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update md files

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François Vieille 2016-10-09 02:43:51 +02:00
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commit 5942b328e7
15 changed files with 110 additions and 102 deletions
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2
man/VT.difft.Rd
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@ -1,4 +1,4 @@
% Generated by roxygen2 (4.1.1): do not edit by hand % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/difft.R % Please edit documentation in R/difft.R
\docType{class} \docType{class}
\name{VT.difft} \name{VT.difft}

2
man/VT.forest.double.Rd
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@ -1,4 +1,4 @@
% Generated by roxygen2 (4.1.1): do not edit by hand % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/forest.double.R % Please edit documentation in R/forest.double.R
\docType{class} \docType{class}
\name{VT.forest.double} \name{VT.forest.double}

2
man/VT.forest.fold.Rd
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@ -1,4 +1,4 @@
% Generated by roxygen2 (4.1.1): do not edit by hand % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/forest.fold.R % Please edit documentation in R/forest.fold.R
\docType{class} \docType{class}
\name{VT.forest.fold} \name{VT.forest.fold}

2
man/VT.forest.one.Rd
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@ -1,4 +1,4 @@
% Generated by roxygen2 (4.1.1): do not edit by hand % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/forest.one.R % Please edit documentation in R/forest.one.R
\docType{class} \docType{class}
\name{VT.forest.one} \name{VT.forest.one}

5
man/VT.object.Rd
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@ -1,4 +1,4 @@
% Generated by roxygen2 (4.1.1): do not edit by hand % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/object.R % Please edit documentation in R/object.R
\docType{class} \docType{class}
\name{VT.object} \name{VT.object}
@ -31,7 +31,7 @@ computation.}
treatments.} treatments.}
\item{\code{type}}{Character : binary or continous. Only binary is currently \item{\code{type}}{Character : binary or continous. Only binary is currently
available.} available.}
}} }}
\section{Methods}{ \section{Methods}{
@ -73,6 +73,7 @@ vt.o$getY(0)
# Print incidences # Print incidences
vt.o$getIncidences() vt.o$getIncidences()
} }
} }
\seealso{ \seealso{
\code{\link{VT.difft}} \code{\link{VT.difft}}

16
man/VT.predict.Rd
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@ -1,4 +1,4 @@
% Generated by roxygen2 (4.1.1): do not edit by hand % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/predict.R % Please edit documentation in R/predict.R
\docType{methods} \docType{methods}
\name{VT.predict} \name{VT.predict}
@ -35,7 +35,7 @@ class.}
predictions are returned.} predictions are returned.}
\item{type}{Must be binary or continous, depending on the outcome. Only \item{type}{Must be binary or continous, depending on the outcome. Only
binary is really available.} binary is really available.}
} }
\value{ \value{
vector \eqn{E(Y=1)} vector \eqn{E(Y=1)}
@ -45,16 +45,16 @@ VT.predict generic function
} }
\section{Methods (by class)}{ \section{Methods (by class)}{
\itemize{ \itemize{
\item \code{rfor = RandomForest,newdata = missing,type = character}: \item \code{rfor = RandomForest,newdata = missing,type = character}: rfor(RandomForest) newdata (missing) type (character)
\item \code{rfor = RandomForest,newdata = data.frame,type = character}: \item \code{rfor = RandomForest,newdata = data.frame,type = character}: rfor(RandomForest) newdata (data.frame) type (character)
\item \code{rfor = randomForest,newdata = missing,type = character}: \item \code{rfor = randomForest,newdata = missing,type = character}: rfor(randomForest) newdata (missing) type (character)
\item \code{rfor = randomForest,newdata = data.frame,type = character}: \item \code{rfor = randomForest,newdata = data.frame,type = character}: rfor(randomForest) newdata (data.frame) type (character)
\item \code{rfor = train,newdata = ANY,type = character}: \item \code{rfor = train,newdata = ANY,type = character}: rfor(train) newdata (ANY) type (character)
\item \code{rfor = train,newdata = missing,type = character}: \item \code{rfor = train,newdata = missing,type = character}: rfor(train) newdata (missing) type (character)
}} }}

2
man/VT.tree.class.Rd
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@ -1,4 +1,4 @@
% Generated by roxygen2 (4.1.1): do not edit by hand % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/tree.class.R % Please edit documentation in R/tree.class.R
\docType{class} \docType{class}
\name{VT.tree.class} \name{VT.tree.class}

2
man/VT.tree.reg.Rd
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@ -1,4 +1,4 @@
% Generated by roxygen2 (4.1.1): do not edit by hand % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/tree.reg.R % Please edit documentation in R/tree.reg.R
\docType{class} \docType{class}
\name{VT.tree.reg} \name{VT.tree.reg}

6
man/aVirtualTwins.Rd
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@ -1,4 +1,4 @@
% Generated by roxygen2 (4.1.1): do not edit by hand % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/aVirtualTwins.R % Please edit documentation in R/aVirtualTwins.R
\docType{package} \docType{package}
\name{aVirtualTwins} \name{aVirtualTwins}
@ -10,9 +10,9 @@ aVirtualTwins is written mainly with reference classes. Briefly, there is three
\itemize{ \itemize{
\item \code{\link{VT.object}} class to represent RCT dataset used by aVirtualTwins. To format correctly RCT dataset, use \code{\link{formatRCTDataset}}. \item \code{\link{VT.object}} class to represent RCT dataset used by aVirtualTwins. 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.difft}} class to compute difference between twins. Family \code{\link{VT.forest}} extends it to compute twins by random forest.
\code{\link{vt.forest()}} is users function. \code{\link{vt.forest}} is users function.
\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. \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.
\code{\link{vt.tree()}} is users function. \code{\link{vt.tree}} is users function.
} }
} }
\section{TODO LIST}{ \section{TODO LIST}{

7
man/formatRCTDataset.Rd
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@ -1,4 +1,4 @@
% Generated by roxygen2 (4.1.1): do not edit by hand % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/formatRCTDataset.R % Please edit documentation in R/formatRCTDataset.R
\name{formatRCTDataset} \name{formatRCTDataset}
\alias{formatRCTDataset} \alias{formatRCTDataset}
@ -14,7 +14,7 @@ formatRCTDataset(dataset, outcome.field, treatment.field, interactions = TRUE)
\item{treatment.field}{name of the treatment's field in \code{dataset}} \item{treatment.field}{name of the treatment's field in \code{dataset}}
\item{interactions}{logical. If running VirtualTwins with treatment's \item{interactions}{logical. If running VirtualTwins with treatment's
interactions, set to TRUE (default value)} interactions, set to TRUE (default value)}
} }
\value{ \value{
return data.frame with good format (explained in details section) to run VirtualTwins return data.frame with good format (explained in details section) to run VirtualTwins
@ -39,5 +39,8 @@ running VirtualTwins with interaction, it creates dummy variables.
\dontrun{ \dontrun{
data.format <- formatRCTDataset(data, "outcome", "treatment", TRUE) data.format <- formatRCTDataset(data, "outcome", "treatment", TRUE)
} }
} }

6
man/sepsis.Rd
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@ -1,4 +1,4 @@
% Generated by roxygen2 (4.1.1): do not edit by hand % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/data.R % Please edit documentation in R/data.R
\docType{data} \docType{data}
\name{sepsis} \name{sepsis}
@ -16,7 +16,7 @@
\item{BLADL}{Baseline activity of daily living score} \item{BLADL}{Baseline activity of daily living score}
\item{BLLBILI}{Baseline local bilirubin} }} \item{BLLBILI}{Baseline local bilirubin} }}
\source{ \source{
\url{http://biopharmnet.com/wiki/Software_for_subgroup_identification_and_analysis} \url{http://biopharmnet.com/subgroup-analysis-software/}
} }
\usage{ \usage{
data(sepsis) data(sepsis)
@ -27,7 +27,7 @@ details.
} }
\details{ \details{
This dataset is taken from This dataset is taken from
\href{http://biopharmnet.com/wiki/Software_for_subgroup_identification_and_analysis}{SIDES \href{http://biopharmnet.com/subgroup-analysis-software/}{SIDES
method}. method}.
\code{Sepsis} contains simulated data on 470 subjects with a binary outcome \code{Sepsis} contains simulated data on 470 subjects with a binary outcome

3
man/vt.data.Rd
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@ -1,4 +1,4 @@
% Generated by roxygen2 (4.1.1): do not edit by hand % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/object.wrapper.R % Please edit documentation in R/object.wrapper.R
\name{vt.data} \name{vt.data}
\alias{vt.data} \alias{vt.data}
@ -31,5 +31,6 @@ a VT.object object.
data(sepsis) data(sepsis)
formatRCTdataset(sepsis, "survival", "THERAPY", T) formatRCTdataset(sepsis, "survival", "THERAPY", T)
} }
} }

5
man/vt.forest.Rd
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@ -1,4 +1,4 @@
% Generated by roxygen2 (4.1.1): do not edit by hand % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/forest.wrapper.R % Please edit documentation in R/forest.wrapper.R
\name{vt.forest} \name{vt.forest}
\alias{vt.forest} \alias{vt.forest}
@ -26,7 +26,7 @@ randomForest, train or cforest. Is only used with forest.type = "one". If
NULL, a randomForest model is grown inside the function. NULL is default.} NULL, a randomForest model is grown inside the function. NULL is default.}
\item{model_trt1}{see model_trt0 explanation and \item{model_trt1}{see model_trt0 explanation and
\code{\link{VT.double.forest}} details.} \code{\link{VT.forest.double}} details.}
\item{model_trt0}{works the same as model parameter. Is only used with \item{model_trt0}{works the same as model parameter. Is only used with
forest.type = "double". If NULL, a randomForest model is grown inside the forest.type = "double". If NULL, a randomForest model is grown inside the
@ -67,5 +67,6 @@ parameter forest.type, any of these class can be used with its own parameter.
vt.f <- vt.forest("one", vt.o, mtry = 3, nodesize = 15) vt.f <- vt.forest("one", vt.o, mtry = 3, nodesize = 15)
# ... # ...
} }
} }

7
man/vt.subgroups.Rd
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@ -1,11 +1,11 @@
% Generated by roxygen2 (4.1.1): do not edit by hand % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/tools.R % Please edit documentation in R/tools.R
\name{vt.subgroups} \name{vt.subgroups}
\alias{vt.subgroups} \alias{vt.subgroups}
\title{Visualize subgroups} \title{Visualize subgroups}
\usage{ \usage{
vt.subgroups(vt.trees, only.leaf = T, only.fav = T, tables = F, vt.subgroups(vt.trees, only.leaf = T, only.fav = T, tables = F,
verbose = F) verbose = F, compete = F)
} }
\arguments{ \arguments{
\item{vt.trees}{\code{\link{VT.tree}} object. Or return of \item{vt.trees}{\code{\link{VT.tree}} object. Or return of
@ -22,7 +22,7 @@ default.}
\item{verbose}{print infos during computation. FALSE is default.} \item{verbose}{print infos during computation. FALSE is default.}
\item{compete}{print competitors rules thanks to competitors computation of \item{compete}{print competitors rules thanks to competitors computation of
the tree} the tree}
} }
\value{ \value{
data.frame of rules data.frame of rules
@ -44,5 +44,6 @@ rpart.plot must be loaded. See \code{\link{VT.tree}} for details.
# change options you'll be surprised ! # change options you'll be surprised !
vt.subgroups(vt.tr, verbose = T, tables = T) vt.subgroups(vt.tr, verbose = T, tables = T)
} }
} }

3
man/vt.tree.Rd
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@ -1,4 +1,4 @@
% Generated by roxygen2 (4.1.1): do not edit by hand % Generated by roxygen2: do not edit by hand
% Please edit documentation in R/tree.wrapper.R % Please edit documentation in R/tree.wrapper.R
\name{vt.tree} \name{vt.tree}
\alias{vt.tree} \alias{vt.tree}
@ -54,5 +54,6 @@ See \code{\link{VT.tree}}, \code{\link{VT.tree.class}} and
vt.tr$tree1$getInfos() vt.tr$tree1$getInfos()
# ... # ...
} }
} }