Hi,
I am using the adonis function in the vegan package to determine effects of
different environmental factors in forest plant community composition in
different regions. I would like to first use adonis to remove the region
effect, this is, to fit a model like
adonis_region- adonis(community ~
Dear Alicia Valdés,
On 18/03/2014, at 13:53 PM, Alicia Valdés wrote:
My problem is that I cannot figure out how to get residual values from the
adonis model.
You cannot get residuals from the output of adonis().
We could change the function so that this is possible, but the current
Dear Alicia and Jari,
just a thought:
Couldn't be capscale or betadisper be used for this?
- To obtain the distances to the group centroid?
But than: How to convert this from distances to abundances?
Eduard Szöcs
On 03/18/2014 01:21 PM, Jari Oksanen wrote:
Dear Alicia Valdés,
On
On 18/03/2014, at 15:23 PM, Eduard Szöcs wrote:
Dear Alicia and Jari,
just a thought:
Couldn't be capscale or betadisper be used for this?
- To obtain the distances to the group centroid?
But than: How to convert this from distances to abundances?
You can *almost* do this with
Hi and many thanks for your replies,
I have had a look at capscale() and betadisper(), but as you said, this
could only provide residuals in fhe form of dissimilarities, and what I
actually would like to have are true residuals, negative and positive.
I have also looked into ecodist, but I did
You ought to be very careful about using residuals from one analysis as the
response variable in another analysis as the inferences about the second
analysis will almost certainly be flawed. Best to try and do this another
way if at all possible.
Brian
Brian S. Cade, PhD
U. S. Geological
Hi,
Yes, I know there are issues about using residuals as response variable,
and contrasting opinions about that.
However, what I attempt to do is to perform an indicator species analysis
(ISA) with these residuals. I want to see if I can find species which are
indicators for different
Dear Alicia,
the mvabund package enables to fit Multivariate Generalized Linear Model
for presence/abscence data. I guess you could extract residuals.
HTH,
Pierre
*Pierre THIRIET*
Doctorant en écologie marine - Marine Ecology PhD student
On Tue, Mar 18, 2014 at 5:02 PM, Alicia Valdés
aliciavaldes1...@gmail.com wrote:
...
However, what I attempt to do is to perform an indicator species analysis
(ISA) with these residuals. I want to see if I can find species which are
indicators for different environmental conditions, but first I
Thanks for so many thoughts!
Arne: I could use Condition() for that but something like
capscale(communitydistances ~ environmentalvar+Condition(region))
would not attempt what I need, because I need to fit a model only with
region, extract residuals, and then do another analysis (ISA) with these
Alicia
One more thought. I wonder if part of the problem is that you're
attempting to use ISA to do something it was not designed to deal with.
Sometimes that can work and result in a clever new approach, but in this
case, I don't see how it can work. As a recall, ISA is done by taking the
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