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crabs

An R package for visualizing congruence classes.

https://github.com/afmagee/crabs

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
  • ○
    .zenodo.json file
  • ✓
    DOI references
    Found 9 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ✓
    Committers with academic emails
    1 of 8 committers (12.5%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (6.0%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

An R package for visualizing congruence classes.

Basic Info
  • Host: GitHub
  • Owner: afmagee
  • License: gpl-3.0
  • Language: R
  • Default Branch: main
  • Homepage:
  • Size: 27 MB
Statistics
  • Stars: 7
  • Watchers: 3
  • Forks: 1
  • Open Issues: 1
  • Releases: 2
Created over 5 years ago · Last pushed over 2 years ago
Metadata Files
Readme License

README.md

CRABS: Congruent Rate Analysis in Birth-death Scenarios

DOI

A package for investigating and visualizing the congruence class (Louca & Pennell 2020) of a phylogenetic birth-death model. Previously, this package went by the acronym ACDC.

Installation:

The stable version can be installed from CRAN:

install.packages("CRABS")

The developmental version can be installed from the github repository. The package devtools makes this convenient:

install.packages("devtools")
library(devtools)
install_github("afmagee/CRABS")

Documentation

There is documentation for each function in R (type ?CRABS in the R-console), as well as a long-form vignette with an example workflow.

References

  • Louca, S., & Pennell, M. W. (2020). Extant timetrees are consistent with a myriad of diversification histories. Nature, 580(7804), 502-505.
  • Höhna, S., Kopperud, B. T., & Magee, A. F. (2022). CRABS: Congruent rate analyses in birth–death scenarios. Methods in Ecology and Evolution, 13, 2709– 2718. https://doi.org/10.1111/2041-210X.13997
  • Kopperud, B. T., Magee, A. F., & Höhna, S. (2023). Rapidly Changing Speciation and Extinction Rates Can Be Inferred in Spite of Nonidentifiability. Proceedings of the National Academy of Sciences 120 (7): e2208851120. https://doi.org/10.1073/pnas.2208851120.
  • Andreoletti J. & Morlon, H. (2023). Exploring congruent diversification histories with flexibility and parsimony. Methods in Ecology and Evolution. https://doi.org/10.1111/2041-210X.14240.

Owner

  • Name: Andy Magee
  • Login: afmagee
  • Kind: user

afmagee.github.io

GitHub Events

Total
Last Year

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 188
  • Total Committers: 8
  • Avg Commits per committer: 23.5
  • Development Distribution Score (DDS): 0.372
Past Year
  • Commits: 19
  • Committers: 4
  • Avg Commits per committer: 4.75
  • Development Distribution Score (DDS): 0.579
Top Committers
Name Email Commits
Bjorn Tore Kopperud k****d@p****m 118
Sebastian Hoehna s****a@g****m 24
Andrew Magee a****e@u****u 21
Jérémy Andréoletti 4****i 8
Andy Magee a****e@g****m 8
Sebastian Hoehna s****a@w****t 5
Jeremy-Andreoletti j****i@g****m 2
Sebastian Hoehna S****a@g****m 2
Committer Domains (Top 20 + Academic)
wma065.palmuc.intranet: 1 uw.edu: 1

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 4
  • Total pull requests: 3
  • Average time to close issues: 3 months
  • Average time to close pull requests: 4 days
  • Total issue authors: 3
  • Total pull request authors: 2
  • Average comments per issue: 3.0
  • Average comments per pull request: 2.0
  • Merged pull requests: 3
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • burbrink (2)
  • davidcerny (1)
  • kopperud (1)
Pull Request Authors
  • Jeremy-Andreoletti (2)
  • kopperud (1)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • cran 215 last-month
  • Total docker downloads: 21,613
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 2
  • Total maintainers: 1
cran.r-project.org: CRABS

Congruent Rate Analyses in Birth-Death Scenarios

  • Versions: 2
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 215 Last month
  • Docker Downloads: 21,613
Rankings
Stargazers count: 21.1%
Forks count: 21.9%
Dependent packages count: 29.8%
Average: 34.4%
Dependent repos count: 35.5%
Downloads: 63.7%
Maintainers (1)
kopperud@protonmail.com
Last synced: 11 months ago

Dependencies

DESCRIPTION cran
  • R >= 3.5.0 depends
  • ggplot2 * depends
  • ape * imports
  • colorspace * imports
  • deSolve * imports
  • dplyr * imports
  • latex2exp * imports
  • magrittr * imports
  • patchwork * imports
  • pracma * imports
  • tibble * imports
  • tidyr * imports
  • knitr * suggests
  • rmarkdown * suggests