Vax dedup #26
Vax dedup #26
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…odel that not ready yet.
* add sft tests * Add broadcast co_event and doc for intervention * Add path to manifest.py so we can run test at any dir * Added README.md for tests * Add unittests coverage test * Add coverage_check.py * Change coverage test file name to get_unittest_coverage.py
Adding new examples for Pakistan provinces and various coverage regimes.
| elif deduplication_policy == "combine": | ||
| intervention.Enable_Intervention_Replacement = 0 | ||
| else: | ||
| raise ValueError( f"duplication_policy needs to be 'replace' or 'combine', not '{duplication_policy}'." ) |
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{duplication_policy} should be {deduplication_policy}
| @@ -150,7 +150,10 @@ def add_vax_intervention(campaign, values, min_age=0.75, max_age=15, binary_immu | |||
| import emodpy_typhoid.interventions.typhoid_vaccine as tv | |||
| print(f"Telling emod-api to use {manifest.schema_file} as schema.") | |||
| campaign.set_schema(manifest.schema_file) | |||
| camp_coverage = values['coverage'] | |||
| if 'coverage' in values: | |||
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This is not working for run('Coverage_RIA') case.
I changed to following to replace line 153 to line 156 which seems working for all cases
for key in values.keys():
if 'coverage' in key:
camp_coverage = values[key]
break
| @@ -25,7 +25,7 @@ def new_intervention( camp, efficacy=0.82, mode="Shedding", constant_period=0, d | |||
| constant_period (float, optional): The constant period of the waning effect in days. Default is 0. | |||
| decay_constant (float, optional): The decay time constant for the waning effect. Default is 6935.0. | |||
| expected_expiration (float, optional): The mean duration before efficacy becomes 0. If this is set to non-zero value, the constant_period and decay_constant are ignored. These are two different modes of waning. | |||
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| deduplication_policy (string, optional): Defaults to 'replace'. Can also be 'combine'. | |||
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line 28 for docstring should not be here. Should be moved to def new_vax function's doc string
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I am comparing new build dev07 and dev05 for emod-typhoid with same examples, I got different populations: old: |
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Thanks for the review @shchen-idmod. Making those changes now. That's very surprising about the population difference just from the builds! And a great catch. I'll look into that. |
| @@ -73,7 +73,7 @@ def new_vax( camp, efficacy=0.82, mode="Acquisition", constant_period=0, decay_c | |||
| elif deduplication_policy == "combine": | |||
| intervention.Enable_Intervention_Replacement = 0 | |||
| else: | |||
| raise ValueError( f"duplication_policy needs to be 'replace' or 'combine', not '{duplication_policy}'." ) | |||
| raise ValueError( f"deduplication_policy needs to be 'replace' or 'combine', not '{duplication_policy}'." ) | |||
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Still need to change the last word in this line
| if 'coverage' in key: | ||
| camp_coverage = values[key] | ||
| break | ||
| else: |
This PR adds support for vaccine de-duplication which enables boosting. It requires a new version of the model: emod_typhoid==0.0.4.dev7
https://github.com/InstituteforDiseaseModeling/emodpy-typhoid/pull/26/files#diff-512107aeda10e42e2086b731f9e875a96c5b1e5d265acfa1163ef625fdef459fR5