Implementation in R using NTT

RF_NTTfromPy.R

@@ -0,0 +1,167 @@
+#note to chanage the options to options("digits"=22) and options("scipen"=100)
+
+library("ape")
+library("phangorn")
+library("readtext")
+setwd("/Users/maryam/Desktop/Research/RF_improvment/FinalCodes")
+options("digits"=22)
+options("scipen"=100)
+#Beta function
+Beta=function(m){
+  if(m<=0){ans=1}
+  else {
+    ans=1
+    for (i in 1:m) {
+      ans=ans*(2*i+1)
+    }
+  }
+  return(ans)
+}
+
+# the function for computing the number of internal edges
+internaledges <- function(tree,ntip){
+  intedges=array(0,c(1,ntip-1))
+  edges=tree$edge
+  for (i in (2*ntip-1):(ntip+1)) {
+    children=which(edges[,1]==i)
+    child1=edges[children[1],2]
+    child2=edges[children[2],2]
+    if(child1 <= ntip&child2 <= ntip){intedges[i-ntip]=0}
+    else if(child1<= ntip & child2 > ntip){intedges[i-ntip]=intedges[child2-ntip]+1}
+    else if(child2<= ntip & child1 > ntip){intedges[i-ntip]=intedges[child1-ntip]+1}
+    else {intedges[i-ntip]=intedges[child2-ntip]+intedges[child1-ntip]+2}
+  }
+  return(intedges)
+}
+
+# the function for computing the number of internal children
+internalchildren <- function(tree,v,ntip){
+  edges=tree$edge
+  children=which(edges[,1]==v)
+  child1=edges[children[1],2]
+  child2=edges[children[2],2]
+  if(child1 > ntip & child2 > ntip){result=c(2,child1,child2)}
+  else if(child1 > ntip & child2 <= ntip){result=c(1,child1)}
+  else if(child2 > ntip & child1 <= ntip){result=c(1,child2)}
+  else {result=0}
+  return(result)
+}
+
+RF_Convolve=function(tree,n){
+  tt=0
+  t=(n-4)*(n-2)*3
+  L= 2^ceiling(log(t)/log(2)) 
+  #L=16384
+  ntip=n-1
+  N=tree$Nnode
+  R=rep(list(matrix(0,(ntip-1),(ntip-1))),N)
+  edges=internaledges(tree,ntip)
+  B=c()
+  for (k in 0:(n-2)) {
+    B[k+1]=Beta(k)        
+  }
+  for (v in N:1) {
+    intchild=internalchildren(tree,v+ntip,ntip)
+    intedges=edges[v]
+    if(intchild[1]==0){
+      R[[v]][1,1]=1
+    }
+    else if(intchild[1]==1){
+      Rchild=R[[intchild[2]-ntip]]
+      R[[v]][1,intedges+1]=1
+      R[[v]][2:(ntip-1),1]=rowSums(t(t(Rchild[1:(ntip-2),])*B[1:(ntip-1)]))
+      R[[v]][2:(ntip-1),2:(ntip-1)]=Rchild[2:(ntip-1),1:((ntip-2))]
+    }
+    else {
+      Rchild1=R[[intchild[2]-ntip]]
+      Rchild2=R[[intchild[3]-ntip]]
+      R[[v]][1,intedges+1]=1
+      R[[v]][3,1]=sum(t(t(Rchild1[1,])*B[1:(ntip-1)]))*sum(t(t(Rchild2[1,])*B[1:(ntip-1)]))
+      for (s in 4:(ntip-1)) {
+        R[[v]][s,1]=sum(rowSums(t(t(Rchild1[1:(s-2),])*B[1:(ntip-1)]))*rowSums(t(t(Rchild2[(s-2):1,])*B[1:(ntip-1)])))
+      }
+      sum1=matrix(0,(ntip-2),(ntip-2))
+      sum1[1,1:(ntip-2)]=sum(t(t(Rchild1[1,])*B[1:(ntip-1)]))*Rchild2[1,1:(ntip-2)]
+      for (s in 3:(ntip-1)) {
+        temp=colSums(rowSums(t(t(Rchild1[1:(s-1),])*B[1:(ntip-1)]))*Rchild2[(s-1):1,1:(ntip-2)])
+        sum1[s-1,1:(ntip-2)]=temp
+      }
+      sum2=matrix(0,(ntip-2),(ntip-2))
+      sum2[1,1:(ntip-2)]=sum(t(t(Rchild2[1,])*B[1:(ntip-1)]))*Rchild1[1,1:(ntip-2)]
+      for (s in 3:(ntip-1)) {
+        temp=colSums(rowSums(t(t(Rchild2[1:(s-1),])*B[1:(ntip-1)]))*Rchild1[(s-1):1,1:(ntip-2)])
+        sum2[s-1,1:(ntip-2)]=temp
+      }
+
+      R1=Rchild1[1:(ntip-1),1:(ntip-3)]
+      #R1aug=numeric(nrow(R1)*(2*ncol(R1)-1))
+      R1aug=numeric(L)
+      t=1
+      for(i in 1:ncol(R1)){
+        R1aug[t:(t+nrow(R1)-1)]=R1[,i]
+        t=t+3*nrow(R1)
+      }
+      R2=Rchild2[1:(ntip-1),1:(ntip-3)]
+      #R2aug=numeric(nrow(R2)*(2*ncol(R2)-1))
+      R2aug=numeric(L)
+      t=1
+      for(i in 1:ncol(R2)){
+        R2aug[t:(t+nrow(R2)-1)]=R2[,i]
+        t=t+3*nrow(R2)
+      }
+
+      #write(L,"testNTT.txt",ncolumns=L,append = TRUE)
+      write(R1aug,"testNTT.txt",ncolumns=L,append = TRUE)
+      write(R2aug,"testNTT.txt",ncolumns=L,append = TRUE)
+
+      #read the output of Python
+
+      system('python  /Users/maryam/Desktop/Research/RF_improvment/FinalCodes/python_code/ntt_fromR.py')
+
+      U=as.matrix(read.csv("/Users/maryam/Desktop/Research/RF_improvment/FinalCodes/outNTT.txt",header = FALSE, quote=""))
+
+      Matc=ceiling(length(R1aug)/(3*nrow(R1)))
+      sum3=matrix(c(U,numeric(Matc*3*nrow(R1)-length(R1aug))),nrow=3*nrow(R1))[1:nrow(R1),1:ncol(R1)]
+      sum3=cbind(array(0, dim=c(nrow(R1)-1,1)),sum3[2:nrow(R1),])
+      R[[v]][2:(ntip-1),2:(ntip-1)]=sum1+sum2+sum3
+      file.remove("testNTT.txt")
+
+    }
+  }
+
+  return(R)
+
+}
+
+
+
+#==========================================
+RsT=function(R,n,s){
+  B=c()
+  for (k in 0:(n-2)) {
+    B[k+1]=Beta(k)        
+  }
+  rst =sum(t(t(R[[1]][s+1,1:(n-2-s)])*B[1:(n-2-s)]))
+  return(rst)
+}
+
+#Compute the value of q_m(T)
+qmT=function(R,n,m){
+  qmt=0
+  for (s in m:(n-3)) {
+    rst=RsT(R,n,s)
+    qmt=qmt+(factorial(s)/(factorial(m)*factorial(s-m)))*rst*(-1)^(s-m)
+  }
+  return(qmt)
+}
+
+polynomial=function(tree,n){
+  Coef=numeric()
+  R=RF_Convolve(tree,n)
+  for (i in seq(0,2*(n-3),2)) {
+    Coef=c(Coef,qmT(R,n,n-3-(i/2)))
+  }
+  return(Coef)
+}
+
+