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

Jens Oldeland oldeland at gmx.de
Wed Oct 14 09:12:05 CEST 2009 

Dear Sarah, Jari and Peter,

let me summarize what has been written so far

1) Jari said that: dbRDA needs rectangular data on right hand side of 
the formula --> dist.matrix on RHS leads to a lack of independence *no 
optimal solution*
2) Sarah suggests *MRM *
3) Peter suggests *Monmonier's maximum-difference barriers algorithm*   
(especially useful for genetic distances) *
*
it seems that there is still need for case studies testing and 
discussion on that topic,

My colleague and I will first dig a bit deeper into that problem, 
reading the suggested literature, then testing the different options and 
after that I will write our findings on R-sig-eco list again.

We like to thank you all for that very interesting discussion!!

many thanks so far!

Jens & Jan

PS: any further hints on literature would be great!


Peter Solymos schrieb:
> Dear All,
>
> Perhaps, there is another way of approaching this problem: the
> Monmonier's maximum-difference barriers algorithm.
>
> Monmonier, M. (1973) Maximum-difference barriers: an alternative
> numerical regionalization method. Geographic Analysis, 3, 245–261.
> Manni, F., Guerard, E. and Heyer, E. (2004) Geographic patterns of
> (genetic, morphologic, linguistic) variation: how barriers can be
> detected by "Monmonier's algorithm". Human Biology, 76, 173–190
>
> Nice documantation and a free software Barrier here:
> http://www.mnhn.fr/mnhn/ecoanthropologie/software/barrier.html
> The R implementation has been done by Thibaut Jombart in the adegenet
> package (function monmonier), that is slightly different in handling
> tessellation at the margin. Permutation test are discussed in the
> Manni paper as I recall and implemented in Barrier. This is especially
> useful for genetic distances (and NOT for biotic data, because of
> profoundly different dispersal mechanisms involved in shaping genetic
> vs. community structures).
>
> Yours,
>
> Peter
>
> Péter Sólymos
> Alberta Biodiversity Monitoring Institute
> Department of Biological Sciences
> CW 405, Biological Sciences Bldg
> University of Alberta
> Edmonton, Alberta, T6G 2E9, Canada
> Phone: 780.492.8534
> Fax: 780.492.7635
> email <- paste("solymos", "ualberta.ca", sep = "@")
>
>
>
> On Tue, Oct 13, 2009 at 10:07 AM, Jari Oksanen <jari.oksanen at oulu.fi> wrote:
>   
>>
>> On 13/10/09 18:44 PM, "Jens Oldeland" <oldeland at gmx.de> wrote:
>>
>>     
>>> 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 55:1703­1705
>>> Castellano, S. and E. Balletto. 2002. Is the partial Mantel test
>>> inadequate? Evolution 56:1871­1873.
>>>
>>>
>>> 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."
>>>       
>> Jens,
>>
>> There has been a very similar discussion in the Ecology recently between my
>> good friends, Hanna Tuomisto & co vs. Pierre Legendre & co. However, the
>> point here and above exactly was that you cannot use dissimilarities on the
>> RHS (lack of independence), but you must use rectangular data in dbRDA. If
>> you use distances on the RHS you won't have dbRDA but you get Mantel family
>> methods (like MRM in ecodist). The problem, of course, is how to map
>> distances onto Euclidean space (= rectangular data) *and* still study the
>> effects of the distances instead of the effects of *location*. I don't know
>> any really good solution here, but all proposed solutions have their
>> problems. Pierre Legendre, Daniel Borcard and Hanna Tuomisto have all tried
>> to convince me of their point of view, and while all their conflicting
>> arguments make sense, they are not yet an optimal solution.
>>
>> Cheers, Jari Oksanen
>>     
>>> 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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>>
>>
>>     
>
>   


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Dipl.Biol. Jens Oldeland
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Germany

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