--- a
+++ b/man/calc.llk.tree.Rd
@@ -0,0 +1,24 @@
+% 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
+}