NEWS.md

In PhylogeneticEM: Automatic Shift Detection using a Phylogenetic EM

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.

PhylogeneticEM documentation built on June 22, 2024, 6:46 p.m.