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.