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From |
Rikke Esberg Kirkfeldt <REKI@svf.au.dk> |

To |
"statalist@hsphsun2.harvard.edu" <statalist@hsphsun2.harvard.edu> |

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

Date |
Mon, 17 Jun 2013 08:46:01 +0000 |

Dear Nick, But of course :-) Thank you! Best regards, Rikke Rikke Kirkfeldt, MD, PhD Department of Cardiology Aarhus University Hospital Denmark ________________________________________ Fra: owner-statalist@hsphsun2.harvard.edu [owner-statalist@hsphsun2.harvard.edu] på vegne af Nick Cox [njcoxstata@gmail.com] Sendt: 17. juni 2013 10:38 Til: statalist@hsphsun2.harvard.edu Emne: Re: st: SV: SV: stcompet and cumulative incidence at a specific point in time Stata version is not the problem here. Make sure that noi table `2' if _t<`1' & _cif_<., c(max _t max _cif_ max _ciflo max _cifhi) format(%04.3f) appears as one logical command line in your program. Nick njcoxstata@gmail.com On 17 June 2013 09:31, Rikke Esberg Kirkfeldt <REKI@svf.au.dk> wrote: > 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? Adam Olszewski > 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. On Mon, Jun 17, 2013 at 3:06 AM, Rikke Esberg Kirkfeldt <REKI@svf.au.dk> 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: owner-statalist@hsphsun2.harvard.edu [owner-statalist@hsphsun2.harvard.edu] på 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] på 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' >> } * * 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/

**References**:**st: stcompet and cumulative incidence at a specific point in time***From:*Enzo Coviello <enzo.coviello@tin.it>

**st: SV: stcompet and cumulative incidence at a specific point in time***From:*Katja Maretty Nielsen <KATJA.MARETTY.NIELSEN@ki.au.dk>

**st: SV: SV: stcompet and cumulative incidence at a specific point in time***From:*Rikke Esberg Kirkfeldt <REKI@svf.au.dk>

**Re: st: SV: SV: stcompet and cumulative incidence at a specific point in time***From:*Adam Olszewski <adam.olszewski@gmail.com>

**SV: st: SV: SV: stcompet and cumulative incidence at a specific point in time***From:*Rikke Esberg Kirkfeldt <REKI@svf.au.dk>

**Re: st: SV: SV: stcompet and cumulative incidence at a specific point in time***From:*Nick Cox <njcoxstata@gmail.com>

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