merge with remote

[valse.git] / test / generateRunSaveTest_EMGrank.R

diff --git a/test/generateRunSaveTest_EMGrank.R b/test/generateRunSaveTest_EMGrank.R
index 9969620..f6a3314 100644 (file)
--- a/test/generateRunSaveTest_EMGrank.R
+++ b/test/generateRunSaveTest_EMGrank.R
@@ -1,22 +1,21 @@
 source("helper.R")
 library(valse)
 
-generateRunSaveTest_EMGrank = function(n=200, p=15, m=10, k=3, mini=5, maxi=10, gamma=1.0,
-       rank = c(1,2,4))
+generateRunSaveTest_EMGrank = function(n=200, p=15, m=10, k=3, mini=5, maxi=10, gamma=1.0, rank = c(1,2,4))
 {
   eps = 1e-6
-  pi = rep(1.0/k, k)
-  rho = array(dim=c(m,m,k))
+  Pi = rep(1.0/k, k)
+  Rho = array(dim=c(m,m,k))
   for(i in 1:k)
-    rho[,,i] = diag(1,m)
+    Rho[,,i] = diag(1,m)
   xy = generateXYdefault(n, p, m, k)
 
-  testFolder = "../data/"
+  testFolder = "./data/"
   dir.create(testFolder, showWarnings=FALSE, mode="0755")
   #save inputs
-  write.table(as.double(rho), paste(testFolder,"rho",sep=""),
+       write.table(as.double(Pi), paste(testFolder,"Pi",sep=""),
                row.names=F, col.names=F)
-       write.table(as.double(pi), paste(testFolder,"pi",sep=""),
+  write.table(as.double(Rho), paste(testFolder,"Rho",sep=""),
                row.names=F, col.names=F)
   write.table(as.integer(mini), paste(testFolder,"mini",sep=""),
                row.names=F, col.names=F)
@@ -33,7 +32,7 @@ generateRunSaveTest_EMGrank = function(n=200, p=15, m=10, k=3, mini=5, maxi=10,
   write.table(as.integer(c(n,p,m,k)), paste(testFolder,"dimensions",sep=""),
                row.names=F, col.names=F)
 
-  res = valse::EMGrank(pi,rho,mini,maxi,xy$X,xy$Y,eps,rank,fast=FALSE)
+  res = valse::EMGrank(Pi,Rho,mini,maxi,xy$X,xy$Y,eps,rank,fast=FALSE)
 
   #save output
   write.table(as.double(res$phi),paste(testFolder,"phi",sep=""),row.names=F,col.names=F)