cutLM: Create landmark data set

In dynpred: Companion Package to "Dynamic Prediction in Clinical Survival Analysis"

Description

Create landmark data set from original data, which can be either in wide or long format, see details.

Usage

cutLM(data, outcome, LM, horizon, covs, format = c("wide", "long"), id, rtime,
  right = TRUE)

Arguments

data	Data frame from which to construct landmark dataset
outcome	List with items time and status, containing character strings identifying the names of time and status variables, respectively, of the survival outcome
LM	Scalar, the value of the landmark time point
horizon	Scalar, the value of the horizon. Administrative censoring is applied at horizon.
covs	List with items fixed and varying, containing character strings specifying column names in the data containing time-fixed and time-varying covariates, respectively
format	Character string specifying whether the original data are in wide (default) or in long format
id	Character string specifying the column name in data containing the subject id; only needed if format="long"
rtime	Character string specifying the column name in data containing the (running) time variable associated with the time-varying covariate(s); only needed if format="long"
right	Boolean (default=TRUE), indicating if the intervals for the time-varying covariates are closed on the right (and open on the left) or vice versa, see cut

Details

For a given landmark time point LM, patients who have reached the event of interest (outcome) or are censored before or at LM are removed. Administrative censoring is applied at the time horizon. Time-varying covariates are evaluated at the landmark time point LM. Time-varying covariates can be specified in the varying item of the covs argument, in two ways. In the first way (data in long format) different values of time-dependent covariate(s) are stored different rows of the data, with id identifying which values belong to the same subject; the column specified through rtime then contains the time points at which the value of the covariate changes value; with right=TRUE (default), it is assumed that the covariate changes value at the time point specified in rtime (and hence is not used for prediction of an event at rtime), while with right=FALSE, it is assumed that the covariate changes value just before the time point specified in rtime. The second way (data in wide format) can only be used for a specific type of time-varying covariates, often used to model whether some other event has occurred or not, namely those that change value from 0 (event not yet occurred) to 1 (event has occurred).

Value

A landmark data set, containing the outcome and the values of time-fixed and time-varying covariates taken at the landmark time points. The value of the landmark time point is stored in column LM.

Author(s)

Hein Putter [e-mail]

References

van Houwelingen HC, Putter H (2012). Dynamic Prediction in Clinical Survival Analysis. Chapman & Hall.

Examples

test0 <- data.frame(id=c(1,1,1,2,2,2),survyrs=c(2.3,2.3,2.3,2.7,2.7,2.7),
  survstat=c(1,1,1,0,0,0),age=c(76,76,76,68,68,68),gender=c(1,1,1,2,2,2),
  bp=c(80,84,88,92,90,89),bptime=c(1,2,2.2,0,1,2))
cutLM(test0, outcome=list(time="survyrs", status="survstat"),
  LM=1, horizon=2.5, covs=list(fixed=c("age","gender"),varying="bp"),
  format="long", id="id", rtime="bptime")
# Note how the previous example does not use the value of the time-varying
# covariate AT time=LM, only just before (if available). This is in line
# with the time-varying covariates being predictable.
# If you want the value of the time-varying covariate at time=LM if it
# changes value at LM, then use right=FALSE
cutLM(test0, outcome=list(time="survyrs", status="survstat"),
  LM=1, horizon=2.5, covs=list(fixed=c("age","gender"),varying="bp"),
  format="long", id="id", rtime="bptime", right=FALSE)

# An example of a time-varying covariate in wide format; recyrs and recstat
# are time and status of a (cancer) recurrence. Here it is assumed that the
# value of the time-varying covariate is 0 and changes value to 1 at recyrs.
# The status variable is not used!
test1 <- data.frame(id=1:4,survyrs=c(7.6,8.4,5.3,2.6),survstat=c(0,1,1,0),
  age=c(48,52,76,18),gender=c(1,2,2,1),recyrs=c(7.6,5.2,0.8,2.6),
  recstat=c(0,1,1,0))
cutLM(test1, outcome=list(time="survyrs", status="survstat"),
  LM=3, horizon=8, covs=list(fixed=c("id","age","gender"),varying="recyrs"))

# The same example in long format, similar to (but not the same as) the way
# one would use a time-varying covariate in long format.
test2 <- data.frame(id=c(1,2,2,3,3,4),survyrs=c(7.6,8.4,8.4,5.3,5.3,2.6),
  survstat=c(0,1,1,1,1,0),age=c(48,52,52,76,76,18),gender=c(1,2,2,2,2,1),
  rec=c(0,0,1,0,1,0),rectime=c(0,0,5.2,0,0.8,0))
cutLM(test2, outcome=list(time="survyrs", status="survstat"),
  LM=3, horizon=8, covs=list(fixed=c("age","gender"),varying="rec"),
  format="long", id="id", rtime="rectime")

Example output

Loading required package: survival
  id survyrs survstat age gender bp bptime LM
1  1     2.3        1  76      1 NA     NA  1
4  2     2.5        0  68      2 92      0  1
  id survyrs survstat age gender bp bptime LM
1  1     2.3        1  76      1 80      1  1
4  2     2.5        0  68      2 90      1  1
  survyrs survstat id age gender recyrs LM
1     7.6        0  1  48      1      0  3
2     8.0        0  2  52      2      0  3
3     5.3        1  3  76      2      1  3
  id survyrs survstat age gender rec rectime LM
1  1     7.6        0  48      1   0     0.0  3
2  2     8.0        0  52      2   0     0.0  3
4  3     5.3        1  76      2   1     0.8  3

dynpred documentation built on May 2, 2019, 5:07 a.m.