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