Merge pull request #44 from rcpch/eatyourpeas/issue43

adds midparental height functions

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 4.2.1
+current_version = 4.2.3
 tag = False
 commit = True
 

rcpchgrowth/__init__.py

@@ -1,15 +1,16 @@
+from .age_advice_strings import comment_prematurity_correction
+from .bmi_functions import bmi_from_height_weight, weight_for_bmi_height
+from .cdc import select_reference_data_for_cdc_chart
+from .centile_bands import centile_band_for_centile
+from .chart_functions import create_chart, generate_custom_sds_line
+from .constants import *
 from .date_calculations import chronological_decimal_age, corrected_decimal_age, chronological_calendar_age, estimated_date_delivery, corrected_gestational_age
+from .dynamic_growth import create_thrive_line, return_correlation, create_thrive_lines
 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
-from .dynamic_growth import create_thrive_line, return_correlation, create_thrive_lines
-from .uk_who import select_reference_data_for_uk_who_chart
-from .turner import select_reference_data_for_turner
+from .measurement import Measurement
+from .mid_parental_height import *
 from .trisomy_21 import select_reference_data_for_trisomy_21
 from .trisomy_21_aap import select_reference_data_for_trisomy_21_aap
-from .measurement import Measurement
-from .chart_functions import create_chart, generate_custom_sds_line
-from .constants import *
+from .turner import select_reference_data_for_turner
+from .uk_who import select_reference_data_for_uk_who_chart

rcpchgrowth/mid_parental_height.py

@@ -0,0 +1,50 @@
+from .constants import HEIGHT, MALE, FEMALE, UK_WHO
+from .global_functions import sds_for_measurement
+"""
+Functions to calculate mid-parental height
+
+cf 
+Tanner JM, Whitehouse RH, Takaishi M. Standards from birth to maturity for height, weight, height velocity, and weight velocity: British children, 1965. I. Arch Dis Child. 1966;41(219):454-471.
+The strengths and limitations of parental heights as a predictor of attained height, Charlotte M Wright, Tim D Cheetham, Arch Dis Child 1999;81:257–260
+"""
+
+def mid_parental_height(maternal_height, paternal_height, sex):
+    """
+    Calculate mid-parental height
+    """
+    if sex == MALE:
+        return (maternal_height + paternal_height + 13) / 2
+    else:
+        return (maternal_height + paternal_height - 13) / 2
+
+def mid_parental_height_z(maternal_height, paternal_height, reference=UK_WHO):
+    """
+    Calculate mid-parental height standard deviation
+    """
+
+    # convert parental heights to z-scores
+    maternal_height_z = sds_for_measurement(reference=reference, age=20.0, measurement_method=HEIGHT, observation_value=maternal_height, sex=FEMALE)
+    paternal_height_z = sds_for_measurement(reference=reference, age=20.0, measurement_method=HEIGHT, observation_value=paternal_height, sex=MALE)
+
+    # take the measn of the z-scores and apply the regression coefficient of 0.5 - simplifed: (MatHtz +PatHtz)/4
+    mid_parental_height_z_score = (maternal_height_z + paternal_height_z) / 4.0
+
+    return mid_parental_height_z_score
+
+def expected_height_z_from_mid_parental_height_z(mid_parental_height_z):
+    """
+    Calculate expected height z score from mid-parental height z-score
+
+    Ninety per cent of children had values within 1.4 SDS of their expected SDS (just over two
+    centile spaces) and only 1% had values > 2 SDS (three centile spaces) below (cf Wright et al)
+    """
+
+    return mid_parental_height_z * 0.5
+
+def lower_and_upper_limits_of_expected_height_z(mid_parental_height_z):
+    """
+    Calculate lower and upper limits of expected height z score from mid-parental height z-score
+    Returns a tuple of (lower, upper) limits
+    """
+
+    return mid_parental_height_z - 1.4, mid_parental_height_z + 1.4

rcpchgrowth/tests/test_mid_parental_height.py

@@ -0,0 +1,16 @@
+import pytest
+
+from rcpchgrowth.constants import MALE, FEMALE, UK_WHO, CDC
+from rcpchgrowth.mid_parental_height import mid_parental_height, mid_parental_height_z, expected_height_z_from_mid_parental_height_z
+
+maternal_height = 151
+paternal_height = 167
+ACCURACY = 1e-3
+
+
+def test_midparental_height():
+    assert mid_parental_height(maternal_height=maternal_height, paternal_height=paternal_height, sex=MALE) == 165.5 
+    assert mid_parental_height(maternal_height=maternal_height, paternal_height=paternal_height, sex=FEMALE) == 152.5
+    assert mid_parental_height_z(maternal_height=maternal_height, paternal_height=paternal_height, reference=UK_WHO) == pytest.approx(-0.8943229, ACCURACY)
+    assert mid_parental_height_z(maternal_height=maternal_height, paternal_height=paternal_height, reference=CDC) == pytest.approx(-0.8177165233046019, ACCURACY)
+    assert expected_height_z_from_mid_parental_height_z(mid_parental_height_z=-0.8943229) == pytest.approx(-0.44716145, ACCURACY)

setup.py

@@ -8,7 +8,7 @@
 
 setup(
     name="rcpchgrowth",
-    version="4.2.1",
+    version="4.2.3",
     description="SDS and Centile calculations for UK Growth Data",
     long_description=long_description,
     url="https://github.com/rcpch/digital-growth-charts/blob/master/README.md",