setA-class

setA

A-class

Represents the abiotic component (environmental suitability) in the BAM framework.
Contains raster-based niche models and their sparse matrix representations.

Species Distribution Modeling (SDM) is a practical
methodology that aims to estimate the area of distribution of a
species. However, most of the work has focused on estimating static
expressions of the correlation between environmental variables. The
outputs of correlative species distribution models can be interpreted
as maps of the suitable environment for a species but not generally as
maps of its actual distribution. Soberón and Peterson (2005)
<doi:10.17161/bi.v2i0.4> presented the BAM scheme, a heuristic
framework that states that the occupied area of a species occurs on
sites that have been accessible through dispersal (M) and have both
favorable biotic (B) and abiotic conditions (A). The 'bamm' package
implements classes and functions to operate on each element of the BAM
and by using a cellular automata model where the occupied area of a
species at time t is estimated by the multiplication of three binary
matrices: one matrix represents movements (M), another abiotic -niche-
tolerances (A), and a third, biotic interactions (B). The theoretical
background of the package can be found in Soberón and Osorio-Olvera
(2023) <doi:10.1111/jbi.14587>.

Luis Osorio-Olvera

bamm

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

Jorge Soberón

Rusby G. Contreras-Díaz

setA-class function

<dl>
<dt><code>niche_model</code></dt>
<dd>A <code>RasterLayer</code> or <code>RasterStack</code> representing the
environmental suitability model (binary or continuous)</dd></dl>
<dt><code>suit_threshold</code></dt>
<dd>Numeric value used to binarize continuous models</dd>
<dt><code>cellIDs</code></dt>
<dd>Numeric vector of raster cell IDs with non-NA values</dd>
<dt><code>suit_values</code></dt>
<dd>Numeric vector of suitability values for continuous models</dd>
<dt><code>sparse_model</code></dt>
<dd>A sparse matrix (<code>dgCMatrix</code>) representation of the niche model</dd>

Slots

The <code>niche_model</code> slot must be either a <code>RasterLayer</code> or <code>RasterStack</code>.

Validity

Luis Osorio-Olvera &amp; Jorge Soberón

Author

Class for the A (Abiotic) Set of BAM Diagram — setA-class

<dl>
<dt><code>niche_model</code></dt>
<dd>A <code>RasterLayer</code> or <code>RasterStack</code> representing the
environmental suitability model (binary or continuous)</dd>


<dt><code>suit_threshold</code></dt>
<dd>Numeric value used to binarize continuous models</dd>


<dt><code>cellIDs</code></dt>
<dd>Numeric vector of raster cell IDs with non-NA values</dd>


<dt><code>suit_values</code></dt>
<dd>Numeric vector of suitability values for continuous models</dd>


<dt><code>sparse_model</code></dt>
<dd>A sparse matrix (<code>dgCMatrix</code>) representation of the niche model</dd>


</dl>

The <code>niche_model</code> slot must be either a <code>RasterLayer</code> or <code>RasterStack</code>.

setA-class: Class for the A (Abiotic) Set of BAM Diagram

Description

Arguments

Value

Slots

Validity

Author

See Also