Index

A

add_blood_meal_mortality() (in module emodpy_malaria.malaria_config) (in module emodpy_malaria.vector_config) add_campaign_event() (in module emodpy_malaria.interventions.common) (in module emodpy_malaria.interventions.outbreak) add_challenge_trial() (in module emodpy_malaria.interventions.malaria_challenge) add_community_health_worker() (in module emodpy_malaria.interventions.community_health_worker) add_coordinator_event_recorder() (in module emodpy_malaria.reporters.builtin) add_diagnostic_survey() (in module emodpy_malaria.interventions.diag_survey) add_drug_campaign() (in module emodpy_malaria.interventions.drug_campaign) add_drug_resistance() (in module emodpy_malaria.malaria_config) add_drug_status_report() (in module emodpy_malaria.reporters.builtin) add_event_recorder() (in module emodpy_malaria.reporters.builtin) add_fMDA() (in module emodpy_malaria.interventions.drug_campaign) add_genes_and_alleles() (in module emodpy_malaria.vector_config) add_habitat_reduction_event() (in module emodpy_malaria.interventions.scale_larval_habitats) add_human_migration_tracking() (in module emodpy_malaria.reporters.builtin) add_initial_vectors_per_species() (emodpy_malaria.demographics.MalariaDemographics.MalariaDemographics method) add_initial_vectors_per_species_from_csv() (emodpy_malaria.demographics.MalariaDemographics.MalariaDemographics method) add_insecticide_resistance() (in module emodpy_malaria.malaria_config) (in module emodpy_malaria.vector_config) add_IPTi() (in module emodpy_malaria.interventions.drug_campaign) add_itn_scheduled() (in module emodpy_malaria.interventions.bednet) add_itn_triggered() (in module emodpy_malaria.interventions.bednet) add_larval_habitat_multiplier() (emodpy_malaria.demographics.MalariaDemographics.MalariaDemographics method) add_larvicide() (in module emodpy_malaria.interventions.larvicide) add_malaria_cotransmission_report() (in module emodpy_malaria.reporters.builtin) add_malaria_immunity_report() (in module emodpy_malaria.reporters.builtin) add_malaria_patient_json_report() (in module emodpy_malaria.reporters.builtin) add_malaria_summary_report() (in module emodpy_malaria.reporters.builtin) add_malaria_survey_analyzer() (in module emodpy_malaria.reporters.builtin) add_MDA() (in module emodpy_malaria.interventions.drug_campaign) add_microsporidia() (in module emodpy_malaria.malaria_config) (in module emodpy_malaria.vector_config) add_MSAT() (in module emodpy_malaria.interventions.drug_campaign) add_mutation() (in module emodpy_malaria.vector_config) add_node_event_recorder() (in module emodpy_malaria.reporters.builtin) add_outbreak_individual() (in module emodpy_malaria.interventions.outbreak) add_outbreak_malaria_genetics() (in module emodpy_malaria.interventions.outbreak) add_outbreak_malaria_var_genes() (in module emodpy_malaria.interventions.outbreak) add_outdoorrestkill() (in module emodpy_malaria.interventions.outdoorrestkill) add_report_event_counter() (in module emodpy_malaria.reporters.builtin) add_report_fpg_output() (in module emodpy_malaria.reporters.builtin) add_report_infection_stats_malaria() (in module emodpy_malaria.reporters.builtin) add_report_intervention_pop_avg() (in module emodpy_malaria.reporters.builtin) add_report_malaria_filtered() (in module emodpy_malaria.reporters.builtin) add_report_malaria_filtered_intrahost() (in module emodpy_malaria.reporters.builtin) add_report_microsporidia() (in module emodpy_malaria.reporters.builtin) add_report_node_demographics() (in module emodpy_malaria.reporters.builtin) add_report_node_demographics_malaria() (in module emodpy_malaria.reporters.builtin) add_report_node_demographics_malaria_genetics() (in module emodpy_malaria.reporters.builtin)

add_report_simulation_stats() (in module emodpy_malaria.reporters.builtin) add_report_vector_genetics() (in module emodpy_malaria.reporters.builtin) add_report_vector_migration() (in module emodpy_malaria.reporters.builtin) add_report_vector_stats() (in module emodpy_malaria.reporters.builtin) add_report_vector_stats_malaria_genetics() (in module emodpy_malaria.reporters.builtin) add_rfMDA() (in module emodpy_malaria.interventions.drug_campaign) add_rfMSAT() (in module emodpy_malaria.interventions.drug_campaign) add_scale_larval_habitats() (in module emodpy_malaria.interventions.scale_larval_habitats) add_scheduled_antimalarial_drug() (in module emodpy_malaria.interventions.drug) add_scheduled_input_eir() (in module emodpy_malaria.interventions.inputeir) add_scheduled_irs_housing_modification() (in module emodpy_malaria.interventions.irs) add_scheduled_ivermectin() (in module emodpy_malaria.interventions.ivermectin) add_scheduled_mosquito_release() (in module emodpy_malaria.interventions.mosquitorelease) add_scheduled_space_spraying() (in module emodpy_malaria.interventions.spacespraying) add_scheduled_sugar_trap() (in module emodpy_malaria.interventions.sugartrap) add_scheduled_usage_dependent_bednet() (in module emodpy_malaria.interventions.usage_dependent_bednet) add_scheduled_vaccine() (in module emodpy_malaria.interventions.vaccine) add_spatial_report_malaria_filtered() (in module emodpy_malaria.reporters.builtin) add_species() (in module emodpy_malaria.malaria_config) (in module emodpy_malaria.vector_config) add_species_drivers() (in module emodpy_malaria.vector_config) add_sql_report_malaria() (in module emodpy_malaria.reporters.builtin) add_sql_report_malaria_genetics() (in module emodpy_malaria.reporters.builtin) add_trait() (in module emodpy_malaria.vector_config) add_treatment_seeking() (in module emodpy_malaria.interventions.treatment_seeking) add_triggered_campaign_delay_event() (in module emodpy_malaria.interventions.common) add_triggered_irs_housing_modification() (in module emodpy_malaria.interventions.irs) add_triggered_ivermectin() (in module emodpy_malaria.interventions.ivermectin) add_triggered_usage_dependent_bednet() (in module emodpy_malaria.interventions.usage_dependent_bednet) add_triggered_vaccine() (in module emodpy_malaria.interventions.vaccine) add_vector_habitat_report() (in module emodpy_malaria.reporters.builtin) add_vector_migration() (in module emodpy_malaria.vector_config) add_vector_surveillance_event_coordinator() (in module emodpy_malaria.interventions.vector_surveillance) add_visualizations() (in module emodpy_malaria.reporters.builtin) adherent_drug() (in module emodpy_malaria.interventions.adherentdrug) agent-based model AgesYears (emodpy_malaria.migration.vector_migration.VectorMigration property) AIR_MIGRATION (emodpy_malaria.migration.convert_json_to_bin.MigrationTypes attribute) (emodpy_malaria.migration.convert_txt_to_bin.MigrationTypes attribute) AIR_TEMPERATURE (emodpy_malaria.weather.weather_variable.WeatherVariable attribute) all_vectors_if_none() (in module emodpy_malaria.reporters.builtin) ALLELE_FREQ (emodpy_malaria.interventions.vector_surveillance.CountType attribute) antibodies antibody antigen antigens attributes (emodpy_malaria.weather.weather_metadata.WeatherMetadata property) (emodpy_malaria.weather.weather_set.WeatherSet property) attributes_dict (emodpy_malaria.weather.weather_metadata.WeatherAttributes property) Author (emodpy_malaria.migration.vector_migration.VectorMigration property) author (emodpy_malaria.weather.weather_metadata.WeatherAttributes property)

B

barcode (emodpy_malaria.serialization.replace_genomes.Genome property)

Boost boxcar function

C

campaign campaign event campaign file channel check_age() (in module emodpy_malaria.migration.convert_json_to_bin) check_ages_array() (in module emodpy_malaria.migration.convert_json_to_bin) check_gender_data_type() (in module emodpy_malaria.migration.convert_json_to_bin) check_in_json() (in module emodpy_malaria.migration.convert_json_to_bin) check_interpolation_type() (in module emodpy_malaria.migration.convert_json_to_bin) check_migration_type() (in module emodpy_malaria.migration.convert_json_to_bin) check_rates_size() (in module emodpy_malaria.migration.convert_json_to_bin) check_vectors() (in module emodpy_malaria.reporters.builtin) circumsporozoite protein (CSP) class factory Clausius-Clayperon relation cohort model compartmental model config() (emodpy_malaria.reporters.builtin.MalariaImmunityReport method) (emodpy_malaria.reporters.builtin.MalariaPatientJSONReport method) (emodpy_malaria.reporters.builtin.MalariaSummaryReport method) (emodpy_malaria.reporters.builtin.MalariaSurveyJSONAnalyzer method) (emodpy_malaria.reporters.builtin.ReportDrugStatus method) (emodpy_malaria.reporters.builtin.ReportEventCounter method) (emodpy_malaria.reporters.builtin.ReportFpgOutputForObservationalModel method) (emodpy_malaria.reporters.builtin.ReportHumanMigrationTracking method) (emodpy_malaria.reporters.builtin.ReportInfectionStatsMalaria method) (emodpy_malaria.reporters.builtin.ReportInterventionPopAvg method) (emodpy_malaria.reporters.builtin.ReportMalariaFiltered method) (emodpy_malaria.reporters.builtin.ReportMalariaFilteredIntraHost method) (emodpy_malaria.reporters.builtin.ReportMicrosporidia method) (emodpy_malaria.reporters.builtin.ReportNodeDemographics method) (emodpy_malaria.reporters.builtin.ReportNodeDemographicsMalaria method) (emodpy_malaria.reporters.builtin.ReportNodeDemographicsMalariaGenetics method) (emodpy_malaria.reporters.builtin.ReportSimpleMalariaTransmission method) (emodpy_malaria.reporters.builtin.ReportSimulationStats method) (emodpy_malaria.reporters.builtin.ReportVectorGenetics method) (emodpy_malaria.reporters.builtin.ReportVectorMigration method) (emodpy_malaria.reporters.builtin.ReportVectorStats method) (emodpy_malaria.reporters.builtin.ReportVectorStatsMalariaGenetics method) (emodpy_malaria.reporters.builtin.SpatialReportMalariaFiltered method) (emodpy_malaria.reporters.builtin.SqlReportMalaria method) (emodpy_malaria.reporters.builtin.SqlReportMalariaGenetics method) (emodpy_malaria.reporters.builtin.VectorHabitatReport method)

configuration file configure_linear_spline() (in module emodpy_malaria.malaria_config) (in module emodpy_malaria.vector_config) convert_char_to_int() (emodpy_malaria.serialization.replace_genomes.Genome method) core CountType (class in emodpy_malaria.interventions.vector_surveillance) create_genome() (emodpy_malaria.serialization.replace_genomes.Genome method) create_trait() (in module emodpy_malaria.vector_config) CRISPR csv_to_weather() (in module emodpy_malaria.weather) cytokine

D

data (emodpy_malaria.weather.weather_data.WeatherData property) data_id (emodpy_malaria.weather.weather_request.WeatherRequest property) data_years (emodpy_malaria.weather.weather_metadata.WeatherAttributes property) DataFrameInfo (class in emodpy_malaria.weather.weather_data) DataSource (class in emodpy_malaria.weather.weather_request) datavalue_count (emodpy_malaria.weather.weather_metadata.WeatherMetadata property) DatavalueCount (emodpy_malaria.migration.vector_migration.Layer property) (emodpy_malaria.migration.vector_migration.VectorMigration property) date_created (emodpy_malaria.weather.weather_metadata.WeatherAttributes property) DateCreated (emodpy_malaria.migration.vector_migration.VectorMigration property) demographics file

destination node detect_columns() (emodpy_malaria.weather.weather_data.DataFrameInfo class method) deterministic diffusive migration dir_path (emodpy_malaria.weather.weather_set.WeatherSet property) disability-adjusted life years (DALY) disease-specific build download (emodpy_malaria.weather.weather_request.RequestReport attribute) download() (emodpy_malaria.weather.weather_request.WeatherRequest method) drug_configs_from_code() (in module emodpy_malaria.interventions.drug_campaign) DrugResistantAndHRPStatisticType (class in emodpy_malaria.reporters.builtin) dynamic link library (DLL)

E

emodpy_malaria module emodpy_malaria.demographics module emodpy_malaria.demographics.MalariaDemographics module emodpy_malaria.interventions module emodpy_malaria.interventions.adherentdrug module emodpy_malaria.interventions.bednet module emodpy_malaria.interventions.common module emodpy_malaria.interventions.community_health_worker module emodpy_malaria.interventions.diag_survey module emodpy_malaria.interventions.drug module emodpy_malaria.interventions.drug_campaign module emodpy_malaria.interventions.inputeir module emodpy_malaria.interventions.irs module emodpy_malaria.interventions.ivermectin module emodpy_malaria.interventions.larvicide module emodpy_malaria.interventions.malaria_challenge module emodpy_malaria.interventions.mosquitorelease module emodpy_malaria.interventions.outbreak module emodpy_malaria.interventions.outdoorrestkill module emodpy_malaria.interventions.scale_larval_habitats module emodpy_malaria.interventions.spacespraying module emodpy_malaria.interventions.sugartrap module emodpy_malaria.interventions.treatment_seeking module emodpy_malaria.interventions.usage_dependent_bednet module emodpy_malaria.interventions.vaccine module emodpy_malaria.interventions.vector_surveillance module emodpy_malaria.malaria_config module emodpy_malaria.malaria_vector_species_params module

emodpy_malaria.migration module emodpy_malaria.migration.convert_csv_to_bin_vector_migration module emodpy_malaria.migration.convert_json_to_bin module emodpy_malaria.migration.convert_txt_to_bin module emodpy_malaria.migration.vector_migration module emodpy_malaria.reporters module emodpy_malaria.reporters.builtin module emodpy_malaria.serialization module emodpy_malaria.serialization.replace_genomes module emodpy_malaria.serialization.replace_genomes_get_next_barcode module emodpy_malaria.serialization.serialization_support module emodpy_malaria.serialization.zero_infections module emodpy_malaria.vector_config module emodpy_malaria.weather module emodpy_malaria.weather.data_sources module emodpy_malaria.weather.weather_data module emodpy_malaria.weather.weather_metadata module emodpy_malaria.weather.weather_request module emodpy_malaria.weather.weather_set module emodpy_malaria.weather.weather_utils module emodpy_malaria.weather.weather_variable module EMODule entomological inoculation rate (EIR) epidemic Epidemiological MODeling software (EMOD) epitope Eradication.exe Euler method event coordinator examine_file() (in module emodpy_malaria.migration.vector_migration) exp( EXPONENTIAL (emodpy_malaria.vector_config.ModifierEquationType attribute) exposed

F

file_names (emodpy_malaria.weather.weather_set.WeatherSet property) file_prefix (emodpy_malaria.weather.weather_request.DataSource property) files (emodpy_malaria.weather.weather_request.WeatherRequest property) files_exist (emodpy_malaria.weather.weather_request.WeatherRequest property) flattened file fmda_cfg() (in module emodpy_malaria.interventions.drug_campaign) force of infection (FoI) format_create_date() (emodpy_malaria.weather.weather_metadata.WeatherAttributes class method) from_csv() (emodpy_malaria.weather.weather_data.WeatherData class method) (emodpy_malaria.weather.weather_set.WeatherSet class method) (in module emodpy_malaria.demographics.MalariaDemographics) (in module emodpy_malaria.migration.vector_migration)

from_dataframe() (emodpy_malaria.weather.weather_data.WeatherData class method) (emodpy_malaria.weather.weather_set.WeatherSet class method) from_demog_and_param_gravity_webservice() (in module emodpy_malaria.migration.vector_migration) from_demographics_and_gravity_params() (in module emodpy_malaria.migration.vector_migration) from_dict() (emodpy_malaria.weather.weather_data.WeatherData class method) from_file() (emodpy_malaria.weather.weather_data.WeatherData class method) (emodpy_malaria.weather.weather_metadata.WeatherMetadata class method) (in module emodpy_malaria.migration.vector_migration) from_files() (emodpy_malaria.weather.weather_set.WeatherSet class method) from_params() (in module emodpy_malaria.demographics.MalariaDemographics) (in module emodpy_malaria.migration.vector_migration) from_pop_csv() (in module emodpy_malaria.demographics.MalariaDemographics) from_template_node() (in module emodpy_malaria.demographics.MalariaDemographics)

G

gametocyte gametocytes GenderDataType (class in emodpy_malaria.migration.convert_csv_to_bin_vector_migration) (class in emodpy_malaria.migration.convert_json_to_bin) (emodpy_malaria.migration.vector_migration.VectorMigration property) gene drive mosquito generate() (emodpy_malaria.weather.weather_request.WeatherRequest method) generate_weather() (in module emodpy_malaria.weather) Genome (class in emodpy_malaria.serialization.replace_genomes) GENOME_FRACTION (emodpy_malaria.interventions.vector_surveillance.CountType attribute)

get_drug_params() (in module emodpy_malaria.malaria_config) get_file_from_http() (in module emodpy_malaria.malaria_config) get_next_barcode() (in module emodpy_malaria.serialization.replace_genomes_get_next_barcode) get_next_genome() (in module emodpy_malaria.serialization.replace_genomes) get_node_offsets() (emodpy_malaria.migration.vector_migration.VectorMigration method) get_species_params() (in module emodpy_malaria.malaria_config) (in module emodpy_malaria.vector_config) get_summary_data() (in module emodpy_malaria.migration.convert_csv_to_bin_vector_migration) (in module emodpy_malaria.migration.convert_json_to_bin) gonotrophic

H

hash_series() (in module emodpy_malaria.weather.weather_utils) hashcode (emodpy_malaria.serialization.replace_genomes.Genome property) hepatocyte herd immunity

Heterogeneous Intra-Node Transmission (HINT) high-performance computing (HPC) home node homing endonuclease gene (HEG)

I

id_reference (emodpy_malaria.weather.weather_metadata.WeatherAttributes property) IdReference (emodpy_malaria.migration.vector_migration.VectorMigration property) immune incidence individual mosquito model individual properties indoor residual spraying (IRS) infectious input files

insecticide-treated nets (ITN) inset chart InterpolationType (emodpy_malaria.migration.vector_migration.VectorMigration property) InterpolationTypes (class in emodpy_malaria.migration.convert_json_to_bin) intervention invert_dict() (in module emodpy_malaria.weather.weather_utils) irs_configuration() (in module emodpy_malaria.interventions.irs) is_number() (in module emodpy_malaria.migration.convert_csv_to_bin_vector_migration) items() (emodpy_malaria.weather.weather_set.WeatherSet method)

J

JSON (JavaScript Object Notation)

K

Keyhole Markup Language (KML)

keys() (emodpy_malaria.weather.weather_set.WeatherSet method) Koppen-Geiger Climate Classification System

L

LAND_TEMPERATURE (emodpy_malaria.weather.weather_variable.WeatherVariable attribute) larval habitat larvicide Layer (class in emodpy_malaria.migration.vector_migration) LINEAR (emodpy_malaria.vector_config.ModifierEquationType attribute) LINEAR_INTERPOLATION (emodpy_malaria.migration.convert_json_to_bin.InterpolationTypes attribute) (emodpy_malaria.migration.vector_migration.VectorMigration attribute)

Link-Time Code Generation (LTCG) list() (emodpy_malaria.weather.weather_variable.WeatherVariable class method) local_dir (emodpy_malaria.weather.weather_request.WeatherRequest property) LOCAL_MIGRATION (emodpy_malaria.migration.convert_json_to_bin.MigrationTypes attribute) (emodpy_malaria.migration.convert_txt_to_bin.MigrationTypes attribute) (emodpy_malaria.migration.vector_migration.VectorMigration attribute) loss to follow-up (LTFU) LTFU

M

make_file_paths() (emodpy_malaria.weather.weather_set.WeatherSet class method) make_path() (in module emodpy_malaria.weather.weather_utils) MalariaDemographics (class in emodpy_malaria.demographics.MalariaDemographics) MalariaImmunityReport (class in emodpy_malaria.reporters.builtin) MalariaPatientJSONReport (class in emodpy_malaria.reporters.builtin) MalariaSummaryReport (class in emodpy_malaria.reporters.builtin) MalariaSurveyJSONAnalyzer (class in emodpy_malaria.reporters.builtin) mass drug administration (MDA) merozoite merozoite surface protein (MSP) merozoites Message Passing Interface (MPI) MetaData (class in emodpy_malaria.migration.convert_csv_to_bin_vector_migration) metadata (emodpy_malaria.weather.weather_data.WeatherData property) metadata_defaults_dict() (emodpy_malaria.weather.weather_metadata.WeatherAttributes class method) microsolver MigrationType (emodpy_malaria.migration.vector_migration.VectorMigration property) MigrationTypes (class in emodpy_malaria.migration.convert_json_to_bin) (class in emodpy_malaria.migration.convert_txt_to_bin) ModifierEquationType (class in emodpy_malaria.vector_config) module emodpy_malaria emodpy_malaria.demographics emodpy_malaria.demographics.MalariaDemographics emodpy_malaria.interventions emodpy_malaria.interventions.adherentdrug emodpy_malaria.interventions.bednet emodpy_malaria.interventions.common emodpy_malaria.interventions.community_health_worker emodpy_malaria.interventions.diag_survey emodpy_malaria.interventions.drug emodpy_malaria.interventions.drug_campaign emodpy_malaria.interventions.inputeir emodpy_malaria.interventions.irs emodpy_malaria.interventions.ivermectin emodpy_malaria.interventions.larvicide emodpy_malaria.interventions.malaria_challenge emodpy_malaria.interventions.mosquitorelease emodpy_malaria.interventions.outbreak emodpy_malaria.interventions.outdoorrestkill emodpy_malaria.interventions.scale_larval_habitats emodpy_malaria.interventions.spacespraying emodpy_malaria.interventions.sugartrap emodpy_malaria.interventions.treatment_seeking emodpy_malaria.interventions.usage_dependent_bednet emodpy_malaria.interventions.vaccine emodpy_malaria.interventions.vector_surveillance emodpy_malaria.malaria_config emodpy_malaria.malaria_vector_species_params emodpy_malaria.migration emodpy_malaria.migration.convert_csv_to_bin_vector_migration emodpy_malaria.migration.convert_json_to_bin emodpy_malaria.migration.convert_txt_to_bin emodpy_malaria.migration.vector_migration emodpy_malaria.reporters emodpy_malaria.reporters.builtin emodpy_malaria.serialization emodpy_malaria.serialization.replace_genomes emodpy_malaria.serialization.replace_genomes_get_next_barcode emodpy_malaria.serialization.serialization_support emodpy_malaria.serialization.zero_infections emodpy_malaria.vector_config emodpy_malaria.weather emodpy_malaria.weather.data_sources emodpy_malaria.weather.weather_data emodpy_malaria.weather.weather_metadata emodpy_malaria.weather.weather_request emodpy_malaria.weather.weather_set emodpy_malaria.weather.weather_utils emodpy_malaria.weather.weather_variable

monolithic build Monte Carlo method

N

name (emodpy_malaria.weather.weather_request.DataSource property) new_intervention_as_file() (in module emodpy_malaria.interventions.bednet) (in module emodpy_malaria.interventions.drug) (in module emodpy_malaria.interventions.inputeir) (in module emodpy_malaria.interventions.irs) (in module emodpy_malaria.interventions.larvicide) (in module emodpy_malaria.interventions.mosquitorelease) (in module emodpy_malaria.interventions.spacespraying) (in module emodpy_malaria.interventions.sugartrap) (in module emodpy_malaria.interventions.usage_dependent_bednet) (in module emodpy_malaria.interventions.vaccine) node node properties

node-targeted intervention node_column (emodpy_malaria.weather.weather_data.DataFrameInfo property) node_count (emodpy_malaria.weather.weather_metadata.WeatherMetadata property) node_offset_str (emodpy_malaria.weather.weather_metadata.WeatherMetadata property) node_offsets (emodpy_malaria.weather.weather_metadata.WeatherMetadata property) NodeCount (emodpy_malaria.migration.vector_migration.Layer property) (emodpy_malaria.migration.vector_migration.VectorMigration property) NodeOffsets (emodpy_malaria.migration.vector_migration.VectorMigration property) nodes Nodes (emodpy_malaria.migration.vector_migration.VectorMigration property) nodes (emodpy_malaria.weather.weather_metadata.WeatherMetadata property) NUM_INFECTIONS (emodpy_malaria.reporters.builtin.DrugResistantAndHRPStatisticType attribute) NUM_PEOPLE_WITH_RESISTANT_INFECTION (emodpy_malaria.reporters.builtin.DrugResistantAndHRPStatisticType attribute)

O

offset_nodes (emodpy_malaria.weather.weather_metadata.WeatherMetadata property) ONE_FOR_EACH_GENDER (emodpy_malaria.migration.convert_csv_to_bin_vector_migration.GenderDataType attribute) (emodpy_malaria.migration.convert_json_to_bin.GenderDataType attribute) (emodpy_malaria.migration.vector_migration.VectorMigration attribute)

ordinary differential equation (ODE) origin node output report overlay file oviposition

P

parse_date() (in module emodpy_malaria.weather.weather_utils) PIECEWISE_CONSTANT (emodpy_malaria.migration.convert_json_to_bin.InterpolationTypes attribute) (emodpy_malaria.migration.vector_migration.VectorMigration attribute) Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1) pre-erythrocytic

pre-erythrocytic vaccine (PEV) prevalence preview print_hashcodes() (in module emodpy_malaria.serialization.replace_genomes) provenance (emodpy_malaria.weather.weather_metadata.WeatherAttributes property)

R

RAINFALL (emodpy_malaria.weather.weather_variable.WeatherVariable attribute) read_json() (in module emodpy_malaria.migration.convert_json_to_bin) recovered REGIONAL_MIGRATION (emodpy_malaria.migration.convert_json_to_bin.MigrationTypes attribute) (emodpy_malaria.migration.convert_txt_to_bin.MigrationTypes attribute) (emodpy_malaria.migration.vector_migration.VectorMigration attribute) regression test RELATIVE_HUMIDITY (emodpy_malaria.weather.weather_variable.WeatherVariable attribute) release replace_genomes() (in module emodpy_malaria.serialization.replace_genomes) report (emodpy_malaria.weather.weather_request.WeatherRequest property) ReportDrugStatus (class in emodpy_malaria.reporters.builtin) reporter ReportEventCounter (class in emodpy_malaria.reporters.builtin) ReportFpgOutputForObservationalModel (class in emodpy_malaria.reporters.builtin) ReportHumanMigrationTracking (class in emodpy_malaria.reporters.builtin) ReportInfectionStatsMalaria (class in emodpy_malaria.reporters.builtin)

ReportInterventionPopAvg (class in emodpy_malaria.reporters.builtin) ReportMalariaFiltered (class in emodpy_malaria.reporters.builtin) ReportMalariaFilteredIntraHost (class in emodpy_malaria.reporters.builtin) ReportMicrosporidia (class in emodpy_malaria.reporters.builtin) ReportNodeDemographics (class in emodpy_malaria.reporters.builtin) ReportNodeDemographicsMalaria (class in emodpy_malaria.reporters.builtin) ReportNodeDemographicsMalariaGenetics (class in emodpy_malaria.reporters.builtin) ReportSimpleMalariaTransmission (class in emodpy_malaria.reporters.builtin) ReportSimulationStats (class in emodpy_malaria.reporters.builtin) ReportVectorGenetics (class in emodpy_malaria.reporters.builtin) ReportVectorMigration (class in emodpy_malaria.reporters.builtin) ReportVectorStats (class in emodpy_malaria.reporters.builtin) ReportVectorStatsMalariaGenetics (class in emodpy_malaria.reporters.builtin) reproductive number RequestReport (class in emodpy_malaria.weather.weather_request) required_metadata_defaults_dict() (emodpy_malaria.weather.weather_metadata.WeatherAttributes class method) routine immunization (RI)

S

SAME_FOR_BOTH_GENDERS (emodpy_malaria.migration.convert_csv_to_bin_vector_migration.GenderDataType attribute) (emodpy_malaria.migration.convert_json_to_bin.GenderDataType attribute) (emodpy_malaria.migration.vector_migration.VectorMigration attribute) save_json() (in module emodpy_malaria.weather.weather_utils) scenario schema schizont SEA_MIGRATION (emodpy_malaria.migration.convert_json_to_bin.MigrationTypes attribute) (emodpy_malaria.migration.convert_txt_to_bin.MigrationTypes attribute) SEIR model SEIRS model select_weather_files() (emodpy_malaria.weather.weather_set.WeatherSet class method) series_count (emodpy_malaria.weather.weather_metadata.WeatherMetadata property) series_len (emodpy_malaria.weather.weather_metadata.WeatherMetadata property) series_unique_count (emodpy_malaria.weather.weather_metadata.WeatherMetadata property) set_allele_roots() (emodpy_malaria.serialization.replace_genomes.Genome method) set_drug_param() (in module emodpy_malaria.malaria_config) set_max_larval_capacity() (in module emodpy_malaria.malaria_config) (in module emodpy_malaria.vector_config) set_parasite_genetics_params() (in module emodpy_malaria.malaria_config) set_risk_high() (emodpy_malaria.demographics.MalariaDemographics.MalariaDemographics method) set_risk_lowmedium() (emodpy_malaria.demographics.MalariaDemographics.MalariaDemographics method) set_species_param() (in module emodpy_malaria.malaria_config) (in module emodpy_malaria.vector_config) set_team_defaults() (in module emodpy_malaria.malaria_config) (in module emodpy_malaria.vector_config) set_team_drug_params() (in module emodpy_malaria.malaria_config) show_usage() (in module emodpy_malaria.migration.convert_txt_to_bin) SI model simulation simulation burn-in

simulation type SIR model SIRS model SIS model solvers spatial repellent spatial_resolution (emodpy_malaria.weather.weather_metadata.WeatherAttributes property) SpatialReportMalariaFiltered (class in emodpy_malaria.reporters.builtin) species_params() (in module emodpy_malaria.malaria_vector_species_params) sporogony sporozoite SqlReportMalaria (class in emodpy_malaria.reporters.builtin) SqlReportMalariaGenetics (class in emodpy_malaria.reporters.builtin) Standard Template Library (STL) state transition event STATE_ADULT (emodpy_malaria.reporters.builtin.VectorState attribute) STATE_EGG (emodpy_malaria.reporters.builtin.VectorState attribute) STATE_IMMATURE (emodpy_malaria.reporters.builtin.VectorState attribute) STATE_INFECTED (emodpy_malaria.reporters.builtin.VectorState attribute) STATE_INFECTIOUS (emodpy_malaria.reporters.builtin.VectorState attribute) STATE_LARVA (emodpy_malaria.reporters.builtin.VectorState attribute) STATE_MALE (emodpy_malaria.reporters.builtin.VectorState attribute) step_column (emodpy_malaria.weather.weather_data.DataFrameInfo property) stochastic stochastic die-out subpatent sugar-baited trap SummaryData (class in emodpy_malaria.migration.convert_json_to_bin) superinfection supplemental immunization activity (SIA) susceptible

T

test_replace_genomes() (in module emodpy_malaria.serialization.replace_genomes) time step to_csv() (emodpy_malaria.weather.weather_data.WeatherData method) (emodpy_malaria.weather.weather_set.WeatherSet method) (in module emodpy_malaria.migration.vector_migration) to_dataframe() (emodpy_malaria.weather.weather_data.WeatherData method) (emodpy_malaria.weather.weather_set.WeatherSet method) to_dict() (emodpy_malaria.weather.weather_data.WeatherData method) to_dtk_dict() (emodpy_malaria.serialization.replace_genomes.Genome method) to_dtk_map_entry() (emodpy_malaria.serialization.replace_genomes.Genome method)

to_file() (emodpy_malaria.migration.vector_migration.VectorMigration method) (emodpy_malaria.weather.weather_data.WeatherData method) (emodpy_malaria.weather.weather_metadata.WeatherMetadata method) to_files() (emodpy_malaria.weather.weather_set.WeatherSet method) Tool (emodpy_malaria.migration.vector_migration.VectorMigration property) tool (emodpy_malaria.weather.weather_metadata.WeatherAttributes property) total_value_count (emodpy_malaria.weather.weather_metadata.WeatherMetadata property) transmissibility (\beta) transmission-blocking vaccine (TBV) tutorial

U

update() (emodpy_malaria.weather.weather_metadata.WeatherAttributes method)

update_resolution (emodpy_malaria.weather.weather_metadata.WeatherAttributes property)

V

vaccine intervention types validate() (emodpy_malaria.weather.weather_data.WeatherData method) (emodpy_malaria.weather.weather_metadata.WeatherAttributes method) (emodpy_malaria.weather.weather_metadata.WeatherMetadata method) (emodpy_malaria.weather.weather_request.WeatherArgs method) (emodpy_malaria.weather.weather_set.WeatherSet method) validate_str_value() (in module emodpy_malaria.weather.weather_utils) validate_types() (emodpy_malaria.weather.weather_variable.WeatherVariable class method) value_column (emodpy_malaria.weather.weather_data.DataFrameInfo property) values() (emodpy_malaria.weather.weather_set.WeatherSet method) vector

vector model VECTOR_BOTH_GENDERS (emodpy_malaria.interventions.vector_surveillance.VectorGender attribute) VECTOR_FEMALE (emodpy_malaria.interventions.vector_surveillance.VectorGender attribute) VECTOR_MALE (emodpy_malaria.interventions.vector_surveillance.VectorGender attribute) VECTOR_MIGRATION_BY_GENETICS (emodpy_malaria.migration.convert_csv_to_bin_vector_migration.GenderDataType attribute) (emodpy_malaria.migration.convert_json_to_bin.GenderDataType attribute) VectorGender (class in emodpy_malaria.interventions.vector_surveillance) VectorHabitatReport (class in emodpy_malaria.reporters.builtin) vectorial capacity VectorMigration (class in emodpy_malaria.migration.vector_migration) VectorState (class in emodpy_malaria.reporters.builtin) virulence

W

WAIFW matrix weather_columns (emodpy_malaria.weather.weather_set.WeatherSet property) weather_to_csv() (in module emodpy_malaria.weather) weather_variables (emodpy_malaria.weather.weather_request.DataSource property) (emodpy_malaria.weather.weather_set.WeatherSet property) WeatherArgs (class in emodpy_malaria.weather.weather_request) WeatherAttributes (class in emodpy_malaria.weather.weather_metadata) WeatherData (class in emodpy_malaria.weather.weather_data) WeatherMetadata (class in emodpy_malaria.weather.weather_metadata) WeatherRequest (class in emodpy_malaria.weather.weather_request)

WeatherSet (class in emodpy_malaria.weather.weather_set) WeatherVariable (class in emodpy_malaria.weather.weather_variable) Weibull distribution Wolbachia working directory write_bin_file() (in module emodpy_malaria.migration.convert_csv_to_bin_vector_migration) (in module emodpy_malaria.migration.convert_json_to_bin) write_bin_file_gender() (in module emodpy_malaria.migration.convert_json_to_bin) write_metadata_file() (in module emodpy_malaria.migration.convert_csv_to_bin_vector_migration) (in module emodpy_malaria.migration.convert_json_to_bin) write_out_humans_data() (in module emodpy_malaria.serialization.serialization_support)

Y

ymd() (in module emodpy_malaria.weather.weather_utils)

Z

zero_human_infections() (in module emodpy_malaria.serialization.zero_infections) zero_infection_path() (in module emodpy_malaria.serialization.zero_infections)

zero_infections() (in module emodpy_malaria.serialization.zero_infections) zero_vector_infections() (in module emodpy_malaria.serialization.zero_infections)