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mmod

Differentiation statistics in R

https://github.com/dwinter/mmod

Science Score: 20.0%

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
    Links to: zenodo.org
  • ✓
    Committers with academic emails
    1 of 6 committers (16.7%) from academic institutions
  • ○
    Institutional organization owner
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    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (14.0%) to scientific vocabulary
Last synced: 11 months ago · JSON representation

Repository

Differentiation statistics in R

Basic Info
  • Host: GitHub
  • Owner: dwinter
  • License: other
  • Language: R
  • Default Branch: master
  • Homepage:
  • Size: 8.54 MB
Statistics
  • Stars: 11
  • Watchers: 3
  • Forks: 5
  • Open Issues: 8
  • Releases: 0
Created over 14 years ago · Last pushed about 9 years ago
Metadata Files
Readme License

README.md

Travis-CI Build Status Current CRAN Release Coverage Status

Modern Measures of Differentiation

mmod is an R package for calculating modern population divergence statistics.

Quickstart

Install

mmod is on CRAN, so you can install the latest stable version using install.packages("mmod"). This github repository may be running ahead of the version on CRAN, if you really want the latest version you can use devtools to install the code in thes repo:

r library(devtools) install_github("dwinter/mmod")

Usage

Once it's up an running all you need is genepop (or fstat) file with your data

    >library(mmod)
    >my_data <- read.genepop("my_file.gen")
    >diff_stats(my_data)

Overview

Population geneticists have traditionally used Nei's Gst (often confusingly called Fst...) to measure divergence between populations. It turns out, Gst doesn't really measure divergence so, a set of new measures have been developed

mmod is a package that brings two of these measures; Hedricks (2005, 2011) G''st Jost's (2008) D and Meirman's (2005) φ'st to R, along with a function that calculates Nei's Gst using nearly unbiased estimators for Hs and Ht (the two key parameters from which most of these stats are calculated). All these functions work on genind objects from the package adegenet so data can be read in from standard genepop for fstat files. An overview of a typical usage is provided in a vignette called "demo", acessable from vignette("demo", package="mmod"), I suggest new users read this before that start.

Help

All functions are documented and there is Vignette describing a basic usage of the pacakge.

Owner

  • Name: David Winter
  • Login: dwinter
  • Kind: user
  • Location: Wellington, New Zealand

Computational evolutionary biology using R, Python and (sometimes) C++

GitHub Events

Total
Last Year

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 167
  • Total Committers: 6
  • Avg Commits per committer: 27.833
  • Development Distribution Score (DDS): 0.293
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
David Winter w****2@s****z 118
David Winter d****r@g****m 43
Zhian Kamvar k****z@s****u 2
david d****d@a****) 2
Thierry Gosselin t****n@i****m 1
pitakakariki p****i@g****m 1
Committer Domains (Top 20 + Academic)
apollo-u.(null): 1 science.oregonstate.edu: 1 student.otago.ac.nz: 1

Issues and Pull Requests

Last synced: over 1 year ago

All Time
  • Total issues: 12
  • Total pull requests: 3
  • Average time to close issues: 7 days
  • Average time to close pull requests: 1 day
  • Total issue authors: 10
  • Total pull request authors: 3
  • Average comments per issue: 1.5
  • Average comments per pull request: 1.0
  • Merged pull requests: 3
  • 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: 0.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • dwinter (2)
  • zkamvar (2)
  • JeannieKlein (1)
  • elewitus (1)
  • wchengadfg (1)
  • LinaValencia85 (1)
  • shofmon88 (1)
  • nek001 (1)
  • OrsonMM (1)
  • dionnecargy (1)
Pull Request Authors
  • thierrygosselin (1)
  • pitakakariki (1)
  • zkamvar (1)
Top Labels
Issue Labels
maintenance (1)
Pull Request Labels

Packages

  • Total packages: 2
  • Total downloads:
    • cran 1,319 last-month
  • Total dependent packages: 6
    (may contain duplicates)
  • Total dependent repositories: 8
    (may contain duplicates)
  • Total versions: 13
  • Total maintainers: 1
cran.r-project.org: mmod

Modern Measures of Population Differentiation

  • Versions: 12
  • Dependent Packages: 5
  • Dependent Repositories: 8
  • Downloads: 1,319 Last month
Rankings
Dependent packages count: 8.2%
Dependent repos count: 10.5%
Forks count: 10.8%
Average: 11.5%
Downloads: 11.6%
Stargazers count: 16.5%
Maintainers (1)
david.winter@gmail.com
Last synced: 11 months ago
conda-forge.org: r-mmod
  • Versions: 1
  • Dependent Packages: 1
  • Dependent Repositories: 0
Rankings
Dependent packages count: 28.8%
Dependent repos count: 34.0%
Average: 39.8%
Forks count: 46.0%
Stargazers count: 50.2%
Last synced: 11 months ago

Dependencies

DESCRIPTION cran
  • R >= 2.6.0 depends
  • adegenet >= 2.0 depends
  • pegas * imports
  • stats * imports
  • covr * suggests
  • testthat * suggests