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.


Reference manual

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1.1.0 by Paul Bastide, 3 months ago

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Authors: Paul Bastide [aut, cre], Mahendra Mariadassou [ctb]

Documentation:   PDF Manual  

GPL (>= 2) | file LICENSE license

Imports capushe, foreach, glmnet, graphics, grDevices, grplasso, LINselect, MASS, methods, plyr, Rcpp, robustbase, stats, utils

Depends on ape, Matrix

Suggests combinat, doParallel, phytools, Rphylopars, testthat, TreeSim, knitr, rmarkdown

Linking to Rcpp, RcppArmadillo

See at CRAN