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. 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 name	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 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
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
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