[R] manipulate a matrix2

From: Jon Hak <Jon_Hak_at_natureserve.org>
Date: Fri, 18 Jul 2008 11:10:40 -0400


Building upon Jim's answer below (Thanks Jim, that helped a lot), I need to pickup where this thread left off. I'm using Vegan to calculate the Jaccard's Index and the Row.Names and column names are represented in my matrix as seen here.

      [,3] [,5] [,6] [,9] [,11]

[3,] 0 6 11 16 21

[5,] 2 0 12 17 22

[6,] 3 8 0 18 23

[9,] 4 9 14 0 24

[11,] 5 10 15 20 0  

When I use the command;
xy <- cbind(row=as.vector(row.names(x)), col=as.vector(colnames(x)), value=as.vector(x))  

I get the list (the column value is the issue);  

      row    col   value
 [1,]   3     1     0
 [2,]   5     1     2
 [3,]   6     1     3
 [4,]   9     1     4
 [5,]   11   1     5
 [6,]   3     2     6
 [7,]   5     2     0
 [8,]   6     2     8
 [9,]   9     2     9
[10,]   11  2    10

[11,] 3 3 11
[12,] 5 3 0  

I would really like the col value to equal the actual name, not the column number. What am I missing? The analysis is very large, 6k x6k matrix so automating the process is a high priority.  

Thanks,
Jon      

From: jim holtman <jholtman_at_gmail.com <mailto:jholtman_at_gmail.com?Subject=Re:%20%5BR%5D%20manipulate%20a%20m atrix> >
Date: Mon, 25 Jun 2007 12:39:46 -0400

Is this what you want?

> x

     [,1] [,2] [,3] [,4] [,5]

[1,]    1    6   11   16   21
[2,]    2    7   12   17   22
[3,]    3    8   13   18   23
[4,]    4    9   14   19   24
[5,]    5   10   15   20   25


 

cbind(row=as.vector(row(x)), col=as.vector(col(x)), value=as.vector(x))

      row col value
 [1,]   1   1     1
 [2,]   2   1     2
 [3,]   3   1     3
 [4,]   4   1     4
 [5,]   5   1     5
 [6,]   1   2     6
 [7,]   2   2     7
 [8,]   3   2     8
 [9,]   4   2     9
[10,]   5   2    10
[11,]   1   3    11
[12,]   2   3    12
[13,]   3   3    13
[14,]   4   3    14
[15,]   5   3    15
[16,]   1   4    16
[17,]   2   4    17
[18,]   3   4    18
[19,]   4   4    19
[20,]   5   4    20
[21,]   1   5    21

[22,] 2 5 22
[23,] 3 5 23

[24,] 4 5 24
[25,] 5 5 25
>

On 6/25/07, Jon Hak <Jon_Hak_at_natureserve.org> wrote:
>
> I have read everything I can find on how to manipulate a results
matrix in
<http://tolstoy.newcastle.edu.au/R/e2/help/07/06/19875.html#19887qlink1>

> 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,
>
>
>
>
> ***********************************************************
> John Hak
> Senior GIS Analyst/Sr. Ecologist
> NatureServe
> 4001 Discovery Drive
> Boulder, CO 80303
> (703) 797-4809
>
> There is perhaps no better demonstration of the folly of human
conceits
> than this distant image of our tiny world. To me, it underscores our
> responsibility to deal more kindly with one another, and to preserve
and
> cherish the pale blue dot, the only home we've ever known. --Carl
Sagan
>

>
> ______________________________________________
> R-help_at_stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

-- 
Jim Holtman
Cincinnati, OH
+1 513 646 9390
 
What is the problem you are trying to solve?
 
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Received on Fri 18 Jul 2008 - 15:14:59 GMT

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