[R] Error on distance matrix

[Gavin Simpson]

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?

Marc,

Take a look at distance in package analogue and method = "mixed" which
implements Gower's general dissimilarity coefficient for mixed data. It
can deal quite happily with binary data and where there is missing-ness.
Binary data are handled through a simple matching coefficient, 1 if
variable i present in both samples, 0 otherwise, and then summed over
all variables i. You should probably read up on how the missing-ness is
handled with this method and what properties the resulting dissimilarity
has.

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

HTH

G

> 
> Thank you,
> Marc. 
> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
> 
> SCRI, Invergowrie, Dundee, DD2 5DA.  
> The Scottish Crop Research Institute is a charitable company limited by guarantee. 
> Registered in Scotland No: SC 29367.
> Recognised by the Inland Revenue as a Scottish Charity No: SC 006662.
> 
> 
> DISCLAIMER:
> 
> This email is from the Scottish Crop Research Institute, but the views 
> expressed by the sender are not necessarily the views of SCRI and its 
> subsidiaries.  This email and any files transmitted with it are confidential 
> to the intended recipient at the e-mail address to which it has been 
> addressed.  It may not be disclosed or used by any other than that addressee.
> If you are not the intended recipient you are requested to preserve this 
> confidentiality and you must not use, disclose, copy, print or rely on this 
> e-mail in any way. Please notify postmaster at scri.ac.uk quoting the 
> name of the sender and delete the email from your system.
> 
> Although SCRI has taken reasonable precautions to ensure no viruses are 
> present in this email, neither the Institute nor the sender accepts any 
> responsibility for any viruses, and it is your responsibility to scan the email 
> and the attachments (if any).
> 
> 
> ______________________________________________
> 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.
-- 
%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%
 Dr. Gavin Simpson             [t] +44 (0)20 7679 0522
 ECRC, UCL Geography,          [f] +44 (0)20 7679 0565
 Pearson Building,             [e] gavin.simpsonATNOSPAMucl.ac.uk
 Gower Street, London          [w] http://www.ucl.ac.uk/~ucfagls/
 UK. WC1E 6BT.                 [w] http://www.freshwaters.org.uk
%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%