[R] Memory Efficiency of Symmetric Matrix

[Steven McKinney]

See also the dist() function documentation.
If you use indexing as described in ?dist
it is straightforward to maintain and
use a vector of the distances.

Steven McKinney

Statistician
Molecular Oncology and Breast Cancer Program
British Columbia Cancer Research Centre

email: smckinney +at+ bccrc +dot+ ca

tel: 604-675-8000 x7561

BCCRC
Molecular Oncology
675 West 10th Ave, Floor 4
Vancouver B.C. 
V5Z 1L3
Canada




-----Original Message-----
From: r-help-bounces at r-project.org on behalf of Søren Højsgaard
Sent: Tue 1/6/2009 4:36 PM
To: Nathan S. Watson-Haigh; r-help at r-project.org
Subject: Re: [R] Memory Efficiency of Symmetric Matrix
 
You can do
mat[lower.tri(mat, diag=F)]
Søren

 
________________________________

Fra: r-help-bounces at r-project.org på vegne af Nathan S. Watson-Haigh
Sendt: on 07-01-2009 01:28
Til: r-help at r-project.org
Emne: [R] Memory Efficiency of Symmetric Matrix



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I'm generating a symmetric correlation matrix using a data matrix as input:
mat <- cor(data.mat)

My question is:
Is there a more memory efficient way to store this data? For instance, since:
all(mat == t(mat))
every value is duplicated, and I should be able to almost half the memory usage for large matrices.

Any thoughts/comments?

Cheers,
Nathan


- --
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Dr. Nathan S. Watson-Haigh
OCE Post Doctoral Fellow
CSIRO Livestock Industries
Queensland Bioscience Precinct
St Lucia, QLD 4067
Australia

Tel: +61 (0)7 3214 2922
Fax: +61 (0)7 3214 2900
Web: http://www.csiro.au/people/Nathan.Watson-Haigh.html
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