>>>>> "GS" == Gavin Simpson <[EMAIL PROTECTED]> >>>>> 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. _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ >> _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ >> >> 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 >> [EMAIL PROTECTED] 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@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. GS> -- GS> %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% GS> Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL GS> Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] GS> gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w] GS> http://www.ucl.ac.uk/~ucfagls/ UK. WC1E 6BT. [w] GS> http://www.freshwaters.org.uk GS> %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% GS> ______________________________________________ GS> R-help@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. ______________________________________________ R-help@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.