boot_ebmstate: Bootstrap samples and bootstrap interval estimates
In ebmstate: Empirical Bayes Multi-State Cox Model

Description Usage Arguments Details Value Author(s)

View source: R/bootstrap_and_leave_one_out.R

This function computes bootstrap samples of regression coefficients, cumulative hazard functions, and transition probability functions.

boot_ebmstate(
  mstate_data_expanded = NULL,
  which_group = NULL,
  min_nr_samples = NULL,
  patient_data = NULL,
  initial_state = NULL,
  tmat = NULL,
  time_model = NULL,
  backup_file = NULL,
  input_file = NULL,
  coxrfx_args = NULL,
  msfit_args = NULL,
  probtrans_args = NULL
)

`mstate_data_expanded`	Data in 'long format', possibly with 'expanded' covariates (as obtained by running mstate::expand.covs). See details.
`which_group`	A character vector with the same meaning as the 'groups' argument of the function `CoxRFX` but named (with the covariate names).
`min_nr_samples`	The confidence interval of any coefficient is based on a number of bootstrap samples at least as high as this argument. See details.
`patient_data`	The covariate data for which the estimates of cumulative hazards and transition probabilities are computed. Must contain: one row of data for each transition, all the covariate columns in the fitted model, and also the 'strata' column.
`initial_state`	The initial state for which transition probability estimates should be computed
`tmat`	Transition matrix for the multi-state model, as obtained by running `mstate::transMat`
`time_model`	The model of time-dependency: either 'clockforward' or 'clockreset'.
`backup_file`	Path to file. Objects generated while the present function is running are stored in this file. This avoids losing all estimates if and when the algorithm breaks down. See argument `input_file`.
`input_file`	Path to `backup_file` (see argument `backup_file`). If this argument is given, all other arguments should be `NULL`.
`coxrfx_args`	Named list with arguments to the `CoxRFX` function other than `Z`,`surv` and `groups`.
`msfit_args`	Named list with arguments to the `msfit_generic.coxrfx` function other than `object`,`newdata` and `trans`.
`probtrans_args`	Named list with arguments to the `probtrans_ebmstate` function other than `initia_state`,`cumhaz` and `model`.

In a given bootstrap sample there might not be enough information to generate estimates for all coefficients. If a covariate has little or no variation in a given bootstrap sample, no estimate of its coefficient will be computed. The present function will keep taking bootstrap samples until every coefficient has been estimated at least min_nr_samples times. After expansion, the original covariates should be excluded from mstate_data_expanded.

A list with: 95% bootstrap intervals for each regression coefficient and for transition probabilities; bootstrap samples of regression coefficients, cumulative hazards and transition probabilities.

Rui Costa

ebmstate documentation built on Dec. 20, 2021, 5:07 p.m.