60 lines
2.1 KiB
R
60 lines
2.1 KiB
R
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library(survival)
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options(na.action=na.exclude) # preserve missings
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options(contrasts=c('contr.treatment', 'contr.poly')) #ensure constrast type
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aeq <- function(x, y, ...) all.equal(as.vector(x), as.vector(y), ...)
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#
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# Test out all of the routines on a more complex data set
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#
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temp <- survfit(Surv(time, status) ~ ph.ecog, lung)
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summary(temp, times=c(30*1:11, 365*1:3))
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print(temp[2:3])
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temp <- survfit(Surv(time, status)~1, lung, type='fleming',
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conf.int=.9, conf.type='log-log', error='tsiatis')
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summary(temp, times=30 *1:5)
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temp <- survdiff(Surv(time, status) ~ inst, lung, rho=.5)
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print(temp, digits=6)
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# verify that the zph routine does the actual score test
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dtime <- lung$time[lung$status==2]
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lung2 <- survSplit(Surv(time, status) ~ ., lung, cut=dtime)
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cfit1 <-coxph(Surv(time, status) ~ ph.ecog + ph.karno + pat.karno + wt.loss
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+ sex + age + strata(inst), lung)
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cfit2 <-coxph(Surv(tstart, time, status) ~ ph.ecog + ph.karno + pat.karno +
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wt.loss + sex + age + strata(inst), lung2)
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all.equal(cfit1$loglik, cfit2$loglik)
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all.equal(coef(cfit1), coef(cfit2))
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# the above verifies that the data set is correct
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zp1 <- cox.zph(cfit1, transform="log")
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zp2 <- cox.zph(cfit2, transform="log")
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# everything should match but the call
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icall <- match("Call", names(zp1))
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all.equal(unclass(zp2)[-icall], unclass(zp1)[-icall])
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# now compute score tests one variable at a time
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ncoef <- length(coef(cfit2))
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check <- double(ncoef)
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cname <- names(coef(cfit2))
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for (i in 1:ncoef) {
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temp <- log(lung2$time) * lung2[[cname[i]]]
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# score test for this new variable
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tfit <- coxph(Surv(tstart, time, status) ~ ph.ecog + ph.karno + pat.karno +
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wt.loss + sex + age + strata(inst) +
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temp, lung2, init=c(cfit2$coefficients, 0), iter=0)
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check[i] <- tfit$score
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}
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aeq(check, zp1$table[1:ncoef,1]) # skip the 'global' test
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#
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# Tests of using "."
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#
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fit1 <- coxph(Surv(time, status) ~ . - meal.cal - wt.loss - inst, lung)
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fit2 <- update(fit1, .~. - ph.karno)
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fit3 <- coxph(Surv(time, status) ~ age + sex + ph.ecog + pat.karno, lung)
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all.equal(fit2, fit3)
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