CRAN fixes and updates to CI

.Rbuildignore

@@ -1,7 +1,6 @@
 ^.*\.Rproj$
 ^\.Rhistory$
 ^\.Rproj\.user$
-^\.travis\.yml$
 ^docs$
 ^_pkgdown\.yml$
 ^README\.Rmd$
@@ -11,3 +10,5 @@
 ^LICENSE\.md$
 ^NOTES\.md$
 ^CRAN-RELEASE$
+^\.github$
+^tools$

.github/.gitignore

@@ -0,0 +1 @@
+*.html

.github/workflows/R-CMD-check.yaml

@@ -0,0 +1,50 @@
+# 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:
+  push:
+    branches: [main, master]
+  pull_request:
+
+name: R-CMD-check.yaml
+
+permissions: read-all
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macos-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v6
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

.github/workflows/pkgdown.yaml

@@ -0,0 +1,47 @@
+# 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:
+  push:
+    branches: [main, master]
+  pull_request:
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: pkgdown.yaml
+
+permissions: read-all
+
+jobs:
+  pkgdown:
+    runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v6
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::pkgdown, local::.
+          needs: website
+
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
+
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/github-pages-deploy-action@d92aa235d04922e8f08b40ce78cc5442fcfbfa2f # v4.8.0
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

.gitignore

@@ -2,3 +2,5 @@
 .Rproj.user
 .RData
 .Rhistory
+*~
+docs/

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: deconvolveR
 Title: Empirical Bayes Estimation Strategies
-Version: 1.2-1
+Version: 1.2-2
 VignetteBuilder: knitr
 Suggests: cowplot, ggplot2, knitr, rmarkdown
 Authors@R: c(person("Bradley", "Efron", role=c("aut"),
@@ -23,4 +23,4 @@ LazyData: true
 Imports:
     splines,
     stats
-RoxygenNote: 7.1.0
+Config/roxygen2/version: 8.0.0

NEWS.md

@@ -1,3 +1,11 @@
+# deconvolveR 1.2-2
+
+- Fixed documentation markup flagged by CRAN (`checkRd` "Lost braces"
+  NOTE in `deconv.Rd`)
+- Switched CI from Travis to GitHub Actions; pkgdown site is now
+  built and deployed via GitHub Actions
+- Added a package logo and updated badges
+
 # deconvolveR 1.2-1
 
 - Fixed URL per CRAN

R/deconv.R

@@ -45,9 +45,9 @@
 #'     where it was referred to as \eqn{R(\alpha)}} \item{cov}{the
 #'     covariance matrix for the mle} \item{cov.g}{the covariance
 #'     matrix for the \eqn{g}} \item{stats}{an m by 6 or 7 matrix
-#'     containing columns for \eqn{theta}, \eqn{g}, \eqn{\tilde{g}}
+#'     containing columns for \eqn{\theta}, \eqn{g}, \eqn{\tilde{g}}
 #'     which is \eqn{g} with thinning correction applied and named
-#'     \code{tg}, std. error of \eqn{g}, \eqn{G} (the cdf of {g}),
+#'     \code{tg}, std. error of \eqn{g}, \eqn{G} (the cdf of \eqn{g}),
 #'     std. error of \eqn{G}, and the bias of \eqn{g}}
 #'     \item{loglik}{the negative log-likelihood function for the data
 #'     taking a \eqn{p}-vector argument} \item{statsFunction}{a
@@ -56,7 +56,7 @@
 #' @section Details:
 #' The data \code{X} is always required with two exceptions. In the Poisson case,
 #' \code{y} alone may be specified and \code{X} omitted, in which case the sample space of
-#' the observations $\eqn{X}$ is assumed to be 1, 2, .., \code{length(y)}. The second exception is
+#' the observations \eqn{X} is assumed to be 1, 2, .., \code{length(y)}. The second exception is
 #' for experimentation with other exponential families besides the three implemented here:
 #' \code{y}, \code{P} and \code{Q} can be specified together.
 #'

R/deconvolveR-package.R

@@ -5,9 +5,6 @@
 #' paper reference below and this package includes a vignette
 #' containing a number of examples.
 #'
-#' @docType package
-#' @name deconvolveR-package
-#'
 #' @references Bradley Efron. Empirical Bayes Deconvolution
 #'     Estimates. Biometrika 103(1), 1-20, ISSN
 #'     0006-3444. doi:10.1093/biomet/asv068.
@@ -19,7 +16,7 @@
 #'     Efron. deconvolveR: A G-Modeling Program for Deconvolution and
 #'     Empirical Bayes Estimation. doi:10.18637/jss.v094.i11
 #'
-NULL
+"_PACKAGE"
 
 #' Shakespeare word counts in the entire canon: 14,376 distinct words
 #' appeared exactly once, 4343 words appeared twice etc.

README.md

@@ -1,9 +1,13 @@
-Empirical Bayes Deconvolution
-=============================
+# deconvolveR <img src="man/figures/logo.png" align="right" height="139" alt="deconvolveR hex logo" />
 
-[![Travis-CI Build
-Status](https://travis-ci.org/bnaras/deconvolveR.svg?branch=master)](https://travis-ci.org/bnaras/deconvolveR)
-[![CRAN_Status_Badge](https://www.r-pkg.org/badges/version/deconvolveR)](https://cran.r-project.org/package=deconvolveR)
+<!-- badges: start -->
+[![R-CMD-check](https://github.com/bnaras/deconvolveR/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/bnaras/deconvolveR/actions/workflows/R-CMD-check.yaml)
+[![CRAN status](https://www.r-pkg.org/badges/version/deconvolveR)](https://cran.r-project.org/package=deconvolveR)
+[![Monthly downloads](https://cranlogs.r-pkg.org/badges/deconvolveR)](https://cran.r-project.org/package=deconvolveR)
+[![Total downloads](https://cranlogs.r-pkg.org/badges/grand-total/deconvolveR)](https://cran.r-project.org/package=deconvolveR)
+<!-- badges: end -->
+
+## Empirical Bayes Deconvolution
 
 An unknown prior density $g(\theta)$ has yielded (unobservable)
 $\Theta_1, \Theta_2,\ldots,\Theta_N$, and each $\Theta_i$ produces an

_pkgdown.yml

@@ -1,7 +1,11 @@
-authors:
+url: https://bnaras.github.io/deconvolveR/
 
-  Balasubramanian Narasimhan:
-    href: https://web.stanford.edu/~naras
+template:
+  bootstrap: 5
+  math-rendering: mathjax
 
+authors:
+  Balasubramanian Narasimhan:
+    href: https://naras.su.domains
   Bradley Efron:
-    href: http://statweb.stanford.edu/~ckirby/brad/
+    href: https://efron.ckirby.su.domains/