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ReportFpgNewInfections

The full parasite genetics new infections report (ReportFpgNewInfections.csv) provides very detailed information on new human infections for simulations where Malaria_Model is set to MALARIA_MECHANISTIC_MODEL_WITH_PARASITE_GENETICS.

Seealso

FPG model — For an overview of the FPG model, genome configuration, and the full FPG workflow.

When Report_Crossover_Data_Instead is set to true, it provides less detailed information on the new infections and includes GenomeCrossoverLocations data column that provides a list of crossovers that created this new infection's genome.

Configuration

To generate this 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.
Report_Crossover_Data_Instead boolean NA NA False If true (1), instead of reporting new infections in detail, the report will contain basic new infection information with the crossover locations that created this infection's genome. 
{
    "Reports": [
        {
            "Start_Day": 500,
            "End_Day": 1000,
            "Filename_Suffix": "Crossovers",
            "Node_IDs_Of_Interest": [],
            "Min_Age_Years": 0,
            "Max_Age_Years": 1000,
            "Must_Have_IP_Key_Value": "",
            "Must_Have_Intervention": "",
            "Report_Crossover_Data_Instead": 1,
            "class": "ReportFpgNewInfections"
        }
    ],
    "Use_Defaults": 1
}

Output data with Report_Crossover_Data_Instead = 0

Each row of the report is one new human infection. The report contains the following stratification columns:

Parameter Data type Description
SporozoiteToHuman_Time float The day of the simulation this infection happened.
SporozoiteToHuman_NodeID integer The ID of the node in which this infection happened.
SporozoiteToHuman_VectorID integer The ID of the vector from which the human got this infection.
SporozoiteToHuman_BiteID integer The ID of the bite from which the human got this infection.
SporozoiteToHuman_HumanID integer The ID of the human that got this infection.
SporozoiteToHuman_NewInfectionID integer The ID of this infection.
SporozoiteToHuman_NewGenomeID integer The genome ID of this infection.
HomeNodeID integer The home node ID of the human (the node in which they started the simulation) who received this new infection.
GametocyteToVector_Time float The day the vector acquired gametocytes (bit an infectious human) that eventually became this new infection.
GametocyteToVector_NodeID integer The ID of the node in which the vector acquired gametocytes.
GametocyteToVector_VectorID integer The ID of the vector from which the human got this infection.
GametocyteToVector_BiteID integer The ID of the bite during which the vector acquired gametocytes that became this new infection.
GametocyteToVector_HumanID integer The ID of the human from whom the vector acquired gametocytes that became this new infection.
FemaleGametocyteToVector_InfectionID integer The ID of the vector to human infection that generated female gametocytes that were acquired by the vector that became this infection.
FemaleGametocyteToVector_GenomeID integer The genome ID of the female gametocytes that were acquired by the vector that became this infection.
MaleGametocyteToVector_InfectionID integer The ID of the vector to human infection that generated male gametocytes that were acquired by the vector that became this infection.
MaleGametocyteToVector_GenomeID integer The genome ID of the male gametocytes that were acquired by the vector that became this infection.

Output data with Report_Crossover_Data_Instead = 1

Each row of the report is one new human infection. This is the output when Report_Crossover_Data_Instead is set to true (1). The report contains the following stratification columns:

Parameter Data type Description
SporozoiteToHuman_Time float The day of the simulation this infection happened.
SporozoiteToHuman_NewInfectionID integer The ID of this infection.
SporozoiteToHuman_NewGenomeID integer The genome ID of this infection.
FemaleGametocyteToVector_InfectionID integer The ID of the vector to human infection that generated female gametocytes that were acquired by the vector that became this infection.
FemaleGametocyteToVector_GenomeID integer The genome ID of the female gametocytes that were acquired by the vector that became this infection.
MaleGametocyteToVector_InfectionID integer The ID of the vector to human infection that generated male gametocytes that were acquired by the vector that became this infection.
MaleGametocyteToVector_GenomeID integer The genome ID of the male gametocytes that were acquired by the vector that became this infection.
GenomeCrossoverLocations array of integers The genome locations of crossovers that happened during the recombination to create the genome of this infection.

Examples

The following is an example of ReportFpgNewInfections.csv with Report_Crossover_Data_Instead = 0

SporozoiteToHuman_Time SporozoiteToHuman_NodeID SporozoiteToHuman_VectorID SporozoiteToHuman_BiteID SporozoiteToHuman_HumanID SporozoiteToHuman_NewInfectionID SporozoiteToHuman_NewGenomeID HomeNodeID GametocyteToVector_Time GametocyteToVector_NodeID GametocyteToVector_VectorID GametocyteToVector_BiteID GametocyteToVector_HumanID FemaleGametocyteToVector_InfectionID FemaleGametocyteToVector_GenomeID MaleGametocyteToVector_InfectionID MaleGametocyteToVector_GenomeID
144 340461476 87041 259801 995 21 10 340461476 126 340461476 87041 214221 391 5 10 5 10
146 340461476 89151 264739 269 22 4 340461476 128 340461476 89151 219021 234 2 4 2 4
146 340461476 89043 265052 307 23 2 340461476 128 340461476 89043 219322 151 1 2 1 2
147 340461476 87041 267498 59 24 10 340461476 126 340461476 87041 214221 391 5 10 5 10
147 340461476 83540 268831 638 25 2 340461476 129 340461476 83540 223200 151 1 2 1 2
147 340461476 78028 268224 775 26 16 340461476 129 340461476 78028 222559 732 8 16 8 16
148 340461476 67511 270334 800 27 22 340461476 130 340461476 67511 224640 72 11 22 11 22
149 340461476 76880 273618 217 28 10 340461476 128 340461476 76880 220281 391 5 10 5 10
149 340461476 92056 272405 250 29 32 340461476 131 340461476 92056 226692 549 16 32 16 32
149 340461476 77455 272243 447 30 8 340461476 131 340461476 77455 226517 381 4 8 4 8
149 340461476 94895 272637 922 31 22 340461476 131 340461476 94895 226930 72 11 22 11 22
149 340461476 89043 272674 976 32 2 340461476 128 340461476 89043 219322 151 1 2 1 2
149 340461476 89151 272378 987 33 4 340461476 128 340461476 89151 219021 234 2 4 2 4
150 340461476 93152 274679 70 34 12 340461476 132 340461476 93152 228859 398 6 12 6 12
150 340461476 93023 275047 192 35 16 340461476 129 340461476 93023 221667 732 8 16 8 16
150 340461476 83808 275775 249 36 2 340461476 132 340461476 83808 229975 151 1 2 1 2
150 340461476 92732 275663 557 37 40 340461476 132 340461476 92732 229866 961 20 40 20 40
150 340461476 92602 275983 587 38 38 340461476 132 340461476 92602 230196 758 19 38 19 38

The following is an example of ReportFpgNewInfections.csv with Report_Crossover_Data_Instead = 1

SporozoiteToHuman_Time SporozoiteToHuman_NewInfectionID SporozoiteToHuman_NewGenomeID FemaleGametocyteToVector_InfectionID FemaleGametocyteToVector_GenomeID MaleGametocyteToVector_InfectionID MaleGametocyteToVector_GenomeID GenomeCrossoverLocations
361 19618 2 12015 2 12636 2
361 19619 4 12388 4 12388 4
361 19620 100133 12009 30811 10931 21493 [736683,1123071,3767781,4665481,5134460,6486626,6797543,7945769,9125435,9989921,10944371,11695580,13533588,15305190,17023334,17539046,19256500,19308207,20763756]
361 19621 22680 11373 22680 11373 22680 [300156,1115495,1932077,8015804,9694659,12015158,12142621,12719223,15028305,15182934,15720251,21186350,21725912,21806766]
361 19622 100575 12019 6 12432 29764 [1025699,1435425,2191534,2444542,2999518,4432303,5775490,9442554,10039560,11419887,12772577,15130766,21936435,22569061]
361 19623 100578 12019 6 12432 29764 [10346,626944,1304093,2191534,2444542,4648851,6005961,6346237,6661639,8179080,10419415,17872858,19015981,20127173,21289218,21586296,21936435]
361 19624 31871 12409 31871 12409 31871 [952741,2554833,3176450,4142765,7965407,8264687,8864824,12821151,13107285,14987306,17954160,19045532]
361 19625 12 12384 12 12384 12
361 19626 4 12057 4 12057 4
361 19627 98122 10213 14284 10215 22 [763126,5407414,6726809,11679005,14649104,16047690,17259818,19084487,19690936,19983120,20311989]
361 19628 32639 12584 32639 12584 32639 [324483,1276162,5032573,10708169,11960555,12346071,14750352,15877594,17127953,17166277,17532989,21467132]
361 19629 26 11651 26 11651 26
361 19630 94615 11511 12 11640 22 [386681,1558378,4567443,5383740,5769900,8496723,8848571,12355762,12573292,13695361,15387094,16252566,16752539,17039027,18915578,19985916]
361 19631 40 10721 40 10721 40
361 19632 28 11155 28 11155 28
361 19633 28 11155 28 11156 28
361 19634 101143 11080 25494 12422 34119 [4800487,9000736,11237108,13993703,14708352,18499728,20289497,21139008,21666227]
361 19635 100807 11081 25495 12422 34119 [1526158,1599200,2038887,5532347,6717723,7773462,11559883,12899345,14080998,14453270,15928554,18973376,19238683,20107010,21841003]
361 19636 32573 12219 32573 12219 32573 [1978245,2624677,2785809,3022483,5120357,5524840,6585099,9586163,10524060,11348618,12387976,13121675,13724817,14120187,14384682,14516097,16359290,18172255,19932626,21907110]
361 19637 27655 11387 27655 11387 27655 [2185598,2847574,3561106,4685365,5636763,8966706,10091860,11097087,11516142,11962824,12804400,14003150,18064128,19248535,20034111]
361 19638 97539 11110 14601 11919 16 [117455,720343,1175032,3536007,4903695,5655050,7048920,10949034,11424219,12314248,18099728,18533894,21385858]
361 19639 97949 9708 16567 12265 30 [510685,2758662,3707940,5074592,7170938,8036134,10665545,15356778,17519326,18759494,21456109,22289229]
361 19640 86758 9331 38 8358 10 [447327,1203983,2738216,4003497,4658684,5415225,7992109,10902225,16705393]
361 19641 101155 10499 18611 10351 7755 [680292,2490255,3098692,8794669,10041006,10605268,11283353,12536006,13290246,14157844,17610340,20673367,21313825]
361 19642 101158 10499 18611 10351 7755 [590017,2086179,3798762,6739982,7621580,8794669,12536006,14157844,19575069,22669151]
361 19643 101159 10350 7754 10352 17470 [465183,946085,1791171,3377171,5989069,6965506,8884666,10234437,10837585,13350865,17078346,19039223,22487975,22592620]
361 19644 32229 12199 32229 12199 32229 [1503777,2325316,4749285,5154862,5799040,6857477,7756337,9931186,12405677,15257243,15718646,16134980,17410826,20719121,21657573]
361 19645 101196 12632 35454 12631 35451 [2459489,3656833,7118530,7806296,8898723,9799911,11330287,13418547,13778577,16239642,16751927,19795868,21709570]
361 19646 40 9504 40 11568 40