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Rphylopars

Phylogenetic Comparative Tools for Missing Data and Within-Species Variation

https://github.com/ericgoolsby/rphylopars

Science Score: 10.0%

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
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    1 of 3 committers (33.3%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (9.4%) to scientific vocabulary
Last synced: 11 months ago · JSON representation

Repository

Phylogenetic Comparative Tools for Missing Data and Within-Species Variation

Basic Info
  • Host: GitHub
  • Owner: ericgoolsby
  • Language: R
  • Default Branch: master
  • Homepage:
  • Size: 893 KB
Statistics
  • Stars: 32
  • Watchers: 8
  • Forks: 11
  • Open Issues: 11
  • Releases: 0
Created about 11 years ago · Last pushed over 3 years ago
Metadata Files
Readme

README.md

Rphylopars

Rphylopars is an R package for conducting multivariate phylogenetic comparative analyses on datasets with missing observations and missing data. Rphylopars uses a fast linear-time algorithm and incorporate a variety of evolutionary models, including estimation of tree transformation parameters (Early-Burst, Ornstein-Uhlenbeck, lambda, kappa, delta) as well as the multivariate Ornstein-Uhlenbeck model.

For download information and tutorials, visit the Rphylopars wiki.

Current versions available

CRAN: 0.3.9

GitHub master branch - 0.3.9

GitHub devel branch - 0.3.9

Version notes

  • Version 0.3.9 - Added get_cov_CIs as option to phylopars to estimate 95% confidence intervals for trait covariance parameters. Clean up write.phylopars() function Also removed dependency on geiger, which is set to be archived on CRAN.
  • Version 0.3.8 - Fixes sim.traits() error which previously set root value to 1.
  • Version 0.3.7 - Converts trait_data to data.frame to prevent errors from tibbles
  • Version 0.3.6 - New experimental internal function Rphylopars:::get_cov_CIs to estimate 95% CIs for trait covariance parameters from a fitted phylopars object.
  • Version 0.3.5 - Checks that all species names in trait_data$species have an exact match in tree$tip.label
  • Version 0.3.4 - Fixes printing error when only one variable is included in phylopars()
  • Version 0.3.3 - Prevents R from crashing when is.na(species) (e.g. trailing blank rows at the end of a spreadsheet).
  • Version 0.3.1 and 0.3.2 - Removed broken links from fast.SSC.Rd and Rphylopars-package.Rd help files (resolves CRAN notes)
  • Version 0.3.0 - R 4.0 compatibility
  • Version 0.2.11 - Fixed confidence intervals (previously too large) and installation issues

Owner

  • Name: Eric W. Goolsby
  • Login: ericgoolsby
  • Kind: user
  • Company: University of Central Florida

GitHub Events

Total
  • Watch event: 4
Last Year
  • Watch event: 4

Committers

Last synced: almost 3 years ago

All Time
  • Total Commits: 59
  • Total Committers: 3
  • Avg Commits per committer: 19.667
  • Development Distribution Score (DDS): 0.136
Past Year
  • Commits: 2
  • Committers: 1
  • Avg Commits per committer: 2.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Eric W. Goolsby e****n@g****m 51
Roberto Toro r****o@g****m 7
Tamora James t****1@s****k 1
Committer Domains (Top 20 + Academic)
sheffield.ac.uk: 1

Issues and Pull Requests

Last synced: 12 months ago

All Time
  • Total issues: 27
  • Total pull requests: 32
  • Average time to close issues: 7 months
  • Average time to close pull requests: 24 days
  • Total issue authors: 23
  • Total pull request authors: 4
  • Average comments per issue: 2.59
  • Average comments per pull request: 0.06
  • Merged pull requests: 31
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 1
  • Pull requests: 0
  • Average time to close issues: 3 days
  • Average time to close pull requests: N/A
  • Issue authors: 1
  • Pull request authors: 0
  • Average comments per issue: 2.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • nick-youngblut (3)
  • jakeberv (2)
  • Jigyasa3 (2)
  • santelmovasconcelos (1)
  • qdread (1)
  • diogoprov (1)
  • daskandalis (1)
  • James-Thorson-NOAA (1)
  • rianbreak (1)
  • amalicea09 (1)
  • NevMagi (1)
  • itchyshin (1)
  • cecileane (1)
  • brmagalis (1)
  • r03ert0 (1)
Pull Request Authors
  • ericgoolsby (29)
  • r03ert0 (1)
  • eddelbuettel (1)
  • tdjames1 (1)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 2
  • Total downloads:
    • cran 407 last-month
  • Total docker downloads: 21,154
  • Total dependent packages: 3
    (may contain duplicates)
  • Total dependent repositories: 4
    (may contain duplicates)
  • Total versions: 13
  • Total maintainers: 1
cran.r-project.org: Rphylopars

Phylogenetic Comparative Tools for Missing Data and Within-Species Variation

  • Versions: 11
  • Dependent Packages: 3
  • Dependent Repositories: 4
  • Downloads: 407 Last month
  • Docker Downloads: 21,154
Rankings
Forks count: 6.3%
Stargazers count: 10.2%
Dependent packages count: 10.9%
Docker downloads count: 12.5%
Average: 13.5%
Dependent repos count: 14.5%
Downloads: 26.4%
Maintainers (1)
eric.goolsby.evolution@gmail.com
Last synced: 12 months ago
conda-forge.org: r-rphylopars
  • Versions: 2
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent repos count: 34.0%
Forks count: 40.9%
Average: 42.6%
Stargazers count: 44.2%
Dependent packages count: 51.2%
Last synced: 12 months ago

Dependencies

DESCRIPTION cran
  • ape * depends
  • MASS * imports
  • Matrix * imports
  • Rcpp * imports
  • doBy * imports
  • numDeriv * imports
  • phylolm * imports
  • phytools * imports