Nothing
#' CONTIG (patch level)
#'
#' @description Contiguity index (Shape metric)
#'
#' @param landscape A categorical raster object: SpatRaster; Raster* Layer, Stack, Brick; stars or a list of SpatRasters.
#' @param directions The number of directions in which patches should be
#' connected: 4 (rook's case) or 8 (queen's case).
#'
#' @details
#' \deqn{CONTIG = \frac{\Bigg[\frac{\sum\limits_{r=1}^z c_{ijr}}{a_{ij}}\Bigg] - 1 }{ v - 1} }
#'
#' where \eqn{c_{ijr}} is the contiguity value for pixel r in patch ij,
#' \eqn{a_{ij}} the area of the respective patch (number of cells) and \eqn{v} is
#' the size of the filter matrix (13 in this case).
#'
#' CONTIG is a 'Shape metric'. It asses the spatial connectedness (contiguity) of
#' cells in patches. CONTIG coerces patch values to a value of 1 and the background
#' to NA. A nine cell focal filter matrix:
#'
#' ```
#' filter_matrix <- matrix(c(1, 2, 1,
#' 2, 1, 2,
#' 1, 2, 1), 3, 3, byrow = T)
#' ```
#' ... is then used to weight orthogonally contiguous pixels more heavily than
#' diagonally contiguous pixels. Therefore, larger and more connections between
#' patch cells in the rookie case result in larger contiguity index values.
#'
#' \subsection{Units}{None}
#' \subsection{Range}{0 >= CONTIG <= 1}
#' \subsection{Behaviour}{Equals 0 for one-pixel patches and increases to a limit
#' of 1 (fully connected patch).}
#'
#' @seealso
#' \code{\link{lsm_c_contig_mn}},
#' \code{\link{lsm_c_contig_sd}},
#' \code{\link{lsm_c_contig_cv}}, \cr
#' \code{\link{lsm_l_contig_mn}},
#' \code{\link{lsm_l_contig_sd}},
#' \code{\link{lsm_l_contig_cv}}
#'
#' @return tibble
#'
#' @examples
#' landscape <- terra::rast(landscapemetrics::landscape)
#' lsm_p_contig(landscape)
#'
#' @aliases lsm_p_contig
#' @rdname lsm_p_contig
#'
#' @references
#' McGarigal K., SA Cushman, and E Ene. 2023. FRAGSTATS v4: Spatial Pattern Analysis
#' Program for Categorical Maps. Computer software program produced by the authors;
#' available at the following web site: https://www.fragstats.org
#'
#' LaGro, J. 1991. Assessing patch shape in landscape mosaics.
#' Photogrammetric Engineering and Remote Sensing, 57(3), 285-293
#'
#' @export
lsm_p_contig <- function(landscape, directions = 8) {
landscape <- landscape_as_list(landscape)
result <- lapply(X = landscape,
FUN = lsm_p_contig_calc,
directions = directions)
layer <- rep(seq_along(result),
vapply(result, nrow, FUN.VALUE = integer(1)))
result <- do.call(rbind, result)
tibble::add_column(result, layer, .before = TRUE)
}
lsm_p_contig_calc <- function(landscape, directions) {
# convert to matrix
if (!inherits(x = landscape, what = "matrix")) {
landscape <- terra::as.matrix(landscape, wide = TRUE)
}
# all values NA
if (all(is.na(landscape))) {
return(tibble::tibble(level = "patch",
class = as.integer(NA),
id = as.integer(NA),
metric = "contig",
value = as.double(NA)))
}
# get unique values
classes <- get_unique_values_int(landscape, verbose = FALSE)
# diagonal neighbours
diagonal_matrix <- matrix(c(1, NA, 1,
NA, 0, NA,
1, NA, 1), 3, 3, byrow = TRUE)
# x-y neighbours
straigth_matrix <- matrix(c(NA, 1, NA,
1, 0, 1,
NA, 1, NA), 3, 3, byrow = TRUE)
contig_patch <- do.call(rbind,
lapply(classes, function(patches_class) {
# get connected patches
patch_mat <- get_patches_int(landscape,
directions = directions,
class = patches_class)[[1]]
# get number of cells for each patch
n_cells <- rcpp_get_composition_vector(patch_mat)
# get number of patches
n_patches <- length(n_cells)
# get diagonal neighbours of same patch
diagonal_neighbours <- rcpp_get_coocurrence_matrix_diag(patch_mat,
directions = as.matrix(diagonal_matrix))
# get straight neighbours of same patch weighted twice
straigth_neighbours <- rcpp_get_coocurrence_matrix_diag(patch_mat,
directions = as.matrix(straigth_matrix)) * 2
# calculated contiguity
contiguity <- (((diagonal_neighbours + straigth_neighbours + n_cells) /
n_cells) - 1) / 12
class <- patches_class
rm(patch_mat)
gc(verbose = FALSE)
tibble::tibble(class = class,
value = contiguity)
})
)
tibble::tibble(
level = "patch",
class = as.integer(contig_patch$class),
id = as.integer(seq_len(nrow(contig_patch))),
metric = "contig",
value = as.double(contig_patch$value)
)
}
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.