arma::is_finite(val) to
std::isfinite(val)merge_rotation now works for trait with more than 2
dimensions.merge_alpha_grids to merge
PhyloEM runs on the same data set but with separate grids
of alpha values.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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