Welcome to emodpy-tbhiv¶

emodpy-tbhiv is a collection of Python scripts and utilities created to streamline user interactions with EMOD and idmtools for modeling measles.

Installation¶

You can install emodpy-tbhiv using the instructions in the GitHub repository README.

emodpy_tbhiv¶

emodpy_tbhiv package¶

The emodpy-tbhiv module is intended to house scripts and tools that enable disease modelers to work more easily with the IDM EMOD TBHIV model.

Subpackages¶

emodpy_tbhiv.demographics package¶

Submodules¶

emodpy_tbhiv.demographics.TBHIVDemographics module¶

class emodpy_tbhiv.demographics.TBHIVDemographics.TBHIVDemographics(nodes=None, idref='Gridded world grump2.5arcmin', base_file=None)¶

Bases: emod_api.demographics.Demographics.Demographics

This class is derived from emod_api.demographics’ Demographics class so that we can set certain defaults for TBHIV in construction. Keen observers will note thatt SetDefaultProperties does not look like a TBHIV-specific function. But as we add other disease types the generatlizations and speicfics will become clearer. The architectural point is solid.

SetHIVCoInfectionDistribution()¶: Insert some notion of a default HIVCoInfection distribution.

SetHIVTBCoInfectionMortalityDistribution()¶: Insert some notion of a default HIVTBCoInfection Mortality distribution.

class emodpy_tbhiv.demographics.TBHIVDemographics.TBHIVDemographicsWithGenderExtrapolation(file_male, file_female, pop=1000000.0, regression_interval=[1970, 1980], which_point='mid', predict_horizon=2050)¶

Bases: emodpy_tbhiv.demographics.TBHIVDemographics.TBHIVDemographics

do_extrapolation(add_to_list=True)¶

makeplots(save=None)¶

create_json_overlay(template, output_name='Extract_demog.json', csv_out=False, n=0, results_scale_factor=0.0027397260273972603)¶: This almost certainly needs to be refactored to use the base class ‘generate_file’ functionality.

emodpy_tbhiv.demographics.TBHIVDemographics.fromBasicNode(lat=0, lon=0, pop=1000000.0, name=1, forced_id=1, implicit_config_fns=None)¶: This function creates a single-node TBHIVDemographics instance from the params you give it.

emodpy_tbhiv.demographics.TBHIVDemographics.fromData(pop=1000000.0, filename_male='Malawi_male_mortality.csv', filename_female='Malawi_female_mortality.csv')¶

emodpy_tbhiv.interventions package¶

Submodules¶

emodpy_tbhiv.interventions.active_diagnostic module¶

emodpy_tbhiv.interventions.active_diagnostic.ActiveDiagnostic(camp, trigger_treatment_list, active_sensitivity=1.0, active_specificity=1.0, pos_event='TBTestPositive', treatment_fraction=1, start_day=0, duration=- 1, property_restrictions_list=[], nodeIDs=[], black_period=0, black_trigger='Blackout', event_name='TB Diagnosis Active Simple')¶: :param TBD Note start_day is initialized as 1, recommend that this be aligned with the start of the simulation

emodpy_tbhiv.interventions.active_diagnostic.new_intervention_as_file(camp, start_day=1, filename=None)¶

emodpy_tbhiv.interventions.art module¶

emodpy_tbhiv.interventions.art.ART(camp, trigger_treatment_list, start_day=0, duration=- 1, property_restrictions_list=[], nodeIDs=[], black_period=0, black_trigger='Blackout', event_name='ART')¶: :param TBD Note start_day is initialized as 1, recommend that this be aligned with the start of the simulation

emodpy_tbhiv.interventions.art.new_intervention_as_file(camp, filename=None)¶

emodpy_tbhiv.interventions.bcg module¶

emodpy_tbhiv.interventions.bcg.BCG(camp, trigger_treatment_list, initial_efficacy=1.0, vaccine_take=1, age_take_decay=1.0, box_duration=365, immune_decay=3650, start_day=0, duration=- 1, property_restrictions_list=[], nodeIDs=[], black_period=0, black_trigger='Blackout', event_name='Vaccine Health Seeking')¶: BCG Vaccine :param TBD Note start_day is initialized as 1, recommend that this be aligned with the start of the simulation

emodpy_tbhiv.interventions.bcg.new_intervention_as_file(camp, filename=None)¶

emodpy_tbhiv.interventions.cd4diag module¶

emodpy_tbhiv.interventions.cd4diag.get_thresh(name, low, high, camp)¶

emodpy_tbhiv.interventions.cd4diag.get_threshes(group_names, camp)¶

emodpy_tbhiv.interventions.cd4diag.CD4Diag(camp, trigger_treatment_list, event_200='Below200', event_350='Below350', event_500='Below500', event_above_500='Above500', start_day=0, duration=- 1, property_restrictions_list=[], nodeIDs=[], black_period=0, black_trigger='Blackout', event_name='CD4 Diagnostic')¶: ART :param TBD Note start_day is initialized as 1, recommend that this be aligned with the start of the simulation

emodpy_tbhiv.interventions.cd4diag.new_intervention_as_file(camp, filename=None)¶

emodpy_tbhiv.interventions.diag_treat_neg module¶

emodpy_tbhiv.interventions.diag_treat_neg.DiagnosticTreatNeg(camp, trigger_treatment_list, base_sensitivity_smearpos=1.0, base_sensitivity_smearneg=1.0, pos_event='TBTestPositive', neg_event='TBTestNegative', def_event='TBTestDefault', treatment_fraction=1, start_day=0, duration=- 1, property_restrictions_list=[], nodeIDs=[], black_period=0, black_trigger='Blackout', event_name='TB Diagnosis')¶: :param TBD Note start_day is initialized as 1, recommend that this be aligned with the start of the simulation

emodpy_tbhiv.interventions.diag_treat_neg.new_intervention_as_file(camp, filename=None)¶

emodpy_tbhiv.interventions.hiv_diag module¶

emodpy_tbhiv.interventions.hiv_diag.HIVDiagnostic(camp, trigger_treatment_list, base_sensitivity=1.0, base_specificity=1.0, pos_event='HIVTestedPositive', neg_event='HIVTestedNegative', treatment_fraction=1, start_day=0, duration=- 1, property_restrictions_list=[], nodeIDs=[], black_period=0, black_trigger='Blackout', event_name='HIV Diagnostic')¶: :param TBD Note start_day is initialized as 1, recommend that this be aligned with the start of the simulation

emodpy_tbhiv.interventions.hiv_diag.new_intervention_as_file(camp, filename=None)¶

emodpy_tbhiv.interventions.hiv_seeding module¶

emodpy_tbhiv.interventions.hiv_seeding.HIV(camp, time_offset=0, disease='HIV', reps=- 1, interval=1, start_day=0, nodeIDs=[], event_name='HIV Incidence')¶

emodpy_tbhiv.interventions.hiv_seeding.new_intervention_as_file(camp, filename=None)¶

emodpy_tbhiv.interventions.hsb module¶

emodpy_tbhiv.interventions.hsb.HSB(camp, trigger_treatment_list, output_event, probability_per_step=1.0, start_day=0, duration=- 1, property_restrictions_list=[], nodeIDs=[], black_period=0, black_trigger='Blackout', event_name='HSB')¶: :param TBD Note start_day is initialized as 1, recommend that this be aligned with the start of the simulation

emodpy_tbhiv.interventions.hsb.new_intervention_as_file(camp, filename=None)¶

emodpy_tbhiv.interventions.ramp_dtn module¶

emodpy_tbhiv.interventions.ramp_dtn.RampDTN(camp, trigger_treatment_list, ramp_time=30, base_sensitivity_smearpos=1.0, base_sensitivity_smearneg=1.0, base_sensitivity_smearpos2=1.0, base_sensitivity_smearneg2=1.0, treatment_fraction=1.0, treatment_fraction2=1.0, pos_event='TBTestPositive', neg_event='TBTestNegative', defaulters_event='TBTestDefault', pos_event2='TBTestPositive', neg_event2='TBTestNegative', defaulters_event2='TBTestDefault', start_day=0, duration=- 1, property_restrictions_list=[], nodeIDs=[], black_period=0, black_trigger='Blackout', event_name='RampDTN')¶: :param TBD Note start_day is initialized as 1, recommend that this be aligned with the start of the simulation

emodpy_tbhiv.interventions.ramp_dtn.new_intervention_as_file(camp, filename=None)¶

emodpy_tbhiv.interventions.resist_diag module¶

emodpy_tbhiv.interventions.resist_diag.ResistanceDiagnostic(camp, trigger_treatment_list, sensitivity=1.0, specificity=1.0, pos_event='TBMDRTestPositive', neg_event='TBMDRTestNegative', def_event='TBMDRTestDefault', treatment_fraction=1, treatment_fraction_negative_test=1, start_day=0, duration=- 1, property_restrictions_list=[], nodeIDs=[], black_period=0, black_trigger='Blackout', event_name='TB Diagnosis MDR')¶: :param TBD Note start_day is initialized as 1, recommend that this be aligned with the start of the simulation

emodpy_tbhiv.interventions.resist_diag.new_intervention_as_file(camp, filename=None)¶

emodpy_tbhiv.interventions.smear_diag module¶

emodpy_tbhiv.interventions.smear_diag.SmearDiagnostic(camp, trigger_treatment_list, base_sensitivity_smearpos=1.0, base_sensitivity_smearneg=1.0, pos_event='TestPositiveOnSmear', treatment_fraction=1, start_day=0, duration=- 1, property_restrictions_list=[], nodeIDs=[], black_period=0, black_trigger='Blackout', event_name='TB Diagnosis Smear Simple')¶: :param TBD Note start_day is initialized as 1, recommend that this be aligned with the start of the simulation

emodpy_tbhiv.interventions.smear_diag.new_intervention_as_file(camp, filename=None)¶

emodpy_tbhiv.interventions.tb_treat_basic module¶

emodpy_tbhiv.interventions.tb_treat_basic.TBDrugTreatment(camp, trigger_treatment_list, drug_name='DOTS', inactivation_rate=0, mortality_rate=0, clearance_rate=0, resistance_rate=0, relapse_rate=0, reduced_transmit=1.0, start_day=0, treatment_duration=180, duration=- 1, property_restrictions_list=[], nodeIDs=[], black_period=0, black_trigger='Blackout', event_name='TBDrugTreatment')¶: :param TBD Note start_day is initialized as 1, recommend that this be aligned with the start of the simulation

emodpy_tbhiv.interventions.tb_treat_basic.new_intervention_as_file(camp, filename=None)¶

emodpy_tbhiv.interventions.tbhiv_treat module¶

emodpy_tbhiv.interventions.tbhiv_treat.TBHIVDrugTreatment(camp, trigger_treatment_list, drug_name, latent_multiplier=1.0, active_multiplier=1.0, start_day=0, duration=- 1, property_restrictions_list=[], nodeIDs=[], black_period=0, black_trigger='Blackout', event_name='TBHIVDrugTreatment')¶: :param TBD Note start_day is initialized as 1, recommend that this be aligned with the start of the simulation

emodpy_tbhiv.interventions.tbhiv_treat.new_intervention_as_file(camp, filename=None)¶

emodpy_tbhiv.interventions.triggered_pvc module¶

emodpy_tbhiv.interventions.triggered_pvc.TPVC(camp, trigger_treatment_list, property_to_change, final_prop_value, revert=0, daily_prob=1, start_day=0, duration=- 1, property_restrictions_list=[], nodeIDs=[], black_period=0, black_trigger='Blackout', event_name='PropertyValueChanger')¶: Triggered Property Value Changer :param TBD Note start_day is initialized as 1, recommend that this be aligned with the start of the simulation

emodpy_tbhiv.interventions.triggered_pvc.new_intervention_as_file(camp, filename=None)¶

emodpy_tbhiv.interventions.vaccine module¶

emodpy_tbhiv.interventions.vaccine.Vaccine(camp, trigger_treatment_list, initial_efficacy=1.0, vaccine_take=1, vtype='AcquisitionBlocking', box_duration=365, immune_decay=3650, start_day=0, duration=- 1, property_restrictions_list=[], nodeIDs=[], black_period=0, black_trigger='Blackout', event_name='Vaccine')¶: :param TBD Note start_day is initialized as 1, recommend that this be aligned with the start of the simulation

emodpy_tbhiv.interventions.vaccine.new_intervention_as_file(camp, filename=None)¶