BT_single: Input files for a single BT run

In cromanpa94/rBT: A wrapper for BayesTraits

Description

This function creates all input files for a single analysis under the BayesTraits MultiState model.

Usage

BT_single(
  tree,
  dataset,
  ML = F,
  model = "PriorAll",
  vrates = T,
  Iterations = 10000,
  Burnin = 100,
  dist = "exp",
  val_prior = 10,
  name = "Default",
  run = T,
  LinuxMac = T,
  path = NULL
)

Arguments

tree	A fully-bifurcating phylo object
dataset	A data.frame object with two columns (tip name + state)
ML	logic whether parameters should be optimized under a Maximum Likelihood approach. MCMC analyses are available under ML=F
model	A character vector used to set the analysis to a "PriorAll" or "RevJump" model
vrates	Whether a VarRates model should be abalyzed, logic
Iterations	The number of iterations under a bayesian optimization (only when ML=F)
Burnin	Total number of generations assumed as burnin under a bayesian optimization (only when ML=F)
dist	A character vector indicating whether the distribution is "exp" (exponential) or "uniform" (uniform)
val_prior	A vector of class numeric with the parameters for the "exp" (1 parameter) or "uniform (2 parameters) distribution
name	The name of the run. This name is used to create a subfolder within the working directory
run	logic whether analyses should start after input files are created
LinuxMac	logic Are you in MacOs or Linux?
path	Path to BayesTraits

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