diff --git a/.Rbuildignore b/.Rbuildignore
index 97b1bb3d..3240997f 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -10,3 +10,4 @@ LICENSE
man-roxygen/*
images/*
^\.github$
+^pkgdown$
diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
new file mode 100644
index 00000000..fa85f77e
--- /dev/null
+++ b/.github/workflows/pkgdown.yaml
@@ -0,0 +1,56 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+ # build dev site on merged pushes
+ push:
+ branches: [main, master]
+ # build full site on releases
+ release:
+ types: [published]
+ workflow_dispatch:
+
+name: pkgdown.yaml
+
+jobs:
+ pkgdown:
+ runs-on: ubuntu-latest
+ # Only restrict concurrency for non-PR jobs
+ concurrency:
+ group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
+ cancel-in-progress: true
+ env:
+ GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+ permissions:
+ contents: write
+ steps:
+ - uses: actions/checkout@v4
+
+ - uses: r-lib/actions/setup-pandoc@v2
+
+ - uses: r-lib/actions/setup-r@v2
+ with:
+ use-public-rspm: true
+
+ - uses: r-lib/actions/setup-r-dependencies@v2
+ with:
+ extra-packages: any::pkgdown, local::., any::withr, stan-dev/pkgdown-config, stan-dev/cmdstanr
+
+ - name: Build site
+ run: |
+ withr::with_envvar(
+ c("NOT_CRAN" = "true"), # this should already be set by setup-r@v2? keeping because vignettes don't build otherwise
+ pkgdown::build_site_github_pages(
+ lazy = FALSE, # change to TRUE if runner times out.
+ run_dont_run = FALSE, # shinystan is interactive so hangs
+ examples = FALSE,
+ new_process = TRUE
+ )
+ )
+ shell: Rscript {0}
+
+ - name: Deploy to GitHub pages 🚀
+ uses: JamesIves/github-pages-deploy-action@v4
+ with:
+ clean: false
+ branch: gh-pages
+ folder: docs
diff --git a/R/shinystan-package.R b/R/shinystan-package.R
index e3d23b59..1a3d4def 100644
--- a/R/shinystan-package.R
+++ b/R/shinystan-package.R
@@ -10,7 +10,6 @@
# You should have received a copy of the GNU General Public License along with
# this program; if not, see .
-
#' \pkg{shinystan} R package ('ShinyStan' graphical user interface)
#'
#' @docType package
@@ -18,7 +17,7 @@
#'
#' @description
#' \if{html}{
-#' \figure{stanlogo.png}{options: width="50" alt="mc-stan.org"}
+#' \figure{logo.svg}{options: width="50" alt="mc-stan.org"}
#' \emph{Stan Development Team}
#' }
#'
@@ -54,7 +53,7 @@
#' publication.
#'
#' The \code{\link{deploy_shinystan}} function lets you easily deploy your own
-#' ShinyStan apps online for any of your models using the shinyapps.io
+#' ShinyStan apps online for any of your models using the shinyapps.io
#' service from 'RStudio'. Each of your apps (each of your models) will have a
#' unique url and will be compatible with most web browsers.
#'
@@ -79,7 +78,7 @@
#' @template seealso-as.shinystan
#' @template seealso-demo
#' @template seealso-launch
-#'
+#'
#' @template reference-muth
#' @template reference-bayesvis
#'
diff --git a/README.md b/README.md
index a9cd59bf..f603f101 100644
--- a/README.md
+++ b/README.md
@@ -1,4 +1,4 @@
-# ShinyStan 
+# ShinyStan 
[](http://cran.r-project.org/web/packages/shinystan)
@@ -46,7 +46,7 @@ launch_shinystan_demo()
### Screenshots
-
+
### About ShinyStan
diff --git a/_pkgdown.yml b/_pkgdown.yml
new file mode 100644
index 00000000..11f73ae4
--- /dev/null
+++ b/_pkgdown.yml
@@ -0,0 +1,80 @@
+url: https://mc-stan.org/shinystan
+
+destination: "."
+
+development:
+ mode: auto
+
+template:
+ package: pkgdownconfig
+
+navbar:
+ title: "shinystan"
+
+ structure:
+ left: [home, vignettes, functions, news, pkgs, stan]
+ right: [search, bluesky, forum, github, lightswitch]
+
+ components:
+ pkgs:
+ text: Other Packages
+ menu:
+ - text: bayesplot
+ href: https://mc-stan.org/bayesplot
+ - text: cmdstanr
+ href: https://mc-stan.org/cmdstanr
+ - text: "loo"
+ href: https://mc-stan.org/loo
+ - text: posterior
+ href: https://mc-stan.org/posterior
+ - text: projpred
+ href: https://mc-stan.org/projpred
+ - text: rstan
+ href: https://mc-stan.org/rstan
+ - text: rstanarm
+ href: https://mc-stan.org/rstanarm
+ - text: rstantools
+ href: https://mc-stan.org/rstantools
+
+articles:
+ - title: "Getting Started"
+ desc: >
+ The best way to get started is to play around with the demo by running
+ launch_shinystan_demo(). The document below provides additional
+ information about some of the R functions in the package.
+ contents:
+ - shinystan-package
+ - title: "Hosting your App"
+ desc: >
+ The document below explains one way to host a shinystan app online.
+ contents:
+ - deploy_shinystan
+
+reference:
+ - title: "Package overview"
+ desc: >
+ Details about the shinystan R package.
+ contents:
+ - shinystan-package
+ - title: "Launching the app"
+ desc: >
+ Functions for launching the app using a particular model or launching a demo of the app.
+ contents:
+ - launch_shinystan
+ - launch_shinystan_demo
+ - title: "shinystan objects"
+ desc: >
+ Functions for creating, examining, and modifying shinystan objects.
+ contents:
+ - as.shinystan
+ - shinystan-class
+ - shinystan-metadata
+ - retrieve
+ - drop_parameters
+ - update_sso
+ - generate_quantity
+ - title: "Deploying apps"
+ desc: >
+ Functions for deploying shinystan apps on shinyapps.io.
+ contents:
+ - deploy_shinystan
diff --git a/inst/ShinyStan/ui_utils.R b/inst/ShinyStan/ui_utils.R
index 7a153309..9e6198ce 100644
--- a/inst/ShinyStan/ui_utils.R
+++ b/inst/ShinyStan/ui_utils.R
@@ -18,25 +18,28 @@ save_and_close_button <- function() {
shinystan_version <- function() {
# prevents error when deployed to shinyapps.io
ver <- try(utils::packageVersion("shinystan"))
- if (inherits(ver, "try-error"))
+ if (inherits(ver, "try-error")) {
return()
- else
+ } else {
strong(paste("Version", ver))
+ }
}
logo_and_name <- function() {
- div(div(
- img(
- src = "wide_ensemble.png",
- class = "wide-ensemble",
- width = "100%"
- )
- ),
div(
- style = "margin-top: 25px",
- img(src = "stan_logo.png", class = "stan-logo"),
- div(id = "shinystan-title", "ShinyStan")
- ))
+ div(
+ img(
+ src = "wide_ensemble.png",
+ class = "wide-ensemble",
+ width = "100%"
+ )
+ ),
+ div(
+ style = "margin-top: 25px",
+ img(src = "stan_logo.svg", class = "stan-logo"),
+ div(id = "shinystan-title", "ShinyStan")
+ )
+ )
}
@@ -56,34 +59,42 @@ save_and_close_reminder <- function(id) {
# show/hide options/glossary ---------------------------------------------
a_options <- function(name) {
- lab <- if (name == "table")
- "Table Options" else "Show/Hide Options"
- div(class = "aoptions",
- checkboxInput(
- inputId = paste0(name, "_options_show"),
- label = strong(style = "margin-top: 20px; color: #222222;", lab),
- value = FALSE
- ))
+ lab <- if (name == "table") {
+ "Table Options"
+ } else {
+ "Show/Hide Options"
+ }
+ div(
+ class = "aoptions",
+ checkboxInput(
+ inputId = paste0(name, "_options_show"),
+ label = strong(style = "margin-top: 20px; color: #222222;", lab),
+ value = FALSE
+ )
+ )
}
a_glossary <- function(id) {
- div(class = "aoptions",
- actionLink(
- inputId = id,
- label = strong(style = "margin-top: 20px; color: #222222;", "Glossary"),
- icon = icon("book", lib = "glyphicon")
- ))
+ div(
+ class = "aoptions",
+ actionLink(
+ inputId = id,
+ label = strong(style = "margin-top: 20px; color: #222222;", "Glossary"),
+ icon = icon("book", lib = "glyphicon")
+ )
+ )
}
-
# plotOutput generators ---------------------------------------------------
-dygraphOutput_175px <- function(id)
+dygraphOutput_175px <- function(id) {
dygraphs::dygraphOutput(id, height = "175px")
-plotOutput_200px <- function(id, ...)
+}
+plotOutput_200px <- function(id, ...) {
plotOutput(id, height = "200px")
-plotOutput_400px <- function(id, ...)
+}
+plotOutput_400px <- function(id, ...) {
plotOutput(id, height = "400px")
-
+}
# conditionalPanel generator for EXPLORE/density -------------------------
@@ -91,25 +102,39 @@ condPanel_dens_together <- function(...) {
conditionalPanel(condition = "input.dens_chain_split == 'Together'", ...)
}
condPanel_dens_prior <- function(dist, ...) {
- cond <- paste0("input.dens_prior ==","'", dist,"'")
+ cond <- paste0("input.dens_prior ==", "'", dist, "'")
conditionalPanel(cond, ...)
}
# conditional transparency settings ---------------------------------------
alpha_calc_pt <- function(N) {
- if (N <= 100) return(1)
- else if (N <= 200) return(0.75)
- else if (N >= 1500) return(0.15)
- else 1 - pnorm(N/1500)
+ if (N <= 100) {
+ return(1)
+ } else if (N <= 200) {
+ return(0.75)
+ } else if (N >= 1500) {
+ return(0.15)
+ } else {
+ 1 - pnorm(N / 1500)
+ }
}
alpha_calc_lines <- function(N) {
- if (N < 50) return(0.5)
- if (N < 500) return(0.4)
- if (N < 1000) return(0.3)
- if (N < 5000) return(0.2)
- else return(0.1)
+ if (N < 50) {
+ return(0.5)
+ }
+ if (N < 500) {
+ return(0.4)
+ }
+ if (N < 1000) {
+ return(0.3)
+ }
+ if (N < 5000) {
+ return(0.2)
+ } else {
+ return(0.1)
+ }
}
@@ -125,28 +150,38 @@ transformation_selectInput <- function(id) {
transform_helpText <- function(var = "x") {
div(
- if (var == "x")
- helpText(style = "font-size: 13px;",
- "To apply a transformation",
- "select a function and click",
- code("Transform"))
- else if (var == "x,y")
- helpText(style = "font-size: 13px;",
- "To apply transformations",
- "select a function for x and/or y",
- "and click", code("Transform"))
- else
- helpText(style = "font-size: 13px;",
- "To apply transformations",
- "select a function for x, y, and/or z",
- "and click", code("Transform"))
+ if (var == "x") {
+ helpText(
+ style = "font-size: 13px;",
+ "To apply a transformation",
+ "select a function and click",
+ code("Transform")
+ )
+ } else if (var == "x,y") {
+ helpText(
+ style = "font-size: 13px;",
+ "To apply transformations",
+ "select a function for x and/or y",
+ "and click",
+ code("Transform")
+ )
+ } else {
+ helpText(
+ style = "font-size: 13px;",
+ "To apply transformations",
+ "select a function for x, y, and/or z",
+ "and click",
+ code("Transform")
+ )
+ }
)
}
# diagnostics help text ---------------------------------------------------
-hT11 <- function(...)
+hT11 <- function(...) {
helpText(style = "font-size: 11px;", ...)
+}
help_interval <- hT11("Highlighted interval shows \\(\\bar{x} \\pm sd(x)\\)")
help_lines <- hT11("Lines are mean (solid) and median (dashed)")
help_max_td <- hT11("Horizontal line indicates the max_treedepth setting")
@@ -162,7 +197,6 @@ help_dynamic <- hT11(
)
-
# ppcheck plot descriptions ----------------------------------------------
plot_descriptions <-
c(
@@ -175,7 +209,6 @@ plot_descriptions <-
)
-
# stan manual reference ---------------------------------------------------
stan_manual <- function() {
helpText(
@@ -209,8 +242,10 @@ if (!exists(".SHINYSTAN_OBJECT")) {
isTRUE(.SHINYSTAN_OBJECT@misc$stanreg) &&
!is.null(.SHINYSTAN_OBJECT@misc$pp_check_plots)
-if (exists("object"))
+if (exists("object")) {
rm(object)
-if (exists(".SHINYSTAN_OBJECT"))
+}
+if (exists(".SHINYSTAN_OBJECT")) {
rm(.SHINYSTAN_OBJECT)
+}
gc()
diff --git a/man/figures/logo.svg b/man/figures/logo.svg
index b4c09fc5..496f0402 100644
--- a/man/figures/logo.svg
+++ b/man/figures/logo.svg
@@ -1,96 +1 @@
-
-
-
-
+
\ No newline at end of file
diff --git a/man/figures/stanlogo.png b/man/figures/stanlogo.png
deleted file mode 100644
index 4a4f06aa..00000000
Binary files a/man/figures/stanlogo.png and /dev/null differ
diff --git a/man/shinystan-package.Rd b/man/shinystan-package.Rd
index 525a57f2..f1d621eb 100644
--- a/man/shinystan-package.Rd
+++ b/man/shinystan-package.Rd
@@ -6,7 +6,7 @@
\title{\pkg{shinystan} R package ('ShinyStan' graphical user interface)}
\description{
\if{html}{
- \figure{stanlogo.png}{options: width="50" alt="mc-stan.org"}
+ \figure{logo.svg}{options: width="50" alt="mc-stan.org"}
\emph{Stan Development Team}
}