cohort_simulation: Runs a cohort discrete event simulation

In stulacy/RDES: Utility Functions for Parametric Multi-State Models

Description

Runs a cohort discrete event simulation

Usage

cohort_simulation(
  models,
  newdata,
  trans_mat,
  start_time = 0,
  start_state = 1,
  time_limit = NULL,
  tcovs = NULL,
  M = 1000,
  ci = FALSE,
  ci_margin = 0.95,
  agelimit = FALSE,
  agecol = "age",
  agescale = 365.25
)

Arguments

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.
start_time	Entry times of individuals specified in newdata. Can either be a single time that everyone enters at, or have as many values as rows in newdata. Defaults to everyone starting at time 0.
start_state	The starting state of the individuals specified in newdata. States can be represented by an integer (the row/column number of the state in trans_mat), or as a string giving the name of the state in trans_mat. Can either be a single value when everyone starts in the same state, or have as many values as rows in newdata. Defaults to everyone starting in state 1.
time_limit	The maximum time to run the simulation for. If not provided then the simulation runs until all the individuals have obtained a sink state.
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.
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.

Value

A data frame with state entry times for each individual.

Examples

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')
})

sim <- cohort_simulation(models, ebmt3, tmat)

stulacy/RDES documentation built on Feb. 14, 2021, 2:31 a.m.