[R-sig-eco] vegan RDA triplot species arrows

[Tyler Smith]

Jari Oksanen <jari.oksanen at oulu.fi> writes:

>> Why does vegan not plot species as arrows in plot? I know how to use
>> scores() and arrows() to create my own arrows, but it seems odd that
>> this feature is not built in. Is there ever a situation where species
>> *should* be plotted as points rather than arrows?
>> 
>
> Not using arrows for species is a design decision, and it is mainly
> for practical reasons. Ordination graphics are usually very messy with
> points, and if you add arrows they get messier beyond grasp.

Thanks for your detailed response. I disagree with your conclusion,
though. Granted, all those arrows do make the plots messy, I think the
better solution would be to drop the shorter arrows (which are less
meaningful), rather than the lines of all arrows.

My reasoning is that whether or not you plot the lines, the species are
in fact arrow heads. Suppressing the lines makes them look like
centroids. This leads to confusion between a CCA plot, with species
plotted as true centroids, and an RDA plot, with arrows that appear to
be centroids. This is an issue I've seen in a number of the projects
submitted as part of a grad course in ordination here.

Whether arrows are preferable to centroids or response surfaces is a
separate issue, and I think there are strong points supporting each of
the three representations depending on the circumstances. One of the
strongest arguments for using species arrows on an RDA is convention:
the method produces arrows by design, so you ought to have a very good
reason to use some other representation of species.

In any case, if you are interested I would be happy to attempt to add
code to plot.cca to do what I'd prefer. If not, no worries, I can make a
wrapper function to get what I want without modifying vegan.

Thanks,

Tyler