individual_intervention
ARTDropout
Bases: IndividualIntervention
The ARTDropout intervention class removes an individual from antiretroviral therapy (ART) and interrupts their progress through the cascade of care. The individual's infectiousness will return to a non-suppressed level, and a new prognosis will be assigned.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
campaign
|
(campaign, required)
|
An instance of the emod_api.campaign module. |
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_hiv/campaign/individual_intervention.py
ARTMortalityTable
Bases: IndividualIntervention
The ARTMortalityTable intervention class allows the user to modify an individual's life expectancy based on different levels of ART adherence; the user defines parameters for age, CD4 count, and time on ART in a multidimensional table which is then used to determine mortality rate. Note: If you have different adherence levels for each gender, then you will need to configure your campaign to distribute an ARTMortalityTable for each gender and adherence level.
Additional considerations when using this intervention
- The model will not allow someone who is HIV negative to be put on ART.
- A person who has not previously been on ART is considered to be 'starting ART' at the time this intervention is applied; the model will track this start time/duration.
- If a person is already on ART from another intervention, receiving a second ART intervention will have no effect.
- If a person is on already ART and receives the ARTMortalityTable intervention, the original ART start time will be used to calculate the duration from enrollment to ART AIDS Death. The duration since starting ART will not change; it will continue to increase.
- If a person is on ART and receives the ARTDropout intervention, the person will go off ART and the duration will be reset; if receiving a new ART intervention, this new start time/duration will be used in any calculations.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
campaign
|
(campaign, required)
|
An instance of the emod_api.campaign module. |
required |
mortality_table
|
(list[list[list[float]]], required)
|
Three-dimensional array of mortality rates used to determine the number of days until AIDS death. Dimensioned by the values specified in art_duration_days_bins, age_years_bins, and cd4_count_bins. |
required |
art_duration_days_bins
|
(list[float], required)
|
An array of bins representing the person's duration on ART, in days (greater than or equal to the value of the bin, but less than the value of the next bin). Each value represents the outer dimension of the mortality_table. Must be in ascending order. |
required |
age_years_bins
|
(list[float], required)
|
An array of bins representing the age of the person, in years, at the time they received the intervention (greater than or equal to the value of the bin, but less than the value of the next bin). If they are new to ART, then it is the age that they started ART. If they are changing their adherence, then it is the age at that time. This bin is used to select the second dimension of the mortality_table. Must be in ascending order. |
required |
cd4_count_bins
|
(list[float], required)
|
An array of bins representing a person's CD4 count at the time they received the intervention (started ART or changed adherence). For each value in the array, there will be one value in the associated row in the mortality_table. A mortality rate will be selected from the table as follows: * Person's CD4 is less than first value in array: Use first mortality rate * Person's CD4 is greater than the last value in the array: Use the last mortality rate * Person's CD4 is between two values: Use linear interpolation to find the mortality rate associated with the person's CD4 Must be in ascending order. |
required |
days_to_achieve_viral_suppression
|
float
|
The number of days after ART initiation over which infectiousness declines linearly until the art_multiplier_on_transmission_prob_per_act takes full effect. Minimum value: 0 Maximum value: 3.40282e+38 Default value: 183 |
183
|
art_multiplier_on_transmission_prob_per_act
|
float
|
Multiplier acting on Base_Infectivity to determine the per-act transmission probability of a virally suppressed HIV+ individual. Minimum value: 0 Maximum value: 1 Default value: 0.08 |
0.08
|
art_is_active_against_mortality_and_transmission
|
bool
|
If set to true (1), ART will suppress viral load and extend prognosis. Default value: True |
True
|
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
Creating an ARTMortalityTable intervention with comprehensive mortality data: - 5 ART duration bins (0-6mo, 6-12mo, 12-24mo, 24-36mo, 36+mo) - 2 age groups (under 40, 40 and over) - 7 CD4 count bins reflecting different immune system states - Higher mortality rates for early ART duration and lower CD4 counts - Reduced mortality over time as patients stabilize on treatment
>>> from emodpy_hiv.campaign.individual_intervention import ARTMortalityTable
>>> from emodpy_hiv.campaign.common import CommonInterventionParameters
>>> import emodpy_hiv.campaign as api_campaign
>>>
>>> art_duration_days_bins=[0, 183, 365, 730, 1095] # 0, 6mo, 1yr, 2yr, 3yr in days
>>> age_years_bins=[0, 40] # Under 40, 40+
>>> cd4_count_bins=[0, 25, 74.5, 149.5, 274.5, 424.5, 624.5] # CD4 count thresholds
>>> # Define mortality table: 5 duration bins x 2 age bins x 7 CD4 bins
>>> mortality_table = [
>>> [ # Duration bin 0 (0-6 months)
>>> [0.2015, 0.2015, 0.1128, 0.0625, 0.0312, 0.0206, 0.0162], # Age 0-40
>>> [0.0875, 0.0875, 0.0490, 0.0271, 0.0136, 0.0062, 0.0041] # Age 40+
>>> ],
>>> [ # Duration bin 1 (6-12 months)
>>> [0.0271, 0.0271, 0.0184, 0.0149, 0.0074, 0.0048, 0.0048],
>>> [0.0171, 0.0171, 0.0116, 0.0094, 0.0047, 0.0030, 0.0030]
>>> ],
>>> [ # Duration bin 2 (12-24 months)
>>> [0.0095, 0.0095, 0.0065, 0.0052, 0.0026, 0.0026, 0.0026],
>>> [0.0095, 0.0095, 0.0065, 0.0052, 0.0026, 0.0026, 0.0026]
>>> ],
>>> [ # Duration bin 3 (24-36 months)
>>> [0.0075, 0.0075, 0.0051, 0.0041, 0.0021, 0.0021, 0.0021],
>>> [0.0075, 0.0075, 0.0051, 0.0041, 0.0021, 0.0021, 0.0021]
>>> ],
>>> [ # Duration bin 4 (36+ months)
>>> [0.0060, 0.0060, 0.0041, 0.0033, 0.0017, 0.0017, 0.0017],
>>> [0.0060, 0.0060, 0.0041, 0.0033, 0.0017, 0.0017, 0.0017]
>>> ]
>>> ]
>>>
>>> # Create the intervention
>>> art_intervention = ARTMortalityTable(campaign=api_campaign,
>>> mortality_table=mortality_table,
>>> art_duration_days_bins=art_duration_days_bins,
>>> age_years_bins=age_years_bins,
>>> cd4_count_bins=cd4_count_bins,
>>> days_to_achieve_viral_suppression=183.0,
>>> art_multiplier_on_transmission_prob_per_act=0.08,
>>> art_is_active_against_mortality_and_transmission=True,
>>> common_intervention_parameters=CommonInterventionParameters(cost=1)
>>> )
Source code in emodpy_hiv/campaign/individual_intervention.py
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AgeDiagnostic
Bases: IndividualIntervention
The AgeDiagnostic allows you to broadcast different events based on the individual's age. For example, you could distribute this intervention to people who are high risk and use the intervention to have different things happen (because of the broadcasted events) based on their age.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
campaign
|
(campaign, required)
|
An instance of the emod_api.campaign module. |
required |
age_thresholds
|
list[RangeThreshold]
|
Used to associate age ranges for individuals. Default value: None |
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
|
Source code in emodpy_hiv/campaign/individual_intervention.py
AntiretroviralTherapy
Bases: IndividualIntervention
The AntiretroviralTherapy intervention class begins antiretroviral therapy (ART) for specified individuals.
To remove an individual from ART, use ARTDropout. Please refer to the documentation for
AntiretroviralTherapy at the following link:
:doc:emod-hiv:emod/hiv-model-healthcare-systems.
Additional considerations when using this intervention
- The model will not allow someone who is HIV negative to be put on ART.
- A person who has not previously been on ART is considered to be 'starting ART' at the time this intervention is applied; the model will track this start time/duration.
- If a person is already on ART from another intervention, receiving a second ART intervention will have no effect.
- If a person is on already ART and receives the ARTMortalityTable intervention, the original ART start time will be used to calculate the duration from enrollment to ART AIDS Death. The duration since starting ART will not change; it will continue to increase.
- If a person is on ART and receives the ARTDropout intervention, the person will go off ART and the duration will be reset; if receiving a new ART intervention, this new start time/duration will be used in any calculations.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
campaign
|
(campaign, required)
|
An instance of the emod_api.campaign module. |
required |
days_to_achieve_viral_suppression
|
float
|
The number of days after ART initiation over which infectiousness declines linearly until the art_multiplier_on_transmission_prob_per_act takes full effect. Minimum value: 0 Maximum value: 3.40282e+38 Default value: 183 |
183
|
art_survival_who_stage_threshold_for_cox
|
float
|
If the person receiving ART has a WHO Stage greater than or equal to this threshold, then use the hazard ratio determined by the parameter art_survival_hazard_ratio_who_stage_3plus. Minimum value: 0 Maximum value: 5 Default value: 3 |
3
|
art_survival_hazard_ratio_who_stage_3plus
|
float
|
The hazard ratio comparing those starting ART in WHO stage >= 3 to those in WHO stage < 3. Minimum value: 1e-06 Maximum value: 1000000.0 Default value: 2.7142 |
2.7142
|
art_survival_hazard_ratio_female
|
float
|
The hazard ratio comparing survival female to male survival for those starting ART. Minimum value: 1e-06 Maximum value: 1000000.0 Default value: 0.6775 |
0.6775
|
art_survival_hazard_ratio_cd4_slope
|
float
|
The slope value to sue when calculating the hazard for for the person based on their CD4 count. multiplier = exp(cd4_slope * cd4 + cd4_intercept) Minimum value: -1000000.0 Maximum value: 1000000.0 Default value: -0.00758256 |
-0.00758256
|
art_survival_hazard_ratio_cd4_intercept
|
float
|
The Y-intercept to use when calculating the hazard ratio for the person based on their CD4 count. multiplier = exp(cd4_slope * cd4 + cd4_intercept) Minimum value: -1000000.0 Maximum value: 1000000.0 Default value: 0.282852 |
0.282852
|
art_survival_hazard_ratio_body_weight_kg_slope
|
float
|
The slope to use when calculating the hazard ratio for the person's body weight. The body weight is determined by WHO stage: * WHO Stage 0 = 65.0 kg * WHO Stage 1-2 = 62.1 kg * WHO Stage 2-3 = 57.0 kg * WHO Stage 3-4 = 50.0 kg * WHO Stage 4+ = 40.1 kg multiplier = exp(weight_slope * weight + weight_intercept) Minimum value: -1000000.0 Maximum value: 1000000.0 Default value: -0.073153 |
-0.073153
|
art_survival_hazard_ratio_body_weight_kg_intercept
|
float
|
The Y-intercept to use when calculating the hazard ratio for the person's body weight. The body weight is determined by WHO stage:
multiplier = exp(weight_slope * weight + weight_intercept) Minimum value: -1000000.0 Maximum value: 1000000.0 Default value: 3.05043 |
3.05043
|
art_survival_hazard_ratio_age_over_40yr
|
float
|
The hazard ratio comparing the survival time of those starting ART over 40 years of age compared to those starting ART <40 years. Minimum value: 1e-06 Maximum value: 1000000.0 Default value: 1.4309 |
1.4309
|
art_survival_baseline_hazard_weibull_shape
|
float
|
Shape parameter for a Weibull distribution of survival time in years for a male < 40 with WHO stage of 1 or 2 starting ART (base case). Minimum value: 0 Maximum value: 10 Default value: 0.34 |
0.34
|
art_survival_baseline_hazard_weibull_scale
|
float
|
Scale parameter for a Weibull distribution of survival time in years for a male < 40 with WHO stage of 1 or 2 starting ART (base case). Minimum value: 1e-06 Maximum value: 1000000.0 Default value: 123.83 |
123.83
|
art_multiplier_on_transmission_prob_per_act
|
float
|
Multiplier acting on Base_Infectivity to determine the per-act transmission probability of a virally suppressed HIV+ individual. Minimum value: 0 Maximum value: 1 Default value: 0.08 |
0.08
|
art_is_active_against_mortality_and_transmission
|
bool
|
If set to true (1), ART will suppress viral load and extend prognosis. Default value: True |
True
|
art_cd4_at_initiation_saturating_reduction_in_mortality
|
float
|
The duration from ART enrollment to on-ART HIV-cause death increases with CD4 at ART initiation up to a threshold determined by this parameter value. This is the maximum value that CD4 is allowed to have in the hazard ratio calculation for CD4. Minimum value: 0 Maximum value: 3.40282e+38 Default value: 350 |
350
|
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_hiv/campaign/individual_intervention.py
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AntiretroviralTherapyFull
Bases: IndividualIntervention
The AntriretroviralTherapyFull intervention class begins antiretroviral therapy (ART) on the person receiving the intervention. This class is similar to the standard AntiretroviralTherapy, but enhances it with two key features: 1) a built-in delay timer such that when the delay expires, the person will come off of ART (ARTDropout should NOT be used with this intervention), and 2) persistence with the individual so the user can track this intervention using ReferenceTrackingEventCoordinator.
Additional considerations when using this intervention
- The model will not allow someone who is HIV negative to be put on ART.
- A person who has not previously been on ART is considered to be 'starting ART' at the time this intervention is applied; the model will track this start time/duration.
- If a person is already on ART from another intervention, receiving a second ART intervention will have no effect.
- If a person is on already ART and receives the ARTMortalityTable intervention, the original ART start time will be used to calculate the duration from enrollment to ART AIDS Death. The duration since starting ART will not change; it will continue to increase.
- If a person is on ART and receives the ARTDropout intervention, the person will go off ART and the duration will be reset; if receiving a new ART intervention, this new start time/duration will be used in any calculations.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
campaign
|
(campaign, required)
|
An instance of the emod_api.campaign module. |
required |
time_on_art_distribution
|
(BaseDistribution, required)
|
The type of distribution to use when determine how long a person will be on ART. Please use the following distribution classes from emodpy_hiv.utils.distributions to define the distribution: * ConstantDistribution * UniformDistribution * GaussianDistribution * ExponentialDistribution * PoissonDistribution * LogNormalDistribution * DualConstantDistribution * WeibullDistribution * DualExponentialDistribution |
required |
stop_art_event
|
str
|
This event is broadcast when the person drops off ART. This could happen either via the timer
running out or the intervention detected a disqualifying property. See
:doc: |
None
|
days_to_achieve_viral_suppression
|
float
|
The number of days after ART initiation over which infectiousness declines linearly until the ART_Multiplier_On_Transmission_Prob_Per_Act takes full effect. Minimum value: 0 Maximum value: 3.40282e+38 Default value: 183 |
183
|
art_survival_who_stage_threshold_for_cox
|
float
|
If the person receiving ART has a WHO Stage greater than or equal to this threshold, then use the hazard ratio determined by the parameter ART_Survival_Hazard_Ratio_WHO_Stage_3Plus. Minimum value: 0 Maximum value: 5 Default value: 3 |
3
|
art_survival_hazard_ratio_who_stage_3plus
|
float
|
The hazard ratio comparing those starting ART in WHO stage >= 3 to those in WHO stage < 3. Minimum value: 1e-06 Maximum value: 1000000.0 Default value: 2.7142 |
2.7142
|
art_survival_hazard_ratio_female
|
float
|
The hazard ratio comparing survival female to male survival for those starting ART. Minimum value: 1e-06 Maximum value: 1000000.0 Default value: 0.6775 |
0.6775
|
art_survival_hazard_ratio_cd4_slope
|
float
|
The slope value to sue when calculating the hazard for for the person based on their CD4 count. multiplier = exp(cd4_slope * cd4 + cd4_intercept) Minimum value: -1000000.0 Maximum value: 1000000.0 Default value: -0.00758256 |
-0.00758256
|
art_survival_hazard_ratio_cd4_intercept
|
float
|
The Y-intercept to use when calculating the hazard ratio for the person based on their CD4 count. multiplier = exp(cd4_slope * cd4 + cd4_intercept) Minimum value: -1000000.0 Maximum value: 1000000.0 Default value: 0.282852 |
0.282852
|
art_survival_hazard_ratio_body_weight_kg_slope
|
float
|
The slope to use when calculating the hazard ratio for the person's body weight. The body weight is determined by WHO stage: * WHO Stage 0 = 65.0 kg * WHO Stage 1-2 = 62.1 kg * WHO Stage 2-3 = 57.0 kg * WHO Stage 3-4 = 50.0 kg * WHO Stage 4+ = 40.1 kg multiplier = exp(weight_slope * weight + weight_intercept) Minimum value: -1000000.0 Maximum value: 1000000.0 Default value: -0.073153 |
-0.073153
|
art_survival_hazard_ratio_body_weight_kg_intercept
|
float
|
The Y-intercept to use when calculating the hazard ratio for the person's body weight. The body weight is determined by WHO stage:
multiplier = exp(weight_slope * weight + weight_intercept) Minimum value: -1000000.0 Maximum value: 1000000.0 Default value: 3.05043 |
3.05043
|
art_survival_hazard_ratio_age_over_40yr
|
float
|
The hazard ratio comparing the survival time of those starting ART over 40 years of age compared to those starting ART <40 years. Minimum value: 1e-06 Maximum value: 1000000.0 Default value: 1.4309 |
1.4309
|
art_survival_baseline_hazard_weibull_shape
|
float
|
Shape parameter for a Weibull distribution of survival time in years for a male < 40 with WHO stage of 1 or 2 starting ART (base case). Minimum value: 0 Maximum value: 10 Default value: 0.34 |
0.34
|
art_survival_baseline_hazard_weibull_scale
|
float
|
Scale parameter for a Weibull distribution of survival time in years for a male < 40 with WHO stage of 1 or 2 starting ART (base case). Minimum value: 1e-06 Maximum value: 1000000.0 Default value: 123.83 |
123.83
|
art_multiplier_on_transmission_prob_per_act
|
float
|
Multiplier acting on Base_Infectivity to determine the per-act transmission probability of a virally suppressed HIV+ individual. Minimum value: 0 Maximum value: 1 Default value: 0.08 |
0.08
|
art_is_active_against_mortality_and_transmission
|
bool
|
If set to true (1), ART will suppress viral load and extend prognosis. Default value: True |
True
|
art_cd4_at_initiation_saturating_reduction_in_mortality
|
float
|
The duration from ART enrollment to on-ART HIV-cause death increases with CD4 at ART initiation up to a threshold determined by this parameter value. This is the maximum value that CD4 is allowed to have in the hazard ratio calculation for CD4. Minimum value: 0 Maximum value: 3.40282e+38 Default value: 350 |
350
|
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_hiv/campaign/individual_intervention.py
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CD4Diagnostic
Bases: IndividualIntervention
The CD4Diagnostic allows you to have different things happen to a person based on their actual CD4 count. For example, if a person was given an HIVRapidDiagnostic and tested positive, you could give that person the CD4Diagnositic. The diagnostic would broadcast different events based on their current CD4 count. If the CD4 count was high, you could broadcast an event that would give the person a delay that would have the person re-test in three months. If the CD4 count was low, you could broadcast an event that would cause them to go on ART immediately.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
campaign
|
(campaign, required)
|
An instance of the emod_api.campaign module. |
required |
cd4_thresholds
|
list[RangeThreshold]
|
This parameter associates ranges of CD4 counts with events that should occur for individuals whose CD4 counts fall into those ranges. Default value: None |
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
|
Source code in emodpy_hiv/campaign/individual_intervention.py
CoitalActRiskFactors
Bases: IndividualIntervention
The CoitalActRiskFactors intervention class provides a method of modifying an individual's risk/probability of acquiring or transmitting an STI. If other risk multipliers are active (across other interventions), the values will be multiplied together; the resulting value will be multiplied with any active STI co-infection factors. When the intervention expires, the individual's risk factor multiplier returns to one. Since this intervention persists, it can be used with Distributors.add_intervention_tracker(). NOTE: An individual can have multiple of these interventions with each one being multiplied times the other.
The risk multiplier for a coital act has three contributions:
1. *Coital Act Risk Factors* - The factors from the use of this intervention.
2. *Co-Infection* - A person can get a co-infection by using the **ModifyStiCoInfectionStatus**
intervention. If the person has a co-infection, then the configuration paameters **STI_Coinfection_Transmission_Multiplier**
or **STI_Coinfection_Acquisition_Multiplier** depending on whether the person has HIV (transmitter)
or not (aquirer). The maximum value of the multiplier between the transmitter and acquirer is used.
3. *Condom Transmission Blocking* - If condoms were used in this coital act, then the
configuration parameter **Condom_Transmission_Blocking_Probability** is included.
The value of the multiplier is calculated as follows:
>>> co_inf_transmission = infected_individual.STI_Coinfection_Transmission_Multiplier if co-infected else 1
>>> co_inf_acquisition = uninfected_individual.STI_Coinfection_Acquisition_Multiplier if co-infected else 1
>>> risk_multiplier = max( co_inf_transmission, co_inf_acquisition )
>>>
>>> risk_factor_transmission = infected_individual.CoitalActsRiskFactors.Transmission_Multiplier
>>> risk_factor_acquisition = uninfected_individual.CoitalActsRiskFactors.Acquisition_Multiplier
>>> risk_multiplier *= risk_factor_transmission * risk_factor_acquisition;
>>>
>>> risk_multiplier *= (1 - Condom_Transmission_Blocking_Probability) if using_condom else 1
This risk multiplier is then used to determine if the uninfected person becomes infected:
>>> probability_infected = risk_multiplier
>>> * transmission_probability
>>> * acquisition_probability
Acquisition Probability
There are three things that contribute to the probability that an uninfected person can acquire HIV from a coital act with an infected person. They are:
1. *Male Circumcision* - If the uninfected person is male and has been circumcised, their probability
of acquisition is reduced. The male individual will have the **MaleCircumcision** intervention and its
**Circumcision_Reduced_Acquire** parameter will be used.
2. *Female Susceptibility By Age* - If the uninfected person is female, then their current age is used
to determine the a factor from the configuration parameters **Male_To_Female_Relative_Infectivity_Ages**
and **Male_To_Female_Relative_Infectivity_Multipliers**. Their age is used with linear interpolation
to calculate a multiplier.
3. *PrEP / Vaccine* - If the uninfected person has a vaccine or PrEP, their probability of acquisition
is also reduced.
>>> probability_acquire = 1.0
>>> probability_acquire *= MaleCircumcision.Circumcision_Reduced_Acquire if male and circumcised else 1
>>> probability_acquire *= get_female_susceptibility( person.age ) if female else 1
>>> probability_acquire *= vaccine_reduced_acquire if person has vaccine else 1
Transmission Probability
In EMOD, the probability of a person transmitting HIV comes down to whether nor not the person has been vaccinated and how infectious they are.
1. *Vaccine* - If the infected person has a vaccine that reduces transmission, its probability of
transmission reduction is used.
2. *Infectiousness* - The infectiousness of a person depends on the following four factors:
2a. *Base Infectivity* - The configuration parameter **Base_Infectivity** determines the starting
amount of infectiousness. It is the starting point of the calculation and is assumed to be
female-to-male transmission.
2b. *Heterogeneity* - To represent the heterogeneity in people, the **Base_Infectivity** is
multiplied by a value from a Log Normal distribution based on the configuration parameter
**Heterogeneous_Infectiousness_LogNormal_Scale**.
>>> median = -0.5 * Heterogeneous_Infectiousness_LogNormal_Scale**2
>>> heterogeneity_factor = median + eGauss() * Heterogeneous_Infectiousness_LogNormal_Scale
where eGauss() is a gaussian distributed random number between 0 and 1.
2c. *Stage of Infection* - The mount the infection has progressed also impacts the amount of
infectiousness. If the person is in the 'acute' stage, then we multiply the **Base_Infectivity**
times the configuration parameter **Acute_Stage_Infectivity_Multiplier**. If the person is in
the 'AIDS' stage, we multiply by the configuration parameter **AIDS_Stage_Infectivity_Multiplier**.
If they are in the 'latent' stage, we do not adjust the **Base_Infectivity**.
2d. *ART Suppression* - If a person has been given an ART intervention (**AntiretroviralTherapy**,
**AntiretroviralTherapyFull**, or **ARTMortalityTable**) and has not dropped off of art (**ARTDropout**),
then ART can suppress the person's infectiousness. This amount of suppression is determined by
the intervention parameters **ART_Multiplier_On_Transmission_Prob_Per_Act** and
**Days_To_Achieve_Viral_Suppression**. If the person has been on ART less than
**Days_To_Achieve_Viral_Suppression**, the **ART_Multiplier_On_Transmission_Prob_Per_Act**
will be reduced proportionally.
These different factors are combined as follows:
>>> infectiousness = Base_Infectivity
>>> infectiousness *= heterogeneity_factor
>>>
>>> if hiv_stage == ACUTE:
>>> infectiousness *= Acute_Stage_Infectivity_Multiplier
>>> elif hiv_stage == AIDS:
>>> infectiousness *= AIDS_Stage_Infectivity_Multiplier
>>>
>>> suppression = ART_Multiplier_On_Transmission_Prob_Per_Act
>>> if Days_To_Achieve_Viral_Suppression > 0:
>>> art_mult = ART_Multiplier_On_Transmission_Prob_Per_Act
>>> days_to_achieve = Days_To_Achieve_Viral_Suppression
>>> suppression = 1 - ((1 - art_mult) / days_to_achieve) * time_since_starting_ART
>>> infectiousness *= suppression
The transmission probability is then calculated as:
>>> probability_transmission = infectiousness * vaccine_reduced_transmission
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
campaign
|
(campaign, required)
|
An instance of the emod_api.campaign module. |
required |
transmission_multiplier
|
float
|
Multiplier for STI transmission probability per coital act. Minimum value: 0 Maximum value: 100 Default value: 1 |
1
|
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_hiv.utils.distributions to define the distribution: * ConstantDistribution * UniformDistribution * GaussianDistribution * ExponentialDistribution * PoissonDistribution * LogNormalDistribution * DualConstantDistribution * WeibullDistribution * DualExponentialDistribution |
required |
expiration_event_trigger
|
str
|
When the intervention expires, this individual-level event will be broadcast. See
:doc: |
None
|
acquisition_multiplier
|
float
|
Multiplier for STI acquisition probability per coital act. Minimum value: 0 Maximum value: 100 Default value: 1 |
1
|
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_hiv/campaign/individual_intervention.py
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FemaleContraceptive
Bases: IndividualIntervention
The FemaleContraceptive intervention is used to reduce the fertility rate of females of reproductive age (14 to 45 years old), based on a distribution set by the user. This intervention can only be distributed to females, and ignores the waning condition expiration (as women could still use a contraceptive, even if it is ineffective). Note: the Birth_Rate_Dependence configuration parameter must be set to INDIVIDUAL_PREGNANCIES or INDIVIDUAL_PREGNANCIES_BY_AGE_AND_YEAR or an error will result.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
campaign
|
(campaign, required)
|
An instance of the emod_api.campaign module. |
required |
waning_config
|
(AbstractWaningConfig, required)
|
A WaningConfig object used to control the efficacy of the contraceptive, typically over time. Specify how this effect decays over time using one of the Waning Config classes in emodpy_hiv.campaign.waning_config. |
required |
usage_expiration_event
|
str
|
When the woman stops using the contraceptive, this event will be broadcast. See
:doc: |
required |
usage_duration_distribution
|
(BaseDistribution, required)
|
For the distribution of each contraceptive, a randomly selected duration from this distribution will determine when the woman stops using the contraceptive. This is independent of how long the contraceptive is effective. Please use the following distribution classes from emodpy_hiv.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: cost, intervention_name, new_property_value, disqualifying_properties, dont_allow_duplicates. Default value: None |
None
|
Source code in emodpy_hiv/campaign/individual_intervention.py
HIVARTStagingByCD4Diagnostic
Bases: IndividualIntervention
The HIVARTStagingByCD4Diagnostic intervention class checks for treatment eligibility based on CD4 count. It uses the lowest-ever recorded CD4 count for that individual, based on the history of past CD4 counts conducted using the HIVDrawBlood intervention. To specify the outcome based on age bins instead of CD4 testing, use HIVARTStagingCD4AgnosticDiagnostic.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
campaign
|
(campaign, required)
|
An instance of the emod_api.campaign module. |
required |
cd4_threshold
|
(ValueMap, required)
|
It is a piecewise table of years to CD4 and the individual's CD4 count must be below this threshold in order to get a positive 'diagnosis'. |
required |
if_pregnant
|
(ValueMap, required)
|
If the individual does not pass the diagnostic from the cd4_threshold or if_active_TB, and the individual is pregnant, then the individual's CD4 is compared to the value found in the ValueMap matrix. |
required |
if_active_tb
|
(ValueMap, required)
|
If the individual's CD4 is not below the threshold in the cd4_threshold table and the individual has TB, then the individual's CD4 will be compared to the CD4 value retrieved from the ValueMap matrix based on the current year. Whether a person has TB is determined by the value of an Individual Property as determined by the parameters individual_property_active_tb_key(typically 'HasActiveTB') and individual_property_active_tb_value(typically 'Yes'). |
required |
positive_diagnosis_event
|
(str, required)
|
If the test is positive, this specifies an event that will be broadcast. See
:doc: |
required |
negative_diagnosis_event
|
str
|
If the test is negative, this specifies an event that will be broadcast.
See :doc: |
None
|
individual_property_active_tb_value
|
str
|
The IndividualProperty value ('Yes') used to determine whether the individual has TB. If you want to use this feature, you will need to define the property in the demographics Default value: None |
None
|
individual_property_active_tb_key
|
str
|
The IndividualProperty key ('HasActiveTB') used to determine whether the individual has TB. If you want to use this feature, you will need to define the property in the demographics Default value: None |
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
|
Source code in emodpy_hiv/campaign/individual_intervention.py
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HIVARTStagingCD4AgnosticDiagnostic
Bases: IndividualIntervention
The HIVARTStagingCD4AgnosticDiagnostic intervention class checks for treatment eligibility based on age. It uses the individual's age and the adult_treatment_age argument to determine if the person should be usin the adult or child requirements. To specify the outcome based on CD4 testing, use HIVARTStagingByCD4Diagnostic.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
campaign
|
(campaign, required)
|
An instance of the emod_api.campaign module. |
required |
child_treat_under_age_in_years_threshold
|
(ValueMap, required)
|
Determines the age at which children are eligible for ART regardless of CD4, WHO stage, or other factors. This parameter uses ValueMap to define Times (by year) and Values for the history and expected treatment guidelines for future years. |
required |
child_by_who_stage
|
(ValueMap, required)
|
Determines the WHO stage at or above which children are eligible for ART. This parameter uses ValueMap to define Times (by year) and Values for the history and expected treatment guidelines for future years. |
required |
child_by_tb
|
(ValueMap, required)
|
Determines the WHO stage at or above which children having active TB are eligible for ART. This parameter uses ValueMap to define Times (by year) and Values for the history and expected treatment guidelines for future years. Whether a child has TB is determined by the value of an Individual Property as determined by the parameters individual_property_active_tb_key(typically 'HasActiveTB') and individual_property_active_tb_value(typically 'Yes'). |
required |
adult_by_who_stage
|
(ValueMap, required)
|
Determines the WHO stage at or above which adults are eligible for ART. This parameter uses ValueMap to define Times (by year) and Values for the history and expected treatment guidelines for future years. |
required |
adult_by_tb
|
(ValueMap, required)
|
Determines the WHO stage at or above which adults having active TB are eligible for ART. This parameter uses ValueMap to define Times (by year) and Values for the history and expected treatment guidelines for future years. Whether an adult has TB is determined by the value of an Individual Property as determined by the parameters individual_property_active_tb_key(typically 'HasActiveTB') and individual_property_active_tb_value(typically 'Yes'). |
required |
adult_by_pregnant
|
(ValueMap, required)
|
Determines the WHO stage at or above which pregnant adults are eligible for ART. This parameter uses ValueMap to define Times (by year) and Values for the history and expected treatment guidelines for future years. |
required |
positive_diagnosis_event
|
(str, required)
|
If an individual tests positive, this specifies an event that may trigger another intervention when
the event occurs. See :doc: |
required |
negative_diagnosis_event
|
str
|
If an individual tests negative, this specifies an event that will be broadcast and may trigger another
intervention. See
:doc: |
None
|
individual_property_active_tb_value
|
str
|
The IndividualProperty value ('Yes') used to determine whether the individual has TB. Default value: None |
None
|
individual_property_active_tb_key
|
str
|
The IndividualProperty key ('HasActiveTB') used to determine whether the individual has TB. Default value: None |
None
|
adult_treatment_age
|
float
|
The age (in years) that delineates adult patients from pediatric patients for the purpose of treatment eligibility. Patients younger than this age may be eligible on the basis of their pediatric patient status. Minimum value: -1 Maximum value: 3.40282e+38 Default value: 5 |
5
|
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_hiv/campaign/individual_intervention.py
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HIVDrawBlood
Bases: IndividualIntervention
The HIVDrawBlood intervention class represents a test where blood is drawn and the person's CD4 or viral load are determined. It allows for a test result to be recorded and used for future health care decisions, but does not intrinsically lead to a health care event. A future health care decision will use this recorded CD4 count or viral load, even if the actual CD4/viral load has changed since last phlebotomy. The result can be updated by distributing another HIVDrawBlood intervention.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
campaign
|
(campaign, required)
|
An instance of the emod_api.campaign module. |
required |
positive_diagnosis_event
|
(str, required)
|
If an individual tests positive, this specifies an event that may trigger another intervention when
the event occurs. See :doc: |
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_hiv/campaign/individual_intervention.py
HIVMuxer
Bases: IndividualIntervention
The HIVMuxer intervention class is a method of placing groups of individuals into a waiting pattern for the next event, and is based on DelayedIntervention. HIVMuxer adds the ability to limit the number of times an individual can be registered with the delay, which ensures that an individual is only provided with the delay one time. For example, without HIVMuxer, an individual could be given an exponential delay twice, effectively doubling the rate of leaving the delay.
Please refer to the documentation for HIVMuxer at the following link:
:doc:emod-hiv:emod/parameter-campaign-individual-hivmuxer
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
campaign
|
(campaign, required)
|
An instance of the emod_api.campaign module. |
required |
muxer_name
|
(str, required)
|
A name used to identify the delay and check whether individuals have entered it multiple times. If the same name is used at multiple points in the health care process, then the number of entries is combined when max_entries is applied. |
required |
delay_period_distribution
|
(BaseDistribution, required)
|
The distribution type to use for assigning the delay period for distributing interventions. Each assigned value is a random draw from the distribution. Please use the following distribution classes from emodpy_hiv.utils.distributions to define the distribution: * ConstantDistribution * UniformDistribution * GaussianDistribution * ExponentialDistribution * PoissonDistribution * LogNormalDistribution * DualConstantDistribution * WeibullDistribution * DualExponentialDistribution |
required |
max_entries
|
int
|
The maximum number of times the individual can be registered with the HIVMuxer delay. Determines what should happen if an individual reaches the HIVMuxer stage of health care multiple times. For example, registering for an exponential delay two times effectively doubles the rate of leaving the delay. Setting max_entries to 1 prevents the rate from doubling. Minimum value: 0 Maximum value: 2147480000.0 Default value: 1 |
1
|
expiration_period
|
float
|
A fixed time period, in days, after which the broadcast_on_expiration_event occurs instead of the broadcast_delay_complete_event. Only applied if the expiration_period occurs earlier than the end of the delay period. For example, if loss to follow-up (LTFU) occurs at a high rate for the first 6 months of care, and then later transitions to a lower rate, then the Expiration_Period should be set to 183 days and Broadcast_On_Expiration_Event can link to another delay intervention with a longer average delay time until LTFU. If LTFU does not occur in the first 6 months, then the expiration will allow the first rate to give way to the post-6-month rate. Minimum value: 0 Maximum value: 3.40282e+38 Default value: 3.40282e+38 |
3.40282e+38
|
broadcast_on_expiration_event
|
str
|
If the delay intervention expires before arriving at the end of the delay period, this specifies
the event that should occur. For example, if loss to follow-up occurs at a high rate for the first
6 months of care, and then later transitions to a lower rate, then the Expiration_Period should
be set to 183 days and Broadcast_On_Expiration_Event can link to another delay intervention
with a longer average delay time until loss to follow up (LTFU). If LTFU does not occur in the
first 6 months, then the expiration will allow the first rate to give way to the post-6-month rate.
See the list of available events for possible values. See :doc: |
None
|
broadcast_delay_complete_event
|
str
|
The event that should occur at the end of the delay period. See
:doc: |
None
|
common_intervention_parameters
|
CommonInterventionParameters
|
The CommonInterventionParameters object that contains the 4 common parameters: intervention_name, new_property_value, disqualifying_properties, dont_allow_duplicates. The following parameters are not valid for this intervention: cost Default value: None |
None
|
Source code in emodpy_hiv/campaign/individual_intervention.py
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HIVPiecewiseByYearAndSexDiagnostic
Bases: IndividualIntervention
The HIVPiecewiseByYearAndSexDiagnostic intervention class is used to model the roll-out of an intervention over time. Unlike HIVSigmoidByYearAndSexDiagnostic, which requires the time trend to have a sigmoid shape, this intervention allows for any trend of time to be configured using piecewise or linear interpolation. The trends over time can be configured differently for males and females. Note that the term "diagnosis" is used, but this intervention is typically used more like a trend in behavior or coverage over time.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
campaign
|
(campaign, required)
|
An instance of the emod_api.campaign module. |
required |
time_value_map
|
(ValueMap, required)
|
Please use the ValueMap class from emodpy_hiv.campaign.common to define the time_value_map. The years (times) and matching probabilities for test results. This parameter uses ValueMap to define Times (by year) and Values for the history and expected treatment guidelines for future years. This creates a JSON structure containing one array of Times and one for Values, which allows for a time-variable probability that can take on any shape over time. When queried at a simulation year corresponding to one of the listed Times, it returns the corresponding Value. When queried earlier than the first listed Time, it returns the default Value. When queried in between listed Times, it either returns the Value for the most recent past time (when linear_interpolation is False) or linearly interpolates Values between Times (when linear_interpolation is True). When queried after the last Time in the list, it returns the last Value. The Times and Values must be of equal length, and can consist of a single value. Times must monotonically increase. |
required |
positive_diagnosis_event
|
(str, required)
|
If an individual tests positive, this specifies an event that may trigger another intervention when
the event occurs. See :doc: |
required |
negative_diagnosis_event
|
str
|
If an individual tests negative, this specifies an event that may trigger another intervention when
the event occurs. See :doc: |
None
|
linear_interpolation
|
bool
|
When set to False, interpolation between values in the time_value_map is zero-order ('staircase'). When set to True, interpolation between values in the time_value_map is linear. The final value is held constant for all times after the last time specified in the time_value_map. Default value: False |
False
|
female_multiplier
|
float
|
Allows for the probabilities in the time_value_map to be different for males and females, by multiplying the female probabilities by a constant value. Minimum value: 0 Maximum value: 3.40282e+38 Default value: 1 |
1
|
default_value
|
float
|
The probability of positive diagnosis if the intervention is used before the earliest specified time in the time_value_map. Minimum value: 0 Maximum value: 1 Default value: 0 |
0
|
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_hiv/campaign/individual_intervention.py
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HIVRandomChoice
Bases: IndividualIntervention
The HIVRandomChoice intervention class is used to change the logic in how and where treatment is applied to individuals based on specified probabilities.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
campaign
|
(campaign, required)
|
An instance of the emod_api.campaign module. |
required |
choice_probabilities
|
(list[float], required)
|
An array of probabilities that the event will be selected, used with choice_names. Values in map must be normalized to sum to one. |
None
|
choice_names
|
(list[str], required)
|
An array of event names to be broadcast if randomly selected, used with choice_probabilities. |
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
|
Source code in emodpy_hiv/campaign/individual_intervention.py
HIVRapidHIVDiagnostic
Bases: IndividualIntervention
The HIVRapidHIVDiagnostic intervention class builds on StandardDiagnostic by also updating the individual's knowledge of their HIV status. This can affect their access to ART in the future as well as other behaviors. This intervention should be used only if the individual's knowledge of their status should impact a voluntary male circumcision campaign.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
campaign
|
(campaign, required)
|
An instance of the emod_api.campaign module. |
required |
positive_diagnosis_event
|
(str, required)
|
If the test is positive, this specifies an event that will be broadcast.
See :doc: |
required |
base_sensitivity
|
float
|
Use this parameter to set a constant value for sensitivity of the diagnostic. If you want to set the sensitivity over time, use the sensitivity_versus_time parameter instead. You need to set either base_sensitivity or sensitivity_versus_time. This sets the proportion of the time that individuals with the condition being tested receive a positive diagnostic test. When set to 1, the diagnostic always accurately reflects the condition. When set to zero, then individuals who have the condition always receive a false-negative diagnostic test. Minimum value: 0 Maximum value: 1 Default value: None |
None
|
sensitivity_versus_time
|
(ValueMap, Optional)
|
Use this parameter to set the sensitivity of the diagnostic test over time. If you want to set a constant value for sensitivity, use the base_sensitivity parameter instead. You need to set either base_sensitivity or sensitivity_versus_time. This expects a ValueMap object (from emodpy_hiv.campaign.common) that contains two arrays: The 'Times' values are the duration from when the person became infected. 'Values' is the sensitivity of the diagnostic for the given age of the infection. Default value: None |
None
|
base_specificity
|
float
|
The specificity of the diagnostic. This sets the proportion of the time that individuals without the condition being tested receive a negative diagnostic test. When set to 1, the diagnostic always accurately reflects the lack of having the condition. When set to zero, then individuals who do not have the condition always receive a false-positive diagnostic test. Minimum value: 0 Maximum value: 1 Default value: 1 |
1
|
probability_received_result
|
float
|
The probability that an individual received the results of a diagnostic test. Minimum value: 0 Maximum value: 1 Default value: 1 |
1
|
negative_diagnosis_event
|
str
|
If the test is negative, this event will be broadcast. See
:doc: |
None
|
enable_is_symptomatic
|
bool
|
If true, requires an infection to be symptomatic to return a positive test. Default value: True |
False
|
days_to_diagnosis
|
float
|
The number of days from diagnosis (which is done when the intervention is distributed) until a positive response is performed. The response to a negative diagnosis is done immediately when the diagnosis is made (at distribution of the intervention). 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: cost, intervention_name, new_property_value, disqualifying_properties, dont_allow_duplicates. Default value: None |
None
|
Source code in emodpy_hiv/campaign/individual_intervention.py
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HIVSigmoidByYearAndSexDiagnostic
Bases: IndividualIntervention
The HIVSigmoidByYearAndSexDiagnostic intervention class broadcasts a positive 'diagnosis' event by selecting a probability of that event from a sigmoidal curve versus time. For a linear approach, use HIVPiecewiseByYearandSexDiagnostic.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
campaign
|
(campaign, required)
|
An instance of the emod_api.campaign module. |
required |
positive_diagnosis_event
|
(str, required)
|
If an individual tests positive, this specifies an event that may trigger another intervention when
the event occurs. See :doc: |
required |
year_sigmoid
|
(Sigmoid, required)
|
Defines a sigmoidal curve for the probability of a positive diagnosis versus time (year). |
required |
female_multiplier
|
float
|
Allows for the sigmoid time-varying probability to be different for males and females, by multiplying the female probability by a constant value. Minimum value: 0 Maximum value: 3.40282e+38 Default value: 1 |
1
|
negative_diagnosis_event
|
str
|
If an individual tests negative, this specifies an event that may trigger another intervention when
the event occurs. See
:doc: |
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
|
Source code in emodpy_hiv/campaign/individual_intervention.py
InterventionForCurrentPartners
Bases: IndividualIntervention
The InterventionForCurrentPartners intervention class provides a mechanism for the partners of individuals in the care system to also seek care. Partners do not need to seek testing at the same time; a delay may occur between the initial test and the partner's test. If a relationship has been paused, such as when a partner migrates to a different node, the partner will not be contacted.
Either the intervention_config or broadcast_event parameter must be set, but not both.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
campaign
|
(campaign, required)
|
An instance of the emod_api.campaign module. |
required |
intervention_config
|
IndividualIntervention
|
The intervention definition that is immediately distributed to the partner. This parameter is required if broadcast_event is not set. Default value: None |
None
|
broadcast_event
|
str
|
The event that is immediately broadcast to the partner.
See :doc: |
None
|
prioritize_partners_by
|
PrioritizePartnersBy
|
How to prioritize partners for the intervention, as long as they have been in a relationship longer than minimum_duration_years. Expect PrioritizePartnersBy enum from emodpy_hiv.utils.emod_enum. Possible values are: * NO_PRIORTIZATION - All partners are contacted. * CHOSEN_AT_RANDOM - Partners are randomly selected until maximum_partners have received the intervention. * LONGER_TIME_IN_RELATIONSHIP - Partners are sorted in descending order of the duration of the relationship. Partners are contacted from the beginning of this list until maximum_partners have received the intervention. * SHORTER_TIME_IN RELATIONSHIP - Partners are sorted in ascending order of the duration of the relationship. Partners are contacted from the beginning of the list until maximum_partners have received the intervention. * OLDER_AGE - Partners are sorted in descending order of their age. Partners are contacted from the beginning of this list until maximum_partners have received the intervention. * YOUNGER_AGE - Partners sorted in ascending order of the duration of the relationship. Partners are contacted from the beginning of this list until maximum_partners have received the intervention. * RELATIONSHIP_TYPE - Partners are sorted based on the order of relationship types defined in the relationship_types array. For example, 'relationship_types' : ['MARITAL', 'INFORMAL', 'TRANSITORY', 'COMMERCIAL'], will prioritize marital first, then informal, then transitory, then commercial, with random selection between mulitple partners of the same type. Default value: PrioritizePartnersBy.NO_PRIORITIZATION |
NO_PRIORITIZATION
|
relationship_types
|
list[RelationshipTypes]
|
An array listing all possible relationship types for which partners can qualify for the intervention. Expect RelationshipTypes enum emodpy_hiv.utils.emod_enum. Possible values are: TRANSITORY, INFORMAL, MARITAL, and COMMERCIAL. If prioritize_partners_by is set to PrioritizePartnersBy.RELATIONSHIP_TYPE, then the order of these types is used. The array may not contain duplicates, and cannot be empty. Default value: None |
None
|
minimum_duration_years
|
float
|
The minimum amount of time, in years, between relationship formation and the current time for the partner to qualify for the intervention. Minimum value: 0 Maximum value: 200 Default value: 0 |
0
|
maximum_partners
|
float
|
The maximum number of partners that will receive the intervention. Required when Prioritize_Partners_By is not set to NO_PRIORITIZATION. Minimum value: 0 Maximum value: 100 Default value: 100 |
100
|
common_intervention_parameters
|
CommonInterventionParameters
|
The CommonInterventionParameters object that contains the 4 common parameters: intervention_name, new_property_value, disqualifying_properties, dont_allow_duplicates. The following parameters are not valid for this intervention: cost Default value: None |
None
|
Source code in emodpy_hiv/campaign/individual_intervention.py
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MaleCircumcision
Bases: IndividualIntervention
The MaleCircumcision intervention class introduces male circumcision as a method to control HIV transmission. Voluntary medical male circumcision (VMMC) permanently reduces a male's likelihood of acquiring HIV; successful distribution results in a reduction in the probability of transmission.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
campaign
|
(campaign, required)
|
An instance of the emod_api.campaign module. |
required |
distributed_event_trigger
|
str
|
The name of the event to be broadcast when the intervention is distributed to an individual. See
:doc: |
None
|
circumcision_reduced_acquire
|
float
|
The reduction of susceptibility to STI by voluntary male medical circumcision (VMMC). Minimum value: 0 Maximum value: 1 Default value: 0.6 |
0.6
|
apply_if_higher_reduced_acquire
|
bool
|
If set to False, the MaleCircumcision intervention can never be applied to someone who already has a MaleCircumcision intervention. If set to True, a male who already has a MaleCircumcision intervention, but whose pre-existing MaleCircumcision intervention has a lower efficacy parameter (circumcision_reduced_acquire) than the one about to be applied, will receive the higher-efficacy MaleCircumcision. Default value: False |
False
|
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_hiv/campaign/individual_intervention.py
ModifyStiCoInfectionStatus
Bases: IndividualIntervention
The ModifyStiCoInfectionStatus intervention class creates or removes STI co-infections (which influence the rate of HIV transmission). This intervention can be used to represent things like STI treatment programs or STI outbreaks.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
campaign
|
(campaign, required)
|
An instance of the emod_api.campaign module. |
required |
new_sti_coinfection_status
|
(bool, required)
|
Determines whether to apply STI co-infection, or cure/remove STI co-infection. Set to True to include co-infection; set to False to remove co-infection. |
required |
Source code in emodpy_hiv/campaign/individual_intervention.py
PMTCT
Bases: IndividualIntervention
The PMTCT (Prevention of Mother-to-Child Transmission) intervention class is used to define the efficacy of PMTCT treatment at time of birth. This can only be used for mothers who are not on suppressive ART and will automatically expire 40 weeks after distribution. Efficacy will be reset to 0 once it expires.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
campaign
|
(campaign, required)
|
An instance of the emod_api.campaign module. |
required |
efficacy
|
float
|
Represents the efficacy of a Prevention of Mother to Child Transmission (PMTCT) intervention, defined as the rate ratio of mother to child transmission (MTCT) between women receiving the intervention and women not receiving the intervention. A setting of 1 is equivalent to 100% blocking efficacy, and 0 reverts to the default probability of transmission, configured through the config.json parameter Maternal_Transmission_Probability. Minimum value: 0 Maximum value: 1 Default value: 0.5 |
0.5
|
common_intervention_parameters
|
CommonInterventionParameters
|
The CommonInterventionParameters object that contains the 4 common parameters: intervention_name, new_property_value, disqualifying_properties, dont_allow_duplicates. The following parameters are not valid for this intervention: cost Default value: None |
None
|
Source code in emodpy_hiv/campaign/individual_intervention.py
RangeThreshold
An element of a look-up table where if a value (age in AgeDiagnostic or CD4 in CD4Diagnostic) is greater-than-or-equal-to the 'Low' value and less-than the 'High' value, the 'Event' will be broadcasted.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
low
|
float
|
The low end of the diagnostic level. For this 'Event' to be selected, the value must be greater-than-or-equal-to (>=) this threshold. Minimum value: 0 Maximum value: 2000 Default value: 0 |
0
|
high
|
float
|
The high end of the diagnostic level. For this 'Event' to be selected, the value must be less-than this threshold. Minimum value: 0 Maximum value: 2000 Default value: 2000 |
2000
|
event_to_broadcast
|
(str, required)
|
If 'low' <= value < 'high, then this event will be broadcast.
See :doc: |
required |
Source code in emodpy_hiv/campaign/individual_intervention.py
to_schema_dict(campaign)
A function that converts the Sigmoid object to a schema dictionary.
Source code in emodpy_hiv/campaign/individual_intervention.py
STIBarrier
Bases: IndividualIntervention
The STIBarrier intervention is used to reduce the probability of STI or HIV transmission by applying a time-variable probability of condom usage. Each STIBarrier intervention is directed at a specific relationship type, and must be configured as a sigmoid trend over time.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
campaign
|
(campaign, required)
|
An instance of the emod_api.campaign module. |
required |
usage_expiration_event
|
str
|
When the person stops using the STIBarrier, this event will be broadcasted. See
:doc: |
required |
usage_duration_distribution
|
(BaseDistribution, required)
|
For the distribution of each STIBarrier, a randomly selected duration from this distribution will determine when the man stops using the intervention and revert back to condom usage based on the relationship type. Please use the following distribution classes from emodpy_hiv.utils.distributions to define the distribution: * ConstantDistribution * UniformDistribution * GaussianDistribution * ExponentialDistribution * PoissonDistribution * LogNormalDistribution * DualConstantDistribution * WeibullDistribution * DualExponentialDistribution |
required |
relationship_type
|
RelationshipType
|
The relationship type to which the condom usage probability is applied. Possible values are: * TRANSITORY * INFORMAL * MARITAL * COMMERCIAL Default value: TRANSITORY |
TRANSITORY
|
condom_usage_sigmoid
|
(Sigmoid, required)
|
The new sigmoid to use when determining the probability that a condom is used during a coital act within the specified relationship. This overrides the Condom_Usage_Probablility for the relationship type as defined in the Demographics file. If None (default), the Condom_Usage_Probablility is not overridden. - WARNING: For STIBarrier, the 'min' and 'max' values of the sigmoid must be between 0 and 1. |
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
|
Source code in emodpy_hiv/campaign/individual_intervention.py
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STIIsPostDebut
Bases: IndividualIntervention
The STIIsPostDebut intervention class checks to see if the individual is post-STI debut. Note that this is not connected to IndividualProperties in the demographics file.
User can either set the diagnosis_config parameters:
- positive_diagnosis_config (required)
- negative_diagnosis_config (optional)
or set the diagnosis_event parameters:
- positive_diagnosis_event (required)
- negative_diagnosis_event (optional)
but not both.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
campaign
|
campaign
|
An instance of the emod_api.campaign module. |
required |
positive_diagnosis_config
|
IndividualIntervention
|
The intervention distributed to individuals if they test positive. Default value: None |
None
|
negative_diagnosis_config
|
IndividualIntervention
|
The intervention distributed to individuals if they test negative. Default value: None |
None
|
positive_diagnosis_event
|
str
|
The event to be broadcast on a positive test result. See
:doc: |
None
|
negative_diagnosis_event
|
str
|
The event to be broadcast on a negative test result. See
:doc: |
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
|
Source code in emodpy_hiv/campaign/individual_intervention.py
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SetSexualDebutAge
Bases: IndividualIntervention
The SetSexualDebutAge intervention class is used to set the age of the individual when they start seeking sexual relationships. If the individual's current age is greater than the age being set, they will immediately debut.
This intervention is typically used when setting the configuration parameter Sexual_Debut_Age_Setting_Type to FROM_INTERVENTION. This setting causes all individuals to be initialized with a very large sexual debut age (max float) so that they never debut. The intervention is used to target specific individuals and set their debut age.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
campaign
|
(campaign, required)
|
An instance of the emod_api.campaign module. |
required |
setting_type
|
SettingType
|
Use Weibull distribution to initialize sexual debut age or an intervention. Default value: CURRENT_AGE |
CURRENT_AGE
|
distributed_event_trigger
|
str
|
The name of the event to be broadcast when the intervention is distributed to an individual. See
:doc: |
None
|
age_years
|
float
|
The age (in years) at which the person receiving the intervention will start seeking sexual relationships. If the person is already order than this age, they will start seeking relationships immediately. You must set Setting_Type to USER_SPECIFIED for the parameter to become activated. Minimum value: 0 Maximum value: 3.40282e+38 Default value: 125 |
125
|
common_intervention_parameters
|
CommonInterventionParameters
|
The CommonInterventionParameters object that contains the 4 common parameters: intervention_name, new_property_value, disqualifying_properties, dont_allow_duplicates. The following parameters are not valid for this intervention: cost Default value: None |
None
|
Source code in emodpy_hiv/campaign/individual_intervention.py
Sigmoid
Defines a sigmoidal curve that can be used to define probabilities versus time.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
min
|
float
|
The left asymptote for the sigmoid trend over time. The min value must be smaller than the max value. Minimum value: -1 Maximum value: 1 Default value: 0 |
0
|
max
|
float
|
The right asymptote for the sigmoid trend over time. The max value must be larger than the min value. Minimum value: -1 Maximum value: 1 Default value: 1 |
1
|
mid
|
float
|
The time of the infection point in the sigmoid trend over time. Minimum value: 1900 Maximum value: 2200 Default value: 2000 |
2000
|
rate
|
float
|
The slope of the inflection point in the sigmoid trend over time. A Rate of 1 sets the slope to a 25% change in probability per year. Specify a negative Rate (e.g. -1) to achieve a negative sigmoid. Minimum value: -100 Maximum value: 100 Default value: 1 |
1
|
Source code in emodpy_hiv/campaign/individual_intervention.py
to_schema_dict(campaign)
A function that converts the Sigmoid object to a schema dictionary.
Source code in emodpy_hiv/campaign/individual_intervention.py
StartNewRelationship
Bases: IndividualIntervention
The StartNewRelationship intervention class provides a method of triggering the formation of a relationship following a user-specified event. The parameters of the relationship that is formed can also be customized by the user, such as individual properties required of the partner, or modified condom usage probability within the relationship. Note: These new relationships can be made by people of any age (the intervention disregards IsPostDebut and Sexual_Debut_Age_Min). Additionally, these relationships are considered outside of the Pair Formation Algorithm (PFA), and do not impact/are not impacted by concurrency or pair formation parameters. Coital act and condom usage rate are as per the corresponding relationship type, unless modified by the user.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
campaign
|
(campaign, required)
|
An instance of the emod_api.campaign module. |
required |
relationship_type
|
RelationshipType
|
The type of the relationship to start for this person. Possible values are: * TRANSITORY * INFORMAL * MARITAL * COMMERCIAL Default value: TRANSITORY |
TRANSITORY
|
partner_has_ip
|
str
|
The IndividualProperty key:value pair that the potential partner must have. Empty string
implies no filtering. See :ref: |
''
|
relationship_created_event
|
str
|
The event trigger to broadcast when a new relationship is created due to the intervention. See
:doc: |
''
|
condom_usage_sigmoid
|
(Sigmoid, required)
|
The new sigmoid to use when determining the probability that a condom is used during a coital act within the specified relationship. This overrides the Condom_Usage_Probablility for the relationship type as defined in the Demographics file. If None (default), the Condom_Usage_Probablility is not overridden. - WARNING: For StartNewRelationship, the 'min' and 'max' values of the sigmoid must be between 0 and 1. |
None
|
common_intervention_parameters
|
CommonInterventionParameters
|
The CommonInterventionParameters object that contains the 4 common parameters: intervention_name, new_property_value, disqualifying_properties, dont_allow_duplicates. The following parameters are not valid for this intervention: cost Default value: None |
None
|
Source code in emodpy_hiv/campaign/individual_intervention.py
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