# Tools for Biological Survey Planning

## Documentation for package ‘biosurvey’ version 0.1.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## 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