Multivariate Comparative Tools for Fitting Evolutionary Models to Morphometric Data

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Documentation for package ‘mvMORPH’ version 1.1.9

• 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'