fix generateRunTest for constructionModelesEMGrank; remove man pages (will be roxygen...

[valse.git] / src / test / generate_test_data / generateRunSaveTest_EMGrank.R

diff --git a/src/test/generate_test_data/generateRunSaveTest_EMGrank.R b/src/test/generate_test_data/generateRunSaveTest_EMGrank.R
index 3740b58..a690cf5 100644 (file)
--- a/src/test/generate_test_data/generateRunSaveTest_EMGrank.R
+++ b/src/test/generate_test_data/generateRunSaveTest_EMGrank.R
@@ -1,18 +1,16 @@
 generateRunSaveTest_EMGrank = function(n=200, p=15, m=10, k=3, mini=5, maxi=10, gamma=1.0,
        rank = c(1,2,4))
 {
-  testFolder = "data/"
-  dir.create(testFolder, showWarnings=FALSE, mode="0755")
-
   tau = 1e-6
   pi = rep(1.0/k, k)
-  rho = array(0, dim=c(m,m,k))
-  for(i in 1:k){
+  rho = array(dim=c(m,m,k))
+  for(i in 1:k)
     rho[,,i] = diag(1,m)
-  }
        require(valse)
-  io = valse:::generateIOdefault(n, p, m, k)
+  xy = valse:::generateXYdefault(n, p, m, k)
 
+  testFolder = "data/"
+  dir.create(testFolder, showWarnings=FALSE, mode="0755")
   #save inputs
   write.table(as.double(rho), paste(testFolder,"rho",sep=""),
                row.names=F, col.names=F)
@@ -22,18 +20,18 @@ generateRunSaveTest_EMGrank = function(n=200, p=15, m=10, k=3, mini=5, maxi=10,
                row.names=F, col.names=F)
   write.table(as.integer(maxi), paste(testFolder,"maxi",sep=""),
                row.names=F, col.names=F)
-  write.table(as.double(io$X), paste(testFolder,"X",sep=""),
+  write.table(as.double(xy$X), paste(testFolder,"X",sep=""),
                row.names=F, col.names=F)
-  write.table(as.double(io$Y), paste(testFolder,"Y",sep=""),
+  write.table(as.double(xy$Y), paste(testFolder,"Y",sep=""),
                row.names=F, col.names=F)
   write.table(as.double(tau), paste(testFolder,"tau",sep=""),
                row.names=F, col.names=F)
   write.table(as.integer(rank), paste(testFolder,"rank",sep=""),
                row.names=F, col.names=F)
-  write.table(as.integer(c(n,p,m,k)), paste(testFolder,"dimensions",sep=""),
+  write.table(as.integer(c(n,p,m,k)), paste(testFolder,"dimensxyns",sep=""),
                row.names=F, col.names=F)
 
-  res = EMGrank(pi,rho,mini,maxi,io$X,io$Y,tau,rank)
+  res = EMGrank(pi,rho,mini,maxi,xy$X,xy$Y,tau,rank)
 
   #save output
   write.table(as.double(res$phi), paste(testFolder,"phi",sep=""), row.names=F,col.names=F)