emodpy_malaria.reporters.builtin module¶

emodpy_malaria.reporters.builtin.add_report_vector_genetics(task, manifest, start_day: int = 0, duration_days: int = 365000, nodes: list = None, species: str = None, gender: str = 'VECTOR_FEMALE', include_vector_state: int = 1, stratify_by: str = 'GENOME', combine_similar_genomes: int = 0, specific_genome_combinations_for_stratification: list = None, allele_combinations_for_stratification: list = None, alleles_for_stratification: list = None, report_description: str = '')¶

Adds ReportVectorGenetics to the simulation. See class definition for description of 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
start_day – the day of the simulation to start reporting data
duration_days – number of days over which to report data
nodes – the list of nodes in which to collect data, empty or None means all nodes
species – the species to include information on
gender – gender of species to include information on. Default: “VECTOR_FEMALE”, other options: “VECTOR_MALE”, “VECTOR_BOTH_GENDERS”
include_vector_state – if 1(true), adds the columns for vectors in the different states (i.e Eggs, Larva, etc)
stratify_by – the way to stratify data. Default: “GENOME”, other options: “SPECIFIC_GENOME”, “ALLELE”, “ALLELE_FREQ”
combine_similar_genomes –
if 1(true), genomes are combined if for each locus (ignoring gender) the set of allele of the two genomes are the same (i.e. 1-0 is similar to 0-1). Depends on: “GENOME”, “SPECIFIC_GENOME” specific_genome_combinations_for_stratification: if stratifying by “SPECIFIC_GENOME”, then use these genomes to stratify by. Example:
```
[{"Allele_Combination": [[ "a0",  "*" ], [ "b1", "b0" ]]},
{"Allele_Combination": [[ "a1", "a0" ], [ "b0",  "*" ]]}]
```
allele_combinations_for_stratification –
if stratifying by “ALLELE”, then also add these allele name combos to the stratification, Example:
```
[[ "a0", "b0" ], [ "a1", "b1" ]]
```
alleles_for_stratification –
For example:
```
[ "a0", "a1", "b0", "b1" ]
```
report_description – adds the description to the filename of the report to differentiate it from others

Returns

Nothing

emodpy_malaria.reporters.builtin.add_report_vector_stats(task, manifest, species_list: list = None, stratify_by_species: int = 0, include_wolbachia: int = 0, include_gestation: int = 0)¶

Adds ReportVectorStats report to the simulation. See class definition for description of the report. :param task: task to which to add the reporter, if left as None, reporter is returned (used for unittests) :param manifest: schema path file :param species_list: a list of species to include information on :param stratify_by_species: if 1(true), data will break out each the species for each node :param include_wolbachia: if 1(true), add a column for each type of Wolbachia :param include_gestation: if 1(true), adds columns for feeding and gestation

Returns: Nothing

emodpy_malaria.reporters.builtin.add_malaria_summary_report(task, manifest, start_day: int = 0, duration_days: int = 365000, nodes: list = None, reporting_interval: float = 1000000, age_bins: list = None, individual_property_filter: str = '', infectiousness_bins: list = None, max_number_reports: int = 100, parasitemia_bins: list = None, pretty_format: int = 0, report_description: str = '')¶

Adds MalariaSummaryReport to the simulation. See class definition for description of 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
start_day – the day of the simulation to starts collecting data for the report
duration_days – The duration of simulation days over which to report events. The report will stop collecting data when the simulation day is greater than Start_Day + Duration_Days.
nodes – a list of nodes from which to collect data for the report
reporting_interval – Defines the cadence of the report by specifying how many time steps to collect data before writing to the file
age_bins – The max age in years per bin, listed in ascending order. Use a large value for the last bin, to collect all remaining individuals
individual_property_filter – the individual ‘property:value’ to filter on. The default of an empty string means the report is not filtered. Example: “Risk:HIGH”
infectiousness_bins – infectiousness Bins to aggregate within for the report
max_number_reports – the maximum number of report output files that will be produced for a given simulation
parasitemia_bins – Parasitemia bins on which to aggregate. A value <= 0 in the first bin indicates that uninfected individuals are added to this bin. You must sort your input data from low to high.
pretty_format – if 1(true) sets pretty JSON formatting, which includes carriage returns, line feeds, and spaces for easier readability. The default, 0 (false), saves space where everything is on one line.
report_description – adds the description to the filename of the report to differentiate it from others

Returns

Nothing

emodpy_malaria.reporters.builtin.add_malaria_patient_json_report(task, manifest)¶

Adds MalariaPatientJSONReport report to the simulation. See class definition for description of the report. You do not need to configure any data parameters to generate this report. :param task: task to which to add the reporter, if left as None, reporter is returned (used for unittests) :param manifest: schema path file

Returns: Nothing

emodpy_malaria.reporters.builtin.add_malaria_transmission_report(task, manifest, start_day: int = 0, duration_days: int = 365000, nodes: list = None, pretty_format: int = 0, report_description: str = '')¶

Adds ReportSimpleMalariaTransmissionJSON report to the simulation. See class definition for description of 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
start_day – the day to start collecting data for the report.
duration_days – The duration of simulation days over which to report events. The report will stop collecting data when the simulation day is greater than Start_Day + Duration_Days
nodes – list of nodes for which to collect data for the report
pretty_format – if 1(true) sets pretty JSON formatting, which includes carriage returns, line feeds, and spaces for easier readability. The default, 0 (false), saves space where everything is on one line.
report_description – adds the description to the filename of the report to differentiate it from others

Returns

Nothing

emodpy_malaria.reporters.builtin.add_report_malaria_filtered(task, manifest, start_day: int = 0, end_day: int = 365000, nodes: list = None, report_filename: str = 'ReportMalariaFiltered.json', min_age_years: float = 0, max_age_years: float = 125, has_interventions: list = None, include_30day_avg_infection_duration: bool = True)¶

Adds ReportMalariaFiltered report to the simulation. See class definition for description of 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
start_day – the day of the simulation to start collecting data
end_day – the day of simulation to stop collecting data
nodes – list of nodes for which to collect the data, None or [] collects all the nodes
report_filename – name of the file to be written
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
has_interventions – A channel is added to the report for each InterventionName provided. The channel name will be Has_<InterventionName> and will be the fraction of the population that has that intervention. The Intervention_Name in the campaign should be the values in this parameter
include_30day_avg_infection_duration – If set to True (1), the 30-Day Avg Infection channel is included in the report

Returns

Nothing

emodpy_malaria.reporters.builtin.add_spatial_report_malaria_filtered(task, manifest, start_day: int = 0, end_day: int = 365000, reporting_interval: int = 365000, nodes: list = None, report_filename: str = 'SpatialReportMalariaFiltered.json', spatial_output_channels: list = None)¶

Adds SpatialReportMalariaFiltered report to the simulation. See class definition for description of 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
start_day – the day of the simulation to start collecting data
end_day – the day of simulation to stop collecting data
reporting_interval – defines the cadence of the report by specifying how many time steps to collect data before writing to the file.
nodes – list of nodes for which to collect the data
report_filename – name of the file to be written
spatial_output_channels – list of names of channels you want to have output for. Available channels are: “Adult_Vectors”, “Air_Temperature”, “Births”, “Blood_Smear_Gametocyte_Prevalence”, “Blood_Smear_Parasite_Prevalence”, “Campaign_Cost”, “Daily_Bites_Per_Human”, “Daily_EIR”, “Disease_Deaths”, “Fever_Prevalence”, “Human_Infectious_Reservoir”, “Infected”, “Infectious_Vectors”, “Land_Temperature”, “Mean_Parasitemia”, “New_Clinical_Cases”, “New_Infections”, “New_Reported_Infections”, “New_Severe_Cases”, “PCR_Gametocyte_Prevalence”, “PCR_Parasite_Prevalence”, “PfHRP2_Prevalence”, “Population”, “Prevalence”, “Rainfall”, “Relative_Humidity”, “True_Prevalence” Defaults: [“Blood_Smear_Parasite_Prevalence”, “New_Clinical_Cases”, “Population”]

Returns

Nothing

emodpy_malaria.reporters.builtin.add_report_event_counter(task, manifest, start_day: int = 0, duration_days: int = 365000, event_trigger_list: list = None, nodes: list = None, report_description: str = '')¶

Adds ReportEventCounter report to the simulation. See class definition for description of the report. :param task: task to which to add the reporter, if left as None, reporter is returned (used for unittests) :param manifest: schema path file :param start_day: the day of the simulation to start counting events :param duration_days: number of days for which to count events :param event_trigger_list: list of events which to count :param nodes: list of nodes in which to count the events :param report_description: used by reports and custom reports. Augments the filename of the report.

Returns: Nothing

emodpy_malaria.reporters.builtin.add_malaria_sql_report(task, manifest, start_day: int = 0, end_day: int = 365000, include_infection_table: int = 1, include_health_table: int = 1, include_drug_table: int = 0)¶

Adds MalariaSqlReport report to the simulation. See class definition for description of 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
start_day – the day of the simulation to start collecting data
end_day – the day of the simulation to stop collecting data
include_infection_table – if 1(true), include the table that provides data at each time step for each active infection
include_health_table – if 1(true), include the table that provides data at each time step for a person’s health
include_drug_status – if 1(true), include the table that provides data at each time step for each drug used

Returns

Nothing

emodpy_malaria.reporters.builtin.add_vector_habitat_report(task, manifest)¶

Adds VectorHabitatReport report to the simulation. See class definition for description of the report. You do not need to configure any data parameters to generate this 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

Nothing

emodpy_malaria.reporters.builtin.add_malaria_immunity_report(task, manifest, start_day: int = 0, duration_days: int = 365000, reporting_interval: int = 365000, max_number_reports: int = 365000, nodes: list = None, age_bins: list = None, pretty_format: int = 0, report_description: str = '')¶

Adds MalariaImmunityReport report to the simulation. See class definition for description of 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
start_day – the day of the simulation to start collecting data
duration_days – number of days over which to report data
reporting_interval – defines the cadence of the report by specifying how many time steps to collect data before writing to the file.
max_number_reports – the maximum number of report output files that will be produced for a given simulation
nodes – list of nodes for which to collect data
age_bins – The max age in years per bin, listed in ascending order. Use a large value for the last bin, to collect all remaining individuals
pretty_format – if 1(true) sets pretty JSON formatting, which includes carriage returns, line feeds, and spaces for easier readability. The default, 0 (false), saves space where everything is on one line.
report_description – adds the description to the filename of the report to differentiate it from others

Returns

Nothing

emodpy_malaria.reporters.builtin.add_malaria_survey_analyzer(task, manifest, start_day: int = 0, duration_days: int = 365000, event_trigger_list: list = None, reporting_interval: float = 1000000.0, max_number_reports: int = 365000, nodes: list = None, individual_property_to_collect: str = '', pretty_format: int = 0, report_description: str = '')¶

Adds MalariaSurveyJSONAnalyzer report to the simulation. See class definition for description of 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
start_day – the day of the simulation to start collecting data
duration_days – number of days over which to report data
reporting_interval – defines the cadence of the report by specifying how many time steps to collect data before writing to the file
event_trigger_list – list of individual events to include into the report
max_number_reports – the maximum number of report output files that will be produced for a given simulation
nodes – list of nodes for which to collect data
individual_property_to_collect – name of the Individual Property Key whose value to collect. Empty string means collect values for all Individual Properties
pretty_format – if 1(true) sets pretty JSON formatting, which includes carriage returns, line feeds, and spaces for easier readability. The default, 0 (false), saves space where everything is on one line
report_description – adds the description to the filename of the report to differentiate it from others

Returns:

emodpy_malaria.reporters.builtin.add_drug_status_report(task, manifest, start_day: int = 0, end_day: int = 365000)¶

Adds ReportDrugStatus report to the simulation. See class definition for description of 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
start_day – the day of the simulation to start collecting data
end_day – the day of the simulation to stop collecting data

Returns

Nothing

emodpy_malaria.reporters.builtin.add_human_migration_tracking(task, manifest)¶

Adds ReportHumanMigrationTracking report to the simulation. There are no special parameter that need to be configured to generate the report. However, the simulation must have migration enabled.

Parameters

task – task to which to add the reporter, if left as None, reporter is returned (used for unittests)
manifest – schema path file

Returns

Nothing

emodpy_malaria.reporters.builtin.add_report_node_demographics(task, manifest, age_bins: list = None, individual_property_to_collect: str = '', stratify_by_gender: int = 1)¶

Adds ReportNodeDemographics report to the simulation. See class definition for description of 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
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.
individual_property_to_collect – The name of theIndividualProperties key by which to stratify the report. An empty string does not stratify by Individual Properties
stratify_by_gender – if 1(true), to stratify by gender. Set to false (0) to not stratify by gender.

Returns

Nothing

emodpy_malaria.reporters.builtin.add_report_node_demographics_malaria(task, manifest, age_bins: list = None, individual_property_to_collect: str = '', stratify_by_gender: int = 1)¶

Adds ReportNodeDemographicsMalaria report to the simulation. See class definition for description of 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
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.
individual_property_to_collect – The name of theIndividualProperties key by which to stratify the report. An empty string does not stratify by Individual Properties
stratify_by_gender – if 1(true), to stratify by gender. Set to false (0) to not stratify by gender.

Returns

Nothing

emodpy_malaria.reporters.builtin.add_report_node_demographics_malaria_genetics(task, manifest, barcodes: list = None, drug_resistant_strings: list = None, drug_resistant_statistic_type: str = 'NUM_PEOPLE_WITH_RESISTANT_INFECTION', age_bins: list = None, individual_property_to_collect: str = '', stratify_by_gender: int = 1)¶

Adds ReportNodeDemographicsMalariaGenetics report to the simulation. See class definition for description of 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
barcodes – a list of barcode strings. The report contains the number of human infections with each barcode. Use ‘*’ for a wild card at a loci to include all values at that loci. For example, “A*T” includes AAT, ACT, AGT, and ATT. The report contains a BarcodeOther column for barcodes that are not defined. Note: There is no validation that the barcode strings are valid barcodes for the scenario.
drug_resistant_strings – a list of strings representing the set of drug resistant markers. A column will be created with the number of humans infetions with that barcode. One can use ‘*’ for a wild card. A ‘BarcodeOther’ column will be created for barcodes not define
drug_resistant_statistic_type – indicates the statistic in the Drug Resistant columns: NUM_PEOPLE_WITH_RESISTANT_INFECTION = A person is counted if they have one infection with that drug resistant marker; NUM_INFECTIONS = The total number of infections with that marker.
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.
individual_property_to_collect – The name of theIndividualProperties key by which to stratify the report. An empty string does not stratify by Individual Properties
stratify_by_gender – if 1(true), to stratify by gender. Set to false (0) to not stratify by gender.

Returns

Nothing

emodpy_malaria.reporters.builtin.add_report_vector_migration(task, manifest, start_day: int = 0, end_day: int = 365000)¶

Adds ReportVectorMigration report to the simulation. See class definition for description of 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
start_day – the day of the simulation to start collecting data
end_day – the day of the simulation to stop collecting data

Returns

Nothing

emodpy_malaria.reporters.builtin.add_report_vector_stats_malaria_genetics(task, manifest, species_list: list = None, stratify_by_species: int = 0, include_wolbachia: int = 0, include_gestation: int = 0, barcodes: list = None)¶

Adds ReportVectorStatsMalariaGenetics report to the simulation. See class definition for description of 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
species_list – a list of species to include information on
stratify_by_species – if 1(true), data will break out each the species for each node
include_wolbachia – if 1(true), add a column for each type of Wolbachia
include_gestation – if 1(true), adds columns for feeding and gestation
barcodes – a list of barcode strings. The report contains the number of human infections with each barcode. Use ‘*’ for a wild card at a loci to include all values at that loci. For example, “A*T” includes AAT, ACT, AGT, and ATT. The report contains a BarcodeOther column for barcodes that are not defined. Note: There is no validation that the barcode strings are valid barcodes for the scenario.

Returns

Nothing

emodpy_malaria.reporters.builtin.add_event_recorder(task, event_list, only_include_events_in_list=True, ips_to_record=None)¶

Adds ReportEventRecorder report to the simulation. See class definition for description of the report.

Parameters

task – task to which to add the reporter
event_list – a list of events to record or exclude, depending on value of only_include_events_in_list
only_include_events_in_list – if True, only record events listed. if False, record ALL events EXCEPT for the ones listed
ips_to_record – list of individual properties to include in report

Returns

Nothing

emodpy_malaria.reporters.builtin.add_report_intervention_pop_avg(task, manifest, start_day: int = 0, duration_days: int = 36500000, report_description: str = '', nodes: list = None)¶

Adds ReportInterventionPopAvg reporter. See class definition for description of 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
start_day – The day of the simulation to start collecting data
duration_days – The number of days over which to collect report data
report_description – Augments the filename of the report. If multiple CSV reports are being generated, this allows you to distinguish among the multiple reports
nodes – List of nodes for which to collect data

Returns

Nothing

class emodpy_malaria.reporters.builtin.ReportVectorGenetics(class_name: str = None, parameters: dict = <factory>, Enabled: bool = True, Pretty_Format: bool = True)¶

Bases: emodpy.reporters.base.BuiltInReporter

The vector genetics report is a CSV-formatted report (ReportVectorGenetics.csv) that collects information on how many vectors of each genome/allele combination exist at each time, node, and vector state. Information can only be collected on one species per report.

config(config_builder, manifest)¶

parameters: dict¶

class emodpy_malaria.reporters.builtin.ReportVectorStats(class_name: str = None, parameters: dict = <factory>, Enabled: bool = True, Pretty_Format: bool = True)¶

Bases: emodpy.reporters.base.BuiltInReporter

The vector statistics report is a CSV-formatted report (ReportVectorStats.csv) that provides detailed life-cycle data on the vectors in the simulation. The report is stratified by time, node ID, and (optionally) species.

config(config_builder, manifest)¶

parameters: dict¶

class emodpy_malaria.reporters.builtin.MalariaSummaryReport(class_name: str = None, parameters: dict = <factory>, Enabled: bool = True, Pretty_Format: bool = True)¶

Bases: emodpy.reporters.base.BuiltInReporter

The population-level malaria summary report is a JSON-formatted report (MalariaSummaryReport.json) that provides a summary of malaria data across the population. The data are grouped into different bins such as age, parasitemia, and infectiousness.

config(config_builder, manifest)¶

parameters: dict¶

class emodpy_malaria.reporters.builtin.MalariaPatientJSONReport(class_name: str = None, parameters: dict = <factory>, Enabled: bool = True, Pretty_Format: bool = True)¶

Bases: emodpy.reporters.base.BuiltInReporter

The malaria patient data report is a JSON-formatted report (MalariaPatientReport.json) that provides medical data for each individual on each day of the simulation. For example, for a specified number of time steps, each “patient” has information collected on the temperature of their fever, their parasite counts, treatments they received, and other relevant data.

config(config_builder, manifest)¶

parameters: dict¶

class emodpy_malaria.reporters.builtin.ReportSimpleMalariaTransmissionJSON(class_name: str = None, parameters: dict = <factory>, Enabled: bool = True, Pretty_Format: bool = True)¶

Bases: emodpy.reporters.base.BuiltInReporter

The simple malaria transmission report (ReportSimpleMalariaTransmissionJSON.json) is a JSON-formatted report that provides data on malaria transmission, by tracking who transmitted malaria to whom. The report can only be used when the simulation setup parameter Malaria_Model is set to MALARIA_MECHANISTIC_MODEL_WITH_CO_TRANSMISSION. This report is typically used as input to the GenEpi model.

config(config_builder, manifest)¶

parameters: dict¶

class emodpy_malaria.reporters.builtin.ReportMalariaFiltered(class_name: str = None, parameters: dict = <factory>, Enabled: bool = True, Pretty_Format: bool = True)¶

Bases: emodpy.reporters.base.BuiltInReporter

The malaria filtered report (ReportMalariaFiltered.json) is the same as the default InsetChart report, but provides filtering options to enable the user to select the data to be displayed for each time step or for each node. See InsetChart for more information about InsetChart.json.

config(config_builder, manifest)¶

parameters: dict¶

class emodpy_malaria.reporters.builtin.SpatialReportMalariaFiltered(class_name: str = None, parameters: dict = <factory>, Enabled: bool = True, Pretty_Format: bool = True)¶

Bases: emodpy.reporters.base.BuiltInReporter

The filtered malaria spatial report (SpatialReportMalariaFiltered.bin) provides spatial information on malaria simulations and allows for filtering the data and collection over different intervals. This report is similar to the Spatial output report but allows for data collection and filtering over different intervals using the Start_Day and a Reporting_Interval parameters

config(config_builder, manifest)¶

parameters: dict¶

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

Bases: emodpy.reporters.base.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_malaria.reporters.builtin.MalariaSqlReport(class_name: str = None, parameters: dict = <factory>, Enabled: bool = True, Pretty_Format: bool = True)¶

Bases: emodpy.reporters.base.BuiltInReporter

The MalariaSQL report outputs epidemiological and transmission data. Because of the quantity and complexity of the data, the report output is a multi-table SQLite relational database (see https://sqlitebrowser.org/). Use the configuration parameters to manage the size of the database.

config(config_builder, manifest)¶

parameters: dict¶

class emodpy_malaria.reporters.builtin.VectorHabitatReport(class_name: str = None, parameters: dict = <factory>, Enabled: bool = True, Pretty_Format: bool = True)¶

Bases: emodpy.reporters.base.BuiltInReporter

The vector habitat report is a JSON-formatted file (VectorHabitatReport.json) containing habitat data for each vector species included in the simulation. It focuses on statistics relevant to mosquito developmental stages (e.g. eggs and larvae), such as egg capacity and larval crowding.

config(config_builder, manifest)¶

parameters: dict¶

class emodpy_malaria.reporters.builtin.MalariaImmunityReport(class_name: str = None, parameters: dict = <factory>, Enabled: bool = True, Pretty_Format: bool = True)¶

Bases: emodpy.reporters.base.BuiltInReporter

The malaria immunity report is a JSON-formatted file (MalariaImmunityReport.json) that provides statistics for several antibody types for specified age bins over a specified reporting duration. Specifically, the report tracks the average and standard deviation in the fraction of observed antibodies for merozoite surface protein ( MSP), Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1), and non-specific (and less immunogenic) minor surface epitopes. The total possible is determined by parameters Falciparum_MSP_Variants, Falciparum_PfEMP1_Variants, and Falciparum_Nonspecific_Types. The greater the fraction, the more antibodies the individual has against possible new infections. The smaller the fraction, the more naïve the individual’s immune system is to malaria.

config(config_builder, manifest)¶

parameters: dict¶

class emodpy_malaria.reporters.builtin.MalariaSurveyJSONAnalyzer(class_name: str = None, parameters: dict = <factory>, Enabled: bool = True, Pretty_Format: bool = True)¶

Bases: emodpy.reporters.base.BuiltInReporter

config(config_builder, manifest)¶

parameters: dict¶

class emodpy_malaria.reporters.builtin.ReportDrugStatus(class_name: str = None, parameters: dict = <factory>, Enabled: bool = True, Pretty_Format: bool = True)¶

Bases: emodpy.reporters.base.BuiltInReporter

The drug status report provides status information on the drugs that an individual has taken or is waiting to take. Because the report provides information for each drug, for each individual, and for each time step, you may want to use the Start_Day and End_Day parameters to limit the size the output file.

config(config_builder, manifest)¶

parameters: dict¶

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

Bases: emodpy.reporters.base.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_malaria.reporters.builtin.ReportNodeDemographics(class_name: str = None, parameters: dict = <factory>, Enabled: bool = True, Pretty_Format: bool = True)¶

Bases: emodpy.reporters.base.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¶

class emodpy_malaria.reporters.builtin.ReportNodeDemographicsMalaria(class_name: str = None, parameters: dict = <factory>, Enabled: bool = True, Pretty_Format: bool = True)¶

Bases: emodpy.reporters.base.BuiltInReporter

This report extends the data collected in the ReportNodeDemographics by adding data about the number of infections with specific barcodes. The malaria node demographics genetics report does not include columns for Genome_Markers because this report assumes that the simulation setup parameter Malaria_Model is set to MALARIA_MECHANISTIC_MODEL_WITH_PARASITE_GENETICS.

Note: If you need detailed data on the infections with different barcodes, use the MalariaSqlReport. That report contains data on all barcodes, without specifying what they are.

config(config_builder, manifest)¶

parameters: dict¶

class emodpy_malaria.reporters.builtin.ReportNodeDemographicsMalariaGenetics(class_name: str = None, parameters: dict = <factory>, Enabled: bool = True, Pretty_Format: bool = True)¶

Bases: emodpy.reporters.base.BuiltInReporter

This report extends the data collected in the ReportNodeDemographics by adding data about the number of infections with specific barcodes. The malaria node demographics genetics report does not include columns for Genome_Markers because this report assumes that the simulation setup parameter Malaria_Model is set to MALARIA_MECHANISTIC_MODEL_WITH_PARASITE_GENETICS.

Note: If you need detailed data on the infections with different barcodes, use the MalariaSqlReport. That report contains data on all barcodes, without specifying what they are.

config(config_builder, manifest)¶

parameters: dict¶

class emodpy_malaria.reporters.builtin.ReportVectorMigration(class_name: str = None, parameters: dict = <factory>, Enabled: bool = True, Pretty_Format: bool = True)¶

Bases: emodpy.reporters.base.BuiltInReporter

This report provides detailed information on where and when vectors are migrating. Because there can be one line for each migrating vector, you may want to use the Start_Day and End_Day parameters to limit the size the output file.

config(config_builder, manifest)¶

parameters: dict¶

class emodpy_malaria.reporters.builtin.ReportVectorStatsMalariaGenetics(class_name: str = None, parameters: dict = <factory>, Enabled: bool = True, Pretty_Format: bool = True)¶

Bases: emodpy.reporters.base.BuiltInReporter

This report extends the data collected in the ReportVectorStats by adding data about the number of infections with specific barcodes. The malaria node demographics genetics report does not include columns for Genome_Markers because this report assumes that the simulation setup parameter Malaria_Model is set to MALARIA_MECHANISTIC_MODEL_WITH_PARASITE_GENETICS.

config(config_builder, manifest)¶

parameters: dict¶

class emodpy_malaria.reporters.builtin.ReportInterventionPopAvg(class_name: str = None, parameters: dict = <factory>, Enabled: bool = True, Pretty_Format: bool = True)¶

Bases: emodpy.reporters.base.BuiltInReporter

ReportInterventionPopAvg is a CSV-formatted report that gives population average data on the usage of interventions. It provides data on the fraction of people or nodes that have an intervention as well as averages on the intervention’s efficacy. For each persistent intervention that has been distributed to a node or person, the report provides one line in the CSV for each intervention used in that node. Since node-level intervention (usually vector control) can only have one per node, the data will be for that one intervention. The individual-level interventions will have data for the people in that node.

config(config_builder, manifest)¶

parameters: dict¶