Merge pull request #378 from stan-dev/new-pkgdown-setup

New pkgdown theme

Author: jgabry

.Rbuildignore

@@ -3,7 +3,7 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
 LICENSE
-^\.travis\.yml$
+^\_pkgdown\.yml$
 ^README\.md$
 .gitignore
 .git/*

.github/workflows/pkgdown.yml

@@ -0,0 +1,55 @@
+# 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
+
+      - 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 = TRUE,
+              new_process = TRUE
+            )
+          )
+        shell: Rscript {0}
+
+      - name: Deploy to GitHub pages 🚀
+        uses: JamesIves/[email protected]
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

R/bayesplot-package.R

@@ -8,7 +8,7 @@
 #'
 #' @description
 #' \if{html}{
-#'    \figure{stanlogo.png}{options: width="50" alt="mc-stan.org"}
+#'    \figure{logo.svg}{options: width="50" alt="mc-stan.org"}
 #' }
 #' *Stan Development Team*
 #'

README.md

@@ -1,9 +1,9 @@
-# bayesplot <img src="man/figures/stanlogo.png" align="right" width="120" />
+# bayesplot <img src="man/figures/logo.svg" align="right" width="120" />
 
 <!-- badges: start -->
 [![CRAN_Status_Badge](https://www.r-pkg.org/badges/version/bayesplot?color=blue)](https://cran.r-project.org/web/packages/bayesplot)
 [![Downloads](https://cranlogs.r-pkg.org/badges/bayesplot?color=blue)](https://cran.rstudio.com/package=bayesplot)
-[![R-CMD-check](https://github.com/stan-dev/bayesplot/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/stan-dev/bayesplot/actions/workflows/R-CMD-check.yaml)
+[![R-CMD-check](https://github.com/stan-dev/bayesplot/actions/workflows/R-CMD-check.yaml/badge.svg)](https://raw.githubusercontent.com/stan-dev/bayesplot/actions/workflows/R-CMD-check.yaml)
 [![codecov](https://codecov.io/gh/stan-dev/bayesplot/branch/master/graph/badge.svg)](https://codecov.io/gh/stan-dev/bayesplot)
 <!-- badges: end -->
 
@@ -35,17 +35,17 @@ and the paper _Visualization in Bayesian workflow_:
 _J. R. Stat. Soc. A_, 182: 389-402. doi:10.1111/rssa.12378. 
 ([journal version](https://rss.onlinelibrary.wiley.com/doi/full/10.1111/rssa.12378),
 [arXiv preprint](https://arxiv.org/abs/1709.01449),
-[code on GitHub](https://github.com/jgabry/bayes-vis-paper))
+[code on GitHub](https://raw.githubusercontent.com/jgabry/bayes-vis-paper))
 
 ### Resources
 
 * [mc-stan.org/bayesplot](https://mc-stan.org/bayesplot) (online documentation, vignettes)
 * [Ask a question](https://discourse.mc-stan.org) (Stan Forums on Discourse)
-* [Open an issue](https://github.com/stan-dev/bayesplot/issues) (GitHub issues for bug reports, feature requests)
+* [Open an issue](https://raw.githubusercontent.com/stan-dev/bayesplot/issues) (GitHub issues for bug reports, feature requests)
 
 ### Contributing 
 
-We are always looking for new contributors! See [CONTRIBUTING.md](https://github.com/stan-dev/bayesplot/blob/master/.github/CONTRIBUTING.md) for details and/or reach out via the issue tracker.
+We are always looking for new contributors! See [CONTRIBUTING.md](https://raw.githubusercontent.com/stan-dev/bayesplot/master/.github/CONTRIBUTING.md) for details and/or reach out via the issue tracker.
 
 ### Installation
 
@@ -55,7 +55,7 @@ We are always looking for new contributors! See [CONTRIBUTING.md](https://github
 install.packages("bayesplot")
 ```
 
-* Install latest development version from GitHub (requires [devtools](https://github.com/hadley/devtools) package):
+* Install latest development version from GitHub (requires [devtools](https://raw.githubusercontent.com/hadley/devtools) package):
 
 ```r
 if (!require("devtools")) {
@@ -88,15 +88,15 @@ mcmc_areas(posterior,
            prob = 0.8) + plot_title
 ```
 
-<img src=https://github.com/stan-dev/bayesplot/blob/master/images/mcmc_areas-rstanarm.png width=50%/>
+<img src="https://raw.githubusercontent.com/stan-dev/bayesplot/master/images/mcmc_areas-rstanarm.png" width="50%">
 
 ```r
 color_scheme_set("red")
 ppc_dens_overlay(y = fit$y, 
                  yrep = posterior_predict(fit, draws = 50))
 ```
 
-<img src=https://github.com/stan-dev/bayesplot/blob/master/images/ppc_dens_overlay-rstanarm.png width=50%/>
+<img src=https://raw.githubusercontent.com/stan-dev/bayesplot/master/images/ppc_dens_overlay-rstanarm.png width=50%/>
 
 ```r
 # also works nicely with piping
@@ -110,7 +110,7 @@ fit %>%
 
 ```
 
-<img src=https://github.com/stan-dev/bayesplot/blob/master/images/ppc_stat_grouped-rstanarm.png width=50%/>
+<img src=https://raw.githubusercontent.com/stan-dev/bayesplot/master/images/ppc_stat_grouped-rstanarm.png width=50%/>
 
 ```r
 # with rstan demo model
@@ -124,7 +124,7 @@ p <- mcmc_trace(posterior2,  pars = c("mu", "tau"), n_warmup = 300,
 p + facet_text(size = 15)
 ```
 
-<img src=https://github.com/stan-dev/bayesplot/blob/master/images/mcmc_trace-rstan.png width=50% />
+<img src=https://raw.githubusercontent.com/stan-dev/bayesplot/master/images/mcmc_trace-rstan.png width=50% />
 
 ```r
 # scatter plot also showing divergences
@@ -137,15 +137,15 @@ mcmc_scatter(
 )
 ```
 
-<img src=https://github.com/stan-dev/bayesplot/blob/master/images/mcmc_scatter-rstan.png width=50% />
+<img src=https://raw.githubusercontent.com/stan-dev/bayesplot/master/images/mcmc_scatter-rstan.png width=50% />
 
 ```r
 color_scheme_set("red")
 np <- nuts_params(fit2)
 mcmc_nuts_energy(np) + ggtitle("NUTS Energy Diagnostic")
 ```
 
-<img src=https://github.com/stan-dev/bayesplot/blob/master/images/mcmc_nuts_energy-rstan.png width=50% />
+<img src=https://raw.githubusercontent.com/stan-dev/bayesplot/master/images/mcmc_nuts_energy-rstan.png width=50% />
 
 ```r
 # another example with rstanarm
@@ -168,4 +168,4 @@ ppc_intervals(
   grid_lines(color = "white")
 ```
 
-<img src=https://github.com/stan-dev/bayesplot/blob/master/images/ppc_intervals-rstanarm.png width=55% />
+<img src=https://raw.githubusercontent.com/stan-dev/bayesplot/master/images/ppc_intervals-rstanarm.png width=55% />

_pkgdown.yml

@@ -0,0 +1,131 @@
+url: https://mc-stan.org/bayesplot
+
+development:
+  mode: auto
+
+destination: "."
+
+template:
+  package: pkgdownconfig
+
+navbar:
+  title: "bayesplot"
+
+  structure:
+    left: [home, vignettes, functions, news, pkgs, stan]
+    right: [search, bluesky, forum, github, lightswitch]
+
+  components:
+    pkgs:
+      text: Other Packages
+      menu:
+        - 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
+        - text: shinystan
+          href: https://mc-stan.org/shinystan
+
+articles:
+  - title: "Getting Started"
+    desc: >
+      These vignettes provide an introduction to visualizing MCMC draws and
+      diagnostics and performing graphical posterior predictive checks using
+      the **bayesplot** package.
+    contents:
+      - plotting-mcmc-draws
+      - visual-mcmc-diagnostics
+      - graphical-ppcs
+
+reference:
+  - title: "Overview"
+    desc: >
+      Package overview
+    contents:
+      - bayesplot-package
+  - title: "Aesthetics"
+    desc: >
+      Functions for setting the color scheme and ggplot theme used
+      by **bayesplot**. (Also see the separate **ggplot helpers** section
+      below.)
+    contents:
+      - bayesplot-colors
+      - bayesplot_theme_get
+      - theme_default
+  - title: "PPC"
+    desc: >
+      Functions for carrying out a wide variety of graphical model checks
+      based on comparing observed data to draws from the posterior or prior
+      predictive distribution.
+    contents:
+      - PPC-overview
+      - starts_with("ppc")
+      - pp_check
+  - title: "PPD"
+    desc: >
+      Functions for creating graphical displays of simulated data from the
+      posterior or prior predictive distribution (PPD). These plots are essentially
+      the same as the corresponding PPC plots but without comparing to any observed
+      data.
+    contents:
+      - PPD-overview
+      - starts_with("ppd")
+  - title: "MCMC"
+    desc: >
+      Functions for creating plots of MCMC draws of model parameters and
+      general MCMC diagnostics.
+    contents:
+      - MCMC-overview
+      - MCMC-diagnostics
+      - MCMC-distributions
+      - MCMC-intervals
+      - MCMC-recover
+      - MCMC-scatterplots
+      - MCMC-parcoord
+      - MCMC-traces
+      - MCMC-combos
+  - title: "HMC/NUTS diagnostics"
+    desc: >
+      Functions for plotting diagnostics specific to Hamiltonian Monte Carlo (HMC)
+      and the No-U-Turn Sampler (NUTS). Some of the general MCMC plotting functions
+      (`mcmc_parcoord()`, `mcmc_pairs()`, `mcmc_scatter()`, `mcmc_trace()`) can also
+      show HMC/NUTS diagnostic information if optional arguments are specified,
+      but the special functions below are _only_ intended for use with HMC/NUTS.
+    contents:
+      - MCMC-nuts
+  - title: "Tidy parameter selection for MCMC plots"
+    desc: >
+      Helper functions for tidy parameter selection and examples of using
+      **bayesplot** with [**dplyr**](https://dplyr.tidyverse.org/).
+    contents:
+      - tidy-params
+  - title: "ggplot helpers"
+    desc: >
+      Convenience functions for arranging multiple plots, adding features
+      to plots, and shortcuts for modifying individual ggplot theme elements.
+    contents:
+      - bayesplot_grid
+      - bayesplot-helpers
+  - title: "Extractors"
+    desc: >
+      Functions extracting various quantities needed for plotting from different
+      types of fitted model objects.
+    contents:
+      - bayesplot-extractors
+  - title: "Miscellaneous"
+    desc: >
+      Functions for generating data for examples and listing available
+      plotting functions.
+    contents:
+      - example-data
+      - available_ppc