PhylogeneticEM: Automatic Shift Detection using a Phylogenetic EM

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.

Version: 1.0.0
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)
LinkingTo: Rcpp, RcppArmadillo
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
Published: 2017-01-31
Author: Paul Bastide [aut, cre], Mahendra Mariadassou [ctb]
Maintainer: Paul Bastide <paul.bastide at m4x.org>
BugReports: https://github.com/pbastide/PhylogeneticEM/issues
License: GPL-2 | GPL-3 | file LICENSE [expanded from: GPL (≥ 2) | file LICENSE]
URL: https://github.com/pbastide/PhylogeneticEM
NeedsCompilation: yes
Citation: PhylogeneticEM citation info
CRAN checks: PhylogeneticEM results

Downloads:

Reference manual: PhylogeneticEM.pdf
Vignettes: Tutorial
Package source: PhylogeneticEM_1.0.0.tar.gz
Windows binaries: r-devel: PhylogeneticEM_1.0.0.zip, r-release: PhylogeneticEM_1.0.0.zip, r-oldrel: PhylogeneticEM_1.0.0.zip
OS X Mavericks binaries: r-release: PhylogeneticEM_1.0.0.tgz, r-oldrel: PhylogeneticEM_1.0.0.tgz

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