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. See Bastide et al. (2017) and Bastide et al. (2018) .


PhylogeneticEM 1.2.1

  • CRAN maintenance
    • Added references in Description
    • Reduce checking and vignette building time

PhylogeneticEM 1.2.0

  • Added Options:
    • option_is.ultrametric to control the ape::is.ultrametric check.
  • Deprecation Fix:
    • Go back to updated version of gglasso (faster than grplasso). This should not change the results of PhylogeneticEM.
  • Added functions:
    • Functions find_rotation and merge_rotations to deal with datasets that are equal up to a rotation.
    • Functions get_criterion and plot_criterion to get and plot the criterion used for model selection easilly.
  • New feature:
    • Function PhyloEM can now allow for negative values of alpha, to fit an EB model.
  • Bug fix:
    • In function plot, fixed bug that led to the wrong parameters being selected when doing ancestral trait reconstruction.

PhylogeneticEM 1.1.0

  • Deprecation Fix:
    • Remove dependency from gglasso (replaced with grplasso). This should not change the results of PhylogeneticEM.
  • Bug Fixes:
    • Issue an error message when the tree has some zero-length branches.
  • Minor Changes:
    • Added options to plot.equivalent_shifts.

PhylogeneticEM 1.0.1

  • Minor Changes:
    • Impose a maximum value for alpha in find_grid_alpha to respect machine max double.
  • New Features
    • added argument label_font to plot function to control the label font.
    • added argument axis_las to plot function to control the axis las.
  • Bug fixes:
    • Plotting missing values correctly in plot.PhyloEM.
    • Bug fixes in plotting PhyloEM object when p = 1.
    • When p=1 and nbr_alpha is not missing, do not switch to estimated mode for alpha.
  • Technical:
    • registration of c++ code to comply with R 3.4 new standards.

PhylogeneticEM 1.0.0

Initial Release.

Reference manual

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1.4.0 by Paul Bastide, a year ago

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Browse source code at

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

Documentation:   PDF Manual  

GPL (>= 2) | file LICENSE license

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

Depends on ape, Matrix

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

Linking to Rcpp, RcppArmadillo

See at CRAN