[R] distance coefficient for amatrix with ngative valus

[R. Michael Weylandt]

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
<benaragamad at 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.weylandt at gmail.com>
> To: dilshan benaragama <benaragamad at yahoo.com>; r-help
> <r-help at 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
> <benaragamad at 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]]
>>
>>
>> ______________________________________________
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>> 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.
>>
>>
>
>
>