[R] Error on distance matrix

[Martin Maechler]

>>>>> "GS" == Gavin Simpson <gavin.simpson at ucl.ac.uk>
>>>>>     on Thu, 10 Jan 2008 14:16:36 +0000 writes:

    GS> On Thu, 2008-01-10 at 10:48 +0000, Marc Moragues wrote:
    >> Hi,
    >> 
    >> I am trying to calculate a distance matrix on a binary
    >> data frame using dist.binary() {ade4}. This is the code I
    >> run and the error I get:
    >> 
    >> > sjlc.dist <- dist.binary(as.data.frame(data), method=2)
    >> #D = (a+d) / (a+b+c+d) Error in if (any(df < 0))
    >> stop("non negative value expected in df") : missing value
    >> where TRUE/FALSE needed
    >> 
    >> I don't know if the problem are the missing values in my
    >> data. If so how can I handle them?

    GS> Marc,

    GS> Take a look at distance in package analogue and method =
    GS> "mixed" which implements Gower's general dissimilarity
    GS> coefficient for mixed data. 

daisy() in recommended package 'cluster' has been doing this
for"ever". Has there been a reason for reimplementing that?

    GS> It can deal quite happily
    GS> with binary data and where there is missing-ness.
    GS> Binary data are handled through a simple matching
    GS> coefficient, 1 if variable i present in both samples, 0
    GS> otherwise, and then summed over all variables i. You
    GS> should probably read up on how the missing-ness is
    GS> handled with this method and what properties the
    GS> resulting dissimilarity has.

    GS> Note that distance() outputs full dissimilarity
    GS> matrices. To get something to plug into functions that
    GS> require a dist object, just use as.dist() on the output
    GS> from distance().

    GS> HTH

    GS> G

    >> 
    >> Thank you, Marc.  _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
    >> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
    >> 
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    >> ______________________________________________
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    GS> --
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    GS> Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL
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    GS> ______________________________________________
    GS> R-help at r-project.org mailing list
    GS> https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do
    GS> read the posting guide
    GS> http://www.R-project.org/posting-guide.html and provide
    GS> commented, minimal, self-contained, reproducible code.