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Fix bug documentation

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prise6 2015-06-12 00:34:25 +02:00
parent cdf25aed08
commit 39b1757fb5
12 changed files with 22 additions and 14 deletions
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2
R/VirtualTwins.R
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@ -5,7 +5,7 @@
#' \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.
#' \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.
#' }
#'
#' @section TODO LIST:

8
R/data.R
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@ -3,10 +3,10 @@
#' Simulated clinical trial with two groups treatment about sepsis desease. See details.
#'
#' This dataset is taken from
#' \link[=http://biopharmnet.com/wiki/Software_for_subgroup_identification_and_analysis]{SIDES
#' \href{http://biopharmnet.com/wiki/Software_for_subgroup_identification_and_analysis}{SIDES
#' method}.
#'
#' \code{Sepsis} contains simulated data on 470 subjects with a binary outcome
#' \code{Sepsis} contains simulated data on 454 subjects with a binary outcome
#' survival, that stores survival status for patient after 28 days of treatment,
#' value of 1 for subjects who died after 28 days and 0 otherwise. There are 11
#' covariates, listed below, all of which are numerical variables.
@ -16,7 +16,7 @@
#'
#' True subgroup is \emph{PRAPACHE <= 26 & AGE <= 49.80}
#'
#' @format 470 patients and 13 variables.
#' @format 454 patients and 13 variables.
#' \describe{
#' \item{survival}{binary outcome}
#' \item{THERAPY}{1 for active treatment, 0 for control treatment}
@ -33,6 +33,8 @@
#' \item{BLLBILI}{Baseline local bilirubin}
#' }
#'
#' @usage data(sepsis)
#' @docType data
#' @source \url{http://biopharmnet.com/wiki/Software_for_subgroup_identification_and_analysis}
#' @name sepsis
NULL

2
R/forest.R
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@ -6,7 +6,7 @@
#'
#' \code{VT.forest} extends \code{VT.difft}
#'
#' @field ... see fields of \linkS4class{VT.difft}
#' @field ... see fields of \code{\link{VT.difft}}
#'
#' @include difft.R predict.R
#'

2
R/forest.fold.R
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@ -17,7 +17,7 @@
#' @field fold numeric, number of fold, i.e. number of forest (k)
#' @field ratio numeric experimental, use to balance sampsize. Defaut to 1.
#' @field groups vector Define which observations belong to which group
#' @field ... field from parent class : \linkS4class{VT.forest}
#' @field ... field from parent class : \code{\link{VT.forest}}
#'
#' @name VT.forest.fold
#'

2
R/forest.one.R
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@ -16,7 +16,7 @@
#'
#' @field model is a caret/RandomForest/randomForest class object
#' @field interactions logical set TRUE if model has been computed with interactions
#' @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.double}}
#'

2
R/formatRCTDataset.R
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@ -27,6 +27,8 @@
#' \dontrun{
#' data.format <- formatRCTDataset(data, "outcome", "treatment", TRUE)
#' }
#'
#'
#'
#' @export
formatRCTDataset <- function(dataset, outcome.field, treatment.field, interactions = TRUE){

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data/sepsis.rdata
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2
man/VT.forest.Rd
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@ -13,7 +13,7 @@ An abstract reference class to compute twin via random forests
\section{Fields}{
\describe{
\item{\code{...}}{see fields of \linkS4class{VT.difft}}
\item{\code{...}}{see fields of \code{\link{VT.difft}}}
}}
\section{Methods}{

2
man/VT.forest.fold.Rd
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@ -26,7 +26,7 @@ interactions}
\item{\code{groups}}{vector Define which observations belong to which group}
\item{\code{...}}{field from parent class : \linkS4class{VT.forest}}
\item{\code{...}}{field from parent class : \code{\link{VT.forest}}}
}}
\section{Methods}{

2
man/VT.forest.one.Rd
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@ -22,7 +22,7 @@ what \code{computeTwin1()} and \code{computeTwin2()} functions do.
\item{\code{interactions}}{logical set TRUE if model has been computed with interactions}
\item{\code{...}}{field from parent class : \linkS4class{VT.forest}}
\item{\code{...}}{field from parent class : \code{\link{VT.forest}}}
}}
\section{Methods}{

2
man/VirtualTwins.Rd
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@ -10,7 +10,7 @@ VirtualTwins is written mainly with reference classes. Briefly, there is three k
\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.
\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.
}
}
\section{TODO LIST}{

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man/sepsis.Rd
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@ -1,9 +1,10 @@
% Generated by roxygen2 (4.1.1): do not edit by hand
% Please edit documentation in R/data.R
\docType{data}
\name{sepsis}
\alias{sepsis}
\title{Clinical Trial for Sepsis desease}
\format{470 patients and 13 variables.
\format{454 patients and 13 variables.
\describe{
\item{survival}{binary outcome}
\item{THERAPY}{1 for active treatment, 0 for control treatment}
@ -22,15 +23,18 @@
\source{
\url{http://biopharmnet.com/wiki/Software_for_subgroup_identification_and_analysis}
}
\usage{
data(sepsis)
}
\description{
Simulated clinical trial with two groups treatment about sepsis desease. See details.
}
\details{
This dataset is taken from
\link[=http://biopharmnet.com/wiki/Software_for_subgroup_identification_and_analysis]{SIDES
\href{http://biopharmnet.com/wiki/Software_for_subgroup_identification_and_analysis}{SIDES
method}.
\code{Sepsis} contains simulated data on 470 subjects with a binary outcome
\code{Sepsis} contains simulated data on 454 subjects with a binary outcome
survival, that stores survival status for patient after 28 days of treatment,
value of 1 for subjects who died after 28 days and 0 otherwise. There are 11
covariates, listed below, all of which are numerical variables.