imputed_traits | R Documentation |
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 class '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, ... )
x |
an object of class |
... |
further arguments to be passed on to
|
trait |
an integer giving the trait to extract. Default to 1. |
save_all |
if TRUE, arguments |
where |
either "nodes" for ancestral state reconstruction, or "tips" for data imputation. |
what |
the quantity to retrieve. Either the imputed traits (default), their conditional variances, or the simple expectations under the selected process. |
params |
(optional) some user-specified parameters.
Must be of class |
method.selection |
(optional) the method selection to be used. One of "LINselect", "DDSE", "Djump". Default to "LINselect". |
reconstructed_states |
if the reconstructed states have already been
computed (by a previous call of the function, with |
A matrix or array with the computed quantities.
PhyloEM
: PhyloEM
object
params_process.PhyloEM
, PhyloEM
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