Mantel
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
P?ter S?lymos
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, Data Analysis, Modelling and Training (mobile) 0410 689 945 (fax) +612 4782 9023 chris at trickysolutions.com.au Disclaimer: The information in this email and any attachments to it are confidential and may contain legally privileged information.?If you are not the named or intended recipient, please delete this communication and contact us immediately.?Please note you are not authorised to copy, use or disclose this communication or any attachments without our consent. Although this email has been checked by anti-virus software, there is a risk that email messages may be corrupted or infected by viruses or other interferences. No responsibility is accepted for such interference. Unless expressly stated, the views of the writer are not those of the company. Tricky Solutions always does our best to provide accurate forecasts and analyses based on the data supplied, however it is possible that some important predictors were not included in the data sent to us. Information provided by us should not be solely relied upon when making decisions and clients should use their own judgement. -----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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