cens.ipw: Censoring patient initiating the other arm treatment and...

In ipcwswitch: Inverse Probability of Censoring Weights to Deal with Treatment Switch in Randomized Clinical Trials

Description

Censoring patient initiating the other arm treatment and building a treatment censoring indicator cens

Usage

cens.ipw(
  data,
  id,
  tstart,
  tstop,
  event,
  censTime,
  arm,
  realtrt = FALSE,
  trt.start = NULL,
  trt.stop = NULL
)

Arguments

data	a dataframe containing the following variables
id	the patient's id
tstart	the date of the beginning of the follow-up (in numeric format)
tstop	the date of the end of the follow-up (in numeric format)
event	the indicator of failure (a death is denoted by 1 at the end of the follow-up)
censTime	the chosen time to censor the patients (in numeric format)
arm	the randomized treatment (2-levels factor)
realtrt	the randomized treatment (2-levels factor)
trt.start	the time of initiation of the randomized treatment (NULL by default)
trt.stop	the time of termination of the randomized treatment (NULL by default)

Value

a dataframe in the long format, with the data being censored according to the input date, censTime. a treatment censoring indicator, cens, is thus added to the previous dataset to indicate such a switch. Note that this function provides the option to include in the data the treatment really taken with the corresponding dates. Then, the treatment really taken is a 3-levels factor, i.e., the two from the randomized arms and a third indicating the no-treatment case (None).

References

Graffeo, N., Latouche, A., Le Tourneau C., Chevret, S. (2019) "ipcwswitch: an R package for inverse probability of censoring weighting with an application to switches in clinical trials". Computers in biology and medicine, 111, 103339. doi : "10.1016/j.compbiomed.2019.103339"

See Also

SHIdat, timesTokeep, wideToLongTDC

Examples

# To obtain the times parameter, we can apply the timesTokeep function on the same
# dataframe in the wide format
kept.t <- timesTokeep(toydata, id = "id",
tstart = "randt", tstop = "lastdt",
mes.cov = list(c("ps1", "ps2", "ps3")),
time.cov = list(c("randt", "dt2", "dt3")))
# Now, we can build the long format
toy.long <- wideToLongTDC(data = toydata, id = "id",
tstart = "randt", tstop = "lastdt", event = "status",
bas.cov = c("age", "arm", "swtrtdt"),
mes.cov = list(TDconf = c("ps1", "ps2", "ps3")),
time.cov = list(c("randt", "dt2", "dt3")),
times = kept.t[[1]])
# Put dates in numeric format with tstart at 0
toy.long$tstart <- as.numeric(toy.long$tstart)
toy.long$tstop <- as.numeric(toy.long$tstop)
toy.long$swtrtdt <- as.numeric(toy.long$swtrtdt)
tabi <- split(toy.long, toy.long$id)
L.tabi   <- length(tabi)
tablist <- lapply(1:L.tabi, function(i){
    refstart <- tabi[[i]]$tstart[1]
    tabi[[i]]$tstart  <- tabi[[i]]$tstart - refstart
    tabi[[i]]$tstop <- tabi[[i]]$tstop - refstart
    tabi[[i]]$swtrtdt <- tabi[[i]]$swtrtdt - refstart
    return(tabi[[i]])
    })
    toy.long <- do.call( rbind, tablist )
# Patients are censored when initiating the other arm treatment, that is, at time swtrtdt
toy.long2 <- cens.ipw(toy.long, id = "id", tstart = "tstart", tstop = "tstop",
event = "event", arm = "arm",
realtrt = FALSE, censTime ="swtrtdt")
# Before censoring:
toy.long
# Ater censoring:
toy.long2

Example output

Loading required package: survival
  id tstart tstop event age arm swtrtdt TDconf
1  1      0    49     1  20   A      48      0
2  2      0    38     0  50   B      NA      1
3  2     38    41     1  50   B      NA      2
4  3      0   227     0  40   A      NA      0
5  3    227   229     0  40   A      NA      1
  id tstart tstop event age arm swtrtdt TDconf cens
1  1      0    48     0  20   A      48      0    1
2  2      0    38     0  50   B      NA      1    0
3  2     38    41     1  50   B      NA      2    0
4  3      0   227     0  40   A      NA      0    0
5  3    227   229     0  40   A      NA      1    0

ipcwswitch documentation built on Feb. 17, 2021, 9:05 a.m.