Package: mvSLOUCH 2.7.6

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>. 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_2.7.6.tar.gz
mvSLOUCH_2.7.6.tar.gz(r-4.5-noble)mvSLOUCH_2.7.6.tar.gz(r-4.4-noble)
mvSLOUCH_2.7.6.tgz(r-4.4-emscripten)mvSLOUCH_2.7.6.tgz(r-4.3-emscripten)
mvSLOUCH.pdf |mvSLOUCH.html✨
mvSLOUCH/json (API)

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

Peer review:

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

20 exports 1.31 score 40 dependencies 1 dependents 3 mentions 59 scripts 748 downloads

Last updated 10 months agofrom:3324f833b1. Checks:OK: 1 NOTE: 1. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 16 2024
R-4.5-linuxNOTESep 16 2024

Exports:BrownianMotionModeldrawPhylProcessestimate.evolutionary.modelfitch.mvslgenerate.model.setupsmvslouchModelOU_phylregOU_RSSOU_xVzouchModelparametric.bootstrapphyltree_pathsplot.clustered_phylosimulate_clustered_phylogenysimulBMProcPhylTreesimulMVSLOUCHProcPhylTreesimulOUCHProcPhylTreeSummarizeBMSummarizeMVSLOUCHSummarizeOUCH

Dependencies:abindapeclicolorspacedata.tabledigestexpmfansifarverggplot2gluegtableisobandlabelinglatticelifecyclemagrittrMASSMatrixmatrixcalcmgcvmunsellmvtnormnlmeouchPCMBasepillarpkgconfigR6RColorBrewerRcpprlangscalessubplextibbleutf8vctrsviridisLitewithrxtable

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

Jesualdo Fuentes Gonzalez, Jason Pienaar and Krzysztof Bartoszek

Rendered frommvSLOUCH_Carnivorans.Rmdusingknitr::rmarkdownon Sep 16 2024.

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

Readme and manuals

Help Manual

Help pageTopics
Multivariate Ornstein-Uhlenbeck type stochastic differential equation models for phylogenetic comparative data.mvSLOUCH-package mvSLOUCH
Estimate parameters under a Brownian motion model of evolutionBrownianMotionModel
Plots the realization of a process evolving on a phylogenetic treedrawPhylProcess
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 statesfitch.mvsl
Generate a list of model setups for the function 'estimate.evolutionary.model'.generate.model.setups
Estimate parameters under a (multivariate) OUBM model of evolutionmvslouchModel
Performs a phylogenetic regression under a given OU model of evolutionOU_phylreg
Calculates the RSS under a (multivariate) phylogenetic OU model of evolutionOU_RSS
Performs a vector matrix vector multiplcation under a (multivariate) phylogenetic OU model of evolutionOU_xVz
Estimate parameters under a (multivariate) OU model of evolutionouchModel
Parametric bootstrap for confidence intervalsparametric.bootstrap
Extract path information from a phylogenetic treephyltree_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 modelsimulBMProcPhylTree
Simulate data on a phylogeny under a (multivariate) OUBM modelsimulMVSLOUCHProcPhylTree
Simulate data on a phylogeny under a (multivariate) OU modelsimulOUCHProcPhylTree
Summarize parameters estimated under a Brownian motion modelSummarizeBM
Summarize parameters estimated under a multivariate OUBM motion modelSummarizeMVSLOUCH
Summarize parameters estimated under a (multivariate) OU motion modelSummarizeOUCH