bivariatemaps (version 1.7)

betagrid: betagrid: Calculates Beta Diversity for all the Grid Cells in Comparison with Their Nearest Neighbor Cells

Description

Uses a 'gridded' shapefile and its corresponding community data matrix to calculate beta diversity for each focal grid cell in relation to its neighbor cells (for example, 8 nearest neighbors).

Usage

betagrid(
  gridshp,
  comp,
  xfeature,
  yfeature,
  radius,
  phylotree,
  phylobeta = F,
  index = "sorensen"
)

Value

A data frame with values of mean turnover, mean nestedness, and mean beta diversity for each grid cell.

Arguments

gridshp

Gridded Shapefile ("SpatialPolygonsDataFrame").

comp

community data matrix (species occurrence on each grid cell).

xfeature

number of the feature within the gridded shapefile corresponding to the longitude.

yfeature

number of the feature within the grid shapefile corresponding to the latitude.

radius

the radius (in degrees) that define the maximum distance to select neighbor cells (for example, use the resolution of the gridded shapefile).

phylotree

optional phylogenetic tree ("phylo" class). It can also be a "phylo" class functional dendrogram.

phylobeta

Optional boolean whether or not to calculate or not phylogenetic beta diversity (see "phylo.beta.pair" function in "betapart" package) instead of the usual beta diversity (see "beta.pair" function in "betapart" package). Default is F.

index

to calculate "sorensen" or "jaccard". Default is "sorensen".

Examples

# https://rfunctions.blogspot.com/2015/08/calculating-beta-diversity-on-grid.html