emodpy_hiv.reporters.builtin module

emodpy_hiv.reporters.builtin.add_report_hiv_by_age_and_gender(task, start_year: float = 1900, end_year: float = 2200, collect_gender_data: bool = False, collect_age_bins_data: list[float] | None = None, collect_circumcision_data: bool = False, collect_hiv_data: bool = False, collect_hiv_stage_data: bool = False, collect_on_art_data: bool = False, collect_ip_data: list[str] | None = None, collect_intervention_data: list[str] | None = None, add_transmitters: bool = False, stratify_infected_by_cd4: bool = False, event_counter_list: list[str] | None = None, add_relationships: bool = False, add_concordant_relationships: bool = False)

The age- and gender-stratified HIV report (ReportHIVByAgeAndGender.csv) provides a detailed set of HIV-related statistics, with numerous ways to customize and stratify the output. The report format facilitates further analysis using a pivot table.

Some results, such as population size or number infected, are reported as single “snapshots” at the end of the reporting period. Other values, such as deaths or new infections, are aggregated for the entire reporting period. Further information on the output data types can be seen in the Output file data section: https://docs.idmod.org/projects/emod-hiv/en/latest/software-report-age-gender.html#output-file-data

Parameters:

• task – task to which to add the reporter

• start_year – The simulation time in years to start collecting data. Default is 1900.

• end_year – The simulation time in years to stop collecting data. Default is 2200.

• collect_gender_data – When True, the report will be stratified by gender.

• collect_age_bins_data – A list of bins (age in years) used to stratify the report by age. Each value defines the minimum value (inclusive) of that bin, while the next value defines the maximum value (exclusive) of the bin. The values cannot be equal and must be listed in ascending order. Leave the array empty to not stratify the report by age. The maximum number of age bins is 100.

• collect_circumcision_data – When True, the IsCircumcised column is included in the output report. The report data will be stratified by those who do or do not have the MaleCircumcision intervention, with IsCircumcised = 1 for those with the intervention. Note: setting this to True doubles the number of rows in the output report.

• collect_hiv_data – When True, the HasHIV column is included in the output report. The report data will be stratified by those who do or do not have HIV. HasHIV = 1 for those with HIV. Cannot be used with Report_HIV_ByAgeAndGender_Collect_HIV_Stage_Data. Note: setting this to 1 doubles the number of rows in the output report.

• collect_hiv_stage_data – When True, the HIV_Stage column is included in the output report. The report data will be stratified by HIV Infection Stage (NOT_INFECTED, ACUTE, LATENT, AIDS, ON_ART). Cannot be used with collect_hiv_data (Report_HIV_ByAgeAndGender_Collect_HIV_Data) or collect_on_art_data (Report_HIV_ByAgeAndGender_Collect_On_Art_Data.) Note: setting this to True x5 the number of rows in the output report.

• collect_on_art_data – When set to 1, the On_ART column is included in the output report. The report data will be stratified by those individuals who are on ART (1) and those who are not (0). Cannot be used with Report_HIV_ByAgeAndGender_Collect_HIV_Stage_Data. Note: setting this to 1 doubles the number of rows in the output report.

• collect_ip_data – A list of individual property (IP) keys used to stratify the report. A column will be added to the report for each IP listed and a row for each possible IP Key:Value pair. Specify the IP keys and values by adding an IndividualProperties parameter in your demographics. For information on IndividualProperties, see https://docs.idmod.org/projects/emod-hiv/en/latest/model-properties.html

• collect_intervention_data – A list of interventions used to stratify the report. This allows for reporting on a subset (or all) of the interventions that an individual has been on, of those listed in the Intervention_Name campaign parameter. Note: this can only be used with interventions that remain with an individual for a period of time, such as VMMC, vaccine/PrEP, or those with a delay state in the cascade of care. For a list of possible interventions, see https://docs.idmod.org/projects/emod-hiv/en/latest/parameter-campaign-individual-interventions.html

• add_transmitters – When True, the Transmitters column is included in the output report. It indicates the total number of the individuals in that row who transmitted HIV during this reporting period. This may not add up to the number of new infections in the reporting period if any of the new infections were due to the OutbreakIndividual intervention or maternal transmission.

• stratify_infected_by_cd4 – When True, the number of infected individuals will be segregated into four columns based on CD4 count (“Infected CD4 Under 200 (Not On ART)”, “Infected CD4 200 to 349 (Not On ART)”, “Infected CD4 350 to 499 (Not On ART)”, “Infected CD4 500 Plus (Not On ART)”) Note: this creates additional polling columns, but not more stratification rows.

• event_counter_list – A list of individual-level events to be used to stratify the report. A column will be added to the report for each event listed, showing the number of times the event occurred during the reporting for the people in the row. To be counted, the individual must qualify for the row stratification at the time the event occurred, not necessarily at the end of the reporting period (the individual themselves might end up being counted in a different row. See Built-In Event and Custom_Individual_Events lists for possible event values.

• add_relationships – When True, the report will contain data on the population currently in a relationship and ever in a relationship for each relationship type (TRANSITORY, INFORMAL, MARITAL, and COMMERCIAL), eight columns total. Additionally, columns containing a sum of individuals in two or more partnerships (Has Concurrent Partners) and a sum of the lifetime number of relationships (Lifetime Partners) will be included.

• add_concordant_relationships – When True, a Concordant column for each relationship type (TRANSITORY, INFORMAL, MARITAL, and COMMERCIAL) is included in the output report. These contain totals for each relationship of each type where both partners have the same HIV status.

Returns:

Nothing

emodpy_hiv.reporters.builtin.add_report_relationship_start(task, start_year: float = 1900, end_year: float = 2200, node_ids: list | None = None, max_age_years: float | None = None, min_age_years: float | None = None, include_hiv_disease_statistics: bool = False, include_other_relationship_statistics: bool = False, individual_properties: list[str] | None = None, must_have_ip_key_value: str = '', must_have_intervention: str = '')

The relationship formation report (RelationshipStart.csv) provides information about each relationship and its members, evaluated at the time of relationship formation. The report includes the relationship type, start time, scheduled end time, and detailed information about each participant: ID, gender, age, infection status, circumcision status for males, co-infections, number of relationships (active, recent, lifetime), and individual properties. The male in the relationship is indicated on the report as participant “A”, and the female as participant “B”.

For more information, please see: https://docs.idmod.org/projects/emod-hiv/en/latest/software-report-relationship-start.html

Parameters:

• task – task to which to add the reporter

• start_year – The simulation time in years to start collecting data. Default is 1900.

• end_year – The simulation time in years to stop collecting data. Default is 2200.

• node_ids – A list of nodes from which to collect data for the report. Leave the array empty None to collect data from all nodes.

• max_age_years – The age that of one of the partners must be less than or equal to for the relationship to be reported.

• min_age_years – The age that of one of the partners must be greater than or equal to for the relationship to be reported.

• include_hiv_disease_statistics – When True, the report will include information on CD4 count, viral load, disease stage, HIV positivity, and HIV testing results for each partner at the start of the relationship.

• include_other_relationship_statistics – When True, the report will include information on the number of active and lifetime relationships of each type (TRANSITORY, INFORMAL, MARITAL, and COMMERCIAL) for each partner in the relationship, as well as total relationships in the past six month and total lifetime relationships. Additionally, a bitmask column will indicate which types of concurrent relationships are allowed; these are configured using the Concurrency_Configuration parameter in the demographics, see: https://docs.idmod.org/projects/emod-hiv/en/latest/parameter-demographics.html#concurrency-configuration

• individual_properties – A list of strings individual property (IP) keys that will be included in the report as applicable to each partner at the start of the relationship. One column will be added to the report for each partner, for each key in the list. Specify the IP keys and values by adding an IndividualProperties parameter in your demographics. For information on IndividualProperties, see: https://docs.idmod.org/projects/emod-hiv/en/latest/model-properties.html

• must_have_ip_key_value – A string in format of “Key:Value”, denoting specific IndividualProperty key and value, that one of the partners must have for the relationship to be reported. Empty string is to not filter by IndividualProperties, include everyone. For information on IndividualProperties, see: https://docs.idmod.org/projects/emod-hiv/en/latest/model-properties.html

• must_have_intervention – The name of an individual-level intervention (Intervention_Name parameter in campaign) that the one of the partners must have in order for the relationship to be reported. Empty string is to not filter by presence of individual, include everyone. For more information, see https://docs.idmod.org/projects/emod-hiv/en/latest/parameter-campaign-individual-interventions.html

Returns:

Nothing

emodpy_hiv.reporters.builtin.add_report_relationship_consummated(task, start_year: float = 1900, end_year: float = 2200, node_ids: list | None = None, max_age_years: float | None = None, min_age_years: float | None = None, relationship_type: str | None = None, has_intervention_with_name: bool = False, must_have_intervention: str = '', individual_properties: list[str] | None = None, partners_with_ip_key_value: list[str] | None = None, must_have_ip_key_value: str = '')

The coital act report (RelationshipConsummated.csv) provides detailed information about each coital act that occurs during the simulation. The report includes unique identifiers for each coital act and relationship; the relationship type, number of acts, whether a condom was used, and whether transmission occurred; and detailed information about each participant, including age, gender, infection status, circumcision status, co-infection status, and treatment status. Each participant in a relationship is referred to as either participant “A” or participant “B”.

One row of data is returned per coital act, and results are ordered on a per-relationship basis. Note: if a person is engaged in coital acts in multiple relationships during a time step, the order of those acts is unknown, only in which relationship they occurred. Additionally, if a person gets infected during a time step, they cannot re-transmit that infection during the same time step. The report does record during which coital act transmission occurred.

If an uninfected person has coital acts with multiple infected partners during the same time step, all acts with the possibility of transmission are randomly ordered, so that the person has an equal chance of getting infected from any one of their partners. The probability of transmission from any one of these coital acts is still determined by the simulation parameters (number of acts, acquisition multipliers, etc.)

For more information, please see: https://docs.idmod.org/projects/emod-hiv/en/latest/software-report-relationship-consummated.html

Parameters:

• task – task to which to add the reporter

• start_year – The simulation time in years to start collecting data. Default is 1900.

• end_year – The simulation time in years to stop collecting data. Default is 2200.

• node_ids – A list of nodes from which to collect data for the report. Leave the array empty None to collect data from all nodes.

• max_age_years – The age that of one of the partners must be less than or equal to for the relationship to be reported.

• min_age_years – The age that of one of the partners must be greater than or equal to for the relationship to be reported.

• relationship_type – A string indicating the type of relationship the coital act has to occur in to be reported. Options are TRANSITORY, INFORMAL, MARITAL, and COMMERCIAL. Leave empty of None to include all relationship types.

• has_intervention_with_name – An array of intervention names where a column is added for each name. 1 if the person has the intervention, else 0.

• must_have_intervention – The name of an individual-level intervention (Intervention_Name parameter in campaign) that the one of the partners must have in order for the relationship to be reported. Empty string or None is to not filter by presence of individual, include everyone. For more information, see https://docs.idmod.org/projects/emod-hiv/en/latest/parameter-campaign-individual-interventions.html

• individual_properties – A list of strings individual property (IP) keys that will be included in the report as columns. Each person will have the value of that key in their row. You can specify the IP keys and values by adding an IndividualProperties parameter in your demographics. For information on IndividualProperties, see: https://docs.idmod.org/projects/emod-hiv/en/latest/model-properties.html

• partners_with_ip_key_value – A list of strings in format of “Key:Value”, denoting specific IndividualProperty key:value pair. For each IP Key:Value string in the list, two columns will be added - one for each partner indicating the number of their partners for whom that IP Key:Value applies. For information on IndividualProperties, see: https://docs.idmod.org/projects/emod-hiv/en/latest/model-properties.html

• must_have_ip_key_value – A string in format of “Key:Value”, denoting specific IndividualProperty key and value, that one of the partners must have for the relationship to be reported. Empty string or None is to not filter by IndividualProperties, include everyone. For information on IndividualProperties, see: https://docs.idmod.org/projects/emod-hiv/en/latest/model-properties.html

Returns:

Nothing

emodpy_hiv.reporters.builtin.add_report_relationship_end(task)

The relationship dissolution report (RelationshipEnd.csv) provides detailed information about each relationship and its members, evaluated at the time of relationship dissolution. The report includes the relationship type, start time, scheduled end time, actual end time (which may differ from the scheduled end time, for instance, due to the death of a partner), and information about each participant.

For more information, please see: https://docs.idmod.org/projects/emod-hiv/en/latest/software-report-relationship-end.html

Parameters:

task – task to which to add the reporter

Returns:

Nothing

emodpy_hiv.reporters.builtin.add_transmission_report(task)

The HIV relationship transmission report (TransmissionReport.csv) provides detailed information about each transmission event and relationship members, evaluated at the time of disease transmission within the relationship. It includes the time/date of transmission and information about the transmitter and recipient, including: age, gender, current and lifetime number of relationships, infection stage, circumcision status for males, co-infections, and disease-specific biomarkers, if applicable.

For more information, please see: https://docs.idmod.org/projects/emod-hiv/en/latest/software-report-transmission.html

Parameters:

task – task to which to add the reporter

Returns:

Nothing

emodpy_hiv.reporters.builtin.add_report_simulation_stats(task, manifest)

Adds ReportSimulationStats to collect data on the computational performance of the model (duration, memory, number of persisted interventions, etc.).

There are no special parameter that need to be configured to generate the report.

Parameters:

• task – task to which to add the reporter, if left as None, reporter is returned (used for unittests)

• manifest – schema path file

Returns:

if task is not set, returns the configured reporter, otherwise returns nothing

emodpy_hiv.reporters.builtin.add_report_event_counter(task, manifest, start_day: int = 0, end_day: int | None = None, node_ids: list | None = None, event_trigger_list: list | None = None, min_age_years: float = 0, max_age_years: float | None = None, must_have_ip_key_value: str = '', must_have_intervention: str = '', filename_suffix: str = '')

The event counter report (ReportEventCounter.json) is a JSON-formatted file that keeps track of how many of each individual-level event types occur during a time step. The report produced is similar to the InsetChart.json channel report, where there is one channel for each event defined in the configuration file (config.json). This report only counts events; a similar report, ReportEventRecorder, will provide information about the person at the time of the event.

Parameters:

• task – task to which to add the reporter, if left as None, reporter is returned (used for unittests)

• manifest – schema path file

• start_day – the day of the simulation to start collecting data

• end_day – the day of simulation to stop collecting data

• node_ids – list of nodes in which to count the events

• event_trigger_list – list of individual-level events which to count

• min_age_years – Minimum age in years of people to collect data on

• max_age_years – Maximum age in years of people to collect data on

• must_have_ip_key_value – a “Key:Value” pair that the individual must have in order to be included. Empty string means don’t look at IPs (individual properties)

• must_have_intervention – the name of the intervention that the person must have in order to be included. Empty string means don’t look at the interventions

• filename_suffix – augments the filename of the report. If multiple reports are being generated, this allows you to distinguish among the multiple reports

Returns:

if task is not set, returns the configured reporter, otherwise returns nothing

emodpy_hiv.reporters.builtin.add_report_node_demographics(task, manifest, age_bins: list[float] | None = None, ip_key_to_collect: str = '', stratify_by_gender: bool = True)

The node demographics report (ReportNodeDemographics.csv) is a CSV-formatted report that provides population information stratified by node. For each time step, the report will collect data on each node and age bin.

For more information: https://docs.idmod.org/projects/emod-hiv/en/latest/software-report-node-demographics.html

Parameters:

• task – task to which to add the reporter, if left as None, reporter is returned (used for unittests)

• manifest – schema path file

• age_bins – the age bins (in years) to aggregate within and report. An empty array does not stratify by age. You must sort your input data from low to high.

• ip_key_to_collect – The name of the Individual Properties Key by which to stratify the report. An empty string or None does not stratify by Individual Properties

• stratify_by_gender – if True, to stratify by gender. False to not stratify by gender.

Returns:

if task is not set, returns the configured reporter, otherwise returns nothing

emodpy_hiv.reporters.builtin.add_event_recorder(task, event_list: list[str] | None = None, only_include_events_in_list: bool = True, ips_to_record: list[str] | None = None, start_day: int = 0, end_day: int | None = None, node_ids: list | None = None, min_age_years: float = 0, max_age_years: float | None = None, must_have_ip_key_value: str = '', must_have_intervention: str = '', property_change_ip_to_record: str = '')

The health events and interventions report (ReportEventRecorder.csv) provides information on each individual’s demographics and health status at the time of an event. Additionally, it is possible to see the value of specific IndividualProperties, as assigned in the demographics file.

For more information: https://docs.idmod.org/projects/emod-malaria/en/latest/software-report-event-recorder.html

Parameters:

• task – task to which to add the reporter

• event_list – The list of individual-level events to include or exclude in the output report, based on how only_include_events_in_list is set.

• only_include_events_in_list – if True, only record events listed. if False, record ALL events EXCEPT for the ones listed.

• ips_to_record – A list of strings individual property (IP) keys that will be included in the report as applicable to each partner at the start of the relationship. One column will be added to the report for each partner, for each key in the list. Specify the IP keys and values by adding an IndividualProperties parameter in your demographics. For information on IndividualProperties, see: https://docs.idmod.org/projects/emod-hiv/en/latest/model-properties.html

• start_day – The day of the simulation to start collecting data

• end_day – The day of the simulation to stop collecting data.

• node_ids – Data will be collected for the nodes in this list, if None or [] - all nodes have data collected.

• min_age_years – Minimum age in years of people to collect data on

• max_age_years – Maximum age in years of people to collect data on

• must_have_ip_key_value – A “Key:Value” pair string that the individual must have in order to be included. Empty string means don’t look at IndividualProperties.

• must_have_intervention – The name of an individual-level intervention (Intervention_Name parameter in campaign) that the one of the partners must have in order for the relationship to be reported. Empty string or None is to not filter by presence of individual, include everyone. For more information, see https://docs.idmod.org/projects/emod-hiv/en/latest/parameter-campaign-individual-interventions.html

• property_change_ip_to_record – IndividualProperty key string for which recorder will add the PropertyChange event to the list of events that the report is listening to. However, it will only record the events where the property changed the value of this given key. For information on IndividualProperties, see: https://docs.idmod.org/projects/emod-hiv/en/latest/model-properties.html

Returns:

Nothing

emodpy_hiv.reporters.builtin.add_report_hiv_art(task)

The ART initiation and discontinuation report (ReportHIVART.csv) provides information on individuals at time of ART initiation and discontinuation, including ID, age, gender, and CD4 count at ART initiation.

For more information: https://docs.idmod.org/projects/emod-hiv/en/latest/software-report-hivart.html

Parameters:

task – task to which to add the reporter

Returns:

Nothing

emodpy_hiv.reporters.builtin.add_report_hiv_infection(task, start_year: float = 1900, end_year: float = 2200)

The HIV disease progression report (ReportHIVInfection.csv) provides information on each individual’s disease state at each time step, including age, gender, CD4 count, survival prognosis, ART status, and factors impacting transmission and acquisition.

For more information: https://docs.idmod.org/projects/emod-hiv/en/latest/software-report-hivinfection.html

Parameters:

• task – task to which to add the reporter

• start_year – The simulation time in years to start collecting data. Default is 1900.

• end_year – The simulation time in years to stop collecting data. Default is 2200.

Returns:

Nothing

emodpy_hiv.reporters.builtin.add_report_hiv_mortality(task)

The HIV mortality report (HIVMortality.csv) provides information about individuals at the time of their death, including disease status, CD4 count, medical history, and relationship history.

For more information: https://docs.idmod.org/projects/emod-hiv/en/latest/software-report-hivmort.html

Parameters:

task – task to which to add the reporter

Returns:

Nothing

emodpy_hiv.reporters.builtin.add_report_relationship_migration_tracking(task, manifest, start_year: float = 1900, end_year: float = 2200, node_ids: list[int] | None = None, min_age_years: float = 0, max_age_years: float | None = None, must_have_ip_key_value: str = '', must_have_intervention: str = '', filename_suffix: str = '')

The relationship migration tracking report (ReportRelationshipMigrationTracking.csv) provides information about the relationships a person has when they are migrating. It will give information when they are leaving and entering a node. When leaving a node, the information will be about the status of the relationships just before they leave. When entering the new node, the information will be about the relationships that have been updated. For example, a person could leave with a relationship paused, find their partner in the new node, and get their relationship back to normal. This helps to know about how the status of the relationships have changed—migrated, paused, or terminated.

The person initiating a migration event will first have their relationships listed in the state before migrating starts. If a partner is asked to migrate with them, then that partner’s relationships will also be listed. When the people are immigrating into the new node, the list of relationships that are continuing in the new node will be listed. Any migrated partner should only have the relationship with the partner initiating migration. Their other relationships will have been terminated.

For more information: https://docs.idmod.org/projects/emod-hiv/en/latest/software-report-relationship-migration-tracking.html

Parameters:

• task – task to which to add the reporter, if left as None, reporter is returned (used for unittests)

• manifest – schema path file

• start_year – The simulation time in years to start collecting data. Default is 1900.

• end_year – The simulation time in years to stop collecting data. Default is 2200.

• node_ids – A list of nodes from which to collect data for the report. Leave the array empty None to collect data from all nodes.

• max_age_years – The age that of one of the partners must be less than or equal to for the relationship to be reported.

• min_age_years – The age that of one of the partners must be greater than or equal to for the relationship to be reported.

• must_have_intervention – The name of an individual-level intervention (Intervention_Name parameter in campaign) that the one of the partners must have in order for the relationship to be reported. Empty string or None is to not filter by presence of individual, include everyone. For more information, see https://docs.idmod.org/projects/emod-hiv/en/latest/parameter-campaign-individual-interventions.html

• must_have_ip_key_value – A string in format of “Key:Value”, denoting specific IndividualProperty key and value, that one of the partners must have for the relationship to be reported. Empty string or None is to not filter by IndividualProperties, include everyone. For information on IndividualProperties, see: https://docs.idmod.org/projects/emod-hiv/en/latest/model-properties.html

• filename_suffix – Augments the filename of the report. This allows you to generate multiple reports by distinguishing among them.

Returns:

if task is not set, returns the configured reporter, otherwise returns nothing

emodpy_hiv.reporters.builtin.add_human_migration_tracking(task, manifest)

The human migration tracking report (ReportHumanMigrationTracking.csv) is a CSV-formatted report that provides details about human travel during simulations. The finished report will provide one line for each surviving individual that migrates during the simulation. The simulation must have migration enabled.

For more information: https://docs.idmod.org/projects/emod-hiv/en/latest/software-report-human-migration.html

Parameters:

• task – task to which to add the reporter, if left as None, reporter is returned (used for unittests)

• manifest – schema path file

Returns:

if task is not set, returns the configured reporter, otherwise returns nothing

class emodpy_hiv.reporters.builtin.ReportHumanMigrationTracking(class_name: str | None = None, parameters: dict = <factory>, Enabled: bool = True, Pretty_Format: bool = True)

Bases: BuiltInReporter

The human migration tracking report is a CSV-formatted report (ReportHumanMigrationTracking.csv) that provides details about human travel during simulations. The report provides one line for each surviving individual who migrates during the simulation.

config(config_builder, manifest)

parameters: dict

class emodpy_hiv.reporters.builtin.ReportRelationshipMigrationTracking(class_name: str | None = None, parameters: dict = <factory>, Enabled: bool = True, Pretty_Format: bool = True)

Bases: BuiltInReporter

See add_report_relationship_migration_tracking for more information.

config(config_builder, manifest)

parameters: dict

class emodpy_hiv.reporters.builtin.ReportEventCounter(class_name: str | None = None, parameters: dict = <factory>, Enabled: bool = True, Pretty_Format: bool = True)

Bases: BuiltInReporter

The event counter report is a JSON-formatted file (ReportEventCounter.json) that keeps track of how many of each event types occurs during a time step. The report produced is similar to the InsetChart.json channel report, where there is one channel for each event defined in the configuration file (config.json).

config(config_builder, manifest)

parameters: dict

class emodpy_hiv.reporters.builtin.ReportSimulationStats(class_name: str | None = None, parameters: dict = <factory>, Enabled: bool = True, Pretty_Format: bool = True)

Bases: BuiltInReporter

Adds ReportSimulationStats to collect data on the computational performance of the model (duration, memory, number of persisted interventions, etc).

config(config_builder, manifest)

parameters: dict

class emodpy_hiv.reporters.builtin.ReportNodeDemographics(class_name: str | None = None, parameters: dict = <factory>, Enabled: bool = True, Pretty_Format: bool = True)

Bases: BuiltInReporter

The node demographics report is a CSV-formatted report (ReportNodeDemographics.csv) that provides population information stratified by node. For each time step, the report collects data on each node and age bin.

config(config_builder, manifest)

parameters: dict