Function reference • biosurvey

Package description

biosurvey: biosurvey: Tools for Biological Survey Planning

Data preparation

prepare_master_matrix(): Prepare a base object to perform further analyses

prepare_base_PAM(): Presence-absence matrix (PAM) linked to a spatial grid

make_blocks(): Creates a block-like regionalization of environmental space

prepare_PAM_CS(): Preparing data for new range-diversity plot

Sampling site selection

EG_selection(): Selection of survey sites maximizing uniformity in environmental space considering geographic structure

random_selection(): Random selection of survey sites

uniformE_selection(): Selection of survey sites maximizing uniformity in environmental space

uniformG_selection(): Selection of survey sites maximizing uniformity in geography

Effectiveness tests

subset_PAM(): Subset PAM according to selected sites

selected_sites_DI(): Dissimilarity indices from PAM_subset

selected_sites_SAC(): Species accumulation curves from PAM_subset

Construct, save, and read objects

new_master_matrix(): Constructor of S3 objects of class master_matrix

new_base_PAM(): Constructor of S3 objects of class base_PAM

new_master_selection(): Constructor of S3 objects of class master_selection

new_PAM_subset(): Constructor of S3 objects of class PAM_subset

new_PAM_CS(): Constructor of S3 objects of class PAM_CS

save_master() read_master(): Functions to save and read master objects

save_PAM() read_PAM(): Functions to save and read PAM objects

Summary and print

print(<master_matrix>) print(<master_selection>) print(<base_PAM>) print(<PAM_subset>) print(<PAM_CS>): Print a short version of elements in master and base objects

summary(<master_matrix>) summary(<master_selection>) summary(<base_PAM>) summary(<PAM_subset>) summary(<PAM_CS>): Summary of attributes and results

Visualization and plotting

compare_SAC(): Comparative plots of species accumulation curves

DI_dendrogram(): Plot dissimilarities withing and among sets of selected sites as a dendrogram

explore_data_EG(): Plots to explore environmental factors in environmental and geographic space

legend_bar(): Helper to add a bar image legend to plots

plot_blocks_EG() plot_blocks_E() plot_blocks_G(): Representation of environmental blocks in geography and environment

plot_DI(): Plotting dissimilarity indices withing and among sets of selected sites

plot_PAM_CS() plot_PAM_CS_geo(): Representations of diversity and dispersion indices

plot_PAM_geo(): Plot of PAM indices in geography

plot_SAC(): Plotting lists of species accumulation curves

plot_sites_EG() plot_sites_E() plot_sites_G(): Representation of sites selected to be surveyed

purplow() darkros() daright() greeple() bluered(): Simple color palettes

Data included

b_pam: Example of object obtained from using the function base_PAM

dist_list: A list of vectors of distances

mx: Example of spatial polygon for a region of interest

m_matrix: Example of a master_matrix object with no preselected sites

m_matrix_pre: Example of a master_matrix object containing preselected sites

m_selection: Example of a master_selection object from using functions for selecting sites

preselected: Example of a data.frame of preselected sites

species_data: Example of species ranges as a SpatVector

sp_data: Example of a data.frame of species' found in distinct positions

sp_layers: Example of raster layers of suitable and unsuitable conditions for species

sp_occurrences: Occurrence records for the species Parides gundlachianus

variables: Example of variables to be used for preparing a master matrix

Helpers for selection analyses

assign_blocks(): Helper to assign block numbers to data according to variables and limits

block_sample(): Selection of blocks in environmental space

closest_to_centroid(): Detection of the closest points to the centroid of a cloud of points

dis_loop(): Helper to calculate dissimilarities in loop

distance_filter(): Helper to filter sets of sites by median distance among all points

find_clusters(): Detection of clusters in 2D spaces

find_modes(): Find modes in a multimodal distribution

point_sample(): Sample points from a 2D environmental space

point_sample_cluster(): Sample points from a 2D environmental space potentially disjoint in geography

point_thinning(): Helps in thinning points either in geographic or environmental space

preselected_dist_mask(): Helper to create objects to detect points to close to preselected sites

unimodal_test(): Unimodality test for list of one or multiple sets of values

Helpers for PAM analyses

files_2data(): Creates a data.frame of species' references from files in a directory

grid_from_region(): Creates grid for a given geographic region

match_rformat(): Helper function to find raster extension

PAM_from_table(): Creates presence-absence matrix from a data.frame

PAM_indices(): Biodiversity indices derived from PAM

randomize_matrix_cb(): Randomize matrix using the curve ball algorithm

refill_PAM_indices(): Helper to refill a list of PAM indices with new or more results

rlist_2data(): Creates a data.frame of species' references from a list of raster layers

selected_sites_PAM(): Helper to subset PAM according to selected sites

spdf_2data(): Creates a data.frame of species' references from SpatVector

stack_2data(): Creates a data.frame of species' references from SpatRaster

wgs84_2aed_laea(): Project spatial points from geographic coordinates