R: Get Species or Site Scores from an Ordination

scores {vegan} | R Documentation

## Get Species or Site Scores from an Ordination

### Description

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.

### Usage

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

### Arguments

`x` | An ordination result.
`choices` | Ordination axes. If missing, default method returns all axes.
`display` | Partial match to access scores for `sites` or `species`.
`...` | Other parameters (unused).

### Details

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.

### Value

The function returns a matrix of scores.

### Author(s)

Jari Oksanen

### See Also

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.

### Examples

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

[Package vegan version 2.4-3 Index]