Function reference • bamm

All functions

adj_mat(): adj_mat: Function to compute the adjacency matrix of an area.

bam-class bam: Class bam digram

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.

bioindex-class bioindex biodiversity_index: Class bioindex

bioindex_sparse-class bioindex_sparse biodiversity_index_sparse: Class bioindex_sparse

community_sim-class community_bam community-class: Class community_sim digram

community_sim(): community_bam: Community bamm

csd-class csd: Class csd

csd_estimate(): csd_estimate: Estimate the connectivity suitability and dispersal plot

csim2pam(): csim2pam: Converts community simulation to a Presence Absence Matrix (PAM)

diversity_range-class diversity_range diversityrange: Class diversity_range

diversity_range_analysis(): range_diversity_analysis: diversity analysis

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

eigen_bam(): eigen_bam: Compute the Eigen system of two bam objects

g_area-class g_area coordinates-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: Class leaflet leaflet

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 PAM: 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(<diversity_range>,<ANY>): Plot method for objects of class diversity_range bamm.

predict(<bam>): Predict method of the package bamm.

sdm_sim(): sdm_sim: Simulate single species dispersal dynamics using the BAM framework.

setA-class setA A-class: Class for the A set of the BAM diagram

setM-class setM M-class: Class for the M set of the bamm diagram

shape2Grid(): shape2Grid: Function to create a grid given a spatial polygon

show(<setA>) show(<csd>) show(<pam>) show(<bioindex_sparse>) show(<setM>) show(<diversity_range>): Show information in setA class bamm.

sim2Animation(): sim2Animation: Animate BAM simulation object.

sim2Raster(): sim2Raster: Convert a BAM simulation object to RasterStack