tests/tmerge2.R

In survival: Survival Analysis

library(survival)

# This test is based on a user report that a 0/1 variable would not reset
#  to zero.  It turned out to be a bug when data2 was not sorted

baseline <- data.frame(idd=1:5,  futime=c(20, 30, 40, 30, 20),
                       status= c(0, 1, 0, 1, 0))
tests <- data.frame(idd = c(2,3,3,3,4,4,5),
                    date = c(25, -1, 15, 23, 17, 19, 14),
                    onoff= c( 1, 1, 0, 1, 1, 0, 1))
tests <- tests[c(7,2,6,3,4,1,5),]  #scramble data2

mydata <- tmerge(baseline, baseline, id=idd, death=event(futime, status))
mydata <- tmerge(mydata, tests, id=idd, ondrug=tdc(date, onoff))

all.equal(mydata$ondrug, c(NA, NA,1, 1,0,1, NA, 1,0, NA, 1))


# Check out addition of a factor, character, and logical
tests$ff <- factor(tests$onoff, 0:1, letters[4:5])
tests$fchar <- as.character(tests$ff)
tests$logic <- as.logical(tests$onoff)
tests$num <- rep(1:3, length=nrow(tests))

mydata <- tmerge(mydata, tests, id=idd, fgrp= tdc(date, ff),
                 chgrp = tdc(date, fchar), 
                 options=list(tdcstart="new"))
all.equal(mydata$fgrp, 
          factor(c(3,3,2,2,1,2,3,2,1,3,2), labels=c("d", "e", "new")))
all.equal(mydata$chgrp, 
          c("d", "e", "new")[c(3,3,2,2,1,2,3,2,1,3,2)])

mydat2  <-  tmerge(mydata, tests, id=idd, 
                 logic1 = tdc(date, logic), logic2= event(date, logic))
all.equal(mydat2$logic1, c(FALSE, TRUE, NA)[as.numeric(mydat2$fgrp)])
all.equal(mydat2$logic2, c(FALSE, TRUE, FALSE, FALSE, TRUE, FALSE, TRUE,
                           FALSE, FALSE, TRUE, FALSE))

mydat3 <- tmerge(mydata, tests, id=idd,
                 xx = tdc(date, num), options=list(tdcstart=5))
all.equal(mydat3$xx, c(5,5,3,2,1,2,5,1,3,5,1))
temp <- tmerge(mydata, tests, id=idd, xx=tdc(date, num, 5)) # alternate default
all.equal(mydat3$xx, temp$xx)

# Multiple chained calls. 
temp <- outer(cgd0$id, 100*0:6, "+")
colnames(temp) <- paste0("x", 1:7)   # add a time dependent covariate too 
test <- cbind(cgd0, temp)

newcgd <- tmerge(data1=cgd0[, 1:13], data2=cgd0, id=id, tstop=futime)
newcgd <- tmerge(newcgd, test, id=id, infect = event(etime1), xx=cumtdc(etime1, x1, 0)) 
newcgd <- tmerge(newcgd, test, id=id, infect = event(etime2), xx=cumtdc(etime2, x2)) 
newcgd <- tmerge(newcgd, test, id=id, infect = event(etime3), xx=cumtdc(etime3, x3)) 
newcgd <- tmerge(newcgd, test, id=id, infect = event(etime4), xx=cumtdc(etime4, x4)) 
newcgd <- tmerge(newcgd, test, id=id, infect = event(etime5), xx=cumtdc(etime5, x5)) 
newcgd <- tmerge(newcgd, test, id=id, infect = event(etime6), xx=cumtdc(etime6, x6)) 
newcgd <- tmerge(newcgd, test, id=id, infect = event(etime7), xx=cumtdc(etime7, x7)) 
newcgd <- tmerge(newcgd, newcgd, id, enum=cumtdc(tstart))
all.equal(dim(newcgd), c(203,18))
all.equal(as.vector(table(newcgd$infect)), c(127, 76))
temp <- with(newcgd, ifelse(enum==1, 0, id + (enum-2)*100))
temp2 <- tapply(temp, newcgd$id, cumsum)
all.equal(newcgd$xx, unlist(temp2), check.attributes=FALSE)
tcount <- attr(newcgd, "tcount")
all(tcount[,1:3] ==0)  # no early, late, or gap

# table with number of subjects who have etime1 < futime (row 1)
#  and  etime1==futime (row 2)
# the table command ignores the missings
temp <- subset(cgd0, select=etime1:etime7)
counts <- sapply(temp, function(x) 
    as.vector(table(factor(x>= cgd0$futime, c(FALSE, TRUE)))))

all(tcount[c(1,3,5,7,9,11,13), c("within", "trailing")] == t(counts))


#
# Merging with a date as the time variable.  In this case tstart/tstop are required
#  A default start of 0 has no meaning
#
base2 <- baseline
base2$date1 <- as.Date("1953-03-10")   # everyone enrolled that day
base2$date2 <- as.Date("1953-03-10") + base2$futime
base2$futime <- NULL
test2 <- tests
test2$date <- as.Date("1953-03-10") + test2$date

mydata2 <- tmerge(base2, base2, id=idd, death=event(date2, status), 
                 tstart = date1, tstop= date2,
                 options=list(tstartname="date1", tstopname="date2"))
mydata2 <- tmerge(mydata2, test2, id=idd, ondrug=tdc(date, onoff))
all.equal(mydata$ondrug, c(NA, NA,1, 1,0,1, NA, 1,0, NA, 1))