fix github actions

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

@@ -0,0 +1,49 @@
+# 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:
+ branches: [main, master]
+
+name: R-CMD-check
+
+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@v3
+
+ - 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 }}
+ use-public-rspm: true
+
+ - 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

.github/workflows/test-coverage.yaml

@@ -1,48 +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
+ branches: [main, master]
  pull_request:
- branches:
- - main
- - master
+ branches: [main, master]
 
 name: test-coverage
 
 jobs:
  test-coverage:
- runs-on: macOS-latest
+ runs-on: ubuntu-latest
  env:
  GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
  steps:
- - uses: actions/checkout@v2
+ - uses: actions/checkout@v3
 
- - uses: r-lib/actions/setup-r@v1
+ - uses: r-lib/actions/setup-r@v2
+ with:
+ use-public-rspm: true
 
- - uses: r-lib/actions/setup-pandoc@v1
+ - uses: r-lib/actions/setup-r-dependencies@v2
+ with:
+ extra-packages: any::covr
+ needs: coverage
 
- - name: Query dependencies
+ - name: Test coverage
  run: |
- install.packages('remotes')
- saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
- writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
+ covr::codecov(
+ quiet = FALSE,
+ clean = FALSE,
+ install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
+ )
  shell: Rscript {0}
 
- - name: Restore R package cache
- uses: actions/cache@v2
- with:
- path: ${{ env.R_LIBS_USER }}
- key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
- restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
-
- - name: Install dependencies
+ - name: Show testthat output
+ if: always()
  run: |
- install.packages(c("remotes"))
- remotes::install_deps(dependencies = TRUE)
- remotes::install_cran("covr")
- shell: Rscript {0}
+ ## --------------------------------------------------------------------
+ find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
+ shell: bash
 
- - name: Test coverage
- run: covr::codecov()
- shell: Rscript {0}
+ - name: Upload test results
+ if: failure()
+ uses: actions/upload-artifact@v3
+ with:
+ name: coverage-test-failures
+ path: ${{ runner.temp }}/package

README.Rmd

@@ -19,6 +19,7 @@ knitr::opts_chunk$set(
 [![R-CMD-check](https://github.com/imbi-heidelberg/blindrecalc/workflows/R-CMD-check/badge.svg)](https://github.com/imbi-heidelberg/blindrecalc/actions)
 [![Codecov test coverage](https://codecov.io/gh/imbi-heidelberg/blindrecalc/branch/master/graph/badge.svg)](https://app.codecov.io/gh/imbi-heidelberg/blindrecalc?branch=master)
 [![CRAN status](https://www.r-pkg.org/badges/version/blindrecalc)](https://cran.r-project.org/package=blindrecalc)
+[![R-CMD-check](https://github.com/imbi-heidelberg/blindrecalc/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/imbi-heidelberg/blindrecalc/actions/workflows/R-CMD-check.yaml)
 <!-- badges: end -->
 
 # blindrecalc

README.md

@@ -7,6 +7,7 @@
 coverage](https://codecov.io/gh/imbi-heidelberg/blindrecalc/branch/master/graph/badge.svg)](https://app.codecov.io/gh/imbi-heidelberg/blindrecalc?branch=master)
 [![CRAN
 status](https://www.r-pkg.org/badges/version/blindrecalc)](https://cran.r-project.org/package=blindrecalc)
+[![R-CMD-check](https://github.com/imbi-heidelberg/blindrecalc/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/imbi-heidelberg/blindrecalc/actions/workflows/R-CMD-check.yaml)
 <!-- badges: end -->
 
 # blindrecalc
@@ -65,7 +66,7 @@ size recalculation, use `toer`:
 
 ``` r
 toer(design, n1 = c(30, 60, 90), nuisance = 10, recalculation = TRUE)
-#> [1] 0.0263 0.0271 0.0242
+#> [1] 0.0270 0.0249 0.0230
 ```
 
 `n1` refers to the sample size of the internal pilot study
@@ -76,18 +77,23 @@ To compute the power of the design, use `pow`:
 
 ``` r
 pow(design, n1 = c(30, 60, 90), nuisance = 10, recalculation = TRUE)
-#> [1] 0.7979 0.7938 0.8067
+#> [1] 0.7869 0.7975 0.7999
 ```
 
 To calculate the distribution of the total sample sizes use `n_dist`:
 
 ``` r
 n_dist(design, n1 = c(30, 60, 90), nuisance = 10)
 #> n_1 = 30 n_1 = 60 n_1 = 90 
-#> Min. : 40.0 Min. : 64.0 Min. : 90.0 
-#> 1st Qu.:109.0 1st Qu.:117.0 1st Qu.:120.0 
-#> Median :131.0 Median :133.0 Median :133.0 
-#> Mean :134.2 Mean :133.9 Mean :134.1 
-#> 3rd Qu.:156.0 3rd Qu.:149.0 3rd Qu.:147.0 
-#> Max. :305.0 Max. :251.0 Max. :219.0
+#> Min. : 30.0 Min. : 62.0 Min. : 90.0 
+#> 1st Qu.:110.0 1st Qu.:117.0 1st Qu.:120.0 
+#> Median :132.0 Median :132.0 Median :133.0 
+#> Mean :134.8 Mean :134.2 Mean :133.8 
+#> 3rd Qu.:157.0 3rd Qu.:150.0 3rd Qu.:147.0 
+#> Max. :297.0 Max. :242.0 Max. :219.0
 ```
+
+## Reference
+
+A paper describing blindrecalc can be found
+[here](https://journal.r-project.org/articles/RJ-2022-001/).