Implementation of the automatic shift detection method for Brownian Motion (BM) or Ornstein–Uhlenbeck (OU) models of trait evolution on phylogenies. Some tools to handle equivalent shifts configurations are also available.

Documentation

Manual: PhylogeneticEM.pdf
Vignette: Tutorial

Maintainer: Paul Bastide <paul.bastide at m4x.org>

Author(s): Paul Bastide*, Mahendra Mariadassou*

Install package and any missing dependencies by running this line in your R console:

install.packages("PhylogeneticEM")

Depends ape(>=3.5), Matrix(>=1.2.3), R (>= 3.2.1),
Imports capushe(>=1.1.1), foreach(>=1.4.3), gglasso(>=1.3), glmnet(>=2.0.5), graphics (>= 3.2.1), grDevices (>= 3.2.1), LINselect(>=0.0.2), MASS(>=7.3.45), methods (>= 3.2.1), plyr(>=1.8.4), Rcpp(>=0.12.6), robustbase(>=0.92.6), stats (>= 3.2.1), utils (>= 3.2.1)
Suggests combinat(>=0.0.8), doParallel(>=1.0.10), phytools(>=0.5.38), Rphylopars(>=0.2.9), testthat(>=1.0.2), TreeSim(>=2.2), knitr, rmarkdown
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Package PhylogeneticEM
Materials
URL https://github.com/pbastide/PhylogeneticEM
Task Views
Version 1.0.0
Published 2017-01-31
License GPL (>= 2) | file LICENSE
BugReports https://github.com/pbastide/PhylogeneticEM/issues
SystemRequirements
NeedsCompilation yes
Citation
CRAN checks PhylogeneticEM check results
Package source PhylogeneticEM_1.0.0.tar.gz