bam_clusters {bamm}

R Documentation

bam_clusters: Function to estimate the connectivity of suitable areas

Description

Function to estimate the connectivity of suitable areas given an adjacency matrix.

Usage

bam_clusters(model, ngbs = 1, plot_model = FALSE)

Arguments

model	A niche model in raster format or a setA object (see model2sparse).
ngbs	Numeric. Number of neighbors (see details).
plot_model	Logical. Indicates whether to plot the niche model using a leaflet map, connected suitable cells shown in the same color.

Details

The main result of the function is the Connectivity-Suitability-Diagram (CSD). In this diagram connected suitable cells make clusters of pixels. For more details about the CSD see (Soberon and Osorio-Olvera, 2022).

Value

An object of class csd. It contains three slots. 1) connections: a data.frame with three columns where first and the second represent (x and y) centroid coordinates of the niche model and the third column with the cluster ID where they belong. 2) interactive_map: a leaflet map of connected suitable pixels shown in the same color. 3) A RasterLayer of connected suitable pixels.

Author(s)

Luis Osorio-Olvera & Jorge Soberón

References

Soberón J, Osorio-Olvera L (2022). “A Dynamic Theory of the Area of Distribution.” doi:10.48550/ARXIV.2212.06308, https://arxiv.org/abs/2212.06308..

Examples

set.seed(891)
model_path <- system.file("extdata/Lepus_californicus_cont.tif",
                          package = "bamm")
model <- raster::raster(model_path)
model <- model > 0.7
clusterin <- bamm::bam_clusters(model,ngbs=1,plot_model=TRUE)
raster::plot(clusterin@raster_map)

clusterin@interactive_map

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