94 lines
3.2 KiB
Plaintext
94 lines
3.2 KiB
Plaintext
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R Under development (unstable) (2019-07-02 r76765) -- "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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> #
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> library(survival)
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>
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> # Some simple tests of the Surv function
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> # The first two are motivated by a bug, pointed out by Kevin Buhr,
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> # where a mixture of NAs and invalid values didn't work right
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> # Even for the simplest things a test case is good.
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> # All but the third should produce warning messages
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> aeq <- function(x,y) all.equal(as.vector(x), as.vector(y))
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> temp <- Surv(c(1, 10, 20, 30), c(2, NA, 0, 40), c(1,1,1,1))
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Warning message:
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In Surv(c(1, 10, 20, 30), c(2, NA, 0, 40), c(1, 1, 1, 1)) :
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Stop time must be > start time, NA created
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> aeq(temp, c(1,10,NA,30, 2,NA,0,40, 1,1,1,1))
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[1] TRUE
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>
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> temp <- Surv(c(1, 10, 20, 30), c(2, NA, 0, 40), type='interval2')
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Warning message:
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In Surv(c(1, 10, 20, 30), c(2, NA, 0, 40), type = "interval2") :
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Invalid interval: start > stop, NA created
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> aeq(temp, c(1,10,20,30, 2,1,1,40, 3,0,NA,3))
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[1] TRUE
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>
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> #No error
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> temp <- Surv(1:5)
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> aeq(temp, c(1:5, 1,1,1,1,1))
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[1] TRUE
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>
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> temp1 <- Surv(c(1,10,NA, 30, 30), c(1,NA,10,20, 40), type='interval2')
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Warning message:
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In Surv(c(1, 10, NA, 30, 30), c(1, NA, 10, 20, 40), type = "interval2") :
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Invalid interval: start > stop, NA created
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> temp2 <- Surv(c(1,10,10,30,30), c(9, NA, 5, 20,40), c(1, 0, 2,3,3),
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+ type='interval')
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Warning message:
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In Surv(c(1, 10, 10, 30, 30), c(9, NA, 5, 20, 40), c(1, 0, 2, 3, :
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Invalid interval: start > stop, NA created
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> aeq(temp1, temp2)
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[1] TRUE
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> aeq(temp1, c(1,10,10,30,30, 1,1,1,1, 40, 1,0,2,NA,3))
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[1] TRUE
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>
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> # Use of inf
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> temp1 <- Surv(c(1,10,NA, 30, 30), c(1,NA,10,30, 40), type='interval2')
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> temp2 <- Surv(c(1,10,-Inf, 30, 30), c(1,Inf,10,30, 40), type='interval2')
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> aeq(temp1, temp2)
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[1] TRUE
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>
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> # Verify sorting and order routines
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> # These fail in 3.4, succeed in 3.5 due to a system change in how
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> # xtfrm.Surv is used.
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> x1 <- Surv(c(4, 6, 3, 2, 1, NA, 2), c(1,0, NA, 0,1,1,1))
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> all.equal(order(x1), c(5,7, 4, 1, 2, 3, 6))
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[1] TRUE
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> all.equal(order(x1, decreasing=TRUE), c(2,1,4,7,5, 3, 6))
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[1] TRUE
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> all.equal(sort(x1), x1[c(5,7,4,1,2)])
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[1] TRUE
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>
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> x2 <- Surv(c(4, 6, 3, 2, 1, NA, 2), c(1,0, NA, 0,1,1,1), type='left')
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> all.equal(order(x2), c(5,4, 7, 1, 2, 3, 6))
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[1] TRUE
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>
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> x3 <- Surv(c(1,5,NA,7, 9), c(6, 6, 4, NA, 9), type="interval2")
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> all.equal(sort(x3), x3[c(1,3,2,4,5)])
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[1] TRUE
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>
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> x4 <- Surv(c(1,5,6,5,2, 4), c(3, 7, 7, 6, 3, NA), factor(c(1, 2, 0, 1, 1, 0)))
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> all.equal(sort(x4), x4[c(1, 5, 4, 2,3)])
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[1] TRUE
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> all.equal(sort(x4, na.last=FALSE), x4[c(6,1,5,4,2,3)])
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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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0.738 0.033 0.764
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