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PhyloCoalSimulations

https://github.com/juliaphylo/phylocoalsimulations.jl

Science Score: 44.0%

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

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (6.6%) to scientific vocabulary
Last synced: 6 months ago · JSON representation ·

Repository

Basic Info
  • Host: GitHub
  • Owner: JuliaPhylo
  • License: mit
  • Language: Julia
  • Default Branch: main
  • Size: 714 KB
Statistics
  • Stars: 14
  • Watchers: 3
  • Forks: 2
  • Open Issues: 2
  • Releases: 5
Created almost 4 years ago · Last pushed 6 months ago
Metadata Files
Readme License Citation

README.md

PhyloCoalSimulations

stable dev Build Status Coverage Code Style: Blue ColPrac: Contributor's Guide on Collaborative Practices for Community Packages PkgEval

PhyloCoalSimulations is a Julia package to simulate phylogenies under the coalescent. It implements the network multi-species coalescent model with possible inheritance correlation: please see CITATION and documentation (links above).

Owner

  • Name: JuliaPhylo
  • Login: JuliaPhylo
  • Kind: organization

Citation (CITATION.bib) 

% reference for the software itself
@misc{PhyloCoalSimulations.jl,
	author  = {C{\'e}cile An{\'e} <cecileane@users.noreply.github.com>, John Fogg <70609062+fogg-uw@users.noreply.github.com>, Joshua Justison <jjustison@users.noreply.github.com>, and contributors},
	title   = {PhyloCoalSimulations.jl},
	url     = {https://github.com/JuliaPhylo/PhyloCoalSimulations.jl},
	version = {v1.0.0},
	year    = {2024},
	month   = {12}
}
% reference for the package, and for the correlated inheritance model
@article{2023fogg_phylocoalsimulations,
  author = {Fogg, John and Allman, Elizabeth S and An{\'e}, C{\'e}cile},
  title = {{PhyloCoalSimulations}: A simulator for network multispecies coalescent
        models, including a new extension for the inheritance of gene flow},
  journal = {Systematic Biology},
  year = {2023},
  volume = {72},
  number = {5},
  pages = {1171-1179},
  doi = {10.1093/sysbio/syad030},
}
% older bioRxiv preprint
@article{2023fogg_phylocoalsimulations_bioRxiv,
  author = {Fogg, John and Allman, Elizabeth S and An{\'e}, C{\'e}cile},
  title = {{PhyloCoalSimulations}: A simulator for network multispecies coalescent
        models, including a new extension for the inheritance of gene flow},
  elocation-id = {2023.01.11.523690},
  year = {2023},
  doi = {10.1101/2023.01.11.523690},
  journal = {bioRxiv}
}

% reference for the PhyloNetworks package, which this package depends on
@article{2017SolislemusBastideAne_PhyloNetworks,
  author = {Sol{\'\i}s-Lemus, Claudia and Bastide, Paul and An{\'e}, C{\'e}cile},
  title = {PhyloNetworks: A Package for Phylogenetic Networks},
  journal = {Molecular Biology and Evolution},
  year = {2017},
  volume = {34},
  number = {12},
  pages = {3292-3298},
  doi = {10.1093/molbev/msx235},
}

GitHub Events

Total
  • Create event: 8
  • Commit comment event: 2
  • Release event: 1
  • Issues event: 1
  • Watch event: 1
  • Delete event: 7
  • Issue comment event: 21
  • Push event: 39
  • Pull request review event: 2
  • Pull request event: 12
  • Fork event: 1
Last Year
  • Create event: 8
  • Commit comment event: 2
  • Release event: 1
  • Issues event: 1
  • Watch event: 1
  • Delete event: 7
  • Issue comment event: 21
  • Push event: 39
  • Pull request review event: 2
  • Pull request event: 12
  • Fork event: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 3
  • Total pull requests: 20
  • Average time to close issues: 2 days
  • Average time to close pull requests: 6 days
  • Total issue authors: 3
  • Total pull request authors: 5
  • Average comments per issue: 3.0
  • Average comments per pull request: 1.7
  • Merged pull requests: 12
  • Bot issues: 0
  • Bot pull requests: 7
Past Year
  • Issues: 0
  • Pull requests: 9
  • Average time to close issues: N/A
  • Average time to close pull requests: 6 days
  • Issue authors: 0
  • Pull request authors: 3
  • Average comments per issue: 0
  • Average comments per pull request: 2.11
  • Merged pull requests: 4
  • Bot issues: 0
  • Bot pull requests: 5
View more stats
Top Authors
Issue Authors
  • arleyc (1)
  • fogg-uw (1)
  • JuliaTagBot (1)
  • crsl4 (1)
Pull Request Authors
  • cecileane (10)
  • dependabot[bot] (8)
  • jjustison (4)
  • github-actions[bot] (2)
  • fogg-uw (2)
Top Labels
Issue Labels
Pull Request Labels
dependencies (8) github_actions (2)

Packages

  • Total packages: 1
  • Total downloads:
    • julia 329 total
  • Total dependent packages: 1
  • Total dependent repositories: 0
  • Total versions: 5
juliahub.com: PhyloCoalSimulations
  • Versions: 5
  • Dependent Packages: 1
  • Dependent Repositories: 0
  • Downloads: 329 Total
Rankings
Dependent repos count: 9.9%
Dependent packages count: 23.0%
Average: 30.1%
Stargazers count: 34.1%
Forks count: 53.5%
Last synced: 6 months ago

Dependencies

.github/workflows/CI.yml actions
  • actions/checkout v2 composite
  • codecov/codecov-action v2 composite
  • julia-actions/cache v1 composite
  • julia-actions/julia-buildpkg v1 composite
  • julia-actions/julia-docdeploy v1 composite
  • julia-actions/julia-processcoverage v1 composite
  • julia-actions/julia-runtest v1 composite
  • julia-actions/setup-julia v1 composite
  • r-lib/actions/setup-r v2 composite
.github/workflows/TagBot.yml actions
  • JuliaRegistries/TagBot v1 composite
.github/workflows/doccleanup.yml actions
  • actions/checkout v2 composite
.github/workflows/CompatHelper.yml actions