Move rfdistr git repository into this repository

.gitignore

@@ -0,0 +1,4 @@
+.Rproj.user
+.Rhistory
+.RData
+.Ruserdata

rfdistr/DESCRIPTION

@@ -1,13 +1,11 @@
 Package: rfdistr
 Type: Package
-Title: RF distribution
+Title: What the Package Does (Title Case)
 Version: 0.1.0
-Author: Maryam Hayati
-Maintainer: The package maintainer <[email protected]>
-Description: These codes implement an improved version of the RF distribution computation by Bryant et al. 
-Here, we modified the dynamic programming algorithm introduced by Bryant et al for computing the distribution of RF distance 
-for a given tree by leveraging the Number-Theoretic Transform (NTT), and improve the running time from O(l^5) to O(l^3log(l)), 
-where l is the number of tips of the tree. 
+Author: Who wrote it
+Maintainer: The package maintainer <[email protected]>
+Description: More about what it does (maybe more than one line)
+    Use four spaces when indenting paragraphs within the Description.
 License: What license is it under?
 Encoding: UTF-8
 LazyData: true

rfdistr/R/RF_FFT.R

@@ -39,7 +39,7 @@ internalchildren <- function(tree,v,ntip){
 }
 
 
-RF_Convolve=function(tree,n){
+fft_RF_Convolve=function(tree,n){
   ntip=n-1
   N=tree$Nnode
   R=rep(list(matrix(0,(ntip-1),(ntip-1))),N)
@@ -117,7 +117,7 @@ qmT=function(R,n,m){
 }
 
 fft_polynomial=function(tree,n){
-  R=RF_Convolve(tree,n)
+  R=fft_RF_Convolve(tree,n)
   for (i in seq(0,2*(n-3),2)) {
     print(qmT(R,n,n-3-(i/2)))
   }

rfdistr/R/RF_NTTfromPy.R

@@ -46,7 +46,7 @@ internalchildren <- function(tree,v,ntip){
   return(result)
 }
 
-RF_Convolve=function(tree,n){
+ntt_RF_Convolve=function(tree,n){
   tt=0
   t=(n-4)*(n-2)*3
   L= 2^ceiling(log(t)/log(2))
@@ -115,7 +115,7 @@ RF_Convolve=function(tree,n){
 
       #read the output of Python
 
-      system('python  /python_code/ntt_fromR.py')
+      system('python  ntt_fromR.py')
 
       U=as.matrix(read.csv("outNTT.txt",header = FALSE, quote=""))
 
@@ -157,7 +157,7 @@ qmT=function(R,n,m){
 #this function computes the RF distribution
 ntt_polynomial=function(tree,n){
   Coef=numeric()
-  R=RF_Convolve(tree,n)
+  R=ntt_RF_Convolve(tree,n)
   for (i in seq(0,2*(n-3),2)) {
     Coef=c(Coef,qmT(R,n,n-3-(i/2)))
   }