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
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 1.1.0
- This is the version 1.1.0:
- Penalized Likelihood methods for High-Dimensional datasets (mvgls)
- Multivariate GLS (mvgls)
- PCA on GLS covariance estimate (mvgls)
- Some minor bugs corrections (see NEWS)
- 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 (1.0.9) 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)
install_github("JClavel/mvMORPH", build_vignettes = 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] (https://cran.r-project.org/bin/windows/Rtools/) and for [Mac] (http://r.research.att.com) (and [Tools] (https://r.research.att.com/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. DOI: 10.1111/2041-210X.12420