R/format_table1.R

In martingerdin/rofi: Utility Functions for the Opportunities For Improvement Project

format_table1 <- function(data) {
  
  ### Require package "labelled"
  
  dpc <- data
  dpc$intub <- with(dpc, ifelse(`pre_intubated` == 1 & is.na(dpc$pre_intubated) == FALSE, 3, `ed_intubated`))  
  #####################################
  # Change factors to readable names ##
  #####################################
  # "korrekt_triage"  
  #dpc$korrekt_triage <- factor(      ##### Ta bort!?!?!
  #  dpc$korrekt_triage,
  #  levels = c("Ja", "Nej", "Övertag annat sjukhus"), 
  #  labels = c("Korrekt triage",
  #             "Incorrect triage",
  #             "Transfer from other hosptial"))
  
  #"host_transfered" 
  dpc$host_transfered <- factor(
    dpc$host_transfered,
    levels = c(1, 2, 3, 4), 
    labels = c("Not moved",
               "Moved to KUH",
               "Moved from KUH",
               "Moved both to and from KUH")) 
  
  ## "ed_tta"
  
  # ###### TA BORT - registrerat t.om   2017-11-06
  #  dpc$ed_tta <- factor(
  #    dpc$ed_tta,
  #    levels = c(1, 2), 
  #    labels = c("Trauma team activation",
  #               "No trauma team activation"))   
  
  # ed_emerg_proc_other
  dpc$ed_emerg_proc_other <- factor(
    dpc$ed_emerg_proc_other,
    levels = c(1, 2, 3, 4, 5), 
    labels = c("Chest drain",
               "External fixation of fracture",
               "Major fracture surgery",
               "Wound revision in OR",
               "Other action")) 
  
  # "ed_emerg_proc" 
  dpc$ed_emerg_proc <- factor(
    dpc$ed_emerg_proc,
    levels = c(1, 2, 3, 4, 5, 6, 7, 8), 
    labels = c("Thoracotomy",
               "Laparotomy",
               "Pelvis Packing",
               "Revascularization",
               "Radiological intervention",
               "Craniotomy",
               "Intracranial pressure measurement",
               "Other")) 
  
  #"pre_transport" 
  dpc$pre_transport <- factor(
    dpc$pre_transport,
    levels = c(1, 2, 3, 4, 5, 6, 7), 
    labels = c("Ground ambulance",
               "Helicopter ambulance",
               "Ambulance flight",
               "Private/public vehicle",
               "Walking",
               "Police",
               "other")) 
  
  # "ed_intub_type" 
  dpc$ed_intub_type <- factor(
    dpc$ed_intub_type,
    levels = c(1, 2, 3, 4), 
    labels = c("Intubation/surgical airway with medication",
               "Supraglottic airway using medication",
               "Intubation/surgical airway without medication",
               "Supraglottic airway without medication")) 
  
    #  "ed_intubated" - ihopslagen med pre intub i var intub 
    dpc$ed_intubated <- factor(
      dpc$ed_intubated,
      levels = c(1, 2), 
      labels = c("Yes",
                 "No"))
  
  # "pre_intub_type" 
  dpc$pre_intub_type <- factor(
    dpc$pre_intub_type,
    levels = c(1, 2, 3, 4), 
    labels = c("Intubation/surgical airway with medication",
               "Supraglottic airway using medication",
               "Intubation/surgical airway without medication",
               "Supraglottic airway without medication"))  
  
  #  #  "pre_intubated" ihopslagning med i var intub
    dpc$pre_intubated <- factor(
      dpc$pre_intubated,
      levels = c(1, 2), 
      labels = c("Yes",
                 "No"))  
  
  # "pre_provided"
  dpc$pre_provided <- factor(
    dpc$pre_provided,
    levels = c(1, 3, 4), 
    labels = c("No prehospital care",
               "treatment without physician",
               "treatment with physician"))          
  
  # "FirstTraumaDT_NotDone"  
  dpc$FirstTraumaDT_NotDone <- factor(
    dpc$FirstTraumaDT_NotDone,
    levels = c(0, 1), 
    labels = c("CT done",
               "CT not done"))
  
  # "AlarmRePrioritised" - Ev ta bort pga reg tid från 2017?
  dpc$AlarmRePrioritised <- factor(
    dpc$AlarmRePrioritised,
    levels = c(1, 2, 3, 4), 
    labels = c("no reprioritization",
               "reprioritization to level 1",
               "reprioritization to level 2",
               "Alarm cancelled"))
  
  # "TraumaAlarmAtHospital" - Ev ta bort pga reg tid från 2017
  dpc$TraumaAlarmAtHospital <- factor(
    dpc$TraumaAlarmAtHospital,
    levels = c(1, 2, 99), 
    labels = c("Trauma alarm level 1",
               "Trauma alarm level 2",
               "No trauma alarm"))
  
  # "TraumaAlarmCriteria" 
  
  #  ### Behövs denna????
  #  dpc$TraumaAlarmCriteria <- factor(
  #    dpc$TraumaAlarmCriteria,
  #    levels = c(1, 2, 3), 
  #    labels = c("National, 2 levels",
  #               "National, 1 level",
  #               "local"))
  
  
  #  "hosp_dischg_dest"
  dpc$hosp_dischg_dest <- factor(
    dpc$hosp_dischg_dest,
    levels = c(1, 2, 3, 4, 5, 6, 7), 
    labels = c("Home",
               "Rehab",
               "Morgue",
               "ICU (higher care level)",
               "ICU (same care level)",
               "Other department",
               "psychiatric care"))
  
  # "host_vent_days_NotDone"
  dpc$host_vent_days_NotDone <- factor(
    dpc$host_vent_days_NotDone,
    levels = c(0, 1),
    labels = c("On ventilator", "Not on ventilator"))
  
  # "ed_be_art_NotDone"
  
  #  ######  OBS - Inkongruent/fel jmf med övrig BE kolumn  
  #  
  #  dpc$ed_be_art_NotDone <- factor(
  #    dpc$ed_be_art_NotDone,
  #    levels = c(0, 1),
  #    labels = c("Done", "Not done"))
  
  # "ed_inr_NotDone"   
  dpc$ed_inr_NotDone <- factor(
    dpc$ed_inr_NotDone,
    levels = c(0, 1),
    labels = c("Done", "Not done"))
  
  
  #"pt_asa_preinjury"       
  dpc$pt_asa_preinjury <- factor(
    dpc$pt_asa_preinjury,
    levels = c(1, 2, 3, 4), 
    labels = c("A healthy patient",
               "Mild systemic disease",
               "Severe systemic disease",
               "Life threatening disease"))
  
  #"pre_card_arrest" 
  dpc$pre_card_arrest <- factor(
    dpc$pre_card_arrest,
    levels = c(1, 2),
    labels = c("Yes", "No"))
  
  #"inj_dominant"
  dpc$inj_dominant <- factor(
    dpc$inj_dominant,
    levels = c(1, 2),
    labels = c("Blunt", "Penetrating"))
  
  # "inj_mechanism"  
  dpc$inj_mechanism <- factor(
    dpc$inj_mechanism,
    levels = c(1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12), 
    labels = c("Motor vehicle accident",
               "Motorcycle accident",
               "Bicycle accident",
               "Injured pedestrian",
               "Other vehicle accident",
               "Gunshot wound",
               "Injury from sharp object",
               "Struck by a blunt object",
               "low energy fall",
               "High energy fall",
               "Explosion",
               "Other injury"))
  
  # "inj_intention" 
  dpc$inj_intention <- factor(
    dpc$inj_intention,
    levels = c(1, 2, 3),
    labels = c("Accident", "Self-inflicted", "Abuse"))
  
  #"intub"  
  dpc$intub <- factor(
    dpc$intub,
    levels = c(1, 2, 3),
    labels = c("Inhospital", "Not intubated", "Prehospital"))
  
  #"host_care_level" 
  dpc$host_care_level <- factor(
    dpc$host_care_level,
    levels = c(1, 2, 3, 4, 5), 
    labels = c("Emergency department",
               "General ward",
               "Surgical ward",
               "Specialist ward/Intermediate ward",
               "Intensive care unit"))
  
  #"pt_Gender"              
  dpc$pt_Gender <- factor(
    dpc$pt_Gender,
    levels = c(2, 1),
    labels = c("Female", "Male"))
  
  # "res_survival"
  dpc$res_survival <- factor(
    dpc$res_survival,
    levels = c(1, 2),     
    labels = c("Yes", "No"))
  
  # "ofi" 
  dpc$ofi <- factor(
    dpc$ofi,
    levels = c("Yes", "No"),
    labels = c("Opportunity for improvement", "No opportunity for improvement"))
  
  #########################
  ## Change column names ##
  #########################
  
  var_label(dpc) <- list(
    ofi = "Opportunity for improvement",
    ed_gcs_sum = "ED GCS",
    ed_sbp_value = "ED Systolic Blood Pressure",
    dt_ed_first_ct = "Time to first CT",
    dt_ed_emerg_proc = "Time to definitive treatment",
    intub = "Intubated",
    host_care_level = "Highest level of care",
    pt_age_yrs = "Age",
    ed_rr_value = "Respiratory rate",
    ISS = "Injury severity score",
    pt_Gender = "Gender",
    res_survival = "Dead at 30 days",
    hosp_los_days = "Days in hospital", 
    inj_dominant ="Injury type",          
    inj_mechanism ="Injury mechanism",
    inj_intention ="Injury intention",
    pt_asa_preinjury ="ASA-score before injury",      
    pre_card_arrest ="PH cardiac arrest",
    pre_gcs_sum ="PH GCS",
    pre_gcs_motor ="PH GCS - Motor response",         
    ed_gcs_motor ="ED GCS",
    pre_sbp_value ="PH systolic blood preassure",         
    pre_rr_value ="PH respiratory rate",
    ed_be_art ="First base excess",     
    ed_inr ="First INR",
    ed_inr_NotDone ="INR not meassured",
    hosp_vent_days ="Days on ventilator",        
    host_vent_days_NotDone ="Ventilator not required",
    hosp_dischg_dest ="Discharge destination",      
    res_gos_dischg ="Discharge glascow outcome scale",
    TraumaAlarmAtHospital ="Type of trauma alarm",
    AlarmRePrioritised ="reprioritizations",
    NISS ="New Injury Severity Score",
    FirstTraumaDT_NotDone ="CT not done",
    dt_alarm_hosp ="Time, alarm to hospital arrival",         
    pre_provided ="Highest PH competence",
    pre_intub_type ="PH airway management",        
    ed_intub_type ="Hospital airway management",
    pre_transport ="Arrival mode",         
    ed_emerg_proc ="Emergency procedure",
    ed_emerg_proc_other ="Other emergency prodecures",
    host_transfered ="Transfer status",
    dt_alarm_scene ="Injury scene time",        
    dt_ed_norm_be ="Time to normal base excess",
    NumberOfActions ="Number of interventions",
    NumberOfInjuries ="Number of injuries") ##Requires library(labelled)
  
  
  formated.data <- dpc
  return(formated.data)
}