from emod_api import schema_to_class as s2c
from emod_api.interventions import utils
from emodpy_malaria.interventions.common import add_campaign_event
def _larval_microsporidia(
campaign,
strain_name: str,
habitat_coverage: float = 1.0,
habitat_target: str = "ALL_HABITATS",
initial_infectivity: float = 1,
box_duration: int = 100,
decay_time_constant: float = 0.0,
intervention_name: str = "LarvalMicrosporidiaIntervention",
cost_to_consumer: float = 0):
"""
Create a LarvalMicrosporidiaIntervention to be used in a campaign event.
Args:
campaign: The campaign object to which the intervention will be added. Provides the schema path.
strain_name: The microsporidia strain with which to treat the habitat. This must be a known strain defined in
the vector species parameters. This parameter is required to create the intervention, and there is no default value.
habitat_coverage: Portion of habitat that is treated with the intervention. Values must be between 0 and 1. Default is 1.0.
habitat_target: The type of habitat to target with the intervention. Default is "ALL_HABITATS".
Habitat target is limited to habitats defined for the species that the microsporidia strain infects.
initial_infectivity: The initial infectivity of the intervention, which defines the portion of larvae that
are infected each day the intervention exists. Must be between 0 and 1. Default is 1.
box_duration: The duration, in days, of the initial infectivity before it begins to wane.
If box_duration = -1, the intervention will have a constant effect and decay_time_constant will be
ignored. If box_duration = 0 and decay_time_constant > 0, the intervention will have an exponential
decaying effect. If box_duration > 0 and decay_time_constant = 0, the intervention will have a
box-shaped waning effect. If box_duration > 0 and decay_time_constant > 0, the intervention will
have a box-shaped waning effect followed by an exponential decay. Default is 100.
decay_time_constant: The time constant for the exponential decay of the intervention's effect, in days. Only
relevant if box_duration = 0 or > 0 as described above in box_duration. Default is 0.0.
intervention_name: The name of the intervention, for organizational purposes. Default
is "LarvalMicrosporidiaIntervention".
cost_to_consumer: The cost to consumer for each distribution of this intervention, if any. Default is 0.
Returns:
Configured LarvalMicrosporidiaIntervention object that can be added to a campaign event.
"""
if not strain_name:
raise ValueError("strain_name is required to create a LarvalMicrosporidiaIntervention. Please provide "
"a valid strain_name that is defined in the vector species parameters.")
intervention = s2c.get_class_with_defaults("LarvalMicrosporidiaIntervention", campaign.schema_path)
intervention.Intervention_Name = intervention_name
intervention.Habitat_Coverage = habitat_coverage
intervention.Habitat_Target = habitat_target
intervention.Cost_To_Consumer = cost_to_consumer
intervention.Strain_Name = strain_name
intervention.Infectivity_Config = utils.get_waning_from_params(campaign.schema_path,
initial=initial_infectivity,
box_duration=box_duration,
decay_time_constant=decay_time_constant)
return intervention
[docs]
def add_larval_microsporidia(
campaign,
strain_name: str,
start_day: int = 1,
num_repetitions: int = 1,
timesteps_between_reps: int = 365,
node_ids: list = None,
node_property_restrictions: list[dict] = None,
habitat_coverage: float = 1.0,
habitat_target: str = "ALL_HABITATS",
initial_infectivity: float = 1,
box_duration: int = 100,
decay_time_constant: float = 0.0,
intervention_name: str = "LarvalMicrosporidiaIntervention",
cost_to_consumer: float = 0
):
"""
Create a new scheduled Larval Microsporidia intervention and add it to the campaign.
This is a Node-level intervention that mimics seeding water bodies with microsporidia to infect mosquito
larvae, reducing their ability to transmit malaria. The intervention can be configured with a habitat target
(e.g., specific types of water bodies) and an initial infectivity which defines the portion of larvae that are
infected each day the intervention exists. The effect of the intervention can wane over time, and the
waning can be configured with a box_duration and decay_time_constant parameters.
The intervention expires and is removed when infectivity reaches near-zero.
Already existing Larval Microsporidia intervention(s) continue(s) to exist together with any new
Larval Microsporidia interventions. Their effects, when affecting the same species in the same habitat,
are resolved with the algorithm that can be found here: https://emod-hub.github.io/emodpy-malaria/emod/parameter-campaign-node-larvalmicrosporidiaintervention.html
Args:
campaign: The campaign object to which the intervention will be added. Provides the schema path.
strain_name: The microsporidia strain with which to treat the habitat. This must be a known strain defined in the vector species parameters.
start_day: the day to distribute the LarvalMicrosporidiaIntervention
num_repetitions: Number of times to distribute the intervention. If num_repetitions > 1,
the intervention will be distributed every timesteps_between_reps days after the initial start_day.
num_repetitions = 1 distributes intervention once on start_day, num_repetitions = 2 distributes
intervention on start_day and start_day + timesteps_between_reps, etc. num_repetitions = -1 distributes
intervention on start_day and every timesteps_between_reps indefinitely.
timesteps_between_reps: Number of days between repeated distributions of the intervention. Only relevant if num_repetitions > 1 or -1.
node_ids: List of node IDs to which the intervention will be applied. If None, the intervention will be applied to all nodes.
node_property_restrictions: A list of dictionaries of NodeProperties which the node must have to receive the intervention. If left at None, all nodes in node_ids receive the intervention.
habitat_coverage: Portion of habitat that is treated with the intervention. Value must be between 0 and 1. Default is 1.0.
habitat_target: The type of habitat to target with the intervention. Default is "ALL_HABITATS". Habitat target is limited to habitats defined for the species that the microsporidia strain infects.
initial_infectivity: The initial infectivity of the intervention, which defines the portion of larvae that are infected each day the intervention exists. Must be between 0 and 1.
box_duration: The duration, in days, of the initial infectivity before it begins to wane.
If box_duration = -1, the intervention will have a constant effect and decay_time_constant will be
ignored. If box_duration = 0 and decay_time_constant > 0, the intervention will have an exponential
decaying effect. If box_duration > 0 and decay_time_constant = 0, the intervention will have a
box-shaped waning effect. If box_duration > 0 and decay_time_constant > 0, the intervention will
have a box-shaped waning effect followed by an exponential decay.
decay_time_constant: The time constant for the exponential decay of the intervention's effect, in days. Only relevant if box_duration = 0 or > 0 as described above in box_duration.
intervention_name: (Optional) The name of the intervention, for organizational purposes. Default is "LarvalMicrosporidiaIntervention".
cost_to_consumer: The cost to consumer for each distribution of this intervention, if any. Default is 0.
Returns:
None
"""
node_intervention = _larval_microsporidia(campaign=campaign,
habitat_coverage=habitat_coverage,
habitat_target=habitat_target,
initial_infectivity=initial_infectivity,
box_duration=box_duration,
decay_time_constant=decay_time_constant,
strain_name=strain_name,
intervention_name=intervention_name,
cost_to_consumer=cost_to_consumer)
add_campaign_event(campaign=campaign,
start_day=start_day,
node_ids=node_ids,
repetitions=num_repetitions,
timesteps_between_repetitions=timesteps_between_reps,
node_intervention=node_intervention,
node_property_restrictions=node_property_restrictions)
