 Dear all,

First of all I want to apologise for send the previous message to the wrong
list. I am very grateful to Dr. J. Oksanen for his reply.

As J. Oksanen answered:

plot(vare.cca, scaling=2, type="n")
text(vare.cca, dis="species", scaling=2, cex=0.6)
with(varespec, ordiellipse(vare.cca, rep(1, 24), show= TRUE, display="lc",
scaling=2, w= Cet.niv, col=2))

>From this function I assume that the standard error will be supplied with
ordiellipse function. I refered as "se" (standard error) as the error that
will be calculated for species centroids displayed in the previous function
with *dis="species"*, some similar to confidence intervals. In the papers
that I read the mention it like "*Data represents means +-SE".*

I am deepening in the parameters of the function ordiellipse and I think
that will be useful to define some arguments like kind:

with(varespec, ordiellipse(vare.cca, rep(1, 24), show= TRUE,
display="lc",kind="se"
scaling=2, w= Cet.niv, col=2))

However, when I applied this function to my particular data set, it returns
an error message like:

Error in cov.wt(X, W) : weights must be non-negative and not all zero

I looked for an error like this, but I do not find any answer yet. I would
appreciate any comment or references to this matter. Again, I apologize for
my previous e-mail send to wrong list.

Best regards,

Paloma

 ---------- Forwarded message ----------
prb <eco.prb <at> gmail.com> writes:
  > Dear all,
>
> I realised a correspondence analysis with function cca() of vegan library.
> Just like in Okansen (2010) in the example of R help:
>
> library(vegan)
> data(varespec)
> data(varechem)
> vare.cca<-cca(varespec~ Al + P + K, varechem)
>
> With plot.cca() function I represented the species matrix in the next way:
> plot(vare.cca,display="species")
>
> Being similar to:
> plot((c(-2,2)),(c(-2,2)), type="n", xlab="AXIS 1", ylab="AXIS 2")
> points(vare.cca,display='species')
>
> Now, I want to add to this graph a standard error in 'x' and 'y'
direction.
> How can I add it? I tried different options but I do not get it. It will
be
> just like the function ordiellipse of ellipse library and others like
> ordihull of vegan library, but without add any factor level. The program
CAP
> of Anderson realice this kind of output and I am wondering if in R exists
> some function implemented that deals with it. Some examples of these
> graphics will be found in Quero et al., 2008 Basic and Applied Ecology 9:
> 635-644; Maestre et al., 2009 Ecology Letters 12: 930 - 941.
>
Paloma,


This is a question on specific package, and I'm not sure that general R News
is
a suitable forum to answer this. I suggest you re-send this message to
r-sig-ecol...@r-project.org (see special interest groups at

http://www.r-project.org/mail.html for more info). Although vegan indeed is
a
special, questions related to vegan are regularly discussed there and the
subject may be tolerated at that forum (or we may assume as long as we are
not
told to go away). Another alternative is to use vegan fora at
http://vegan.r-forge.r-project.org/ which are dedicated to vegan questions.

Then a brief preliminary aswer to your question: you should tell us what is
"species standard error". I can guess what you mean, and if I guess
correctly,
this can be done. Here is one way how to do this for one species continuing
your
example:

plot(vare.cca, scaling=2, type="n")
text(vare.cca, dis="species", scaling=2, cex=0.6)
with(varespec, ordiellipse(vare.cca, rep(1, 24), show= TRUE, display="lc",
scaling=2, w= Cet.niv, col=2))

Why this works and what this means is better explained in some more
dedicated
news group: there are many fine details. This is also based on the
hypothesis
that I guessed correctly what you wanted to do.

Cheers, Jari Okansen

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