Merge pull request #91 from jasenfinch/devel

v0.15.0

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

@@ -1,4 +1,4 @@
-# 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:
@@ -18,7 +18,7 @@ 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 +29,21 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-      - 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

.github/workflows/pkgdown.yaml

@@ -1,8 +1,10 @@
-# 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:
@@ -12,24 +14,33 @@ name: pkgdown
 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 }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-      - 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 "$GITHUB_ACTOR"
-          git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com"
-          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/github-pages-deploy-action@v4.4.1
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

.github/workflows/test-coverage.yaml

@@ -1,4 +1,4 @@
-# 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:
@@ -15,16 +15,36 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-      - 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
+          needs: coverage
 
       - name: Test coverage
-        run: covr::codecov()
+        run: |
+          covr::codecov(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
+          )
         shell: Rscript {0}
+
+      - 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@v3
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package

DESCRIPTION

@@ -1,9 +1,9 @@
 Package: metabolyseR
 Title: Methods for Pre-Treatment, Data Mining and Correlation Analyses of Metabolomics Data
-Version: 0.14.10
+Version: 0.15.0
 Authors@R: person("Jasen", "Finch", email = "jsf9@aber.ac.uk", role = c("aut", "cre"))
 Description: A tool kit for pre-treatment, modelling, feature selection and correlation analyses of metabolomics data.
-URL: https://jasenfinch.github.io/metabolyseR
+URL: https://jasenfinch.github.io/metabolyseR/
 BugReports: https://github.com/jasenfinch/metabolyseR/issues
 biocViews: Metabolomics
 Depends: R (>= 3.4.0)
@@ -38,7 +38,7 @@ Imports: Hmisc,
 License: GPL (>= 3)
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.3
 Suggests: knitr,
     rmarkdown,
     readr,
@@ -47,7 +47,7 @@ Suggests: knitr,
     prettydoc,
     covr,
     kableExtra
-Collate: allClasses.R
+Collate: all-classes.R
     analysis-accessors.R
     aggregate.R
     analysisData.R
@@ -61,7 +61,7 @@ Collate: allClasses.R
     metabolyse.R
     metabolyseR.R
     modelling.R
-    modellingPlots.R
+    modelling-plots.R
     nlda.R
     occupancy.R
     parameters.R
@@ -80,6 +80,11 @@ Collate: allClasses.R
     QC.R
     reexports.R
     remove.R
+    randomForest-permute.R
+    randomForest-classification.R
+    randomForest-regression.R
+    randomForest-internals.R
+    randomForest-unsupervised.R
     randomForest.R
     rsd.R
     roc.R

NAMESPACE

@@ -75,6 +75,7 @@ export(preTreatmentElements)
 export(preTreatmentMethods)
 export(preTreatmentParameters)
 export(predict)
+export(predictions)
 export(proximity)
 export(randomForest)
 export(raw)
@@ -138,12 +139,14 @@ importFrom(dplyr,mutate_all)
 importFrom(dplyr,mutate_at)
 importFrom(dplyr,mutate_if)
 importFrom(dplyr,n)
+importFrom(dplyr,pull)
 importFrom(dplyr,relocate)
 importFrom(dplyr,rename)
 importFrom(dplyr,rename_with)
 importFrom(dplyr,rowwise)
 importFrom(dplyr,select)
 importFrom(dplyr,select_if)
+importFrom(dplyr,slice)
 importFrom(dplyr,summarise)
 importFrom(dplyr,summarise_all)
 importFrom(dplyr,ungroup)
@@ -152,6 +155,7 @@ importFrom(forestControl,fpr_fs)
 importFrom(furrr,furrr_options)
 importFrom(furrr,future_map)
 importFrom(furrr,future_map2)
+importFrom(furrr,future_map_dfr)
 importFrom(future,plan)
 importFrom(ggdendro,dendro_data)
 importFrom(ggplot2,aes)
@@ -204,6 +208,7 @@ importFrom(magrittr,set_names)
 importFrom(magrittr,set_rownames)
 importFrom(methods,"slot<-")
 importFrom(methods,as)
+importFrom(methods,is)
 importFrom(methods,new)
 importFrom(methods,show)
 importFrom(methods,slot)
@@ -217,10 +222,12 @@ importFrom(purrr,map_chr)
 importFrom(purrr,map_dbl)
 importFrom(purrr,map_depth)
 importFrom(purrr,map_df)
+importFrom(purrr,map_dfr)
 importFrom(purrr,map_lgl)
 importFrom(purrr,walk)
 importFrom(randomForest,margin)
 importFrom(rlang,":=")
+importFrom(rlang,squash)
 importFrom(rlang,sym)
 importFrom(stats,cmdscale)
 importFrom(stats,cov)
@@ -243,6 +250,7 @@ importFrom(stringr,str_replace_all)
 importFrom(stringr,str_split)
 importFrom(stringr,str_split_fixed)
 importFrom(stringr,str_sub)
+importFrom(stringr,str_to_title)
 importFrom(tibble,as_tibble)
 importFrom(tibble,deframe)
 importFrom(tibble,rowid_to_column)

NEWS.md

@@ -1,3 +1,25 @@
+# metabolyseR 0.15.0
+
+* It is now possible to specify multiple `cls` arguments to the [aggregation methods](https://jasenfinch.github.io/metabolyseR/reference/aggregate.html).
+
+* Correlation thresholds are now available for both coefficient and total number using the `minCoef` and `maxCor` arguments in the [`correlations()`](https://jasenfinch.github.io/metabolyseR/reference/correlations.html) method.
+
+* Added the [`predictions()`]() accessor method for the [`RandomForest`](https://jasenfinch.github.io/metabolyseR/reference/RandomForest-class.html) S4 class to enable the retrieval of the out of bag model response predictions.
+
+* The [occupancy filtering methods](https://jasenfinch.github.io/metabolyseR/reference/occupancyFilter.html) now error if the value supplied to argument `occupancy` is non-numeric.
+
+* Memory usage and performance improvements for the [`randomForest()`](https://jasenfinch.github.io/metabolyseR/reference/randomForest.html) method.
+
+* Added [`type()`](https://jasenfinch.github.io/metabolyseR/reference/modelling-accessors.html) and [`response()`](https://jasenfinch.github.io/metabolyseR/reference/modelling-accessors.html) methods for the [`Univariate`](https://jasenfinch.github.io/metabolyseR/reference/Univariate-class.html) S4 class.
+
+* [`plotLDA()`](https://jasenfinch.github.io/metabolyseR/reference/plotLDA.html) now returns a warning and skips plotting if an error is encountered during PC-LDA.
+
+* The value `pre-treated` is now the default for argument `type` in the [`Analysis`](https://jasenfinch.github.io/metabolyseR/reference/Analysis-class.html) S4 class [accessor methods](https://jasenfinch.github.io/metabolyseR/reference/analysis-accessors.html).
+
+* Added the `value` argument to the [`explanatoryFeatures()`](https://jasenfinch.github.io/metabolyseR/reference/modelling-accessors.html) method to allow the specification of on which importance value to apply the specified `threshold`.
+
+* The specified `cls` argument is now correctly displayed on the x-axis title of the resulting plots from the [`plotFeature()`](https://jasenfinch.github.io/metabolyseR/reference/plotFeature.html) method.
+
 # metabolyseR 0.14.10
 
 * Added the method [`predict()`](https://jasenfinch.github.io/metabolyseR/reference/predict.html) for the [`RandomForest`](https://jasenfinch.github.io/metabolyseR/reference/RandomForest-class.html) S4 class to predict model response values.

R/QC.R

@@ -80,7 +80,7 @@ setMethod('QCimpute',signature = 'AnalysisData',
 
             dat(d)[d %>% 
                      sinfo() %>% 
-                     select(cls) %>%
+                     select(all_of(cls)) %>%
                      deframe() %>%
                      {. == QCidx},] <- QC %>%
               dat()