R/sumstatEXP.R

In vnminin/phylomap: Phylogenetic Stochastic Mapping

pruningwiseedgeorder<-function(x){
 returnme<-seq(1:dim(x$edge)[1])
 y<-reorder(x,order="pruningwise")
 for(i in 1:dim(x$edge)[1]){
  for(j in 1:dim(x$edge)[1]){
   if(x$edge[i,1]==y$edge[j,1]&x$edge[i,2]==y$edge[j,2]) returnme[j]<-i
  }
 }
 return(returnme)
}
makenodelist<-function(x){
 rm<-NULL
 for(i in 1:(x$Nnode-1)){
  rm[i]<-reorder(x,order="pruningwise")$edge[length(x$edge[,1])-2*i,1]
 }
 return(rm)
}
myreorder<-function(x) reorder(x,order="pruningwise")$edge[dim(x$edge)[1],1]


sumstatEXP<-function(z,Q,pid,N) {
 nen=pruningwiseedgeorder(z)
 nodelist=makenodelist(z)
 root = myreorder(z)

 uer<-eigen(Q)
 lefts<-(uer$vectors)
 rights<-solve(lefts)
 d<-diag(uer$values)

 ss<-maketreelistEXP(z,Q,pid,nen,nodelist,root,N,lefts,rights,d)
 return(ss)
}