getVectorIndex {vectorsurvR}

Get Vector Index

Description

'getVectorIndex()'requires at least five years prior to the target_year of arthro collections data to calculate for the specified parameters. The function uses the methods of the Gateway Abundance Anomaly calculator, and will not work if there is fewer than five years of data present.

Usage

getVectorIndex(
  collections,
  pools,
  interval,
  target_disease,
  pt_estimate,
  scale = 1000,
  species_list = NULL,
  trap_list = NULL
)

Arguments

collections

Collections data retrieved from 'getArthroCollections()'

pools

Pools data retrieved from 'getPools()'

interval

Calculation interval for vector index, accepts “collection_date”,“Biweek”,“Week”, and “Month

target_disease

The disease to calculate infection rate for–i.e. “WNV”. Disease acronyms are the accepted input. To see a list of disease acronyms, run 'unique(pools$target_acronym)'

pt_estimate

The estimation type for infection rate. Options include: “mle”,“bc-”mle”, “mir”

scale

Constant to multiply infection rate

species_list

Species filter for calculating abundance. Species_display_name is the accepted notation. To see a list of species present in your data run 'unique(pools$species_display_name)'. If species is unspecified, the default 'NULL' will return data for all species in data.

trap_list

Trap filter for calculating abundance. Trap_acronym is the is the accepted notation. Run 'unique(pools$trap_acronym)' to see trap types present in your data. If trap_list is unspecified, the default 'NULL' will return data for all trap types.

Value

Vector index calculation

Examples

getVectorIndex(sample_collections, sample_pools, "Month", "WNV", "mle" )