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 1.1.6

This is the version 1.1.6:

fix issue in the estimation of GIC with “BMM” model in mvgls. The GIC was lower than expected due to formatting issues in the scaling of the rates.
implements the ‘mvols’ function, a wrapper to the more general ‘mvgls’ function to fit ordinary multivariate regressions (possibly regularized).

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 (1.1.6) 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] (https://mac.r-project.org/) (and [Tools] (https://mac.r-project.org/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.