emodpy_malaria.interventions.outbreak module

emodpy_malaria.interventions.outbreak.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 = 1000, 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

emodpy_malaria.interventions.outbreak.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 = 1000, 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

emodpy_malaria.interventions.outbreak.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 = 1000, 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

emodpy_malaria.interventions.outbreak.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 = 1000, 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