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