Added description and export

DESCRIPTION

@@ -3,7 +3,7 @@ Type: Package
 Title: Adaptation of Virtual Twins method from Jared Foster.
 Version: 0.0.0.1000
 Date: 2015-05-31
-Author: François Vieille
+Author: Francois Vieille
 Maintainer: <vieille.francois@gmail.com>
 Description: Research of subgroups in random clinical trials with binary
     outcome and two treatments groups.

NAMESPACE

@@ -1,5 +1,11 @@
 # Generated by roxygen2 (4.1.1): do not edit by hand
 
+export(VT.difft)
+export(VT.forest.double)
+export(VT.forest.one)
+export(VT.object)
+export(VT.tree.class)
+export(VT.tree.reg)
 export(formatRCTDataset)
 import(methods)
 importClassesFrom(party,RandomForest)

R/VirtualTwins.R

@@ -0,0 +1,24 @@
+
+#' VirtualTwins : An adapation of VirtualTwins method created by Jared Foster.
+#' 
+#' VirtualTwins is written mainly with reference classes. Briefly, there is three kinds of class :
+#' \itemize{
+#'  \item \code{\link{VT.object}} class to represent RCT dataset used by VirtualTwins. To format correctly RCT dataset, use \code{\link{formatRCTDataset}}.
+#'  \item \code{\link{VT.difft}} class to compute difference between twins. Family \code{\link{VT.forest}} extends it to compute twins by random forest.
+#'  \item \code{\link{VT.tree}} class to find subgroups from \code{\link{difft}} by CART trees. \code{\link{VT.tree.class}} and \code{\link{VT.tree.reg}} extend it.
+#' }
+#'  
+#' @section TODO LIST:
+#' \emph{last update : 11.06.2015}
+#' \itemize{
+#'  \item More detailed documentation and vignettes 
+#'  \item Write wrappers for classes
+#'  \item Write examples
+#'  \item ...
+#' }
+#'
+#' @docType package
+#' @name VirtualTwins
+#' @aliases VirtualTwins-package
+#'
+NULL

R/difft.R

@@ -17,6 +17,8 @@
 #'   
 #' @name VT.difft
 #'  
+#' @export VT.difft
+#'  
 #' @seealso \code{\link{VT.forest}}, \code{\link{VT.forest.one}}, \code{\link{VT.forest.double}}
 #' 
 #' @import methods

R/forest.double.R

@@ -23,11 +23,13 @@
 #'   1
 #' @field model_trt0 a caret/RandomForest/randomForest object for treatment T =
 #'   0
-#' @field ... field from parent class : \linkS4class{VT.forest}
+#' @field ... field from parent class : \code{\link{VT.forest}}
 #'   
 #' @seealso \code{\link{VT.difft}}, \code{\link{VT.forest}},
 #'   \code{\link{VT.forest.one}}
 #'   
+#' @export VT.forest.double
+#'   
 #' @name VT.forest.double
 #'   
 #' @import methods

R/forest.one.R

@@ -22,6 +22,8 @@
 #' 
 #' @name VT.forest.one
 #' 
+#' @export VT.forest.one
+#' 
 #' @import methods
 VT.forest.one <- setRefClass(
   Class = "VT.forest.one",

R/object.R

@@ -4,19 +4,18 @@
 #' 
 #' A Reference Class to deal with RCT dataset
 #' 
-#' Currently working with binary response only. Continous will come, one day.
+#' Currently working with binary response only. Continous will come, one day. 
 #' Two-levels treatment only as well.
 #' 
 #' \code{data} field should be as described, however if virtual twins won't used
-#' interactions, there is no need to transform factors. A tool function to 
+#' interactions, there is no need to transform factors. See
-#' transform factor will come soon.
+#' \link{formatRCTDataset} for more details.
 #' 
 #' 
 #' @field data Data.frame with format: \eqn{Y,T,X_{1}, \ldots, X_{p}}. Y must be
 #'   two levels factor if type is binary. T must be numeric or integer.
-#' @field alpha Numeric, no need in this current version. Set to \code{1}.
+#' @field screening Logical, set to \code{FALSE} Set to \code{TRUE} to use
-#' @field screening Logical, set to \code{FALSE} Set to \code{TRUE} to use \code{varimp} in trees 
+#'   \code{varimp} in trees computation.
-#'   computation.
 #' @field varimp Character vector of important variables to use in trees 
 #'   computation.
 #' @field delta Numeric representing the difference of incidence between 
@@ -28,6 +27,8 @@
 #'   
 #' @name VT.object
 #'   
+#' @export VT.object
+#'   
 #' @examples
 #' \dontrun{
 #' # Default use :
@@ -49,14 +50,13 @@
 #' vt.o$getIncidences()
 #' }
 #' 
-#' @seealso \code{\linkS4class{VT.difft}}
+#' @seealso \code{\link{VT.difft}}
 #'   
 VT.object <- setRefClass(
   Class = "VT.object",
   
   fields = list(
     data = "data.frame",
-    alpha = "numeric",
     screening = "logical",
     varimp = "character",
     delta = "numeric",
@@ -64,14 +64,12 @@ VT.object <- setRefClass(
   ),
   
   methods = list(
-    initialize = function(screening = F, alpha = 1, type = "binary", ...){
+    initialize = function(screening = F, type = "binary", ...){
       
       .self$screening <- screening
       
       .self$type <- type
-      
+            
-      .self$alpha <- alpha
-      
       .self$initFields(...)
     },
     

R/tree.class.R

@@ -8,6 +8,8 @@
 #' 
 #' @name VT.tree.class
 #' 
+#' @export VT.tree.class
+#' 
 #' @import methods
 VT.tree.class <- setRefClass(
   Class = "VT.tree.class",

R/tree.reg.R

@@ -6,6 +6,8 @@
 #'
 #' @include tree.R
 #' 
+#' @export VT.tree.reg
+#' 
 #' @name VT.tree.reg
 
 VT.tree.reg <- setRefClass(

man/VT.forest.double.Rd

@@ -29,7 +29,7 @@ This is what \code{computeTwin2()} does.
 \item{\code{model_trt0}}{a caret/RandomForest/randomForest object for treatment T =
 0}
 
-\item{\code{...}}{field from parent class : \linkS4class{VT.forest}}
+\item{\code{...}}{field from parent class : \code{\link{VT.forest}}}
 }}
 \section{Methods}{
 

man/VT.object.Rd

@@ -12,8 +12,8 @@ Currently working with binary response only. Continous will come, one day.
 Two-levels treatment only as well.
 
 \code{data} field should be as described, however if virtual twins won't used
-interactions, there is no need to transform factors. A tool function to
+interactions, there is no need to transform factors. See
-transform factor will come soon.
+\link{formatRCTDataset} for more details.
 }
 \section{Fields}{
 
@@ -21,10 +21,8 @@ transform factor will come soon.
 \item{\code{data}}{Data.frame with format: \eqn{Y,T,X_{1}, \ldots, X_{p}}. Y must be
 two levels factor if type is binary. T must be numeric or integer.}
 
-\item{\code{alpha}}{Numeric, no need in this current version. Set to \code{1}.}
+\item{\code{screening}}{Logical, set to \code{FALSE} Set to \code{TRUE} to use
-
+\code{varimp} in trees computation.}
-\item{\code{screening}}{Logical, set to \code{FALSE} Set to \code{TRUE} to use \code{varimp} in trees
-computation.}
 
 \item{\code{varimp}}{Character vector of important variables to use in trees
 computation.}
@@ -75,6 +73,6 @@ vt.o$getIncidences()
 }
 }
 \seealso{
-\code{\linkS4class{VT.difft}}
+\code{\link{VT.difft}}
 }
 

man/VirtualTwins-package.Rd

@@ -1,32 +0,0 @@
-\name{VirtualTwins-package}
-\alias{VirtualTwins-package}
-\alias{VirtualTwins}
-\docType{package}
-\title{
-\packageTitle{VirtualTwins}
-}
-\description{
-\packageDescription{VirtualTwins}
-}
-\details{
-
-The DESCRIPTION file:
-\packageDESCRIPTION{VirtualTwins}
-\packageIndices{VirtualTwins}
-~~ An overview of how to use the package, including the most important functions ~~
-}
-\author{
-\packageAuthor{VirtualTwins}
-
-Maintainer: \packageMaintainer{VirtualTwins}
-}
-\references{
-~~ Literature or other references for background information ~~
-}
-
-\keyword{ package }
-\seealso{
-~~ \code{\link[<pkg>:<pkg>-package]{<pkg>}} ~~
-}
-\examples{
-}

man/VirtualTwins.Rd

@@ -0,0 +1,29 @@
+% Generated by roxygen2 (4.1.1): do not edit by hand
+% Please edit documentation in R/VirtualTwins.R
+\docType{package}
+\name{VirtualTwins}
+\alias{VirtualTwins}
+\alias{VirtualTwins-package}
+\title{VirtualTwins : An adapation of VirtualTwins method created by Jared Foster.}
+\description{
+VirtualTwins is written mainly with reference classes. Briefly, there is three kinds of class :
+\itemize{
+ \item \code{\link{VT.object}} class to represent RCT dataset used by VirtualTwins. To format correctly RCT dataset, use \code{\link{formatRCTDataset}}.
+ \item \code{\link{VT.difft}} class to compute difference between twins. Family \code{\link{VT.forest}} extends it to compute twins by random forest.
+ \item \code{\link{VT.tree}} class to find subgroups from \code{\link{difft}} by CART trees. \code{\link{VT.tree.class}} and \code{\link{VT.tree.reg}} extend it.
+}
+}
+\details{
+\encoding{UTF-8}
+}
+\section{TODO LIST}{
+
+\emph{last update : 11.06.2015}
+\itemize{
+ \item More detailed documentation and vignettes
+ \item Write wrappers for classes
+ \item Write examples
+ \item ...
+}
+}
+