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ReportMicrosporidia

The microsporidia report (ReportMicrosporidia.csv) tracks vector population counts broken down by species and microsporidia strain at each time step. For every combination of species and strain — including a "NoMicrosporidia" row representing uninfected vectors — it reports the number of vectors in each life stage. This report is useful for monitoring how microsporidia spreads through vector populations over time.

This report is available for VECTOR_SIM and MALARIA_SIM simulations.

Configuration

To generate this report, add the following to the custom_reports.json file. This report has no configurable parameters beyond the class name.

{
    "Reports": [
        {
            "class": "ReportMicrosporidia"
        }
    ],
    "Use_Defaults": 1
}

Output file data

The output file is named ReportMicrosporidia.csv. One row is written per time step, per node, per species, and per microsporidia strain. A row with MicrosporidiaStrain = NoMicrosporidia is included for each species and represents vectors not carrying any microsporidia strain.

Parameter Data type Description
Time float The simulation time in days when the data was collected.
NodeID integer The external ID of the node that the data is being collected for.
Species string The name of the vector species.
MicrosporidiaStrain string The name of the microsporidia strain. A value of NoMicrosporidia indicates vectors not infected with any strain.
VectorPopulation integer The total number of adult female vectors in this species/strain group (STATE_INFECTIOUS + STATE_INFECTED + STATE_ADULT).
STATE_INFECTIOUS integer The number of adult female vectors that are infectious.
STATE_INFECTED integer The number of adult female vectors that are infected but not yet infectious.
STATE_ADULT integer The number of uninfected adult female vectors.
STATE_MALE integer The number of adult male vectors.
STATE_IMMATURE integer The number of immature vectors (male and female).
STATE_LARVA integer The number of larvae (male and female).
STATE_EGG integer The number of eggs (male and female).

Example

The following is an example of ReportMicrosporidia.csv.

Time NodeID Species MicrosporidiaStrain VectorPopulation STATE_INFECTIOUS STATE_INFECTED STATE_ADULT STATE_MALE STATE_IMMATURE STATE_LARVA STATE_EGG
0 340461476 SillySkeeter NoMicrosporidia 8742 0 0 8742 9033 0 0 613800
0 340461476 SillySkeeter Strain_A 0 0 0 0 0 0 0 0
0 340461476 SillySkeeter Strain_B 0 0 0 0 0 0 0 0
1 340461476 SillySkeeter NoMicrosporidia 7652 0 0 7652 8139 0 20576 548000
1 340461476 SillySkeeter Strain_A 0 0 0 0 0 0 0 0
1 340461476 SillySkeeter Strain_B 0 0 0 0 0 0 0 0
2 340461476 SillySkeeter NoMicrosporidia 6724 0 0 6724 7391 0 27219 481000
2 340461476 SillySkeeter Strain_A 0 0 0 0 0 0 0 0
2 340461476 SillySkeeter Strain_B 0 0 0 0 0 0 0 0