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st: SV: SV: stcompet and cumulative incidence at a specific point in time


From   Rikke Esberg Kirkfeldt <REKI@svf.au.dk>
To   "statalist@hsphsun2.harvard.edu" <statalist@hsphsun2.harvard.edu>
Subject   st: SV: SV: stcompet and cumulative incidence at a specific point in time
Date   Mon, 17 Jun 2013 07:06:04 +0000

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: owner-statalist@hsphsun2.harvard.edu [owner-statalist@hsphsun2.harvard.edu] p&#229; vegne af Katja Maretty Nielsen [KATJA.MARETTY.NIELSEN@ki.au.dk]
Sendt: 16. juni 2013 08:42
Til: statalist@hsphsun2.harvard.edu
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: katja.maretty.nielsen@ki.au.dk
________________________________________
Fra: owner-statalist@hsphsun2.harvard.edu [owner-statalist@hsphsun2.harvard.edu] p&#229; vegne af Enzo Coviello [enzo.coviello@tin.it]
Sendt: 16. juni 2013 08:14
Til: statalist@hsphsun2.harvard.edu
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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