[R-sig-eco] using two distance metrices in formula

[Jens Oldeland]

Hi again,

our distance matrices are 1) genetic distance (Jaccard) and 2) 
3D-Euclidean Distance and the question we want to solve is if there is 
an effect called "Isolation by Distance" (IBD) in our data (genetic and 
"real"-distances of snails on the island of crete) or not. There was a 
debate on the topic if the mantel test or the partial mantel test (isn´t 
this similar to MRM?) in several papers mainly in evolution-journals:

Raufaste, N. and F. Rousset. 2001. Are partial Mantel tests adequate? 
Evolution 55:1703–1705
Castellano, S. and E. Balletto. 2002. Is the partial Mantel test 
inadequate? Evolution 56:1871–1873.


Geffen, E., Anderson, M.J., & Wayne, R.K. (2004). Climate and habitat 
barriers to dispersal in the highly mobile grey wolf. Molecular Ecology, 
13, 2481-2490
explain it nicely on page p.2483 (LHS)

"The problem arises due to the lack of independence of individual 
distances in a distance matrix. Although a simple Mantel test overcomes 
this issue by the
use of permutations, a permutational approach does not necessarily solve 
problems introduced by several uncontrolled nuisance parameters in the 
case of more than one
regressor (i.e. partial tests). Thus, we do not use a Mantel approach 
here, but rather use the distance-based multivariate approach of McArdle 
& Anderson (2001). The important point is that, for dbRDA, the 
individual distances are not treated as a single univariate response 
variable, as in the Mantel test, but rather the individual sites are the 
units of observation for analysis, about which we have calculated 
distances using an entire set of genetic variables. The distance matrix 
is therefore treated as information regarding multivariate 
response.Taking this multivariate approach avoids the problems 
associated with the partial Mantel test."

so we thought it would be a good idea not to use mantel and friends 
since the problem of IBD seems to need a different approach here.

best,
Jens





Sarah Goslee schrieb:
> That doesn't make much sense to me. You'd need an entirely different method
> than capscale.
>
> Perhaps what you're looking for is more like multiple regression on distance
> matrices (implemented in MRM in ecodist)?
>
>      Lichstein, J. 2007. Multiple regression on distance matrices: A
>      multivariate spatial analysis tool. Plant Ecology 188: 117-131.
>
>      Legendre, P.; Lapointe, F. and Casgrain, P. 1994. Modeling brain
>      evolution from behavior: A permutational regression approach.
>      Evolution 48: 1487-1499.
>
> Sarah
>
> On Tue, Oct 13, 2009 at 11:13 AM, Jens Oldeland <oldeland at gmx.de> wrote:
>   
>> Dear Sarah dear Jari,
>>
>> many thanks for your explanations. However, it wasnt what I thought about,
>> sorry I definitely have to be more specific about the problem.
>>
>> Okay I try be more precise:
>>
>> the problem was that for example  capscale accepts   "capscale(dist.matrix.1
>> ~ N + P + K *Ag, data=varechem)"
>> but I need  "capscale(dist.matrix.1 ~ dist.matrix.2, data=dist.matrix.2)"
>>  so the trick was not on how to create a distance matrix but how to use a
>> second on in a formula.
>>
>> We are trying a similar analysis like the the "distlm" program by Marti
>> Anderson does, however we had a problem with that and wanted to try the
>> analysis in R.
>>
>> thanks already for all your comments !
>>
>> best
>> Jens
>>     
>
>
>
>   


-- 
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Dipl.Biol. Jens Oldeland
University of Hamburg
Biocentre Klein Flottbek and Botanical Garden
Ohnhorststr. 18
22609 Hamburg,
Germany

Tel:    0049-(0)40-42816-407
Fax:    0049-(0)40-42816-543
Mail: 	Oldeland at botanik.uni-hamburg.de
        Jens.Oldeland at DLR.de  (for attachments > 2mb!!)
http://www.biologie.uni-hamburg.de/bzf/fbda005/fbda005.htm
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