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removed setting drug parameters from inside interventions as it is no…
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… longer possible. Drug parameters will need to be set in config builder separately from campaign builder.
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@stitova-idm
stitova-idm committed Nov 27, 2024
1 parent 6ef6958 commit 4f7c5ff
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Showing 2 changed files with 48 additions and 67 deletions.
4 changes: 2 additions & 2 deletions snt/helpers_add_interventions.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -519,7 +519,7 @@ def add_hfca_vaccsmc(campaign, smc_df, hfca, effective_coverage_resistance_multi
target_group={'agemin': age_min_list[ii],
'agemax': age_max_list[ii]},
ind_property_restrictions=[{'SMCAccess': access_list[ii]}],
receiving_drugs_event=False) ## If False uses vaccSMC with automatic offset of 17 days, if True, uses vaccDrugSMC
also_deploy_drugs=False) ## If False uses vaccSMC with automatic offset of 17 days, if True, uses vaccDrugSMC

return len(df)

Expand Down Expand Up @@ -869,7 +869,7 @@ def add_ds_vaccpmc(campaign, pmc_df, hfca):
'delay_distribution_mean': df['distribution_mean'],
'delay_distribution_std': df['distribution_std']},
num_iiv_groups=num_iiv_groups,
receiving_drugs_event=False) ## use vaccine effects only with default offset of -10 days
also_deploy_drugs=False) ## use vaccine effects only with default offset of -10 days

return len(pmc_df)

Expand Down
111 changes: 46 additions & 65 deletions snt/support_files/malaria_vaccdrug_campaigns.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -19,13 +19,17 @@ def add_vaccdrug_campaign(campaign, campaign_type: str = 'SMC', start_days: list
receiving_vaccine_event_name: str = None,
receiving_drugs_event_name: str = None,
num_iiv_groups: int = 1,
receiving_drugs_event: bool = True):
also_deploy_drugs: bool = True):
"""
Add a vaccine + vehicle drug intervention to approximate efficacy of SMC or PMC, as specified in **campaign_type**,
to the campaign. This intervention uses default parameters corresponding to SMC with SPAQ and PMC with SP, if not
otherwise specified via vacc_param_dic, drug_param_dic. The vehicle drug instantly clear parasites (blood stage +
liver stage) and the prophylactic effect is added by the vaccine event.
Note: To change drug parameters (including "Vehicle" drug) you will need to do that separately in the
config builder section of your code, because drug parameters need to be updated in the config object.
You can import make_vehicle_drug function into the config builder and use it there.
Campaign type specifications:
For SMC, the drug event (MDA drug campaign) is initiated at the specified simdays and generates a broadcast event
that is used to trigger the vaccine event without delay.
Expand Down Expand Up @@ -69,13 +73,6 @@ def add_vaccdrug_campaign(campaign, campaign_type: str = 'SMC', start_days: list
{'vaccine_initial_effect': 0.598, 'vaccine_box_duration': 21.7, 'vaccine_decay_duration': 1.18}
drug_param_dict: Dictionary of three parameters for initial parasite clearing efficacy (drug campaign).
Default: Fitted parameters for SMC-SPAQ and PMC-SP.
Examples::
{'drug_irbc_killing': 18.6, 'drug_hep_killing': 1.5, 'drug_box_day': 2.0}
delay_distribution_dict: Dictionary of lists of distribution parameters. Distributions allowed:
"GAUSSIAN_DISTRIBUTION","LOG_NORMAL_DISTRIBUTION", "CONSTANT_DISTRIBUTION".
for age-touchpoints, there is also an internal offset (please see code)
Expand Down Expand Up @@ -115,7 +112,7 @@ def add_vaccdrug_campaign(campaign, campaign_type: str = 'SMC', start_days: list
num_iiv_groups: Number of individual drug response groups.
If >1, ind_property_restrictions is set to {'DrugResponseGroup': val} if campaign_type = PMC, not used for
SMC. Default: SMC: Not used. PMC: 1, IIV only acts on the vaccine event, not the drug event
receiving_drugs_event: Specify whether to deploy the parasite clearing drug event or the vaccine event only.
also_deploy_drugs: Specify whether to deploy the parasite clearing drug event or the vaccine event only.
Default: True
Exception: for PMC, set to False
Expand All @@ -128,11 +125,11 @@ def add_vaccdrug_campaign(campaign, campaign_type: str = 'SMC', start_days: list
receiving_vaccine_event_name = f'Received_{campaign_type}_VaccDrug'

if campaign_type == 'SMC':
if receiving_drugs_event:
if also_deploy_drugs:
add_vaccdrug_smc(campaign, start_days=start_days, coverages=coverages,
vaccine_param_dict=vaccine_param_dict, drug_param_dict=drug_param_dict,
vaccine_param_dict=vaccine_param_dict,
target_group=target_group,
receiving_drugs_event=receiving_drugs_event_name,
receiving_drugs_event_name=receiving_drugs_event_name,
receiving_vaccine_event=receiving_vaccine_event_name,
node_ids=node_ids,
ind_property_restrictions=ind_property_restrictions,
Expand All @@ -153,12 +150,11 @@ def add_vaccdrug_campaign(campaign, campaign_type: str = 'SMC', start_days: list
raise ValueError(
'You passed in a trigger_condition for campaign_type PMC that is per default triggered by "Births". '
'trigger_condition_list needs to be empty.\n')
if receiving_drugs_event:
if also_deploy_drugs:
add_vaccdrug_pmc(campaign, start_days=start_days, coverages=coverages,
target_group=target_group, num_iiv_groups=num_iiv_groups,
vaccine_param_dict=vaccine_param_dict,
drug_param_dict=drug_param_dict,
receiving_drugs_event=receiving_drugs_event_name,
receiving_drugs_event_name=receiving_drugs_event_name,
receiving_vaccine_event=receiving_vaccine_event_name,
delay_distribution_dict=delay_distribution_dict,
node_ids=node_ids,
Expand All @@ -180,26 +176,36 @@ def add_vaccdrug_campaign(campaign, campaign_type: str = 'SMC', start_days: list
raise ValueError('Invalid campaign_type specified, valid options: "SMC" or "PMC"')


def make_vehicle_drug(campaign, drug_box_day: float = 0, drug_irbc_killing: float = 0, drug_hep_killing: float = 0):
def make_vehicle_drug(config, drug_box_day: float = 0, drug_irbc_killing: float = 0, drug_hep_killing: float = 0):
"""
Note: To change drug parameters (including "Vehicle" drug) you will need to do that separately in the
config builder section of your code, because drug parameters need to be updated in the config object.
You can import make_vehicle_drug function (see set_param_drug) into the config builder and use it there.
"""

if drug_box_day:
set_drug_param(campaign, "Vehicle", "Drug_Decay_T1", drug_box_day)
set_drug_param(campaign, "Vehicle", "Drug_Decay_T2", drug_box_day)
set_drug_param(config, "Vehicle", "Drug_Decay_T1", drug_box_day)
set_drug_param(config, "Vehicle", "Drug_Decay_T2", drug_box_day)
if drug_irbc_killing:
set_drug_param(campaign, "Vehicle", "Max_Drug_IRBC_Kill", drug_irbc_killing)
set_drug_param(config, "Vehicle", "Max_Drug_IRBC_Kill", drug_irbc_killing)
if drug_hep_killing:
set_drug_param(campaign, "Vehicle", "Drug_Hepatocyte_Killrate", drug_hep_killing)
set_drug_param(config, "Vehicle", "Drug_Hepatocyte_Killrate", drug_hep_killing)

return {'drug_box_day': drug_box_day,
'drug_irbc_killing': drug_irbc_killing,
'drug_hep_killing': drug_hep_killing}


def add_vaccdrug_smc(campaign, start_days: list, coverages: list,
def add_vaccdrug_smc(campaign, start_days: list,
coverages: list,
target_group: dict = None,
node_ids: list = None,
vaccine_param_dict: dict = None, drug_param_dict: dict = None,
receiving_vaccine_event: str = None, receiving_drugs_event: str = None,
listening_duration: int = -1, trigger_condition_list: list = None,
vaccine_param_dict: dict = None,
receiving_vaccine_event: str = None,
receiving_drugs_event_name: str = None,
listening_duration: int = -1,
trigger_condition_list: list = None,
ind_property_restrictions: dict = None,
target_residents_only: int = 1,
check_eligibility_at_trigger: bool = False):
Expand All @@ -209,6 +215,10 @@ def add_vaccdrug_smc(campaign, start_days: list, coverages: list,
The vehicle drug instantly clear parasites (blood stage + liver stage) and the prophylactic effect is added
by the vaccine event.
Note: To change drug parameters (including "Vehicle" drug) you will need to do that separately in the
config builder section of your code, because drug parameters need to be updated in the config object.
You can import make_vehicle_drug function into the config builder and use it there.
Campaign type specifications:
For SMC, the drug event (MDA drug campaign) is initiated at the specified simdays and generates a broadcast event
that is used to trigger the vaccine event without delay.
Expand All @@ -232,12 +242,9 @@ def add_vaccdrug_smc(campaign, start_days: list, coverages: list,
vaccine_decay_duration/log(2)
Example and Default: {'vaccine_initial_effect': 0.598, 'vaccine_box_duration': 21.7,
'vaccine_decay_duration': 1.18}
drug_param_dict: dictionary of parameters for a drug to use with this intervention, these will be assigned
to the 'Vehicle' drug. Example and Default: {'drug_box_day': 2.0, 'drug_irbc_killing': 10.8,
'drug_hep_killing': 3.64}
receiving_vaccine_event: Event to send out when person received vaccine.
Default: 'Received_<campaign_type>_VaccDrug'
receiving_drugs_event: Event to send out when person received drugs.
receiving_drugs_event_name: Event to send out when person received drugs.
Event name needs to include 'Received_Vehicle' in it, as otherwise overwritten in drug_campaigns function
(see drug_campaigns.py L247)
Default: SMC: 'Received_Vehicle'
Expand All @@ -254,16 +261,6 @@ def add_vaccdrug_smc(campaign, start_days: list, coverages: list,
option to check individual/node's eligibility at the initial trigger
or when the event is actually distributed after delay. (for example, a person might've aged out of the
intervention before the initial trigger and the intervention distribution)
receiving_drugs_event_name: Event to send out when person received drugs.
Event name needs to include 'Received_Vehicle' in it, as otherwise overwritten in drug_campaigns function
(see drug_campaigns.py L247)
Default: SMC: 'Received_Vehicle'; PMC: 'Received_Vehicle_X' with X being number of PMC dose
num_iiv_groups: Number of individual drug response groups.
If >1, ind_property_restrictions is set to {'DrugResponseGroup': val} if campaign_type = PMC, not used for
SMC. Default: SMC: Not used; PMC: 1, IIV only acts on the vaccine event, not the drug event
receiving_drugs_event: Specify whether to deploy the parasite clearing drug event or the vaccine event only.
Default: True
Exception: for PMC, set to False
Returns:
dictionary of tags
Expand All @@ -278,20 +275,11 @@ def add_vaccdrug_smc(campaign, start_days: list, coverages: list,
target_age_max = target_group['agemax']
if not vaccine_param_dict:
vaccine_param_dict = {'vacc_initial_effect': 0.598, 'vacc_box_duration': 21.7, 'vacc_decay_duration': 1.18}
if not drug_param_dict:
# drug_param_dic = {'drug_irbc_killing': 18.6, 'drug_hep_killing': 1.5, 'drug_box_day': 2.0}
drug_param_dict = {'drug_box_day': 2.0, 'drug_irbc_killing': 10.8, 'drug_hep_killing': 3.64}

vaccine_initial_effect = vaccine_param_dict['vacc_initial_effect']
vaccine_box_duration = vaccine_param_dict['vacc_box_duration']
vaccine_decay_duration = vaccine_param_dict['vacc_decay_duration']

drug_box_day = drug_param_dict['drug_box_day']
drug_irbc_killing = drug_param_dict['drug_irbc_killing']
drug_hep_killing = drug_param_dict['drug_hep_killing']
make_vehicle_drug(campaign, drug_box_day=drug_box_day, drug_irbc_killing=drug_irbc_killing,
drug_hep_killing=drug_hep_killing)

for (d, cov) in zip(start_days, coverages):
add_drug_campaign(campaign, campaign_type='MDA',
drug_code='Vehicle',
Expand All @@ -304,7 +292,7 @@ def add_vaccdrug_smc(campaign, start_days: list, coverages: list,
listening_duration=listening_duration,
target_group=target_group,
ind_property_restrictions=ind_property_restrictions,
receiving_drugs_event_name=receiving_drugs_event,
receiving_drugs_event_name=receiving_drugs_event_name,
trigger_condition_list=trigger_condition_list,
target_residents_only=target_residents_only,
node_ids=node_ids,
Expand All @@ -313,7 +301,7 @@ def add_vaccdrug_smc(campaign, start_days: list, coverages: list,
add_triggered_vaccine(campaign,
start_day=start_days[0], # otherwise it won't "hear" the first round of drugs
demographic_coverage=1,
trigger_condition_list=[receiving_drugs_event],
trigger_condition_list=[receiving_drugs_event_name],
listening_duration=listening_duration,
target_age_min=target_age_min,
target_age_max=target_age_max,
Expand Down Expand Up @@ -394,9 +382,11 @@ def add_vacc_smc(campaign, start_days, coverages, target_group: dict = None,
def add_vaccdrug_pmc(campaign, start_days: list, coverages: list,
target_group: dict = None,
num_iiv_groups: int = 1,
vaccine_param_dict: dict = None, drug_param_dict: dict = None,
receiving_vaccine_event: str = None, receiving_drugs_event: str = None,
listening_duration: int = -1, node_ids: list = None,
vaccine_param_dict: dict = None,
receiving_vaccine_event: str = None,
receiving_drugs_event_name: str = None,
listening_duration: int = -1,
node_ids: list = None,
delay_distribution_dict: dict = None,
ind_property_restrictions: dict = None, target_residents_only: int = 1,
check_eligibility_at_trigger: bool = False):
Expand All @@ -409,9 +399,8 @@ def add_vaccdrug_pmc(campaign, start_days: list, coverages: list,
target_group:
num_iiv_groups:
vaccine_param_dict:
drug_param_dict:
receiving_vaccine_event:
receiving_drugs_event:
receiving_drugs_event_name:
listening_duration:
node_ids:
delay_distribution_dict:
Expand All @@ -425,19 +414,11 @@ def add_vaccdrug_pmc(campaign, start_days: list, coverages: list,

if not vaccine_param_dict:
vaccine_param_dict = {'vacc_initial_effect': 0.85, 'vacc_box_duration': 13.20, 'vacc_decay_duration': 11.53}
if not drug_param_dict:
drug_param_dict = {'drug_irbc_killing': 16.03, 'drug_hep_killing': 0.92, 'drug_box_day': 2.0}

vaccine_initial_effect = vaccine_param_dict['vacc_initial_effect']
vaccine_box_duration = vaccine_param_dict['vacc_box_duration']
vaccine_decay_duration = vaccine_param_dict['vacc_decay_duration']

drug_box_day = drug_param_dict['drug_box_day']
drug_irbc_killing = drug_param_dict['drug_irbc_killing']
drug_hep_killing = drug_param_dict['drug_hep_killing']
make_vehicle_drug(campaign, drug_box_day=drug_box_day, drug_irbc_killing=drug_irbc_killing,
drug_hep_killing=drug_hep_killing)

pmc_touchpoints = list(target_group.values())
pmc_event_names = [f'PMC_{x + 1}' for x in range(len(pmc_touchpoints))]
if len(pmc_touchpoints) != len(coverages) or len(pmc_touchpoints) != len(
Expand Down Expand Up @@ -488,7 +469,7 @@ def add_vaccdrug_pmc(campaign, start_days: list, coverages: list,
listening_duration=listening_duration,
trigger_condition_list=[event_name],
ind_property_restrictions=ind_property_restrictions,
receiving_drugs_event_name=f'{receiving_drugs_event}_{i + 1}',
receiving_drugs_event_name=f'{receiving_drugs_event_name}_{i + 1}',
node_ids=node_ids,
target_residents_only=target_residents_only,
check_eligibility_at_trigger=check_eligibility_at_trigger
Expand All @@ -512,7 +493,7 @@ def add_vaccdrug_pmc(campaign, start_days: list, coverages: list,

add_triggered_vaccine(campaign,
start_day=start_days[0],
trigger_condition_list=[f'{receiving_drugs_event}_{i + 1}'],
trigger_condition_list=[f'{receiving_drugs_event_name}_{i + 1}'],
demographic_coverage=1,
ind_property_restrictions=[{'DrugResponseGroup': val}],
broadcast_event=receiving_vaccine_event,
Expand All @@ -526,7 +507,7 @@ def add_vaccdrug_pmc(campaign, start_days: list, coverages: list,
else:
add_triggered_vaccine(campaign,
start_day=start_days[0],
trigger_condition_list=[f'{receiving_drugs_event}_{i + 1}'],
trigger_condition_list=[f'{receiving_drugs_event_name}_{i + 1}'],
demographic_coverage=1,
ind_property_restrictions=ind_property_restrictions,
broadcast_event=receiving_vaccine_event,
Expand Down

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