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.