34 lines
1.0 KiB
R
34 lines
1.0 KiB
R
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#
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# Test out anova, with strata terms
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#
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options(na.action=na.omit)
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library(survival)
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fit1 <- coxph(Surv(time, status) ~ ph.ecog + wt.loss + strata(sex) +
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poly(age,3), lung)
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ztemp <- anova(fit1)
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tdata <- na.omit(lung[, c('time', 'status', 'ph.ecog', 'wt.loss', 'sex', 'age')])
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fit2 <- coxph(Surv(time, status)~ ph.ecog + wt.loss + poly(age,3) + strata(sex),
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data=tdata)
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ztemp2 <- anova(fit2)
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all.equal(ztemp, ztemp2)
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fit2 <- coxph(Surv(time, status) ~ ph.ecog + wt.loss + strata(sex), tdata)
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fit3 <- coxph(Surv(time, status) ~ ph.ecog + strata(sex), tdata)
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all.equal(ztemp$loglik, c(fit1$loglik[1], fit3$loglik[2], fit2$loglik[2],
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fit1$loglik[2]))
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all.equal(ztemp$Chisq[-1], 2* diff(ztemp$loglik))
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all.equal(ztemp$Df[-1], c(1,1,3))
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ztemp2 <- anova(fit3, fit2, fit1)
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all.equal(ztemp2$loglik, ztemp$loglik[-1])
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all.equal(ztemp2$Chisq[2:3], ztemp$Chisq[3:4])
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# Change from ztemp2$P; it's a data frame and in R 3.0.2 abbreviated names
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# give a warning
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all.equal(ztemp2[[4]][2:3], ztemp[[4]][3:4])
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