NicheOverlap {EnvNicheR} | R Documentation |
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)