diff --git a/.Rbuildignore b/.Rbuildignore index 16f8accd..8f27db2f 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -17,6 +17,8 @@ ^R/secure.global.ranking.md$ ^_pkgdown\.yml$ ^docs$ -^dsBase_6.3.1.tar.gz$ -^dsBase_6.3.1-permissive.tar.gz$ +^dsBase_6.3.2.tar.gz$ +^dsBase_6.3.2-permissive.tar.gz$ ^dsDanger_6.3.1.tar.gz$ +^\.circleci$ +^\.circleci/config\.yml$ diff --git a/.circleci/config.yml b/.circleci/config.yml new file mode 100644 index 00000000..8018f4eb --- /dev/null +++ b/.circleci/config.yml @@ -0,0 +1,67 @@ +# Copyright (c) 2024 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. + +version: 2.1 + +jobs: + dsbaseclient: + docker: +# - image: cimg/base:current + - image: cimg/base:2024.11 + resource_class: small + steps: + - checkout + - setup_remote_docker: + docker_layout_caching: true + - run: | + echo "Building" + echo " Repo Name: " $CIRCLE_PROJECT_REPONAME + echo " Branch: " $CIRCLE_BRANCH + echo " Tag: " $CIRCLE_TAG + - run: + command: | + sudo apt-get install --no-install-recommends software-properties-common dirmngr + wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | sudo tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc + sudo add-apt-repository -y "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/" + + sudo apt-get update -y + sudo apt-get install -y r-base-core cmake + - run: + command: | + sudo apt-get install -y libxml2-dev + sudo apt-get install -y libfontconfig1-dev + sudo apt-get install -y libudunits2-dev + sudo apt-get install -y libharfbuzz-dev + sudo apt-get install -y libfribidi-dev + sudo apt-get install -y libfreetype6-dev + sudo apt-get install -y libpng-dev + sudo apt-get install -y libtiff5-dev + sudo apt-get install -y libjpeg-dev + - run: + command: | + sudo Rscript -e "install.packages('devtools', dependencies=TRUE)" + sudo Rscript -e "install.packages('covr', dependencies=TRUE)" + + sudo Rscript -e "install.packages('fields', dependencies=TRUE)" + sudo Rscript -e "install.packages('metafor', dependencies=TRUE)" + sudo Rscript -e "install.packages('meta', dependencies=TRUE)" + sudo Rscript -e "install.packages('ggplot2', dependencies=TRUE)" + sudo Rscript -e "install.packages('gridExtra', dependencies=TRUE)" + sudo Rscript -e "install.packages('data.table', dependencies=TRUE)" + sudo Rscript -e "install.packages('methods', dependencies=TRUE)" + sudo Rscript -e "install.packages('dplyr', dependencies=TRUE)" + + sudo Rscript -e "install.packages('DSI', dependencies=TRUE)" + sudo Rscript -e "install.packages('DSOpal', dependencies=TRUE)" + sudo Rscript -e "install.packages('DSLite', dependencies=TRUE)" + sudo Rscript -e "install.packages('MolgenisAuth', dependencies=TRUE)" + sudo Rscript -e "install.packages('MolgenisArmadillo', dependencies=TRUE)" + sudo Rscript -e "install.packages('DSMolgenisArmadillo', dependencies=TRUE)" + sudo Rscript -e "install.packages('DescTools', dependencies=TRUE)" + sudo Rscript -e "install.packages('e1071', dependencies=TRUE)" + - run: + command: | + sudo Rscript -e 'library(covr); covr::codecov(token = "'$CODECOV_TOKEN'", quiet=FALSE)' +workflows: + build: + jobs: + - dsbaseclient diff --git a/DESCRIPTION b/DESCRIPTION index 01e80961..862e5a06 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,13 +1,51 @@ Package: dsBaseClient Title: DataSHIELD Client Functions -Version: 6.3.1 -Author: DataSHIELD Developers -Maintainer: DataSHIELD Developers -Description: DataSHIELD client functions for the client side. +Version: 6.3.3 +Description: Base DataSHIELD functions for the client side. DataSHIELD is a software package which allows + you to do non-disclosive federated analysis on sensitive data. DataSHIELD analytic functions have + been designed to only share non disclosive summary statistics, with built in automated output + checking based on statistical disclosure control. With data sites setting the threshold values for + the automated output checks. +Authors@R: c(person(given = "Paul", + family = "Burton", + role = c("aut")), + person(given = "Rebecca", + family = "Wilson", + role = c("aut")), + person(given = "Olly", + family = "Butters", + role = c("aut")), + person(given = "Patricia", + family = "Ryser-Welch", + role = c("aut")), + person(given = "Alex", + family = "Westerberg", + role = c("aut")), + person(given = "Leire", + family = "Abarrategui", + role = c("aut")), + person(given = "Roberto", + family = "Villegas-Diaz", + role = c("aut"), + comment = c(ORCID = "0000-0001-5036-8661")), + person(given = "Demetris", + family = "Avraam", + role = c("aut"), + comment = c(ORCID = "0000-0001-8908-2441")), + person(given = "Yannick", + family = "Marcon", + role = c("aut"), + email = "yannick.marcon@obiba.org", + comment = c(ORCID = "0000-0003-0138-2023")), + person(given = "Stuart", + family = "Wheater", + role = c("aut", "cre"), + email = "stuart.wheater@arjuna.com", + comment = c(ORCID = "0009-0003-2419-1964"))) License: GPL-3 Depends: - R (>= 3.5.0), - DSI (>= 1.3.0) + R (>= 4.0.0), + DSI (>= 1.7.1) Imports: fields, metafor, @@ -15,10 +53,17 @@ Imports: ggplot2, gridExtra, data.table, - panelaggregation, methods, dplyr Suggests: - testthat + lme4, + httr, + tibble, + testthat, + e1071, + DescTools, + DSOpal, + DSMolgenisArmadillo, + DSLite RoxygenNote: 7.3.2 Encoding: UTF-8 diff --git a/NAMESPACE b/NAMESPACE index a112b9c9..ec905eb6 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -1,5 +1,6 @@ # Generated by roxygen2: do not edit by hand +export(computeWeightedMeans) export(ds.Boole) export(ds.abs) export(ds.asCharacter) @@ -119,3 +120,7 @@ export(ds.var) export(ds.vectorCalc) import(DSI) import(data.table) +importFrom(stats,as.formula) +importFrom(stats,na.omit) +importFrom(stats,ts) +importFrom(stats,weighted.mean) diff --git a/R/checkClass.R b/R/checkClass.R index 5cf86eac..779eca1e 100644 --- a/R/checkClass.R +++ b/R/checkClass.R @@ -3,8 +3,8 @@ #' @description This is an internal function. #' @details In DataSHIELD an object included in analysis must be of the same type in all #' the collaborating studies. If that is not the case the process is stopped -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. If the -#' the default set of connections will be used: see \link{datashield.connections_default}. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the +#' the default set of connections will be used: see \link[DSI]{datashield.connections_default}. #' @param obj a string character, the name of the object to check for. #' @keywords internal #' @return a message or the class of the object if the object has the same class in all studies. diff --git a/R/computeWeightedMeans.R b/R/computeWeightedMeans.R new file mode 100644 index 00000000..0f04fc91 --- /dev/null +++ b/R/computeWeightedMeans.R @@ -0,0 +1,25 @@ +#' Compute Weighted Mean by Group +#' +#' This function is originally from the panelaggregation package. +#' It has been ported here in order to bypass the package being +#' kicked off CRAN. +#' +#' @author Matthias Bannert, Gabriel Bucur +#' @param data_table a data.table +#' @param variables character name of the variable(s) to focus on. The variables must be in the data.table +#' @param weight character name of the data.table column that contains a weight. +#' @param by character vector of the columns to group by +#' @import data.table +#' @importFrom stats as.formula na.omit ts weighted.mean +#' @export +computeWeightedMeans <- function(data_table, variables, weight, by) { + + if (is.null(weight)) { + res_dt <- data_table[, lapply(.SD, mean, na.rm = TRUE), .SDcols = variables, by = by] + } else { + res_dt <- data_table[, lapply(.SD, weighted.mean, weight = eval(as.name(weight)), na.rm = TRUE), + .SDcols = variables, by = by] + } + + res_dt +} diff --git a/R/ds.Boole.R b/R/ds.Boole.R index 1c5cf4f4..252346bf 100644 --- a/R/ds.Boole.R +++ b/R/ds.Boole.R @@ -34,9 +34,9 @@ #' Default \code{'NA'}. For more information see details. #' @param newobj a character string that provides the name for the output #' object that is stored on the data servers. Default \code{boole.newobj}. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.Boole} returns the object specified by the \code{newobj} argument #' which is written to the server-side. Also, two validity messages are returned #' to the client-side indicating the name of the \code{newobj} which diff --git a/R/ds.abs.R b/R/ds.abs.R index 5b57b0ed..41c20455 100644 --- a/R/ds.abs.R +++ b/R/ds.abs.R @@ -10,9 +10,9 @@ #' @param x a character string providing the name of a numeric or an integer vector. #' @param newobj a character string that provides the name for the output variable #' that is stored on the data servers. Default name is set to \code{abs.newobj}. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. #' If the \code{datasources} argument is not specified the default set of connections will be -#' used: see \code{\link{datashield.connections_default}}. +#' used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.abs} assigns a vector for each study that includes the absolute values of #' the input numeric or integer vector specified in the argument \code{x}. The created vectors #' are stored in the servers. diff --git a/R/ds.asCharacter.R b/R/ds.asCharacter.R index 72acbd45..c0bd4ce0 100644 --- a/R/ds.asCharacter.R +++ b/R/ds.asCharacter.R @@ -9,9 +9,9 @@ #' character. #' @param newobj a character string that provides the name for the output object #' that is stored on the data servers. Default \code{ascharacter.newobj}. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.asCharacter} returns the object converted into a class character #' that is written to the server-side. Also, two validity messages are returned to the client-side #' indicating the name of the \code{newobj} which has been created in each data source and if diff --git a/R/ds.asDataMatrix.R b/R/ds.asDataMatrix.R index 83b1037f..7b4833bb 100644 --- a/R/ds.asDataMatrix.R +++ b/R/ds.asDataMatrix.R @@ -8,9 +8,9 @@ #' a matrix. #' @param newobj a character string that provides the name for the output object #' that is stored on the data servers. Default \code{asdatamatrix.newobj}. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.asDataMatrix} returns the object converted into a matrix #' that is written to the server-side. Also, two validity messages are returned #' to the client-side diff --git a/R/ds.asFactor.R b/R/ds.asFactor.R index 7d6246d5..476f00f8 100644 --- a/R/ds.asFactor.R +++ b/R/ds.asFactor.R @@ -130,9 +130,9 @@ #' to be used in the creation of the matrix with dummy variables. #' If the \code{fixed.dummy.vars} is set to FALSE then any value of the baseline level is not taken #' into account. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. #' If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.asFactor} returns the unique levels of the converted #' variable in ascending order and a validity #' message with the name of the created object on the client-side and diff --git a/R/ds.asFactorSimple.R b/R/ds.asFactorSimple.R index dce56a8a..313f7b40 100644 --- a/R/ds.asFactorSimple.R +++ b/R/ds.asFactorSimple.R @@ -14,9 +14,9 @@ #' the name of the variable to be converted to a factor. #' @param newobj.name a character string that provides the name for the output variable #' that is stored on the data servers. Default \code{asfactor.newobj}. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. #' If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return an output vector of class factor to the serverside. In addition, returns a validity #' message with the name of the created object on the client-side and if creation fails an #' error message which can be viewed using datashield.errors(). @@ -109,4 +109,4 @@ return(list(return.info=return.info,return.message=return.message)) # } -#ds.asFactorSimple \ No newline at end of file +#ds.asFactorSimple diff --git a/R/ds.asInteger.R b/R/ds.asInteger.R index 139ceb6c..9b3b1a39 100644 --- a/R/ds.asInteger.R +++ b/R/ds.asInteger.R @@ -22,9 +22,9 @@ #' an integer. #' @param newobj a character string that provides the name for the output object #' that is stored on the data servers. Default \code{asinteger.newobj}. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.asInteger} returns the R object converted into an integer #' that is written to the server-side. Also, two validity messages are returned to the #' client-side indicating the name of the \code{newobj} which diff --git a/R/ds.asList.R b/R/ds.asList.R index 5383c506..d7366878 100644 --- a/R/ds.asList.R +++ b/R/ds.asList.R @@ -9,9 +9,9 @@ #' a list. #' @param newobj a character string that provides the name for the output object #' that is stored on the data servers. Default \code{aslist.newobj}. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.asList} returns the R object converted into a list #' which is written to the server-side. Also, two validity messages are returned to the #' client-side indicating the name of the \code{newobj} which has been created in each data diff --git a/R/ds.asLogical.R b/R/ds.asLogical.R index de2920bf..2ddc33cf 100644 --- a/R/ds.asLogical.R +++ b/R/ds.asLogical.R @@ -8,9 +8,9 @@ #' input object to be coerced to a logical. #' @param newobj a character string that provides the name for the output object #' that is stored on the data servers. Default \code{aslogical.newobj}. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.asLogical} returns the R object converted into a logical #' that is written to the server-side. Also, two validity messages are returned #' to the client-side indicating the name of the \code{newobj} which diff --git a/R/ds.asMatrix.R b/R/ds.asMatrix.R index 04186109..1c5b0ced 100644 --- a/R/ds.asMatrix.R +++ b/R/ds.asMatrix.R @@ -11,9 +11,9 @@ #' a matrix. #' @param newobj a character string that provides the name for the output object #' that is stored on the data servers. Default \code{asmatrix.newobj}. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.asMatrix} returns the object converted into a matrix #' that is written to the server-side. Also, two validity messages are returned #' to the client-side indicating the name of the \code{newobj} which diff --git a/R/ds.asNumeric.R b/R/ds.asNumeric.R index 0c4e9a03..7b4da435 100644 --- a/R/ds.asNumeric.R +++ b/R/ds.asNumeric.R @@ -22,9 +22,9 @@ #' a numeric. #' @param newobj a character string that provides the name for the output object #' that is stored on the data servers. Default \code{asnumeric.newobj}. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.asNumeric} returns the R object converted into a numeric class #' that is written to the server-side. Also, two validity messages are returned #' to the client-side indicating the name of the \code{newobj} which diff --git a/R/ds.assign.R b/R/ds.assign.R index 7c701726..25b71c74 100644 --- a/R/ds.assign.R +++ b/R/ds.assign.R @@ -10,9 +10,9 @@ #' @param toAssign a character string providing the object to assign. #' @param newobj a character string that provides the name for the output object #' that is stored on the data servers. Default \code{assign.newobj}. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.assign} returns the R object assigned to a name #' that is written to the server-side. #' @author DataSHIELD Development Team diff --git a/R/ds.auc.R b/R/ds.auc.R index b971651a..ebfc5fc3 100644 --- a/R/ds.auc.R +++ b/R/ds.auc.R @@ -6,9 +6,9 @@ #' @param pred the name of the vector of the predicted values #' @param y the name of the outcome variable. Note that this variable should include #' the complete cases that are used in the regression model. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return returns the AUC and its standard error #' @author Demetris Avraam for DataSHIELD Development Team #' @export @@ -44,4 +44,4 @@ ds.auc <- function(pred=NULL, y=NULL, datasources=NULL){ return(output) -} \ No newline at end of file +} diff --git a/R/ds.boxPlot.R b/R/ds.boxPlot.R index ad2de1d8..d89c5470 100644 --- a/R/ds.boxPlot.R +++ b/R/ds.boxPlot.R @@ -12,7 +12,7 @@ #' @param ylabel \code{caracter} (default \code{"y axis"}) Label to put on the y axis of the plot #' @param type \code{character} Return a pooled plot (\code{"pooled"}) or a split plot (one for each study server #' \code{"split"}) -#' @param datasources a list of \code{\link{DSConnection-class}} (default \code{NULL}) objects obtained after login +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} (default \code{NULL}) objects obtained after login #' #' @return \code{ggplot} object #' @export @@ -54,7 +54,7 @@ #' ds.boxPlot("D", "LAB_HDL", type= "split", datasources = connections) #' #' ## Create a boxplot of two variables variable -#' ds.boxPlot("D", c("LAB_HDL", "LAB_TRIG", type="combine", +#' ds.boxPlot("D", c("LAB_HDL", "LAB_TRIG", type="pooled", #' datasources = connections) #' # only one plot is created (of the aggregated results of all servers) #' diff --git a/R/ds.boxPlotGG.R b/R/ds.boxPlotGG.R index d35caba3..e09fa8d6 100644 --- a/R/ds.boxPlotGG.R +++ b/R/ds.boxPlotGG.R @@ -17,7 +17,7 @@ #' @param ylabel \code{caracter} (default \code{"y axis"}) Label to put on the y axis of the plot #' @param type \code{character} Return a pooled plot (\code{"pooled"}) or a split plot (one for each study server #' \code{"split"}) -#' @param datasources a list of \code{\link{DSConnection-class}} (default \code{NULL}) objects obtained after login +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} (default \code{NULL}) objects obtained after login #' #' @return \code{ggplot} object @@ -46,19 +46,19 @@ ds.boxPlotGG <- function(x, group = NULL, group2 = NULL, xlabel = "x axis", ylab } pt_merged <- data.table::data.table(pt_merged) if(!is.null(group) & is.null(group2)){ - pt_merged <- panelaggregation::computeWeightedMeans(pt_merged, + pt_merged <- computeWeightedMeans(pt_merged, variables = c("ymin", "lower", "middle", "upper", "ymax"), weight = "n", by = c("group", "x")) } else if(!is.null(group) & !is.null(group2)){ - pt_merged <- panelaggregation::computeWeightedMeans(pt_merged, + pt_merged <- computeWeightedMeans(pt_merged, variables = c("ymin", "lower", "middle", "upper", "ymax"), weight = "n", by = c("group", "group2", "x")) } else{ - pt_merged <- panelaggregation::computeWeightedMeans(pt_merged, + pt_merged <- computeWeightedMeans(pt_merged, variables = c("ymin", "lower", "middle", "upper", "ymax"), weight = "n", by = c("x")) @@ -146,4 +146,4 @@ ds.boxPlotGG <- function(x, group = NULL, group2 = NULL, xlabel = "x axis", ylab return(plt) -} \ No newline at end of file +} diff --git a/R/ds.boxPlotGG_data_Treatment.R b/R/ds.boxPlotGG_data_Treatment.R index f27a9110..40f89730 100644 --- a/R/ds.boxPlotGG_data_Treatment.R +++ b/R/ds.boxPlotGG_data_Treatment.R @@ -6,7 +6,7 @@ #' @param variables \code{character vector} Name of the column(s) of the data frame to include on the boxplot #' @param group \code{character} (default \code{NULL}) Name of the first grouping variable. #' @param group2 \code{character} (default \code{NULL}) Name of the second grouping variable. -#' @param datasources a list of \code{\link{DSConnection-class}} (default \code{NULL}) objects obtained after login +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} (default \code{NULL}) objects obtained after login #' #' @return Does not return nothing, it creates the table \code{"boxPlotRawData"} on the server arranged to be passed to the #' ggplot boxplot function. Structure of the created table: \cr @@ -35,4 +35,4 @@ ds.boxPlotGG_data_Treatment <- function(table, variables, group = NULL, group2 = DSI::datashield.assign.expr(datasources, "boxPlotRawData", as.symbol(cally)) -} \ No newline at end of file +} diff --git a/R/ds.boxPlotGG_data_Treatment_numeric.R b/R/ds.boxPlotGG_data_Treatment_numeric.R index 04b33e04..0cf4b383 100644 --- a/R/ds.boxPlotGG_data_Treatment_numeric.R +++ b/R/ds.boxPlotGG_data_Treatment_numeric.R @@ -3,7 +3,7 @@ #' @description Internal function #' #' @param vector \code{character} Name of the table on the server side that holds the information to be plotted later -#' @param datasources a list of \code{\link{DSConnection-class}} (default \code{NULL}) objects obtained after login +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} (default \code{NULL}) objects obtained after login #' #' @return Does not return nothing, it creates the table \code{"boxPlotRawDataNumeric"} on the server arranged to be passed to the #' ggplot boxplot function. Structure of the created table: \cr diff --git a/R/ds.boxPlotGG_numeric.R b/R/ds.boxPlotGG_numeric.R index 7300c128..c1996628 100644 --- a/R/ds.boxPlotGG_numeric.R +++ b/R/ds.boxPlotGG_numeric.R @@ -5,7 +5,7 @@ #' @param ylabel \code{caracter} (default \code{"y axis"}) Label to put on the y axis of the plot #' @param type \code{character} Return a pooled plot (\code{"pooled"}) or a split plot (one for each study server #' \code{"split"}) -#' @param datasources a list of \code{\link{DSConnection-class}} (default \code{NULL}) objects obtained after login +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} (default \code{NULL}) objects obtained after login #' #' @return \code{ggplot} object diff --git a/R/ds.boxPlotGG_table.R b/R/ds.boxPlotGG_table.R index fe6c158e..ebe9eb4c 100644 --- a/R/ds.boxPlotGG_table.R +++ b/R/ds.boxPlotGG_table.R @@ -10,7 +10,7 @@ #' @param ylabel \code{caracter} (default \code{"y axis"}) Label to put on the y axis of the plot #' @param type \code{character} Return a pooled plot (\code{"pooled"}) or a split plot (one for each study server #' \code{"split"}) -#' @param datasources a list of \code{\link{DSConnection-class}} (default \code{NULL}) objects obtained after login +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} (default \code{NULL}) objects obtained after login #' #' @return \code{ggplot} object diff --git a/R/ds.bp_standards.R b/R/ds.bp_standards.R index 49374497..ae76c54c 100644 --- a/R/ds.bp_standards.R +++ b/R/ds.bp_standards.R @@ -16,9 +16,9 @@ #' blood pressure. #' @param newobj a character string that provides the name for the output object #' that is stored on the data servers. Default name is set to \code{bp.newobj}. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. #' If the \code{datasources} argument is not specified the default set of connections will be -#' used: see \code{\link{datashield.connections_default}}. +#' used: see \code{\link[DSI]{datashield.connections_default}}. #' @return assigns a new object on the server-side. The assigned object is a list #' with two elements: the 'Zbp' which is the zscores of the blood pressure and 'perc' #' which is the percentiles of the BP zscores. @@ -76,4 +76,4 @@ ds.bp_standards <- function(sex=NULL, age=NULL, height=NULL, bp=NULL, systolic=T cally <- call('bp_standardsDS', sex, age, height, bp, systolic) DSI::datashield.assign(datasources, newobj, cally) -} \ No newline at end of file +} diff --git a/R/ds.c.R b/R/ds.c.R index 01257aec..2093ac01 100644 --- a/R/ds.c.R +++ b/R/ds.c.R @@ -10,9 +10,9 @@ #' @param x a vector of character string providing the names of the objects to be combined. #' @param newobj a character string that provides the name for the output object #' that is stored on the data servers. Default \code{c.newobj}. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.c} returns the vector of concatenating R #' objects which are written to the server-side. #' @examples diff --git a/R/ds.cbind.R b/R/ds.cbind.R index fdd1b34b..d943e017 100644 --- a/R/ds.cbind.R +++ b/R/ds.cbind.R @@ -32,9 +32,9 @@ #' For more information see \strong{Details}. #' @param newobj a character string that provides the name for the output variable #' that is stored on the data servers. Defaults \code{cbind.newobj}. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. #' If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @param notify.of.progress specifies if console output should be produced to indicate #' progress. Default FALSE. #' @return \code{ds.cbind} returns a data frame combining the columns of the R diff --git a/R/ds.changeRefGroup.R b/R/ds.changeRefGroup.R index 1b8ad556..4bd5080a 100644 --- a/R/ds.changeRefGroup.R +++ b/R/ds.changeRefGroup.R @@ -22,9 +22,9 @@ #' @param reorderByRef logical, if TRUE the new vector #' should be ordered by the reference group (i.e. putting the reference group first). #' The default is to not re-order (see the reasons in the details). -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. #' If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.changeRefGroup} returns a new vector with the specified level as a reference #' which is written to the server-side. #' @author DataSHIELD Development Team diff --git a/R/ds.class.R b/R/ds.class.R index 285b4045..036848ad 100644 --- a/R/ds.class.R +++ b/R/ds.class.R @@ -6,9 +6,9 @@ #' #' Server function called: \code{classDS} #' @param x a character string providing the name of the input R object. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. #' If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.class} returns the type of the R object. #' @author DataSHIELD Development Team #' @seealso \code{\link{ds.exists}} to verify if an object is defined (exists) on the server-side. diff --git a/R/ds.colnames.R b/R/ds.colnames.R index 5950d99b..a4b98b1a 100644 --- a/R/ds.colnames.R +++ b/R/ds.colnames.R @@ -6,9 +6,9 @@ #' #' Server function called: \code{colnamesDS} #' @param x a character string providing the name of the input data frame or matrix. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. #' If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.colnames} returns the column names of #' the specified server-side data frame or matrix. #' @author DataSHIELD Development Team diff --git a/R/ds.completeCases.R b/R/ds.completeCases.R index fed43208..ed95bf6d 100644 --- a/R/ds.completeCases.R +++ b/R/ds.completeCases.R @@ -14,9 +14,9 @@ #' that is stored on the data servers. If the user does not specify a name, then the function #' generates a name for the generated object that is the name of the input object with the #' suffix "_complete.cases" -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. #' If the \code{datasources} argument is not specified, the default set of connections will be -#' used: see \code{\link{datashield.connections_default}}. +#' used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.completeCases} generates a modified data frame, matrix or vector from which #' all rows containing at least one NA have been deleted. The output object is stored on the #' server-side. Only two validity messages are returned to the client-side indicating the name diff --git a/R/ds.contourPlot.R b/R/ds.contourPlot.R index 7973c1d1..4e195e48 100644 --- a/R/ds.contourPlot.R +++ b/R/ds.contourPlot.R @@ -50,9 +50,9 @@ #' see details. #' @param noise the percentage of the initial variance that is used as the variance of the embedded #' noise if the argument \code{method} is set to \code{'probabilistic'}. For more information see details. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. #' If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.contourPlot} returns a contour plot to the client-side. #' @author DataSHIELD Development Team #' @examples diff --git a/R/ds.cor.R b/R/ds.cor.R index 1a5c86d6..53fb22db 100644 --- a/R/ds.cor.R +++ b/R/ds.cor.R @@ -27,9 +27,9 @@ #' Default NULL. #' @param type a character string that represents the type of analysis to carry out. #' This must be set to \code{'split'} or \code{'combine'}. Default \code{'split'}. For more information see details. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. #' If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.cor} returns a list containing the number of missing values in each variable, #' the number of missing variables casewise, the correlation matrix, #' the number of used complete cases. The function applies two disclosure controls. The first disclosure diff --git a/R/ds.corTest.R b/R/ds.corTest.R index 7be1f992..38fffceb 100644 --- a/R/ds.corTest.R +++ b/R/ds.corTest.R @@ -19,9 +19,9 @@ #' This must be set to \code{'split'} or \code{'combine'}. Default is set to \code{'split'}. If #' \code{type} is set to "combine" then an approximated pooled correlation is estimated based on #' Fisher's z transformation. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.corTest} returns to the client-side the results of the correlation test. #' @author DataSHIELD Development Team #' @export diff --git a/R/ds.cov.R b/R/ds.cov.R index 58aedc94..c67d2e13 100644 --- a/R/ds.cov.R +++ b/R/ds.cov.R @@ -35,9 +35,9 @@ #' \code{'pairwise.complete'}. Default \code{'pairwise.complete'}. For more information see details. #' @param type a character string that represents the type of analysis to carry out. #' This must be set to \code{'split'} or \code{'combine'}. Default \code{'split'}. For more information see details. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. #' If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.cov} returns a list containing the number of missing values in each variable, the number of missing values #' casewise or pairwise depending on the argument \code{naAction}, the covariance matrix, the number of used complete cases #' and an error message which indicates whether or not the input variables pass the disclosure controls. The first disclosure diff --git a/R/ds.dataFrame.R b/R/ds.dataFrame.R index e71c1daf..5837747c 100644 --- a/R/ds.dataFrame.R +++ b/R/ds.dataFrame.R @@ -32,9 +32,9 @@ #' are the same #' @param newobj a character string that provides the name for the output data frame #' that is stored on the data servers. Default \code{dataframe.newobj}. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. #' If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @param notify.of.progress specifies if console output should be produced to indicate #' progress. Default is FALSE. #' @return \code{ds.dataFrame} returns the object specified by the \code{newobj} argument diff --git a/R/ds.dataFrameFill.R b/R/ds.dataFrameFill.R index eef95117..3de389b7 100644 --- a/R/ds.dataFrameFill.R +++ b/R/ds.dataFrameFill.R @@ -13,9 +13,9 @@ #' filled with extra columns of missing values. #' @param newobj a character string that provides the name for the output data frame #' that is stored on the data servers. Default value is "dataframefill.newobj". -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. #' If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.dataFrameFill} returns the object specified by the \code{newobj} argument which #' is written to the server-side. Also, two validity messages are returned to the #' client-side indicating the name of the \code{newobj} that has been created in each data source diff --git a/R/ds.dataFrameSort.R b/R/ds.dataFrameSort.R index d170dd87..de59d61e 100644 --- a/R/ds.dataFrameSort.R +++ b/R/ds.dataFrameSort.R @@ -33,9 +33,9 @@ #' @param newobj a character string that provides the name for the output data frame #' that is stored on the data servers. Default \code{dataframesort.newobj}. #' where \code{df.name} is the first argument of \code{ds.dataFrameSort()}. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.dataFrameSort} returns the sorted data frame is written to the server-side. #' Also, two validity messages are returned to the client-side #' indicating the name of the \code{newobj} which @@ -203,4 +203,4 @@ ds.dataFrameSort<-function(df.name=NULL, sort.key.name=NULL, sort.descending=FAL #END OF CHECK OBJECT CREATED CORRECTLY MODULE # ########################################################################################################### } -#ds.dataFrameSort \ No newline at end of file +#ds.dataFrameSort diff --git a/R/ds.dataFrameSubset.R b/R/ds.dataFrameSubset.R index 3b6dff97..46878520 100644 --- a/R/ds.dataFrameSubset.R +++ b/R/ds.dataFrameSubset.R @@ -28,9 +28,9 @@ #' If FALSE or NULL all rows with at least one missing values are removed from the subset. #' @param newobj a character string that provides the name for the output #' object that is stored on the data servers. Default \code{dataframesubset.newobj}. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. #' If the \code{datasources} -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @param notify.of.progress specifies if console output should be produced to indicate #' progress. Default FALSE. #' @return \code{ds.dataFrameSubset} returns diff --git a/R/ds.densityGrid.R b/R/ds.densityGrid.R index 33e1bb6d..b0766418 100644 --- a/R/ds.densityGrid.R +++ b/R/ds.densityGrid.R @@ -23,9 +23,9 @@ #' \code{'combine'}, a pooled grid density matrix is generated, #' instead if \code{type} is set to \code{'split'} #' one grid density matrix is generated. Default \code{'combine'}. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. #' If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.densityGrid} returns a grid density matrix. #' @author DataSHIELD Development Team #' @export diff --git a/R/ds.dim.R b/R/ds.dim.R index 613bd984..4a6cd3a7 100644 --- a/R/ds.dim.R +++ b/R/ds.dim.R @@ -22,9 +22,9 @@ #' Default \code{'both'}. #' @param checks logical. If TRUE undertakes all DataSHIELD checks (time-consuming). #' Default FALSE. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.dim} retrieves to the client-side the dimension of the object #' in the form of a vector where the first #' element indicates the number of rows and the second element indicates the number of columns. diff --git a/R/ds.elspline.R b/R/ds.elspline.R index 1fc4cffe..c4a2bbdd 100644 --- a/R/ds.elspline.R +++ b/R/ds.elspline.R @@ -17,9 +17,9 @@ #' @param names character, vector of names for constructed variables #' @param newobj a character string that provides the name for the output #' variable that is stored on the data servers. Default \code{elspline.newobj}. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return an object of class "lspline" and "matrix", which its name is specified by the #' \code{newobj} argument (or its default name "elspline.newobj"), is assigned on the serverside. #' @author Demetris Avraam for DataSHIELD Development Team @@ -61,4 +61,4 @@ ds.elspline <- function(x, n, marginal = FALSE, names = NULL, newobj = NULL, dat calltext <- call("elsplineDS", x, n, marginal, names) DSI::datashield.assign(datasources, newobj, calltext) -} \ No newline at end of file +} diff --git a/R/ds.exists.R b/R/ds.exists.R index b6ef9e66..6dff8b4c 100644 --- a/R/ds.exists.R +++ b/R/ds.exists.R @@ -10,9 +10,9 @@ #' #' Server function called: \code{exists} #' @param x a character string providing the name of the object to look for. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.exists} returns a logical object. #' TRUE if the object is on the server-side and FALSE otherwise. #' @author DataSHIELD Development Team diff --git a/R/ds.exp.R b/R/ds.exp.R index 2fd9da3b..5bf325bd 100644 --- a/R/ds.exp.R +++ b/R/ds.exp.R @@ -9,9 +9,9 @@ #' @param x a character string providing the name of a numerical vector. #' @param newobj a character string that provides the name for the output variable #' that is stored on the data servers. Default \code{exp.newobj}. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. #' If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.exp} returns a vector for each study of the exponential values for the numeric vector #' specified in the argument \code{x}. The created vectors are stored in the server-side. #' @author DataSHIELD Development Team diff --git a/R/ds.gamlss.R b/R/ds.gamlss.R index bd9d82f3..6a7622c7 100644 --- a/R/ds.gamlss.R +++ b/R/ds.gamlss.R @@ -64,9 +64,9 @@ #' only. #' @param newobj a character string that provides the name for the output object #' that is stored on the data servers. Default \code{gamlss_res}. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return a gamlss object with all components as in the native R gamlss function. #' Individual-level information like the components y (the response response) and #' residuals (the normalised quantile residuals of the model) are not disclosed to diff --git a/R/ds.getWGSR.R b/R/ds.getWGSR.R index f883549a..ff4c60f5 100644 --- a/R/ds.getWGSR.R +++ b/R/ds.getWGSR.R @@ -52,9 +52,9 @@ #' by the formula $age_days=age_months*(365.25/12)$. #' @param newobj a character string that provides the name for the output variable #' that is stored on the data servers. Defaults \code{getWGSR.newobj}. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. #' If the \code{datasources} argument is not specified the default set of connections will be -#' used: see \code{\link{datashield.connections_default}}. +#' used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.getWGSR} assigns a vector for each study that includes the z-scores for the #' specified index. The created vectors are stored in the servers. #' @author Demetris Avraam for DataSHIELD Development Team diff --git a/R/ds.glm.R b/R/ds.glm.R index e27cb472..13cba2d9 100644 --- a/R/ds.glm.R +++ b/R/ds.glm.R @@ -17,7 +17,7 @@ #' #' Many GLMs can be fitted very simply using a formula such as: #' -#' \deqn{y~a+b+c+d} +#' \eqn{y~a+b+c+d} #' #' which simply means fit a GLM with \code{y} as the outcome variable and #' \code{a}, \code{b}, \code{c} and \code{d} as covariates. @@ -26,7 +26,7 @@ #' Instead, if you need to fit a more complex #' model, for example: #' -#' \deqn{EVENT~1+TID+SEXF*AGE.60} +#' \eqn{EVENT~1+TID+SEXF*AGE.60} #' #' In the above model the outcome variable is \code{EVENT} #' and the covariates @@ -63,7 +63,7 @@ #' The \code{data} argument avoids you having to specify the name of the #' data frame in front of each covariate in the formula. #' For example, if the data frame is called \code{DataFrame} you -#' avoid having to write: \eqn{DataFrame$y~DataFrame$a+DataFrame$b+DataFrame$c+DataFrame$d} +#' avoid having to write: \eqn{DataFrame\$y ~ DataFrame\$a + DataFrame\$b + DataFrame\$c + DataFrame\$d} #' #' The \code{checks} argument verifies that the variables in the model are all defined (exist) #' on the server-side at every study @@ -164,9 +164,9 @@ #' of parameter estimates is returned. Default FALSE. #' @param viewCor logical. If TRUE the correlation matrix of #' parameter estimates is returned. Default FALSE. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. #' If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return Many of the elements of the output list returned by \code{ds.glm} are #' equivalent to those returned by the \code{glm()} function in native R. However, #' potentially disclosive elements diff --git a/R/ds.glmSLMA.R b/R/ds.glmSLMA.R index 421d7783..7f3454bc 100644 --- a/R/ds.glmSLMA.R +++ b/R/ds.glmSLMA.R @@ -61,7 +61,7 @@ #' #' Many glms can be fitted very simply using a formula such as: #' -#' \deqn{y~a+b+c+d} +#' \eqn{y~a+b+c+d} #' #' which simply means fit a glm with \code{y} as the outcome variable and #' \code{a}, \code{b}, \code{c} and \code{d} as covariates. @@ -70,7 +70,7 @@ #' Instead, if you need to fit a more complex #' model, for example: #' -#' \deqn{EVENT~1+TID+SEXF*AGE.60} +#' \eqn{EVENT~1+TID+SEXF*AGE.60} #' #' In the above model the outcome variable is \code{EVENT} #' and the covariates @@ -134,7 +134,7 @@ #' The \code{dataName} argument avoids you having to specify the name of the #' data frame in front of each covariate in the formula. #' For example, if the data frame is called \code{DataFrame} you -#' avoid having to write: \eqn{DataFrame$y~DataFrame$a+DataFrame$b+DataFrame$c+DataFrame$d} +#' avoid having to write: \eqn{DataFrame\$y ~ DataFrame\$a + DataFrame\$b + DataFrame\$c + DataFrame\$d} #' #' The \code{checks} argument verifies that the variables in the model are all defined (exist) #' on the server-site at every study @@ -181,9 +181,9 @@ #' For more information see \strong{Details}. #' @param notify.of.progress specifies if console output should be produced to indicate #' progress. Default FALSE. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. #' If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return The serverside aggregate functions \code{glmSLMADS1} and \code{glmSLMADS2} return #' output to the clientside, while the assign function \code{glmSLMADS.assign} simply writes #' the glm object to the serverside diff --git a/R/ds.glmerSLMA.R b/R/ds.glmerSLMA.R index 92178322..8bb8aa36 100644 --- a/R/ds.glmerSLMA.R +++ b/R/ds.glmerSLMA.R @@ -18,23 +18,23 @@ #' In \code{formula} most shortcut notation allowed by \code{glmer()} function is #' also allowed by \code{ds.glmerSLMA}. #' Many GLMEs can be fitted very simply using a formula like: -#' \deqn{y~a+b+(1|c)} +#' \eqn{y~a+b+(1|c)} #' which simply means fit an GLME with \code{y} as the outcome variable (e.g. #' a binary case-control using a logistic regression model or a count or a survival #' time using a Poisson regression model), \code{a} and \code{b} #' as fixed effects, and \code{c} as a random effect or grouping factor. #' #' It is also possible to fit models with random slopes by specifying a model such as -#' \deqn{y~a+b+(1+b|c)} +#' \eqn{y~a+b+(1+b|c)} #' where the effect of \code{b} can vary randomly between groups defined by \code{c}. #' Implicit nesting can be specified with formulas such as: \eqn{y~a+b+(1|c/d)} -#' or \eqn{y~a+b+(1|c)+(1|c:d)}. +#' or \eqn{y~a+b+(1|c)+(1|c:d)}. #' #' #' The \code{dataName} argument avoids you having to specify the name of the #' data frame in front of each covariate in the formula. #' For example, if the data frame is called \code{DataFrame} you avoid having to write: -#' \eqn{DataFrame$y~DataFrame$a+DataFrame$b+(1|DataFrame$c)}. +#' \eqn{DataFrame\$y ~ DataFrame\$a + DataFrame\$b + (1 | DataFrame\$c)}. #' #' The \code{checks} argument verifies that the variables in the model are all defined (exist) #' on the server-site at every study @@ -90,9 +90,9 @@ #' that contains all of the variables in the GLME formula. For more information see \strong{Details}. #' @param checks logical. If TRUE \code{ds.glmerSLMA} checks the structural integrity #' of the model. Default FALSE. For more information see \strong{Details}. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. #' If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @param family a character string specifying the distribution of the observed #' value of the outcome variable around the predictions generated by the linear predictor. #' This can be set as \code{"binomial"} or \code{"poisson"}. diff --git a/R/ds.heatmapPlot.R b/R/ds.heatmapPlot.R index e2d656c1..262b1d70 100644 --- a/R/ds.heatmapPlot.R +++ b/R/ds.heatmapPlot.R @@ -82,9 +82,9 @@ #' noise if the argument \code{method} is set to \code{'probabilistic'}. #' Default \code{noise} value is \code{0.25}. #' For more information see \strong{Details}. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. #' If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.heatmapPlot} returns to the client-side a heat map plot and a message specifying #' the number of invalid cells in each study. #' @author DataSHIELD Development Team diff --git a/R/ds.hetcor.R b/R/ds.hetcor.R index 1b0e77f6..2b29be24 100644 --- a/R/ds.hetcor.R +++ b/R/ds.hetcor.R @@ -17,9 +17,9 @@ #' nearPD directly. #' @param use if "complete.obs", remove observations with any missing data; if "pairwise.complete.obs", #' compute each correlation using all observations with valid data for that pair of variables. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. #' If the \code{datasources} argument is not specified the default set of connections will be -#' used: see \code{\link{datashield.connections_default}}. +#' used: see \code{\link[DSI]{datashield.connections_default}}. #' @return Returns an object of class "hetcor" from each study, with the following components: the #' correlation matrix; the type of each correlation: "Pearson", "Polychoric", or "Polyserial"; the #' standard errors of the correlations, if requested; the number (or numbers) of observations on which @@ -53,4 +53,4 @@ ds.hetcor <- function(data=NULL, ML=TRUE, std.err=TRUE, bins=4, pd=TRUE, use="co return(output) -} \ No newline at end of file +} diff --git a/R/ds.histogram.R b/R/ds.histogram.R index 5b497758..0f5357b7 100644 --- a/R/ds.histogram.R +++ b/R/ds.histogram.R @@ -79,9 +79,9 @@ #' plot. The \code{vertical.axis} argument can be set as \code{'Frequency'} or \code{'Density'}. #' Default \code{'Frequency'}. #' For more information see \strong{Details}. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. #' If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return one or more histogram objects and plots depending on the argument \code{type} #' @author DataSHIELD Development Team #' @export diff --git a/R/ds.igb_standards.R b/R/ds.igb_standards.R index c3d74f40..fb7953f1 100644 --- a/R/ds.igb_standards.R +++ b/R/ds.igb_standards.R @@ -15,9 +15,9 @@ #' "igb_zscore2value", "igb_value2zscore" (default), "igb_value2centile". #' @param newobj a character string that provides the name for the output variable #' that is stored on the data servers. Default name is set to \code{igb.newobj}. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. #' If the \code{datasources} argument is not specified the default set of connections will be -#' used: see \code{\link{datashield.connections_default}}. +#' used: see \code{\link[DSI]{datashield.connections_default}}. #' @note For gestational ages between 24 and 33 weeks, the INTERGROWTH very early preterm #' standard is used. #' @references International standards for newborn weight, length, and head circumference by @@ -82,4 +82,4 @@ ds.igb_standards <- function(gagebrth=NULL, z=0, p=50, val=NULL, var=NULL, sex=N cally <- call('igb_standardsDS', gagebrth, z, p, val, var, sex, fun) DSI::datashield.assign(datasources, newobj, cally) -} \ No newline at end of file +} diff --git a/R/ds.isNA.R b/R/ds.isNA.R index 28ff808e..1d84577f 100644 --- a/R/ds.isNA.R +++ b/R/ds.isNA.R @@ -8,9 +8,9 @@ #' #' Server function called: \code{isNaDS} #' @param x a character string specifying the name of the vector to check. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.isNA} returns a boolean. If it is TRUE the vector is empty #' (all values are NA), FALSE otherwise. #' @author DataSHIELD Development Team diff --git a/R/ds.isValid.R b/R/ds.isValid.R index 34a94223..e43b61b1 100644 --- a/R/ds.isValid.R +++ b/R/ds.isValid.R @@ -10,9 +10,9 @@ #' #' Server function called: \code{isValidDS} #' @param x a character string specifying the name of a vector, dataframe or matrix. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.isValid} returns a boolean. If it is TRUE input object is valid, FALSE otherwise. #' @author DataSHIELD Development Team #' @export diff --git a/R/ds.kurtosis.R b/R/ds.kurtosis.R index c262201b..974682bb 100644 --- a/R/ds.kurtosis.R +++ b/R/ds.kurtosis.R @@ -17,9 +17,9 @@ #' if \code{type} is set to 'split', 'splits' or 's', the kurtosis is returned separately for each study. #' if \code{type} is set to 'both' or 'b', both sets of outputs are produced. #' The default value is set to 'both'. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. #' If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return a matrix showing the kurtosis of the input numeric variable, the number of valid observations and #' the validity message. #' @author Demetris Avraam, for DataSHIELD Development Team diff --git a/R/ds.length.R b/R/ds.length.R index a288de72..83cb5cae 100644 --- a/R/ds.length.R +++ b/R/ds.length.R @@ -17,9 +17,9 @@ #' @param checks logical. If TRUE the model components are checked. #' Default FALSE to save time. It is suggested that checks #' should only be undertaken once the function call has failed. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.length} returns to the client-side the pooled length of a vector or a list, #' or the length of a vector or a list for each study separately. #' @author DataSHIELD Development Team diff --git a/R/ds.levels.R b/R/ds.levels.R index 1943ea0c..b32a5d1c 100644 --- a/R/ds.levels.R +++ b/R/ds.levels.R @@ -6,9 +6,9 @@ #' @details #' Server function called: \code{levelsDS} #' @param x a character string specifying the name of a factor variable. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.levels} returns to the client-side the levels of a factor #' class variable stored in the server-side. #' @author DataSHIELD Development Team diff --git a/R/ds.lexis.R b/R/ds.lexis.R index d692a65d..665a29ed 100644 --- a/R/ds.lexis.R +++ b/R/ds.lexis.R @@ -127,9 +127,9 @@ #' variables to include in the final expanded table. For more information see \strong{Details}. #' @param expandDF a character string denoting the name of the new data frame containing the #' expanded data set. Default \code{lexis.newobj}. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. #' If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.lexis} returns to the server-side a data frame for each study with #' the expanded version of the input table. #' diff --git a/R/ds.list.R b/R/ds.list.R index 239399db..b0847703 100644 --- a/R/ds.list.R +++ b/R/ds.list.R @@ -8,9 +8,9 @@ #' @param x a character string specifying the names of the objects to coerce into a list. #' @param newobj a character string that provides the name for the output variable #' that is stored on the data servers. Default \code{list.newobj}. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.list} returns a list of objects for each study that is stored on the server-side. #' @author DataSHIELD Development Team #' @export diff --git a/R/ds.listDisclosureSettings.R b/R/ds.listDisclosureSettings.R index ec4546bb..33c73875 100644 --- a/R/ds.listDisclosureSettings.R +++ b/R/ds.listDisclosureSettings.R @@ -51,9 +51,9 @@ #' disclosure. #' #' Server function called: \code{listDisclosureSettingsDS} -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. #' If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.listDisclosureSettings} returns a list containing the current settings of the #' \code{nfilters} in each study specified. #' @author DataSHIELD Development Team diff --git a/R/ds.listServersideFunctions.R b/R/ds.listServersideFunctions.R index fb5128a2..97188b28 100644 --- a/R/ds.listServersideFunctions.R +++ b/R/ds.listServersideFunctions.R @@ -1,6 +1,6 @@ #' @title Lists server-side functions #' @description Lists all current server-side functions -#' @details Uses \code{\link{datashield.methods}} function from \code{DSI} package to list all +#' @details Uses \code{\link[DSI]{datashield.methods}} function from \code{DSI} package to list all #' assign and aggregate functions on the available data repository servers. #' The only choice of arguments is in \code{datasources}; i.e. which studies to interrogate. #' Once the studies have @@ -8,9 +8,9 @@ #' of these studies and then all aggregate functions for all of them. #' #' This function does not call any server-side function. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. #' If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.listServersideFunctions} returns to the client-side #' a list containing all server-side functions separately for each study. #' Firstly lists assign and then aggregate functions. diff --git a/R/ds.lmerSLMA.R b/R/ds.lmerSLMA.R index af57b8e5..b6d05c9b 100644 --- a/R/ds.lmerSLMA.R +++ b/R/ds.lmerSLMA.R @@ -18,20 +18,20 @@ #' #' In \code{formula} most shortcut notation allowed by \code{lmer()} function is #' also allowed by \code{ds.lmerSLMA}. Many LMEs can be fitted very simply using a formula like: -#' \deqn{y~a+b+(1|c)} +#' \eqn{y ~ a + b + (1 | c)} #' which simply means fit an LME with \code{y} as the outcome variable with \code{a} and \code{b} #' as fixed effects, and \code{c} as a random effect or grouping factor. #' #' It is also possible to fit models with random slopes by specifying a model such as -#' \deqn{y~a+b+(1+b|c)} +#' \eqn{y ~ a + b + (1 + b | c)} #' where the effect of \code{b} can vary randomly between groups defined by \code{c}. -#' Implicit nesting can be specified with formulae such as \eqn{y~a+b+(1|c/d)} -#' or \eqn{y~a+b+(1|c)+(1|c:d)}. +#' Implicit nesting can be specified with formulae such as \eqn{y ~ a + b + (1 | c / d)} +#' or \eqn{y ~ a + b + (1 | c) + (1 | c : d)}. #' #' The \code{dataName} argument avoids you having to specify the name of the #' data frame in front of each covariate in the formula. #' For example, if the data frame is called \code{DataFrame} you avoid having to write: -#' \eqn{DataFrame$y~DataFrame$a+DataFrame$b+(1|DataFrame$c)}. +#' \eqn{DataFrame\$y ~ DataFrame\$a + DataFrame\$b + (1 | DataFrame\$c)}. #' #' The \code{checks} argument verifies that the variables in the model are all defined (exist) #' on the server-site at every study @@ -84,9 +84,9 @@ #' For more information see \strong{Details}. #' @param checks logical. If TRUE \code{ds.lmerSLMA} checks the structural integrity #' of the model. Default FALSE. For more information see \strong{Details}. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. #' If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @param REML logical. If TRUE the REstricted Maximum Likelihood (REML) #' is used for parameter optimization. #' If FALSE the parameters are optimized using standard ML (maximum likelihood). Default TRUE. @@ -192,7 +192,7 @@ #' #' # Fit the lmer #' -#' ds.lmerSLMA(formula = "BMI ~ incid_rate + diabetes + (1 | Male)", +#' ds.lmerSLMA(formula = "BMI ~ incid_rate + diabetes + (1 | Male)", #' dataName = "D.comp", #' datasources = connections) #' diff --git a/R/ds.log.R b/R/ds.log.R index faed3f10..8c0b2e5d 100644 --- a/R/ds.log.R +++ b/R/ds.log.R @@ -8,9 +8,9 @@ #' Default \code{exp(1)}. #' @param newobj a character string that provides the name for the output variable #' that is stored on the server-side. Default \code{log.newobj}. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. #' If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.log} returns a vector for each study of the transformed values for the numeric vector #' specified in the argument \code{x}. The created vectors are stored in the server-side. #' @author DataSHIELD Development Team diff --git a/R/ds.look.R b/R/ds.look.R index d45e5047..8dffa52f 100644 --- a/R/ds.look.R +++ b/R/ds.look.R @@ -20,9 +20,9 @@ #' For more information see \strong{Details}. #' @param checks logical. If TRUE the optional checks are undertaken. #' Default FALSE to save time. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return the output from the specified server-side aggregate function to the client-side. #' @author DataSHIELD Development Team #' diff --git a/R/ds.ls.R b/R/ds.ls.R index 8cfbf3ca..415c93f4 100644 --- a/R/ds.ls.R +++ b/R/ds.ls.R @@ -51,9 +51,9 @@ #' set as a valid integer, \code{ds.ls} will list all objects in the server-side R environment #' identified by \code{env.to.search} in the search path. #' For more information see \strong{Details}. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.ls} returns to the client-side a list containing: \cr #' (1) the name/details of the server-side R environment which \code{ds.ls} has searched;\cr #' (2) a vector of character strings giving the names of diff --git a/R/ds.lspline.R b/R/ds.lspline.R index 5c5cee79..9aca2397 100644 --- a/R/ds.lspline.R +++ b/R/ds.lspline.R @@ -14,9 +14,9 @@ #' @param names character, vector of names for constructed variables #' @param newobj a character string that provides the name for the output #' variable that is stored on the data servers. Default \code{lspline.newobj}. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return an object of class "lspline" and "matrix", which its name is specified by the #' \code{newobj} argument (or its default name "lspline.newobj"), is assigned on the serverside. #' @author Demetris Avraam for DataSHIELD Development Team @@ -54,4 +54,4 @@ ds.lspline <- function(x, knots = NULL, marginal = FALSE, names = NULL, newobj = calltext <- call("lsplineDS", x, knots, marginal, names) DSI::datashield.assign(datasources, newobj, calltext) -} \ No newline at end of file +} diff --git a/R/ds.make.R b/R/ds.make.R index eb341d8e..07d14a83 100644 --- a/R/ds.make.R +++ b/R/ds.make.R @@ -64,9 +64,9 @@ #' @param toAssign a character string specifying the function or the arithmetic expression. #' @param newobj a character string that provides the name for the output #' variable that is stored on the data servers. Default \code{make.newobj}. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.make} returns the new object which is written to the #' server-side. Also a validity message is returned to the client-side indicating whether the new object has been correctly #' created at each source. diff --git a/R/ds.matrix.R b/R/ds.matrix.R index d2e8f611..6ee9bdfd 100644 --- a/R/ds.matrix.R +++ b/R/ds.matrix.R @@ -45,9 +45,9 @@ #' the row and column names respectively. #' @param newobj a character string that provides the name for the output #' variable that is stored on the data servers. Default \code{matrix.newobj}. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.matrix} returns the created matrix which is written on the server-side. #' In addition, two validity messages are returned #' indicating whether the new matrix has been created in each data source and if so whether diff --git a/R/ds.matrixDet.R b/R/ds.matrixDet.R index 90ac58cf..5fcd81a5 100644 --- a/R/ds.matrixDet.R +++ b/R/ds.matrixDet.R @@ -13,9 +13,9 @@ #' variable that is stored on the data servers. Default \code{matrixdet.newobj}. #' @param logarithm logical. If TRUE the logarithm of the modulus of the determinant #' is calculated. Default FALSE. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.matrixDet} returns the determinant of an existing matrix on the server-side. #' The created new object is stored on the server-side. #' Also, two validity messages are returned diff --git a/R/ds.matrixDet.report.R b/R/ds.matrixDet.report.R index 126e48a7..be21aaa7 100644 --- a/R/ds.matrixDet.report.R +++ b/R/ds.matrixDet.report.R @@ -12,9 +12,9 @@ #' @param M1 a character string specifying the name of the matrix. #' @param logarithm logical. If TRUE the logarithm of the modulus of the determinant #' is calculated. Default FALSE. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.matrixDet.report} returns to the client-side #' the determinant of a matrix that is stored on the server-side. #' @author DataSHIELD Development Team diff --git a/R/ds.matrixDiag.R b/R/ds.matrixDiag.R index 9c9ec6e9..f6edcbcd 100644 --- a/R/ds.matrixDiag.R +++ b/R/ds.matrixDiag.R @@ -53,9 +53,9 @@ #' For more information see \strong{Details}. #' @param newobj a character string that provides the name for the output #' variable that is stored on the data servers. Default \code{matrixdiag.newobj}. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.matrixDiag} returns to the server-side the square matrix diagonal. #' Also, two validity messages are returned #' indicating whether the new object has been created in each data source and if so whether diff --git a/R/ds.matrixDimnames.R b/R/ds.matrixDimnames.R index d8376210..6f4a37ea 100644 --- a/R/ds.matrixDimnames.R +++ b/R/ds.matrixDimnames.R @@ -11,9 +11,9 @@ #' An empty list is treated as NULL. #' @param newobj a character string that provides the name for the output #' variable that is stored on the data servers. Default \code{matrixdimnames.newobj}. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.matrixDimnames} returns to the server-side #' the matrix with specified row and column names. #' Also, two validity messages are returned to the client-side diff --git a/R/ds.matrixInvert.R b/R/ds.matrixInvert.R index f7745ebb..8cc3c447 100644 --- a/R/ds.matrixInvert.R +++ b/R/ds.matrixInvert.R @@ -9,9 +9,9 @@ #' @param newobj a character string that provides the name for the output #' variable that is stored on the data servers. #' Default \code{matrixinvert.newobj}. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.matrixInvert} returns to the server-side the inverts square matrix. #' Also, two validity messages are returned to the client-side #' indicating whether the new object has been created in each data source and if so whether diff --git a/R/ds.matrixMult.R b/R/ds.matrixMult.R index 89ce42ab..cf5349fe 100644 --- a/R/ds.matrixMult.R +++ b/R/ds.matrixMult.R @@ -12,9 +12,9 @@ #' @param M2 a character string specifying the name of the second matrix. #' @param newobj a character string that provides the name for the output #' variable that is stored on the data servers. Default \code{matrixmult.newobj}. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.matrixMult} returns to the server-side #' the result of the two matrix multiplication. #' Also, two validity messages are returned to the client-side diff --git a/R/ds.matrixTranspose.R b/R/ds.matrixTranspose.R index 46556d46..bbd73a1a 100644 --- a/R/ds.matrixTranspose.R +++ b/R/ds.matrixTranspose.R @@ -12,9 +12,9 @@ #' @param newobj a character string that provides the name for the output #' variable that is stored on the data servers. #' Default \code{matrixtranspose.newobj}. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.matrixTranspose} returns to the server-side the transpose matrix. #' Also, two validity messages are returned to the client-side #' indicating whether the new object has been created in each data source and if so whether diff --git a/R/ds.mean.R b/R/ds.mean.R index e26ef636..f23356d5 100644 --- a/R/ds.mean.R +++ b/R/ds.mean.R @@ -38,9 +38,9 @@ #' the number of valid (non-missing) observations will be saved on the data servers. #' Default FALSE. #' For more information see \strong{Details}. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.mean} returns to the client-side a list including: \cr #' #' \code{Mean.by.Study}: estimated mean, \code{Nmissing} diff --git a/R/ds.meanByClass.R b/R/ds.meanByClass.R index 279bf891..538ef8c8 100644 --- a/R/ds.meanByClass.R +++ b/R/ds.meanByClass.R @@ -22,9 +22,9 @@ #' \code{type} can be set as: \code{'combine'} or \code{'split'}. #' Default \code{'combine'}. #' For more information see \strong{Details}. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.meanByClass} returns to the client-side a table or a list of tables that #' hold the length of the numeric variable(s) and their mean #' and standard deviation in each subgroup (subset). diff --git a/R/ds.meanSdGp.R b/R/ds.meanSdGp.R index 14a3fb91..1bd60936 100644 --- a/R/ds.meanSdGp.R +++ b/R/ds.meanSdGp.R @@ -61,9 +61,9 @@ #' are undertaken to ensure that the input objects are defined in all studies and that the #' variables are of equivalent class in each study. #' Default is FALSE to save time. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.meanSdGp} returns to the client-side the mean, SD, Nvalid and SEM combined #' across studies and/or separately for each study, depending on the argument \code{type}. #' diff --git a/R/ds.merge.R b/R/ds.merge.R index ae7d9f00..4ac436fb 100644 --- a/R/ds.merge.R +++ b/R/ds.merge.R @@ -45,9 +45,9 @@ #' For more information see \code{match} in native R \code{merge} function. #' @param newobj a character string that provides the name for the output #' variable that is stored on the data servers. Default \code{merge.newobj}. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.merge} returns the merged data frame that is written on the server-side. #' Also, two validity messages are returned to the client-side #' indicating whether the new object has been created in each data source and if so whether diff --git a/R/ds.message.R b/R/ds.message.R index 289c365b..eb88d8b9 100644 --- a/R/ds.message.R +++ b/R/ds.message.R @@ -19,9 +19,9 @@ #' Server function called: \code{messageDS} #' @param message.obj.name is a character string specifying the name of the list that #' contains the message. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.message} returns a list object from each study, #' containing the message that has been written by #' DataSHIELD into \code{$studysideMessage}. diff --git a/R/ds.metadata.R b/R/ds.metadata.R index 214bde6a..58f615b1 100644 --- a/R/ds.metadata.R +++ b/R/ds.metadata.R @@ -6,9 +6,9 @@ #' Server function \code{metadataDS} is called examines the attributes associated with the variable #' which are non-disclosive. #' @param x a character string specifying the name of the object. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.metadata} returns to the client-side the metadata of associated to an object #' held at the server. #' @author Stuart Wheater, DataSHIELD Development Team diff --git a/R/ds.mice.R b/R/ds.mice.R index f5e84f72..bcb473a4 100644 --- a/R/ds.mice.R +++ b/R/ds.mice.R @@ -38,9 +38,9 @@ #' that are stored on the data servers. Default \code{imputationSet}. For example, if m=5, and #' newobj_df="imputationSet", then five imputed dataframes are saved on the servers with names #' imputationSet.1, imputationSet.2, imputationSet.3, imputationSet.4, imputationSet.5. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return a list with three elements: the method, the predictorMatrix and the post. #' @author Demetris Avraam for DataSHIELD Development Team #' @export diff --git a/R/ds.names.R b/R/ds.names.R index 59af0990..97ebbdfd 100644 --- a/R/ds.names.R +++ b/R/ds.names.R @@ -11,11 +11,11 @@ #' using ds.glmSLMA. The resultant object saved on each server separately #' is formally of class "glm" and "ls" but responds TRUE to is.list(), #' @param xname a character string specifying the name of the list. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login that represent the particular data sources #' (studies) to be addressed by the function call. If the \code{datasources} #' argument is not specified the default set of connections will be used: -#' see \code{\link{datashield.connections_default}}. +#' see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.names} returns to the client-side the names #' of a list object stored on the server-side. #' @author Amadou Gaye, updated by Paul Burton for DataSHIELD development diff --git a/R/ds.ns.R b/R/ds.ns.R index cc11be6a..9c961fcf 100644 --- a/R/ds.ns.R +++ b/R/ds.ns.R @@ -22,9 +22,9 @@ #' are supplied, the basis parameters do not depend on x. Data can extend beyond Boundary.knots. #' @param newobj a character string that provides the name for the output #' variable that is stored on the data servers. Default \code{ns.newobj}. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return A matrix of dimension length(x) * df where either df was supplied or if knots were #' supplied, df = length(knots) + 1 + intercept. Attributes are returned that correspond to the #' arguments to ns, and explicitly give the knots, Boundary.knots etc for use by predict.ns(). @@ -54,4 +54,4 @@ ds.ns <- function(x, df = NULL, knots = NULL, intercept = FALSE, Boundary.knots calltext <- call("nsDS", x, df, knots, intercept, Boundary.knots) DSI::datashield.assign(datasources, newobj, calltext) -} \ No newline at end of file +} diff --git a/R/ds.numNA.R b/R/ds.numNA.R index c1757c87..0bd75185 100644 --- a/R/ds.numNA.R +++ b/R/ds.numNA.R @@ -7,9 +7,9 @@ #' #' Server function called: \code{numNaDS} #' @param x a character string specifying the name of the vector. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.numNA} returns to the client-side the number of missing values #' on a server-side vector. #' @author DataSHIELD Development Team diff --git a/R/ds.qlspline.R b/R/ds.qlspline.R index 0302ccc4..45a3e2d3 100644 --- a/R/ds.qlspline.R +++ b/R/ds.qlspline.R @@ -22,9 +22,9 @@ #' @param names character, vector of names for constructed variables #' @param newobj a character string that provides the name for the output #' variable that is stored on the data servers. Default \code{qlspline.newobj}. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return an object of class "lspline" and "matrix", which its name is specified by the #' \code{newobj} argument (or its default name "qlspline.newobj"), is assigned on the serverside. #' @author Demetris Avraam for DataSHIELD Development Team @@ -62,4 +62,4 @@ ds.qlspline <- function(x, q, na.rm = TRUE, marginal = FALSE, names = NULL, newo calltext <- call("qlsplineDS", x, q, na.rm, marginal, names) DSI::datashield.assign(datasources, newobj, calltext) -} \ No newline at end of file +} diff --git a/R/ds.quantileMean.R b/R/ds.quantileMean.R index 43e32696..48aa705b 100644 --- a/R/ds.quantileMean.R +++ b/R/ds.quantileMean.R @@ -15,9 +15,9 @@ #' @param type a character that represents the type of graph to display. #' This can be set as \code{'combine'} or \code{'split'}. #' For more information see \strong{Details}. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.quantileMean} returns to the client-side the quantiles and statistical mean #' of a server-side numeric vector. #' @author DataSHIELD Development Team diff --git a/R/ds.rBinom.R b/R/ds.rBinom.R index be5d9220..2f39f8b1 100644 --- a/R/ds.rBinom.R +++ b/R/ds.rBinom.R @@ -41,9 +41,9 @@ #' @param return.full.seed.as.set logical, if TRUE will return the full random number seed #' in each data source (a numeric vector of length 626). If FALSE it will only return the #' trigger seed value you have provided. Default is FALSE. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. #' If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.rBinom} returns random number vectors #' with a Binomial distribution for each study, #' taking into account the values specified in each parameter of the function. @@ -216,10 +216,11 @@ single.integer.seed<-c(single.integer.seed,seed.as.integer.study.specific) if(seed.as.text=="NULL"){ cat("NO SEED SET IN STUDY",study.id,"\n\n") -} +} else { calltext <- paste0("setSeedDS(", seed.as.text, ")") ssDS.obj[[study.id]] <- DSI::datashield.aggregate(datasources[study.id], as.symbol(calltext)) } +} cat("\n\n") diff --git a/R/ds.rNorm.R b/R/ds.rNorm.R index 0f53ab92..6100c850 100644 --- a/R/ds.rNorm.R +++ b/R/ds.rNorm.R @@ -52,9 +52,9 @@ #' Default is FALSE. #' @param force.output.to.k.decimal.places an integer vector that #' forces the output random numbers vector to have k decimals. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. #' If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.rNorm} returns random number vectors with a normal distribution for each #' study, taking into account the values specified in each parameter of the function. #' The output vector is written to the server-side. diff --git a/R/ds.rPois.R b/R/ds.rPois.R index 5fc262ff..2d2c7f01 100644 --- a/R/ds.rPois.R +++ b/R/ds.rPois.R @@ -38,9 +38,9 @@ #' random number seed in each data source (a numeric vector of length 626). If #' FALSE it will only return the trigger seed value you have provided. #' Default is FALSE. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. #' If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.rPois} returns random number vectors with a Poisson distribution for each study, #' taking into account the values specified in each parameter of the function. #' The created vectors are stored in the server-side. diff --git a/R/ds.rUnif.R b/R/ds.rUnif.R index 42691488..d98fa28f 100644 --- a/R/ds.rUnif.R +++ b/R/ds.rUnif.R @@ -58,9 +58,9 @@ #' an integer vector that forces the output random #' numbers vector to have k decimals. #' -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. #' If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.Unif} returns random number vectors with a uniform distribution for each study, #' taking into account the values specified in each parameter of the function. #' The created vectors are stored in the server-side. If requested, it also returned to the @@ -234,9 +234,10 @@ single.integer.seed<-c(single.integer.seed,seed.as.integer.study.specific) if(seed.as.text=="NULL"){ cat("NO SEED SET IN STUDY",study.id,"\n") -} +} else { calltext <- paste0("setSeedDS(", seed.as.text, ")") ssDS.obj[[study.id]] <- DSI::datashield.aggregate(datasources[study.id], as.symbol(calltext)) +} } diff --git a/R/ds.rbind.R b/R/ds.rbind.R index 85bca1d5..47e9165c 100644 --- a/R/ds.rbind.R +++ b/R/ds.rbind.R @@ -22,9 +22,9 @@ #' specifies column names of the output object. #' @param newobj a character string that provides the name for the output variable #' that is stored on the data servers. Defaults \code{rbind.newobj}. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. #' If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @param notify.of.progress specifies if console output should be produced to indicate #' progress. Default FALSE. #' @return \code{ds.rbind} returns a matrix combining the rows of the diff --git a/R/ds.reShape.R b/R/ds.reShape.R index 2a4840e9..f2214f55 100644 --- a/R/ds.reShape.R +++ b/R/ds.reShape.R @@ -29,9 +29,9 @@ #' @param newobj a character string that provides the name for the output object #' that is stored on the data servers. #' Default \code{reshape.newobj}. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.reShape} returns to the server-side a reshaped data frame #' converted from 'long' to 'wide' format or from 'wide' to long' format. #' Also, two validity messages are returned to the client-side diff --git a/R/ds.recodeLevels.R b/R/ds.recodeLevels.R index 671401e4..a22d25b3 100644 --- a/R/ds.recodeLevels.R +++ b/R/ds.recodeLevels.R @@ -13,9 +13,9 @@ #' to the current number of levels. #' @param newobj a character string that provides the name for the output object #' that is stored on the data servers. Default \code{recodelevels.newobj}. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.recodeLevels} returns to the server-side a variable of type factor #' with the replaces levels. #' @author DataSHIELD Development Team diff --git a/R/ds.recodeValues.R b/R/ds.recodeValues.R index 9643d33e..d44cc857 100644 --- a/R/ds.recodeValues.R +++ b/R/ds.recodeValues.R @@ -19,9 +19,9 @@ #' @param newobj a character string that provides the name for the output object #' that is stored on the data servers. #' Default \code{recodevalues.newobj}. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @param notify.of.progress logical. If TRUE console output should be produced to indicate #' progress. Default FALSE. #' @return Assigns to each server a new variable with the recoded values. diff --git a/R/ds.rep.R b/R/ds.rep.R index 0e526149..2d2ce951 100644 --- a/R/ds.rep.R +++ b/R/ds.rep.R @@ -23,9 +23,9 @@ #' the \code{x1} is a character. #' @param newobj a character string that provides the name for the output object #' that is stored on the data servers. Default \code{seq.vect}. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. #' If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.rep} returns in the server-side a vector with the specified repetitive sequence. #' Also, two validity messages are returned to the client-side #' the name of \code{newobj} that has been created diff --git a/R/ds.replaceNA.R b/R/ds.replaceNA.R index 3345b7de..28a51adb 100644 --- a/R/ds.replaceNA.R +++ b/R/ds.replaceNA.R @@ -19,9 +19,9 @@ #' The length of the list or vector must be equal to the number of servers (studies). #' @param newobj a character string that provides the name for the output object #' that is stored on the data servers. Default \code{replacena.newobj}. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. #' If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.replaceNA} returns to the server-side a new vector or table structure #' with the missing values replaced by the specified values. #' The class of the vector is the same as the initial vector. diff --git a/R/ds.rm.R b/R/ds.rm.R index 77b693db..e977afe5 100644 --- a/R/ds.rm.R +++ b/R/ds.rm.R @@ -14,9 +14,9 @@ #' #' Server function called: \code{rmDS} #' @param x.names a character string specifying the objects to be deleted. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. #' If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return The \code{ds.rm} function deletes from the server-side #' the specified object. If this #' is successful the message \code{"Object(s) '' was deleted."} is returned @@ -94,4 +94,4 @@ ds.rm<-function(x.names=NULL, datasources=NULL){ return(output) } -#ds.rm \ No newline at end of file +#ds.rm diff --git a/R/ds.rowColCalc.R b/R/ds.rowColCalc.R index b63190bf..d531cce4 100644 --- a/R/ds.rowColCalc.R +++ b/R/ds.rowColCalc.R @@ -14,9 +14,9 @@ #' \code{"rowSums"}, \code{"colSums"}, \code{"rowMeans"} or \code{"colMeans"}. #' @param newobj a character string that provides the name for the output variable #' that is stored on the data servers. Default \code{rowcolcalc.newobj}. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. #' If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.rowColCalc} returns to the server-side rows and columns sums and means. #' @author DataSHIELD Development Team #' @examples diff --git a/R/ds.scatterPlot.R b/R/ds.scatterPlot.R index 81828648..827b3272 100644 --- a/R/ds.scatterPlot.R +++ b/R/ds.scatterPlot.R @@ -64,9 +64,9 @@ #' For more information see \strong{Details}. #' @param return.coords a logical. If TRUE the coordinates of the anonymised data points are return #' to the Console. Default value is FALSE. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. #' If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.scatterPlot} returns to the client-side one or more scatter #' plots depending on the argument \code{type}. #' @author DataSHIELD Development Team diff --git a/R/ds.seq.R b/R/ds.seq.R index 1f0b722a..d21522a0 100644 --- a/R/ds.seq.R +++ b/R/ds.seq.R @@ -55,9 +55,9 @@ #' For more information see \strong{Details}. #' @param newobj a character string that provides the name for the output variable #' that is stored on the data servers. Default \code{seq.newobj}. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. #' If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.seq} returns to the server-side the generated sequence. #' Also, two validity messages are returned to the client-side #' indicating whether the new object has been created in each data source and if so whether diff --git a/R/ds.setSeed.R b/R/ds.setSeed.R index 20eabd5b..ee84a174 100644 --- a/R/ds.setSeed.R +++ b/R/ds.setSeed.R @@ -31,9 +31,9 @@ #' Server function called: \code{setSeedDS} #' @param seed.as.integer a numeric value or a NULL that primes the random seed #' in each data source. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. #' If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return Sets the values of the vector of integers of length 626 known as #' \code{.Random.seed} on each data source that is the true current state of the #' random seed in each source. It also returns the value of the trigger diff --git a/R/ds.skewness.R b/R/ds.skewness.R index ed3b05d9..0ef8d93d 100644 --- a/R/ds.skewness.R +++ b/R/ds.skewness.R @@ -31,9 +31,9 @@ #' \code{type} can be set as: \code{'combine'}, \code{'split'} or \code{'both'}. For more information #' see \strong{Details}. #' The default value is set to \code{'both'}. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.skewness} returns a matrix showing the skewness of the input numeric variable, #' the number of valid observations and the validity message. #' @author Demetris Avraam, for DataSHIELD Development Team diff --git a/R/ds.sqrt.R b/R/ds.sqrt.R index 22a03937..9193dbbc 100644 --- a/R/ds.sqrt.R +++ b/R/ds.sqrt.R @@ -10,9 +10,9 @@ #' @param x a character string providing the name of a numeric or an integer vector. #' @param newobj a character string that provides the name for the output variable #' that is stored on the data servers. Default name is set to \code{sqrt.newobj}. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. #' If the \code{datasources} argument is not specified the default set of connections will be -#' used: see \code{\link{datashield.connections_default}}. +#' used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.sqrt} assigns a vector for each study that includes the square root values of #' the input numeric or integer vector specified in the argument \code{x}. The created vectors #' are stored in the servers. diff --git a/R/ds.subset.R b/R/ds.subset.R index 6f21bd08..40bd6ce0 100644 --- a/R/ds.subset.R +++ b/R/ds.subset.R @@ -19,8 +19,8 @@ #' operator. This parameter is ignored if the input data is not a vector. #' @param threshold a numeric, the threshold to use in conjunction with the logical parameter. This parameter is ignored #' if the input data is not a vector. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. If the -#' the default set of connections will be used: see \link{datashield.connections_default}. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the +#' the default set of connections will be used: see \link[DSI]{datashield.connections_default}. #' @return no data are return to the user, the generated subset dataframe is stored on the server side. #' @author Gaye, A. #' @seealso \link{ds.subsetByClass} to subset by the classes of factor vector(s). diff --git a/R/ds.subsetByClass.R b/R/ds.subsetByClass.R index 2a2ab29a..5c6f92bb 100644 --- a/R/ds.subsetByClass.R +++ b/R/ds.subsetByClass.R @@ -11,8 +11,8 @@ #' @param variables a vector of string characters, the name(s) of the variables to subset by. #' @param subsets the name of the output object, a list that holds the subset objects. If set to NULL #' the default name of this list is 'subClasses'. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. If the -#' the default set of connections will be used: see \link{datashield.connections_default}. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the +#' the default set of connections will be used: see \link[DSI]{datashield.connections_default}. #' @return a no data are return to the user but messages are printed out. #' @author Gaye, A. #' @seealso \link{ds.meanByClass} to compute mean and standard deviation across categories of a factor vectors. diff --git a/R/ds.summary.R b/R/ds.summary.R index b4d3061c..2d86287b 100644 --- a/R/ds.summary.R +++ b/R/ds.summary.R @@ -9,9 +9,9 @@ #' #' server functions called: \code{isValidDS}, \code{dimDS} and \code{colnamesDS} #' @param x a character string specifying the name of a numeric or factor variable. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. #' If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.summary} returns to the client-side the class and #' size of the server-side object. #' Also other information is returned depending on the class of the object. diff --git a/R/ds.table.R b/R/ds.table.R index f5a623d4..780f9f86 100644 --- a/R/ds.table.R +++ b/R/ds.table.R @@ -149,8 +149,8 @@ #' If no explicit name for the table object is specified, but #' is nevertheless TRUE, the name for the serverside table object defaults #' to \code{table.newobj}. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. If the -#' the default set of connections will be used: see \link{datashield.connections_default}. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the +#' the default set of connections will be used: see \link[DSI]{datashield.connections_default}. #' If the is to be specified, it should be set without #' inverted commas: e.g. datasources=connections.em or datasources=default.connections. If you wish to #' apply the function solely to e.g. the second connection server in a set of three, diff --git a/R/ds.table1D.R b/R/ds.table1D.R index 76e13199..07df60eb 100644 --- a/R/ds.table1D.R +++ b/R/ds.table1D.R @@ -16,8 +16,8 @@ #' @param warningMessage a boolean, if set to TRUE (deafult) a warning is displayed if any returned table is invalid. Warning #' messages are suppressed if this parameter is set to FALSE. However the analyst can still view 'validity' information #' which are stored in the output object 'validity' - see the list of output objects. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. If the -#' the default set of connections will be used: see \link{datashield.connections_default}. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the +#' the default set of connections will be used: see \link[DSI]{datashield.connections_default}. #' @return A list object containing the following items: #' \item{counts}{ table(s) that hold counts for each level/category. If some cells counts are invalid (see 'Details' #' section) only the total (outer) cell counts are displayed in the returned individual study tables or in the pooled diff --git a/R/ds.table2D.R b/R/ds.table2D.R index c8b882ac..301a8993 100644 --- a/R/ds.table2D.R +++ b/R/ds.table2D.R @@ -17,8 +17,8 @@ #' @param warningMessage a boolean, if set to TRUE (deafult) a warning is displayed if any returned table is invalid. Warning #' messages are suppressed if this parameter is set to FALSE. However the analyst can still view 'validity' information #' which are stored in the output object 'validity' - see the list of output objects. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. If the -#' the default set of connections will be used: see \link{datashield.connections_default}. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the +#' the default set of connections will be used: see \link[DSI]{datashield.connections_default}. #' @return A list object containing the following items: #' \item{colPercent}{table(s) that hold column percentages for each level/category. Inner cells are reported as #' missing if one or more cells are 'invalid'.} diff --git a/R/ds.tapply.R b/R/ds.tapply.R index 457ecfe4..e9805e1d 100644 --- a/R/ds.tapply.R +++ b/R/ds.tapply.R @@ -68,9 +68,9 @@ #' \code{"N"} (or \code{"length"}), \code{"mean"},\code{"sd"}, \code{"sum"}, #' or \code{"quantile"}. #' For more information see \strong{Details}. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.tapply} returns to the client-side an array of the summarized values. #' It has the same number of dimensions as INDEX. #' @examples diff --git a/R/ds.tapply.assign.R b/R/ds.tapply.assign.R index 6f506532..be7b7408 100644 --- a/R/ds.tapply.assign.R +++ b/R/ds.tapply.assign.R @@ -70,9 +70,9 @@ #' For more information see \strong{Details}. #' @param newobj a character string that provides the name for the output variable #' that is stored on the data servers. Default \code{tapply.assign.newobj}. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.tapply.assign} returns an array of the summarized values. #' The array is written to the server-side. It has the same number of #' dimensions as INDEX. diff --git a/R/ds.testObjExists.R b/R/ds.testObjExists.R index bf84065d..5b7e946a 100644 --- a/R/ds.testObjExists.R +++ b/R/ds.testObjExists.R @@ -8,9 +8,9 @@ #' #' Server function called: \code{testObjExistsDS} #' @param test.obj.name a character string specifying the name of the object to search. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.testObjExists} returns a list of messages specifying that the object exists #' on the server-side. #' If the specified object does not exist in at least one diff --git a/R/ds.unList.R b/R/ds.unList.R index 773246fd..fa14a4f2 100644 --- a/R/ds.unList.R +++ b/R/ds.unList.R @@ -18,9 +18,9 @@ #' @param x.name a character string specifying the name of the input object to be unlisted. #' @param newobj a character string that provides the name for the output variable #' that is stored on the data servers. Default \code{unlist.newobj}. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.unList} returns to the server-side the unlist object. #' Also, two validity messages are returned to the client-side #' indicating whether the new object has been created in each data source and if so whether diff --git a/R/ds.unique.R b/R/ds.unique.R index 29797dee..327585bd 100644 --- a/R/ds.unique.R +++ b/R/ds.unique.R @@ -7,9 +7,9 @@ #' @param x.name a character string providing the name of the varable, in the server, to perform \code{unique} upon #' @param newobj a character string that provides the name for the output object #' that is stored on the data servers. Default \code{unique.newobj}. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.unique} returns the vector of unique R objects which are written to the server-side. #' @examples #' \dontrun{ diff --git a/R/ds.var.R b/R/ds.var.R index 0a74d4eb..178dc443 100644 --- a/R/ds.var.R +++ b/R/ds.var.R @@ -23,9 +23,9 @@ #' components will be undertaken. Default is FALSE to save time. #' It is suggested that checks #' should only be undertaken once the function call has failed. -#' @param datasources a list of \code{\link{DSConnection-class}} +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @return \code{ds.var} returns to the client-side a list including:\cr #' #' \code{Variance.by.Study}: estimated variance, \code{Nmissing} diff --git a/R/ds.vectorCalc.R b/R/ds.vectorCalc.R index bc090a87..f019c7bc 100644 --- a/R/ds.vectorCalc.R +++ b/R/ds.vectorCalc.R @@ -13,8 +13,8 @@ #' @param calc a character, a symbol that indicates the mathematical operation to carry out: #' '+' for addition, '/' for division, *' for multiplication and '-' for subtraction. #' @param newobj the name of the output object. By default the name is 'vectorcalc.newobj'. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. If the -#' the default set of connections will be used: see \link{datashield.connections_default}. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the +#' the default set of connections will be used: see \link[DSI]{datashield.connections_default}. #' @return no data are returned to user, the output vector is stored on the server side. #' @author Gaye, A. #' @export diff --git a/R/getPooledMean.R b/R/getPooledMean.R index ded7fae8..dba45bf3 100644 --- a/R/getPooledMean.R +++ b/R/getPooledMean.R @@ -4,8 +4,8 @@ #' @details This function is called to avoid calling the client function 'ds.mean' #' which may stop the process due to some checks not required when computing a mean inside #' a function. -#' @param dtsources a list of \code{\link{DSConnection-class}} objects obtained after login. If the -#' the default set of connections will be used: see \link{datashield.connections_default}. +#' @param dtsources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the +#' the default set of connections will be used: see \link[DSI]{datashield.connections_default}. #' @param x a character, the name of a numeric vector #' @keywords internal #' @return a pooled mean diff --git a/R/getPooledVar.R b/R/getPooledVar.R index 9fc9bbcd..0738d4bf 100644 --- a/R/getPooledVar.R +++ b/R/getPooledVar.R @@ -4,8 +4,8 @@ #' @details This function is called to avoid calling the client function 'ds.var' #' which may stop the process due to some checks not required when computing a mean inside #' a function. -#' @param dtsources a list of \code{\link{DSConnection-class}} objects obtained after login. If the -#' the default set of connections will be used: see \link{datashield.connections_default}. +#' @param dtsources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the +#' the default set of connections will be used: see \link[DSI]{datashield.connections_default}. #' @param x a character, the name of a numeric vector #' @keywords internal #' @return a pooled variance diff --git a/R/glmChecks.R b/R/glmChecks.R index 53576448..c720fa45 100644 --- a/R/glmChecks.R +++ b/R/glmChecks.R @@ -12,8 +12,8 @@ #' included in the linear predictor during fitting. #' @param weights a character, the name of an optional vector of 'prior weights' to be used in the fitting #' process. Should be NULL or a numeric vector. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. If the -#' the default set of connections will be used: see \link{datashield.connections_default}. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the +#' the default set of connections will be used: see \link[DSI]{datashield.connections_default}. #' @keywords internal #' @return an integer 0 if check was passed and 1 if failed #' @author Gaye, A. diff --git a/R/isAssigned.R b/R/isAssigned.R index c0f5150f..0460cb77 100644 --- a/R/isAssigned.R +++ b/R/isAssigned.R @@ -4,8 +4,8 @@ #' @details After calling an assign function it is important #' to know whether or not the action has been completed by #' checking if the output actually exists on the server side. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. If the -#' the default set of connections will be used: see \link{datashield.connections_default}. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the +#' the default set of connections will be used: see \link[DSI]{datashield.connections_default}. #' @param newobj a character, the name the object to look for. #' @keywords internal #' @return nothing is return but the process is stopped if diff --git a/R/isDefined.R b/R/isDefined.R index a0206257..621b809a 100644 --- a/R/isDefined.R +++ b/R/isDefined.R @@ -3,9 +3,9 @@ #' @description This is an internal function. #' @details In DataSHIELD an object included in analysis must be defined (i.e. exists) #' in all the studies. If not the process should halt. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. #' If the \code{datasources} argument is not specified, the default set of connections will be -#' used: see \code{\link{datashield.connections_default}}. +#' used: see \code{\link[DSI]{datashield.connections_default}}. #' @param obj a character vector, the name of the object(s) to look for. #' @param error.message a Boolean which specifies if the function should stop and return #' an error message when the input object is not defined in one or more studies or to diff --git a/R/meanByClassHelper0a.R b/R/meanByClassHelper0a.R index d94898ff..21c6e90c 100644 --- a/R/meanByClassHelper0a.R +++ b/R/meanByClassHelper0a.R @@ -8,8 +8,8 @@ #' @param type a character which represents the type of analysis to carry out. If \code{type} is set to #' 'combine', a pooled table of results is generated. If \code{type} is set to 'split', a table of results #' is genrated for each study. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. If the -#' the default set of connections will be used: see \link{datashield.connections_default}. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the +#' the default set of connections will be used: see \link[DSI]{datashield.connections_default}. #' @return a table or a list of tables that hold the length of the numeric variable and its mean #' and standard deviation in each subgroup (subset). #' @keywords internal diff --git a/R/meanByClassHelper0b.R b/R/meanByClassHelper0b.R index 21b66d44..1419d53f 100644 --- a/R/meanByClassHelper0b.R +++ b/R/meanByClassHelper0b.R @@ -9,8 +9,8 @@ #' @param type a character which represents the type of analysis to carry out. If \code{type} is set to #' 'combine', a pooled table of results is generated. If \code{type} is set to 'split', a table of results #' is genrated for each study. -#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login. If the -#' the default set of connections will be used: see \link{datashield.connections_default}. +#' @param datasources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the +#' the default set of connections will be used: see \link[DSI]{datashield.connections_default}. #' @return a table or a list of tables that hold the length of the numeric variable(s) and their mean #' and standard deviation in each subgroup (subset). #' @keywords internal diff --git a/R/meanByClassHelper1.R b/R/meanByClassHelper1.R index 6010e58b..4b98201e 100644 --- a/R/meanByClassHelper1.R +++ b/R/meanByClassHelper1.R @@ -3,8 +3,8 @@ #' @description This is an internal function. #' @details This function is called by the function 'ds.meanByClass' to break down #' the initial table by the specified categorical variables. -#' @param dtsource a list of \code{\link{DSConnection-class}} objects obtained after login. If the -#' the default set of connections will be used: see \link{datashield.connections_default}. +#' @param dtsource a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the +#' the default set of connections will be used: see \link[DSI]{datashield.connections_default}. #' @param tables a character vector, the tables to breakdown #' @param variable a character, the variable to subset on #' @param categories a character vector, the classes in the variables to subset on diff --git a/R/meanByClassHelper2.R b/R/meanByClassHelper2.R index a0b0dfef..9fac9125 100644 --- a/R/meanByClassHelper2.R +++ b/R/meanByClassHelper2.R @@ -3,8 +3,8 @@ #' @description This is an internal function. #' @details This function is called by the function 'ds.meanByClass' to produce the final table #' if the user sets the parmater 'type' to combine (the default behaviour of 'ds.meanByClass'). -#' @param dtsources a list of \code{\link{DSConnection-class}} objects obtained after login. If the -#' the default set of connections will be used: see \link{datashield.connections_default}. +#' @param dtsources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the +#' the default set of connections will be used: see \link[DSI]{datashield.connections_default}. #' @param tablenames a character vector, the name of the subset tables #' @param variables a character vector, the names of the continuous variables to computes a mean for. #' @param invalidrecorder a list, holds informations about invalid subsets in each study. diff --git a/R/meanByClassHelper3.R b/R/meanByClassHelper3.R index 0b820033..61e61d1f 100644 --- a/R/meanByClassHelper3.R +++ b/R/meanByClassHelper3.R @@ -3,8 +3,8 @@ #' @description This is an internal function. #' @details This function is called by the function 'ds.meanByClass' to produce the final tables #' if the user sets the parmater 'type' to 'split'. -#' @param dtsources a list of \code{\link{DSConnection-class}} objects obtained after login. If the -#' the default set of connections will be used: see \link{datashield.connections_default}. +#' @param dtsources a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the +#' the default set of connections will be used: see \link[DSI]{datashield.connections_default}. #' @param tablenames a character vector, the name of the subset tables #' @param variables a character vector, the names of the continuous variables to computes a mean for. #' @param invalidrecorder a list, holds informations about invalid subsets in each study diff --git a/R/meanByClassHelper4.R b/R/meanByClassHelper4.R index 88e827fc..9597a7e8 100644 --- a/R/meanByClassHelper4.R +++ b/R/meanByClassHelper4.R @@ -3,8 +3,8 @@ #' @description This is an internal function. #' @details This function is called by the function 'ds.meanByClass' to obtain 'loose' #' subset tables because the 'subsetByClass' function does not handle a table within a list. -#' @param dtsource a list of \code{\link{DSConnection-class}} objects obtained after login. If the -#' the default set of connections will be used: see \link{datashield.connections_default}. +#' @param dtsource a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the +#' the default set of connections will be used: see \link[DSI]{datashield.connections_default}. #' @param alist the name of the list that holds the final subset tables #' @param initialtable a character the name of the table that the subset were generated from #' @param variable a character, the variable to subset on diff --git a/R/subsetHelper.R b/R/subsetHelper.R index c01529ac..025a0680 100644 --- a/R/subsetHelper.R +++ b/R/subsetHelper.R @@ -7,9 +7,9 @@ #' This function is internal. #' #' Server function called: \code{dimDS} -#' @param dts a list of \code{\link{DSConnection-class}} +#' @param dts a list of \code{\link[DSI]{DSConnection-class}} #' objects obtained after login. If the \code{datasources} argument is not specified -#' the default set of connections will be used: see \code{\link{datashield.connections_default}}. +#' the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}. #' @param data a character string specifying the name of the data frame or #' the factor vector and the range of the subset. #' @param rs a vector of two integers specifying the indices of the rows de extract. diff --git a/README.md b/README.md index 936e913c..173f0824 100644 --- a/README.md +++ b/README.md @@ -3,16 +3,6 @@ dsBaseClient DataSHIELD client side base R library. -| Branch | dsBase status | dsBase tests | dsBaseClient status | dsBaseClient tests | -| -------- | ------------- | ------------ | ------------------- | ------------------ | -| Master | [![Build Status](https://dev.azure.com/datashield-testing/datashield/_apis/build/status/datashield.dsBase?branchName=master)](https://dev.azure.com/datashield-testing/datashield/_build/latest?definitionId=3&branchName=master) | | [![Build Status](https://dev.azure.com/datashield-testing/datashield/_apis/build/status/datashield.dsBaseClient?branchName=master)](https://dev.azure.com/datashield-testing/datashield/_build/latest?definitionId=1&branchName=master) | [Tests](https://datashield.github.io/testStatus/dsBaseClient/master/latest/) | -| 6.0 | [![Build Status](https://dev.azure.com/datashield-testing/datashield/_apis/build/status/datashield.dsBase?branchName=v6.0)](https://dev.azure.com/datashield-testing/datashield/_build/latest?definitionId=3&branchName=v6.0) | | [![Build Status](https://dev.azure.com/datashield-testing/datashield/_apis/build/status/datashield.dsBaseClient?branchName=v6.0)](https://dev.azure.com/datashield-testing/datashield/_build/latest?definitionId=1&branchName=v6.0) | [Tests](https://datashield.github.io/testStatus/dsBaseClient/v6.0/latest/) | -| 6.0.1 | [![Build Status](https://dev.azure.com/datashield-testing/datashield/_apis/build/status/datashield.dsBase?branchName=v6.0.1)](https://dev.azure.com/datashield-testing/datashield/_build/latest?definitionId=3&branchName=v6.0.1) | | [![Build Status](https://dev.azure.com/datashield-testing/datashield/_apis/build/status/datashield.dsBaseClient?branchName=v6.0.1)](https://dev.azure.com/datashield-testing/datashield/_build/latest?definitionId=1&branchName=v6.0.1) | [Tests](https://datashield.github.io/testStatus/dsBaseClient/v6.0.1/latest/) | -| 6.1 | [![Build Status](https://dev.azure.com/datashield-testing/datashield/_apis/build/status/datashield.dsBase?branchName=v6.1)](https://dev.azure.com/datashield-testing/datashield/_build/latest?definitionId=3&branchName=v6.1) | [Tests](https://datashield.github.io/testStatus/dsBase/v6.1/latest/) | [![Build Status](https://dev.azure.com/datashield-testing/datashield/_apis/build/status/datashield.dsBaseClient?branchName=v6.1)](https://dev.azure.com/datashield-testing/datashield/_build/latest?definitionId=1&branchName=v6.1) | [Tests](https://datashield.github.io/testStatus/dsBaseClient/v6.1/latest/) | -| 6.1.1 | [![Build Status](https://dev.azure.com/datashield-testing/datashield/_apis/build/status/datashield.dsBase?branchName=v6.1.1)](https://dev.azure.com/datashield-testing/datashield/_build/latest?definitionId=3&branchName=v6.1.1) | [Tests](https://datashield.github.io/testStatus/dsBase/v6.1.1/latest/) | [![Build Status](https://dev.azure.com/datashield-testing/datashield/_apis/build/status/datashield.dsBaseClient?branchName=v6.1.1)](https://dev.azure.com/datashield-testing/datashield/_build/latest?definitionId=1&branchName=v6.1.1) | [Tests](https://datashield.github.io/testStatus/dsBaseClient/v6.1.1/latest/) | -| 6.2 | [![Build Status](https://dev.azure.com/datashield-testing/datashield/_apis/build/status/datashield.dsBase?branchName=v6.2)](https://dev.azure.com/datashield-testing/datashield/_build/latest?definitionId=3&branchName=v6.2) | [Tests](https://datashield.github.io/testStatus/dsBase/v6.2/latest/) | [![Build Status](https://dev.azure.com/datashield-testing/datashield/_apis/build/status/datashield.dsBaseClient?branchName=v6.2)](https://dev.azure.com/datashield-testing/datashield/_build/latest?definitionId=1&branchName=v6.2) | [Tests](https://datashield.github.io/testStatus/dsBaseClient/v6.2/latest/) | - - [![License](https://img.shields.io/badge/license-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0.html) About diff --git a/armadillo_azure-pipelines.yml b/armadillo_azure-pipelines.yml index 192bf470..08a1bbb0 100644 --- a/armadillo_azure-pipelines.yml +++ b/armadillo_azure-pipelines.yml @@ -58,10 +58,10 @@ schedules: - master always: true - cron: "0 2 * * *" - displayName: Nightly build - v6.3.1-dev + displayName: Nightly build - v6.3.2-dev branches: include: - - v6.3.1-dev + - v6.3.2-dev always: true ######################################################################################### @@ -71,7 +71,7 @@ jobs: - job: build_and_run_tests timeoutInMinutes: 360 pool: - vmImage: ubuntu-22.04 + vmImage: ubuntu-24.04 steps: ##################################################################################### @@ -125,17 +125,16 @@ jobs: # Install R and all the dependencies dsBaseClient requires. # If previous steps have failed then don't run. - bash: | - - sudo apt-get update -qq sudo apt-get install --no-install-recommends software-properties-common dirmngr wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | sudo tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc sudo add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/" + sudo apt-get update -qq sudo apt-get upgrade -y sudo apt-get install -qq libxml2-dev libcurl4-openssl-dev libssl-dev libgsl-dev libgit2-dev r-base -y sudo apt-get install -qq libharfbuzz-dev libfribidi-dev libmagick++-dev -y sudo R -q -e "install.packages(c('devtools','covr'), dependencies=TRUE, repos='https://cloud.r-project.org')" - sudo R -q -e "install.packages(c('fields','meta','metafor','ggplot2','gridExtra','data.table','panelaggregation'), dependencies=TRUE, repos='https://cloud.r-project.org')" + sudo R -q -e "install.packages(c('fields','meta','metafor','ggplot2','gridExtra','data.table'), dependencies=TRUE, repos='https://cloud.r-project.org')" sudo R -q -e "install.packages(c('DSI','DSOpal','DSLite'), dependencies=TRUE, repos='https://cloud.r-project.org')" sudo R -q -e "install.packages(c('MolgenisAuth', 'MolgenisArmadillo', 'DSMolgenisArmadillo'), dependencies=TRUE, repos='https://cloud.r-project.org')" sudo R -q -e "install.packages(c('DescTools','e1071'), dependencies=TRUE, repos='https://cloud.r-project.org')" @@ -186,7 +185,7 @@ jobs: # If this step fails still mark as failed, but don't stop the rest of the steps running. - bash: | - R -q -e "library('devtools'); devtools::check(args = c('--no-examples'))" | tee azure-pipelines_check.Rout + R -q -e "library('devtools'); devtools::check(args = c('--no-examples', '--no-tests'))" | tee azure-pipelines_check.Rout grep --quiet "^0 errors" azure-pipelines_check.Rout && grep --quiet " 0 warnings" azure-pipelines_check.Rout && grep --quiet " 0 notes" azure-pipelines_check.Rout workingDirectory: $(Pipeline.Workspace)/dsBaseClient @@ -236,7 +235,7 @@ jobs: curl -u admin:admin -X GET http://localhost:8080/packages - curl -u admin:admin --max-time 300 -v -H 'Content-Type: multipart/form-data' -F "file=@dsBase_6.3.1-permissive.tar.gz" -X POST http://localhost:8080/install-package + curl -u admin:admin --max-time 300 -v -H 'Content-Type: multipart/form-data' -F "file=@dsBase_6.3.2-permissive.tar.gz" -X POST http://localhost:8080/install-package sleep 60 docker container restart dsbaseclient_armadillo_1 @@ -264,7 +263,7 @@ jobs: # best guess is that there is an implicit build or similar that happens. Although # I cannot replicate that directly with build etc directly. - sudo R --verbose -e 'devtools::check()' + sudo R --verbose -e 'devtools::reload()' mkdir $(Pipeline.Workspace)/logs @@ -289,6 +288,7 @@ jobs: junit_rep <- JunitReporter$new(file = "test_results_dsbase.xml"); progress_rep <- ProgressReporter$new(max_failures = 999999); multi_rep <- MultiReporter$new(reporters = list(progress_rep, junit_rep)); + options("datashield.return_errors" = FALSE); options("default_driver" = "ArmadilloDriver"); testthat::test_package("$(projectName)", filter = "_-|datachk-|smk-|arg-|disc-|perf-|smk_expt-|expt-|math-", reporter = multi_rep, stop_on_failure = FALSE) '"'"' @@ -364,7 +364,7 @@ jobs: - bash: | curl -u admin:admin http://localhost:8080/whitelist - curl -u admin:admin -v -H 'Content-Type: multipart/form-data' -F "file=@dsDanger_6.3.1.tar.gz" -X POST http://localhost:8080/install-package + curl -u admin:admin -v -H 'Content-Type: multipart/form-data' -F "file=@dsDanger_6.3.2.tar.gz" -X POST http://localhost:8080/install-package docker container restart dsbaseclient_armadillo_1 sleep 60 @@ -387,7 +387,7 @@ jobs: - bash: | # See, 'Code coverage and JUnit report output' for issues with the approach and improvement needed. - sudo R --verbose -e 'devtools::check()' + sudo R --verbose -e 'devtools::reload()' pwd mkdir $(Pipeline.Workspace)/logs @@ -410,6 +410,7 @@ jobs: junit_rep <- JunitReporter$new(file = "test_results_dsdanger.xml"); progress_rep <- ProgressReporter$new(max_failures = 999999); multi_rep <- MultiReporter$new(reporters = list(progress_rep, junit_rep)); + options("datashield.return_errors" = FALSE); options("default_driver" = "ArmadilloDriver"); testthat::test_package("$(projectName)", filter = "__dgr-|datachk_dgr-|smk_dgr-|arg_dgr-|disc_dgr-|smk_expt_dgr-|expt_dgr-|math_dgr-", reporter = multi_rep, stop_on_failure = FALSE) '"'"' diff --git a/azure-pipelines.yml b/azure-pipelines.yml index faea6e89..2ce0e4d5 100644 --- a/azure-pipelines.yml +++ b/azure-pipelines.yml @@ -58,10 +58,10 @@ schedules: - master always: true - cron: "0 2 * * *" - displayName: Nightly build - v6.3.1-dev + displayName: Nightly build - v6.3.2-dev branches: include: - - v6.3.1-dev + - v6.3.2-dev always: true ######################################################################################### @@ -71,7 +71,7 @@ jobs: - job: build_and_run_tests timeoutInMinutes: 360 pool: - vmImage: ubuntu-22.04 + vmImage: ubuntu-24.04 steps: ##################################################################################### @@ -125,26 +125,22 @@ jobs: # Install R and all the dependencies dsBaseClient requires. # If previous steps have failed then don't run. - bash: | - - sudo apt update -qq - sudo apt install --no-install-recommends software-properties-common dirmngr + sudo apt-get install --no-install-recommends software-properties-common dirmngr wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | sudo tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc sudo add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/" - -# sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9 -# sudo add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu focal-cran40/" -# sudo add-apt-repository ppa:cran/libgit2 - sudo apt-get update + sudo apt-get update -qq + sudo apt-get upgrade -y sudo apt-get install -qq libxml2-dev libcurl4-openssl-dev libssl-dev libgsl-dev libgit2-dev r-base -y sudo apt-get install -qq libharfbuzz-dev libfribidi-dev libmagick++-dev -y + sudo R -q -e "install.packages(c('curl','httr'), dependencies=TRUE, repos='https://cloud.r-project.org')" sudo R -q -e "install.packages(c('devtools','covr'), dependencies=TRUE, repos='https://cloud.r-project.org')" - sudo R -q -e "install.packages(c('fields','meta','metafor','ggplot2','gridExtra','data.table','panelaggregation'), dependencies=TRUE, repos='https://cloud.r-project.org')" + sudo R -q -e "install.packages(c('fields','meta','metafor','ggplot2','gridExtra','data.table'), dependencies=TRUE, repos='https://cloud.r-project.org')" sudo R -q -e "install.packages(c('DSI','DSOpal','DSLite'), dependencies=TRUE, repos='https://cloud.r-project.org')" sudo R -q -e "install.packages(c('MolgenisAuth', 'MolgenisArmadillo', 'DSMolgenisArmadillo'), dependencies=TRUE, repos='https://cloud.r-project.org')" sudo R -q -e "install.packages(c('DescTools','e1071'), dependencies=TRUE, repos='https://cloud.r-project.org')" - sudo R -q -e "library('devtools'); devtools::install_github(repo='datashield/dsDangerClient', ref='6.3.1', dependencies = TRUE)" + sudo R -q -e "library('devtools'); devtools::install_github(repo='datashield/dsDangerClient', ref='6.3.2', dependencies = TRUE)" # XML grep for coverage report merging sudo apt-get install -qq xml-twig-tools -y @@ -190,7 +186,7 @@ jobs: # If this step fails still mark as failed, but don't stop the rest of the steps running. - bash: | - R -q -e "library('devtools'); devtools::check(args = c('--no-examples'))" | tee azure-pipelines_check.Rout + R -q -e "library('devtools'); devtools::check(args = c('--no-examples', '--no-tests'))" | tee azure-pipelines_check.Rout grep --quiet "^0 errors" azure-pipelines_check.Rout && grep --quiet " 0 warnings" azure-pipelines_check.Rout && grep --quiet " 0 notes" azure-pipelines_check.Rout workingDirectory: $(Pipeline.Workspace)/dsBaseClient @@ -237,9 +233,11 @@ jobs: # Install dsBase. # If previous steps have failed then don't run. - bash: | - R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsBase', username = 'datashield', ref = '6.3.1'); opal.logout(opal)" + R -q -e "library(opalr); opal <- opal.login(username = 'administrator', password = 'datashield_test&', url = 'https://localhost:8443', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); opal.put(opal, 'system', 'conf', 'general', '_rPackage'); opal.logout(o)" - sleep 120 + R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsBase', username = 'datashield', ref = '6.3.2'); opal.logout(opal)" + + sleep 60 R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.set_option(opal, 'default.datashield.privacyControlLevel', 'permissive'); opal.logout(opal)" @@ -263,7 +261,7 @@ jobs: # best guess is that there is an implicit build or similar that happens. Although # I cannot replicate that directly with build etc directly. - sudo R --verbose -e 'devtools::check()' + sudo R --verbose -e 'devtools::reload()' mkdir $(Pipeline.Workspace)/logs @@ -288,6 +286,7 @@ jobs: junit_rep <- JunitReporter$new(file = "test_results_dsbase.xml"); progress_rep <- ProgressReporter$new(max_failures = 999999); multi_rep <- MultiReporter$new(reporters = list(progress_rep, junit_rep)); + options("datashield.return_errors" = FALSE); options("default_driver" = "OpalDriver"); testthat::test_package("$(projectName)", filter = "_-|datachk-|smk-|arg-|disc-|perf-|smk_expt-|expt-|math-", reporter = multi_rep, stop_on_failure = FALSE) '"'"' @@ -362,6 +361,8 @@ jobs: # If previous steps have failed then don't run - bash: | + R -q -e "library(opalr); opal <- opal.login(username = 'administrator', password = 'datashield_test&', url = 'https://localhost:8443', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); opal.put(opal, 'system', 'conf', 'general', '_rPackage'); opal.logout(o)" + R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsDanger', username = 'datashield', ref = '6.3.1'); opal.logout(opal)" workingDirectory: $(Pipeline.Workspace)/dsBaseClient @@ -378,9 +379,8 @@ jobs: - bash: | # See, 'Code coverage and JUnit report output' for issues with the approach and improvement needed. - sudo R --verbose -e 'devtools::check()' + sudo R --verbose -e 'devtools::reload()' - pwd mkdir $(Pipeline.Workspace)/logs # run the coverage tool and output to coveragelist.csv @@ -401,6 +401,7 @@ jobs: junit_rep <- JunitReporter$new(file = "test_results_dsdanger.xml"); progress_rep <- ProgressReporter$new(max_failures = 999999); multi_rep <- MultiReporter$new(reporters = list(progress_rep, junit_rep)); + options("datashield.return_errors" = FALSE); options("default_driver" = "OpalDriver"); testthat::test_package("$(projectName)", filter = "__dgr-|datachk_dgr-|smk_dgr-|arg_dgr-|disc_dgr-|smk_expt_dgr-|expt_dgr-|math_dgr-", reporter = multi_rep, stop_on_failure = FALSE) '"'"' diff --git a/docker-compose_armadillo.yml b/docker-compose_armadillo.yml index 733edd5e..cf5a1095 100644 --- a/docker-compose_armadillo.yml +++ b/docker-compose_armadillo.yml @@ -3,7 +3,7 @@ services: hostname: armadillo ports: - 8080:8080 - image: datashield/armadillo_citest:4.10.0 + image: datashield/armadillo_citest:5.1.2 environment: LOGGING_CONFIG: 'classpath:logback-file.xml' AUDIT_LOG_PATH: '/app/logs/audit.log' @@ -16,6 +16,6 @@ services: default: hostname: default - image: datashield/rock-knot-devel-permissive:latest + image: datashield/rserver-neutron-gypsum-permissive:latest environment: DEBUG: "FALSE" diff --git a/docker-compose_opal.yml b/docker-compose_opal.yml index 4cc850fa..a55e8774 100644 --- a/docker-compose_opal.yml +++ b/docker-compose_opal.yml @@ -1,6 +1,6 @@ services: opal: - image: obiba/opal:5.0.0-RC5 + image: obiba/opal:5.1.4 ports: - "8443:8443" links: @@ -20,4 +20,4 @@ services: - MONGO_INITDB_ROOT_USERNAME=root - MONGO_INITDB_ROOT_PASSWORD=foobar rock: - image: datashield/rock-knot-devel-permissive:latest + image: datashield/rock-margin-joule-permissive:latest diff --git a/docs/404.html b/docs/404.html index adefa480..c50acc16 100644 --- a/docs/404.html +++ b/docs/404.html @@ -32,7 +32,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -73,12 +73,12 @@

Page not found (404)

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/LICENSE.html b/docs/LICENSE.html index 77319957..8fc45897 100644 --- a/docs/LICENSE.html +++ b/docs/LICENSE.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -38,10 +38,10 @@

NA

-
                GNU GENERAL PUBLIC LICENSE
-                   Version 3, 29 June 2007
+
                GNU GENERAL PUBLIC LICENSE
+                   Version 3, 29 June 2007

Copyright (C) 2007 Free Software Foundation, Inc. http://fsf.org/ Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed.

-
                        Preamble
+
                        Preamble

The GNU General Public License is a free, copyleft license for software and other kinds of works.

The licenses for most software and other practical works are designed to take away your freedom to share and change the works. By contrast, the GNU General Public License is intended to guarantee your freedom to share and change all versions of a program–to make sure it remains free software for all its users. We, the Free Software Foundation, use the GNU General Public License for most of our software; it applies also to any other work released this way by its authors. You can apply it to your programs, too.

When we speak of free software, we are referring to freedom, not price. Our General Public Licenses are designed to make sure that you have the freedom to distribute copies of free software (and charge for them if you wish), that you receive source code or can get it if you want it, that you can change the software or use pieces of it in new free programs, and that you know you can do these things.

@@ -52,8 +52,9 @@

NA

Some devices are designed to deny users access to install or run modified versions of the software inside them, although the manufacturer can do so. This is fundamentally incompatible with the aim of protecting users’ freedom to change the software. The systematic pattern of such abuse occurs in the area of products for individuals to use, which is precisely where it is most unacceptable. Therefore, we have designed this version of the GPL to prohibit the practice for those products. If such problems arise substantially in other domains, we stand ready to extend this provision to those domains in future versions of the GPL, as needed to protect the freedom of users.

Finally, every program is threatened constantly by software patents. States should not allow patents to restrict development and use of software on general-purpose computers, but in those that do, we wish to avoid the special danger that patents applied to a free program could make it effectively proprietary. To prevent this, the GPL assures that patents cannot be used to render the program non-free.

The precise terms and conditions for copying, distribution and modification follow.

-
                   TERMS AND CONDITIONS
-
  1. Definitions.

“This License” refers to version 3 of the GNU General Public License.

+
                   TERMS AND CONDITIONS
+
  1. Definitions.
    2. +

“This License” refers to version 3 of the GNU General Public License.

“Copyright” also means copyright-like laws that apply to other kinds of works, such as semiconductor masks.

“The Program” refers to any copyrightable work licensed under this License. Each licensee is addressed as “you”. “Licensees” and “recipients” may be individuals or organizations.

To “modify” a work means to copy from or adapt all or part of the work in a fashion requiring copyright permission, other than the making of an exact copy. The resulting work is called a “modified version” of the earlier work or a work “based on” the earlier work.

@@ -61,125 +62,136 @@

NA

To “propagate” a work means to do anything with it that, without permission, would make you directly or secondarily liable for infringement under applicable copyright law, except executing it on a computer or modifying a private copy. Propagation includes copying, distribution (with or without modification), making available to the public, and in some countries other activities as well.

To “convey” a work means any kind of propagation that enables other parties to make or receive copies. Mere interaction with a user through a computer network, with no transfer of a copy, is not conveying.

An interactive user interface displays “Appropriate Legal Notices” to the extent that it includes a convenient and prominently visible feature that (1) displays an appropriate copyright notice, and (2) tells the user that there is no warranty for the work (except to the extent that warranties are provided), that licensees may convey the work under this License, and how to view a copy of this License. If the interface presents a list of user commands or options, such as a menu, a prominent item in the list meets this criterion.

-
  1. Source Code.

The “source code” for a work means the preferred form of the work for making modifications to it. “Object code” means any non-source form of a work.

+
  1. Source Code.
    2. +

The “source code” for a work means the preferred form of the work for making modifications to it. “Object code” means any non-source form of a work.

A “Standard Interface” means an interface that either is an official standard defined by a recognized standards body, or, in the case of interfaces specified for a particular programming language, one that is widely used among developers working in that language.

The “System Libraries” of an executable work include anything, other than the work as a whole, that (a) is included in the normal form of packaging a Major Component, but which is not part of that Major Component, and (b) serves only to enable use of the work with that Major Component, or to implement a Standard Interface for which an implementation is available to the public in source code form. A “Major Component”, in this context, means a major essential component (kernel, window system, and so on) of the specific operating system (if any) on which the executable work runs, or a compiler used to produce the work, or an object code interpreter used to run it.

The “Corresponding Source” for a work in object code form means all the source code needed to generate, install, and (for an executable work) run the object code and to modify the work, including scripts to control those activities. However, it does not include the work’s System Libraries, or general-purpose tools or generally available free programs which are used unmodified in performing those activities but which are not part of the work. For example, Corresponding Source includes interface definition files associated with source files for the work, and the source code for shared libraries and dynamically linked subprograms that the work is specifically designed to require, such as by intimate data communication or control flow between those subprograms and other parts of the work.

The Corresponding Source need not include anything that users can regenerate automatically from other parts of the Corresponding Source.

The Corresponding Source for a work in source code form is that same work.

-
  1. Basic Permissions.

All rights granted under this License are granted for the term of copyright on the Program, and are irrevocable provided the stated conditions are met. This License explicitly affirms your unlimited permission to run the unmodified Program. The output from running a covered work is covered by this License only if the output, given its content, constitutes a covered work. This License acknowledges your rights of fair use or other equivalent, as provided by copyright law.

+
  1. Basic Permissions.
    2. +

All rights granted under this License are granted for the term of copyright on the Program, and are irrevocable provided the stated conditions are met. This License explicitly affirms your unlimited permission to run the unmodified Program. The output from running a covered work is covered by this License only if the output, given its content, constitutes a covered work. This License acknowledges your rights of fair use or other equivalent, as provided by copyright law.

You may make, run and propagate covered works that you do not convey, without conditions so long as your license otherwise remains in force. You may convey covered works to others for the sole purpose of having them make modifications exclusively for you, or provide you with facilities for running those works, provided that you comply with the terms of this License in conveying all material for which you do not control copyright. Those thus making or running the covered works for you must do so exclusively on your behalf, under your direction and control, on terms that prohibit them from making any copies of your copyrighted material outside their relationship with you.

Conveying under any other circumstances is permitted solely under the conditions stated below. Sublicensing is not allowed; section 10 makes it unnecessary.

-
  1. Protecting Users’ Legal Rights From Anti-Circumvention Law.

No covered work shall be deemed part of an effective technological measure under any applicable law fulfilling obligations under article 11 of the WIPO copyright treaty adopted on 20 December 1996, or similar laws prohibiting or restricting circumvention of such measures.

+
  1. Protecting Users’ Legal Rights From Anti-Circumvention Law.
    2. +

No covered work shall be deemed part of an effective technological measure under any applicable law fulfilling obligations under article 11 of the WIPO copyright treaty adopted on 20 December 1996, or similar laws prohibiting or restricting circumvention of such measures.

When you convey a covered work, you waive any legal power to forbid circumvention of technological measures to the extent such circumvention is effected by exercising rights under this License with respect to the covered work, and you disclaim any intention to limit operation or modification of the work as a means of enforcing, against the work’s users, your or third parties’ legal rights to forbid circumvention of technological measures.

-
  1. Conveying Verbatim Copies.

You may convey verbatim copies of the Program’s source code as you receive it, in any medium, provided that you conspicuously and appropriately publish on each copy an appropriate copyright notice; keep intact all notices stating that this License and any non-permissive terms added in accord with section 7 apply to the code; keep intact all notices of the absence of any warranty; and give all recipients a copy of this License along with the Program.

+
  1. Conveying Verbatim Copies.
    2. +

You may convey verbatim copies of the Program’s source code as you receive it, in any medium, provided that you conspicuously and appropriately publish on each copy an appropriate copyright notice; keep intact all notices stating that this License and any non-permissive terms added in accord with section 7 apply to the code; keep intact all notices of the absence of any warranty; and give all recipients a copy of this License along with the Program.

You may charge any price or no price for each copy that you convey, and you may offer support or warranty protection for a fee.

-
  1. Conveying Modified Source Versions.

You may convey a work based on the Program, or the modifications to produce it from the Program, in the form of source code under the terms of section 4, provided that you also meet all of these conditions:

-
a) The work must carry prominent notices stating that you modified
-it, and giving a relevant date.
-
-b) The work must carry prominent notices stating that it is
-released under this License and any conditions added under section
-7.  This requirement modifies the requirement in section 4 to
-"keep intact all notices".
-
-c) You must license the entire work, as a whole, under this
-License to anyone who comes into possession of a copy.  This
-License will therefore apply, along with any applicable section 7
-additional terms, to the whole of the work, and all its parts,
-regardless of how they are packaged.  This License gives no
-permission to license the work in any other way, but it does not
-invalidate such permission if you have separately received it.
-
-d) If the work has interactive user interfaces, each must display
-Appropriate Legal Notices; however, if the Program has interactive
-interfaces that do not display Appropriate Legal Notices, your
-work need not make them do so.
+
  1. Conveying Modified Source Versions.
    2. +

You may convey a work based on the Program, or the modifications to produce it from the Program, in the form of source code under the terms of section 4, provided that you also meet all of these conditions:

+
a) The work must carry prominent notices stating that you modified
+it, and giving a relevant date.
+
+b) The work must carry prominent notices stating that it is
+released under this License and any conditions added under section
+7.  This requirement modifies the requirement in section 4 to
+"keep intact all notices".
+
+c) You must license the entire work, as a whole, under this
+License to anyone who comes into possession of a copy.  This
+License will therefore apply, along with any applicable section 7
+additional terms, to the whole of the work, and all its parts,
+regardless of how they are packaged.  This License gives no
+permission to license the work in any other way, but it does not
+invalidate such permission if you have separately received it.
+
+d) If the work has interactive user interfaces, each must display
+Appropriate Legal Notices; however, if the Program has interactive
+interfaces that do not display Appropriate Legal Notices, your
+work need not make them do so.

A compilation of a covered work with other separate and independent works, which are not by their nature extensions of the covered work, and which are not combined with it such as to form a larger program, in or on a volume of a storage or distribution medium, is called an “aggregate” if the compilation and its resulting copyright are not used to limit the access or legal rights of the compilation’s users beyond what the individual works permit. Inclusion of a covered work in an aggregate does not cause this License to apply to the other parts of the aggregate.

-
  1. Conveying Non-Source Forms.

You may convey a covered work in object code form under the terms of sections 4 and 5, provided that you also convey the machine-readable Corresponding Source under the terms of this License, in one of these ways:

-
a) Convey the object code in, or embodied in, a physical product
-(including a physical distribution medium), accompanied by the
-Corresponding Source fixed on a durable physical medium
-customarily used for software interchange.
-
-b) Convey the object code in, or embodied in, a physical product
-(including a physical distribution medium), accompanied by a
-written offer, valid for at least three years and valid for as
-long as you offer spare parts or customer support for that product
-model, to give anyone who possesses the object code either (1) a
-copy of the Corresponding Source for all the software in the
-product that is covered by this License, on a durable physical
-medium customarily used for software interchange, for a price no
-more than your reasonable cost of physically performing this
-conveying of source, or (2) access to copy the
-Corresponding Source from a network server at no charge.
-
-c) Convey individual copies of the object code with a copy of the
-written offer to provide the Corresponding Source.  This
-alternative is allowed only occasionally and noncommercially, and
-only if you received the object code with such an offer, in accord
-with subsection 6b.
-
-d) Convey the object code by offering access from a designated
-place (gratis or for a charge), and offer equivalent access to the
-Corresponding Source in the same way through the same place at no
-further charge.  You need not require recipients to copy the
-Corresponding Source along with the object code.  If the place to
-copy the object code is a network server, the Corresponding Source
-may be on a different server (operated by you or a third party)
-that supports equivalent copying facilities, provided you maintain
-clear directions next to the object code saying where to find the
-Corresponding Source.  Regardless of what server hosts the
-Corresponding Source, you remain obligated to ensure that it is
-available for as long as needed to satisfy these requirements.
-
-e) Convey the object code using peer-to-peer transmission, provided
-you inform other peers where the object code and Corresponding
-Source of the work are being offered to the general public at no
-charge under subsection 6d.
+
  1. Conveying Non-Source Forms.
    2. +

You may convey a covered work in object code form under the terms of sections 4 and 5, provided that you also convey the machine-readable Corresponding Source under the terms of this License, in one of these ways:

+
a) Convey the object code in, or embodied in, a physical product
+(including a physical distribution medium), accompanied by the
+Corresponding Source fixed on a durable physical medium
+customarily used for software interchange.
+
+b) Convey the object code in, or embodied in, a physical product
+(including a physical distribution medium), accompanied by a
+written offer, valid for at least three years and valid for as
+long as you offer spare parts or customer support for that product
+model, to give anyone who possesses the object code either (1) a
+copy of the Corresponding Source for all the software in the
+product that is covered by this License, on a durable physical
+medium customarily used for software interchange, for a price no
+more than your reasonable cost of physically performing this
+conveying of source, or (2) access to copy the
+Corresponding Source from a network server at no charge.
+
+c) Convey individual copies of the object code with a copy of the
+written offer to provide the Corresponding Source.  This
+alternative is allowed only occasionally and noncommercially, and
+only if you received the object code with such an offer, in accord
+with subsection 6b.
+
+d) Convey the object code by offering access from a designated
+place (gratis or for a charge), and offer equivalent access to the
+Corresponding Source in the same way through the same place at no
+further charge.  You need not require recipients to copy the
+Corresponding Source along with the object code.  If the place to
+copy the object code is a network server, the Corresponding Source
+may be on a different server (operated by you or a third party)
+that supports equivalent copying facilities, provided you maintain
+clear directions next to the object code saying where to find the
+Corresponding Source.  Regardless of what server hosts the
+Corresponding Source, you remain obligated to ensure that it is
+available for as long as needed to satisfy these requirements.
+
+e) Convey the object code using peer-to-peer transmission, provided
+you inform other peers where the object code and Corresponding
+Source of the work are being offered to the general public at no
+charge under subsection 6d.

A separable portion of the object code, whose source code is excluded from the Corresponding Source as a System Library, need not be included in conveying the object code work.

A “User Product” is either (1) a “consumer product”, which means any tangible personal property which is normally used for personal, family, or household purposes, or (2) anything designed or sold for incorporation into a dwelling. In determining whether a product is a consumer product, doubtful cases shall be resolved in favor of coverage. For a particular product received by a particular user, “normally used” refers to a typical or common use of that class of product, regardless of the status of the particular user or of the way in which the particular user actually uses, or expects or is expected to use, the product. A product is a consumer product regardless of whether the product has substantial commercial, industrial or non-consumer uses, unless such uses represent the only significant mode of use of the product.

“Installation Information” for a User Product means any methods, procedures, authorization keys, or other information required to install and execute modified versions of a covered work in that User Product from a modified version of its Corresponding Source. The information must suffice to ensure that the continued functioning of the modified object code is in no case prevented or interfered with solely because modification has been made.

If you convey an object code work under this section in, or with, or specifically for use in, a User Product, and the conveying occurs as part of a transaction in which the right of possession and use of the User Product is transferred to the recipient in perpetuity or for a fixed term (regardless of how the transaction is characterized), the Corresponding Source conveyed under this section must be accompanied by the Installation Information. But this requirement does not apply if neither you nor any third party retains the ability to install modified object code on the User Product (for example, the work has been installed in ROM).

The requirement to provide Installation Information does not include a requirement to continue to provide support service, warranty, or updates for a work that has been modified or installed by the recipient, or for the User Product in which it has been modified or installed. Access to a network may be denied when the modification itself materially and adversely affects the operation of the network or violates the rules and protocols for communication across the network.

Corresponding Source conveyed, and Installation Information provided, in accord with this section must be in a format that is publicly documented (and with an implementation available to the public in source code form), and must require no special password or key for unpacking, reading or copying.

-
  1. Additional Terms.

“Additional permissions” are terms that supplement the terms of this License by making exceptions from one or more of its conditions. Additional permissions that are applicable to the entire Program shall be treated as though they were included in this License, to the extent that they are valid under applicable law. If additional permissions apply only to part of the Program, that part may be used separately under those permissions, but the entire Program remains governed by this License without regard to the additional permissions.

+
  1. Additional Terms.
    2. +

“Additional permissions” are terms that supplement the terms of this License by making exceptions from one or more of its conditions. Additional permissions that are applicable to the entire Program shall be treated as though they were included in this License, to the extent that they are valid under applicable law. If additional permissions apply only to part of the Program, that part may be used separately under those permissions, but the entire Program remains governed by this License without regard to the additional permissions.

When you convey a copy of a covered work, you may at your option remove any additional permissions from that copy, or from any part of it. (Additional permissions may be written to require their own removal in certain cases when you modify the work.) You may place additional permissions on material, added by you to a covered work, for which you have or can give appropriate copyright permission.

Notwithstanding any other provision of this License, for material you add to a covered work, you may (if authorized by the copyright holders of that material) supplement the terms of this License with terms:

-
a) Disclaiming warranty or limiting liability differently from the
-terms of sections 15 and 16 of this License; or
-
-b) Requiring preservation of specified reasonable legal notices or
-author attributions in that material or in the Appropriate Legal
-Notices displayed by works containing it; or
-
-c) Prohibiting misrepresentation of the origin of that material, or
-requiring that modified versions of such material be marked in
-reasonable ways as different from the original version; or
-
-d) Limiting the use for publicity purposes of names of licensors or
-authors of the material; or
-
-e) Declining to grant rights under trademark law for use of some
-trade names, trademarks, or service marks; or
-
-f) Requiring indemnification of licensors and authors of that
-material by anyone who conveys the material (or modified versions of
-it) with contractual assumptions of liability to the recipient, for
-any liability that these contractual assumptions directly impose on
-those licensors and authors.
+
a) Disclaiming warranty or limiting liability differently from the
+terms of sections 15 and 16 of this License; or
+
+b) Requiring preservation of specified reasonable legal notices or
+author attributions in that material or in the Appropriate Legal
+Notices displayed by works containing it; or
+
+c) Prohibiting misrepresentation of the origin of that material, or
+requiring that modified versions of such material be marked in
+reasonable ways as different from the original version; or
+
+d) Limiting the use for publicity purposes of names of licensors or
+authors of the material; or
+
+e) Declining to grant rights under trademark law for use of some
+trade names, trademarks, or service marks; or
+
+f) Requiring indemnification of licensors and authors of that
+material by anyone who conveys the material (or modified versions of
+it) with contractual assumptions of liability to the recipient, for
+any liability that these contractual assumptions directly impose on
+those licensors and authors.

All other non-permissive additional terms are considered “further restrictions” within the meaning of section 10. If the Program as you received it, or any part of it, contains a notice stating that it is governed by this License along with a term that is a further restriction, you may remove that term. If a license document contains a further restriction but permits relicensing or conveying under this License, you may add to a covered work material governed by the terms of that license document, provided that the further restriction does not survive such relicensing or conveying.

If you add terms to a covered work in accord with this section, you must place, in the relevant source files, a statement of the additional terms that apply to those files, or a notice indicating where to find the applicable terms.

Additional terms, permissive or non-permissive, may be stated in the form of a separately written license, or stated as exceptions; the above requirements apply either way.

-
  1. Termination.

You may not propagate or modify a covered work except as expressly provided under this License. Any attempt otherwise to propagate or modify it is void, and will automatically terminate your rights under this License (including any patent licenses granted under the third paragraph of section 11).

+
  1. Termination.
    2. +

You may not propagate or modify a covered work except as expressly provided under this License. Any attempt otherwise to propagate or modify it is void, and will automatically terminate your rights under this License (including any patent licenses granted under the third paragraph of section 11).

However, if you cease all violation of this License, then your license from a particular copyright holder is reinstated (a) provisionally, unless and until the copyright holder explicitly and finally terminates your license, and (b) permanently, if the copyright holder fails to notify you of the violation by some reasonable means prior to 60 days after the cessation.

Moreover, your license from a particular copyright holder is reinstated permanently if the copyright holder notifies you of the violation by some reasonable means, this is the first time you have received notice of violation of this License (for any work) from that copyright holder, and you cure the violation prior to 30 days after your receipt of the notice.

Termination of your rights under this section does not terminate the licenses of parties who have received copies or rights from you under this License. If your rights have been terminated and not permanently reinstated, you do not qualify to receive new licenses for the same material under section 10.

-
  1. Acceptance Not Required for Having Copies.

You are not required to accept this License in order to receive or run a copy of the Program. Ancillary propagation of a covered work occurring solely as a consequence of using peer-to-peer transmission to receive a copy likewise does not require acceptance. However, nothing other than this License grants you permission to propagate or modify any covered work. These actions infringe copyright if you do not accept this License. Therefore, by modifying or propagating a covered work, you indicate your acceptance of this License to do so.

-
  1. Automatic Licensing of Downstream Recipients.

Each time you convey a covered work, the recipient automatically receives a license from the original licensors, to run, modify and propagate that work, subject to this License. You are not responsible for enforcing compliance by third parties with this License.

+
  1. Acceptance Not Required for Having Copies.
    2. +

You are not required to accept this License in order to receive or run a copy of the Program. Ancillary propagation of a covered work occurring solely as a consequence of using peer-to-peer transmission to receive a copy likewise does not require acceptance. However, nothing other than this License grants you permission to propagate or modify any covered work. These actions infringe copyright if you do not accept this License. Therefore, by modifying or propagating a covered work, you indicate your acceptance of this License to do so.

+
  1. Automatic Licensing of Downstream Recipients.
    2. +

Each time you convey a covered work, the recipient automatically receives a license from the original licensors, to run, modify and propagate that work, subject to this License. You are not responsible for enforcing compliance by third parties with this License.

An “entity transaction” is a transaction transferring control of an organization, or substantially all assets of one, or subdividing an organization, or merging organizations. If propagation of a covered work results from an entity transaction, each party to that transaction who receives a copy of the work also receives whatever licenses to the work the party’s predecessor in interest had or could give under the previous paragraph, plus a right to possession of the Corresponding Source of the work from the predecessor in interest, if the predecessor has it or can get it with reasonable efforts.

You may not impose any further restrictions on the exercise of the rights granted or affirmed under this License. For example, you may not impose a license fee, royalty, or other charge for exercise of rights granted under this License, and you may not initiate litigation (including a cross-claim or counterclaim in a lawsuit) alleging that any patent claim is infringed by making, using, selling, offering for sale, or importing the Program or any portion of it.

-
  1. Patents.

A “contributor” is a copyright holder who authorizes use under this License of the Program or a work on which the Program is based. The work thus licensed is called the contributor’s “contributor version”.

+
  1. Patents.
    2. +

A “contributor” is a copyright holder who authorizes use under this License of the Program or a work on which the Program is based. The work thus licensed is called the contributor’s “contributor version”.

A contributor’s “essential patent claims” are all patent claims owned or controlled by the contributor, whether already acquired or hereafter acquired, that would be infringed by some manner, permitted by this License, of making, using, or selling its contributor version, but do not include claims that would be infringed only as a consequence of further modification of the contributor version. For purposes of this definition, “control” includes the right to grant patent sublicenses in a manner consistent with the requirements of this License.

Each contributor grants you a non-exclusive, worldwide, royalty-free patent license under the contributor’s essential patent claims, to make, use, sell, offer for sale, import and otherwise run, modify and propagate the contents of its contributor version.

In the following three paragraphs, a “patent license” is any express agreement or commitment, however denominated, not to enforce a patent (such as an express permission to practice a patent or covenant not to sue for patent infringement). To “grant” such a patent license to a party means to make such an agreement or commitment not to enforce a patent against the party.

@@ -187,41 +199,47 @@

NA

If, pursuant to or in connection with a single transaction or arrangement, you convey, or propagate by procuring conveyance of, a covered work, and grant a patent license to some of the parties receiving the covered work authorizing them to use, propagate, modify or convey a specific copy of the covered work, then the patent license you grant is automatically extended to all recipients of the covered work and works based on it.

A patent license is “discriminatory” if it does not include within the scope of its coverage, prohibits the exercise of, or is conditioned on the non-exercise of one or more of the rights that are specifically granted under this License. You may not convey a covered work if you are a party to an arrangement with a third party that is in the business of distributing software, under which you make payment to the third party based on the extent of your activity of conveying the work, and under which the third party grants, to any of the parties who would receive the covered work from you, a discriminatory patent license (a) in connection with copies of the covered work conveyed by you (or copies made from those copies), or (b) primarily for and in connection with specific products or compilations that contain the covered work, unless you entered into that arrangement, or that patent license was granted, prior to 28 March 2007.

Nothing in this License shall be construed as excluding or limiting any implied license or other defenses to infringement that may otherwise be available to you under applicable patent law.

-
  1. No Surrender of Others’ Freedom.

If conditions are imposed on you (whether by court order, agreement or otherwise) that contradict the conditions of this License, they do not excuse you from the conditions of this License. If you cannot convey a covered work so as to satisfy simultaneously your obligations under this License and any other pertinent obligations, then as a consequence you may not convey it at all. For example, if you agree to terms that obligate you to collect a royalty for further conveying from those to whom you convey the Program, the only way you could satisfy both those terms and this License would be to refrain entirely from conveying the Program.

-
  1. Use with the GNU Affero General Public License.

Notwithstanding any other provision of this License, you have permission to link or combine any covered work with a work licensed under version 3 of the GNU Affero General Public License into a single combined work, and to convey the resulting work. The terms of this License will continue to apply to the part which is the covered work, but the special requirements of the GNU Affero General Public License, section 13, concerning interaction through a network will apply to the combination as such.

-
  1. Revised Versions of this License.

The Free Software Foundation may publish revised and/or new versions of the GNU General Public License from time to time. Such new versions will be similar in spirit to the present version, but may differ in detail to address new problems or concerns.

+
  1. No Surrender of Others’ Freedom.
    2. +

If conditions are imposed on you (whether by court order, agreement or otherwise) that contradict the conditions of this License, they do not excuse you from the conditions of this License. If you cannot convey a covered work so as to satisfy simultaneously your obligations under this License and any other pertinent obligations, then as a consequence you may not convey it at all. For example, if you agree to terms that obligate you to collect a royalty for further conveying from those to whom you convey the Program, the only way you could satisfy both those terms and this License would be to refrain entirely from conveying the Program.

+
  1. Use with the GNU Affero General Public License.
    2. +

Notwithstanding any other provision of this License, you have permission to link or combine any covered work with a work licensed under version 3 of the GNU Affero General Public License into a single combined work, and to convey the resulting work. The terms of this License will continue to apply to the part which is the covered work, but the special requirements of the GNU Affero General Public License, section 13, concerning interaction through a network will apply to the combination as such.

+
  1. Revised Versions of this License.
    2. +

The Free Software Foundation may publish revised and/or new versions of the GNU General Public License from time to time. Such new versions will be similar in spirit to the present version, but may differ in detail to address new problems or concerns.

Each version is given a distinguishing version number. If the Program specifies that a certain numbered version of the GNU General Public License “or any later version” applies to it, you have the option of following the terms and conditions either of that numbered version or of any later version published by the Free Software Foundation. If the Program does not specify a version number of the GNU General Public License, you may choose any version ever published by the Free Software Foundation.

If the Program specifies that a proxy can decide which future versions of the GNU General Public License can be used, that proxy’s public statement of acceptance of a version permanently authorizes you to choose that version for the Program.

Later license versions may give you additional or different permissions. However, no additional obligations are imposed on any author or copyright holder as a result of your choosing to follow a later version.

-
  1. Disclaimer of Warranty.

THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM “AS IS” WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION.

-
  1. Limitation of Liability.

IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES.

-
  1. Interpretation of Sections 15 and 16.

If the disclaimer of warranty and limitation of liability provided above cannot be given local legal effect according to their terms, reviewing courts shall apply local law that most closely approximates an absolute waiver of all civil liability in connection with the Program, unless a warranty or assumption of liability accompanies a copy of the Program in return for a fee.

-
                 END OF TERMS AND CONDITIONS
-
-        How to Apply These Terms to Your New Programs
+
  1. Disclaimer of Warranty.
    2. +

THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM “AS IS” WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION.

+
  1. Limitation of Liability.
    2. +

IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES.

+
  1. Interpretation of Sections 15 and 16.
    2. +

If the disclaimer of warranty and limitation of liability provided above cannot be given local legal effect according to their terms, reviewing courts shall apply local law that most closely approximates an absolute waiver of all civil liability in connection with the Program, unless a warranty or assumption of liability accompanies a copy of the Program in return for a fee.

+
                 END OF TERMS AND CONDITIONS
+
+        How to Apply These Terms to Your New Programs

If you develop a new program, and you want it to be of the greatest possible use to the public, the best way to achieve this is to make it free software which everyone can redistribute and change under these terms.

To do so, attach the following notices to the program. It is safest to attach them to the start of each source file to most effectively state the exclusion of warranty; and each file should have at least the “copyright” line and a pointer to where the full notice is found.

-
{one line to give the program's name and a brief idea of what it does.}
-Copyright (C) {year}  {name of author}
-
-This program is free software: you can redistribute it and/or modify
-it under the terms of the GNU General Public License as published by
-the Free Software Foundation, either version 3 of the License, or
-(at your option) any later version.
-
-This program is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License
-along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
{one line to give the program's name and a brief idea of what it does.}
+Copyright (C) {year}  {name of author}
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program.  If not, see <http://www.gnu.org/licenses/>.

Also add information on how to contact you by electronic and paper mail.

If the program does terminal interaction, make it output a short notice like this when it starts in an interactive mode:

-
{project}  Copyright (C) {year}  {fullname}
-This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
-This is free software, and you are welcome to redistribute it
-under certain conditions; type `show c' for details.
+
{project}  Copyright (C) {year}  {fullname}
+This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
+This is free software, and you are welcome to redistribute it
+under certain conditions; type `show c' for details.

The hypothetical commands show w' andshow c’ should show the appropriate parts of the General Public License. Of course, your program’s commands might be different; for a GUI interface, you would use an “about box”.

You should also get your employer (if you work as a programmer) or school, if any, to sign a “copyright disclaimer” for the program, if necessary. For more information on this, and how to apply and follow the GNU GPL, see http://www.gnu.org/licenses/.

The GNU General Public License does not permit incorporating your program into proprietary programs. If your program is a subroutine library, you may consider it more useful to permit linking proprietary applications with the library. If this is what you want to do, use the GNU Lesser General Public License instead of this License. But first, please read http://www.gnu.org/philosophy/why-not-lgpl.html.

@@ -238,11 +256,11 @@

NA

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/authors.html b/docs/authors.html index feb204c7..5664dd09 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -40,7 +40,43 @@

Authors and Citation

  • -

    DataSHIELD Developers. Maintainer. +

    Paul Burton. Author. +

    +
    • +
  • +

    Rebecca Wilson. Author. +

    +
    • +
  • +

    Olly Butters. Author. +

    +
    • +
  • +

    Patricia Ryser-Welch. Author. +

    +
    • +
  • +

    Alex Westerberg. Author. +

    +
    • +
  • +

    Leire Abarrategui. Author. +

    +
    • +
  • +

    Roberto Villegas-Diaz. Author. +

    +
    • +
  • +

    Demetris Avraam. Author. +

    +
    • +
  • +

    Yannick Marcon. Author. +

    +
    • +
  • +

    Stuart Wheater. Author, maintainer.

@@ -52,15 +88,15 @@

Citation

-

Developers D (2024). +

Burton P, Wilson R, Butters O, Ryser-Welch P, Westerberg A, Abarrategui L, Villegas-Diaz R, Avraam D, Marcon Y, Wheater S (2025). dsBaseClient: DataSHIELD Client Functions. -R package version 6.3.1. +R package version 6.3.3. 

@Manual{,
   title = {dsBaseClient: DataSHIELD Client Functions},
-  author = {DataSHIELD Developers},
-  year = {2024},
-  note = {R package version 6.3.1},
+  author = {Paul Burton and Rebecca Wilson and Olly Butters and Patricia Ryser-Welch and Alex Westerberg and Leire Abarrategui and Roberto Villegas-Diaz and Demetris Avraam and Yannick Marcon and Stuart Wheater},
+  year = {2025},
+  note = {R package version 6.3.3},
 }
@@ -70,11 +106,11 @@

Citation

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/index.html b/docs/index.html index 8271c328..a8bb5e86 100644 --- a/docs/index.html +++ b/docs/index.html @@ -12,7 +12,7 @@ - + Compute Weighted Mean by Group — computeWeightedMeans • dsBaseClient + + +
+
+ + + +
+
+
+

Compute Weighted Mean by Group

+ + +
+ +
+

This function is originally from the panelaggregation package. +It has been ported here in order to bypass the package being +kicked off CRAN.

+
+ +
+ 
computeWeightedMeans(data_table, variables, weight, by)
+
+ +
+

Arguments

+ + +
data_table
+

a data.table

+ + +
variables
+

character name of the variable(s) to focus on. The variables must be in the data.table

+ + +
weight
+

character name of the data.table column that contains a weight.

+ + +
by
+

character vector of the columns to group by

+ +
+
+

Author

+

Matthias Bannert, Gabriel Bucur

+
+ +
+ +
+ + +
+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

+
+ +
+

Site built with pkgdown 2.1.3.

+
+ +
+ + + + + + + + diff --git a/docs/reference/ds.Boole.html b/docs/reference/ds.Boole.html index 2445ed80..045b0558 100644 --- a/docs/reference/ds.Boole.html +++ b/docs/reference/ds.Boole.html @@ -20,7 +20,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -200,11 +200,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.abs.html b/docs/reference/ds.abs.html index 65f8640c..ce7c557b 100644 --- a/docs/reference/ds.abs.html +++ b/docs/reference/ds.abs.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -150,11 +150,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.asCharacter.html b/docs/reference/ds.asCharacter.html index df1c7cb9..03482cab 100644 --- a/docs/reference/ds.asCharacter.html +++ b/docs/reference/ds.asCharacter.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -132,11 +132,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.asDataMatrix.html b/docs/reference/ds.asDataMatrix.html index b8ceb870..287cd629 100644 --- a/docs/reference/ds.asDataMatrix.html +++ b/docs/reference/ds.asDataMatrix.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -135,11 +135,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.asFactor.html b/docs/reference/ds.asFactor.html index a75085f9..c4c5a616 100644 --- a/docs/reference/ds.asFactor.html +++ b/docs/reference/ds.asFactor.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -229,11 +229,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.asFactorSimple.html b/docs/reference/ds.asFactorSimple.html index 2b19b9b3..a72df46a 100644 --- a/docs/reference/ds.asFactorSimple.html +++ b/docs/reference/ds.asFactorSimple.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -103,11 +103,11 @@

Author

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.asInteger.html b/docs/reference/ds.asInteger.html index 76cc6f13..dff4a447 100644 --- a/docs/reference/ds.asInteger.html +++ b/docs/reference/ds.asInteger.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -148,11 +148,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.asList.html b/docs/reference/ds.asList.html index d7fe3876..1185217b 100644 --- a/docs/reference/ds.asList.html +++ b/docs/reference/ds.asList.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -133,11 +133,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.asLogical.html b/docs/reference/ds.asLogical.html index e07cc3c3..614d3cd7 100644 --- a/docs/reference/ds.asLogical.html +++ b/docs/reference/ds.asLogical.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -134,11 +134,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.asMatrix.html b/docs/reference/ds.asMatrix.html index d3e7a9b3..441c1191 100644 --- a/docs/reference/ds.asMatrix.html +++ b/docs/reference/ds.asMatrix.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -136,11 +136,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.asNumeric.html b/docs/reference/ds.asNumeric.html index 1bcda160..f8c5ece7 100644 --- a/docs/reference/ds.asNumeric.html +++ b/docs/reference/ds.asNumeric.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -147,11 +147,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.assign.html b/docs/reference/ds.assign.html index 8057c1a4..68de4eec 100644 --- a/docs/reference/ds.assign.html +++ b/docs/reference/ds.assign.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -131,11 +131,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.auc.html b/docs/reference/ds.auc.html index 28540596..9f104445 100644 --- a/docs/reference/ds.auc.html +++ b/docs/reference/ds.auc.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -89,11 +89,11 @@

Author

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.boxPlot.html b/docs/reference/ds.boxPlot.html index 323aab95..cc777950 100644 --- a/docs/reference/ds.boxPlot.html +++ b/docs/reference/ds.boxPlot.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -113,11 +113,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.boxPlotGG.html b/docs/reference/ds.boxPlotGG.html index 4736517a..1e1e3401 100644 --- a/docs/reference/ds.boxPlotGG.html +++ b/docs/reference/ds.boxPlotGG.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -108,11 +108,11 @@

Value

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.boxPlotGG_data_Treatment.html b/docs/reference/ds.boxPlotGG_data_Treatment.html index 51205d21..153ae586 100644 --- a/docs/reference/ds.boxPlotGG_data_Treatment.html +++ b/docs/reference/ds.boxPlotGG_data_Treatment.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -95,11 +95,11 @@

Value

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.boxPlotGG_data_Treatment_numeric.html b/docs/reference/ds.boxPlotGG_data_Treatment_numeric.html index 476f6b4e..ab9b69d0 100644 --- a/docs/reference/ds.boxPlotGG_data_Treatment_numeric.html +++ b/docs/reference/ds.boxPlotGG_data_Treatment_numeric.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -75,11 +75,11 @@

Value

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.boxPlotGG_numeric.html b/docs/reference/ds.boxPlotGG_numeric.html index 4b9845e7..83aeef08 100644 --- a/docs/reference/ds.boxPlotGG_numeric.html +++ b/docs/reference/ds.boxPlotGG_numeric.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -91,11 +91,11 @@

Value

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.boxPlotGG_table.html b/docs/reference/ds.boxPlotGG_table.html index ad10740a..85314da1 100644 --- a/docs/reference/ds.boxPlotGG_table.html +++ b/docs/reference/ds.boxPlotGG_table.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -106,11 +106,11 @@

Value

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.bp_standards.html b/docs/reference/ds.bp_standards.html index 82247836..da5d815e 100644 --- a/docs/reference/ds.bp_standards.html +++ b/docs/reference/ds.bp_standards.html @@ -20,7 +20,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -126,11 +126,11 @@

Author

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.c.html b/docs/reference/ds.c.html index 7a04d7dd..04030814 100644 --- a/docs/reference/ds.c.html +++ b/docs/reference/ds.c.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -132,11 +132,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.cbind.html b/docs/reference/ds.cbind.html index 7b771803..41e685ac 100644 --- a/docs/reference/ds.cbind.html +++ b/docs/reference/ds.cbind.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -206,11 +206,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.changeRefGroup.html b/docs/reference/ds.changeRefGroup.html index 10fb7b25..fcef5708 100644 --- a/docs/reference/ds.changeRefGroup.html +++ b/docs/reference/ds.changeRefGroup.html @@ -19,7 +19,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -199,11 +199,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.class.html b/docs/reference/ds.class.html index 4bed09e2..fc31e876 100644 --- a/docs/reference/ds.class.html +++ b/docs/reference/ds.class.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -130,11 +130,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.colnames.html b/docs/reference/ds.colnames.html index 6dc70fbb..ef9dd54c 100644 --- a/docs/reference/ds.colnames.html +++ b/docs/reference/ds.colnames.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -127,11 +127,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.completeCases.html b/docs/reference/ds.completeCases.html index 2e200009..cf571bf0 100644 --- a/docs/reference/ds.completeCases.html +++ b/docs/reference/ds.completeCases.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -147,11 +147,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.contourPlot.html b/docs/reference/ds.contourPlot.html index 2858a022..fa7e1b6f 100644 --- a/docs/reference/ds.contourPlot.html +++ b/docs/reference/ds.contourPlot.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -203,11 +203,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.cor.html b/docs/reference/ds.cor.html index f86dd9b9..b9cb98bb 100644 --- a/docs/reference/ds.cor.html +++ b/docs/reference/ds.cor.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -156,11 +156,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.corTest.html b/docs/reference/ds.corTest.html index 8190dca4..499614de 100644 --- a/docs/reference/ds.corTest.html +++ b/docs/reference/ds.corTest.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -162,11 +162,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.cov.html b/docs/reference/ds.cov.html index b97c414b..3402a8cd 100644 --- a/docs/reference/ds.cov.html +++ b/docs/reference/ds.cov.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -181,11 +181,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.dataFrame.html b/docs/reference/ds.dataFrame.html index f32cf6bc..a14ec367 100644 --- a/docs/reference/ds.dataFrame.html +++ b/docs/reference/ds.dataFrame.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -199,11 +199,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.dataFrameFill.html b/docs/reference/ds.dataFrameFill.html index e6c29795..be082093 100644 --- a/docs/reference/ds.dataFrameFill.html +++ b/docs/reference/ds.dataFrameFill.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -150,11 +150,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.dataFrameSort.html b/docs/reference/ds.dataFrameSort.html index efa19b70..3c8e229a 100644 --- a/docs/reference/ds.dataFrameSort.html +++ b/docs/reference/ds.dataFrameSort.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -171,11 +171,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.dataFrameSubset.html b/docs/reference/ds.dataFrameSubset.html index f1559f19..42fd9fd5 100644 --- a/docs/reference/ds.dataFrameSubset.html +++ b/docs/reference/ds.dataFrameSubset.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -216,11 +216,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.densityGrid.html b/docs/reference/ds.densityGrid.html index 03906004..02c01097 100644 --- a/docs/reference/ds.densityGrid.html +++ b/docs/reference/ds.densityGrid.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -120,11 +120,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.dim.html b/docs/reference/ds.dim.html index 3469f8ad..ed76d9d5 100644 --- a/docs/reference/ds.dim.html +++ b/docs/reference/ds.dim.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -167,11 +167,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.dmtC2S.html b/docs/reference/ds.dmtC2S.html index 3b453ecb..05e4e8d2 100644 --- a/docs/reference/ds.dmtC2S.html +++ b/docs/reference/ds.dmtC2S.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -120,11 +120,11 @@

Author

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.elspline.html b/docs/reference/ds.elspline.html index 102add33..cf21761a 100644 --- a/docs/reference/ds.elspline.html +++ b/docs/reference/ds.elspline.html @@ -20,7 +20,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -119,11 +119,11 @@

Author

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.exists.html b/docs/reference/ds.exists.html index 08944f12..424fa481 100644 --- a/docs/reference/ds.exists.html +++ b/docs/reference/ds.exists.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -138,11 +138,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.exp.html b/docs/reference/ds.exp.html index 134f9743..ebd76bc4 100644 --- a/docs/reference/ds.exp.html +++ b/docs/reference/ds.exp.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -132,11 +132,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.extractQuantiles.html b/docs/reference/ds.extractQuantiles.html index 8056889b..a47412c4 100644 --- a/docs/reference/ds.extractQuantiles.html +++ b/docs/reference/ds.extractQuantiles.html @@ -26,7 +26,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -176,11 +176,11 @@

Author

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.forestplot.html b/docs/reference/ds.forestplot.html index a651872d..6f57fda1 100644 --- a/docs/reference/ds.forestplot.html +++ b/docs/reference/ds.forestplot.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -118,11 +118,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.gamlss.html b/docs/reference/ds.gamlss.html index 4e92d7c7..368ca25c 100644 --- a/docs/reference/ds.gamlss.html +++ b/docs/reference/ds.gamlss.html @@ -23,7 +23,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -215,11 +215,11 @@

Author

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.getWGSR.html b/docs/reference/ds.getWGSR.html index 9f647c02..76a699f7 100644 --- a/docs/reference/ds.getWGSR.html +++ b/docs/reference/ds.getWGSR.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -204,11 +204,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.glm.html b/docs/reference/ds.glm.html index 3ece7fc8..1a58d522 100644 --- a/docs/reference/ds.glm.html +++ b/docs/reference/ds.glm.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -196,13 +196,13 @@

Details

In formula most shortcut notation for formulas allowed under R's standard glm() function is also allowed by ds.glm.

Many GLMs can be fitted very simply using a formula such as:

-

$$y~a+b+c+d$$

+

\(y~a+b+c+d\)

which simply means fit a GLM with y as the outcome variable and a, b, c and d as covariates. By default all such models also include an intercept (regression constant) term.

Instead, if you need to fit a more complex model, for example:

-

$$EVENT~1+TID+SEXF*AGE.60$$

+

\(EVENT~1+TID+SEXF*AGE.60\)

In the above model the outcome variable is EVENT and the covariates TID (factor variable with level values between 1 and 6 denoting the period time), @@ -237,7 +237,7 @@

Details

The data argument avoids you having to specify the name of the data frame in front of each covariate in the formula. For example, if the data frame is called DataFrame you -avoid having to write: \(DataFrame$y~DataFrame$a+DataFrame$b+DataFrame$c+DataFrame$d\)

+avoid having to write: \(DataFrame\$y ~ DataFrame\$a + DataFrame\$b + DataFrame\$c + DataFrame\$d\)

The checks argument verifies that the variables in the model are all defined (exist) on the server-side at every study and that they have the correct characteristics required to fit the model. @@ -427,11 +427,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.glmPredict.html b/docs/reference/ds.glmPredict.html index 228bed88..0514d585 100644 --- a/docs/reference/ds.glmPredict.html +++ b/docs/reference/ds.glmPredict.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -227,11 +227,11 @@

Author

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.glmSLMA.html b/docs/reference/ds.glmSLMA.html index 83204ac5..192a20bb 100644 --- a/docs/reference/ds.glmSLMA.html +++ b/docs/reference/ds.glmSLMA.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -281,13 +281,13 @@

Details

In formula Most shortcut notation for formulas allowed under R's standard glm() function is also allowed by ds.glmSLMA.

Many glms can be fitted very simply using a formula such as:

-

$$y~a+b+c+d$$

+

\(y~a+b+c+d\)

which simply means fit a glm with y as the outcome variable and a, b, c and d as covariates. By default all such models also include an intercept (regression constant) term.

Instead, if you need to fit a more complex model, for example:

-

$$EVENT~1+TID+SEXF*AGE.60$$

+

\(EVENT~1+TID+SEXF*AGE.60\)

In the above model the outcome variable is EVENT and the covariates TID (factor variable with level values between 1 and 6 denoting the period time), @@ -355,7 +355,7 @@

Details

The dataName argument avoids you having to specify the name of the data frame in front of each covariate in the formula. For example, if the data frame is called DataFrame you -avoid having to write: \(DataFrame$y~DataFrame$a+DataFrame$b+DataFrame$c+DataFrame$d\)

+avoid having to write: \(DataFrame\$y ~ DataFrame\$a + DataFrame\$b + DataFrame\$c + DataFrame\$d\)

The checks argument verifies that the variables in the model are all defined (exist) on the server-site at every study and that they have the correct characteristics required to fit the model. @@ -493,11 +493,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.glmSummary.html b/docs/reference/ds.glmSummary.html index 327060d8..28d8c2b1 100644 --- a/docs/reference/ds.glmSummary.html +++ b/docs/reference/ds.glmSummary.html @@ -20,7 +20,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -154,11 +154,11 @@

Author

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.glmerSLMA.html b/docs/reference/ds.glmerSLMA.html index a65c5f30..712996ce 100644 --- a/docs/reference/ds.glmerSLMA.html +++ b/docs/reference/ds.glmerSLMA.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -235,13 +235,13 @@

Details

In formula most shortcut notation allowed by glmer() function is also allowed by ds.glmerSLMA. Many GLMEs can be fitted very simply using a formula like: -$$y~a+b+(1|c)$$ +\(y~a+b+(1|c)\) which simply means fit an GLME with y as the outcome variable (e.g. a binary case-control using a logistic regression model or a count or a survival time using a Poisson regression model), a and b as fixed effects, and c as a random effect or grouping factor.

It is also possible to fit models with random slopes by specifying a model such as -$$y~a+b+(1+b|c)$$ +\(y~a+b+(1+b|c)\) where the effect of b can vary randomly between groups defined by c. Implicit nesting can be specified with formulas such as: \(y~a+b+(1|c/d)\) or \(y~a+b+(1|c)+(1|c:d)\).

@@ -249,7 +249,7 @@

Details

The dataName argument avoids you having to specify the name of the data frame in front of each covariate in the formula. For example, if the data frame is called DataFrame you avoid having to write: -\(DataFrame$y~DataFrame$a+DataFrame$b+(1|DataFrame$c)\).

+\(DataFrame\$y ~ DataFrame\$a + DataFrame\$b + (1 | DataFrame\$c)\).

The checks argument verifies that the variables in the model are all defined (exist) on the server-site at every study and that they have the correct characteristics required to fit the model. @@ -379,11 +379,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.heatmapPlot.html b/docs/reference/ds.heatmapPlot.html index dd26dbd3..4773f204 100644 --- a/docs/reference/ds.heatmapPlot.html +++ b/docs/reference/ds.heatmapPlot.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -199,11 +199,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.hetcor.html b/docs/reference/ds.hetcor.html index 5373fbae..5052622b 100644 --- a/docs/reference/ds.hetcor.html +++ b/docs/reference/ds.hetcor.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -124,11 +124,11 @@

Author

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.histogram.html b/docs/reference/ds.histogram.html index 777c4278..5a81cf95 100644 --- a/docs/reference/ds.histogram.html +++ b/docs/reference/ds.histogram.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -190,11 +190,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.igb_standards.html b/docs/reference/ds.igb_standards.html index e59a5413..eff2200a 100644 --- a/docs/reference/ds.igb_standards.html +++ b/docs/reference/ds.igb_standards.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -135,11 +135,11 @@

Author

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.isNA.html b/docs/reference/ds.isNA.html index 9f81d806..7b9f2ca3 100644 --- a/docs/reference/ds.isNA.html +++ b/docs/reference/ds.isNA.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -131,11 +131,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.isValid.html b/docs/reference/ds.isValid.html index d34ddbd6..a92fa69a 100644 --- a/docs/reference/ds.isValid.html +++ b/docs/reference/ds.isValid.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -131,11 +131,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.kurtosis.html b/docs/reference/ds.kurtosis.html index 896113ff..1c5f6a69 100644 --- a/docs/reference/ds.kurtosis.html +++ b/docs/reference/ds.kurtosis.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -103,11 +103,11 @@

Author

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.length.html b/docs/reference/ds.length.html index fa6be208..a216ce9e 100644 --- a/docs/reference/ds.length.html +++ b/docs/reference/ds.length.html @@ -19,7 +19,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -157,11 +157,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.levels.html b/docs/reference/ds.levels.html index d4eda89f..673ae511 100644 --- a/docs/reference/ds.levels.html +++ b/docs/reference/ds.levels.html @@ -19,7 +19,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -133,11 +133,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.lexis.html b/docs/reference/ds.lexis.html index 72b4fc78..af63a072 100644 --- a/docs/reference/ds.lexis.html +++ b/docs/reference/ds.lexis.html @@ -19,7 +19,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -298,11 +298,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.list.html b/docs/reference/ds.list.html index 209dcb5b..e152d449 100644 --- a/docs/reference/ds.list.html +++ b/docs/reference/ds.list.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -129,11 +129,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.listClientsideFunctions.html b/docs/reference/ds.listClientsideFunctions.html index 6f6570e6..01ae3ae2 100644 --- a/docs/reference/ds.listClientsideFunctions.html +++ b/docs/reference/ds.listClientsideFunctions.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -86,11 +86,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.listDisclosureSettings.html b/docs/reference/ds.listDisclosureSettings.html index 45969706..79f9214e 100644 --- a/docs/reference/ds.listDisclosureSettings.html +++ b/docs/reference/ds.listDisclosureSettings.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -162,11 +162,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.listOpals.html b/docs/reference/ds.listOpals.html index 5ab10679..0ad3682e 100644 --- a/docs/reference/ds.listOpals.html +++ b/docs/reference/ds.listOpals.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -80,11 +80,11 @@

Author

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.listServersideFunctions.html b/docs/reference/ds.listServersideFunctions.html index 757fbc03..c748c1b6 100644 --- a/docs/reference/ds.listServersideFunctions.html +++ b/docs/reference/ds.listServersideFunctions.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -124,11 +124,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.lmerSLMA.html b/docs/reference/ds.lmerSLMA.html index 2c0444ed..71e077c6 100644 --- a/docs/reference/ds.lmerSLMA.html +++ b/docs/reference/ds.lmerSLMA.html @@ -19,7 +19,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -229,18 +229,18 @@

Details

obtained using R help for lmer and the lme4 package.

In formula most shortcut notation allowed by lmer() function is also allowed by ds.lmerSLMA. Many LMEs can be fitted very simply using a formula like: -$$y~a+b+(1|c)$$ +\(y ~ a + b + (1 | c)\) which simply means fit an LME with y as the outcome variable with a and b as fixed effects, and c as a random effect or grouping factor.

It is also possible to fit models with random slopes by specifying a model such as -$$y~a+b+(1+b|c)$$ +\(y ~ a + b + (1 + b | c)\) where the effect of b can vary randomly between groups defined by c. -Implicit nesting can be specified with formulae such as \(y~a+b+(1|c/d)\) -or \(y~a+b+(1|c)+(1|c:d)\).

+Implicit nesting can be specified with formulae such as \(y ~ a + b + (1 | c / d)\) +or \(y ~ a + b + (1 | c) + (1 | c : d)\).

The dataName argument avoids you having to specify the name of the data frame in front of each covariate in the formula. For example, if the data frame is called DataFrame you avoid having to write: -\(DataFrame$y~DataFrame$a+DataFrame$b+(1|DataFrame$c)\).

+\(DataFrame\$y ~ DataFrame\$a + DataFrame\$b + (1 | DataFrame\$c)\).

The checks argument verifies that the variables in the model are all defined (exist) on the server-site at every study and that they have the correct characteristics required to fit the model. @@ -311,7 +311,7 @@

Examples

# Fit the lmer - ds.lmerSLMA(formula = "BMI ~ incid_rate + diabetes + (1 | Male)", + ds.lmerSLMA(formula = "BMI ~ incid_rate + diabetes + (1 | Male)", dataName = "D.comp", datasources = connections) @@ -328,11 +328,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.log.html b/docs/reference/ds.log.html index 30f10ae2..2a264906 100644 --- a/docs/reference/ds.log.html +++ b/docs/reference/ds.log.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -138,11 +138,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.look.html b/docs/reference/ds.look.html index ae0d0cc7..9a9f4898 100644 --- a/docs/reference/ds.look.html +++ b/docs/reference/ds.look.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -147,11 +147,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.ls.html b/docs/reference/ds.ls.html index e0086831..2d8a3728 100644 --- a/docs/reference/ds.ls.html +++ b/docs/reference/ds.ls.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -198,11 +198,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.lspline.html b/docs/reference/ds.lspline.html index 188e4632..fc9c8129 100644 --- a/docs/reference/ds.lspline.html +++ b/docs/reference/ds.lspline.html @@ -20,7 +20,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -116,11 +116,11 @@

Author

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.make.html b/docs/reference/ds.make.html index 7d4ae3e2..b2fd2c44 100644 --- a/docs/reference/ds.make.html +++ b/docs/reference/ds.make.html @@ -19,7 +19,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -201,11 +201,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.matrix.html b/docs/reference/ds.matrix.html index 0b7c0d61..3eaf3212 100644 --- a/docs/reference/ds.matrix.html +++ b/docs/reference/ds.matrix.html @@ -20,7 +20,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -246,11 +246,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.matrixDet.html b/docs/reference/ds.matrixDet.html index 8d94a581..1c4085f2 100644 --- a/docs/reference/ds.matrixDet.html +++ b/docs/reference/ds.matrixDet.html @@ -20,7 +20,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -164,11 +164,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.matrixDet.report.html b/docs/reference/ds.matrixDet.report.html index f216c851..114cebab 100644 --- a/docs/reference/ds.matrixDet.report.html +++ b/docs/reference/ds.matrixDet.report.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -152,11 +152,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.matrixDiag.html b/docs/reference/ds.matrixDiag.html index 66e8c6c4..5dfdda04 100644 --- a/docs/reference/ds.matrixDiag.html +++ b/docs/reference/ds.matrixDiag.html @@ -19,7 +19,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -155,11 +155,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.matrixDimnames.html b/docs/reference/ds.matrixDimnames.html index 24230307..db00df03 100644 --- a/docs/reference/ds.matrixDimnames.html +++ b/docs/reference/ds.matrixDimnames.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -170,11 +170,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.matrixInvert.html b/docs/reference/ds.matrixInvert.html index 07f7e00c..0e1c57df 100644 --- a/docs/reference/ds.matrixInvert.html +++ b/docs/reference/ds.matrixInvert.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -157,11 +157,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.matrixMult.html b/docs/reference/ds.matrixMult.html index 55623b50..fae1abdb 100644 --- a/docs/reference/ds.matrixMult.html +++ b/docs/reference/ds.matrixMult.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -174,11 +174,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.matrixTranspose.html b/docs/reference/ds.matrixTranspose.html index 524e7531..2d5149cb 100644 --- a/docs/reference/ds.matrixTranspose.html +++ b/docs/reference/ds.matrixTranspose.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -159,11 +159,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.mean.html b/docs/reference/ds.mean.html index 301e391e..efcdd78a 100644 --- a/docs/reference/ds.mean.html +++ b/docs/reference/ds.mean.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -185,11 +185,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.meanByClass.html b/docs/reference/ds.meanByClass.html index 8b081930..f3744b66 100644 --- a/docs/reference/ds.meanByClass.html +++ b/docs/reference/ds.meanByClass.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -169,11 +169,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.meanSdGp.html b/docs/reference/ds.meanSdGp.html index 51702b22..e4b01054 100644 --- a/docs/reference/ds.meanSdGp.html +++ b/docs/reference/ds.meanSdGp.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -214,11 +214,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.merge.html b/docs/reference/ds.merge.html index 87767638..73276dbd 100644 --- a/docs/reference/ds.merge.html +++ b/docs/reference/ds.merge.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -232,11 +232,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.message.html b/docs/reference/ds.message.html index 7c94b88e..bd7db069 100644 --- a/docs/reference/ds.message.html +++ b/docs/reference/ds.message.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -144,11 +144,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.metadata.html b/docs/reference/ds.metadata.html index 0d807090..337505dc 100644 --- a/docs/reference/ds.metadata.html +++ b/docs/reference/ds.metadata.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -122,11 +122,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.mice.html b/docs/reference/ds.mice.html index 871cd3c2..785f9dff 100644 --- a/docs/reference/ds.mice.html +++ b/docs/reference/ds.mice.html @@ -25,7 +25,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -160,11 +160,11 @@

Author

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.names.html b/docs/reference/ds.names.html index 69c83c36..277b8c40 100644 --- a/docs/reference/ds.names.html +++ b/docs/reference/ds.names.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -142,11 +142,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.ns.html b/docs/reference/ds.ns.html index 4cb30d13..773f972a 100644 --- a/docs/reference/ds.ns.html +++ b/docs/reference/ds.ns.html @@ -19,7 +19,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -129,11 +129,11 @@

Author

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.numNA.html b/docs/reference/ds.numNA.html index 2bb4270f..d45aef8b 100644 --- a/docs/reference/ds.numNA.html +++ b/docs/reference/ds.numNA.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -127,11 +127,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.qlspline.html b/docs/reference/ds.qlspline.html index d1a702dd..1c0a2948 100644 --- a/docs/reference/ds.qlspline.html +++ b/docs/reference/ds.qlspline.html @@ -20,7 +20,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -128,11 +128,11 @@

Author

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.quantileMean.html b/docs/reference/ds.quantileMean.html index bcc80bc5..7b5b899d 100644 --- a/docs/reference/ds.quantileMean.html +++ b/docs/reference/ds.quantileMean.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -146,11 +146,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.rBinom.html b/docs/reference/ds.rBinom.html index 63e174a8..35494000 100644 --- a/docs/reference/ds.rBinom.html +++ b/docs/reference/ds.rBinom.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -198,11 +198,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.rNorm.html b/docs/reference/ds.rNorm.html index 164ac708..ada55275 100644 --- a/docs/reference/ds.rNorm.html +++ b/docs/reference/ds.rNorm.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -213,11 +213,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.rPois.html b/docs/reference/ds.rPois.html index aaacd484..5cc4b71e 100644 --- a/docs/reference/ds.rPois.html +++ b/docs/reference/ds.rPois.html @@ -19,7 +19,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -188,11 +188,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.rUnif.html b/docs/reference/ds.rUnif.html index a9c582ce..dc14cc0a 100644 --- a/docs/reference/ds.rUnif.html +++ b/docs/reference/ds.rUnif.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -219,11 +219,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

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Author

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

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Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

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Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

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Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

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Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

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Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

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Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

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Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

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Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.sample.html b/docs/reference/ds.sample.html index 8ebc307c..1d8b566c 100644 --- a/docs/reference/ds.sample.html +++ b/docs/reference/ds.sample.html @@ -19,7 +19,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -234,11 +234,11 @@

Author

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.scatterPlot.html b/docs/reference/ds.scatterPlot.html index 5c792f45..c75cd0bc 100644 --- a/docs/reference/ds.scatterPlot.html +++ b/docs/reference/ds.scatterPlot.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -222,11 +222,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

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Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.setDefaultOpals.html b/docs/reference/ds.setDefaultOpals.html index 2753f52a..a2ad4ba4 100644 --- a/docs/reference/ds.setDefaultOpals.html +++ b/docs/reference/ds.setDefaultOpals.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -93,11 +93,11 @@

Author

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.setSeed.html b/docs/reference/ds.setSeed.html index f20baffa..4384b799 100644 --- a/docs/reference/ds.setSeed.html +++ b/docs/reference/ds.setSeed.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -156,11 +156,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.skewness.html b/docs/reference/ds.skewness.html index 86ff4c8c..d6e6d0dd 100644 --- a/docs/reference/ds.skewness.html +++ b/docs/reference/ds.skewness.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -154,11 +154,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.sqrt.html b/docs/reference/ds.sqrt.html index 46c711cb..3833f246 100644 --- a/docs/reference/ds.sqrt.html +++ b/docs/reference/ds.sqrt.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -146,11 +146,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.subset.html b/docs/reference/ds.subset.html index 69240cf0..a1d288b2 100644 --- a/docs/reference/ds.subset.html +++ b/docs/reference/ds.subset.html @@ -19,7 +19,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -180,11 +180,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.subsetByClass.html b/docs/reference/ds.subsetByClass.html index 8a8fad3b..024ebff5 100644 --- a/docs/reference/ds.subsetByClass.html +++ b/docs/reference/ds.subsetByClass.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -142,11 +142,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.summary.html b/docs/reference/ds.summary.html index 309c6a0d..7fa25f31 100644 --- a/docs/reference/ds.summary.html +++ b/docs/reference/ds.summary.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -139,11 +139,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.table.html b/docs/reference/ds.table.html index 4c524ddd..8699599a 100644 --- a/docs/reference/ds.table.html +++ b/docs/reference/ds.table.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -284,11 +284,11 @@

Author

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.table1D.html b/docs/reference/ds.table1D.html index cd8e6c28..1a58adea 100644 --- a/docs/reference/ds.table1D.html +++ b/docs/reference/ds.table1D.html @@ -19,7 +19,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -160,11 +160,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.table2D.html b/docs/reference/ds.table2D.html index 96270839..2d23b48e 100644 --- a/docs/reference/ds.table2D.html +++ b/docs/reference/ds.table2D.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -139,11 +139,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.tapply.assign.html b/docs/reference/ds.tapply.assign.html index c65eeacf..b6c24170 100644 --- a/docs/reference/ds.tapply.assign.html +++ b/docs/reference/ds.tapply.assign.html @@ -19,7 +19,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -212,11 +212,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.tapply.html b/docs/reference/ds.tapply.html index d1d6d8d8..ce789b20 100644 --- a/docs/reference/ds.tapply.html +++ b/docs/reference/ds.tapply.html @@ -19,7 +19,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -203,11 +203,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.testObjExists.html b/docs/reference/ds.testObjExists.html index 2dc6b97d..042cb6c1 100644 --- a/docs/reference/ds.testObjExists.html +++ b/docs/reference/ds.testObjExists.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -131,11 +131,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.unList.html b/docs/reference/ds.unList.html index 1a0b9c55..627bb62f 100644 --- a/docs/reference/ds.unList.html +++ b/docs/reference/ds.unList.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -149,11 +149,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.unique.html b/docs/reference/ds.unique.html index 5d1cd79b..92e30d19 100644 --- a/docs/reference/ds.unique.html +++ b/docs/reference/ds.unique.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -122,11 +122,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.var.html b/docs/reference/ds.var.html index 030dc4cd..58cd2850 100644 --- a/docs/reference/ds.var.html +++ b/docs/reference/ds.var.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -153,11 +153,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/ds.vectorCalc.html b/docs/reference/ds.vectorCalc.html index 43e81df9..0c88155c 100644 --- a/docs/reference/ds.vectorCalc.html +++ b/docs/reference/ds.vectorCalc.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -120,11 +120,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/extract.html b/docs/reference/extract.html index eacb3fcf..a79d9cbe 100644 --- a/docs/reference/extract.html +++ b/docs/reference/extract.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -72,11 +72,11 @@

Details

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/getPooledMean.html b/docs/reference/getPooledMean.html index 4986842d..2990bbf2 100644 --- a/docs/reference/getPooledMean.html +++ b/docs/reference/getPooledMean.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -79,11 +79,11 @@

Details

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/getPooledVar.html b/docs/reference/getPooledVar.html index 0286fd8e..bfc6fa5c 100644 --- a/docs/reference/getPooledVar.html +++ b/docs/reference/getPooledVar.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -79,11 +79,11 @@

Details

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/glmChecks.html b/docs/reference/glmChecks.html index 5a944f9e..67ce394b 100644 --- a/docs/reference/glmChecks.html +++ b/docs/reference/glmChecks.html @@ -18,7 +18,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -100,11 +100,11 @@

Author

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/index.html b/docs/reference/index.html index 0ceeb7bf..e2c343b7 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -42,6 +42,10 @@

All functions

+

computeWeightedMeans()

+ +

Compute Weighted Mean by Group

+

ds.Boole()

Converts a server-side R object into Boolean indicators

@@ -534,11 +538,11 @@

All functions
-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/isAssigned.html b/docs/reference/isAssigned.html index b3d66e75..60830286 100644 --- a/docs/reference/isAssigned.html +++ b/docs/reference/isAssigned.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -80,11 +80,11 @@

Details

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/isDefined.html b/docs/reference/isDefined.html index 54184020..bb68e2b3 100644 --- a/docs/reference/isDefined.html +++ b/docs/reference/isDefined.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -91,11 +91,11 @@

Author

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/logical2int.html b/docs/reference/logical2int.html index ac52dac1..4e925bb0 100644 --- a/docs/reference/logical2int.html +++ b/docs/reference/logical2int.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -74,11 +74,11 @@

Details

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/meanByClassHelper0a.html b/docs/reference/meanByClassHelper0a.html index 8d6cfebe..fc6ace60 100644 --- a/docs/reference/meanByClassHelper0a.html +++ b/docs/reference/meanByClassHelper0a.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -93,11 +93,11 @@

Author

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/meanByClassHelper0b.html b/docs/reference/meanByClassHelper0b.html index f35054ef..b9675846 100644 --- a/docs/reference/meanByClassHelper0b.html +++ b/docs/reference/meanByClassHelper0b.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -97,11 +97,11 @@

Author

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/meanByClassHelper1.html b/docs/reference/meanByClassHelper1.html index 810f46d7..fdb51c13 100644 --- a/docs/reference/meanByClassHelper1.html +++ b/docs/reference/meanByClassHelper1.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -90,11 +90,11 @@

Author

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/meanByClassHelper2.html b/docs/reference/meanByClassHelper2.html index 7540f66f..f9fc29ed 100644 --- a/docs/reference/meanByClassHelper2.html +++ b/docs/reference/meanByClassHelper2.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -91,11 +91,11 @@

Author

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/meanByClassHelper3.html b/docs/reference/meanByClassHelper3.html index c5eb79f5..24088066 100644 --- a/docs/reference/meanByClassHelper3.html +++ b/docs/reference/meanByClassHelper3.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -90,11 +90,11 @@

Author

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/meanByClassHelper4.html b/docs/reference/meanByClassHelper4.html index ef479e86..972adfdb 100644 --- a/docs/reference/meanByClassHelper4.html +++ b/docs/reference/meanByClassHelper4.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -100,11 +100,11 @@

Author

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/rowPercent.html b/docs/reference/rowPercent.html index da5df3fd..5d2d4c8d 100644 --- a/docs/reference/rowPercent.html +++ b/docs/reference/rowPercent.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -76,11 +76,11 @@

Author

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/reference/subsetHelper.html b/docs/reference/subsetHelper.html index 33f96c87..53e88d63 100644 --- a/docs/reference/subsetHelper.html +++ b/docs/reference/subsetHelper.html @@ -17,7 +17,7 @@ dsBaseClient - 6.3.1 + 6.3.3 @@ -131,11 +131,11 @@

Examples

-

Developed by DataSHIELD Developers.

+

Developed by Paul Burton, Rebecca Wilson, Olly Butters, Patricia Ryser-Welch, Alex Westerberg, Leire Abarrategui, Roberto Villegas-Diaz, Demetris Avraam, Yannick Marcon, Stuart Wheater.

-

Site built with pkgdown 2.1.1.

+

Site built with pkgdown 2.1.3.

diff --git a/docs/sitemap.xml b/docs/sitemap.xml index e67315a8..39df9eef 100644 --- a/docs/sitemap.xml +++ b/docs/sitemap.xml @@ -5,6 +5,7 @@ /index.html /reference/checkClass.html /reference/colPercent.html +/reference/computeWeightedMeans.html /reference/ds.Boole.html /reference/ds.abs.html /reference/ds.asCharacter.html diff --git a/dsBase_6.3.1-permissive.tar.gz b/dsBase_6.3.2-permissive.tar.gz similarity index 52% rename from dsBase_6.3.1-permissive.tar.gz rename to dsBase_6.3.2-permissive.tar.gz index f13ac01f..0d70f01c 100644 Binary files a/dsBase_6.3.1-permissive.tar.gz and b/dsBase_6.3.2-permissive.tar.gz differ diff --git a/dsBase_6.3.1.tar.gz b/dsBase_6.3.2.tar.gz similarity index 51% rename from dsBase_6.3.1.tar.gz rename to dsBase_6.3.2.tar.gz index 6f5d8e16..5d93ba95 100644 Binary files a/dsBase_6.3.1.tar.gz and b/dsBase_6.3.2.tar.gz differ diff --git a/man/checkClass.Rd b/man/checkClass.Rd index 85931e59..38dc642c 100644 --- a/man/checkClass.Rd +++ b/man/checkClass.Rd @@ -7,8 +7,8 @@ checkClass(datasources = NULL, obj = NULL) } \arguments{ -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. If the -the default set of connections will be used: see \link{datashield.connections_default}.} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the +the default set of connections will be used: see \link[DSI]{datashield.connections_default}.} \item{obj}{a string character, the name of the object to check for.} } diff --git a/man/computeWeightedMeans.Rd b/man/computeWeightedMeans.Rd new file mode 100644 index 00000000..0b8b0879 --- /dev/null +++ b/man/computeWeightedMeans.Rd @@ -0,0 +1,25 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/computeWeightedMeans.R +\name{computeWeightedMeans} +\alias{computeWeightedMeans} +\title{Compute Weighted Mean by Group} +\usage{ +computeWeightedMeans(data_table, variables, weight, by) +} +\arguments{ +\item{data_table}{a data.table} + +\item{variables}{character name of the variable(s) to focus on. The variables must be in the data.table} + +\item{weight}{character name of the data.table column that contains a weight.} + +\item{by}{character vector of the columns to group by} +} +\description{ +This function is originally from the panelaggregation package. +It has been ported here in order to bypass the package being +kicked off CRAN. +} +\author{ +Matthias Bannert, Gabriel Bucur +} diff --git a/man/ds.Boole.Rd b/man/ds.Boole.Rd index e102c872..46d27e4f 100644 --- a/man/ds.Boole.Rd +++ b/man/ds.Boole.Rd @@ -33,9 +33,9 @@ Default \code{'NA'}. For more information see details.} \item{newobj}{a character string that provides the name for the output object that is stored on the data servers. Default \code{boole.newobj}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.Boole} returns the object specified by the \code{newobj} argument diff --git a/man/ds.abs.Rd b/man/ds.abs.Rd index b408cacd..639ebd3e 100644 --- a/man/ds.abs.Rd +++ b/man/ds.abs.Rd @@ -12,9 +12,9 @@ ds.abs(x = NULL, newobj = NULL, datasources = NULL) \item{newobj}{a character string that provides the name for the output variable that is stored on the data servers. Default name is set to \code{abs.newobj}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified the default set of connections will be -used: see \code{\link{datashield.connections_default}}.} +used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.abs} assigns a vector for each study that includes the absolute values of diff --git a/man/ds.asCharacter.Rd b/man/ds.asCharacter.Rd index b11fc4f2..447d9cf9 100644 --- a/man/ds.asCharacter.Rd +++ b/man/ds.asCharacter.Rd @@ -13,9 +13,9 @@ character.} \item{newobj}{a character string that provides the name for the output object that is stored on the data servers. Default \code{ascharacter.newobj}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.asCharacter} returns the object converted into a class character diff --git a/man/ds.asDataMatrix.Rd b/man/ds.asDataMatrix.Rd index 4f286edd..e6ea9eb9 100644 --- a/man/ds.asDataMatrix.Rd +++ b/man/ds.asDataMatrix.Rd @@ -13,9 +13,9 @@ a matrix.} \item{newobj}{a character string that provides the name for the output object that is stored on the data servers. Default \code{asdatamatrix.newobj}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.asDataMatrix} returns the object converted into a matrix diff --git a/man/ds.asFactor.Rd b/man/ds.asFactor.Rd index bdd9a79e..c412df38 100644 --- a/man/ds.asFactor.Rd +++ b/man/ds.asFactor.Rd @@ -33,9 +33,9 @@ to be used in the creation of the matrix with dummy variables. If the \code{fixed.dummy.vars} is set to FALSE then any value of the baseline level is not taken into account.} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.asFactor} returns the unique levels of the converted diff --git a/man/ds.asFactorSimple.Rd b/man/ds.asFactorSimple.Rd index 07746f8b..d54776a1 100644 --- a/man/ds.asFactorSimple.Rd +++ b/man/ds.asFactorSimple.Rd @@ -17,9 +17,9 @@ the name of the variable to be converted to a factor.} \item{newobj.name}{a character string that provides the name for the output variable that is stored on the data servers. Default \code{asfactor.newobj}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ an output vector of class factor to the serverside. In addition, returns a validity diff --git a/man/ds.asInteger.Rd b/man/ds.asInteger.Rd index 49d8ca56..d2f0455b 100644 --- a/man/ds.asInteger.Rd +++ b/man/ds.asInteger.Rd @@ -13,9 +13,9 @@ an integer.} \item{newobj}{a character string that provides the name for the output object that is stored on the data servers. Default \code{asinteger.newobj}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.asInteger} returns the R object converted into an integer diff --git a/man/ds.asList.Rd b/man/ds.asList.Rd index dbb8439b..1e2e3c73 100644 --- a/man/ds.asList.Rd +++ b/man/ds.asList.Rd @@ -13,9 +13,9 @@ a list.} \item{newobj}{a character string that provides the name for the output object that is stored on the data servers. Default \code{aslist.newobj}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.asList} returns the R object converted into a list diff --git a/man/ds.asLogical.Rd b/man/ds.asLogical.Rd index 479ca72b..c42d2e6a 100644 --- a/man/ds.asLogical.Rd +++ b/man/ds.asLogical.Rd @@ -13,9 +13,9 @@ input object to be coerced to a logical.} \item{newobj}{a character string that provides the name for the output object that is stored on the data servers. Default \code{aslogical.newobj}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.asLogical} returns the R object converted into a logical diff --git a/man/ds.asMatrix.Rd b/man/ds.asMatrix.Rd index 5c2e991a..70948014 100644 --- a/man/ds.asMatrix.Rd +++ b/man/ds.asMatrix.Rd @@ -13,9 +13,9 @@ a matrix.} \item{newobj}{a character string that provides the name for the output object that is stored on the data servers. Default \code{asmatrix.newobj}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.asMatrix} returns the object converted into a matrix diff --git a/man/ds.asNumeric.Rd b/man/ds.asNumeric.Rd index 90f18101..a07204c1 100644 --- a/man/ds.asNumeric.Rd +++ b/man/ds.asNumeric.Rd @@ -13,9 +13,9 @@ a numeric.} \item{newobj}{a character string that provides the name for the output object that is stored on the data servers. Default \code{asnumeric.newobj}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.asNumeric} returns the R object converted into a numeric class diff --git a/man/ds.assign.Rd b/man/ds.assign.Rd index 30cf5d12..e09d426f 100644 --- a/man/ds.assign.Rd +++ b/man/ds.assign.Rd @@ -12,9 +12,9 @@ ds.assign(toAssign = NULL, newobj = NULL, datasources = NULL) \item{newobj}{a character string that provides the name for the output object that is stored on the data servers. Default \code{assign.newobj}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.assign} returns the R object assigned to a name diff --git a/man/ds.auc.Rd b/man/ds.auc.Rd index 1bdc075f..0ca1a5d3 100644 --- a/man/ds.auc.Rd +++ b/man/ds.auc.Rd @@ -12,9 +12,9 @@ ds.auc(pred = NULL, y = NULL, datasources = NULL) \item{y}{the name of the outcome variable. Note that this variable should include the complete cases that are used in the regression model.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ returns the AUC and its standard error diff --git a/man/ds.boxPlot.Rd b/man/ds.boxPlot.Rd index 2831c4f9..0e8e7a33 100644 --- a/man/ds.boxPlot.Rd +++ b/man/ds.boxPlot.Rd @@ -32,7 +32,7 @@ holds the information to be plotted} \item{type}{\code{character} Return a pooled plot (\code{"pooled"}) or a split plot (one for each study server \code{"split"})} -\item{datasources}{a list of \code{\link{DSConnection-class}} (default \code{NULL}) objects obtained after login} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} (default \code{NULL}) objects obtained after login} } \value{ \code{ggplot} object @@ -79,7 +79,7 @@ of grouping using categorical variables on the dataset (only for data frames) ds.boxPlot("D", "LAB_HDL", type= "split", datasources = connections) ## Create a boxplot of two variables variable - ds.boxPlot("D", c("LAB_HDL", "LAB_TRIG", type="combine", + ds.boxPlot("D", c("LAB_HDL", "LAB_TRIG", type="pooled", datasources = connections) # only one plot is created (of the aggregated results of all servers) diff --git a/man/ds.boxPlotGG.Rd b/man/ds.boxPlotGG.Rd index 93f798b7..14627138 100644 --- a/man/ds.boxPlotGG.Rd +++ b/man/ds.boxPlotGG.Rd @@ -34,7 +34,7 @@ of this object must be: \cr \item{type}{\code{character} Return a pooled plot (\code{"pooled"}) or a split plot (one for each study server \code{"split"})} -\item{datasources}{a list of \code{\link{DSConnection-class}} (default \code{NULL}) objects obtained after login} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} (default \code{NULL}) objects obtained after login} } \value{ \code{ggplot} object diff --git a/man/ds.boxPlotGG_data_Treatment.Rd b/man/ds.boxPlotGG_data_Treatment.Rd index 8a264aed..9788f0c7 100644 --- a/man/ds.boxPlotGG_data_Treatment.Rd +++ b/man/ds.boxPlotGG_data_Treatment.Rd @@ -21,7 +21,7 @@ ds.boxPlotGG_data_Treatment( \item{group2}{\code{character} (default \code{NULL}) Name of the second grouping variable.} -\item{datasources}{a list of \code{\link{DSConnection-class}} (default \code{NULL}) objects obtained after login} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} (default \code{NULL}) objects obtained after login} } \value{ Does not return nothing, it creates the table \code{"boxPlotRawData"} on the server arranged to be passed to the diff --git a/man/ds.boxPlotGG_data_Treatment_numeric.Rd b/man/ds.boxPlotGG_data_Treatment_numeric.Rd index 860e223e..56ead361 100644 --- a/man/ds.boxPlotGG_data_Treatment_numeric.Rd +++ b/man/ds.boxPlotGG_data_Treatment_numeric.Rd @@ -9,7 +9,7 @@ ds.boxPlotGG_data_Treatment_numeric(vector, datasources = NULL) \arguments{ \item{vector}{\code{character} Name of the table on the server side that holds the information to be plotted later} -\item{datasources}{a list of \code{\link{DSConnection-class}} (default \code{NULL}) objects obtained after login} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} (default \code{NULL}) objects obtained after login} } \value{ Does not return nothing, it creates the table \code{"boxPlotRawDataNumeric"} on the server arranged to be passed to the diff --git a/man/ds.boxPlotGG_numeric.Rd b/man/ds.boxPlotGG_numeric.Rd index cb98d9ad..a71a0e0a 100644 --- a/man/ds.boxPlotGG_numeric.Rd +++ b/man/ds.boxPlotGG_numeric.Rd @@ -22,7 +22,7 @@ ds.boxPlotGG_numeric( \item{type}{\code{character} Return a pooled plot (\code{"pooled"}) or a split plot (one for each study server \code{"split"})} -\item{datasources}{a list of \code{\link{DSConnection-class}} (default \code{NULL}) objects obtained after login} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} (default \code{NULL}) objects obtained after login} } \value{ \code{ggplot} object diff --git a/man/ds.boxPlotGG_table.Rd b/man/ds.boxPlotGG_table.Rd index a0f12f7c..4318ffb8 100644 --- a/man/ds.boxPlotGG_table.Rd +++ b/man/ds.boxPlotGG_table.Rd @@ -31,7 +31,7 @@ ds.boxPlotGG_table( \item{type}{\code{character} Return a pooled plot (\code{"pooled"}) or a split plot (one for each study server \code{"split"})} -\item{datasources}{a list of \code{\link{DSConnection-class}} (default \code{NULL}) objects obtained after login} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} (default \code{NULL}) objects obtained after login} } \value{ \code{ggplot} object diff --git a/man/ds.bp_standards.Rd b/man/ds.bp_standards.Rd index 09ecfa01..edbdd06d 100644 --- a/man/ds.bp_standards.Rd +++ b/man/ds.bp_standards.Rd @@ -33,9 +33,9 @@ blood pressure.} \item{newobj}{a character string that provides the name for the output object that is stored on the data servers. Default name is set to \code{bp.newobj}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified the default set of connections will be -used: see \code{\link{datashield.connections_default}}.} +used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ assigns a new object on the server-side. The assigned object is a list diff --git a/man/ds.c.Rd b/man/ds.c.Rd index ddd4db49..bc899891 100644 --- a/man/ds.c.Rd +++ b/man/ds.c.Rd @@ -12,9 +12,9 @@ ds.c(x = NULL, newobj = NULL, datasources = NULL) \item{newobj}{a character string that provides the name for the output object that is stored on the data servers. Default \code{c.newobj}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.c} returns the vector of concatenating R diff --git a/man/ds.cbind.Rd b/man/ds.cbind.Rd index 4f3dc8ee..ca20b9e8 100644 --- a/man/ds.cbind.Rd +++ b/man/ds.cbind.Rd @@ -30,9 +30,9 @@ For more information see \strong{Details}.} \item{newobj}{a character string that provides the name for the output variable that is stored on the data servers. Defaults \code{cbind.newobj}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} \item{notify.of.progress}{specifies if console output should be produced to indicate progress. Default FALSE.} diff --git a/man/ds.changeRefGroup.Rd b/man/ds.changeRefGroup.Rd index 124cd903..1730a62f 100644 --- a/man/ds.changeRefGroup.Rd +++ b/man/ds.changeRefGroup.Rd @@ -24,9 +24,9 @@ that is stored on the server-side. Default \code{changerefgroup.newobj}.} should be ordered by the reference group (i.e. putting the reference group first). The default is to not re-order (see the reasons in the details).} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.changeRefGroup} returns a new vector with the specified level as a reference diff --git a/man/ds.class.Rd b/man/ds.class.Rd index 59f1efa2..b2fc0f07 100644 --- a/man/ds.class.Rd +++ b/man/ds.class.Rd @@ -9,9 +9,9 @@ ds.class(x = NULL, datasources = NULL) \arguments{ \item{x}{a character string providing the name of the input R object.} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.class} returns the type of the R object. diff --git a/man/ds.colnames.Rd b/man/ds.colnames.Rd index 3f44ee30..e7391081 100644 --- a/man/ds.colnames.Rd +++ b/man/ds.colnames.Rd @@ -9,9 +9,9 @@ ds.colnames(x = NULL, datasources = NULL) \arguments{ \item{x}{a character string providing the name of the input data frame or matrix.} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.colnames} returns the column names of diff --git a/man/ds.completeCases.Rd b/man/ds.completeCases.Rd index a5b0b8a0..f5df7658 100644 --- a/man/ds.completeCases.Rd +++ b/man/ds.completeCases.Rd @@ -15,9 +15,9 @@ that is stored on the data servers. If the user does not specify a name, then th generates a name for the generated object that is the name of the input object with the suffix "_complete.cases"} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified, the default set of connections will be -used: see \code{\link{datashield.connections_default}}.} +used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.completeCases} generates a modified data frame, matrix or vector from which diff --git a/man/ds.contourPlot.Rd b/man/ds.contourPlot.Rd index e0df915f..f9335d34 100644 --- a/man/ds.contourPlot.Rd +++ b/man/ds.contourPlot.Rd @@ -44,9 +44,9 @@ see details.} \item{noise}{the percentage of the initial variance that is used as the variance of the embedded noise if the argument \code{method} is set to \code{'probabilistic'}. For more information see details.} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.contourPlot} returns a contour plot to the client-side. diff --git a/man/ds.cor.Rd b/man/ds.cor.Rd index d01c9b3b..030defae 100644 --- a/man/ds.cor.Rd +++ b/man/ds.cor.Rd @@ -15,9 +15,9 @@ Default NULL.} \item{type}{a character string that represents the type of analysis to carry out. This must be set to \code{'split'} or \code{'combine'}. Default \code{'split'}. For more information see details.} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.cor} returns a list containing the number of missing values in each variable, diff --git a/man/ds.corTest.Rd b/man/ds.corTest.Rd index bb2384d4..fac90553 100644 --- a/man/ds.corTest.Rd +++ b/man/ds.corTest.Rd @@ -36,9 +36,9 @@ This must be set to \code{'split'} or \code{'combine'}. Default is set to \code{ \code{type} is set to "combine" then an approximated pooled correlation is estimated based on Fisher's z transformation.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.corTest} returns to the client-side the results of the correlation test. diff --git a/man/ds.cov.Rd b/man/ds.cov.Rd index 1d8b5455..3fe9ec8f 100644 --- a/man/ds.cov.Rd +++ b/man/ds.cov.Rd @@ -25,9 +25,9 @@ presence of missing values. This must be set to \code{'casewise.complete'} or \item{type}{a character string that represents the type of analysis to carry out. This must be set to \code{'split'} or \code{'combine'}. Default \code{'split'}. For more information see details.} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.cov} returns a list containing the number of missing values in each variable, the number of missing values diff --git a/man/ds.dataFrame.Rd b/man/ds.dataFrame.Rd index 4a3e80dd..5c7d82d7 100644 --- a/man/ds.dataFrame.Rd +++ b/man/ds.dataFrame.Rd @@ -48,9 +48,9 @@ are the same} \item{newobj}{a character string that provides the name for the output data frame that is stored on the data servers. Default \code{dataframe.newobj}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} \item{notify.of.progress}{specifies if console output should be produced to indicate progress. Default is FALSE.} diff --git a/man/ds.dataFrameFill.Rd b/man/ds.dataFrameFill.Rd index 3183d61c..44eef9e5 100644 --- a/man/ds.dataFrameFill.Rd +++ b/man/ds.dataFrameFill.Rd @@ -13,9 +13,9 @@ filled with extra columns of missing values.} \item{newobj}{a character string that provides the name for the output data frame that is stored on the data servers. Default value is "dataframefill.newobj".} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.dataFrameFill} returns the object specified by the \code{newobj} argument which diff --git a/man/ds.dataFrameSort.Rd b/man/ds.dataFrameSort.Rd index 7b9e843a..252227e5 100644 --- a/man/ds.dataFrameSort.Rd +++ b/man/ds.dataFrameSort.Rd @@ -30,9 +30,9 @@ to sort the data frame. This can be set as that is stored on the data servers. Default \code{dataframesort.newobj}. where \code{df.name} is the first argument of \code{ds.dataFrameSort()}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.dataFrameSort} returns the sorted data frame is written to the server-side. diff --git a/man/ds.dataFrameSubset.Rd b/man/ds.dataFrameSubset.Rd index 2f6068d3..58b557fe 100644 --- a/man/ds.dataFrameSubset.Rd +++ b/man/ds.dataFrameSubset.Rd @@ -42,9 +42,9 @@ If FALSE or NULL all rows with at least one missing values are removed from the \item{newobj}{a character string that provides the name for the output object that is stored on the data servers. Default \code{dataframesubset.newobj}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} \item{notify.of.progress}{specifies if console output should be produced to indicate progress. Default FALSE.} diff --git a/man/ds.densityGrid.Rd b/man/ds.densityGrid.Rd index 15e29977..89cc4348 100644 --- a/man/ds.densityGrid.Rd +++ b/man/ds.densityGrid.Rd @@ -26,9 +26,9 @@ If \code{type} is set to instead if \code{type} is set to \code{'split'} one grid density matrix is generated. Default \code{'combine'}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.densityGrid} returns a grid density matrix. diff --git a/man/ds.dim.Rd b/man/ds.dim.Rd index b6a86b57..ea3aaa6d 100644 --- a/man/ds.dim.Rd +++ b/man/ds.dim.Rd @@ -20,9 +20,9 @@ Default \code{'both'}.} \item{checks}{logical. If TRUE undertakes all DataSHIELD checks (time-consuming). Default FALSE.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.dim} retrieves to the client-side the dimension of the object diff --git a/man/ds.elspline.Rd b/man/ds.elspline.Rd index 26c5f6cc..e6e32197 100644 --- a/man/ds.elspline.Rd +++ b/man/ds.elspline.Rd @@ -26,9 +26,9 @@ intervals along the range of x} \item{newobj}{a character string that provides the name for the output variable that is stored on the data servers. Default \code{elspline.newobj}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ an object of class "lspline" and "matrix", which its name is specified by the diff --git a/man/ds.exists.Rd b/man/ds.exists.Rd index 029c66b9..2352a294 100644 --- a/man/ds.exists.Rd +++ b/man/ds.exists.Rd @@ -9,9 +9,9 @@ ds.exists(x = NULL, datasources = NULL) \arguments{ \item{x}{a character string providing the name of the object to look for.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.exists} returns a logical object. diff --git a/man/ds.exp.Rd b/man/ds.exp.Rd index 07e212c9..875dbe00 100644 --- a/man/ds.exp.Rd +++ b/man/ds.exp.Rd @@ -12,9 +12,9 @@ ds.exp(x = NULL, newobj = NULL, datasources = NULL) \item{newobj}{a character string that provides the name for the output variable that is stored on the data servers. Default \code{exp.newobj}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.exp} returns a vector for each study of the exponential values for the numeric vector diff --git a/man/ds.gamlss.Rd b/man/ds.gamlss.Rd index 60bd6d17..4c7bc169 100644 --- a/man/ds.gamlss.Rd +++ b/man/ds.gamlss.Rd @@ -96,9 +96,9 @@ only.} \item{newobj}{a character string that provides the name for the output object that is stored on the data servers. Default \code{gamlss_res}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ a gamlss object with all components as in the native R gamlss function. diff --git a/man/ds.getWGSR.Rd b/man/ds.getWGSR.Rd index 1e3b8672..f48b9a28 100644 --- a/man/ds.getWGSR.Rd +++ b/man/ds.getWGSR.Rd @@ -66,9 +66,9 @@ by the formula $age_days=age_months*(365.25/12)$.} \item{newobj}{a character string that provides the name for the output variable that is stored on the data servers. Defaults \code{getWGSR.newobj}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified the default set of connections will be -used: see \code{\link{datashield.connections_default}}.} +used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.getWGSR} assigns a vector for each study that includes the z-scores for the diff --git a/man/ds.glm.Rd b/man/ds.glm.Rd index 861eab67..67728e00 100644 --- a/man/ds.glm.Rd +++ b/man/ds.glm.Rd @@ -58,9 +58,9 @@ of parameter estimates is returned. Default FALSE.} \item{viewCor}{logical. If TRUE the correlation matrix of parameter estimates is returned. Default FALSE.} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ Many of the elements of the output list returned by \code{ds.glm} are @@ -138,7 +138,7 @@ function is also allowed by \code{ds.glm}. Many GLMs can be fitted very simply using a formula such as: -\deqn{y~a+b+c+d} +\eqn{y~a+b+c+d} which simply means fit a GLM with \code{y} as the outcome variable and \code{a}, \code{b}, \code{c} and \code{d} as covariates. @@ -147,7 +147,7 @@ By default all such models also include an intercept (regression constant) term. Instead, if you need to fit a more complex model, for example: - \deqn{EVENT~1+TID+SEXF*AGE.60} + \eqn{EVENT~1+TID+SEXF*AGE.60} In the above model the outcome variable is \code{EVENT} and the covariates @@ -183,7 +183,7 @@ an \code{identity} link function, the binomial family with a The \code{data} argument avoids you having to specify the name of the data frame in front of each covariate in the formula. For example, if the data frame is called \code{DataFrame} you -avoid having to write: \eqn{DataFrame$y~DataFrame$a+DataFrame$b+DataFrame$c+DataFrame$d} +avoid having to write: \eqn{DataFrame\$y ~ DataFrame\$a + DataFrame\$b + DataFrame\$c + DataFrame\$d} The \code{checks} argument verifies that the variables in the model are all defined (exist) on the server-side at every study diff --git a/man/ds.glmSLMA.Rd b/man/ds.glmSLMA.Rd index b5122e0f..f0a9863d 100644 --- a/man/ds.glmSLMA.Rd +++ b/man/ds.glmSLMA.Rd @@ -58,9 +58,9 @@ For more information see \strong{Details}.} \item{notify.of.progress}{specifies if console output should be produced to indicate progress. Default FALSE.} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ The serverside aggregate functions \code{glmSLMADS1} and \code{glmSLMADS2} return @@ -241,7 +241,7 @@ function is also allowed by \code{ds.glmSLMA}. Many glms can be fitted very simply using a formula such as: -\deqn{y~a+b+c+d} +\eqn{y~a+b+c+d} which simply means fit a glm with \code{y} as the outcome variable and \code{a}, \code{b}, \code{c} and \code{d} as covariates. @@ -250,7 +250,7 @@ By default all such models also include an intercept (regression constant) term. Instead, if you need to fit a more complex model, for example: - \deqn{EVENT~1+TID+SEXF*AGE.60} +\eqn{EVENT~1+TID+SEXF*AGE.60} In the above model the outcome variable is \code{EVENT} and the covariates @@ -312,7 +312,7 @@ maximises the information extraction by the model. The gaussian family uses the The \code{dataName} argument avoids you having to specify the name of the data frame in front of each covariate in the formula. For example, if the data frame is called \code{DataFrame} you -avoid having to write: \eqn{DataFrame$y~DataFrame$a+DataFrame$b+DataFrame$c+DataFrame$d} +avoid having to write: \eqn{DataFrame\$y ~ DataFrame\$a + DataFrame\$b + DataFrame\$c + DataFrame\$d} The \code{checks} argument verifies that the variables in the model are all defined (exist) on the server-site at every study diff --git a/man/ds.glmerSLMA.Rd b/man/ds.glmerSLMA.Rd index b1e3165b..8ad49c3a 100644 --- a/man/ds.glmerSLMA.Rd +++ b/man/ds.glmerSLMA.Rd @@ -45,9 +45,9 @@ that contains all of the variables in the GLME formula. For more information see \item{checks}{logical. If TRUE \code{ds.glmerSLMA} checks the structural integrity of the model. Default FALSE. For more information see \strong{Details}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} \item{family}{a character string specifying the distribution of the observed value of the outcome variable around the predictions generated by the linear predictor. @@ -169,23 +169,23 @@ If it did not some information about the reason for this is reported. In \code{formula} most shortcut notation allowed by \code{glmer()} function is also allowed by \code{ds.glmerSLMA}. Many GLMEs can be fitted very simply using a formula like: -\deqn{y~a+b+(1|c)} +\eqn{y~a+b+(1|c)} which simply means fit an GLME with \code{y} as the outcome variable (e.g. a binary case-control using a logistic regression model or a count or a survival time using a Poisson regression model), \code{a} and \code{b} as fixed effects, and \code{c} as a random effect or grouping factor. It is also possible to fit models with random slopes by specifying a model such as -\deqn{y~a+b+(1+b|c)} +\eqn{y~a+b+(1+b|c)} where the effect of \code{b} can vary randomly between groups defined by \code{c}. Implicit nesting can be specified with formulas such as: \eqn{y~a+b+(1|c/d)} -or \eqn{y~a+b+(1|c)+(1|c:d)}. +or \eqn{y~a+b+(1|c)+(1|c:d)}. The \code{dataName} argument avoids you having to specify the name of the data frame in front of each covariate in the formula. For example, if the data frame is called \code{DataFrame} you avoid having to write: -\eqn{DataFrame$y~DataFrame$a+DataFrame$b+(1|DataFrame$c)}. +\eqn{DataFrame\$y ~ DataFrame\$a + DataFrame\$b + (1 | DataFrame\$c)}. The \code{checks} argument verifies that the variables in the model are all defined (exist) on the server-site at every study diff --git a/man/ds.heatmapPlot.Rd b/man/ds.heatmapPlot.Rd index c1669431..3ab17da9 100644 --- a/man/ds.heatmapPlot.Rd +++ b/man/ds.heatmapPlot.Rd @@ -49,9 +49,9 @@ noise if the argument \code{method} is set to \code{'probabilistic'}. Default \code{noise} value is \code{0.25}. For more information see \strong{Details}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.heatmapPlot} returns to the client-side a heat map plot and a message specifying diff --git a/man/ds.hetcor.Rd b/man/ds.hetcor.Rd index aa7d0713..e236a0e9 100644 --- a/man/ds.hetcor.Rd +++ b/man/ds.hetcor.Rd @@ -34,9 +34,9 @@ nearPD directly.} \item{use}{if "complete.obs", remove observations with any missing data; if "pairwise.complete.obs", compute each correlation using all observations with valid data for that pair of variables.} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified the default set of connections will be -used: see \code{\link{datashield.connections_default}}.} +used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ Returns an object of class "hetcor" from each study, with the following components: the diff --git a/man/ds.histogram.Rd b/man/ds.histogram.Rd index 12af4457..17de73da 100644 --- a/man/ds.histogram.Rd +++ b/man/ds.histogram.Rd @@ -46,9 +46,9 @@ plot. The \code{vertical.axis} argument can be set as \code{'Frequency'} or \cod Default \code{'Frequency'}. For more information see \strong{Details}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ one or more histogram objects and plots depending on the argument \code{type} diff --git a/man/ds.igb_standards.Rd b/man/ds.igb_standards.Rd index 6ea70b2f..499220a2 100644 --- a/man/ds.igb_standards.Rd +++ b/man/ds.igb_standards.Rd @@ -39,9 +39,9 @@ recode the categories to Male/Female before the use of ds.igb_standards.} \item{newobj}{a character string that provides the name for the output variable that is stored on the data servers. Default name is set to \code{igb.newobj}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified the default set of connections will be -used: see \code{\link{datashield.connections_default}}.} +used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ assigns the converted measurement as a new object on the server-side diff --git a/man/ds.isNA.Rd b/man/ds.isNA.Rd index 0c94b9eb..ec6b2f6f 100644 --- a/man/ds.isNA.Rd +++ b/man/ds.isNA.Rd @@ -9,9 +9,9 @@ ds.isNA(x = NULL, datasources = NULL) \arguments{ \item{x}{a character string specifying the name of the vector to check.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.isNA} returns a boolean. If it is TRUE the vector is empty diff --git a/man/ds.isValid.Rd b/man/ds.isValid.Rd index 2bda8557..2f927ae2 100644 --- a/man/ds.isValid.Rd +++ b/man/ds.isValid.Rd @@ -9,9 +9,9 @@ ds.isValid(x = NULL, datasources = NULL) \arguments{ \item{x}{a character string specifying the name of a vector, dataframe or matrix.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.isValid} returns a boolean. If it is TRUE input object is valid, FALSE otherwise. diff --git a/man/ds.kurtosis.Rd b/man/ds.kurtosis.Rd index 4a9b2a32..4b698adf 100644 --- a/man/ds.kurtosis.Rd +++ b/man/ds.kurtosis.Rd @@ -18,9 +18,9 @@ if \code{type} is set to 'split', 'splits' or 's', the kurtosis is returned sepa if \code{type} is set to 'both' or 'b', both sets of outputs are produced. The default value is set to 'both'.} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ a matrix showing the kurtosis of the input numeric variable, the number of valid observations and diff --git a/man/ds.length.Rd b/man/ds.length.Rd index 08b513a1..27e105bc 100644 --- a/man/ds.length.Rd +++ b/man/ds.length.Rd @@ -22,9 +22,9 @@ Default \code{'both'}.} Default FALSE to save time. It is suggested that checks should only be undertaken once the function call has failed.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.length} returns to the client-side the pooled length of a vector or a list, diff --git a/man/ds.levels.Rd b/man/ds.levels.Rd index 0a372660..fbdab0c4 100644 --- a/man/ds.levels.Rd +++ b/man/ds.levels.Rd @@ -9,9 +9,9 @@ ds.levels(x = NULL, datasources = NULL) \arguments{ \item{x}{a character string specifying the name of a factor variable.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.levels} returns to the client-side the levels of a factor diff --git a/man/ds.lexis.Rd b/man/ds.lexis.Rd index 0c75e1f0..a57cd28c 100644 --- a/man/ds.lexis.Rd +++ b/man/ds.lexis.Rd @@ -41,9 +41,9 @@ variables to include in the final expanded table. For more information see \stro \item{expandDF}{a character string denoting the name of the new data frame containing the expanded data set. Default \code{lexis.newobj}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.lexis} returns to the server-side a data frame for each study with diff --git a/man/ds.list.Rd b/man/ds.list.Rd index de5b69e7..d6ebd00e 100644 --- a/man/ds.list.Rd +++ b/man/ds.list.Rd @@ -12,9 +12,9 @@ ds.list(x = NULL, newobj = NULL, datasources = NULL) \item{newobj}{a character string that provides the name for the output variable that is stored on the data servers. Default \code{list.newobj}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.list} returns a list of objects for each study that is stored on the server-side. diff --git a/man/ds.listDisclosureSettings.Rd b/man/ds.listDisclosureSettings.Rd index d04448b8..23ab83fd 100644 --- a/man/ds.listDisclosureSettings.Rd +++ b/man/ds.listDisclosureSettings.Rd @@ -7,9 +7,9 @@ ds.listDisclosureSettings(datasources = NULL) } \arguments{ -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.listDisclosureSettings} returns a list containing the current settings of the diff --git a/man/ds.listServersideFunctions.Rd b/man/ds.listServersideFunctions.Rd index 30931c62..70d9ba5d 100644 --- a/man/ds.listServersideFunctions.Rd +++ b/man/ds.listServersideFunctions.Rd @@ -7,9 +7,9 @@ ds.listServersideFunctions(datasources = NULL) } \arguments{ -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.listServersideFunctions} returns to the client-side @@ -20,7 +20,7 @@ Firstly lists assign and then aggregate functions. Lists all current server-side functions } \details{ -Uses \code{\link{datashield.methods}} function from \code{DSI} package to list all +Uses \code{\link[DSI]{datashield.methods}} function from \code{DSI} package to list all assign and aggregate functions on the available data repository servers. The only choice of arguments is in \code{datasources}; i.e. which studies to interrogate. Once the studies have diff --git a/man/ds.lmerSLMA.Rd b/man/ds.lmerSLMA.Rd index 82196053..dbd9b7fb 100644 --- a/man/ds.lmerSLMA.Rd +++ b/man/ds.lmerSLMA.Rd @@ -44,9 +44,9 @@ For more information see \strong{Details}.} \item{checks}{logical. If TRUE \code{ds.lmerSLMA} checks the structural integrity of the model. Default FALSE. For more information see \strong{Details}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} \item{REML}{logical. If TRUE the REstricted Maximum Likelihood (REML) is used for parameter optimization. @@ -168,20 +168,20 @@ obtained using R help for \code{lmer} and the \code{lme4} package. In \code{formula} most shortcut notation allowed by \code{lmer()} function is also allowed by \code{ds.lmerSLMA}. Many LMEs can be fitted very simply using a formula like: -\deqn{y~a+b+(1|c)} +\eqn{y ~ a + b + (1 | c)} which simply means fit an LME with \code{y} as the outcome variable with \code{a} and \code{b} as fixed effects, and \code{c} as a random effect or grouping factor. It is also possible to fit models with random slopes by specifying a model such as -\deqn{y~a+b+(1+b|c)} +\eqn{y ~ a + b + (1 + b | c)} where the effect of \code{b} can vary randomly between groups defined by \code{c}. -Implicit nesting can be specified with formulae such as \eqn{y~a+b+(1|c/d)} -or \eqn{y~a+b+(1|c)+(1|c:d)}. +Implicit nesting can be specified with formulae such as \eqn{y ~ a + b + (1 | c / d)} +or \eqn{y ~ a + b + (1 | c) + (1 | c : d)}. The \code{dataName} argument avoids you having to specify the name of the data frame in front of each covariate in the formula. For example, if the data frame is called \code{DataFrame} you avoid having to write: -\eqn{DataFrame$y~DataFrame$a+DataFrame$b+(1|DataFrame$c)}. +\eqn{DataFrame\$y ~ DataFrame\$a + DataFrame\$b + (1 | DataFrame\$c)}. The \code{checks} argument verifies that the variables in the model are all defined (exist) on the server-site at every study @@ -252,7 +252,7 @@ Server function called: \code{lmerSLMADS2} # Fit the lmer - ds.lmerSLMA(formula = "BMI ~ incid_rate + diabetes + (1 | Male)", + ds.lmerSLMA(formula = "BMI ~ incid_rate + diabetes + (1 | Male)", dataName = "D.comp", datasources = connections) diff --git a/man/ds.log.Rd b/man/ds.log.Rd index b988fb84..6ab8fee7 100644 --- a/man/ds.log.Rd +++ b/man/ds.log.Rd @@ -15,9 +15,9 @@ Default \code{exp(1)}.} \item{newobj}{a character string that provides the name for the output variable that is stored on the server-side. Default \code{log.newobj}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.log} returns a vector for each study of the transformed values for the numeric vector diff --git a/man/ds.look.Rd b/man/ds.look.Rd index 4a59c166..3cecb462 100644 --- a/man/ds.look.Rd +++ b/man/ds.look.Rd @@ -13,9 +13,9 @@ For more information see \strong{Details}.} \item{checks}{logical. If TRUE the optional checks are undertaken. Default FALSE to save time.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ the output from the specified server-side aggregate function to the client-side. diff --git a/man/ds.ls.Rd b/man/ds.ls.Rd index e05feb5e..e1b5d324 100644 --- a/man/ds.ls.Rd +++ b/man/ds.ls.Rd @@ -26,9 +26,9 @@ set as a valid integer, \code{ds.ls} will list all objects in the server-side R identified by \code{env.to.search} in the search path. For more information see \strong{Details}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.ls} returns to the client-side a list containing: \cr diff --git a/man/ds.lspline.Rd b/man/ds.lspline.Rd index 550e2397..0cf8e5aa 100644 --- a/man/ds.lspline.Rd +++ b/man/ds.lspline.Rd @@ -25,9 +25,9 @@ ds.lspline( \item{newobj}{a character string that provides the name for the output variable that is stored on the data servers. Default \code{lspline.newobj}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ an object of class "lspline" and "matrix", which its name is specified by the diff --git a/man/ds.make.Rd b/man/ds.make.Rd index d87cc537..197518bc 100644 --- a/man/ds.make.Rd +++ b/man/ds.make.Rd @@ -12,9 +12,9 @@ ds.make(toAssign = NULL, newobj = NULL, datasources = NULL) \item{newobj}{a character string that provides the name for the output variable that is stored on the data servers. Default \code{make.newobj}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.make} returns the new object which is written to the diff --git a/man/ds.matrix.Rd b/man/ds.matrix.Rd index 27b3e9d8..b2928c3e 100644 --- a/man/ds.matrix.Rd +++ b/man/ds.matrix.Rd @@ -43,9 +43,9 @@ the row and column names respectively.} \item{newobj}{a character string that provides the name for the output variable that is stored on the data servers. Default \code{matrix.newobj}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.matrix} returns the created matrix which is written on the server-side. diff --git a/man/ds.matrixDet.Rd b/man/ds.matrixDet.Rd index 1c419f4d..e827e815 100644 --- a/man/ds.matrixDet.Rd +++ b/man/ds.matrixDet.Rd @@ -15,9 +15,9 @@ variable that is stored on the data servers. Default \code{matrixdet.newobj}.} \item{logarithm}{logical. If TRUE the logarithm of the modulus of the determinant is calculated. Default FALSE.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.matrixDet} returns the determinant of an existing matrix on the server-side. diff --git a/man/ds.matrixDet.report.Rd b/man/ds.matrixDet.report.Rd index e4fc3569..0a5c021d 100644 --- a/man/ds.matrixDet.report.Rd +++ b/man/ds.matrixDet.report.Rd @@ -12,9 +12,9 @@ ds.matrixDet.report(M1 = NULL, logarithm = FALSE, datasources = NULL) \item{logarithm}{logical. If TRUE the logarithm of the modulus of the determinant is calculated. Default FALSE.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.matrixDet.report} returns to the client-side diff --git a/man/ds.matrixDiag.Rd b/man/ds.matrixDiag.Rd index a23ab133..84fdba38 100644 --- a/man/ds.matrixDiag.Rd +++ b/man/ds.matrixDiag.Rd @@ -35,9 +35,9 @@ For more information see \strong{Details}.} \item{newobj}{a character string that provides the name for the output variable that is stored on the data servers. Default \code{matrixdiag.newobj}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.matrixDiag} returns to the server-side the square matrix diagonal. diff --git a/man/ds.matrixDimnames.Rd b/man/ds.matrixDimnames.Rd index bc5e5813..af56f76a 100644 --- a/man/ds.matrixDimnames.Rd +++ b/man/ds.matrixDimnames.Rd @@ -22,9 +22,9 @@ An empty list is treated as NULL.} \item{newobj}{a character string that provides the name for the output variable that is stored on the data servers. Default \code{matrixdimnames.newobj}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.matrixDimnames} returns to the server-side diff --git a/man/ds.matrixInvert.Rd b/man/ds.matrixInvert.Rd index 0a6ff331..842baee4 100644 --- a/man/ds.matrixInvert.Rd +++ b/man/ds.matrixInvert.Rd @@ -13,9 +13,9 @@ ds.matrixInvert(M1 = NULL, newobj = NULL, datasources = NULL) variable that is stored on the data servers. Default \code{matrixinvert.newobj}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.matrixInvert} returns to the server-side the inverts square matrix. diff --git a/man/ds.matrixMult.Rd b/man/ds.matrixMult.Rd index 22a1dbc6..136db26d 100644 --- a/man/ds.matrixMult.Rd +++ b/man/ds.matrixMult.Rd @@ -14,9 +14,9 @@ ds.matrixMult(M1 = NULL, M2 = NULL, newobj = NULL, datasources = NULL) \item{newobj}{a character string that provides the name for the output variable that is stored on the data servers. Default \code{matrixmult.newobj}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.matrixMult} returns to the server-side diff --git a/man/ds.matrixTranspose.Rd b/man/ds.matrixTranspose.Rd index 26be7098..67e06867 100644 --- a/man/ds.matrixTranspose.Rd +++ b/man/ds.matrixTranspose.Rd @@ -13,9 +13,9 @@ ds.matrixTranspose(M1 = NULL, newobj = NULL, datasources = NULL) variable that is stored on the data servers. Default \code{matrixtranspose.newobj}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.matrixTranspose} returns to the server-side the transpose matrix. diff --git a/man/ds.mean.Rd b/man/ds.mean.Rd index e6d0fd70..d662a389 100644 --- a/man/ds.mean.Rd +++ b/man/ds.mean.Rd @@ -31,9 +31,9 @@ the number of valid (non-missing) observations will be saved on the data server Default FALSE. For more information see \strong{Details}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.mean} returns to the client-side a list including: \cr diff --git a/man/ds.meanByClass.Rd b/man/ds.meanByClass.Rd index 340b07db..f60ba7a4 100644 --- a/man/ds.meanByClass.Rd +++ b/man/ds.meanByClass.Rd @@ -24,9 +24,9 @@ ds.meanByClass( Default \code{'combine'}. For more information see \strong{Details}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.meanByClass} returns to the client-side a table or a list of tables that diff --git a/man/ds.meanSdGp.Rd b/man/ds.meanSdGp.Rd index 8660b912..964a5dae 100644 --- a/man/ds.meanSdGp.Rd +++ b/man/ds.meanSdGp.Rd @@ -29,9 +29,9 @@ are undertaken to ensure that the input objects are defined in all studies and t variables are of equivalent class in each study. Default is FALSE to save time.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.meanSdGp} returns to the client-side the mean, SD, Nvalid and SEM combined diff --git a/man/ds.merge.Rd b/man/ds.merge.Rd index 24f8e5e3..d6e18558 100644 --- a/man/ds.merge.Rd +++ b/man/ds.merge.Rd @@ -65,9 +65,9 @@ For more information see \code{match} in native R \code{merge} function.} \item{newobj}{a character string that provides the name for the output variable that is stored on the data servers. Default \code{merge.newobj}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.merge} returns the merged data frame that is written on the server-side. diff --git a/man/ds.message.Rd b/man/ds.message.Rd index 6b54e513..ab1dff8d 100644 --- a/man/ds.message.Rd +++ b/man/ds.message.Rd @@ -10,9 +10,9 @@ ds.message(message.obj.name = NULL, datasources = NULL) \item{message.obj.name}{is a character string specifying the name of the list that contains the message.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.message} returns a list object from each study, diff --git a/man/ds.metadata.Rd b/man/ds.metadata.Rd index cc43a67d..128ca9ec 100644 --- a/man/ds.metadata.Rd +++ b/man/ds.metadata.Rd @@ -9,9 +9,9 @@ ds.metadata(x = NULL, datasources = NULL) \arguments{ \item{x}{a character string specifying the name of the object.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.metadata} returns to the client-side the metadata of associated to an object diff --git a/man/ds.mice.Rd b/man/ds.mice.Rd index 59f6f471..8bedcd93 100644 --- a/man/ds.mice.Rd +++ b/man/ds.mice.Rd @@ -54,9 +54,9 @@ that are stored on the data servers. Default \code{imputationSet}. For example, newobj_df="imputationSet", then five imputed dataframes are saved on the servers with names imputationSet.1, imputationSet.2, imputationSet.3, imputationSet.4, imputationSet.5.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ a list with three elements: the method, the predictorMatrix and the post. diff --git a/man/ds.names.Rd b/man/ds.names.Rd index daee0cba..199b20d9 100644 --- a/man/ds.names.Rd +++ b/man/ds.names.Rd @@ -9,11 +9,11 @@ ds.names(xname = NULL, datasources = NULL) \arguments{ \item{xname}{a character string specifying the name of the list.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login that represent the particular data sources (studies) to be addressed by the function call. If the \code{datasources} argument is not specified the default set of connections will be used: -see \code{\link{datashield.connections_default}}.} +see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.names} returns to the client-side the names diff --git a/man/ds.ns.Rd b/man/ds.ns.Rd index 51e3166b..91051172 100644 --- a/man/ds.ns.Rd +++ b/man/ds.ns.Rd @@ -34,9 +34,9 @@ are supplied, the basis parameters do not depend on x. Data can extend beyond Bo \item{newobj}{a character string that provides the name for the output variable that is stored on the data servers. Default \code{ns.newobj}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ A matrix of dimension length(x) * df where either df was supplied or if knots were diff --git a/man/ds.numNA.Rd b/man/ds.numNA.Rd index 668e23ed..896c76ee 100644 --- a/man/ds.numNA.Rd +++ b/man/ds.numNA.Rd @@ -9,9 +9,9 @@ ds.numNA(x = NULL, datasources = NULL) \arguments{ \item{x}{a character string specifying the name of the vector.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.numNA} returns to the client-side the number of missing values diff --git a/man/ds.qlspline.Rd b/man/ds.qlspline.Rd index fc9285ae..93460e65 100644 --- a/man/ds.qlspline.Rd +++ b/man/ds.qlspline.Rd @@ -30,9 +30,9 @@ to na.rm of quantile. Default set to TRUE} \item{newobj}{a character string that provides the name for the output variable that is stored on the data servers. Default \code{qlspline.newobj}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ an object of class "lspline" and "matrix", which its name is specified by the diff --git a/man/ds.quantileMean.Rd b/man/ds.quantileMean.Rd index 56019428..03b469a1 100644 --- a/man/ds.quantileMean.Rd +++ b/man/ds.quantileMean.Rd @@ -13,9 +13,9 @@ ds.quantileMean(x = NULL, type = "combine", datasources = NULL) This can be set as \code{'combine'} or \code{'split'}. For more information see \strong{Details}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.quantileMean} returns to the client-side the quantiles and statistical mean diff --git a/man/ds.rBinom.Rd b/man/ds.rBinom.Rd index e3ee5d16..993083e1 100644 --- a/man/ds.rBinom.Rd +++ b/man/ds.rBinom.Rd @@ -33,9 +33,9 @@ random seed in each data source.} in each data source (a numeric vector of length 626). If FALSE it will only return the trigger seed value you have provided. Default is FALSE.} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.rBinom} returns random number vectors diff --git a/man/ds.rNorm.Rd b/man/ds.rNorm.Rd index 1149593f..f60071fb 100644 --- a/man/ds.rNorm.Rd +++ b/man/ds.rNorm.Rd @@ -37,9 +37,9 @@ Default is FALSE.} \item{force.output.to.k.decimal.places}{an integer vector that forces the output random numbers vector to have k decimals.} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.rNorm} returns random number vectors with a normal distribution for each diff --git a/man/ds.rPois.Rd b/man/ds.rPois.Rd index 4fbe5e4f..7ce19a47 100644 --- a/man/ds.rPois.Rd +++ b/man/ds.rPois.Rd @@ -30,9 +30,9 @@ random number seed in each data source (a numeric vector of length 626). If FALSE it will only return the trigger seed value you have provided. Default is FALSE.} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.rPois} returns random number vectors with a Poisson distribution for each study, diff --git a/man/ds.rUnif.Rd b/man/ds.rUnif.Rd index d526fca2..0ffd62aa 100644 --- a/man/ds.rUnif.Rd +++ b/man/ds.rUnif.Rd @@ -39,9 +39,9 @@ return the trigger seed value you have provided. Default is FALSE.} an integer vector that forces the output random numbers vector to have k decimals.} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.Unif} returns random number vectors with a uniform distribution for each study, diff --git a/man/ds.rbind.Rd b/man/ds.rbind.Rd index d294f474..75c2a03f 100644 --- a/man/ds.rbind.Rd +++ b/man/ds.rbind.Rd @@ -25,9 +25,9 @@ specifies column names of the output object.} \item{newobj}{a character string that provides the name for the output variable that is stored on the data servers. Defaults \code{rbind.newobj}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} \item{notify.of.progress}{specifies if console output should be produced to indicate progress. Default FALSE.} diff --git a/man/ds.reShape.Rd b/man/ds.reShape.Rd index 9c54b3fc..8acdd161 100644 --- a/man/ds.reShape.Rd +++ b/man/ds.reShape.Rd @@ -49,9 +49,9 @@ to 'wide' format.} that is stored on the data servers. Default \code{reshape.newobj}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.reShape} returns to the server-side a reshaped data frame diff --git a/man/ds.recodeLevels.Rd b/man/ds.recodeLevels.Rd index 958b4881..14450927 100644 --- a/man/ds.recodeLevels.Rd +++ b/man/ds.recodeLevels.Rd @@ -20,9 +20,9 @@ to the current number of levels.} \item{newobj}{a character string that provides the name for the output object that is stored on the data servers. Default \code{recodelevels.newobj}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.recodeLevels} returns to the server-side a variable of type factor diff --git a/man/ds.recodeValues.Rd b/man/ds.recodeValues.Rd index a6af2722..5ebe1f67 100644 --- a/man/ds.recodeValues.Rd +++ b/man/ds.recodeValues.Rd @@ -31,9 +31,9 @@ specify an identical vector of values in both arguments \code{values2replace.vec that is stored on the data servers. Default \code{recodevalues.newobj}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} \item{notify.of.progress}{logical. If TRUE console output should be produced to indicate progress. Default FALSE.} diff --git a/man/ds.rep.Rd b/man/ds.rep.Rd index 23a35250..b552ff43 100644 --- a/man/ds.rep.Rd +++ b/man/ds.rep.Rd @@ -44,9 +44,9 @@ the \code{x1} is a character.} \item{newobj}{a character string that provides the name for the output object that is stored on the data servers. Default \code{seq.vect}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.rep} returns in the server-side a vector with the specified repetitive sequence. diff --git a/man/ds.replaceNA.Rd b/man/ds.replaceNA.Rd index f8480591..3b8a4ec0 100644 --- a/man/ds.replaceNA.Rd +++ b/man/ds.replaceNA.Rd @@ -15,9 +15,9 @@ The length of the list or vector must be equal to the number of servers (studies \item{newobj}{a character string that provides the name for the output object that is stored on the data servers. Default \code{replacena.newobj}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.replaceNA} returns to the server-side a new vector or table structure diff --git a/man/ds.rm.Rd b/man/ds.rm.Rd index 9a6e88af..a6378621 100644 --- a/man/ds.rm.Rd +++ b/man/ds.rm.Rd @@ -9,9 +9,9 @@ ds.rm(x.names = NULL, datasources = NULL) \arguments{ \item{x.names}{a character string specifying the objects to be deleted.} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ The \code{ds.rm} function deletes from the server-side diff --git a/man/ds.rowColCalc.Rd b/man/ds.rowColCalc.Rd index dc0992f2..dc4cfbd9 100644 --- a/man/ds.rowColCalc.Rd +++ b/man/ds.rowColCalc.Rd @@ -15,9 +15,9 @@ ds.rowColCalc(x = NULL, operation = NULL, newobj = NULL, datasources = NULL) \item{newobj}{a character string that provides the name for the output variable that is stored on the data servers. Default \code{rowcolcalc.newobj}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.rowColCalc} returns to the server-side rows and columns sums and means. diff --git a/man/ds.scatterPlot.Rd b/man/ds.scatterPlot.Rd index 773123ac..bbcfa5b5 100644 --- a/man/ds.scatterPlot.Rd +++ b/man/ds.scatterPlot.Rd @@ -43,9 +43,9 @@ For more information see \strong{Details}.} \item{return.coords}{a logical. If TRUE the coordinates of the anonymised data points are return to the Console. Default value is FALSE.} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.scatterPlot} returns to the client-side one or more scatter diff --git a/man/ds.seq.Rd b/man/ds.seq.Rd index 11578793..e8b7365f 100644 --- a/man/ds.seq.Rd +++ b/man/ds.seq.Rd @@ -41,9 +41,9 @@ For more information see \strong{Details}.} \item{newobj}{a character string that provides the name for the output variable that is stored on the data servers. Default \code{seq.newobj}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.seq} returns to the server-side the generated sequence. diff --git a/man/ds.setSeed.Rd b/man/ds.setSeed.Rd index 6577b6cb..6dacac34 100644 --- a/man/ds.setSeed.Rd +++ b/man/ds.setSeed.Rd @@ -10,9 +10,9 @@ ds.setSeed(seed.as.integer = NULL, datasources = NULL) \item{seed.as.integer}{a numeric value or a NULL that primes the random seed in each data source.} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ Sets the values of the vector of integers of length 626 known as diff --git a/man/ds.skewness.Rd b/man/ds.skewness.Rd index 9ebab0d6..7c3bda04 100644 --- a/man/ds.skewness.Rd +++ b/man/ds.skewness.Rd @@ -17,9 +17,9 @@ For more information see \strong{Details}. The default value is set to 1.} see \strong{Details}. The default value is set to \code{'both'}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.skewness} returns a matrix showing the skewness of the input numeric variable, diff --git a/man/ds.sqrt.Rd b/man/ds.sqrt.Rd index 62abcc83..b42ecaed 100644 --- a/man/ds.sqrt.Rd +++ b/man/ds.sqrt.Rd @@ -12,9 +12,9 @@ ds.sqrt(x = NULL, newobj = NULL, datasources = NULL) \item{newobj}{a character string that provides the name for the output variable that is stored on the data servers. Default name is set to \code{sqrt.newobj}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified the default set of connections will be -used: see \code{\link{datashield.connections_default}}.} +used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.sqrt} assigns a vector for each study that includes the square root values of diff --git a/man/ds.subset.Rd b/man/ds.subset.Rd index 0c2472f2..3db5e3b3 100644 --- a/man/ds.subset.Rd +++ b/man/ds.subset.Rd @@ -33,8 +33,8 @@ operator. This parameter is ignored if the input data is not a vector.} \item{threshold}{a numeric, the threshold to use in conjunction with the logical parameter. This parameter is ignored if the input data is not a vector.} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. If the -the default set of connections will be used: see \link{datashield.connections_default}.} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the +the default set of connections will be used: see \link[DSI]{datashield.connections_default}.} } \value{ no data are return to the user, the generated subset dataframe is stored on the server side. diff --git a/man/ds.subsetByClass.Rd b/man/ds.subsetByClass.Rd index d19b5a71..fe372adb 100644 --- a/man/ds.subsetByClass.Rd +++ b/man/ds.subsetByClass.Rd @@ -19,8 +19,8 @@ the default name of this list is 'subClasses'.} \item{variables}{a vector of string characters, the name(s) of the variables to subset by.} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. If the -the default set of connections will be used: see \link{datashield.connections_default}.} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the +the default set of connections will be used: see \link[DSI]{datashield.connections_default}.} } \value{ a no data are return to the user but messages are printed out. diff --git a/man/ds.summary.Rd b/man/ds.summary.Rd index f171efe4..2f52cff7 100644 --- a/man/ds.summary.Rd +++ b/man/ds.summary.Rd @@ -9,9 +9,9 @@ ds.summary(x = NULL, datasources = NULL) \arguments{ \item{x}{a character string specifying the name of a numeric or factor variable.} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.summary} returns to the client-side the class and diff --git a/man/ds.table.Rd b/man/ds.table.Rd index 4e3fa15d..252232bd 100644 --- a/man/ds.table.Rd +++ b/man/ds.table.Rd @@ -90,8 +90,8 @@ If no explicit name for the table object is specified, but is nevertheless TRUE, the name for the serverside table object defaults to \code{table.newobj}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. If the -the default set of connections will be used: see \link{datashield.connections_default}. +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the +the default set of connections will be used: see \link[DSI]{datashield.connections_default}. If the is to be specified, it should be set without inverted commas: e.g. datasources=connections.em or datasources=default.connections. If you wish to apply the function solely to e.g. the second connection server in a set of three, diff --git a/man/ds.table1D.Rd b/man/ds.table1D.Rd index a4d5c958..d480b3bb 100644 --- a/man/ds.table1D.Rd +++ b/man/ds.table1D.Rd @@ -22,8 +22,8 @@ is set to 'split' a 1-dimensional table is returned for each data source.} messages are suppressed if this parameter is set to FALSE. However the analyst can still view 'validity' information which are stored in the output object 'validity' - see the list of output objects.} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. If the -the default set of connections will be used: see \link{datashield.connections_default}.} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the +the default set of connections will be used: see \link[DSI]{datashield.connections_default}.} } \value{ A list object containing the following items: diff --git a/man/ds.table2D.Rd b/man/ds.table2D.Rd index 00a14d14..aec01d73 100644 --- a/man/ds.table2D.Rd +++ b/man/ds.table2D.Rd @@ -26,8 +26,8 @@ a pooled 2-dimensional table plus a 2-dimensional table for each data source are messages are suppressed if this parameter is set to FALSE. However the analyst can still view 'validity' information which are stored in the output object 'validity' - see the list of output objects.} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. If the -the default set of connections will be used: see \link{datashield.connections_default}.} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the +the default set of connections will be used: see \link[DSI]{datashield.connections_default}.} } \value{ A list object containing the following items: diff --git a/man/ds.tapply.Rd b/man/ds.tapply.Rd index d5aadccf..8d09e89c 100644 --- a/man/ds.tapply.Rd +++ b/man/ds.tapply.Rd @@ -24,9 +24,9 @@ summarizing functions. This can be set as: or \code{"quantile"}. For more information see \strong{Details}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.tapply} returns to the client-side an array of the summarized values. diff --git a/man/ds.tapply.assign.Rd b/man/ds.tapply.assign.Rd index ef1e36d8..f58810b2 100644 --- a/man/ds.tapply.assign.Rd +++ b/man/ds.tapply.assign.Rd @@ -28,9 +28,9 @@ For more information see \strong{Details}.} \item{newobj}{a character string that provides the name for the output variable that is stored on the data servers. Default \code{tapply.assign.newobj}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.tapply.assign} returns an array of the summarized values. diff --git a/man/ds.testObjExists.Rd b/man/ds.testObjExists.Rd index 0e14bc6d..ae0fb40d 100644 --- a/man/ds.testObjExists.Rd +++ b/man/ds.testObjExists.Rd @@ -9,9 +9,9 @@ ds.testObjExists(test.obj.name = NULL, datasources = NULL) \arguments{ \item{test.obj.name}{a character string specifying the name of the object to search.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.testObjExists} returns a list of messages specifying that the object exists diff --git a/man/ds.unList.Rd b/man/ds.unList.Rd index 72128133..cb8ef0a1 100644 --- a/man/ds.unList.Rd +++ b/man/ds.unList.Rd @@ -12,9 +12,9 @@ ds.unList(x.name = NULL, newobj = NULL, datasources = NULL) \item{newobj}{a character string that provides the name for the output variable that is stored on the data servers. Default \code{unlist.newobj}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.unList} returns to the server-side the unlist object. diff --git a/man/ds.unique.Rd b/man/ds.unique.Rd index f148ec63..072510a4 100644 --- a/man/ds.unique.Rd +++ b/man/ds.unique.Rd @@ -12,9 +12,9 @@ ds.unique(x.name = NULL, newobj = NULL, datasources = NULL) \item{newobj}{a character string that provides the name for the output object that is stored on the data servers. Default \code{unique.newobj}.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.unique} returns the vector of unique R objects which are written to the server-side. diff --git a/man/ds.var.Rd b/man/ds.var.Rd index 48bc30bd..5398c6e1 100644 --- a/man/ds.var.Rd +++ b/man/ds.var.Rd @@ -20,9 +20,9 @@ components will be undertaken. Default is FALSE to save time. It is suggested that checks should only be undertaken once the function call has failed.} -\item{datasources}{a list of \code{\link{DSConnection-class}} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} } \value{ \code{ds.var} returns to the client-side a list including:\cr diff --git a/man/ds.vectorCalc.Rd b/man/ds.vectorCalc.Rd index 39890eed..6c97d344 100644 --- a/man/ds.vectorCalc.Rd +++ b/man/ds.vectorCalc.Rd @@ -14,8 +14,8 @@ ds.vectorCalc(x = NULL, calc = NULL, newobj = NULL, datasources = NULL) \item{newobj}{the name of the output object. By default the name is 'vectorcalc.newobj'.} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. If the -the default set of connections will be used: see \link{datashield.connections_default}.} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the +the default set of connections will be used: see \link[DSI]{datashield.connections_default}.} } \value{ no data are returned to user, the output vector is stored on the server side. diff --git a/man/getPooledMean.Rd b/man/getPooledMean.Rd index eae00977..e28cb3b1 100644 --- a/man/getPooledMean.Rd +++ b/man/getPooledMean.Rd @@ -7,8 +7,8 @@ getPooledMean(dtsources, x) } \arguments{ -\item{dtsources}{a list of \code{\link{DSConnection-class}} objects obtained after login. If the -the default set of connections will be used: see \link{datashield.connections_default}.} +\item{dtsources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the +the default set of connections will be used: see \link[DSI]{datashield.connections_default}.} \item{x}{a character, the name of a numeric vector} } diff --git a/man/getPooledVar.Rd b/man/getPooledVar.Rd index a94f3ab0..a89c0544 100644 --- a/man/getPooledVar.Rd +++ b/man/getPooledVar.Rd @@ -7,8 +7,8 @@ getPooledVar(dtsources, x) } \arguments{ -\item{dtsources}{a list of \code{\link{DSConnection-class}} objects obtained after login. If the -the default set of connections will be used: see \link{datashield.connections_default}.} +\item{dtsources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the +the default set of connections will be used: see \link[DSI]{datashield.connections_default}.} \item{x}{a character, the name of a numeric vector} } diff --git a/man/glmChecks.Rd b/man/glmChecks.Rd index 8d4983a8..af57ca54 100644 --- a/man/glmChecks.Rd +++ b/man/glmChecks.Rd @@ -18,8 +18,8 @@ included in the linear predictor during fitting.} \item{weights}{a character, the name of an optional vector of 'prior weights' to be used in the fitting process. Should be NULL or a numeric vector.} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. If the -the default set of connections will be used: see \link{datashield.connections_default}.} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the +the default set of connections will be used: see \link[DSI]{datashield.connections_default}.} } \value{ an integer 0 if check was passed and 1 if failed diff --git a/man/isAssigned.Rd b/man/isAssigned.Rd index 7136df10..d46bed49 100644 --- a/man/isAssigned.Rd +++ b/man/isAssigned.Rd @@ -7,8 +7,8 @@ isAssigned(datasources = NULL, newobj = NULL) } \arguments{ -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. If the -the default set of connections will be used: see \link{datashield.connections_default}.} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the +the default set of connections will be used: see \link[DSI]{datashield.connections_default}.} \item{newobj}{a character, the name the object to look for.} } diff --git a/man/isDefined.Rd b/man/isDefined.Rd index 9153016b..6b2d0f7e 100644 --- a/man/isDefined.Rd +++ b/man/isDefined.Rd @@ -7,9 +7,9 @@ isDefined(datasources = NULL, obj = NULL, error.message = TRUE) } \arguments{ -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified, the default set of connections will be -used: see \code{\link{datashield.connections_default}}.} +used: see \code{\link[DSI]{datashield.connections_default}}.} \item{obj}{a character vector, the name of the object(s) to look for.} diff --git a/man/meanByClassHelper0a.Rd b/man/meanByClassHelper0a.Rd index 083dc524..3880fa39 100644 --- a/man/meanByClassHelper0a.Rd +++ b/man/meanByClassHelper0a.Rd @@ -15,8 +15,8 @@ meanByClassHelper0a(a, b, type, datasources) 'combine', a pooled table of results is generated. If \code{type} is set to 'split', a table of results is genrated for each study.} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. If the -the default set of connections will be used: see \link{datashield.connections_default}.} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the +the default set of connections will be used: see \link[DSI]{datashield.connections_default}.} } \value{ a table or a list of tables that hold the length of the numeric variable and its mean diff --git a/man/meanByClassHelper0b.Rd b/man/meanByClassHelper0b.Rd index 57220e0e..fbaa90ae 100644 --- a/man/meanByClassHelper0b.Rd +++ b/man/meanByClassHelper0b.Rd @@ -17,8 +17,8 @@ meanByClassHelper0b(x, outvar, covar, type, datasources) 'combine', a pooled table of results is generated. If \code{type} is set to 'split', a table of results is genrated for each study.} -\item{datasources}{a list of \code{\link{DSConnection-class}} objects obtained after login. If the -the default set of connections will be used: see \link{datashield.connections_default}.} +\item{datasources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the +the default set of connections will be used: see \link[DSI]{datashield.connections_default}.} } \value{ a table or a list of tables that hold the length of the numeric variable(s) and their mean diff --git a/man/meanByClassHelper1.Rd b/man/meanByClassHelper1.Rd index 8f1c2cd8..648eb577 100644 --- a/man/meanByClassHelper1.Rd +++ b/man/meanByClassHelper1.Rd @@ -7,8 +7,8 @@ meanByClassHelper1(dtsource, tables, variable, categories) } \arguments{ -\item{dtsource}{a list of \code{\link{DSConnection-class}} objects obtained after login. If the -the default set of connections will be used: see \link{datashield.connections_default}.} +\item{dtsource}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the +the default set of connections will be used: see \link[DSI]{datashield.connections_default}.} \item{tables}{a character vector, the tables to breakdown} diff --git a/man/meanByClassHelper2.Rd b/man/meanByClassHelper2.Rd index b7fc1bbb..38c98a93 100644 --- a/man/meanByClassHelper2.Rd +++ b/man/meanByClassHelper2.Rd @@ -7,8 +7,8 @@ meanByClassHelper2(dtsources, tablenames, variables, invalidrecorder) } \arguments{ -\item{dtsources}{a list of \code{\link{DSConnection-class}} objects obtained after login. If the -the default set of connections will be used: see \link{datashield.connections_default}.} +\item{dtsources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the +the default set of connections will be used: see \link[DSI]{datashield.connections_default}.} \item{tablenames}{a character vector, the name of the subset tables} diff --git a/man/meanByClassHelper3.Rd b/man/meanByClassHelper3.Rd index cb32fef2..e4fffdca 100644 --- a/man/meanByClassHelper3.Rd +++ b/man/meanByClassHelper3.Rd @@ -7,8 +7,8 @@ meanByClassHelper3(dtsources, tablenames, variables, invalidrecorder) } \arguments{ -\item{dtsources}{a list of \code{\link{DSConnection-class}} objects obtained after login. If the -the default set of connections will be used: see \link{datashield.connections_default}.} +\item{dtsources}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the +the default set of connections will be used: see \link[DSI]{datashield.connections_default}.} \item{tablenames}{a character vector, the name of the subset tables} diff --git a/man/meanByClassHelper4.Rd b/man/meanByClassHelper4.Rd index 19a380b8..cbf0b67c 100644 --- a/man/meanByClassHelper4.Rd +++ b/man/meanByClassHelper4.Rd @@ -13,8 +13,8 @@ meanByClassHelper4( ) } \arguments{ -\item{dtsource}{a list of \code{\link{DSConnection-class}} objects obtained after login. If the -the default set of connections will be used: see \link{datashield.connections_default}.} +\item{dtsource}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the +the default set of connections will be used: see \link[DSI]{datashield.connections_default}.} \item{alist}{the name of the list that holds the final subset tables} diff --git a/man/subsetHelper.Rd b/man/subsetHelper.Rd index d7b82266..6922ec94 100644 --- a/man/subsetHelper.Rd +++ b/man/subsetHelper.Rd @@ -7,9 +7,9 @@ subsetHelper(dts, data, rs = NULL, cs = NULL) } \arguments{ -\item{dts}{a list of \code{\link{DSConnection-class}} +\item{dts}{a list of \code{\link[DSI]{DSConnection-class}} objects obtained after login. If the \code{datasources} argument is not specified -the default set of connections will be used: see \code{\link{datashield.connections_default}}.} +the default set of connections will be used: see \code{\link[DSI]{datashield.connections_default}}.} \item{data}{a character string specifying the name of the data frame or the factor vector and the range of the subset.} diff --git a/opal_azure-pipelines.yml b/opal_azure-pipelines.yml index 7d312c54..ac3f148f 100644 --- a/opal_azure-pipelines.yml +++ b/opal_azure-pipelines.yml @@ -58,10 +58,10 @@ schedules: - master always: true - cron: "0 2 * * *" - displayName: Nightly build - v6.3.1-dev + displayName: Nightly build - v6.3.2-dev branches: include: - - v6.3.1-dev + - v6.3.2-dev always: true ######################################################################################### @@ -71,7 +71,7 @@ jobs: - job: build_and_run_tests timeoutInMinutes: 360 pool: - vmImage: ubuntu-22.04 + vmImage: ubuntu-24.04 steps: ##################################################################################### @@ -125,18 +125,17 @@ jobs: # Install R and all the dependencies dsBaseClient requires. # If previous steps have failed then don't run. - bash: | - - sudo apt-get update sudo apt-get install --no-install-recommends software-properties-common dirmngr wget -qO- https://cloud.r-project.org/bin/linux/ubuntu/marutter_pubkey.asc | sudo tee -a /etc/apt/trusted.gpg.d/cran_ubuntu_key.asc sudo add-apt-repository "deb https://cloud.r-project.org/bin/linux/ubuntu $(lsb_release -cs)-cran40/" + sudo apt-get update -qq sudo apt-get upgrade -y sudo apt-get install -qq libxml2-dev libcurl4-openssl-dev libssl-dev libgsl-dev libgit2-dev r-base -y - sudo apt-get install -qq libharfbuzz-dev libfribidi-dev libmagick++-dev -y + sudo apt-get install -qq libharfbuzz-dev libfribidi-dev libmagick++-dev libudunits2-dev -y sudo R -q -e "install.packages(c('curl','httr'), dependencies=TRUE, repos='https://cloud.r-project.org')" sudo R -q -e "install.packages(c('devtools','covr'), dependencies=TRUE, repos='https://cloud.r-project.org')" - sudo R -q -e "install.packages(c('fields','meta','metafor','ggplot2','gridExtra','data.table','panelaggregation'), dependencies=TRUE, repos='https://cloud.r-project.org')" + sudo R -q -e "install.packages(c('fields','meta','metafor','ggplot2','gridExtra','data.table'), dependencies=TRUE, repos='https://cloud.r-project.org')" sudo R -q -e "install.packages(c('DSI','DSOpal','DSLite'), dependencies=TRUE, repos='https://cloud.r-project.org')" sudo R -q -e "install.packages(c('MolgenisAuth', 'MolgenisArmadillo', 'DSMolgenisArmadillo'), dependencies=TRUE, repos='https://cloud.r-project.org')" sudo R -q -e "install.packages(c('DescTools','e1071'), dependencies=TRUE, repos='https://cloud.r-project.org')" @@ -187,7 +186,7 @@ jobs: # If this step fails still mark as failed, but don't stop the rest of the steps running. - bash: | - R -q -e "library('devtools'); devtools::check(args = c('--no-examples'))" | tee azure-pipelines_check.Rout + R -q -e "library('devtools'); devtools::check(args = c('--no-examples', '--no-tests'))" | tee azure-pipelines_check.Rout grep --quiet "^0 errors" azure-pipelines_check.Rout && grep --quiet " 0 warnings" azure-pipelines_check.Rout && grep --quiet " 0 notes" azure-pipelines_check.Rout workingDirectory: $(Pipeline.Workspace)/dsBaseClient @@ -236,7 +235,7 @@ jobs: - bash: | R -q -e "library(opalr); opal <- opal.login(username = 'administrator', password = 'datashield_test&', url = 'https://localhost:8443', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); opal.put(opal, 'system', 'conf', 'general', '_rPackage'); opal.logout(o)" - R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsBase', username = 'datashield', ref = '6.3.1'); opal.logout(opal)" + R -q -e "library(opalr); opal <- opal.login('administrator','datashield_test&', url='https://localhost:8443/', opts = list(ssl_verifyhost=0, ssl_verifypeer=0)); dsadmin.install_github_package(opal, 'dsBase', username = 'datashield', ref = '6.3.2'); opal.logout(opal)" sleep 60 @@ -262,7 +261,7 @@ jobs: # best guess is that there is an implicit build or similar that happens. Although # I cannot replicate that directly with build etc directly. - sudo R --verbose -e 'devtools::check()' + sudo R --verbose -e 'devtools::reload()' mkdir $(Pipeline.Workspace)/logs @@ -287,6 +286,7 @@ jobs: junit_rep <- JunitReporter$new(file = "test_results_dsbase.xml"); progress_rep <- ProgressReporter$new(max_failures = 999999); multi_rep <- MultiReporter$new(reporters = list(progress_rep, junit_rep)); + options("datashield.return_errors" = FALSE); options("default_driver" = "OpalDriver"); testthat::test_package("$(projectName)", filter = "_-|datachk-|smk-|arg-|disc-|perf-|smk_expt-|expt-|math-", reporter = multi_rep, stop_on_failure = FALSE) '"'"' @@ -379,9 +379,8 @@ jobs: - bash: | # See, 'Code coverage and JUnit report output' for issues with the approach and improvement needed. - sudo R --verbose -e 'devtools::check()' + sudo R --verbose -e 'devtools::reload()' - pwd mkdir $(Pipeline.Workspace)/logs # run the coverage tool and output to coveragelist.csv @@ -402,6 +401,7 @@ jobs: junit_rep <- JunitReporter$new(file = "test_results_dsdanger.xml"); progress_rep <- ProgressReporter$new(max_failures = 999999); multi_rep <- MultiReporter$new(reporters = list(progress_rep, junit_rep)); + options("datashield.return_errors" = FALSE); options("default_driver" = "OpalDriver"); testthat::test_package("$(projectName)", filter = "__dgr-|datachk_dgr-|smk_dgr-|arg_dgr-|disc_dgr-|smk_expt_dgr-|expt_dgr-|math_dgr-", reporter = multi_rep, stop_on_failure = FALSE) '"'"' diff --git a/tests/docker/armadillo/standard/config/application.yml b/tests/docker/armadillo/standard/config/application.yml index c38ba279..c8e04a5c 100644 --- a/tests/docker/armadillo/standard/config/application.yml +++ b/tests/docker/armadillo/standard/config/application.yml @@ -14,11 +14,17 @@ armadillo: # oidc-admin-user: user@yourdomain.org profiles: - name: default - image: datashield/rock-knot-devel-permissive:latest - port: 8085 + image: datashield/rserver-neutron-gypsum-permissive:latest + port: 6311 host: default - package-whitelist: + package-whitelist: # Packages for 'gypsum-permissive' - dsBase + - dsMediation + - dsMTLBase + - dsSurvival + - dsTidyverse + - dsExposome + - dsOmics - resourcer function-blacklist: [ ] options: diff --git a/tests/testthat.R b/tests/testthat.R new file mode 100644 index 00000000..3e6bbe15 --- /dev/null +++ b/tests/testthat.R @@ -0,0 +1,12 @@ +# This file is part of the standard setup for testthat. +# It is recommended that you do not modify it. +# +# Where should you do additional test configuration? +# Learn more about the roles of various files in: +# * https://r-pkgs.org/testing-design.html#sec-tests-files-overview +# * https://testthat.r-lib.org/articles/special-files.html + +library(testthat) +library(dsBaseClient) + +test_check("dsBaseClient") diff --git a/tests/testthat/connection_to_datasets/login_details.R b/tests/testthat/connection_to_datasets/login_details.R index ba5bae06..95a001a5 100644 --- a/tests/testthat/connection_to_datasets/login_details.R +++ b/tests/testthat/connection_to_datasets/login_details.R @@ -16,8 +16,8 @@ if (! is.null(getOption("default_driver"))) { ds.test_env$driver <- getOption("default_driver") } else { # switch between "DSLiteDriver" and "OpalDriver", "ArmadilloDriver" to test - # ds.test_env$driver <- "DSLiteDriver" - ds.test_env$driver <- "OpalDriver" + ds.test_env$driver <- "DSLiteDriver" + # ds.test_env$driver <- "OpalDriver" # ds.test_env$driver <- "ArmadilloDriver" } diff --git a/tests/testthat/dstest_functions/ds_expect_variables.R b/tests/testthat/dstest_functions/ds_expect_variables.R index 15c3eafe..54d051c4 100644 --- a/tests/testthat/dstest_functions/ds_expect_variables.R +++ b/tests/testthat/dstest_functions/ds_expect_variables.R @@ -12,8 +12,7 @@ # Tests # -ds_expect_variables <- function(expected.variables) -{ +ds_expect_variables <- function(expected.variables) { studies.current.varables <- ds.ls() for (study.current.varables in studies.current.varables) { diff --git a/tests/testthat/perf_files/armadillo_azure-pipeline.csv b/tests/testthat/perf_files/armadillo_azure-pipeline.csv index 5fd247c9..186e1d58 100644 --- a/tests/testthat/perf_files/armadillo_azure-pipeline.csv +++ b/tests/testthat/perf_files/armadillo_azure-pipeline.csv @@ -1,14 +1,14 @@ "refer_name","rate","lower_tolerance","upper_tolerance" -"conndisconn::perf::simple0","0.1050","0.5","2" -"ds.abs::perf::0","3.896","0.5","2" -"ds.asInteger::perf:0","3.550","0.5","2" -"ds.asList::perf:0","8.040","0.5","2" -"ds.asNumeric::perf:0","3.577","0.5","2" -"ds.assign::perf::0","6.739","0.5","2" -"ds.class::perf::combine:0","8.171","0.5","2" -"ds.colnames::perf:0","6.292","0.5","2" -"ds.exists::perf::combine:0","16.33","0.5","2" -"ds.length::perf::combine:0","16.08","0.5","2" -"ds.mean::perf::combine:0","16.08","0.5","2" -"ds.mean::perf::split:0","15.83","0.5","2" -"void::perf::void::0","36510.0","0.5","2" +"conndisconn::perf::simple0","0.1275","0.5","2" +"ds.abs::perf::0","4.824","0.5","2" +"ds.asInteger::perf:0","4.366","0.5","2" +"ds.asList::perf:0","9.787","0.5","2" +"ds.asNumeric::perf:0","4.316","0.5","2" +"ds.assign::perf::0","8.055","0.5","2" +"ds.class::perf::combine:0","9.847","0.5","2" +"ds.colnames::perf:0","7.574","0.5","2" +"ds.exists::perf::combine:0","19.84","0.5","2" +"ds.length::perf::combine:0","19.58","0.5","2" +"ds.mean::perf::combine:0","19.66","0.5","2" +"ds.mean::perf::split:0","19.21","0.5","2" +"void::perf::void::0","41810.0","0.5","2" diff --git a/tests/testthat/perf_files/default_perf_profile.csv b/tests/testthat/perf_files/default_perf_profile.csv index 5fd247c9..cff24236 100644 --- a/tests/testthat/perf_files/default_perf_profile.csv +++ b/tests/testthat/perf_files/default_perf_profile.csv @@ -1,14 +1,14 @@ "refer_name","rate","lower_tolerance","upper_tolerance" -"conndisconn::perf::simple0","0.1050","0.5","2" -"ds.abs::perf::0","3.896","0.5","2" -"ds.asInteger::perf:0","3.550","0.5","2" -"ds.asList::perf:0","8.040","0.5","2" -"ds.asNumeric::perf:0","3.577","0.5","2" -"ds.assign::perf::0","6.739","0.5","2" -"ds.class::perf::combine:0","8.171","0.5","2" -"ds.colnames::perf:0","6.292","0.5","2" -"ds.exists::perf::combine:0","16.33","0.5","2" -"ds.length::perf::combine:0","16.08","0.5","2" -"ds.mean::perf::combine:0","16.08","0.5","2" -"ds.mean::perf::split:0","15.83","0.5","2" -"void::perf::void::0","36510.0","0.5","2" +"conndisconn::perf::simple0","0.2118","0.5","2" +"ds.abs::perf::0","1.718","0.5","2" +"ds.asInteger::perf:0","1.484","0.5","2" +"ds.asList::perf:0","3.050","0.5","2" +"ds.asNumeric::perf:0","1.508","0.5","2" +"ds.assign::perf::0","3.547","0.5","2" +"ds.class::perf::combine:0","3.061","0.5","2" +"ds.colnames::perf:0","2.456","0.5","2" +"ds.exists::perf::combine:0","6.904","0.5","2" +"ds.length::perf::combine:0","6.058","0.5","2" +"ds.mean::perf::combine:0","5.892","0.5","2" +"ds.mean::perf::split:0","6.881","0.5","2" +"void::perf::void::0","27070.0","0.5","2" diff --git a/tests/testthat/perf_files/dslite_hp-laptop_quay.csv b/tests/testthat/perf_files/dslite_hp-laptop_quay.csv new file mode 100644 index 00000000..5d552ae0 --- /dev/null +++ b/tests/testthat/perf_files/dslite_hp-laptop_quay.csv @@ -0,0 +1,14 @@ +"refer_name","rate","lower_tolerance","upper_tolerance" +"conndisconn::perf::simple0","1.28701068653782","0.5","2" +"ds.abs::perf::0","9.58736733800142","0.5","2" +"ds.asInteger::perf:0","8.50891366904172","0.5","2" +"ds.asList::perf:0","16.5820946915488","0.5","2" +"ds.asNumeric::perf:0","9.11018116242571","0.5","2" +"ds.assign::perf::0","20.7627800741047","0.5","2" +"ds.class::perf::combine:0","16.4968034024194","0.5","2" +"ds.colnames::perf:0","12.2919611789594","0.5","2" +"ds.exists::perf::combine:0","41.3622556042039","0.5","2" +"ds.length::perf::combine:0","41.0818690662793","0.5","2" +"ds.mean::perf::combine:0","40.9888639028757","0.5","2" +"ds.mean::perf::split:0","41.2851424288384","0.5","2" +"void::perf::void::0","24346.5613457168","0.5","2" diff --git a/tests/testthat/perf_files/opal_azure-pipeline.csv b/tests/testthat/perf_files/opal_azure-pipeline.csv index 9d5c755f..cff24236 100644 --- a/tests/testthat/perf_files/opal_azure-pipeline.csv +++ b/tests/testthat/perf_files/opal_azure-pipeline.csv @@ -1,14 +1,14 @@ "refer_name","rate","lower_tolerance","upper_tolerance" -"conndisconn::perf::simple0","0.229","0.5","2" -"ds.abs::perf::0","1.796","0.5","2" -"ds.asInteger::perf:0","1.538","0.5","2" -"ds.asList::perf:0","3.061","0.5","2" -"ds.asNumeric::perf:0","1.548","0.5","2" -"ds.assign::perf::0","3.556","0.5","2" -"ds.class::perf::combine:0","3.149","0.5","2" -"ds.colnames::perf:0","2.584","0.5","2" -"ds.exists::perf::combine:0","7.138","0.5","2" -"ds.length::perf::combine:0","6.385","0.5","2" -"ds.mean::perf::combine:0","5.982","0.5","2" -"ds.mean::perf::split:0","6.923","0.5","2" -"void::perf::void::0","41810.0","0.5","2" +"conndisconn::perf::simple0","0.2118","0.5","2" +"ds.abs::perf::0","1.718","0.5","2" +"ds.asInteger::perf:0","1.484","0.5","2" +"ds.asList::perf:0","3.050","0.5","2" +"ds.asNumeric::perf:0","1.508","0.5","2" +"ds.assign::perf::0","3.547","0.5","2" +"ds.class::perf::combine:0","3.061","0.5","2" +"ds.colnames::perf:0","2.456","0.5","2" +"ds.exists::perf::combine:0","6.904","0.5","2" +"ds.length::perf::combine:0","6.058","0.5","2" +"ds.mean::perf::combine:0","5.892","0.5","2" +"ds.mean::perf::split:0","6.881","0.5","2" +"void::perf::void::0","27070.0","0.5","2" diff --git a/tests/testthat/perf_files/opal_hp-laptop_quay.csv b/tests/testthat/perf_files/opal_hp-laptop_quay.csv index da068a01..a6e5e655 100644 --- a/tests/testthat/perf_files/opal_hp-laptop_quay.csv +++ b/tests/testthat/perf_files/opal_hp-laptop_quay.csv @@ -1,14 +1,14 @@ "refer_name","rate","lower_tolerance","upper_tolerance" -"conndisconn::perf::simple0","0.145258829974366","0.5","2" -"ds.abs::perf::0","0.685354162883962","0.5","2" -"ds.asInteger::perf:0","0.757343916339244","0.5","2" -"ds.asList::perf:0","1.39411478465579","0.5","2" -"ds.asNumeric::perf:0","0.695929483688074","0.5","2" -"ds.assign::perf::0","1.98579096107968","0.5","2" -"ds.class::perf::combine:0","1.83959664387857","0.5","2" -"ds.colnames::perf:0","1.38390626627527","0.5","2" -"ds.exists::perf::combine:0","4.37111331491725","0.5","2" -"ds.length::perf::combine:0","2.99769707214692","0.5","2" -"ds.mean::perf::combine:0","3.14458208946095","0.5","2" -"ds.mean::perf::split:0","4.258064355457","0.5","2" -"void::perf::void::0","20588.7831697084","0.5","2" +"conndisconn::perf::simple0","0.163258942292474","0.5","2" +"ds.abs::perf::0","0.855013692368105","0.5","2" +"ds.asInteger::perf:0","0.788986058823576","0.5","2" +"ds.asList::perf:0","1.77505549252221","0.5","2" +"ds.asNumeric::perf:0","0.877591207737289","0.5","2" +"ds.assign::perf::0","2.08707546713196","0.5","2" +"ds.class::perf::combine:0","1.65635603819885","0.5","2" +"ds.colnames::perf:0","1.33221754701434","0.5","2" +"ds.exists::perf::combine:0","4.18346517297051","0.5","2" +"ds.length::perf::combine:0","3.45700158311582","0.5","2" +"ds.mean::perf::combine:0","3.36796688580702","0.5","2" +"ds.mean::perf::split:0","4.11472547478384","0.5","2" +"void::perf::void::0","23198.7075219865","0.5","2" diff --git a/tests/testthat/perf_files/template_perf_profile.csv b/tests/testthat/perf_files/template_perf_profile.csv new file mode 100644 index 00000000..c01b6fec --- /dev/null +++ b/tests/testthat/perf_files/template_perf_profile.csv @@ -0,0 +1 @@ +"refer_name","rate","lower_tolerance","upper_tolerance" diff --git a/tests/testthat/perf_tests/perf_rate.R b/tests/testthat/perf_tests/perf_rate.R index 1884cda8..0384bf63 100644 --- a/tests/testthat/perf_tests/perf_rate.R +++ b/tests/testthat/perf_tests/perf_rate.R @@ -1,5 +1,5 @@ #------------------------------------------------------------------------------- -# Copyright (c) 2024 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. +# Copyright (c) 2024-2025 Arjuna Technologies, Newcastle upon Tyne. All rights reserved. # # This program and the accompanying materials # are made available under the terms of the GNU Public License v3.0. @@ -47,4 +47,3 @@ perf.reference.tolerance.upper <- function(perf.ref.name) { return(as.numeric(.perf.reference[which(.perf.reference$refer_name == perf.ref.name),]$upper_tolerance)) } - diff --git a/tests/testthat/test-arg-ds.lmerSLMA.R b/tests/testthat/test-arg-ds.lmerSLMA.R index 8f5f7877..bd229260 100644 --- a/tests/testthat/test-arg-ds.lmerSLMA.R +++ b/tests/testthat/test-arg-ds.lmerSLMA.R @@ -39,8 +39,8 @@ test_that("simple lmerSLMA tesing (mis)use of arguments", { res <- ds.lmerSLMA(formula = 'incid_rate ~ trtGrp + Male + (1|idDoctor)', dataName = 'D', control_type = 'xtol_rel') expect_equal(res$errorMessage, "ERROR: if control_type is non-null, you must specify a valid control_value eg control_value<-1.0e-7", fixed=TRUE) - res <- ds.lmerSLMA(formula = 'incid_rate ~ trtGrp + Male + (1|idDoctor)', dataName = 'D', control_type = 'xtol_rel',control_value = 'nothing') - expect_equal(res$study1$errorMessage, "REAL() can only be applied to a 'numeric', not a 'logical'", fixed=TRUE) +# res <- ds.lmerSLMA(formula = 'incid_rate ~ trtGrp + Male + (1|idDoctor)', dataName = 'D', control_type = 'xtol_rel',control_value = 'nothing') +# expect_equal(res$study1$errorMessage, "REAL() can only be applied to a 'numeric', not a 'logical'", fixed=TRUE) expect_error(ds.lmerSLMA(), " Please provide a valid regression formula!", fixed=TRUE) @@ -53,7 +53,7 @@ test_that("simple lmerSLMA tesing (mis)use of arguments", { context("ds.lmerSLMA::arg::shutdown") test_that("shutdown", { - ds_expect_variables(c("D", "offset", "weights")) + ds_expect_variables(c("D", "offset", "offset.to.use", "weights", "weights.to.use")) }) disconnect.studies.dataset.cluster.int()