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You are able to store such a huge matrix in R, if you ask for it...
Furthermore, "table" command might help you:

Help page for "table" says:

Cross Tabulation and Table Creation
Description:
     'table' uses the cross-classifying factors to build a contingency
     table of the counts at each combination of factor levels.

Take a look at the examples on the Help page.

- --vst


Des Callaghan wrote:
> Dear all,
> 
> I have a set of data that is 2 columns wide and 35,000 rows long (see
> extract below).  The first column contains codes for tetrads (2km x 2km
> squares within NW England) and the second column has the names of moss
> species present within each tetrad.  I wish to convert this into a matrix
> where rows are labelled by 'Tetrad', columns are labelled by 'Moss species'
> and each cell contains a 1 or 0 to denote the presence or absence of the
> moss species within each tetrad.  This would be a matrix measuring 796 rows
> by 417 columns.  Am I able to do this within R?  I ran into problems trying
> to do it using the crosstab query in MS Access and the pivot table function
> on MS Excel because there are too many columns for these software to handle.
> Thanks very much in advance for any help.
> 
> All the best,
> Des
> 
> Tetrad        Moss species
> SD20S Amblystegium serpens var. serpens
> SD20S Barbula convoluta
> SD21S Brachythecium albicans
> SD20J Brachythecium rutabulum
> SD30S Bryum argenteum
> SD20S Bryum capillare
> 
> ______________________________________________
> [email protected] mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
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