BT_multiple: Input files for multiple BT runs

In cromanpa94/rBT: A wrapper for BayesTraits

Description

This function creates imput files for a large combination of the parameters under the BayesTraits MultiState model.

Usage

BT_multiple(
  tree,
  dataset,
  run = F,
  name_general,
  ML = F,
  it = 1.1e+07,
  bur = 1e+06
)

Arguments

tree	A fully-bifurcating Phy object
dataset	A data.frame object with two columns (tip name + state)
run	logic whether analyses should start after input files are created
name_general	A character indicating the name of the analuysis (use unique per analysis)
ML	logic whether parameters should be optimized under a Maximum Likelihood approach. MCMC analyses are available under ML=F
it	The number of iterations under a bayesian optimization (only when ML=F)
bur	Total number of generations assumed as burnin under a bayesian optimization (only when ML=F)

Details

Specifically, this function is designed to run models differing in the following parameters: (1) "PriorAll" vs. "RevJump", (2) Variable rates vs. non-Variable rates, and (3) uniform vs. exponential distributions.

cromanpa94/rBT documentation built on Dec. 19, 2021, 6:20 p.m.