Tools for Biological Survey Planning


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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