"biplot"(x, choices = c(1, 2), scaling = "species", display = c("sites", "species"), type, xlim, ylim, col = c(1,2), const, correlation = FALSE, ...)
rda
result object.2
) or site (1
) scores are scaled by eigenvalues, and
the other set of scores is left unscaled, or with 3
both are
scaled symmetrically by square root of eigenvalues. With negative
scaling values in rda
, species scores are divided by standard
deviation of each species and multiplied with an equalizing
constant. Unscaled raw scores stored in the result can be accessed
with scaling = 0
. The type of scores can also be specified as one of "none"
,
"sites"
, "species"
, or "symmetric"
, which
correspond to the values 0
, 1
, 2
, and 3
respectively. Argument correlation
can be used in combination
with these character descriptions to get the corresponding negative
value.
scaling
is a character
description of the scaling type, correlation
can be used to
select correlation-like scores for PCA. See argument scaling
for details."species"
for species scores, and/or "sites"
for site
scores.text
for text labels, points
for points, and none
for
setting frames only. If omitted, text
is selected for
smaller data sets, and points
for larger. Can be of length 2
(e.g. type = c("text", "points")
), in which case the first
element describes how species scores are handled, and the second how
site scores are drawn.scores.rda
.plot
function returns invisibly a plotting structure which
can be used by identify.ordiplot
to identify
the points or other functions in the ordiplot
family.
rda
. It is common for the "species" scores in a PCA to
be drawn as biplot arrows that point in the direction of increasing
values for that variable. The biplot.rda
function provides a
wrapper to plot.cca
to allow the easy production of such a
plot. biplot.rda
is only suitable for unconstrained models. If
used on an ordination object with constraints, an error is issued.
If species scores are drawn using "text"
, the arrows are drawn
from the origin to 0.85 * species score, whilst the labels are
drawn at the species score. If the type used is "points"
, then
no labels are drawn and therefore the arrows are drawn from the origin
to the actual species score.
plot.cca
, rda
for something to
plot, ordiplot
for an alternative plotting routine
and more support functions, and text
,
points
and arrows
for the basic routines.data(dune)
mod <- rda(dune, scale = TRUE)
biplot(mod, scaling = "symmetric")
## different type for species and site scores
biplot(mod, scaling = "symmetric", type = c("text", "points"))
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