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 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 1.0.8

This is the version 1.0.8:

Allows estimating the missing cases (NA)
Allows estimating trends
User defined constrained models and parameterizations
Return the log-likelihood function
Simulating traits on package vignette
Multivariate models for time-series (TS)
Partial implementation of a tests-suite

TODO:

Incorporation of a tests-suite
Implement the sampler (upcomming mvMORPH)
Code improvements
Extend the shift model to TS
Formula option for independent variables

The current stable version of the mvMORPH package (1.0.8) is on the CRAN repository. https://cran.r-project.org/package=mvMORPH

Package Installation

You can download the current beta version (1.0.8) binaries for Windows and Mac OS X from the release page

You can also install it 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

Download version with appended supplementary material.