Calculate epidemic onset

Usage

calc_epidemic_onset(start, end, c_closure, weather, cultivar_sus = 5)

Arguments

start: POSIXct, start date in which to begin calculating the epidemic onset, if not specified, the first date in the weather data will be used.
end: POSIXct, end date, last date to complete calculating the epidemic onset, if not specified, the last date in the weather data will be used.
c_closure: POSIXct formatted date to start the model running the model This is usually at canopy closure (Wolf)
weather: data.table, formatted with format_weather
cultivar_sus: numeric, susceptibility of the cultivar on the 'bsa' https://www.bundessortenamt.de variety list. Susceptibility rating must range between 1 and 9. 1 = resistant, 9 = susceptible. Default is 5.

Value

If the input weather is conducive for epidemic, the function returns a POSIX_ct date when epidemic commences. If no epidemic occurs, a numeric, proportion indicating the progress an epidemic is returned

Examples

wethr <- read.csv(system.file("extdata", "clean_weather.csv",
                  package = "cercospoRa"))
wethr <- format_weather(wethr,time_zone = "UTC")

calc_epidemic_onset(start = as.POSIXct("2022-04-25",tz = "UTC"),
                    end = as.POSIXct("2022-09-30",tz = "UTC"),
                    c_closure = as.POSIXct("2022-07-01",tz = "UTC"),
                    weather = wethr)
#> [1] "2022-07-26 UTC"