getInfectionRate {vectorsurvR} | R Documentation |
Calculate infection rate
Description
'getInfectionRate()' Calculates infection rate from pools data
Usage
getInfectionRate(
pools,
interval,
target_disease,
pt_estimate = "bc-mle",
scale = 1000,
agency = NULL,
species = NULL,
trap = NULL,
sex = "female",
separate_by = NULL
)
Arguments
pools |
Pools data retrieved from 'getPools()' |
interval |
Calculation interval for infection rate, 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$test_target_acronym)' |
pt_estimate |
The estimation type for infection rate. Options include: “mle”,“bc-mle”, “mir” |
scale |
Constant to multiply infection rate by |
agency |
An optional vector for filtering agency by character code |
species |
An optional vector for filtering species. Species_display_name is the accepted notation.To see a list of species present in your data run unique(collections$species_display_name). If species is unspecified, the default NULL will return data for all species in data. |
trap |
An optional vector for filtering trap type by acronym. Trap_acronym is the is the accepted notation. Run unique(collections$trap_acronym) to see trap types present in your data. If trap is unspecified, the default NULL will return data for all trap types. |
sex |
An optional vector for filtering sex type. Accepts 'male', 'female',or 'other'. If sex is unspecified, the default NULL will return data for female sex. |
separate_by |
Separate/group the calculation by 'trap','species' or 'agency'. Default NULL does not separate. |
Value
Dataframe of infection rate calculation