R help - Sep 2016 - Cumulative Incident Function does not go to end of dataset

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 ?

-- 
- Don

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

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> 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]]
> 
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> 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.
David Winsemius
Alameda, CA, USA

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]]
> >
> > ______________________________________________
> > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> > 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.
>
> David Winsemius
> Alameda, CA, USA
>
>

-- 
- Don

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

	[[alternative HTML version deleted]]