R/calc_c_closure.R

In cercospoRa: Process Based Epidemiological Model for Cercospora Leaf Spot of Sugar Beet

#' Calculate canopy closure date
#'
#' @details
#'  Calculates canopy closure dates from LAI and growth rate parameters
#'
#'
#' @param param_rxt Output of the function \link{calc_r_x0}, which produces a
#'  list containing parameters that are necessary to calculate \code{c_closure}.
#'  These parameters are \code{r}, the growth rate, \code{x0}, the initial LAI
#'  value, and \code{t0}, the initial date and the associated dates
#' @param x1 LAI value at which 90% canopy closure is reached. It is fixed to
#'  1.3 for sugar beet.
#' @param k carrying capacity, which is the maximum LAI that can be attained.
#'  This value can be cultivar-dependent. The default is fixed to 6
#'
#' @return \code{c_closure} date at which 90% canopy closure is reached at each
#'  location.
#'
#' @export
#' @examples
#' img_dir <- system.file("extdata", "uav_img",package = "cercospoRa")
#' epidemic_onset_param <-
#'   read_sb_growth_parameter(img_files = list.files(img_dir,pattern = "tif",
#'                                                   full.names = TRUE),
#'                            img_dates = as.POSIXct(
#'                              c("2022-06-14","2022-06-28"),tz = "UTC"),
#'                            target_res = 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 )
calc_c_closure <- function(param_rxt,
                           x1 = 1.3,
                           k=6 ){
  x0 <- param_rxt$x0
  r <- param_rxt$r
  t0 <- param_rxt$t0
  c_closure <- as.numeric(t0)/(24*60*60) + round(log( x1*(k-x0)/(x0*(k-x1)))/r,0)
  return(c_closure)
}