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

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

diff --git a/src/test/generate_test_data/generateRunSaveTest_constructionModelesLassoMLE.R b/src/test/generate_test_data/generateRunSaveTest_constructionModelesLassoMLE.R
index 500ce2f..95aaf1e 100644 (file)
--- a/src/test/generate_test_data/generateRunSaveTest_constructionModelesLassoMLE.R
+++ b/src/test/generate_test_data/generateRunSaveTest_constructionModelesLassoMLE.R
@@ -1,22 +1,24 @@
 generateRunSaveTest_constructionModelesLassoMLE = function(n=200, p=15, m=10, k=3, mini=5,
        maxi=10, gamma=1.0, glambda=list(0.0,0.01,0.02,0.03,0.05,0.1,0.2,0.3,0.5,0.7,0.85,0.99))
 {
-  testFolder = "data/"
-  dir.create(testFolder, showWarnings=FALSE, mode="0755")
-
-       require(valse)
-  params = valse:::basic_Init_Parameters(n, p, m, k)
-  A2 = array(0, dim=c(p, m+1, L))
+       tau = 1e-6;
+       seuil = 1e-15;
+       L = length(glambda);
   A1 = array(0, dim=c(p, m+1, L))
+  A2 = array(0, dim=c(p, m+1, L))
   for (i in 1:L)
        {
-    A2[,1,i] = seq_len(p)
-    A2[,2,i] = seq_len(5)
     A1[,1,i] = seq_len(p)
-    A1[,2,i] = seq_len(5)
+    A1[1:5,2,i] = seq_len(5)
+    A2[,1,i] = seq_len(p)
+    A2[1:5,2,i] = seq_len(5)
   }
-  io = generateIOdefault(n, p, m, k)
+       require(valse)
+  params = valse:::basicInitParameters(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(params$phiInit), paste(testFolder,"phiInit",sep=""),
                row.names=F, col.names=F)
@@ -34,18 +36,24 @@ generateRunSaveTest_constructionModelesLassoMLE = function(n=200, p=15, m=10, k=
                row.names=F, col.names=F)
   write.table(as.double(lambda), paste(testFolder,"lambda",sep=""),
                row.names=F, col.names=F)
-  write.table(as.double(io$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(seuil), paste(testFolder,"seuil",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(c(n,p,m,k)), paste(testFolder,"dimensions",sep=""),
+  write.table(as.double(A1), paste(testFolder,"A1",sep=""),
+               row.names=F, col.names=F)
+  write.table(as.double(A2), paste(testFolder,"A2",sep=""),
+               row.names=F, col.names=F)
+  write.table(as.integer(c(n,p,m,k,L)), paste(testFolder,"dimensions",sep=""),
                row.names=F, col.names=F)
 
   res = constructionModelesLassoMLE(
                params$phiInit,params$rhoInit,params$piInit,params$gamInit,
-               mini,maxi,gamma,glambda,io$X,io$Y,seuil,tau,A1,A2)
+               mini,maxi,gamma,glambda,xy$X,xy$Y,seuil,tau,A1,A2)
 
   #save output
   write.table(as.double(res$phi), paste(testFolder,"phi",sep=""), row.names=F, col.names=F)