Kohonen Package

Hi All,

I am still learning R, but making, IMO, great strides.  I learned about Kohonen/Self-Organizing Maps in class and I would like to try to replicate some of the things we have seen in class.

Below is my code.  I am trying to create a u-matrix.  In the documentation on page 9 it appears the type of plot, dist.neighbours should do the trick, however, I am getting an error:
(Error in match.arg(type) : 'arg' should be one of "codes", "changes", "counts", "mapping", "property", "quality")

Since I am new to R, I figure I am missing something obvious.  Any help you can provide will be greatly appreciated!

Thanks in advance,

Brock

library(kohonen)

data("wines")
wines.sc <- scale(wines)

som <- som(wines.sc, grid=somgrid(5, 5, "hexagonal"))
plot(som)
plot(som, type="dist.neighbours" )

I haven't used pkg:kohonen, so this is just guessing:

1. are you using an old version of the package?

packageDescription("kohonen")$Version

2. don't call the output of function som() 'som'. As
people around here might say: would you call your
iguana 'iguana'?

3. have you used str() on your object to check what
it really contains? I would guess that it should be
of class som and have a component 'distances'.

If none of that helps then it's beyond me.

  -Peter Ehlers


Brock Tibert wrote:

Hi All,

I am still learning R, but making, IMO, great strides.  I learned about Kohonen/Self-Organizing Maps in class and I would like to try to replicate some of the things we have seen in class.

Below is my code.  I am trying to create a u-matrix.  In the documentation on page 9 it appears the type of plot, dist.neighbours should do the trick, however, I am getting an error:
(Error in match.arg(type) : 'arg' should be one of "codes", "changes", "counts", "mapping", "property", "quality")

Since I am new to R, I figure I am missing something obvious.  Any help you can provide will be greatly appreciated!

Thanks in advance,

Brock

library(kohonen)

data("wines")
wines.sc <- scale(wines)

som <- som(wines.sc, grid=somgrid(5, 5, "hexagonal"))
plot(som)
plot(som, type="dist.neighbours" )

From: Gavin Simpson <gavin.simpson at ucl.ac.uk>
Subject: Re: [R] Kohonen Package
To: "Peter Ehlers" <ehlers at ucalgarywas.ca>
Cc: "Brock Tibert" <btibert3 at yahoo.com>, r-help at r-project.org
Date: Sunday, November 29, 2009, 6:21 AM
On Sat, 2009-11-28 at 17:16 -0700,
Peter Ehlers wrote:

I haven't used pkg:kohonen, so this is just guessing:

1. are you using an old version of the package?

I deleted the original email, so I'll reply here instead.
The example
provided by the OP works for me with on R 2.10-patched
and:

packageDescription("kohonen")$Version

[1] "2.0.5"

Looking at the CHANGES file in the package,
"dist.neighbours" was added
in version 2.0.5, so I suspect the OP was using an older
version, but
reading a newer version of the help as a PDF.

2. don't call the output of function som() 'som'. As
people around here might say: would you call your
iguana 'iguana'?

Indeed:

##install.packages("fortunes") ## uncomment if not
installed
require("fortunes")
fortune("dog")

HTH

G

3. have you used str() on your object to check what
it really contains? I would guess that it should be
of class som and have a component 'distances'.

If none of that helps then it's beyond me.

???-Peter Ehlers


Brock Tibert wrote:

Hi All,

I am still learning R, but making, IMO, great

strides.? I learned about Kohonen/Self-Organizing Maps
in class and I would like to try to replicate some of the
things we have seen in class.

Below is my code.? I am trying to create a

u-matrix.? In the documentation on page 9 it appears
the type of plot, dist.neighbours should do the trick,
however, I am getting an error:

(Error in match.arg(type) : 'arg' should be one

of "codes", "changes", "counts", "mapping", "property",
"quality")

Since I am new to R, I figure I am missing

something obvious.? Any help you can provide will be
greatly appreciated!

Thanks in advance,

Brock

library(kohonen)

data("wines")
wines.sc <- scale(wines)

som <- som(wines.sc, grid=somgrid(5, 5,

"hexagonal"))

plot(som)
plot(som, type="dist.neighbours" )

mailing list

reproducible code.

mailing list

reproducible code.
-- 
%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%
 Dr. Gavin Simpson? ? ? ? ?
???[t] +44 (0)20 7679 0522
 ECRC, UCL Geography,? ? ? ? ? [f]
+44 (0)20 7679 0565
 Pearson Building,? ? ? ? ?
???[e] gavin.simpsonATNOSPAMucl.ac.uk
 Gower Street, London? ? ? ? ? [w]
http://www.ucl.ac.uk/~ucfagls/
 UK. WC1E 6BT.? ? ? ? ? ?
? ???[w] http://www.freshwaters.org.uk
%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%

Many thanks, Peter, Gavin.  That is exactly what it was...and old version.  I was running R 2.7 (needed it to integrate with SPSS 17). 

I know I am a pain, but one last question.  Is it possible to overlay a value label onto the maps?  In some of the SOMs we have worked through in class, we saw examples that overlay the observation's label onto the map so we could see where each observation fell.  

Again, many, many, many thanks.  In just working through this one example, I have learned a ton about R.

- Brock



--- On Sun, 11/29/09, Gavin Simpson <gavin.simpson at ucl.ac.uk> wrote:

From: Gavin Simpson <gavin.simpson at ucl.ac.uk>
Subject: Re: [R] Kohonen Package
To: "Peter Ehlers" <ehlers at ucalgarywas.ca>
Cc: "Brock Tibert" <btibert3 at yahoo.com>, r-help at r-project.org
Date: Sunday, November 29, 2009, 6:21 AM
On Sat, 2009-11-28 at 17:16 -0700,
Peter Ehlers wrote:

I haven't used pkg:kohonen, so this is just guessing:

1. are you using an old version of the package?

I deleted the original email, so I'll reply here instead.
The example
provided by the OP works for me with on R 2.10-patched
and:

packageDescription("kohonen")$Version

[1] "2.0.5"

Looking at the CHANGES file in the package,
"dist.neighbours" was added
in version 2.0.5, so I suspect the OP was using an older
version, but
reading a newer version of the help as a PDF.

2. don't call the output of function som() 'som'. As
people around here might say: would you call your
iguana 'iguana'?

Indeed:

##install.packages("fortunes") ## uncomment if not
installed
require("fortunes")
fortune("dog")

HTH

G

3. have you used str() on your object to check what
it really contains? I would guess that it should be
of class som and have a component 'distances'.

If none of that helps then it's beyond me.

   -Peter Ehlers


Brock Tibert wrote:

Hi All,

I am still learning R, but making, IMO, great

strides.  I learned about Kohonen/Self-Organizing Maps
in class and I would like to try to replicate some of the
things we have seen in class.

Below is my code.  I am trying to create a

u-matrix.  In the documentation on page 9 it appears
the type of plot, dist.neighbours should do the trick,
however, I am getting an error:

(Error in match.arg(type) : 'arg' should be one

of "codes", "changes", "counts", "mapping", "property",
"quality")

Since I am new to R, I figure I am missing

something obvious.  Any help you can provide will be
greatly appreciated!

Thanks in advance,

Brock

library(kohonen)

data("wines")
wines.sc <- scale(wines)

som <- som(wines.sc, grid=somgrid(5, 5,

"hexagonal"))

plot(som)
plot(som, type="dist.neighbours" )

mailing list

reproducible code.

mailing list

reproducible code.
-- 
%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%
 Dr. Gavin Simpson         
   [t] +44 (0)20 7679 0522
 ECRC, UCL Geography,          [f]
+44 (0)20 7679 0565
 Pearson Building,         
   [e] gavin.simpsonATNOSPAMucl.ac.uk
 Gower Street, London          [w]
http://www.ucl.ac.uk/~ucfagls/
 UK. WC1E 6BT.           
     [w] http://www.freshwaters.org.uk
%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%