From: emilie <emilie@devijver.org>
Date: Tue, 4 Apr 2017 08:57:21 +0000 (+0200)
Subject: update main.R and fix some errors
X-Git-Url: https://git.auder.net/variants/current/css/doc/html/packages.html?a=commitdiff_plain;h=19041906b8d80eb9a7dac7bffebf3992bcec6ccf;p=valse.git

update main.R and fix some errors
---

diff --git a/pkg/DESCRIPTION b/pkg/DESCRIPTION
index 8ec8b8a..eb71b76 100644
--- a/pkg/DESCRIPTION
+++ b/pkg/DESCRIPTION
@@ -19,7 +19,7 @@ Depends:
     R (>= 3.0.0)
 Imports:
     MASS,
-		parallel
+    parallel
 Suggests:
     capushe,
     roxygen2,
@@ -27,3 +27,16 @@ Suggests:
 URL: http://git.auder.net/?p=valse.git
 License: MIT + file LICENSE
 RoxygenNote: 5.0.1
+Collate:
+    'plot.R'
+    'main.R'
+    'selectVariables.R'
+    'filterModels.R'
+    'constructionModelesLassoRank.R'
+    'constructionModelesLassoMLE.R'
+    'computeGridLambda.R'
+    'initSmallEM.R'
+    'EMGrank.R'
+    'EMGLLF.R'
+    'generateXY.R'
+    'A_NAMESPACE.R'
diff --git a/pkg/R/computeGridLambda.R b/pkg/R/computeGridLambda.R
index a051441..e2b6303 100644
--- a/pkg/R/computeGridLambda.R
+++ b/pkg/R/computeGridLambda.R
@@ -24,9 +24,8 @@ computeGridLambda = function(phiInit, rhoInit, piInit, gamInit, X, Y,
 	m = dim(phiInit)[2]
 	k = dim(phiInit)[3]
 
-	# TODO: explain why gamma=1 instad of just 'gamma'?
-  list_EMG = EMGLLF(phiInit, rhoInit, piInit, gamInit, mini, maxi,
-		gamma=1, lamba=0, X, Y, tau)
+	list_EMG = EMGLLF(phiInit, rhoInit, piInit, gamInit, mini, maxi,
+		gamma, lambda=0, X, Y, tau)
 	grid = array(0, dim=c(p,m,k))
 	for (i in 1:p)
 	{
@@ -34,6 +33,5 @@ computeGridLambda = function(phiInit, rhoInit, piInit, gamInit, X, Y,
 			grid[i,j,] = abs(list_EMG$S[i,j,]) / (n*list_EMG$pi^gamma)
 	}
 	grid = unique(grid)
-	grid = grid[grid <= 1]
 	grid
 }
diff --git a/pkg/R/main.R b/pkg/R/main.R
index ab25daf..8f845f4 100644
--- a/pkg/R/main.R
+++ b/pkg/R/main.R
@@ -87,11 +87,13 @@ valse = function(X, Y, procedure='LassoMLE', selecMod='DDSE', gamma=1, mini=10,
 
 	# List (index k) of lists (index lambda) of models
 	models_list <-
-		if (ncores_k > 1)
+		#if (ncores_k > 1)
+	  if (ncores_outer > 1)
 			parLapply(cl, kmin:kmax, computeModels)
 		else
 			lapply(kmin:kmax, computeModels)
-	if (ncores_k > 1)
+	#if (ncores_k > 1)
+	if (ncores_outer > 1)
 		parallel::stopCluster(cl)
 
 	if (! requireNamespace("capushe", quietly=TRUE))
@@ -102,11 +104,11 @@ valse = function(X, Y, procedure='LassoMLE', selecMod='DDSE', gamma=1, mini=10,
 
 	# Get summary "tableauRecap" from models ; TODO: jusqu'à ligne 114 à mon avis là c'est faux :/
 	tableauRecap = t( sapply( models_list, function(models) {
-		llh = do.call(rbind, lapply(models, function(model) model$llh)
+		llh = do.call(rbind, lapply(models, function(model) model$llh))
     LLH = llh[-1,1]
     D = llh[-1,2]
 		c(LLH, D, rep(k, length(model)), 1:length(model))
-	) } ) )
+	} ))
 	if (verbose)
 		print('Model selection')
   tableauRecap = tableauRecap[rowSums(tableauRecap[, 2:4])!=0,]