You avoid the call to cmdscale() by supplying your own starting configuration (see the manual page for the y= argument). You could still hit other barriers within isoMDS() or insufficient memory on your computer.
------------------------------------- David L Carlson Department of Anthropology Texas A&M University College Station, TX 77840-4352 -----Original Message----- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Kawashima, Masayuki Sent: Wednesday, November 5, 2014 10:51 PM To: r-help@r-project.org Subject: [R] limit of cmdscale function Hi We have a few questions regarding the use of the "isoMDS" function. When we run "isoMDS" function using 60,000 x 60,000 data matrix, we get the following error message: ------------------------------------ cmdscale(d, k) : invalid value of 'n' Calls: isoMDS -> cmdscale ------------------------------------ We checked the source code of "cmdscale" and found the following limitation: ------------------------------------ ## we need to handle nxn internally in dblcen if(is.na(n) || n > 46340) stop("invalid value of 'n'") ------------------------------------ 1. This cmdscale limitation ('n > 46340') is due to the limitation of BLAS and LAPACK variables(int4) which can only handle '2^31-1' amount of data? 2. Is there any workaround to run isoMDS using large data (i.e. greater than 46340)? We would like to run isoMDS using a maximum of 150,000x150,000 data matrix. Best regards Masayuki Kawashima Email: kawasim...@jp.fujitsu.com ______________________________________________ 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. ______________________________________________ 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.
