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 |