65 lines
2.2 KiB
R
65 lines
2.2 KiB
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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# 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$flag, c(2,0,0,0,0))
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aeq(fit1$overlap$row, 3:4)
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aeq(fit1$overlap$id, 2)
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aeq(fit1$transitions[1,], c(2,1,1,1))
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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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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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aeq(fit2$flag , c(1,2,0,0,0))
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aeq(fit2$transition, rbind(c(3,0,0,0), c(0,2,1,0), c(0,0,0,1), 0))
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(fit2$overlap$id == 'B')
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(fit2$overlap$row ==5)
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all(fit2$gap$id == c("B", "C"))
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aeq(fit2$gap$row, c(6,8))
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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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# 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$flag , c(1,1,0,0,0))
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aeq(fit2b$transition, rbind(c(3,0,0), c(0,2,1), 0,0))
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(fit2b$overlap$id == 'B')
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(fit2b$overlap$row ==5)
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all(fit2b$gap$id == "C")
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aeq(fit2b$gap$row, 8)
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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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aeq(fit3$flag, c(1, 1, 1, 2, 0))
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aeq(fit3$transitions, rbind(c(3,0,0,0), 0, c(0,2,1,1), 0))
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all.equal(fit3$overlap, fit2$overlap)
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all(fit3$teleport$id == c("A", "C"))
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all(fit3$teleport$row == c(3,9))
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all(fit3$jump$id == "C")
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all(fit3$jump$row == 8)
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all.equal(fit3$gap, list(row=6L, id= "B"))
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