fix memory leaks on EMGLLF, test OK for EMGrank

[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 b6ff68c..500ce2f 100644 (file)
--- a/src/test/generate_test_data/generateRunSaveTest_constructionModelesLassoMLE.R
+++ b/src/test/generate_test_data/generateRunSaveTest_constructionModelesLassoMLE.R
@@ -1,46 +1,55 @@
-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)){
+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")
-  delimiter = " "
-  
-  #Generate phiInit,piInit,...
+
        require(valse)
   params = valse:::basic_Init_Parameters(n, p, m, k)
-
-  #save inputs
-  write.table(paste(testFolder,"phiInit",sep=""), params$phiInit, sep=delimiter)
-  write.table(paste(testFolder,"rhoInit",sep=""), params$rhoInit, sep=delimiter)
-  write.table(paste(testFolder,"piInit",sep=""), params$piInit, sep=delimiter)
-  write.table(paste(testFolder,"gamInit",sep=""), params$gamInit, sep=delimiter)
-  write.table(paste(testFolder,"mini",sep=""), mini, sep=delimiter)
-  write.table(paste(testFolder,"maxi",sep=""), maxi, sep=delimiter)
-  write.table(paste(testFolder,"gamma",sep=""), gamma, sep=delimiter)
-  write.table(paste(testFolder,"lambda",sep=""), lambda, sep=delimiter)
-  write.table(paste(testFolder,"X",sep=""), io$X, sep=delimiter)
-  write.table(paste(testFolder,"Y",sep=""), io$Y, sep=delimiter)
-  write.table(paste(testFolder,"tau",sep=""), tau, sep=delimiter)
-  write.table(paste(testFolder,"dimensions",sep=""), c(n,p,m,k), sep=delimiter)
-  
   A2 = array(0, dim=c(p, m+1, L))
   A1 = array(0, dim=c(p, m+1, L))
-  for(i in 1:L){
-    A2[,1,i] = seq(1,p)
-    A2[,2,i] = seq(1,5)
-    A1[,1, i] = seq(1,p)
-    A1[,2,i] = seq(1,5)
+  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)
   }
-  
-  #Generate X and Y
-  generateIOdef = generateIOdefault(n, p, m, k)
-  construct_LME = constructionModelesLassoMLE(params$phiInit,params$rhoInit,params$piInit,params$gamInit,mini,maxi,gamma,glambda,generateIOdef$X,generateIOdef$Y,seuil,tau,A1,A2)
-  phi = construct_LME$phi
-  rho = construct_LME$rho
-  pi = construct_LME$pi
-  lvraisemblance = construct_LME$lvraisemblance
-  
+  io = generateIOdefault(n, p, m, k)
+
+  #save inputs
+  write.table(as.double(params$phiInit), paste(testFolder,"phiInit",sep=""),
+               row.names=F, col.names=F)
+  write.table(as.double(params$rhoInit), paste(testFolder,"rhoInit",sep=""),
+               row.names=F, col.names=F)
+  write.table(as.double(params$piInit), paste(testFolder,"piInit",sep=""),
+               row.names=F, col.names=F)
+  write.table(as.double(params$gamInit), paste(testFolder,"gamInit",sep=""),
+               row.names=F, col.names=F)
+  write.table(as.integer(mini), paste(testFolder,"mini",sep=""),
+               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(gamma), paste(testFolder,"gamma",sep=""),
+               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$X), paste(testFolder,"X",sep=""),
+               row.names=F, col.names=F)
+  write.table(as.double(io$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(c(n,p,m,k)), 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)
+
   #save output
-  write.table(paste(testFolder,"phi",sep=""), construct_LME$phi, sep=delimiter)
-  write.table(paste(testFolder,"rho",sep=""), construct_LME$rho, sep=delimiter)
-  write.table(paste(testFolder,"pi",sep=""), construct_LME$pi, sep=delimiter)
-  write.table(paste(testFolder,"lvraisemblance",sep=""), construct_LME$lvraisemblance, sep=delimiter)
+  write.table(as.double(res$phi), paste(testFolder,"phi",sep=""), row.names=F, col.names=F)
+  write.table(as.double(res$rho), paste(testFolder,"rho",sep=""), row.names=F, col.names=F)
+  write.table(as.double(res$pi), paste(testFolder,"pi",sep=""), row.names=F, col.names=F)
+  write.table(as.double(res$llh), paste(testFolder,"llh",sep=""), row.names=F, col.names=F)
 }