Changes in version 1.8.1 (2025-09-23)                  

  - Deprecation fix:
      - change arma::is_finite(val) to std::isfinite(val)

                 Changes in version 1.8.0 (2025-02-14)                  

  - Bug fix:
      - merge_rotation now works for trait with more than 2 dimensions.
      - Fix documentation notes on CRAN checks.
  - New functions and features:
      - Function merge_alpha_grids to merge PhyloEM runs on the same
        data set but with separate grids of alpha values.

                 Changes in version 1.7.0 (2024-01-31)                  

  - 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.

                 Changes in version 1.6.0 (2022-08-31)                  

  - 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.

                 Changes in version 1.5.0 (2021-09-16)                  

  - 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.

                 Changes in version 1.4.0 (2020-02-11)                  

  - 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.

                 Changes in version 1.3.0 (2019-10-03)                  

  - 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).

                 Changes in version 1.2.1 (2018-09-11)                  

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

                        Changes in version 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.

                 Changes in version 1.1.0 (2017-09-08)                  

  - 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.

                 Changes in version 1.0.1 (2017-05-01)                  

  - 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.

                 Changes in version 1.0.0 (2017-01-31)                  

Initial Release.