[BioC] Why daisy() in cluster library failed to exclude NA when computing dissimilarity

[James W. MacDonald]

Hi Gundala,

This question isn't about a Bioconductor package, so should be asked on 
R-help instead.

Best,

Jim

On Sunday, December 08, 2013 2:11:12 AM, Gundala Viswanath wrote:
> Hi,
>
>
> According to daisy function from cluster documentation, it can compute
> dissimilarity when NA (missing) value(s) is present.
>
> http://stat.ethz.ch/R-manual/R-devel/library/cluster/html/daisy.html
>
> But why when I tried this code
>
> library(cluster)
> x <- c(1.115,NA,NA,0.971,NA)
> y <- c(NA,1.006,NA,NA,0.645)
> df <- as.data.frame(rbind(x,y))
> daisy(df,metric="gower")
>
> It gave this message:
>
> Dissimilarities :
>     x
> y NA
>
> Metric :  mixed ;  Types = I, I, I, I, I
> Number of objects : 2
> Warning messages:
> 1: In min(x) : no non-missing arguments to min; returning Inf
> 2: In max(x) : no non-missing arguments to max; returning -Inf
>
> I welcome other alternative than gower.
>
> I expect the dissimilarity output gives a non-NA value e.g. 0. What's
> the right way to do it?
>
> G.V.
>
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--
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
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Seattle WA 98105-6099