[R-sig-eco] Community composition variance partitioning?

[Steve Brewer]

Alexandre,

I'll leave it to Sarah to advise you on MRM (and I agree with Jari that
the method you're describing is not going to work). I'll just add that it
is not clear to me why the predictors (even geographic distance) have to
be treated as distances to partition the variance in composition. I'm
assuming the environmental variables were not originally in the form of
euclidean distance matrices and that the raw measurements are available?
As for the geographic distances, if you have lat and long coordinates, why
not treat both lat and long as predictors and do the necessary analyses as
partial distance-based redundancy analyses using capscale? In one analysis
the geographic predictors could be partialled out (with the result
explaining the fraction explained by the environment). In another, the
environmental predictors could be partialled out (with the result
explaining the fraction explained by the geographic distance) and in a
third both geographic and environmental predictors could be considered
with no conditioning covariates (which will give the total variance
explained by both combined).

Best
Steve


J. Stephen Brewer 
Professor 
Department of Biology
PO Box 1848
 University of Mississippi
University, Mississippi 38677-1848
 Brewer web page - http://home.olemiss.edu/~jbrewer/
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Phone - 662-915-1077




On 12/4/13 11:50 AM, "Alexandre Fadigas de Souza" <alexsouza at cb.ufrn.br>
wrote:

>Dear friends,
>
>   My name is Alexandre and I am trying to analyze a dataset on floristic
>composition of tropical coastal vegetation by means of variance
>partition, according to the outlines of a Tuomisto's recent papers,
>specially
>
>Tuomisto, H., Ruokolainen, L., Ruokolainen, K., 2012. Modelling niche and
>neutral dynamics : on the ecological interpretation of variation
>partitioning results. Ecography (Cop.). 35, 961­971.
>
>   I have a doubt, could you please give your opinion on it?
>
>   We are proceeding a variance partition of the bray-curtis floristic
>distance using as explanatory fractions soil nutrition, topography,
>canopy openess and geographical distances (all as euclidean distance
>matrices).
>
>We are using the MRM function of the ecodist package:
>
>mrm <- MRM(dist(species) ~ dist(soil) + dist(topograph) + dist(light) +
>dist(xy), data=my.data, nperm=10000
>
>The idea is that the overall R2 of this multiple regression should be
>used to assess the contributions of the spatial and environmental
>fractions through subtraction :
>
>Three separate multiple regression analyses are needed
>to assess the relative explanatory power of geographical
>and environmental distances. All of these have the same
>response variable (the compositional dissimilarity matrix),
>but each analysis uses a diff erent set of the explanatory
>variables. In these analyses the explanatory variables are:
>(I) the geographical distance matrix only, (II) the environmental
>diff erence matrices only, and (III) all the explanatory
>variables used in (I) or (II). Comparing the R 2 values
>from these three analyses allows partitioning the variance
>of the response dissimilarity matrix to four fractions.
>Fraction A is explained uniquely by the environmental
>diff erence matrices and equals R2 (III) R2 (I). Fraction B
>is explained jointly by the environmental and geographical
>distances and equals R2 (I) R2 (II) R2 (III). Fraction C
>is explained uniquely by geographical distances and
>equals R2 (III) R2 (II). Fraction D is unexplained by the
>available environmental and geographical dissimilarity
>matrices and equals 100% R2 (III) (throughout the present
>paper, R2 values are expressed as percentages rather
>than proportions). [Tuomisto et al. 2012]
>
>The problem is that the R2 of the overall model (containing all the
>explanatory variables) is smaller than most of the R2 of models
>containing each of the explanatory matrices. So it seems not possible to
>proceed with the approach proposed.
>
>    
>    Sincerely,
>
>    Alexandre
>
>Dr. Alexandre F. Souza
>Professor Adjunto II Departamento de Botanica, Ecologia e Zoologia
>Universidade Federal do Rio Grande do Norte (UFRN)
>http://www.docente.ufrn.br/alexsouza  Curriculo:
>lattes.cnpq.br/7844758818522706
>
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