111 lines
3.2 KiB
Plaintext
111 lines
3.2 KiB
Plaintext
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R Under development (unstable) (2020-03-27 r78086) -- "Unsuffered Consequences"
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Copyright (C) 2020 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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> library(survival)
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> aeq <- function(x, y, ...) all.equal(as.vector(x), as.vector(y), ...)
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>
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> # dummy data 1, simple survival
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> data1 <- data.frame(id=c(1,2,2,2,3,4), time=c(10, 20, 25, 30, 30, 10),
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+ status=factor(c(0,0,1,1, 2,3)))
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> fit1 <- survcheck(Surv(time, status) ~ 1, data1, id=id)
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> aeq(fit1$flag, c(2,0,0,0,0))
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[1] TRUE
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> aeq(fit1$overlap$row, 3:4)
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[1] TRUE
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> aeq(fit1$overlap$id, 2)
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[1] TRUE
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> aeq(fit1$transitions[1,], c(2,1,1,1))
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[1] TRUE
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>
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>
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> # dummy data 2, no initial values, start stop data
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> # A: (0, 10, 0), (10, 20, 1), (20, 30, 2) # no issues
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> # B: (0, 20, 1), (15, 24, 2), (25,26, 0)
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> # C: (10,13, 1), (15, 18, 0), (18,25,3)
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>
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> data2 <- data.frame(id=rep(LETTERS[1:3], each=3),
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+ t1 = c(0, 10, 20, 0, 15,25, 10, 15, 18),
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+ t2 = c(10, 20,30, 20, 24, 26, 13, 18, 25),
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+ status= factor(c(0, 1, 2, 1,2, 0, 1, 0, 3)),
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+ x = c(1:5, NA, 7:9),
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+ stringsAsFactors = FALSE)
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> fit2 <- survcheck(Surv(t1, t2, status) ~ 1, data2, id=id)
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>
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> aeq(fit2$flag , c(1,2,0,0,0))
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[1] TRUE
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> aeq(fit2$transition, rbind(c(3,0,0,0), c(0,2,1,0), c(0,0,0,1), 0))
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[1] TRUE
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> (fit2$overlap$id == 'B')
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[1] TRUE
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> (fit2$overlap$row ==5)
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[1] TRUE
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> all(fit2$gap$id == c("B", "C"))
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[1] TRUE
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> aeq(fit2$gap$row, c(6,8))
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[1] TRUE
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>
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> # scramble
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> reord <- c(9,2,1,4,3,5,6,8,7)
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> tfit <- survcheck(Surv(t1, t2, status) ~ 1, data2[reord,], id=id)
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> all.equal(fit2[1:4], tfit[1:4])
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[1] TRUE
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>
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> # let a missing value in
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> fit2b <- survcheck(Surv(t1, t2, status) ~ x, data2, id=id)
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> aeq(fit2b$flag , c(1,1,0,0,0))
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[1] TRUE
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> aeq(fit2b$transition, rbind(c(3,0,0), c(0,2,1), 0,0))
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[1] TRUE
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> (fit2b$overlap$id == 'B')
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[1] TRUE
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> (fit2b$overlap$row ==5)
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[1] TRUE
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> all(fit2b$gap$id == "C")
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[1] TRUE
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> aeq(fit2b$gap$row, 8)
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[1] TRUE
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>
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> # designed to trigger all 4 error types
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> data3 <- data2
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> levels(data3$status) <- c("cens", "mgus", "recur", "death")
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> data3$istate <- c("entry", "entry", "recur", "entry", "recur", "recur",
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+ "entry", "recur", "recur")
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> fit3 <- survcheck(Surv(t1, t2, status) ~ 1, data3, id=id, istate=istate)
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>
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> aeq(fit3$flag, c(1, 1, 1, 2, 0))
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[1] TRUE
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> aeq(fit3$transitions, rbind(c(3,0,0,0), 0, c(0,2,1,1), 0))
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[1] TRUE
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> all.equal(fit3$overlap, fit2$overlap)
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[1] TRUE
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> all(fit3$teleport$id == c("A", "C"))
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[1] TRUE
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> all(fit3$teleport$row == c(3,9))
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[1] TRUE
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> all(fit3$jump$id == "C")
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[1] TRUE
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> all(fit3$jump$row == 8)
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[1] TRUE
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> all.equal(fit3$gap, list(row=6L, id= "B"))
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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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0.879 0.044 0.914
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