fix EMGRank.R, and add some lines in the roxygen code for some functions

[valse.git] / pkg / R / constructionModelesLassoMLE.R

diff --git a/pkg/R/constructionModelesLassoMLE.R b/pkg/R/constructionModelesLassoMLE.R
index ac54319..ba6f125 100644 (file)
--- a/pkg/R/constructionModelesLassoMLE.R
+++ b/pkg/R/constructionModelesLassoMLE.R
@@ -2,21 +2,33 @@
 #'
 #' Construct a collection of models with the Lasso-MLE procedure.
 #' 
 #'
 #' Construct a collection of models with the Lasso-MLE procedure.
 #' 

+#' @param phiInit an initialization for phi, get by initSmallEM.R
+#' @param rhoInit an initialization for rho, get by initSmallEM.R
+#' @param piInit an initialization for pi, get by initSmallEM.R
+#' @param gamInit an initialization for gam, get by initSmallEM.R
+#' @param mini integer, minimum number of iterations in the EM algorithm, by default = 10
+#' @param maxi integer, maximum number of iterations in the EM algorithm, by default = 100
+#' @param gamma integer for the power in the penaly, by default = 1
+#' @param X matrix of covariates (of size n*p)
+#' @param Y matrix of responses (of size n*m)
+#' @param eps real, threshold to say the EM algorithm converges, by default = 1e-4
+#' @param S output of selectVariables.R
+#' @param ncores Number of cores, by default = 3
+#' @param fast TRUE to use compiled C code, FALSE for R code only
+#' @param verbose TRUE to show some execution traces
+#' 
+#' @return a list with several models, defined by phi, rho, pi, llh

 #'
 #'

-#' @param ...
-#'
-#' @return ...
-#'
-#' export
-constructionModelesLassoMLE = function(phiInit, rhoInit, piInit, gamInit, mini, maxi,
-       gamma, X, Y, thresh, tau, S, ncores=3, fast=TRUE, verbose=FALSE)
+#' @export
+constructionModelesLassoMLE = function( phiInit, rhoInit, piInit, gamInit, mini, maxi,gamma, X, Y,
+        eps, S, ncores=3, fast=TRUE, verbose=FALSE)

 {
        if (ncores > 1)
        {
                cl = parallel::makeCluster(ncores, outfile='')
                parallel::clusterExport( cl, envir=environment(),
 {
        if (ncores > 1)
        {
                cl = parallel::makeCluster(ncores, outfile='')
                parallel::clusterExport( cl, envir=environment(),

-                       varlist=c("phiInit","rhoInit","gamInit","mini","maxi","gamma","X","Y","thresh",
-                       "tau","S","ncores","verbose") )
+                       varlist=c("phiInit","rhoInit","gamInit","mini","maxi","gamma","X","Y","eps",
+                       "S","ncores","fast","verbose") )

        }
 
        # Individual model computation
        }
 
        # Individual model computation


@@ -40,7 +52,7 @@ constructionModelesLassoMLE = function(phiInit, rhoInit, piInit, gamInit, mini,
 
                # lambda == 0 because we compute the EMV: no penalization here
                res = EMGLLF(phiInit[col.sel,,],rhoInit,piInit,gamInit,mini,maxi,gamma,0,
 
                # lambda == 0 because we compute the EMV: no penalization here
                res = EMGLLF(phiInit[col.sel,,],rhoInit,piInit,gamInit,mini,maxi,gamma,0,

-                       X[,col.sel], Y, tau, fast)
+                       X[,col.sel], Y, eps, fast)

                
                # Eval dimension from the result + selected
                phiLambda2 = res$phi
                
                # Eval dimension from the result + selected
                phiLambda2 = res$phi