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

[Jari Oksanen]

On 4/05/11 22:44 PM, "Tyler Smith" <tyler.smith at eku.edu> wrote:

> Hi,
> 
> 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?
> 
> I checked ?plot.cca, vegan-decision, and google, but I didn't find
> anything, (excepting the possibility of using biplot.rda, but only for
> unconstrained analyses).
> 
Tyler,

Do you mean something like

library(vegan)
data(dune)
m <- rda(dune)
plot(m, dis="si")
plot(envfit(m ~ ., dune), add=TRUE)

Like Gavin said in another message: I hate this. My feelings shouldn't stop
you.

There was an earlier discussion in this group for using species arrows in
dbRDA (capscale in vegan). Search for that.

For constrained ordination, you got to base envfit on "lc" scores instead of
"sites".

Cheers, Jari