diff --git a/DESCRIPTION b/DESCRIPTION index c82f275..c856b82 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -19,6 +19,7 @@ Depends: methods Collate: 'VirtualTwins.R' + 'data.R' 'object.R' 'difft.R' 'setClass.R' diff --git a/R/data.R b/R/data.R new file mode 100644 index 0000000..fc5dead --- /dev/null +++ b/R/data.R @@ -0,0 +1,38 @@ +#' Clinical Trial for Sepsis desease +#' +#' 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 +#' method}. +#' +#' \code{Sepsis} contains simulated data on 470 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. +#' +#' Note that contrary to the original dataset used in SIDES, missing values have +#' been imputed by random forest \code{(randomForest::rfImpute())} +#' +#' True subgroup is \emph{PRAPACHE <= 26 & AGE <= 49.80} +#' +#' @format 470 patients and 13 variables. +#' \describe{ +#' \item{survival}{binary outcome} +#' \item{THERAPY}{1 for active treatment, 0 for control treatment} +#' \item{TIMFIRST}{Time from first sepsis-organ fail to start drug} +#' \item{AGE}{Patient age in years} +#' \item{BLLPLAT}{Baseline local platelets} +#' \item{blSOFA}{Sum of baselin sofa (cardiovascular, hematology, hepaticrenal, and respiration scores)} +#' \item{BLLCREAT}{Base creatinine} +#' \item{ORGANNUM}{Number of baseline organ failures} +#' \item{PRAPACHE}{Pre-infusion apache-ii score} +#' \item{BLGCS}{Base GLASGOW coma scale score} +#' \item{BLIL6}{Baseline serum IL-6 concentration} +#' \item{BLADL}{Baseline activity of daily living score} +#' \item{BLLBILI}{Baseline local bilirubin} +#' } +#' +#' @source \url{http://biopharmnet.com/wiki/Software_for_subgroup_identification_and_analysis} +#' @name sepsis +NULL diff --git a/data/sepsis.RData b/data/sepsis.rdata similarity index 100% rename from data/sepsis.RData rename to data/sepsis.rdata diff --git a/man/VirtualTwins.Rd b/man/VirtualTwins.Rd index 5f669f8..0048537 100644 --- a/man/VirtualTwins.Rd +++ b/man/VirtualTwins.Rd @@ -13,9 +13,6 @@ VirtualTwins is written mainly with reference classes. Briefly, there is three k \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} diff --git a/man/sepsis.Rd b/man/sepsis.Rd new file mode 100644 index 0000000..2973876 --- /dev/null +++ b/man/sepsis.Rd @@ -0,0 +1,43 @@ +% Generated by roxygen2 (4.1.1): do not edit by hand +% Please edit documentation in R/data.R +\name{sepsis} +\alias{sepsis} +\title{Clinical Trial for Sepsis desease} +\format{470 patients and 13 variables. +\describe{ + \item{survival}{binary outcome} + \item{THERAPY}{1 for active treatment, 0 for control treatment} + \item{TIMFIRST}{Time from first sepsis-organ fail to start drug} + \item{AGE}{Patient age in years} + \item{BLLPLAT}{Baseline local platelets} + \item{blSOFA}{Sum of baselin sofa (cardiovascular, hematology, hepaticrenal, and respiration scores)} + \item{BLLCREAT}{Base creatinine} + \item{ORGANNUM}{Number of baseline organ failures} + \item{PRAPACHE}{Pre-infusion apache-ii score} + \item{BLGCS}{Base GLASGOW coma scale score} + \item{BLIL6}{Baseline serum IL-6 concentration} + \item{BLADL}{Baseline activity of daily living score} + \item{BLLBILI}{Baseline local bilirubin} +}} +\source{ +\url{http://biopharmnet.com/wiki/Software_for_subgroup_identification_and_analysis} +} +\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 +method}. + +\code{Sepsis} contains simulated data on 470 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. + +Note that contrary to the original dataset used in SIDES, missing values have +been imputed by random forest \code{(randomForest::rfImpute())} + +True subgroup is \emph{PRAPACHE <= 26 & AGE <= 49.80} +} +