You still haven't explained what's wrong with *almost every metric there is*, but if you want other distance metrics have you considered those in the package you are using, via the function dsvdis(). Consider, for example:
library(labdsv) X <- get(data(bryceveg)); X[, sample(NROW(X))] <- (-1)*X[, sample(NROW(X))] # Put some negative values in all willy nilly like.... Y <- pco( dsvdis(X, index="bray/curtis") ) print(any(X < 0)) If you want more explanation, please provide actual details of what you are asking, as requested in my first email. Michael Weylandt On Mon, Oct 3, 2011 at 9:23 PM, dilshan benaragama <benaraga...@yahoo.com> wrote: > I am using (labdsv). If I can use euclidean distance I can do it with PCA > instead of PCO, so I am trying an alternative to PCA, but I cannot find a > disimilarity coefficient for that. > > From: R. Michael Weylandt <michael.weyla...@gmail.com> > To: dilshan benaragama <benaraga...@yahoo.com>; r-help > <r-help@r-project.org> > Sent: Monday, October 3, 2011 3:27:53 PM > Subject: Re: [R] distance coefficient for amatrix with ngative valus > > One order of the usual coming right up! > > 1 course of "Why does XXX not work for you?" a la francaise, where XXX > is, in your case, the Euclidean distance. Specifically, any metric > worth its salt (in a normed space) satisfies dist(a,b) = dist(a+c,b+c) > so why are negative values a problem?... > > 2 sides: a "Minimal Working Example" with a light buttery sauce and a > fried "what package/code are you using" > > and, for desert, a Winsemian special of: "read the posting guide!" > > Michael Weylandt, who is putting together a menu for a fancy dinner > even as he types > > On Mon, Oct 3, 2011 at 12:55 PM, dilshan benaragama > <benaraga...@yahoo.com> wrote: >> Hi, >> I need to run a PCoA (PCO) for a data set wich has both positive and >> negative values for variables. I could not find any distancecoefficient >> other than euclidean distace running for the data set. Are there any other >> coefficient works with negtive values.Also I cannot get summary out put (the >> eigen values) for PCO as for PCA. >> >> Thanks. >> Dilshan >> [[alternative HTML version deleted]] >> >> >> ______________________________________________ >> 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. >> >> > > > ______________________________________________ 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.
