emodpy_hiv.country_model module#

class emodpy_hiv.country_model.DefaultZambiaData[source]#

Bases: object

This class contains the default data file paths for Zambia.

data_root = Path('/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.9/site-packages/emodpy_hiv-1.4.6-py3.9.egg', 'emodpy_hiv/country_data/zambia/')#

historical_vmmc_data_file = Path('/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.9/site-packages/emodpy_hiv-1.4.6-py3.9.egg', 'emodpy_hiv/country_data/zambia/historical_vmmc_data.csv')#

initial_age_distribution_file = Path('/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.9/site-packages/emodpy_hiv-1.4.6-py3.9.egg', 'emodpy_hiv/country_data/zambia/initial_age_distribution.csv')#

initial_population_file = Path('/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.9/site-packages/emodpy_hiv-1.4.6-py3.9.egg', 'emodpy_hiv/country_data/zambia/initial_population.csv')#

female_mortality_file = Path('/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.9/site-packages/emodpy_hiv-1.4.6-py3.9.egg', 'emodpy_hiv/country_data/zambia/parsed_mortality--female.csv')#

male_mortality_file = Path('/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.9/site-packages/emodpy_hiv-1.4.6-py3.9.egg', 'emodpy_hiv/country_data/zambia/parsed_mortality--male.csv')#

fertility_file = Path('/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.9/site-packages/emodpy_hiv-1.4.6-py3.9.egg', 'emodpy_hiv/country_data/zambia/parsed_fertility.csv')#

class emodpy_hiv.country_model.Country(country_name: str, base_year: float = 1960.5)[source]#

Bases: ABC

initialize_campaign(schema_path, base_year)[source]#

static load_nchooser_distribution_data(file_path: str) → dict[source]#

Load target distribution data into a dataframe format that works for Nchooser and group by node_id. :param file_path: path to the csv file that contains the data

Returns:: a dictionary that has node_id as the key and a dataframe as the value. The dataframe contains the distribution data for Nchooser.
Return type:: dict

add_male_circumcision(campaign, historical_vmmc_data_filepath, traditional_male_circumcision_coverages_per_node)[source]#

add_historical_vmmc_nchooser(campaign, historical_vmmc_data_filepath: str, historical_vmmc_reduced_acquire=0.6, historical_vmmc_start_year=2008)[source]#

add_traditional_male_circumcision(campaign, traditional_male_circumcision_coverages_per_node: dict)[source]#

add_vmmc_reference_tracking(campaign)[source]#

seed_infections(campaign)[source]#

add_csw(campaign)[source]#

add_post_debut_coinfection(campaign)[source]#

add_pmtct(campaign)[source]#

add_health_care_testing(campaign: <module 'emod_api.campaign' from '/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.9/site-packages/emod_api/campaign.py'>, hct_start_year: float = 1990)[source]#

add_ART_cascade(campaign, art_cascade_start_year: float = 1990)[source]#

add_state_TestingOnANC(campaign: <module 'emod_api.campaign' from '/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.9/site-packages/emod_api/campaign.py'>)[source]#

add_state_TestingOnChild6w(campaign: <module 'emod_api.campaign' from '/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.9/site-packages/emod_api/campaign.py'>)[source]#

add_state_HCTUptakeAtDebut(campaign: <module 'emod_api.campaign' from '/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.9/site-packages/emod_api/campaign.py'>, start_day: int)[source]#

add_state_HCTUptakePostDebut(campaign: <module 'emod_api.campaign' from '/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.9/site-packages/emod_api/campaign.py'>, start_day: int)[source]#

add_state_HCTTestingLoop(campaign: <module 'emod_api.campaign' from '/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.9/site-packages/emod_api/campaign.py'>, start_day: int)[source]#

add_state_TestingOnSymptomatic(campaign: <module 'emod_api.campaign' from '/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.9/site-packages/emod_api/campaign.py'>, start_day: int)[source]#

add_state_ARTStagingDiagnosticTest(campaign: <module 'emod_api.campaign' from '/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.9/site-packages/emod_api/campaign.py'>, start_day: int)[source]#

add_state_ARTStaging(campaign: <module 'emod_api.campaign' from '/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.9/site-packages/emod_api/campaign.py'>, start_day: int)[source]#

add_state_LinkingToPreART(campaign: <module 'emod_api.campaign' from '/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.9/site-packages/emod_api/campaign.py'>, start_day: int)[source]#

add_state_OnPreART(campaign: <module 'emod_api.campaign' from '/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.9/site-packages/emod_api/campaign.py'>, start_day: int)[source]#

add_state_LinkingToART(campaign: <module 'emod_api.campaign' from '/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.9/site-packages/emod_api/campaign.py'>, start_day: int)[source]#

add_state_OnART(campaign: <module 'emod_api.campaign' from '/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.9/site-packages/emod_api/campaign.py'>, start_day: int)[source]#

add_state_LostForever(campaign: <module 'emod_api.campaign' from '/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.9/site-packages/emod_api/campaign.py'>, start_day: int)[source]#

build_campaign(schema_path: str, base_year: float, historical_vmmc_data_filepath: str | Traversable, traditional_male_circumcision_coverages_per_node: dict)[source]#

A method to pass into EMODTask to build campaign events for Emod.

Parameters:

schema_path (str) – file path to the schema file.
base_year (float) – base year for the Simulation.
historical_vmmc_data_filepath (str) – file path to the historical vmmc data csv file.
traditional_male_circumcision_coverages_per_node(Dict[int – float]): coverage of traditional male circumcision per node.

Returns:

class emodpy_hiv.country_model.Zambia(country_name='Zambia')[source]#

Bases: Country

Zambia country model class. This class is a subclass of the Country class and implements the build_campaign method to build campaign object to be used with EMODTask.

Example

>>> from emodpy_hiv.country_model import Zambia
>>> from emodpy.emod_task import EMODTask
>>> import manifest
>>> from functools import partial
>>> zambia = Zambia()
>>> # Define a campaign_builder function to pass in the required arguments for the zambia.build_campaign() method.
>>> def campaign_builder():
>>>     return zambia.build_campaign(schema_path=manifest.schema_file, base_year=1960.5)
>>> # Alternatively, you can use the partial function to pass in the required arguments for the
>>> # zambia.build_campaign() method. For example:
>>> # campaign_builder = partial(zambia.build_campaign, schema_path=manifest.schema_file, base_year=1960.5)
>>> # Create an EMODTask object using the campaign_builder function
>>> task = EMODTask.from_default2(config_path="config.json",
>>>                               eradication_path=manifest.eradication_path,
>>>                               campaign_builder=campaign_builder, ...)

build_config(config)[source]#

build_campaign(schema_path: str, base_year: float = 1960.5, historical_vmmc_data_filepath: str | Traversable = Path('/home/docs/checkouts/readthedocs.org/user_builds/institute-for-disease-modeling-emodpy-hiv/envs/latest/lib/python3.9/site-packages/emodpy_hiv-1.4.6-py3.9.egg', 'emodpy_hiv/country_data/zambia/historical_vmmc_data.csv'), traditional_male_circumcision_coverages_per_node: Dict[int, float] | None = None)[source]#

A method to pass into EMODTask to build campaign events for Emod.

Parameters:

schema_path (str) – file path to the schema file.
base_year (float) – base year for the Simulation.
historical_vmmc_data_filepath (str) – file path to the historical vmmc data csv file.
traditional_male_circumcision_coverages_per_node(Dict[int – float]): coverage of traditional male circumcision per node.

Returns:

build_demographics()[source]#