getAncLiks: Returns ancestral likelihoods at each node. Based on code...

In nclark-lab/RERconverge: Analysis of Convergence Between Organismal Traits and DNA/Protein Sequences

Returns ancestral likelihoods at each node. Based on code from ace in ape and fitMk/rerootingMethod in phytools

Description

Returns ancestral likelihoods at each node. Based on code from ace in ape and fitMk/rerootingMethod in phytools

Usage

getAncLiks(tree, tipvals, Q = NULL, rate_model = "ER", root_prior = "auto")

Arguments

tree	Object of class phylo that has been pruned to only contain the species in tipvals
tipvals	The phenotype data for the extant species in the tree in the same order as tree$tip.label and mapped to integers
Q	A transition matrix, if NULL the transition matrix is fit with fit_mk from castor package
rate_model	The rate model to use for fitting the transition matrix if one is not provided
root_prior	The root prior used when fitting the transition matrix if one is not provided

Value

The ancestral likelihoods at each node in the tree

nclark-lab/RERconverge documentation built on March 2, 2024, 8:51 a.m.