tests/tmerge3.R

In survival: Survival Analysis

# 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))

all.equal(b2$got_flu, c(0,0,1,0,0,0,3,0))


# 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$x1, c(NA, 1, 0, NA, NA, 2,2, 4,4,4))
all.equal(b3$x2, c(NA, 1, 1, NA, NA, 2,2, 9,9,9))
all.equal(b3$x3, c(1,0,0,0,2,0,4,0,0,0))
all.equal(b3$x4, c(1,0,0,0,2,0,9,0,0,0))

# 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")
            }
)

# 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)

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")
            }
)