mmcif_fit: Fits a Mixed Competing Risk Model

In mmcif: Mixed Multivariate Cumulative Incidence Functions

Fits a Mixed Competing Risk Model

Description

Fits mixed cumulative incidence functions model by maximizing the log composite likelihood function.

Usage

mmcif_fit(
  par,
  object,
  n_threads = 1L,
  control.outer = list(itmax = 100L, method = "nlminb", kkt2.check = FALSE, trace =
    FALSE),
  control.optim = list(eval.max = 10000L, iter.max = 10000L),
  ghq_data = object$ghq_data,
  ...
)

Arguments

par	numeric vector with parameters. This is using a log Cholesky decomposition for the covariance matrix.
object	an object from mmcif_data.
n_threads	the number of threads to use.
control.outer, control.optim, ...	arguments passed to auglag.
ghq_data	the Gauss-Hermite quadrature nodes and weights to use. It should be a list with two elements called "node" and "weight". The argument can also be a list with lists with different sets of quadrature nodes. In this case, fits are successively made using the previous fit as the starting value. This may reduce the computation time by starting with fewer quadrature nodes.

Value

The output from auglag.

References

Cederkvist, L., Holst, K. K., Andersen, K. K., & Scheike, T. H. (2019). Modeling the cumulative incidence function of multivariate competing risks data allowing for within-cluster dependence of risk and timing. Biostatistics, Apr 1, 20(2), 199-217.

See Also

mmcif_data, mmcif_start_values and mmcif_sandwich.

Examples

if(require(mets)){
  # prepare the data
  data(prt)

  # truncate the time
  max_time <- 90
  prt <- within(prt, {
    status[time >= max_time] <- 0
    time <- pmin(time, max_time)
  })

  # select the DZ twins and re-code the status
  prt_use <- subset(prt, zyg == "DZ") |>
    transform(status = ifelse(status == 0, 3L, status))

  # randomly sub-sample
  set.seed(1)
  prt_use <- subset(
    prt_use, id %in% sample(unique(id), length(unique(id)) %/% 10L))

  n_threads <- 2L
  mmcif_obj <- mmcif_data(
    ~ country - 1, prt_use, status, time, id, max_time,
    2L, strata = country)

  # get the staring values
  start_vals <- mmcif_start_values(mmcif_obj, n_threads = n_threads)

  # estimate the parameters
  ests <- mmcif_fit(start_vals$upper, mmcif_obj, n_threads = n_threads)

  # show the estimated covariance matrix of the random effects
  tail(ests$par, 10L) |> log_chol_inv() |> print()

  # gradient is ~ zero
  mmcif_logLik_grad(
    mmcif_obj, ests$par, is_log_chol = TRUE, n_threads = n_threads) |>
    print()
}

mmcif documentation built on July 18, 2022, 1:06 a.m.