updating actg repo for package

README.Rmd

+---
+title: "AIDS Clinical Trial Group (ACTG) Study Dataset"
+author: "Sara Levintow"
+date: "8/28/2017"
+output: md_document
+---
+# AIDS Clinical Trial Group (ACTG) Study Dataset #
+
+The ACTG study 320 compared a combination of three antiretroviral drugs against a pair. 
+
+### Installation
+
+You can install the package from Bitbucket
+
+```{r setup, include=FALSE, warning=FALSE}
+knitr::opts_chunk$set(echo = TRUE)
+  library("devtools")
+  devtools::install_bitbucket("levintow/actg")
+  library(actg)
+```
+
+```{r, eval=FALSE}
+  library("devtools")
+  devtools::install_bitbucket("levintow/actg")
+  library(actg)
+```
+
+### List of Variables (variable name: definition) ###
+
+* id: patient identifier
+* male: 1=male, 0=female
+* black: 1=black, 0=non-black
+* hispanic: 1=hispanic, 0=non-hispanic
+* idu: 1=history of injection drug use, 0=no history
+* art: 1=triple therapy, 0=double therapy
+* delta: 1=endpoint (AIDS or death), 0=no endpoint
+* drop: 1=loss to follow up, 0=not
+* r: 1=in subcohort, 0=not
+* age: years of age at randomization
+* karnof: Karnofsky score (100=normal, 0=dead)
+* days: days from randomization to endpoint of censoring
+* cd4: CD4 count in cells/mm^3 at randomization
+* stop: day therapy stopped, missing if not stopped
+
+### Notes ###
+
+* There is one record per patient in the dataset.
+* r is a constructed variable to illustrate confounding.

README.md

-# AIDS Clinical Trial Group (ACTG) Study Dataset #
-
-The ACTG study 320 compared a combination of three antiretroviral drugs against a pair. 
-
-### List of Variables (variable name: definition) ###
-
-* id: patient identifier
-* male: 1=male, 0=female
-* black: 1=black, 0=non-black
-* hispanic: 1=hispanic, 0=non-hispanic
-* idu: 1=history of injection drug use, 0=no history
-* art: 1=triple therapy, 0=double therapy
-* delta: 1=endpoint (AIDS or death), 0=no endpoint
-* drop: 1=loss to follow up, 0=not
-* r: 1=in subcohort, 0=not
-* age: years of age at randomization
-* karnof: Karnofsky score (100=normal, 0=dead)
-* days: days from randomization to endpoint of censoring
-* cd4: CD4 count in cells/mm^3 at randomization
-* stop: day therapy stopped, missing if not stopped
-
-### Notes ###
-
-* There is one record per patient in the dataset.
-* r is a constructed variable to illustrate confounding.
+AIDS Clinical Trial Group (ACTG) Study Dataset
+==============================================
+
+The ACTG study 320 compared a combination of three antiretroviral drugs
+against a pair.
+
+### Installation
+
+You can install the package from Bitbucket
+
+      library("devtools")
+      devtools::install_bitbucket("levintow/actg")
+      library(actg)
+
+### List of Variables (variable name: definition)
+
+-   id: patient identifier
+-   male: 1=male, 0=female
+-   black: 1=black, 0=non-black
+-   hispanic: 1=hispanic, 0=non-hispanic
+-   idu: 1=history of injection drug use, 0=no history
+-   art: 1=triple therapy, 0=double therapy
+-   delta: 1=endpoint (AIDS or death), 0=no endpoint
+-   drop: 1=loss to follow up, 0=not
+-   r: 1=in subcohort, 0=not
+-   age: years of age at randomization
+-   karnof: Karnofsky score (100=normal, 0=dead)
+-   days: days from randomization to endpoint of censoring
+-   cd4: CD4 count in cells/mm^3 at randomization
+-   stop: day therapy stopped, missing if not stopped
+
+### Notes
+
+-   There is one record per patient in the dataset.
+-   r is a constructed variable to illustrate confounding.

data-raw/read_actg.R → data-raw/read_data.R

+# read_data.R
+# Purpose: read-in ACTG data for inclusion in package
+# This file is run to rebuild the actg data for the package
+# Authors: Sara Levintow and Alan Brookhart
+
 library(devtools)
+library(tidyverse)
 library(readr)
 use_data_raw()
 
 # Reading in ACTG data set
-actg<-read.table("/Users/salevintow/Documents/R Software Development/actg/data-raw/actg320.23nov16.dat.txt")
+actg<-read.table("./data-raw/actg320.23nov16.dat.txt")
 colnames(actg)<-c("id","male","black","hispanic","idu","art","delta","drop","r","age","karnof","days","cd4","stop")
 
 # Review variables and make sure data read in correctly
@@ -14,11 +20,17 @@ actg$stop<-as.character(actg$stop)
 actg$stop<-ifelse(actg$stop=="."," ",actg$stop)
 actg$stop<-as.numeric(actg$stop)
 
-## Creating event time and censoring time variables
+# Creating event time and censoring time variables
 actg$Y <- ifelse(actg$delta==1,actg$days,NA) #Y is time of event (AIDS or death)
-actg$C <- ifelse(actg$delta==0,actg$days,NA) #C is time of censoring
 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"))
+
+# Deleting indicators of outcome and drop-out
+actg$delta<-NULL
+actg$drop<-NULL
+
 # Save R data set in the actg package
 devtools::use_data(actg,overwrite = TRUE)