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Param Revamp - Malaria #1736

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Param Revamp - Malaria #1736

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475049b
param revamp malaria
mmsuarezcosta Oct 24, 2025
41f248f
param revamp malaria
mmsuarezcosta Oct 24, 2025
c1cd0a4
fix linting errors
mmsuarezcosta Oct 24, 2025
93d7649
fix itn param rename errors
mmsuarezcosta Oct 25, 2025
4770910
update paraam 'itn_projected_future_coverage' name in test_htm_scaleu…
mmsuarezcosta Oct 27, 2025
e304f1d
delete unused files
mmsuarezcosta Oct 27, 2025
fa10ff7
change nomenclature itn_projected_future_coverage back to itn, update…
mmsuarezcosta Oct 27, 2025
9b40d12
update additional param files
mmsuarezcosta Oct 27, 2025
c97429a
add param labels, temp soln for rdt_testing_rates with col 'param_label'
mmsuarezcosta Oct 28, 2025
17b2348
revisit itn param nomenclature and df indexing
mmsuarezcosta Oct 28, 2025
621a4fa
Merge branch '1649-malaria' of https://github.com/UCL/TLOmodel into 1…
mmsuarezcosta Oct 28, 2025
01c778e
revert file deletion
mmsuarezcosta Oct 30, 2025
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4 changes: 2 additions & 2 deletions resources/malaria/ResourceFile_malaria/MAP_IRSrates.csv
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4 changes: 2 additions & 2 deletions resources/malaria/ResourceFile_malaria/MAP_ITNrates.csv
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4 changes: 2 additions & 2 deletions resources/malaria/ResourceFile_malaria/WHO_TestData2023.csv
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4 changes: 2 additions & 2 deletions resources/malaria/ResourceFile_malaria/parameters.csv
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4 changes: 2 additions & 2 deletions resources/malaria/ResourceFile_malaria/scaleup_parameters.csv
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173 changes: 125 additions & 48 deletions src/tlo/methods/malaria.py
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6 changes: 3 additions & 3 deletions tests/test_htm_scaleup.py
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Original file line number Diff line number Diff line change
Expand Up @@ -189,15 +189,15 @@ def test_htm_scale_up(seed):
files="scaleup_parameters")

assert sim.modules["Malaria"].parameters["prob_malaria_case_tests"] == new_mal_params.loc[
new_mal_params.parameter == "prob_malaria_case_tests", "target_value"].values[0]
new_mal_params.parameter_name == "prob_malaria_case_tests", "value"].values[0]
assert sim.modules["Malaria"].parameters["rdt_testing_rates"]["Rate_rdt_testing"].eq(new_mal_params.loc[
new_mal_params.parameter == "rdt_testing_rates", "target_value"].values[0]).all()
new_mal_params.parameter_name == "rdt_testing_rates", "value"].values[0]).all()

# some irs coverage levels should now = 1.0
assert sim.modules["Malaria"].itn_irs['irs_rate'].any() == 1.0
# itn rates for 2019 onwards
assert sim.modules["Malaria"].parameters["itn"] == new_mal_params.loc[
new_mal_params.parameter == "itn", "target_value"].values[0]
new_mal_params.parameter_name == "itn", "value"].values[0]

# check tb parameters changed
new_tb_params = read_csv_files(resourcefilepath / 'ResourceFile_TB', files="scaleup_parameters")
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