1.1_table1_descriptive_stats.Rmd

---
title: "table1"
author: "Aiyi Zhang"
date: "November 29, 2017"
output:
  word_document: default
  pdf_document: default
  html_document: default
---
```{r setup, include=FALSE}
require(arsenal)
require(knitr)
library(readr)
setwd("~/Macabi/data_generated/method9.3")
sample <- read_csv("~/Macabi/data_generated/method9.3/sample.csv")
sample$X1=NULL
```

```{r, echo=F, results="asis"}
options(width = 10000)
labels(sample)  <- c(age="Age",
                  SEX="Sex",
                  deathYN="Death Status",
                  DISEASE_GROUPUP_CD="Cancer Types")
sample$diab[which(sample$diab==0)]="non Diabetic"
sample$diab[which(sample$diab==1)]="Diabetic"
sample$deathYN[which(sample$deathYN==0)]="alive"
sample$deathYN[which(sample$deathYN==1)]="Deceased"
sample$deathYN[which(sample$deathYN==1)]="Deceased"

sample$DISEASE_GROUPUP_CD[which(sample$DISEASE_GROUPUP_CD==2000)]="Colon"
  sample$DISEASE_GROUPUP_CD[which(sample$DISEASE_GROUPUP_CD==3000)]="Lung"
  sample$DISEASE_GROUPUP_CD[which(sample$DISEASE_GROUPUP_CD==4000)]="Breast"
  sample$DISEASE_GROUPUP_CD[which(sample$DISEASE_GROUPUP_CD==7000)]="Female Genital"
  sample$DISEASE_GROUPUP_CD[which(sample$DISEASE_GROUPUP_CD==8000)]="Male Genital"
  sample$DISEASE_GROUPUP_CD[which(sample$DISEASE_GROUPUP_CD==14000)]="Hematologic Neoplasm"
summary(tableby(diab~age+SEX+deathYN+BMI+HBA1C+CREATININE+DISEASE_GROUPUP_CD, data=sample))
```