Origin/v6.4.0 dev feat/standardise df

.Rbuildignore

@@ -3,20 +3,8 @@
 ^\.Rproj\.user$
 ^LICENSE.md$
 ^azure-pipelines\.yml$
-^opal_azure-pipelines\.yml$
-^armadillo_azure-pipelines\.yml$
 ^azure-pipelines_site\.pp$
 ^azure-pipelines_site-dsdanger\.pp$
 ^azure-pipelines_check\.Rout$
 ^azure-pipelines_test\.Rout$
-^tests/docker/armadillo/standard/log/.gitkeep$
 ^checkDocumentationUpdated\.sh$
-^docker-compose_armadillo\.yml$
-^docker-compose_opal\.yml$
-^docker-compose\.yml$
-^R/secure.global.ranking.md$
-^_pkgdown\.yml$
-^docs$
-^dsBase_6.3.1.tar.gz$
-^dsBase_6.3.1-permissive.tar.gz$
-^dsDanger_6.3.1.tar.gz$

.gitignore

@@ -10,5 +10,3 @@
 inst/tests/test-template.R
 azure-pipelines.Rout
 tests/testthat/connection_to_datasets/local_settings.csv
-tests/docker/armadillo/standard/logs/
-tests/docker/armadillo/standard/data/

DESCRIPTION

@@ -1,24 +1,20 @@
 Package: dsBaseClient
 Title: DataSHIELD Client Functions
-Version: 6.3.1
-Author: DataSHIELD Developers <datashield@liverpool.ac.uk>
-Maintainer: DataSHIELD Developers <datashield@liverpool.ac.uk>
+Version: 6.1.1
+Author: DataSHIELD Developers <datashield@newcastle.ac.uk>
+Maintainer: DataSHIELD Developers <datashield@newcastle.ac.uk>
 Description: DataSHIELD client functions for the client side.
 License: GPL-3
 Depends:
     R (>= 3.5.0),
-    DSI (>= 1.3.0)
+    DSI (>= 1.2.0)
 Imports:
     fields,
     metafor,
-    meta,
     ggplot2,
     gridExtra,
     data.table,
     panelaggregation,
-    methods,
-    dplyr
-Suggests:
-    testthat
-RoxygenNote: 7.3.2
+    methods
+RoxygenNote: 7.1.1
 Encoding: UTF-8

NAMESPACE

@@ -5,16 +5,13 @@ export(ds.abs)
 export(ds.asCharacter)
 export(ds.asDataMatrix)
 export(ds.asFactor)
-export(ds.asFactorSimple)
 export(ds.asInteger)
 export(ds.asList)
 export(ds.asLogical)
 export(ds.asMatrix)
 export(ds.asNumeric)
 export(ds.assign)
-export(ds.auc)
 export(ds.boxPlot)
-export(ds.bp_standards)
 export(ds.c)
 export(ds.cbind)
 export(ds.changeRefGroup)
@@ -31,22 +28,16 @@ export(ds.dataFrameSort)
 export(ds.dataFrameSubset)
 export(ds.densityGrid)
 export(ds.dim)
-export(ds.dmtC2S)
-export(ds.elspline)
 export(ds.exists)
 export(ds.exp)
-export(ds.forestplot)
-export(ds.gamlss)
 export(ds.getWGSR)
 export(ds.glm)
 export(ds.glmPredict)
 export(ds.glmSLMA)
 export(ds.glmSummary)
 export(ds.glmerSLMA)
 export(ds.heatmapPlot)
-export(ds.hetcor)
 export(ds.histogram)
-export(ds.igb_standards)
 export(ds.isNA)
 export(ds.isValid)
 export(ds.kurtosis)
@@ -62,7 +53,6 @@ export(ds.lmerSLMA)
 export(ds.log)
 export(ds.look)
 export(ds.ls)
-export(ds.lspline)
 export(ds.make)
 export(ds.matrix)
 export(ds.matrixDet)
@@ -77,18 +67,13 @@ export(ds.meanByClass)
 export(ds.meanSdGp)
 export(ds.merge)
 export(ds.message)
-export(ds.metadata)
-export(ds.mice)
 export(ds.names)
-export(ds.ns)
 export(ds.numNA)
-export(ds.qlspline)
 export(ds.quantileMean)
 export(ds.rBinom)
 export(ds.rNorm)
 export(ds.rPois)
 export(ds.rUnif)
-export(ds.ranksSecure)
 export(ds.rbind)
 export(ds.reShape)
 export(ds.recodeLevels)
@@ -114,8 +99,6 @@ export(ds.tapply)
 export(ds.tapply.assign)
 export(ds.testObjExists)
 export(ds.unList)
-export(ds.unique)
 export(ds.var)
 export(ds.vectorCalc)
 import(DSI)
-import(data.table)

R/ds.Boole.R

@@ -24,7 +24,7 @@
 #' 
 #' @param V1 A character string specifying the name of the vector to which the Boolean operator
 #' is to be applied. 
-#' @param V2 A character string specifying the name of the vector to compare with \code{V1}. 
+#' @param V2 A character string specifying the name of the vector  to compare with \code{V1}. 
 #' @param Boolean.operator A character string specifying one of six possible Boolean operators:
 #' \code{'==', '!=', '>', '>=', '<'} and \code{'<='}. 
 #' @param numeric.output logical. If TRUE the output variable should be of class numeric (\code{1/0}).
@@ -177,7 +177,7 @@ ds.Boole<-function(V1=NULL, V2=NULL, Boolean.operator=NULL, numeric.output=TRUE,
     newobj <- paste0(V1,"_Boole")
   }
 
-  # CALL THE MAIN SERVER SIDE FUNCTION
+# CALL THE MAIN SERVER SIDE FUNCTION
   calltext <- call("BooleDS", V1, V2, BO.n, na.assign,numeric.output)
   DSI::datashield.assign(datasources, newobj, calltext)
 
@@ -209,7 +209,7 @@ for(j in 1:num.datasources){																			 	#
 	if(!object.info[[j]]$test.obj.exists){																 	#
 		obj.name.exists.in.all.sources<-FALSE															 	#
 		}																								 	#
-	if(is.null(object.info[[j]]$test.obj.class) || ("ABSENT" %in% object.info[[j]]$test.obj.class)){														 	#
+	if(is.null(object.info[[j]]$test.obj.class) || object.info[[j]]$test.obj.class=="ABSENT"){														 	#
 		obj.non.null.in.all.sources<-FALSE																 	#
 		}																								 	#
 	}																									 	#

R/ds.abs.R

@@ -86,15 +86,26 @@ ds.abs <- function(x=NULL, newobj=NULL, datasources=NULL){
     stop("Please provide the name of the input object!", call.=FALSE)
   }
 
-  # check if the input object is defined in all the studies
-  isDefined(datasources, x)
+  # the input variable might be given as column table (i.e. D$x)
+  # or just as a vector not attached to a table (i.e. x)
+  # we have to make sure the function deals with each case
+  xnames <- extract(x)
+  varname <- xnames$elements
+  obj2lookfor <- xnames$holders
+
+  # check if the input object(s) is(are) defined in all the studies
+  if(is.na(obj2lookfor)){
+    defined <- isDefined(datasources, varname)
+  }else{
+    defined <- isDefined(datasources, obj2lookfor)
+  }
 
   # call the internal function that checks the input object is of the same class in all studies.
   typ <- checkClass(datasources, x)
 
   # call the internal function that checks the input object(s) is(are) of the same class in all studies.
   if(!('numeric' %in% typ) && !('integer' %in% typ)){
-    stop("Only objects of type 'numeric' or 'integer' are allowed.", call.=FALSE)
+      stop("Only objects of type 'numeric' or 'integer' are allowed.", call.=FALSE)
   }
 
   # create a name by default if the user did not provide a name for the new variable

R/ds.asCharacter.R

@@ -1,4 +1,3 @@
-#' 
 #' @title Converts a server-side R object into a character class
 #' @description Converts the input object into a character class. 
 #' This function is based on the native R function \code{as.character}.
@@ -14,7 +13,8 @@
 #' the default set of connections will be used: see \code{\link{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 
+#' indicating the name of the \code{newobj} which 
+#' has been created in each data source and if 
 #' it is in a valid form.
 #' @examples 
 #' \dontrun{
@@ -54,7 +54,6 @@
 #' }   
 #' @author DataSHIELD Development Team
 #' @export
-#' 
 ds.asCharacter <- function(x.name=NULL, newobj=NULL, datasources=NULL){
 
   # look for DS connections
@@ -70,9 +69,7 @@ ds.asCharacter <- function(x.name=NULL, newobj=NULL, datasources=NULL){
   if(is.null(x.name)){
     stop("Please provide the name of the input vector!", call.=FALSE)
   }
-
-  # check if the input object is defined in all the studies
-  isDefined(datasources, x.name)
+
 
   # create a name by default if user did not provide a name for the new variable
   if(is.null(newobj)){
@@ -110,7 +107,7 @@ for(j in 1:num.datasources){																			 	#
 	if(!object.info[[j]]$test.obj.exists){																 	#
 		obj.name.exists.in.all.sources<-FALSE															 	#
 		}																								 	#
-	if(is.null(object.info[[j]]$test.obj.class) || ("ABSENT" %in% object.info[[j]]$test.obj.class)){														 	#
+	if(is.null(object.info[[j]]$test.obj.class) || object.info[[j]]$test.obj.class=="ABSENT"){														 	#
 		obj.non.null.in.all.sources<-FALSE																 	#
 		}																								 	#
 	}																									 	#

R/ds.asDataMatrix.R

@@ -55,7 +55,6 @@
 #' }   
 #' @author DataSHIELD Development Team
 #' @export
-#' 
 ds.asDataMatrix <- function(x.name=NULL, newobj=NULL, datasources=NULL){
 
   # look for DS connections
@@ -71,17 +70,17 @@ ds.asDataMatrix <- function(x.name=NULL, newobj=NULL, datasources=NULL){
   if(is.null(x.name)){
     stop("Please provide the name of the input vector!", call.=FALSE)
   }
-
-  # check if the input object is defined in all the studies
-  isDefined(datasources, x.name)
-
+
+
   # create a name by default if user did not provide a name for the new variable
   if(is.null(newobj)){
     newobj <- "asdatamatrix.newobj"
   }
 
-  # call the server side function that does the job
+    # call the server side function that does the job
+
 	calltext <- call("asDataMatrixDS", x.name)
+
 	DSI::datashield.assign(datasources, newobj, calltext)
 
 
@@ -109,7 +108,7 @@ for(j in 1:num.datasources){																			 	#
 	if(!object.info[[j]]$test.obj.exists){																 	#
 		obj.name.exists.in.all.sources<-FALSE															 	#
 		}																								 	#
-	if(is.null(object.info[[j]]$test.obj.class) || ("ABSENT" %in% object.info[[j]]$test.obj.class)){														 	#
+	if(is.null(object.info[[j]]$test.obj.class) || object.info[[j]]$test.obj.class=="ABSENT"){														 	#
 		obj.non.null.in.all.sources<-FALSE																 	#
 		}																								 	#
 	}																									 	#