If the goal is to *use* the Mahalanobis distance, rather than to learn how to write your own code, there are several existing implementations. rseek.org is a good place to find functions.
Sarah On Fri, Jan 29, 2010 at 9:48 PM, Robert Lonsinger <rob.lonsin...@gmail.com> wrote: > Hello, > I am a new R user and trying to learn how to implement the mahalanobis > function to measure the distance between to 2 population centroids. I > have used STATISTICA to calculate these differences, but was hoping to learn > to do the analysis in R. I have implemented the code as below, but my > results are very different from that of STATISTICA, and I believe I may not > have interpreted the help correctly and may have implemented the > code incorrectly. > > Though I am not certain, I believe that my error may be in calculating the > common covariance matrix (the third argument supplied to the mahalanobis > funtion). > > Any help or guidance would be greatly appreciated. > > Thank you! RL > > CODE > > fit<-lda(pop~v1 + v2 + v3 +...+vn, data=my.data) > > x1<-subset(my.data, pop==1) > > x2<-subset(my.data, pop==2) > > > > #Save Covariance Matices for each group > cov1<-cov(x1) > cov2<-cov(x2) > > > > #Determine number of rows in each matrix > n1<-nrow(x1); n2<-nrow(x2); > n.rows<-c(n1,n2) > > > #store mean vectors from lda object > mu1<-fit$means[1,] > mu2<-fit$means[2,] > > > > #Calculate the common Covariance Matrix > S<-(((n.rows[1]-1)*cov1)+((n.rows[2]-1)*cov2)/ (sum(n.rows[1:2])-1)) > > #Calculate the common Covariance Matrix > mahalanobis(mu1, mu2, S) > > [[alternative HTML version deleted]] > > ______________________________________________ > 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. > -- Sarah Goslee http://www.functionaldiversity.org ______________________________________________ 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.