Merge pull request #132 from stan-dev/v2.2.1

Version 2.2.1

.travis.yml

@@ -3,6 +3,7 @@ r: devel
 cache: packages
 
 r_github_packages:
+  - HenrikBengtsson/matrixStats@develop
   - jimhester/covr
 
 after_success:

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: shinystan
 Title: Interactive Visual and Numerical Diagnostics and Posterior Analysis for
     Bayesian Models
-Version: 2.2.0
-Date: 2016-05-23
+Version: 2.2.1
+Date: 2016-08-31
 Authors@R: c(person("Jonah", "Gabry", role = c("aut", "cre"),
     email = "jsg2201@columbia.edu"),
       person(family = "Stan Development Team", role = "ctb"),
@@ -36,7 +36,8 @@ Suggests:
     rstanarm (>= 2.9.0-3),
     testthat
 Imports:
-    DT (>= 0.1),
+    colourpicker,
+    DT (>= 0.2),
     dygraphs (>= 0.4.5),
     ggplot2 (>= 2.1.0),
     gridExtra,
@@ -47,7 +48,7 @@ Imports:
     rsconnect (>= 0.4.2),
     rstan (>= 2.9.0-3),
     stats,
-    shinyjs (>= 0.1.0),
+    shinyjs (>= 0.6.0),
     shinythemes (>= 1.0.1),
     threejs (>= 0.2.1),
     utils,

NAMESPACE

@@ -22,13 +22,13 @@ import(threejs)
 import(utils)
 import(xts)
 importFrom(DT,datatable)
+importFrom(colourpicker,colourInput)
 importFrom(gridExtra,arrangeGrob)
 importFrom(gridExtra,grid.arrange)
 importFrom(gtools,mixedsort)
 importFrom(markdown,markdownToHTML)
 importFrom(reshape2,melt)
 importFrom(rsconnect,deployApp)
-importFrom(shinyjs,colourInput)
 importFrom(shinyjs,useShinyjs)
 importFrom(shinythemes,shinytheme)
 importFrom(stats,acf)

NEWS.md

@@ -1,3 +1,14 @@
+### Version 2.2.1
+* Better compatibility with latest releases of 'shinyjs' and 'DT' packages
+* `shinystan::launch_shinystan_demo()` now works without first having to load 
+the package with a call to `library`
+* Unless running on a server, the app now stops running when browser tab is 
+closed
+
+### Version 2.2.0-1
+* Fix bug in `deploy_shinystan` preventing some ShinyStan apps from being
+deployed
+
 ### Version 2.2.0
 * Add optional argument `pars` to the `as.shinystan` method for stanfit objects,
 allowing a subset of parameters to be selected for inclusion in the resulting

R/deploy_shinystan.R

@@ -2,85 +2,86 @@
 # 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.
-# 
+#
 # shinystan 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/>.
 
 
 #' Deploy a ShinyStan app on the web using shinyapps.io by RStudio
-#' 
-#' Requires a (free or paid) ShinyApps account. Visit 
+#'
+#' Requires a (free or paid) ShinyApps account. Visit
 #' \url{http://www.shinyapps.io/} to sign up.
-#' 
+#'
 #' @export
 #' @template args-sso
 #' @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.io account username. Only required if more than one 
+#' @param account shinyapps.io account username. Only required if more than one
 #'   account is configured on the system.
 #' @param ... Optional arguments. See Details.
-#' @param deploy Should the app be deployed? The only reason for this to be 
+#' @param deploy Should the app be deployed? The only reason for this to be
 #'   \code{FALSE} is if you just want to check that the preprocessing before
 #'   deployment is successful.
-#' 
-#' @return \link[=invisible]{Invisibly}, \code{TRUE} if deployment succeeded 
-#'   (did not encounter an error) or, if \code{deploy} argument is set to 
-#'   \code{FALSE}, the path to the temporary directory containing the app ready 
+#'
+#' @return \link[=invisible]{Invisibly}, \code{TRUE} if deployment succeeded
+#'   (did not encounter an error) or, if \code{deploy} argument is set to
+#'   \code{FALSE}, the path to the temporary directory containing the app ready
 #'   for deployment (also invisibly).
-#' 
-#' @details In \code{...}, the arguments \code{ppcheck_data} and 
+#'
+#' @details In \code{...}, the arguments \code{ppcheck_data} and
 #'   \code{ppcheck_yrep} can be specified. \code{ppcheck_data} should be a
 #'   vector of observations to use for graphical posterior predictive checking
 #'   and \code{ppcheck_yrep} should be a character string naming the parameter
 #'   in \code{sso} containing the posterior predictive simulations/replications.
 #'   The value of \code{ppcheck_yrep} is only used to preselect the appropriate
-#'   parameter/generated quantity to use for the posterior predictive checking. 
+#'   parameter/generated quantity to use for the posterior predictive checking.
 #'   \code{ppcheck_yrep} (but not \code{ppcheck_data}) can also be set
 #'   interactively on shinyapps.io when using the app.
-#'   
-#' @seealso The example in the \emph{Deploying to shinyapps.io} vignette that 
+#'
+#' @seealso The example in the \emph{Deploying to shinyapps.io} vignette that
 #'   comes with this package.
-#' 
+#'
 #'   \url{http://www.shinyapps.io/} to sign up for a free or paid ShinyApps
 #'   account and for details on how to configure your account on your local
 #'   system using RStudio's \pkg{\link[rsconnect]{rsconnect}} package.
-#' 
+#'
 #' @examples
 #' \dontrun{
-#' # 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.io username is 'username'. 
+#' # 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.io username is 'username'.
 #'
-#' deploy_shinystan(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. 
+#' # If you only have one ShinyApps account configured then you can also omit
+#' # the 'account' argument.
 #'
 #' deploy_shinystan(sso, appName = "my-model")
 #' }
-#' 
+#'
 #' @importFrom rsconnect deployApp
-#' 
+#'
 deploy_shinystan <- function(sso, appName, account = NULL, ..., deploy = TRUE) {
   sso_check(sso)
   if (missing(appName))
     stop("'appName' is required.")
-  
+
   # copy contents to temporary directory and write necessary additional lines to
   # ui, server, and global
   appDir <- tempdir()
   deployDir <- file.path(appDir, "ShinyStan")
   contents <- system.file("ShinyStan", package = "shinystan")
   file.copy(from = contents, to = appDir, recursive = TRUE)
-  
+
   server_pkgs <- c(
     "shiny",
     "shinyjs",
+    "colourpicker",
     "markdown",
     "shinythemes"
   )
@@ -99,25 +100,22 @@ deploy_shinystan <- function(sso, appName, account = NULL, ..., deploy = TRUE) {
   server_lines <- paste0("library(", server_pkgs, ");")
   ui_lines <- paste0("library(", ui_pkgs, ");")
   global_lines <- paste(
-    "load('sso.RData');", 
+    "load('sso.RData');",
     "if (file.exists('y.RData')) load('y.RData')"
   )
   for (ff in c("ui", "server", "global")) {
     file_name <- file.path(deployDir, paste0(ff, ".R"))
     fconn <- file(file_name, 'r+')
     original_content <- readLines(fconn)
-    if (ff %in% c("ui", "server")) {
-      sel <- grep(".SHINYSTAN_OBJECT", original_content)
-      original_content <- original_content[-sel]
-    }
     new_lines <- get(paste0(ff, "_lines"))
     writeLines(c(new_lines, original_content), con = fconn)
     close(fconn)
   }
-    
+
   # save sso to deployDir
-  object <- sso
-  save(object, file = file.path(deployDir, "sso.RData"))
+  .SHINYSTAN_OBJECT <- sso
+  save(.SHINYSTAN_OBJECT, file = file.path(deployDir, "sso.RData"))
+
   # save ppcheck_data and set ppcheck defaults
   pp <- list(...)
   if ("ppcheck_data" %in% names(pp)) {
@@ -130,10 +128,10 @@ deploy_shinystan <- function(sso, appName, account = NULL, ..., deploy = TRUE) {
         y_name = "y"
       )
   }
-    
+
   if (!deploy)
     return(invisible(deployDir))
-  
+
   rsconnect::deployApp(
     appDir = deployDir,
     appName = appName,
@@ -144,24 +142,17 @@ deploy_shinystan <- function(sso, appName, account = NULL, ..., deploy = TRUE) {
 
 
 
-# functions to set defaults for ppcheck shiny::selectInput for y and y_rep 
+# functions to set defaults for ppcheck shiny::selectInput for y and y_rep
 set_ppcheck_defaults <- function(appDir, yrep_name, y_name = "y") {
-  stopifnot(is.character(yrep_name), is.character(y_name), 
+  stopifnot(is.character(yrep_name), is.character(y_name),
             length(yrep_name) == 1, length(y_name) == 1)
   fileDir <- file.path(appDir, "server_files", "pages", "diagnose", "ppcheck", "ui")
-  y_file <- file.path(fileDir, "pp_y_from_r.R")
-  yrep_file <- file.path(fileDir, "pp_yrep_from_sso.R")
-  for (file in c("y_file", "yrep_file")) {
-    f <- get(file)
-    if (file.exists(f)) {
-      file.remove(f)
-      file.create(f)
-    }
+  ppc_file <- file.path(fileDir, "pp_get_y_and_yrep.R")
+  if (file.exists(ppc_file)) {
+    file.remove(ppc_file)
+    file.create(ppc_file)
   }
-  .write_files(
-    files = c(y_file, yrep_file),
-    lines = c(.y_lines(y_name), .yrep_lines(yrep_name))
-  )
+  .write_files(files = ppc_file, lines = .ppc_lines(y_name, yrep_name))
 }
 
 .write_files <- function(files, lines) {
@@ -173,25 +164,22 @@ set_ppcheck_defaults <- function(appDir, yrep_name, y_name = "y") {
   }
 }
 
-.y_lines <- function(y_name = "y") {
+.ppc_lines <- function(y_name = "y", yrep_name) {
   paste0(
-    "output$ui_pp_y_from_r <- renderUI({
+    "output$ui_pp_get_y <- renderUI({
       choices <- objects(envir = .GlobalEnv)
-      selectizeInput('y_name', label = span(style = 'color: #337ab7;', 'y, a vector of observations'), 
-      choices = c('', choices), 
+      selectizeInput('y_name', label = span(style = 'color: #337ab7;', 'y, a vector of observations'),
+      choices = c('', choices),
       selected = '", y_name,"')
-    })")
-}
+      })
 
-.yrep_lines <- function(yrep_name) {
-  paste0(
-    "output$ui_pp_yrep_from_sso <- renderUI({
-      choices <- param_names
+    output$ui_pp_get_yrep <- renderUI({
+      choices <- PARAM_NAMES
       choices <- strsplit(choices, split = '[', fixed = TRUE)
       choices <- lapply(choices, function(i) return(i[1]))
       choices <- unique(unlist(choices))
-      selectizeInput('yrep_name', 
-      label = span(style = 'color: #337ab7;', 'y_rep, posterior predictive replications'), 
+      selectizeInput('yrep_name',
+      label = span(style = 'color: #337ab7;', 'y_rep, posterior predictive replications'),
       choices = c('', choices),
       selected = '", yrep_name,"')
     })"

R/launch_shinystan.R

@@ -123,8 +123,8 @@ launch_shinystan_demo <- function(demo_name = "eight_schools",
                                   rstudio = getOption("shinystan.rstudio"),
                                   ...) {
   demo_name <- match.arg(demo_name)
-  demo_object <- get(demo_name)
-  invisible(launch(demo_object, rstudio = rstudio, ...))
+  data(list = demo_name, package = "shinystan", envir = environment())
+  invisible(launch(get(demo_name, inherits = FALSE), rstudio = rstudio, ...))
 }
 
 # Internal launch function