Calculate epidemic onset from image

Usage

calc_epidemic_onset_from_image(start, end, cc_r, 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.
cc_r: spatRast map of canopy closure dates formatted an integer of days since 1970-01-01. It defines the date to start running the model (Wolf)
weather: data.table, formatted with format_weather
cultivar_sus: character, susceptibility of the cultivar in "R" resistant, "S" susceptible, "MR" moderately resistant etc.

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")

img_dir <- system.file("extdata", "uav_img",package = "cercospoRa")

epidemic_onset_param <-
   read_sb_growth_parameter(
      list.files(img_dir,pattern = "tif",
                 full.names = TRUE),
      img_dates = as.POSIXct(c("2022-06-14","2022-06-28"),
                             tz = "UTC"),
      10)
param_rxt <- calc_r_x0(epidemic_onset_param,
                       min_r = 0.02,
                       max_r = 0.05,
                       k = 6)
c_closure_map <- calc_c_closure(param_rxt,
                                x1 = 1.3,
                                k=6 )
 # this takes about 20 sec to run
epidemic_onset_map <- calc_epidemic_onset_from_image(start = as.POSIXct("2022-04-25",tz = "UTC"),
                                                     end = as.POSIXct("2022-09-30",tz = "UTC"),
                                                     cc_r = c_closure_map,
                                                     weather = wethr)

terra::plot(epidemic_onset_map)