R/expand_trials.R

In CAM-Roche/RandomisedTrialsEmulation: Causal Analysis of Observational Time-to-Event Data

expand_trials_trial_seq <- function(object) {
  # Avoid NOTE for data.table
  period <- eligible <- NULL

  data <- object@data@data
  # Use the observed min/max periods if they are within the specified limits
  first_period <- max(c(object@expansion@first_period, object@data@data[eligible == 1, min(period)]))
  last_period <- min(c(object@expansion@last_period, object@data@data[eligible == 1, max(period)]))
  chunk_size <- object@expansion@chunk_size
  censor_at_switch <- object@expansion@censor_at_switch

  outcome_adj_vars <- unique(object@outcome_model@adjustment_vars)
  keeplist <- unique(c(
    "id", "trial_period", "followup_time", "outcome", "weight", "treatment",
    outcome_adj_vars, object@outcome_model@treatment_var
  ))

  wt <- NULL
  if (is.null(data$wt)) data[, wt := 1]

  all_ids <- unique(data$id)
  ids_split <- if (chunk_size == 0) {
    list(all_ids)
  } else if (chunk_size > 0) {
    split(all_ids, ceiling(seq_along(all_ids) / chunk_size))
  }
  for (ids in ids_split) {
    switch_data <- expand(
      sw_data = data[list(ids), ],
      outcomeCov_var = outcome_adj_vars,
      where_var = NA,
      use_censor = censor_at_switch,
      minperiod = first_period,
      maxperiod = last_period,
      keeplist = keeplist
    )
    object@expansion@datastore <- save_expanded_data(object@expansion@datastore, switch_data)
  }
  object
}