79 lines
2.8 KiB
Plaintext
79 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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> 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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> library(survival)
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>
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> # Create a "counting process" version of the simplest test data set
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> #
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> test1 <- data.frame(time= c(9, 3,1,1,6,6,8),
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+ status=c(1,NA,1,0,1,1,0),
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+ x= c(0, 2,1,1,1,0,0))
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>
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> test1b<- list(start= c(0, 3, 0, 0, 5, 0, 6,14, 0, 0, 10,20,30, 0),
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+ stop = c(3,10, 10, 5,20, 6,14,20, 30, 10,20,30,40, 10),
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+ status=c(0, 1, 0, 0, 1, 0, 0, 1, 0, 0, 0, 0, 1, 0),
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+ x= c(1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, NA),
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+ id = c(3, 3, 4, 5, 5, 6, 6, 6, 7, 1, 1, 1, 1, 2))
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>
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> aeq <- function(x,y) all.equal(as.vector(x), as.vector(y))
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> #
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> # Check out the various residuals under an Efron approximation
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> #
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> fit0 <- coxph(Surv(time, status)~ x, test1, iter=0)
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> fit <- coxph(Surv(time, status) ~x, test1)
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> fit0b <- coxph(Surv(start, stop, status) ~ x, test1b, iter=0)
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> fitb <- coxph(Surv(start, stop, status) ~x, test1b)
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> fitc <- coxph(Surv(time, status) ~ offset(fit$coefficients*x), test1)
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> fitd <- coxph(Surv(start, stop, status) ~ offset(fit$coefficients*x), test1b)
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>
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> aeq(fit0b$coefficients, fit0$coefficients)
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[1] TRUE
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>
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> aeq(resid(fit0), resid(fit0b, collapse=test1b$id))
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[1] TRUE
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> aeq(resid(fit), resid(fitb, collapse=test1b$id))
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[1] TRUE
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> aeq(resid(fitc), resid(fitd, collapse=test1b$id))
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[1] TRUE
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> aeq(resid(fitc), resid(fit))
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[1] TRUE
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>
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> aeq(resid(fit0, type='score'), resid(fit0b, type='score', collapse=test1b$id))
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[1] TRUE
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> aeq(resid(fit, type='score'), resid(fitb, type='score', collapse=test1b$id))
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[1] TRUE
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>
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> aeq(resid(fit0, type='scho'), resid(fit0b, type='scho', collapse=test1b$id))
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[1] TRUE
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> aeq(resid(fit, type='scho'), resid(fitb, type='scho', collapse=test1b$id))
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[1] TRUE
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>
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> # The two survivals will have different censoring times
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> # nrisk, nevent, surv, and std should be the same
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> temp1 <- survfit(fit, list(x=1), censor=FALSE)
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> temp2 <- survfit(fitb, list(x=1), censor=FALSE)
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> all.equal(unclass(temp1)[c(3,4,6,8)], unclass(temp2)[c(3,4,6,8)])
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[1] TRUE
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>
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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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0.436 0.012 0.445
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