centipede.plot: Plots species optima and tolerances

Description Usage Arguments Details Value Author(s) Examples

View source: R/centipede.plot.r

Description

Plots species optima and tolerances as calculated by a WA model.

Usage

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centipede.plot(x,keep=TRUE, xlab="", xlim, ...)

Arguments

x

A WA model.

keep

A logical vector of which taxa to include in the plot. Defaults to all taxa.

xlab

The xlab of the plot

xlim

xlims for the plot. Defaults to a sensible range.

...

Extra arguments to plot, for example of the cex, col, and pch of the points.

Details

Extracts, sorts and plots WA optima and tolerances. Tends only to work well when there are a reasonable number of taxa, otherwise it is difficult to read the names on the axis. If rare taxa are not excluded via the keep argument, the tol.cut argument in WA may need to be set to prevent very small tolerances of these taxa.

Value

None

Author(s)

Richard Telford [email protected]

Examples

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require(rioja)
data(SWAP)
mod<-WA(SWAP$spec, SWAP$pH, tolDW=TRUE)
keep<-colSums(SWAP$spec)>40#only common taxa
opar<-par(no.readonly = TRUE)
par(mar=c(5.1,6.1,2.1,1.1))#extra space on left side of plot for names
centipede.plot(x=mod, keep=keep, pch=20, cex.axis=.7)
par(opar)

palaeoSig documentation built on May 29, 2017, 9:11 a.m.