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update md files
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% Generated by roxygen2 (4.1.1): do not edit by hand
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% Generated by roxygen2: do not edit by hand
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% Please edit documentation in R/difft.R
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\docType{class}
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\name{VT.difft}
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% Generated by roxygen2 (4.1.1): do not edit by hand
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% Generated by roxygen2: do not edit by hand
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% Please edit documentation in R/forest.double.R
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\docType{class}
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\name{VT.forest.double}
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% Generated by roxygen2 (4.1.1): do not edit by hand
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% Generated by roxygen2: do not edit by hand
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% Please edit documentation in R/forest.fold.R
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\docType{class}
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\name{VT.forest.fold}
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% Generated by roxygen2 (4.1.1): do not edit by hand
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% Generated by roxygen2: do not edit by hand
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% Please edit documentation in R/forest.one.R
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\docType{class}
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\name{VT.forest.one}
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% Generated by roxygen2 (4.1.1): do not edit by hand
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% Generated by roxygen2: do not edit by hand
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% Please edit documentation in R/object.R
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\docType{class}
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\name{VT.object}
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@ -31,7 +31,7 @@ computation.}
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treatments.}
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\item{\code{type}}{Character : binary or continous. Only binary is currently
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available.}
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available.}
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}}
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\section{Methods}{
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@ -73,6 +73,7 @@ vt.o$getY(0)
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# Print incidences
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vt.o$getIncidences()
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}
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}
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\seealso{
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\code{\link{VT.difft}}
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% Generated by roxygen2 (4.1.1): do not edit by hand
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% Generated by roxygen2: do not edit by hand
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% Please edit documentation in R/predict.R
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\docType{methods}
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\name{VT.predict}
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@ -35,7 +35,7 @@ class.}
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predictions are returned.}
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\item{type}{Must be binary or continous, depending on the outcome. Only
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binary is really available.}
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binary is really available.}
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}
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\value{
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vector \eqn{E(Y=1)}
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@ -45,16 +45,16 @@ VT.predict generic function
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}
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\section{Methods (by class)}{
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\itemize{
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\item \code{rfor = RandomForest,newdata = missing,type = character}:
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\item \code{rfor = RandomForest,newdata = missing,type = character}: rfor(RandomForest) newdata (missing) type (character)
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\item \code{rfor = RandomForest,newdata = data.frame,type = character}:
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\item \code{rfor = RandomForest,newdata = data.frame,type = character}: rfor(RandomForest) newdata (data.frame) type (character)
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\item \code{rfor = randomForest,newdata = missing,type = character}:
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\item \code{rfor = randomForest,newdata = missing,type = character}: rfor(randomForest) newdata (missing) type (character)
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\item \code{rfor = randomForest,newdata = data.frame,type = character}:
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\item \code{rfor = randomForest,newdata = data.frame,type = character}: rfor(randomForest) newdata (data.frame) type (character)
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\item \code{rfor = train,newdata = ANY,type = character}:
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\item \code{rfor = train,newdata = ANY,type = character}: rfor(train) newdata (ANY) type (character)
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\item \code{rfor = train,newdata = missing,type = character}:
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\item \code{rfor = train,newdata = missing,type = character}: rfor(train) newdata (missing) type (character)
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}}
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% Generated by roxygen2 (4.1.1): do not edit by hand
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% Generated by roxygen2: do not edit by hand
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% Please edit documentation in R/tree.class.R
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\docType{class}
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\name{VT.tree.class}
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% Generated by roxygen2 (4.1.1): do not edit by hand
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% Generated by roxygen2: do not edit by hand
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% Please edit documentation in R/tree.reg.R
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\docType{class}
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\name{VT.tree.reg}
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% Generated by roxygen2 (4.1.1): do not edit by hand
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% Generated by roxygen2: do not edit by hand
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% Please edit documentation in R/aVirtualTwins.R
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\docType{package}
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\name{aVirtualTwins}
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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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\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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\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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% Generated by roxygen2 (4.1.1): do not edit by hand
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% Generated by roxygen2: do not edit by hand
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% Please edit documentation in R/formatRCTDataset.R
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\name{formatRCTDataset}
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\alias{formatRCTDataset}
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\item{treatment.field}{name of the treatment's field in \code{dataset}}
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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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interactions, set to TRUE (default value)}
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}
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\value{
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return data.frame with good format (explained in details section) to run VirtualTwins
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\dontrun{
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data.format <- formatRCTDataset(data, "outcome", "treatment", TRUE)
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}
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}
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% Generated by roxygen2 (4.1.1): do not edit by hand
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% Generated by roxygen2: do not edit by hand
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% Please edit documentation in R/data.R
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\docType{data}
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\name{sepsis}
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\item{BLADL}{Baseline activity of daily living score}
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\item{BLLBILI}{Baseline local bilirubin} }}
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\source{
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\url{http://biopharmnet.com/wiki/Software_for_subgroup_identification_and_analysis}
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\url{http://biopharmnet.com/subgroup-analysis-software/}
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}
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\usage{
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data(sepsis)
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}
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\details{
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This dataset is taken from
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\href{http://biopharmnet.com/wiki/Software_for_subgroup_identification_and_analysis}{SIDES
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\href{http://biopharmnet.com/subgroup-analysis-software/}{SIDES
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method}.
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\code{Sepsis} contains simulated data on 470 subjects with a binary outcome
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% Generated by roxygen2 (4.1.1): do not edit by hand
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% Generated by roxygen2: do not edit by hand
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% Please edit documentation in R/object.wrapper.R
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\name{vt.data}
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\alias{vt.data}
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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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% Generated by roxygen2 (4.1.1): do not edit by hand
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% Generated by roxygen2: do not edit by hand
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% Please edit documentation in R/forest.wrapper.R
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\name{vt.forest}
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\alias{vt.forest}
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NULL, a randomForest model is grown inside the function. NULL is default.}
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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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\code{\link{VT.forest.double}} details.}
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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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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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% Generated by roxygen2 (4.1.1): do not edit by hand
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% Generated by roxygen2: do not edit by hand
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% Please edit documentation in R/tools.R
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\name{vt.subgroups}
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\alias{vt.subgroups}
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\title{Visualize subgroups}
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\usage{
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vt.subgroups(vt.trees, only.leaf = T, only.fav = T, tables = F,
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verbose = F)
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verbose = F, compete = F)
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}
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\arguments{
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\item{vt.trees}{\code{\link{VT.tree}} object. Or return of
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\item{verbose}{print infos during computation. FALSE is default.}
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\item{compete}{print competitors rules thanks to competitors computation of
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the tree}
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the tree}
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}
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\value{
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data.frame of rules
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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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% Generated by roxygen2 (4.1.1): do not edit by hand
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% Generated by roxygen2: do not edit by hand
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% Please edit documentation in R/tree.wrapper.R
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\name{vt.tree}
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\alias{vt.tree}
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vt.tr$tree1$getInfos()
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# ...
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}
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}
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