Merge pull request #131 from r-spatialecology/main

mhesselbarth · web-flow · commit 66f668fdd87f · 2024-01-09T11:40:45.000+01:00
v2.2.1
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Type: Package
 Package: shar
 Title: Species-Habitat Associations
-Version: 2.2
+Version: 2.2.1
 Authors@R: c(person("Maximilian H.K.", "Hesselbarth", email = "mhk.hesselbarth@gmail.com",
              role = c("aut", "cre"), comment = c(ORCID = "0000-0003-1125-9918")),
              person("Marco", "Sciaini", email = "marco.sciaini@posteo.net",
diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,7 @@
+# shar 2.2.1
+* Improvements
+  * Simplify roxygen2 docs
+
 # shar 2.2
 * Improvements
   * Added a new function `reconstruct_pattern_multi()` including several internal functions and methods
diff --git a/R/calc_gest.R b/R/calc_gest.R
@@ -14,9 +14,6 @@
 #'
 #' @return data.frame
 #'
-#' @aliases calc_gest
-#' @rdname calc_gest
-#'
 #' @keywords internal
 calc_gest <- function(dist, r, n_points){
 
diff --git a/R/calc_moments.R b/R/calc_moments.R
@@ -19,9 +19,6 @@
 #'
 #' @return matrix
 #'
-#' @aliases calc_moments
-#' @rdname calc_moments
-#'
 #' @keywords internal
 calc_moments <- function(fn,
                          p,
diff --git a/R/calculate_energy.R b/R/calculate_energy.R
@@ -33,9 +33,6 @@
 #' calculate_energy(marks_recon, return_mean = FALSE)
 #' }
 #'
-#' @aliases calculate_energy
-#' @rdname calculate_energy
-#'
 #' @references
 #' Kirkpatrick, S., Gelatt, C.D.Jr., Vecchi, M.P., 1983. Optimization by simulated
 #' annealing. Science 220, 671–680. <https://doi.org/10.1126/science.220.4598.671>
diff --git a/R/classify_habitats.R b/R/classify_habitats.R
@@ -27,9 +27,6 @@
 #' landscape_classified <- classify_habitats(terra::rast(landscape), style = "fixed",
 #' fixedBreaks = c(0, 0.25, 0.75, 1.0), return_breaks = TRUE)
 #'
-#' @aliases classify_habitats
-#' @rdname classify_habitats
-#'
 #' @references
 #' Armstrong, M.P., Xiao, N., Bennett, D.A., 2003. Using genetic algorithms to create
 #' multicriteria class intervals for choropleth maps. Annals of the Association of
diff --git a/R/classint_to_vector.R b/R/classint_to_vector.R
@@ -16,9 +16,6 @@
 #' classint_to_vector(x = landscape_classified$breaks, digits = 4)
 #' }
 #'
-#' @aliases classint_to_vector
-#' @rdname classint_to_vector
-#'
 #' @keywords internal
 classint_to_vector <- function(x, digits = NULL) {
 
diff --git a/R/compute_statistics.R b/R/compute_statistics.R
@@ -15,9 +15,6 @@
 #'
 #' @return list
 #'
-#' @aliases compute_statistics
-#' @rdname compute_statistics
-#'
 #' @keywords internal
 compute_statistics <- function(x, y, k, xr, yr, w_statistics, bw, divisor, kernel_arg, r) {
 
diff --git a/R/create_neighbourhood.R b/R/create_neighbourhood.R
@@ -22,9 +22,6 @@
 #' create_neighbourhood(cell_id, mat)
 #' }
 #'
-#' @aliases create_neighbourhood
-#' @rdname create_neighbourhood
-#'
 #' @keywords internal
 create_neighbourhood <- function(cells, matrix, directions = 4) {
 
diff --git a/R/dummy_transf.R b/R/dummy_transf.R
@@ -11,9 +11,6 @@
 #'
 #' @return matrix
 #'
-#' @aliases dummy_transf
-#' @rdname dummy_transf
-#'
 #' @keywords internal
 to_dummy <- function(f) {
   x <- matrix(0, length(f), nlevels(f), dimnames=list(names(f), levels(f)))
diff --git a/R/energy_fun.R b/R/energy_fun.R
@@ -24,9 +24,6 @@
 #'
 #' @return vector
 #'
-#' @aliases energy_fun
-#' @rdname energy_fun
-#'
 #' @keywords internal
 #'
 Energy_fun <- function(f, f0, statistics, f_, f0_, statistics_, fn, p, p_, Lp, w_statistics) {
diff --git a/R/extract_points.R b/R/extract_points.R
@@ -19,9 +19,6 @@
 #' extract_points(raster = landscape_classified, pattern = species_b)
 #' }
 #'
-#' @aliases extract_points
-#' @rdname extract_points
-#'
 #' @keywords internal
 extract_points <- function(raster, pattern){
 
diff --git a/R/fit_point_process.R b/R/fit_point_process.R
@@ -22,9 +22,6 @@
 #' @examples
 #' pattern_fitted <- fit_point_process(pattern = species_a, n_random = 39)
 #'
-#' @aliases fit_point_process
-#' @rdname fit_point_process
-#'
 #' @references
 #' Plotkin, J.B., Potts, M.D., Leslie, N., Manokaran, N., LaFrankie, J.V.,
 #' Ashton, P.S., 2000. Species-area curves, spatial aggregation, and habitat specialization
diff --git a/R/get_dist_pairs.R b/R/get_dist_pairs.R
@@ -13,9 +13,6 @@
 #'
 #' @return matrix
 #'
-#' @aliases get_dist_pairs
-#' @rdname get_dist_pairs
-#'
 #' @keywords internal
 get_dist_pairs <- function(X, rmax){
 
diff --git a/R/list_to_randomized.R b/R/list_to_randomized.R
@@ -27,9 +27,6 @@
 #' list_to_randomized(list = fit_list, observed = species_a)
 #' }
 #'
-#' @aliases list_to_randomized
-#' @rdname list_to_randomized
-#'
 #' @export
 list_to_randomized <- function(list, observed = NULL) {
 
diff --git a/R/pack_randomized.R b/R/pack_randomized.R
@@ -21,9 +21,6 @@
 #' x <- pack_randomized(raster = landscape_random)
 #' }
 #'
-#' @aliases pack_randomized
-#' @rdname pack_randomized
-#'
 #' @export
 pack_randomized <- function(raster) {
 
diff --git a/R/plot.rd_mar.R b/R/plot.rd_mar.R
@@ -38,10 +38,6 @@
 #' plot(marks_recon)
 #' }
 #'
-#'
-#' @aliases plot.rd_mar
-#' @rdname plot.rd_mar
-#'
 #' @export
 plot.rd_mar <- function(x, what = "sf", n = NULL, probs = c(0.025, 0.975),
                         ask = TRUE, verbose = TRUE, ...) {
diff --git a/R/plot.rd_multi.R b/R/plot.rd_multi.R
@@ -16,9 +16,6 @@
 #'
 #' @return void
 #'
-#' @aliases plot.rd_multi
-#' @rdname plot.rd_multi
-#'
 #' @export
 plot.rd_multi <- function(x, verbose = TRUE, ...) {
 
diff --git a/R/plot.rd_pat.R b/R/plot.rd_pat.R
@@ -38,9 +38,6 @@
 #' plot(pattern_recon)
 #' }
 #'
-#' @aliases plot.rd_pat
-#' @rdname plot.rd_pat
-#'
 #' @export
 plot.rd_pat <- function(x, what = "sf", n = NULL, probs = c(0.025, 0.975),
                         ask = TRUE, verbose = TRUE, ...) {
diff --git a/R/plot.rd_ras.R b/R/plot.rd_ras.R
@@ -28,9 +28,6 @@
 #' plot(landscape_random)
 #' }
 #'
-#' @aliases plot.rd_ras
-#' @rdname plot.rd_ras
-#'
 #' @export
 plot.rd_ras <- function(x, n = NULL, col, verbose = TRUE, nrow, ncol, ...) {
 
diff --git a/R/plot_energy.R b/R/plot_energy.R
@@ -28,9 +28,6 @@
 #' plot_energy(marks_recon)
 #' }
 #'
-#' @aliases plot_energy
-#' @rdname plot_energy
-#'
 #' @export
 plot_energy <- function(pattern,
                         col = NULL){
diff --git a/R/print.rd_mar.R b/R/print.rd_mar.R
@@ -24,9 +24,6 @@
 #' print(marks_recon)
 #' }
 #'
-#' @aliases print.rd_mar
-#' @rdname print.rd_mar
-#'
 #' @export
 print.rd_mar <- function(x, digits = 4, ...) {
 
diff --git a/R/print.rd_pat.R b/R/print.rd_pat.R
@@ -25,9 +25,6 @@
 #' print(pattern_recon)
 #' }
 #'
-#' @aliases print.rd_pat
-#' @rdname print.rd_pat
-#'
 #' @export
 print.rd_pat <- function(x,
                          digits = 4,
diff --git a/R/print.rd_ras.R b/R/print.rd_ras.R
@@ -23,9 +23,6 @@
 #' print(landscape_random)
 #' }
 #'
-#' @aliases print.rd_ras
-#' @rdname print.rd_ras
-#'
 #' @export
 print.rd_ras <- function(x, ...) {
 
diff --git a/R/randomize_raster.R b/R/randomize_raster.R
@@ -32,9 +32,6 @@
 #' landscape_random <- randomize_raster(landscape_classified, n_random = 19)
 #' }
 #'
-#' @aliases randomize_raster
-#' @rdname randomize_raster
-#'
 #' @references
 #' Harms, K.E., Condit, R., Hubbell, S.P., Foster, R.B., 2001. Habitat associations of
 #' trees and shrubs in a 50-ha neotropical forest plot. Journal of Ecology 89, 947–959.
diff --git a/R/reconstruct_algorithm.R b/R/reconstruct_algorithm.R
@@ -23,9 +23,6 @@
 #'
 #' @return list
 #'
-#' @aliases reconstruct_algorithm
-#' @rdname reconstruct_algorithm
-#'
 #' @keywords internal
 reconstruct_algorithm <- function(pattern,
                                   method,
diff --git a/R/reconstruct_pattern.R b/R/reconstruct_pattern.R
@@ -69,9 +69,6 @@
 #' pattern_recon <- reconstruct_pattern(species_b, n_random = 19, max_runs = 1000)
 #' }
 #'
-#' @aliases reconstruct_pattern
-#' @rdname reconstruct_pattern
-#'
 #' @references
 #' Kirkpatrick, S., Gelatt, C.D.Jr., Vecchi, M.P., 1983. Optimization by simulated
 #' annealing. Science 220, 671–680. <https://doi.org/10.1126/science.220.4598.671>
diff --git a/R/reconstruct_pattern_marks.R b/R/reconstruct_pattern_marks.R
@@ -49,9 +49,6 @@
 #' n_random = 19, max_runs = 1000)
 #' }
 #'
-#' @aliases reconstruct_pattern_marks
-#' @rdname reconstruct_pattern_marks
-#'
 #' @references
 #' Kirkpatrick, S., Gelatt, C.D.Jr., Vecchi, M.P., 1983. Optimization by simulated
 #' annealing. Science 220, 671–680. <https://doi.org/10.1126/science.220.4598.671>
diff --git a/R/reconstruct_pattern_multi.R b/R/reconstruct_pattern_multi.R
@@ -94,9 +94,6 @@
 #' max_steps = 10000)
 #' }
 #'
-#' @aliases reconstruct_pattern_multi
-#' @rdname reconstruct_pattern_multi
-#'
 #' @references
 #' Kirkpatrick, S., Gelatt, C.D.Jr., Vecchi, M.P., 1983. Optimization by simulated
 #' annealing. Science 220, 671–680. <https://doi.org/10.1126/science.220.4598.671>
diff --git a/R/results_habitat_association.R b/R/results_habitat_association.R
@@ -36,9 +36,6 @@
 #' species_a_random <- fit_point_process(species_a, n_random = 199)
 #' results_habitat_association(pattern = species_a_random, raster = landscape_classified)
 #'
-#' @aliases results_habitat_association
-#' @rdname results_habitat_association
-#'
 #' @references
 #' Harms, K.E., Condit, R., Hubbell, S.P., Foster, R.B., 2001. Habitat associations of
 #' trees and shrubs in a 50-ha neotropical forest plot. Journal of Ecology 89, 947–959.
diff --git a/R/sample_randomized.R b/R/sample_randomized.R
@@ -18,9 +18,6 @@
 #' sample_randomized(randomized = reconstruction$randomized, n = c(5, 10, 15))
 #' }
 #'
-#' @aliases sample_randomized
-#' @rdname sample_randomized
-#'
 #' @keywords internal
 sample_randomized <- function(randomized, n = NULL, verbose = TRUE) {
 
diff --git a/R/select_kernel.R b/R/select_kernel.R
@@ -17,9 +17,6 @@
 #'
 #' @return list
 #'
-#' @aliases select_kernel
-#' @rdname select_kernel
-#'
 #' @keywords internal
 #'
 select_kernel <- function(kernel_arg, bw, rmax, divisor) {
diff --git a/R/translate_raster.R b/R/translate_raster.R
@@ -32,9 +32,6 @@
 #' steps_x = 1:10, steps_y = 1:5)
 #' }
 #'
-#' @aliases translate_raster
-#' @rdname translate_raster
-#'
 #' @references
 #' Harms, K.E., Condit, R., Hubbell, S.P., Foster, R.B., 2001. Habitat associations
 #' of trees and shrubs in a 50-ha neotropical forest plot. Journal of Ecology 89, 947–959.
diff --git a/R/unpack_randomized.R b/R/unpack_randomized.R
@@ -23,9 +23,6 @@
 #' y <- unpack_randomized(raster = y)
 #' }
 #'
-#' @aliases unpack_randomized
-#' @rdname unpack_randomized
-#'
 #' @export
 unpack_randomized <- function(raster) {
 
diff --git a/codemeta.json b/codemeta.json
diff --git a/cran-comments.md b/cran-comments.md
diff --git a/man/energy_fun.Rd b/man/energy_fun.Rd
diff --git a/man/plot.rd_mar.Rd b/man/plot.rd_mar.Rd
diff --git a/man/to_dummy.Rd b/man/to_dummy.Rd
