Merge pull request #25 from R-Computing-Lab/dev

Add between-family and faster regressions

Author: smasongarrison

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

@@ -0,0 +1,54 @@
+on:
+  push:
+    branches: [dev]
+    paths:
+      - '**.Rmd'
+      - '**.Rd'
+      - '**.R'
+  pull_request:
+    branches: [dev]
+
+name: Dev Branch
+
+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', rtools: ''}
+          - {os: windows-latest, r: 'release', rtools: '42'}
+          - {os: ubuntu-latest, r: 'devel', rtools: '', http-user-agent: 'release'}
+          - {os: ubuntu-latest, r: 'release', rtools: ''}
+          - {os: ubuntu-latest, r: 'oldrel-1', rtools: ''}
+
+    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 }}
+          rtools-version: ${{ matrix.config.rtools }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          cache-version: 3
+          extra-packages: |
+            any::rcmdcheck
+          upgrade: 'TRUE'
+          needs: check
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true

.github/workflows/codecov.yaml

@@ -0,0 +1,36 @@
+# For more configuration details:
+# https://docs.codecov.com/docs/codecov-yaml
+
+# Check if this file is valid by running in bash:
+# curl -X POST --data-binary @.codecov.yml https://codecov.io/validate
+
+# Settings related to codecov job
+codecov:
+  require_ci_to_pass: yes  # Only report if CI runs successfully
+  notify:
+    wait_for_ci: yes       # Wait for other jobs to finish
+    manual_trigger: true   # Notify when manually triggered
+
+# Settings related to code coverage analysis
+coverage:
+  status:
+    # Checks how the PR changes overall coverage.
+    project:
+      default:
+        # For each PR, auto compare coverage to previous commit.
+        target: auto  # Desired coverage
+        base: auto    # Compares against the base branch
+        threshold: 2% # Allows slight drops before failing
+    # Checks the relative coverage of the new PR code only.
+    patch:
+      default:
+         target: auto
+         base: auto
+         threshold: 2%
+
+# Settings related to the comment that Codecov posts on the PR
+comment:
+  layout: "diff, flags, files"
+  behavior: default             # Uses default commenting behavior
+  require_changes: false        # Always post the comment, even if coverage did not change
+  hide_project_coverage: false  # Always show coverage for both project and patch

.github/workflows/test-coverage.yaml

@@ -0,0 +1,61 @@
+# 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,dev]
+  pull_request:
+
+name: test-coverage.yaml
+
+permissions: read-all
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr, any::xml2
+          needs: coverage
+
+      - name: Test coverage
+        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 if error if not on PR, or if on PR and token is given
+          fail_ci_if_error: ${{ github.event_name != 'pull_request' || secrets.CODECOV_TOKEN }}
+          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

@@ -2,7 +2,6 @@ Package: discord
 Type: Package
 Title: Functions for Discordant Kinship Modeling
 Version: 1.2.4
-Date: 2025-04-29
 Authors@R: c(person("S. Mason", "Garrison", email = "garrissm@wfu.edu",
                   role = c("aut", "cre", "cph"),
            comment = c(ORCID = "0000-0002-4804-6003")),
@@ -29,6 +28,7 @@ Suggests:
     dplyr,
     grid,
     gridExtra,
+    ggplot2,
     janitor,
     kableExtra,
     knitr,

NAMESPACE

@@ -1,7 +1,9 @@
 # Generated by roxygen2: do not edit by hand
 
+export(discord_between_model)
 export(discord_data)
 export(discord_regression)
+export(discord_within_model)
 export(kinsim)
 importFrom(stats,formula)
 importFrom(stats,lm)

NEWS.md

@@ -1,6 +1,11 @@
+
+
 # discord 1.2.4
 * Added a new vignette demonstrating ways to visualize discordant kinship data using the `ggplot2` package. 
 * Added a new vignette demonstrating how to conduct a power analysis.
+* Vectorizing `discord_data()` to improve performance.
+* Adding tests to ensure comparability between optimized and non-optimized versions of `discord_data()`.
+* Adding `discord_between_model()` to get the between-family model
 
 # discord 1.2.3.1
 * More mild improvements to documentation