boxgradient: Display Species Response along Gradients as Boxplots or...
In jarioksa/gravy: Gradient Analysis of Vegetation

Description Usage Arguments Details Value Author(s) See Also Examples

The function display species responses along ecological gradients using either boxplot or a polygon displaying fitted Gaussian responses.

boxgradient(x, grad, horizontal = TRUE, xlab, freq.lim = 5,
    cex.species= 0.7, axes = TRUE, ...)
gaussgradient(x, grad, family = poisson, xlab, freq.lim = 5,
    cex.species = 0.7, axes = TRUE, ...)

`x`	Community data
`grad`	Gradient vector
`horizontal`	Use horizontal `boxplot`.
`family`	Errof `family` used in fitting the Gaussian model using `glm`. The `link` function will always be `log`, and some families cannot be fitted with this link.
`xlab`	Label of the gradient. Variable name used as default.
`freq.lim`	Frequency of rarest species displayed.
`cex.species`	Size multiplier for species labels. Species labela are printed horizontally, and typically you must reduces their size with this parameter or increase the margin (see `mar` in `par`), or `abbreviate` names.
`axes`	Draw `axis` with labels.
`...`	Other parameters passed to underlying functions `boxplot` or `polygon`.

The functions are intended for simultaneous display of species responses along an ecological gradient.

Function boxgradient will draw boxplots of species presences. In addition, it puts points at weighted avarages. The boxplots are based on presence data only, but weighted averages are based on the original quantitative information. Boxes are arranged by medians, but breaking ties by weighted averages. The function also adds lines of quartiles and median for the whole gradient, and adds a rug of gradient values.

Function gaussgradient draws fitted Gaussian response models. The curves are adjusted to the same area so that narrower responses will look higher, but the heights have no relation to the original abundances. The responses are fitted using glm, and species with failed fitting (“inverted” responses) will not be displayed. The fitted responses are ordered by the location of the top (‘optimum’).

The functions are used to draw plots. Function boxpgradient returns invisibly the object returned by boxplot. Function gaussgradient returns invisibly a list of fitted optima and tolerances.

Jari Oksanen

boxplot, polygon, axis, par.

data(mtf01)
data(mtf.alt)
attach(mtf.alt)
op <- par(no.readonly=TRUE)
par(mfrow=c(2,1))
par(mar=c(4,6,1,1))
boxgradient(mtf01, Altitude, col="pink", border="blue", notch=TRUE)
gaussgradient(mtf01, Altitude, col="pink", border="blue")
par(op)