Merge pull request #3 from astamm/master

Code migration for repo transfer

.Rbuildignore

@@ -1,5 +1,11 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
-.travis.yml
 codecov.yml
-vignettes/Roahd.html
+^\.github$
+^revdep$
+^cran-comments\.md$
+^CRAN-RELEASE$
+^README\.Rmd$
+^_pkgdown\.yml$
+^docs$
+^pkgdown$

.github/.gitignore

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

.github/workflows/check-standard.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/pkgdown.yaml

@@ -0,0 +1,33 @@
+# 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]
+    tags: ['*']
+
+name: pkgdown
+
+jobs:
+  pkgdown:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-pandoc@v1
+
+      - uses: r-lib/actions/setup-r@v1
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v1
+        with:
+          extra-packages: pkgdown
+          needs: website
+
+      - name: Deploy package
+        run: |
+          git config --local user.name "$GITHUB_ACTOR"
+          git config --local user.email "[email protected]"
+          Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE)'

.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}

.gitignore

@@ -2,6 +2,5 @@
 .Rhistory
 .RData
 Rplots.pdf
-
-vignettes/Roahd.R
-vignettes/Roahd.html
+docs
+*.DS_Store

DESCRIPTION

@@ -1,41 +1,67 @@
 Package: roahd
 Type: Package
 Title: Robust Analysis of High Dimensional Data
-Version: 1.4.1
-Date: 2018-08-18
-Authors@R: c( person("Nicholas", "Tarabelloni", role = c("aut", "cre"),
-                     email = "[email protected]"),
-              person("Ana", "Arribas-Gil", role = "aut",
-                      email = "[email protected]" ),
-              person("Francesca", "Ieva", role = "aut",
-                      email = "[email protected]" ),
-              person("Anna Maria", "Paganoni", role = "aut",
-                     email = "[email protected]" ),
-              person("Juan", "Romo", role = "aut",
-                      email = "[email protected]"),
-              person("Francesco", "Palma", role = "ctb",
-                      email = "[email protected]") )
-Author: Nicholas Tarabelloni [aut, cre],
-    Ana Arribas-Gil [aut],
-    Francesca Ieva [aut],
-    Anna Maria Paganoni [aut],
-    Juan Romo [aut],
-    Francesco Palma [ctb]
-Maintainer: Nicholas Tarabelloni <[email protected]>
+Version: 1.4.3.9000
+Authors@R: c( 
+    person(given = "Nicholas", 
+           family = "Tarabelloni", 
+           role = "aut", 
+           email = "[email protected]"), 
+    person(given = "Ana", 
+           family = "Arribas-Gil", 
+           role = "aut", 
+           email = "[email protected]"), 
+    person(given = "Francesca", 
+           family = "Ieva", 
+           role = "aut", 
+           email = "[email protected]"), 
+    person(given = "Anna Maria", 
+           family = "Paganoni", 
+           role = "aut", 
+           email = "[email protected]"), 
+    person(given = "Juan", 
+           family = "Romo", 
+           role = "aut", 
+           email = "[email protected]"), 
+    person(given = "Francesco", 
+           family = "Palma", 
+           role = "ctb", 
+           email = "[email protected]"),
+    person(given = "Aymeric",
+           family = "Stamm",
+           role = c("ctb", "cre"), 
+           email = "[email protected]",
+           comment = c(ORCID = "0000-0002-8725-3654")),
+    person(given = "Antonio",
+           family = "Elias-Fernandez",
+           role = "ctb"))
 Description: A collection of methods for the robust analysis of univariate and
     multivariate functional data, possibly in high-dimensional cases, and hence
-    with attention to computational efficiency and simplicity of use.
+    with attention to computational efficiency and simplicity of use. See the R 
+    Journal publication of Ieva et al. (2019) <doi:10.32614/RJ-2019-032> for an 
+    in-depth presentation of the 'roahd' package. See Aleman-Gomez et al. (2021) 
+    <arXiv:2103.08874> for details about the concept of depthgram.
 Depends: R (>= 2.10)
 License: GPL-3
+Encoding: UTF-8
 LazyData: yes
 Suggests:
-    testthat,
+    testthat (>= 3.0.0),
     knitr,
-    rmarkdown
+    rmarkdown,
+    withr,
+    vdiffr
 Imports:
     scales,
     robustbase,
     magrittr,
-    dplyr
+    dplyr,
+    ggplot2,
+    plotly
 VignetteBuilder: knitr
-RoxygenNote: 6.0.1
+RoxygenNote: 7.1.2
+Roxygen: list(markdown = TRUE)
+URL: https://astamm.github.io/roahd/, https://github.com/astamm/roahd
+BugReports: https://github.com/astamm/roahd/issues
+Language: en-US
+Config/testthat/edition: 3

NAMESPACE

@@ -29,6 +29,9 @@ S3method(MHRD,fData)
 S3method(as.mfData,list)
 S3method(cov_fun,fData)
 S3method(cov_fun,mfData)
+S3method(depthgram,default)
+S3method(depthgram,fData)
+S3method(depthgram,mfData)
 S3method(fbplot,fData)
 S3method(fbplot,mfData)
 S3method(mean,fData)
@@ -42,8 +45,10 @@ S3method(multiMEI,mfData)
 S3method(multiMHI,default)
 S3method(multiMHI,mfData)
 S3method(plot,Cov)
+S3method(plot,depthgram)
 S3method(plot,fData)
 S3method(plot,mfData)
+export("%>%")
 export(BCIntervalSpearman)
 export(BCIntervalSpearmanMultivariate)
 export(BD)
@@ -66,6 +71,7 @@ export(cor_kendall)
 export(cor_spearman)
 export(cor_spearman_accuracy)
 export(cov_fun)
+export(depthgram)
 export(exp_cov_function)
 export(fDColorPalette)
 export(fData)
@@ -89,27 +95,5 @@ export(toListOfValues)
 export(toRowMatrixForm)
 export(unfold)
 export(warp)
-importFrom(dplyr,filter)
-importFrom(dplyr,group_by)
-importFrom(dplyr,summarize)
-importFrom(grDevices,col2rgb)
-importFrom(grDevices,dev.cur)
-importFrom(grDevices,dev.set)
-importFrom(grDevices,rgb)
-importFrom(graphics,image)
-importFrom(graphics,lines)
-importFrom(graphics,matplot)
-importFrom(graphics,par)
-importFrom(graphics,plot)
-importFrom(graphics,points)
-importFrom(graphics,polygon)
-importFrom(graphics,text)
+import(ggplot2)
 importFrom(magrittr,"%>%")
-importFrom(stats,approx)
-importFrom(stats,cor)
-importFrom(stats,cov)
-importFrom(stats,pnorm)
-importFrom(stats,qnorm)
-importFrom(stats,quantile)
-importFrom(stats,rnorm)
-importFrom(stats,uniroot)