Calculate epidemic onset from image

Calculate epidemic onset from image

Usage

calc_epidemic_onset_from_image(
  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

map of canopy closure dates formatted as number 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 <- 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"),
                                                     c_closure = c_closure,
                                                     weather = wethr)

terra::plot(epidemic_onset_map)