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Param Revamp - Schisto #1720

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Param Revamp - Schisto #1720

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c3326cd
param revamp schisto
mmsuarezcosta Sep 29, 2025
b6ccece
Parameterize scenario parameters mda_execute and single_district
mmsuarezcosta Oct 7, 2025
e1f1e0c
update schisto files based on parameterization of schisto.py, add dis…
mmsuarezcosta Oct 7, 2025
74f9647
remove param mda_coverage_upper_limit, add date interval parameters, …
mmsuarezcosta Oct 7, 2025
de99c53
remove param mda_coverage_upper_limit, add date interval parameters, …
mmsuarezcosta Oct 7, 2025
eeb3d96
clean param file
mmsuarezcosta Oct 7, 2025
1fdfbee
linting fixes
mmsuarezcosta Oct 7, 2025
d23ec0b
remove mda_execute from schisto_analysis.py
mmsuarezcosta Oct 8, 2025
ec2f8da
delete unused files and add param_label 'calibration data' for all da…
mmsuarezcosta Oct 8, 2025
95ca91f
revert function try_cast_to_float, refactor file name
mmsuarezcosta Oct 10, 2025
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3 changes: 0 additions & 3 deletions resources/ResourceFile_Schisto/DALYs.csv
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4 changes: 2 additions & 2 deletions resources/ResourceFile_Schisto/District_Params_haematobium.csv
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4 changes: 2 additions & 2 deletions resources/ResourceFile_Schisto/District_Params_mansoni.csv
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3 changes: 0 additions & 3 deletions resources/ResourceFile_Schisto/ESPEN.csv
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4 changes: 2 additions & 2 deletions resources/ResourceFile_Schisto/ESPEN_MDA.csv
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3 changes: 0 additions & 3 deletions resources/ResourceFile_Schisto/ESPEN_codebook.csv
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3 changes: 0 additions & 3 deletions resources/ResourceFile_Schisto/InitialData_haematobium.csv
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3 changes: 0 additions & 3 deletions resources/ResourceFile_Schisto/InitialData_mansoni.csv
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4 changes: 2 additions & 2 deletions resources/ResourceFile_Schisto/LatestData_haematobium.csv
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4 changes: 2 additions & 2 deletions resources/ResourceFile_Schisto/LatestData_mansoni.csv
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3 changes: 0 additions & 3 deletions resources/ResourceFile_Schisto/MDA_historical_Coverage.csv
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3 changes: 0 additions & 3 deletions resources/ResourceFile_Schisto/Parameters.csv
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3 changes: 0 additions & 3 deletions resources/ResourceFile_Schisto/Symptoms.csv
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3 changes: 3 additions & 0 deletions resources/ResourceFile_Schisto/parameter_values.csv
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4 changes: 1 addition & 3 deletions src/scripts/schistosomiasis/baseline_run.py
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Original file line number Diff line number Diff line change
Expand Up @@ -89,9 +89,7 @@ def modules(self):
bladder_cancer.BladderCancer(resourcefilepath=self.resources),
diarrhoea.Diarrhoea(resourcefilepath=self.resources),
hiv.Hiv(resourcefilepath=self.resources),
schisto.Schisto(resourcefilepath=self.resources,
mda_execute=self.mda_execute,
single_district=self.single_district),
schisto.Schisto(resourcefilepath=self.resources),
stunting.Stunting(resourcefilepath=self.resources),
tb.Tb(resourcefilepath=self.resources),
wasting.Wasting(resourcefilepath=self.resources),
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6 changes: 3 additions & 3 deletions src/scripts/schistosomiasis/schisto_analysis.py
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Expand Up @@ -16,7 +16,7 @@
from tlo.util import read_csv_files


def run_simulation(popsize=10000, haem=True, mansoni=True, mda_execute=True):
def run_simulation(popsize=10000, haem=True, mansoni=True):
outputpath = Path("./outputs") # folder for convenience of storing outputs
# The resource files
resourcefilepath = Path("./resources")
Expand All @@ -41,7 +41,7 @@ def run_simulation(popsize=10000, haem=True, mansoni=True, mda_execute=True):
sim.register(healthsystem.HealthSystem())
sim.register(healthburden.HealthBurden())
sim.register(contraception.Contraception())
sim.register(schisto.Schisto(mda_execute=mda_execute))
sim.register(schisto.Schisto())
if haem:
sim.register(schisto.Schisto_Haematobium(symptoms_and_HSI=False))
if mansoni:
Expand All @@ -59,7 +59,7 @@ def run_simulation(popsize=10000, haem=True, mansoni=True, mda_execute=True):
return sim, output


sim, output = run_simulation(popsize=10000, haem=True, mansoni=False, mda_execute=False)
sim, output = run_simulation(popsize=10000, haem=True, mansoni=False)


# ---------------------------------------------------------------------------------------------------------
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5 changes: 4 additions & 1 deletion src/scripts/schistosomiasis/schisto_calibration_check.py
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Original file line number Diff line number Diff line change
Expand Up @@ -65,9 +65,12 @@ def run_simulation(popsize=popsize, mda_execute=True):
healthburden.HealthBurden(),
healthsystem.HealthSystem(),
simplified_births.SimplifiedBirths(),
schisto.Schisto(mda_execute=mda_execute),
schisto.Schisto(),
)

# Override schisto parameters
sim.modules["Schisto"].parameters["mda_execute"] = mda_execute

# initialise the population
sim.make_initial_population(n=popsize)

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6 changes: 4 additions & 2 deletions src/scripts/schistosomiasis/schisto_single_run_local.py
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Original file line number Diff line number Diff line change
Expand Up @@ -72,10 +72,12 @@ def run_simulation(popsize,
healthsystem.HealthSystem(disable_and_reject_all=hs_disable_and_reject_all,
cons_availability='all'),
simplified_births.SimplifiedBirths(),
schisto.Schisto(mda_execute=mda_execute,
single_district=single_district),
schisto.Schisto(),
)

# Override schisto parameters
sim.modules["Schisto"].parameters["mda_execute"] = mda_execute
sim.modules["Schisto"].parameters["single_district"] = single_district
# sim.modules["Schisto"].parameters["calibration_scenario"] = 0
# sim.modules["Schisto"].parameters["scaleup_WASH"] = 0.0 # 1.0=True
# sim.modules["Schisto"].parameters["scaleup_WASH_start_year"] = 2011
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