R/slm.R

In spEDM: Spatial Empirical Dynamic Modeling

.slm_sf_method = \(data, x = NULL, y = NULL, z = NULL,
                   k = 4, step = 15, alpha_x = 0.28, alpha_y = 0.25, alpha_z = 0.22,
                   beta_xy = 0.05, beta_xz = 0.05, beta_yx = 0.2, beta_yz = 0.2, beta_zx = 0.35, beta_zy = 0.35,
                   threshold = Inf, transient = 1, nb = NULL){
  vx = .uni_lattice(data,x,FALSE)
  vy = .uni_lattice(data,y,FALSE)
  vz = .uni_lattice(data,z,FALSE)
  if (is.null(nb)) nb = .internal_lattice_nb(data)
  return(.bind_slm(RcppSLMTri4Lattice(vx,vy,vz,nb,k,step,alpha_x,alpha_y,alpha_z,beta_xy,beta_xz,beta_yx,beta_yz,beta_zx,beta_zy,threshold),x,y,z,transient))
}

.slm_spatraster_method = \(data, x = NULL, y = NULL, z = NULL,
                           k = 4, step = 15, alpha_x = 0.28, alpha_y = 0.25, alpha_z = 0.22,
                           beta_xy = 0.05, beta_xz = 0.05, beta_yx = 0.2, beta_yz = 0.2, beta_zx = 0.35, beta_zy = 0.35,
                           threshold = Inf, transient = 1){
  mx = .uni_grid(data,x,FALSE)
  my = .uni_grid(data,y,FALSE)
  mz = .uni_grid(data,z,FALSE)
  return(.bind_slm(RcppSLMTri4Grid(mx,my,mz,k,step,alpha_x,alpha_y,alpha_z,beta_xy,beta_xz,beta_yx,beta_yz,beta_zx,beta_zy,threshold),x,y,z,transient))
}

#' spatial logistic map
#'
#' @param data observation data.
#' @param x (optional) name of first spatial variable.
#' @param y (optional) name of second spatial variable.
#' @param z (optional) name of third spatial variable.
#' @param k (optional) number of neighbors to used.
#' @param step (optional) number of simulation time steps.
#' @param alpha_x (optional) growth parameter for x.
#' @param alpha_y (optional) growth parameter for y.
#' @param alpha_z (optional) growth parameter for y.
#' @param beta_xy (optional) cross-inhibition from x to y.
#' @param beta_xz (optional) cross-inhibition from x to z.
#' @param beta_yx (optional) cross-inhibition from y to x.
#' @param beta_yz (optional) cross-inhibition from y to z.
#' @param beta_zx (optional) cross-inhibition from z to x.
#' @param beta_zy (optional) cross-inhibition from z to y.
#' @param threshold (optional) set to `NaN` if the absolute value exceeds this threshold.
#' @param transient (optional) transients to be excluded from the results.
#' @param nb (optional) neighbours list.
#'
#' @return A list
#' @export
#' @name slm
#' @aliases slm,sf-method
#' @references
#' Willeboordse, F.H., The spatial logistic map as a simple prototype for spatiotemporal chaos, Chaos, 533–540 (2003).
#'
#' @examples
#' columbus = sf::read_sf(system.file("case/columbus.gpkg", package="spEDM"))
#' columbus$inc = sdsfun::normalize_vector(columbus$inc)
#' slm(columbus,"inc")
#'
methods::setMethod("slm", "sf", .slm_sf_method)

#' @rdname slm
methods::setMethod("slm", "SpatRaster", .slm_spatraster_method)