boxPlotTest: Compares prediction accuracy under different rate models and...

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

Compares prediction accuracy under different rate models and represents the results as a series of boxplots

Description

Compares prediction accuracy under different rate models and represents the results as a series of boxplots

Usage

boxPlotTest(
  treesObj,
  phenvals,
  rate_models,
  nsims = 100,
  confidence_threshold = NULL,
  ...
)

Arguments

treesObj	the trees object returned by readTrees
phenvals	the named phenotype vector with names matching the tip labels in the trees object
rate_models	a list of rate models to compare
nsims	the number of simulations to perform for each model of evolution (each rate model)
confidence_threshold	if not NULL, only compares prediction accuracy for nodes whose maximum likelihood is greater than the confidence threshold. Must be between 0 and 1.

Value

a list of boxplots for each rate model

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