cdc #36
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cdc #36
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… use the CDC adapted version
…ve the data fix three percent centiles to remove 5% and create five percent centiles
… create_data_point not default to UK_WHO
…sults matching cdc explainers
…dc is linearly interpolated so this added to global_functions. Single fail for CDC height in a 2.5y girl: assert 1.3882029662677624 == 1.3893 ± 1.0e-03
…D. This test therefore is amended erroneously to pass:
{
"birth_date": "2015-04-01",
"observation_date": "2017-10-04",
"gestation_weeks": 30,
"gestation_days": 2,
"sex": "female",
"measurement_method": "height",
"chronological_age": 2.5106,
"corrected_age": 2.3244,
"observation_value": 95.3,
"corrected_sds": 1.8348,
"chronological_sds": 1.2788,
"age": 30.1273,
"height": 95.3,
"haz": 1.3893,
"hap": 91.7623,
"p50": 16.0277,
"p95": 18.6016,
"mod_haz": 1.3864,
"z_score": 1.3893
},
…r, do not calculate CDC results for preterm babies and signpost to user
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Overview
This PR includes the CDC reference data and integrates the calculations into the code base. It will be a minor version change.
A few things about this:
CDC is made up of WHO (0-2) and CDC (2+). The WHO version used by CDC though has been tweaked, presumably to make the disjunction between the references less marked. The effect is that the code base now has 2 versions of WHO - the WHO one and the US interpretation.
CDC BMI is included and for BMI measurements > 95th centile some clever maths is introduced to prevent some of the issues that have been detailed in conversations about the accuracy of z scores.
Note that there is no preterm data for the moment. The Canadian Fenton data is what is typically used, but this is licensed and conversations about the legals are ongoing. This means that for all corrected ages < 0 no values are returned, but a meaningful error is included.
There is also a fix to the confusing error raised when EDD has not yet been reached in a preterm baby.
There are also tests for the same test subjects used in UK-WHO, but recalculated for CDC using the excellent R package [cdcanthro] (https://github.com/CDC-DNPAO/CDCAnthro) by David Freedman, author of the CDC BMI reference.
Code changes
cdc.py: selects the correct array for LMS values to pass to functions. Excludes Fenton for the time being and returns an empty string.chart_functions.py: updatescreate_chartto acceptcdcand creates a new functions to generate the correct json object. Keys are 'cdc_infant' and 'cdc_child'age_constants.pyandreference_constants: includes some new constants relevant to CDC cutoffs. Also includes values important for Fenton although not implemented yetdata_tables/: the data filesglobal_functions:measurement_from_sdshas extra code that inspects the array for thesigmakey that is found only in CDC BMI reference. This is used to calculate the correct SDS and centiles for BMI values > 95%measurement.py: adds a conditional to not return any data in preterm babies and a suitable error messagetests/cdc/...: test files and gold standardsDocumentation changes (done or required as a result of this PR)
Documentation will be added separately to the documentation repo
Please describe any changes to documentation here.
Related Issues
Closes #35