mvMORPH
mvMORPH: an R package for fitting multivariate evolutionary models to morphometric data
Science Score: 23.0%
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○CITATION.cff file
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○.zenodo.json file
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○DOI references
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○Academic publication links
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✓Committers with academic emails
3 of 8 committers (37.5%) from academic institutions -
○Institutional organization owner
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○Scientific vocabulary similarity
Low similarity (13.4%) to scientific vocabulary
Repository
mvMORPH: an R package for fitting multivariate evolutionary models to morphometric data
Basic Info
- Host: GitHub
- Owner: JClavel
- Language: R
- Default Branch: master
- Size: 10.9 MB
Statistics
- Stars: 18
- Watchers: 3
- Forks: 5
- Open Issues: 6
- Releases: 1
Metadata Files
README.md
mvMORPH
mvMORPH: an R package for fitting multivariate evolutionary models to morphometric data
This package allows the fitting of multivariate evolutionary models (Ornstein-Uhlenbeck, Brownian motion, Early burst, Shift models) on species trees and time series. It also provides functions to compute log-likelihood of users specified models with fast methods (e.g., for Bayesian approaches or customized comparative methods), simulates correlated traits under various models, constrain various parts of multivariate models...
The package implement now efficient methods for high-dimensional multivariate comparative methods (mvgls) based on Penalized likelihood as well as associated tests (Wilks, Pillai...)
The package is designed to handle ultrametric and non-ultrametric trees (i.e. with fossil species) and missing data in multivariate datasets (NA values), SIMMAP mapping of discrete traits, measurement error, etc...
See the packages vignettes for details and examples: browseVignettes("mvMORPH").
mvMORPH 1.2.1
This is the version 1.2.1:
- Check the NEWS file for detailled updates
TODO:
- Incorporation of a tests-suite
- Implement the sampler (upcomming mvMORPH)
- Code improvements
- Extend the shift model to TS
- Improved mvOU model
- Threshold model for categorical data
The current stable version of the mvMORPH package (1.2.0) is on the CRAN repository. https://cran.r-project.org/package=mvMORPH
Package Installation
You can install the package directly from gitHub through devtools:
``` library(devtools)
installgithub("JClavel/mvMORPH", buildvignettes = TRUE)
```
(The installation may crash if your dependencies are not up to date. Note that you may also need to install Rtools to compile the C codes included in the package. For Windows and for Mac (and Tools )
Report an issue
Any bugs encountered when using the package can be reported here
Package citation
Clavel, J., Escarguel, G., Merceron, G. 2015. mvMORPH: an R package for fitting multivariate evolutionary models to morphometric data. Methods in Ecology and Evolution, 6(11):1311-1319.
Owner
- Login: JClavel
- Kind: user
- Repositories: 1
- Profile: https://github.com/JClavel
GitHub Events
Total
- Issue comment event: 2
- Push event: 4
Last Year
- Issue comment event: 2
- Push event: 4
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Clavel Julien | j****l@h****r | 124 |
| JClavel | j****l@b****l | 9 |
| JClavel | j****l@i****r | 7 |
| JClavel | j****l@i****r | 3 |
| JClavel | j****l@p****e | 2 |
| JClavel | j****l@i****r | 1 |
| thauffe | t****e@g****m | 1 |
| shreeramsenthi | 3****i | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 11 months ago
All Time
- Total issues: 15
- Total pull requests: 3
- Average time to close issues: about 2 months
- Average time to close pull requests: 5 months
- Total issue authors: 15
- Total pull request authors: 3
- Average comments per issue: 2.27
- Average comments per pull request: 1.33
- 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: 2.0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- CamilleAnna (1)
- meireles (1)
- sz-1002 (1)
- DPANN (1)
- emaseculi (1)
- Wxdeyyy (1)
- cdmuir (1)
- MKeao (1)
- charlllie (1)
- acope3 (1)
- gaballench (1)
- r03ert0 (1)
- corinthiablack (1)
- rafmarcondes (1)
- jakeberv (1)
Pull Request Authors
- thauffe (1)
- shreeramsenthi (1)
- rvosa (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- cran 707 last-month
- Total docker downloads: 21,777
- Total dependent packages: 5
- Total dependent repositories: 7
- Total versions: 22
- Total maintainers: 1
cran.r-project.org: mvMORPH
Multivariate Comparative Tools for Fitting Evolutionary Models to Morphometric Data
- Homepage: https://github.com/JClavel/mvMORPH
- Documentation: http://cran.r-project.org/web/packages/mvMORPH/mvMORPH.pdf
- License: GPL-2 | GPL-3 [expanded from: GPL (≥ 2.0)]
-
Latest release: 1.2.1
published almost 2 years ago
Rankings
Maintainers (1)
Dependencies
- R >= 2.9.1 depends
- ape * depends
- corpcor * depends
- phytools * depends
- subplex * depends
- glassoFast * imports
- graphics * imports
- parallel * imports
- pbmcapply * imports
- spam * imports
- stats * imports
- utils * imports
- car * suggests
- knitr * suggests