Please keep the discussion on the list. It is hard to answer your question without context. You give us a warning message from a function that is not in base R. Perhaps it is in package ade? You also don’t include anything about the data or the commands that produced the warning message. A dist object does not contain a diagonal so your comment suggests that you did not convert the matrix to a dist object.
David C From: Nick Jeffery [mailto:nick.w.jeffe...@gmail.com] Sent: Wednesday, May 6, 2015 9:34 AM To: David L Carlson Subject: Re: [R] Mantel test Hi, Thanks for the help. I get these warnings when I run the Mantel test however - is this because the diagonal of the matrix is all 0s? Both are symmetrical matrices about the diagonal line of zeroes. Warning messages: 1: In is.euclid(m1) : Zero distance(s) 2: In is.euclid(m2) : Zero distance(s) Thanks for your time, Nick On Mon, May 4, 2015 at 3:48 PM, David L Carlson <dcarl...@tamu.edu<mailto:dcarl...@tamu.edu>> wrote: Assuming the 'matrix' format is a symmetrical distance 'matrix' stored as a data frame (which read.csv creates) rather a rectangular data 'matrix,' you can convert it to a dist object with as.dist(). ?dist ------------------------------------- David L Carlson Department of Anthropology Texas A&M University College Station, TX 77840-4352 -----Original Message----- From: R-help [mailto:r-help-boun...@r-project.org<mailto:r-help-boun...@r-project.org>] On Behalf Of Nick Jeffery Sent: Monday, May 4, 2015 10:49 AM To: r-help@r-project.org<mailto:r-help@r-project.org> Subject: [R] Mantel test Dear R users, I'm having trouble getting my data into R in the correct format to run a Mantel test. I'm testing genome size differences by genetic distances of the 28S gene for ~30 species. I'm able to get my genome size data (as a single column of data) into matrix and dist formats in R but the genetic distances output by MEGA are already in 'matrix' format so I don't know how to load this CSV file into R without it calculating new genetic distances when I convert it to the dist form required by the test. Thanks in advance, Nick -- Nick Jeffery, PhD Candidate Integrative Biology SCIE 1453 University of Guelph Guelph, Ontario, Canada [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org<mailto:R-help@r-project.org> mailing list -- To UNSUBSCRIBE and more, see 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. -- Nick Jeffery, PhD Candidate Integrative Biology SCIE 1453 University of Guelph Guelph, Ontario, Canada [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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.
