[R-sig-eco] Mantel

[Chris Howden]

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,
Data Analysis, Modelling and Training
(mobile) 0410 689 945
(fax) +612 4782 9023
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
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