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Merge pull request #132 from stan-dev/v2.2.1
Version 2.2.1
2 parents 41ca2b4 + cecb75c commit 9c24c52

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‎.travis.yml

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cache: packages
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r_github_packages:
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- HenrikBengtsson/matrixStats@develop
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- jimhester/covr
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after_success:

‎DESCRIPTION

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

‎NAMESPACE

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

‎NEWS.md

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

‎R/deploy_shinystan.R

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# terms of the GNU General Public License as published by the Free Software
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# Foundation; either version 3 of the License, or (at your option) any later
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# version.
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#
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#
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# shinystan is distributed in the hope that it will be useful, but WITHOUT ANY
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# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
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# A PARTICULAR PURPOSE. See the GNU General Public License for more details.
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#
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#
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# You should have received a copy of the GNU General Public License along with
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# this program; if not, see <http://www.gnu.org/licenses/>.
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#' Deploy a ShinyStan app on the web using shinyapps.io by RStudio
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#'
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#' Requires a (free or paid) ShinyApps account. Visit
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#'
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#' Requires a (free or paid) ShinyApps account. Visit
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#' \url{http://www.shinyapps.io/} to sign up.
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#'
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#'
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#' @export
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#' @template args-sso
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#' @param appName The name to use for the application. Application names must be
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#' at least four characters long and may only contain letters, numbers, dashes
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#' and underscores.
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#' @param account shinyapps.io account username. Only required if more than one
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#' @param account shinyapps.io account username. Only required if more than one
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#' account is configured on the system.
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#' @param ... Optional arguments. See Details.
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#' @param deploy Should the app be deployed? The only reason for this to be
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#' @param deploy Should the app be deployed? The only reason for this to be
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#' \code{FALSE} is if you just want to check that the preprocessing before
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#' deployment is successful.
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#'
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#' @return \link[=invisible]{Invisibly}, \code{TRUE} if deployment succeeded
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#' (did not encounter an error) or, if \code{deploy} argument is set to
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#' \code{FALSE}, the path to the temporary directory containing the app ready
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#'
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#' @return \link[=invisible]{Invisibly}, \code{TRUE} if deployment succeeded
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#' (did not encounter an error) or, if \code{deploy} argument is set to
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#' \code{FALSE}, the path to the temporary directory containing the app ready
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#' for deployment (also invisibly).
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#'
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#' @details In \code{...}, the arguments \code{ppcheck_data} and
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#'
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#' @details In \code{...}, the arguments \code{ppcheck_data} and
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#' \code{ppcheck_yrep} can be specified. \code{ppcheck_data} should be a
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#' vector of observations to use for graphical posterior predictive checking
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#' and \code{ppcheck_yrep} should be a character string naming the parameter
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#' in \code{sso} containing the posterior predictive simulations/replications.
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#' The value of \code{ppcheck_yrep} is only used to preselect the appropriate
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#' parameter/generated quantity to use for the posterior predictive checking.
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#' parameter/generated quantity to use for the posterior predictive checking.
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#' \code{ppcheck_yrep} (but not \code{ppcheck_data}) can also be set
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#' interactively on shinyapps.io when using the app.
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#'
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#' @seealso The example in the \emph{Deploying to shinyapps.io} vignette that
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#'
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#' @seealso The example in the \emph{Deploying to shinyapps.io} vignette that
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#' comes with this package.
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#'
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#'
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#' \url{http://www.shinyapps.io/} to sign up for a free or paid ShinyApps
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#' account and for details on how to configure your account on your local
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#' system using RStudio's \pkg{\link[rsconnect]{rsconnect}} package.
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#'
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#'
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#' @examples
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#' \dontrun{
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#' # For this example assume sso is the name of the shinystan object for
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#' # the model you want to use. Assume also that you want to name your app
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#' # 'my-model' and that your shinyapps.io username is 'username'.
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#' # For this example assume sso is the name of the shinystan object for
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#' # the model you want to use. Assume also that you want to name your app
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#' # 'my-model' and that your shinyapps.io username is 'username'.
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#'
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#' deploy_shinystan(sso, appName = "my-model", account = "username")
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#' deploy_shinystan(sso, appName = "my-model", account = "username")
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#'
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#' # If you only have one ShinyApps account configured then you can also omit
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#' # the 'account' argument.
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#' # If you only have one ShinyApps account configured then you can also omit
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#' # the 'account' argument.
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#'
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#' deploy_shinystan(sso, appName = "my-model")
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#' }
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#'
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#'
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#' @importFrom rsconnect deployApp
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#'
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#'
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deploy_shinystan <- function(sso, appName, account = NULL, ..., deploy = TRUE) {
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sso_check(sso)
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if (missing(appName))
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stop("'appName' is required.")
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# copy contents to temporary directory and write necessary additional lines to
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# ui, server, and global
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appDir <- tempdir()
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deployDir <- file.path(appDir, "ShinyStan")
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contents <- system.file("ShinyStan", package = "shinystan")
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file.copy(from = contents, to = appDir, recursive = TRUE)
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server_pkgs <- c(
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"shiny",
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"shinyjs",
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"colourpicker",
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"markdown",
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"shinythemes"
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)
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server_lines <- paste0("library(", server_pkgs, ");")
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ui_lines <- paste0("library(", ui_pkgs, ");")
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global_lines <- paste(
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"load('sso.RData');",
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"load('sso.RData');",
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"if (file.exists('y.RData')) load('y.RData')"
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)
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for (ff in c("ui", "server", "global")) {
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file_name <- file.path(deployDir, paste0(ff, ".R"))
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fconn <- file(file_name, 'r+')
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original_content <- readLines(fconn)
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if (ff %in% c("ui", "server")) {
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sel <- grep(".SHINYSTAN_OBJECT", original_content)
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original_content <- original_content[-sel]
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}
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new_lines <- get(paste0(ff, "_lines"))
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writeLines(c(new_lines, original_content), con = fconn)
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close(fconn)
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}
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# save sso to deployDir
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object <- sso
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save(object, file = file.path(deployDir, "sso.RData"))
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.SHINYSTAN_OBJECT <- sso
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save(.SHINYSTAN_OBJECT, file = file.path(deployDir, "sso.RData"))
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# save ppcheck_data and set ppcheck defaults
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pp <- list(...)
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if ("ppcheck_data" %in% names(pp)) {
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y_name = "y"
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)
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}
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if (!deploy)
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return(invisible(deployDir))
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rsconnect::deployApp(
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appDir = deployDir,
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appName = appName,
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# functions to set defaults for ppcheck shiny::selectInput for y and y_rep
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# functions to set defaults for ppcheck shiny::selectInput for y and y_rep
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set_ppcheck_defaults <- function(appDir, yrep_name, y_name = "y") {
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stopifnot(is.character(yrep_name), is.character(y_name),
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stopifnot(is.character(yrep_name), is.character(y_name),
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length(yrep_name) == 1, length(y_name) == 1)
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fileDir <- file.path(appDir, "server_files", "pages", "diagnose", "ppcheck", "ui")
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y_file <- file.path(fileDir, "pp_y_from_r.R")
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yrep_file <- file.path(fileDir, "pp_yrep_from_sso.R")
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for (file in c("y_file", "yrep_file")) {
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f <- get(file)
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if (file.exists(f)) {
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file.remove(f)
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file.create(f)
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}
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ppc_file <- file.path(fileDir, "pp_get_y_and_yrep.R")
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if (file.exists(ppc_file)) {
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file.remove(ppc_file)
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file.create(ppc_file)
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}
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.write_files(
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files = c(y_file, yrep_file),
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lines = c(.y_lines(y_name), .yrep_lines(yrep_name))
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)
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.write_files(files = ppc_file, lines = .ppc_lines(y_name, yrep_name))
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}
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.write_files <- function(files, lines) {
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}
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}
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.y_lines <- function(y_name = "y") {
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.ppc_lines <- function(y_name = "y", yrep_name) {
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paste0(
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"output$ui_pp_y_from_r <- renderUI({
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"output$ui_pp_get_y <- renderUI({
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choices <- objects(envir = .GlobalEnv)
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selectizeInput('y_name', label = span(style = 'color: #337ab7;', 'y, a vector of observations'),
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choices = c('', choices),
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selectizeInput('y_name', label = span(style = 'color: #337ab7;', 'y, a vector of observations'),
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choices = c('', choices),
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selected = '", y_name,"')
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})")
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}
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})
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.yrep_lines <- function(yrep_name) {
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paste0(
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"output$ui_pp_yrep_from_sso <- renderUI({
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choices <- param_names
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output$ui_pp_get_yrep <- renderUI({
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choices <- PARAM_NAMES
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choices <- strsplit(choices, split = '[', fixed = TRUE)
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choices <- lapply(choices, function(i) return(i[1]))
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choices <- unique(unlist(choices))
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selectizeInput('yrep_name',
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label = span(style = 'color: #337ab7;', 'y_rep, posterior predictive replications'),
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selectizeInput('yrep_name',
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label = span(style = 'color: #337ab7;', 'y_rep, posterior predictive replications'),
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choices = c('', choices),
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selected = '", yrep_name,"')
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})"

‎R/launch_shinystan.R

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

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