jarioksa/vegan — Issue #4: `scores` method returns only two site-axes by default, should return all
Author: joey711
Created: 2012-02-24 00:00:27+00:00
State: open

The documentation for the `scores` method `choices` argument states that, "If missing, default method returns all axes." However, recently, I've found that it is actually defaulting to only the first two axes. I would prefer the stated default because otherwise I will need to add an additional line accessing some aspect of the `cca` object in order to determine (at least) the number of axes I should request explicitly in a `choices` argument. This is somewhat antithetical to (one of) the goal(s) of `scores`, which is to abstract the action of accessing the axes values of an ordination result from the internal structure of various ordination objects.

Reproducible example: Perform correspondence analysis on `dune`
```R
library(vegan)
data(dune)
dune.cca <- cca(dune)
```

Attempt to get all site scores using default
```R
scores(dune.cca, display="sites")
```
But this just returns a 2-column `matrix`.

One undesirable work-around that I can use, for now, is to dig into the `CA$eig` element and ask how long that vector is:
```R
scores(dune.cca, choices=1:length(dune.cca$CA$eig), display="sites")
```
However, this won't work if the object is the result of a constrained correspondence analysis, because in that case there should be `CCA` axes as well, and so the hack would need to be extended. Is there an obvious replacement / alternative? Is this a bug, and the current documentation is describing the expected (but missing) behavior?