ReportVectorMigration#

The vector migration report (ReportVectorMigration.csv) provides detailed information on when and where vectors are migrating. As there will be one line for each migrating vector or cohort, it is beneficial to use the parameters to limit the size of the output file.

See Vector migration for more information on how to create vector migration files.

Configuration#

To generate the report, configure the following parameters in the custom_reports.json file:

Parameter

Data type

Min

Max

Default

Description

End_Day

float

0

3.40E+38

3.40E+38

The day to stop collecting data for the report.

Start_Day

float

0

3.40E+38

0

The day to start collecting data for the report.

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.

Must_Be_In_State

array of enums

NA

NA

[ ]

A list of vector states for which you want to record the migration. Only STATE_MALE, STATE_ADULT, STATE_INFECTED, STATE_INFECTIOUS migrate.

Must_Be_From_Node

array of integers

1

2147480000

[ ]

A list of node IDs. A vector must be travelling FROM one of these nodes to be recorded into the report. Empty list means vectors traveling from any/all nodes will be recorded.

Must_Be_To_Node

array of integers

1

2147480000

[ ]

A list of node IDs. A vector must be travelling TO one of these nodes to be recorded into the report. Empty list means vectors traveling from any/all nodes will be recorded.

Include_Genome_Data

boolean

NA

NA

0

If set to true (1), adds a Genome column for migrating vectors. Vectors with no custom alleles will still have their sex alleles listed.

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.

{
    "Reports": [
        {
            "class": "ReportVectorMigration",
            "Start_Day": 366.0,
            "End_Day": 375.0,
            "Include_Genome_Data": 1,
            "Must_Be_In_State": ["STATE_INFECTIOUS", "STATE_INFECTED"],
            "Must_Be_From_Node": [23, 24],
            "Must_Be_To_Node": [23, 24],
            "Species_List": [
                "funestus"
            ],
            "Filename_Suffix": "funestus"
        },
    ],
    "Use_Defaults": 1
}

Report structure and data channel descriptions#

The file contains the following data channels:

Data channel

Data type

Description

Time

integer

The day that the vector migrated.

ID

integer

The ID of the vector or cohort. Note that when using the cohort model, a cohort may need to split such that some of the cohort migrates to the node and some do not, creating new cohort IDs. This may make it difficult to follow cohorts by ID.

FromNodeID

integer

The ID of the node that the vector was migrating from.

ToNodeID

integer

The ID of the node that the vector traveled to.

State

string

The state of the migrating vector.

Species

string

The name of the species of vector.

Age

integer

The number of days the vector has been alive.

Genome

string

Full genome of the migrating vector.

Population

integer

The number of migrating vectors per line depends on the Vector_Sampling_Type setting. If Vector_Sampling_Type is set to TRACK_ALL_VECTORS or SAMPLE_INDIVIDUAL_VECTORS, female vectors migrate individually, so this number will always be 1. For male vectors, or for female vectors when Vector_Sampling_Type is set to VECTOR_COMPARTMENTS_NUMBER or VECTOR_COMPARTMENTS_PERCENT, the number can be greater than 1. This indicates that ‘X’ vectors of the same age, state, genome, and species are migrating between the specific nodes.

Example#

The following is an example of ReportVectorMigration.csv:

Time

ID

FromNodeID

ToNodeID

State

Genome

Species

Age

Population

400

220742554

1487745020

1487810556

STATE_INFECTED

X:X

arabiensis

29

10

400

211244943

1487745020

1487679485

STATE_INFECTIOUS

X:X

arabiensis

34

10

400

256543649

1487745020

1487810555

STATE_ADULT

X:X

arabiensis

3

10

400

259247278

1487745020

1487745019

STATE_MALE

X:Y

funestus

0

5

400

259248701

1487745020

1487810557

STATE_MALE

X:Y

funestus

0

2

400

259250124

1487745020

1487810556

STATE_MALE

X:Y

funestus

0

2

400

259251547

1487745020

1487679484

STATE_MALE

X:Y

funestus

0

1

400

259252970

1487745020

1487679485

STATE_MALE

X:Y

funestus

0

1