R Under development (unstable) (2024-12-13 r87441 ucrt) -- "Unsuffered Consequences"
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> library(survival)
> aeq <- function(x, y, ...) all.equal(as.vector(x), as.vector(y), ...)
> 
> # dummy data 1, simple survival
> data1 <- data.frame(id=c(1,2,2,2,3,4), time=c(10, 20, 25, 30, 30, 10),
+                     status=factor(c(0,0,1,1, 2,3)))
> fit1 <- survcheck(Surv(time, status) ~ 1, data1, id=id)
> aeq(fit1$flag, c(2,0,0,0,0))
[1] TRUE
> aeq(fit1$overlap$row, 3:4)
[1] TRUE
> aeq(fit1$overlap$id, 2)
[1] TRUE
> aeq(fit1$transitions[1,], c(2,1,1,1))
[1] TRUE
> 
> 
> # dummy data 2, no initial values, start stop data
> # A: (0, 10, 0), (10, 20, 1), (20, 30, 2)   # no issues
> # B: (0, 20, 1), (15, 24, 2), (25,26, 0)
> # C: (10,13, 1), (15, 18, 0), (18,25,3)
> 
> data2 <- data.frame(id=rep(LETTERS[1:3], each=3),
+                     t1 = c(0, 10, 20, 0, 15,25, 10, 15, 18),
+                     t2 = c(10, 20,30, 20, 24, 26, 13, 18, 25),
+                     status= factor(c(0, 1, 2, 1,2, 0, 1, 0, 3)),
+                     x = c(1:5, NA, 7:9),
+                     stringsAsFactors = FALSE)
> fit2 <- survcheck(Surv(t1, t2, status) ~ 1, data2, id=id)
> 
> aeq(fit2$flag , c(1,2,0,0,0))
[1] TRUE
> aeq(fit2$transition, rbind(c(3,0,0,0), c(0,2,1,0), c(0,0,0,1), 0))
[1] TRUE
> (fit2$overlap$id == 'B')
[1] TRUE
> (fit2$overlap$row ==5)
[1] TRUE
> all(fit2$gap$id == c("B", "C"))
[1] TRUE
> aeq(fit2$gap$row, c(6,8))
[1] TRUE
> 
> # scramble
> reord <- c(9,2,1,4,3,5,6,8,7) 
> tfit <- survcheck(Surv(t1, t2, status) ~ 1, data2[reord,], id=id)
> all.equal(fit2[1:4], tfit[1:4])   
[1] TRUE
> 
> # let a missing value in
> fit2b <- survcheck(Surv(t1, t2, status) ~ x, data2, id=id)
> aeq(fit2b$flag , c(1,1,0,0,0))
[1] TRUE
> aeq(fit2b$transition, rbind(c(3,0,0), c(0,2,1), 0,0))
[1] TRUE
> (fit2b$overlap$id == 'B')
[1] TRUE
> (fit2b$overlap$row ==5)
[1] TRUE
> all(fit2b$gap$id == "C")
[1] TRUE
> aeq(fit2b$gap$row, 8)
[1] TRUE
> 
> # designed to trigger all 4 error types
> data3 <- data2
> levels(data3$status) <- c("cens", "mgus", "recur", "death")
> data3$istate <- c("entry", "entry", "recur",  "entry", "recur", "recur",
+                   "entry", "recur", "recur")
> fit3 <- survcheck(Surv(t1, t2, status) ~ 1, data3, id=id, istate=istate)
> 
> aeq(fit3$flag, c(1, 1, 1, 2, 0))
[1] TRUE
> aeq(fit3$transitions, rbind(c(3,0,0,0), 0, c(0,2,1,1), 0))
[1] TRUE
> all.equal(fit3$overlap, fit2$overlap)
[1] TRUE
> all(fit3$teleport$id == c("A", "C"))
[1] TRUE
> all(fit3$teleport$row == c(3,9))
[1] TRUE
> all(fit3$jump$id == "C")
[1] TRUE
> all(fit3$jump$row == 8)
[1] TRUE
> all.equal(fit3$gap, list(row=6L, id= "B"))
[1] TRUE
> 
> 
> 
> proc.time()
   user  system elapsed 
   0.79    0.09    0.87