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PhylogeneticEM 1.7.0

  • Bug fixes:
    • Fix documentation notes on CRAN checks.
  • New functions and features:
    • Function node_optimal_values for optimal values computation at each nodes.
    • Trait names are now inherited by the params_process objects.

PhylogeneticEM 1.6.0

  • Deprecation fix:
    • Update code to comply with Matrix 1.4-2 new coding standards.
  • API change:
    • Function compute_stationary_variance now always return a dpoMatrix, using Matrix::nearPD if needed. The change only impacts computations with full variance and selection strength matrices, which are never used in a typical PhyloEM analysis, but could impact direct calls to the function or simulations under complex scenarios.
  • Bug Fix:
    • In plot.equivalent_shifts make sure the colors of the regimes are consistent for all equivalent solutions.

PhylogeneticEM 1.5.0

  • Bug fix:
    • merge_rotations now accepts datasets with entire species missing, and throws an error when the missing data pattern is not compatible with a rotation.
  • Warnings:
    • The function now throws a warning when two traits are very highly correlated.
  • CI:
    • Replace Travis with Github Actions.
    • Build doc automatically with GHA.

PhylogeneticEM 1.4.0

  • New option:
    • Add an option "show_axis_traits" to control the trait axis in a plot.
  • New Feature
    • Function simul_process can now handle an "OU/BM" process (i.e. an OU with some eigen values equal to zero).
  • Bug fix:
    • Documented arguments not in usage in documentation object equivalent_shifts.
    • Check with "R_CHECK_FORCE_SUGGESTS=FALSE" now runs.

PhylogeneticEM 1.3.0

  • Bug fix:
    • Bug fix in plot function for univariate result.
    • Tree does not need to be ultrametric for a BM
    • Change tol to tol_EM in estimateEM for actual binding
    • Bug fixes in plot function for displaying traits.
  • New Option:
    • Add option "name_trait" to plot function for ancestral state reconstruction.
  • API Change
    • For a univariate trait, the BM re-scaling is now applied by default.
  • Deprecation Fix:
    • Update ape, and replace is.binary.tree by is.binary.
    • Remove dependency to Rphylopars (no longer on CRAN).

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 easily.
  • 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.