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ReportNodeDemographicsMalaria

The malaria node demographics report is a CSV-formatted report that extends the ReportNodeDemographics report (see ReportNodeDemographics) by adding malaria-specific statistics. The report still contains population information stratified by node, but the data columns now also contain information about malaria parasite counts.

Configuration

To generate this report, the following parameters must be configured in the custom_reports.json file:

Parameter Data type Min Max Default Description
Age_Bins array of floats -3.04E+38 3.04E+38 [] The age bins (in years, in ascending order) to aggregate within and report. An empty array does not stratify by age.
IP_Key_To_Collect string NA NA (empty string) The name of the IndividualProperties (IP) key by which to stratify the report. An empty string means the report is not stratified by IP.
Stratify_By_Gender boolean 0 1 1 Set to true (1) to stratify by gender; a value of 0 will not stratify by gender.
Stratify_By_Has_Clinical_Symptoms boolean NA NA 1 If set to 1, the data will have an extra stratification for people who have clinical symptoms and those that do not. Default is 0 or no extra stratification. 
{
    "Reports": [
        {
            "class": "ReportNodeDemographicsMalaria",
            "Age_Bins": [10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 125],
            "IP_Key_To_Collect": "",
            "Stratify_by_Gender": 1,
            "Stratify_By_Has_Clinical_Symptoms": 0
        }
    ],
    "Use_Defaults": 1
}

Output file data

The report will contain the following output data, divided between stratification columns and data columns.

Stratification columns

Parameter Data type Description
Time float The day of the simulation that the data was collected.
NodeID integer The External ID of the node for the data in the row in the report.
Gender enum Possible values are M or F; the gender of the individuals in the row in the report. This column only appears if Stratify_By_Gender = 1.
AgeYears float The max age in years of the bin for the individuals in the row in the report. If Age_Bins is empty, this column does not appear.
IndividualProp string The value of the IP for the individuals in the row in the report. If IP_Key_To_Collect is an empty string, then this column does not appear.
HasClinicalSymptoms enum T implies that the people in the row are having clinical symptoms. F implies they do not. This column only appears if Stratify_By_Has_Clinical_Symptoms = 1.

Data columns

Parameter Data type Description
NumIndividuals integer The number of individuals that meet the stratification values.
NumInfected integer The number of infected individuals that meet the stratification values.
NodeProp = <Node Property Keys> string For each possible Node Property, there is one column where the data in the column is the value of that particular property. If there are no NodeProperties, then there are no columns.
AvgInfectiousness float The average infectiousness to mosquitoes for the individuals of this row. Infectiousness is based on the number of mature gametocytes that the person has.
AvgParasiteDensity float The average true parasite density for the individuals of this row.
AvgGametocyteDensity float The average true gametocyte density for the individuals of this row.
AvgVariantFractionPfEMP1Major float For each individual, a count is made of the number of PfEMP1 Major antibodies the individual has and is divided by the total number of possible variants (Falciparum_PfEMP1_Variants). This is the average of this value for all the individuals represented in this row.
AvgNumInfections float The average number of infections for the people of this row.
AvgInfectionClearedDuration float The average duration to clear infections for the people of this row.
NumInfectionsCleared integer The number of cleared infections for the people of this row.
NumHasFever integer The number of people in the row that have a fever according to the diagnostic using the Report_Detection_Threshold_Fever parameter.
NumHasClinicalSymptoms integer If Stratify_By_Has_Clinical_Symptoms = 0, then this column is present with the number of people in the row that are considered to have 'clinical' symptoms.

Example

The following is an example of ReportNodeDemographicsMalaria.csv.

Time NodeID Gender AgeYears IndividualProp=StudyGroups HasClinicalSymptoms NumIndividuals NumInfected AvgInfectiousness AvgParasiteDensity AvgGametocyteDensity AvgVariantFractionPfEMP1Major AvgNumInfections AvgInfectionClearedDuration NumInfectionsCleared NumHasFever
50 1 M 10 arm1 F 366 0 0 0 0 0 0 0 0 0
50 1 M 10 arm1 T 151 151 0.00593093 112435 1.06936 0.0165342 1 0 0 151
50 1 M 10 arm2 F 1256 0 0 0 0 0 0 0 0 0
50 1 M 10 arm2 T 292 292 0.00615811 111366 1.11031 0.0165525 1 0 0 292
50 1 M 10 arm3 F 2744 0 0 0 0 0 0 0 0 0
50 1 M 10 arm3 T 282 282 0.00600333 111783 1.08239 0.0165839 1 0 0 282
50 1 M 100 arm1 F 335 0 0 0 0 0 0 0 0 0
50 1 M 100 arm1 T 159 159 0.00205596 140531 0.371012 0.0166038 1 0 0 159
50 1 M 100 arm2 F 946 0 0 0 0 0 0 0 0 0
50 1 M 100 arm2 T 588 588 0.00205613 140583 0.371029 0.0165647 1 0 0 588
50 1 M 100 arm3 F 2645 0 0 0 0 0 0 0 0 0
50 1 M 100 arm3 T 297 297 0.00205629 140105 0.371017 0.0165545 1 0 0 297
50 1 F 10 arm1 F 379 0 0 0 0 0 0 0 0 0
50 1 F 10 arm1 T 164 164 0.00606003 110326 1.09222 0.0165447 1 0 0 164
50 1 F 10 arm2 F 1143 0 0 0 0 0 0 0 0 0
50 1 F 10 arm2 T 288 288 0.00595153 111696 1.07296 0.0165162 1 0 0 288
50 1 F 10 arm3 F 2809 0 0 0 0 0 0 0 0 0
50 1 F 10 arm3 T 302 302 0.00597365 111095 1.07672 0.0165011 1 0 0 302
50 1 F 100 arm1 F 355 0 0 0 0 0 0 0 0 0
50 1 F 100 arm1 T 144 144 0.00205568 141105 0.37102 0.0166435 1 0 0 144
50 1 F 100 arm2 F 887 0 0 0 0 0 0 0 0 0
50 1 F 100 arm2 T 579 579 0.00205593 140874 0.371017 0.0165688 1 0 0 579
50 1 F 100 arm3 F 2584 0 0 0 0 0 0 0 0 0
50 1 F 100 arm3 T 305 305 0.00205636 140043 0.371022 0.0165465 1 0 0 305
50 2 M 10 arm1 F 340 0 0 0 0 0 0 0 0 0
50 2 M 10 arm1 T 147 147 0.00608663 112032 1.09768 0.016644 1 0 0 147
50 2 M 10 arm2 F 1161 0 0 0 0 0 0 0 0 0
50 2 M 10 arm2 T 311 311 0.00599196 111639 1.08021 0.0165274 1 0 0 311
50 2 M 10 arm3 F 2742 0 0 0 0 0 0 0 0 0
50 2 M 10 arm3 T 285 285 0.00596162 112175 1.07493 0.0165731 1 0 0 285
50 2 M 100 arm1 F 327 0 0 0 0 0 0 0 0 0
50 2 M 100 arm1 T 160 160 0.0020567 139714 0.371016 0.0164792 1 0 0 160
50 2 M 100 arm2 F 899 0 0 0 0 0 0 0 0 0
50 2 M 100 arm2 T 583 583 0.00205599 140620 0.371006 0.0165638 1 0 0 583
50 2 M 100 arm3 F 2697 0 0 0 0 0 0 0 0 0
50 2 M 100 arm3 T 278 278 0.00205585 141016 0.371021 0.0165828 1 0 0 278
50 2 F 10 arm1 F 332 0 0 0 0 0 0 0 0 0
50 2 F 10 arm1 T 160 160 0.00600168 112563 1.08236 0.0166042 1 0 0 160
50 2 F 10 arm2 F 1184 0 0 0 0 0 0 0 0 0
50 2 F 10 arm2 T 333 333 0.00607677 111940 1.09565 0.0165566 1 0 0 333
50 2 F 10 arm3 F 2731 0 0 0 0 0 0 0 0 0
50 2 F 10 arm3 T 294 294 0.00601945 111251 1.08511 0.0165306 1 0 0 294
50 2 F 100 arm1 F 341 0 0 0 0 0 0 0 0 0
50 2 F 100 arm1 T 156 156 0.00205657 139663 0.371027 0.0165171 1 0 0 156
50 2 F 100 arm2 F 914 0 0 0 0 0 0 0 0 0
50 2 F 100 arm2 T 626 626 0.00205598 140771 0.371019 0.0165549 1 0 0 626
50 2 F 100 arm3 F 2728 0 0 0 0 0 0 0 0 0
50 2 F 100 arm3 T 271 271 0.00205597 140890 0.370996 0.0165068 1 0 0 271