ReportNodeDemographicsMalariaGenetics

The malaria genetics node demographics report (ReportNodeDemographcsMalariaGenetics.csv) extends the data collected in the malaria node demographics report by adding data about the number of infections with specific gentic 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.

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.
Barcodes array of strings NA NA [ ] 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 an OtherBarcodes column for barcodes that are not defined. Note: There is no validation that the barcode strings are valid barcodes for the scenario.
Drug_Resistant_Statistic_Type enum NA NA NUM_PEOPLE_WITH_RESISTANT_INFECTION Indicates the statistic in the DrugResistant columns. Possible values are: 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.
Drug_Resistant_Strings array of strings NA NA [ ] A list of strings representing the set of drug resistant markers. A column will be created with the number of human infections with that barcode. One can use a ‘*’ for a wild card. An ‘OtherBarcodes’ column will be created for barcodes not defined.
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 bool NA NA 1 Set to true (1) to stratify by gender. Set to false (0) to not stratify by gender.
Stratify_By_Has_Clinical_Symptoms bool 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": "ReportNodeDemographicsMalariaGenetics",
            "Age_Bins": [
                10,
                100
            ],
            "Barcodes": [
                "TA",
                "AT",
                "TT"
            ],
            "Drug_Resistant_Stat_Type": "NUM_INFECTIONS",
            "Drug_Resistant_Strings": [
                "TA",
                "AT",
                "TT"
            ],
            "IP_Key_To_Collect": "",
            "Stratify_By_Gender": 0,
            "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 who meet the stratification values.
NumInfected integer The number of infected individuals who 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 Node Properties, then there are no columns.
AvgInfectiousness float The average infectiousness to mosquitos 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.
[barcodes] integer The number of human infections with the barcode that is the column header. If you used a wild card at a loci, it includes all the barcodes that match the other loci exactly but ignores differences at this loci. For example, A*T includes AAT, ACT, AGT, and ATT. There will be one column for each barcode.
OtherBarcodes integer The number of human infections whose barcode is not counted by the other columns.

Example

The following is an example of a ReportNodeDemographicsMalariaGenetics.csv

Time NodeID AgeYears NumIndividuals NumInfected AvgInfectiousness AvgParasiteDensity AvgGametocyteDensity AvgVariantFractionPfEMP1Major AvgNumInfections AvgInfectionClearedDuration NumInfectionsCleared NumHasFever NumHasClinicalSymptoms TA AT TT OtherBarcodes TA AT TT NoDrugResistance
200 4 10 339 339 0.61637 12162.5 1038.6 0.180659 8.50443 61.6944 72 153 199 1491 1094 163 135 1491 1094 163 135
200 4 100 661 661 0.627337 12805.6 1084.05 0.174226 8.72315 64.2336 107 275 374 2989 2206 276 295 2989 2206 276 295
200 3 10 343 343 0.610594 10458.5 1086.55 0.180894 8.43149 61.4211 57 123 172 0 2892 0 0 0 2892 0 0
200 3 100 657 657 0.639379 14241.1 1074.46 0.175525 8.78691 64.4853 136 260 359 0 5773 0 0 0 5773 0 0
200 2 10 330 330 0.62785 15945.3 1107.33 0.173889 8.56364 61.6377 69 134 179 2826 0 0 0 2826 0 0 0
200 2 100 670 670 0.649023 13305.3 1150.4 0.175338 8.68806 64.8 115 268 361 5821 0 0 0 5821 0 0 0
200 1 10 321 321 0.650348 12543.2 1097.84 0.173842 8.64486 61.678 59 134 191 0 0 0 2775 0 0 0 2775
200 1 100 679 679 0.65758 14437.5 1330.21 0.170324 8.72607 65.3988 100 295 408 0 0 0 5925 0 0 0 5925
201 4 10 339 339 0.605389 11346.4 995.784 0.183186 8.39233 61.7711 83 145 202 1465 1075 163 142 1465 1075 163 142
201 4 100 661 661 0.625909 13623.3 1074.37 0.175986 8.66566 63.8224 133 286 376 2960 2191 277 300 2960 2191 277 300
201 3 10 342 342 0.616016 10373.4 1081.56 0.183762 8.43275 62.6765 68 142 176 0 2884 0 0 0 2884 0 0
201 3 100 658 658 0.631187 12559.5 1054.92 0.177351 8.71125 65.0115 141 259 350 0 5732 0 0 0 5732 0 0
201 2 10 330 330 0.618134 13675.8 1121.95 0.176455 8.52424 61.2059 68 137 184 2813 0 0 0 2813 0 0 0
201 2 100 670 670 0.648521 13363.5 1191.18 0.177448 8.68507 64.4876 121 269 359 5819 0 0 0 5819 0 0 0
201 1 10 321 321 0.655716 12432.2 1214.83 0.175867 8.65732 62.1475 61 134 180 0 0 0 2779 0 0 0 2779
201 1 100 679 679 0.644713 13488.7 1274.26 0.172356 8.67894 65.386 114 283 400 0 0 0 5893 0 0 0 5893
202 4 10 339 339 0.598077 10570.8 975.812 0.185811 8.38053 62.5556 72 149 204 1454 1076 165 146 1454 1076 165 146
202 4 100 661 661 0.613423 12068.9 1060.33 0.178084 8.65053 64.641 117 270 372 2950 2183 281 304 2950 2183 281 304
202 3 10 342 342 0.593883 10130.2 1061.35 0.185741 8.41521 62.3333 63 132 186 0 2878 0 0 0 2878 0 0
202 3 100 658 658 0.625583 12888.2 1052.63 0.179271 8.68541 64.9604 139 256 347 0 5715 0 0 0 5715 0 0
202 2 10 330 330 0.606342 14340 1131.78 0.17805 8.44545 61.1493 67 137 182 2787 0 0 0 2787 0 0 0
202 2 100 670 670 0.637783 12996.4 1159.33 0.179343 8.67015 64.4728 115 260 362 5809 0 0 0 5809 0 0 0
202 1 10 321 321 0.646784 12130 1165.26 0.177684 8.64486 61.4776 67 131 179 0 0 0 2775 0 0 0 2775
202 1 100 679 679 0.641917 13286.9 1271.64 0.174335 8.69072 65.7283 115 280 399 0 0 0 5901 0 0 0 5901