Merge pull request #36 from rcpch/eatyourpeas/issue35

cdc

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 4.0.2
+current_version = 4.1.0
 tag = False
 commit = True
 

.gitignore

@@ -133,3 +133,6 @@ dmypy.json
 
 # MacOS DS_Store files
 .DS_Store
+
+# Fenton data is licenced and not to be shared
+rcpchgrowth/data_tables/fenton/*.*

rcpchgrowth/__init__.py

@@ -1,6 +1,7 @@
 from .date_calculations import chronological_decimal_age, corrected_decimal_age, chronological_calendar_age, estimated_date_delivery, corrected_gestational_age
-from .global_functions import centile, sds_for_measurement, measurement_from_sds, percentage_median_bmi, mid_parental_height, measurement_for_z
+from .global_functions import centile, sds_for_measurement, measurement_from_sds, percentage_median_bmi, mid_parental_height, measurement_for_z, cubic_interpolation, linear_interpolation
 from .centile_bands import centile_band_for_centile
+from .cdc import select_reference_data_for_cdc_chart
 from .bmi_functions import bmi_from_height_weight, weight_for_bmi_height
 from .age_advice_strings import comment_prematurity_correction
 from .fictional_child import generate_fictional_child_data

rcpchgrowth/age_advice_strings.py

@@ -15,7 +15,7 @@ def comment_prematurity_correction(
             clinician_chronological_decimal_age_comment = "Born Term. No correction has been made for gestation."
     elif chronological_decimal_age > corrected_decimal_age or chronological_decimal_age < corrected_decimal_age:
         ## adjustment for gestational age has been made - even if >=37 weeks
-        lay_corrected_decimal_age_comment = f"Because your child was born at {gestation_weeks}+{gestation_days} weeks gestation, an adjustment has been made to take this into account."
+        lay_corrected_decimal_age_comment = f"Because your child was born at {gestation_weeks}+{gestation_days} weeks gestation an adjustment has been made to take this into account."
         clinician_corrected_decimal_age_comment = "Correction for gestational age has been made."
         lay_chronological_decimal_age_comment = "This is your child's age without taking into account their gestation at birth."
         clinician_chronological_decimal_age_comment = "No correction has been made for gestational age."

rcpchgrowth/cdc.py

@@ -0,0 +1,173 @@
+"""
+Handles CDC-specific reference data selection
+"""
+
+# standard imports
+import json
+from importlib import resources
+from pathlib import Path
+
+# rcpch imports
+from .constants import *
+
+"""
+birth_date: date of birth
+observation_date: date of observation
+sex: sex (string, MALE or FEMALE)
+decimal_age: chronological, decimal
+corrected_age: corrected for prematurity, decimal
+measurement_method: height, weight, bmi, ofc (decimal)
+observation: value (float)
+gestation_weeks: gestational age(weeks), integer
+gestation_days: supplementary days of gestation
+lms: L, M or S
+reference: reference data
+"""
+
+# load the reference data
+data_directory = resources.files("rcpchgrowth.data_tables")
+
+# data_path = Path(data_directory,"fenton", "fenton.json")  # 23 weeks to 50 weeks - currently not in the code base
+# with open(data_path) as json_file:
+#     FENTON_DATA = json.load(json_file)
+#     json_file.close()
+FENTON_DATA = []
+
+data_path = Path(data_directory, "cdc_infants.json")  # CDC interpretation of WHO 0-2y
+with open(data_path) as json_file:
+    CDC_INFANT_DATA = json.load(json_file)
+    json_file.close()
+
+data_path = Path(data_directory, "cdc2-20.json")  # 2 years to 20 years
+with open(data_path) as json_file:
+    CDC_CHILD_DATA = json.load(json_file)
+    json_file.close()
+# public functions
+
+
+def reference_data_absent(age: float, measurement_method: str, sex: str):
+    """
+    Helper function.
+    Returns boolean
+    Tests presence of valid reference data for a given measurement request
+
+    Reference data is not complete for all ages/sexes/measurements.
+    - WHO data is used from 0-2 years
+    - CDC data is used from 2-20 years
+    """
+
+    # if age < 0:
+    #     return True, "CDC data does not exist below 40 weeks."
+    if age > TWENTY_YEARS:  # upper threshold of UK90 data
+        return True, "CDC data does not exist above 20 years."
+    if measurement_method == HEAD_CIRCUMFERENCE and age > THREE_YEARS:
+        return True, "CDC data does not exist for head circumference above 3 years."
+    if measurement_method == BMI and age < TWO_YEARS:
+        return True, "CDC data does not exist for BMI below 2 years."
+    else:
+        return False, None
+
+
+def cdc_reference(age: float, measurement_method, default_youngest_reference: bool = False) -> json:
+    """
+    The purpose of this function is to choose the correct reference for calculation.
+    The CDC standard is an unusual case because it combines two different reference sources: the 1977 National Center for Health Statistics (NCHS) and the WHO2006.
+    - CDC reference runs from 2.04 y to 20 y
+    - WHO 2006 runs from 0  to 2 years
+    - Preterm data is handled by Fenton (which is Canadian data)
+    The function return the appropriate reference file as json
+    """
+
+    # These conditionals are to select the correct reference
+    if age < FENTON_LOWER_THRESHOLD:
+        # Below the range for which we have reference data, we can't provide a calculation.
+        raise ValueError(
+            "There is no reference data for ages below 22 weeks gestation."
+        )
+    elif age < 0:
+        # Below 40 weeks, Fenton data is always used
+        return FENTON_DATA
+
+    elif age < 2 or (age == 2 and default_youngest_reference) or (measurement_method == HEAD_CIRCUMFERENCE and age <= 3):
+        # Below 2 years, CDC interpretation of WHO is used
+        return CDC_INFANT_DATA
+
+    elif age <= CDC_UPPER_THRESHOLD:
+        # CDC data is used for all children 2-20 years
+        return CDC_CHILD_DATA 
+
+    else:
+        return ValueError("There is no CDC reference data above the age of 20 years.")
+
+
+def cdc_lms_array_for_measurement_and_sex(
+    age: float,
+    measurement_method: str,
+    sex: str,
+    default_youngest_reference: bool = False,
+) -> list:
+
+    # selects the correct lms data array from the patchwork of references that make up UK-WHO
+
+    try:
+        selected_reference = cdc_reference(
+            age=age, measurement_method=measurement_method, default_youngest_reference=default_youngest_reference
+        )
+    except:  #  there is no reference for the age supplied
+        return LookupError("There is no CDC reference for the age supplied.")
+
+    # Check that the measurement requested has reference data at that age
+
+    invalid_data, data_error = reference_data_absent(
+        age=age, measurement_method=measurement_method, sex=sex
+    )
+
+    if invalid_data:
+        raise LookupError(data_error)
+    else:
+        return selected_reference["measurement"][measurement_method][sex]
+
+
+def select_reference_data_for_cdc_chart(
+    cdc_reference_name: str,
+    measurement_method: str,
+    sex: str,
+    default_youngest_reference: bool = False,
+):
+
+    # takes a cdc reference name (see parameter constants), measurement_method and sex to return
+    # reference data - NOTE for the moment Fenton is not implemented as license not yet secured and reference data therefore not committed to the repo
+
+    if cdc_reference_name == FENTON:
+        try:
+            fenton_preterm_reference = cdc_lms_array_for_measurement_and_sex(
+                age=-0.01, # an arbritrary age to select the preterm data
+                measurement_method=measurement_method,
+                sex=sex,
+                default_youngest_reference=False # should never need younger reference in this calculation
+            )
+        except:
+            fenton_preterm_reference = []
+        return fenton_preterm_reference
+    elif cdc_reference_name == CDC_INFANT:
+        try:
+            cdc_infant_reference = cdc_lms_array_for_measurement_and_sex(
+                age=0.04, # an arbritrary age to select the infant data
+                measurement_method=measurement_method,
+                sex=sex,
+                default_youngest_reference=default_youngest_reference
+            )
+        except:
+            cdc_infant_reference = []
+        return cdc_infant_reference
+    else:
+        try:
+            cdc_children_reference = cdc_lms_array_for_measurement_and_sex(
+                age=3, # an arbritrary age to select the child data
+                measurement_method=measurement_method,
+                sex=sex,
+                default_youngest_reference=False # There is no younger reference data for CDC
+            )
+        except:
+            cdc_children_reference = []
+        return cdc_children_reference