Hi Gavin,
I have been analyzing real data (sorry but I am not allowed to post
these data here) and what I got was this,
mydistmat_f.cap - capscale(distmat_f ~ F + L + F:L, mfactors_frame)
Warning messages:
1: some of the first 30 eigenvalues are 0 in: cmdscale(X, k = k, eig =
TRUE, add = add)
On Mon, 2006-11-27 at 15:37 +0100, Alicia Amadoz wrote:
Hi Gavin,
I have been analyzing real data (sorry but I am not allowed to post
these data here) and what I got was this,
mydistmat_f.cap - capscale(distmat_f ~ F + L + F:L, mfactors_frame)
I believe you can write that formula as:
Hello,
Thank you for your help. I have tried to perform the analysis I wanted
with data of example, I mean not real data because I can't provide it
here. So, what I have tried is this,
matrix
[,1] [,2] [,3]
[1,] 0.00 0.13 0.59
[2,] 0.13 0.00 0.55
[3,] 0.59 0.55 0.00
dist_mat
12
On Fri, 2006-11-17 at 12:18 +0100, Alicia Amadoz wrote:
Hello,
Thank you for your help. I have tried to perform the analysis I wanted
with data of example, I mean not real data because I can't provide it
here. So, what I have tried is this,
Hi Alicia,
It would have been more helpful if
Hello Gavin,
Thank you very much for your help. I'm sorry I forgot to include all
commands that I used but next time I will try to write all of them. I
will try with my real data and see how it goes. I think I finally have
understood how capscale works with this kind of data. Thank you.
Regards,
On Fri, 2006-11-17 at 12:26 +, Gavin Simpson wrote:
On Fri, 2006-11-17 at 12:18 +0100, Alicia Amadoz wrote:
Hello,
Thank you for your help. I have tried to perform the analysis I wanted
with data of example, I mean not real data because I can't provide it
here. So, what I have
Hello,
I am interested in using the capscale function of vegan package of R. I
already have a dissimilarity matrix and I am intended to use it as
'distance' argument. But then, I don't know what kind of data must be in
'comm' argument. I don't understand what type of data must be referred
as
Hi Alicia,
On 11/16/06, Alicia Amadoz [EMAIL PROTECTED] wrote:
'comm' argument. I don't understand what type of data must be referred
as 'species scores' and 'community data frame' since my data refer to
nucleic distances between different sequences.
comm would be the original data from
Sorry, one additional note:
You don't need to specify comm to use capscale. Ignore what I said about
modifying the function.
Sarah
--
Sarah Goslee
http://www.functionaldiversity.org
__
R-help@stat.math.ethz.ch mailing list
On Thu, 2006-11-16 at 17:25 +0100, Alicia Amadoz wrote:
Hello,
I am interested in using the capscale function of vegan package of R. I
already have a dissimilarity matrix and I am intended to use it as
'distance' argument. But then, I don't know what kind of data must be in
'comm' argument.
Nice catch, Gavin - I missed that part of the original post. The
nucleic distances need to be included as the left-hand-side of
the formula, not as the distance argument.
comm is still optional, though, but it's not a good idea to omit
it if there's any way you can provide the original data. From
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