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)

- `PhyloEM`: `PhyloEM` object

### See Also

`params_process.PhyloEM`, `PhyloEM`

[Package PhylogeneticEM version 1.1.0 Index]