Package: mvSLOUCH
Type: Package
Title: Multivariate Stochastic Linear Ornstein-Uhlenbeck Models for
        Phylogenetic Comparative Hypotheses
Version: 2.7.7
Date: 2025-07-24
Authors@R: c(person(family="Bartoszek",given="Krzysztof",role=c("cre","aut"),email="krzbar@protonmail.ch"),
	    person(family="Clarke", given="John", email="j.clarke.paleo@gmail.com",role=c("ctb")),
	    person(family="Fuentes-Gonzalez", given="Jesualdo", email="jafuentesgonzalez@ua.edu",role=c("ctb")),
	    person(family="Pienaar", given="Jason", email="jason.pienaar@ua.edu",role=c("ctb")))
Maintainer: Krzysztof Bartoszek <krzbar@protonmail.ch>
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) <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/>. 
Depends: R(>= 3.5.0), abind
License: GPL (>= 2) | file LICENCE
LazyLoad: yes
Collate: bootstrap.R evolmodelest.R matrixexps.R phylgls.R
        sdecovariancephyl.R wrappers.R ci.R fitch.mvsl.R
        calls_to_matrixcalc.R matrixparametrizations.R PhyloSDEestim.R
        sdemoments.R estimBM.R getESS.R modelparams.R phyltree_paths.R
        simulVasicekprocphyl.R estimGLSGC.R loglik.R
        modelparamssummary.R precalcs.R simulVasicekproc.R
        estimMAXLIK.R make.states.mvsl.R modelparamstransform.R
        regimes.R trees2slouch.mvsl.R simulclustphyl.R
        OUphylregression.R sdemeanphyl.R
Imports: ape (>= 5.3), graphics, methods, mvtnorm, Matrix, ouch,
        PCMBase (>= 1.2.10), stats, matrixcalc
Suggests: PCMBaseCpp (>= 0.1.9), ggplot2, knitr, rmarkdown, mvMORPH,
        testthat
VignetteBuilder: knitr, rmarkdown
NeedsCompilation: no
Packaged: 2025-07-24 07:36:54 UTC; kbart
Author: Krzysztof Bartoszek [cre, aut],
  John Clarke [ctb],
  Jesualdo Fuentes-Gonzalez [ctb],
  Jason Pienaar [ctb]
Repository: CRAN
Date/Publication: 2025-07-24 14:40:02 UTC
Built: R 4.4.3; ; 2025-12-08 03:39:20 UTC; windows
