R Under development (unstable) (2024-12-13 r87441 ucrt) -- "Unsuffered Consequences"
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> #
> # Test out anova, with strata terms
> #
> options(na.action=na.omit)
> library(survival)
> 
> fit1 <- coxph(Surv(time, status) ~ ph.ecog + wt.loss + strata(sex) + 
+               poly(age,3), lung)
> ztemp <- anova(fit1)
> 
> tdata <- na.omit(lung[, c('time', 'status', 'ph.ecog', 'wt.loss', 'sex', 'age')])
> fit2 <- coxph(Surv(time, status)~ ph.ecog + wt.loss + poly(age,3) + strata(sex),
+               data=tdata)
> ztemp2 <- anova(fit2)
> all.equal(ztemp, ztemp2)
[1] TRUE
> 
> 
> fit2 <-  coxph(Surv(time, status) ~ ph.ecog + wt.loss + strata(sex), tdata)
> fit3 <-  coxph(Surv(time, status) ~ ph.ecog + strata(sex), tdata)
> 
> all.equal(ztemp$loglik, c(fit1$loglik[1], fit3$loglik[2], fit2$loglik[2],
+                          fit1$loglik[2]))
[1] TRUE
> all.equal(ztemp$Chisq[-1], 2* diff(ztemp$loglik))
[1] TRUE
> all.equal(ztemp$Df[-1], c(1,1,3))
[1] TRUE
> 
> ztemp2 <- anova(fit3, fit2, fit1)
> all.equal(ztemp2$loglik, ztemp$loglik[-1])
[1] TRUE
> all.equal(ztemp2$Chisq[2:3], ztemp$Chisq[3:4])
[1] TRUE
> # Change from ztemp2$P; it's a data frame and in R 3.0.2 abbreviated names
> #   give a warning
> all.equal(ztemp2[[4]][2:3], ztemp[[4]][3:4])
[1] TRUE
> 
> 
> 
> proc.time()
   user  system elapsed 
   0.85    0.04    0.90