57 lines
1.8 KiB
Plaintext
57 lines
1.8 KiB
Plaintext
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R version 2.14.0 (2011-10-31)
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Copyright (C) 2011 The R Foundation for Statistical Computing
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ISBN 3-900051-07-0
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Platform: i686-pc-linux-gnu (32-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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> #
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> # Ensure that factors work in prediction
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> #
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> library(survival)
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Loading required package: splines
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>
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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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> tfit <- coxph(Surv(time, status) ~ age + factor(ph.ecog), lung)
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> p1 <- predict(tfit, type='risk')
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>
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> # Testing NA handling is important too
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> keep <- (is.na(lung$ph.ecog) | lung$ph.ecog !=1)
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> lung2 <- lung[keep,]
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> p2 <- predict(tfit, type='risk', newdata=lung[keep,])
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> aeq(p1[keep], p2)
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[1] TRUE
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>
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> # Same, for survreg
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> tfit <- survreg(Surv(time, status) ~ age + factor(ph.ecog), lung)
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> p1 <- predict(tfit, type='response')
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> p2 <- predict(tfit, type='response', newdata=lung2)
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> aeq(p1[keep], p2)
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[1] TRUE
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>
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>
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> # Now repeat it tossing the missings
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> options(na.action=na.omit)
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> keep2 <- (lung$ph.ecog[!is.na(lung$ph.ecog)] !=1)
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>
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> tfit2 <- survreg(Surv(time, status) ~ age + factor(ph.ecog), lung)
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> p3 <- predict(tfit2, type='response')
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> p4 <- predict(tfit2, type='response', newdata=lung2, na.action=na.omit)
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> aeq(p3[keep2] , p4)
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[1] TRUE
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>
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