from emod_api import schema_to_class as s2c
from emod_api.interventions.common import utils, BroadcastEvent, MultiInterventionDistributor
[docs]def add_outbreak_individual(campaign,
start_day: int = 1,
demographic_coverage: float = 1.0,
target_num_individuals: int = None,
node_ids: list = None,
repetitions: int = 1,
timesteps_between_repetitions: int = 365,
ind_property_restrictions: list = None,
target_age_min: int = 0,
target_age_max: int = 125,
target_gender: str = "All",
ignore_immunity: bool = True,
incubation_period_override: int = -1,
antigen: int = 0,
genome: int = 0,
broadcast_event: str = None):
"""
Adds a scheduled OutbreakIndividual intervention. This is set up to be used with Malaria-Ongoing branch.
Args:
campaign: campaign object to which the intervention will be added, and schema_path container
start_day: The day the intervention is given out.
demographic_coverage: This value is the probability that each individual in the target population will
receive the intervention. It does not guarantee that the exact fraction of the target population set by
Demographic_Coverage receives the intervention.
target_num_individuals: The exact number of people to select out of the targeted group. If this value is set,
demographic_coverage parameter is ignored
node_ids: List of nodes to which to distribute the intervention. [] or None, indicates all nodes
will get the intervention
repetitions: The number of times an intervention is given, used with timesteps_between_repetitions. -1 means
the intervention repeats forever. Sets **Number_Repetitions**
timesteps_between_repetitions: The interval, in timesteps, between repetitions. Ignored if repetitions = 1.
Sets **Timesteps_Between_Repetitions**
ind_property_restrictions: A list of dictionaries of IndividualProperties, which are needed for the individual
to receive the intervention. Sets the **Property_Restrictions_Within_Node**
target_age_min: The lower end of ages targeted for an intervention, in years. Sets **Target_Age_Min**
target_age_max: The upper end of ages targeted for an intervention, in years. Sets **Target_Age_Max**
target_gender: The gender targeted for an intervention: All, Male, or Female.
ignore_immunity: Individuals will be force-infected (with a specific strain) regardless of actual
immunity level when set to True (1). Default is True (1). The person will or will not get an infection
based on their immunity level if this is set to False.
incubation_period_override: The incubation period, in days, that infected individuals will go through before
becoming infectious. This value overrides the incubation period set in the configuration file.
Set to -1 to honor the configuration parameter settings
antigen: The antigenic base strain ID of the outbreak infection
genome: The genetic substrain ID of the outbreak infection
broadcast_event: Optional event that will be sent out at the same time as outbreak is distributed
Returns:
Nothing
"""
schema_path = campaign.schema_path
# configuring the intervention itself
intervention = s2c.get_class_with_defaults("OutbreakIndividual", schema_path)
intervention.Antigen = antigen
intervention.Genome = genome
intervention.Ignore_Immunity = 1 if ignore_immunity else 0
intervention.Incubation_Period_Override = incubation_period_override
if broadcast_event:
intervention = MultiInterventionDistributor(campaign, [intervention,
BroadcastEvent(campaign, Event_Trigger=broadcast_event)])
add_campaign_event(campaign, start_day=start_day, demographic_coverage=demographic_coverage,
repetitions=repetitions,
timesteps_between_repetitions=timesteps_between_repetitions,
ind_property_restrictions=ind_property_restrictions,
target_age_min=target_age_min, target_age_max=target_age_max, target_gender=target_gender,
target_num_individuals=target_num_individuals, node_ids=node_ids, intervention=intervention)
[docs]def add_outbreak_malaria_genetics(campaign,
start_day: int = 1,
demographic_coverage: float = 1.0,
target_num_individuals: int = None,
node_ids: list = None,
repetitions: int = 1,
timesteps_between_repetitions: int = 365,
ind_property_restrictions: list = None,
target_age_min: int = 0,
target_age_max: int = 125,
target_gender: str = "All",
ignore_immunity: bool = True,
incubation_period_override: int = -1,
create_nucleotide_sequence_from: str = "BARCODE_STRING",
barcode_string: str = None,
drug_resistant_string: str = None,
msp_variant_value: int = None,
pfemp1_variants_values: list = None,
barcode_allele_frequencies_per_genome_location: list = None,
drug_resistant_allele_frequencies_per_genome_location: list = None,
hrp_allele_frequencies_per_genome_location: list = None,
hrp_string: str = None,
broadcast_event: str = None):
"""
Creates a scheduled OutbreakIndividualMalariaGenetics CampaignEvent which can then
be added to a campaign.
Args:
campaign: campaign object to which the intervention will be added, and schema_path container
start_day: The day the intervention is given out.
demographic_coverage: This value is the probability that each individual in the target population will
receive the intervention. It does not guarantee that the exact fraction of the target population set by
Demographic_Coverage receives the intervention.
target_num_individuals: The exact number of people to select out of the targeted group. If this value is set,
demographic_coverage parameter is ignored.
node_ids: List of nodes to which to distribute the intervention. [] or None, indicates all nodes
will get the intervention
repetitions: The number of times an intervention is given, used with timesteps_between_repetitions. -1 means
the intervention repeats forever. Sets **Number_Repetitions**
timesteps_between_repetitions: The interval, in timesteps, between repetitions. Ignored if repetitions = 1.
Sets **Timesteps_Between_Repetitions**
ind_property_restrictions: A list of dictionaries of IndividualProperties, which are needed for the individual
to receive the intervention. Sets the **Property_Restrictions_Within_Node**
target_age_min: The lower end of ages targeted for an intervention, in years. Sets **Target_Age_Min**
target_age_max: The upper end of ages targeted for an intervention, in years. Sets **Target_Age_Max**
target_gender: The gender targeted for an intervention: All, Male, or Female.
ignore_immunity: Individuals will be force-infected (with a specific strain) regardless of actual
immunity level when set to True (1). Default is True (1). The person will or will not get an infection
based on their immunity level if this is set to False.
incubation_period_override: The incubation period, in days, that infected individuals will go through before
becoming infectious. This value overrides the incubation period set in the configuration file.
Set to -1 to honor the configuration parameter settings
create_nucleotide_sequence_from: A string that indicates how the genomes are created.
Possible values are: BARCODE_STRING, ALLELE_FREQUENCIES, NUCLEOTIDE_SEQUENCE.
barcode_string: Used with 'BARCODE_STRING' or 'NUCLEOTIDE_SEQUENCE'. A series of nucleotide base letters
(A, C, G, T) that represent the values at locations in the genome. The length of the string depends on the
number of locations defined in config.Parasite_Genetics.Barcode_Genome_Locations. Each character of the
string corresponds to one of the locations. The locations are assumed to be in ascending order.
drug_resistant_string: Used with 'BARCODE_STRING' or 'NUCLEOTIDE_SEQUENCE'. A series of nucleotide base
letters (A, C, G, T) that represent the values at locations in the genome. The length of the string depends
on the number of locations defined in config.Parasite_Genetics.Drug_Resistant_Genome_Locations. Each
character of the string corresponds to one of the locations. The locations are assumed to be in ascending
order.
msp_variant_value: Used with 'NUCLEOTIDE_SEQUENCE'. The Merozoite Surface Protein value used to determine how
the antibodies recognizes the merzoites. This value depends on config.Falciparum_MSP_Variants and must be
less than or equal to it.
pfemp1_variants_values: Used with 'NUCLEOTIDE_SEQUENCE'. The PfEMP1 Variant values / major epitopes used to
define how the antibodies recognize the infected red blood cells. The values of the array depend on
config. Falciparum_PfEMP1_Variants and must be less than or equal to it.
There must be exactly 50 values – one for each epitope.
barcode_allele_frequencies_per_genome_location: Used with 'ALLELE_FREQUENCIES'. The fractions of allele
occurrences for each location in the barcode. This 2D array should have one array for each
location/character in the barcode. For each location, there should be four values between 0 and 1
indicating the probability that specific character appears. The possible letters are: A=0, C=1, G=2, T=3.
The frequencies should sum up to 1.
drug_resistant_allele_frequencies_per_genome_location:Used with 'ALLELE_FREQUENCIES'. The fractions of allele
occurrences for each location in the drug resistant markers. This 2D array should have one array for each
drug resistant location. For each location, there should be four values between 0 and 1 indicating the
probability that specific character will appear. The possible letters are S'A'=0, 'C'=1, 'G'=2, 'T'=3.
The frequencies should sum up to 1.
hrp_allele_frequencies_per_genome_location: Used with 'ALLELE_FREQUENCIES'. The fractions of allele occurrences
for each location in the HRP markers. This 2D array should have one array for each HRP location.
For each location, there should be four values between 0 and 1 indicating the probability that specific
character will appear. The possible letters are 'A'=0, 'C'=1, 'G'=2, 'T'=3.
hrp_string: Used with 'BARCODE_STRING' or 'NUCLEOTIDE_SEQUENCE'. A series of nucleotide base letters (A, C, G, T)
that represent the HRP values at locations in the genome. There must be one character for each location
defined in <config>.Parasite_Genetics.HRP_Genome_Locations. 'A' means HRP marker is present and a
non-'A' means it isn't.
broadcast_event: Optional event that will be sent out at the same time as outbreak is distributed
Returns:
CampaignEvent which then can be added to the campaign file
"""
if create_nucleotide_sequence_from == "BARCODE_STRING" and not barcode_string:
raise ValueError(f"You must define barcode_string with {create_nucleotide_sequence_from} setting.\n")
elif create_nucleotide_sequence_from == "BARCODE_STRING" and (msp_variant_value or pfemp1_variants_values
or barcode_allele_frequencies_per_genome_location or
hrp_allele_frequencies_per_genome_location):
raise ValueError(f"With {create_nucleotide_sequence_from} setting does not use msp_variant_value or "
f"pfemp1_variants_values or barcode_allele_frequencies_per_genome_location or "
f"hrp_allele_frequencies_per_genome_location. Please do not set them.\n")
elif create_nucleotide_sequence_from == "NUCLEOTIDE_SEQUENCE" and not (
msp_variant_value and pfemp1_variants_values):
raise ValueError(f"You must define msp_variant_value and pfemp1_variants_values with "
f"{create_nucleotide_sequence_from} setting.\n")
elif create_nucleotide_sequence_from == "NUCLEOTIDE_SEQUENCE" and (barcode_string or
barcode_allele_frequencies_per_genome_location or
hrp_allele_frequencies_per_genome_location):
raise ValueError(f"With {create_nucleotide_sequence_from} setting does not use barcode_string "
f"or barcode_allele_frequencies_per_genome_location or "
f"hrp_allele_frequencies_per_genome_location. Please do not set them.\n")
elif create_nucleotide_sequence_from == "ALLELE_FREQUENCIES" and not barcode_allele_frequencies_per_genome_location:
raise ValueError(f"You must define barcode_allele_frequencies_per_genome_location with "
f"{create_nucleotide_sequence_from} setting.\n")
elif create_nucleotide_sequence_from == "ALLELE_FREQUENCIES" and (barcode_string or hrp_string or
msp_variant_value or pfemp1_variants_values):
raise ValueError(f"With {create_nucleotide_sequence_from} setting does not use barcode_string "
f"or msp_variant_value or pfemp1_variants_values or hrp_string. Please do not set them.\n")
schema_path = campaign.schema_path
intervention = s2c.get_class_with_defaults("OutbreakIndividualMalariaGenetics", schema_path)
if create_nucleotide_sequence_from == "BARCODE_STRING":
intervention.Barcode_String = barcode_string
if drug_resistant_string:
intervention.Drug_Resistant_String = drug_resistant_string
if hrp_string:
intervention.HRP_String = hrp_string
elif create_nucleotide_sequence_from == "NUCLEOTIDE_SEQUENCE":
intervention.MSP_Variant_Value = msp_variant_value
intervention.Barcode_String = barcode_string
intervention.PfEMP1_Variants_Values = pfemp1_variants_values
if drug_resistant_string:
intervention.Drug_Resistant_String = drug_resistant_string
if hrp_string:
intervention.HRP_String = hrp_string
elif create_nucleotide_sequence_from == "ALLELE_FREQUENCIES":
intervention.Barcode_Allele_Frequencies_Per_Genome_Location = barcode_allele_frequencies_per_genome_location
if drug_resistant_allele_frequencies_per_genome_location:
intervention.Drug_Resistant_Allele_Frequencies_Per_Genome_Location = drug_resistant_allele_frequencies_per_genome_location
if hrp_allele_frequencies_per_genome_location:
intervention.HRP_Allele_Frequencies_Per_Genome_Location = hrp_allele_frequencies_per_genome_location
else:
raise ValueError(f"Unknown create_nucleotide_sequence_from option - {create_nucleotide_sequence_from}.\n")
intervention.Create_Nucleotide_Sequence_From = create_nucleotide_sequence_from
intervention.Ignore_Immunity = 1 if ignore_immunity else 0
intervention.Incubation_Period_Override = incubation_period_override
if broadcast_event:
intervention = MultiInterventionDistributor(campaign, [intervention,
BroadcastEvent(campaign, Event_Trigger=broadcast_event)])
add_campaign_event(campaign, start_day=start_day, demographic_coverage=demographic_coverage,
repetitions=repetitions,
timesteps_between_repetitions=timesteps_between_repetitions,
ind_property_restrictions=ind_property_restrictions,
target_age_min=target_age_min, target_age_max=target_age_max, target_gender=target_gender,
target_num_individuals=target_num_individuals, node_ids=node_ids, intervention=intervention)
[docs]def add_outbreak_malaria_var_genes(campaign,
start_day: int = 1,
demographic_coverage: float = 1.0,
target_num_individuals: int = None,
node_ids: list = None,
repetitions: int = 1,
timesteps_between_repetitions: int = 365,
ind_property_restrictions: list = None,
target_age_min: int = 0,
target_age_max: int = 125,
target_gender: str = "All",
ignore_immunity: bool = True,
incubation_period_override: int = -1,
irbc_type: list = None,
minor_epitope_type: list = None,
msp_type: int = None):
"""
Creates a scheduled OutbreakIndividualMalariaGenetics CampaignEvent which can then
be added to a campaign.
Args:
campaign: campaign object to which the intervention will be added, and schema_path container
start_day: The day the intervention is given out.
demographic_coverage: This value is the probability that each individual in the target population will
receive the intervention. It does not guarantee that the exact fraction of the target population set by
Demographic_Coverage receives the intervention.
target_num_individuals: The exact number of people to select out of the targeted group. If this value is set,
demographic_coverage parameter is ignored
node_ids: List of nodes to which to distribute the intervention. [] or None, indicates all nodes
will get the intervention
repetitions: The number of times an intervention is given, used with timesteps_between_repetitions. -1 means
the intervention repeats forever. Sets **Number_Repetitions**
timesteps_between_repetitions: The interval, in timesteps, between repetitions. Ignored if repetitions = 1.
Sets **Timesteps_Between_Repetitions**
ind_property_restrictions: A list of dictionaries of IndividualProperties, which are needed for the individual
to receive the intervention. Sets the **Property_Restrictions_Within_Node**
target_age_min: The lower end of ages targeted for an intervention, in years. Sets **Target_Age_Min**
target_age_max: The upper end of ages targeted for an intervention, in years. Sets **Target_Age_Max**
target_gender: The gender targeted for an intervention: All, Male, or Female.
ignore_immunity: Individuals will be force-infected (with a specific strain) regardless of actual
immunity level when set to True (1). Default is True (1). The person will or will not get an infection
based on their immunity level if this is set to False.
incubation_period_override: The incubation period, in days, that infected individuals will go through before
becoming infectious. This value overrides the incubation period set in the configuration file.
Set to -1 to honor the configuration parameter settings
irbc_type: The array PfEMP1 Major epitope variant values. There must be exactly 50 values. Min value = 0,
MAX value = config.Falciparum_PfEMP1_Variants.
minor_epitope_type: The array PfEMP1 Minor epitope variant values. There must be exactly 50 values.
Min value = 0, MAX value = config.Falciparum_Nonspecific_Types * MINOR_EPITOPE_VARS_PER_SET(=5) .
msp_type: The Merozoite Surface Protein variant value of this infection. Min value = 0,
MAX value = config.Falciparum_MSP_Variants.
Returns:
CampaignEvent which then can be added to the campaign file
"""
if not irbc_type or not minor_epitope_type or not msp_type:
raise ValueError(f"irbc_type, minor_epitope_type, msp_type all must be defined.\n")
elif irbc_type and len(irbc_type) != 50:
raise ValueError(f"irbc_type needs to have 50 values, you have {len(irbc_type)}.\n")
elif minor_epitope_type and len(minor_epitope_type) != 50:
raise ValueError(f"minor_epitope_type needs to have 50 values, you have {len(minor_epitope_type)}.\n")
schema_path = campaign.schema_path
intervention = s2c.get_class_with_defaults("OutbreakIndividualMalariaVarGenes", schema_path)
intervention.MSP_Type = msp_type
intervention.Minor_Epitope_Type = minor_epitope_type
intervention.IRBC_Type = irbc_type
intervention.Ignore_Immunity = 1 if ignore_immunity else 0
intervention.Incubation_Period_Override = incubation_period_override
add_campaign_event(campaign, start_day=start_day, demographic_coverage=demographic_coverage,
repetitions=repetitions,
timesteps_between_repetitions=timesteps_between_repetitions,
ind_property_restrictions=ind_property_restrictions,
target_age_min=target_age_min, target_age_max=target_age_max, target_gender=target_gender,
target_num_individuals=target_num_individuals, node_ids=node_ids, intervention=intervention)
[docs]def add_campaign_event(campaign,
start_day: int = 1,
demographic_coverage: float = 1.0,
target_num_individuals: int = None,
node_ids: list = None,
repetitions: int = 1,
timesteps_between_repetitions: int = 365,
ind_property_restrictions: list = None,
target_age_min: int = 0,
target_age_max: int = 125,
target_gender: str = "All",
intervention: any = None):
"""
Adds a campaign event to the campaign with a passed in intervention.
Args:
campaign: campaign object to which the intervention will be added, and schema_path container
start_day: The day the intervention is given out.
demographic_coverage: This value is the probability that each individual in the target population will
receive the intervention. It does not guarantee that the exact fraction of the target population set by
Demographic_Coverage receives the intervention.
target_num_individuals: The exact number of people to select out of the targeted group. If this value is set,
demographic_coverage parameter is ignored
node_ids: List of nodes to which to distribute the intervention. [] or None, indicates all nodes
will get the intervention
repetitions: The number of times an intervention is given, used with timesteps_between_repetitions. -1 means
the intervention repeats forever. Sets **Number_Repetitions**
timesteps_between_repetitions: The interval, in timesteps, between repetitions. Ignored if repetitions = 1.
Sets **Timesteps_Between_Repetitions**
ind_property_restrictions: A list of dictionaries of IndividualProperties, which are needed for the individual
to receive the intervention. Sets the **Property_Restrictions_Within_Node**
target_age_min: The lower end of ages targeted for an intervention, in years. Sets **Target_Age_Min**
target_age_max: The upper end of ages targeted for an intervention, in years. Sets **Target_Age_Max**
target_gender: The gender targeted for an intervention: All, Male, or Female.
intervention: Intervention or a list of interventions to be distributed by this event
Returns:
Nothing, add the CampaignEvent to the campaign
"""
schema_path = campaign.schema_path
event = s2c.get_class_with_defaults("CampaignEvent", schema_path)
event.Start_Day = start_day
event.Nodeset_Config = utils.do_nodes(schema_path, node_ids)
if isinstance(intervention, list):
multi_intervention_distributor = s2c.get_class_with_defaults("MultiInterventionDistributor", schema_path)
multi_intervention_distributor.Intervention_List = intervention
intervention = multi_intervention_distributor
# configuring the coordinator
coordinator = s2c.get_class_with_defaults("StandardEventCoordinator", schema_path)
if target_num_individuals is not None:
coordinator.Target_Num_Individuals = target_num_individuals
else:
coordinator.Demographic_Coverage = demographic_coverage
coordinator.Number_Repetitions = repetitions
coordinator.Timesteps_Between_Repetitions = timesteps_between_repetitions
coordinator.Property_Restrictions_Within_Node = ind_property_restrictions if ind_property_restrictions else []
coordinator.Property_Restrictions = [] # not using; Property_Restrictions_Within_Node are more flexible
if target_age_min > 0 or target_age_max < 125:
coordinator.Target_Age_Min = target_age_min
coordinator.Target_Age_Max = target_age_max
if target_gender != "All":
coordinator.Target_Gender = target_gender
coordinator.Target_Demographic = "ExplicitAgeRangesAndGender"
event.Event_Coordinator_Config = coordinator
coordinator.Intervention_Config = intervention
campaign.add(event)