Merge pull request #77 from jasenfinch/devel

v0.14.0
jasenfinch · Apr 16, 2021 · 0a1aca3 · 0a1aca3
2 parents 2094515 + e118fad
commit 0a1aca3
Show file tree

Hide file tree

Showing 461 changed files with 41,268 additions and 7,240 deletions.
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -1,5 +1,10 @@
-^appveyor\.yml$
 ^.*\.Rproj$
 ^\.Rproj\.user$
-.travis.yml
+README.Rmd
+^_pkgdown\.yml$
+^docs$
+^pkgdown$
 ^\.github$
+^codecov\.yml$
+^doc$
+^Meta$
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -68,7 +68,7 @@ jobs:
       - name: Install dependencies
         run: |
           remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("rcmdcheck")
+          remotes::install_cran(c("rcmdcheck","goodpractice"))
         shell: Rscript {0}
 
       - name: Check
@@ -77,6 +77,10 @@ jobs:
         run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
         shell: Rscript {0}
 
+      - name: Goodpractice
+        run: goodpractice::goodpractice()
+        shell: Rscript {0}
+
       - name: Test coverage
         run: covr::codecov()
         shell: Rscript {0}

diff --git a/.gitignore b/.gitignore
@@ -3,3 +3,7 @@
 .RData
 .Ruserdata
 inst/doc
+doc
+Meta
+/doc/
+/Meta/
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,14 +1,14 @@
 Package: metabolyseR
-Title: Methods for Pre-Treatment, Classification, Feature Selection and Correlation Analyses of Metabolomics Data
-Version: 0.13.4
+Title: Methods for Pre-Treatment, Data Mining and Correlation Analyses of Metabolomics Data
+Version: 0.14.0
 Authors@R: person("Jasen", "Finch", email = "jsf9@aber.ac.uk", role = c("aut", "cre"))
-Description: Methods for pre-treatment, classification, feature selection and correlation analyses of metabolomics data.
+Description: A tool kit for pre-treatment, modelling, feature selection and correlation analyses of metabolomics data.
+URL:  https://jasenfinch.github.io/metabolyseR
+BugReports: https://github.com/jasenfinch/metabolyseR/issues
 biocViews: Metabolomics
-Depends: R (>= 3.4.0),
-         parallel
+Depends: R (>= 3.4.0)
 Imports: Hmisc,
          dplyr,
-         magrittr,
          missForest,
          randomForest,
          stringr,
@@ -19,76 +19,72 @@ Imports: Hmisc,
          ggthemes,
          ggdendro,
          purrr,
-         doParallel,
+         doFuture,
          e1071,
-         MASS,
          forestControl,
          crayon,
          yaml,
          cli,
          lubridate,
          ggrepel,
-         ROCR,
          patchwork,
          yardstick,
          broom,
          rlang,
-         tidyselect
+         tidyselect,
+         magrittr,
+         furrr,
+         future
 License: GPL (>= 3)
 Encoding: UTF-8
 LazyData: true
+Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.1.1
 Suggests: knitr,
     rmarkdown,
-    DiagrammeR,
     readr,
     testthat,
     metaboData,
     prettydoc,
-    covr
-Collate: allGenerics.R
-    allClasses.R
-    aggregateMethods.R
+    covr,
+    kableExtra
+Collate: allClasses.R
+    analysis-accessors.R
+    aggregate.R
     analysisData.R
-    analysisParameters.R
-    changeParameter.R
-    correctionMethods.R
-    correlations-method.R
-    correlationResults-method.R
-    imputeMethods.R
+    correction.R
+    correlations.R
+    impute.R
+    info.R
+    join.R
+    keep.R
     metabolyse.R
     metabolyseR.R
-    nlda.R
-    occupancyMethods.R
-    parseParameters.R
-    plotExplanatoryHeatmap-method.R
-    plotFeature-method.R
-    plotLDA-method.R
-    plotPCA-method.R
-    plotRSD-method.R
-    plotSupervisedRF-method.R
-    plotTIC-method.R
-    plotUnsupervisedRF-method.R
-    preTreat-method.R
-    preTreatedData-method.R
-    preTreatedInfo-method.R
-    preTreatMethods.R
-    QCMethods.R
-    rawData-method.R
-    rawInfo-method.R
-    reAnalyse.R
-    reexports.R
-    removeMethods.R
-    show-method.R
-    transformMethods.R
-    univariateMethods.R
     modelling.R
-    randomForest.R
     modellingPlots.R
-    keepMethods.R
-    info.R
+    nlda.R
+    occupancy.R
+    parameters.R
+    plotExplanatoryHeatmap.R
+    plotFeature.R
+    plotLDA.R
     plotOccupancy.R
-    join.R
+    plotPCA.R
+    plotRSD.R
+    plotSupervisedRF.R
+    plotTIC.R
+    plotting.R
+    plotUnsupervisedRF.R
+    pre-treatment.R
+    QC.R
+    reexports.R
+    remove.R
+    randomForest.R
+    rsd.R
+    show-method.R
     split.R
+    transform.R
+    univariate.R
+    modelling-accessors.R
 VignetteBuilder: knitr
 Remotes: aberHRML/metaboData