# Multivariate Stochastic Linear Ornstein-Uhlenbeck Models for Phylogenetic Comparative Hypotheses

## Documentation for package ‘mvSLOUCH’ version 2.7.7

- 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