More tests and consumables for CMD #1625
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| @@ -376,6 +376,17 @@ def add_record(df: pd.DataFrame, record: Dict): | |||
| 'Unit_Cost': np.nan}, | |||
| ) | |||
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| cons = add_record( | |||
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I see this chnage to the script generating the consumables... but I don't see a new version of the resulting ResourceFile (ResourceFile_Consumables_Items_and_Packages.csv)... please commit that too.
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ALso - do you want to declare an availability for it? By not doing so (as currently) it will follow the average for other consumables, which may be fine.
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I tried to do it in line 1675 but I commented it out because the 40% of the availability isn't accurate (just a placeholder). I am working on finding more accurate data.
| # If medication is available, flag as being on medication | ||
| df.at[person_id, f'nc_{self.condition}_on_medication'] = True | ||
| # Determine if the medication will work to prevent death | ||
| df.at[person_id, f'nc_{self.condition}_medication_prevents_death'] = \ | ||
| self.module.rng.rand() < self.module.parameters[f'{self.condition}_hsi'].pr_treatment_works | ||
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| #todo review logic of diabetes second and third line drugs |
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this is causing the test_analysis.py to fail because medication_item_code_second_line is not defined anywhere.
| @@ -1700,12 +1778,15 @@ def apply(self, person_id, squeeze_factor): | |||
| # lower back pain - 2400mg aspirin daily (2400*30.5), CIHD - 75mg aspirin daily (75*30.5) | |||
| dose = {'diabetes': 30_500, | |||
| 'hypertension': 610, | |||
| 'chronic_kidney_disease': 1, | |||
| 'chronic_kidney_disease': 12, | |||
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thank you. here,. are you able to add a commment in-line to give justication for the change?
| @@ -1671,8 +1747,10 @@ def __init__(self, module, person_id, condition): | |||
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| self.TREATMENT_ID = 'CardioMetabolicDisorders_Treatment' | |||
| self.EXPECTED_APPT_FOOTPRINT = self.make_appt_footprint({'Over5OPD': 1}) | |||
| self.ACCEPTED_FACILITY_LEVEL = '1b' | |||
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| if condition == 'chronic_kidney_disease': | |||
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suggest (just for neatness) to do this in one line:
self.ACCEPTED_FACILITY_LEVEL = '3' if conditon == 'chronic_kidney_disease' else '1b'
| @@ -15,6 +15,7 @@ | |||
| import math | |||
| from itertools import combinations | |||
| from pathlib import Path | |||
| from random import random | |||
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this line can be removed as this import is not used (which is correct, for all random things, use the module's rng)
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That was added when we were trying to check availability of consumables (which has been commented out, as stated in the earlier comment) but has been removed for now.
| # Select all eligible individuals (men & women w/o condition and in age range) | ||
| sample_eligible(men_wo_cond & (df.age_range == _age_range), p[f'm_{_age_range}'], condition) | ||
| sample_eligible(women_wo_cond & (df.age_range == _age_range), p[f'f_{_age_range}'], condition) | ||
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I can't see what is intended with this change: don't think this any effect and so change should be rolled-back
(probably this a rememant of some experiments you were doing?!)
| @@ -1362,7 +1371,8 @@ def proportion_of_something_in_a_groupby_ready_for_logging(_df, something, group | |||
| {'count': x['nc_n_conditions'].count()})) | |||
| n_comorbidities_all.loc[:, num] = col['count'] | |||
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| prop_comorbidities_all = n_comorbidities_all.div(n_comorbidities_all.sum(axis=1), axis=0) | |||
| row_sums = n_comorbidities_all.sum(axis=1) | |||
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is this change to avoid some divisions by zero? Looks fine but wondering if the same effect (suppression of na's) could be accomplished by stick .fillna(0.) on the end of the original?
| @@ -1484,6 +1494,9 @@ def do_for_each_condition(self, _c) -> bool: | |||
| hs = self.sim.modules['HealthSystem'] | |||
| df = self.sim.population.props | |||
| person_id = self.target | |||
| m = self.module | |||
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no purpose for change, so roll back?
| of the initial treatment. They are not second and third line drugs. | ||
| """ | ||
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| medication_codes = self.module.parameters[f'{self.condition}_hsi'].get('medication_item_code') |
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from where are these being read?
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This file is found in resources\cmd\ResourceFile_cmd_condition_hsi\diabetes.csv
# Conflicts: # src/tlo/methods/cardio_metabolic_disorders.py
Reviewing and adding tests and consumables for CMD. Fixes #1607