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mvSLOUCH (version 2.7.7)

Multivariate Stochastic Linear Ornstein-Uhlenbeck Models for Phylogenetic Comparative Hypotheses

Description

Fits multivariate Ornstein-Uhlenbeck types of models to continues trait data from species related by a common evolutionary history. See K. Bartoszek, J, Pienaar, P. Mostad, S. Andersson, T. F. Hansen (2012) and K. Bartoszek, and J. Tredgett Clarke, J. Fuentes-Gonzalez, V. Mitov, J. Pienaar, M. Piwczynski, R. Puchalka, K. Spalik, K. L. Voje (2024) . The suggested PCMBaseCpp package (which significantly speeds up the likelihood calculations) can be obtained from .

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Version

Install

install.packages('mvSLOUCH')

Monthly Downloads

309

Version

2.7.7

License

GPL (>= 2) | file LICENCE

Maintainer

Krzysztof Bartoszek

Last Published

July 24th, 2025

Functions in mvSLOUCH (2.7.7)

fitch.mvsl

Unordered Fitch parsimony reconstruction of discrete character states
SummarizeMVSLOUCH

Summarize parameters estimated under a multivariate OUBM motion model
estimate.evolutionary.model

Wrapper function to find best (out of BM, OU, OUOU, OUBM) fitting evolutionary model and estimate its parameters.
OU_phylreg

Performs a phylogenetic regression under a given OU model of evolution
BrownianMotionModel

Estimate parameters under a Brownian motion model of evolution
drawPhylProcess

Plots the realization of a process evolving on a phylogenetic tree
OU_xVz

Performs a vector matrix vector multiplcation under a (multivariate) phylogenetic OU model of evolution
SummarizeBM

Summarize parameters estimated under a Brownian motion model
OU_RSS

Calculates the RSS under a (multivariate) phylogenetic OU model of evolution
SummarizeOUCH

Summarize parameters estimated under a (multivariate) OU motion model
simulMVSLOUCHProcPhylTree

Simulate data on a phylogeny under a (multivariate) OUBM model
parametric.bootstrap

Parametric bootstrap for confidence intervals
plot.clustered_phylo

Plots a clustered_phylo object.
mvSLOUCH-internal

Internal mvSLOUCH objects
phyltree_paths

Extract path information from a phylogenetic tree
mvslouchModel

Estimate parameters under a (multivariate) OUBM model of evolution
mvSLOUCH-package

Multivariate Ornstein-Uhlenbeck type stochastic differential equation models for phylogenetic comparative data.
generate.model.setups

Generate a list of model setups for the function estimate.evolutionary.model.
simulate_clustered_phylogeny

Simulate a phylogenetic tree with a specified number of clades.
ouchModel

Estimate parameters under a (multivariate) OU model of evolution
simulOUCHProcPhylTree

Simulate data on a phylogeny under a (multivariate) OU model
simulBMProcPhylTree

Simulate data on a phylogeny under a (multivariate) Brownian motion model