From: Benjamin Auder <benjamin.auder@somewhere>
Date: Fri, 10 Feb 2017 14:13:49 +0000 (+0100)
Subject: fix valse pkg functions callings in src/test/generate
X-Git-Url: https://git.auder.net/variants/current/css/doc/img/%7B%7B%20targetUrl%20%7D%7D?a=commitdiff_plain;h=9ade3f1b66fa07ad9f1a3b09fc05462c783841de;p=valse.git

fix valse pkg functions callings in src/test/generate
---

diff --git a/R/vec_bin.R b/R/vec_bin.R
index ece7280..27f771b 100644
--- a/R/vec_bin.R
+++ b/R/vec_bin.R
@@ -20,4 +20,4 @@ vec_bin = function(X,r)
 			Z[i] = 0
 	}
 	return (list(Z=Z,indice=indice))
-}
\ No newline at end of file
+}
diff --git a/src/test/generate_test_data/generateRunSaveTest_EMGLLF.R b/src/test/generate_test_data/generateRunSaveTest_EMGLLF.R
index 60ac6c5..2c2dc2a 100644
--- a/src/test/generate_test_data/generateRunSaveTest_EMGLLF.R
+++ b/src/test/generate_test_data/generateRunSaveTest_EMGLLF.R
@@ -6,7 +6,8 @@ generateRunSaveTest_EMGLLF = function(n=200, p=15, m=10, k=3, mini=5, maxi=10,
 	delimiter = " "
 
 	#save inputs
-	params = basicInitParameters(n, p, m, k)
+	require(valse)
+	params = valse:::basic_Init_Parameters(n, p, m, k)
 	io = generateIOdefault(n, p, m, k)
 	write.table(paste(testFolder,"phiInit",sep=""), params$phiInit, sep=delimiter);
 	write.table(paste(testFolder,"rhoInit",sep=""), params$rhoInit, sep=delimiter);
diff --git a/src/test/generate_test_data/generateRunSaveTest_EMGrank.R b/src/test/generate_test_data/generateRunSaveTest_EMGrank.R
index 6fc812a..0f97995 100644
--- a/src/test/generate_test_data/generateRunSaveTest_EMGrank.R
+++ b/src/test/generate_test_data/generateRunSaveTest_EMGrank.R
@@ -13,7 +13,8 @@ generateRunSaveTest_EMGrank = function(n=200, p=15, m=10, k=3, mini=5, maxi=10,
   }
 
   #Generate X and Y
-  generateIOdef = generateIOdefault(n, p, m, k)
+	require(valse)
+  generateIOdef = valse:::generateIOdefault(n, p, m, k)
   
   #save inputs
   write.table(paste(testFolder,"rho",sep=""), rho, sep=delimiter)
diff --git a/src/test/generate_test_data/generateRunSaveTest_constructionModelesLassoMLE.R b/src/test/generate_test_data/generateRunSaveTest_constructionModelesLassoMLE.R
index 104cb3f..b6ff68c 100644
--- a/src/test/generate_test_data/generateRunSaveTest_constructionModelesLassoMLE.R
+++ b/src/test/generate_test_data/generateRunSaveTest_constructionModelesLassoMLE.R
@@ -4,7 +4,8 @@ generateRunSaveTest_constructionModelesLassoMLE = function(n=200, p=15, m=10, k=
   delimiter = " "
   
   #Generate phiInit,piInit,...
-  params = basicInitParameters(n, p, m, k)
+	require(valse)
+  params = valse:::basic_Init_Parameters(n, p, m, k)
 
   #save inputs
   write.table(paste(testFolder,"phiInit",sep=""), params$phiInit, sep=delimiter)
diff --git a/src/test/generate_test_data/generateRunSaveTest_constructionModelesLassoRank.R b/src/test/generate_test_data/generateRunSaveTest_constructionModelesLassoRank.R
index 09d9823..dfb2736 100644
--- a/src/test/generate_test_data/generateRunSaveTest_constructionModelesLassoRank.R
+++ b/src/test/generate_test_data/generateRunSaveTest_constructionModelesLassoRank.R
@@ -17,7 +17,8 @@ generateRunSaveTest_constructionModelesLassoRank = function(n=200, p=15, m=10, L
     }
   }
   #Generate X and Y
-  generateIOdef = generateIOdefault(n, p, m, k)
+	require(valse)
+  generateIOdef = valse:::generateIOdefault(n, p, m, k)
   
   A1 = matrix(0,p,L)
   for(i in 1:L){
@@ -42,4 +43,4 @@ generateRunSaveTest_constructionModelesLassoRank = function(n=200, p=15, m=10, L
   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
index b366ec9..adfe26c 100644
--- a/src/test/generate_test_data/generateRunSaveTest_selectiontotale.R
+++ b/src/test/generate_test_data/generateRunSaveTest_selectiontotale.R
@@ -3,11 +3,13 @@ generateRunSaveTest_selectiontotale= function(n=200, p=15, m=10, k=3, mini=5, ma
   dir.create(testFolder, showWarnings=FALSE, mode="0755")
   delimiter = " "
   
+	require(valse)
+
   #Generate phiInit,piInit,...
-  params = basicInitParameters(n, p, m, k)
+  params = valse:::basic_Init_Parameters(n, p, m, k)
   
   #Generate X and Y
-  generateIOdef = generateIOdefault(n, p, m, k)
+  generateIOdef = valse:::generateIOdefault(n, p, m, k)
   
   #save inputs
   write.table(paste(testFolder,"phiInit",sep=""), params$phiInit, sep=delimiter)
diff --git a/src/test/generate_test_data/helpers/EMGrank.R b/src/test/generate_test_data/helpers/EMGrank.R
index e34e0be..a1e3df7 100644
--- a/src/test/generate_test_data/helpers/EMGrank.R
+++ b/src/test/generate_test_data/helpers/EMGrank.R
@@ -1,4 +1,3 @@
-source("/home/goehry/Documents/valse/valse/R/vec_bin.R")
 require(MASS)
 EMGrank = function(Pi, Rho, mini, maxi, X, Y, tau, rank){
   #matrix dimensions
@@ -24,7 +23,7 @@ EMGrank = function(Pi, Rho, mini, maxi, X, Y, tau, rank){
   while(ite<=mini || (ite<=maxi && sumDeltaPhi>tau)){
     #M step: Mise à jour de Beta (et donc phi)
     for(r in 1:k){
-      Z_bin = vec_bin(Z,r)
+      Z_bin = valse:::vec_bin(Z,r)
       Z_vec = Z_bin$vec #vecteur 0 et 1 aux endroits o? Z==r
       Z_indice = Z_bin$indice 
       if(sum(Z_indice) == 0){
@@ -82,4 +81,4 @@ EMGrank = function(Pi, Rho, mini, maxi, X, Y, tau, rank){
   
   }
   return(list(phi=phi, LLF=LLF))
-}
\ No newline at end of file
+}
diff --git a/src/test/generate_test_data/helpers/constructionModelesLassoRank.R b/src/test/generate_test_data/helpers/constructionModelesLassoRank.R
index c319c61..183a6d1 100644
--- a/src/test/generate_test_data/helpers/constructionModelesLassoRank.R
+++ b/src/test/generate_test_data/helpers/constructionModelesLassoRank.R
@@ -9,9 +9,9 @@ constructionModelesLassoRank = function(Pi,Rho,mini,maxi,X,Y,tau,A1,rangmin,rang
   deltaRank = rangmax - rangmin + 1
   Size = deltaRank^k
   Rank = matrix(0, Size, k)
-  for(r in 1:k){
-    Rank[,r] = rangmin + 
-  }
+#  for(r in 1:k) {
+#    Rank[,r] = rangmin +  <--- #FIXME:
+#  }
   
   phi = array(0, dim=c(p,m,k,L*Size))
   lvraisemblance = matrix(0, L*Size, 2)
@@ -31,4 +31,4 @@ constructionModelesLassoRank = function(Pi,Rho,mini,maxi,X,Y,tau,A1,rangmin,rang
     }
   }
   return(list(phi=phi, lvraisemblance = lvraisemblance))
-}
\ No newline at end of file
+}