Package: mvSLOUCH 2.7.7

Krzysztof Bartoszek

mvSLOUCH: Multivariate Stochastic Linear Ornstein-Uhlenbeck Models for Phylogenetic Comparative Hypotheses

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) <doi:10.1016/j.jtbi.2012.08.005> and K. Bartoszek, and J. Tredgett Clarke, J. Fuentes-Gonzalez, V. Mitov, J. Pienaar, M. Piwczynski, R. Puchalka, K. Spalik, K. L. Voje (2024) <doi:10.1111/2041-210X.14376>. The suggested PCMBaseCpp package (which significantly speeds up the likelihood calculations) can be obtained from <https://github.com/venelin/PCMBaseCpp/>.

Authors:Krzysztof Bartoszek [cre, aut], John Clarke [ctb], Jesualdo Fuentes-Gonzalez [ctb], Jason Pienaar [ctb]

mvSLOUCH_2.7.7.tar.gz
mvSLOUCH_2.7.7.tar.gz(r-4.7-any)mvSLOUCH_2.7.7.tar.gz(r-4.6-any)
mvSLOUCH_2.7.7.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
mvSLOUCH/json (API)

# Install 'mvSLOUCH' in R:

install.packages('mvSLOUCH', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

3.83 score 1 packages 75 scripts 437 downloads 3 mentions 20 exports 32 dependencies

Last updated from:59a2ec8a5b. Checks:4 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	200
source / vignettes	OK	230
linux-release-x86_64	OK	202
wasm-release	OK	123

Exports:BrownianMotionModel drawPhylProcess estimate.evolutionary.model fitch.mvsl generate.model.setups mvslouchModel OU_phylreg OU_RSS OU_xVz ouchModel parametric.bootstrap phyltree_paths plot.clustered_phylo simulate_clustered_phylogeny simulBMProcPhylTree simulMVSLOUCHProcPhylTree simulOUCHProcPhylTree SummarizeBM SummarizeMVSLOUCH SummarizeOUCH

Dependencies:abind ape cli cpp11 data.table digest expm farver ggplot2 glue gtable isoband labeling lattice lifecycle Matrix matrixcalc mvtnorm nlme ouch PCMBase R6 RColorBrewer Rcpp rlang S7 scales subplex vctrs viridisLite withr xtable

Analysis of locomotion and forelimb morphology in carnivorans using the mvSLOUCH R-package

Introduction | Data: Locomotion and forelimb morphology in carnivorans

Rendered frommvSLOUCH_Carnivorans.Rmdusingknitr::rmarkdown

Last update: 2022-05-04
Started: 2021-03-09

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

Package: mvSLOUCH 2.7.7

mvSLOUCH: Multivariate Stochastic Linear Ornstein-Uhlenbeck Models for Phylogenetic Comparative Hypotheses

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