getRates: Extract rates of evolution from fitted models

In Caetanods/sequence-trait: Phylogenetic Comparative Methods to Study Sequence Traits and Correlated Evolution

Extract rates of evolution from fitted models

Description

Extracts and summarize the estimates of rates of evolution from the fitted models.

Usage

getRates(x, Q.model = "ER", gap.char = "-")

Arguments

x	a model fit result.
Q.model	one of "ER" or "DEL". Default is "ER".
gap.char	the charactaed state used to identify gaps. Default is "-".

Details

Returns a vector if the model has a global rate (i.e., model "ER"). If the estimated model was of type "DEL", this function will return a matrix with the distinct rates for the observed states and between the observed states and gaps.

This functions will substitute invariant positions for NA when necessary.

Please check the help for 'fitCorrSeq' for more information.

Value

a vector or a matrix with the evolutionary rates estimated for each sequence position.

Author(s)

Daniel Caetano

Caetanods/sequence-trait documentation built on Nov. 25, 2022, 4:32 p.m.