plotPAC: Function to draw a circular plot to visualise potential...

In bipartite: Visualising Bipartite Networks and Calculating Some (Ecological) Indices

Function to draw a circular plot to visualise potential apparent competition (PAC)

Description

Visualises the Potential for Apparent Competition as a circular graph with species represented by circles and shared parasitoids/predators/pollinators as connecting lines. Area of circles is proportional to species' abundance, filling of circles proportional to self-loops (e.g. parasitoids emerging from this species and then attacking it again) and width of connecting lines is proportional to “export” of parasitoids. The function is modelled after the example given in Morris et al. (2005)

Usage

plotPAC(web, scaling = 1, plot.scale = 1, fill.col = rgb(0.2, 0.2, 0.2, 0.5), 
arrow.col = rgb(0.5, 0.5, 0.5, 0.5), outby = 1, label=TRUE, text = TRUE, 
circles = FALSE, radius = 1, text.cex=1)

Arguments

web	A community matrix with lower trophic level in rows and higher trophic level in columns.
scaling	A factor scaling the size of species-circles. The default of 1 may cause overlap when there are many species or some are very large. Smaller values yield smaller circles.
plot.scale	Scales the whole plot to the plotting region. If you want to add labels, you may want more space around the plot and hence choose smaller values for plot.scale.
fill.col	Colour of the species-circles. Note that the default is using transparency, which is the fourth parameter in the rgb-function.
arrow.col	Colour(s) of the arrows (in fact polygons) connecting species. As for fill.col, the default uses transparency. If more than one colour is provided, the links will be coloured in a somewhat complicated sequence, starting with the species with most interactions and then down. So it might require some playing around if you want to colour a specific arrow.
outby	A factor determining by how much the text labels should be moved out from the species-circles. Values smaller than 1 will move them inside the circle-plot.
label	Logical; if TRUE (default), a number will be plotted next to each species-circle.
text	Logical; if TRUE (default), the name (as provided by the row names of the input matrix) will be plotted.
circles	Logical; shall species labels be put into a circle (as in the original plot of Morris et al. 2005)? Defaults to FALSE.
radius	A factor modifying the size of the label-circles.
text.cex	A multiplier to scale the point labels by; defaults to 1.

Details

The function is modelled after Morris et al. (2005). The whole idea and application is explained there, too. The only change to their plotting is the default choice of transparency for clarity of the visual effect.

Value

None. The function is invoked for its side effects (i.e. printing).

Author(s)

Carsten F. Dormann [e-mail]

References

Morris, R. J., Lewis, O. T. and Godfray, H. C. J. 2005. Apparent competition and insect community structure: towards a spatial perspective. Annales Zoologica Fennici 42, 449–462.

See Also

See also comments and notes in PAC!

Examples

## Not run: 
data(kevan1970)
plotPAC(kevan1970)
plotPAC(kevan1970, arrow.col=rainbow(30))

data(Safariland)
plotPAC(Safariland, plot.scale=1, fill.col="red", arrow.col="orange", 
	circles=TRUE, radius=1)
	

## End(Not run)

bipartite documentation built on May 29, 2024, 2:23 a.m.