upd

Author: explodecomputer

.Rbuildignore

@@ -1 +1,2 @@
 ^LICENSE\.md$
+^\.github$

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

@@ -0,0 +1,51 @@
+# 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@v4
+
+      - 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
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

DESCRIPTION

@@ -10,3 +10,6 @@ License: MIT + file LICENSE
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.3
+Suggests: 
+    testthat (>= 3.0.0)
+Config/testthat/edition: 3

README.md

@@ -0,0 +1,17 @@
+
+# rhds.rpackage
+
+<!-- badges: start -->
+[![R-CMD-check](https://github.com/MRCIEU/rhds.rpackage/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/MRCIEU/rhds.rpackage/actions/workflows/R-CMD-check.yaml)
+<!-- badges: end -->
+
+Example package for the RHDS short course
+
+## Installation
+
+You can install the development version of rhds.rpackage from [GitHub](https://github.com/) with:
+
+``` r
+remotes::install_github("MRCIEU/rhds.rpackage")
+```
+

tests/testthat.R

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+# This file is part of the standard setup for testthat.
+# It is recommended that you do not modify it.
+#
+# Where should you do additional test configuration?
+# Learn more about the roles of various files in:
+# * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
+# * https://testthat.r-lib.org/articles/special-files.html
+
+library(testthat)
+library(rhds.rpackage)
+
+test_check("rhds.rpackage")

tests/testthat/test_extract.r

@@ -0,0 +1,18 @@
+library(testthat)
+
+test_that("extract.participant extracts participant ID correctly", {
+  # Test basic TCGA ID format
+  expect_equal(extract.participant("TCGA-AB-1234-01A"), "1234")
+  
+  # Test with different project code
+  expect_equal(extract.participant("TCGA-XY-5678-11B"), "5678")
+  
+  # Test with longer suffix
+  expect_equal(extract.participant("TCGA-CD-9999-01A-01D-1234-08"), "9999")
+  
+  # Test with minimal valid format
+  expect_equal(extract.participant("TCGA-AB-123-01"), "123")
+  
+  # Test that non-matching format returns original string
+  expect_equal(extract.participant("invalid-id"), "invalid-id")
+})