bichrom_optim: Calculates the maximum likelihood estimate and the value of...

In roszenil/chromploid: Chromosome Number and Ploidy Evolution Models

Description

Calculates the maximum likelihood estimate and the value of the likelihood at the MLE of a BiChroM and BiChroM reduced models

Usage

bichrom_optim(phy.tree, tip.values, model = "bichrom",
  model.args = list(size = 50), starting.val, root.dist,
  optim.options = list(algorithm = "NLOPT_LN_SBPLX", ftol_rel = 1e-08,
  print_level = 1, maxtime = 1.7e+08, maxeval = 1000))

Arguments

phy.tree	phylogenetic tree
tip.values	A vector with chromosome numbers and/or binary trait states. See Zenil-Ferguson et al 2017 supplement for an explanation of BichroM model.
model	options are "bichrom" or "reducedbichrom"
model.args	List of arguments passed in each specified model other than parameters like size (default size is 50 chromosomes)
starting.val	vector of parameters in log scale that help with the optimization of the likelihood
root.dist	vector of probabilities for the states at the root
optim.options	See opts from nloptr package, optimization options for the likelihood function

Author(s)

Rosana Zenil-Ferguson

roszenil/chromploid documentation built on March 19, 2018, 4:42 p.m.