Re: [R] system is computationally singular: reciprocal condition number

2012-10-26 Thread langvince
Adding a small random value (0,0001-0,0009) to all values helped to solve the problem. Thank You everyone, who helped. -- View this message in context: http://r.789695.n4.nabble.com/system-is-computationally-singular-reciprocal-condition-number-tp4647472p4647540.html Sent from the R help mail

Re: [R] system is computationally singular: reciprocal condition number

2012-10-26 Thread langvince
Hi Thomas, thanks for the comment. I had a similar idea, so got rid of the rounding (these are laboratory measurement based data, thats why I have rounded to only 2 decimal values, but I also tried with 4 and got the same. I will try to get rid of the many 0s with random noise, hopefully it will

Re: [R] system is computationally singular: reciprocal condition number

2012-10-25 Thread langvince
Hey David, my answers are delayed here, although I am not using my gmail email address:) Yep thats right, those bands of zeros are one of the most important values to define one group, and have a nice distance from the rest of the groups :). I cannot really get rid of those, I bet it would not h

Re: [R] system is computationally singular: reciprocal condition number

2012-10-25 Thread langvince
Hey Bert, thanks for your fast reply. Yes, based on svd it is singular. The "no way" statement was because of the source of the dataset. I would not expect that. I never used the stats Maha dist calc, but after giving it a shot, not a surprise still singular. Any idea how to manipulate the data

Re: [R] system is computationally singular: reciprocal condition number

2012-10-25 Thread Thomas Lumley
On Fri, Oct 26, 2012 at 12:14 PM, langvince wrote: > 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 up

Re: [R] system is computationally singular: reciprocal condition number

2012-10-25 Thread David Winsemius
On Oct 25, 2012, at 4:41 PM, Bert Gunter wrote: > 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 va

Re: [R] system is computationally singular: reciprocal condition number

2012-10-25 Thread Bert Gunter
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

[R] system is computationally singular: reciprocal condition number

2012-10-25 Thread langvince
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 "s