[R] how to convert a data.frame to a list of dist objects for individual differences MDS?

[Michael Friendly]

I have a 45 x 16 data frame consisting of dissimilarities among 10 
colors, giving in each
column the 45 = 10*9/2 pairwise judgments for one of 16 subjects.  The 
rownames
identify each pair of colors, e.g, "AC" = ("A","C"), and the pairs are 
ordered by columns
in the lower triangle of each distance matrix.

 > helm.raw <- 
read.table("http://euclid.psych.yorku.ca/datavis/Private/mdshelm.dat", 
header=TRUE, row.names=1)
 > head(helm.raw)
      N1   N2   N3   N4   N5  N6a  N6b   N7   N8  N9  N10  CD1 CD2a 
CD2b  CD3  CD4
AC  6.8  5.9  7.1  7.5  6.6  5.2  5.8  6.2  7.5 6.0  9.2 11.5  9.3  9.0 
10.4  9.9
AE 12.5 11.1 10.2 10.3 10.5  9.4 10.5 10.8  9.1 9.4 10.8 13.1 10.7 10.0 
12.4 13.2
AG 13.8 18.8 11.1 10.7 10.2 11.4 13.4  9.9 10.2 9.5  9.7 12.6 10.7 10.4 
12.8 12.3
AI 14.2 17.3 12.5 11.6  9.6 13.3 14.0 11.1 12.1 9.5 10.1 10.6 11.9 10.0 
13.7 11.1
AK 12.5 16.6 11.8 10.6 10.8 12.0 13.2 10.3 12.5 9.8 10.3 10.6 11.0  9.3 
11.8  8.7
AM 11.0 16.5  9.9  9.7  9.7 12.3 11.7  8.8  9.7 8.7  9.7 10.8  9.8  8.6  
4.3  5.6
 > row.names(helm.raw)
  [1] "AC" "AE" "AG" "AI" "AK" "AM" "AO" "AQ" "AS" "CE" "CG" "CI" "CK" 
"CM" "CO" "CQ" "CS" "EG" "EI" "EK"
[21] "EM" "EO" "EQ" "ES" "GI" "GK" "GM" "GO" "GQ" "GS" "IK" "IM" "IO" 
"IQ" "IS" "KM" "KO" "KQ" "KS" "MO"
[41] "MQ" "MS" "OQ" "OS" "QS"
 >

To analyse this (with individual differences MDS, e.g., smacofDiff()), I 
need to:

(a) convert this to a list of objects of class "dist", one for each 
column of  helm.raw
(b) rename the 1-letter codes to color name abbreviations as row/col 
labels for each distance matrix,
according to:
   'A'='RPur'
   'C'='Red'
   'E'='Yel'
   'G'='Gy1'
   'I'='Gy2'
   'K'='Green'
   'M'='Blue'
   'O'='BlP'
   'Q'='Pur1'
   'S'='Pur2'

I've done this in SAS, but I don't know how to do it in R because 
neither dist() nor
as.dist() seem to be able to work with data in this format.  I could try 
brute-force,
but maybe there is an easier way.  Can someone help?

As a distance matrix, the column helm.raw$CD1 for subject CD1 should 
appear something like
shown below (without the Obs column, where stim is the rowname)

--------------------------------- Subject=CD1 
----------------------------------

      Obs  stim   RPur   Red   Yel   Gy1   Gy2  Green  Blue  BlP  Pur1  Pur2

        1  RPur     .     .     .     .     .      .     .    .     .     .
        2  Red    11.5    .     .     .     .      .     .    .     .     .
        3  Yel    13.1   6.0    .     .     .      .     .    .     .     .
        4  Gy1    12.6   7.9   6.2    .     .      .     .    .     .     .
        5  Gy2    10.6   8.4   8.4   5.2    .      .     .    .     .     .
        6  Green  10.6   9.4   9.9   6.5   4.1     .     .    .     .     .
        7  Blue   10.8  10.2  10.3   8.8   7.0    6.4    .    .     .     .
        8  BlP     7.3  11.3  12.7  11.2  10.4    9.9   4.2   .     .     .
        9  Pur1    5.4  11.5  12.9  11.7  10.8    9.4   8.4  4.5    .     .
       10  Pur2    5.0  11.5  10.7  10.2  10.6   10.1   8.1  6.4    3     .


-- 
Michael Friendly     Email: friendly AT yorku DOT ca
Professor, Psychology Dept.
York University      Voice: 416 736-5115 x66249 Fax: 416 736-5814
4700 Keele Street    Web:   http://www.datavis.ca
Toronto, ONT  M3J 1P3 CANADA