[R-sig-eco] null models with continuous abundance data

[Carsten Dormann]

Hi Etienne,

the double constraint is observed by two functions:

swap.web in package bipartite

and

commsimulator in vegan (at least in the r-forge version)

Both build on the r2dtable approach, i.e. you have, as you propose, to 
turn the low values into higher-value integers.

The algorithm is described in the help to swap.web.


HTH,

Carsten



On 06/01/2010 08:55, Etienne Laliberté wrote:
> Hi,
>
> Let's say I have measured plant biomass for a total of 5 species from 3
> sites (i.e. plots), such that I end with the following data matrix
>
> mat<- matrix(c(0.35, 0.12, 0.61, 0, 0, 0.28, 0, 0.42, 0.31, 0.19, 0.82,
> 0, 0, 0, 0.25), 3, 5, byrow = T)
>
> dimnames(mat)<- list(c("site1", "site2", "site3"), c("sp1", "sp2",
> "sp3", "sp4", "sp5"))
>
> Data is therefore continuous. I want to generate n random community
> matrices which both respect the following constraints:
>
> 1) row and column totals are kept constant, such that "productivity" of
> each site is maintained, and that rare species at a "regional" level
> stay rare (and vice-versa).
>
> 2) number of species in each plot is kept constant, i.e. each row
> maintains the same number of zeros, though these zeros should not stay
> fixed.
>
> To deal with continuous data, my initial idea was to transform the
> continuous data in mat to integer data by
>
> mat2<- floor(mat * 100 / min(mat[mat>  0]) )
>
> where multiplying by 100 is only used to reduce the effect of rounding
> to nearest integer (a bit arbitrary). In a way, shuffling mat could now
> be seen as re-allocating "units of biomass" randomly to plots. However,
> doing so results in a matrix with large number of "individuals" to
> reshuffle, which can slow things down quite a bit. But this is only part
> of the problem.
>
> My main problem has been to find an algorithm that can actually respect
> constraints 1 and 2. Despite trying various R functions (r2dtable,
> permatfull, etc), I have not yet been able to find one that can do
> this.
>
> I've had some kind help from Peter Solymos who suggested that I try the
> aylmer package, and it's *almost* what I need, but the problem is that
> their algorithm does not allow for the zeros to move within the matrix;
> they stay fixed. I want the number of zeros to stay constant within each
> row, but I want them to move freely betweem columns.
>
> Any help would be very much appreciated.
>
> Thanks
>
>    

-- 
Dr. Carsten F. Dormann
Department of Computational Landscape Ecology
Helmholtz Centre for Environmental Research-UFZ
Permoserstr. 15
04318 Leipzig
Germany

Tel: ++49(0)341 2351946
Fax: ++49(0)341 2351939
Email: carsten.dormann at ufz.de
internet: http://www.ufz.de/index.php?de=4205