KM estimation for interval censoring?

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KM estimation for interval censoring?

gallon li
Does anybody know if there is such a function to estimate the distribution
for interval censored data?

survfit doesn't work for this type of data as I tried various references.

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Re: KM estimation for interval censoring?

David Winsemius
"gallon li" <[hidden email]> wrote in
news:[hidden email]:

> Does anybody know if there is such a function to estimate the
> distribution for interval censored data?
>
> survfit doesn't work for this type of data as I tried various
> references.

My reading of R-help posts by Therneau and Lumley is that interval
censoring is only available for parametric estimates in the survival
package.

It's not KM, but perhaps this will be of interest:

"Turnbull's Nonparametric Estimator for Interval-Censored Data"
Suely Ruiz Giolo

<http://www.est.ufpr.br/rt/suely04a.pdf>

Giolo cites KLEIN, J. P, MOESCHBERGER, M. Survival Analysis. New York:
Springer Verlag, 1997, for the algorithm.

This MIT-CSAIL report says they have an available R package that handles
interval censoring and time-dependent covariates:

http://dspace.mit.edu/bitstream/1721.1/33957/1/MIT-CSAIL-TR-2006-055.pdf

--
David Winsemius

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Re: KM estimation for interval censoring?

Robert Gentleman
The Icens package implements a number of different estimation paradigms.
Briefly, for interval censored data, the KM does not apply, but
Turnbull's method does. Relevant citations for Icens are in it.

For a Cox model approach, there was at one time a package, not at CRAN,
by Commenges (and a Biometrics paper, I believe), Google suggests that
Dr. Commenges is pretty active in this area.


David Winsemius wrote:

> "gallon li" <[hidden email]> wrote in
> news:[hidden email]:
>
>> Does anybody know if there is such a function to estimate the
>> distribution for interval censored data?
>>
>> survfit doesn't work for this type of data as I tried various
>> references.
>
> My reading of R-help posts by Therneau and Lumley is that interval
> censoring is only available for parametric estimates in the survival
> package.
>
> It's not KM, but perhaps this will be of interest:
>
> "Turnbull's Nonparametric Estimator for Interval-Censored Data"
> Suely Ruiz Giolo
>
> <http://www.est.ufpr.br/rt/suely04a.pdf>
>
> Giolo cites KLEIN, J. P, MOESCHBERGER, M. Survival Analysis. New York:
> Springer Verlag, 1997, for the algorithm.
>
> This MIT-CSAIL report says they have an available R package that handles
> interval censoring and time-dependent covariates:
>
> http://dspace.mit.edu/bitstream/1721.1/33957/1/MIT-CSAIL-TR-2006-055.pdf
>

--
Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
206-667-7700
[hidden email]

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Re: KM estimation for interval censoring?

Martin Maechler
>>>>> "RobG" == Robert Gentleman <[hidden email]>
>>>>>     on Mon, 28 Jan 2008 08:18:06 -0800 writes:

    RobG> The Icens package implements a number of different estimation paradigms.
    RobG> Briefly, for interval censored data, the KM does not apply, but
    RobG> Turnbull's method does. Relevant citations for Icens are in it.

    RobG> For a Cox model approach, there was at one time a package, not at CRAN,
    RobG> by Commenges (and a Biometrics paper, I believe), Google suggests that
    RobG> Dr. Commenges is pretty active in this area.

Further, Marloes Maathuis is active in this field, too.
Her (CRAN) R package is  'MLEcens'
which computes the (nonparametric!) MLE for (bivariate or univariate)
interval censored data, which -- I think -- is what the
KM estimator is for the one-sided censoring.

Martin Maechler, ETH Zurich


    RobG> David Winsemius wrote:
    >> "gallon li" <[hidden email]> wrote in
    >> news:[hidden email]:
    >>
    >>> Does anybody know if there is such a function to estimate the
    >>> distribution for interval censored data?
    >>>
    >>> survfit doesn't work for this type of data as I tried various
    >>> references.
    >>
    >> My reading of R-help posts by Therneau and Lumley is that interval
    >> censoring is only available for parametric estimates in the survival
    >> package.
    >>
    >> It's not KM, but perhaps this will be of interest:
    >>
    >> "Turnbull's Nonparametric Estimator for Interval-Censored Data"
    >> Suely Ruiz Giolo
    >>
    >> <http://www.est.ufpr.br/rt/suely04a.pdf>
    >>
    >> Giolo cites KLEIN, J. P, MOESCHBERGER, M. Survival Analysis. New York:
    >> Springer Verlag, 1997, for the algorithm.
    >>
    >> This MIT-CSAIL report says they have an available R package that handles
    >> interval censoring and time-dependent covariates:
    >>
    >> http://dspace.mit.edu/bitstream/1721.1/33957/1/MIT-CSAIL-TR-2006-055.pdf
    >>

    RobG> --
    RobG> Robert Gentleman, PhD
    RobG> Program in Computational Biology
    RobG> Division of Public Health Sciences
    RobG> Fred Hutchinson Cancer Research Center
    RobG> 1100 Fairview Ave. N, M2-B876
    RobG> PO Box 19024
    RobG> Seattle, Washington 98109-1024
    RobG> 206-667-7700
    RobG> [hidden email]

    RobG> ______________________________________________
    RobG> [hidden email] mailing list
    RobG> https://stat.ethz.ch/mailman/listinfo/r-help
    RobG> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
    RobG> and provide commented, minimal, self-contained, reproducible code.

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