ordisurf {vegan} | R Documentation

## 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.

### 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`).

### Value

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

### Note

The default is to use thinplate splines. These make sense in ordination as they have equal smoothing in all directions and are rotation invariant.

### Author(s)

Dave Roberts and Jari Oksanen

### 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))

[Package vegan version 1.8-8 Index]