boxgradient | R Documentation |
The function display species responses along ecological gradients
using either boxplot
or a polygon
displaying fitted Gaussian responses.
boxgradient(x, grad, horizontal = TRUE, xlab, freq.lim = 5,
cex.species= 0.7, axes = TRUE, ...)
gaussgradient(x, grad, family = poisson, xlab, freq.lim = 5,
cex.species = 0.7, axes = TRUE, ...)
x |
Community data |
grad |
Gradient vector |
horizontal |
Use horizontal |
family |
Errof |
xlab |
Label of the gradient. Variable name used as default. |
freq.lim |
Frequency of rarest species displayed. |
cex.species |
Size multiplier for species labels. Species labela
are printed horizontally, and typically you must reduces their size
with this parameter or increase the margin (see |
axes |
Draw |
... |
Other parameters passed to underlying functions
|
The functions are intended for simultaneous display of species responses along an ecological gradient.
Function boxgradient
will draw boxplot
s of species presences. In addition,
it puts points at weighted avarages. The boxplots are based on
presence data only, but weighted averages are based on the original
quantitative information. Boxes are arranged by medians, but breaking
ties by weighted averages. The
function also adds lines of quartiles and median for the whole
gradient, and adds a rug
of gradient values.
Function gaussgradient
draws fitted Gaussian response models.
The curves are adjusted to the same area so that narrower responses
will look higher, but the heights have no relation to the original
abundances. The responses are fitted using glm
, and
species with failed fitting (“inverted” responses) will not be
displayed. The fitted responses are ordered by the location of the
top (‘optimum’).
The functions are used to draw plots. Function boxpgradient
returns
invisibly the object returned by boxplot
. Function
gaussgradient
returns invisibly a list
of fitted optima
and tolerances.
Jari Oksanen
boxplot
, polygon
,
axis
, par
.
data(mtf01)
data(mtf.alt)
attach(mtf.alt)
op <- par(no.readonly=TRUE)
par(mfrow=c(2,1))
par(mar=c(4,6,1,1))
boxgradient(mtf01, Altitude, col="pink", border="blue", notch=TRUE)
gaussgradient(mtf01, Altitude, col="pink", border="blue")
par(op)
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