bootstrap_helper: Bootstrap Observed Data and Simulate Under All Interventions
In CausalInference/gfoRmula: Parametric G-Formula

bootstrap_helper

R Documentation

Bootstrap Observed Data and Simulate Under All Interventions

Description

This internal function bootstraps the observed data (i.e., resamples the observed data set with replacement to construct bootstrap confidence intervals and standard errors). Then, the function simulates data using the resampled dataset to estimate the survival outcome, binary end-of-follow-up outcome, or continuous end-of-follow-up outcome.

Usage

bootstrap_helper(
  r,
  time_points,
  obs_data,
  bootseeds,
  outcome_type,
  intvars,
  interventions,
  int_times,
  ref_int,
  covparams,
  covnames,
  covtypes,
  covfits_custom,
  covpredict_custom,
  basecovs,
  histvars,
  histvals,
  histories,
  ymodel,
  ymodel_fit_custom,
  ymodel_predict_custom,
  yrestrictions,
  compevent_restrictions,
  restrictions,
  comprisk,
  compevent_model,
  time_name,
  outcome_name,
  compevent_name,
  ranges,
  parallel,
  ncores,
  max_visits,
  hazardratio,
  intcomp,
  boot_diag,
  nsimul,
  baselags,
  below_zero_indicator,
  min_time,
  show_progress,
  pb,
  int_visit_type,
  sim_trunc,
  ...
)

Arguments

`r`	Integer specifying the index of the current iteration of the bootstrap.
`time_points`	Number of time points to simulate.
`obs_data`	Data table containing the observed data.
`bootseeds`	Vector of integers specifying the seeds. One seed is used to initialize each bootstrap iteration.
`outcome_type`	Character string specifying the "type" of the outcome. The possible "types" are: `"survival"`, `"continuous_eof"`, and `"binary_eof"`.
`intvars`	List, whose elements are vectors of character strings. The kth vector in `intvars` specifies the name(s) of the variable(s) to be intervened on in each round of the simulation under the kth intervention in `interventions`.
`interventions`	List, whose elements are lists of vectors. Each list in `interventions` specifies a unique intervention on the relevant variable(s) in `intvars`. Each vector contains a function implementing a particular intervention on a single variable, optionally followed by one or more "intervention values" (i.e., integers used to specify the treatment regime).
`int_times`	List, whose elements are lists of vectors. The kth list in `int_times` corresponds to the kth intervention in `interventions`. Each vector specifies the time points in which the relevant intervention is applied on the corresponding variable in `intvars`. When an intervention is not applied, the simulated natural course value is used. By default, this argument is set so that all interventions are applied in all time points.
`ref_int`	Integer denoting the intervention to be used as the reference for calculating the risk ratio and risk difference. 0 denotes the natural course, while subsequent integers denote user-specified interventions in the order that they are named in `interventions`.
`covparams`	List of vectors, where each vector contains information for one parameter used in the modeling of the time-varying covariates (e.g., model statement, family, link function, etc.). Each vector must be the same length as `covnames` and in the same order. If a parameter is not required for a certain covariate, it should be set to `NA` at that index.
`covnames`	Vector of character strings specifying the names of the time-varying covariates in `obs_data`.
`covtypes`	Vector of character strings specifying the "type" of each time-varying covariate included in `covnames`. The possible "types" are: `"binary"`, `"normal"`, `"categorical"`, `"bounded normal"`, `"zero-inflated normal"`, `"truncated normal"`, `"absorbing"`, `"categorical time"`, and `"custom"`.
`covfits_custom`	Vector containing custom fit functions for time-varying covariates that do not fall within the pre-defined covariate types. It should be in the same order `covnames`. If a custom fit function is not required for a particular covariate (e.g., if the first covariate is of type `"binary"` but the second is of type `"custom"`), then that index should be set to `NA`.
`covpredict_custom`	Vector containing custom prediction functions for time-varying covariates that do not fall within the pre-defined covariate types. It should be in the same order as `covnames`. If a custom prediction function is not required for a particular covariate, then that index should be set to `NA`.
`basecovs`	Vector of character strings specifying the names of baseline covariates in `obs_data`.
`histvars`	List of vectors. The kth vector specifies the names of the variables for which the kth history function in `histories` is to be applied.
`histvals`	List of length two. The first element is a numeric vector specifying the lags used in the model statements (e.g., if `lag1_varname` and `lag2_varname` were included in the model statements, this vector would be `c(1,2)`). The second element is a numeric vector specifying the lag averages used in the model statements.
`histories`	Vector of history functions to apply to the variables specified in `histvars`.
`ymodel`	Model statement for the outcome variable.
`ymodel_fit_custom`	Function specifying a custom outcome model. See the vignette "Using Custom Outcome Models in gfoRmula" for details.
`ymodel_predict_custom`	Function obtaining predictions from the custom outcome model specified in `ymodel_fit_custom`. See the vignette "Using Custom Outcome Models in gfoRmula" for details.
`yrestrictions`	List of vectors. Each vector containins as its first entry a condition and its second entry an integer. When the condition is `TRUE`, the outcome variable is simulated according to the fitted model; when the condition is `FALSE`, the outcome variable takes on the value in the second entry.
`compevent_restrictions`	List of vectors. Each vector containins as its first entry a condition and its second entry an integer. When the condition is `TRUE`, the competing event variable is simulated according to the fitted model; when the condition is `FALSE`, the competing event variable takes on the value in the second entry.
`restrictions`	List of vectors. Each vector contains as its first entry a covariate for which a priori knowledge of its distribution is available; its second entry a condition under which no knowledge of its distribution is available and that must be `TRUE` for the distribution of that covariate given that condition to be estimated via a parametric model or other fitting procedure; its third entry a function for estimating the distribution of that covariate given the condition in the second entry is false such that a priori knowledge of the covariate distribution is available; and its fourth entry a value used by the function in the third entry. The default is `NA`.
`comprisk`	Logical scalar indicating the presence of a competing event.
`compevent_model`	Model statement for the competing event variable.
`time_name`	Character string specifying the name of the time variable in `obs_data`.
`outcome_name`	Character string specifying the name of the outcome variable in `obs_data`.
`compevent_name`	Character string specifying the name of the competing event variable in `obs_data`.
`ranges`	List of vectors. Each vector contains the minimum and maximum values of one of the covariates in `covnames`.
`parallel`	Logical scalar indicating whether to parallelize simulations of different interventions to multiple cores.
`ncores`	Integer specifying the number of cores to use in parallel simulation.
`max_visits`	A vector of one or more values denoting the maximum number of times a binary covariate representing a visit process may be missed before the individual is censored from the data (in the observed data) or a visit is forced (in the simulated data). Multiple values exist in the vector when the modeling of more than covariate is attached to a visit process. A value of `NA` should be provided when there is no visit process.
`hazardratio`	Logical scalar indicating whether the hazard ratio should be computed between two interventions.
`intcomp`	List of two numbers indicating a pair of interventions to be compared by a hazard ratio. The default is `NA`, resulting in no hazard ratio calculation.
`boot_diag`	Logical scalar indicating whether to return the coefficients, standard errors, and variance-covariance matrices of the parameters of the fitted models in the bootstrap samples. The default is `FALSE`.
`nsimul`	Number of subjects for whom to simulate data. By default, this argument is set equal to the number of subjects in `obs_data`.
`baselags`	Logical scalar for specifying the convention used for lagi and lag_cumavgi terms in the model statements when pre-baseline times are not included in `obs_data` and when the current time index, `t`, is such that `t < i`. If this argument is set to `FALSE`, the value of all lagi and lag_cumavgi terms in this context are set to 0 (for non-categorical covariates) or the reference level (for categorical covariates). If this argument is set to `TRUE`, the value of lagi and lag_cumavgi terms are set to their values at time 0. The default is `FALSE`.
`below_zero_indicator`	Logical scalar indicating whether the observed data set contains rows for time `t < 0`.
`min_time`	Numeric scalar specifying lowest value of time `t` in the observed data set.
`show_progress`	Logical scalar indicating whether to print a progress bar for the number of bootstrap samples completed in the R console. This argument is only applicable when `parallel` is set to `FALSE` and bootstrap samples are used (i.e., `nsamples` is set to a value greater than 0). The default is `TRUE`.
`pb`	Progress bar R6 object. See `progress_bar` for further details.
`int_visit_type`	Vector of logicals. The kth element is a logical specifying whether to carry forward the intervened value (rather than the natural value) of the treatment variables(s) when performing a carry forward restriction type for the kth intervention in `interventions`. When the kth element is set to `FALSE`, the natural value of the treatment variable(s) in the kth intervention in `interventions` will be carried forward. By default, this argument is set so that the intervened value of the treatment variable(s) is carried forward for all interventions.
`sim_trunc`	Logical scalar indicating whether to truncate simulated covariates to their range in the observed data set. This argument is only applicable for covariates of type `"normal"`, `"bounded normal"`, `"truncated normal"`, and `"zero-inflated normal"`.
`...`	Other arguments

Value

A list with the following components:

`Result`	Matrix containing risks over time under the natural course and under each user-specific intervention.
`ResultRatio`	Matrix containing risk ratios over time under the natural course and under each user-specific intervention.
`ResultDiff`	Matrix containing risk differences over time under the natural course and under each user-specific intervention.
`bootcoeffs`	List of the coefficients of the fitted models. If the argument `boot_diag` is set to `FALSE`, a value of `NA` is given.
`bootstderrs`	List of the standard errors of the coefficients of the fitted models. If the argument `boot_diag` is set to `FALSE`, a value of `NA` is given.