new tests + correction

diff --git a/src/test/generate_test_data/generateRunSaveTest_EMGrank.R b/src/test/generate_test_data/generateRunSaveTest_EMGrank.R
new file mode 100644 (file)
index 0000000..6fc812a
--- /dev/null
+++ b/src/test/generate_test_data/generateRunSaveTest_EMGrank.R
@@ -0,0 +1,34 @@
+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")
+  delimiter = " "
+  
+  tau = 1e-6
+  
+  pi = rep(1.0/k, k)
+  rho = array(0, dim=c(m,m,k))
+  
+  for(i in 1:k){
+    rho[,,i] = diag(1,m)
+  }
+
+  #Generate X and Y
+  generateIOdef = generateIOdefault(n, p, m, k)
+  
+  #save inputs
+  write.table(paste(testFolder,"rho",sep=""), rho, sep=delimiter)
+  write.table(paste(testFolder,"pi",sep=""), pi, sep=delimiter)
+  write.table(paste(testFolder,"mini",sep=""), mini, sep=delimiter)
+  write.table(paste(testFolder,"maxi",sep=""), maxi, sep=delimiter)
+  write.table(paste(testFolder,"X",sep=""), generateIOdef$X sep=delimiter)
+  write.table(paste(testFolder,"Y",sep=""), generateIOdef$Y, sep=delimiter)
+  write.table(paste(testFolder,"tau",sep=""), tau, sep=delimiter)
+  write.table(paste(testFolder,"rank",sep=""), rank, sep=delimiter)
+  write.table(paste(testFolder,"dimensions",sep=""), c(n,p,m,k), sep=delimiter)
+  
+  EMG_rank = EMG(pi,rho,mini,maxi,X,Y,tau,rank)
+  
+  #save output
+  write.table(paste(testFolder,"phi",sep=""), EMG_rank$phi, sep=delimiter)
+  write.table(paste(testFolder,"LLF",sep=""), EMG_rank$LLF, sep=delimiter)
+}

diff --git a/src/test/generate_test_data/generateRunSaveTest_constructionModelesLassoMLE.R b/src/test/generate_test_data/generateRunSaveTest_constructionModelesLassoMLE.R
index d367bfd..104cb3f 100644 (file)
--- a/src/test/generate_test_data/generateRunSaveTest_constructionModelesLassoMLE.R
+++ b/src/test/generate_test_data/generateRunSaveTest_constructionModelesLassoMLE.R
@@ -1,76 +1,45 @@
-generateRunSaveTest_constructionModelesLassoMLE = function(n, p, m, k, mini, maxi, gamma, glambda, varargin){
-  #set defaults for optional inputs
-  optargs = c(200 15 10 3 5 10 1.0 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))
-  #replace defaults by user parameters
-  optargs[1:length(varargin)] = varargin
-  n = optargs[1]
-  p = optargs[2]
-  m = optargs[3]
-  k = optargs[4]
-  mini = optargs[5]
-  maxi = optargs[6]
-  gamma = optargs[7]
-  glambda = optargs[8]
-  tau = 1e-6
-  seuil = 1e-15
-  L = length(glambda)
+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,...
-  basicInit = basicInitParameters(n, p, m, k)
-  phiInit = basicInit$phiInit
-  rhoInit = basicInit$rhoInit
-  piInit = basicInit$piInit
-  gamInit = basicInit$gamInit
-  
-  #Generate X and Y
-  generateIOdef = generateIOdefault(n, p, m, k)
-  X = generateIOdef$X
-  Y = generateIOdef$Y
+  params = basicInitParameters(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){
-    for(j in 1:p){
-      A2[j, 1, i] = j
-      A1[j, 1, i] = j
-    }
-    for(k in 1:5){
-      A2[k,2,i] = k
-      A1[k,2,i] = k
-    }
+    A2[,1,i] = seq(1,p)
+    A2[,2,i] = seq(1,5)
+    A1[,1, i] = seq(1,p)
+    A1[,2,i] = seq(1,5)
   }
-
-  testFolder = 'data/'
-  dir.create(testFolder)
-  delimiter = ' '
   
-  
-  #save inputs
-  write(strcat(testFolder,'phiInit'), reshape(phiInit,1), delimiter)
-  write(strcat(testFolder,'rhoInit'), reshape(rhoInit,1), delimiter)
-  write(strcat(testFolder,'piInit'), piInit, delimiter)
-  write(strcat(testFolder,'gamInit'), reshape(gamInit,1), delimiter)
-  write(strcat(testFolder,'mini'), mini, delimiter)
-  write(strcat(testFolder,'maxi'), maxi, delimiter)
-  write(strcat(testFolder,'gamma'), gamma, delimiter)
-  write(strcat(testFolder,'glambda'), glambda, delimiter)
-  write(strcat(testFolder,'X'), reshape(X,1), delimiter)
-  write(strcat(testFolder,'Y'), reshape(Y,1), delimiter)
-  mwrite(strcat(testFolder,'seuil'), seuil, delimiter)
-  write(strcat(testFolder,'tau'), tau, delimiter)
-  write(strcat(testFolder,'A1'), reshape(A1,1), delimiter)
-  write(strcat(testFolder,'A2'), reshape(A2,1), delimiter)
-  write(strcat(testFolder,'dimensions'), [n,p,m,k,L], delimiter)
-  
-  construct_LME = constructionModelesLassoMLE(phiInit,rhoInit,piInit,gamInit,mini,maxi,gamma,glambda,X,Y,seuil,tau,A1,A2)
+  #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
   
   #save output
-  write(strcat(testFolder,'phi'), reshape(phi,1), delimiter);
-  write(strcat(testFolder,'rho'), reshape(rho,1), delimiter);
-  write(strcat(testFolder,'pi'), reshape(pi,1), delimiter);
-  write(strcat(testFolder,'lvraisemblance'), reshape(lvraisemblance,1), delimiter);
+  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)
 }

diff --git a/src/test/generate_test_data/generateRunSaveTest_constructionModelesLassoRank.R b/src/test/generate_test_data/generateRunSaveTest_constructionModelesLassoRank.R
new file mode 100644 (file)
index 0000000..09d9823
--- /dev/null
+++ b/src/test/generate_test_data/generateRunSaveTest_constructionModelesLassoRank.R
@@ -0,0 +1,45 @@
+generateRunSaveTest_constructionModelesLassoRank = function(n=200, p=15, m=10, L=12, mini=5, maxi=10, gamma=1.0, rangmin=3, rangmax=6){
+  testFolder = "data/"
+  dir.create(testFolder, showWarnings=FALSE, mode="0755")
+  delimiter = " "
+  
+  tau = 1e-6
+  
+  
+  pi = matrix(0, k,L)
+  for(i in 1:L){
+    pi[,i] = rep(1.0/k, k)
+  }
+  rho = array(0, dim=c(m,m,k,L))
+  for(l in 1:L){
+    for(r in 1:k){
+      rho[,,r,l] = diag(1,m)
+    }
+  }
+  #Generate X and Y
+  generateIOdef = generateIOdefault(n, p, m, k)
+  
+  A1 = matrix(0,p,L)
+  for(i in 1:L){
+    A1[,i] = seq(1,p)
+  }
+  #save inputs
+  write.table(paste(testFolder,"rho",sep=""), rho, sep=delimiter)
+  write.table(paste(testFolder,"pi",sep=""), pi, sep=delimiter)
+  write.table(paste(testFolder,"mini",sep=""), mini, sep=delimiter)
+  write.table(paste(testFolder,"maxi",sep=""), maxi, sep=delimiter)
+  write.table(paste(testFolder,"X",sep=""), generateIOdef$X sep=delimiter)
+  write.table(paste(testFolder,"Y",sep=""), generateIOdef$Y, sep=delimiter)
+  write.table(paste(testFolder,"tau",sep=""), tau, sep=delimiter)
+  write.table(paste(testFolder,"A1",sep=""), A1, sep=delimiter)
+  write.table(paste(testFolder,"rangmin",sep=""), rangmin, sep=delimiter)
+  write.table(paste(testFolder,"rangmax",sep=""), rangmax, sep=delimiter)
+  write.table(paste(testFolder,"dimensions",sep=""), c(n,p,m,k), sep=delimiter)
+  
+  construct = constructionModelesLassoRank(pi,rho,mini,maxi,X,Y,tau,A1,rangmin,rangmax))
+  
+  #save output
+  write.table(paste(testFolder,"phi",sep=""), construct$phi, sep=delimiter)
+  write.table(paste(testFolder,"lvraisemblance",sep=""), construct$lvraisemblance, sep=delimiter)
+  
+}
\ No newline at end of file

diff --git a/src/test/generate_test_data/generateRunSaveTest_selectiontotale.R b/src/test/generate_test_data/generateRunSaveTest_selectiontotale.R
new file mode 100644 (file)
index 0000000..b366ec9
--- /dev/null
+++ b/src/test/generate_test_data/generateRunSaveTest_selectiontotale.R
@@ -0,0 +1,34 @@
+generateRunSaveTest_selectiontotale= 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,...
+  params = basicInitParameters(n, p, m, k)
+  
+  #Generate X and Y
+  generateIOdef = generateIOdefault(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=""), glambda, 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)
+  
+  
+  selec = selectiontotale(params$phiInit,params$rhoInit,params$piInit,params$gamInit,mini,maxi,gamma,glambda,generateIOdef$X,generateIOdef$Y,seuil, tau)
+  
+  #save output
+  write.table(paste(testFolder,"A1",sep=""), selec$A1, sep=delimiter)
+  write.table(paste(testFolder,"A2",sep=""), selec$A2, sep=delimiter)
+  write.table(paste(testFolder,"rho",sep=""), selec$rho, sep=delimiter)
+  write.table(paste(testFolder,"pi",sep=""), selec$pi, sep=delimiter)
+}