length_of_stay: Estimates length of stay
In multistateutils: Utility Functions for Parametric Multi-State Models

Description Usage Arguments Value Examples

Estimates length of stay in each state of an individual's passage through a multi-state model by discrete event simulation.

length_of_stay(
  models,
  newdata,
  trans_mat,
  times,
  start_state = 1,
  tcovs = NULL,
  N = 1e+05,
  M = 1000,
  ci = FALSE,
  ci_margin = 0.95,
  agelimit = FALSE,
  agecol = "age",
  agescale = 365.25
)

`models`	List of `flexsurvreg` objects.
`newdata`	Data frame with covariates of individual to simulate times for. Must contain all fields required by models.
`trans_mat`	Transition matrix, such as that used in `mstate`.
`times`	Times at which to estimate length of stay.
`start_state`	Starting state. Either number or character name in `trans_mat`.
`tcovs`	As in `flexsurv::pmatrix.simfs`, this is the names of covariates that need to be incremented by the simulation clock at each transition, such as age when modelled as age at state entry.
`N`	Number of times to repeat the individual
`M`	Number of times to run the simulations in order to obtain confidence interval estimates.
`ci`	Whether to calculate confidence intervals. See `flexsurv::pmatrix.simfs` for details.
`ci_margin`	Confidence interval range to use if `ci` is set to `TRUE`.
`agelimit`	Whether to automatically assign people to an 'early death' state. This is useful as otherwise individuals can be assigned unrealistic time-to-events due to the nature of sampling times from a random number distribution. If this value is `FALSE` then no limit is applied, otherwise provide the time-limit to be used. This limit must be in the same time-scale as the time-to-event models.
`agecol`	The name of the column in `newdata` that holds an individual's age.
`agescale`	Any multiplication to be applied to the age covariate to put it onto the same time-scale as the simulation. This is often useful as time-to-event may be measured on a day-based time-scale while age is typically measured in years.

A data frame containing length of stay estimates.

library(multistateutils)
library(mstate)
library(flexsurv)

# Convert data to long
data(ebmt3)
tmat <- trans.illdeath()
long <- msprep(time=c(NA, 'prtime', 'rfstime'),
               status=c(NA, 'prstat', 'rfsstat'),
               data=ebmt3,
               trans=tmat,
               keep=c('age', 'dissub'))

# Fit parametric models
models <- lapply(1:3, function(i) {
    flexsurvreg(Surv(time, status) ~ age + dissub, data=long, dist='weibull')
})

# New individual to estimate transition probabilities for
newdata <- data.frame(age="20-40", dissub="AML")

# Estimate length of stay in each state after a year, given starting in state 1
length_of_stay(models,
               newdata=newdata,
               tmat, times=365.25,
               start=1)