R/01 - Create Patient Time Periods.R

In mjkarlsen/traumaR: This package was created to manipulate the Pennsylvania Trauma Outcome System (PTOS) data.

#' Create Patient Time Periods and Intervals
#'
#' @param .patient_df Patient Dataframe
#'
#' @return Dataframe of dates, times, and period intervals
#' @export
create_patient_timeframe <- function(.patient_df) {

  .patient_timeframe <- .patient_df %>%
    filter.(fltr_procedure == T,
            # fltr_fasciotomy == T,
    ) %>%
    mutate_across.(ends_with.("_tm"), as.ITime) %>%
    mutate_across.(ends_with.("_dt"), mdy) %>%
    select.(
      id,
      sex,
      race,
      age_in_yrs,
      age_grp,
      peds_adult_flag,
      payor_class_primary,
      primary_injury_type,
      place_of_injury,
      cause_of_injury_e_code,
      injury_desc,
      patient_county,
      zip_code,
      arrival_dt,
      arrival_tm,
      forearm_fx_dt,
      forearm_fx_tm,
      forearm_fx_loc,
      forearm_fx_desc,
      fasciotomy_dt,
      fasciotomy_tm,
      fasciotomy_loc,
      discharge_dt,
      discharge_tm,
      deathdischargetransfer_dt,
      deathdischargetransfer_tm,
      discharge_status,
      fltr_fasciotomy,
      fltr_procedure
    ) %>%
    # drop_na.() %>%
    mutate.(arrival_dtime = ymd_hms(paste(arrival_dt, arrival_tm)),
            forearm_fx_dtime = ymd_hms(paste(forearm_fx_dt, forearm_fx_tm)),
            fasciotomy_dtime = ymd_hms(paste(fasciotomy_dt, fasciotomy_tm)),
            discharge_dtime = ymd_hms(paste(discharge_dt, discharge_tm)),
            total_stay_time = as.period(lubridate::interval(arrival_dtime,  discharge_dtime)),
            arrival_to_forearm_time = as.period(lubridate::interval(arrival_dtime, forearm_fx_dtime)),
            arrival_to_fasciotomy_time = as.period(lubridate::interval(arrival_dtime, fasciotomy_dtime)),
            forearm_to_fasciotomy_time = as.period(lubridate::interval(forearm_fx_dtime,  fasciotomy_dtime)),
            fasciotomy_to_discharge_time = as.period(lubridate::interval(fasciotomy_dtime,  discharge_dtime)))

  # Create the patient_df dataframe
  assign(paste("patient_periods"), data.frame(.patient_timeframe), envir = .GlobalEnv)

}