R/S4classes.R

In IsoriX: Isoscape Computation and Inference of Spatial Origins using Mixed Models

# This S4 definitions of classes are required for saveRDS to work and interact properly with the package terra.

#' Class ISOSCAPE
#'
#' @slot isoscapes a SpatRaster storing the isoscapes
#' @slot sp_points a list of spatial points
#'
#' @export
#' @rdname ISOSCAPE-class
#'
setClass("ISOSCAPE", slots = c(
  isoscapes = "SpatRaster",
  sp_points = "list"
))


#' Class CALIBFIT
#'
#' @slot method a character string indicating the method used for the calibration
#' @slot species_rand a logical indicating whether the species random effect is included in the model
#' @slot site_rand a logical indicating whether the site random effect is included in the model
#' @slot param the fixed-effect estimates of the calibration function
#' @slot fixefCov the covariance matrix of the fixed effects
#' @slot phi the residual variance of the calibration fit
#' @slot calib_fit the fitted calibration model (if applicable)
#' @slot iso_fit the fitted calibration model (if applicable)
#' @slot data the calibration data
#' @slot sp_points a list of spatial points used for calibration
#'
#' @export
#' @rdname CALIBFIT-class
#'
setClass("CALIBFIT", slots = c(
  method = "character",
  species_rand = "logical",
  site_rand = "logical",
  param = "numeric",
  fixefCov = "matrix",
  phi = "numeric",
  calib_fit = "list",
  iso_fit = "list",
  data = "data.frame",
  sp_points = "list"
))


#' Class ISOFIND
#'
#' @slot sample a list of SpatRaster objects storing the assignment info for each sample
#' @slot group a SpatRaster storing the group assignment info
#' @slot sp_points a list of SpatVector storing the spatial points for sources, calibration and assignment samples
#'
#' @export
#' @rdname ISOFIND-class
#'
setClass("ISOFIND", slots = c(
  sample = "list",
  group = "SpatRaster",
  sp_points = "list"
))