Updating readme and dataset to code treatment as a factor variable

README.Rmd

@@ -6,7 +6,7 @@ output: md_document
 ---
 # AIDS Clinical Trial Group (ACTG) Study Dataset #
 
-The ACTG study 320 compared a combination of three antiretroviral drugs against a pair. 
+The AIDS Clinical Trials Group (ACTG) 320 compared a combination of three antiretroviral drugs (two nucleoside analogues, zidovudine and lamivudine, plus a protease inhibitor, indinavir) against a pair (zidovudine and lamivudine alone). The dataset consists of 1,156 HIV-positive patients enrolled in the trial between January 29, 1996 and January 27, 1997. At screening, all patients had a CD4 cell count ≤200 cells per cubic millimeter, at least 3 months of prior zidovudine therapy, and no previous treatment with lamivudine or protease inhibitors. Patients were stratified based on CD4 count (≤50 vs. 51-200) and randomly assigned to the three-drug or two-drug regimen. The outcome of interest was the occurrence of AIDS or death, and the findings from the trial were reported in Hammer's 1997 paper in the New England Journal of Medicine. Trial participants were followed until AIDS diagnosis, death, loss to follow-up, or administrative censoring. Covariates measured at baseline and available in the dataset are age, sex, race, ethnicity, Karnofsky score, CD4 cell count, and history of injection drug use. 
 
 ### Installation
 
@@ -31,9 +31,9 @@ knitr::opts_chunk$set(echo = TRUE)
 * male: 1=male, 0=female
 * black: 1=black, 0=non-black
 * hispanic: 1=hispanic, 0=non-hispanic
-* idu: numeric variable for exposure (1=history of injection drug use, 0=no history)
-* idu_f: factor variable for exposure (1=history of injection drug use, 0=no history)
-* art: 1=triple therapy, 0=double therapy
+* idu: 1=history of injection drug use, 0=no history of injection drug use
+* art: 1=triple therapy, 0=dual therapy
+* art_f: factor variable for treatment group (1=triple therapy, 0=dual therapy)
 * r: 1=in subcohort, 0=not
 * age: years of age at randomization
 * karnof: Karnofsky score (100=normal, 0=dead)

data-raw/read_data.R

@@ -25,8 +25,8 @@ actg$Y <- ifelse(actg$delta==1,actg$days,NA) #Y is time of event (AIDS or death)
 actg$C1 <- ifelse(actg$drop==1,actg$days,NA) #C1 is time of censoring due to drop-out
 actg$C2 <- ifelse(actg$delta==0 & actg$drop==0,actg$days,NA) #C2 is time of censoring not due to drop-out
 
-# Exposure (idu) as a factor variable
-actg$idu_f <- factor(actg$idu,levels = c(0,1), labels = c("No IDU","History of IDU"))
+# Treatment (art) as a factor variable
+actg$art_f <- factor(actg$art,levels = c(0,1), labels = c("Dual therapy","Triple therapy"))
 
 # Deleting indicators of outcome and drop-out
 actg$delta<-NULL