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

[Jari Oksanen]

On 9/05/11 17:55 PM, "Tyler Smith" <tyler.smith at eku.edu> wrote:

> 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.
>e 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.
> 
Tyler,

Vegan has two general design principles: (1) there are design principles,
(2) they can be overruled.

I'll be happy to accept plot.cca amendment -- providing they are
"acceptable". I'm not quite sure how to code this new plotting option
without breaking other conventions. Like you wrote, you probably need to
drop some of the arrows, and this is different from ordinary plot(). I have
consciously opted to have all species/sites in plots and not to drop some of
those automatically. CanoDraw (IIRC) uses goodness-of-fit which usually drop
rare species which cannot have a good linear fit. You suggested dropping
shorter arrows. So you need to decide how to control the kept arrows, and
how to allow the user control to overrule your choice (that is always needed
in vegan style).

I do think that if you go for arrows, you must go completely. This means
that you need to get rid of absolute scaling of the locations of the arrow
heads (now points). The location of arrow heads have no special meaning wrt
site points. All features you must preserve are relative lengths of arrows
wrt each other, and their directions. So you need an automatic rescaling of
coordinates so that the arrows fill the graphics space.

Finally a comment about arrows as a convention in RDA: I disagree -- it is
not a convention in RDA, but a convention in CanoDraw and its heirs. I never
liked it when CanoDraw introduced this for the reasons I gave earlier
(messy). Points were quite common in displaying PCA results even earlier,
although some people used arrows, especially with small data sets.

Cheers, Jari Oksanen