scores | R Documentation |

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.

## Default S3 method: scores(x, choices, display=c("sites", "species", "both"), tidy = FALSE, ...)

`x` |
An ordination result. |

`choices` |
Ordination axes. If missing, default method returns all axes. |

`display` |
Partial match to access scores for |

`tidy` |
Return |

`...` |
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 if one type is requested, or a
named list of matrices if `display = "both"`

, or a
ggplot2 compatible data frame if `tidy = TRUE`

.

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.

data(varespec) vare.pca <- prcomp(varespec) scores(vare.pca, choices=c(1,2))

vegan documentation built on Oct. 11, 2022, 5:06 p.m.

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