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diemr

Diagnostic index expectation maximisation (diem) algorithm implementations

https://github.com/stuartjebaird/diem

Science Score: 26.0%

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    Found 4 DOI reference(s) in README
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    Low similarity (5.9%) to scientific vocabulary
Last synced: 11 months ago · JSON representation

Repository

Diagnostic index expectation maximisation (diem) algorithm implementations

Basic Info
  • Host: GitHub
  • Owner: StuartJEBaird
  • Language: R
  • Default Branch: main
  • Size: 1.05 MB
Statistics
  • Stars: 9
  • Watchers: 3
  • Forks: 0
  • Open Issues: 4
  • Releases: 1
Created about 4 years ago · Last pushed over 1 year ago
Metadata Files
Readme

README.md

diem: Diagnostic index expectation maximisation

Alt text

diem is a genome polarisation algorithm that finds which alleles of genomic markers belong to which side of a barrier, co-estimating which individuals belong on either side. diem is a deterministic expectation maximisation algorithm and so uses the likelihood inference framework.

The diem algorithm has been implemented in several programming languages, with core functions and accompanying tools stored in this repository.

  1. diemr - R implementation. The package is available through https://CRAN.R-project.org/package=diemr.
  2. diempy - Python implementation.
  3. diemmca - Mathematica implementation. Soon also to be available at https://www.notebookarchive.org

When using any of the diem algorithm implementations, cite:

Stuart J. E. Baird, Jan Petružela, Izar Jaroň, Pavel Škrabánek, Natália Martínková. 2022. Genome polarisation for detecting barriers to geneflow. bioRxiv 2022.03.24.485605; doi: https://doi.org/10.1101/2022.03.24.485605.

Stuart J. E. Baird, Jan Petružela, Izar Jaroň, Pavel Škrabánek, Natália Martínková. 2023. Genome polarisation for detecting barriers to geneflow. Methods in Ecology and Evolution; doi: https://doi.org/10.1111/2041-210X.14010.

Owner

  • Name: Stuart
  • Login: StuartJEBaird
  • Kind: user

GitHub Events

Total
  • Watch event: 2
  • Issue comment event: 1
  • Push event: 3
Last Year
  • Watch event: 2
  • Issue comment event: 1
  • Push event: 3

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 36
  • Total Committers: 2
  • Avg Commits per committer: 18.0
  • Development Distribution Score (DDS): 0.194
Past Year
  • Commits: 2
  • Committers: 1
  • Avg Commits per committer: 2.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Stuart S****d@g****m 29
Natália Martínková 1****a 7

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 5
  • Total pull requests: 2
  • Average time to close issues: over 1 year
  • Average time to close pull requests: less than a minute
  • Total issue authors: 4
  • Total pull request authors: 1
  • Average comments per issue: 13.0
  • Average comments per pull request: 0.0
  • Merged pull requests: 2
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 1
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 1
  • Pull request authors: 0
  • Average comments per issue: 1.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • simonharnqvist (2)
  • wmy-m (1)
  • kfpbennett (1)
  • MengLu-flw (1)
Pull Request Authors
  • nmartinkova (2)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • cran 312 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 12
  • Total maintainers: 1
cran.r-project.org: diemr

Diagnostic Index Expectation Maximisation in R

  • Versions: 12
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 312 Last month
Rankings
Dependent packages count: 29.8%
Dependent repos count: 35.5%
Average: 38.6%
Downloads: 50.6%
Maintainers (1)
martinkova@ivb.cz
Last synced: 11 months ago