update valse.R

diff --git a/.gitignore b/.gitignore
index b1cd49c..56843bc 100644 (file)
--- a/.gitignore
+++ b/.gitignore
@@ -1,7 +1,7 @@
-/NAMESPACE
+.Rproj.user

 .Rhistory
 .RData
 .Rhistory
 .RData

-*.swp
-*~
-/man/*
-!/man/*-package.Rd
+.Ruserdata
+src/*.o
+src/*.so
+src/*.dll

diff --git a/DESCRIPTION b/DESCRIPTION
index f8f5a29..9d8a677 100644 (file)
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -16,7 +16,8 @@ Maintainer: Benjamin Auder <Benjamin.Auder@math.u-psud.fr>
 Depends:
     R (>= 3.0.0)
 Imports:
 Depends:
     R (>= 3.0.0)
 Imports:

-    MASS
+    MASS,
+    methods

 Suggests:
     parallel,
     testthat,
 Suggests:
     parallel,
     testthat,

diff --git a/R/gridLambda.R b/R/gridLambda.R
index 855b4a6..e7946ae 100644 (file)
--- a/R/gridLambda.R
+++ b/R/gridLambda.R
@@ -1,8 +1,11 @@
 #' Construct the data-driven grid for the regularization parameters used for the Lasso estimator
 #' @param phiInit value for phi
 #' Construct the data-driven grid for the regularization parameters used for the Lasso estimator
 #' @param phiInit value for phi

-#' @param rhoInt       value for rho
+#' @param rhoInit      value for rho

 #' @param piInit       value for pi
 #' @param gamInit value for gamma
 #' @param piInit       value for pi
 #' @param gamInit value for gamma

+#' @param X matrix of covariates (of size n*p)
+#' @param Y matrix of responses (of size n*m)
+#' @param gamma power of weights in the penalty

 #' @param mini         minimum number of iterations in EM algorithm
 #' @param maxi         maximum number of iterations in EM algorithm
 #' @param tau          threshold to stop EM algorithm
 #' @param mini         minimum number of iterations in EM algorithm
 #' @param maxi         maximum number of iterations in EM algorithm
 #' @param tau          threshold to stop EM algorithm

diff --git a/R/initSmallEM.R b/R/initSmallEM.R
index e2157b2..399f39f 100644 (file)
--- a/R/initSmallEM.R
+++ b/R/initSmallEM.R
@@ -3,11 +3,12 @@
 #' @param k number of components
 #' @param X matrix of covariates (of size n*p)
 #' @param Y matrix of responses (of size n*m)
 #' @param k number of components
 #' @param X matrix of covariates (of size n*p)
 #' @param Y matrix of responses (of size n*m)

-#' @param tau threshold to stop EM algorithm

 #'
 #' @return a list with phiInit, rhoInit, piInit, gamInit
 #' @export
 #'
 #' @return a list with phiInit, rhoInit, piInit, gamInit
 #' @export

-initSmallEM = function(k,X,Y,tau)
+#' @importFrom methods new
+#' @importFrom stats cutree dist hclust runif
+initSmallEM = function(k,X,Y)

 {
        n = nrow(Y)
        m = ncol(Y)
 {
        n = nrow(Y)
        m = ncol(Y)


@@ -34,9 +35,13 @@ initSmallEM = function(k,X,Y,tau)
                {
                        Z = Zinit1[,repet]
                        Z_indice = seq_len(n)[Z == r] #renvoit les indices où Z==r
                {
                        Z = Zinit1[,repet]
                        Z_indice = seq_len(n)[Z == r] #renvoit les indices où Z==r

-                       
+                       if (length(Z_indice) == 1) {
+                         betaInit1[,,r,repet] = ginv(crossprod(t(X[Z_indice,]))) %*%
+                           crossprod(t(X[Z_indice,]), Y[Z_indice,])
+                       } else {

                        betaInit1[,,r,repet] = ginv(crossprod(X[Z_indice,])) %*%
                                crossprod(X[Z_indice,], Y[Z_indice,])
                        betaInit1[,,r,repet] = ginv(crossprod(X[Z_indice,])) %*%
                                crossprod(X[Z_indice,], Y[Z_indice,])

+                       }

                        sigmaInit1[,,r,repet] = diag(m)
                        phiInit1[,,r,repet] = betaInit1[,,r,repet] #/ sigmaInit1[,,r,repet]
                        rhoInit1[,,r,repet] = solve(sigmaInit1[,,r,repet])
                        sigmaInit1[,,r,repet] = diag(m)
                        phiInit1[,,r,repet] = betaInit1[,,r,repet] #/ sigmaInit1[,,r,repet]
                        rhoInit1[,,r,repet] = solve(sigmaInit1[,,r,repet])


@@ -58,7 +63,7 @@ initSmallEM = function(k,X,Y,tau)
                maxiInit = 11
                
                new_EMG = .Call("EMGLLF_core",phiInit1[,,,repet],rhoInit1[,,,repet],piInit1[repet,],
                maxiInit = 11
                
                new_EMG = .Call("EMGLLF_core",phiInit1[,,,repet],rhoInit1[,,,repet],piInit1[repet,],

-                       gamInit1[,,repet],miniInit,maxiInit,1,0,X,Y,tau)
+                       gamInit1[,,repet],miniInit,maxiInit,1,0,X,Y,1e-4)

                LLFEessai = new_EMG$LLF
                LLFinit1[repet] = LLFEessai[length(LLFEessai)]
        }
                LLFEessai = new_EMG$LLF
                LLFinit1[repet] = LLFEessai[length(LLFEessai)]
        }

diff --git a/R/main.R b/R/main.R
index 42852d3..1908021 100644 (file)
--- a/R/main.R
+++ b/R/main.R
@@ -92,7 +92,7 @@ Valse = setRefClass(
                        #smallEM initializes parameters by k-means and regression model in each component,
                        #doing this 20 times, and keeping the values maximizing the likelihood after 10
                        #iterations of the EM algorithm.
                        #smallEM initializes parameters by k-means and regression model in each component,
                        #doing this 20 times, and keeping the values maximizing the likelihood after 10
                        #iterations of the EM algorithm.

-                       init = initSmallEM(k,X,Y,eps)
+                       init = initSmallEM(k,X,Y)

                        phiInit <<- init$phi0
                        rhoInit <<- init$rho0
                        piInit  <<- init$pi0
                        phiInit <<- init$phi0
                        rhoInit <<- init$rho0
                        piInit  <<- init$pi0