name change

[ci skip]

DESCRIPTION

@@ -1,7 +1,7 @@
-Package: shinyStan
+Package: shinystan
 Title: Interactive Visual Summaries and Analysis for MCMC
 Version: 2.0.0
-Date: 2015-08-01
+Date: 2015-08-03
 Authors@R: c(person("Jonah", "Gabry", role = c("aut", "cre"),
     email = "jsg2201@columbia.edu", comment = "Stan Development Team"),
       person("Michael", "Andreae", role = "ctb"),
@@ -10,9 +10,10 @@ Authors@R: c(person("Jonah", "Gabry", role = c("aut", "cre"),
 Maintainer: Jonah Gabry <jsg2201@columbia.edu>
 Description: Immediate, informative, customizable visual and numerical summaries 
     of model parameters and convergence diagnostics for MCMC simulations. 
-    shinyStan can be used to explore the output of MCMC programs written in 
-    any programming language (and has additional features for Stan models).
-    Users can also deploy their own shinyStan apps online using 
+    The ShinyStan app provided in the shinystan package can be used to explore 
+    the output of MCMC programs written in any programming language 
+    (and has additional features for Stan models).
+    Users can also deploy their own ShinyStan apps online using 
     RStudio's ShinyApps service. Note: to use this feature the user must install 
     the shinyapps package available from RStudio (Github url in 
     Additional_repositories).

NAMESPACE

@@ -13,7 +13,6 @@ import(dygraphs)
 import(ggplot2)
 import(methods)
 import(shiny)
-import(shinyBS)
 import(stats)
 import(threejs)
 import(xts)
@@ -25,6 +24,7 @@ importFrom(markdown,markdownToHTML)
 importFrom(plyr,ddply)
 importFrom(plyr,summarize)
 importFrom(reshape2,melt)
+importFrom(shinyBS,bsModal)
 importFrom(shinyjs,colourInput)
 importFrom(shinyjs,useShinyjs)
 importFrom(xtable,print.xtable)

R/array2shinystan.R

@@ -1,19 +1,18 @@
-# This file is part of shinyStan
-# Copyright (C) 2015 Jonah Sol Gabry & Stan Development Team
+# This file is part of shinystan
+# Copyright (C) Jonah Gabry
 #
-# shinyStan is free software; you can redistribute it and/or modify it under the
+# 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
 # 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
+# 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/>.
 
-
 # Convert 3D array to shinystan object
 # 
 # @param X A 3D array of posterior simulations with dimensions corresponding to 

R/as.shinystan.R

@@ -1,12 +1,12 @@
-# This file is part of shinyStan
-# Copyright (C) 2015 Jonah Sol Gabry & Stan Development Team
+# This file is part of shinystan
+# Copyright (C) Jonah Gabry
 #
-# shinyStan is free software; you can redistribute it and/or modify it under the
+# 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
 # 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
+# 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.
 # 
@@ -30,7 +30,7 @@
 #' @param Y An object to test.
 #' @param ... Additional arguments. See \strong{Details}, below, for instructions.
 #' @return For \code{as.shinystan} an object of class \code{shinystan} that can
-#' be used with \code{\link[shinyStan]{launch_shinystan}}. For
+#' be used with \code{{launch_shinystan}}. For
 #' \code{is.shinystan} a logical value indicating whether the tested object
 #' is a \code{shinystan} object.
 #' @details If \code{X} is a \code{stanfit} object then no additional arguments
@@ -45,11 +45,11 @@
 #'   For scalar parameters use \code{0} as the dimension. See \strong{Examples}.}
 #'   \item{\code{model_code}}{A character string with the code you used to run your model.
 #'   This can also be added to your \code{shinystan} object later using the
-#'   \code{\link[shinyStan]{include_model_code}} function. See \code{\link[shinyStan]{include_model_code}}
+#'   \code{\link{include_model_code}} function. See \code{\link{include_model_code}}
 #'   for additional formatting instructions. After launching the app \code{model_code}
 #'   will be viewable in the \strong{Model Code} tab.}
 #' }
-#' @seealso \code{\link[shinyStan]{launch_shinystan}}, \code{\link[shinyStan]{launch_shinystan_demo}}
+#' @seealso \code{\link{launch_shinystan}}, \code{\link{launch_shinystan_demo}}
 #' @export
 #'
 #' @examples
@@ -96,15 +96,18 @@ as.shinystan <- function(X, ...) {
   if (what_X_is == "shinystan") {
     message(
       paste0(Xname, " is already a shinystan object.\n",
-             "You can use launch_shinystan(", Xname, ") to launch shinyStan.")
+             "You can use launch_shinystan(", Xname, 
+             ") to launch ShinyStan.")
     )
     return(X)
   }
   if (what_X_is == "stanfit") return(stan2shinystan(X, ...))
   if (what_X_is == "mcmclist") return(mcmc2shinystan(X, ...))
   if (what_X_is == "chainlist") return(chains2shinystan(X, ...))
   if (what_X_is == "other") {
-    if (!is.array(X)) stop(paste(Xname, "is not a valid input type. See ?as.shinystan"), call. = FALSE)
+    if (!is.array(X)) 
+      stop(paste(Xname, "is not a valid input type. See ?as.shinystan"), 
+           call. = FALSE)
     array2shinystan(X, ...)
   }
 

R/chains2shinystan.R

@@ -1,12 +1,12 @@
-# This file is part of shinyStan
-# Copyright (C) 2015 Jonah Sol Gabry & Stan Development Team
+# This file is part of shinystan
+# Copyright (C) Jonah Gabry
 #
-# shinyStan is free software; you can redistribute it and/or modify it under the
+# 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
 # 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
+# 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.
 # 

R/convenience.R

@@ -1,18 +1,17 @@
-# This file is part of shinyStan
-# Copyright (C) 2015 Jonah Sol Gabry & Stan Development Team
+# This file is part of shinystan
+# Copyright (C) Jonah Gabry
 #
-# shinyStan is free software; you can redistribute it and/or modify it under the
+# 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
 # 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
+# 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/>.
-
 
 retrieve_rhat <- function(sso, pars) {
   if (missing(pars)) {

R/deploy_shinystan.R

@@ -1,20 +1,20 @@
-# This file is part of shinyStan
-# Copyright (C) 2015 Jonah Sol Gabry & Stan Development Team
+# This file is part of shinystan
+# Copyright (C) Jonah Gabry
 #
-# shinyStan is free software; you can redistribute it and/or modify it under the
+# 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
 # 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
+# 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 to shinyapps.io
+#' Deploy a ShinyStan app to shinyapps.io
 #' 
 #' Requires a (free or paid) ShinyApps account. Visit 
 #' \url{http://www.shinyapps.io/} to sign up. Also requires the \pkg{shinyapps} 
@@ -63,7 +63,7 @@
 deploy_shinystan <- function(sso, appName, account = NULL, ...) {
   sso_check(sso)
   if (!requireNamespace("shinyapps", quietly = TRUE)) 
-    stop("Deploying a shinyStan app requires the shinyapps package.",
+    stop("Deploying a ShinyStan app requires the shinyapps package.",
         "\nTo install use devtools::install_github('rstudio/shinyapps')", 
         call. = FALSE)
   if (missing(appName)) 
@@ -73,8 +73,8 @@ deploy_shinystan <- function(sso, appName, account = NULL, ...) {
   # 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")
+  deployDir <- file.path(appDir, "shinystan")
+  contents <- system.file("shinystan", package = "shinystan")
   file.copy(from = contents, to = appDir, recursive = TRUE)
   server_pkgs <- c("shiny", "shinyBS", "shinyjs", "markdown")
   ui_pkgs <- c(server_pkgs, "ggplot2", "gtools", "plyr", "reshape2", 

R/eight_schools.R

@@ -1,21 +1,21 @@
-# This file is part of shinyStan
-# Copyright (C) 2015 Jonah Sol Gabry & Stan Development Team
+# This file is part of shinystan
+# Copyright (C) Jonah Gabry
 #
-# shinyStan is free software; you can redistribute it and/or modify it under the
+# 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
 # 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
+# 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/>.
 
-#' shinyStan demo: Eight Schools 
+#' ShinyStan demo: Eight Schools 
 #'
-#' A shinyStan object for the Stan "Eight Schools" demo model 
-#' 
+#' A shinystan object for the Stan "Eight Schools" demo model 
+#' @seealso \code{\link{launch_shinystan_demo}}
 #' @format An S4 object of class \code{shinystan}
 "eight_schools"

R/generate_quantity.R

@@ -1,12 +1,12 @@
-# This file is part of shinyStan
-# Copyright (C) 2015 Jonah Sol Gabry & Stan Development Team
+# This file is part of shinystan
+# Copyright (C) Jonah Gabry
 #
-# shinyStan is free software; you can redistribute it and/or modify it under the
+# 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
 # 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
+# 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.
 # 
@@ -24,7 +24,7 @@
 #' @param param2 Optional. Name of second paramter as character string.
 #' @param new_name Name for the new parameter as character string.
 #' @return A \code{shinystan} object with \code{new_name} included as a parameter.
-#' @seealso \code{\link[shinyStan]{as.shinystan}}, \code{\link[shinyStan]{launch_shinystan_demo}}
+#' @seealso \code{\link{as.shinystan}}, \code{\link{launch_shinystan_demo}}
 #' @export
 #'
 #' @examples

R/include_model_code.R

@@ -1,12 +1,12 @@
-# This file is part of shinyStan
-# Copyright (C) 2015 Jonah Sol Gabry & Stan Development Team
+# This file is part of shinystan
+# Copyright (C) Jonah Gabry
 #
-# shinyStan is free software; you can redistribute it and/or modify it under the
+# 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
 # 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
+# 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.
 # 
@@ -17,15 +17,16 @@
 #' Add model code to a \code{shinystan} object
 #'
 #' @param sso A \code{shinystan} object.
-#' @param code The code you want to add. See \strong{Details} below for
-#' formatting instructions.
-#' @return The \code{shinystan} object \code{sso} with \code{code} in the
-#' \code{model_code} slot.
-#'
-#' @details \code{code} should be a character string that can be used as an argument
-#' to \code{cat}. See \strong{Examples}, below.
-#' @note This is intended for users who did not run their models using \pkg{rstan}.
-#' For \pkg{rstan} users the model code will be automatically available. 
+#' @param code The code you want to add. See \strong{Details} below for 
+#'   formatting instructions.
+#' @return The \code{shinystan} object \code{sso} with \code{code} in the 
+#'   \code{model_code} slot.
+#'   
+#' @details \code{code} should be a character string that can be used as an
+#'   argument to \code{cat}. See \strong{Examples}, below.
+#' @note This is intended for users who did not run their models using
+#'   \pkg{rstan}. For \pkg{rstan} users the model code will be automatically
+#'   available.
 #' 
 #' @seealso \code{cat}
 #' @export

R/launch_shinystan.R

@@ -1,41 +1,32 @@
-# This file is part of shinyStan
-# Copyright (C) 2015 Jonah Sol Gabry & Stan Development Team
+# This file is part of shinystan
+# Copyright (C) Jonah Gabry
 #
-# shinyStan is free software; you can redistribute it and/or modify it under the
+# 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
 # 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
+# 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/>.
 
-
-#' Launch shinyStan app
+#' ShinyStan app
 #' 
 #' @export
 #' 
-#' @param object An object of class \code{shinystan} or \code{stanfit}. See
-#'   \code{\link[shinyStan]{as.shinystan}} for converting to a 
-#'   \code{shinystan} object (sso).
-#' @param ... Optional arguments to pass to \code{\link[shiny]{runApp}}. See 
-#'   Details (RStudio users in particular).
+#' @param object An object of class \code{shinystan}, \code{stanfit}, or 
+#'   \code{stanreg}. See \code{\link{as.shinystan}} for converting other
+#'   objects to a \code{shinystan} object (sso).
+#' @param rstudio For RStudio users, should the app launch in RStudio's Viewer? 
+#'   The default (FALSE) is to launch the app in the default web browser.
+#' @param ... Optional arguments to pass to \code{\link[shiny]{runApp}}.
 #' @return An S4 object of class \code{shinystan}.
-#' 
-#' @details Unless you are using RStudio, \code{launch_shinystan} will open the
-#'   app in your system's default web browser. For RStudio users
-#'   \strong{shinyStan} will launch in RStudio's (pop-up) Viewer pane by
-#'   default. If you prefer to use \strong{shinyStan} in your web browser (or if
-#'   you are having trouble with the RStudio Viewer pane) you can 
-#'   specify \code{launch.browser = TRUE} in \code{...}. Alternatively, if 
-#'   \strong{shinyStan} is open in the RStudio Viewer pane you can click on 
-#'   'Open in Browser' (at the top left of the Viewer pane).
 #'
-#' @seealso \code{\link[shinyStan]{as.shinystan}}, 
-#'   \code{\link[shinyStan]{launch_shinystan_demo}}
+#' @seealso \code{\link{as.shinystan}}, 
+#'   \code{\link{launch_shinystan_demo}}
 #' @examples
 #' \dontrun{
 #' # If X is a stanfit object (or shinystan object (sso))
@@ -45,18 +36,20 @@
 #' X_sso <- launch_shinystan(as.shinystan(X, model_name = "Example"))
 #' }
 #'
-launch_shinystan <- function(object, launch.browser = TRUE, ...) {
+launch_shinystan <- function(object, rstudio = FALSE, ...) {
   name <- deparse(substitute(object))
   no_name <- substr(name, 1, 12) == "as.shinystan"
   if (missing(object)) 
     stop("Please specify a shinystan or stanfit object.")
-
-  if (!is.shinystan(object) && !inherits(object, "stanreg") 
-      && !inherits(object, "stanfit"))
-    stop(paste(name, "is not a shinystan or stanfit object."))
+  if (inherits(object, "stanreg"))
+    object <- object$stanfit
+  if (inherits(object, "stanfit"))
+    object <- stan2shinystan(object)
+  if (!is.shinystan(object))
+    stop(paste(name, "is not a valid input. See ?launch_shinystan"))
   message(paste("\n Loading... \n", 
-                "For large models shinyStan may take a few moments to launch."))
+                "For large models ShinyStan may take a few moments to launch."))
   on.exit(cleanup_shinystan())
-  launch(object, launch.browser, ...)
+  launch(object, rstudio, ...)
   invisible(return_sso())
 }