Re: st: intcens: how to estimate mean and variance after intcens

[Yoann Madec <yoann.madec@pasteur.fr>]

Thanks Steve for your messages.

However, I may have to provide some clarifications.

I used :
stset date_deb_periode1, scale(365.25) origin(seroco_d)

1- date_deb_periode1 and seroco_d are dates, and scale(365.25) enables 
results to be expressed in years. But I could easily omit the scale option.

2- All patients experienced the event, this is why failure() does not 
appear in the stset command.

3- The event I am interested in occurs between seroco_d and 
date_deb_periode1, thus the use of interval-censored methods.


In the help document regarding stpm, it is said:
left(leftvar) specifies that some or all of the survival-time 
observations are interval-censored. The rules for specifying
        values of leftvar and their meanings in terms of interval 
censoring are as follows:
        -------------------------------------------------------------------
        Value of leftvar   _d   Meaning
        -------------------------------------------------------------------
        . or _t             0   Right censored at _t
        . or _t             1   Event at _t
        0                   0   Right censored at _t
        0                   1   Interval censored, event in (0,_t]
        <_t                 0   Late entry at leftvar, right censored at _t
        <_t                 1   Interval censored, event in [leftvar,_t]
        -------------------------------------------------------------------

In order to test whether stpm was working ok with simple data, I first 
omitted the left command (as if all events occured at time _t).
That worked ok.

Then I used the left(seroco_d) option. I know that for every patient 
seroco_d is strictly before date_deb_periode1.
Still:
xi: stpm i.gender if num_v==1, stpmdf(6) scale(hazard) left(seroco_d)
i.gender          _Igender_1-2        (naturally coded; _Igender_1 omitted)
seroco_d>_t in some observations

While it is not true that seroco_d is >date_deb_periode1.

I thought that maybe the fact that within the stset, I also used 
seroco_d in the origin() option.
Therfore, I created artificially a new variable simply the mid-point 
between seroco_d and date_deb_periode1, but still have the same problem 
and the same error message.

I hope someone can help.

Yoann






Le 26/10/2012 03:20, Steve Samuels a écrit :
> If the origin of observation is truly seroco_d, your date of left
> censoring, then you do not have left-censored or interval-censored data.
> You have ordinary right-censored data.
>
> In that case, you can use -stpm2- (from SSC), which does not accept
> interval-censored data, but otherwise has some advantages over -stpm-.
>
> I suggest that study the section "Two concepts of time" in of the Manual
> entry for -stset- .
>
>
> Steve
>
>
>
> Steve
>
> On Oct 25, 2012, at 4:43 AM, Yoann Madec wrote:
>
> Thanks steve for your comments, and sorry not to have mention the source of the intcens command.
>
> After reading the help page for stpm, I still do not manage to make it work with interval-censored data.
>
> As a test, I have written:
>
> 	gen date_left_censoring=seroco_d
> 	
> 	stset date_deb_periode1, scale(365.25) origin(seroco_d)
>
> 	failure(hiv_controleur_bis)
>
> In this case, I should have no interval-censored data, but strictly right-censored data.
> However, here is what STATA states:
>
> .         xi: stpm i.gender if num_v==1, stpmdf(6) scale(hazard) left(date_left_censoring)
> i.gender          _Igender_1-2        (naturally coded; _Igender_1 omitted)
> date_left_censoring>_t in some observations
>
>
> I have been trying many things without success.
>
> I hope someone can help.
>
> Best regards,
> Yoann
>
> Le 12/10/2012 19:48, Steve Samuels a écrit :
> > Yoann, The FAQ ask that you state the source of unofficial commands.
> > -intcens- was written by Jamie Griffin and is available from SSC.
> >
> > The usual sample descriptive statistics cannot be calculated for
> > interval-censored data.
> >
> > One approach is to apply Patrick Royston's command -stpm-, also at SSC,
> > which fits flexible distributions. You can estimate survival curves and
> > percentiles of the unconditional as well as covariate-conditional,
> > distributions. You won't get standard errors for the percentiles, but
> > you could -bootstrap- these. Means and SDs can be estimated with a lot
> > more work, but I don't think these are useful descriptive stats for
> > most survival data problems.
> >
> > In fact, I recommend -stpm-, not -intcens- for your main analysis. Some
> > reasons: 1) Both fit parametric models, but -stpm- adapts to the shape
> > of the distribution, saving you the need to select a "best" theoretical
> > distribution. 2) -stpm- has excellent postestimtion options; -intcens-
> > has none. (You can estimate survival curves&   statistics starting with
> > the supplied e(b) matrix, but you must do it by hand.) 3) -stpm- allows
> > coefficients to vary with time (i.e. time-predictor interactions,);
> > -intcens- does not.
> >
> >
> > Steve
> >
> >
> >
> > On Oct 11, 2012, at 12:35 PM, Yoann Madec wrote:
> >
> > Dear Stata users,
> >
> > In order to describe the time to an event I used the command intcens. Indeed, for all my subjects, I know that the event took place within a time-interval, but do not have thje exact date.
> >
> > Using intcens, I vcan test whether some factors influence this time to event.
> >
> > However, I would like to summarize the time to event and provide a confidence interval for this time.
> > I have not been able to fin how to estimate a mean and variance after intcens.
> >
> > i hope that someone will be able to help.
> >
> > Best regards,
> >
> > Yoann
> >
> > *
> > *   For searches and help try:
> > *   http://www.stata.com/help.cgi?search
> > *   http://www.stata.com/support/faqs/resources/statalist-faq/
> > *   http://www.ats.ucla.edu/stat/stata/
> >
> >
> > *
> > *   For searches and help try:
> > *   http://www.stata.com/help.cgi?search
> > *   http://www.stata.com/support/faqs/resources/statalist-faq/
> > *   http://www.ats.ucla.edu/stat/stata/
*
*   For searches and help try:
*   http://www.stata.com/help.cgi?search
*   http://www.stata.com/support/faqs/resources/statalist-faq/
*   http://www.ats.ucla.edu/stat/stata/