diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
new file mode 100644
index 0000000..37084ab
--- /dev/null
+++ b/.github/workflows/pkgdown.yaml
@@ -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
+ with:
+ clean: false
+ branch: gh-pages
+ folder: docs
diff --git a/DESCRIPTION b/DESCRIPTION
index 7d27a6f..2a9d70f 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -53,6 +53,6 @@ Suggests:
roxygen2 (>= 6.0.1),
rmarkdown,
rstudioapi
-RoxygenNote: 7.3.2
+RoxygenNote: 7.3.3
VignetteBuilder: knitr
Roxygen: list(markdown = TRUE)
diff --git a/R/rstan_create_package.R b/R/rstan_create_package.R
index f3a9236..caa15c1 100644
--- a/R/rstan_create_package.R
+++ b/R/rstan_create_package.R
@@ -21,7 +21,7 @@
#' @aliases rstan_package_skeleton
#'
#' @description
-#' \if{html}{\figure{stanlogo.png}{options: width="25" alt="https://mc-stan.org/about/logo/"}}
+#' \if{html}{\figure{logo.svg}{options: width="25" alt="https://mc-stan.org/about/logo/"}}
#' The `rstan_create_package()` function helps get you started developing a
#' new \R package that interfaces with Stan via the \pkg{rstan} package. First
#' the basic package structure is set up via [usethis::create_package()].
diff --git a/R/rstantools-package.R b/R/rstantools-package.R
index c347516..130e549 100644
--- a/R/rstantools-package.R
+++ b/R/rstantools-package.R
@@ -5,7 +5,7 @@
#'
#' @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*
#'
#' The \pkg{rstantools} package provides various tools for developers of \R
diff --git a/README.md b/README.md
index ef5e8aa..e5a2fe5 100644
--- a/README.md
+++ b/README.md
@@ -1,4 +1,4 @@
-# rstantools 
+# rstantools 
[](https://cran.r-project.org/web/packages/rstantools)
diff --git a/_pkgdown.yml b/_pkgdown.yml
new file mode 100644
index 0000000..2c57c4d
--- /dev/null
+++ b/_pkgdown.yml
@@ -0,0 +1,83 @@
+url: https://mc-stan.org/rstantools
+
+destination: "."
+
+template:
+ package: pkgdownconfig
+
+development:
+ mode: auto
+
+navbar:
+ title: "rstantools"
+
+ 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: shinystan
+ href: https://mc-stan.org/shinystan
+
+articles:
+ - title: "Recommendations for R package development with Stan"
+ desc: >
+ This vignette provides many recommendations for developers interested in
+ creating an R package that interface with Stan. Topics include
+ development best practices, precompiling Stan programs, R code and
+ documentation, and more.
+ contents:
+ - developer-guidelines
+ - title: "Step-by-step guide"
+ desc: >
+ This vignette walks through the steps required to set up a package with
+ a precompiled Stan model, from creating the initial package structure to
+ adding the precompiled Stan program and writing the R function that users
+ will call to fit the model.
+ contents:
+ - minimal-rstan-package
+
+reference:
+ - title: "Package structure"
+ desc: >
+ Creating the basic structure of a Stan-based R package or add
+ Stan programs to an existing package.
+ contents:
+ - rstantools-package
+ - rstan_create_package
+ - use_rstan
+ - rstan_config
+ - rstantools_load_code
+ - title: "Generics"
+ desc: >
+ S3 generics (and some default methods) for adding functionality
+ to your package using the same naming conventions as **rstanarm**
+ and other Stan-based R packages.
+ contents:
+ - bayes_R2
+ - log_lik
+ - loo-prediction
+ - posterior_interval
+ - posterior_epred
+ - posterior_linpred
+ - posterior_predict
+ - predictive_error
+ - predictive_interval
+ - prior_summary
diff --git a/man/figures/logo.svg b/man/figures/logo.svg
index b4c09fc..496f040 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 4a4f06a..0000000
Binary files a/man/figures/stanlogo.png and /dev/null differ
diff --git a/man/rstan_create_package.Rd b/man/rstan_create_package.Rd
index a3a987a..d7bfeb6 100644
--- a/man/rstan_create_package.Rd
+++ b/man/rstan_create_package.Rd
@@ -48,7 +48,7 @@ file. If \code{TRUE} (the default) adds the \verb{GPL (>= 3)} license (see
whenever the package gets installed (see \strong{Details}). Defaults to \code{TRUE}.}
}
\description{
-\if{html}{\figure{stanlogo.png}{options: width="25" alt="https://mc-stan.org/about/logo/"}}
+\if{html}{\figure{logo.svg}{options: width="25" alt="https://mc-stan.org/about/logo/"}}
The \code{rstan_create_package()} function helps get you started developing a
new \R package that interfaces with Stan via the \pkg{rstan} package. First
the basic package structure is set up via \code{\link[usethis:create_package]{usethis::create_package()}}.
diff --git a/man/rstantools-package.Rd b/man/rstantools-package.Rd
index 7b6a5b2..327d82d 100644
--- a/man/rstantools-package.Rd
+++ b/man/rstantools-package.Rd
@@ -7,7 +7,7 @@
\title{Tools for Developing \R Packages Interfacing with Stan}
\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}
The \pkg{rstantools} package provides various tools for developers of \R
@@ -40,7 +40,7 @@ Useful links:
}
\author{
-\strong{Maintainer}: Jonah Gabry \email{jsg2201@columbia.edu}
+\strong{Maintainer}: Jonah Gabry \email{jgabry@gmail.com}
Authors:
\itemize{
diff --git a/vignettes/minimal-rstan-package.Rmd b/vignettes/minimal-rstan-package.Rmd
index 050b451..e0fa99e 100644
--- a/vignettes/minimal-rstan-package.Rmd
+++ b/vignettes/minimal-rstan-package.Rmd
@@ -8,7 +8,7 @@ output:
params:
EVAL: !r identical(Sys.getenv("NOT_CRAN"), "true")
vignette: >
- %\VignetteIndexEntry{Step by step guide}
+ %\VignetteIndexEntry{Step by step guide for creating a package that depends on RStan}
%\VignetteEngine{knitr::rmarkdown}
%\VignetteEncoding{UTF-8}
---
@@ -235,13 +235,14 @@ information about the package.
With __roxygen__ documentation enabled, we need to generate the documentation
for `lm_stan` and update the `NAMESPACE` so the function is exported, i.e.,
-available to users when the package is installed. This can be done with the
+available to users when the package is installed. This can be done with the
function `roxygen2::roxygenize()`, which needs to be called twice initially.
```{r, eval = FALSE}
try(roxygen2::roxygenize(load_code = rstantools_load_code), silent = TRUE)
roxygen2::roxygenize()
```
+
```{r, echo=FALSE, results="hide"}
try(roxygen2::roxygenize(PATH, load_code = rstantools_load_code), silent = TRUE)
roxygen2::roxygenize(PATH)