Description Usage Arguments Details Value Author(s) See Also Examples
Function to access either species or site scores for specified axes
in some ordination methods. The scores
function is generic in
vegan, and vegan ordination functions have their own
scores
functions that are documented separately with the
method (see e.g. scores.cca
,
scores.metaMDS
, scores.decorana
). This
help file documents the default scores
method that is only
used for non-vegan ordination objects.
1 2 |
x |
An ordination result. |
choices |
Ordination axes. If missing, default method returns all axes. |
display |
Partial match to access scores for |
... |
Other parameters (unused). |
Function scores
is a generic method in vegan. Several
vegan functions have their own scores
methods with their
own defaults and with some new arguments. This help page describes
only the default method. For other methods, see, e.g.,
scores.cca
, scores.rda
,
scores.decorana
.
All vegan ordination functions should have a scores
method which should be used to extract the scores instead of
directly accessing them. Scaling and transformation of scores should
also happen in the scores
function. If the scores
function is available, the results can be plotted using
ordiplot
, ordixyplot
etc., and the
ordination results can be compared in procrustes
analysis.
The scores.default
function is used to extract scores from
non-vegan ordination results. Many standard ordination
methods of libraries do not have a specific class
, and no
specific method can be written for them. However,
scores.default
guesses where some commonly used functions
keep their site scores and possible species scores.
If x
is a matrix, scores.default
returns the chosen
columns of that matrix, ignoring whether species or sites were
requested (do not regard this as a bug but as a feature, please).
Currently the function seems to work at least for isoMDS
,
prcomp
, princomp
and some ade4 objects.
It may work in other cases or fail mysteriously.
The function returns a matrix of scores.
Jari Oksanen
Specific scores
functions include (but are not limited to)
scores.cca
, scores.rda
,
scores.decorana
, scores.envfit
,
scores.metaMDS
, scores.monoMDS
and
scores.pcnm
. These have somewhat different interface
– scores.cca
in particular – but all work with
keywords display="sites"
and return a matrix. However, they
may also return a list of matrices, and some other scores
methods will have quite different arguments.
1 2 3 |
Loading required package: permute
Loading required package: lattice
This is vegan 2.4-4
PC1 PC2
18 -10.7847878 18.7094315
15 -27.8036826 -11.7414745
24 -25.6919559 -14.5399684
27 -31.7820166 -31.2216800
23 -19.6315869 -2.5541193
19 -0.2413294 -11.4974077
22 -26.6771373 -12.3140897
16 -21.9230366 0.4449159
28 -39.6083051 -41.8877392
13 -4.0664328 20.4191153
14 -18.4416245 5.4406988
20 -17.3999191 2.3653380
25 -25.1673547 -13.2508067
7 -11.4065430 41.7356300
5 -8.4243752 45.3805255
6 -2.0759474 36.9311222
3 39.8617580 8.0590041
4 13.1065901 12.8377217
2 57.6827011 -4.8983565
9 63.3138332 -22.4481549
12 44.1073111 -10.1653935
10 64.9418975 -16.7633564
11 11.5313633 3.9720890
21 -3.4194194 -3.0130455
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.