getVectorIndex: Calculate vector index

Description

`getVectorIndex()` Calculates vector index from pools and collections data

Usage

getVectorIndex(
  collections,
  pools,
  interval,
  target_disease,
  pt_estimate = "bc-mle",
  scale = 1000,
  agency = NULL,
  species = NULL,
  trap = NULL,
  sex = NULL,
  trapnight_min = 1,
  trapnight_max = NULL,
  separate_by = NULL
)

Value

Dataframe containing the vector index calculation

Arguments

collections: Collections data retrieved from `getArthroCollections()`
pools: Pools data retrieved from `getPools()`
interval: Calculation interval for vector index, accepts "CollectionDate","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$target_acronym)`
pt_estimate: The estimation type for infection rate. Options include: "mle","bc-"mle", "mir"
scale: Constant to multiply infection rate, default is 1000
agency: Character vector for filtering agency by character code
species: Character vector for filtering species. View species in your data `unique(data$species_display_name)`. Defaults to all species if no selection
trap: Character vector for filtering trap type by acronym. View trap types in your data`unique(data$trap_acronym`. Defaults to all trap types
sex: Character vector for filtering sex type. View sex options `unique(data$sex_type`). Defaults to "female".
trapnight_min: Minimum trap night restriction for calculation. Default is 1.
trapnight_max: Maximum trap night restriction for calculation. Default is no restriction.
separate_by: Separate/group the calculation by 'trap','species' or 'agency'. Default NULL does not separate.

Examples

Run this code

getVectorIndex(collections=sample_collections,
pools=sample_pools, interval="Month", target_disease = "WNV", pt_estimate="mle")

Run the code above in your browser using DataLab