Merge pull request #642 from stan-dev/New-pkgdown-theme

jgabry · web-flow · commit 1b8c4cea95ad · 2025-12-10T15:03:31.000-07:00
New pkgdown theme
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -22,3 +22,4 @@ dev-notes/*
 revdep/*
 
 ^\.github$
+^_pkgdown\.yml$
diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
@@ -0,0 +1,52 @@
+# 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::., stan-dev/pkgdown-config
+
+      - name: Build site
+        run: |
+          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/NEWS.md b/NEWS.md
@@ -1,3 +1,32 @@
+# rstanarm v2.32.2
+
+* Update recommendations for responding to convergence warnings by @jgabry in https://github.com/stan-dev/rstanarm/pull/617
+* Replace Stan R Packages repo with R-Universe by @andrjohns in https://github.com/stan-dev/rstanarm/pull/624
+* Fix mistaken ')' alignment in output test by @MichaelChirico in https://github.com/stan-dev/rstanarm/pull/636
+* Default to not computing r_eff for loo by @jgabry in https://github.com/stan-dev/rstanarm/pull/638
+* migrate formula machinery from lme4 to reformulas by @bbolker in https://github.com/stan-dev/rstanarm/pull/639
+* Fix documentations to address CRAN NOTEs by @yoshidk6 in https://github.com/stan-dev/rstanarm/pull/641
+* Use vectorized abs() by @HPCurtis in https://github.com/stan-dev/rstanarm/pull/632
+* Use rstantools - Fix Build/Export Errors by @andrjohns in https://github.com/stan-dev/rstanarm/pull/625
+
+# rstanarm v2.32.1
+
+* Avoid error for 1-D unit_vector by @jgabry in https://github.com/stan-dev/rstanarm/pull/606
+* Update .set_nreps by @avehtari in https://github.com/stan-dev/rstanarm/pull/612
+* Use LTO during compilation 
+
+
+# rstanarm 2.26.1
+
+This release updates rstanarm to use the latest syntax supported by rstan. 
+
+* wells dataset wrong variable name by @storopoli in https://github.com/stan-dev/rstanarm/pull/552
+* add logo to be displayed in r-universe by @avehtari in https://github.com/stan-dev/rstanarm/pull/569
+* Fix CRAN NOTEs and failures by @andrjohns in https://github.com/stan-dev/rstanarm/pull/587
+* Implement posterior::as_draws() for rstanarm objects by @jgabry in https://github.com/stan-dev/rstanarm/pull/596
+* Array syntax by @bgoodri in https://github.com/stan-dev/rstanarm/pull/597
+
+
 # rstanarm 2.21.3
 
 ### Bug fixes
diff --git a/R/doc-rstanarm-package.R b/R/doc-rstanarm-package.R
@@ -37,7 +37,7 @@
 #'
 #' @description
 #' \if{html}{
-#'    \figure{stanlogo.png}{options: width="50" alt="https://mc-stan.org/about/logo/"}
+#'    \figure{logo.svg}{options: width="50" alt="https://mc-stan.org/about/logo/"}
 #'    \emph{Stan Development Team}
 #' }
 #'
diff --git a/R/pp_validate.R b/R/pp_validate.R
@@ -92,7 +92,7 @@
 #' }
 #' }
 #' @importFrom ggplot2 rel geom_point geom_segment scale_x_continuous element_line
-#'
+#' @keywords internal
 pp_validate <- function(object, nreps = 20, seed = 12345, ...) {
   # based on Samantha Cook's BayesValidate::validate
   quant <- function(draws) {
diff --git a/R/stan_betareg.R b/R/stan_betareg.R
@@ -17,7 +17,7 @@
 
 #' Bayesian beta regression models via Stan
 #'
-#' \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/"}}
 #' Beta regression modeling with optional prior distributions for the 
 #' coefficients, intercept, and auxiliary parameter \code{phi} (if applicable).
 #'
diff --git a/R/stan_biglm.R b/R/stan_biglm.R
@@ -17,7 +17,7 @@
 
 #' Bayesian regularized linear but big models via Stan
 #' 
-#' \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/"}}
 #' This is the same model as with \code{\link{stan_lm}} but it utilizes the
 #' output from \code{\link[biglm]{biglm}} in the \pkg{biglm} package in order to
 #' proceed when the data is too large to fit in memory.
@@ -92,4 +92,3 @@ stan_biglm <- function(biglm, xbar, ybar, s_y, ...,
                  prior_PD = prior_PD, algorithm = match.arg(algorithm), 
                  adapt_delta = adapt_delta)
 }
-
diff --git a/R/stan_clogit.R b/R/stan_clogit.R
@@ -17,7 +17,7 @@
 
 #' Conditional logistic (clogit) regression models via Stan
 #'
-#' \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/"}}
 #' A model for case-control studies with optional prior distributions for the
 #' coefficients, intercept, and auxiliary parameters.
 #'
diff --git a/R/stan_gamm4.R b/R/stan_gamm4.R
@@ -19,7 +19,7 @@
 #' Bayesian generalized linear additive models with optional group-specific
 #' terms via Stan
 #' 
-#' \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/"}}
 #' Bayesian inference for GAMMs with flexible priors.
 #' 
 #' @export
diff --git a/R/stan_glm.R b/R/stan_glm.R
@@ -17,7 +17,7 @@
 
 #' Bayesian generalized linear models via Stan
 #'
-#' \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/"}}
 #' Generalized linear modeling with optional prior distributions for the
 #' coefficients, intercept, and auxiliary parameters.
 #'
diff --git a/R/stan_glmer.R b/R/stan_glmer.R
@@ -17,7 +17,7 @@
 
 #' Bayesian generalized linear models with group-specific terms via Stan
 #' 
-#' \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/"}}
 #' Bayesian inference for GLMs with group-specific coefficients that have 
 #' unknown covariance matrices with flexible priors.
 #' 
diff --git a/R/stan_jm.R b/R/stan_jm.R
@@ -18,7 +18,7 @@
 
 #' Bayesian joint longitudinal and time-to-event models via Stan
 #' 
-#' \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/"}}
 #' Fits a shared parameter joint model for longitudinal and time-to-event 
 #' (e.g. survival) data under a Bayesian framework using Stan.
 #' 
@@ -650,4 +650,3 @@ stan_jm <- function(formulaLong, dataLong, formulaEvent, dataEvent, time_var,
   out <- stanmvreg(fit)
   return(out)
 }
-
diff --git a/R/stan_lm.R b/R/stan_lm.R
@@ -17,7 +17,7 @@
 
 #' Bayesian regularized linear models via Stan
 #' 
-#' \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/"}}
 #' Bayesian inference for linear modeling with regularizing priors on the model
 #' parameters that are driven by prior beliefs about \eqn{R^2}, the proportion
 #' of variance in the outcome attributable to the predictors. See
diff --git a/R/stan_mvmer.R b/R/stan_mvmer.R
@@ -19,7 +19,7 @@
 #' Bayesian multivariate generalized linear models with correlated 
 #' group-specific terms via Stan
 #' 
-#' \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/"}}
 #' Bayesian inference for multivariate GLMs with group-specific coefficients 
 #' that are assumed to be correlated across the GLM submodels.
 #' 
@@ -209,4 +209,3 @@ stan_mvmer <- function(formula, data, family = gaussian, weights,
   out <- stanmvreg(fit)
   return(out)
 }
-
diff --git a/R/stan_nlmer.R b/R/stan_nlmer.R
@@ -17,7 +17,7 @@
 
 #' Bayesian nonlinear models with group-specific terms via Stan
 #' 
-#' \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/"}}
 #' Bayesian inference for NLMMs with group-specific coefficients that have 
 #' unknown covariance matrices with flexible priors.
 #'
diff --git a/R/stan_polr.R b/R/stan_polr.R
@@ -18,7 +18,7 @@
 
 #' Bayesian ordinal regression models via Stan
 #'
-#' \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/"}}
 #' Bayesian inference for ordinal (or binary) regression models under a
 #' proportional odds assumption.
 #'
diff --git a/R/stan_polr.fit.R b/R/stan_polr.fit.R
@@ -191,4 +191,3 @@ summarize_polr_prior <- function(prior, prior_counts, shape=NULL, rate=NULL) {
   
   return(prior_list)
 }
-
diff --git a/README.md b/README.md
@@ -1,4 +1,4 @@
-# rstanarm <img src="man/figures/stanlogo.png" align="right" width="120" />
+# rstanarm <img src="man/figures/logo.svg" align="right" width="120" />
 
 <!-- badges: start -->
 [![CRAN\_Status\_Badge](https://www.r-pkg.org/badges/version/rstanarm?color=blue)](https://cran.r-project.org/package=rstanarm)
diff --git a/_pkgdown.yml b/_pkgdown.yml
@@ -0,0 +1,107 @@
+url: https://mc-stan.org/rstanarm
+
+destination: "."
+
+development:
+  mode: auto
+
+template:
+  package: pkgdownconfig
+
+navbar:
+  title: "rstanarm"
+
+  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: rstantools
+          href: https://mc-stan.org/rstantools
+        - text: shinystan
+          href: https://mc-stan.org/shinystan
+
+articles:
+  - title: "Getting Started"
+    desc: >
+      These vignettes provide a preliminary introduction to rstanarm and 
+      discuss the prior distributions available.
+    contents:
+    - rstanarm
+    - priors
+  - title: "Modeling functions"
+    desc: >
+      These vignettes provide instructions on how to use the modeling 
+      functions in rstanarm.
+    contents:
+    - binomial
+    - count
+    - continuous
+    - aov
+    - lm
+    - betareg
+    - polr
+    - glmer
+    - jm
+  - title: "Additional tutorials on specific modeling techniques and applications"
+    desc: >
+      These vignettes provide additional tutorials on using rstanarm 
+      for specific purposes once you are comfortable using the package
+      in general.
+    contents:
+    - mrp
+    - pooling
+    - ab-testing
+
+reference:
+  - title: "About rstanarm"
+    desc: >
+      These pages provides a summary of the functionality available in rstanarm.
+    contents:
+      - rstanarm-package
+      - available-models
+      - available-algorithms
+  - title: "Fitting models"
+    desc: >
+      Functions for model fitting.
+    contents:
+      - starts_with("stan_")
+      - priors
+  - title: "Methods"
+    desc: >
+      Functions to work with fitted model objects.
+    contents:
+      - stanreg-objects
+      - ends_with("stanreg")
+      - starts_with("posterior_")
+      - ps_check
+      - ends_with("stanmvreg")
+      - ends_with("stanjm")
+  - title: "Additional documentation"
+    desc: >
+      Misc. other help pages.
+    contents:
+      - rstanarm-datasets
+      - example_model
+      - example_jm
+      - stanreg_list
+      - adapt_delta
+      - QR-argument
+      - neg_binomial_2
+      - rstanarm-deprecated
+      - logit
diff --git a/man/figures/logo.svg b/man/figures/logo.svg
diff --git a/man/figures/stanlogo.png b/man/figures/stanlogo.png
diff --git a/man/pp_validate.Rd b/man/pp_validate.Rd
diff --git a/man/rstanarm-datasets.Rd b/man/rstanarm-datasets.Rd
diff --git a/man/rstanarm-package.Rd b/man/rstanarm-package.Rd
diff --git a/vignettes/lm.Rmd b/vignettes/lm.Rmd

Original file line number	Diff line number	Diff line change
`@@ -22,3 +22,4 @@ dev-notes/*`
`22`	`22`	`revdep/*`
`23`	`23`
`24`	`24`	`^\.github$`
	`25`	`+^_pkgdown\.yml$`