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From |
May Boggess <mboggess@stata.com> |

To |
statalist@hsphsun2.harvard.edu |

Subject |
RE: st: Stcurve following stcox, strata |

Date |
07 Apr 2004 10:36:34 -0500 |

On Tuesday, Trey asked how to plot survival curves after a stratified Cox regression. The command -stcurve- can be used for plotting survival and hazard curves after -stcox- and -streg- in most circumstances. But if we have a more complicated model than usual, say we have continuously time-varying covariates, or, as in Trey's case, the model is stratified, we need to generate the survival function and plot it using -twoway- as follows: clear sysuse cancer drop if drug==3 qui stset st,failure(di) sum age gen meanage=age-r(mean) stcox meanage, basesurv(baseline) strata(drug) nolog gen s1=baseline if drug==1 label var s1 "drug=1" gen s2=baseline if drug==2 label var s2 "drug=2" sort _t twoway line s1 _t, connect(stairstep) || /* */ line s2 _t, connect(stairstep) ||, /* */ legend(rows(1)) title("Survival at average age")/* */ xtitle("analysis time") In this example I am plotting the survival curves for each strata. Trey also has a binary covariate and wants to plot the survival curves, for each strata, at each covariate value, as follows: clear sysuse cancer drop if drug==3 set seed 12345 gen x1 =uniform()>0.5 stset studytime,failure(died) sort _t sum age gen meanage=age-r(mean) stcox x1 meanage, strata(drug) basesurv(baseline) nolog gen s1=baseline^exp(_b[x1]*x1) if drug==1 label var s1 "drug=1" gen s2=baseline^exp(_b[x1]*x1) if drug==2 label var s2 "drug=2" twoway line s1 _t, connect(stairstep) || /* */ line s2 _t, connect(stairstep)||, by(x1) There are number of different ways to set out the plot, but the important point to note is that the survival function is different for each strata, so if you just try to plot it for the two values of x1, you don't get the plot you are looking for: clear sysuse cancer drop if drug==3 set seed 12345 gen x1 =uniform()>0.5 stset studytime,failure(died) sort _t sum age gen meanage=age-r(mean) stcox x1 meanage, strata(drug) basesurv(baseline) nolog gen s=baseline^exp(_b[x1]*x1) twoway line s _t, by(x1) If you want to put all four survival functions on one plot, you just break the baseline up into four bits: clear sysuse cancer drop if drug==3 set seed 12345 gen x1 =uniform()>0.5 stset studytime,failure(died) sort _t sum age gen meanage=age-r(mean) stcox x1 meanage, strata(drug) basesurv(baseline) nolog gen s11=baseline^exp(_b[x1]) if drug==1 & x1==1 label var s11 "drug=1, x1=1" gen s21=baseline^exp(_b[x1]) if drug==2 & x1==1 label var s21 "drug=2, x1=1" gen s10=baseline if drug==1 & x1==0 label var s10 "drug=1, x1=0" gen s20=baseline if drug==2 & x1==0 label var s20 "drug=2, x1=0" twoway line s11 _t, connect(stairstep) || /* */ line s21 _t, connect(stairstep)||/* */ line s10 _t, connect(stairstep)||/* */ line s20 _t, connect(stairstep) Lastly, you may be wondering why I created the variable meanage, and used that in the -stcox-, rather than just using age. The baseline survival function is the the survival evaluated with all the covariates set to zero. If the covariate equal to zero is a sensible value for your dataset, then you expect sensible values. But in my example, age=0 was not anywhere near the values in my dataset. The range of age was from 47 to 67. By shifting my age variable, I am protecting myself against numerical problems that sometimes occur when we calculate the baseline at a value way outside the range of the data. To see how I would do the above without this shift: clear sysuse cancer drop if drug==3 set seed 12345 gen x1 =uniform()>0.5 stset studytime,failure(died) sort _t gen copy=age stcox x1 age, strata(drug) basesurv(baseline) nolog sum age replace age=r(mean) predict xb,xb gen t11=baseline^exp(xb) if drug==1 & x1==1 gen t21=baseline^exp(xb) if drug==2 & x1==1 gen t10=baseline^exp(xb) if drug==1 & x1==0 gen t20=baseline^exp(xb) if drug==2 & x1==0 drop baseline xb replace age=copy sum age gen meanage=age-r(mean) stcox x1 meanage, strata(drug) basesurv(baseline) nolog gen s11=baseline^exp(_b[x1]) if drug==1 & x1==1 gen s21=baseline^exp(_b[x1]) if drug==2 & x1==1 gen s10=baseline if drug==1 & x1==0 gen s20=baseline if drug==2 & x1==0 sum t11 s11 sum t21 s21 sum t10 s10 sum t20 s20 -- May mmb@stata.com * * For searches and help try: * http://www.stata.com/support/faqs/res/findit.html * http://www.stata.com/support/statalist/faq * http://www.ats.ucla.edu/stat/stata/

**References**:**RE: st: Stcurve following stcox, strata***From:*Ricardo Ovaldia <ovaldia@yahoo.com>

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