# Multivariate Comparative Tools for Fitting Evolutionary Models to Morphometric Data

## Documentation for package ‘mvMORPH’ version 1.2.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

mvMORPH-package | Multivariate Comparative Methods for Fitting Evolutionary Models to Morphometric Data
aicw | Akaike weights
ancestral | Estimation of traits ancestral states.
coef.mvgls | Extract multivariate gls (or ols) model coefficients
dfaShape | Projection of 2D and 3D shapes (from geometric morphometric datasets) on Discriminant axes
effectsize | Multivariate measure of association/effect size for objects of class "manova.gls"
EIC | Extended Information Criterion (EIC) to compare models fit with 'mvgls' (or 'mvols') by Maximum Likelihood (ML) or Penalized Likelihood (PL)
estim | Ancestral states reconstructions and missing value imputation with phylogenetic/time-series models
fitted.mvgls | Extract multivariate gls (or ols) model fitted values
GIC | Generalized Information Criterion (GIC) to compare models fit with 'mvgls' (or 'mvols') by Maximum Likelihood (ML) or Penalized Likelihood (PL)
halflife | The phylogenetic half-life for an Ornstein-Uhlenbeck process
LRT | Likelihood Ratio Test
manova.gls | Multivariate Analysis of Variance
mv.Precalc | Model parameterization for the various mvMORPH functions
mvBM | Multivariate Brownian Motion models of continuous traits evolution
mvEB | Multivariate Early Burst model of continuous traits evolution
mvgls | Fit linear model using Generalized Least Squares to multivariate (high-dimensional) data sets
mvgls.dfa | Discriminant Function Analysis (DFA) - also called Linear Discriminant Analysis (LDA) or Canonical Variate Analysis (CVA) - based on multivariate GLS (or OLS) model fit
mvgls.pca | Principal Component Analysis (PCA) based on GLS (or OLS) estimate of the traits variance-covariance matrix (possibly regularized)
mvLL | Multivariate (and univariate) algorithms for log-likelihood estimation of arbitrary covariance matrix/trees
mvMORPH | Multivariate Comparative Methods for Fitting Evolutionary Models to Morphometric Data
mvols | Fit linear model using Ordinary Least Squares to multivariate (high-dimensional) data sets
mvOU | Multivariate Ornstein-Uhlenbeck model of continuous traits evolution
mvOUTS | Multivariate continuous trait evolution for a stationary time series (Ornstein-Uhlenbeck model)
mvqqplot | Quantile-Quantile plots for multivariate models fit with 'mvgls' or 'mvols'
mvRWTS | Multivariate Brownian motion / Random Walk model of continuous traits evolution on time series
mvSHIFT | Multivariate change in mode of continuous trait evolution
mvSIM | Simulation of (multivariate) continuous traits on a phylogeny
pairwise.contrasts | Pairwise contrasts
pairwise.glh | Pairwise multivariate tests between levels of a factor
pcaShape | Projection of 2D and 3D shapes (from geometric morphometric datasets) on Principal Component Axes (PCA)
phyllostomid | Phylogeny and trait data for a sample of Phyllostomid bats
predict.mvgls | Predictions from (multivariate) gls or ols model fit
predict.mvgls.dfa | Predictions from Discriminant analysis conducted with a mvgls model fit
pruning | Pruning algorithm to compute the square root of the phylogenetic covariance matrix and its determinant.
residuals.mvgls | Extract gls (or ols) model residuals
stationary | The stationary variance of an Ornstein-Uhlenbeck process
vcov.mvgls | Calculate variance-covariance matrix for a fitted object of class 'mvgls'