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treebase

An R interface to the treeBASE API (now on CRAN)

https://github.com/ropensci/treebase

Science Score: 26.0%

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
    Found 2 DOI reference(s) in README
  • ○
    Academic publication links
  • ○
    Committers with academic emails
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    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (8.9%) to scientific vocabulary

Keywords

r r-package rstats

Keywords from Contributors

genome metadata-standard eml-metadata eml darwin-core taxonomic-databases itis phylogenetics doi crossref-api
Last synced: 10 months ago · JSON representation

Repository

An R interface to the treeBASE API (now on CRAN)

Basic Info
Statistics
  • Stars: 10
  • Watchers: 6
  • Forks: 4
  • Open Issues: 7
  • Releases: 0
Topics
r r-package rstats
Created over 14 years ago · Last pushed over 2 years ago
Metadata Files
Readme Changelog License

README.md

treebase

An R package for discovery, access and manipulation of online phylogenies

  • [Publication in Methods in Ecology and Evolution doi:10.1111/j.2041-210X.2012.00247.x

Installation

treebase is available from CRAN. You can install the latest version from the development website on github using the devtools package from within R. Make sure you have the latest version for the best experience.

r library(devtools) install_github("ropensci/treebase")

Getting Started

Use of the treebase package should be relatively straight forward:

r library(treebase) Phylogenies_from_Huelsenbeck <- search_treebase("Huelsenbeck", "author")

More interesting examples will take advantage of R to loop over large amounts of treebase data that would be to tiresome to search for, download and analyze by hand. Welcome to the era of big data phylogenetics.

References

  • Carl Boettiger, Duncan Temple Lang (2012). Treebase: An R package for discovery, access and manipulation of online phylogenies, Methods in Ecology and Evolution. doi:10.1111/j.2041-210X.2012.00247.x

Owner

  • Name: rOpenSci
  • Login: ropensci
  • Kind: organization
  • Email: info@ropensci.org
  • Location: Berkeley, CA

GitHub Events

Total
  • Issues event: 1
  • Issue comment event: 1
Last Year
  • Issues event: 1
  • Issue comment event: 1

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 205
  • Total Committers: 4
  • Avg Commits per committer: 51.25
  • Development Distribution Score (DDS): 0.063
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Carl Boettiger c****g@g****m 192
Scott Chamberlain m****s@g****m 11
Duncan Temple Lang d****n@r****g 1
rOpenSci Bot m****t@g****m 1
Committer Domains (Top 20 + Academic)
r-project.org: 1

Issues and Pull Requests

Last synced: over 1 year ago

All Time
  • Total issues: 17
  • Total pull requests: 0
  • Average time to close issues: 4 months
  • Average time to close pull requests: N/A
  • Total issue authors: 10
  • Total pull request authors: 0
  • Average comments per issue: 1.24
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • 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
  • sckott (5)
  • cboettig (4)
  • cmzambranat (1)
  • ms609 (1)
  • hadley (1)
  • EvoLandEco (1)
  • rdinnager (1)
  • bomeara (1)
  • widdowquinn (1)
  • DylanCarbone (1)
Pull Request Authors
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 2
  • Total downloads:
    • cran 342 last-month
  • Total docker downloads: 110,395
  • Total dependent packages: 2
    (may contain duplicates)
  • Total dependent repositories: 9
    (may contain duplicates)
  • Total versions: 12
  • Total maintainers: 1
cran.r-project.org: treebase

Discovery, Access and Manipulation of 'TreeBASE' Phylogenies

  • Versions: 11
  • Dependent Packages: 2
  • Dependent Repositories: 9
  • Downloads: 342 Last month
  • Docker Downloads: 110,395
Rankings
Docker downloads count: 0.0%
Dependent repos count: 9.8%
Dependent packages count: 13.7%
Forks count: 14.2%
Average: 14.8%
Stargazers count: 17.4%
Downloads: 33.8%
Maintainers (1)
cboettig@gmail.com
Last synced: 11 months ago
conda-forge.org: r-treebase
  • Versions: 1
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Stargazers count: 52.3%
Average: 53.0%
Forks count: 53.7%
Last synced: 11 months ago

Dependencies

DESCRIPTION cran
  • R >= 2.15 depends
  • ape * depends
  • RCurl * imports
  • XML * imports
  • httr * imports
  • methods * imports
  • utils * imports
  • knitr * suggests
  • rmarkdown * suggests
  • testthat * suggests
.github/workflows/R-CMD-check.yaml actions
  • actions/checkout v4 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