vegan (version 1.11-0)

ordisurf: Fit and Plot Smooth Surfaces of Variables on Ordination.

Description

Function ordisurf fits a smooth surface for given variable and plots the result on ordination diagram.

Usage

ordisurf(x, y, choices=c(1, 2), knots=10, family="gaussian", col="red",
     thinplate = TRUE, add = FALSE, display = "sites",
     w = weights(x), main, nlevels = 10, levels, labcex = 0.6,  ...)

Arguments

x

Ordination configuration, either a matrix or a result known by scores.

y

Variable to be plotted.

choices

Ordination axes.

knots

Number of initial knots in gam (one more than degrees of freedom).

family

Error distribution in gam.

col

Colour of contours.

thinplate

Use thinplate splines in gam.

add

Add contours on an existing diagram or draw a new plot.

display

Type of scores known by scores: typically "sites" for ordinary site scores or "lc" for linear combination scores.

w

Prior weights on the data. Concerns mainly cca and decorana results which have nonconstant weights.

main

The main title for the plot, or as default the name of plotted variable in a new plot.

nlevels, levels

Either a vector of levels for which contours are drawn, or suggested number of contours in nlevels if levels are not supplied.

labcex

Label size in contours. Setting this zero will suppress labels.

...

Other graphical parameters.

Value

• Function is usually called for its side effect of drawing the contour plot, but it returns the result object of gam.

Details

Function ordisurf fits a smooth surface using thinplate splines in gam, and uses predict.gam to find fitted values in a regular grid. Function plots the fitted contours with convex hull of data poitns either over an existing ordination diagram or draws a new plot The function uses scores to extract ordination scores, and x can be any result object known by that function.

User can supply a vector of prior weights w. If the ordination object has weights, these will be used. In practise this means that the row totals are used as weights with cca or decorana results. If you do not like this, but want to give equal weights to all sites, you should set w = NULL. The behaviour is consistent with envfit. For complete accordance with constrained cca, you should set display = "lc" (and possibly scaling = 2).

See Also

For basic routines gam, and scores. Function envfit provides a more traditional and compact alternative.

Examples

data(varespec)
data(varechem)
library(MASS)
vare.dist <- vegdist(varespec)
vare.mds <- isoMDS(vare.dist)
with(varechem, ordisurf(vare.mds, Baresoil))
## Cover of Cladina arbuscula
with(varespec, ordisurf(vare.mds, Cla.arb, family=quasipoisson))