[R] cumulative incidence plot vs survival plot

[array chip]

Alan,

Let's say that I code censoring as "0", recurrence as "1" for fstat and 
death/competing risk as "2". If a patient did not have recurrence and lost 
follow-up at 2 years in terms of recurrence monitoring, but he also died at 5 
years. How should I code this patient? I think I still code this patient as 0 
(censoring) because lost-of-followup occurred before death, am I correct?

Thanks very much!

John





----- Original Message ----
From: alanm (Alan Mitchell) <alanm at crab.org>
To: array chip <arrayprofile at yahoo.com>; David Winsemius 
<dwinsemius at comcast.net>
Cc: r-help at r-project.org
Sent: Tue, June 28, 2011 9:20:22 AM
Subject: RE: [R] cumulative incidence plot vs survival plot

John,

Since death precludes recurrence, censoring deaths would violate the KM
estimator assumption that additional follow-up would eventually lead to
an event.  If your goal is to estimate the probability of recurrence,
then you want CI with deaths as a competing risk.  The cuminc function
in the cmprsk package is a great place to start.  

Gooley has a great paper on the difference between CI and 1-KM (See
Statistics in Medicine, 18, 695-706 (1999)).  

HTH,

Alan Mitchell, MSc
Biostatistician
alanm at crab.org

-----Original Message-----
From: array chip [mailto:arrayprofile at yahoo.com] 
Sent: Monday, June 27, 2011 2:04 PM
To: David Winsemius
Cc: r-help at r-project.org
Subject: Re: [R] cumulative incidence plot vs survival plot

Hi David,

Thanks for responding, and plain text ...(didn't realized I was in rich
text).

The endpoint is disease recurrence, I was producing a regular KM plot of
recurrence-free probability. Then someone recommend using cumulative
incidence is preferred because death was censored in the dataset. I did
a little googling, I found CI was used often in the context of competing
risk. I am totally new to competing risk and trying to understand what
competing risk means and why CI is preferred than KM survival in this
context. If you could share your thoughts helping me to understand,
greatly appreciated.

Searched archive, found people talking about cmprsk package for
estimating and plotting CI. would that be the same as the code you
suggested: plot(time,
cumsum(dead))

Thanks very much!

John




________________________________
From: David Winsemius <dwinsemius at comcast.net>

Cc: r-help at r-project.org
Sent: Mon, June 27, 2011 1:45:35 PM
Subject: Re: [R] cumulative incidence plot vs survival plot


On Jun 27, 2011, at 4:31 PM, array chip wrote:

> Hi, I am wondering if anyone can explain to me if cumulative incidence

> (CI) is just "1 minus kaplan-Meier survival"?

First tell us what you think CI is defined as. I suspect it is not the
same. The 

KM estimator is cumulative product of (alive-n(dead))/alive so is the
product of 

interval survival probabilities. I doubt that your definition of CI has
a similar denominator.


> Under what circumstance, you should use
> cumulative incidence vs KM survival? If the relationship is just CI =
> 1-survival, then what difference it makes to use one vs. the other?
> 
> And in R how I can draw a cumulative incidence plot.

plot(time, cumsum(dead)) ...?

> I know I can make a
> Kaplan-Meier survival plot using plot(survfit()), for example:
> 
> fit<-survfit(Surv(time,status)~group,data=data)
> plot(fit, col=1:2)
> 
> How to draw CI plot then?

As above. Specify what you are seeking.

There is a well-defined relationship between S(t) and the cumulative
hazard. 
Maybe you should do a little study of those terms in texts regarding
survival 
analysis.

> Thanks very much!
> 
> John
>     [[alternative HTML version deleted]]

Isn't it time you learned to post in plain text?

--
David Winsemius, MD
West Hartford, CT