skeleton for working out ICNARC acute physiology score

icnarc score.R

-
  fname: icnarc_score
  sqltype: tinyint
  varlab: ICNARC acute physiology score
  derived: True
  derived_missing_ok: True
  primaryfields:
    - hrate
    - bpsys
    - temperature
    - rrate
    - pao2
    - abgfio2
    - rxfio2
    - ph
    - urea
    - creatinine
    - sodium
    - urine_vol
    - urine_period
    - v_timestamp
    - wcc
    - gcst
  code:
    python: |
      # CHANGED: 2013-02-08 - since rxfio2 is now an integer code
      rxfio2_dict = {0:'r', 1:'w', 2:'v', 3:'b', 4:'c', 5:'n', 6:'p', 7:'o'}
      if rxfio2 in rxfio2_dict:
        rxfio2 = rxfio2_dict[rxfio2]
      else:
        rxfio2 = ''
      # derive intermediate vars uvol24 and pf
      if urine_period is not None and v_timestamp is not None and urine_vol is not None:
        if urine_period in [1, 2, 3]:
            uvol24 = urine_vol / {1:1,2:6, 3:12}[urine_period] * 24
        elif urine_period == 4 and v_timestamp.hour != 0:
            uvol24 = urine_vol / v_timestamp.hour * 24
      else:
          uvol24 = None
      if (pao2 is not None) and (abgfio2 is not None):
          # ensure that one var is float else get integer division in python 2.x
          pf = round(float(pao2) * 7.6 / abgfio2 * 100)
      else:
          pf = None
      i = 0
      # heart rate
      if hrate is None:
        pass
      elif hrate <= 39:
        i += 14
      elif hrate >= 140:
        i += 3
      elif hrate >= 120:
        i += 2
      elif hrate >= 110:
        i += 1
      # systolic bp
      if bpsys is None:
        pass
      elif bpsys <= 49:
        i += 15
      elif bpsys <=59:
        i += 9
      elif bpsys <=69:
        i += 6
      elif bpsys <= 79:
        i += 4
      elif bpsys <= 99:
        i += 2
      elif bpsys >= 220:
        i += 16
      elif bpsys >= 180:
        i += 7
      # temperature
      if temperature is None:
        pass
      elif temperature <= 33.9:
        i += 12
      elif temperature <= 35.9:
        i += 7
      elif temperature <= 38.4:
        i += 1
      elif temperature >= 41:
        i += 5
      # respiratory rate
      if rrate is None:
        pass
      elif rrate <= 5:
        i += 1
      elif rrate >= 25:
        i += 5
      elif rrate >= 14:
        i += 2
      elif rrate >= 12:
        i += 1
      # p:f ratio
      if pf is None:
        pass
      elif pf <= 99 and rxfio2 not in list('cnp'):
        i += 6
      elif pf <= 199 and rxfio2 not in list('cnp'):
        i += 3
      elif pf <= 99 and rxfio2 in list('cnp'):
        i += 8
      elif pf <= 199 and rxfio2 in list('cnp'):
        i += 5
      elif pf >= 200 and rxfio2 in list('cnp'):
        i += 3
      # pH
      if ph is None:
        pass
      elif ph <= 7.14:
        i += 4
      elif ph <= 7.24:
        i += 2
      elif ph >= 7.5:
        i += 4
      elif ph >= 7.33:
        i += 1
      # urea
      if urea is None:
        pass
      elif urea >= 14.4:
        i += 5
      elif urea >= 7.2:
        i += 3
      elif urea >= 6.2:
        i += 1
      # creatinine
      if creatinine is None:
        pass
      elif creatinine > 1.5 * 88.4:
        i += 4
      elif creatinine > 0.6 * 88.4:
        i += 2
      # sodium
      if sodium is None:
        pass
      elif sodium <= 129:
        i += 4
      elif sodium >= 160:
        i += 8
      elif sodium >= 155:
        i += 7
      elif sodium >= 150:
        i += 4
      # urine volume
      if uvol24 is None:
        pass
      elif uvol24 <= 399:
        i += 7
      elif uvol24 <= 599:
        i += 6
      elif uvol24 <= 899:
        i += 5
      elif uvol24 <= 1499:
        i += 3
      elif uvol24 <= 1999:
        i += 1
      # white cell count
      if wcc is None:
        pass
      elif wcc <= 0.9:
        i += 6
      elif wcc <= 2.9:
        i += 3
      elif wcc >= 40:
        i += 4
      elif wcc >= 15:
        i += 2
      # gcs
      if gcst is None:
        pass
      elif gcst <= 3:
        i += 11
      elif gcst <=4:
        i += 9
      elif gcst <= 5:
        i += 6
      elif gcst <= 6:
        i += 4
      elif gcst <= 13:
        i += 2
      elif gcst <= 14:
        i += 1
      derived_var = i