1. I don't know what StatMatch is. Try using stats::mahalanobis. 2. It's the covariance matrix that is **numerically** singular and can't be inverted. Why do you claim that there's "no way" this could be true when there are hundreds of variables (= dimensions).
3. Try calculating the svd of your matrix and see what you get if you haven't already done so. Cheers, Bert On Thu, Oct 25, 2012 at 4:14 PM, langvince <[email protected]> wrote: > Hi folks, > > I know, this is a fairly common question and I am really disappointed that I > could not find a solution. > I am trying to calculate Mahanalobis distances in a data frame, where I have > several hundreds groups and several hundreds of variables. > > Whatever I do, however I subset it I get the "system is computationally > singular: reciprocal condition number" error. > I know what it means and I know what should be the problem, but there is no > way this is a singular matrix. > > I have uploaded the input file to my ftp: > http://mkk.szie.hu/dep/talt/lv/CentInpDuplNoHeader.txt > It is a tab delimited txt file with no headers. > > I tried the StatMatch Mahanalobis function and also this function: > > mahal_dist <-function (data, nclass, nvariable) { > dist <- matrix(0, nclass, nclass) > n=0 > w <- cov(data) > print(w) > for(i in 1:nclass) { > > for(c in 1:nclass){ > diffl <- vector(length = nvariable) > for(l in 1:nvariable){ > diffl[l]=abs(data[i,l]-data[c,l]) > > } > ### matrixes > print(diffl) > dist[i,c]= (t(diffl))%*%(solve(w))%*%(diffl) > } > > n=n+1 > print(n) > } > return(dist) > sqrt_dist <- sqrt(dist) > print(sqrt_dist) } > > > I have a deadline for this project (not a homework:)), and I could always > use this codes, so I thought I will be able to quit the calculations short, > but now I am just lost. > > I would really appreciate any help. > > Thanks for any help > > > > -- > View this message in context: > http://r.789695.n4.nabble.com/system-is-computationally-singular-reciprocal-condition-number-tp4647472.html > Sent from the R help mailing list archive at Nabble.com. > > ______________________________________________ > [email protected] 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. -- Bert Gunter Genentech Nonclinical Biostatistics Internal Contact Info: Phone: 467-7374 Website: http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm ______________________________________________ [email protected] 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.
