ReportVectorStats#

The vector statistics report (ReportVectorStats.csv) is a CSV-formatted report that provides detailed life-cycle data on the vectors in the simulation. The report is stratified by time, node ID, and (optionally) species.

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 at death. It adds two columns for each of the following states: ADULT, INFECTED, INFECTIOUS, and MALE.
Include_Microsporidia_Columns	boolean	NA	NA	0	If set to true (1), columns will be added for each state and the value in the column will be the number of vectors that have microsporidia in that state during this time step.

{
    "Reports": [
        {
            "class": "ReportVectorStats",
            "Species_List":  [
                "arabiensis",
                "funestus"
            ],
            "Stratify_By_Species": 1,
            "Include_Wolbachia_Columns": 0,
            "Include_Gestation_Columns": 1,
            "Include_Microsporidia_Columns": 0,
            "Include_Death_By_State_Columns": 1
        }
    ],
    "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	This is the number of vectors that died indoors while attempting to feed (e.g. due to bed nets).
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 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 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 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 the mature male vectors that died during this time step.
AvgDurationLarvaeToImmature	float	Average time, in days, it takes larva to become immature adults.
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.
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.
HasMicrosporidia-STATE_XXX	integer	If Include_Microsporidia_Columns = 1, then the columns contain number of vectors in that state that have microsporidia.
NoMicrosporidia-STATE_XXX	integer	If Include_Microsporidia_Columns = 1, then the columns contain number of vectors in that state that do not have microsporidia.

Example#

The following are examples of ReportVectorStats.csv files. The examples do not include the Death By State columns.

This example includes Wolbachia columns:

STATE_ADULT	STATE_MALE	STATE_IMMATURE	STATE_LARVA	STATE_EGG	NewEggsCount	IndoorBitesCount	IndoorBitesCount-Infectious	OutdoorBitesCount	OutdoorBitesCount-Infectious	NewAdults	DiedBeforeFeeding	DiedDuringFeedingIndoor	DiedDuringFeedingOutdoor	VECTOR_WOLBACHIA_FREE	VECTOR_WOLBACHIA_A	MigrationFromCountRegional	arabiensis_AvailableHabitat	funestus_AvailableHabitat	gambiae_AvailableHabitat	arabiensis_EggCrowdingCorrection	funestus_EggCrowdingCorrection	gambiae_EggCrowdingCorrection	NumInfectousBitesGiven	NumInfectousBitesReceived	InfectiousBitesGivenMinusReceived
16220	36576	17593	147016	1541720	770860	8537	202	2426	75	1469	2788	844	245	0	137427	0	8991.45	4123.95	10026.9 0.00706801	0.0259187	0.00710855	277	136	141	0
14635	34183	17098	152982	958640	479320	4756	479	1366	128	1047	2501	517	121	15087	0	0	3873.64	3814.74	4504.05	0.0133491	0.0316351	0.0135903	607	295	312
13247	32339	12849	150692	1264080	632040	5812	296	1559	92	1339	2287	643	159	66443	0	0	3662.45	2833.68	4034.73	0.00908111	0.0593457	0.00962815	388	219	169
12066	30731	14408	140976	1452320	726160	6700	270	1803	76	1564	2100	637	171	0	130007	0	8211.71	3889.12	9207.12	0.00671468	0.0242195	0.00670622	346	178	168
12590	30509	10898	145816	794440	397220	4239	455	1166	129	2672	1969	466	134	15105	0	0	2797.77	3512.56	3192.74	0.0129099	0.0288083	0.0135152	584	274	310
11243	28771	10887	138512	954720	477360	5676	312	1556	128	1134	1928	610	153	59130	0	6894.61	3493.81	7625.89	0.00798359	0.049113	0.00857158	440	227	213	0
8933	26075	14491	138662	1112920	556460	5247	329	1429	92	0	1884	604	131	0	136952	0	14562.2	4190.82	16253.6	0.0172538	0.0315782	0.0171569	421	240	181
9541	25515	9959	159705	705280	352640	2854	347	746	106	1965	1575	286	84	12354	0	0	1660.21	3321.22	2031.23	0.0308546	0.035052	0.031173	453	221	232
8604	24184	14841	143138	946320	473160	5224	418	1312	111	1070	1549	552	130	4545	0	0	5737.64	3498.29	6278.16	0.00562629	0.0425362	0.00611594	529	250	279
7951	22936	16030	140226	860880	430440	4290	310	1058	86	1048	1454	435	117	0	137234	0	3113.21	3527.66	3467.57	0.014121	0.0311236	0.0146823	396	208	188
8216	22242	15596	132199	463280	231640	2584	344	685	109	1552	1391	299	68	15421	0	0	1562.56	3622.39	1707.29	0.00863056	0.0325911	0.00884764	453	214	239
6553	20374	17428	122419	854320	427160	4512	421	1178	111	248	1482	490	140	63235	0	0	3282.25	3217.14	3811.39	0.00827453	0.0702558	0.00766011	532	263	269
8015	21173	12487	118951	683640	341820	3003	376	741	94	2646	1204	346	76	0	136025	0	2047.61	3347.56	2169.57	0.00896889	0.0306045	0.00994518	470	233	237
7913	20868	8126	115273	420600	210300	3489	299	927	70	1585	1298	357	82	14010	0	0	1894.64	2482.64	2145.04	0.00736232	0.0335831	0.0070938	369	172	197
7560	20286	8209	107152	734040	367020	4018	384	1079	109	1393	1290	449	102	59413	0	0	2474.93	3355.48	2673.81	0.0110462	0.046009	0.0109935	493	241	252
7525	19644	6876	103579	476880	238440	2978	375	665	90	1292	1279	323	61	0	125487	0	1868.86	3167.59	2158.96	0.00808167	0.0314773	0.00832445	465	218	247

This table includes gestation columns:

Time	NodeID	Population	VectorPopulation	STATE_INFECTIOUS	STATE_INFECTED	STATE_ADULT	STATE_MALE	STATE_IMMATURE	STATE_LARVA	STATE_EGG	NumLookingToFeed	NumFedCount	NumGestatingBegin	NumGestatingEnd	NumAttemptFeedIndoor	NumAttemptFeedOutdoor	NumAttemptButNotFeed	NewEggsCount	IndoorBitesCount	IndoorBitesCount-Infectious	OutdoorBitesCount	OutdoorBitesCount-Infectious	NewAdults	DiedBeforeFeeding	DiedDuringFeedingIndoor	DiedDuringFeedingOutdoor	NumGestatingOnDay_0	NumGestatingOnDay_1	NumGestatingOnDay_2	NumGestatingOnDay_3	NumGestatingOnDay_4
350	1	1000	88760	2171	16352	70237	100715	124862	1699008	1647000	29944	16393	48447	64840	8098	8154	11915	823500	8	1	8	0	12005	10422	820	816	9823	11150	12887	14587	16393
351	1	1000	88451	2127	16377	69947	100900	124843	1699680	1641840	29839	16278	48381	64659	8059	8021	11911	820920	8	0	8	1	11881	10540	848	802	9772	11285	12856	14468	16278
352	1	1000	88312	2110	16283	69919	100936	125391	1697598	1619120	29630	16020	48388	64408	7970	7859	12004	809560	7	2	7	2	11900	10433	803	803	9901	11347	12790	14350	16020
353	1	1000	88477	2117	16291	70069	101167	125234	1698069	1655960	29957	16285	48062	64347	8014	8127	12029	827980	8	1	8	0	12101	10293	807	836	9964	11265	12681	14152	16285
354	1	1000	88617	2154	16232	70231	101057	125605	1697983	1669440	30280	16509	47938	64447	8045	8214	12183	834720	8	0	8	0	11987	10259	790	798	9889	11158	12502	14389	16509
355	1	1000	88480	2154	16217	70109	101222	125573	1698350	1649840	30097	16393	47995	64388	8120	8083	12069	824920	8	0	8	1	12023	10525	813	822	9715	11030	12662	14588	16393

This table includes microsporidia columns:

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	NumDiedInfectious	NumDiedInfected	NumDiedAdults	NumDiedMale	AvgAgeAtDeathInfectious	AvgAgeAtDeathInfected	AvgAgeAtDeathAdults	AvgAgeAtDeathMale	AvgDurationLarvaeToImmature	NoMicrosporidia-STATE_INFECTIOUS	NoMicrosporidia-STATE_INFECTED	NoMicrosporidia-STATE_ADULT	NoMicrosporidia-STATE_MALE	NoMicrosporidia-STATE_IMMATURE	NoMicrosporidia-STATE_LARVA	NoMicrosporidia-STATE_EGG	SillySkeeter_AvailableHabitat	SillySkeeter_EggCrowdingCorrection
34	340461476	1000	8595	12	209	8374	10936	12679	81106	302440	151220	2603	0	1227	873	264	0	18	1119	1048	0	8.44444	5.95085	7.46183	11	12	209	8374	10936	12679	81106	302440	11593.8	0.0357489
35	340461476	1000	8694	26	210	8458	11051	12616	81384	315720	157860	2713	1	1221	831	291	0	29	1093	1069	0	8.58621	6.36688	7.7521	11	26	210	8458	11051	12616	81384	315720	11437.7	0.0383342
36	340461476	1000	8802	38	211	8553	11286	13262	80529	344080	172040	2841	4	1196	796	292	5	30	1053	1040	12.2	9.4	6.24691	7.78462	11	38	211	8553	11286	13262	80529	344080	12400.3	0.0362274
37	340461476	1000	9000	46	215	8739	11420	13336	81294	337560	168780	2783	5	1246	761	287	4	26	1018	1109	14.5	10.3077	6.11002	8.17764	11	46	215	8739	11420	13336	81294	337560	11730.2	0.0360389
38	340461476	1000	9140	50	229	8861	11428	13306	81547	343280	171640	2853	4	1300	855	305	6	18	1136	1173	16.6667	7.33333	6.70158	8.22677	11	50	229	8861	11428	13306	81547	343280	11561	0.03475
39	340461476	1000	9177	58	226	8893	11535	13517	81669	359000	179500	2993	8	1186	846	303	4	30	1115	1068	14.75	10.3333	6.53453	8	11	58	226	8893	11535	13517	81669	359000	11512.9	0.0336779
40	340461476	1000	9428	67	221	9140	11866	13201	81574	355160	177580	2847	5	1425	871	303	6	26	1142	1128	12.8333	9.69231	6.50613	8.34486	11	67	221	9140	11866	13201	81574	355160	11673.1	0.0320693
41	340461476	1000	9510	73	224	9213	12055	13208	81606	365520	182760	3126	6	1260	876	302	8	26	1144	1143	15.875	8.76923	6.38112	8.55731	11	73	224	9213	12055	13208	81606	365520	11698.6	0.0328671