scoresfunction is generic in vegan, and vegan ordination functions have their own
scoresfunctions that are documented separately with the method (see e.g.
scores.decorana). This help file documents the default
scoresmethod that is only used for non-vegan ordination objects.
"scores"(x, choices, display=c("sites", "species"), ...)
scoresis a generic method in vegan. Several vegan functions have their own
scoresmethods with their own defaults and with some new arguments. This help page describes only the default method. For other methods, see, e.g.,
All vegan ordination functions should have a
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
function is available, the results can be plotted using
ordixyplot etc., and the
ordination results can be compared in
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.
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
princomp and some ade4 objects.
It may work in other cases or fail mysteriously.
scoresfunctions include (but are not limited to)
scores.pcnm. These have somewhat different interface --
scores.ccain particular -- but all work with keywords
display="sites"and return a matrix. However, they may also return a list of matrices, and some other
scoresmethods will have quite different arguments.