[R] Cumulative Incident Function does not go to end of dataset

[Donald Catanzaro]

Hi All,

Thank you David, I see now that what I need to do is something like

plot(attr(ci,"survfit"), col=c("red","green"))


and I will get the plot with the two CIFs in different colors.

On Sat, Sep 24, 2016 at 9:17 AM, David Winsemius <dwinsemius at comcast.net>
wrote:

>
> > On Sep 23, 2016, at 8:58 PM, Donald Catanzaro <dgcatanzaro at gmail.com>
> wrote:
> >
> > Hi All,
> >
> > I have been working on a Competing Risks analysis using the mstate
> package
> > and when I run my analysis I was surprised to see the cumulative incident
> > function ending substantially before my data set did.
> >
> > You can reproduce the behavior (kind of) using the data that was provided
> > with mstate:
> >
> > library(mstate)
> > data(aidssi)
> > ci <- Cuminc(time=aidssi$time, status=aidssi$status)
> >
> >
> > and you can see that ci goes to 10.448
> >
> > However, when you use the cmprsk package, the CIF goes pretty much to the
> > end of the data
> >
> >
> > library(cmprsk)
> > CI.overall <- cuminc(ftime =aidssi$time, fstatus=aidssi$status)
> >
> > and you can see that CI.overall ends at 12
> >
> > Using the data provided in the package, a difference of < 2 years is not
> > terrible but with my dataset mstate ends at 1.02 while cmprsk ends at 4
> (my
> > max for event time is 4.9) and that is a substantial difference.
> >
> > I believe I must be missing something here.  Is there a way to get
> mstate to
> > report the entire CIF ?
>
>
> If you compare the output of plot(ci) and plot(CI.overall) they appear
> identical, modulo a difference in the range of the plot.
>
> The help page for Cuminc says that: "Cuminc is now simply a wrapper around
> survfit of the survival package with type="mstate", only maintained for
> backward compatibility. The survfit object is kept as attribute
> (attr("survfit")), and the print, plot and summary functions are simply
> print, plot and summary applied to the survfit object."  So it would seem
> that you should be extracting your desired estimates from that  attribute.
>
> >
> > --
> > - Don
> >
> > Donald Catanzaro PhD
> > dgcatanzaro at gmail.com
> > 16144 Sigmond Lane
> > Lowell, AR 72745
> > 479-721-2533
> >
> >       [[alternative HTML version deleted]]
> >
> > ______________________________________________
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> > PLEASE do read the posting guide http://www.R-project.org/
> posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
>
> David Winsemius
> Alameda, CA, USA
>
>


-- 
- Don

Donald Catanzaro PhD
dgcatanzaro at gmail.com
16144 Sigmond Lane
Lowell, AR 72745
479-721-2533

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