ReportVectorStatsMalariaGenetics

The vector statistics and malaria genetics report (ReportVectorStatsMalariaGenetics.csv) is a CSV-formatted report similar to the software-report-vector-stats report. It provides genetic barcode information in addition to detailed life-cycle data on the vectors in the simulation. The report is stratified by time, node ID, and (optionally) species.

When Malaria_Model is set to MALARIA_MECHANISTIC_MODEL_WITH_PARASITE_GENETICS, this report will provide detailed insight into the status of the parasites in the vector population, including details on the oocysts, sporozoites, biting, etc.

Seealso

malaria-model-fpg for more information on the FPG model.

Configuration

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

Parameter	Data type	Min	Max	Default	Description
`Species_List`	array of strings	NA	NA	[]	The species for which to include information. If the list is empty or absent, then data for all species will be collected.
`Stratify_By_Species`	boolean	NA	NA	0	If set to true (1), then data will be stratified by species for each node.
`Include_Wolbachia_Columns`	boolean	NA	NA	0	If set to true (1), columns will be added for each type of Wolbachia. Summation of columns should be equal to VectorPopulation.
`Include_Gestation_Columns`	boolean	NA	NA	0	If set to true (1), columns will be added for feeding and gestation.
`Include_Death_By_State_Columns`	boolean	NA	NA	0	Adds columns for the number of vectors that died in this state during this time step as well as the average age. It adds two columns for each of the following states: ADULT, INFECTED, INFECTIOUS, and MALE.
`Barcodes`	array of strings	NA	NA	[]	A list of barcode strings where a column will be created with the number of vectors with sporozoites with that barcode. Use '' for a wild card. An OtherBarcodes* column will be created for those not defined.

{
    "Reports": [
        {
            "class": "ReportVectorStatsMalariaGenetics",
            "Species_List": ["arabiensis", "funestus"],
            "Stratify_By_Species": 1,
            "Include_Wolbachia_Columns": 0,
            "Include_Gestation_Columns": 1,
            "Barcodes": ["AAAAAA", "AAAATTA"]
        }
    ],
    "Use_Defaults": 1
}

Output file data

The output report will contain the following information.

Stratification columns

Parameter	Data type	Description
`Time`	integer	The day of the simulation that the data was collected.
`NodeID`	integer	The External ID of the node that the data is being collected for.
`Species`	string	If Stratify_By_Species = 1, then the species column will contain the name of the species for the given row.

Data columns

Parameter	Data type	Description
`Population`	integer	The number of people in the node.
`VectorPopulation`	integer	The number of adult female vectors that are in the STATE_INFECTIOUS, STATE_INFECTED, and 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.
`STATE_ADULT`	integer	The number of adult female vectors.
`STATE_MALE`	integer	The number of adult male vectors.
`STATE_IMMATURE`	integer	The number of immature vectors, includes male and female.
`STATE_LARVA`	integer	The number of larva, includes male and female.
`STATE_EGG`	integer	The number of eggs, includes male and female.
`NumLookingToFeed`	integer	If Include_Gestation_Columns = 1, then this column contains the number of adult female vectors that were looking to feed during this time step.
`NumFedCount`	integer	If Include_Gestation_Columns = 1, then this column contains the number of adult female vectors that had a blood meal during this time step.
`NumGestatingBegin`	integer	If Include_Gestation_Columns = 1, then this column contains the number of adult female vectors that were gestating and did not die due to non-feeding mortality.
`NumGestatingEnd`	integer	If Include_Gestation_Columns = 1, then this column contains the number of adult female vectors that were gestating at the end of the time step.
`NumAttemptFeedIndoor`	integer	If Include_Gestation_Columns = 1, then this column contains the number of adult female vectors that attempt to feed indoors. This group of vectors can still die indoors before they feed on a human.
`NumAttemptFeedOutdoor`	integer	If Include_Gestation_Columns = 1, then this column contains the number of adult female vectors that attempt to feed outdoors. This group of vectors can still die outdoors before they feed on a human.
`NumAttemptButNotFeed`	integer	If Include_Gestation_Columns = 1, then this column contains the number of adult female vectors that were attempting to feed indoors or outdoors but did not die or feed on a human. They will look to feed during the next day.
`NewEggsCount`	integer	The number of eggs that were laid this day.
`IndoorBitesCount`	float	The number of bites made on humans indoors. This includes vectors that live for another day as well as those that die trying to get away.
`IndoorBitesCountInfectious`	float	The number of bites made by infectious vectors on humans indoors. This includes vectors that live for another day as well as those that die trying to get away.
`OutdoorBitesCount`	float	The number of bites made on humans outdoors. This includes vectors that live for another day as well as those that die trying to get away.
`OutdoorBitesCountInfectious`	float	The number of bites made by infectious vectors on humans outdoors. This includes vectors that live for another day as well as those that die trying to get away.
`UnmatedAdults`	float	The number of adult females that have not mated. This can be an important statistic when the male vector population is suppressed. When the male population is low, females moving from immature to adult might not find a male to mate with for several days. The female continues to feed but she does not produce fertile eggs.
`NewAdults`	integer	The number of female vectors that matured to adulthood this day.
`DiedBeforeFeeding`	integer	The number of vectors that died this time step due to local mortality, sugar feeding, outdoor area killing, etc.
`DiedDuringFeedingIndoor`	integer	The number of vectors that died indoors while attempting to feed (e.g. due to bed nets).
`DiedDuringFeedingOutdoor`	integer	The number of vectors that died outdoors while attempting to feed.
`NumDiedInfectious`	integer	If Include_Death_By_State_Columns = 1, then this column contains the number of infectious, mature, female vectors that died during this time step.
`NumDiedInfected`	integer	If Include_Death_By_State_Columns = 1, then this column contains the number of infected, mature, female vectors that died during this time step.
`NumDiedAdults`	integer	If Include_Death_By_State_Columns = 1, then this column contains the number of mature female vectors that are neither infected or infectious that died during this time step.
`NumDiedMale`	integer	If Include_Death_By_State_Columns = 1, then this column contains the number of mature male vectors that died during this time step.
`AvgAgeAtDeathInfectious`	float	If Include_Death_By_State_Columns = 1, then this column contains the average age (in days) of the infectious, mature, female vectors that died during this time step.
`AvgAgeAtDeathInfected`	float	If Include_Death_By_State_Columns = 1, then this column contains the average age (in days) of the infected, mature, female vectors that died during this time step.
`AvgAgeAtDeathAdults`	float	If Include_Death_By_State_Columns = 1, then this column contains the average age (in days) of the mature, female vectors that are neither infected or infectious that died during this time step.
`AvgAgeAtDeathMale`	float	If Include_Death_By_State_Columns = 1, then this column contains the average age (in days) of the mature male vectors that died during this time step.
`NumGestatingOnDay_0`	integer	If Include_Gestation_Columns = 1, then this column contains the number of vectors that are gestating but with 0 more days before attempting to feed.
`NumGestatingOnDay_1`	integer	If Include_Gestation_Columns = 1, then this column contains the number of vectors that are gestating but with 1 more days before attempting to feed.
`NumGestatingOnDay_2`	integer	If Include_Gestation_Columns = 1, then this column contains the number of vectors that are gestating but with 2 more days before attempting to feed.
`NumGestatingOnDay_3`	integer	If Include_Gestation_Columns = 1, then this column contains the number of vectors that are gestating but with 3 more days before attempting to feed.
`NumGestatingOnDay_4`	integer	If Include_Gestation_Columns = 1, then this column contains the number of vectors that are gestating but with 4 more days before attempting to feed.
`NumGestatingOnDay_5`	integer	If Include_Gestation_Columns = 1, then this column contains the number of vectors that are gestating but with 5 more days before attempting to feed.
`NumGestatingOnDay_6`	integer	If Include_Gestation_Columns = 1, then this column contains the number of vectors that are gestating but with 6 more days before attempting to feed.
`NumGestatingOnDay_7`	integer	If Include_Gestation_Columns = 1, then this column contains the number of vectors that are gestating but with 7 more days before attempting to feed.
`VECTOR_WOLBACHIA_FREE`	integer	If Include_Wolbachia_Columns = 1, then this column contains the number of adult female vectors that are Wolbachia free.
`VECTOR_WOLBACHIA_A`	integer	If Include_Wolbachia_Columns = 1, then this column contains the number of adult female vectors that have Wolbachia A.
`VECTOR_WOLBACHIA_B`	integer	If Include_Wolbachia_Columns = 1, then this column contains the number of adult female vectors that have Wolbachia B.
`VECTOR_WOLBACHIA_AB`	integer	If Include_Wolbachia_Columns = 1, then this column contains the number of adult female vectors that have Wolbachia AB.
`MigrationFromCountLocal`	integer	The number of adult female vectors that made a local migration trip away from this node.
`MigrationFromCountRegional`	integer	The number of adult female vectors that made a regional migration trip away from this node.
`XXX_AvailableHabitat`	integer	If Stratify_By_Species = 0, then this column title does not have the species name in it. If Stratify_By_Species = 1, then there is a column for each species. This column contains the number of larva that the habitat could add (e.g. number of spots open); equal to current capacity - current larval count.
`XXX_EggCrowdingCorrection`	float	If Stratify_By_Species = 0, then this column title does not have the species name in it. If Stratify_By_Species = 1, then there is a column for each species. This column contains the probability that eggs die due to overcrowding.
`NumVectorsNone`	integer	The number of uninfected/noninfectious vectors; they contain neither oocysts nor sporozoites.
`NumVectorsOnlyOocysts`	integer	The number of vectors that are infected and contain only oocysts. The lack of sporozoites implies that the vectors are infected but not infectious. This is the stage before the oocysts turn into sporozoites.
`NumVectorsOnlySporozoites`	integer	The number of vectors that are infected and contain only sporozoites. The fact that the vectors have sporozoites means that they are infectious and give the sporozoites to humans.
`NumVectorsBothOocystsSporozoites`	integer	The number of vectors that have both oocysts and sporozoites. A vector can have both due to getting infected at different times by different bites.
`NumBitesAdults`	integer	The number of bites on humans made by uninfected vectors, neither infected or infectious. The vector that did the biting could have lived, died during feed, or died after feed.
`NumBitesInfected`	integer	The number of bites on humans made by a vector that is infected but not infectious. That is, a vector that only has oocysts.
`NumBitesInfectious`	integer	The number of bites on humans made by an infectious vector, e.g. has sporozoites. The vector could have both oocysts and sporozoites. This biting vector could die during feeding, after feeding, or live to the next day.
`NumDiedAdults`	integer	The number of uninfected vectors that died this day. They could have died from interventions, while trying to feed, or just old age.
`NumDiedInfected`	integer	The number of infected vectors that died this day. These vectors had oocysts but no sporozoites.
`NumDiedInfectious`	integer	The number of infectious vectors that died this day. These vectors must have had sporozoites, but they could have had oocysts as well.
`NumParasiteCohortsOocysts`	integer	The number of parasite cohorts in the oocyst state counted from all of the infected vectors. Each cohort is unique based on the vector it is in, the age, and the parasite genome.
`NumParasiteCohortsSporozoites`	integer	The number of parasite cohorts in the sporozoite state counted from all of the vectors that contain them. Each cohort is unique based on the vector it is in, the age, and the parasite genome.
`NumOocysts`	integer	The number of oocysts in the vector population.
`NumSporozoites`	integer	The number of sporozoites in the vector population.
`NumInfectiousToAdult`	integer	The number of vectors that transitioned from infectious (had sporozoites) to adult (having no sporozoites or oocysts).
`NumInfectiousToInfected`	integer	The number of vectors that transitioned from infectious (had sporozoites) to infected (having only oocysts).
`\<Barcode\>`	integer	Number of vectors with sporozoites with the indicated barcode. If a wild card ('') is used, then it is the number of vectors in that group that contain sporozoites. The barcode indicated is provided by the user in the Barcodes* parameter.
`OtherBarcodes`	integer	The number of vectors with sporozoites having a barcode different from those specified by the user. This column only appears when the user specifies barcodes in the Barcodes parameter.

Example

The following is an example of a ReportVectorStatsMalariaGenetics.csv file.

Time	NodeID	Population	VectorPopulation	STATE_INFECTIOUS	STATE_INFECTED	STATE_ADULT	STATE_MALE	STATE_IMMATURE	STATE_LARVA	STATE_EGG	NewEggsCount	IndoorBitesCount	IndoorBitesCount-Infectious	NewAdults	DiedBeforeFeeding	DiedDuringFeedingIndoor	SillySkeeter_AvailableHabitat	SillySkeeter_EggCrowdingCorrection	NumInfectousBitesGiven	NumInfectousBitesReceived	NumVectorsNone	NumVectorsOnlyOocysts	NumVectorsOnlySporozoites	NumVectorsBothOocystsSporozoites	NumBitesAdults	NumBitesInfected	NumBitesInfectious	NumDiedAdults	NumDiedInfected	NumDiedInfectious	NumParasiteCohortsOocysts	NumParasiteCohortsSporozoites	NumOocysts	NumSporozoites	AAAAAAAAAAAAAAAAAAAAAAAA	TAAAAAAAAAAAAAAAAAAAAAAA	AAAAAAAAAAAAAAAAAAAAAAAT	TAAAAAAAAAAAAAAAAAAAAAAT
270	3	52	785	0	10	775	1046	1037	25045	37360	18680	260	0	99	69	30	2490.64	0.0669741	0	0	775	10	0	0	259	1	0	99	0	0	18	0	46	0	0	0	0	0
270	1	50	747	58	479	210	1067	1054	24802	28920	14460	246	15	83	76	20	2733.64	0.0787309	15	15	210	479	0	58	115	116	15	31	61	4	1895	829	3353	3.68346e+06	44	39	40	47
270	4	53	776	57	383	336	1061	1021	24880	29960	14980	244	20	110	67	22	2655.64	0.0821259	20	20	336	383	7	50	132	92	20	39	43	7	730	123	2263	2.50476e+06	4	3	2	56
270	2	50	782	0	0	782	1050	1018	24844	34600	17300	249	0	89	65	23	2691.64	0.0677958	0	0	782	0	0	0	249	0	0	88	0	0	0	0	0	0	0	0	0	0
271	3	52	787	0	12	775	1031	1102	24918	36240	18120	262	0	94	75	18	2617.69	0.066666	0	0	775	12	0	0	258	4	0	92	1	0	21	0	53	0	0	0	0	0
271	1	50	767	53	479	235	1059	1047	24872	28440	14220	228	13	108	70	18	2663.69	0.0945243	13	13	235	479	0	53	101	114	13	25	52	11	1864	788	3368	3.63207e+06	39	35	33	43
271	4	53	786	53	372	361	1064	993	24997	29800	14900	257	13	108	72	25	2538.69	0.0886396	13	13	361	372	6	47	139	105	13	41	45	11	691	124	2193	2.59086e+06	4	3	2	52
271	2	50	777	0	0	777	1055	1003	24796	36400	18200	238	0	101	73	33	2739.69	0.0777931	0	0	777	0	0	0	238	0	0	106	0	0	0	0	0	0	0	0	0	0
272	3	52	787	0	18	769	1028	1099	24819	38280	19140	266	0	99	67	32	2716.73	0.072232	0	0	769	18	0	0	263	3	0	99	0	0	33	0	81	0	0	0	0	0
272	1	50	756	55	467	234	1047	1039	24834	35040	17520	290	20	95	76	30	2701.73	0.09366	20	20	234	467	1	54	132	138	20	38	62	6	1932	811	3507	3.54281e+06	41	36	35	46
272	4	53	778	53	362	363	1064	1007	24839	33880	16940	271	12	98	81	25	2696.73	0.0851909	12	12	363	362	5	48	157	102	12	46	50	10	679	97	2147	2.55488e+06	1	1	1	53
272	2	50	768	0	0	768	1063	1024	24823	42400	21200	290	0	91	73	27	2712.73	0.0752662	0	0	768	0	0	0	290	0	0	100	0	0	0	0	0	0	0	0	0	0
273	3	52	787	0	21	766	1053	1073	24869	37880	18940	265	0	108	73	35	2666.78	0.0709701	0	0	766	21	0	0	262	3	0	108	0	0	39	0	95	0	0	0	0	0
273	1	50	768	59	474	235	1069	1053	24934	29200	14600	240	18	93	66	16	2601.78	0.0771043	18	18	235	474	1	58	106	116	18	28	49	5	1912	864	3489	3.83343e+06	46	43	39	48
273	4	53	778	56	363	359	1054	984	24803	31560	15780	251	17	90	70	19	2732.78	0.0795966	17	17	359	363	3	53	149	85	17	45	39	5	668	98	2119	2.62942e+06	1	1	1	56
273	2	50	773	0	0	773	1063	1040	24838	35600	17800	245	0	105	76	24	2697.78	0.0639796	0	0	773	0	0	0	245	0	0	100	0	0	0	0	0	0	0	0	0	0
274	3	52	799	0	29	770	1069	1078	24915	37400	18700	267	0	100	58	31	2620.82	0.0704007	0	0	770	29	0	0	263	4	0	88	1	0	53	0	115	0	0	0	0	0
274	1	50	790	61	475	254	1070	1036	24919	28360	14180	231	14	112	69	21	2616.82	0.089102	14	14	254	475	1	60	109	108	14	29	54	7	1944	782	3536	3.46932e+06	44	44	41	45
274	4	53	771	59	349	363	1033	1008	24794	32720	16360	254	19	85	71	20	2741.82	0.0865899	19	19	363	349	3	56	153	82	19	45	41	5	648	95	2048	2.42879e+06	0	0	0	59
274	2	50	766	0	0	766	1054	1008	24911	33600	16800	261	0	97	72	32	2624.82	0.0757803	0	0	766	0	0	0	261	0	0	104	0	0	0	0	0	0	0	0	0	0