R/LogLik_bounds_est_root.R

In BBMV: Models for Continuous Traits Evolving in Macroevolutionary Landscapes of any Shape

LogLik_bounds_est_root <-
function(tree,trait ,dCoeff,V, x0_pos,bounds){
Npts_tot=length(V)		
tree_formatted=FormatTree_bounds(tree,trait,V,bounds)		
dMat=DiffMat_backwards(V)
pMat=prep_mat_exp(dCoeff,dMat,bounds) # edited
tree_formatted2= tree_formatted
logFactor=0
for (i in 1:dim(tree_formatted2$tab)[1]){
	tree_formatted2$Pos[[tree_formatted2$tab[i,1]]]= tree_formatted2$Pos[[tree_formatted2$tab[i,1]]]*ConvProp_bounds(X=tree_formatted2$Pos[[tree_formatted2$tab[i,2]]],t=tree_formatted2$tab[i,3],prep_mat=pMat) # edited with prep_mat for faster calculations
	norm=sum(tree_formatted2$Pos[[tree_formatted2$tab[i,1]]])
	tree_formatted2$Pos[[tree_formatted2$tab[i,1]]]= tree_formatted2$Pos[[tree_formatted2$tab[i,1]]]/norm
	logFactor=logFactor+log(norm)
}
return(log(tree_formatted2$Pos[[tree_formatted2$tab[i,1]]][x0_pos])+logFactor) # extraction of the likelihood for a given root value (in the ML optimization version, we take max(tree_formatted2$Pos[[tree_formatted2$tab[i,1]]]))
}