86 lines
2.8 KiB
Plaintext
86 lines
2.8 KiB
Plaintext
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R Under development (unstable) (2024-04-17 r86441) -- "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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> library(survival)
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> #
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> # Check that the survival curves from a Cox model with beta=0
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> # match ordinary survival
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> #
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> # Aalen
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> surv1 <- survfit(Surv(time,status) ~ sex, data=lung, stype=2)
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> fit1 <- coxph(Surv(time, status) ~ age + strata(sex), data=lung, iter=0,
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+ ties='breslow')
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> fit1$var <- 0*fit1$var #sneaky, causes the extra term in the Cox variance
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> # calculation to be zero
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> surv2 <- survfit(fit1, stype=2)
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> surv3 <- survfit(fit1)
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>
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> arglist <- c('n', 'time', 'n.risk','n.event', 'n.censor', 'surv', 'strata',
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+ 'std.err', 'upper', 'lower')
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> all.equal(unclass(surv1)[arglist], unclass(surv2)[arglist])
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[1] TRUE
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> all.equal(unclass(surv1)[arglist], unclass(surv3)[arglist])
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[1] TRUE
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>
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>
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> # Efron method
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> surv1 <- survfit(Surv(time,status) ~ sex, data=lung, stype=2, ctype=2)
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> surv2 <- survfit(fit1, ctype=2)
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> all.equal(unclass(surv1)[arglist], unclass(surv2)[arglist])
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[1] TRUE
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>
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> # Kaplan-Meier
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> surv1 <- survfit(Surv(time,status) ~ sex, data=lung)
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> surv2 <- survfit(fit1, stype=1)
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> all.equal(unclass(surv1)[arglist], unclass(surv2)[arglist])
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[1] TRUE
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>
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>
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> # Now add some random weights
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> rwt <- runif(nrow(lung), .5, 3)
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> surv1 <- survfit(Surv(time,status) ~ sex, data=lung, stype=2, weights=rwt,
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+ robust=FALSE)
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> fit1 <- coxph(Surv(time, status) ~ age + strata(sex), data=lung, iter=0,
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+ ties='breslow', weights=rwt, robust=FALSE)
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> fit1$var <- 0*fit1$var #sneaky
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> surv2 <- survfit(fit1, stype=2, ctype=1)
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> surv3 <- survfit(fit1)
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>
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> all.equal(unclass(surv1)[arglist], unclass(surv2)[arglist])
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[1] TRUE
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> all.equal(unclass(surv1)[arglist], unclass(surv3)[arglist])
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[1] TRUE
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>
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>
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> # Efron method
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> surv1 <- survfit(Surv(time,status) ~ sex, data=lung, stype=2, ctype=2,
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+ weights=rwt, robust=FALSE)
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> surv2 <- survfit(fit1, ctype=2, robust=FALSE)
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> all.equal(unclass(surv1)[arglist], unclass(surv2)[arglist])
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[1] TRUE
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>
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> # Kaplan-Meier
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> surv1 <- survfit(Surv(time,status) ~ sex, data=lung, weights=rwt, robust=FALSE)
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> surv2 <- survfit(fit1, stype=1, robust=FALSE)
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> all.equal(unclass(surv1)[arglist], unclass(surv2)[arglist])
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[1] TRUE
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>
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>
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> proc.time()
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user system elapsed
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0.412 0.023 0.433
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