Species Distribution Models as a Function of Biotic, Abiotic and Movement Factors (BAM)

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Documentation for package ‘bamm’ version 0.5.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

A-class	Class for the A set of the BAM diagram
adj_mat	adj_mat: Function to compute the adjacency matrix of an area.
bam	Class 'bam' digram
bam-class	Class 'bam' digram
bam-method	Predict method of the package 'bamm'.
bam_clusters	bam_clusters: Function to estimate the connectivity of suitable areas
bam_sim	bam_sim: Simulate dispersal dynamics using the set B of the BAM framework.
bam_ssim	bam_ssim: Simulate dispersal dynamics using the set B of the BAM framework.
biodiversity_index	Class 'bioindex'
biodiversity_index_sparse	Class 'bioindex_sparse'
bioindex	Class 'bioindex'
bioindex-class	Class 'bioindex'
bioindex_sparse	Class 'bioindex_sparse'
bioindex_sparse-class	Class 'bioindex_sparse'
community-class	Class 'community_sim' digram
community_bam	Class 'community_sim' digram
community_sim	community_bam: Community 'bamm'
community_sim-class	Class 'community_sim' digram
coordinates-class	S4 classes to organize data and results of 'bamm' objects
csd	Class 'csd'
csd-class	Class 'csd'
csd_estimate	csd_estimate: Estimate the connectivity suitability and dispersal plot
csim2pam	csim2pam: Converts community simulation to a Presence Absence Matrix (PAM)
diversityrange	Class 'diversity_range'
diversity_range	Class 'diversity_range'
diversity_range-class	Class 'diversity_range'
diversity_range_analysis	range_diversity_analysis: diversity analysis
eigen_bam	eigen_bam: Compute the Eigen system of two bam objects
g_area	S4 classes to organize data and results of 'bamm' objects
g_area-class	S4 classes to organize data and results of 'bamm' objects
jaccard	jaccard: Estimates the Jaccard index for comparing two binary maps
leaflet	Class 'leaflet' leaflet
leaflet-class	Class 'leaflet' leaflet
M-class	Class for the M set of the 'bamm' diagram
model2sparse	model2sparse: Converts a niche model into a diagonal sparse matrix
models2pam	models2pam: Converts binary rasters to a PAM
null_dispersion_field_distribution	null_dispersion_field_distribution: Null distribution of the dispersion field
occs2sparse	occs2sparse: Converts occurrence data into a sparse matrix object
PAM	Class 'pam' Presence-Absence Matrix
pam	Class 'pam' Presence-Absence Matrix
pam-class	Class 'pam' Presence-Absence Matrix
pam2bioindex	pam2bioindex: PAM to biodiversity index
pam2richness	pam2richness: Converts Presence Absence Matrix (pam object) to richness raster
permute_pam	permute_pam: Function to permute a Presence-Absence-Matrix.
plot-method	Plot method for objects of class diversity_range 'bamm'.
predict	Predict method of the package 'bamm'.
predict-method	Predict method of the package 'bamm'.
sdm_sim	sdm_sim: Simulate single species dispersal dynamics using the BAM framework.
setA	Class for the A set of the BAM diagram
setA-class	Class for the A set of the BAM diagram
setM	Class for the M set of the 'bamm' diagram
setM-class	Class for the M set of the 'bamm' diagram
shape2Grid	shape2Grid: Function to create a grid given a spatial polygon
show-method	Show information in setA class 'bamm'.
sim2Animation	sim2Animation: Animate BAM simulation object.
sim2Raster	sim2Raster: Convert a BAM simulation object to RasterStack