NicheOverlap: Niche overlap between two taxa

In EnvNicheR: Niche Estimation

Niche overlap between two taxa

Description

This function shows in a plot the niche overlap between two taxa, at any level of the taxonomy (order, family, genus or species), using the file Polar coordinates.CSV obtained from the function Niche.

Usage

NicheOverlap(data, Level1, Taxon1, Level2=Level1, Taxon2,
colA=hsv(h=0,s=1,v=1,alpha=0.4), colB=hsv(h=0.7,s=1,v=1, alpha=0.4),
xlab="Polar coordinate X in pixel", ylab="Polar coordinate Y in pixels",
cex=1.57, cex.lab=1.5,font.lab=1, main="", cex.main = 2, font.main=2,
family="serif", digits =2, xlegend="topleft", ylegend=NULL, pch=15, bty="n",
text.font=3, cex.legend=1.2, ncol=1, x.intersp=1, y.intersp=1, legend=TRUE)

Arguments

data	The file Polar coodinates.CSV obtained from the function Niche().
Level1	Taxonomic level to be selected, i.e., Class, Order, Family, or Genus, of the first taxon.
Taxon1	Name of the taxon of the first taxonomic level.
Level2	Taxonomic level to be selected, i.e., Class, Order, Family, or Genus, of the second taxon. If missing the default value is Level1.
Taxon2	Name of the taxon of the second taxonomic level.
colA	Color of Taxon1.
colB	Color of Taxon2.
xlab	Label for x-axis.
ylab	Label for y-axis.
cex	Size of the symbols.This argument and the function omi() are useful to adjust the overlap among symbols and to avoid white lines.
cex.lab	Magnification used for text in axis labels relative to the current setting of cex.
font.lab	The font to be used for x and y labels.
main	Title of the plot.
cex.main	Magnification used for title relative to the current setting of cex.
font.main	The font to be used for plot main titles.
family	The name of a font family for drawing text.
digits	Integer indicating the number of decimal places of the overlap values.
xlegend	The x co-ordinates to be used to position the legend.
ylegend	The y co-ordinates to be used to position the legend.
pch	The plotting symbols appearing in the plot and in the legend.
bty	The type of box to be drawn around the legend. The allowed values are "o" and "n" (the default).
text.font	The font used for the legend text, see text.
cex.legend	Character expansion factor relative to current par("cex") of the legend.
ncol	The number of columns in which to set the legend items.
x.intersp	Character interspacing factor for horizontal (x) spacing of the legend.
y.intersp	Character interspacing factor for vertical (y) spacing of the legend.
legend	If TRUE the legend is shown.

Details

The plot shows the niche overlap between two taxa using the file Polar coordinates.CSV obtained from the function Niche(). The overlap is estimated counting the overlapping pixels.

Value

A plot shows the values of niche overlap for both taxa and the overlapping area.

Author(s)

Cástor Guisande González, Universidad de Vigo, Spain.

Examples

## Not run: 

data(Polar.coordinates)

NicheOverlap(Polar.coordinates, Level1="Species", Taxon1="Panthera onca",
Taxon2="Panthera leo")

#Remove the data set
rm(Polar.coordinates)

## End(Not run)

EnvNicheR documentation built on Oct. 8, 2023, 1:07 a.m.