Multivariate Comparative Tools for Fitting Evolutionary Models to Morphometric Data


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Documentation for package ‘mvMORPH’ version 1.1.0

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mvMORPH-package Multivariate Comparative Methods for Fitting Evolutionary Models to Morphometric Data
aicw Akaike weights
coef.mvgls Extract multivariate gls model coefficients
estim Ancestral states reconstructions and missing value imputation with phylogenetic/time-series models
fitted.mvgls Extract multivariate gls model fitted values
GIC Generalized Information Criterion (GIC) to compare models fit with 'mvgls' by Maximum Likelihood (ML) or Penalized Likelihood (PL).
halflife The phylogenetic half-life for an Ornstein-Uhlenbeck process
LRT Likelihood Ratio Test
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.pca Principal Component Analysis (PCA) based on GLS 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
mvOU Multivariate Ornstein-Uhlenbeck model of continuous traits evolution
mvOUTS Multivariate continuous trait evolution for a stationary time series (Ornstein-Uhlenbeck model)
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
pruning Pruning algorithm to compute the square root of the phylogenetic covariance matrix and it's determinant.
residuals.mvgls Extract gls model residuals
stationary The stationary variance of an Ornstein-Uhlenbeck process
vcov.mvgls Calculate variance-covariance matrix for a fitted object of class 'mvgls'