Update to v2023.9.12

Merge dev branch into master branch

Author: sunroofgod

.Rbuildignore

@@ -1,13 +1,14 @@
-^Meta$
-^doc$
-^CRAN-RELEASE$
 ^.*\.Rproj$
 ^\.Rproj\.user$
-^\.travis\.yml$
-^cran-comments\.md$
+^LICENSE\.md$
+^_pkgdown\.yml$
+^docs$
+^pkgdown$
+^\.github$
 ^README\.Rmd$
-^README-.*\.png$
 ^CODE_OF_CONDUCT.md$
 ^CONTRIBUTING.MD$
-^packrat/
-^\.Rprofile$
+^figures$
+^dabestr.Rmd$
+^cran-comments\.md$
+^revdep$

.github/.gitignore

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

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

@@ -0,0 +1,29 @@
+# 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: [dev, master]
+  pull_request:
+    branches: [dev, master]
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2

.github/workflows/pkgdown.yaml

@@ -0,0 +1,48 @@
+# 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: [master]
+  pull_request:
+    branches: [master]
+  release:
+    types: [published]
+  workflow_dispatch:
+
+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 }}
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::pkgdown, local::.
+          needs: website
+
+      - 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

.gitignore

@@ -1,16 +1,17 @@
-Meta
-doc
+# Byte-compiled / optimized / DLL files
+
+# Testing Files
+dabestr.Rmd
+
+# Mac
+**/.DS_Store
+
+# RProj
 .Rproj.user
-.Rhistory
 .RData
+.Rhistory
 .Ruserdata
-.Rprofile
-.DS_Store
-*.DS_Store
+.RProfile
+docs
 inst/doc
-# revdevcheck temp folder
-revdep
-# test figures
-tests/testthat/Rplots.pdf
-packrat/lib*/
-packrat/src/
+figures

.travis.yml

@@ -1,60 +1,72 @@
 Package: dabestr
 Type: Package
 Title: Data Analysis using Bootstrap-Coupled Estimation
-Version: 0.3.0
+Version: 2023.9.12
 Authors@R: c(
-    person("Joses W.", "Ho",
-          email = "joseshowh@gmail.com", role = c("cre", "aut")),
-    person("Tayfun", "Tumkaya",
-          role = c("aut"))
-          )
-Maintainer: Joses W. Ho <joseshowh@gmail.com>
+  person("Yishan", "Mai", email = "maiyishan@u.duke.nus.edu", role = c("cre", "ctb"),
+         comment = c(ORCID = "0000-0002-7199-380X")),
+  person("Kah Seng", "Lian", email = "kahseng@u.nus.edu", role = c("aut")),
+  person("Zhuoyu", "Wang", email = "wzhuoyu21@u.nus,edu", role = "aut"),
+  person("Jun Yang", "Liao", email = "name@example.com", role = "aut"),
+  person("Joses W.", "Ho", email = "joseshowh@gmail.com", role = "aut",
+         comment = c(ORCID = "0000-0002-9186-6322")),
+  person("Tayfun", "Tumkaya", role = "aut",
+         comment = c(ORCID = "0000-0001-8425-3360")),
+  person("Felicia", "Low", role = "aut", email = "lowminhuifelicia@gmail.com"),
+  person("Adam", "Claridge-Chang", role = "ctb",
+         comment = c(ORCID = "0000-0002-4583-3650")),
+  person("Hyungwon", "Choi", role = "ctb",
+         comment = c(ORCID = "0000-0002-6687-3088")),
+  person("Sangyu", "Xu", role = "ctb",
+         comment = c(ORCID = "0000-0002-4927-9204")),
+  person("ACCLAB", role = c("cph", "fnd")))
 Description: Data Analysis using Bootstrap-Coupled ESTimation.
-    Estimation statistics is a simple framework that avoids the pitfalls of
-    significance testing. It uses familiar statistical concepts: means,
-    mean differences, and error bars. More importantly, it focuses on the
-    effect size of one's experiment/intervention, as opposed to a false
-    dichotomy engendered by P values.
-    An estimation plot has two key features:
-    1. It presents all datapoints as a swarmplot, which orders each point to
-    display the underlying distribution.
-    2. It presents the effect size as a bootstrap 95% confidence interval on a
-    separate but aligned axes.
-    Estimation plots are introduced in Ho et al., Nature Methods 2019, 1548-7105.
-    <doi:10.1038/s41592-019-0470-3>.
-    The free-to-view PDF is located at <https://rdcu.be/bHhJ4>.
-License: file LICENSE
-URL: https://github.com/ACCLAB/dabestr
-BugReports: https://github.com/ACCLAB/dabestr/issues
+  Estimation statistics is a simple framework that avoids the pitfalls of
+  significance testing. It uses familiar statistical concepts: means,
+  mean differences, and error bars. More importantly, it focuses on the
+  effect size of one's experiment/intervention, as opposed to a false
+  dichotomy engendered by P values.
+  An estimation plot has two key features:
+  1. It presents all datapoints as a swarmplot, which orders each point to
+  display the underlying distribution.
+  2. It presents the effect size as a bootstrap 95% confidence interval on a
+  separate but aligned axes.
+  Estimation plots are introduced in Ho et al., Nature Methods 2019, 1548-7105.
+  <doi:10.1038/s41592-019-0470-3>.
+  The free-to-view PDF is located at <https://www.nature.com/articles/s41592-019-0470-3.epdf?author_access_token=Euy6APITxsYA3huBKOFBvNRgN0jAjWel9jnR3ZoTv0Pr6zJiJ3AA5aH4989gOJS_dajtNr1Wt17D0fh-t4GFcvqwMYN03qb8C33na_UrCUcGrt-Z0J9aPL6TPSbOxIC-pbHWKUDo2XsUOr3hQmlRew%3D%3D>.
+License: Apache License (>= 2)
 Encoding: UTF-8
-LazyData: true
+URL: https://github.com/ACCLAB/dabestr,
+    https://acclab.github.io/dabestr/
 Depends:
-    R (>= 3.5.0),
-    magrittr,
-    stats,
-    utils
-Imports:
-    boot,
-    cowplot,
-    dplyr,
-    effsize,
-    ellipsis,
-    ggplot2 (>= 3.2),
-    forcats,
-    ggforce,
-    ggbeeswarm,
-    plyr,
-    RColorBrewer,
-    rlang,
-    simpleboot,
-    stringr,
-    tibble,
-    tidyr,
-RoxygenNote: 7.1.0
-Suggests:
+  R (>= 2.10)
+Imports: 
+  ggplot2, 
+  cowplot, 
+  tidyr, 
+  dplyr, 
+  tibble,
+  rlang, 
+  magrittr, 
+  ggbeeswarm,
+  effsize,
+  grid,
+  scales,
+  ggsci,
+  cli,
+  boot,
+  stats,
+  stringr,
+  brunnermunzel,
+  methods
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.2.3
+Suggests: 
+    testthat (>= 3.0.0),
+    vdiffr,
     knitr,
     rmarkdown,
-    tufte,
-    testthat,
-    vdiffr
-VignetteBuilder: knitr
+    kableExtra
+Config/testthat/edition: 3
+LazyData: true
+VignetteBuilder: knitr, kableExtra