# Code for the Kaplan-meier chapter
# next line may not be necessary if you installed it sometime earlier
install.packages("survival", dependencies=TRUE)
library(survival)
Now load the dataset into R with the following command:
mydataframe <- read.delim("http://www.robin-beaumont.co.uk/virtualclassroom/book2data/survival_collett_p290.dat", header=TRUE)
names(mydataframe)
mydataframe
Now create the regression model:
library(survival)

attach(mydataframe)
# now create a survival object/dataset note the upper case S 
mysurv <- Surv(time, cens)
# now create a survival curve object note the lower case S 
myKMest <- survfit(mysurv~treat, conf.int=FALSE )
plot(myKMest, 
lty=c(1,3), col=c("blue","red")) 
title(main= "survival ovarian cancer n=26", 
xlab="Time (days )", 
ylab=" % surviving, S(t)") 
legend(x=10,y=0.2, legend=c("monotherapy","combined"),col=c("blue","red"),lty=c(1,1))
summary(myKMest)


# from http://biostat.mc.vanderbilt.edu/wiki/Main/TatsukiRcode 
# http://biostat.mc.vanderbilt.edu/wiki/pub/Main/TatsukiRcode/TatsukiRcodeKMplot.r
# local copy available at:
#http://www.robin-beaumont.co.uk/virtualclassroom/book2data/r_code/TatsukiRcodeKMplot.r",
# You can use the source command to read a bit of R code from somewhere else
# source(file)
####################

source("http://www.robin-beaumont.co.uk/virtualclassroom/book2data/r_code/TatsukiRcodeKMplot.r")

kmplot(myKMest, mark='|', simple=FALSE,
	xaxis.at=c(0,200, 400, 600, 800, 1000, 1200), xaxis.lab=c(0,200, 400, 600, 800, 1000, 1200),         # n.risk.at
	lty.surv=c(1,2), lwd.surv=1, col.surv=c(1,4),    # survival.curves
	col.ci=0, # confidence intervals not plotted
	group.names=c('monotherapy','combined'),
	group.order=c(1,2), # order of appearance in the n.risk.at table and legend.
	extra.left.margin=6, label.n.at.risk=TRUE, draw.lines=TRUE,
	cex.axis=.8, xlab='days', ylab='Survival Probability', # labels
	grid=TRUE, lty.grid=1, lwd.grid=1, col.grid=grey(.9),
	legend=TRUE, loc.legend='bottomleft',
	cex.lab=.8, xaxs='r', bty='L', las=1, tcl=-.2 ,  # other parameters passed to plot()
)

title(main='Chemotherapy for Ovarian cancer', adj=.1, font.main=1, line=0.5, cex.main=1)



# let kma = myKmest
kmplot(myKMest, mark='', simple=FALSE,
	xaxis.at=c(0,.5,1:9)*365, xaxis.lab=c(0,.5,1:9),         # n.risk.at
	lty.surv=c(1,2), lwd.surv=1, col.surv=c(1,1,2,2,4,4),    # survival.curves
	col.ci=0, # confidence intervals not plotted
	group.names=c('Obs ','Obs tumor adh','Lev','Lev tumor adh','Lev+5FU ','Lev+5FU tumor adh'),
	group.order=c(5,3,1,6,4,2), # order of appearance in the n.risk.at table and legend.
	extra.left.margin=6, label.n.at.risk=FALSE, draw.lines=TRUE,
	cex.axis=.8, xlab='Years', ylab='Survival Probability', # labels
	grid=TRUE, lty.grid=1, lwd.grid=1, col.grid=grey(.9),
	legend=TRUE, loc.legend='bottomleft',
	cex.lab=.8, xaxs='r', bty='L', las=1, tcl=-.2  # other parameters passed to plot()
)
title(main='Chemotherapy for stage B/C colon cancer', adj=.1, font.main=1, line=0.5, cex.main=1)