plotDistri: Plot function to represent density of trait values

In cati: Community Assembly by Traits: Individuals and Beyond

Plot function to represent density of trait values

Description

Plot function to represent density of trait values

Usage

	plotDistri(traits = NULL, var.1 = NULL, var.2 = NULL, col.dens = NULL, 
	plot.ask = TRUE, ylim.cex = 1, cex.leg = 0.8, polyg = TRUE, 
	multipanel = TRUE, leg = TRUE, xlim = NULL, ylim = NULL, 
	main = "default", ...)

Arguments

traits	Matrix of traits with traits in column.
var.1	The first variable defines the division of each plots, in most case either a vector of species or name of sites.
var.2	The second variable define the division by color, in most case either a vector of species or name of sites.
col.dens	A vector of colors for the second variable.
plot.ask	Logical value; ask for plotting the next plot or not.
ylim.cex	Numeric value; the magnification to be used for range of y axe
cex.leg	Numeric value; the magnification to be used for legend relative to the current setting of cex
polyg	Logical value; do the mean distribution is full or empty
multipanel	Logical value. If TRUE divides the device to shown several traits graphics in the same device.
leg	Logical value; if TRUE print the legend.
ylim	Numeric vectors of length 2, giving the y coordinates range
xlim	Numeric vectors of length 2, giving the y coordinates range
main	Title for the plot. Default set automatic title using informations in the input dataset.
...	Any additional arguments are passed to the plot function creating the core of the plot and can be used to adjust the look of resulting graph.

Value

None; used for the side-effect of producing a plot.

Author(s)

Adrien Taudiere

See Also

plotSpPop

Examples

	
data(finch.ind)

## Not run: 
	#Plot the distribution of trait values for populations, 
	#species, sites and regional scales. 
	
	### First, let try the distribution for all populations 
	#of Darwin finches.
	
	par(mfrow = c(4,4), cex = 0.5)
	plotDistri(traits.finch, sp.finch, ind.plot.finch, ylim.cex = 3, 
	plot.ask = FALSE, multipanel = FALSE, leg = FALSE)
	
	### Then we can inverse the second and the third arguments 
	#to plot the distribution for all finches species. 
	
	par(mfrow = c(4,4), cex = 0.5)
	plotDistri(traits.finch, ind.plot.finch, sp.finch, ylim.cex = 8, 
	plot.ask = FALSE, multipanel = FALSE, leg = FALSE)
	
	### Only one trait to plot using leg = TRUE to plot the legend

	par(mfrow=c(2,3))
	plotDistri(as.matrix(traits.finch[,1]), ind.plot.finch, sp.finch, 
    ylim.cex=8, plot.ask = FALSE, multipanel = FALSE, leg = TRUE, cex.leg=0.5)

	### You can also plot trait distribution for all species in the region
	
	par(mfrow = c(1,1), cex = 1)
	plotDistri(traits.finch, rep("region", times = dim(traits.finch)[1]), 
	sp.finch, ylim.cex = 6, plot.ask = FALSE, leg = FALSE)
	
	### You can also plot trait distribution for all sites
	#without taking into account species identity

	plotDistri(traits.finch, rep("toutes_sp", times = dim(traits.finch)[1]), 
	ind.plot.finch, ylim.cex = 3, plot.ask = FALSE)


## End(Not run)
	

cati documentation built on March 18, 2022, 5:43 p.m.