Merge pull request #180 from ACCLAB/dev

Added swarm bars, forest plot function

Author: maiyishan

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,28 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: enhancement
+assignees: ''
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Is a dataset available for testing out the functionality**
+
+If yes, please leave a Google Drive link 
+
+**Additional context**
+
+Add any other context or screenshots about the feature request here.

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,28 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: enhancement
+assignees: ''
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Is a dataset available for testing out the functionality**
+
+If yes, please leave a Google Drive link 
+
+**Additional context**
+
+Add any other context or screenshots about the feature request here.

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

@@ -14,6 +14,7 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       R_KEEP_PKG_SOURCE: yes
+      CI: true
     steps:
       - uses: actions/checkout@v3
 

CONTRIBUTING.md

@@ -12,13 +12,13 @@ Please note that dabestr is released with a [Contributor Code of Conduct](CODE_O
 
 Ensure the bug was not already reported by searching in [Issues](https://github.com/ACCLAB/dabestr/issues). Be sure to also check that the bug hasn't been addressed in a closed issue.
 
-If the bug isn't being addressed, open a new one. 
+If the bug isn't being addressed, open a new issue using the Bug report template. 
 
-Be sure to include a title and clear description, and a [minimally reproducible code sample](http://adv-r.had.co.nz/Reproducibility.html) demonstrating the expected behavior that is not occurring. 
+Be sure to fill in the necessary information, and a [minimally reproducible code sample](http://adv-r.had.co.nz/Reproducibility.html) demonstrating the expected behavior that is not occurring. 
 
 ## Feature Requests
 
-You may suggest by opening an issue and adding an Enhancement tag.
+You may suggest by opening an issue using the Feature request template.
 
 ## Pull requests
 

DESCRIPTION

@@ -1,72 +1,77 @@
-Package: dabestr
 Type: Package
+Package: dabestr
 Title: Data Analysis using Bootstrap-Coupled Estimation
-Version: 2023.9.12
+Version: 2025.3.14
 Authors@R: c(
-  person("Joses W.", "Ho", email = "joseshowh@gmail.com", role = "aut",
-         comment = c(ORCID = "0000-0002-9186-6322")),
-  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("Felicia", "Low", role = "aut", email = "lowminhuifelicia@gmail.com"),
-  person("Tayfun", "Tumkaya", role = "aut",
-         comment = c(ORCID = "0000-0001-8425-3360")),
-  person("Yishan", "Mai", email = "maiyishan@u.duke.nus.edu", role = c("cre", "ctb"),
-         comment = c(ORCID = "0000-0002-7199-380X")),
-  person("Sangyu", "Xu", role = "ctb",
-         comment = c(ORCID = "0000-0002-4927-9204")),
-  person("Hyungwon", "Choi", role = "ctb",
-         comment = c(ORCID = "0000-0002-6687-3088")),
-  person("Adam", "Claridge-Chang", role = "ctb",
-         comment = c(ORCID = "0000-0002-4583-3650")),
-  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://www.nature.com/articles/s41592-019-0470-3.epdf?author_access_token=Euy6APITxsYA3huBKOFBvNRgN0jAjWel9jnR3ZoTv0Pr6zJiJ3AA5aH4989gOJS_dajtNr1Wt17D0fh-t4GFcvqwMYN03qb8C33na_UrCUcGrt-Z0J9aPL6TPSbOxIC-pbHWKUDo2XsUOr3hQmlRew%3D%3D>.
+    person("Joses W.", "Ho", , "joseshowh@gmail.com", role = "aut",
+           comment = c(ORCID = "0000-0002-9186-6322")),
+    person("Kah Seng", "Lian", , "kahseng@u.nus.edu", role = "aut"),
+    person("Ana Rosa", "Castillo", , "arosacastillo@protonmail.com", role = "aut"),
+    person("Zhuoyu", "Wang", , "wzhuoyu21@u.nus,edu", role = "aut"),
+    person("Jun Yang", "Liao", , "name@example.com", role = "aut"),
+    person("Felicia", "Low", , "lowminhuifelicia@gmail.com", role = "aut"),
+    person("Tayfun", "Tumkaya", , role = "aut",
+           comment = c(ORCID = "0000-0001-8425-3360")),
+    person("Jonathan", "Anns", , role = "ctb",
+           comment = c(ORCID = "0009-0005-8349-4986")),
+    person("Yishan", "Mai", ,"maiyishan@u.duke.nus.edu", role = c("cre", "ctb"), 
+           comment = c(ORCID = "0000-0002-7199-380X")),
+    person("Sangyu", "Xu", , role = "ctb",
+           comment = c(ORCID = "0000-0002-4927-9204")),
+    person("Hyungwon", "Choi", , role = "ctb",
+           comment = c(ORCID = "0000-0002-6687-3088")),
+    person("Adam", "Claridge-Chang", , role = "ctb",
+           comment = c(ORCID = "0000-0002-4583-3650")),
+    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://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
-URL: https://github.com/ACCLAB/dabestr,
-    https://acclab.github.io/dabestr/
+URL: https://github.com/ACCLAB/dabestr, https://acclab.github.io/dabestr/
 Depends:
-  R (>= 2.10)
+    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
+    boot,
+    brunnermunzel,
+    cli,
+    cowplot,
+    dplyr,
+    effsize,
+    ggbeeswarm,
+    ggplot2 (>= 3.5.1),
+    ggsci,
+    grid,
+    magrittr,
+    RColorBrewer,
+    rlang,
+    scales,
+    stats,
+    stringr,
+    tibble,
+    tidyr,
+    viridisLite
 Suggests: 
-    testthat (>= 3.0.0),
-    vdiffr,
+    kableExtra,
     knitr,
     rmarkdown,
-    kableExtra
+    testthat (>= 3.0.0),
+    vdiffr
+VignetteBuilder: 
+    kableExtra,
+    knitr
 Config/testthat/edition: 3
+Encoding: UTF-8
 LazyData: true
-VignetteBuilder: knitr, kableExtra
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.2.3

NAMESPACE

@@ -7,9 +7,11 @@ export(cliffs_delta)
 export(cohens_d)
 export(cohens_h)
 export(dabest_plot)
+export(forest_plot)
 export(hedges_g)
 export(load)
 export(mean_diff)
 export(median_diff)
 importFrom(ggplot2,.pt)
 importFrom(magrittr,"%>%")
+importFrom(rlang,.data)

NEWS.md

@@ -1,3 +1,10 @@
+# dabestr v2025.3.14
+This release implements quite a couple of new features, matching up with the current DABEST in python.
+
+### New features
+* Plots now include swarm bars, contrast bars and delta dots
+* Forest plots
+
 # dabestr v2023.9.12
 This release is a complete rebuild of dabestr.