Merge pull request #64 from Lifebrain/doctype

Doctype

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

@@ -1,13 +1,15 @@
-# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# 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, develop]
+    branches: [main, master]
   pull_request:
-    branches: [main, master, develop]
+    branches: [main, master]
 
 name: R-CMD-check
 
+permissions: read-all
+
 jobs:
   R-CMD-check:
     runs-on: ${{ matrix.config.os }}
@@ -18,7 +20,7 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: macOS-latest,   r: 'release'}
+          - {os: macos-latest,   r: 'release'}
           - {os: windows-latest, r: 'release'}
           - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
           - {os: ubuntu-latest,   r: 'release'}
@@ -29,18 +31,22 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
-      - uses: r-lib/actions/setup-pandoc@v1
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
           http-user-agent: ${{ matrix.config.http-user-agent }}
           use-public-rspm: true
 
-      - uses: r-lib/actions/setup-r-dependencies@v1
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: rcmdcheck
+          extra-packages: any::rcmdcheck
+          needs: check
 
-      - uses: r-lib/actions/check-r-package@v1
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

.github/workflows/test-coverage.yaml

@@ -1,30 +1,61 @@
-# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# 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, develop]
+    branches: [main, master]
   pull_request:
-    branches: [main, master, develop]
+    branches: [main, master]
 
 name: test-coverage
 
+permissions: read-all
+
 jobs:
   test-coverage:
     runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
 
-      - uses: r-lib/actions/setup-r-dependencies@v1
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: covr
+          extra-packages: any::covr, any::xml2
+          needs: coverage
 
       - name: Test coverage
-        run: covr::codecov()
+        run: |
+          cov <- covr::package_coverage(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
+          )
+          covr::to_cobertura(cov)
         shell: Rscript {0}
+
+      - uses: codecov/codecov-action@v4
+        with:
+          fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }}
+          file: ./cobertura.xml
+          plugin: noop
+          disable_search: true
+          token: ${{ secrets.CODECOV_TOKEN }}
+
+      - name: Show testthat output
+        if: always()
+        run: |
+          ## --------------------------------------------------------------------
+          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package

DESCRIPTION

@@ -31,7 +31,7 @@ Imports:
     ggplot2,
     metafor,
     rlang
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Suggests: 
     roxygen2,
     knitr,

R/metagam_package.R

@@ -14,8 +14,7 @@
 #'   \code{\link{plot_heterogeneity}} can be used to study the meta-analytic fit
 #'   computed by \code{\link{strip_rawdata}}.
 #'
-#' @docType package
 #' @name metagam-package
 #'
 #' @importFrom rlang .data
-NULL
+"_PACKAGE"

README.Rmd

@@ -21,6 +21,7 @@ devtools::load_all(".")
 [![R-CMD-check](https://github.com/Lifebrain/metagam/workflows/R-CMD-check/badge.svg)](https://github.com/Lifebrain/metagam/actions)
 [![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
 [![Codecov test coverage](https://codecov.io/gh/Lifebrain/metagam/branch/master/graph/badge.svg)](https://app.codecov.io/gh/Lifebrain/metagam?branch=master)
+[![R-CMD-check](https://github.com/Lifebrain/metagam/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/Lifebrain/metagam/actions/workflows/R-CMD-check.yaml)
 <!-- badges: end -->
 
 

README.md

@@ -12,6 +12,7 @@ status](https://www.r-pkg.org/badges/version/metagam)](https://CRAN.R-project.or
 experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
 [![Codecov test
 coverage](https://codecov.io/gh/Lifebrain/metagam/branch/master/graph/badge.svg)](https://app.codecov.io/gh/Lifebrain/metagam?branch=master)
+[![R-CMD-check](https://github.com/Lifebrain/metagam/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/Lifebrain/metagam/actions/workflows/R-CMD-check.yaml)
 <!-- badges: end -->
 
 ## Overview
@@ -31,10 +32,10 @@ Zanobetti (2000) and Crippa, Thomas, and Orsini (2018).
 Currently, GAMs objects created with the following functions are
 supported:
 
--   From package [mgcv](https://cran.r-project.org/package=mgcv):
-    `bam()`, `gam()` and `gamm()`.
--   From package [gamm4](https://cran.r-project.org/package=gamm4):
-    `gamm4()`.
+- From package [mgcv](https://cran.r-project.org/package=mgcv): `bam()`,
+  `gam()` and `gamm()`.
+- From package [gamm4](https://cran.r-project.org/package=gamm4):
+  `gamm4()`.
 
 This package is under development, so changes to the interface can be
 expected. Suggestions for improvements and bug reports are warmly
@@ -65,7 +66,7 @@ remotes::install_github("lifebrain/metagam")
 library("metagam")
 library("mgcv")
 #> Loading required package: nlme
-#> This is mgcv 1.8-38. For overview type 'help("mgcv-package")'.
+#> This is mgcv 1.9-1. For overview type 'help("mgcv-package")'.
 ```
 
 Simulate three datasets and fit a GAM to each of them. Then use
@@ -91,7 +92,7 @@ participant data. We can then meta-analyze them using `metagam()`.
 ``` r
 meta_analysis <- metagam(models)
 summary(meta_analysis)
-#> Meta-analysis of GAMs from 3 cohorts, using method FE.
+#> Meta-analysis of GAMs from  cohorts, using method FE.
 #> 
 #> Smooth terms analyzed: s(x2).
 ```
@@ -108,7 +109,8 @@ By contributing to this project, you agree to abide by its terms.
 
 ## References
 
-<div id="refs" class="references csl-bib-body hanging-indent">
+<div id="refs" class="references csl-bib-body hanging-indent"
+entry-spacing="0">
 
 <div id="ref-Crippa2018" class="csl-entry">