getInfectionRate {vectorsurvR}

Get Infection Rate

Description

'getInfectionRate()' 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

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

Arguments

pools

Pools data retrieved from 'getPools()'

interval

Calculation interval for infection rate, 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 by

species_list

Species filter for calculating infection rate 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 infection rate. 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

Infection rate calculation

Examples

getInfectionRate(sample_pools,
                 interval = "Biweek",
                 target_disease = "WNV",
                 pt_estimate = "mle",
                 scale = 1000,
                 species_list = list("Cx pipiens"),
                 trap_list = list("CO2"))