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PhylogeneticEM

Implementation of the EM algorithm for the detection of shifts in a phylogeny.

https://github.com/pbastide/phylogeneticem

Science Score: 36.0%

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

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    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
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    .zenodo.json file
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    DOI references
    Found 4 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: wiley.com
  • ○
    Committers with academic emails
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    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (9.5%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

Implementation of the EM algorithm for the detection of shifts in a phylogeny.

Basic Info
Statistics
  • Stars: 18
  • Watchers: 9
  • Forks: 4
  • Open Issues: 4
  • Releases: 10
Created over 11 years ago · Last pushed over 1 year ago
Metadata Files
Readme Changelog License

README.md

PhylogeneticEM

R-CMD-check codecov CRAN_Status_Badge

Implementation of the EM algorithm for the detection of shifts in a phylogeny.

Installation

Stable version on the CRAN.

To get the latest (and possibly unstable) version, you can use the devtools package: R install.packages("devtools") devtools::install_github(repo = "pbastide/PhylogeneticEM", ref = "develop")

Documentation

See package documentation (references and vignettes) here: http://pbastide.github.io/PhylogeneticEM/

(Built with pkgdown).

References:

Bastide, P., Mariadassou, M. and Robin, S. (2017), Detection of adaptive shifts on phylogenies by using shifted stochastic processes on a tree. Journal of the Royal Statistical Society: Series B (Statistical Methodology), 79(4):1067-1093, doi:10.1111/rssb.12206.

Bastide, P., Ané, C., Robin, S. and Mariadassou, M. (2018), Inference of Adaptive Shifts for Multivariate Correlated Traits. Systematic Biology, 67(4), 662–680. doi:10.1093/sysbio/syy005.

Owner

  • Name: Paul Bastide
  • Login: pbastide
  • Kind: user
  • Location: Montpellier, France
  • Company: CNRS - Université de Montpellier

GitHub Events

Total
  • Release event: 1
  • Watch event: 1
  • Push event: 7
  • Fork event: 1
  • Create event: 1
Last Year
  • Release event: 1
  • Watch event: 1
  • Push event: 7
  • Fork event: 1
  • Create event: 1

Committers

Last synced: about 1 year ago

All Time
  • Total Commits: 777
  • Total Committers: 4
  • Avg Commits per committer: 194.25
  • Development Distribution Score (DDS): 0.018
Past Year
  • Commits: 9
  • Committers: 1
  • Avg Commits per committer: 9.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
pbastide p****e@g****m 763
Mahendra Mariadassou m****u@g****m 7
olivroy 5****y 6
“pbastide” “****e@g****” 1
Committer Domains (Top 20 + Academic)
gmail.com”: 1

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 15
  • Total pull requests: 11
  • Average time to close issues: 5 months
  • Average time to close pull requests: about 2 hours
  • Total issue authors: 6
  • Total pull request authors: 2
  • Average comments per issue: 2.0
  • Average comments per pull request: 0.27
  • Merged pull requests: 11
  • 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
  • pbastide (6)
  • jakeberv (4)
  • oscarIM (2)
  • ptitle (1)
  • saurabh-mk (1)
  • mahendra-mariadassou (1)
Pull Request Authors
  • pbastide (10)
  • olivroy (2)
Top Labels
Issue Labels
bug (2) invalid (2) enhancement (1)
Pull Request Labels

Packages

  • Total packages: 2
  • Total downloads:
    • cran 325 last-month
  • Total dependent packages: 0
    (may contain duplicates)
  • Total dependent repositories: 0
    (may contain duplicates)
  • Total versions: 15
  • Total maintainers: 1
cran.r-project.org: PhylogeneticEM

Automatic Shift Detection using a Phylogenetic EM

  • Versions: 10
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 325 Last month
Rankings
Stargazers count: 14.2%
Forks count: 14.9%
Average: 26.4%
Dependent packages count: 29.8%
Dependent repos count: 35.5%
Downloads: 37.9%
Maintainers (1)
paul.bastide@m4x.org
Last synced: 11 months ago
conda-forge.org: r-phylogeneticem
  • Versions: 5
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent repos count: 34.0%
Average: 46.0%
Stargazers count: 47.3%
Dependent packages count: 51.2%
Forks count: 51.6%
Last synced: 11 months ago

Dependencies

DESCRIPTION cran
  • Matrix >= 1.2.18 depends
  • R >= 3.6.0 depends
  • ape >= 5.3 depends
  • LINselect >= 1.1.1 imports
  • MASS >= 7.3.45 imports
  • Rcpp >= 1.0.2 imports
  • capushe >= 1.1.1 imports
  • foreach >= 1.4.3 imports
  • gglasso >= 1.4 imports
  • glmnet >= 2.0.5 imports
  • grDevices >= 3.6.0 imports
  • graphics >= 3.6.0 imports
  • methods >= 3.6.0 imports
  • plyr >= 1.8.4 imports
  • robustbase >= 0.92.6 imports
  • stats >= 3.6.0 imports
  • utils >= 3.6.0 imports
  • TreeSim >= 2.2 suggests
  • combinat >= 0.0.8 suggests
  • doParallel >= 1.0.10 suggests
  • knitr * suggests
  • phytools >= 0.5.38 suggests
  • rmarkdown * suggests
  • testthat >= 1.0.2 suggests