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

## Documentation for package ‘bamm’ version 0.4.3

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

## Help Pages

.nonzero | Helper function to compute the elements in g0 that have no zero values.The function is taken from the Ringo package
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