Tools for Biological Survey Planning

Documentation for package ‘biosurvey’ version 0.1.1

Help Pages

assign_blocks	Helper to assign block numbers to data according to variables and limits
base_PAM	Constructor of S3 objects of class base_PAM
biosurvey	biosurvey: Tools for Biological Survey Planning
block_sample	Selection of blocks in environmental space
bluered	Simple color palettes
b_pam	Example of object obtained from using the function base_PAM
closest_to_centroid	Detection of the closest points to the centroid of a cloud of points
compare_SAC	Comparative plots of species accumulation curves
daright	Simple color palettes
darkros	Simple color palettes
distance_filter	Helper to filter sets of sites by median distance among all points
dist_list	A list of vectors of distances
dis_loop	Helper to calculate dissimilarities in loop
DI_dendrogram	Plot dissimilarities withing and among sets of selected sites as a dendrogram
EG_selection	Selection of survey sites maximizing uniformity in environmental space considering geographic structure
explore_data_EG	Plots to explore environmental factors in environmental and geographic space
files_2data	Creates a data.frame of species' references from files in a directory
find_clusters	Detection of clusters in 2D spaces
find_modes	Find modes in a multimodal distribution
greeple	Simple color palettes
grid_from_region	Creates grid for a given geographic region
legend_bar	Helper to add a bar image legend to plots
make_blocks	Creates a block-like regionalization of environmental space
master_matrix	Constructor of S3 objects of class master_matrix
master_selection	Constructor of S3 objects of class master_selection
match_rformat	Helper function to find raster extension
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
new_base_PAM	Constructor of S3 objects of class base_PAM
new_master_matrix	Constructor of S3 objects of class master_matrix
new_master_selection	Constructor of S3 objects of class master_selection
new_PAM_CS	Constructor of S3 objects of class PAM_CS
new_PAM_subset	Constructor of S3 objects of class PAM_subset
PAM_CS	Constructor of S3 objects of class PAM_CS
PAM_from_table	Creates presence-absence matrix from a data.frame
PAM_indices	Biodiversity indices derived from PAM
PAM_subset	Constructor of S3 objects of class PAM_subset
plot_blocks_E	Representation of environmental blocks in geography and environment
plot_blocks_EG	Representation of environmental blocks in geography and environment
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	Representations of diversity and dispersion indices
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_E	Representation of sites selected to be surveyed
plot_sites_EG	Representation of sites selected to be surveyed
plot_sites_G	Representation of sites selected to be surveyed
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
prepare_base_PAM	Presence-absence matrix (PAM) linked to a spatial grid
prepare_master_matrix	Prepare a base object to perform further analyses
prepare_PAM_CS	Preparing data for new range-diversity plot
preselected	Example of a data.frame of preselected sites
preselected_dist_mask	Helper to create objects to detect points to close to preselected sites
print	Print a short version of elements in master and base objects
print-method	Print a short version of elements in master and base objects
print.base_PAM	Print a short version of elements in master and base objects
print.master_matrix	Print a short version of elements in master and base objects
print.master_selection	Print a short version of elements in master and base objects
print.PAM_CS	Print a short version of elements in master and base objects
print.PAM_subset	Print a short version of elements in master and base objects
purplow	Simple color palettes
random_selection	Random selection of survey sites
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_DI	Dissimilarity indices from PAM_subset
selected_sites_PAM	Helper to subset PAM according to selected sites
selected_sites_SAC	Species accumulation curves from PAM_subset
spdf_2data	Creates a data.frame of species' references from SpatialPolygonsDataFrame
species_data	Example of species ranges as SpatialPolygonsDataFrame
sp_data	Example of a data.frame of species' found in distinct positions
sp_layers	Example of stack of layers of suitable and unsuitable conditions for species
sp_occurrences	Occurrence records for the species Parides gundlachianus
stack_2data	Creates a data.frame of species' references from RasterStack
subset_PAM	Subset PAM according to selected sites
summary	Summary of attributes and results
summary-method	Summary of attributes and results
summary.base_PAM	Summary of attributes and results
summary.master_matrix	Summary of attributes and results
summary.master_selection	Summary of attributes and results
summary.PAM_CS	Summary of attributes and results
summary.PAM_subset	Summary of attributes and results
uniformE_selection	Selection of survey sites maximizing uniformity in environmental space
uniformG_selection	Selection of survey sites maximizing uniformity in geography
unimodal_test	Unimodality test for list of one or multiple sets of values
variables	Example of variables to be used for preparing a master matrix
wgs84_2aed_laea	Project spatial points from geographic coordinates