[R-sig-eco] Mantel

[Peter Solymos]

Jonathan and Chris,

The mantel function in vegan package contains dist-to-matrix coercion,
so memory requirements for matrices should be setting the limit.

Cheers,

Peter

Péter Sólymos
Alberta Biodiversity Monitoring Institute
and Boreal Avian Modelling project
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 = "@")
http://www.abmi.ca
http://www.borealbirds.ca
http://sites.google.com/site/psolymos



On Thu, Apr 19, 2012 at 7:12 PM, Chris Howden
<chris at trickysolutions.com.au> wrote:
> I can't comment on vegan but R in general can handle a matrix with about
> 2*10^9 elements (for more R memory info look at
> http://stat.ethz.ch/R-manual/R-devel/library/base/html/Memory-limits.html)
>
> I believe distance matrices usually only store either the lower or upper
> diagonal. So the number of elements in a distance matrix are approx 1/2
> the number of elements in a matrix.
>
> I use the following code to see if my data is too big for R.
>
> ## # CHECK: IS DISTANCE MATRIX TOO BIG FOR MEMORY?
> ## # What is the min memory required for the distance matrix, assuming 1
> bit for each distance (which is actually too small)
> ## # CHECK RESULT GB: requires 8GB which is too big for my computer
> ## dim(segment.input)
> ## (nrow(segment.input)^2)/2
> ## (nrow(segment.input)^2)/(2*1000000000)
>
> ## # CHECK RESULT vector length, keeping in mind that I think distance
> matrices only require half the matrix to
> ## # store all the data, max is 2*10^9: Its bigger
> ## (nrow(segment.input)^2)/2 - 2*10^9
>
>
> ## ## interstingly nrow(segment.input)*nrow(segment.input) won't work for
> large numbers we get
> ## ## > nrows*nrows
> ## ## [1] NA
> ## ## Warning message:
> ## ## In nrows * nrows : NAs produced by integer overflow
>
>
> Chris Howden B.Sc. (Hons) GStat.
> Founding Partner
> Evidence Based Strategic Development, IP Commercialisation and Innovation,
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> chris at trickysolutions.com.au
>
>
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> -----Original Message-----
> From: r-sig-ecology-bounces at r-project.org
> [mailto:r-sig-ecology-bounces at r-project.org] On Behalf Of Jonathan Hughes
> Sent: Friday, 20 April 2012 10:24 AM
> To: r-sig-ecology at r-project.org
> Subject: [R-sig-eco] Mantel
>
>
>
> Dear all,
> Does anyone have an expectation of the maximum distance matrix size that
> vegan can handle during a partial Mantel test?
> thanks,
> Jonathan
>        [[alternative HTML version deleted]]
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