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Martin Guetlein

2014-Jul-04 07:12 UTC

[R] sammon fails with duplicates error, but no duplicates there (MASS package)

Hi all,

the sammon mapping fails with message "initial configuration has
duplicates". But there are no duplicates in my data (see example
below).
Apparently, the problem is that row 9 and 10 have an equal distance to
all other rows (but they are not equal, see last two columns).

Any help to get sammon working would be great,
Kind regards,
Martin


library("MASS")
c1 <- c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0)
c2 <- c(0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0)
c3 <- c(1, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0)
c4 <- c(0, 0, 0, 0, 0, 1, 1, 1, 1, 0, 1, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0)
c5 <- c(1, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 0, 1, 0, 0, 1, 1, 0, 0, 0, 0,
0, 0, 0, 0, 0)
c6 <- c(0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 1, 0, 1, 0, 0, 0, 0, 1, 1, 1, 1,
1, 1, 1, 0, 0)
c7 <- c(0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 1, 0,
0, 0, 0, 0, 0)
c8 <- c(1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0)
c9 <- c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 1, 0)
c10<- c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 1)
# working
data <- rbind(c1,c2,c3,c4,c5,c6,c7,c8,c9)
sammon(dist(data))
# not working:
data <- rbind(c1,c2,c3,c4,c5,c6,c7,c8,c9,c10)
sammon(dist(data))

Frede Aakmann Tøgersen

2014-Jul-04 08:02 UTC

head link

[R] sammon fails with duplicates error, but no duplicates there (MASS package)

Hi

It seems to be related to the way that the default start values (y argument of
sammon) are calculated.

Here the last two rows are the same:
> cmdscale(dist(data), 2)           [,1]       [,2]
c1   2.04910556 -0.3627887
c2  -0.01889892 -0.1822057
c3   0.40767629  0.2599026
c4   0.81569304 -0.4165993
c5   0.70362596 -0.3573003
c6  -1.69673266 -1.7209956
c7  -0.65997449 -0.2888096
c8  -0.24449262  0.4502489
c9  -0.67800108  1.3092739
c10 -0.67800108  1.3092739

Try to perturb the start values using jitter(). Like this
> sammon(dist(data), y = jitter(cmdscale(dist(data), 2)))Initial stress        : 0.18304
stress after  10 iters: 0.07867, magic = 0.092
stress after  20 iters: 0.05149, magic = 0.500
stress after  30 iters: 0.05101, magic = 0.500
stress after  40 iters: 0.05096, magic = 0.500
$points
           [,1]       [,2]
c1   2.12900041 -1.7255589
c2   0.32144017 -0.4397770
c3   1.09694083  1.2989299
c4   1.90228818  0.3198121
c5   0.09479179 -1.7229204
c6  -2.35619505 -1.2913663
c7  -0.95749355 -0.2635698
c8  -0.08310984  0.6903391
c9  -1.48236001  1.2443252
c10 -0.66530292  1.8897858

$stress
[1] 0.0509611

$call
sammon(d = dist(data), y = jitter(cmdscale(dist(data), 2)))
> 
Yours sincerely / Med venlig hilsen


Frede Aakmann T?gersen
Specialist, M.Sc., Ph.D.
Plant Performance & Modeling

Technology & Service Solutions
T +45 9730 5135
M +45 2547 6050
frtog at vestas.com
http://www.vestas.com

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> -----Original Message-----
> From: r-help-bounces at r-project.org [mailto:r-help-bounces at
r-project.org]
> On Behalf Of Martin Guetlein
> Sent: 4. juli 2014 09:13
> To: r-help at r-project.org
> Subject: [R] sammon fails with duplicates error, but no duplicates there
> (MASS package)
> 
> Hi all,
> 
> the sammon mapping fails with message "initial configuration has
> duplicates". But there are no duplicates in my data (see example
> below).
> Apparently, the problem is that row 9 and 10 have an equal distance to
> all other rows (but they are not equal, see last two columns).
> 
> Any help to get sammon working would be great,
> Kind regards,
> Martin
> 
> 
> library("MASS")
> c1 <- c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
> 0, 0, 0, 0, 0)
> c2 <- c(0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0,
> 0, 0, 0, 0, 0)
> c3 <- c(1, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0,
> 0, 0, 0, 0, 0)
> c4 <- c(0, 0, 0, 0, 0, 1, 1, 1, 1, 0, 1, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0,
> 0, 0, 0, 0, 0)
> c5 <- c(1, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 0, 1, 0, 0, 1, 1, 0, 0, 0, 0,
> 0, 0, 0, 0, 0)
> c6 <- c(0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 1, 0, 1, 0, 0, 0, 0, 1, 1, 1, 1,
> 1, 1, 1, 0, 0)
> c7 <- c(0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 1, 0,
> 0, 0, 0, 0, 0)
> c8 <- c(1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0,
> 0, 0, 0, 0, 0)
> c9 <- c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
> 0, 0, 0, 1, 0)
> c10<- c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
> 0, 0, 0, 0, 1)
> # working
> data <- rbind(c1,c2,c3,c4,c5,c6,c7,c8,c9)
> sammon(dist(data))
> # not working:
> data <- rbind(c1,c2,c3,c4,c5,c6,c7,c8,c9,c10)
> sammon(dist(data))
> 
> ______________________________________________
> 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.

R help - Jul 2014 - sammon fails with duplicates error, but no duplicates there (MASS package)

[R] sammon fails with duplicates error, but no duplicates there (MASS package)

[R] sammon fails with duplicates error, but no duplicates there (MASS package)