inst/shiny-examples/respineappv2/disper_time.R

In ajpelu/respine: Evaluate RESilience of Mediterranean PINE plantations

#' Propagule input into pine plantation by time
#'
#' Compute the propagule input from each natural forest patch to pine plantation
#' target using three types of disperser and different equations.
#'
#' @param x A \code{raster} object with the landscape configured
#'
#' @param xr A \code{raster} object with richness computed
#'
#' @param msb A \code{raster} object with small bird contribution on target pine plantation
#'
#' @param mmb A \code{raster} object with medium bird contribution on target pine plantation
#'
#' @param mab A \code{raster} object with mammal contribution on target pine plantation
#'
#' @param pp_value The value of "Pine plantation" class within the raster
#' (Default value = 1)
#'
#' @param per_sb Percentage of small bird dispersers
#'
#' @param per_mb Percentage of medium bird dispersers
#'
#' @param per_ma Percentage of mammals dispersers
#'
#' @import raster
#' @import rgeos
#' @author Antonio J Perez-Luque


disper_time <- function(msb, mmb, mma,
                        x, xr, pp_value,
                        per_sb, per_mb, per_ma,
                        propaguleInputBird,
                        propaguleInputMammal,
                        time_span){

  # Output stack
  out <- stack()

  # Get richnes of pine plantations
  rich_pp <- calc(stack(x, xr), fun=function(x) ifelse(x[1] == pp_value, x[1]*x[2], NA))

  # Compute propagule input by cell
  seed_input <- ((msb * per_sb) + (mmb * per_mb)) * propaguleInputBird  + (mma * per_ma) * propaguleInputMammal


  for (i in 1:time_span){
    aux <- c()
    propagulo_time <- rich_pp + (seed_input)*i
    names(propagulo_time) <- paste0('y',i)


    rich_time <- calc(stack(x,xr, propagulo_time),
                      fun = function(x) ifelse(
                        x[1] == pp_value, x[1]*x[3], x[2]))

    names(rich_time) <- paste0('rich_y',i)
    rich_time[rich_time == 0] <- NA

    out <- stack(out, rich_time)}

  return(out)
}