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update manual because of new wrappers
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@ -5,17 +5,20 @@
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#' \itemize{
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#' \item \code{\link{VT.object}} class to represent RCT dataset used by aVirtualTwins. To format correctly RCT dataset, use \code{\link{formatRCTDataset}}.
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#' \item \code{\link{VT.difft}} class to compute difference between twins. Family \code{\link{VT.forest}} extends it to compute twins by random forest.
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#' \item \code{\link{VT.tree}} class to find subgroups from \code{difft} by CART trees. \code{\link{VT.tree.class}} and \code{\link{VT.tree.reg}} extend it.
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#' \code{\link{vt.forest()}} is users function.
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#' \item \code{\link{VT.tree}} class to find subgroups from \code{difft} by CART trees. \code{\link{VT.tree.class}} and \code{\link{VT.tree.reg}} extend it.
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#' \code{\link{vt.tree()}} is users function.
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#' }
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#'
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#' @section TODO LIST:
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#' \emph{last update : 24.07.2015}
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#' \emph{last update : 27.07.2015}
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#' \itemize{
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#' \item More detailed documentation and vignettes
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#' \item Write wrappers for classes
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#' \item Write examples
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#' \item ...
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#' }
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#'
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#' See github.com/prise6/aVirtualTwins for last updates.
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#'
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#' @docType package
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#' @name aVirtualTwins
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@ -2,58 +2,92 @@
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#'
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#' Create forest to compute difft
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#'
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#' \code{vt.forest} is a wrapper of \code{\link{VT.forest.one}},
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#' \code{\link{VT.forest.double}} and \code{\link{VT.forest.fold}}.
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#' \code{vt.forest} is a wrapper of \code{\link{VT.forest.one}},
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#' \code{\link{VT.forest.double}} and \code{\link{VT.forest.fold}}. With
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#' parameter forest.type, any of these class can be used with its own parameter.
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#'
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#' @param forest.type character one / double / fold
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#' @param vt.data \code{\link{VT.data}} or return of \code{vt.data()} function
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#' @param forest.type must be a character. "one" to use VT.forest.one class.
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#' "double" to use VT.forest.double. "fold" to use VT.forest.fold.
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#' @param vt.data \code{\link{VT.object}}. Can be return of \code{vt.data()}
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#' function
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#' @param interactions logical. If running VirtualTwins with treatment's
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#' interactions, set to TRUE (default value)
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#' @param method character absolute / relative / logit
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#' @param ... parameters of \code{\link{VT.difft}} or \code{\link{VT.forest}}
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#' @param method character c("absolute", "relative", "logit"). See
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#' \code{\link{VT.difft}}.
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#' @param model allows to give a model you build outside this function. Can be
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#' randomForest, train or cforest. Is only used with forest.type = "one". If
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#' NULL, a randomForest model is grown inside the function. NULL is default.
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#' @param model_trt0 works the same as model parameter. Is only used with
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#' forest.type = "double". If NULL, a randomForest model is grown inside the
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#' function. NULL is default. See \code{\link{VT.forest.double}} for details.
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#' @param model_trt1 see model_trt0 explanation and
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#' \code{\link{VT.double.forest}} details.
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#' @param fold number of fold you want to construct forest with k-fold method.
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#' Is only used with forest.type = "fold". Default to 5. See
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#' \code{\link{VT.forest.fold}}
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#' @param ratio numeric value that allow sampsize to be a bit controlled.
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#' Default to 1. See \code{\link{VT.forest.fold}}.
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#' @param ... randomForest() function parameters. Can be used for any forest.type.
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#'
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#' @return \code{VT.difft}
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#'
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#'
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#' @examples
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#' \dontrun{
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#' # data(sepsis)
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#' vt.o <- vt.data(sepsis, "survival", "THERAPY", T)
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#' # inside model :
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#' vt.f <- vt.forest("one", vt.o)
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#' # ...
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#' # your model :
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#' rf <- randomForest(y = vt.o$getY(),
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#' x = vt.o$getX(int = T),
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#' mtry = 3,
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#' nodesize = 15)
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#' vt.f <- vt.forest("one", vt.o, model = rf)
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#' # ...
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#' # Can also use ... parameters
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#' vt.f <- vt.forest("one", vt.o, mtry = 3, nodesize = 15)
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#' # ...
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#' }
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#'
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#' @include forest.R difft.R
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#'
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#'
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#' @name vt.forest
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#'
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#'
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#' @export vt.forest
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vt.forest <- function(forest.type = "one", vt.data, interactions = T, method = "absolute", ...){
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vt.forest <- function(forest.type = "one", vt.data, interactions = T, method = "absolute",
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model = NULL, model_trt1 = NULL, model_trt0 = NULL, ratio = 1, fold = 10, ...){
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if(!inherits(vt.data, "VT.object"))
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stop("vt.data must be VT.object class")
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params <- list(...)
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if (forest.type == "one"){
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if(! "model" %in% names(params) ){
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rf <- randomForest(x = vt.data$getX(interactions = interactions, trt = NULL),
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if(is.null(model)){
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model <- randomForest(x = vt.data$getX(interactions = interactions, trt = NULL),
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y = vt.data$getY(),
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...)
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} else{
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rf <- params[["model"]]
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}
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rf <- model
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vt.difft <- VT.forest.one(vt.object = vt.data, model = rf, interactions = interactions, method = method)
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} else if (forest.type == "double"){
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if(! "model_trt1" %in% names(params) ){
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rf_trt1 <- randomForest(x = vt.data$getX(trt = 1, interactions = interactions),
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y = vt.data$getY(1),
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...)
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} else
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rf_trt1 <- params[["model_trt1"]]
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if(is.null(model_trt1)){
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model_trt1 <- randomForest(x = vt.data$getX(trt = 1),
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y = vt.data$getY(1),
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...)
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}
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rf_trt1 <- model_trt1
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if(! "model_trt0" %in% names(params) ){
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rf_trt0 <- randomForest(x = vt.data$getX(trt = 1, interactions = interactions),
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y = vt.data$getY(1),
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...)
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} else
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rf_trt0 <- params[["model_trt0"]]
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if(is.null(model_trt0)){
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model_trt0 <- randomForest(x = vt.data$getX(trt = 0),
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y = vt.data$getY(0),
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...)
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}
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rf_trt0 <- model_trt0
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vt.difft <- VT.forest.double(vt.object = vt.data, model_trt1 = rf_trt1, model_trt0 = rf_trt0, method = method)
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} else if (forest.type == "fold"){
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fold <- ifelse(! "fold" %in% names(params) , 5, as.numeric(params["fold"]))
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ratio <- ifelse(! "ratio" %in% names(params) , 1, as.numeric(params["ratio"]))
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vt.difft <- aVirtualTwins:::VT.forest.fold(vt.object = vt.data, fold = fold, ratio = ratio,
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interactions = interactions, method = method)
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#'
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#' Initialize virtual twins data
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#'
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#' \code{vt.data} is a wrapper of \code{\link{formatRCTDataset}} and
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#' \code{\link{VT.object}}.
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#' \code{vt.data} is a wrapper of \code{\link{formatRCTDataset}} and
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#' \code{\link{VT.object}}. Allows to format your data.frame in order to create
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#' a VT.object object.
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#'
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#' @param dataset data.frame representing RCT's
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#' @param outcome.field name of the outcome's field in \code{dataset}
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#' @param treatment.field name of the treatment's field in \code{dataset}
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#' @param interactions logical. If running VirtualTwins with treatment's
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#' @param interactions logical. If running VirtualTwins with treatment's
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#' interactions, set to TRUE (default value)
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#' @param ... parameters of \code{\link{VT.object}}
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#'
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#'
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#' @examples
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#' \dontrun{
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#' data(sepsis)
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#' formatRCTdataset(sepsis, "survival", "THERAPY", T)
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#' }
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#'
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#' @return \code{VT.object}
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#'
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#' @include object.R
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#'
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#'
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#' @include object.R
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#'
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#' @name vt.data
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#'
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#'
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#' @export vt.data
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vt.data <- function(dataset, outcome.field, treatment.field, interactions = TRUE, ...){
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36
R/tools.R
36
R/tools.R
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@ -1,18 +1,38 @@
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#' Visualize subgroups
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#'
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#' @param vt.trees \code{\link{VT.tree}} object (can be a list)
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#' @param only.leaf logical select only leaf of trees
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#' @param only.fav logical select only favorable subgroup (meaning with favorable label of the tree)
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#' @param tables logical show tables of incidence
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#' @param verbose print tables during computation
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#' Function which uses \code{\link{VT.tree}} intern functions. Package
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#' rpart.plot must be loaded. See \code{\link{VT.tree}} for details.
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#'
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#' @param vt.trees \code{\link{VT.tree}} object. Or return of
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#' \code{\link{vt.tree}} function. Can be a list.
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#' @param only.leaf logical to select only leaf of trees. TRUE is default.
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#' @param only.fav logical select only favorable subgroups (meaning with
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#' favorable label of the tree). TRUE is default.
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#' @param tables set to TRUE if tables of incidence must be shown. FALSE is
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#' default.
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#' @param verbose print infos during computation. FALSE is default.
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#'
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#' @return data.frame of rules
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#'
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#' @examples
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#' \dontrun{
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#' # data(sepsis)
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#' vt.o <- vt.data(sepsis, "survival", "THERAPY", T)
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#' # inside model :
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#' vt.f <- vt.forest("one", vt.o)
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#' # use classification tree
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#' vt.tr <- vt.tree("class", vt.f, threshold = c(0.01, 0.05))
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#' # show subgroups
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#' vt.subgroups(vt.tr)
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#' # change options you'll be surprised !
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#' vt.subgroups(vt.tr, verbose = T, tables = T)
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#' }
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#'
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#' @export vt.subgroups
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#'
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#' @name vt.subgroups
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#'
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#'
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#' @name vt.subgroups
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#'
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vt.subgroups <- function(vt.trees, only.leaf = T, only.fav = T, tables = F, verbose = F){
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#' Trees to find Subgroups
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#'
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#' A wrapper of class VT.tree.xxx
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#'
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#' \code{vt.tree} is a wrapper of \code{\link{VT.tree.class}} and
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#' \code{\link{VT.tree.reg}}. With parameter tree.type, any of these two class
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#' can be used with its own parameter.
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#'
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#' See \code{\link{VT.tree}}
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#'
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#' @param tree.type character "class" for classification tree, "reg" for regression tree
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#' @param vt.difft \code{\link{VT.difft}} object
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#' @param sens character c(">","<"). See details.
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#' @param threshold numeric It can be a unique value or a vector
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#'
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#' @return \code{VT.tree} or a list of \code{VT.tree} depending on threshold dimension
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#' See \code{\link{VT.tree}}, \code{\link{VT.tree.class}} and
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#' \code{\link{VT.tree.reg}} classes.
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#'
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#' @param tree.type must be a character. "class" for classification tree, "reg"
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#' for regression tree.
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#' @param vt.difft \code{\link{VT.difft}} object. Or return of
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#' \code{\link{vt.forest}} function.
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#' @param sens must be a character c(">","<"). See \code{\link{VT.tree}} for
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#' details.
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#' @param threshold must be numeric. It can be a unique value or a vector. If
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#' numeric vector, a list is returned. See \code{\link{VT.tree}} for details.
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#' @param screening must be logical. If TRUE, only varimp variables of VT.object
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#' is used to create the tree.
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#' @param ... rpart() function parameters. Can be used for any tree.type.
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#'
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#' @return \code{VT.tree} or a list of \code{VT.tree} depending on threshold
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#' dimension. See examples.
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#'
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#' @examples
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#' \dontrun{
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#' # data(sepsis)
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#' vt.o <- vt.data(sepsis, "survival", "THERAPY", T)
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#' # inside model :
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#' vt.f <- vt.forest("one", vt.o)
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#' # use classification tree
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#' vt.tr <- vt.tree("class", vt.f, threshold = c(0.01, 0.05))
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#' # return a list
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#' class(vt.tr)
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#' # access one of the tree
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#' vt.tr$tree1
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#' # return infos
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#' vt.tr$tree1$getInfos()
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#' # ...
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#' }
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#'
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#' @include tree.R
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#'
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#'
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#' @name vt.tree
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#'
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#'
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#' @export vt.tree
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vt.tree <- function(tree.type = "class", vt.difft, sens = ">", threshold = seq(.5, .8, .1), screening = NULL, ...){
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@ -10,17 +10,20 @@ aVirtualTwins is written mainly with reference classes. Briefly, there is three
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\itemize{
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\item \code{\link{VT.object}} class to represent RCT dataset used by aVirtualTwins. To format correctly RCT dataset, use \code{\link{formatRCTDataset}}.
|
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\item \code{\link{VT.difft}} class to compute difference between twins. Family \code{\link{VT.forest}} extends it to compute twins by random forest.
|
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\code{\link{vt.forest()}} is users function.
|
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\item \code{\link{VT.tree}} class to find subgroups from \code{difft} by CART trees. \code{\link{VT.tree.class}} and \code{\link{VT.tree.reg}} extend it.
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\code{\link{vt.tree()}} is users function.
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}
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}
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\section{TODO LIST}{
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\emph{last update : 24.07.2015}
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\emph{last update : 27.07.2015}
|
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\itemize{
|
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\item More detailed documentation and vignettes
|
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\item Write wrappers for classes
|
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\item Write examples
|
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\item ...
|
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}
|
||||
|
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See github.com/prise6/aVirtualTwins for last updates.
|
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}
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|
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@ -23,6 +23,13 @@ interactions, set to TRUE (default value)}
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}
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\description{
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\code{vt.data} is a wrapper of \code{\link{formatRCTDataset}} and
|
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\code{\link{VT.object}}.
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\code{\link{VT.object}}. Allows to format your data.frame in order to create
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a VT.object object.
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}
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\examples{
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\dontrun{
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data(sepsis)
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formatRCTdataset(sepsis, "survival", "THERAPY", T)
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}
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}
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@ -5,25 +5,67 @@
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\title{Create forest to compute difft}
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\usage{
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vt.forest(forest.type = "one", vt.data, interactions = T,
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method = "absolute", ...)
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method = "absolute", model = NULL, model_trt1 = NULL,
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model_trt0 = NULL, ratio = 1, fold = 10, ...)
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}
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\arguments{
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\item{forest.type}{character one / double / fold}
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\item{forest.type}{must be a character. "one" to use VT.forest.one class.
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"double" to use VT.forest.double. "fold" to use VT.forest.fold.}
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\item{vt.data}{\code{\link{VT.data}} or return of \code{vt.data()} function}
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\item{vt.data}{\code{\link{VT.object}}. Can be return of \code{vt.data()}
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function}
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\item{interactions}{logical. If running VirtualTwins with treatment's
|
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interactions, set to TRUE (default value)}
|
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|
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\item{method}{character absolute / relative / logit}
|
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\item{method}{character c("absolute", "relative", "logit"). See
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\code{\link{VT.difft}}.}
|
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|
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\item{...}{parameters of \code{\link{VT.difft}} or \code{\link{VT.forest}}}
|
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\item{model}{allows to give a model you build outside this function. Can be
|
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randomForest, train or cforest. Is only used with forest.type = "one". If
|
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NULL, a randomForest model is grown inside the function. NULL is default.}
|
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|
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\item{model_trt1}{see model_trt0 explanation and
|
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\code{\link{VT.double.forest}} details.}
|
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|
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\item{model_trt0}{works the same as model parameter. Is only used with
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forest.type = "double". If NULL, a randomForest model is grown inside the
|
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function. NULL is default. See \code{\link{VT.forest.double}} for details.}
|
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|
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\item{ratio}{numeric value that allow sampsize to be a bit controlled.
|
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Default to 1. See \code{\link{VT.forest.fold}}.}
|
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|
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\item{fold}{number of fold you want to construct forest with k-fold method.
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Is only used with forest.type = "fold". Default to 5. See
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\code{\link{VT.forest.fold}}}
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\item{...}{randomForest() function parameters. Can be used for any forest.type.}
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}
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\value{
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\code{VT.difft}
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}
|
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\description{
|
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\code{vt.forest} is a wrapper of \code{\link{VT.forest.one}},
|
||||
\code{\link{VT.forest.double}} and \code{\link{VT.forest.fold}}.
|
||||
\code{\link{VT.forest.double}} and \code{\link{VT.forest.fold}}. With
|
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parameter forest.type, any of these class can be used with its own parameter.
|
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}
|
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\examples{
|
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\dontrun{
|
||||
# data(sepsis)
|
||||
vt.o <- vt.data(sepsis, "survival", "THERAPY", T)
|
||||
# inside model :
|
||||
vt.f <- vt.forest("one", vt.o)
|
||||
# ...
|
||||
# your model :
|
||||
rf <- randomForest(y = vt.o$getY(),
|
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x = vt.o$getX(int = T),
|
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mtry = 3,
|
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nodesize = 15)
|
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vt.f <- vt.forest("one", vt.o, model = rf)
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# ...
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# Can also use ... parameters
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vt.f <- vt.forest("one", vt.o, mtry = 3, nodesize = 15)
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# ...
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}
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}
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||||
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|
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|
@ -8,20 +8,38 @@ vt.subgroups(vt.trees, only.leaf = T, only.fav = T, tables = F,
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|||
verbose = F)
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}
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||||
\arguments{
|
||||
\item{vt.trees}{\code{\link{VT.tree}} object (can be a list)}
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||||
\item{vt.trees}{\code{\link{VT.tree}} object. Or return of
|
||||
\code{\link{vt.tree}} function. Can be a list.}
|
||||
|
||||
\item{only.leaf}{logical select only leaf of trees}
|
||||
\item{only.leaf}{logical to select only leaf of trees. TRUE is default.}
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||||
|
||||
\item{only.fav}{logical select only favorable subgroup (meaning with favorable label of the tree)}
|
||||
\item{only.fav}{logical select only favorable subgroups (meaning with
|
||||
favorable label of the tree). TRUE is default.}
|
||||
|
||||
\item{tables}{logical show tables of incidence}
|
||||
\item{tables}{set to TRUE if tables of incidence must be shown. FALSE is
|
||||
default.}
|
||||
|
||||
\item{verbose}{print tables during computation}
|
||||
\item{verbose}{print infos during computation. FALSE is default.}
|
||||
}
|
||||
\value{
|
||||
data.frame of rules
|
||||
}
|
||||
\description{
|
||||
Visualize subgroups
|
||||
Function which uses \code{\link{VT.tree}} intern functions. Package
|
||||
rpart.plot must be loaded. See \code{\link{VT.tree}} for details.
|
||||
}
|
||||
\examples{
|
||||
\dontrun{
|
||||
# data(sepsis)
|
||||
vt.o <- vt.data(sepsis, "survival", "THERAPY", T)
|
||||
# inside model :
|
||||
vt.f <- vt.forest("one", vt.o)
|
||||
# use classification tree
|
||||
vt.tr <- vt.tree("class", vt.f, threshold = c(0.01, 0.05))
|
||||
# show subgroups
|
||||
vt.subgroups(vt.tr)
|
||||
# change options you'll be surprised !
|
||||
vt.subgroups(vt.tr, verbose = T, tables = T)
|
||||
}
|
||||
}
|
||||
|
||||
|
|
|
@ -8,21 +8,51 @@ vt.tree(tree.type = "class", vt.difft, sens = ">", threshold = seq(0.5,
|
|||
0.8, 0.1), screening = NULL, ...)
|
||||
}
|
||||
\arguments{
|
||||
\item{tree.type}{character "class" for classification tree, "reg" for regression tree}
|
||||
\item{tree.type}{must be a character. "class" for classification tree, "reg"
|
||||
for regression tree.}
|
||||
|
||||
\item{vt.difft}{\code{\link{VT.difft}} object}
|
||||
\item{vt.difft}{\code{\link{VT.difft}} object. Or return of
|
||||
\code{\link{vt.forest}} function.}
|
||||
|
||||
\item{sens}{character c(">","<"). See details.}
|
||||
\item{sens}{must be a character c(">","<"). See \code{\link{VT.tree}} for
|
||||
details.}
|
||||
|
||||
\item{threshold}{numeric It can be a unique value or a vector}
|
||||
\item{threshold}{must be numeric. It can be a unique value or a vector. If
|
||||
numeric vector, a list is returned. See \code{\link{VT.tree}} for details.}
|
||||
|
||||
\item{screening}{must be logical. If TRUE, only varimp variables of VT.object
|
||||
is used to create the tree.}
|
||||
|
||||
\item{...}{rpart() function parameters. Can be used for any tree.type.}
|
||||
}
|
||||
\value{
|
||||
\code{VT.tree} or a list of \code{VT.tree} depending on threshold dimension
|
||||
\code{VT.tree} or a list of \code{VT.tree} depending on threshold
|
||||
dimension. See examples.
|
||||
}
|
||||
\description{
|
||||
A wrapper of class VT.tree.xxx
|
||||
\code{vt.tree} is a wrapper of \code{\link{VT.tree.class}} and
|
||||
\code{\link{VT.tree.reg}}. With parameter tree.type, any of these two class
|
||||
can be used with its own parameter.
|
||||
}
|
||||
\details{
|
||||
See \code{\link{VT.tree}}
|
||||
See \code{\link{VT.tree}}, \code{\link{VT.tree.class}} and
|
||||
\code{\link{VT.tree.reg}} classes.
|
||||
}
|
||||
\examples{
|
||||
\dontrun{
|
||||
# data(sepsis)
|
||||
vt.o <- vt.data(sepsis, "survival", "THERAPY", T)
|
||||
# inside model :
|
||||
vt.f <- vt.forest("one", vt.o)
|
||||
# use classification tree
|
||||
vt.tr <- vt.tree("class", vt.f, threshold = c(0.01, 0.05))
|
||||
# return a list
|
||||
class(vt.tr)
|
||||
# access one of the tree
|
||||
vt.tr$tree1
|
||||
# return infos
|
||||
vt.tr$tree1$getInfos()
|
||||
# ...
|
||||
}
|
||||
}
|
||||
|
||||
|
|
Loading…
Reference in a new issue