Tjerk, This is just a pseudo code outline of what you need to do: M = matrix(0, number of variables, number of variables) V = rep(0, number of variables) N = 0 While (more observations to read) { X <- next observation V <- V + X M <- M + outer(X,X) N <- N+1 } Compute covariance matrix from elements of V,M, and N
You just need to refer to the formula defining covariance. Outlook seems to think all my variables should be upper case. HTH Rex -----Original Message----- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Tsjerk Wassenaar Sent: Monday, March 14, 2011 10:14 AM To: R-help Subject: [R] *Building* a covariance matrix efficiently deaRs, I want to build a covariance matrix out of the data from a binary file, that I can read in chunk by chunk, with each chunk containing a single observation vector X. I wonder how to do that most efficiently, avoiding the calculation of the full symmetric matrices XX'. The trivial non-optimal approach boils down to something like: Q <- matrix(rnorm(100000),ncol=200) M <- matrix(0,ncol=200,nrow=200) for (i in 1:nrow(Q)) M <- M + tcrossprod(Q[i,]) I would appreciate pointers to help me fill this lacuna in my R skills :) Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands ______________________________________________ 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. message may contain confidential information. If you are not the designated recipient, please notify the sender immediately, and delete the original and any copies. Any use of the message by you is prohibited. ______________________________________________ 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.