Merge pull request #153 from stan-dev/develop

v2.4.0

Author: jgabry

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: shinystan
 Title: Interactive Visual and Numerical Diagnostics and Posterior Analysis for
     Bayesian Models
-Version: 2.3.0
-Date: 2017-01-31
+Version: 2.4.0
+Date: 2017-08-01
 Authors@R: c(person("Jonah", "Gabry", role = c("aut", "cre"),
     email = "[email protected]"),
       person(family = "Stan Development Team", role = "ctb"),
@@ -18,18 +18,19 @@ Authors@R: c(person("Jonah", "Gabry", role = c("aut", "cre"),
 Maintainer: Jonah Gabry <[email protected]>
 Description: 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 and rstanarm packages).
-URL: https://github.com/stan-dev/shinystan/, http://mc-stan.org/
+    posterior sample. The interface is powered by the 'Shiny' web
+    application framework from 'RStudio' and works with the output of MCMC 
+    programs written in any programming language (and has extended 
+    functionality for 'Stan' models fit using the 'rstan' and 'rstanarm' 
+    packages).
+URL: http://mc-stan.org/, http://discourse.mc-stan.org
 BugReports: https://github.com/stan-dev/shinystan/issues/
 License: GPL (>=3)
 Depends:
     R (>= 3.1.0),
-    shiny (>= 0.12.1)
+    shiny (>= 1.0.3)
 Imports:
-    bayesplot (>= 1.1.0),
+    bayesplot (>= 1.2.0),
     colourpicker,
     DT (>= 0.2),
     dygraphs (>= 1.1.1.2),
@@ -52,8 +53,8 @@ Suggests:
     coda,
     knitr (>= 1.9),
     rmarkdown (>= 0.8.1),
-    rstanarm (>= 2.14.1),
+    rstanarm (>= 2.15.3),
     testthat
 LazyData: true
 VignetteBuilder: knitr
-RoxygenNote: 5.0.1
+RoxygenNote: 6.0.1

NAMESPACE

@@ -1,5 +1,7 @@
 # Generated by roxygen2: do not edit by hand
 
+S3method(launch_shinystan,default)
+S3method(launch_shinystan,shinystan)
 export(as.shinystan)
 export(deploy_shinystan)
 export(drop_parameters)

NEWS.md

@@ -1,3 +1,10 @@
+### Version 2.4.0
+
+* `launch_shinystan` is now an S3 generic with methods. This allows developers 
+of packages that use __shinystan__ to create their own `launch_shinystan` 
+methods instead of using a different function name or creating a naming 
+conflict.
+
 ### Version 2.3.0
 
 #### Fixes 

R/deploy_shinystan.R

@@ -11,9 +11,9 @@
 # this program; if not, see <http://www.gnu.org/licenses/>.
 
 
-#' Deploy a ShinyStan app on the web using shinyapps.io by RStudio
+#' 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
@@ -46,13 +46,13 @@
 #' @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
+#'   \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.
+#'   system using the \pkg{\link[rsconnect]{rsconnect}} package from 'RStudio'.
 #'
 #' @examples
 #' \dontrun{
-#' # For this example assume sso is the name of the shinystan object for
+#' # For this example assume sso is the name of the \code{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'.
 #'

R/drop_parameters.R

@@ -11,13 +11,14 @@
 # this program; if not, see <http://www.gnu.org/licenses/>.
 
 
-#' Drop parameters from a shinystan object
+#' Drop parameters from a \code{shinystan} object
 #' 
-#' Remove selected parameters from a shinystan object. This is useful if you 
-#' have a very large shinystan object when you only want to look at a subset of 
-#' parameters. With a smaller shinystan object, \code{\link{launch_shinystan}} 
-#' will be faster and you should experience better performance (responsiveness) 
-#' after launching when using the ShinyStan app.
+#' Remove selected parameters from a \code{shinystan} object. This is useful if 
+#' you have a very large \code{shinystan} object when you only want to look at a
+#' subset of parameters. With a smaller \code{shinystan} object, 
+#' \code{\link{launch_shinystan}} will be faster and you should experience 
+#' better performance (responsiveness) after launching when using the
+#' 'ShinyStan' app.
 #'
 #' @export
 #' @template args-sso

R/generate_quantity.R

@@ -21,7 +21,7 @@
 #' @param fun Function to call, i.e. \code{function(param1)} or 
 #'   \code{function(param1,param2)}. See Examples, below.
 #' @param param1 Name of first parameter as character string.
-#' @param param2 Optional. Name of second paramter as character string.
+#' @param param2 Optional. Name of second parameter as character string.
 #' @param new_name Name for the new parameter as character string.
 #'   
 #' @return sso, updated. See Examples.

R/launch_shinystan.R

@@ -11,24 +11,26 @@
 # this program; if not, see <http://www.gnu.org/licenses/>.
 
 
-#' Launch the ShinyStan app
+#' Launch the 'ShinyStan' app
 #' 
-#' Launch the ShinyStan app in the default web browser. RStudio users also have
-#' the option of launching the app in RStudio's pop-up Viewer.
+#' Launch the 'ShinyStan' app in the default web browser. 'RStudio' users also
+#' have the option of launching the app in the pop-up Viewer.
 #' 
 #' @export
-#' @param object An object of class shinystan, stanfit, or stanreg. To use other
-#'   types of objects first create a shinystan object using 
+#' @param object The object to use. For the default method this can be an object
+#'   of class \code{"shinystan"}, \code{"stanfit"}, or \code{"stanreg"}. To use
+#'   other types of objects first create a shinystan object using
 #'   \code{\link{as.shinystan}}.
-#' @param rstudio Only relevant for RStudio users. The default (\code{FALSE}) is
-#'   to launch the app in the user's default web browser rather than RStudio's
-#'   pop-up Viewer. Users can change the default to \code{TRUE} by setting the
-#'   global option \code{options(shinystan.rstudio = TRUE)}.
+#' @param rstudio Only relevant for 'RStudio' users. The default (\code{FALSE})
+#'   is to launch the app in the user's default web browser rather than the 
+#'   pop-up Viewer provided by 'RStudio'. Users can change the default to
+#'   \code{TRUE} by setting the global option \code{options(shinystan.rstudio =
+#'   TRUE)}.
 #' @param ... Optional arguments passed to \code{\link[shiny]{runApp}}.
 #' 
 #' @return The \code{launch_shinystan} function is used for the side effect of 
-#'   starting the ShinyStan app, but it also returns a shinystan object, an
-#'   instance of S4 class \code{"shinystan"}.
+#'   starting the 'ShinyStan' app, but it also returns a \code{shinystan}
+#'   object, an instance of S4 class \code{"shinystan"}.
 #'   
 #' @template seealso-as.shinystan 
 #' @template seealso-update_sso 
@@ -69,31 +71,45 @@
 #' # Example 3: 'fit' is an mcmc.list, array or list of matrices
 #' #######################################
 #'
-#' # First create shinystan object (see ?as.shinystan for full details)
-#' fit_sso <- as.shinystan(fit, model_name = "Example")
-#' 
-#' # Now fit_sso is a shinystan object and so Example 1 (above) applies.
+#' # First create shinystan object (see ?as.shinystan) for full details)
 #' }
 #'
-launch_shinystan <- function(object, 
-                             rstudio = getOption("shinystan.rstudio"), 
-                             ...) {
-  if (is.shinystan(object)) {
-    sso_check(object)
-  } else if (is.stanreg(object) || is.stanfit(object)) {
-    message("\nCreating shinystan object...")
+launch_shinystan <- function(object, ...) {
+  UseMethod("launch_shinystan")
+}
+
+#' @rdname launch_shinystan
+#' @export
+launch_shinystan.default <-
+  function(object,
+           ...,
+           rstudio = getOption("shinystan.rstudio")) {
+    if (!is.shinystan(object) && 
+        !is.stanfit(object) && 
+        !is.stanreg(object)) {
+      stop("object not compatible with 'launch_shinystan'. ",
+           "Try converting to a shinystan object first using 'as.shinystan'.")
+    }
     object <- as.shinystan(object)
+    message("\nLaunching ShinyStan interface... ",
+            "for large models this  may take some time.")
+    invisible(launch(object, rstudio, ...))
+  }
+
+#' @rdname launch_shinystan
+#' @export
+launch_shinystan.shinystan <-
+  function(object,
+           ...,
+           rstudio = getOption("shinystan.rstudio")) {
+    sso_check(object)
+    message("\nLaunching ShinyStan interface... ",
+            "for large models this  may take some time.")
+    invisible(launch(object, rstudio, ...))
   }
-  if (!is.shinystan(object))
-    stop("'object' is not a valid input. See help('launch_shinystan').")
-  
-  message("\nLaunching ShinyStan interface... ",
-          "for large models this  may take some time.")
-  invisible(launch(object, rstudio, ...))
-}
 
 
-#' ShinyStan demo
+#' 'ShinyStan' demo
 #'
 #' @aliases eight_schools
 #' @export
@@ -102,8 +118,8 @@ launch_shinystan <- function(object,
 #'   the only option, but additional demos may be available in future releases.
 #'   \describe{
 #'   \item{\code{eight_schools}}{Hierarchical meta-analysis model. See 
-#'    \emph{Meta Analysis} chapter of the Stan manual (chapter 11.2 in version
-#'    2.9), \url{http://mc-stan.org/documentation/}.}
+#'    \emph{Meta Analysis} chapter of the 'Stan' manual 
+#'    \url{http://mc-stan.org/users/documentation/}.}
 #'   }
 #' @return An S4 shinystan object.
 #'   

R/retrieve.R

@@ -25,15 +25,15 @@
 #'   include/exclude warmup iterations (the default is \code{FALSE}). See
 #'   Details, below.
 #'   
-#' @details The argument \code{what} can take on the values below. Args:
-#'   \code{arg} means that \code{arg} can be specified in \code{...} for this
+#' @details The argument \code{what} can take on the values below. 'Args:
+#'   \code{arg}' means that \code{arg} can be specified in \code{...} for this
 #'   value of \code{what}.
 #' \describe{
 #'   \item{\code{"rhat"}, \code{"Rhat"}, \code{"r_hat"}, or \code{"R_hat"}}{returns: Rhat statistics. Args: \code{pars}}
 #'   \item{\code{"N_eff"}, \code{"n_eff"}, \code{"neff"}, \code{"Neff"}, \code{"ess"}, or \code{"ESS"}}{returns: Effective sample sizes. Args: \code{pars}}
 #'   \item{\code{"mean"}}{returns: Posterior means. Args: \code{pars}}
 #'   \item{\code{"sd"}}{returns: Posterior standard deviations. Args: \code{pars}}
-#'   \item{\code{"se_mean"} or \code{"mcse"}}{returns: Monte carlo standard error. Args: \code{pars}}
+#'   \item{\code{"se_mean"} or \code{"mcse"}}{returns: Monte Carlo standard error. Args: \code{pars}}
 #'   \item{\code{"median"}}{returns: Posterior medians. Args: \code{pars}.}
 #'   \item{\code{"quantiles"} or any string with \code{"quant"} in it (not case sensitive)}{returns: 2.5\%, 25\%, 50\%, 75\%, 97.5\% posterior quantiles. Args: \code{pars}.}
 #'   \item{\code{"avg_accept_stat"} or any string with \code{"accept"} in it (not case sensitive)}{returns: Average value of "accept_stat" (which itself is the average acceptance probability over the NUTS subtree). Args: \code{inc_warmup}}