Learn R Programming
⚠️There's a newer version (2.7.7) of this package.Take me there.

mvSLOUCH (version 2.7.6)

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) . The suggested PCMBaseCpp package (which significantly speeds up the likelihood calculations) can be obtained from .

Copy Link

Version

Install

install.packages('mvSLOUCH')

Monthly Downloads

309

Version

2.7.6

License

GPL (>= 2) | file LICENCE

Maintainer

Krzysztof Bartoszek

Last Published

November 20th, 2023

Functions in mvSLOUCH (2.7.6)

SummarizeBM

Summarize parameters estimated under a Brownian motion model
drawPhylProcess

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

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

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

Estimate parameters under a Brownian motion model of evolution
OU_phylreg

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

Summarize parameters estimated under a multivariate OUBM motion model
fitch.mvsl

Unordered Fitch parsimony reconstruction of discrete character states
estimate.evolutionary.model

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

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

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

Extract path information from a phylogenetic tree
simulBMProcPhylTree

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

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

Parametric bootstrap for confidence intervals
generate.model.setups

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

Simulate data on a phylogeny under a (multivariate) OU model
mvSLOUCH-internal

Internal mvSLOUCH objects
simulate_clustered_phylogeny

Simulate a phylogenetic tree with a specified number of clades.
plot.clustered_phylo

Plots a clustered_phylo object.
mvSLOUCH-package

Multivariate Ornstein-Uhlenbeck type stochastic differential equation models for phylogenetic comparative data.
mvslouchModel

Estimate parameters under a (multivariate) OUBM model of evolution