tmerge {survival}R Documentation

Time based merge for survival data

Description

A common task in survival analysis is the creation of start,stop data sets which have multiple intervals for each subject, along with the covariate values that apply over that interval. This function aids in the creation of such data sets.

Usage

tmerge(data1, data2,  id,..., tstart, tstop, options)

Arguments

data1

the primary data set, to which new variables and/or observation will be added

data2

second data set in which the other arguments will be found

id

subject identifier

...

operations that add new variables or intervals, see below

tstart

optional variable to define the valid time range for each subject, only used on an initial call

tstop

optional variable to define the valid time range for each subject, only used on an initial call

options

a list of options. Valid ones are idname, tstartname, tstopname, delay, na.rm, and tdcstart. See the explanation below.

Details

The program is often run in multiple passes, the first of which defines the basic structure, and subsequent ones that add new variables to that structure. For a more complete explanation of how this routine works refer to the vignette on time-dependent variables.

There are 4 types of optional arguments: a time dependent covariate (tdc), cumulative count (cumtdc), event (event) or cumulative event (cumevent). Time dependent covariates change their values before an event, events are outcomes.

The function adds three new variables to the output data set: tstart, tstop, and id. The options argument can be used to change these names. If data1 contains the tstart variable then that is used as the starting point for the created time intervals, otherwise the initial interval for each id will begin at 0 by default. This will lead to an invalid interval and subsequent error if say a death time were <= 0.

The na.rm option affects creation of time-dependent covariates. Should a data row in data2 that has a missing value for the variable be ignored (na.rm=FALSE, default) or should it generate an observation with a value of NA? The default value leads to "last value carried forward" behavior. The delay option causes a time-dependent covariate's new value to be delayed, see the vignette for an example.

Value

a data frame with two extra attributes tname and tcount. The first contains the names of the key variables; it's persistence from call to call allows the user to avoid constantly reentering the options argument. The tcount variable contains counts of the match types. New time values that occur before the first interval for a subject are "early", those after the last interval for a subject are "late", and those that fall into a gap are of type "gap". All these are are considered to be outside the specified time frame for the given subject. An event of this type will be discarded. A time-dependent covariate value will be applied to later intervals but will not generate a new time point in the output.

The most common type will usually be "within", for those new times that fall inside an existing interval and cause it to be split into two. Observations that fall exactly on the edge of an interval but within the (min, max] time for a subject are counted as being on a "leading" edge, "trailing" edge or "boundary". The first corresponds for instance to an occurrence at 17 for someone with an intervals of (0,15] and (17, 35]. A tdc at time 17 will affect this interval but an event at 17 would be ignored. An event occurrence at 15 would count in the (0,15] interval. The last case is where the main data set has touching intervals for a subject, e.g. (17, 28] and (28,35] and a new occurrence lands at the join. Events will go to the earlier interval and counts to the latter one. A last column shows the number of additions where the id and time point were identical. When this occurs, the tdc and event operators will use the final value in the data (last edit wins), but ignoring missing, while cumtdc and cumevent operators add up the values.

These extra attributes are ephemeral and will be discarded if the dataframe is modified in any way. This is intentional.

Author(s)

Terry Therneau

See Also

neardate

Examples

# The pbc data set contains baseline data and follow-up status
# for a set of subjects with primary biliary cirrhosis, while the
# pbcseq data set contains repeated laboratory values for those
# subjects.  
# The first data set contains data on 312 subjects in a clinical trial plus
# 106 that agreed to be followed off protocol, the second data set has data
# only on the trial subjects.
temp <- subset(pbc, id <= 312, select=c(id:sex, stage)) # baseline data
pbc2 <- tmerge(temp, temp, id=id, endpt = event(time, status))
pbc2 <- tmerge(pbc2, pbcseq, id=id, ascites = tdc(day, ascites),
               bili = tdc(day, bili), albumin = tdc(day, albumin),
               protime = tdc(day, protime), alk.phos = tdc(day, alk.phos))

fit <- coxph(Surv(tstart, tstop, endpt==2) ~ protime + log(bili), data=pbc2)

[Package survival version 2.42-6 Index]