individual_intervention
AdherentDrug
Bases: IndividualIntervention
The AdherentDrug intervention class extends antimalarial drug distribution of the MultiPackComboDrug intervention with adherence modeling. It allows configuring dose schedules, adherence patterns, and non-adherence behaviors, simulating patients who may not take every dose as prescribed.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
campaign
|
(campaign, required)
|
An instance of the emod_api.campaign module. |
required |
doses
|
(list[list[str]], required)
|
A two-dimensional array of drug names defining the drug regimen. Each inner list represents the drugs taken in a single dose. All drug names must match those defined in the simulation's Malaria_Drug_Params. Example -- a standard 3-day AL (Artemether-Lumefantrine) regimen with 6 doses:: Example -- a single-dose SP (Sulfadoxine-Pyrimethamine) for IPTp:: |
required |
adherence_config
|
(AbstractWaningConfig, required)
|
Configuration for the probability of taking a dose. Use a waning effect class to specify how this probability changes over time. Available types are defined in Waning Effects. Example -- 80% adherence that stays constant throughout the regimen:: Example -- adherence that decays from 90% to 50% over the course of a 3-day regimen:: |
required |
non_adherence_options
|
(list[NonAdherenceOption], required)
|
List of options for what happens when a dose is missed. Each entry defines a possible non-adherence behavior; the corresponding probability of each behavior is set in non_adherence_distribution. Use the NonAdherenceOption enum values:
Example -- most people who miss a dose wait for the next scheduled time, but some stop entirely:: |
required |
non_adherence_distribution
|
(list[float], required)
|
Probability distribution across non-adherence options. Must sum to 1.0 and have the same length as non_adherence_options. Each value is the probability of the corresponding non-adherence behavior when a dose is missed. Example -- matching the options above, 90% wait for next dose time, 10% stop:: |
required |
dose_interval
|
float
|
The number of days between doses which are defined in the doses parameter. Minimum value: 0 Maximum value: 100000 Default value: 1 Example -- twice-daily dosing for an AL regimen:: |
1
|
max_dose_consideration_duration
|
float
|
Maximum number of days the person will consider (attempt) taking remaining doses. After this duration, any remaining doses in the regimen are abandoned. Minimum value: 0.0416667 Maximum value: 3.40282e+38 Default value: 3.40282e+38 Example -- give up on the regimen after 7 days regardless of adherence:: |
3.40282e+38
|
took_dose_event
|
str
|
An individual-level event to broadcast each time a dose is successfully taken. Useful for tracking adherence or triggering follow-up actions. Default value: None Example -- broadcast an event to count doses taken:: |
None
|
common_intervention_parameters
|
CommonInterventionParameters
|
The CommonInterventionParameters object that contains the 5 common parameters: cost, intervention_name, new_property_value, disqualifying_properties, dont_allow_duplicates. Default value: None |
None
|
Example
A 3-day AL regimen with once-every-two days, 80% constant adherence, and mixed non-adherence behaviors::
from emodpy_malaria.campaign.individual_intervention import AdherentDrug
from emodpy_malaria.campaign.waning_config import Constant
from emodpy_malaria.utils.emod_enum import NonAdherenceOption
drug = AdherentDrug(
campaign=campaign,
doses=[
["Artemether", "Lumefantrine"],
["Artemether", "Lumefantrine"],
["Artemether", "Lumefantrine"],
["Artemether", "Lumefantrine"],
["Artemether", "Lumefantrine"],
["Artemether", "Lumefantrine"],
],
adherence_config=Constant(campaign, initial_effect=0.8),
non_adherence_options=[
NonAdherenceOption.NEXT_DOSAGE_TIME,
NonAdherenceOption.LOST_TAKE_NEXT,
NonAdherenceOption.STOP,
],
non_adherence_distribution=[0.6, 0.3, 0.1],
dose_interval=2,
max_dose_consideration_duration=7,
took_dose_event="TookALDose",
)
Source code in emodpy_malaria/campaign/individual_intervention.py
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AntimalarialDrug
Bases: IndividualIntervention
The AntimalarialDrug intervention class distributes an antimalarial drug to an individual. The drug's pharmacokinetic and pharmacodynamic parameters are configured in the config file via Malaria_Drug_Params.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
campaign
|
(campaign, required)
|
An instance of the emod_api.campaign module. |
required |
drug_type
|
(str, required)
|
The name of the antimalarial drug to distribute. Must match a drug name configured in the simulation's Malaria_Drug_Params. |
required |
common_intervention_parameters
|
CommonInterventionParameters
|
The CommonInterventionParameters object that contains the 5 common parameters: cost, intervention_name, new_property_value, disqualifying_properties, dont_allow_duplicates. Default value: None |
None
|
Source code in emodpy_malaria/campaign/individual_intervention.py
BitingRisk
Bases: IndividualIntervention
The BitingRisk class allows you to adjust the relative risk that the person is bitten by a vector. As an intervention, it allows you to target specific groups at specific times during the simulation.
The relative risk is population-relative: it controls how likely one individual is to be bitten compared to others in the same node, not the absolute biting rate of the node. For example, setting the entire population to a relative risk of 10 has no effect because everyone's risk is equally scaled — the ratio between individuals is unchanged. The relative risk is only meaningful when some individuals have a different value than others.
The relative biting rate can be initially set using MalariaDemographics.set_risk_distribution(), which gives each new person their own relative risk at their inception.
The relative biting rate can be thought of as having two parts: the relative risk value
and the age dependent value. Age dependence is set using
config.parameters.Age_Dependent_Biting_Risk_Type (set to
AgeDependentBitingRiskType.LINEAR or
AgeDependentBitingRiskType.SURFACE_AREA_DEPENDENT; AgeDependentBitingRiskType.OFF
disables it). These two values (from age dependence and
relative risk) are multiplied to get the resulting rate, which is then used to control how
much contagion is deposited from an infectious individual and the probability that an
infection is acquired.
This intervention expires. To reset it, distribute another BitingRisk intervention that sets it back to the original value. Note that this is a relative biting rate. For example, giving everyone a value of 10 is the same as giving everyone a value of 1. This intervention is used to indicate some individuals are more likely to be bitten than others.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
campaign
|
(campaign, required)
|
An instance of the emod_api.campaign module. |
required |
risk_distribution
|
(BaseDistribution, required)
|
The distribution type to use for assigning the relative risk of being bitten by a mosquito to each individual. Each assigned value is a random draw from the distribution. Please use the following distribution classes from emodpy_malaria.utils.distributions to define the distribution: * ConstantDistribution * UniformDistribution * GaussianDistribution * ExponentialDistribution * PoissonDistribution * LogNormalDistribution * DualConstantDistribution * WeibullDistribution * DualExponentialDistribution |
required |
common_intervention_parameters
|
CommonInterventionParameters
|
The CommonInterventionParameters object that contains the 5 common parameters. Default value: None |
None
|
Source code in emodpy_malaria/campaign/individual_intervention.py
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HumanHostSeekingTrap
Bases: IndividualIntervention
The HumanHostSeekingTrap intervention class applies a trap that attracts and kills indoor host-seeking mosquitoes in the simulation. Human-host-seeking traps are individually-distributed interventions that have attraction and killing rates that decay in an analogous fashion to the killing rates of bednets.
An artificial diet diverts the vector from feeding on the indoor human, resulting in a two-fold benefit: (1) uninfected mosquitoes avoid biting infected humans some of the time, therefore decreasing the amount of human-to-vector transmission, and (2) infectious vectors are diverted to feed on an artificial diet instead of humans, therefore decreasing the amount of vector-to-human transmission.
At a glance:
- Distributed to: Individuals
- Serialized: Yes, if it has been distributed to a person.
- Uses insecticides: No
- Time-based expiration: No
- Purge existing: Yes. A new intervention of this class will replace an existing one.
- Vector killing contributes to: Indoor Die Before Feeding
- Vector effects: Artificial Diet feed instead of Human or Animal Feed
- Vector sexes affected: Females only
- Vector life stage affected: Adult
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
campaign
|
(campaign, required)
|
An instance of the emod_api.campaign module. |
required |
attract_config
|
(AbstractWaningConfig, required)
|
Waning effect for the trap's attractiveness. The vectors that are attracted to the trap will feed on an artificial diet instead of humans, and therefore do not contribute to malaria transmission this feeding cycle. Out of the vectors that are attacted to the trap, some will die due to the killing effect defined by the killing_config. Available types are defined in Waning Effects. |
required |
killing_config
|
(AbstractWaningConfig, required)
|
Waning effect configuration for the trap killing efficacy. The killing effect is applied to indoor meal-seeking vectors that have been attracted to the trap. Available types are defined in Waning Effects. |
required |
common_intervention_parameters
|
CommonInterventionParameters
|
The CommonInterventionParameters object that contains the 5 common parameters. Default value: None |
None
|
Source code in emodpy_malaria/campaign/individual_intervention.py
IRSHousingModification
Bases: IndividualIntervention
The IRSHousingModification intervention class includes Indoor Residual Spraying (IRS) in the simulation. IRS is another key vector control tool in which insecticide is sprayed on the interior walls of a house so that mosquitoes resting on the walls after consuming a blood meal will die. This intervention affects indoor meal-seeking mosquitoes, which may be repelled from entering the house or killed after landing on the wall post-meal. Since this intervention does not kill vectors before feeding, infectious vectors that are not repelled and die from this intervention still contribute to malaria transmission by potentially passing it to humans before they die.
Note that EMOD does not explicitly model houses. IRSHousingModification is distributed to
individuals, which means you can give IRS to some people in the population and not others —
it does not apply uniformly to all individuals in a node the way a node-level intervention
would. Also, because this intervention is tied to the individual, when the individual migrates,
they "take" it with them. We have a node-level IndoorSpaceSpraying intervention that is distributed
to nodes and does not migrate with individuals but rather affects the individuals currently in the node.
At a glance:
- Distributed to: Individuals
- Serialized: Yes, if it has been distributed to a person.
- Uses insecticides: Yes. Can target specific species or other subgroups.
- Time-based expiration: No
- Purge existing: No. Existing interventions of this class continue to exist together with new ones. Efficacies combine as 1-(1-prob1)*(1-prob2).
- Vector killing contributes to: Indoor Die After Feeding
- Vector effects: Repelling and killing
- Vector sexes affected: Indoor meal-seeking females only
- Vector life stage affected: Adult
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
campaign
|
(campaign, required)
|
An instance of the emod_api.campaign module. |
required |
repelling_config
|
(AbstractWaningConfig, required)
|
Waning effect configuration for the IRS repelling efficacy. Repelled vectors survive and do not attempt to feed again until the following day and are not affected by the killing effect of IRS. Available types are defined in Waning Effects. |
required |
killing_config
|
(AbstractWaningConfig, required)
|
Waning effect configuration for the IRS killing efficacy. The killing effect is applied to indoor meal-seeking vectors that have not been repelled, mimicking mosquitoes landing on the wall and being exposed to the insecticide after the meal. Available types are defined in Waning Effects. |
required |
insecticide_name
|
str
|
The name of the insecticide used. Only relevant when modeling insecticide resistance
via the vector genetics system. The name must match an insecticide defined via
|
None
|
common_intervention_parameters
|
CommonInterventionParameters
|
The CommonInterventionParameters object that contains the 5 common parameters. Default value: None |
None
|
Source code in emodpy_malaria/campaign/individual_intervention.py
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IndoorIndividualEmanator
Bases: IndividualIntervention
The IndoorIndividualEmanator intervention class is a house modification intervention that imitates the use of personal mosquito repellents designed for indoor use, such as mosquito coils or vaporizer mats. These interventions release insecticides into the air to repel or kill mosquitoes in the vicinity of the individual using the emanator. The intervention is distributed to individuals, allowing for targeting specific subgroups of the population.
The intervention acts on female vectors seeking a blood meal indoors. Once the vector is indoors, it is first repelled based on the repelling effect. Then, vectors that are not repelled are subjected to the killing effect. Vectors that are not repelled or killed can proceed to try to bite the individual and will be subject to other individual indoor interventions. After the vectors have successfully fed (human or non-human meal), they are subjected again to the killing effect of the emanator before exiting the indoor environment. Hence, the IndoorIndividualEmanator can contribute to both Indoor Die Before Feeding and Indoor Die After Feeding.
At a glance:
- Distributed to: Individuals
- Serialized: Yes, if it has been distributed to a person.
- Uses insecticides: Yes. Can target specific species or other subgroups.
- Time-based expiration: No
- Purge existing: No. Existing interventions continue to exist together with new ones. Efficacies combine as 1-(1-prob1)*(1-prob2).
- Vector killing contributes to: Indoor Die Before Feeding, Indoor Die After Feeding
- Vector effects: Repelling and killing
- Vector sexes affected: Females seeking blood meal indoors only
- Vector life stage affected: Adult
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
campaign
|
(campaign, required)
|
An instance of the emod_api.campaign module. |
required |
repelling_config
|
(AbstractWaningConfig, required)
|
Waning effect configuration for the emanator repelling efficacy. Repelled vectors survive and do not attempt to feed again until the following day and are not affected by the killing effect of the emanator. Available types are defined in Waning Effects. |
required |
killing_config
|
(AbstractWaningConfig, required)
|
Waning effect configuration for the emanator killing efficacy. The killing effect is applied to indoor meal-seeking vectors that have not been repelled by the emanator, mimicking mosquitoes flying through toxic smoke. The killing effect is applied before and, again, after feeding. Available types are defined in Waning Effects. |
required |
insecticide_name
|
str
|
The name of the insecticide used. Only relevant when modeling insecticide resistance
via the vector genetics system. The name must match an insecticide defined via
|
None
|
common_intervention_parameters
|
CommonInterventionParameters
|
The CommonInterventionParameters object that contains the 5 common parameters. Default value: None |
None
|
Source code in emodpy_malaria/campaign/individual_intervention.py
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Ivermectin
Bases: IndividualIntervention
The Ivermectin intervention class modifies the feeding outcome probabilities for both indoor- and outdoor-feeding mosquitoes. Ivermectin works by increasing the mortality of mosquitoes after they blood-feed on a human. It is an individually-distributed intervention that configures the waning of the drug's killing effect on the adult mosquito population. This intervention enables exploration of the impact of giving humans an insecticidal drug, and how the effectiveness and duration of the drug's killing effect interacts with other interventions. For example, you can look at the impact of controlling and eliminating malaria transmission using both anti-parasite drugs that clear existing infections and insecticidal drugs.
At a glance:
- Distributed to: Individuals
- Serialized: Yes, if it has been distributed to a person.
- Uses insecticides: Yes. Can target specific species or other subgroups.
- Time-based expiration: No, but expires if efficacy is below 0.00001.
- Purge existing: No. Existing interventions of this class continue to exist together with new ones. Efficacies combine as 1-(1-prob1)*(1-prob2).
- Vector killing contributes to: Indoor/Outdoor Die After Feeding
- Vector effects: Killing
- Vector sexes affected: Meal-seeking females only
- Vector life stage affected: Adult
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
campaign
|
(campaign, required)
|
An instance of the emod_api.campaign module. |
required |
killing_config
|
(AbstractWaningConfig, required)
|
Waning effect for ivermectin's mosquito-killing efficacy for vectors who have had a blood meal from the treated human. The killing effect is applied after the blood meal, and therefore does not prevent infectious mosquitoes from infecting the human host or getting infected by an infectious human, but it does prevent them from spreading the infection any further. Available types are defined in Waning Effects. |
required |
insecticide_name
|
str
|
The name of the insecticide used. Only relevant when modeling insecticide resistance
via the vector genetics system. The name must match an insecticide defined via
|
None
|
common_intervention_parameters
|
CommonInterventionParameters
|
The CommonInterventionParameters object that contains the 5 common parameters. Default value: None |
None
|
Source code in emodpy_malaria/campaign/individual_intervention.py
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MalariaDiagnostic
Bases: IndividualIntervention
The MalariaDiagnostic intervention class tests an individual for malaria using a specified diagnostic type and broadcasts events based on the result.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
campaign
|
(campaign, required)
|
An instance of the emod_api.campaign module. |
required |
diagnostic_type
|
(DiagnosticType, required)
|
The type of malaria diagnostic to use. The diagnostic type determines how the test measurement is made and what units detection_threshold and measurement_sensitivity use. Use the DiagnosticType enum values:
|
required |
detection_threshold
|
(float, required)
|
The diagnostic detection threshold whose units depend on the diagnostic_type setting. The measurement must be greater than this threshold to trigger a positive diagnosis, therefore the default of 0 generates a positive diagnosis at any positive value. Use the following units based on the diagnostic type:
Minimum value: 0 Maximum value: 1000000 |
0
|
measurement_sensitivity
|
(float, required)
|
The volume of blood tested in microliters, used to simulate Poisson sampling
noise in blood smear diagnostics. Only applies when diagnostic_type is
The diagnostic measurement is calculated as:: where Minimum value: 0 Maximum value: 1000000 Default value: 0.1 |
0.1
|
treatment_fraction
|
float
|
Fraction of positive diagnoses that receive the action specified in positive_diagnosis. This allows modeling imperfect treatment coverage after diagnosis. Negative diagnoses are unaffected regardless of this parameter, all are received. Minimum value: 0 Maximum value: 1 Default value: 1 |
1
|
positive_diagnosis
|
(Union[str, IndividualIntervention], required)
|
The action to take on positive diagnosis. If a string, it is broadcast as an
individual-level event after days_to_diagnosis. If an |
required |
negative_diagnosis
|
Union[str, IndividualIntervention]
|
The action to take on negative diagnosis. If a string, it is broadcast as an
individual-level event immediately. If an |
None
|
days_to_diagnosis
|
float
|
Number of days between test administration and diagnosis result (event broadcast or intervention distribution). This allows modeling delays in receiving test results or seeking treatment after diagnosis. Minimum value: 0 Maximum value: 3.40282e+38 Default value: 0 |
0
|
common_intervention_parameters
|
CommonInterventionParameters
|
The CommonInterventionParameters object that contains the 5 common parameters. Default value: None |
None
|
Example
Test for malaria using blood smear and broadcast an event on positive result::
from emodpy_malaria.campaign.individual_intervention import MalariaDiagnostic
from emodpy_malaria.utils.emod_enum import DiagnosticType
diagnostic = MalariaDiagnostic(
campaign=campaign,
diagnostic_type=DiagnosticType.BLOOD_SMEAR_PARASITES,
detection_threshold=40,
measurement_sensitivity=0.1,
positive_diagnosis="TestedPositive",
negative_diagnosis="TestedNegative",
)
Example
Use an RDT and distribute a drug on positive diagnosis::
from emodpy_malaria.campaign.individual_intervention import MalariaDiagnostic, AntimalarialDrug
from emodpy_malaria.utils.emod_enum import DiagnosticType
diagnostic = MalariaDiagnostic(
campaign=campaign,
diagnostic_type=DiagnosticType.PF_HRP2,
detection_threshold=20,
measurement_sensitivity=0.1,
positive_diagnosis=AntimalarialDrug(campaign, drug_type="Chloroquine"),
)
Source code in emodpy_malaria/campaign/individual_intervention.py
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MultiInsecticideIRSHousingModification
Bases: IndividualIntervention
The MultiInsecticideIRSHousingModification intervention class is an individual-level intervention that builds on IRSHousingModification by enabling the use of multiple insecticides. The killing efficacy of each insecticide can be specified. This class uses Indoor Residual Spraying (IRS), where insecticide is sprayed on the interior walls of houses such that mosquitoes resting on the walls after consuming blood meals will die. The effectiveness of the intervention is combined using the following equation::
Total efficacy = 1.0 - (1.0 - efficacy_1) * (1.0 - efficacy_2) * ... * (1.0 - efficacy_n)
At a glance:
- Distributed to: Individuals
- Serialized: Yes, if it has been distributed to a person.
- Uses insecticides: Yes. Can target specific species or other subgroups.
- Time-based expiration: No
- Purge existing: No. Existing interventions of this class continue to exist together with new ones. Efficacies combine as 1-(1-prob1)*(1-prob2).
- Vector killing contributes to: Indoor Die After Feeding, Indoor Die Before Feeding (when combined with HostSeekingSugarTrap)
- Vector effects: Repelling and killing
- Vector sexes affected: Females only
- Vector life stage affected: Adult
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
campaign
|
(campaign, required)
|
An instance of the emod_api.campaign module. |
required |
insecticides
|
(list[InsecticideWaningEffect], required)
|
A list of
InsecticideWaningEffect
objects with repelling and killing configs (variant |
required |
common_intervention_parameters
|
CommonInterventionParameters
|
The CommonInterventionParameters object that contains the 5 common parameters. Default value: None |
None
|
Source code in emodpy_malaria/campaign/individual_intervention.py
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MultiInsecticideUsageDependentBednet
Bases: IndividualIntervention
The MultiInsecticideUsageDependentBednet intervention class is similar to UsageDependentBednet but allows the addition of multiple insecticides. Each insecticide entry defines its own repelling, blocking, and killing waning effects. The effectiveness of multiple insecticides is combined using the following equation::
Total efficacy = 1.0 - (1.0 - efficacy_1) * (1.0 - efficacy_2) * ... * (1.0 - efficacy_n)
As in UsageDependentBednet, bednet ownership and nightly bednet usage are distinct. Net ownership is configured through the demographic coverage, and the repelling, blocking, and killing rates of mosquitoes are time-dependent. Nightly use of bednets is age-dependent and can vary seasonally. Once a net has been distributed to someone, the nightly net usage is determined by the product of the waning effects in the usage_config_list until the expiration timer runs out and the net is discarded.
At a glance:
- Distributed to: Individuals
- Serialized: Yes, if it has been distributed to a person.
- Uses insecticides: Yes. Can target specific species or other subgroups.
- Time-based expiration: Yes, an expiration timer independent from waning effects can be configured.
- Purge existing: Yes. A new bednet replaces any other bednet intervention.
- Vector killing contributes to: Indoor Die Before Feeding
- Vector effects: Repelling, blocking, killing
- Vector sexes affected: Indoor meal-seeking females only
- Vector life stage affected: Adult
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
campaign
|
(campaign, required)
|
An instance of the emod_api.campaign module. |
required |
insecticides
|
(list[InsecticideWaningEffect], required)
|
A list of
InsecticideWaningEffect
objects with repelling, blocking, and killing configs (variant |
required |
usage_config_list
|
list[AbstractWaningConfig]
|
A list of waning effect configurations that combine to determine whether a net owner sleeps under the net on a given night. Each waning effect in the list produces a value between 0 and 1, and the product of all values is the probability that the person uses the net that night. This allows combining independent usage factors such as age-dependent and seasonal usage patterns. Available types are defined in Waning Effects. Default value: None |
None
|
received_event
|
str
|
An individual-level event to broadcast when a bednet is received. Default value: None |
None
|
using_event
|
str
|
An individual-level event to broadcast when a bednet is being used that night. Default value: None |
None
|
discard_event
|
str
|
An individual-level event to broadcast when a bednet is discarded. Default value: None |
None
|
expiration_period_distribution
|
(BaseDistribution, required)
|
The distribution type to use for setting the expiration of the intervention. Each intervention gets an expiration duration by doing a random draw from the distribution. Please use the following distribution classes from emodpy_malaria.utils.distributions to define the distribution: * ConstantDistribution * UniformDistribution * GaussianDistribution * ExponentialDistribution * PoissonDistribution * LogNormalDistribution * DualConstantDistribution * WeibullDistribution * DualExponentialDistribution |
required |
common_intervention_parameters
|
CommonInterventionParameters
|
The CommonInterventionParameters object that contains the 5 common parameters. Default value: None |
None
|
Source code in emodpy_malaria/campaign/individual_intervention.py
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MultiPackComboDrug
Bases: IndividualIntervention
The MultiPackComboDrug intervention class distributes a combination drug regimen with multiple doses. Similar to AdherentDrug but without adherence modeling.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
campaign
|
(campaign, required)
|
An instance of the emod_api.campaign module. |
required |
doses
|
(list[list[str]], required)
|
A two-dimensional array of drug names defining the drug regimen. Each inner list represents the drugs taken in a single dose. All drug names must match those defined in the simulation's Malaria_Drug_Params. Example -- a standard 3-day AL (Artemether-Lumefantrine) regimen with 6 doses:: Example -- a single-dose SP (Sulfadoxine-Pyrimethamine) for IPTp:: |
required |
dose_interval
|
float
|
The number of days between doses which are defined in the doses parameter. Minimum value: 0 Maximum value: 100000 Default value: 1 Example -- twice-daily dosing for an AL regimen:: |
1
|
common_intervention_parameters
|
CommonInterventionParameters
|
The CommonInterventionParameters object that contains the 5 common parameters. Default value: None |
None
|
Source code in emodpy_malaria/campaign/individual_intervention.py
OutbreakIndividualMalariaGenetics
Bases: IndividualIntervention
The OutbreakIndividualMalariaGenetics intervention class creates an outbreak with a specific malaria parasite genome (barcode, drug resistance alleles, HRP markers). This intervention is part of the Full Parasite Genetics (FPG) model. See Full Parasite Genetics (FPG) Model for details.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
campaign
|
(campaign, required)
|
An instance of the emod_api.campaign module. |
required |
create_nucleotide_sequence_from
|
(NucleotideSequenceOrigin, required)
|
Determines how the parasite genome is created. Use the NucleotideSequenceOrigin enum values:
|
required |
barcode_string
|
str, conditionally required
|
A series of nucleotide base letters (A, C, G, T) that represent the values at
barcode locations in the parasite genome. The length of the string depends on
the number of barcode locations configured via
|
None
|
drug_resistant_string
|
str
|
A series of nucleotide base letters (A, C, G, T) that represent the values at
drug-resistance locations in the parasite genome. The length of the string
depends on the number of locations defined in the drug-resistance locations configured via
|
None
|
hrp_string
|
str
|
A series of nucleotide base letters (A, C, G, T) that represent HRP
(histidine-rich protein) values at locations in the parasite genome. The length
of the string depends on the number of locations defined in the
HRP locations configured via
|
None
|
barcode_allele_frequencies_per_genome_location
|
list[list[float]]
|
The fractions of allele occurrences for each location in the barcode. This 2D
array has an inner array for each location in the barcode. The number of inner
arrays depends on the number of barcode locations configured via
|
None
|
drug_resistant_allele_frequencies_per_genome_location
|
list[list[float]]
|
The fractions of allele occurrences for each drug-resistance location. This 2D
array has an inner array for each location. The number of inner arrays depends
on the number of drug-resistance locations configured via
|
None
|
hrp_allele_frequencies_per_genome_location
|
list[list[float]]
|
The fractions of allele occurrences for each HRP location. This 2D array has
an inner array for each location. The number of inner arrays depends on the
number of HRP locations configured via
|
None
|
msp_variant_value
|
int, conditionally required
|
The Merozoite Surface Protein (MSP) variant value used to determine how
antibodies recognize merozoites during blood-stage infection. This value must
be less than or equal to the |
None
|
pfemp1_variants_values
|
list[int]
|
The PfEMP1 (Plasmodium falciparum Erythrocyte Membrane Protein 1) variant
values, also known as major epitopes, used to define how antibodies recognize
infected red blood cells. Each value in the array must be less than or equal
to the |
None
|
ignore_immunity
|
bool
|
If True, individuals will be force-infected with the specified parasite strain regardless of their actual immunity level. If False, individual's immunity affects whether the infection takes hold. Default value: True |
True
|
incubation_period_override
|
int
|
The incubation period, in days, that infected individuals go through before becoming infectious. This overrides the incubation period set in the configuration file. Set to -1 to use the default incubation period. Range: -1 to 2147480000. Default value: -1 |
-1
|
common_intervention_parameters
|
CommonInterventionParameters
|
The CommonInterventionParameters object that contains the 5 common parameters. Default value: None |
None
|
Example
Create an outbreak with a specific barcode::
from emodpy_malaria.campaign.individual_intervention import OutbreakIndividualMalariaGenetics
from emodpy_malaria.utils.emod_enum import NucleotideSequenceOrigin
outbreak = OutbreakIndividualMalariaGenetics(
campaign=campaign,
create_nucleotide_sequence_from=NucleotideSequenceOrigin.BARCODE_STRING,
barcode_string="AATTCCGG",
drug_resistant_string="AA",
hrp_string="AT"
)
Example
Create an outbreak using allele frequencies::
from emodpy_malaria.campaign.individual_intervention import OutbreakIndividualMalariaGenetics
from emodpy_malaria.utils.emod_enum import NucleotideSequenceOrigin
outbreak = OutbreakIndividualMalariaGenetics(
campaign=campaign,
create_nucleotide_sequence_from=NucleotideSequenceOrigin.ALLELE_FREQUENCIES,
barcode_allele_frequencies_per_genome_location=[
[0.25, 0.25, 0.25, 0.25], # location 1
[0.50, 0.50, 0.00, 0.00], # location 2
],
ignore_immunity=False
)
Source code in emodpy_malaria/campaign/individual_intervention.py
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OutbreakIndividualMalariaVarGenes
Bases: IndividualIntervention
The OutbreakIndividualMalariaVarGenes intervention class creates an outbreak with specific var gene (PfEMP1) variant types for modeling antigenic variation. This intervention is part of the Full Parasite Genetics (FPG) model. See Full Parasite Genetics (FPG) Model for details.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
campaign
|
(campaign, required)
|
An instance of the emod_api.campaign module. |
required |
msp_type
|
int
|
The Merozoite Surface Protein (MSP) variant value of the infection. This value
determines how antibodies recognize merozoites during blood-stage infection and
must be less than or equal to the |
0
|
irbc_type
|
list[int]
|
The array of PfEMP1 major epitope variant values, which define how antibodies
recognize infected red blood cells. Each value in the array must be less than
or equal to the |
None
|
minor_epitope_type
|
list[int]
|
The array of PfEMP1 minor epitope variant values. The array must contain
exactly 50 values. Each value must be less than or equal to
Falciparum_Nonspecific_Types multiplied by 5
( |
None
|
ignore_immunity
|
bool
|
If True, individuals will be force-infected with the specified parasite strain regardless of their actual immunity level. Set to False to have immunity affect whether the infection takes hold. Default value: True |
True
|
incubation_period_override
|
int
|
The incubation period, in days, that infected individuals go through before becoming infectious. This overrides the incubation period set in the configuration file. Set to -1 to use the default incubation period from configuration settings. Range: -1 to 2147480000. Default value: -1 |
-1
|
common_intervention_parameters
|
CommonInterventionParameters
|
The CommonInterventionParameters object that contains the 5 common parameters. Default value: None |
None
|
Source code in emodpy_malaria/campaign/individual_intervention.py
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ScreeningHousingModification
Bases: IndividualIntervention
The ScreeningHousingModification intervention class implements housing screens as a vector control effort. Housing screens are used to decrease the number of mosquitoes that can enter indoors and therefore reduce indoor biting. The vectors that are not repelled by the screens and enter the house might then be killed post-meal from landing on the screen.
This intervention works similarly to IRS. Like IRSHousingModification, it is distributed to individuals rather than applied to a node — EMOD does not explicitly model houses, so this intervention can be given to a subset of the population to represent screened households.
At a glance:
- Distributed to: Individuals
- Serialized: Yes, if it has been distributed to a person.
- Uses insecticides: Yes. Can target specific species or other subgroups.
- Time-based expiration: No
- Purge existing: Yes and No. A new intervention of this class will overwrite any existing intervention of the same class with the same Intervention_Name. If Intervention_Name is different, both interventions will coexist and their efficacies will combine as 1-(1-prob1)*(1-prob2).
- Vector killing contributes to: Die Indoor After Feeding, Die Indoor Before Feeding
- Vector effects: Repelling and killing
- Vector sexes affected: Indoor meal-seeking females only
- Vector life stage affected: Adult
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
campaign
|
(campaign, required)
|
An instance of the emod_api.campaign module. |
required |
repelling_config
|
(AbstractWaningConfig, required)
|
Waning effect configuration for the screen repelling efficacy. Repelled vectors survive and do not attempt to feed again until the following day and are not affected by the killing effect of the screen. Available types are defined in Waning Effects. |
required |
killing_config
|
(AbstractWaningConfig, required)
|
Waning effect configuration for the screen killing efficacy. The killing effect is applied to indoor meal-seeking vectors that have not been repelled, mimicking mosquitoes landing on the screen and being exposed to the insecticide after the meal. Available types are defined in Waning Effects. |
required |
insecticide_name
|
str
|
The name of the insecticide used. Only relevant when modeling insecticide resistance
via the vector genetics system. The name must match an insecticide defined via
|
None
|
common_intervention_parameters
|
CommonInterventionParameters
|
The CommonInterventionParameters object that contains the 5 common parameters. Default value: None |
None
|
Source code in emodpy_malaria/campaign/individual_intervention.py
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SimpleBednet
Bases: IndividualIntervention
The SimpleBednet intervention class implements insecticide-treated nets (ITN) in the simulation. ITNs are a key component of modern malaria control efforts, and have recently been scaled up towards universal coverage in sub-Saharan Africa. Modern bednets are made of a polyethylene or polyester mesh, which is impregnated with a slowly releasing pyrethroid insecticide. When mosquitoes that are seeking a blood meal indoors encounter a net, the feeding attempt may be repelled due to the presence of insecticides or blocked as long as the net retains its physical integrity and has been correctly installed. Blocked feeding attempts also carry the possibility of killing the mosquito. Net ownership is configured through the demographic coverage, and the repelling, blocking, and killing rates of mosquitoes are time-dependent. All the efficacies are also affected by the usage_config parameter -- the usage effect is multiplied by the repelling, blocking, and killing effects to determine the final efficacy of the net on any given day.
SimpleBednet can model the nightly bednet usage of net owners by reducing the daily efficacy. To model individuals using nets intermittently, see UsageDependentBednet. To include multiple insecticides, see MultiInsecticideUsageDependentBednet.
At a glance:
- Distributed to: Individuals
- Serialized: Yes, if it has been distributed to a person.
- Uses insecticides: Yes. Can target specific species or other subgroups via insecticide configuration.
- Time-based expiration: No, but expires if the WaningEffect expires.
- Purge existing: Yes. A new bednet replaces any other bednet intervention for this same user.
- Vector killing contributes to: Indoor Die Before Feeding
- Vector effects: Repelling, blocking, killing
- Vector sexes affected: Indoor meal-seeking females only
- Vector life stage affected: Adult
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
campaign
|
(campaign, required)
|
An instance of the emod_api.campaign module. |
required |
repelling_config
|
(AbstractWaningConfig, required)
|
Waning effect configuration for the bednet's mosquito repelling effect. This is the first effect applied to meal-seeking mosquitoes that encounter the net. Repelled vectors do not enter the netted space — they survive and do not attempt to feed again until the following day and are not affected by the blocking or killing effects. Available types are defined in Waning Effects. |
required |
blocking_config
|
(AbstractWaningConfig, required)
|
Waning effect configuration for the bednet's ability to block meal-seeking mosquito. The blocking_config probabilities are applied to the subset of meal-seeking mosquitoes that have not been repelled. Available types are defined in Waning Effects. |
required |
killing_config
|
(AbstractWaningConfig, required)
|
Waning effect configuration for the bednet's insecticidal killing effect. For meal-seeking vector to be affected, it must be successfully blocked first, mimicking mosquito landing on the bednet, so killing_config probabilities are applied to the subset of mosquitoes that are blocked. Available types are defined in Waning Effects. |
required |
usage_config
|
AbstractWaningConfig
|
Waning effect configuration for nightly bednet usage over time. The usage effect is multiplied with the repelling, blocking, and killing effects to determine the final efficacy of the net on any given night. Available types are defined in Waning Effects. Default value: Constant usage with initial effect of 1 (full usage) |
None
|
insecticide_name
|
str
|
The name of the insecticide used. Only relevant when modeling insecticide resistance
via the vector genetics system. The name must match an insecticide defined via
|
None
|
common_intervention_parameters
|
CommonInterventionParameters
|
The CommonInterventionParameters object that contains the 5 common parameters. Default value: None |
None
|
Source code in emodpy_malaria/campaign/individual_intervention.py
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SimpleHealthSeekingBehavior
Bases: IndividualIntervention
The SimpleHealthSeekingBehavior intervention class models the time delay that typically occurs between when an individual experiences onset of symptoms and when they seek help from a health care provider. Several factors may contribute to such delays including accessibility, cost, and trust in the health care system. This intervention models this time delay as an exponential process; at every time step, the model draws randomly to determine if the individual will receive the specified intervention. As an example, this intervention can be nested in a NodeLevelHealthTriggeredIV so that when an individual is infected or experiences clinical symptoms, they receive a SimpleHealthSeekingBehavior, representing that the individual will now seek care. The individual subsequently seeks care with an exponentially distributed delay and ultimately receives the specified intervention.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
campaign
|
(campaign, required)
|
An instance of the emod_api.campaign module. |
required |
tendency
|
float
|
Probability that the individual will seek care. Minimum value: 0 Maximum value: 1 Default value: 1 |
1
|
single_use
|
bool
|
If True, the intervention expires after first use, set to False, it remains active indefinitely. Default value: True |
True
|
actual_intervention
|
(Union[str, IndividualIntervention], required)
|
The action to take when the individual seeks care. If a string, it is broadcast
as an individual-level event. If an |
required |
common_intervention_parameters
|
CommonInterventionParameters
|
The CommonInterventionParameters object that contains the 5 common parameters. Default value: None |
None
|
Example
Distribute antimalarial treatment when symptomatic individuals seek care::
from emodpy_malaria.campaign.individual_intervention import SimpleHealthSeekingBehavior, AntimalarialDrug
hsb = SimpleHealthSeekingBehavior(
campaign=campaign,
tendency=0.8,
single_use=False,
actual_intervention=AntimalarialDrug(campaign, drug_type="Chloroquine")
)
Example
Broadcast an event when care is sought::
from emodpy_malaria.campaign.individual_intervention import SimpleHealthSeekingBehavior
hsb = SimpleHealthSeekingBehavior(
campaign=campaign,
tendency=0.6,
actual_intervention="SeekingTreatment"
)
Source code in emodpy_malaria/campaign/individual_intervention.py
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SimpleIndividualRepellent
Bases: IndividualIntervention
The SimpleIndividualRepellent intervention class provides protection to individuals against both indoor-feeding and outdoor-feeding mosquito bites.
At a glance:
- Distributed to: Individuals
- Serialized: Yes, when it has been distributed to individuals.
- Uses insecticides: Yes. The vector genome can be used to target specific vectors.
- Time-based expiration: No. It will continue to exist even if efficacy is zero.
- Purge existing: Yes and No. A new intervention of this class will overwrite any existing intervention of the same class with the same Intervention_Name. If Intervention_Name is different, both interventions will coexist and their efficacies will combine as 1-(1-prob1)*(1-prob2).
- Vector killing contributes to: No killing
- Vector effects: Repelling
- Vector sexes affected: All meal-seeking females
- Vector life stage affected: Adult
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
campaign
|
(campaign, required)
|
An instance of the emod_api.campaign module. |
required |
repelling_config
|
(AbstractWaningConfig, required)
|
Waning effect configuration for the IRS repelling efficacy. Repelled vectors survive and do not attempt to feed again until the following day and are not affected by the killing effect of IRS. Available types are defined in Waning Effects. |
required |
insecticide_name
|
str
|
The name of the insecticide used. Only relevant when modeling insecticide resistance
via the vector genetics system. The name must match an insecticide defined via
|
None
|
common_intervention_parameters
|
CommonInterventionParameters
|
The CommonInterventionParameters object that contains the 5 common parameters. Default value: None |
None
|
Source code in emodpy_malaria/campaign/individual_intervention.py
SpatialRepellentHousingModification
Bases: IndividualIntervention
The SpatialRepellentHousingModification intervention class is a housing modification utilizing spatial repellents. The protection provided by this intervention is exclusively against indoor-biting mosquitoes. This intervention is similar to IRSHousingModification and ScreeningHousingModification, but it only has a repelling effect without a killing effect. Repelled vectors survive and do not attempt to feed again until the following day.
At a glance:
- Distributed to: Individuals
- Serialized: Yes, when it has been distributed to individuals.
- Uses insecticides: Yes. The vector genome can be used to target specific vectors.
- Time-based expiration: No. It will continue to exist even if efficacy is zero.
- Purge existing: No. Existing interventions continue to exist together with new ones. Efficacies combine as 1-(1-prob1)*(1-prob2).
- Vector killing contributes to: No killing
- Vector effects: Repelling
- Vector sexes affected: Indoor meal-seeking females only
- Vector life stage affected: Adult
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
campaign
|
(campaign, required)
|
An instance of the emod_api.campaign module. |
required |
repelling_config
|
(AbstractWaningConfig, required)
|
Waning effect configuration for the IRS repelling efficacy. Repelled vectors survive and do not attempt to feed again until the following day and are not affected by the killing effect of IRS. Available types are defined in Waning Effects. |
required |
insecticide_name
|
str
|
The name of the insecticide used. Only relevant when modeling insecticide resistance
via the vector genetics system. The name must match an insecticide defined via
|
None
|
common_intervention_parameters
|
CommonInterventionParameters
|
The CommonInterventionParameters object that contains the 5 common parameters. Default value: None |
None
|
Source code in emodpy_malaria/campaign/individual_intervention.py
UsageDependentBednet
Bases: IndividualIntervention
The UsageDependentBednet intervention class is similar to SimpleBednet, as it distributes insecticide-treated nets to individuals in the simulation. However, bednet ownership and nightly bednet usage are distinct in this intervention. As in SimpleBednet, net ownership is configured through the demographic coverage, and the repelling, blocking, and killing rates of mosquitoes are time-dependent. Nightly use of bednets is age-dependent and can vary seasonally. Once a net has been distributed to someone, the nightly net usage is determined by the product of the seasonal and age-dependent usage probabilities until the net-retention counter runs out, and the net is discarded.
While SimpleBednet usage is applied as a daily reduction in efficacy, UsageDependentBednet uses the usage efficacy to determine whether the person slept under the net that night.
For example, consider a bednet configured with 0% repelling, 100% blocking, 100% killing, and 50% usage effect. A person with a SimpleBednet will have a net with final efficacy of 50% blocking and 50% killing every night. A person with a UsageDependentBednet will have half of their nights with a 100% blocking and 100% killing net and half with no net usage at all.
At a glance:
- Distributed to: Individuals
- Serialized: Yes, if it has been distributed to a person.
- Uses insecticides: Yes. Can target sub-groups using genomes, especially specific species.
- Time-based expiration: Yes, an expiration timer independent from waning effects can be configured.
- Purge existing: Yes. A new bednet replaces any other bednet intervention.
- Vector killing contributes to: Indoor Die Before Feeding
- Vector effects: Repelling, blocking, and killing
- Vector sexes affected: Indoor meal-seeking females only
- Vector life stage affected: Adult
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
campaign
|
(campaign, required)
|
An instance of the emod_api.campaign module. |
required |
repelling_config
|
(AbstractWaningConfig, required)
|
Waning effect configuration for the bednet's mosquito repelling effect. This is the first effect applied to meal-seeking mosquitoes that encounter the net. Repelled vectors do not enter the netted space — they survive and do not attempt to feed again until the following day and are not affected by the blocking or killing effects. Available types are defined in Waning Effects. |
required |
blocking_config
|
(AbstractWaningConfig, required)
|
Waning effect configuration for the bednet's ability to block meal-seeking mosquito. The blocking_config probabilities are applied to the subset of meal-seeking mosquitoes that have not been repelled. Available types are defined in Waning Effects. |
required |
killing_config
|
(AbstractWaningConfig, required)
|
Waning effect configuration for the bednet's insecticidal killing effect. For meal-seeking vector to be affected, it must be successfully blocked first, mimicking mosquito landing on the bednet, so killing_config probabilities are applied to the subset of mosquitoes that are blocked. Available types are defined in Waning Effects. |
required |
usage_config_list
|
list[AbstractWaningConfig]
|
A list of waning effect configurations that combine to determine whether a net owner sleeps under the net on a given night. Each waning effect in the list produces a value between 0 and 1, and the product of all values is the probability that the person uses the net that night. This allows combining independent usage factors such as age-dependent and seasonal usage patterns. Available types are defined in Waning Effects. Default value: None |
None
|
insecticide_name
|
str
|
The name of the insecticide used. Only relevant when modeling insecticide resistance
via the vector genetics system. The name must match an insecticide defined via
|
None
|
received_event
|
str
|
An individual-level event to broadcast when a bednet is received. Default value: None |
None
|
using_event
|
str
|
An individual-level event to broadcast when a bednet is being used that night. Default value: None |
None
|
discard_event
|
str
|
An individual-level event to broadcast when a bednet is discarded. Default value: None |
None
|
expiration_period_distribution
|
(BaseDistribution, required)
|
The distribution type to use for setting the expiration of the intervention. Each intervention gets an expiration duration by doing a random draw from the distribution. Please use the following distribution classes from emodpy_malaria.utils.distributions to define the distribution: * ConstantDistribution * UniformDistribution * GaussianDistribution * ExponentialDistribution * PoissonDistribution * LogNormalDistribution * DualConstantDistribution * WeibullDistribution * DualExponentialDistribution |
required |
common_intervention_parameters
|
CommonInterventionParameters
|
The CommonInterventionParameters object that contains the 5 common parameters. Default value: None |
None
|
Source code in emodpy_malaria/campaign/individual_intervention.py
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