R/set_max_iic_objective.R

In restoptr: Ecological Restoration Planning

#' @include internal.R
NULL

#' Set an objective to maximize the integral index of connectivity
#'
#' Specify that a restoration problem ([restopt_problem()]) should
#' the integral index of connectivity (IIC).
#'
#' @inheritParams set_max_mesh_objective
#' @inherit set_max_mesh_objective return
#'
#' @param distance_threshold `numeric` greater than 0. Minimum distance (in
#' `unit`) between two patches to consider them connected in the computation of
#' the IIC. The default value -1 causes the function to use 1 aggregated cell as
#' the distance threshold.
#'
#' @param unit `unit` object or a `character` that can be coerced to a distance
#' unit (see `unit` package), or "cells" for cell width of aggregated
#' habitat raster. Units of the `distance_threshold` parameter. If the input
#' habitat raster does not use a projected coordinate system, only "cells" is
#' available. Meters by default, expected if `distance_threshold` is set to its
#' default value (-1), which causes the function to use 1 cell by default.
#'
#' @details The integral index of connectivity (IIC) is a graph-based inter-patch
#' connectivity index based on a binary connection model (Pascual-Hortal &
#' Saura, 2006). Its maximization in the context of restoration favours
#' restoring the structural connectivity between large patches. IIC is unitless
#' and comprised between 0 (no connectivity) and 1 (all the landscape is
#' habitat, thus fully connected). The `distance_threshold` parameter indicates
#' to the solver how to construct the habitat graph, i.e. what is the minimum
#' distance between two patches to consider them as connected. Note that, as
#' the computation occurs on aggregated cells, if `distance_threshold` is used
#' with a different unit than "cells", it will be rounded to the closest
#' corresponding number of cells.
#'
#' @return An updated restoration problem ([restopt_problem()] object.
#'
#' @references
#' Pascual-Hortal, L., & Saura, S. (2006).
#' Comparison and development of new graph-based landscape connectivity indices:
#' Towards the priorization of habitat patches and corridors for conservation.
#' Landscape Ecology, 21(7), 959‑967. https://doi.org/10.1007/s10980-006-0013-z
#'
#' @family objectives
#'
#' @examples
#' \dontrun{
#' # load data
#' habitat_data <- rast(
#'   system.file("extdata", "habitat_hi_res.tif", package = "restoptr")
#' )
#'
#' locked_out_data <- rast(
#'  system.file("extdata", "locked_out.tif", package = "restoptr")
#' )
#'
#' # create problem with locked out constraints
#' p <- restopt_problem(
#'     existing_habitat = habitat_data,
#'     aggregation_factor = 16,
#'     habitat_threshold = 0.7
#'   ) %>%
#'   set_max_iic_objective() %>%
#'   add_restorable_constraint(
#'     min_restore = 5,
#'     max_restore = 5,
#'   ) %>%
#'   add_locked_out_constraint(data = locked_out_data) %>%
#'   add_settings(time_limit = 1)
#'
#' # print problem
#' print(p)
#'
#' # solve problem
#' s <- solve(p)
#'
#' # plot solution
#' plot(s)
#' }
#'
#' @export
set_max_iic_objective <- function(problem, distance_threshold = -1, unit = "m") {
  # assert argument is valid
  assertthat::assert_that(inherits(problem, "RestoptProblem"))
  if (distance_threshold < 0) {
    distance_threshold <- 1
    unit <- "cells"
  }
  assertthat::assert_that(
    assertthat::is.number(distance_threshold),
    assertthat::noNA(distance_threshold),
    (unit == "cells" || units::ud_are_convertible(unit, "m"))
  )
  distance_threshold_unitless <- distance_threshold
  if (unit != "cells") {
    width <- cell_width(get_existing_habitat(problem), unit = unit)
    distance_threshold_unitless <- distance_threshold / width
  }
  distance_threshold_unitless <- as.integer(round(distance_threshold_unitless))
  if (distance_threshold_unitless == 0) {
    warning(paste0("The distance threshold was rounded to 1 aggregated cell (",
                   width, ") because it was less than this minimum value"))
    distance_threshold_unitless <- 1L
  }
  # set objective
  set_restopt_objective(
    problem = problem,
    objective = restopt_component(
      name = "Maximize integral index of connectivity",
      class = c("MaxIicObjective", "RestoptObjectve"),
      post = function(jproblem, nb_solutions, precision, time_limit, optimality_gap,
                      verbose=FALSE, search_strategy="", lns=FALSE) {
        rJava::.jcall(
          jproblem, "Ljava/util/List;", "maximizeIIC", nb_solutions, precision,
          distance_threshold_unitless, time_limit, optimality_gap, verbose, search_strategy, lns
        )
      }
    )
  )
}