imputed_traits.PhyloEM takes an object of class PhyloEM,
and returns the imputed traits values, either at the internal nodes (ancestral
state reconstruction) or at the tips (data imputation)
imputed_traits(x, ...)# S3 method for PhyloEM
imputed_traits(
x,
trait = 1,
save_all = FALSE,
where = c("nodes", "tips"),
what = c("imputed", "variances", "expectations"),
params = NULL,
method.selection = NULL,
reconstructed_states = NULL,
...
)
A matrix or array with the computed quantities.
an object of class PhyloEM.
further arguments to be passed on to
params_process.PhyloEM
an integer giving the trait to extract. Default to 1.
if TRUE, arguments where and what are ignored, and
all the moments are kept for further extraction with the same function, specifying
the argument reconstructed_states. Default to FALSE.
either "nodes" for ancestral state reconstruction, or "tips" for data imputation.
the quantity to retrieve. Either the imputed traits (default), their conditional variances, or the simple expectations under the selected process.
(optional) some user-specified parameters.
Must be of class params_process. If left blank, they are extracted
using the method.selection argument (see below).
(optional) the method selection to be used. One of "LINselect", "DDSE", "Djump". Default to "LINselect".
if the reconstructed states have already been
computed (by a previous call of the function, with save_all=TRUE),
they can be passed on here (avoids multiple computations of the E step).
imputed_traits(PhyloEM): PhyloEM object
params_process.PhyloEM, PhyloEM