R/RcppExports.R

In spacc: Fast Spatial Species Accumulation Curves

# Generated by using Rcpp::compileAttributes() -> do not edit by hand
# Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393

cpp_beta_knn_single <- function(species_pa, dist_mat, seed, use_jaccard = FALSE) {
    .Call(`_spacc_cpp_beta_knn_single`, species_pa, dist_mat, seed, use_jaccard)
}

cpp_beta_knn_parallel <- function(species_pa, dist_mat, n_seeds, use_jaccard = FALSE, n_cores = 1L, progress = FALSE) {
    .Call(`_spacc_cpp_beta_knn_parallel`, species_pa, dist_mat, n_seeds, use_jaccard, n_cores, progress)
}

calc_coverage <- function(abundances) {
    .Call(`_spacc_calc_coverage`, abundances)
}

calc_chiu_coverage <- function(abundances, incidences, T_sites) {
    .Call(`_spacc_calc_chiu_coverage`, abundances, incidences, T_sites)
}

cpp_knn_coverage_single <- function(species_mat, dist_mat, seed, coverage_type = 0L) {
    .Call(`_spacc_cpp_knn_coverage_single`, species_mat, dist_mat, seed, coverage_type)
}

cpp_knn_coverage_parallel <- function(species_mat, dist_mat, n_seeds, n_cores = 1L, progress = FALSE, coverage_type = 0L) {
    .Call(`_spacc_cpp_knn_coverage_parallel`, species_mat, dist_mat, n_seeds, n_cores, progress, coverage_type)
}

interpolate_at_coverage <- function(richness, coverage, targets) {
    .Call(`_spacc_interpolate_at_coverage`, richness, coverage, targets)
}

cpp_distance_matrix <- function(x, y, method = "euclidean") {
    .Call(`_spacc_cpp_distance_matrix`, x, y, method)
}

calc_hill_number <- function(abundances, q) {
    .Call(`_spacc_calc_hill_number`, abundances, q)
}

cpp_knn_hill_single <- function(species_mat, dist_mat, seed, q_values) {
    .Call(`_spacc_cpp_knn_hill_single`, species_mat, dist_mat, seed, q_values)
}

cpp_knn_hill_parallel <- function(species_mat, dist_mat, n_seeds, q_values, n_cores = 1L, progress = FALSE) {
    .Call(`_spacc_cpp_knn_hill_parallel`, species_mat, dist_mat, n_seeds, q_values, n_cores, progress)
}

cpp_knn_hill_beta_parallel <- function(species_mat, dist_mat, n_seeds, q_values, n_cores = 1L, progress = FALSE) {
    .Call(`_spacc_cpp_knn_hill_beta_parallel`, species_mat, dist_mat, n_seeds, q_values, n_cores, progress)
}

cpp_knn_hill_coverage_parallel <- function(species_mat, dist_mat, n_seeds, q_values, n_cores = 1L, progress = FALSE) {
    .Call(`_spacc_cpp_knn_hill_coverage_parallel`, species_mat, dist_mat, n_seeds, q_values, n_cores, progress)
}

cpp_kncn_single <- function(species_pa, x, y, seed) {
    .Call(`_spacc_cpp_kncn_single`, species_pa, x, y, seed)
}

cpp_kncn_parallel <- function(species_pa, x, y, n_seeds, n_cores = 1L, progress = FALSE) {
    .Call(`_spacc_cpp_kncn_parallel`, species_pa, x, y, n_seeds, n_cores, progress)
}

cpp_kncn_kdtree_single <- function(species_pa, x, y, seed, distance = "euclidean") {
    .Call(`_spacc_cpp_kncn_kdtree_single`, species_pa, x, y, seed, distance)
}

cpp_kncn_kdtree_parallel <- function(species_pa, x, y, n_seeds, n_cores = 1L, progress = FALSE, distance = "euclidean") {
    .Call(`_spacc_cpp_kncn_kdtree_parallel`, species_pa, x, y, n_seeds, n_cores, progress, distance)
}

cpp_knn_single <- function(species_pa, dist_mat, seed) {
    .Call(`_spacc_cpp_knn_single`, species_pa, dist_mat, seed)
}

cpp_knn_parallel <- function(species_pa, dist_mat, n_seeds, n_cores = 1L, progress = FALSE) {
    .Call(`_spacc_cpp_knn_parallel`, species_pa, dist_mat, n_seeds, n_cores, progress)
}

cpp_knn_parallel_seeds <- function(species_pa, dist_mat, seeds, n_cores = 1L, progress = FALSE) {
    .Call(`_spacc_cpp_knn_parallel_seeds`, species_pa, dist_mat, seeds, n_cores, progress)
}

cpp_knn_kdtree_single <- function(species_pa, x, y, seed, distance = "euclidean") {
    .Call(`_spacc_cpp_knn_kdtree_single`, species_pa, x, y, seed, distance)
}

cpp_knn_kdtree_parallel <- function(species_pa, x, y, n_seeds, n_cores = 1L, progress = FALSE, distance = "euclidean") {
    .Call(`_spacc_cpp_knn_kdtree_parallel`, species_pa, x, y, n_seeds, n_cores, progress, distance)
}

cpp_knn_kdtree_parallel_seeds <- function(species_pa, x, y, seeds, n_cores = 1L, progress = FALSE, distance = "euclidean") {
    .Call(`_spacc_cpp_knn_kdtree_parallel_seeds`, species_pa, x, y, seeds, n_cores, progress, distance)
}

cpp_collector_single <- function(species_pa) {
    .Call(`_spacc_cpp_collector_single`, species_pa)
}

cpp_gaussian_single <- function(species_pa, dist_mat, seed, sigma) {
    .Call(`_spacc_cpp_gaussian_single`, species_pa, dist_mat, seed, sigma)
}

cpp_gaussian_parallel <- function(species_pa, dist_mat, n_seeds, sigma, n_cores = 1L, progress = FALSE) {
    .Call(`_spacc_cpp_gaussian_parallel`, species_pa, dist_mat, n_seeds, sigma, n_cores, progress)
}

cpp_wavefront_single <- function(species_pa, dist_mat, seed, r0, dr, n_steps) {
    .Call(`_spacc_cpp_wavefront_single`, species_pa, dist_mat, seed, r0, dr, n_steps)
}

cpp_wavefront_parallel <- function(species_pa, dist_mat, n_seeds, r0, dr, n_steps, n_cores = 1L, progress = FALSE) {
    .Call(`_spacc_cpp_wavefront_parallel`, species_pa, dist_mat, n_seeds, r0, dr, n_steps, n_cores, progress)
}

cpp_radius_single <- function(species_pa, dist_mat, seed) {
    .Call(`_spacc_cpp_radius_single`, species_pa, dist_mat, seed)
}

cpp_radius_parallel <- function(species_pa, dist_mat, n_seeds, n_cores = 1L, progress = FALSE) {
    .Call(`_spacc_cpp_radius_parallel`, species_pa, dist_mat, n_seeds, n_cores, progress)
}

cpp_cone_single <- function(species_pa, x, y, seed, angle, width) {
    .Call(`_spacc_cpp_cone_single`, species_pa, x, y, seed, angle, width)
}

cpp_cone_parallel <- function(species_pa, x, y, n_seeds, width = 0.785398, n_cores = 1L, progress = FALSE) {
    .Call(`_spacc_cpp_cone_parallel`, species_pa, x, y, n_seeds, width, n_cores, progress)
}

cpp_distance_decay_single <- function(species_pa, dist_mat, seed, breaks) {
    .Call(`_spacc_cpp_distance_decay_single`, species_pa, dist_mat, seed, breaks)
}

cpp_distance_decay_parallel <- function(species_pa, dist_mat, n_seeds, breaks, n_cores = 1L, progress = FALSE) {
    .Call(`_spacc_cpp_distance_decay_parallel`, species_pa, dist_mat, n_seeds, breaks, n_cores, progress)
}

cpp_knn_metrics_parallel <- function(species_pa, dist_mat, n_cores = 1L, progress = FALSE) {
    .Call(`_spacc_cpp_knn_metrics_parallel`, species_pa, dist_mat, n_cores, progress)
}

cpp_kncn_metrics_parallel <- function(species_pa, x_coords, y_coords, n_cores = 1L, progress = FALSE) {
    .Call(`_spacc_cpp_kncn_metrics_parallel`, species_pa, x_coords, y_coords, n_cores, progress)
}

cpp_knn_order <- function(dist_mat, seeds) {
    .Call(`_spacc_cpp_knn_order`, dist_mat, seeds)
}

cpp_kncn_order <- function(x, y, seeds) {
    .Call(`_spacc_cpp_kncn_order`, x, y, seeds)
}

calc_mpd <- function(dist_mat, species_present, abundance_weighted = FALSE, abundances = numeric()) {
    .Call(`_spacc_calc_mpd`, dist_mat, species_present, abundance_weighted, abundances)
}

calc_mntd <- function(dist_mat, species_present, abundance_weighted = FALSE, abundances = numeric()) {
    .Call(`_spacc_calc_mntd`, dist_mat, species_present, abundance_weighted, abundances)
}

calc_rao <- function(dist_mat, abundances) {
    .Call(`_spacc_calc_rao`, dist_mat, abundances)
}

calc_faith_pd <- function(edge, edge_length, n_tips, species_present) {
    .Call(`_spacc_calc_faith_pd`, edge, edge_length, n_tips, species_present)
}

cpp_phylo_knn_single <- function(species_pa, site_dist_mat, phylo_dist_mat, seed, metrics, tree_edge = NULL, tree_edge_length = NULL, tree_n_tips = 0L) {
    .Call(`_spacc_cpp_phylo_knn_single`, species_pa, site_dist_mat, phylo_dist_mat, seed, metrics, tree_edge, tree_edge_length, tree_n_tips)
}

cpp_phylo_knn_parallel <- function(species_pa, site_dist_mat, phylo_dist_mat, n_seeds, metrics, n_cores = 1L, progress = FALSE, tree_edge = NULL, tree_edge_length = NULL, tree_n_tips = 0L) {
    .Call(`_spacc_cpp_phylo_knn_parallel`, species_pa, site_dist_mat, phylo_dist_mat, n_seeds, metrics, n_cores, progress, tree_edge, tree_edge_length, tree_n_tips)
}

calc_fdis <- function(traits, species_present, abundances) {
    .Call(`_spacc_calc_fdis`, traits, species_present, abundances)
}

calc_fric_approx <- function(traits, species_present) {
    .Call(`_spacc_calc_fric_approx`, traits, species_present)
}

calc_rao_traits <- function(traits, abundances) {
    .Call(`_spacc_calc_rao_traits`, traits, abundances)
}

cpp_func_knn_single <- function(species_mat, site_dist_mat, traits, seed, metrics) {
    .Call(`_spacc_cpp_func_knn_single`, species_mat, site_dist_mat, traits, seed, metrics)
}

cpp_func_knn_parallel <- function(species_mat, site_dist_mat, traits, n_seeds, metrics, n_cores = 1L, progress = FALSE) {
    .Call(`_spacc_cpp_func_knn_parallel`, species_mat, site_dist_mat, traits, n_seeds, metrics, n_cores, progress)
}

cpp_random_single <- function(species_pa, order) {
    .Call(`_spacc_cpp_random_single`, species_pa, order)
}

cpp_random_parallel <- function(species_pa, n_seeds, n_cores = 1L, progress = FALSE) {
    .Call(`_spacc_cpp_random_parallel`, species_pa, n_seeds, n_cores, progress)
}

cpp_order_parallel <- function(species_pa, orders, n_cores = 1L, progress = FALSE) {
    .Call(`_spacc_cpp_order_parallel`, species_pa, orders, n_cores, progress)
}