#' @export PCMRegimes.PCM <- function(model, tree = NULL, preorder = if(is.null(tree)) NULL else PCMTreePreorder(tree)) r <- attr(model, "regimes") if(is.integer(r) && !is.null(tree)) PCMTreeUniqueRegimes(tree, preorder)[r] else r Integer vector giving the model type index for each regime

PCMMapModelTypesToRegimes(model, tree, ...)

Arguments

model

a PCM model

tree

a phylo object with an edge.regime member

...

additional parameters passed to methods

Value

an integer vector with elements corresponding to the elements in PCMTreeUniqueRegimes(tree)

Details

This is a generic S3 method. The default implementation for the basic class PCM returns a vector of 1's, because it assumes that a single model type is associated with each regime. The implementation for multi-regime models (MRG) returns the mapping attribute of the MRG object reordered to correspond to PCMTreeUniqueRegimes(tree).