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, ...)
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. |
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
).
Function is usually called for its side effect of drawing the contour
plot, but it returns the result object of 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)) ## Cover of Cladina arbuscula with(varespec, ordisurf(vare.mds, Cla.arb, family=quasipoisson))