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tsdate

Infer the age of ancestral nodes in a tree sequence.

https://github.com/tskit-dev/tsdate

Science Score: 67.0%

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

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    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 4 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: biorxiv.org, science.org
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    Academic email domains
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    Institutional organization owner
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    JOSS paper metadata
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    Scientific vocabulary similarity
    Low similarity (11.0%) to scientific vocabulary
Last synced: 6 months ago · JSON representation ·

Repository

Infer the age of ancestral nodes in a tree sequence.

Basic Info
  • Host: GitHub
  • Owner: tskit-dev
  • License: mit
  • Language: Python
  • Default Branch: main
  • Homepage:
  • Size: 13.4 MB
Statistics
  • Stars: 22
  • Watchers: 9
  • Forks: 11
  • Open Issues: 43
  • Releases: 12
Created over 6 years ago · Last pushed 6 months ago
Metadata Files
Readme Changelog License Citation

README.md

tsdate

CircleCI codecov

tsdate is a scalable method for estimating the age of ancestral nodes in a tree sequence. The method uses a coalescent prior and updates node times on the basis of the number of mutations along each edge of the tree sequence (i.e. using the "molecular clock").

The method is frequently combined with the tsinfer algorithm, which efficiently infers tree sequence topologies from large genetic datasets.

Please refer to the documentation for information on installing and using the software.

The algorithms for the original inside_outside and maximization methods are described in this Science paper (citation below, preprint here, evaluations in another repository). The new variational_gamma method, the default from version 0.2 onwards, has not yet been described in print. For the moment, please cite this github repository if you need a citable reference.

The citation to use for the original tsdate algorithms is:

Anthony Wilder Wohns, Yan Wong, Ben Jeffery, Ali Akbari, Swapan Mallick, Ron Pinhasi, Nick Patterson, David Reich, Jerome Kelleher, and Gil McVean (2022) A unified genealogy of modern and ancient genomes. Science 375: eabi8264; doi: https://doi.org/10.1126/science.abi8264

Owner

  • Name: Tskit developers
  • Login: tskit-dev
  • Kind: organization
  • Email: admin@tskit.dev

Software for the creation and analysis of tree-sequences.

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use tsdate in your work, please cite it as below."
authors:
- given-names: Anthony Wilder
  family-names: Wohns
  orcid: "https://orcid.org/0000-0001-7353-1177"
- given-names: Yan
  family-names: Wong
  orcid: "https://orcid.org/0000-0002-3536-6411"
- given-names: Ben
  family-names: Jeffery
  orcid: "https://orcid.org/0000-0002-1982-6801"
title: "Tsdate"
version: 0.1.4
date-released: 2021-06-30
url: "https://github.com/tskit-dev/tsdate"
license: MIT
preferred-citation:
  type: article
  authors:
  - given-names: Anthony Wilder
    family-names: Wohns
    orcid: "https://orcid.org/0000-0001-7353-1177"
  - given-names: Yan
    family-names: Wong
    orcid: "https://orcid.org/0000-0002-3536-6411"
  - given-names: Ben
    family-names: Jeffery
    orcid: "https://orcid.org/0000-0002-1982-6801"
  - given-names: Ali
    family-names: Akbari
    orcid: "https://orcid.org/0000-0002-5000-5876"
  - given-names: Swapan
    family-names: Mallick
    orcid: "https://orcid.org/0000-0002-4531-4439"
  - given-names: Ron
    family-names: Pinhasi
    orcid: "https://orcid.org/0000-0003-1629-8131"
  - given-names: Nick
    family-names: Patterson
    orcid: "https://orcid.org/0000-0003-0302-684X"
  - given-names: David
    family-names: Reich
    orcid: "https://orcid.org/0000-0002-7037-5292"
  - given-names: Jerome
    family-names: Kelleher
    orcid: "https://orcid.org/0000-0002-7894-5253"
  - given-names: Gil
    family-names: McVean
    orcid: "https://orcid.org/0000-0002-5012-4162"
  doi: "10.1126/science.abi8264"
  journal: "Science"
  start: eabi8264
  title: "A unified genealogy of modern and ancient genomes"
  volume: 375
  year: 2022

GitHub Events

Total
  • Create event: 6
  • Release event: 2
  • Issues event: 37
  • Watch event: 1
  • Delete event: 6
  • Issue comment event: 106
  • Push event: 26
  • Pull request review comment event: 13
  • Pull request review event: 18
  • Pull request event: 54
Last Year
  • Create event: 6
  • Release event: 2
  • Issues event: 37
  • Watch event: 1
  • Delete event: 6
  • Issue comment event: 106
  • Push event: 26
  • Pull request review comment event: 13
  • Pull request review event: 18
  • Pull request event: 54

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 132
  • Total pull requests: 250
  • Average time to close issues: about 1 year
  • Average time to close pull requests: about 1 month
  • Total issue authors: 16
  • Total pull request authors: 10
  • Average comments per issue: 3.7
  • Average comments per pull request: 2.2
  • Merged pull requests: 219
  • Bot issues: 0
  • Bot pull requests: 6
Past Year
  • Issues: 11
  • Pull requests: 47
  • Average time to close issues: about 8 hours
  • Average time to close pull requests: 7 days
  • Issue authors: 5
  • Pull request authors: 5
  • Average comments per issue: 0.27
  • Average comments per pull request: 1.45
  • Merged pull requests: 41
  • Bot issues: 0
  • Bot pull requests: 2
View more stats
Top Authors
Issue Authors
  • hyanwong (86)
  • awohns (16)
  • nspope (13)
  • barneyhill (3)
  • benjeffery (3)
  • swamidass (1)
  • qianfeng2 (1)
  • jeromekelleher (1)
  • nmmahmed (1)
  • stsmall (1)
  • YunDeng98 (1)
  • alxsimon (1)
  • petrelharp (1)
  • hanbin973 (1)
  • agladstein (1)
Pull Request Authors
  • hyanwong (150)
  • benjeffery (38)
  • nspope (33)
  • awohns (16)
  • dependabot[bot] (4)
  • mergify[bot] (2)
  • barneyhill (2)
  • petrelharp (2)
  • hfr1tz3 (2)
  • hossam26644 (1)
Top Labels
Issue Labels
enhancement (8) invalid (2) documentation (1) bug (1) good first issue (1)
Pull Request Labels
dependencies (4) github_actions (2)

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 238 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 5
  • Total versions: 12
  • Total maintainers: 2
pypi.org: tsdate

Infer node ages from a tree sequence topology.

  • Versions: 12
  • Dependent Packages: 0
  • Dependent Repositories: 5
  • Downloads: 238 Last month
Rankings
Dependent repos count: 6.6%
Dependent packages count: 10.1%
Forks count: 12.5%
Average: 13.4%
Stargazers count: 15.2%
Downloads: 22.5%
Maintainers (2)
benjeffery awohns
Last synced: 6 months ago

Dependencies

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docs/requirements.txt pypi
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  • six *
  • sphinx-argparse *
  • sphinx_issues *
  • sphinx_rtd_theme *
  • tqdm *
  • tskit *
requirements.txt pypi
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  • codecov *
  • daiquiri *
  • flake8 *
  • msprime >=1.0.0
  • numba ==0.53.1
  • numpy *
  • pre-commit *
  • pytest *
  • pytest-cov *
  • pytest-xdist *
  • scipy *
  • tqdm *
  • tsinfer >=0.2.0
  • tskit >=0.4.0
setup.py pypi
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  • numba >=0.46.0
  • numpy *
  • scipy >1.2.3
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  • tskit >=0.2.3
pyproject.toml pypi
.github/workflows/docs.yml actions
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