Merge pull request #48 from jakobdanel/feat/distance-n-neighbours

Feat/distance n neighbours

NAMESPACE

@@ -6,26 +6,33 @@ export(get_tiles_path)
 export(is_tile_existing)
 export(lfa_capitalize_first_char)
 export(lfa_check_flag)
+export(lfa_combine_sf_obj)
 export(lfa_create_stacked_distributions_plot)
 export(lfa_create_stacked_histogram)
 export(lfa_create_tile_location_objects)
 export(lfa_detection)
 export(lfa_download)
 export(lfa_download_areas)
+export(lfa_find_n_nearest_trees)
 export(lfa_get_all_areas)
 export(lfa_get_detection_area)
+export(lfa_get_detections)
 export(lfa_get_detections_species)
 export(lfa_get_flag_path)
+export(lfa_get_neighbor_paths)
+export(lfa_get_species)
 export(lfa_ground_correction)
 export(lfa_init)
 export(lfa_init_data_structure)
 export(lfa_intersect_areas)
 export(lfa_load_ctg_if_not_present)
 export(lfa_map_tile_locations)
 export(lfa_merge_and_save)
+export(lfa_modify_gpkg)
 export(lfa_rd_to_qmd)
 export(lfa_rd_to_results)
 export(lfa_read_area_as_catalog)
+export(lfa_save_all_neighbours)
 export(lfa_segmentation)
 export(lfa_set_flag)
 export(read_catalog)

R/combine_sf_obj.R

@@ -0,0 +1,31 @@
+#' Combine Spatial Feature Objects from Multiple GeoPackage Files
+#'
+#' This function reads spatial feature objects (sf) from multiple GeoPackage files and combines them into a single sf object.
+#' Each GeoPackage file is assumed to contain neighbor information for a specific detection area, and the resulting sf object
+#' includes additional columns indicating the corresponding area and species information.
+#'
+#' @param paths A character vector containing file paths to GeoPackage files with neighbor information.
+#' @param area_infos A data frame or list containing information about the corresponding detection areas, including "area" and "specie" columns.
+#' @return A combined sf object with additional columns for area and specie information.
+#' @export
+#'
+#' @examples
+#' # Assuming paths and area_infos are defined
+#' combined_sf <- lfa_combine_sf_obj(paths, area_infos)
+#'
+#' # Print the combined sf object
+#' print(combined_sf)
+#'
+#'@export
+lfa_combine_sf_obj <- function(paths, area_infos) {
+  sf_obj <- sf::st_read(paths[1])
+  sf_obj$area = area_infos$area[1]
+  sf_obj$specie = area_infos$specie[1]
+  for (i in 2:length(paths)) {
+    extend <- sf::st_read(paths[i])
+    extend$area = area_infos$area[i]
+    extend$specie = area_infos$specie[i]
+    sf_obj <- dplyr::bind_rows(sf_obj, extend)
+  }
+  return(sf_obj)
+}

R/find_n_nearest_trees.R

@@ -0,0 +1,48 @@
+#' Find n Nearest Trees
+#'
+#' This function calculates the distances to the n nearest trees for each tree in the input dataset.
+#'
+#' @param trees A sf object containing tree coordinates.
+#' @param n The number of nearest trees to find for each tree (default is 100).
+#' @return A data frame with additional columns representing the distances to the n nearest trees.
+#'
+#' @examples
+#' # Load tree data using lfa_get_detections() (not provided)
+#' tree_data <- lfa_get_detections()
+#'
+#' # Filter tree data for a specific species and area
+#' tree_data = tree_data[tree_data$specie == "pine" & tree_data$area == "greffen", ]
+#'
+#' # Find the 100 nearest trees for each tree in the filtered dataset
+#' tree_data <- lfa_find_n_nearest_trees(tree_data)
+#'
+#'@export
+lfa_find_n_nearest_trees <- function(trees, n = 100) {
+  coordinates <- sf::st_coordinates(trees)
+
+  distances_matrix <- matrix(NA, nrow = nrow(coordinates), ncol = n)
+
+  cat("Calculate ", nrow(coordinates), "entries")
+  for (i in seq_len(nrow(coordinates))) {
+    query_point <- coordinates[i,]
+    neighbors <-
+      spdep::knn2nb(spdep::knearneigh(coordinates, k = n))
+
+    # Extract the coordinates of neighbors and create an sf object
+    neighbor_indices <- unlist(neighbors[[i]])
+    neighbors_sf <- trees[neighbor_indices,]
+
+    # Set CRS for query point
+    query_point_sf <-
+      sf::st_sfc(sf::st_point(c(query_point[1], query_point[2])), crs = sf::st_crs(trees))
+
+    distances <- sf::st_distance(query_point_sf, neighbors_sf)
+    distances <- distances[order(distances)]
+    distances_matrix[i, ] <- distances
+    cat(i, "/", nrow(coordinates), "\n")
+  }
+  distances_matrix <- distances_matrix |> data.frame()
+  colnames(distances_matrix) <- paste0("Neighbor_", 1:n)
+  trees <- dplyr::bind_cols(trees, distances_matrix)
+  return(trees)
+}

R/get_detections.R

@@ -0,0 +1,43 @@
+#' Retrieve aggregated detection data for multiple species.
+#'
+#' This function obtains aggregated detection data for multiple species by iterating
+#' through the list of species obtained from \code{\link{lfa_get_species}}. For each
+#' species, it calls \code{\link{lfa_get_detections_species}} to retrieve the
+#' corresponding detection data and aggregates the results into a single data frame.
+#' The resulting data frame includes columns for the species, tree detection data,
+#' and the area in which the detections occurred.
+#'
+#' @return A data frame containing aggregated detection data for multiple species.
+#'
+#' @export
+#' @seealso
+#' \code{\link{lfa_get_species}}, \code{\link{lfa_get_detections_species}}
+#'
+#' @examples
+#' lfa_get_detections()
+#'
+#' @keywords data manipulation aggregation
+#'
+#' @family data retrieval functions
+#'
+#' @examples
+#' # Retrieve aggregated detection data for multiple species
+#' detections_data <- lfa_get_detections()
+#'
+#' @export
+lfa_get_detections <- function() {
+  species <- lfa_get_species()
+  results <- NULL
+  for(specie in species){
+    trees <- lfa_get_detections_species(specie)
+    trees$specie <- specie
+    if(is.null(results)){
+      results <- trees
+    } else {
+      results <- dplyr::bind_rows(results, trees)
+    }
+  }
+  results$area <- as.factor(results$area)
+  results$specie <- as.factor(results$specie)
+  return(results)
+}

R/get_neighbor_paths.R

@@ -0,0 +1,25 @@
+#' Get Paths to Neighbor GeoPackage Files
+#'
+#' This function retrieves the file paths to GeoPackage files containing neighbor information for each detection area.
+#' The GeoPackage files are assumed to be named "neighbours.gpkg" and organized in a directory structure under the "data" folder.
+#'
+#' @return A character vector containing file paths to GeoPackage files for each detection area's neighbors.
+#' @export
+#'
+#' @examples
+#' # Get paths to neighbor GeoPackage files for all areas
+#' paths <- lfa_get_neighbor_paths()
+#'
+#' # Print the obtained file paths
+#' print(paths)
+#'@export
+lfa_get_neighbor_paths <- function() {
+  all_areas <- lfa::lfa_get_all_areas()
+  return(file.path(
+    getwd(),
+    "data",
+    all_areas$specie,
+    all_areas$area,
+    "neighbours.gpkg"
+  ))
+}

R/get_species.R

@@ -0,0 +1,25 @@
+#' Get a list of species from the data directory.
+#'
+#' This function retrieves a list of species by scanning the "data" directory
+#' located in the current working directory.
+#'
+#' @return A character vector containing the names of species found in the "data" directory.
+#'
+#' @seealso
+#' \code{\link{list.dirs}}
+#'
+#' @references
+#' This function relies on the \code{\link{list.dirs}} function for directory listing.
+#'
+#' @keywords data manipulation file system
+#'
+#' @family data retrieval functions
+#'
+#' @examples
+#' # Retrieve the list of species
+#' species_list <- lfa_get_species()
+#'
+#' @export
+lfa_get_species <- function() {
+  return(file.path(getwd(), "data") |> list.dirs(full.names = FALSE, recursive = FALSE))
+}

R/save_all_neighbours.R

@@ -0,0 +1,24 @@
+#' Save Neighbors for All Areas
+#'
+#' This function iterates through all detection areas, finds the n nearest trees for each tree,
+#' and saves the result to a GeoPackage file for each area.
+#'
+#' @param n The number of nearest trees to find for each tree (default is 100).
+#' @export
+#'
+#' @examples
+#' # Save neighbors for all areas with default value (n=100)
+#' lfa_save_all_neighbours()
+#'
+#' # Save neighbors for all areas with a specific value of n (e.g., n=50)
+#' lfa_save_all_neighbours(n = 50)
+#' @export
+lfa_save_all_neighbours <- function (n = 100) {
+  all_areas <- lfa::lfa_get_all_areas()
+  for (i in 1:nrow(all_areas)) {
+    cat("Find neighbours for", all_areas[i, 1], ",", all_areas[i, 2], "\n")
+    out_path <-
+      file.path(getwd(), "data", all_areas[i, 1], all_areas[i, 2], "neighbours.gpkg")
+    lfa::lfa_get_detection_area(all_areas[i, 1], all_areas[i, 2]) |> lfa::lfa_find_n_nearest_trees(n) |> sf::st_write(out_path, append = F)
+  }
+  }