ordisurf {vegan}R Documentation

Smooths Variables and Plots Contours 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, ...)

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.
... Other graphical parameters.

Details

Function ordisurf fits a smooth surface using thinplate spline fitting in gam, and interpolates the fitted values into a regular grid using interp. Finally, it plots the results either over an existing ordination diagram or draws a new plot with sample plots and fitted contours. The function uses scores to extract ordination scores, and x can be any result object known by that function.

Value

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

Note

The funtion requires libraries mgcv (gam) and akima (interp). In fact, it is a very primitive wrapper for these.

The default is to use thinplate splines. These make sense in ordination as they have equal smoothing in all directions and are rotation invariant. However, they seem to fail badly in some case, and then separate spline smoothing may be used.

The function was called surf in older version of vegan; new names was chosen to avoid name clashes with the labdsv package.

Author(s)

Dave Roberts and Jari Oksanen

See Also

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

Examples

## The examples are not run by `example(ordisurf)' because they need
## libraries `mgcv' and `akima' which may not exist in every system.
## Not run: data(varespec)
## Not run: data(varechem)
## Not run: library(MASS)
## Not run: library(mva)
## Not run: vare.dist <- vegdist(varespec)
## Not run: vare.mds <- isoMDS(vare.dist)
## Not run: attach(varespec)
## Not run: attach(varechem)
## Not run: ordisurf(vare.mds, Baresoil, xlab="Dim1", ylab="Dim2")
## Total cover of reindeer lichens
## Not run: ordisurf(vare.mds, Cla.ste+Cla.arb+Cla.ran, xlab="Dim1", ylab="Dim2") 

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