ReportVectorGenetics

The vector genetics report is a CSV-formatted report that collects information on how many vectors of each genome/allele combination exist at each time, node, and vector state. Information can only be collected on one species per report.

Configuration

To generate this report, the following parameters must be configured in the custom_reports.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.
Allele_Combinations_For_Stratification	array of strings	NA	NA	[]	If stratifying by allele, this will be the list of alleles to stratify by. Depends on Stratify_By = ALLELE.
Alleles_For_Stratification	array of strings	NA	NA	[]	The list of alleles for which to collect frequency counts. If the list is empty, the report uses a list of all possible alleles. Depends on Stratify_By = ALLELE_FREQ
Combine_Similar_Genomes	boolean	NA	NA	[]	If set to true (1), genomes are combined for each locus (ignoring gender) if the set of alleles of the two genomes are the same. Note that ‘1-0’ is considered to be the same as ‘0-1’. Depends on Stratify_By = GENOME or SPECIFIC_GENOME.
Gender	enum	NA	NA	VECTOR_FEMALE	The gender to include in the file; possible values are VECTOR_FEMALE, VECTOR_MALE, and VECTOR_BOTH_GENDERS.
Include_Vector_State_Columns	boolean	NA	NA	1	If set to true (1), the columns for each vector state (Eggs, Larvae, etc) will be included.
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.
Species	string	NA	NA	(if not specified, the first species found will be used)	The species to include information on; the name must exist in Vector_Species_Params in the config.json file. The name will be added to the report name.
Specific_Genome_Combinations_For_Stratification	array of strings	NA	NA	NA	If stratifying by SPECIFIC_GENOME, this is the list of genomes to stratify by. ‘*’ will list all entries at that location, and ‘?’ will combine all entries at that location. Depends on Stratify_By = SPECIFIC_GENOME.
Stratify_By	enum	NA	NA	GENOME	Determines how the report will be stratified; possible values are GENOME, SPECIFIC_GENOME, and ALLELE.

The following is an example of an input file for this report:

{
    "Reports": [{
            "class": "ReportVectorGenetics",
            "Species": "arabiensis2",
            "Gender": "VECTOR_FEMALE",
            "Stratify_By": "GENOME",
            "Start_Day": 365,
            "End_Day": 465,
            "Filename_Suffix": "Node1",
            "Node_IDs_Of_Interest": [ 1 ]
        },
        {
            "class": "ReportVectorGenetics",
            "Species": "arabiensis2",
            "Gender": "VECTOR_BOTH_GENDERS",
            "Stratify_By": "ALLELE_FREQ",
            "Alleles_For_Stratification" : [ "a0", "a1", "b0", "b1" ],
            "Filename_Suffix": "Test67"
        },
        {
            "class": "ReportVectorGenetics",
            "Species": "arabiensis2",
            "Gender": "VECTOR_FEMALE",
            "Stratify_By": "ALLELE",
            "Allele_Combinations_For_Stratification": [
                [ "a0", "b0" ],
                [ "a1", "b1" ]
            ],
            "Include_Vector_State_Columns": 0
        },
        {
            "class": "ReportVectorGenetics",
            "Species": "arabiensis2",
            "Stratify_By": "SPECIFIC_GENOME",
            "Gender": "VECTOR_FEMALE",
            "Specific_Genome_Combinations_For_Stratification": [
                {
                    "Allele_Combination": [
                        [  "X",  "X" ],
                        [ "a0",  "*" ],
                        [ "b1", "b0" ]
                    ]
                },
                {
                    "Allele_Combination": [
                        [  "X",  "X" ],
                        [ "a1", "a0" ],
                        [ "b0",  "*" ]
                    ]
                },
                {
                    "Allele_Combination": [
                        [  "X",  "X" ],
                        [ "a1",  "*" ],
                        [ "b1", "b0" ]
                    ]
                },
                {
                    "Allele_Combination": [
                        [  "X",  "X" ],
                        [ "a1", "a0" ],
                        [ "b1",  "*" ]
                    ]
                }
            ],
            "Combine_Similar_Genomes": 1,
            "Include_Vector_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.
Alleles	string	If Stratify_By = ALLELE, then the column will be all of the possible alleles plus the values in Allele_Combinations_For_Stratification.
Genome	string	If Stratify_By = GENOME or SPECIFIC_GENOME, then this is the ‘Genome’ column and for each time and NodeID, the column will contain the possible combinations of genomes.

Data columns

Parameter	Data type	Description
VectorPopulation	integer	If Gender = VECTOR_BOTH_GENDERS or VECTOR_FEMALE, then this column will contain the number of female vectors that are in the states STATE_INFECTIOUS, STATE_INFECTED, or STATE_ADULT.
STATE_INFECTIOUS	integer	If Gender is VECTOR_BOTH_GENDERS or VECTOR_FEMALE, then this column will contain the number of female vectors that are in this state.
STATE_INFECTED	integer	If Gender is VECTOR_BOTH_GENDERS or VECTOR_FEMALE, then this column will contain the number of female vectors that are in this state.
STATE_ADULT	integer	If Gender is VECTOR_BOTH_GENDERS or VECTOR_FEMALE, then this column will contain the number of female vectors that are in this state.
STATE_MALE	integer	If Gender is VECTOR_BOTH_GENDERS or VECTOR_MALE, then this column will contain the number of mature male vectors.
STATE_IMMATURE	integer	This column contains the number of vectors (male and female) in the ‘immature’ state.
STATE_LARVA	integer	This column contains the number of larva (male and female).
STATE_EGG	integer	This column contains the number of eggs (male and female).
VectorPopulationNumDied	integer	If Include_Death_By_State_Columns is true and Gender = VECTOR_BOTH_GENDERS or VECTOR_FEMALE, then this column will contain the number of female vectors that died and were in states STATE_INFECTIOUS, STATE_INFECTED, or STATE_ADULT.
InfectiousNumDied	integer	If Include_Death_By_State_Columns is true, Include_Vector_State_Columns is true, and Gender = VECTOR_BOTH_GENDERS or VECTOR_FEMALE, then this column will contain the number of infectious, mature, female vectors that died during this time step.
InfectedNumDied	integer	If Include_Death_By_State_Columns is true, Include_Vector_State_Columns is true, and Gender = VECTOR_BOTH_GENDERS or VECTOR_FEMALE, then this column will contain the number of infected, mature, female vectors that died during this time step.
AdultsNumDied	integer	If Include_Death_By_State_Columns is true, Include_Vector_State_Columns is true, and Gender = VECTOR_BOTH_GENDERS or VECTOR_FEMALE, then this column will contain the number of mature female vectors that are neither infected or infectious that died during this time step.
MaleNumDied	integer	If Include_Death_By_State_Columns is true, Include_Vector_State_Columns is true, and Gender = VECTOR_BOTH_GENDERS or VECTOR_MALE, then this column will contain the number of mature male vectors that died during this time step.
VectorPopulationAvgAgeAtDeath	float	If Include_Death_By_State_Columns is true and Gender = VECTOR_BOTH_GENDERS or VECTOR_FEMALE, then this column will contain the average age (in days) of the the infectious, mature, female vectors that died during this time step.
InfectiousAvgAgeAtDeath	float	If Include_Death_By_State_Columns is true, Include_Vector_State_Columns is true, and Gender = VECTOR_BOTH_GENDERS or VECTOR_FEMALE, then this column will contain the average age (in days) of the the infectious, mature, female vectors that died during this time step.
InfectedAvgAgeAtDeath	float	If Include_Death_By_State_Columns is true, Include_Vector_State_Columns is true, and Gender = VECTOR_BOTH_GENDERS or VECTOR_FEMALE, then this column will contain the average age (in days) of the the infected, mature, female vectors that died during this time step.
AdultsAvgAgeAtDeath	float	If Include_Death_By_State_Columns is true, Include_Vector_State_Columns is true, and Gender = VECTOR_BOTH_GENDERS or VECTOR_FEMALE, then this column will contain the average age (in days) of the the mature, female vectors that are neither infected or infectious that died during this time step.
MaleAvgAgeAtDeath	float	If Include_Death_By_State_Columns is true, Include_Vector_State_Columns is true, and Gender = VECTOR_BOTH_GENDERS or VECTOR_MALE, then this column will contain the average age (in days) of the the mature male vectors that died during this time step.

Example

The following are examples of ReportVectorGenetics.csv files. The Death By State columns are not included in the examples.

This table is stratified by genome and female vectors.

Time	NodeID	Genome	VectorPopulation	STATE_INFECTIOUS	STATE_INFECTED	STATE_ADULT	STATE_IMMATURE	STATE_LARVA	STATE_EGG
0	1	X-a0-b0:X-a0-b0	293	0	0	293	0	0	8903
0	1	X-a0-b0:X-a1-b0	181	0	0	181	0	0	5797
0	1	X-a0-b0:X-a0-b1	657	0	0	657	0	0	21948
0	1	X-a0-b0:X-a1-b1	454	0	0	454	0	0	14096
0	1	X-a1-b0:X-a0-b0	194	0	0	194	0	0	6360
0	1	X-a1-b0:X-a1-b0	124	0	0	124	0	0	3934
0	1	X-a1-b0:X-a0-b1	437	0	0	437	0	0	14967
0	1	X-a1-b0:X-a1-b1	285	0	0	285	0	0	9140
0	1	X-a0-b1:X-a0-b0	638	0	0	638	0	0	22200
0	1	X-a0-b1:X-a1-b0	439	0	0	439	0	0	15429
0	1	X-a0-b1:X-a0-b1	1515	0	0	1515	0	0	50901
0	1	X-a0-b1:X-a1-b1	1039	0	0	1039	0	0	33525
0	1	X-a1-b1:X-a0-b0	435	0	0	435	0	0	15209
0	1	X-a1-b1:X-a1-b0	293	0	0	293	0	0	9808
0	1	X-a1-b1:X-a0-b1	1032	0	0	1032	0	0	34564
0	1	X-a1-b1:X-a1-b1	695	0	0	695	0	0	23311
1	1	X-a0-b0:X-a0-b0	261	0	0	261	0	5877	9167
1	1	X-a0-b0:X-a1-b0	157	0	0	157	0	3830	6470
1	1	X-a0-b0:X-a0-b1	564	0	0	564	0	14393	21121
1	1	X-a0-b0:X-a1-b1	397	0	0	397	0	9134	13920
1	1	X-a1-b0:X-a0-b0	167	0	0	167	0	4143	5533
1	1	X-a1-b0:X-a1-b0	104	0	0	104	0	2536	3779
1	1	X-a1-b0:X-a0-b1	377	0	0	377	0	9836	13234
1	1	X-a1-b0:X-a1-b1	243	0	0	243	0	6002	9229
1	1	X-a0-b1:X-a0-b0	564	0	0	564	0	14428	19047
1	1	X-a0-b1:X-a1-b0	381	0	0	381	0	10047	13371
1	1	X-a0-b1:X-a0-b1	1322	0	0	1322	0	33210	47190
1	1	X-a0-b1:X-a1-b1	898	0	0	898	0	21974	31616
1	1	X-a1-b1:X-a0-b0	381	0	0	381	0	9938	12977
1	1	X-a1-b1:X-a1-b0	257	0	0	257	0	6393	9156
1	1	X-a1-b1:X-a0-b1	886	0	0	886	0	22766	30973
1	1	X-a1-b1:X-a1-b1	604	0	0	604	0	15236	20404

This table is stratified by genome and male vectors.

Time	NodeID	Genome	STATE_MALE	STATE_IMMATURE	STATE_LARVA	STATE_EGG
728	1	X-a0-b0:Y-a1-b0	471	234	2889	76019
728	1	X-a0-b0:Y-a0-b1	472	238	2876	77305
728	1	X-a0-b0:Y-a1-b1	6139	3607	44504	1200234
728	1	X-a1-b0:Y-a1-b1	20783	12670	166170	4672298
728	1	X-a0-b1:Y-a1-b1	20879	12732	166591	4748180
728	1	Other	73196	46195	639267	18714288
729	1	X-a0-b0:Y-a1-b0	460	224	2818	76957
729	1	X-a0-b0:Y-a0-b1	461	238	2798	79896
729	1	X-a0-b0:Y-a1-b1	6076	3578	44258	1205125
729	1	X-a1-b0:Y-a1-b1	20824	12630	165392	4658639
729	1	X-a0-b1:Y-a1-b1	20801	12677	166219	4709209
729	1	Other	73268	46247	640706	18831238

This table is stratified by allele and female vectors, with vector state columns included.

Time	NodeID	Alleles	VectorPopulation
604	1	Ad	36238
604	1	Am	60886
604	1	Aw	63143
604	1	Bd	9419
604	1	Bm	13313
604	1	Bw	96119
604	1	Ce	15029
604	1	Cw	96861
604	1	De	12088
604	1	Dw	97095
604	1	X	97469
604	1	Y	0
605	1	Ad	36232
605	1	Am	60897
605	1	Aw	62762
605	1	Bd	9503
605	1	Bm	13334
605	1	Bw	95893
605	1	Ce	14964
605	1	Cw	96645
605	1	De	12253
605	1	Dw	96877
605	1	X	97250
605	1	Y	0