diff --git a/.Rbuildignore b/.Rbuildignore index 91114bf..4b3f9f2 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -1,2 +1,3 @@ ^.*\.Rproj$ ^\.Rproj\.user$ +^data-raw$ diff --git a/R/data.R b/R/data.R index 0ff331c..2bee803 100644 --- a/R/data.R +++ b/R/data.R @@ -6,7 +6,7 @@ #' \href{http://biopharmnet.com/wiki/Software_for_subgroup_identification_and_analysis}{SIDES #' method}. #' -#' \code{Sepsis} contains simulated data on 454 subjects with a binary outcome +#' \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. @@ -16,7 +16,7 @@ #' #' True subgroup is \emph{PRAPACHE <= 26 & AGE <= 49.80} #' -#' @format 454 patients and 13 variables. +#' @format 470 patients and 13 variables. #' \describe{ #' \item{survival}{binary outcome} #' \item{THERAPY}{1 for active treatment, 0 for control treatment} diff --git a/data-raw/sepsis.R b/data-raw/sepsis.R new file mode 100644 index 0000000..2207871 --- /dev/null +++ b/data-raw/sepsis.R @@ -0,0 +1,42 @@ + +# Create sepsis data ------------------------------------------------------ + +# Load some libraries +library(VirtualTwins) +library(randomForest) + +# Sepsis is a csv file available in SIDES example to this address: +# http://biopharmnet.com/wiki/Software_for_subgroup_identification_and_analysis +# type ?sepsis to see details +# I downloaded zip file and extract the sepsis.csv in data-raw folder. +sepsis.csv <- read.csv(file = "data-raw/sepsis.csv", na.strings = ".") + +# Check data +str(sepsis.csv) + +# Count NA's +sum(is.na(sepsis.csv)) +# No NA's in outcome +sum(is.na(sepsis.csv$survival)) + +# For futures computation i need to impute missing values +# I use random forest imputation with randomForest package with simple parameters +# I need to make survival field as factor +sepsis.csv$survival <- factor(sepsis.csv$survival, levels = 0:1) +sepsis.imp <- with(sepsis.csv, rfImpute(y = survival, x = sepsis.csv[, -1], iter = 5, ntree = 500)) +str(sepsis.imp) + +# Change THERAPY levels in 0/1 and type will be numeric +sepsis.imp$THERAPY <- with(sepsis.csv, ifelse(THERAPY == "control", 0, 1)) + +# Change survival into numeric values +sepsis.imp$survival <- as.numeric(as.character(sepsis.imp$survival)) + +# Check data +sepsis <- formatRCTDataset(sepsis.imp, "survival", "THERAPY", T) + +# Save file into data folder +save(sepsis, file = "data/sepsis.rdata") + +# End. + diff --git a/data-raw/sepsis.csv b/data-raw/sepsis.csv new file mode 100644 index 0000000..8cbe9b6 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