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:
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 = 'https://cloud.r-project.org') |
Bug tracker:https://github.com/jclavel/mvmorph/issues6 issues
- phyllostomid - Phylogeny and trait data for a sample of Phyllostomid bats
Last updated 7 months agofrom:61a4326aa6. Checks:1 OK, 2 WARNING. Indexed: no.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Mar 27 2025 |
| R-4.5-linux-x86_64 | WARNING | Mar 27 2025 |
| R-4.4-linux-x86_64 | WARNING | Mar 27 2025 |
Exports:aicwancestraldfaShapeeffectsizeEICestimGIChalflifeLRTmanova.glsmv.PrecalcmvBMmvEBmvglsmvgls.dfamvgls.pcamvLLmvolsmvOUmvOUTSmvqqplotmvRWTSmvSHIFTmvSIMpairwise.contrastspairwise.glhpcaShapepruningstationary
Dependencies:apecliclusterGenerationcodacodetoolscombinatcorpcorcpp11DEoptimdigestdoParalleldotCall64expmfastmatchforeachgenericsglassoFastglueigraphiteratorslatticelifecyclemagrittrmapsMASSMatrixmnormtnlmenumDerivoptimParallelpbmcapplyphangornphytoolspkgconfigquadprogRcpprlangscatterplot3dspamsubplexvctrs
How to use mvMORPH?
Rendered fromHow_to_use_mvMORPH.Rmdusingknitr::rmarkdownon Mar 27 2025.Last update: 2023-03-13
Started: 2016-06-18
mvMORPH: an R package for fitting multivariate evolutionary models
Rendered fromtutorial_mvMORPH.Rmdusingknitr::rmarkdownon Mar 27 2025.Last update: 2016-10-25
Started: 2015-08-23
Citation
To cite package 'mvMORPH' in publications use:
Clavel, J., Escarguel, G., and Merceron, G. (2015) mvMORPH: an R package for fitting multivariate evolutionary models to morphometric data. Methods in Ecology and Evolution, 6(11):1311-1319.<doi:10.1111/2041-210X.12420>
Corresponding BibTeX entry:
@Article{,
author = {Julien Clavel and Gilles Escarguel and Gildas Merceron},
title = {mvMORPH: an R package for fitting multivariate
evolutionary models to morphometric data},
year = {2015},
journal = {Methods in Ecology and Evolution},
volume = {6},
pages = {1311-1319},
}
Readme and manuals
mvMORPH
mvMORPH: an R package for fitting multivariate evolutionary models to morphometric data
This package allows the fitting of multivariate evolutionary models (Ornstein-Uhlenbeck, Brownian motion, Early burst, Shift models) on species trees and time series. It also provides functions to compute log-likelihood of users specified models with fast methods (e.g., for Bayesian approaches or customized comparative methods), simulates correlated traits under various models, constrain various parts of multivariate models...
The package implement now efficient methods for high-dimensional multivariate comparative methods (mvgls) based on Penalized likelihood as well as associated tests (Wilks, Pillai...)
The package is designed to handle ultrametric and non-ultrametric trees (i.e. with fossil species) and missing data in multivariate datasets (NA values), SIMMAP mapping of discrete traits, measurement error, etc...
See the packages vignettes for details and examples: browseVignettes("mvMORPH").
mvMORPH 1.2.1
- This is the version 1.2.1:
- Check the NEWS file for detailled updates
- TODO:
- Incorporation of a tests-suite
- Implement the sampler (upcomming mvMORPH)
- Code improvements
- Extend the shift model to TS
- Improved mvOU model
- Threshold model for categorical data
The current stable version of the mvMORPH package (1.2.0) is on the CRAN repository. https://cran.r-project.org/package=mvMORPH
Package InstallationPackage Installation
You can install the package directly from gitHub through devtools:
library(devtools)
install_github("JClavel/mvMORPH", build_vignettes = TRUE)
(The installation may crash if your dependencies are not up to date. Note that you may also need to install Rtools to compile the C codes included in the package. For [Windows] (https://cran.r-project.org/bin/windows/Rtools/) and for [Mac] (https://mac.r-project.org/) (and [Tools] (https://mac.r-project.org/tools/) )
Report an issueReport an issue
Any bugs encountered when using the package can be reported here
Package citationPackage citation
Clavel, J., Escarguel, G., Merceron, G. 2015. mvMORPH: an R package for fitting multivariate evolutionary models to morphometric data. Methods in Ecology and Evolution, 6(11):1311-1319.
