diff --git a/.Rbuildignore b/.Rbuildignore
index a91bcc13..031ffa55 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -3,7 +3,7 @@
^.*\.Rproj$
^\.Rproj\.user$
LICENSE
-^\.travis\.yml$
+^\_pkgdown\.yml$
^README\.md$
.gitignore
.git/*
diff --git a/.github/workflows/pkgdown.yml b/.github/workflows/pkgdown.yml
new file mode 100644
index 00000000..dc9cce3f
--- /dev/null
+++ b/.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/github-pages-deploy-action@v4.5.0
+ with:
+ clean: false
+ branch: gh-pages
+ folder: docs
diff --git a/R/bayesplot-package.R b/R/bayesplot-package.R
index a2d4531d..4eb23955 100644
--- a/R/bayesplot-package.R
+++ b/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*
#'
diff --git a/README.md b/README.md
index b9b878d6..db75f239 100644
--- a/README.md
+++ b/README.md
@@ -1,9 +1,9 @@
-# bayesplot 
+# bayesplot 
[](https://cran.r-project.org/web/packages/bayesplot)
[](https://cran.rstudio.com/package=bayesplot)
-[](https://github.com/stan-dev/bayesplot/actions/workflows/R-CMD-check.yaml)
+[](https://raw.githubusercontent.com/stan-dev/bayesplot/actions/workflows/R-CMD-check.yaml)
[](https://codecov.io/gh/stan-dev/bayesplot)
@@ -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")) {
@@ -88,7 +88,7 @@ mcmc_areas(posterior,
prob = 0.8) + plot_title
```
-
+
```r
color_scheme_set("red")
@@ -96,7 +96,7 @@ ppc_dens_overlay(y = fit$y,
yrep = posterior_predict(fit, draws = 50))
```
-
+
```r
# also works nicely with piping
@@ -110,7 +110,7 @@ fit %>%
```
-
+
```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)
```
-
+
```r
# scatter plot also showing divergences
@@ -137,7 +137,7 @@ mcmc_scatter(
)
```
-
+
```r
color_scheme_set("red")
@@ -145,7 +145,7 @@ np <- nuts_params(fit2)
mcmc_nuts_energy(np) + ggtitle("NUTS Energy Diagnostic")
```
-
+
```r
# another example with rstanarm
@@ -168,4 +168,4 @@ ppc_intervals(
grid_lines(color = "white")
```
-
+
diff --git a/_pkgdown.yml b/_pkgdown.yml
new file mode 100644
index 00000000..4388eb8c
--- /dev/null
+++ b/_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
diff --git a/man/bayesplot-package.Rd b/man/bayesplot-package.Rd
index ae59ee0e..5ef89271 100644
--- a/man/bayesplot-package.Rd
+++ b/man/bayesplot-package.Rd
@@ -7,7 +7,7 @@
\title{\strong{bayesplot}: Plotting for Bayesian Models}
\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}
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/vignettes/graphical-ppcs.Rmd b/vignettes/graphical-ppcs.Rmd
index 5e866dd4..db649f42 100644
--- a/vignettes/graphical-ppcs.Rmd
+++ b/vignettes/graphical-ppcs.Rmd
@@ -19,6 +19,7 @@ vignette: >
```{r pkgs, include=FALSE}
library("ggplot2")
library("rstanarm")
+bayesplot_theme_set()
set.seed(840)
```
diff --git a/vignettes/plotting-mcmc-draws.Rmd b/vignettes/plotting-mcmc-draws.Rmd
index 38aa1081..0ed21f62 100644
--- a/vignettes/plotting-mcmc-draws.Rmd
+++ b/vignettes/plotting-mcmc-draws.Rmd
@@ -19,6 +19,7 @@ vignette: >
```{r pkgs, include=FALSE}
library("ggplot2")
library("rstanarm")
+bayesplot_theme_set()
```