Science Score: 49.0%
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
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 6 DOI reference(s) in README -
○Academic publication links
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✓Committers with academic emails
3 of 7 committers (42.9%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (9.5%) to scientific vocabulary
Keywords
Repository
R package for breeding program simulations
Basic Info
- Host: GitHub
- Owner: gaynorr
- License: other
- Language: R
- Default Branch: master
- Homepage: https://gaynorr.github.io/AlphaSimR/
- Size: 9.69 MB
Statistics
- Stars: 53
- Watchers: 8
- Forks: 23
- Open Issues: 39
- Releases: 12
Topics
Metadata Files
README.md
README
The successor to the 'AlphaSim' software for breeding program simulation (Faux et al., 2016; https://doi.org/10.3835/plantgenome2016.02.0013). Used for stochastic simulations of breeding programs to the level of DNA sequence for every individual. Contained is a wide range of functions for modeling common tasks in a breeding program, such as selection and crossing. These functions allow for constructing simulations of highly complex plant and animal breeding programs via scripting in the R software environment. Such simulations can be used to evaluate overall breeding program performance and conduct research into breeding program design, such as implementation of genomic selection. Included is the 'Markovian Coalescent Simulator' ('MaCS') for fast simulation of biallelic sequences according to a population demographic history (Chen et al., 2009; https://doi.org/10.1101/gr.083634.108).
Publication
Gaynor, R. Chris, Gregor Gorjanc, and John M. Hickey. 2021. AlphaSimR: an R package for breeding program simulations. G3 Gene|Genomes|Genetics 11(2):jkaa017. https://doi.org/10.1093/g3journal/jkaa017.
Download
AlphaSimR is available on CRAN.
To install use:
install.packages('AlphaSimR')
The development version of AlphaSimR (potentially unstable) can be accessed from the devel branch on GitHub.
To install use:
devtools::install_github(repo="gaynorr/AlphaSimR@devel")
To install with vignettes use:
devtools::install_github(repo="gaynorr/AlphaSimR@devel", build_vignettes=TRUE)
Owner
- Name: Chris Gaynor
- Login: gaynorr
- Kind: user
- Company: Bayer Crop Science
- Repositories: 3
- Profile: https://github.com/gaynorr
GitHub Events
Total
- Create event: 2
- Release event: 2
- Issues event: 13
- Watch event: 10
- Issue comment event: 35
- Push event: 17
- Pull request event: 15
- Fork event: 4
Last Year
- Create event: 2
- Release event: 2
- Issues event: 13
- Watch event: 10
- Issue comment event: 35
- Push event: 17
- Pull request event: 15
- Fork event: 4
Committers
Last synced: over 1 year ago
Top Committers
| Name | Commits | |
|---|---|---|
| GAYNOR Chris | c****r@r****k | 196 |
| Chris Gaynor | g****t@h****m | 151 |
| Gregor Gorjanc | g****c@g****m | 47 |
| MONEY Daniel | D****y@r****k | 14 |
| David Wilson | d****n@r****k | 3 |
| philipbg | 5****g | 2 |
| AudreyAAMartin | 1****n | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 111
- Total pull requests: 56
- Average time to close issues: 4 months
- Average time to close pull requests: 2 days
- Total issue authors: 28
- Total pull request authors: 7
- Average comments per issue: 2.36
- Average comments per pull request: 0.84
- Merged pull requests: 41
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 10
- Pull requests: 11
- Average time to close issues: about 1 month
- Average time to close pull requests: 10 days
- Issue authors: 9
- Pull request authors: 4
- Average comments per issue: 1.6
- Average comments per pull request: 1.0
- Merged pull requests: 4
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- gregorgorjanc (59)
- gaynorr (10)
- rthapa1 (6)
- AudreyAAMartin (5)
- janaobsteter (4)
- jamonterotena (3)
- poca87 (2)
- zjwinn (2)
- marcio-resende (2)
- philipbg (1)
- takosa (1)
- LucianoRogerio (1)
- juliendiot42 (1)
- metwallys (1)
- maxecoulter (1)
Pull Request Authors
- gregorgorjanc (29)
- gaynorr (22)
- philipbg (3)
- domwaters19 (2)
- janaobsteter (2)
- RosCraddock (1)
- Prof-ThiagoOliveira (1)
- AudreyAAMartin (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- cran 1,367 last-month
- Total dependent packages: 2
- Total dependent repositories: 5
- Total versions: 25
- Total maintainers: 1
cran.r-project.org: AlphaSimR
Breeding Program Simulations
- Homepage: https://github.com/gaynorr/AlphaSimR
- Documentation: http://cran.r-project.org/web/packages/AlphaSimR/AlphaSimR.pdf
- License: MIT + file LICENSE
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Latest release: 2.0.0
published 6 months ago
Rankings
Maintainers (1)
Dependencies
- R >= 4.0.0 depends
- R6 * depends
- methods * depends
- Rcpp >= 0.12.7 imports
- knitr * suggests
- rmarkdown * suggests
- testthat * suggests
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- JamesIves/github-pages-deploy-action 4.1.4 composite
- actions/checkout v2 composite
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- r-lib/actions/setup-r v2 composite
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