CRAN/E | PhylogeneticEM

PhylogeneticEM

Automatic Shift Detection using a Phylogenetic EM

Installation

About

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. See Bastide et al. (2017) doi:10.1111/rssb.12206 and Bastide et al. (2018) doi:10.1093/sysbio/syy005.

Citation PhylogeneticEM citation info
github.com/pbastide/PhylogeneticEM
Bug report File report

Key Metrics

Version 1.7.0
R ≥ 3.6.0
Published 2024-01-31 80 days ago
Needs compilation? yes
License GPL-2
License GPL-3
License File
CRAN checks PhylogeneticEM results

Downloads

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Maintainer

Maintainer

Paul Bastide

paul.bastide@m4x.org

Authors

Paul Bastide

aut / cre

Mahendra Mariadassou

ctb

Material

NEWS
Reference manual
Package source

Vignettes

New World Monkeys
Tutorial

macOS

r-release

arm64

r-oldrel

arm64

r-release

x86_64

Windows

r-devel

x86_64

r-release

x86_64

r-oldrel

x86_64

Old Sources

PhylogeneticEM archive

Depends

ape ≥ 5.3
Matrix ≥ 1.2.18
R ≥ 3.6.0

Imports

capushe ≥ 1.1.1
foreach ≥ 1.4.3
gglasso ≥ 1.4
glmnet ≥ 2.0.5
graphics ≥ 3.6.0
grDevices ≥ 3.6.0
LINselect ≥ 1.1.1
MASS ≥ 7.3.45
methods ≥ 3.6.0
plyr ≥ 1.8.4
Rcpp ≥ 1.0.2
robustbase ≥ 0.92.6
stats ≥ 3.6.0
utils ≥ 3.6.0

Suggests

combinat ≥ 0.0.8
doParallel ≥ 1.0.10
phytools ≥0.5.38
testthat ≥ 1.0.2
TreeSim ≥ 2.2
knitr
rmarkdown

LinkingTo

Rcpp
RcppArmadillo