From: Benjamin Auder <benjamin.auder@somewhere>
Date: Mon, 9 Jan 2017 13:44:19 +0000 (+0100)
Subject: update Makevars
X-Git-Url: https://git.auder.net/js/css/%7B%7B?a=commitdiff_plain;h=cad71b2c9e838c8f65313e590e6cf6980b037401;p=valse.git

update Makevars
---

diff --git a/NAMESPACE b/NAMESPACE
index c625f7e..656ff8d 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -9,3 +9,5 @@ export(gridLambda)
 export(indicesSelection)
 export(initSmallEM)
 export(modelSelection)
+export(selectVariables)
+useDynLib(valse)
diff --git a/R/main.R b/R/main.R
index 6633be2..4c4e87c 100644
--- a/R/main.R
+++ b/R/main.R
@@ -1,3 +1,5 @@
+#' @useDynLib valse
+
 Valse = setRefClass(
 	Class = "Valse",
 
diff --git a/R/selectVariables.R b/R/selectVariables.R
index e1a4e33..3f58ea3 100644
--- a/R/selectVariables.R
+++ b/R/selectVariables.R
@@ -15,10 +15,11 @@
 #' @param thres	 threshold to consider a coefficient to be equal to 0
 #' @param tau		 threshold to say that EM algorithm has converged
 #'
-#' @return
-#' @export
+#' @return TODO
+#'
+#' @examples TODO
 #'
-#' @examples
+#' @export
 selectVariables <- function(phiInit,rhoInit,piInit,gamInit,
 	mini,maxi,gamma,glambda,X,Y,thres,tau)
 {
diff --git a/man/basic_Init_Parameters.Rd b/man/basic_Init_Parameters.Rd
index 3be2e2d..981b984 100644
--- a/man/basic_Init_Parameters.Rd
+++ b/man/basic_Init_Parameters.Rd
@@ -3,7 +3,7 @@
 \name{basic_Init_Parameters}
 \alias{basic_Init_Parameters}
 \title{Initialize the parameters in a basic way (zero for the conditional mean,
- uniform for weights, identity for covariance matrices, and uniformly distributed forthe clustering)}
+uniform for weights, identity for covariance matrices, and uniformly distributed forthe clustering)}
 \usage{
 basic_Init_Parameters(n, p, m, k)
 }
@@ -21,6 +21,6 @@ list with phiInit, rhoInit,piInit,gamInit
 }
 \description{
 Initialize the parameters in a basic way (zero for the conditional mean,
- uniform for weights, identity for covariance matrices, and uniformly distributed forthe clustering)
+uniform for weights, identity for covariance matrices, and uniformly distributed forthe clustering)
 }
 
diff --git a/man/discardSimilarModels.Rd b/man/discardSimilarModels.Rd
index 0a73b7e..7cef581 100644
--- a/man/discardSimilarModels.Rd
+++ b/man/discardSimilarModels.Rd
@@ -19,7 +19,7 @@ discardSimilarModels(B1, B2, glambda, rho, pi)
 }
 \value{
 a list with update B1, B2, glambda, rho and pi, and ind the vector of indices
- of selected models.
+of selected models.
 }
 \description{
 Discard models which have the same relevant variables
diff --git a/man/generateIO.Rd b/man/generateIO.Rd
index b420156..bf8fb20 100644
--- a/man/generateIO.Rd
+++ b/man/generateIO.Rd
@@ -7,9 +7,9 @@
 generateIO(covX, covY, pi, beta, n)
 }
 \arguments{
-\item{covX}{covariance for covariates}
+\item{covX}{covariance for covariates (of size p*p*K)}
 
-\item{covY}{covariance for the response vector}
+\item{covY}{covariance for the response vector (of size m*m*K)}
 
 \item{pi}{proportion for each cluster}
 
diff --git a/man/indicesSelection.Rd b/man/indicesSelection.Rd
index 21d8e2d..a727cdf 100644
--- a/man/indicesSelection.Rd
+++ b/man/indicesSelection.Rd
@@ -2,7 +2,7 @@
 % Please edit documentation in R/indicesSelection.R
 \name{indicesSelection}
 \alias{indicesSelection}
-\title{Construct the set of relevant indices}
+\title{Construct the set of relevant indices -> ED: je crois que cette fonction n'est pas utile}
 \usage{
 indicesSelection(phi, thresh = 1e-06)
 }
@@ -13,9 +13,9 @@ indicesSelection(phi, thresh = 1e-06)
 }
 \value{
 a list with A, a matrix with relevant indices (size = p*m) and B, a 
-         matrix with irrelevant indices (size = p*m)
+				matrix with irrelevant indices (size = p*m)
 }
 \description{
-Construct the set of relevant indices
+Construct the set of relevant indices -> ED: je crois que cette fonction n'est pas utile
 }
 
diff --git a/man/modelSelection.Rd b/man/modelSelection.Rd
index c65b678..650bf70 100644
--- a/man/modelSelection.Rd
+++ b/man/modelSelection.Rd
@@ -14,7 +14,7 @@ the second column corresponds to the dimensions of the corresponding models.}
 }
 \value{
 a list with indices, a vector of indices selected models, 
-        and D1, a vector of corresponding dimensions
+			 and D1, a vector of corresponding dimensions
 }
 \description{
 Among a collection of models, this function constructs a subcollection of models with
diff --git a/man/selectVariables.Rd b/man/selectVariables.Rd
new file mode 100644
index 0000000..09a52f2
--- /dev/null
+++ b/man/selectVariables.Rd
@@ -0,0 +1,49 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/selectVariables.R
+\name{selectVariables}
+\alias{selectVariables}
+\title{selectVaribles
+It is a function which construct, for a given lambda, the sets of
+relevant variables and irrelevant variables.}
+\usage{
+selectVariables(phiInit, rhoInit, piInit, gamInit, mini, maxi, gamma, glambda,
+  X, Y, thres, tau)
+}
+\arguments{
+\item{phiInit}{an initial estimator for phi (size: p*m*k)}
+
+\item{rhoInit}{an initial estimator for rho (size: m*m*k)}
+
+\item{piInit}{an initial estimator for pi (size : k)}
+
+\item{gamInit}{an initial estimator for gamma}
+
+\item{mini}{minimum number of iterations in EM algorithm}
+
+\item{maxi}{maximum number of iterations in EM algorithm}
+
+\item{gamma}{power in the penalty}
+
+\item{glambda}{grid of regularization parameters}
+
+\item{X}{matrix of regressors}
+
+\item{Y}{matrix of responses}
+
+\item{thres}{threshold to consider a coefficient to be equal to 0}
+
+\item{tau}{threshold to say that EM algorithm has converged}
+}
+\value{
+TODO
+}
+\description{
+selectVaribles
+It is a function which construct, for a given lambda, the sets of
+relevant variables and irrelevant variables.
+}
+\examples{
+TODO
+
+}
+
diff --git a/src/Makevars b/src/Makevars
index 6068f39..50b7fb6 100644
--- a/src/Makevars
+++ b/src/Makevars
@@ -4,7 +4,7 @@ PKG_CFLAGS=-g -I./sources
 #Prod flags:
 #PKG_CFLAGS=-O2 -I./sources
 
-PKG_LIBS=-lm
+PKG_LIBS=-lm -lgsl -lcblas
 
 SOURCES = $(wildcard adapters/*.c sources/*.c)