NicheOverlap: 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.

Value

area.

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.

Examples

Run this code


data(Polar.coordinates)

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

#Remove the data set
rm(Polar.coordinates)

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