ordisurf {vegan} | R Documentation |

Function `ordisurf`

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

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, bubble = FALSE, cex = 1, ...) ## S3 method for class 'ordisurf': calibrate(object, newdata, ...)

`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). If `knots = 0` or
`knots = 1` the function will fit a linear trend surface, and
if `knots = 2` the function will fit a quadratic trend surface
instead of a smooth surface. |

`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. |

`bubble` |
Use “bubble plot” for points, or vary the point
diameter by the value of the plotted variable. If `bubble` is
numeric, its value is used for the maximum symbol size (as in
`cex` ), or if `bubble = TRUE` , the value of `cex` gives
the maximum. The minimum size will always be `cex = 0.4` . The
option only has an effect if `add = FALSE` . |

`cex` |
Character expansion of plotting symbols. |

`object` |
An `ordisurf` result object. |

`newdata` |
Coordinates in two-dimensional ordination for new points. |

`...` |
Other graphical parameters. |

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 points
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`

).

Function `calibrate`

returns the fitted values of the response
variable. The `newdata`

must be coordinates of points for which
the fitted values are desired. The function is based on
`predict.gam`

and will pass extra arguments to
that function.

Function is usually called for its side effect of drawing the
contour plot. The function returns the result object of class
`"ordisurf"`

that inherits from `gam`

used
internally to fit the surface, but adds an item `grid`

that
contains the data for the grid surface. The item `grid`

has
elements `x`

and `y`

which are vectors of axis coordinates,
and element `z`

that is a matrix of fitted values for
`contour`

. The values outside the convex hull of observed
points are `NA`

in `z`

. The `gam`

component of the result can be used for further analysis like
predicting new values (see `predict.gam`

).

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

Dave Roberts and Jari Oksanen

For basic routines `gam`

,
and `scores`

. Function
`envfit`

provides a more traditional and compact
alternative.

data(varespec) data(varechem) library(MASS) vare.dist <- vegdist(varespec) vare.mds <- isoMDS(vare.dist) with(varechem, ordisurf(vare.mds, Baresoil, bubble = 5)) ## Cover of Cladina arbuscula fit <- with(varespec, ordisurf(vare.mds, Cla.arb, family=quasipoisson)) ## Get fitted values calibrate(fit)

[Package *vegan* version 1.16-32 Index]