Merge pull request #102 from stan-dev/version-2.0.2

Version 2.1.0

Author: jgabry

DESCRIPTION

@@ -1,7 +1,8 @@
 Package: shinystan
-Title: Interactive Visual and Numerical Diagnostics and Posterior Analysis for Bayesian Models
-Version: 2.0.1
-Date: 2015-09-17
+Title: Interactive Visual and Numerical Diagnostics and Posterior Analysis for
+    Bayesian Models
+Version: 2.1.0
+Date: 2016-01-06
 Authors@R: c(person("Jonah", "Gabry", role = c("aut", "cre"),
     email = "[email protected]"),
       person(family = "Stan Development Team", role = "ctb"),
@@ -15,28 +16,29 @@ Authors@R: c(person("Jonah", "Gabry", role = c("aut", "cre"),
       person("Dongying", "Song", role = "ctb"),
       person("Rob", "Trangucci", role = "ctb"))
 Maintainer: Jonah Gabry <[email protected]>
-Description: We provide a graphical user interface for interactive Markov chain 
-  Monte Carlo (MCMC) diagnostics and plots and tables helpful for analyzing a 
-  posterior sample. The interface is powered by RStudio's Shiny web application 
-  framework and works with the output of MCMC programs written in any 
-  programming language (and has extended functionality for Stan models fit 
-  using the rstan package and the No-U-Turn sampler).
-URL: https://github.com/stan-dev/shinystan, http://mc-stan.org/
-BugReports: https://github.com/stan-dev/shinystan/issues
-Depends: 
+Description: We provide a graphical user interface for interactive Markov chain
+    Monte Carlo (MCMC) diagnostics and plots and tables helpful for analyzing a
+    posterior sample. The interface is powered by RStudio's Shiny web application
+    framework and works with the output of MCMC programs written in any programming
+    language (and has extended functionality for Stan models fit using the rstan
+    package and the No-U-Turn sampler).
+URL: https://github.com/stan-dev/shinystan/, http://mc-stan.org/
+BugReports: https://github.com/stan-dev/shinystan/issues/
+Depends:
     R (>= 3.1.0),
     shiny (>= 0.12.1)
 License: GPL (>=3)
 LazyData: true
-Suggests: 
+Suggests:
     coda,
     knitr (>= 1.9),
     rstan (>= 2.7),
+    rmarkdown (>= 0.8.1),
     testthat
-Imports: 
+Imports:
     DT (>= 0.1),
     dygraphs (>= 0.4.5),
-    ggplot2 (>= 1.0.0),
+    ggplot2 (>= 2.0.0),
     gridExtra,
     gtools,
     markdown (>= 0.7.4),
@@ -50,3 +52,4 @@ Imports:
     xtable,
     xts (>= 0.9-7)
 VignetteBuilder: knitr
+RoxygenNote: 5.0.1

NAMESPACE

@@ -1,4 +1,4 @@
-# Generated by roxygen2 (4.1.1): do not edit by hand
+# Generated by roxygen2: do not edit by hand
 
 export(as.shinystan)
 export(deploy_shinystan)

NEWS.md

@@ -1,16 +1,22 @@
 # `shinystan news`
 
+### Version 2.1.0
+* Compatibility with recent ggplot2 update
+* Select parameters via regular expressions in parameters plot ('Estimate' page)
+* Fix error when selecting an entire parameter group in parameters 
+plot ('Estimate' page)
+
 ### Version 2.0.1
 * Fixes small bugs and typos
 * Adds support for stanreg objects
 * Moves ggplot2 from Depends to Imports
 
-### Version 2.0.0 (major update)
+### Version 2.0.0 (major update, initial CRAN release)
 
 Version 2.0.0 has a new look, a new(ish) name, and a lot of new functionality. 
 Many bugs have also been fixed (see GitHub issue tracker). 
 
-It's also now [available on CRAN](https://cran.rstudio.com/web/packages/shinystan/index.html).
+[Available on CRAN](https://cran.rstudio.com/web/packages/shinystan/index.html).
 
 ### New names
 * The name of the R package is **shinystan** and the app/GUI is **ShinyStan**. 

R/array2shinystan.R

@@ -1,5 +1,5 @@
 # This file is part of shinystan
-# Copyright (C) Jonah Gabry
+# Copyright (C) 2015 Jonah Gabry
 #
 # shinystan 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

R/as.shinystan.R

@@ -1,5 +1,5 @@
 # This file is part of shinystan
-# Copyright (C) Jonah Gabry
+# Copyright (C) 2015 Jonah Gabry
 #
 # shinystan 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
@@ -15,10 +15,12 @@
 
 #' Create and test shinystan objects
 #'
+#' @export
 #' @param X An object to be converted to a shinystan object. Can be
 #' one of the following:
 #' \describe{
 #'   \item{stanfit}{An object of class stanfit (\pkg{rstan})}
+#'   \item{stanreg}{An object of class stanreg (\pkg{rstanarm})}
 #'   \item{mcmc.list}{An object of class \code{mcmc.list} (\pkg{coda})}
 #'   \item{3D array}{A 3D array of posterior simulations with dimensions corresponding
 #'   to iterations, chains, and parameters, in that order.}
@@ -35,7 +37,15 @@
 #'   
 #' @details If \code{X} is a stanfit object then no additional arguments should
 #'   be specified in \code{...} (they are taken automatically from the stanfit
-#'   object). If \code{X} is not a stanfit object then the following arguments
+#'   object). 
+#'   
+#'   If \code{X} is a stanreg object the argument \code{ppd} (logical)
+#'   can be specified indicating whether to draw from the posterior predictive
+#'   distribution before launching ShinyStan. The default is \code{TRUE}, 
+#'   although for large objects it can be wise to set it to \code{FALSE} as 
+#'   drawing from the posterior predictive distribution can be time consuming.
+#'   
+#'   If \code{X} is not a stanfit or stanreg object then the following arguments
 #'   can be specified but are not required:
 #'   
 #' \describe{
@@ -50,7 +60,6 @@
 #' }
 #' 
 #' @seealso \code{\link{launch_shinystan}}, \code{\link{launch_shinystan_demo}}
-#' @export
 #'
 #' @examples
 #' \dontrun{
@@ -94,16 +103,14 @@ as.shinystan <- function(X, ...) {
   }
   X_is <- get_type(X)
   if (X_is == "stanfit") return(stan2shinystan(X, ...))
-  if (X_is == "stanreg") return(stan2shinystan(X$stanfit, ...))
+  if (X_is == "stanreg") return(stanreg2shinystan(X, ...))
   if (X_is == "mcmclist") return(mcmc2shinystan(X, ...))
   if (X_is == "chainlist") return(chains2shinystan(X, ...))
   if (X_is == "other") {
     if (!is.array(X)) 
-      stop(paste(Xname, "is not a valid input type. See ?as.shinystan"), 
-           call. = FALSE)
+      stop(paste(Xname, "is not a valid input type. See ?as.shinystan"))
     array2shinystan(X, ...)
   }
-  
 }
 
 #' @rdname as.shinystan

R/chains2shinystan.R

@@ -1,5 +1,5 @@
 # This file is part of shinystan
-# Copyright (C) Jonah Gabry
+# Copyright (C) 2015 Jonah Gabry
 #
 # shinystan 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
@@ -26,19 +26,22 @@
 # 
 
 chains2shinystan <- function(chain_list, ...) {
-
   if (!is.list(chain_list)) {
     name <- deparse(substitute(chain_list))
     stop(paste(name, "is not a list."), call. = FALSE)
   }
-
   nChain <- length(chain_list)
+  for (i in 1:nChain) {
+    nms <- colnames(chain_list[[i]])
+    if (is.null(nms) || !all(nzchar(nms)))
+      stop("Some parameters are missing names. ",
+           "Check the column names for the matrices in your list of chains.")
+  }
   if (nChain > 1) {
     nIter <- sapply(chain_list, nrow)
     same_iters <- length(unique(nIter)) == 1
     if (!same_iters) 
       stop("Each chain should contain the same number of iterations.")
-
     cnames <- sapply(chain_list, colnames)
     if (is.array(cnames)) {
       same_params <- identical(cnames[,1], cnames[,2])
@@ -48,8 +51,8 @@ chains2shinystan <- function(chain_list, ...) {
       param_names <- cnames
     }
     if (!same_params) 
-      stop("The parameters for each chain should be in the same order and have the same names.")
-
+      stop("The parameters for each chain should be in the same order ",
+           "and have the same names.")
     nIter <- nIter[1]
   } else {
     if (nChain == 1) {
@@ -59,19 +62,14 @@ chains2shinystan <- function(chain_list, ...) {
       stop("You don't appear to have any chains.")
     }
   }
-
   param_names <- unique(param_names)
   nParam <- length(param_names)
-
   out <- array(NA, dim = c(nIter, nChain, nParam))
   for(i in 1:nChain) {
     out[,i,] <- chain_list[[i]]
   }
-
   dimnames(out) <- list(iterations = NULL,
-                        chains = paste0("chain:",1:nChain),
+                        chains = paste0("chain:", 1:nChain),
                         parameters = param_names)
-
-  out <- array2shinystan(out, ...)
-  out
+  array2shinystan(out, ...)
 }

R/convenience.R

@@ -1,5 +1,5 @@
 # This file is part of shinystan
-# Copyright (C) Jonah Gabry
+# Copyright (C) 2015 Jonah Gabry
 #
 # shinystan 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

R/deploy_shinystan.R

@@ -1,5 +1,5 @@
 # This file is part of shinystan
-# Copyright (C) Jonah Gabry
+# Copyright (C) 2015 Jonah Gabry
 #
 # shinystan 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
@@ -14,20 +14,19 @@
 # this program; if not, see <http://www.gnu.org/licenses/>.
 
 
-#' Deploy a ShinyStan app to shinyapps.io
+#' Deploy a ShinyStan app on the web using shinyapps.io by RStudio
 #' 
-#' Requires a (free or paid) ShinyApps account. Visit 
-#' \url{http://www.shinyapps.io/} to sign up. 
+#' Requires a (free or paid) shinyapps.io account. Visit 
+#' \url{http://www.shinyapps.io/} to sign up and for details on how to configure
+#' your account on your local system using RStudio's \pkg{rsconnect} package.
 #' 
 #' @export
-#' 
-#' @param sso shinystan object.
+#' @param sso A shinystan object.
 #' @param appName The name to use for the application. Application names must be
 #'   at least four characters long and may only contain letters, numbers, dashes
 #'   and underscores.
-#' @param account ShinyApps account username. Only required if more than one 
-#'   ShinyApps account is configured on the system. See 
-#'   \url{http://www.shinyapps.io/} for help configuring your account.
+#' @param account shinyapps.io account username. Only required if more than one 
+#'   account is configured on the system.
 #' @param ... Optional arguments. See Details.
 #' 
 #' @details In \code{...}, the arguments \code{ppcheck_data} and 
@@ -45,24 +44,23 @@
 #' 
 #' @examples
 #' \dontrun{
-#' # For this example assume my_sso is the name of the shinystan object for 
+#' # For this example assume sso is the name of the shinystan object for 
 #' # the model you want to use. Assume also that you want to name your app 
-#' # 'my-model' and that your ShinyApps username is 'username'. 
+#' # 'my-model' and that your shinyapps.io username is 'username'. 
 #'
-#' deploy_shinystan(sso = my_sso, appName = "my-model", account = "username") 
+#' deploy_shinystan(sso, appName = "my-model", account = "username") 
 #'
 #' # If you only have one ShinyApps account configured then you can also omit 
 #' # the 'account' argument. 
 #'
-#' deploy_shinystan(sso = my_sso, appName = "my-model")
+#' deploy_shinystan(sso, appName = "my-model")
 #' }
 #' 
 
 deploy_shinystan <- function(sso, appName, account = NULL, ...) {
   sso_check(sso)
   if (missing(appName)) 
-    stop("Please specify a name for your app using the 'appName' argument", 
-         call. = FALSE)
+    stop("Please specify a name for your app using the 'appName' argument")
 
   # copy contents to temporary directory and write necessary additional lines to
   # ui, server, and global
@@ -93,7 +91,7 @@ deploy_shinystan <- function(sso, appName, account = NULL, ...) {
   # save shinystan_object to deployDir
   object <- sso
   save(object, file = file.path(deployDir, "shinystan_temp_object.RData"))
-  deploy <- getFromNamespace("deployApp", "shinyapps")
+  deploy <- getFromNamespace("deployApp", "rsconnect")
   # save ppcheck_data and set ppcheck defaults
   pp <- list(...)
   if ("ppcheck_data" %in% names(pp)) {
@@ -103,6 +101,5 @@ deploy_shinystan <- function(sso, appName, account = NULL, ...) {
       set_ppcheck_defaults(appDir = deployDir, yrep_name = pp$ppcheck_yrep, 
                            y_name = "y")
   }
-  deploy(appDir = deployDir, appName = appName, 
-                       account = account, lint = FALSE)
+  deploy(appDir = deployDir, appName = appName, account = account, lint = TRUE)
 }

R/eight_schools.R

@@ -1,5 +1,5 @@
 # This file is part of shinystan
-# Copyright (C) Jonah Gabry
+# Copyright (C) 2015 Jonah Gabry
 #
 # shinystan 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

R/generate_quantity.R

@@ -1,5 +1,5 @@
 # This file is part of shinystan
-# Copyright (C) Jonah Gabry
+# Copyright (C) 2015 Jonah Gabry
 #
 # shinystan 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
@@ -16,16 +16,18 @@
 
 #' Add to shinystan object a new parameter as a function of one or two 
 #' existing parameters
-#'
+#' 
+#' @export
 #' @param sso shinystan object.
 #' @param fun Function to call, i.e. \code{function(param1)} or
 #'   \code{function(param1,param2)}. See \strong{Examples}, below.
 #' @param param1 Name of first parameter as character string.
 #' @param param2 Optional. Name of second paramter as character string.
 #' @param new_name Name for the new parameter as character string.
+#' 
 #' @return sso, updated. See Examples.
+#' 
 #' @seealso \code{\link{as.shinystan}}
-#' @export
 #'
 #' @examples
 #' \dontrun{