Marco Barbàra
2010-Jul-17 11:46 UTC
[R] Adjustment for multiple-comparison for log-rank test
DeaR experts, I was asked for a log-rank pairwise survival comparison. I've a straightforward way to do this using the SAS system: http://support.sas.com/documentation/cdl/en/statug/63033/HTML/default/viewer.htm#/documentation/cdl/en/statug/63033/HTML/default/statug_lifetest_sect019.htm What I've found in R is shown below, but it's not a logrank test, I suppose. (The documentation talks about "Tukey pairwise-comparisons"). Is it possible to carry out a "pairwise" logrank test? Am I totally misguided? Thank you very much for help. ################################### R code #################################################> data(pbc) > pbc$stage <- factor(pbc$stage) > (fit <- coxph(Surv(time,status==2)~stage,data=pbc))Call: coxph(formula = Surv(time, status == 2) ~ stage, data = pbc) coef exp(coef) se(coef) z p stage2 1.10 3.01 0.737 1.50 0.13000 stage3 1.53 4.63 0.722 2.12 0.03400 stage4 2.53 12.57 0.717 3.53 0.00041 Likelihood ratio test=65.1 on 3 df, p=4.84e-14 n=412 (6 observations deleted due to missingness)> summary(glht(fit,linfct=mcp(stage="Tukey"),alternative="g"))Simultaneous Tests for General Linear Hypotheses Multiple Comparisons of Means: Tukey Contrasts Fit: coxph(formula = Surv(time, status == 2) ~ stage, data = pbc) Linear Hypotheses: Estimate Std. Error z value Pr(>z) 2 - 1 <= 0 1.1027 0.7374 1.495 0.237 3 - 1 <= 0 1.5318 0.7224 2.120 0.068 . 4 - 1 <= 0 2.5311 0.7168 3.531 <0.001 *** 3 - 2 <= 0 0.4291 0.2544 1.686 0.169 4 - 2 <= 0 1.4284 0.2375 6.013 <0.001 *** 4 - 3 <= 0 0.9994 0.1816 5.502 <0.001 *** --- Signif. codes: 0 ?***? 0.001 ?**? 0.01 ?*? 0.05 ?.? 0.1 ? ? 1 (Adjusted p values reported -- single-step method)