R: Ancestral State Reconstruction

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"), method.selection = NULL, reconstructed_states = NULL,
  ...)

Arguments

`x`	an object of class `PhyloEM`.
`...`	further arguments to be passed on to `params_process.PhyloEM`
`trait`	an integer giving the trait to extract. Default to 1.
`save_all`	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.
`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.
`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 `save_all=TRUE`), they can be passed on here (avoids multiple computations of the E step).

Value

A matrix or array with the computed quantities.

Methods (by class)