Science Score: 23.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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○codemeta.json file
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○.zenodo.json file
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✓DOI references
Found 7 DOI reference(s) in README -
○Academic publication links
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✓Committers with academic emails
1 of 3 committers (33.3%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (13.6%) to scientific vocabulary
Repository
Statistical Analysis of Mixed Ploidy Populations
Basic Info
- Host: GitHub
- Owner: lpembleton
- Language: R
- Default Branch: master
- Homepage: https://lpembleton.github.io/StAMPP/
- Size: 419 KB
Statistics
- Stars: 1
- Watchers: 1
- Forks: 1
- Open Issues: 3
- Releases: 0
Metadata Files
README.md
StAMPP: Statistical Analysis of Mixed Ploidy Populations 
StAMPP is an R package for the Statistical Analysis of Mixed Ploidy Populations. It allows users to calculate pairwise Nei's Genetic Distances (Nei 1972), pairwise Fixation Indexes (Fst) (Weir & Cockerham 1984) and also Genomic Relationship matrixes following Yang et al. (2010) in mixed and single ploidy populations. Bootstrapping across loci is implemented during Fst calculation to generate confidence intervals and p-values around pairwise Fst values. StAMPP utilises SNP genotype data of any ploidy level (with the ability to handle missing data) and is coded to utilise multithreading where available to allow efficient analysis of large datasets. StAMPP is able to handle genotype data from genlight objects allowing integration with other packages such adegenet.
Installation
You can install the latest stable version of StAMPP from CRAN:
r
install.packages("StAMPP")
Version
This GitHub repository hosts the latest version of StAMPP which may be a pre-alpha/alpha/beta development version. Please check NEWS.md for details.
Vignette
A vignette describing the use of the package is available from within
R (and also here). Load the package
and then use the vignette function.
r
library(StAMPP)
vignette("StAMPP", package="StAMPP")
Citation
LW Pembleton, NOI Cogan & JW Forster, 2013, Molecular Ecology Resources, 13(5), 946-952. doi:10.1111/1755-0998.12129.
Thank you in advance.
Owner
- Name: Luke Pembleton
- Login: lpembleton
- Kind: user
- Location: Melbourne, Victoria
- Company: Barenbrug Global
- Website: https://lpembleton.rbind.io/
- Twitter: lwpembleton
- Repositories: 2
- Profile: https://github.com/lpembleton
Genomic Breeding Scientist | Strategic Science Manager at Barenbrug.
GitHub Events
Total
- Watch event: 1
Last Year
- Watch event: 1
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Luke Pembleton | l****n@b****m | 7 |
| Luke Pembleton (DJPR) | l****n@a****u | 4 |
| Luke Pembleton | 8****n | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: over 2 years ago
All Time
- Total issues: 3
- Total pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Total issue authors: 3
- Total pull request authors: 0
- Average comments per issue: 2.0
- Average comments per pull request: 0
- Merged pull requests: 0
- 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: 2.0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- ne1s0n (1)
- jacquelinemattos (1)
- monis4567 (1)
- laiajulianamu (1)
- pascalangst (1)
Pull Request Authors
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- cran 1,140 last-month
- Total docker downloads: 42,733
- Total dependent packages: 4
- Total dependent repositories: 1
- Total versions: 9
- Total maintainers: 1
cran.r-project.org: StAMPP
Statistical Analysis of Mixed Ploidy Populations
- Homepage: https://github.com/lpembleton/StAMPP
- Documentation: http://cran.r-project.org/web/packages/StAMPP/StAMPP.pdf
- License: GPL-3
-
Latest release: 1.6.3
published almost 5 years ago
Rankings
Maintainers (1)
Dependencies
- R >= 3.2.0 depends
- pegas * depends
- adegenet * imports
- doParallel * imports
- foreach * imports
- methods * imports
- parallel * imports
- utils * imports