R/define_observation_periods.R

In pwatrick/DrugRepurposingToolKit: A High-Throughput Approach Integrating Gene Expression Signatures and Clinical Data to Repurpose Drugs

#' Define baseline and treatment periods
#'
#'
#' @description
#' \code{define_observation_periods} creates baseline and treatment period columns
#'
#' @details
#' This function defines the baseline and treatment period columns from
#' clinical data from electronic health record (EHR) databases that have
#' adopted the Observational Medical Outcomes Partnership (OMOP)
#' Common Data Model (CDM) format.
#'
#' Baseline period = "start_date" to "first_{drug}_exposure".
#' Treatment period = ("first_{drug}_exposure" + 30 days) to "last_{drug}_exposure".
#' If treatment period > 12 months, then treatment period =
#' ("first_{drug}_exposure" + 30 days) to "end_date".
#'
#' Updated: 2021-03-27
#'
#'
#' @param .data   A tibble
#' @export

define_observation_periods <- function(.data, ...) {

  #Calculate number of days between "first_drug_exposure" and "last_drug_exposure"
  .data$drug_length <- lubridate::interval(.data$first_drug_exposure,
                                           .data$last_drug_exposure)
  .data$drug_length <- lubridate::time_length(.data$drug_length, "day")

  #Remove patients with "drug_length" less than 30 days
  .data <- .data %>%
    dplyr::filter(drug_length >= 30)

  #If "last_drug_exposure" occurs before "end_date", set "final_end_date" to "last_drug_exposure", else set to "end_date"
  .data <- .data %>%
    dplyr::mutate(
      final_end_date = dplyr::if_else(last_drug_exposure <= end_date,
                                      last_drug_exposure,
                                      end_date)
    )

  #Get final columns of interest
  .data <- .data %>%
    dplyr::select(person_id, start_date, first_drug_exposure, final_end_date) %>%
    dplyr::distinct()
}