From: <john_philip_lawo_at_baxter.com>

Date: Thu, 17 Apr 2008 10:49:05 +0200

John-Philip Lawo

R-help_at_r-project.org mailing list

https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Received on Thu 17 Apr 2008 - 09:51:09 GMT

Date: Thu, 17 Apr 2008 10:49:05 +0200

Hello everyone,

I was trying to calculate linear contrasts with coxph via the contrasts
function, but I'm not sure if it is correct.
First, all the statistics change, if I state 2 contrasts instead of 3.
Second, stipulating common linear contrasts does not even nearly produce an
expected result (i.e. -1,1,0,0 should lead to nonsignificatn result, as
group A and B are not differing very much)
So, I suppose a contrast like -1,0,0,1 isn't just first versus last group,
but I didn't found anything on that yet.
Do you have an idea?

Kind reagrds,

John

Code:

x <- 40

weeka <- round(rnorm (x,4,0.3),0) weekb <- round(rnorm (x,4,0.4),0) weekc <- round(rnorm (x,8,0.6),0) weekd <- round(rnorm (x,12,0.9),0) week <- c(weeka, weekb,weekc, weekd) cens <- round(runif((4*x),0.4,1),0) # 0 = censored treat <- as.factor(c(rep("A",x),rep("B",x), rep("C",x), rep("D",x)))

S <- Surv(week,cens)

contrasts(treat, how.many=3) <- contr.sum(4); contrasts(treat) summary(coxph(formula=S~treat, robust=TRUE))

contrasts(treat, how.many=2) <- contr.sum(4); contrasts(treat) summary(coxph(formula=S~treat, robust=TRUE))

contrasts(treat, how.many=3) <- matrix(ncol=3, nrow=4, c(-3,-1,1,3,
-1,0,1,0, -1,1,0,0)); contrasts(treat)

summary(coxph(formula=S~treat, robust=TRUE))

John-Philip Lawo

Biostatistician

Baxter Innovations GmbH

Wagramer Straße 17-19

IZD Tower 24th floor

A-1220 Vienna

Phone: +43-(0)1-20100-3480

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