compareRateModels: Performs pairwise likelihood ratio comparisons on a list of...

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

Performs pairwise likelihood ratio comparisons on a list of rate models

Description

Performs pairwise likelihood ratio comparisons on a list of rate models

Usage

compareRateModels(
  rate_models,
  treesObj,
  phenvals,
  nsims = 100,
  nested_only = FALSE,
  return_type = "pvals",
  ...
)

Arguments

rate_models	a named list of rate models in matrix form
treesObj	the trees object returned by readTrees
phenvals	the named phenotype vector with names matching the tip labels on the tree
nsims	the number of simulations to use in getLRnullDistribuutions when the rate models are not nested
nested_only	a boolean indicating whether comparisons should only be made between nested models. If TRUE, this decreases runtime because simulations to get the null distribution are not performed.
return_type	can be "pvals" or "ratios" indicating whether to return p values obtained from the likelihood ratios or the likelihood ratios themselves
...	additional parameters for the castor function, fit_mk used to fit the transition matrix

Value

a square matrix of p-values or likelihood ratios for pairwise comparisons between rate models

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