setup github actions

.Rbuildignore

@@ -7,3 +7,4 @@ R/.create_metrics.R
 ^Meta$
 ^doc/
 ^doc$
+^\.github$

.github/.gitignore

@@ -0,0 +1 @@
+*.html

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

@@ -0,0 +1,58 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/master/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@v2
+
+      - uses: r-lib/actions/setup-pandoc@v1
+
+      - uses: r-lib/actions/setup-r@v1
+        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
+        with:
+          extra-packages: rcmdcheck
+
+      - uses: r-lib/actions/check-r-package@v1
+
+      - name: Show testthat output
+        if: always()
+        run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload check results
+        if: failure()
+        uses: actions/upload-artifact@main
+        with:
+          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
+          path: check

.github/workflows/test-coverage.yaml

@@ -0,0 +1,30 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/master/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: test-coverage
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@v1
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v1
+        with:
+          extra-packages: covr
+
+      - name: Test coverage
+        run: covr::codecov()
+        shell: Rscript {0}

README.Rmd

@@ -20,6 +20,7 @@ knitr::opts_chunk$set(
 [![](http://cranlogs.r-pkg.org/badges/grand-total/mxnorm?color=green)](https://cran.r-project.org/package=mxnorm)
 [![status](https://joss.theoj.org/papers/c18a1df622016c6ea8ed9e67dda73d07/status.svg)](https://joss.theoj.org/papers/c18a1df622016c6ea8ed9e67dda73d07)
 
+[![R-CMD-check](https://github.com/ColemanRHarris/mxnorm/workflows/R-CMD-check/badge.svg)](https://github.com/ColemanRHarris/mxnorm/actions)
 <!-- badges: end -->
 
 A package designed to handle multiplexed imaging data in R, implementing normalization methods and quality metrics detailed in our paper [here](https://doi.org/10.1101/2021.07.16.452359). Further information about the package, usage, the vignettes, and more can be found on [CRAN](https://cran.r-project.org/package=mxnorm).

README.md

@@ -9,6 +9,7 @@
 [![](http://cranlogs.r-pkg.org/badges/grand-total/mxnorm?color=green)](https://cran.r-project.org/package=mxnorm)
 [![status](https://joss.theoj.org/papers/c18a1df622016c6ea8ed9e67dda73d07/status.svg)](https://joss.theoj.org/papers/c18a1df622016c6ea8ed9e67dda73d07)
 
+[![R-CMD-check](https://github.com/ColemanRHarris/mxnorm/workflows/R-CMD-check/badge.svg)](https://github.com/ColemanRHarris/mxnorm/actions)
 <!-- badges: end -->
 
 A package designed to handle multiplexed imaging data in R, implementing
@@ -205,8 +206,8 @@ summary(mx_var)
 #> 
 #> Clustering consistency (UMAP):
 #>       table adj_rand_index cohens_kappa
-#>  normalized          0.052       -0.102
-#>         raw          0.574        0.206
+#>  normalized          0.052        0.090
+#>         raw          0.633        0.522
 #> 
 #> Variance proportions (slide-level):
 #>       table  mean    sd