This package is considered a duplicate. The official version of this package is found at:https://jclavel.r-universe.dev/mvMORPH

Package: mvMORPH 1.2.1

Julien Clavel

mvMORPH: Multivariate Comparative Tools for Fitting Evolutionary Models to Morphometric Data

Fits multivariate (Brownian Motion, Early Burst, ACDC, Ornstein-Uhlenbeck and Shifts) models of continuous traits evolution on trees and time series. 'mvMORPH' also proposes high-dimensional multivariate comparative tools (linear models using Generalized Least Squares and multivariate tests) based on penalized likelihood. See Clavel et al. (2015) <doi:10.1111/2041-210X.12420>, Clavel et al. (2019) <doi:10.1093/sysbio/syy045>, and Clavel & Morlon (2020) <doi:10.1093/sysbio/syaa010>.

Authors:Julien Clavel [aut, cre], with contributions from Aaron King [aut], Emmanuel Paradis [aut]

mvMORPH_1.2.1.tar.gz
mvMORPH_1.2.1.tar.gz(r-4.5-noble)mvMORPH_1.2.1.tar.gz(r-4.4-noble)
mvMORPH_1.2.1.tgz(r-4.4-emscripten)mvMORPH_1.2.1.tgz(r-4.3-emscripten)
mvMORPH.pdf |mvMORPH.html✨
mvMORPH/json (API)
NEWS

# Install 'mvMORPH' in R:

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

Bug tracker:https://github.com/jclavel/mvmorph/issues

Uses libs:

openblas– Optimized BLAS

Datasets:

phyllostomid - Phylogeny and trait data for a sample of Phyllostomid bats

openblas

6.22 score 3 packages 184 scripts 659 downloads 21 mentions 29 exports 41 dependencies

Last updated 4 months agofrom:61a4326aa6. Checks:OK: 1 WARNING: 1. Indexed: no.

Target	Result	Date
Doc / Vignettes	OK	Dec 27 2024
R-4.5-linux-x86_64	WARNING	Dec 27 2024

Exports:aicw ancestral dfaShape effectsize EIC estim GIC halflife LRT manova.gls mv.Precalc mvBM mvEB mvgls mvgls.dfa mvgls.pca mvLL mvols mvOU mvOUTS mvqqplot mvRWTS mvSHIFT mvSIM pairwise.contrasts pairwise.glh pcaShape pruning stationary

Dependencies:ape cli clusterGeneration coda codetools combinat corpcor cpp11 DEoptim digest doParallel dotCall64 expm fastmatch foreach generics glassoFast glue igraph iterators lattice lifecycle magrittr maps MASS Matrix mnormt nlme numDeriv optimParallel pbmcapply phangorn phytools pkgconfig quadprog Rcpp rlang scatterplot3d spam subplex vctrs

How to use mvMORPH?

Rendered fromHow_to_use_mvMORPH.Rmdusingknitr::rmarkdownon Dec 27 2024.

Last update: 2023-03-13
Started: 2016-06-18

mvMORPH: an R package for fitting multivariate evolutionary models

Rendered fromtutorial_mvMORPH.Rmdusingknitr::rmarkdownon Dec 27 2024.

Last update: 2016-10-25
Started: 2015-08-23

Citation

Readme and manuals

Help Manual

Help page	Topics
Multivariate Comparative Methods for Fitting Evolutionary Models to Morphometric Data	mvMORPH-package mvMORPH
Akaike weights	aicw
Estimation of traits ancestral states.	ancestral
Extract multivariate gls (or ols) model coefficients	coef.mvgls
Projection of 2D and 3D shapes (from geometric morphometric datasets) on Discriminant axes	dfaShape
Multivariate measure of association/effect size for objects of class "manova.gls"	effectsize
Extended Information Criterion (EIC) to compare models fit with 'mvgls' (or 'mvols') by Maximum Likelihood (ML) or Penalized Likelihood (PL)	EIC
Ancestral states reconstructions and missing value imputation with phylogenetic/time-series models	estim
Extract multivariate gls (or ols) model fitted values	fitted.mvgls
Generalized Information Criterion (GIC) to compare models fit with 'mvgls' (or 'mvols') by Maximum Likelihood (ML) or Penalized Likelihood (PL)	GIC
The phylogenetic half-life for an Ornstein-Uhlenbeck process	halflife
Likelihood Ratio Test	LRT
Multivariate Analysis of Variance	manova.gls
Model parameterization for the various mvMORPH functions	mv.Precalc
Multivariate Brownian Motion models of continuous traits evolution	mvBM
Multivariate Early Burst model of continuous traits evolution	mvEB
Fit linear model using Generalized Least Squares to multivariate (high-dimensional) data sets	mvgls
Discriminant Function Analysis (DFA) - also called Linear Discriminant Analysis (LDA) or Canonical Variate Analysis (CVA) - based on multivariate GLS (or OLS) model fit	mvgls.dfa
Principal Component Analysis (PCA) based on GLS (or OLS) estimate of the traits variance-covariance matrix (possibly regularized)	mvgls.pca
Multivariate (and univariate) algorithms for log-likelihood estimation of arbitrary covariance matrix/trees	mvLL
Fit linear model using Ordinary Least Squares to multivariate (high-dimensional) data sets	mvols
Multivariate Ornstein-Uhlenbeck model of continuous traits evolution	mvOU
Multivariate continuous trait evolution for a stationary time series (Ornstein-Uhlenbeck model)	mvOUTS
Quantile-Quantile plots for multivariate models fit with 'mvgls' or 'mvols'	mvqqplot
Multivariate Brownian motion / Random Walk model of continuous traits evolution on time series	mvRWTS
Multivariate change in mode of continuous trait evolution	mvSHIFT
Simulation of (multivariate) continuous traits on a phylogeny	mvSIM
Pairwise contrasts	pairwise.contrasts
Pairwise multivariate tests between levels of a factor	pairwise.glh
Projection of 2D and 3D shapes (from geometric morphometric datasets) on Principal Component Axes (PCA)	pcaShape
Phylogeny and trait data for a sample of Phyllostomid bats	phyllostomid
Predictions from (multivariate) gls or ols model fit	predict.mvgls
Predictions from Discriminant analysis conducted with a mvgls model fit	predict.mvgls.dfa
Pruning algorithm to compute the square root of the phylogenetic covariance matrix and its determinant.	pruning
Extract gls (or ols) model residuals	residuals.mvgls
The stationary variance of an Ornstein-Uhlenbeck process	stationary
Calculate variance-covariance matrix for a fitted object of class 'mvgls'	vcov.mvgls