sir.cont: Ventilation status in intensive care unit patients

In aallignol/mvna: Nelson-Aalen estimator of the cumulative hazard in multistate models

Description

Time-dependent ventilation status for intensive care unit (ICU) patients, a random sample from the SIR-3 study.

Usage

data(sir.cont)

Format

A data frame with 1141 rows and 6 columns:

id:

Randomly generated patient id

from:

State from which a transition occurs

to:

State to which a transition occurs

time:

Time when a transition occurs

age:

Age at inclusion

sex:

Sex. F for female and M for male

The possible states are:

0: No ventilation

1: Ventilation

2: End of stay.

And cens stands for censored observations.

Details

This data frame consists in a random sample of the SIR-3 cohort data. It focuses on the effect of ventilation on the length of stay (combined endpoint discharge/death). Ventilation status is considered as a transcient state in an illness-death model.

The data frame is directly formated to be used with the mvna function, i.e., it is transition-oriented with one row per transition.

Source

Beyersmann, J., Gastmeier, P., Grundmann, H., Baerwolff, S., Geffers, C., Behnke, M., Rueden, H., and Schumacher, M. Use of multistate models to assess prolongation of intensive care unit stay due to nosocomial infection. Infection Control and Hospital Epidemiology, 27:493-499, 2006.

Examples

data(sir.cont)

# Matrix of possible transitions
tra <- matrix(ncol=3,nrow=3,FALSE)
tra[1, 2:3] <- TRUE
tra[2, c(1, 3)] <- TRUE

# Modification for patients entering and leaving a state
# at the same date
sir.cont <- sir.cont[order(sir.cont$id, sir.cont$time), ]
for (i in 2:nrow(sir.cont)) {
  if (sir.cont$id[i]==sir.cont$id[i-1]) {
    if (sir.cont$time[i]==sir.cont$time[i-1]) {
      sir.cont$time[i-1] <- sir.cont$time[i-1] - 0.5
    }
  }
}

# Computation of the Nelson-Aalen estimates
  na.cont <- mvna(sir.cont,c("0","1","2"),tra,"cens")

if (require("lattice")) {
  xyplot(na.cont,tr.choice=c("0 2","1 2"),aspect=1,
       strip=strip.custom(bg="white",
         factor.levels=c("No ventilation -- Discharge/Death",
           "Ventilation -- Discharge/Death"),
         par.strip.text=list(cex=0.9)),
       scales=list(alternating=1),xlab="Days",
       ylab="Nelson-Aalen estimates")
}

aallignol/mvna documentation built on May 10, 2019, 3:13 a.m.