Merge branch 'master' of auder.net:valse

diff --combined pkg/R/selectiontotale.R
index 1690386,5b0112c..5b0112c
--- 1/pkg/R/selectiontotale.R
--- 2/R/selectiontotale.R
+++ b/pkg/R/selectiontotale.R
@@@ -1,12 -1,13 +1,13 @@@
  #Return a list of outputs, for each lambda in grid: selected,Rho,Pi
- selectiontotale = function(phiInit,rhoInit,piInit,gamInit,mini,maxi,gamma,glambda,X,Y,thresh,tau){
-   require(parallel)
-     cl = parallel::makeCluster( parallel::detectCores() / 4 ) # <-- ça devrait être un argument
+ selectiontotale = function(phiInit,rhoInit,piInit,gamInit,mini,maxi,gamma,glambda,X,Y,thresh,tau, parallel = FALSE){
+   if (parallel) {
+     require(parallel)
+     cl = parallel::makeCluster( parallel::detectCores() / 4) # <-- ça devrait être un argument
      parallel::clusterExport(cl=cl,
                              varlist=c("phiInit","rhoInit","gamInit","mini","maxi","glambda","X","Y","thresh","tau"),
                              envir=environment())
      #Pour chaque lambda de la grille, on calcule les coefficients
-     out = parLapply( 1:length(glambda), function(lambdaindex)
+     out = parLapply(cl,  1:length(glambda), function(lambdaIndex)
      {
        params = 
          EMGLLF(phiInit,rhoInit,piInit,gamInit,mini,maxi,gamma,glambda[lambdaIndex],X,Y,tau)
@@@ -23,4 -24,27 +24,27 @@@
        list("selected"=selectedVariables,"Rho"=params$Rho,"Pi"=params$Pi)
      })
      parallel::stopCluster(cl)
-   }
+   }
+   else {
+     selectedVariables = list()
+     Rho = list()
+     Pi = list()
+     #Pour chaque lambda de la grille, on calcule les coefficients
+     for (lambdaIndex in 1:length(glambda)){
+       print(lambdaIndex)
+       params = 
+         EMGLLF(phiInit,rhoInit,piInit,gamInit,mini,maxi,gamma,glambda[lambdaIndex],X,Y,tau)
+       p = dim(phiInit)[1]
+       m = dim(phiInit)[2]
+       #selectedVariables: list where element j contains vector of selected variables in [1,m]
+       selectedVariables[[lambdaIndex]] = lapply(1:p, function(j) {
+         #from boolean matrix mxk of selected variables obtain the corresponding boolean m-vector,
+         #and finally return the corresponding indices
+         seq_len(m)[ apply( abs(params$phi[j,,]) > thresh, 1, any ) ]
+       })
+       Rho[[lambdaIndex]] = params$Rho
+       Pi[[lambdaIndex]] = params$Pi
+     }
+     list("selected"=selectedVariables,"Rho"=Rho,"Pi"=Pi)
+   }
+ }