Multivariate Stochastic Linear Ornstein-Uhlenbeck Models for Phylogenetic Comparative Hypotheses

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Documentation for package ‘mvSLOUCH’ version 2.7.6

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

mvSLOUCH-package	Multivariate Ornstein-Uhlenbeck type stochastic differential equation models for phylogenetic comparative data.
BrownianMotionModel	Estimate parameters under a Brownian motion model of evolution
drawPhylProcess	Plots the realization of a process evolving on a phylogenetic tree
estimate.evolutionary.model	Wrapper function to find best (out of BM, OU, OUOU, OUBM) fitting evolutionary model and estimate its parameters.
fitch.mvsl	Unordered Fitch parsimony reconstruction of discrete character states
generate.model.setups	Generate a list of model setups for the function 'estimate.evolutionary.model'.
mvSLOUCH	Multivariate Ornstein-Uhlenbeck type stochastic differential equation models for phylogenetic comparative data.
mvslouchModel	Estimate parameters under a (multivariate) OUBM model of evolution
ouchModel	Estimate parameters under a (multivariate) OU model of evolution
OU_phylreg	Performs a phylogenetic regression under a given OU model of evolution
OU_RSS	Calculates the RSS under a (multivariate) phylogenetic OU model of evolution
OU_xVz	Performs a vector matrix vector multiplcation under a (multivariate) phylogenetic OU model of evolution
parametric.bootstrap	Parametric bootstrap for confidence intervals
phyltree_paths	Extract path information from a phylogenetic tree
plot.clustered_phylo	Plots a clustered_phylo object.
simulate_clustered_phylogeny	Simulate a phylogenetic tree with a specified number of clades.
simulBMProcPhylTree	Simulate data on a phylogeny under a (multivariate) Brownian motion model
simulMVSLOUCHProcPhylTree	Simulate data on a phylogeny under a (multivariate) OUBM model
simulOUCHProcPhylTree	Simulate data on a phylogeny under a (multivariate) OU model
SummarizeBM	Summarize parameters estimated under a Brownian motion model
SummarizeMVSLOUCH	Summarize parameters estimated under a multivariate OUBM motion model
SummarizeOUCH	Summarize parameters estimated under a (multivariate) OU motion model