Gabriel/syphilis - #1885
Gabriel/syphilis#1885Gabbie123king wants to merge 5 commits into
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| df.at[individual_id, 'ps_syphilis_state'] = 'primary' | ||
| df.at[individual_id, 'ps_syphilis_treated'] = False |
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wont this be false already anyway?
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Hi Joe, It will usually already be False, but a woman could have received treatment earlier in the pregnancy before this scheduled incident infection occurs. Resetting it here ensures the new infection is treated as untreated and is not incorrectly prevented from progressing by the earlier treatment flag. Apologies for delays, am addressing some of the comments in the model and updating the write-up for each change, logic and code cleanup. It will be shared soon.
| df.loc[id_or_index, 'ps_premature_rupture_of_membranes'] = False | ||
| df.loc[id_or_index, 'ps_chorioamnionitis'] = False | ||
| df.loc[id_or_index, 'ps_emergency_event'] = False | ||
| self.sim.modules['Syphilis'].reset_pregnancy_syphilis_properties(id_or_index) |
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again, if were having the separate syphilis module i think you can just set the properties within the syphilis module itself (its cleaner)
| self.module.apply_risk_of_premature_rupture_of_membranes_and_chorioamnionitis( | ||
| gestation_of_interest=gestation_of_interest) | ||
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| self.sim.modules['Syphilis'].apply_risk_of_congenital_syphilis( |
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is there an epidemiological reason for only applying the risk of congenital infection starting at 22 weeks gestational age?
| logger = logging.getLogger(__name__) | ||
| logger.setLevel(logging.INFO) | ||
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| DETECTABLE_STAGES = ['primary', 'secondary', 'early_latent', 'late_latent'] |
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what are the 'non-detectable stages'? or is this just a test
| df.at[person, 'ps_congenital_syphilis'] = True | ||
| pregnancy_helper_functions.store_dalys_in_mni( | ||
| person, mni, 'congenital_syphilis_onset', module.sim.date | ||
| ) |
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why does congenital infection have its own DALY weight attached?
| future_stillbirth_weeks = [ | ||
| week for week in CONGENITAL_SYPHILIS_STILLBIRTH_CHECKPOINTS | ||
| if week >= gestation_of_interest | ||
| ] |
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Can you explain whats happening here?
| df.at[child_id, 'nb_early_preterm'] = False | ||
| df.at[child_id, 'nb_late_preterm'] = False | ||
| df.at[child_id, 'nb_preterm_birth_disab'] = 'none' | ||
| self.sim.modules['Syphilis'].do_newborn_congenital_syphilis_handoff(mother_id, child_id) |
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i would move this until after the properties are set and then add a comment explaining whats happening
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also - currently there are no newborn outcomes (death/disability) associated with congential syphils. is that the case?
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| # We assume that treatment is 100% effective at curing infection | ||
| df.at[person_id, 'ps_syphilis'] = False | ||
| self.sim.modules['Syphilis'].treat_maternal_syphilis(person_id) |
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ok if this is the approach thats doing to be taken we need to review the parameters which determine if screening etc are delivered because currently treatment is essentially never delivered
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| def test_congenital_syphilis_stillbirth_risk_is_drawn_once_at_transmission(seed): | ||
| """Changing congenital stillbirth risk after infection should not create later repeated draws.""" |
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i dont follow the logic of this test! maybe some more description needed
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| def test_assigned_congenital_syphilis_stillbirth_is_applied_at_next_checkpoint(seed): | ||
| """A congenital syphilis stillbirth assigned at infection should be applied at the next stillbirth checkpoint.""" |
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i understand the logic here - is there an epidemiological reason as to why you cant apply risk of congenital infection and stillbirth in the same month?
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Summary
This PR introduces a Syphilis module for the TLO model, focusing on maternal infection during pregnancy and its potential consequences for the fetus and newborn.
The current implementation establishes the core disease mechanics required before calibration, intervention analysis, and epidemiological validation.
Changes introduced
The module represents:
Validation
A dedicated
tests/test_syphilis.pytest file has been added to validate the module’s core behaviour, including:Current status
This PR focuses on establishing and reviewing the core disease mechanics. Calibration and full epidemiological validation are outside the scope of this PR.
Further work will include:
PregnancySupervisor,CareOfWomenDuringPregnancy, andNewbornOutcomesProgresses #1884