emodpy_malaria package

Subpackages

• emodpy_malaria.demographics package
  • Submodules
    • emodpy_malaria.demographics.MalariaDemographics module
      • MalariaDemographics
      • from_template_node()
      • from_pop_csv()
      • from_csv()
      • from_params()
• emodpy_malaria.interventions package
  • Submodules
    • emodpy_malaria.interventions.adherentdrug module
      • adherent_drug()
    • emodpy_malaria.interventions.bednet module
      • new_intervention_as_file()
      • add_itn_scheduled()
      • add_itn_triggered()
    • emodpy_malaria.interventions.common module
      • add_triggered_campaign_delay_event()
      • add_campaign_event()
    • emodpy_malaria.interventions.community_health_worker module
      • add_community_health_worker()
    • emodpy_malaria.interventions.diag_survey module
      • add_diagnostic_survey()
    • emodpy_malaria.interventions.drug module
      • add_scheduled_antimalarial_drug()
      • new_intervention_as_file()
    • emodpy_malaria.interventions.drug_campaign module
      • drug_configs_from_code()
      • add_drug_campaign()
      • add_MDA()
      • add_MSAT()
      • add_fMDA()
      • add_rfMSAT()
      • add_rfMDA()
      • fmda_cfg()
      • add_IPTi()
    • emodpy_malaria.interventions.inputeir module
      • add_scheduled_input_eir()
      • new_intervention_as_file()
    • emodpy_malaria.interventions.irs module
      • add_scheduled_irs_housing_modification()
      • add_triggered_irs_housing_modification()
      • irs_configuration()
      • new_intervention_as_file()
    • emodpy_malaria.interventions.ivermectin module
      • add_scheduled_ivermectin()
      • add_triggered_ivermectin()
    • emodpy_malaria.interventions.larvicide module
      • add_larvicide()
      • new_intervention_as_file()
    • emodpy_malaria.interventions.malaria_challenge module
      • add_challenge_trial()
    • emodpy_malaria.interventions.mosquitorelease module
      • add_scheduled_mosquito_release()
      • new_intervention_as_file()
    • emodpy_malaria.interventions.outbreak module
      • add_outbreak_individual()
      • add_outbreak_malaria_genetics()
      • add_outbreak_malaria_var_genes()
      • add_campaign_event()
    • emodpy_malaria.interventions.outdoorrestkill module
      • add_outdoorrestkill()
    • emodpy_malaria.interventions.scale_larval_habitats module
      • add_scale_larval_habitats()
      • add_habitat_reduction_event()
    • emodpy_malaria.interventions.spacespraying module
      • add_scheduled_space_spraying()
      • new_intervention_as_file()
    • emodpy_malaria.interventions.sugartrap module
      • add_scheduled_sugar_trap()
      • new_intervention_as_file()
    • emodpy_malaria.interventions.treatment_seeking module
      • add_treatment_seeking()
    • emodpy_malaria.interventions.usage_dependent_bednet module
      • add_scheduled_usage_dependent_bednet()
      • add_triggered_usage_dependent_bednet()
      • new_intervention_as_file()
    • emodpy_malaria.interventions.vaccine module
      • add_scheduled_vaccine()
      • add_triggered_vaccine()
      • new_intervention_as_file()
    • emodpy_malaria.interventions.vector_surveillance module
      • CountType
      • VectorGender
      • add_vector_surveillance_event_coordinator()
• emodpy_malaria.migration package
  • Submodules
    • emodpy_malaria.migration.convert_csv_to_bin_vector_migration module
      • GenderDataType
      • MetaData
      • write_metadata_file()
      • is_number()
      • get_summary_data()
      • write_bin_file()
    • emodpy_malaria.migration.convert_json_to_bin module
      • check_age()
      • check_ages_array()
      • GenderDataType
      • InterpolationTypes
      • MigrationTypes
      • check_gender_data_type()
      • check_interpolation_type()
      • check_migration_type()
      • check_in_json()
      • check_rates_size()
      • read_json()
      • SummaryData
      • get_summary_data()
      • write_bin_file()
      • write_bin_file_gender()
      • write_metadata_file()
    • emodpy_malaria.migration.convert_txt_to_bin module
      • MigrationTypes
      • show_usage()
    • emodpy_malaria.migration.vector_migration module
      • Layer
      • VectorMigration
      • from_file()
      • examine_file()
      • from_params()
      • from_demog_and_param_gravity_webservice()
      • from_demographics_and_gravity_params()
      • to_csv()
      • from_csv()
• emodpy_malaria.reporters package
  • Submodules
    • emodpy_malaria.reporters.builtin module
      • VectorState
      • DrugResistantAndHRPStatisticType
      • check_vectors()
      • all_vectors_if_none()
      • add_visualizations()
      • add_report_vector_genetics()
      • add_report_vector_stats()
      • add_malaria_summary_report()
      • add_malaria_patient_json_report()
      • add_malaria_cotransmission_report()
      • add_report_malaria_filtered()
      • add_report_malaria_filtered_intrahost()
      • add_spatial_report_malaria_filtered()
      • add_report_event_counter()
      • add_sql_report_malaria()
      • add_sql_report_malaria_genetics()
      • add_vector_habitat_report()
      • add_malaria_immunity_report()
      • add_malaria_survey_analyzer()
      • add_drug_status_report()
      • add_report_infection_stats_malaria()
      • add_human_migration_tracking()
      • add_report_node_demographics()
      • add_report_node_demographics_malaria()
      • add_report_node_demographics_malaria_genetics()
      • add_report_vector_migration()
      • add_report_vector_stats_malaria_genetics()
      • add_event_recorder()
      • add_node_event_recorder()
      • add_coordinator_event_recorder()
      • add_report_intervention_pop_avg()
      • add_report_microsporidia()
      • add_report_fpg_output()
      • add_report_simulation_stats()
      • ReportVectorGenetics
      • ReportInfectionStatsMalaria
      • ReportVectorStats
      • MalariaSummaryReport
      • MalariaPatientJSONReport
      • ReportSimpleMalariaTransmission
      • ReportMalariaFiltered
      • SpatialReportMalariaFiltered
      • ReportMalariaFilteredIntraHost
      • ReportEventCounter
      • SqlReportMalariaGenetics
      • SqlReportMalaria
      • VectorHabitatReport
      • MalariaImmunityReport
      • MalariaSurveyJSONAnalyzer
      • ReportDrugStatus
      • ReportHumanMigrationTracking
      • ReportNodeDemographics
      • ReportNodeDemographicsMalaria
      • ReportNodeDemographicsMalariaGenetics
      • ReportVectorMigration
      • ReportVectorStatsMalariaGenetics
      • ReportInterventionPopAvg
      • ReportFpgOutputForObservationalModel
      • ReportSimulationStats
      • ReportMicrosporidia
• emodpy_malaria.serialization package
  • Submodules
    • emodpy_malaria.serialization.replace_genomes module
      • Genome
      • print_hashcodes()
      • get_next_genome()
      • replace_genomes()
      • test_replace_genomes()
    • emodpy_malaria.serialization.replace_genomes_get_next_barcode module
      • get_next_barcode()
    • emodpy_malaria.serialization.serialization_support module
      • write_out_humans_data()
    • emodpy_malaria.serialization.zero_infections module
      • zero_vector_infections()
      • zero_human_infections()
      • zero_infections()
      • zero_infection_path()
• emodpy_malaria.weather package
  • Main Features
  • generate_weather()
  • csv_to_weather()
  • weather_to_csv()
  • Submodules
    • emodpy_malaria.weather.data_sources module
    • emodpy_malaria.weather.weather_data module
      • WeatherData
      • DataFrameInfo
    • emodpy_malaria.weather.weather_metadata module
      • WeatherAttributes
      • WeatherMetadata
    • emodpy_malaria.weather.weather_request module
      • WeatherArgs
      • RequestReport
      • DataSource
      • WeatherRequest
    • emodpy_malaria.weather.weather_set module
      • WeatherSet
    • emodpy_malaria.weather.weather_utils module
      • invert_dict()
      • hash_series()
      • save_json()
      • make_path()
      • ymd()
      • parse_date()
      • validate_str_value()
    • emodpy_malaria.weather.weather_variable module
      • WeatherVariable

Submodules

• emodpy_malaria.malaria_config module
  • get_file_from_http()
  • set_team_defaults()
  • set_team_drug_params()
  • set_parasite_genetics_params()
  • get_drug_params()
  • set_drug_param()
  • add_drug_resistance()
  • set_species_param()
  • add_species()
  • add_blood_meal_mortality()
  • add_insecticide_resistance()
  • get_species_params()
  • set_max_larval_capacity()
  • add_microsporidia()
  • configure_linear_spline()
• emodpy_malaria.malaria_vector_species_params module
  • species_params()
• emodpy_malaria.vector_config module
  • set_team_defaults()
  • get_species_params()
  • set_species_param()
  • configure_linear_spline()
  • add_species()
  • add_genes_and_alleles()
  • add_mutation()
  • create_trait()
  • add_trait()
  • add_blood_meal_mortality()
  • add_insecticide_resistance()
  • add_species_drivers()
  • set_max_larval_capacity()
  • add_microsporidia()
  • ModifierEquationType
    • ModifierEquationType.EXPONENTIAL
    • ModifierEquationType.LINEAR
  • add_vector_migration()