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 software-migration-vector 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:

Parameter	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:

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