Updated version to 1.3 (#18)

* v1.3.0 (dev)

* Added ggplot2 and missingness

* Update methods-TxpResult-plot.R

added showCenter parameter for showing/removing inner circle

* Update introduction.Rmd

added ggplot method examples and comparisons

* Update DESCRIPTION

Added Jonathon Fleming as author

* Update introduction.Rmd

Adjusted presentation of graphical "paths" and their comparison

* updated with embedded pdf example and new sections for ggplot method

* Intro vignette formatting

* Update introduction.Rmd

Editing text in the Graphics (fka Plotting) section

* Update introduction.Rmd

updated text + swapped out intro figure

* New introductory figure

* Updated version to 1.3

* Patched coord_munch update

* Make coord_munch update compatible with older versions of ggplot2

* added testing for new missingness and plot code

* added extra testing and vignette comments

* Swapped to svg rendering to remove blurriness, removed pdf comparison, fixed workflow image scaling, fixed "rigid lines" in center of plot by removing coord_munch reset

* Updated README to contain updated steps for installing/building package

* reverted to png and set fig.retina parameter to improve plot resolution

* Update README.md

Minor text and line-wrap adjustments

* Update README.md

Minor edits

* updated pkgdown workflow to V2 to replace deprecated version

* updated all files for V2 setup

---------

Co-authored-by: Dayne Filer, MD, PhD <[email protected]>
Co-authored-by: SkylarMarvel <[email protected]>
Co-authored-by: David Reif <[email protected]>
Co-authored-by: Fleming <[email protected]>
Co-authored-by: SkylarMarvel <[email protected]>

Author: 5 people

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

@@ -1,12 +1,14 @@
-# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# 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
+name: R-CMD-check.yaml
+
+permissions: read-all
 
 jobs:
   R-CMD-check:
@@ -18,7 +20,7 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: macOS-latest,   r: 'release'}
+          - {os: macos-latest,   r: 'release'}
           - {os: windows-latest, r: 'release'}
           - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
           - {os: ubuntu-latest,   r: 'release'}
@@ -29,18 +31,22 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
-      - uses: r-lib/actions/setup-pandoc@v1
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - uses: r-lib/actions/setup-r@v1
+      - 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@v1
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: rcmdcheck
+          extra-packages: any::rcmdcheck
+          needs: check
 
-      - uses: r-lib/actions/check-r-package@v1
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

.github/workflows/pkgdown.yaml

@@ -1,35 +1,50 @@
-# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# 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]
   release:
     types: [published]
   workflow_dispatch:
 
-name: pkgdown
+name: pkgdown.yaml
+
+permissions: read-all
 
 jobs:
   pkgdown:
     runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
-      - uses: r-lib/actions/setup-pandoc@v1
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
 
-      - uses: r-lib/actions/setup-r-dependencies@v1
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: pkgdown
+          extra-packages: any::pkgdown, local::.
           needs: website
 
-      - name: Deploy package
-        run: |
-          git config --local user.name "$GITHUB_ACTOR"
-          git config --local user.email "[email protected]"
-          Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE)'
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
+
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/[email protected]
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

.github/workflows/test-coverage.yaml

@@ -1,12 +1,14 @@
-# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# 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: test-coverage
+name: test-coverage.yaml
+
+permissions: read-all
 
 jobs:
   test-coverage:
@@ -15,16 +17,45 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
 
-      - uses: r-lib/actions/setup-r-dependencies@v1
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: covr
+          extra-packages: any::covr, any::xml2
+          needs: coverage
 
       - name: Test coverage
-        run: covr::codecov(token = "${{ secrets.CODECOV_TOKEN }}")
+        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_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }}
+          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

@@ -1,7 +1,7 @@
 Package: toxpiR
 Type: Package
 Title: Create ToxPi Prioritization Models
-Version: 1.2.1
+Version: 1.3.0
 Authors@R: 
     c(person("Dayne L", "Filer", 
              role = c("aut", "cre", "fnd"), 
@@ -14,6 +14,8 @@ Authors@R:
              comment = c(ORCID = "0000-0001-5447-0129")),
       person("Skylar W", "Marvel",
              role = "aut"),
+      person("Jonathon", "Fleming",
+             role = "aut"),
       person("Alison A", "Motsinger-Reif",
              role = c("fnd"),
              comment = c(ORCID = "0000-0003-1346-2493")),
@@ -41,10 +43,11 @@ Imports:
     BiocGenerics,
     pryr,
     tidyr,
-    utils
+    utils,
+    ggplot2
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.3
 Roxygen: list(markdown = TRUE)
 Depends: 
     R (>= 4.0)

NAMESPACE

@@ -44,6 +44,7 @@ exportMethods(plot)
 exportMethods(sort)
 exportMethods(txpCalculateScores)
 exportMethods(txpIDs)
+exportMethods(txpMissing)
 exportMethods(txpModel)
 exportMethods(txpRanks)
 exportMethods(txpResultParam)
@@ -53,6 +54,7 @@ exportMethods(txpSlices)
 exportMethods(txpTransFuncs)
 exportMethods(txpValueNames)
 exportMethods(txpWeights)
+import(ggplot2)
 import(grid)
 import(methods)
 importClassesFrom(S4Vectors,List)

R/allClasses.R

@@ -33,8 +33,8 @@ setClassUnion("TxpTransFunc_OR_NULL", members = c("TxpTransFunc", "NULL"))
 #' @rdname TxpTransFuncList-class
 #' @exportClass TxpTransFuncList
 
-setClass("TxpTransFuncList", 
-         contains = "SimpleList", 
+setClass("TxpTransFuncList",
+         contains = "SimpleList",
          prototype = prototype(elementType = "TxpTransFunc_OR_NULL"))
 
 ##----------------------------------------------------------------------------##
@@ -43,7 +43,7 @@ setClass("TxpTransFuncList",
 #' @rdname TxpSlice-class
 #' @exportClass TxpSlice
 
-setClass("TxpSlice", 
+setClass("TxpSlice",
          slots = c(txpValueNames = "character",
                    txpTransFuncs = "TxpTransFuncList"))
 
@@ -66,8 +66,8 @@ setClass("TxpSliceList",
 #' @rdname TxpModel-class
 #' @exportClass TxpModel
 
-setClass("TxpModel", 
-         slots = c(txpSlices = "TxpSliceList", 
+setClass("TxpModel",
+         slots = c(txpSlices = "TxpSliceList",
                    txpWeights = "numeric",
                    txpTransFuncs = "TxpTransFuncList"))
 
@@ -90,8 +90,8 @@ setClass("TxpModelList",
 #' @name TxpResultParam-class
 #' @exportClass TxpResultParam
 
-setClass("TxpResultParam", 
-         slots = c(rank.ties.method = "character", 
+setClass("TxpResultParam",
+         slots = c(rank.ties.method = "character",
                    negative.value.handling = "character"))
 
 ##----------------------------------------------------------------------------##
@@ -100,10 +100,11 @@ setClass("TxpResultParam",
 #' @name TxpResult-class
 #' @exportClass TxpResult
 
-setClass("TxpResult", 
-         slots = c(txpScores = "numeric", 
+setClass("TxpResult",
+         slots = c(txpScores = "numeric",
                    txpSliceScores = "matrix",
                    txpRanks = "numeric",
+                   txpMissing = "numeric",
                    txpModel = "TxpModel",
                    txpIDs = "character_OR_NULL",
                    txpResultParam = "TxpResultParam"))

R/allGenerics.R

@@ -5,12 +5,12 @@
 
 #' @name txpGenerics
 #' @title toxpiR package generics
-#' @description toxpiR package generics; see class man pages for associated 
+#' @description toxpiR package generics; see class man pages for associated
 #' methods
 #' @param x toxpiR S4 object
 #' @param value Replacement value
 #' @param ... Included for extendability; not currently used
-#' 
+#'
 #' @return See specific methods for details.
 
 NULL
@@ -19,32 +19,32 @@ NULL
 setGeneric("txpValueNames", function(x, ...) standardGeneric("txpValueNames"))
 
 #' @rdname txpGenerics
-setGeneric("txpValueNames<-", 
+setGeneric("txpValueNames<-",
            function(x, ..., value) standardGeneric("txpValueNames<-"))
 
 #' @rdname txpGenerics
 setGeneric("txpTransFuncs", function(x, ...) standardGeneric("txpTransFuncs"))
 
 #' @rdname txpGenerics
-setGeneric("txpTransFuncs<-", 
+setGeneric("txpTransFuncs<-",
            function(x, ..., value) standardGeneric("txpTransFuncs<-"))
 
 #' @rdname txpGenerics
 setGeneric("txpSlices", function(x, ...) standardGeneric("txpSlices"))
 
 #' @rdname txpGenerics
-setGeneric("txpSlices<-", 
+setGeneric("txpSlices<-",
            function(x, ..., value) standardGeneric("txpSlices<-"))
 
 #' @rdname txpGenerics
 setGeneric("txpWeights", function(x, ...) standardGeneric("txpWeights"))
 
 #' @rdname txpGenerics
-setGeneric("txpWeights<-", 
+setGeneric("txpWeights<-",
            function(x, ..., value) standardGeneric("txpWeights<-"))
 
 #' @rdname txpCalculateScores
-setGeneric("txpCalculateScores", 
+setGeneric("txpCalculateScores",
            function(model, input, ...) standardGeneric("txpCalculateScores"))
 
 #' @rdname txpGenerics
@@ -65,5 +65,8 @@ setGeneric("txpIDs<-", function(x, ..., value) standardGeneric("txpIDs<-"))
 #' @rdname txpGenerics
 setGeneric("txpRanks", function(x, ...) standardGeneric("txpRanks"))
 
+#' @rdname txpGenerics
+setGeneric("txpMissing", function(x, ...) standardGeneric("txpMissing"))
+
 #' @rdname txpGenerics
 setGeneric("txpResultParam", function(x, ...) standardGeneric("txpResultParam"))