chromploid_nllike: Calculates the negative log-likelihood of a chromosome or...

Description Usage Arguments Value Author(s)

View source: R/chromploid_nllike.R

Description

Calculates the negative log-likelihood of a chromosome or ploidy model

Usage

1
chromploid_nllike(log.par, phy, tip.values, pi.0, Q.FUN, Q.ARGS)

Arguments

log.par

A vector of parameter values in ln scale. Length of the vector depends on model defined by Q.FUN

phy

Binary rooted phylogenetic tree

tip.values

A data frame with at least two columns first column has tip labels in the same order than phylogenetic tree, second column ploidy or chromosome numbers depending on Q.FUN

pi.0

Probability distribution to be used at the root of phylogeny

Q.FUN

A function that calculates the Q-matrix of the parameters of interest

Q.ARGS

A list of arguments to be passed to Q.FUN

Value

Result is the negative log-likelihood of parameters log.par given the model in Q.FUN

Author(s)

Rosana Zenil-Ferguson


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