[R] manipulate a matrix2

Fri Jul 18 17:56:03 CEST 2008

Is this what you want:

> x
      [,3] [,5] [,6] [,9] [,11]
[,3]     1    6   11   16    21
[,5]     2    7   12   17    22
[,6]     3    8   13   18    23
[,9]     4    9   14   19    24
[,11]    5   10   15   20    25
> library(reshape)
> melt(x)
      X1    X2 value
1   [,3]  [,3]     1
2   [,5]  [,3]     2
3   [,6]  [,3]     3
4   [,9]  [,3]     4
5  [,11]  [,3]     5
6   [,3]  [,5]     6
7   [,5]  [,5]     7
8   [,6]  [,5]     8
9   [,9]  [,5]     9
10 [,11]  [,5]    10
11  [,3]  [,6]    11
12  [,5]  [,6]    12
13  [,6]  [,6]    13
14  [,9]  [,6]    14
15 [,11]  [,6]    15
16  [,3]  [,9]    16
17  [,5]  [,9]    17
18  [,6]  [,9]    18
19  [,9]  [,9]    19
20 [,11]  [,9]    20
21  [,3] [,11]    21
22  [,5] [,11]    22
23  [,6] [,11]    23
24  [,9] [,11]    24
25 [,11] [,11]    25
>

On Fri, Jul 18, 2008 at 11:10 AM, Jon Hak <Jon_Hak at natureserve.org> wrote:
> 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?
>
>        [[alternative HTML version deleted]]
>
>
>
>
>
>
>        [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at r-project.org 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?