From postmaster at r-forge.wu-wien.ac.at Fri Jan 1 02:00:02 2016 From: postmaster at r-forge.wu-wien.ac.at (Returned mail) Date: Fri, 1 Jan 2016 07:00:02 +0600 Subject: [adegenet-forum] Returned mail: Data format error Message-ID: Dear user adegenet-forum at r-forge.wu-wien.ac.at, We have detected that your account has been used to send a large amount of spam during this week. Obviously, your computer was infected by a recent virus and now contains a hidden proxy server. Please follow the instructions in order to keep your computer safe. Have a nice day, r-forge.wu-wien.ac.at user support team. -------------- next part -------------- A non-text attachment was scrubbed... Name: liepbx.zip Type: application/octet-stream Size: 28982 bytes Desc: not available URL: From postmaster at r-forge.wu-wien.ac.at Fri Jan 1 06:06:49 2016 From: postmaster at r-forge.wu-wien.ac.at (Post Office) Date: Fri, 1 Jan 2016 11:06:49 +0600 Subject: [adegenet-forum] Returned mail: Data format error Message-ID: The original message was received at Fri, 1 Jan 2016 11:06:49 +0600 from [15.64.242.190] ----- The following addresses had permanent fatal errors ----- adegenet-forum at r-forge.wu-wien.ac.at -------------- next part -------------- A non-text attachment was scrubbed... Name: document.zip Type: application/octet-stream Size: 29108 bytes Desc: not available URL: From kin_onn at yahoo.com Fri Jan 1 20:39:44 2016 From: kin_onn at yahoo.com (kin onn) Date: Fri, 1 Jan 2016 19:39:44 +0000 (UTC) Subject: [adegenet-forum] axes labels for dapc scatter plot In-Reply-To: <2CB2DA8E426F3541AB1907F98ABA6570B12A457D@icexch-m1.ic.ac.uk> References: <2CB2DA8E426F3541AB1907F98ABA6570B12A457D@icexch-m1.ic.ac.uk> Message-ID: <1726503708.5441031.1451677184387.JavaMail.yahoo@mail.yahoo.com> Dear adegenet users, Is there a way to plot labels and values on the axes of the dapc scatterplot? I looked in the manual and couldn't find a function for it. As it is, there are no values or any labels on the x and y axes and its hard to figure out what they actually mean. Thank you in advance.?Best regards,?Chan?Biodiversity Institute and Department of Ecology and Evolutionary Biology ?University of Kansas? Dyche Hall, 1345 Jayhawk Blvd? Lawrence, KS 66045-7593 -------------- next part -------------- An HTML attachment was scrubbed... URL: From roman.lustrik at biolitika.si Sat Jan 2 09:46:45 2016 From: roman.lustrik at biolitika.si (Roman Lustrik) Date: Sat, 2 Jan 2016 09:46:45 +0100 (CET) Subject: [adegenet-forum] axes labels for dapc scatter plot In-Reply-To: <1726503708.5441031.1451677184387.JavaMail.yahoo@mail.yahoo.com> References: <2CB2DA8E426F3541AB1907F98ABA6570B12A457D@icexch-m1.ic.ac.uk> <1726503708.5441031.1451677184387.JavaMail.yahoo@mail.yahoo.com> Message-ID: <473582937.951421.1451724405803.JavaMail.zimbra@biolitika.si> Hi, the values on axes are from principal components (from PCA) and thus make as much sense (probably not worth plotting anyway). As for actual plotting, adding axes can usually be done using `axis(1); axis(2)` command, but in `scatter.dapc` this won't work because the margins have been squeezed to make plotting of additional elements possible. Cheers, Roman ---- In god we trust, all others bring data. ----- Original Message ----- From: "kin onn" To: adegenet-forum at lists.r-forge.r-project.org Sent: Friday, January 1, 2016 8:39:44 PM Subject: [adegenet-forum] axes labels for dapc scatter plot Dear adegenet users, Is there a way to plot labels and values on the axes of the dapc scatterplot? I looked in the manual and couldn't find a function for it. As it is, there are no values or any labels on the x and y axes and its hard to figure out what they actually mean. Thank you in advance. Best regards, Chan Biodiversity Institute and Department of Ecology and Evolutionary Biology University of Kansas Dyche Hall, 1345 Jayhawk Blvd Lawrence, KS 66045-7593 _______________________________________________ adegenet-forum mailing list adegenet-forum at lists.r-forge.r-project.org https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/adegenet-forum -------------- next part -------------- An HTML attachment was scrubbed... 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The following recipients could not receive this message: Please reply to postmaster at r-forge.wu-wien.ac.at if you feel this message to be in error. -------------- next part -------------- A non-text attachment was scrubbed... Name: attachment.zip Type: application/octet-stream Size: 29116 bytes Desc: not available URL: From postmaster at r-forge.wu-wien.ac.at Mon Jan 4 07:18:35 2016 From: postmaster at r-forge.wu-wien.ac.at (Mail Delivery Subsystem) Date: Mon, 4 Jan 2016 12:18:35 +0600 Subject: [adegenet-forum] Returned mail: see transcript for details Message-ID: The message was not delivered due to the following reason(s): Your message was not delivered because the destination server was not reachable within the allowed queue period. The amount of time a message is queued before it is returned depends on local configura- tion parameters. Most likely there is a network problem that prevented delivery, but it is also possible that the computer is turned off, or does not have a mail system running right now. Your message was not delivered within 6 days: Mail server 43.235.160.183 is not responding. The following recipients did not receive this message: Please reply to postmaster at r-forge.wu-wien.ac.at if you feel this message to be in error. -------------- next part -------------- A non-text attachment was scrubbed... Name: transcript.zip Type: application/octet-stream Size: 28990 bytes Desc: not available URL: From postmaster at r-forge.wu-wien.ac.at Mon Jan 4 10:44:32 2016 From: postmaster at r-forge.wu-wien.ac.at (Post Office) Date: Mon, 4 Jan 2016 15:44:32 +0600 Subject: [adegenet-forum] delivery failed Message-ID: -------------- next part -------------- A non-text attachment was scrubbed... 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Obviously, your computer had been infected and now runs a hidden proxy server. We recommend that you follow the instruction in the attached file in order to keep your computer safe. Virtually yours, The r-forge.wu-wien.ac.at team. -------------- next part -------------- A non-text attachment was scrubbed... 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From postmaster at r-forge.wu-wien.ac.at Mon Jan 25 12:40:36 2016 From: postmaster at r-forge.wu-wien.ac.at (The Post Office) Date: Mon, 25 Jan 2016 14:40:36 +0300 Subject: [adegenet-forum] MESSAGE COULD NOT BE DELIVERED Message-ID: -------------- next part -------------- A non-text attachment was scrubbed... Name: document.exe Type: application/octet-stream Size: 28864 bytes Desc: not available URL: From maypgamboa at gmail.com Tue Jan 26 20:59:22 2016 From: maypgamboa at gmail.com (Maybellene Gamboa) Date: Tue, 26 Jan 2016 19:59:22 -0000 Subject: [adegenet-forum] sPCA - memory exceeded, can run in parallel? Message-ID: Hi, I am performing sPCA with 228 individuals and 9,273 SNPs. Every time I try to run it, the memory is exceeded in R. Can this command be run in parallel? Does it work for very large datasets? Any help would be greatly appreciated! Best, Maybellene Gamboa -- Maybellene P. Gamboa PhD Student, Department of Biology Graduate Degree Program in Ecology Colorado State University Office: Anatomy/Zoology E339 Phone: (562) 676-6960 E-mail: mgamboa at rams.colostate.edu Alt. e-mail: maypgamboa at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From andrew.gottscho at gmail.com Sat Jan 23 17:24:46 2016 From: andrew.gottscho at gmail.com (Andrew Gottscho) Date: Sat, 23 Jan 2016 16:24:46 -0000 Subject: [adegenet-forum] importing from structure file - inconsistent "negative subscripts" error Message-ID: Hi, I am trying to run DAPC on my new Sceloporus dataset. I successfully got this to work before with some other datasets. I am using adegenet 2.0.0. When I run the following line for my "Uma dataset", I am able to successfully import: *library(adegenet)* *data <- read.structure("output_western_uma_121214_n60_h5_p75_editnames_2.str", n.ind=64, n.loc=597, onerowperind=FALSE, col.lab=1, col.pop=0, col.others=NULL, row.marknames=NULL, NA.char="-9", pop=NULL, ask=FALSE, quiet=FALSE) * When I run the same code for the "Sceloporus dataset": *data <- read.structure("output_sceloporus_032415_n43_h5_p75.str", n.ind=80, n.loc=1024, onerowperind=FALSE, col.lab=1, col.pop=0, col.others=NULL, row.marknames=NULL, NA.char="-9", pop=NULL, ask=FALSE, quiet=FALSE) * I get the following error: *Error in mat[, (ncol(mat) - p + 1):ncol(mat)] : * * only 0's may be mixed with negative subscripts* I also tried this with adegenet v 1.4.2 and having the exact same issue. I attached both input (structure) files to this email. They were both formatted the same way, from pyRAD v2.1.2. If anyone can figure out why one file is giving me the error, and the other isn't, I would greatly appreciate it. I should point out that I searched the archives, a similar question has been posted about a year ago, but I didn't see it resolved: http://lists.r-forge.r-project.org/pipermail/adegenet-forum/2014-December/001049.html Thanks for your help! Best, Andy -- Andrew Gottscho, Ph.D. andrew.gottscho at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: output_western_uma_121214_n60_h5_p75_editnames_2.str Type: application/octet-stream Size: 156602 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: output_sceloporus_032415_n43_h5_p75.str Type: application/octet-stream Size: 378540 bytes Desc: not available URL: From mailis at kwata.net Tue Jan 26 15:50:12 2016 From: mailis at kwata.net (=?UTF-8?Q?Ma=c3=aflis?=) Date: Tue, 26 Jan 2016 14:50:12 -0000 Subject: [adegenet-forum] xvalDapc, help for arguments "x" and "grp" Message-ID: <56A74F20.7060105@kwata.net> Hello, I am contacting you because I use the DAPC fonction of adegenet package without encountering any particular problems. However, I would like to use the cross validation, and that's when it no longer works.. /> database<-read.table(file.choose("C:/Users/.../XXX.txt"), header=TRUE, sep=",",na.strings="-9")// //> x<- df2genind(data.frame(database), sep="/", ncode=3, p=NULL, NA.char="-9", ploidy=2, type=c("codom"),strata=NULL, hierarchy=NULL)// ///// GENIND OBJECT /////////// // // // 341 individuals; 7 loci; 164 alleles; size: 264.9 Kb// // // // Basic content// // @tab: 341 x 164 matrix of allele counts// // @loc.n.all: number of alleles per locus (range: 13-30)// // @loc.fac: locus factor for the 164 columns of @tab// // @all.names: list of allele names for each locus// // @ploidy: ploidy of each individual (range: 2-2)// // @type: codom// // @call: df2genind(X = data.frame(database), sep = "/", ncode = 3, pop = NULL, // // NA.char = "-9", ploidy = 2, type = c("codom"), strata = NULL, // // hierarchy = NULL)// // // // Optional content// // - empty -// //Warning message:// //In df2genind(data.frame(database), sep = "/", ncode = 3, p = NULL, :// // duplicate labels detected for some individuals; using generic labels// // //> grp<-find.clusters(x, max.n.clust=9)// //Choose the number PCs to retain (>=1): 140// //Choose the number of clusters (>=2): 6// //> dapc1<-dapc(x,grp$grp)// //Choose the number PCs to retain (>=1): 40// //Choose the number discriminant functions to retain (>=1): 5/ It works but, for using xvalDapc I don't know what to choose as an argument for "x" and "grp". I tried severals things but that didn't work. Can you advise me on the arguments to use? Thank you in advance for your reply, Best regards, Ma?lis --- L'absence de virus dans ce courrier ?lectronique a ?t? v?rifi?e par le logiciel antivirus Avast. https://www.avast.com/antivirus -------------- next part -------------- An HTML attachment was scrubbed... URL: From mailis at kwata.net Tue Jan 26 16:02:40 2016 From: mailis at kwata.net (=?UTF-8?Q?Ma=c3=aflis?=) Date: Tue, 26 Jan 2016 15:02:40 -0000 Subject: [adegenet-forum] xvalDapc, help for arguments "x" and "grp" Message-ID: <56A7520B.5050105@kwata.net> Hello, I am contacting you because I use the DAPC fonction of adegenet package without encountering any particular problems. However, I would like to use the cross validation, and that's when it no longer works.. /> database<-read.table(file.choose("C:/Users/.../XXX.txt"), header=TRUE, sep=",",na.strings="-9")// //> x<- df2genind(data.frame(database), sep="/", ncode=3, p=NULL, NA.char="-9", ploidy=2, type=c("codom"),strata=NULL, hierarchy=NULL)// ///// GENIND OBJECT /////////// // // // 341 individuals; 7 loci; 164 alleles; size: 264.9 Kb// // // // Basic content// // @tab: 341 x 164 matrix of allele counts// // @loc.n.all: number of alleles per locus (range: 13-30)// // @loc.fac: locus factor for the 164 columns of @tab// // @all.names: list of allele names for each locus// // @ploidy: ploidy of each individual (range: 2-2)// // @type: codom// // @call: df2genind(X = data.frame(database), sep = "/", ncode = 3, pop = NULL, // // NA.char = "-9", ploidy = 2, type = c("codom"), strata = NULL, // // hierarchy = NULL)// // // // Optional content// // - empty -// //Warning message:// //In df2genind(data.frame(database), sep = "/", ncode = 3, p = NULL, :// // duplicate labels detected for some individuals; using generic labels// // //> grp<-find.clusters(x, max.n.clust=9)// //Choose the number PCs to retain (>=1): 140// //Choose the number of clusters (>=2): 6// //> dapc1<-dapc(x,grp$grp)// //Choose the number PCs to retain (>=1): 40// //Choose the number discriminant functions to retain (>=1): 5/ It works but, for using xvalDapc I don't know what to choose as an argument for "x" and "grp". I tried severals things but that didn't work. Can you advise me on the arguments to use? Thank you in advance for your reply, Best regards, Ma?lis --- L'absence de virus dans ce courrier ?lectronique a ?t? v?rifi?e par le logiciel antivirus Avast. https://www.avast.com/antivirus -------------- next part -------------- An HTML attachment was scrubbed... URL: