update main.R and fix some errors

diff --git a/pkg/DESCRIPTION b/pkg/DESCRIPTION
index 8ec8b8a..eb71b76 100644 (file)
--- 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 (file)
--- 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 (file)
--- 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,]