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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 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 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 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 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 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