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Avoid use of apply in computing infection status in schisto module #683

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Aug 10, 2022
Merged

Avoid use of apply in computing infection status in schisto module #683

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33 changes: 16 additions & 17 deletions src/tlo/methods/schisto.py
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Original file line number Diff line number Diff line change
Expand Up @@ -518,18 +518,21 @@ def update_infectious_status_and_symptoms(self, idx: pd.Index) -> None:
if not len(idx) > 0:
return

def _inf_status(age: int, agg_wb: int) -> str:
if age < 5:
if agg_wb >= params['high_intensity_threshold_PSAC']:
return 'High-infection'

if agg_wb >= params['high_intensity_threshold']:
return 'High-infection'

if agg_wb >= params['low_intensity_threshold']:
return 'Low-infection'

return 'Non-infected'
def _get_infection_status(population: pd.DataFrame) -> pd.Series:
age = population["age_years"]
agg_wb = population[prop("aggregate_worm_burden")]
status = pd.Series(
"Non-infected",
index=population.index,
dtype=population[prop("infection_status")].dtype
)
high_group = (
(age < 5) & (agg_wb >= params["high_intensity_threshold_PSAC"])
) | (agg_wb >= params["high_intensity_threshold"])
low_group = ~high_group & (agg_wb >= params["low_intensity_threshold"])
status[high_group] = "High-infection"
status[low_group] = "Low-infection"
return status

def _impose_symptoms_of_high_intensity_infection(idx: pd.Index) -> None:
"""Assign symptoms to the person with high intensity infection.
Expand All @@ -547,11 +550,7 @@ def _impose_symptoms_of_high_intensity_infection(idx: pd.Index) -> None:
disease_module=schisto_module
)

correct_status = df.loc[idx].apply(
lambda x: _inf_status(x['age_years'], x[prop('aggregate_worm_burden')]),
axis=1
)

correct_status = _get_infection_status(df.loc[idx])
original_status = df.loc[idx, prop('infection_status')]

# Impose symptoms for those newly having 'High-infection' status
Expand Down