Package: mvMORPH 1.2.2

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_1.2.2.tar.gz
mvMORPH_1.2.2.zip(r-4.7)mvMORPH_1.2.2.zip(r-4.6)mvMORPH_1.2.2.zip(r-4.5)
mvMORPH_1.2.2.tgz(r-4.6-x86_64)mvMORPH_1.2.2.tgz(r-4.6-arm64)mvMORPH_1.2.2.tgz(r-4.5-x86_64)mvMORPH_1.2.2.tgz(r-4.5-arm64)
mvMORPH_1.2.2.tar.gz(r-4.7-arm64)mvMORPH_1.2.2.tar.gz(r-4.7-x86_64)mvMORPH_1.2.2.tar.gz(r-4.6-arm64)mvMORPH_1.2.2.tar.gz(r-4.6-x86_64)
mvMORPH_1.2.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
mvMORPH/json (API)

# Install 'mvMORPH' in R:
install.packages('mvMORPH', repos = c('https://phylotastic.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

On CRAN:

Conda:

openblas

9.98 score 19 stars 3 packages 263 scripts 768 downloads 21 mentions 30 exports 51 dependencies

Last updated from:a053f8a15d. Checks:11 WARNING, 2 OK. Indexed: no.

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source / vignettesOK320
linux-release-arm64WARNING237
linux-release-x86_64WARNING300
macos-release-arm64WARNING148
macos-release-x86_64WARNING222
macos-oldrel-arm64WARNING124
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windows-develWARNING159
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wasm-releaseOK175

Exports:aicwancestraldfaShapeeffectsizeEICestimGIChalflifeLRTmanova.glsmapping.asrmv.PrecalcmvBMmvEBmvglsmvgls.dfamvgls.pcamvLLmvolsmvOUmvOUTSmvqqplotmvRWTSmvSHIFTmvSIMpairwise.contrastspairwise.glhpcaShapepruningstationary

Dependencies:apebackportscheckmatecliclusterGenerationcodacodetoolscombinatcorpcorcpp11DEoptimdigestdoParalleldotCall64expmforeachfuturefuture.applygenericsglassoFastglobalsglueigraphiteratorslatticelifecyclelistenvmagrittrmapsMASSMatrixmnormtnlmenumDerivoptimParallelosqpparallellypbapplypbmcapplyphangornphytoolspkgconfigprogressrRcppRcppArmadillorlangS7scatterplot3dspamsubplexvctrs

How to use mvMORPH?
Trees and Time series | Phylogenetic trees | Time series | Data and Errors | Simulating data | Optimization methods | Likelihood computation methods | error - X X X X X | Multivariate GLS models and High-Dimensional datasets | Model comparison | Treatment of the root | Ancestral state and primary optimum | Multiple phylogenetic means | Directional trends | Constraints | Overview of the various constraint parameterizations in mvMORPH | "User-defined" constraints | The "param" list | The "decomp" and "decompSigma" options | the "vcv" argument | Functions | The loglikelihood function | The matrix parameterization functions | Fossil data | Overview of the functions | Imputing missing values | Ancestral state reconstructions | Tweak mvMORPH | Make your own model! | Reuse of the returned log-likelihood functions | Bayesian mcmc
Rendered fromHow_to_use_mvMORPH.Rmdusingknitr::rmarkdown

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

mvMORPH: an R package for fitting multivariate evolutionary models
Example 1: Models with distinct selective regimes | Type I 0.213 0.22 | Example 2: Tests for evolutionary correlations between two species groups | References:
Rendered fromtutorial_mvMORPH.Rmdusingknitr::rmarkdown

Last update: 2016-10-13
Started: 2015-05-29

Readme and manuals

Help Manual

Help pageTopics
Multivariate Comparative Methods for Fitting Evolutionary Models to Morphometric DatamvMORPH-package mvMORPH
Akaike weightsaicw
Estimation of traits ancestral states.ancestral
Extract multivariate gls (or ols) model coefficientscoef.mvgls
Projection of 2D and 3D shapes (from geometric morphometric datasets) on Discriminant axesdfaShape
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 modelsestim
Extract multivariate gls (or ols) model fitted valuesfitted.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 processhalflife
Likelihood Ratio TestLRT
Multivariate Analysis of Variancemanova.gls
Model parameterization for the various mvMORPH functionsmv.Precalc
Multivariate Brownian Motion models of continuous traits evolutionmvBM
Multivariate Early Burst model of continuous traits evolutionmvEB
Fit linear model using Generalized Least Squares to multivariate (high-dimensional) data setsmvgls
Discriminant Function Analysis (DFA) - also called Linear Discriminant Analysis (LDA) or Canonical Variate Analysis (CVA) - based on multivariate GLS (or OLS) model fitmvgls.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/treesmvLL
Fit linear model using Ordinary Least Squares to multivariate (high-dimensional) data setsmvols
Multivariate Ornstein-Uhlenbeck model of continuous traits evolutionmvOU
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 seriesmvRWTS
Multivariate change in mode of continuous trait evolutionmvSHIFT
Simulation of (multivariate) continuous traits on a phylogenymvSIM
Pairwise contrastspairwise.contrasts
Pairwise multivariate tests between levels of a factorpairwise.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 batsphyllostomid
Predictions from (multivariate) gls or ols model fitpredict.mvgls
Predictions from Discriminant analysis conducted with a mvgls model fitpredict.mvgls.dfa
Pruning algorithm to compute the square root of the phylogenetic covariance matrix and its determinant.pruning
Extract gls (or ols) model residualsresiduals.mvgls
The stationary variance of an Ornstein-Uhlenbeck processstationary
Calculate variance-covariance matrix for a fitted object of class 'mvgls'vcov.mvgls