
R Under development (unstable) (2022-08-09 r82699) -- "Unsuffered Consequences"
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> # Understanding edge cases
> library(survival)
> 
> #
> # this is from a user report of a problem with cumevents.  When there is
> #  a row merged in that is a censor, don't mark it as a cumevent.
> #
> base <- data.frame(
+   id = 1:2, tstart = c(0, 0), tstop  = c(10, 10), got_flu = c(0, 0), 
+   has_flu = factor(c("no", "no"), levels = c("no", "yes")))
> base <- tmerge(base, base, id = id, got_flu = event(tstop, got_flu))
> 
> # add time-varying covariates
> vars <- data.frame(id = c(1, rep(2, 5)), time = c(0, (0:4) * 2), x = rnorm(6))
> base <- tmerge(base, vars, id = id, x = tdc(time, x))
> 
> # add cumevents, using a covariate
> events <- data.frame(
+   id = c(2, 2, 2), 
+   # notice the zero -- the second row should not add an event
+   got_flu = c(1,0,2), 
+   has_flu = c("yes", "no", "yes"),
+   time = c(3, 5, 8))
> b2 <- tmerge(base, events, id = id, got_flu = cumevent(time, got_flu),
+                has_flu = tdc(time, has_flu))
Warning message:
In tmerge(base, events, id = id, got_flu = cumevent(time, got_flu),  :
  replacement of variable 'has_flu'
> 
> all.equal(b2$got_flu, c(0,0,1,0,0,0,3,0))
[1] TRUE
> 
> 
> # Tied times in the merger data set
> # for all of them missings are essentially ignored
> # last obs wins for tdc and event
> tiedat <- data.frame(id=c(1, 1, 1, 2,2,2), time=c(3,4, 4, 3, 5, 5), 
+                      x=c(1, NA,0, 2,3,4))
> b3 <- tmerge(base, tiedat, id=id, x1= tdc(time, x), x2=cumtdc(time, x),
+              x3= event(time, x), x4 = cumevent(time, x))
> all.equal(b3$x1, c(NA, 1, 0, NA, NA, 2,2, 4,4,4))
[1] TRUE
> all.equal(b3$x2, c(NA, 1, 1, NA, NA, 2,2, 9,9,9))
[1] TRUE
> all.equal(b3$x3, c(1,0,0,0,2,0,4,0,0,0))
[1] TRUE
> all.equal(b3$x4, c(1,0,0,0,2,0,9,0,0,0))
[1] TRUE
> 
> # Multiple overlapping time windows in the first step.
> #  Should generate an error message
> test <- tryCatch(
+             {tmerge(pbcseq[, c("id", "trt", "age", "sex")], pbcseq, id,
+                death = event(futime, status==2))},
+             error= function(cond) {
+                 if (grepl("duplicate identifiers", cond)) 
+                     cat("successful tmerge error test\n")
+             }
+ )
successful tmerge error test
> 
> # Using a tdc that depends on more than one variable.  If they are not
> #  exactly the same class, tmerge should fail.
> # Happens with wide data sets
> 
> tdata <- data.frame(id= 1:3, age=c(40,44,38), dtime=c(700, 600, 500),  
+                     t1 = c(111, 211, 311), x1= as.integer(c(4, 5, 6)),
+                     t2 = c(120, 240, 400.3), x2=c( 9, 8, 7),
+                     t3 = c(400, 500, 450), x3=c(12,2, 0))
> # This works
> wide1 <- tmerge(tdata[,1:2], tdata, id=id, death= event(dtime),
+                 x = tdc(t1, x1),  x= tdc(t2, x2), x= tdc(t3, x3))
> 
> r1 <- data.frame(id=rep(1:3, each=4), 
+                  age= tdata$age[rep(1:3, each=4)],
+                  tstart=c(0,111, 120, 400, 0, 211, 240, 500, 0, 311,400.3, 450),
+                  tstop =c(111, 120, 400, 700, 211, 240, 500, 600, 
+                           311, 400.3, 450, 500),
+                  death= rep(c(0,0,0,1), 3),
+                  x= c(NA,4, 9,12, NA, 5, 8, 2, NA, 6,7, 0))
> all.equal(r1, wide1, check.attributes=FALSE)
[1] TRUE
> 
> tdata$x2[2] <- 'c'  # different data type
> test <- tryCatch(
+             {tmerge(tdata[,1:2], tdata, id=id, death= event(dtime),
+                 x = tdc(t1, x1),  x= tdc(t2, x2), x= tdc(t3, x3))},
+              error= function(cond) {
+                 if (grepl("tdc update does not match prior variable type: x", cond)) 
+                     cat("successful tmerge error test\n")
+             }
+ )
successful tmerge error test
> 
> proc.time()
   user  system elapsed 
  1.142   0.080   1.219 
