R/deprecated/deprecated_calculate_mortality_probability.R

In mhesselbarth/rabmp: R agent-based model for plants

#' #' deprecated_calculate_mortality_probability
#' #'
#' #' @description Calculate mortality probability
#' #'
#' #' @param species current species
#' #' @param dbh of current tree
#' #'
#' #' @details
#' #' Calculate the mortality probability depending on the species and the current DBH.
#' #'
#' #' @return vector
#' #'
#' #' @examples
#' #' deprecated_calculate_mortality_probability(species = "Beech", dbh = 25.31)
#' #'
#' #' @aliases deprecated_calculate_mortality_probability
#' #' @rdname deprecated_calculate_mortality_probability
#' #'
#' #' @references
#' #' Holzwarth, F., Kahl, A., Bauhus, J., & Wirth, C. (2013). Many ways to die - partitioning
#' #' tree mortality dynamics in a near-natural mixed deciduous forest. Journal of Ecology, 101(1), 220-230.
#' #'
#' #' @export
#' deprecated_calculate_mortality_probability <- function(species, dbh){
#'
#'   if(species == "Beech"){
#'
#'     # calculate dbh increase
#'     dbh_inc <- exp(-3.4 + 2.1 * (1 - exp(-(-0.00035) * dbh ^ 2.5 ) ) )
#'
#'     # calculate logit for "early phase"
#'     logit_early <- ifelse(test = is.na(1.8 + (-2.1) * log(dbh + 8) + (dbh_inc * -1.4)),
#'                           yes = 0, no = 1.8 + (-2.1) * log(dbh + 8) + (dbh_inc * -1.4))
#'
#'     # calculate logit for late phase
#'     logit_late <- -8.9 + (dbh * 0.052)
#'
#'     # sum both logits
#'     p_early <- 1 / (1 + exp(-logit_early))
#'     p_late <- 1 / (1 + exp(-logit_late))
#'
#'     # calculate prob
#'     p <- p_early + p_late
#'   }
#'
#'   else if(species == "Ash"){
#'
#'     # calculate logit
#'     logit <- 1.3 + (log(dbh) * -1.6)
#'
#'     # calculate prob
#'     p <- 1 / (1 + exp(-logit))
#'   }
#'
#'   else if(species == "Hornbeam"){
#'
#'     # calculate logit
#'     logit <- -2.8 + (dbh * -0.051)
#'
#'     # calculate prob
#'     p <- 1 / (1 + exp(-logit))
#'   }
#'
#'   else if(species == "Sycamore"){
#'
#'     # calculate logit
#'     logit <- -2.8 + (dbh * -0.051)
#'
#'     # calculate prob
#'     p <- 1 / (1 + exp(-logit))
#'   }
#'
#'   else if(species == "others"){
#'
#'     # calculate logit
#'     logit <- -2.8 + (dbh * -0.051)
#'
#'     # calculate prob
#'     p <- 1 / (1 + exp(-logit))
#'   }
#'
#'   else{
#'     print("Please select valid species - returning 0")
#'     p <- 0
#'   }
#'
#'   return(p)
#' }