kestrel99 · billdenney · May 2, 2026 · May 2, 2026 · May 2, 2026 · May 2, 2026
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -12,3 +12,4 @@ pmxTools.Rproj
 ^docs$
 ^pkgdown$
 ^\.github$
+^codecov\.yml$
diff --git a/.github/workflows/R-CMD-check.yaml b/.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")'
diff --git a/.github/workflows/blank.yml b/.github/workflows/blank.yml
diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
@@ -4,12 +4,13 @@ on:
   push:
     branches: [main, master]
   pull_request:
-    branches: [main, master]
   release:
     types: [published]
   workflow_dispatch:
 
-name: pkgdown
+name: pkgdown.yaml
+
+permissions: read-all
 
 jobs:
   pkgdown:
@@ -19,14 +20,14 @@ jobs:
       group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v6
 
       - uses: r-lib/actions/setup-pandoc@v2
 
       - uses: r-lib/actions/setup-r@v2
-        with:
-          use-public-rspm: true
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
@@ -39,7 +40,7 @@ jobs:
 
       - name: Deploy to GitHub pages 🚀
         if: github.event_name != 'pull_request'
-        uses: JamesIves/github-pages-deploy-action@v4.4.1
+        uses: JamesIves/github-pages-deploy-action@d92aa235d04922e8f08b40ce78cc5442fcfbfa2f # v4.8.0
         with:
           clean: false
           branch: gh-pages

diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
@@ -0,0 +1,60 @@
+# 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: test-coverage.yaml
+
+permissions: read-all
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v6
+
+      - uses: r-lib/actions/setup-r@v2
+
+      - 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")
+          )
+          print(cov)
+          covr::to_cobertura(cov)
+        shell: Rscript {0}
+
+      - uses: codecov/codecov-action@57e3a136b779b570ffcdbf80b3bdc90e7fab3de2 # v6
+        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 }}
+          files: ./cobertura.xml
+          plugins: 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@v7
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package
diff --git a/.travis.yml b/.travis.yml
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -13,10 +13,10 @@ Authors@R: c(person("Justin", "Wilkins", email = "justin.wilkins@occams.com", ro
              person("John", "Johnson", email="johndjohnson@gmail.com", role="ctb"))
 Maintainer: Justin Wilkins <justin.wilkins@occams.com>
 Contact: Justin Wilkins <justin.wilkins@occams.com>
-Description: Pharmacometric tools for common data analytical tasks; closed-form solutions for calculating concentrations at given 
-    times after dosing based on compartmental PK models (1-compartment, 2-compartment and 3-compartment, covering infusions, zero- 
-    and first-order absorption, and lag times, after single doses and at steady state, per Bertrand & Mentre (2008) 
-    <https://www.facm.ucl.ac.be/cooperation/Vietnam/WBI-Vietnam-October-2011/Modelling/Monolix32_PKPD_library.pdf>); parametric simulation from NONMEM-generated parameter estimates 
+Description: Pharmacometric tools for common data analytical tasks; closed-form solutions for calculating concentrations at given
+    times after dosing based on compartmental PK models (1-compartment, 2-compartment and 3-compartment, covering infusions, zero-
+    and first-order absorption, and lag times, after single doses and at steady state, per Bertrand & Mentre (2008)
+    <https://www.facm.ucl.ac.be/cooperation/Vietnam/WBI-Vietnam-October-2011/Modelling/Monolix32_PKPD_library.pdf>); parametric simulation from NONMEM-generated parameter estimates
     and other output; and parsing, tabulating and plotting results generated by Perl-speaks-NONMEM (PsN).
 License: GPL-2
 URL: https://github.com/kestrel99/pmxTools,
@@ -40,9 +40,9 @@ Imports:
     magrittr,
     data.tree
 Depends:
-    R (>= 4.00),
+    R (>= 4.0.0),
     patchwork
-Suggests: 
+Suggests:
     testthat,
     vdiffr,
     knitr,

diff --git a/README.md b/README.md
@@ -1,21 +1,24 @@
 # pmxTools
 Pharmacometric Tools for Modeling &amp; Simulation
 
-[![Build Status](https://app.travis-ci.com/kestrel99/pmxTools.png?branch=master)](https://app.travis-ci.com/kestrel99/pmxTools)
+<!-- badges: start -->
+[![R-CMD-check](https://github.com/kestrel99/pmxTools/actions/workflows/R-CMD-check.yaml/badge.svghttps://github.com/kestrel99/pmxTools/actions/workflows/R-CMD-check.yaml/badge.svghttps://github.com/kestrel99/pmxTools/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/kestrel99/pmxTools/actions/workflows/R-CMD-check.yaml)
 [![contributions welcome](https://img.shields.io/badge/contributions-welcome-brightgreen.svg?style=flat)](https://github.com/kestrel99/pmxTools/issues)
 [![](https://www.r-pkg.org/badges/version/pmxTools?color=green)](https://cran.r-project.org/package=pmxTools)
 [![](http://cranlogs.r-pkg.org/badges/grand-total/pmxTools?color=blue)](https://cran.r-project.org/package=pmxTools)
+[![Codecov test coverage](https://codecov.io/gh/kestrel99/pmxTools/graph/badge.svg)](https://app.codecov.io/gh/kestrel99/pmxTools)
+<!-- badges: end -->
 
 <!--[![HitCount](http://hits.dwyl.io/kestrel99/pmxTools.svg)](http://hits.dwyl.io/kestrel99/pmxTools)-->
 
 Developed by **Justin Wilkins**, **Bill Denney** and **Rik Schoemaker**, with contributions from a host of others.
 
-Pharmacometric tools for common data analytical tasks; closed-form solutions for calculating concentrations at given 
-    times after dosing based on compartmental PK models (1-compartment, 2-compartment and 3-compartment, covering infusions, zero- 
-    and first-order absorption, and lag times, after single doses and at steady state, per Bertrand & Mentre (2008) 
-    <https://www.facm.ucl.ac.be/cooperation/Vietnam/WBI-Vietnam-October-2011/Modelling/Monolix32_PKPD_library.pdf>); parametric simulation from NONMEM-generated parameter estimates 
+Pharmacometric tools for common data analytical tasks; closed-form solutions for calculating concentrations at given
+    times after dosing based on compartmental PK models (1-compartment, 2-compartment and 3-compartment, covering infusions, zero-
+    and first-order absorption, and lag times, after single doses and at steady state, per Bertrand & Mentre (2008)
+    <https://www.facm.ucl.ac.be/cooperation/Vietnam/WBI-Vietnam-October-2011/Modelling/Monolix32_PKPD_library.pdf>); parametric simulation from NONMEM-generated parameter estimates
     and other output; and parsing, tabulating and plotting results generated by Perl-speaks-NONMEM (PsN).
-    
+
 To install:
 
 ```{r}

diff --git a/_pkgdown.yml b/_pkgdown.yml
@@ -1,6 +1,3 @@
 url: https://kestrel99.github.io/pmxTools/
 template:
   bootstrap: 5
-
-development:
-  mode: auto
diff --git a/codecov.yml b/codecov.yml
@@ -0,0 +1,14 @@
+comment: false
+
+coverage:
+  status:
+    project:
+      default:
+        target: auto
+        threshold: 1%
+        informational: true
+    patch:
+      default:
+        target: auto
+        threshold: 1%
+        informational: true