% Generated by roxygen2: do not edit by hand

% Please edit documentation in R/calc.llk.tree.R

\name{calc.llk.tree}

\alias{calc.llk.tree}

\title{Function to calculate integrated likelihood for set of variants up tree}

\usage{

calc.llk.tree(pars, data.sub, returnForwardMatrix = FALSE,

  returnGMatrix = FALSE)

}

\arguments{

\item{pars}{A list object as returned by the function set.parameters}

\item{data.sub}{A 3-dimension array (N. SNPs x N. phenotypes x 3) with state likelihoods.}

\item{returnForwardMatrix}{Boolean}

\item{returnGMatrix}{Boolean}

}

\value{

Either a numeric object with the Tree likelihood or a list with FWD and G matrices

}

\description{

Function to calculate integrated likelihood for set of variants up tree

}