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update_antipsychotic_equivalences #10

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c55e38a
Update compute_medication_effects.py
Momo1502 Nov 14, 2025
fd6cac5
Update constants.py
Momo1502 Nov 14, 2025
7fcc834
Update constants.py
Momo1502 Nov 14, 2025
4c2259b
Update compute_medication_effects_by_class.py
Momo1502 Nov 17, 2025
bc86ac1
fix: correct return value and type hints in medication effect functions
dheshanm Apr 9, 2026
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48 changes: 48 additions & 0 deletions formsdb/constants.py
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Original file line number Diff line number Diff line change
Expand Up @@ -413,6 +413,54 @@
"Sulpride (Dolmatil, Sulpitil, Sulparex)": 5000,
}

# Antipsychotic medication (1 mg) equivalent doses to 1 mg Haloperidol using the Leucht table for equivalences
med_idx_drug_equivalent_dose_leucht: Dict[int, float] = {
238: 0.01089, # Amisulpride (Solian) # 'amisulpride/Solian'
305: 0.55043, # Aripiprazole (Abilitat, Abilify) # 'aripiprazole/Abilify'
725: 0.53, # Aripiprazole (Abilitat, Abilify) # 'aripiprazole/Abilify ACUTE INJECTION'
547: 0.38311, # Aripiprazole (Abilitat, Abilify) # 'aripiprazole LAI/Abilify Maintena'
723: 0.43923, # Aripiprazole (Abilitat, Abilify) # 'aripiprazole lauroxil LAI/Aristada'
530: 0.42285, # Asenapine (Saphris) # 'asenapine/Saphris'
732: 0.67191, # Asenapine (Saphris) # 'asenapine patch/Secuado'
574: 1.88204, # Brexpiprazole (Rexulti) # 'brexpiprazole/Rexulti'
721: 0.82962, # Cariprazine (Vraylar) # 'cariprazine/Vraylar'
256: 0.01073, # Chlorpromazine (Largactil) # 'chlorpromazine/Thorazine'
257: 0.05, # Chlorpromazine (Largactil) # 'chlorpromazine/Thorazine ACUTE INJECTION'
69: 0.01043, # Clozapine (Clozaril) # 'clozapine/Clozaril'
403: 0.83454, # Droperidol (Droleptan) # 'droperidol/Inapsine'
727: 3.2, # Droperidol (Droleptan) # 'droperidol/Inapsine ACUTE INJECTION'
220: 1, # Fluphenazine HCL (Anatensol) # 'fluphenazine/Prolixin/Permitil'
222: 4.63634, # Fluphenazine HCL (Anatensol) # 'fluphenazine LAI/Prolixin Decanoate'
122: 1, # Haloperidol (Haldol) # 'haloperidol/Haldol'
123: 1, # Haloperidol (Haldol) # 'haloperidol/Haldol ACUTE INJECTION'
124: 1.54545, # Haloperidol (Haldol) # 'haloperidol LAI/Haldol Decanoate'
532: 0.31446, # Iloperidone (Fanapt) # 'iloperidone/Fanapt'
728: 0.18238, # Lumateperone (Caplyta) # 'lumateperone/Caplyta'
540: 0.04305, # Lurasidone (Latuda) # 'lurasidone/Latuda'
201: 0.41727, # Olanzapine (Zyprexa) # 'olanzapine/Zyprexa/Symbyax/Lybalvi '
726: 0.5, # Olanzapine (Zyprexa) # 'olanzapine/Zyprexa ACUTE INJECTION'
720: 0.31972, # Olanzapine (Zyprexa) # 'olanzapine LAI/Relprevv'
531: 0.47416, # Paliperidone (Invega) # 'paliperidone/Invega'
546: 0.65954, # Paliperidone (Invega) # 'paliperidone palmitate LAI/Invega Sustenna'
722: 0.56532, # Paliperidone (Invega) # 'paliperidone palmitate LAI/Invega Trinza'
408: 1.04318, # Pimozide (Orap) # 'pimozide/Orap'
270: 0.28005, # Perphenazine (Trilafon) # 'perphenazine/Trilafon'
271: 0.5, # Perphenazine (Trilafon) # 'perphenazine/Trilafon ACUTE INJECTION'
235: 0.01313, # Quetiapine Fumarate (Seroquel) # 'quetiapine/Seroquel'
300: 1.01118, # Risperidone (Risperdal) # 'risperidone/Risperdal'
425: 2.42396, # Risperidone (Risperdal) # 'risperidone LAI/Risperdal Consta'
452: 1.987, # Risperidone (Risperdal) # 'risperidone SC LAI/Perseris'
184: 0.27957, # Thiothixene (Navane) # 'thiothixene/Navane'
158: 0.01669, # Thioridazine (Melleril, Aldazine) # 'thioridazine/Mellaril'
244: 0.41727, # Trifluoperazine (Stelazine) # 'trifluoperazine/Stelazine'
245: 1, # Trifluoperazine (Stelazine) # 'trifluoperazine/Stelazine ACUTE INJECTION'
304: 0.03396, # Ziprasidone (Geodon) # 'ziprasidone/Geodon'
724: 0.25, # Ziprasidone (Geodon) # 'ziprasidone/Geodon ACUTE INJECTION'
538: 0.03396, # Ziprasidone (Geodon) # 'ziprasidone/Geodon or placebo (Blinded)'
75: 0.09597, # Prochlorperazine (Compazine) # 'prochlorperazine/Compazine'
76: 0.23, # Prochlorperazine (Compazine) # 'prochlorperazine/Compazine ACUTE INJECTION'
242: 0.02667, # Promazine (Sparine) # 'promazine/Sparine'
}
antidepressant_fluoxetine_40mg_drug_equivalent_dose: Dict[str, float] = {
"fluoxetine": 40,
"agomelatine": 53.2,
Expand Down
52 changes: 46 additions & 6 deletions formsdb/runners/compute/compute_medication_effects.py
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Original file line number Diff line number Diff line change
Expand Up @@ -243,7 +243,7 @@ def get_medication_duaraion_i(

duration = len(dates)
if duration == 0:
return pd.NA, pd.NA, pd.NA # type: ignore[return]
return pd.NA, pd.NA, pd.NA, pd.NA # type: ignore[return]

avg_dosage = sum(total_dosage_by_date.values()) / duration
complied_avg_dosage = sum(complied_total_dosage_by_date.values()) / duration
Expand Down Expand Up @@ -545,7 +545,7 @@ def get_subject_medication_effect_info(
# logger.warning(f"Processing {modality} - {timepoint} for {subject_id} on {subject_date_dt}")
currently_taking, potential_currently_taking, taken_before = (
get_medication_status(
medication_df=subject_medication_data, target_date=subject_date_dt
medication_df=subject_medication_data, target_date=subject_date_dt # type: ignore
)
)

Expand All @@ -567,12 +567,12 @@ def get_subject_medication_effect_info(
ever_used = med_idx in taken_before

result = get_medication_duaraion_i(
medication_df=subject_medication_data,
medication_df=subject_medication_data, # type: ignore
target_medication_idx=med_idx,
target_date=subject_date_dt,
)
is_ongoing = is_medication_ongoing(
medication_df=subject_medication_data,
medication_df=subject_medication_data, # type: ignore
target_medication_idx=med_idx,
target_date=subject_date_dt,
)
Expand All @@ -581,7 +581,7 @@ def get_subject_medication_effect_info(
days_since_last_taken = 0
else:
last_taken_date = date_last_taken(
medication_df=subject_medication_data,
medication_df=subject_medication_data, # type: ignore
target_medication_idx=med_idx,
target_date=subject_date_dt,
)
Expand All @@ -608,6 +608,8 @@ def get_subject_medication_effect_info(
if pd.isna(dosage_prescribed) or pd.isna(duration_prescribed):
ap_equivalent_drug_dose_prescribed = pd.NA
ap_equivalent_drug_dose_estimated_taken = pd.NA
ap_equivalent_drug_dose_prescribed_leucht = pd.NA
ap_equivalent_drug_dose_estimated_taken_leucht = pd.NA
bd_equivalent_drug_dose_prescribed = pd.NA
bd_equivalent_drug_dose_estimated_taken = pd.NA
else:
Expand All @@ -617,6 +619,11 @@ def get_subject_medication_effect_info(
int(med_idx), None
)
)
ap_standard_equivalent_drug_dose_leucht = (
constants.med_idx_drug_equivalent_dose_leucht.get(
int(med_idx), None
)
)
if ap_standard_equivalent_drug_dose is not None:
prescribed_eq_dosage_for_day = dosage_prescribed * (
50 / ap_standard_equivalent_drug_dose
Expand All @@ -643,9 +650,36 @@ def get_subject_medication_effect_info(
# )
ap_equivalent_drug_dose_prescribed = pd.NA
ap_equivalent_drug_dose_estimated_taken = pd.NA
if ap_standard_equivalent_drug_dose_leucht is not None:
prescribed_eq_dosage_for_day_leucht = (
dosage_prescribed * ap_standard_equivalent_drug_dose_leucht
)
ap_equivalent_drug_dose_prescribed_leucht = (
prescribed_eq_dosage_for_day_leucht * duration_prescribed
)

if complied_dosage is not None:
complied_equivalent_drug_dose_for_day_leucht = (
complied_dosage * ap_standard_equivalent_drug_dose_leucht
)
else:
complied_equivalent_drug_dose_for_day_leucht = pd.NA
ap_equivalent_drug_dose_estimated_taken_leucht = (
complied_equivalent_drug_dose_for_day_leucht
* duration_prescribed
)
else:
# logger.warning(
# f"Missing AP Standard Equivalent Drug Dose for "
# f"{med_idx}"
# )
ap_equivalent_drug_dose_prescribed_leucht = pd.NA
ap_equivalent_drug_dose_estimated_taken_leucht = pd.NA
else:
ap_equivalent_drug_dose_prescribed = pd.NA
ap_equivalent_drug_dose_estimated_taken = pd.NA
ap_equivalent_drug_dose_prescribed_leucht = pd.NA
ap_equivalent_drug_dose_estimated_taken_leucht = pd.NA

if med_class == "BENZODIAZEPINE":
bd_med_name: str = med_info[int(med_idx)]["med_name"]
Expand Down Expand Up @@ -718,6 +752,8 @@ def get_subject_medication_effect_info(
if ever_used_inconclusive:
ap_equivalent_drug_dose_prescribed = pd.NA
ap_equivalent_drug_dose_estimated_taken = pd.NA
ap_equivalent_drug_dose_prescribed_leucht = pd.NA
ap_equivalent_drug_dose_estimated_taken_leucht = pd.NA
bd_equivalent_drug_dose_prescribed = pd.NA
bd_equivalent_drug_dose_estimated_taken = pd.NA

Expand All @@ -744,6 +780,8 @@ def get_subject_medication_effect_info(
"days_since_last_taken": days_since_last_taken,
"ap_equivalent_drug_dose_prescribed": ap_equivalent_drug_dose_prescribed,
"ap_equivalent_drug_dose_estimated_taken": ap_equivalent_drug_dose_estimated_taken,
"ap_equivalent_drug_dose_prescribed_leucht": ap_equivalent_drug_dose_prescribed_leucht,
"ap_equivalent_drug_dose_estimated_taken_leucht": ap_equivalent_drug_dose_estimated_taken_leucht,
"bd_equivalent_drug_dose_prescribed": bd_equivalent_drug_dose_prescribed,
"bd_equivalent_drug_dose_estimated_taken": bd_equivalent_drug_dose_estimated_taken,
"med_use": med_use,
Expand Down Expand Up @@ -798,7 +836,7 @@ def compile_medication_effects(
# f"Randomly selected {len(subjects)} subjects for processing (out of {len(all_subjects)} total subjects)."
# )

num_processes = multiprocessing.cpu_count() // 2
num_processes = multiprocessing.cpu_count()
logger.info(f"Using {num_processes} processes for parallel computation.")
params = [(config_file, subject_id) for subject_id in subjects]

Expand All @@ -815,6 +853,8 @@ def compile_medication_effects(
"days_from_consent",
"ap_equivalent_drug_dose_prescribed",
"ap_equivalent_drug_dose_estimated_taken",
"ap_equivalent_drug_dose_prescribed_leucht",
"ap_equivalent_drug_dose_estimated_taken_leucht",
"bd_equivalent_drug_dose_prescribed",
"bd_equivalent_drug_dose_estimated_taken",
"duration_prescribed_days",
Expand Down
12 changes: 12 additions & 0 deletions formsdb/runners/compute/compute_medication_effects_by_class.py
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Original file line number Diff line number Diff line change
Expand Up @@ -179,9 +179,17 @@ def sum_or_none(series: pd.Series) -> Optional[Union[int, float]]:
ap_equivalent_drug_dose_estimated_taken = sum_or_none(
med_class_df["ap_equivalent_drug_dose_estimated_taken"]
)
ap_equivalent_drug_dose_prescribed_leucht = sum_or_none(
med_class_df["ap_equivalent_drug_dose_prescribed_leucht"]
)
ap_equivalent_drug_dose_estimated_taken_leucht = sum_or_none(
med_class_df["ap_equivalent_drug_dose_estimated_taken_leucht"]
)
else:
ap_equivalent_drug_dose_prescribed = None
ap_equivalent_drug_dose_estimated_taken = None
ap_equivalent_drug_dose_prescribed_leucht = None
ap_equivalent_drug_dose_estimated_taken_leucht = None

if med_class == "BENZODIAZEPINE":
bd_equivalent_drug_dose_prescribed = sum_or_none(
Expand Down Expand Up @@ -221,6 +229,8 @@ def sum_or_none(series: pd.Series) -> Optional[Union[int, float]]:
"ever_used": ever_used,
"ap_equivalent_drug_dose_prescribed": ap_equivalent_drug_dose_prescribed,
"ap_equivalent_drug_dose_estimated_taken": ap_equivalent_drug_dose_estimated_taken,
"ap_equivalent_drug_dose_prescribed_leucht": ap_equivalent_drug_dose_prescribed_leucht,
"ap_equivalent_drug_dose_estimated_taken_leucht": ap_equivalent_drug_dose_estimated_taken_leucht,
"bd_equivalent_drug_dose_prescribed": bd_equivalent_drug_dose_prescribed,
"bd_equivalent_drug_dose_estimated_taken": bd_equivalent_drug_dose_estimated_taken,
"prescribed_equivalent_drug_dose_for_day":
Expand Down Expand Up @@ -281,6 +291,8 @@ def compile_medication_effects(
"days_from_consent",
"ap_equivalent_drug_dose_prescribed",
"ap_equivalent_drug_dose_estimated_taken",
"ap_equivalent_drug_dose_prescribed_leucht",
"ap_equivalent_drug_dose_estimated_taken_leucht",
"bd_equivalent_drug_dose_prescribed",
"bd_equivalent_drug_dose_estimated_taken",
"current_use",
Expand Down