imputed_traits {PhylogeneticEM} | R Documentation |
Ancestral State Reconstruction
Description
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)
Usage
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,
...
)
Arguments
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 |
Value
A matrix or array with the computed quantities.
Methods (by class)
-
imputed_traits(PhyloEM)
:PhyloEM
object
See Also
params_process.PhyloEM
, PhyloEM