node_optimal_values
for optimal values computation at each nodes.params_process
objects.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.plot.equivalent_shifts
make sure the colors of the regimes are consistent for
all equivalent solutions.merge_rotations
now accepts datasets with entire species missing,
and throws an error when the missing data pattern is not compatible with a rotation.simul_process
can now handle an "OU/BM" process (i.e. an OU with
some eigen values equal to zero).equivalent_shifts
.tol
to tol_EM
in estimateEM
for actual bindingape
, and replace is.binary.tree
by is.binary
.option_is.ultrametric
to control the ape::is.ultrametric
check.find_rotation
and merge_rotations
to deal with datasets that are
equal up to a rotation.get_criterion
and plot_criterion
to get and plot the criterion used
for model selection easily.label_font
to plot
function to control the label font.axis_las
to plot
function to control the axis las.Initial Release.
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