visCompareTwoRateModels: Visually compare the results of two rate models by plotting...

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

Visually compare the results of two rate models by plotting the differences between them on the phylogenetic tree Relative entropy is calculated with A as the "target" and B as the "estimate" Switching the order of rate model A and rate model B DOES give different relative entropies (relative entropy is not symmetric)

Description

Visually compare the results of two rate models by plotting the differences between them on the phylogenetic tree Relative entropy is calculated with A as the "target" and B as the "estimate" Switching the order of rate model A and rate model B DOES give different relative entropies (relative entropy is not symmetric)

Usage

visCompareTwoRateModels(
  A,
  B,
  treesObj,
  phenvals,
  mode = "entropy",
  cex = 0.5,
  ...
)

Arguments

A	the first rate model
B	teh second rate model
treesObj	the trees object returned by readTrees
phenvals	the named phenotype vector with names matching the tip labels in the trees object
mode	indicates how to represent differences between ancestral reconstructions. When mode is "entropy" the relative entropies between ancestral likelihoods at each node are plotted along the branches of the trees. When mode is "match", nodes are colored red when state assignments are different and red when they are the same.
cex	a graphical argument representing the size of node labels and tip labels

Value

a list of relative entropies or state assignemtns and ancestral likelihoods under each rate model

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