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

In luismurao/bam: Species Distribution Models in the light of the BAM theory

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

Description

Creates an adjacency matrix of an area of interest. This could be the accessible area (M) of a species or any geographic region of interest.

Usage

adj_mat(modelsparse, ngbs = 1, eigen_sys = FALSE, which_eigs = 1)

Arguments

modelsparse	A setA object returned by the function model2sparse.
ngbs	Numeric. Number of neighbors (see details).
eigen_sys	Logical. If TRUE the eigen analsys of the adjancency matrix will be returned.
which_eigs	Numeric. Which eigen value and eigen vector will be returned.

Details

The grid_base raster object is the area where the dispersal process will occur. The number of neighbors depends on the dispersal abilities of the species and the spatial resolution of the grid_base; for example, a species's with big dispersal abilities will move throughout more than 1 km^2 per day, so the idea is to give an approximate number of moving neighbors (pixels) per unit of time.

Value

Returns an adjacency matrix of class sparseMatrix of n+2 x n columns (n number of the non-NA cells of grid_base) with the coordinates of the non-NA cells of grid_base.

Examples

## Not run: 
data("wrld_simpl", package = "maptools")
mx <- wrld_simpl[wrld_simpl$NAME=="Mexico",]
mx_grid <- shape2Grid(mx,0.5)
mx_sparse <- bam::model2sparse(mx_grid)
adj_mx <- adj_mat(mx_sparse,ngbs=1)
# Adjacency matrix from a niche model
model_path <- system.file("extdata/Lepus_californicus_cont.tif",
                          package = "bam")
model <- raster::raster(model_path)

sparse_mod <- bam::model2sparse(model,threshold=0.05)
adj_mod <- adj_mat(sparse_mod,ngbs=1)

## End(Not run)

luismurao/bam documentation built on Nov. 28, 2022, 3:02 p.m.