117 lines
3.6 KiB
Plaintext
117 lines
3.6 KiB
Plaintext
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R Under development (unstable) (2024-04-29 r86493) -- "Unsuffered Consequences"
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Copyright (C) 2024 The R Foundation for Statistical Computing
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Platform: aarch64-unknown-linux-gnu
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R is free software and comes with ABSOLUTELY NO WARRANTY.
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You are welcome to redistribute it under certain conditions.
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Type 'license()' or 'licence()' for distribution details.
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R is a collaborative project with many contributors.
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Type 'contributors()' for more information and
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'citation()' on how to cite R or R packages in publications.
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Type 'demo()' for some demos, 'help()' for on-line help, or
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'help.start()' for an HTML browser interface to help.
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Type 'q()' to quit R.
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> #
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> # Make sure that the newdata argument works for various
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> # predictions
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> # We purposely use a subset of the lung data that has only some
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> # of the levels of ph.ecog
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> library(survival)
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> options(na.action=na.exclude, contrasts=c('contr.treatment', 'contr.poly'))
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> aeq <- function(x,y) all.equal(as.vector(x), as.vector(y))
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>
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> myfit <- coxph(Surv(time, status) ~ age + factor(ph.ecog) + strata(sex), lung)
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>
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> keep <- which(lung$inst<13 & (lung$ph.ecog==1 | lung$ph.ecog==2))
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> p1 <- predict(myfit, type='lp')
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> p2 <- predict(myfit, type="lp", newdata=lung[keep,])
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> p3 <- predict(myfit, type='lp', se.fit=TRUE)
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> p4 <- predict(myfit, type="lp", newdata=lung[keep,], se.fit=TRUE)
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> aeq(p1[keep], p2)
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[1] TRUE
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> aeq(p1, p3$fit)
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[1] TRUE
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> aeq(p1[keep], p4$fit)
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[1] TRUE
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> aeq(p3$se.fit[keep], p4$se.fit)
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[1] TRUE
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>
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> p1 <- predict(myfit, type='risk')
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> p2 <- predict(myfit, type="risk", newdata=lung[keep,])
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> p3 <- predict(myfit, type='risk', se.fit=TRUE)
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> p4 <- predict(myfit, type="risk", newdata=lung[keep,], se.fit=TRUE)
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> aeq(p1[keep], p2)
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[1] TRUE
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> aeq(p1, p3$fit)
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[1] TRUE
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> aeq(p1[keep], p4$fit)
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[1] TRUE
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> aeq(p3$se.fit[keep], p4$se.fit)
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[1] TRUE
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>
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> # The all.equal fails for type=expected, Efron approx, and tied death
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> # times due to use of an approximation. See comments in the source code.
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> myfit <- coxph(Surv(time, status) ~ age + factor(ph.ecog) + strata(sex),
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+ data=lung, method='breslow')
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> p1 <- predict(myfit, type='expected')
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> p2 <- predict(myfit, type="expected", newdata=lung[keep,])
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> p3 <- predict(myfit, type='expected', se.fit=TRUE)
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> p4 <- predict(myfit, type="expected", newdata=lung[keep,], se.fit=TRUE)
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> aeq(p1[keep], p2)
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[1] TRUE
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> aeq(p1, p3$fit)
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[1] TRUE
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> aeq(p1[keep], p4$fit)
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[1] TRUE
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> aeq(p3$se.fit[keep], p4$se.fit)
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[1] TRUE
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>
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> p1 <- predict(myfit, type='terms')
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> p2 <- predict(myfit, type="terms",newdata=lung[keep,])
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> p3 <- predict(myfit, type='terms', se.fit=T)
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> p4 <- predict(myfit, type="terms",newdata=lung[keep,], se.fit=T)
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> aeq(p1[keep,], p2)
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[1] TRUE
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> aeq(p1, p3$fit)
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[1] TRUE
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> aeq(p1[keep,], p4$fit)
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[1] TRUE
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> aeq(p3$se.fit[keep,], p4$se.fit)
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[1] TRUE
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>
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> #
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> # Check out the logic whereby predict does not need to
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> # recover the model frame. The first call should not
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> # need to do so, the second should in each case.
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> #
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> myfit <- coxph(Surv(time, status) ~ age + factor(sex), lung, x=T)
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> p1 <- predict(myfit, type='risk', se=T)
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> myfit2 <- coxph(Surv(time, status) ~ age + factor(sex), lung)
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> p2 <- predict(myfit2, type='risk', se=T)
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> aeq(p1$fit, p2$fit)
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[1] TRUE
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> aeq(p1$se, p2$se)
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[1] TRUE
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>
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> p1 <- predict(myfit, type='expected', se=T)
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> p2 <- predict(myfit2, type='expected', se=T)
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> aeq(p1$fit, p2$fit)
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[1] TRUE
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> aeq(p1$se.fit, p2$se.fit)
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[1] TRUE
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>
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> p1 <- predict(myfit, type='terms', se=T)
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> p2 <- predict(myfit2, type='terms', se=T)
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> aeq(p1$fit, p2$fit)
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[1] TRUE
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> aeq(p1$se.fit, p2$se.fit)
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[1] TRUE
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>
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> proc.time()
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user system elapsed
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0.430 0.027 0.455
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