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SV: st: SV: SV: stcompet and cumulative incidence at a specific point in time
From
Rikke Esberg Kirkfeldt <[email protected]>
To
"[email protected]" <[email protected]>
Subject
SV: st: SV: SV: stcompet and cumulative incidence at a specific point in time
Date
Mon, 17 Jun 2013 08:31:58 +0000
Dear Adam,
Thank you for the program.
Unfortunately, I only have Stata v.11.2, so I had to change the command a bit, and it now reads:
program define ciflist
version 11.2
syntax anything [if]
capture drop _cif*
stcompet _cif_ = ci _cifhi = hi _ciflo = lo `if', compet1(2)
noi table `2' if _t<`1' & _cif_<., c(max _t max _cif_ max _ciflo max
_cifhi) format(%04.3f)
end
When I run the -ciflist 5 outcom- the following happens:
ciflist 5 outcome
) required
r(100);
I've tried to include a -)- that doesn't help. Maybe the Stata version is the problem?
Sincerely,
Rikke
Rikke Kirkfeldt, MD, PhD
Department of Cardiology
Aarhus University Hospital
Denmark
________________________________________
Fra: [email protected] [[email protected]] på vegne af Adam Olszewski [[email protected]]
Sendt: 17. juni 2013 09:28
Til: [email protected]
Emne: Re: st: SV: SV: stcompet and cumulative incidence at a specific point in time
Hi,
You can also use this short program to list the basic CIF and 95% CI:
program define ciflist
version 12.1
syntax anything [if]
capture drop _cif*
stcompet _cif_ = ci _cifhi = hi _ciflo = lo `if', compet1(2)
noi table `2' if _t<`1' & _cif_<., c(max _t max _cif_ max _ciflo max
_cifhi) format(%04.3f)
end
Then you can type e.g.
-ciflist 5 cevent-
where "cevent" is your fail-event variable and 5 is the time you want
the point estimate for. This assumes that value 1 is your event of
interest and value 2 is a competing event.
The downside is that you have to wait for a new stcompet run each
time, but of course you could modify it to run just once.
AO
On Mon, Jun 17, 2013 at 3:06 AM, Rikke Esberg Kirkfeldt <[email protected]> wrote:
> Dear Katja and Enzo,
>
> Thank you so much for your replies.
>
> Katja, indeed the pseudo value approach would be appropriate. However, we plan to use the cumulative incidence curves, and all I wanted was a relatively precise way of estimating the cumulative incidence from the curves generated after stcompet. And I believe, Enzo, that your solution does just that.
>
> Would it be correct to replace –ci- with –lo- and –hi- in order to estimate the confidence intervals, like this?
>
> . stset survtime, failure(outcome==1)
>
> failure event: outcome == 1
> obs. time interval: (0, survtime]
> exit on or before: failure
>
> ------------------------------------------------------------------------------
> 1415 total obs.
> 0 exclusions
> ------------------------------------------------------------------------------
> 1415 obs. remaining, representing
> 247 failures in single record/single failure data
> 6708.504 total analysis time at risk, at risk from t = 0
> earliest observed entry t = 0
> last observed exit t = 10.58179
>
> . stcompet ci=ci hi=hi lo=lo, compet1(2)
>
> . forval i = 1(1)5 {
> 2. qui su _t if _t<=`i'
> 3. local tobs = `r(max)'
> 4. qui su ci if _t<=`i'
> 5. local ciat = `r(max)'
> 6. if `i'==10 di _col(5) "at" _col(18) "Obs Time" _col(33) "Cum Inc"
> 7. di _col(5) `i' _col(20) `tobs' _col(35) `ciat'
> 8. }
> 1 .99657768 .04452297
> 2 1.9986311 .0864664
> 3 2.9952087 .11046968
> 4 3.9972622 .14158537
> 5 4.9993157 .17513161
>
> .
> . forval i = 1(1)5 {
> 2. qui su _t if _t<=`i'
> 3. local tobs = `r(max)'
> 4. qui su lo if _t<=`i'
> 5. local ciat = `r(max)'
> 6. if `i'==10 di _col(5) "at" _col(18) "Obs Time" _col(33) "Cum Inc"
> 7. di _col(5) `i' _col(20) `tobs' _col(35) `ciat'
> 8. }
> 1 .99657768 .03464053
> 2 1.9986311 .07253825
> 3 2.9952087 .09467253
> 4 3.9972622 .12335587
> 5 4.9993157 .15447509
>
> . forval i = 1(1)5 {
> 2. qui su _t if _t<=`i'
> 3. local tobs = `r(max)'
> 4. qui su hi if _t<=`i'
> 5. local ciat = `r(max)'
> 6. if `i'==10 di _col(5) "at" _col(18) "Obs Time" _col(33) "Cum Inc"
> 7. di _col(5) `i' _col(20) `tobs' _col(35) `ciat'
> 8. }
> 1 .99657768 .05616275
> 2 1.9986311 .10186408
> 3 2.9952087 .12760713
> 4 3.9972622 .16104027
> 5 4.9993157 .1968829
>
> Best regards,
>
> Rikke Kirkfeldt, MD, PhD
> Department of Cardiology
> Aarhus University Hospital
> Denmark
>
> ________________________________________
> Fra: [email protected] [[email protected]] på vegne af Katja Maretty Nielsen [[email protected]]
> Sendt: 16. juni 2013 08:42
> Til: [email protected]
> Emne: st: SV: stcompet and cumulative incidence at a specific point in time
>
> Dear Enzo.
>
> I've encountered the same problem, but was advised to use the psudovalue approach with the -stpci-, were you generate pseudo values at the time you are interested in:
>
> gen cevent=(dssstatus==2)
> label variable cevent "competing risk event"
> stpci cevent, at(1 2 3 4 5)
> glm pseudo1, fam(gauss) link(id) vce(robust)
> glm pseudo2, fam(gauss) link(id) vce(robust)
> glm pseudo3, fam(gauss) link(id) vce(robust)
> glm pseudo4, fam(gauss) link(id) vce(robust)
> glm pseudo5, fam(gauss) link(id) vce(robust)
>
> Hope this helps.
>
> Best regards
>
> Katja Maretty Nielsen
>
> MD, Phd-student
> Dept. of Experimental Clinical Oncology
> Aarhus University Hospital
> Noerrebrogade 44, building 5
> DK- 8000 Aarhus C
> Tel.: +45 78462621 / 50904640
> Mail: [email protected]
> ________________________________________
> Fra: [email protected] [[email protected]] på vegne af Enzo Coviello [[email protected]]
> Sendt: 16. juni 2013 08:14
> Til: [email protected]
> Emne: st: stcompet and cumulative incidence at a specific point in time
>
> Hi All,
>
> Is there a Stata command that can be used to list (at specific time
> points e.g. -sts list, at (0 (1) 5)-)
> the cumulative incidence function with confidence intervals from a
> competing risk analysis (after the –stcompet- command)?
>
>
> As far as I know there is not a command.
> The following code should approximately obtain what you need supposing
> that the -ci- is the name of the variable containing the cumulative
> incidence:
>
> forval i = 1(1)5 {
> qui su _t if _t<=`i'
> local tobs = `r(max)'
> qui su ci if _t<=`i'
> local ciat = `r(max)'
> if `i'==10 di _col(5) "at" _col(18) "Obs Time" _col(33) "Cum Inc"
> di _col(5) `i' _col(20) `tobs' _col(35) `ciat'
> }
>
> Best
>
> Enzo
>
> --
> Enzo Coviello
> Epidemiology Unit - Cancer Registry ASL BT
> Piazza Umberto 1
> 76121 BARLETTA (BT)
> Italy
> mobile +39 347 5016016
> tel +39 0883 577329
> fax +39 0883 577288
> Home +39 0883 695055
>
>
> --
> Enzo Coviello
> Epidemiology Unit - Cancer Registry ASL BT
> Piazza Umberto 1
> 76121 BARLETTA (BT)
> Italy
> mobile +39 347 5016016
> tel +39 0883 577329
> fax +39 0883 577288
> Home +39 0883 695055
> *
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