93 lines
3.2 KiB
Plaintext
93 lines
3.2 KiB
Plaintext
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R Under development (unstable) (2019-08-23 r77061) -- "Unsuffered Consequences"
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Copyright (C) 2019 The R Foundation for Statistical Computing
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Platform: x86_64-pc-linux-gnu (64-bit)
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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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> #
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> # Test out the revised model.matrix code
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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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+ z= factor(c('a', 'a', 'b', 'b', 'c', 'c', 'a')),
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+ stringsAsFactors=FALSE)
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>
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> fit1 <- coxph(Surv(time, status) ~ z, test1, iter=1)
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> fit2 <- coxph(Surv(time, status) ~z, test1, x=T, iter=1)
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> all.equal(model.matrix(fit1), fit2$x)
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[1] TRUE
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>
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> # This has no level 'b', make sure dummies recode properly
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> test2 <- data.frame(time= c(9, 3,1,1,6,6,8),
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+ status=c(1,NA,1,0,1,1,0),
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+ x= c(0, 2,1,1,1,0,0),
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+ z= factor(c('a', 'a', 'a', 'a', 'c', 'c', 'a')),
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+ stringsAsFactors=FALSE)
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>
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> ftest <- model.frame(fit1, data=test2)
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> all.equal(levels(ftest$z), levels(test1$z))
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[1] TRUE
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>
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> # xtest will have one more row than the others, since it does not delete
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> # the observation with a missing value for status
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> xtest <- model.matrix(fit1, data=test2)
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> dummy <- fit2$x
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> dummy[,1] <- 0
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> all.equal(xtest[-2,], dummy, check.attributes=FALSE)
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[1] TRUE
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>
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> # The case of a strata by factor interaction
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> # Use iter=0 since there are too many covariates and it won't converge
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> test1$x2 <- factor(rep(1:2, length=7))
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> fit3 <- coxph(Surv(time, status) ~ strata(x2)*z, test1, iter=0)
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> xx <- model.matrix(fit3)
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> all.equal(attr(xx, "assign"), c(2,2,3,3))
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[1] TRUE
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> all.equal(colnames(xx), c("zb", "zc", "strata(x2)2:zb",
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+ "strata(x2)2:zc"))
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[1] TRUE
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> all.equal(attr(xx, "contrasts"),
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+ list("strata(x2)"= "contr.treatment", z="contr.treatment"))
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[1] TRUE
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>
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> fit3b <- coxph(Surv(time, status) ~ strata(x2)*z, test1, iter=0, x=TRUE)
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> all.equal(fit3b$x, xx)
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[1] TRUE
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>
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>
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> # A model with a tt term
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> fit4 <- coxph(Surv(time, status) ~ tt(x) + x, test1, iter=0,
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+ tt = function(x, t, ...) x*t)
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> ff <- model.frame(fit4)
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> # There is 1 subject in the final risk set, 4 at risk at time 6, 6 at time 1
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> # The .strata. variable numbers from last time point to first
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> all.equal(ff$.strata., rep(1:3, c(1, 4,6)))
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[1] TRUE
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> all.equal(ff[["tt(x)"]], ff$x* c(9,6,1)[ff$.strata.])
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[1] TRUE
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>
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> xx <- model.matrix(fit4)
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> all.equal(xx[,1], ff[[2]], check.attributes=FALSE)
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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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0.746 0.041 0.781
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