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
----------------------------------------------------------------------------------------------------------------------------------------
EA 4228 - ECOMERS - /Ecosystèmes Côtiers Marins et Réponses aux Stress/
Université de Nice - Sophia Antipolis, Faculté des Sciences, Parc 
Valrose, 06108 Nice Cedex 2, France
More about my work and my lab. 
<http://www.unice.fr/ecomers/index.php?option=com_comprofiler&task=userProfile&user=101&Itemid=111&lang=fr>
----------------------------------------------------------------------------------------------------------------------------------------
Cell: +336 79 44 91 90
Office: +334 92 07 68 33
Skype: pierre.d.thiriet
Mail: pierre.thiriet@unice.fr
Mail(bis): pierre.d.thiriet@gmail.com


Le 18/03/2014 15:43, Cade, Brian a écrit :
> 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 Survey
> Fort Collins Science Center
> 2150 Centre Ave., Bldg. C
> Fort Collins, CO  80526-8818
>
> email:cadeb@usgs.gov  <brian_cade@usgs.gov>
> tel:  970 226-9326
>
>
>
> On Tue, Mar 18, 2014 at 5:53 AM, Alicia Valdés
> <aliciavaldes1501@gmail.com>wrote:
>
>> 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 ~ region,permutations=999,method="bray")
>>
>>   Where community is a presence/absence data matrix of species in forest
>> patches belonging to different regions.
>>
>> Then I would like to use the residuals of this model as the response
>> variable for some other analyses. I know I could use strata to model region
>> as a block variable, but this does not interest me, as afterwards I want to
>> perform another kind of analysis where I would like the region effect to be
>> removed.
>>
>> My problem is that I cannot figure out how to get residual values from the
>> adonis model.
>>
>> Any hint of some other kind of multivariate analysis that could solve this
>> problem is very welcome.
>>
>> Thanks in advance,
>>
>> --
>> Alicia Valdés
>> Université de Picardie Jules Verne
>> Unité EDYSAN (Ecologie et Dynamique des Systèmes Anthropisés)
>> 1, rue des Louvels
>> F-80037 Amiens Cedex
>> France
>> tel:+33 322825775
>> alicia.valdes@u-picardie.fr
>> http://www.u-picardie.fr/edysan/
>>
>>          [[alternative HTML version deleted]]
>>
>>
>> _______________________________________________
>> R-sig-ecology mailing list
>> R-sig-ecology@r-project.org
>> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
>>
>>
> 	[[alternative HTML version deleted]]
>
>
>
> _______________________________________________
> R-sig-ecology mailing list
> R-sig-ecology@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-ecology




	[[alternative HTML version deleted]]

