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r-spatialecology · Jan 8, 2024 · 943a661 · 943a661
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diff --git a/NEWS.md b/NEWS.md
@@ -1,4 +1,6 @@
 # landscapemetrics 2.1.1
+* Improvements
+    * Simplify roxygen2 docs
 * Bugfixes
     * Bugfix in calculate of clumpy if NA values are present
     * Bugfix in construct_buffer that CRS was lost

diff --git a/R/calculate_correlation.R b/R/calculate_correlation.R
@@ -18,9 +18,6 @@
 #' metrics <- calculate_lsm(landscape, what = c("patch", "class"))
 #' calculate_correlation(metrics, method = "pearson")
 #'
-#' @aliases calculate_correlation
-#' @rdname calculate_correlation
-#'
 #' @export
 calculate_correlation <- function(metrics, method = "pearson",
                                   diag = TRUE, simplify = FALSE) {

diff --git a/R/calculate_lsm.R b/R/calculate_lsm.R
@@ -52,9 +52,6 @@
 #' type = "aggregation metric")
 #' }
 #'
-#' @aliases calculate_lsm
-#' @rdname calculate_lsm
-#'
 #' @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;

diff --git a/R/check_landscape.R b/R/check_landscape.R
@@ -22,9 +22,6 @@
 #' landscape <- terra::rast(landscapemetrics::landscape)
 #' check_landscape(c(landscape, landscape))
 #'
-#' @aliases check_landscape
-#' @rdname check_landscape
-#'
 #' @export
 check_landscape <- function(landscape, verbose = TRUE) {
 

diff --git a/R/construct_buffer.R b/R/construct_buffer.R
@@ -17,9 +17,6 @@
 #' coords <- matrix(c(10, 5, 25, 15, 5, 25), ncol = 2, byrow = TRUE)
 #' construct_buffer(coords = coords, shape = "square", size = 5)
 #'
-#' @aliases construct_buffer
-#' @rdname construct_buffer
-#'
 #' @keywords internal
 #'
 #' @export

diff --git a/R/data_info.R b/R/data_info.R
@@ -17,9 +17,6 @@
 #' landscape <- terra::rast(landscapemetrics::landscape)
 #' data_info(landscape)
 #'
-#' @aliases data_info
-#' @rdname data_info
-#'
 #' @keywords internal
 #'
 #' @export

diff --git a/R/extract_lsm.R b/R/extract_lsm.R
@@ -41,9 +41,6 @@
 #'
 #' }
 #'
-#' @aliases extract_lsm
-#' @rdname extract_lsm
-#'
 #' @export
 extract_lsm <- function(landscape, y,
                         extract_id = NULL, metric = NULL,

diff --git a/R/get_adjacencies.R b/R/get_adjacencies.R
@@ -41,9 +41,6 @@
 #'                             1,  NA,  1), 3, 3, byrow = TRUE)
 #' get_adjacencies(landscape, diagonal_matrix)
 #'
-#' @aliases get_adjacencies
-#' @rdname get_adjacencies
-#'
 #' @export
 get_adjacencies <- function(landscape, neighbourhood = 4, what = "full", upper = FALSE) {
 

diff --git a/R/get_boundaries.R b/R/get_boundaries.R
@@ -26,9 +26,6 @@
 #' get_boundaries(class_1)
 #' get_boundaries(class_1, return_raster = FALSE)
 #'
-#' @aliases get_boundaries
-#' @rdname get_boundaries
-#'
 #' @export
 get_boundaries <- function(landscape,
                            consider_boundary = FALSE, edge_depth = 1,

diff --git a/R/get_centroids.R b/R/get_centroids.R
@@ -21,9 +21,6 @@
 #' landscape <- terra::rast(landscapemetrics::landscape)
 #' get_centroids(landscape)
 #'
-#' @aliases get_centroids
-#' @rdname get_centroids
-#'
 #' @export
 get_centroids <- function(landscape, directions = 8, cell_center = FALSE,
                           return_vec = FALSE, verbose = TRUE) {

diff --git a/R/get_circumscribingcircle.R b/R/get_circumscribingcircle.R
@@ -24,9 +24,6 @@
 #' # get circle around whole class
 #' get_circumscribingcircle(landscape, level = "class")
 #'
-#' @aliases get_circumscribingcircle
-#' @rdname get_circumscribingcircle
-#'
 #' @export
 get_circumscribingcircle <- function(landscape, directions = 8, level = "patch") {
 
@@ -115,7 +112,7 @@ get_circumscribingcircle_calc <- function(landscape, level, directions) {
         circle_class <- rcpp_get_circle(landscape, resolution_xy = resolution[1])
 
         # resulting tibble
-        circle <- tibble::new_tibble(list(level = rep("class", nrow(circle_class)), 
+        circle <- tibble::new_tibble(list(level = rep("class", nrow(circle_class)),
                                  class = as.integer(circle_class$patch_id),
                                  id = rep(as.integer(NA), nrow(circle_class)),
                                  value = circle_class$circle_diameter,

diff --git a/R/get_nearestneighbour.R b/R/get_nearestneighbour.R
@@ -25,9 +25,6 @@
 #' get_nearestneighbour(class_1)
 #' get_nearestneighbour(class_1, return_id = TRUE)
 #'
-#' @aliases get_nearestneighbour
-#' @rdname get_nearestneighbour
-#'
 #' @export
 get_nearestneighbour <- function(landscape, return_id = FALSE) {
 

diff --git a/R/get_patches.R b/R/get_patches.R
@@ -45,9 +45,6 @@
 #' # check for patches of every class
 #' patched_raster <-  get_patches(landscape)
 #'
-#' @aliases get_patches
-#' @rdname get_patches
-#'
 #' @export
 get_patches <- function(landscape, class = "all", directions = 8,
                         to_disk = getOption("to_disk", default = FALSE),

diff --git a/R/get_unique_values.R b/R/get_unique_values.R
@@ -27,9 +27,6 @@
 #' landscape_list <- list(landscape, landscape_matrix, x_vec)
 #' get_unique_values(landscape_list)
 #'
-#' @aliases get_unique_values
-#' @rdname get_unique_values
-#'
 #' @export
 get_unique_values <- function(x, simplify = FALSE, verbose = TRUE) {
 

diff --git a/R/landscape_as_list.R b/R/landscape_as_list.R
@@ -12,9 +12,6 @@
 #' landscape <- terra::rast(landscapemetrics::landscape)
 #' landscape_as_list(c(landscape, landscape))
 #'
-#' @aliases landscape_as_list
-#' @rdname landscape_as_list
-#'
 #' @export
 landscape_as_list <- function(landscape) UseMethod("landscape_as_list")
 

diff --git a/R/list_lsm.R b/R/list_lsm.R
@@ -30,9 +30,6 @@
 #' list_lsm(metric = "area", what = c("patch", "lsm_l_ta"))
 #' list_lsm(what = c("lsm_c_tca", "lsm_l_ta"))
 #'
-#' @aliases list_lsm
-#' @rdname list_lsm
-#'
 #' @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;

diff --git a/R/lsm_c_ai.R b/R/lsm_c_ai.R
@@ -28,9 +28,6 @@
 #' landscape <- terra::rast(landscapemetrics::landscape)
 #' lsm_c_ai(landscape)
 #'
-#' @aliases lsm_c_ai
-#' @rdname lsm_c_ai
-#'
 #' @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;

diff --git a/R/lsm_c_area_cv.R b/R/lsm_c_area_cv.R
@@ -33,9 +33,6 @@
 #' landscape <- terra::rast(landscapemetrics::landscape)
 #' lsm_c_area_cv(landscape)
 #'
-#' @aliases lsm_c_area_cv
-#' @rdname lsm_c_area_cv
-#'
 #' @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;

diff --git a/R/lsm_c_area_mn.R b/R/lsm_c_area_mn.R
@@ -35,9 +35,6 @@
 #' landscape <- terra::rast(landscapemetrics::landscape)
 #' lsm_c_area_mn(landscape)
 #'
-#' @aliases lsm_c_area_mn
-#' @rdname lsm_c_area_mn
-#'
 #' @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;

diff --git a/R/lsm_c_area_sd.R b/R/lsm_c_area_sd.R
@@ -35,9 +35,6 @@
 #' landscape <- terra::rast(landscapemetrics::landscape)
 #' lsm_c_area_sd(landscape)
 #'
-#' @aliases lsm_c_area_sd
-#' @rdname lsm_c_area_sd
-#'
 #' @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;

diff --git a/R/lsm_c_ca.R b/R/lsm_c_ca.R
@@ -34,9 +34,6 @@
 #' landscape <- terra::rast(landscapemetrics::landscape)
 #' lsm_c_ca(landscape)
 #'
-#' @aliases lsm_c_ca
-#' @rdname lsm_c_ca
-#'
 #' @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;

diff --git a/R/lsm_c_cai_cv.R b/R/lsm_c_cai_cv.R
@@ -42,9 +42,6 @@
 #' landscape <- terra::rast(landscapemetrics::landscape)
 #' lsm_c_cai_cv(landscape)
 #'
-#' @aliases lsm_c_cai_cv
-#' @rdname lsm_c_cai_cv
-#'
 #' @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;

diff --git a/R/lsm_c_cai_mn.R b/R/lsm_c_cai_mn.R
@@ -40,9 +40,6 @@
 #' landscape <- terra::rast(landscapemetrics::landscape)
 #' lsm_c_cai_mn(landscape)
 #'
-#' @aliases lsm_c_cai_mn
-#' @rdname lsm_c_cai_mn
-#'
 #' @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;

diff --git a/R/lsm_c_cai_sd.R b/R/lsm_c_cai_sd.R
@@ -42,9 +42,6 @@
 #' landscape <- terra::rast(landscapemetrics::landscape)
 #' lsm_c_cai_sd(landscape)
 #'
-#' @aliases lsm_c_cai_sd
-#' @rdname lsm_c_cai_sd
-#'
 #' @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;

diff --git a/R/lsm_c_circle_cv.R b/R/lsm_c_circle_cv.R
@@ -38,9 +38,6 @@
 #' landscape <- terra::rast(landscapemetrics::landscape)
 #' lsm_c_circle_cv(landscape)
 #'
-#' @aliases lsm_c_circle_cv
-#' @rdname lsm_c_circle_cv
-#'
 #' @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;

diff --git a/R/lsm_c_circle_mn.R b/R/lsm_c_circle_mn.R
@@ -36,9 +36,6 @@
 #' landscape <- terra::rast(landscapemetrics::landscape)
 #' lsm_c_circle_mn(landscape)
 #'
-#' @aliases lsm_c_circle_mn
-#' @rdname lsm_c_circle_mn
-#'
 #' @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;

diff --git a/R/lsm_c_circle_sd.R b/R/lsm_c_circle_sd.R
@@ -36,9 +36,6 @@
 #' landscape <- terra::rast(landscapemetrics::landscape)
 #' lsm_c_circle_sd(landscape)
 #'
-#' @aliases lsm_c_circle_sd
-#' @rdname lsm_c_circle_sd
-#'
 #' @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;

diff --git a/R/lsm_c_clumpy.R b/R/lsm_c_clumpy.R
@@ -29,9 +29,6 @@
 #' landscape <- terra::rast(landscapemetrics::landscape)
 #' lsm_c_clumpy(landscape)
 #'
-#' @aliases lsm_c_clumpy
-#' @rdname lsm_c_clumpy
-#'
 #' @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;

diff --git a/R/lsm_c_cohesion.R b/R/lsm_c_cohesion.R
@@ -32,9 +32,6 @@
 #' landscape <- terra::rast(landscapemetrics::landscape)
 #' lsm_c_cohesion(landscape)
 #'
-#' @aliases lsm_c_cohesion
-#' @rdname lsm_c_cohesion
-#'
 #' @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;
@@ -87,7 +84,7 @@ lsm_c_cohesion_calc <- function(landscape, directions, resolution, extras = NULL
                                   directions = directions,
                                   resolution = resolution,
                                   extras = extras)
-    
+
     # get number of cells for each patch -> area = n_cells * res / 10000
     patch_area$ncells <- patch_area$value * 10000 / prod(resolution)
 

diff --git a/R/lsm_c_contig_cv.R b/R/lsm_c_contig_cv.R
@@ -44,9 +44,6 @@
 #' landscape <- terra::rast(landscapemetrics::landscape)
 #' lsm_c_contig_cv(landscape)
 #'
-#' @aliases lsm_c_contig_cv
-#' @rdname lsm_c_contig_cv
-#'
 #' @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;

diff --git a/R/lsm_c_contig_mn.R b/R/lsm_c_contig_mn.R
@@ -43,9 +43,6 @@
 #' landscape <- terra::rast(landscapemetrics::landscape)
 #' lsm_c_contig_mn(landscape)
 #'
-#' @aliases lsm_c_contig_mn
-#' @rdname lsm_c_contig_mn
-#'
 #' @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;

diff --git a/R/lsm_c_contig_sd.R b/R/lsm_c_contig_sd.R
@@ -44,9 +44,6 @@
 #' landscape <- terra::rast(landscapemetrics::landscape)
 #' lsm_c_contig_sd(landscape)
 #'
-#' @aliases lsm_c_contig_sd
-#' @rdname lsm_c_contig_sd
-#'
 #' @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;

diff --git a/R/lsm_c_core_cv.R b/R/lsm_c_core_cv.R
@@ -37,9 +37,6 @@
 #' landscape <- terra::rast(landscapemetrics::landscape)
 #' lsm_c_core_cv(landscape)
 #'
-#' @aliases lsm_c_core_cv
-#' @rdname lsm_c_core_cv
-#'
 #' @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;

diff --git a/R/lsm_c_core_mn.R b/R/lsm_c_core_mn.R
@@ -36,9 +36,6 @@
 #' landscape <- terra::rast(landscapemetrics::landscape)
 #' lsm_c_core_mn(landscape)
 #'
-#' @aliases lsm_c_core_mn
-#' @rdname lsm_c_core_mn
-#'
 #' @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;

diff --git a/R/lsm_c_core_sd.R b/R/lsm_c_core_sd.R
@@ -38,9 +38,6 @@
 #' landscape <- terra::rast(landscapemetrics::landscape)
 #' lsm_c_core_sd(landscape)
 #'
-#' @aliases lsm_c_core_sd
-#' @rdname lsm_c_core_sd
-#'
 #' @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;

diff --git a/R/lsm_c_cpland.R b/R/lsm_c_cpland.R
@@ -34,9 +34,6 @@
 #' landscape <- terra::rast(landscapemetrics::landscape)
 #' lsm_c_cpland(landscape)
 #'
-#' @aliases lsm_c_cpland
-#' @rdname lsm_c_cpland
-#'
 #' @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;
@@ -93,7 +90,7 @@ lsm_c_cpland_calc <- function(landscape, directions, consider_boundary, edge_dep
     core_area <- lsm_p_core_calc(landscape,
                                  directions = directions,
                                  consider_boundary = consider_boundary,
-                                 edge_depth = edge_depth, 
+                                 edge_depth = edge_depth,
                                  resolution = resolution,
                                  extras = extras)
 

diff --git a/R/lsm_c_dcad.R b/R/lsm_c_dcad.R
@@ -38,9 +38,6 @@
 #' landscape <- terra::rast(landscapemetrics::landscape)
 #' lsm_c_dcad(landscape)
 #'
-#' @aliases lsm_c_dcad
-#' @rdname lsm_c_dcad
-#'
 #' @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;