[R] manipulate a matrix

[Marc Schwartz]

On Mon, 2007-06-25 at 10:58 -0400, Jon Hak wrote:
> I have read everything I can find on how to manipulate a results
> matrix in R and I have to admit I'm stumped.  I have set up a process
> to extract a dataset from ArcGIS to compute a similarity index
> (Jaccards) in Vegan.  The dataset is fairly simple, but large, and
> consists of rows = sample area, and columns = elements.  I've been
> able to view the results in R, but I want to get the results out to a
> database and a matrix that is 6000-rows x 6000-columns can be very
> difficult to manipulate in Windows XP.  I would to rotate the matrix
> so that the output would look like the old condensed format in
> programs like Conoco.  Ideally, I would like format to look something
> like this;
> 
> 
> Site-row Site-col Jaccard
> 1	    1		1
> 1	    2  	.9
> 1	    3  	.6
> 2	    1  	.9
> 2    	    2       1
> 2	    3       .75
> 
> Thanks for any help,

Presuming that your source matrix for the above is:

mat <- matrix(c(1, .9, .6, .9, 1, .75), ncol = 3, byrow = TRUE)

> mat
     [,1] [,2] [,3]
[1,]  1.0  0.9 0.60
[2,]  0.9  1.0 0.75

You can use the following:

t.mat <- t(mat)

Res <- cbind("Site-row" = as.vector(col(t.mat)), 
             "Site-col" = as.vector(row(t.mat)), 
             Jaccard = as.vector(t.mat))

> Res
     Site-row Site-col Jaccard
[1,]        1        1    1.00
[2,]        1        2    0.90
[3,]        1        3    0.60
[4,]        2        1    0.90
[5,]        2        2    1.00
[6,]        2        3    0.75

See ?t and ?row

HTH,

Marc Schwartz