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


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Documentation for package ‘bamm’ version 0.4.3

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.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