manipulate a matrix2

Thanks Jim, that was exactly what I was after.

On a second note, do you have any insight into pulling out the
duplicates in this type of matrix?
I thought that was what the upper=FALSE is in:
csv.dis <- vegdist(csv.m, method='jaccard', binary=FALSE, diag=FALSE,
upper=FALSE).  I just need either the lower or upper portion, with the
zeros (,3 & ,3) being the dividing line.

     [,3] [,5] [,6] [,9] [,11]

 [3,]    0    2   3   4   5

 [5,]    2    0   8   9   10

 [6,]    3    8   0   14   15

 [9,]    4    9   14  0    20

 [11,]   5   10   15  20   0

Thanks again,

Jon



-----Original Message-----
From: jim holtman [mailto:jholtman at gmail.com]
Sent: Friday, July 18, 2008 9:56 AM
To: Jon Hak
Cc: r-help at r-project.org
Subject: Re: [R] manipulate a matrix2

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

matrix so automating the process is a high priority.

Thanks,
Jon



From: jim holtman <jholtman_at_gmail.com

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

R and I have to admit I'm stumped. I have set up a process to

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

--
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]]