From: Jari Oksanen <jari.oksanen_at_oulu.fi>

Date: Thu, 10 Jan 2008 14:06:42 +0000 (UTC)

R-help_at_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. Received on Thu 10 Jan 2008 - 14:09:32 GMT

Date: Thu, 10 Jan 2008 14:06:42 +0000 (UTC)

Jari Oksanen <jari.oksanen <at> oulu.fi> writes:

*>
*

> Marc Moragues <Marc.Moragues <at> scri.ac.uk> writes:

*>
**> >
**> > 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?
**> >
**> Dear Marc Moragues,
**>
**> At least adding NA to a data.frame gave the same error message as you report
**> above. Odds are good for NA being responsible (but we cannot know: we only
**> guess).
*

...clip...

> One solution is to use function designdist in vegan where you can with some

*> acrobary design your own dissimilarity indices.
*

It is a bad habit to comment on yourself, but if you write stupid things, you should tell so: that designdist() "handles" missing values is accidental, unintentional and dangerous. Now you still should figure out *how* they are handled, and the function should warn users if they supply data with missing values. I hope that will be changed.

>Function designdist uses

*> different notations, because its author hates that misleading and dangerous 2x2
**> contingency table notation. The following, however, seems to define the same
**> index as ade4:
**>
**> designdist(data, "sqrt(1-(2*J+P-A-B)/P)")
**>
*

You can make this cuter:

designdist(data, "sqrt((A+B-2*J)/P)")

Cheers, Jari Oksanen

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