Hi Frede, awesome, thanks a lot. Helped me to understand how sammon is working as well.
Martin On 4 July 2014 10:02, Frede Aakmann Tøgersen <fr...@vestas.com> wrote: > 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 Tøgersen > Specialist, M.Sc., Ph.D. > Plant Performance & Modeling > > Technology & Service Solutions > T +45 9730 5135 > M +45 2547 6050 > fr...@vestas.com > http://www.vestas.com > > Company reg. name: Vestas Wind Systems A/S > This e-mail is subject to our e-mail disclaimer statement. > Please refer to www.vestas.com/legal/notice > If you have received this e-mail in error please contact the sender. > >> -----Original Message----- >> From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] >> On Behalf Of Martin Guetlein >> Sent: 4. juli 2014 09:13 >> To: r-help@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@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. -- Dipl-Inf. Martin Gütlein Phone: +49 (0)761 203 8442 (office) +49 (0)177 623 9499 (mobile) Email: guetl...@informatik.uni-freiburg.de ______________________________________________ R-help@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.