SpatialReportMalariaFiltered

The filtered malaria spatial report (SpatialReportMalariaFiltered.bin) provides spatial information on malaria simulations, similar to the SpatialReport, but allows for filtering the data and collection over different intervals. The output of this file differs from the spatial output report by adding Start_Day and a Reporting_Interval.

Configuration

To generate the report, configure the following parameters in the custom_report.json file:

Parameter	Data type	Min	Max	Default	Description
Filename_Suffix	string	NA	NA	(empty string)	Augments the filename of the report. If multiple reports are being generated, this allows you to distinguish among the multiple reports.
Start_Day	float	0	3.40282e+38	0	The day of the simulation to start collecting data.
End_Day	float	0	3.40282e+38	3.40282e+38	The day of the simulation to stop collecting data.
Node_IDs_Of_Interest	array of integers	0	2.14748e+09	[]	Data will be collected for the nodes in this list. Empty list implies all nodes.
Min_Age_Years	float	0	9.3228e+35	0	Minimum age in years of people to collect data on.
Max_Age_Years	float	0	9.3228e+35	9.3228e+35	Maximum age in years of people to collect data on.
Must_Have_IP_Key_Value	string	NA	NA	(empty string)	A Key:Value pair that the individual must have in order to be included. Empty string means to not include IPs in the selection criteria.
Must_Have_Intervention	string	NA	NA	(empty string)	The name of the intervention that the person must have in order to be included. Empty string means to not include interventions in the selection criteria.
Reporting_Interval	float	0	3.40E+38	1	The number of days to collect data and average over.
Spatial_Output_Channels	list of strings	NA	NA	(empty string)	An array of channel names for spatial output by node and time step. The data from each channel will be written to a separate binary file. See the table below for all possible channels.

For more information on spatial reports, see SpatialReport.

Example configuration

{
    "class": "SpatialReportMalariaFiltered",
    "Filename_Suffix": "NewCases",
    "Start_Day": 0,
    "End_Day": 85,
    "Node_IDs_Of_Interest": [1, 2, 3, 4, 5, 6, 7, 8],
    "Min_Age_Years": 5,
    "Max_Age_Years": 10,
    "Must_Have_IP_Key_Value": "Risk:HIGH",
    "Must_Have_Intervention": "UsageDependentBednet",
    "Reporting_Interval": 1,
    "Spatial_Output_Channels": [
        "Population",
        "New_Infections",
        "Prevalence",
        "Adult_Vectors",
        "New_Diagnostic_Prevalence",
        "New_Clinical_Cases"
    ]
}

Report structure and data channel descriptions

The file contains the following data channels:

Data channel	Description
Adult_Vectors	The total number of adult female vectors in the node at each time step. Includes vectors from all species and all infectious sates (not infected, infected, and infectious).
Air_Temperature	The air temperature of that day for that node in Celcius.
Births	The live births cumulative up to that day for that node.
Blood_Smear_Gametocyte_Prevalence	The fraction of the population that is detectable with the BLOOD_SMEAR_GAMETOCYTES version of MalariaDiagnostic. The detectability of the diagnostic is controlled by the parameters Report_Gametocyte_Smear_Sensitivity and Report_Detection_Threshold_Blood_Smear_Gametocytes.
Blood_Smear_Parasite_Prevalence	The fraction of the population that is detectable with the BLOOD_SMEAR_PARASITES version of MalariaDiagnostic. The detectability of the diagnostic is controlled by the parameters Report_Parasite_Smear_Sensitivity and Report_Detection_Threshold_Blood_Smear_Parasites.
Campaign_Cost	The cumulative cost of the interventions that have been distributed to that node. This is based on the Cost_To_Consumer parameter in the interventions used.
Daily_Bites_Per_Human	The average number of mosquito bites received per individual on that day.
Daily_EIR	The number of infectious bites per person in the node made that day/reporting period as determined by the vector model. It includes the infectious bites of all species for both indoor and outdoor bites.
Disease_Deaths	The number of people that died in the node that day. The population for the node at the beginning of the next time step will be the population at this time step minus the number of deaths plus new births.
Fever_Prevalence	This fraction is the number of people whose fever is above the Report_Detection_Threshold_Fever threshold divided by the number of people in the node.
Human_Infectious_Reservoir	The sum of the infectiousness of each person in the node; a person’s infectiousness is the probability of infecting a mosquito during a successful blood meal.
Infected	The fraction of the population currently infected.
Infectious Vectors	The fraction of vectors in the simulation that are currently infected and infectious.
Land_Temperature	The temperature of the land/ground that day in that node in degrees Celsius.
Mean_Parasitemia	The geometric mean number of parasites per microliter of blood.
New_Clinical_Cases	The number of new clinical cases for a given day.
New_Infections	The number of people who received a new infection in that node on that time step.
New_Reported_Infections	The number of people reported to have received a new infection in that node on that time step. This number should be about 50% of the value in New_Infections.
New_Severe_Cases	The number of new severe cases of malaria on that day in the node. An individual is considered to be a severe case if the combined probability of anemia, parasite density, and fever is greater than a uniform random number. This combined probability is the combination of sigmoid using the following parameters: Anemia_Severe_Threshold and Anemia_Severe_Inverse_Width, Parasite_Severe_Threshold and Parasite_Severe_Inverse_Width, and Fever_Severe_Threshold and Fever_Severe_Inverse_Width.
PCR_Gametocyte_Prevalence	The fraction of the population that is detectable with the PCR_GAMETOCYTES version of MalariaDiagnostic. The detectability of the diagnostic is controlled by the parameter Report_Detection_Threshold_PCR_Gametocytes.
PCR_Parasite_Prevalence	The fraction of the population that is detectable with the PCR_PARASITES version of MalariaDiagnostic. The detectability of the diagnostic is controlled by the parameter Report_Detection_Threshold_PCR_Parasites.
PfHRP2_Prevalence	The fraction of the population that is detectable with the PF_HRP2 version of MalariaDiagnostic. The detectability of the diagnostic is controlled by the parameter Report_Detection_Threshold_PCR_PfHRP2.
Population	The total number of individuals in the node on that day.
Prevalence	The fraction of the population currently infected in that node on that day.
Rainfall	The number millimeters of rainfall in that node on that day.
Relative_Humidity	The amount of water vapor present in air expressed as a percentage of the amount needed for saturation at the same temperature for the node on that day.
True_Prevalence	The fraction of the population that is detectable with the TRUE_PARASITE_DENSITY version of MalariaDiagnostic. The detectability of the diagnostic is controlled by the parameter Report_Detection_Threshold_True_Parasite_Density.