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

Description Usage Arguments Author(s)

View source: R/bichrom_optim.R

Description

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

Usage

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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.