# This file is stored as  lworld.R

# This is code for analyzing the World Leisure
# study of endometrial cancer.  Ther are four 
#  controls  for each case and they are matched 
#  on age.  The file contains 315 records with 
#  data on cases and controls from the Leisure 
#  World study of endometrial cancer as related 
#  to treatment with estrogens for menopausal 
#  syptoms and other risk factors.  See the 
#  article by Mack et al in NEJM 294:1262-1267, 
#  1976 for a full description.

# The variables are as follows:

#Number  Name        Description             Codes/Range
#-------------------------------------------------------------------------
#   1    GROUP       Matched set indicator    1-63
#   2    CASE        Case-control indicator  1 = Case; 0 = control
#   3    AGE         Age in years            55-84
#   4    AGEG        Age group indicator     1 = 55-64; 2 = 65-74; 3 = 75+
#   5    EST         Estrogen usage          1 = No; 2 = Yes
#   6    GALL        Gallbladder disease     1 = No; 2 = Yes
#   7    HYP         Hypertension            1 = No; 2 = Yes 
#   8    OB          Obesity                 1 = No; 2 = Yes; 3 = Unknown
#   9    NON         Non-estrogen drug       1 = No; 2 = Yes
#-------------------------------------------------------------------------
#The nine variables may be read either in free format or using the Fortran
#format (1x,9f5.0).  AGEG is based on the age of the case in each matched
#set.



# Enter the data into a data frame.

set1 <- read.table("c:/stat565/lworld.txt",
      header=F, col.names=c("group", "case", "age", "ageg", "est", 
      "gall", "hyp", "ob", "non"))
set1$est <- set1$est-1
set1$gall <-set1$gall-1
set1$hyp <- set1$hyp-1
set1$non <- set1$non-1
set1$oby <- set1$ob
set1$obu <- set1$ob
set1$oby[set1$oby>2] <- 2
set1$oby <- set1$oby-1
set1$obu[set1$obu<3] <- 0
set1$obu <- set1$obu/3

# Load the survival analysis package

 library(survival)

 coxout <- coxph(Surv(group,case) ~ est + gall + hyp + non
            +oby+obu+strata(group), data=set1, method="exact")

summary(coxout)