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RevGadgets

Postprocessing gadgets for output generated by RevBayes

https://github.com/revbayes/revgadgets

Science Score: 33.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ○
    .zenodo.json file
  • ○
    DOI references
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ✓
    Committers with academic emails
    7 of 20 committers (35.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (18.0%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

Postprocessing gadgets for output generated by RevBayes

Basic Info
  • Host: GitHub
  • Owner: revbayes
  • Language: R
  • Default Branch: master
  • Homepage:
  • Size: 155 MB
Statistics
  • Stars: 13
  • Watchers: 10
  • Forks: 8
  • Open Issues: 5
  • Releases: 6
Created over 7 years ago · Last pushed over 1 year ago
Metadata Files
Readme Changelog

README.md

RevGadgets

CRAN downloads R-CMD-check DOI

Postprocessing gadgets for output generated by RevBayes

Through user-friendly data pipelines, RevGadgets guides users through importing RevBayes output into R, processing the output, and producing figures or other summaries of the results. RevGadgets provide paired processing and plotting functions built around commonly implemented analyses, such as tree building and divergence-time estimation, diversification-rate estimation, ancestral-state reconstruction and biogeographic range reconstruction, and posterior predictive simulations.

To install:

First, make sure that you have a recent version of R installed. RevGadgets requires R version 4.0 or greater.

Then, install the devtools R-package:

R install.packages("devtools")

Install RevGadgets directly from GitHub:

R devtools::install_github("revbayes/RevGadgets")

Note about magick dependency:

A few RevGadgets dependencies require magick, which may require you to install the imagemagick software external to R.

On a mac, you can do this with homebrew on terminal:

bash brew install imagemagick

Tutorial:

For an introduction to using RevGadgets, check out the tutorial on the RevBayes website.

Legacy:

Some old RevBayes tutorials reference a legacy version of RevGadgets. To reproduce those tutorials, or the results of papers published using the legacy version, you'll need to install the legacy version of RevGadgets. To use this code, install the package using devtools, specifying the legacy branch:

R devtools::install_github("revbayes/RevGadgets@legacy")

Gists:

Here's a list of useful R scripts for working with RevBayes/RevGadgets, but separate from core RevGadgets functionality. This is a growing list: please let us know if you want to contribute your own!

Contributing:

If you'd like to contribute to RevGadgets, please have a look at our developer guide! For minor changes to existing code, make changes to development. To develop new code or make more substantial changes, create a new feature branch from development and then submit a pull request to merge back with development when the code is ready. No changes should happen directly on the master branch.

Owner

  • Name: revbayes
  • Login: revbayes
  • Kind: organization

GitHub Events

Total
  • Issues event: 2
  • Issue comment event: 6
  • Push event: 3
  • Pull request review comment event: 2
  • Pull request review event: 5
  • Create event: 1
Last Year
  • Issues event: 2
  • Issue comment event: 6
  • Push event: 3
  • Pull request review comment event: 2
  • Pull request review event: 5
  • Create event: 1

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 505
  • Total Committers: 20
  • Avg Commits per committer: 25.25
  • Development Distribution Score (DDS): 0.354
Past Year
  • Commits: 38
  • Committers: 4
  • Avg Commits per committer: 9.5
  • Development Distribution Score (DDS): 0.368
Top Committers
Name Email Commits
cmt2 c****2@b****u 326
Mike m****y@g****m 58
Bjorn Tore Kopperud k****d@p****m 25
JoelleBS j****s@i****u 23
cmt2 c****2@h****u 16
Will Freyman w****n@g****m 14
Andy Magee a****e@u****u 6
Jun Ying Lim j****m@g****m 6
Michael Landis m****s@g****m 6
Jeremy-Andreoletti j****i@g****m 5
zenillab z****b@d****u 5
Sebastian Hoehna s****a@g****m 4
rbillenstein r****n@l****e 3
Jenna T. B. Ekwealor j****e@b****u 2
Luiza Guimaraes Fabreti l****t@w****t 1
Carrie c****e@c****u 1
Sebastian Höhna S****a@g****m 1
rbillenstein r****a@b****m 1
cmt2 c****e@c****n 1
Carrie c****e@m****l 1
Committer Domains (Top 20 + Academic)
berkeley.edu: 2 carries-mbp.lan: 1 billenstein.com: 1 calvisitor-10-105-168-101.calvisitor.1918.berkeley.edu: 1 wla033.palmuc.intranet: 1 lmu.de: 1 dhcp-168-105-84-58.wireless.manoa.hawaii.edu: 1 uw.edu: 1 hawaii.edu: 1 iastate.edu: 1

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 17
  • Total pull requests: 16
  • Average time to close issues: 3 months
  • Average time to close pull requests: about 1 month
  • Total issue authors: 12
  • Total pull request authors: 9
  • Average comments per issue: 1.94
  • Average comments per pull request: 0.75
  • Merged pull requests: 15
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 2
  • Pull requests: 2
  • Average time to close issues: 7 days
  • Average time to close pull requests: 19 days
  • Issue authors: 2
  • Pull request authors: 2
  • Average comments per issue: 1.5
  • Average comments per pull request: 1.5
  • Merged pull requests: 2
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • cmt2 (3)
  • hoehna (3)
  • claudiavaga (2)
  • mhDu (1)
  • abhitims (1)
  • willgearty (1)
  • BenjaminGuinet (1)
  • StromTroopers (1)
  • coyotree (1)
  • chlangley (1)
  • thomasp85 (1)
  • prilau (1)
Pull Request Authors
  • cmt2 (4)
  • mikeryanmay (3)
  • maheessh (2)
  • jenna-tb-ekwealor (2)
  • bjoelle (2)
  • wrightaprilm (2)
  • Jeremy-Andreoletti (1)
  • rbillenstein (1)
  • kopperud (1)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • cran 294 last-month
  • Total docker downloads: 21,613
  • Total dependent packages: 1
  • Total dependent repositories: 1
  • Total versions: 5
  • Total maintainers: 1
cran.r-project.org: RevGadgets

Visualization and Post-Processing of 'RevBayes' Analyses

  • Versions: 5
  • Dependent Packages: 1
  • Dependent Repositories: 1
  • Downloads: 294 Last month
  • Docker Downloads: 21,613
Rankings
Docker downloads count: 0.6%
Forks count: 14.2%
Stargazers count: 15.1%
Average: 16.4%
Dependent packages count: 18.1%
Dependent repos count: 23.8%
Downloads: 26.9%
Maintainers (1)
ctribble09@gmail.com
Last synced: 11 months ago

Dependencies

DESCRIPTION cran
  • R >= 4.0.0 depends
  • ape >= 5.4 imports
  • deeptime >= 0.1.0 imports
  • dplyr >= 1.0.0 imports
  • ggimage * imports
  • gginnards >= 0.0.3 imports
  • ggplot2 >= 3.0.0 imports
  • ggplotify >= 0.0.5 imports
  • ggpp * imports
  • ggthemes >= 4.2.0 imports
  • ggtree >= 3.0.2 imports
  • grDevices >= 4.0.1 imports
  • phytools >= 0.7 imports
  • png >= 0.1 imports
  • reshape >= 0.8.8 imports
  • stats >= 4.0.1 imports
  • tibble >= 3.0.1 imports
  • tidyr >= 1.1.0 imports
  • tidytree >= 0.3.4 imports
  • treeio >= 1.12.0 imports
  • utils >= 4.0.1 imports
  • knitr * suggests
  • rmarkdown * suggests
  • testthat * suggests
.github/workflows/check-standard.yaml actions
  • actions/checkout v3 composite
  • r-lib/actions/check-r-package v2 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite