[R] FW: New package apex 1.0.0 released on CRAN
Dear all, (apologies for multiple posting) On behalf of the apex development team (E. Paradis, K. Schliep, Z. Kamvar, R. Harris and myself), I am happy to announce that apex has been released on CRAN: http://cran.r-project.org/web/packages/apex/index.html This package provides tools for reading, storing, handling and analysing genetic sequences from multiple genes, and is compatible with both ape and phangorn. For more information on apex, questions, requests, or to join us, check our github project at: https://github.com/thibautjombart/apex Best regards Thibaut == Dr Thibaut Jombart MRC Centre for Outbreak Analysis and Modelling Department of Infectious Disease Epidemiology Imperial College - School of Public Health Norfolk Place, London W2 1PG, UK Tel. : 0044 (0)20 7594 3658 http://sites.google.com/site/thibautjombart/ http://sites.google.com/site/therepiproject/ http://adegenet.r-forge.r-project.org/ Twitter: @thibautjombart ___ R-sig-genetics mailing list r-sig-genet...@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-genetics __ 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.
[R] FW: r-sig-genetics is alive!
Dear all, a small "heads up" for R-sig-genetics, a mailing list devoted to population genetics in R. See below, and sorry about the double-posting. All the best Thibaut ------ From: Jombart, Thibaut Sent: 08 April 2015 17:21 To: r-sig-genet...@r-project.org Subject: r-sig-genetics is alive! Dear all, after a rather quiet existence for the last few years, it may be good to send this reminder: r-sig-genetics is alive! Many awesome people have subscribed lately, and I am looking forward to seeing exciting discussions here. Posting guidelines have been freshly updated: https://stat.ethz.ch/mailman/listinfo/r-sig-genetics Coming soon: exciting news regarding future releases of a bunch of population genetics packages. All the best Thibaut == Dr Thibaut Jombart MRC Centre for Outbreak Analysis and Modelling Department of Infectious Disease Epidemiology Imperial College - School of Public Health Norfolk Place, London W2 1PG, UK Tel. : 0044 (0)20 7594 3658 http://sites.google.com/site/thibautjombart/ http://sites.google.com/site/therepiproject/ http://adegenet.r-forge.r-project.org/ Twitter: @thibautjombart __ 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.
Re: [R] Geneland error on unix: Error in MCMC(........ :, unused argument(s) (ploidy = 2, genotypes = geno)
Hello,
you may want to contact directly the maintainer of Geneland for that kind of
issue. In any case, this post would be best suited for R-sig-genetics:
https://stat.ethz.ch/mailman/listinfo/r-sig-genetics
Best regards,
Thibaut
--
##
Dr Thibaut JOMBART
MRC Centre for Outbreak Analysis and Modelling
Department of Infectious Disease Epidemiology
Imperial College - Faculty of Medicine
St Mary’s Campus
Norfolk Place
London W2 1PG
United Kingdom
Tel. : 0044 (0)20 7594 3658
t.jomb...@imperial.ac.uk
http://sites.google.com/site/thibautjombart/
http://adegenet.r-forge.r-project.org/
From: Nevil Amos [nevil.a...@gmail.com]
Sent: 20 May 2010 10:34
To: r-help@r-project.org; Jombart, Thibaut
Subject: Geneland error on unix: Error in MCMC( :, unused argument(s)
(ploidy = 2, genotypes = geno)
I am receiving the above error ( full r session output below) the
script runs OK in windows. and "genotypes" and "ploidy" are both
correct arguments
any suggestions would be most welcome
Nevil Amos
MERG/ACB
Monash University School of Biological Sciences
> library(Geneland)
Loading required package: RandomFields
Loading required package: fields
Loading required package: spam
Package 'spam' is loaded. Spam version 0.21-0 (2010-03-13).
Type demo( spam) for some demos, help( Spam) for an overview
of this package.
Help for individual functions is optained by adding the
suffix '.spam' to the function name, e.g. 'help(chol.spam)'.
Attaching package: 'spam'
The following object(s) are masked from 'package:base':
backsolve, forwardsolve, norm
Try help(fields) for an overview of this library
fields web: http://www.image.ucar.edu/Software/Fields
Loading required package: mapproj
Loading required package: maps
Loading required package: snow
Loading required package: tcltk
Loading Tcl/Tk interface ... done
ooo
oGeneland is loaded o
o o
o* Please * o
o o
oRegister on o
ohttp://www2.imm.dtu.dk/~gigu/Geneland/register.php o
o o
oSee manual ono
ohttp://www2.imm.dtu.dk/~gigu/Geneland/#Manualo
o o
oType citation("Geneland") for a quick citation guide o
o o
oSee http://www2.imm.dtu.dk/~gigu/Geneland/# o
ofor additional referenceso
o o
oThis is Geneland-3.2.1 o
o o
ooo
Warning message:
In fun(...) : no DISPLAY variable so Tk is not available
> DIRLIST<-c("Adult_ALL
NO_ANW/")#,"Adult_Or_ANW/","Adult_Females/","Adult_Males/")
> for(d in DIRLIST){
+ theWd<- paste("/nfs/monash/home/namos/Rwork/",d,sep="")
+ setwd(theWd)
+ SPP.CODES <-"EYR"#c("BT","EYR","FH","SPP","STP")
+ for (sp in SPP.CODES){
+ path.sp<- paste(theWd,sp,"/",sep="")
+ dir.create(path.sp)
+ GENO.TABLE<-paste(theWd,sp,"geno",sep="")
+ XY.TABLE<-paste(theWd,sp,"xy",sep="")
+ MINPOP=1
+ MAXPOP=25
+ INITPOP=1
+ NITS=50
+ THIN=NITS/1000
+ nrun <- 10
+ burnin <- 200
+ geno<-noquote(read.table(GENO.TABLE))
+ coord<-read.table(XY.TABLE)
+
+ ## Loop for multiple runs
+
+ for(irun in 1:nrun)
+ {
+ ## define path to MCMC directory
+
+ path.mcmc <- paste(path.sp,irun,"/",sep="")
+ dir.create(path.mcmc)
+ MCMC(coordinates=coord, ploidy=2, genotypes=geno, varnpop=T,
npopmax=MAXPOP, npopinit=MINPOP, spatial=T, freq.model="Correlated",
nit=NITS, thinning=500, rate.max=nrow(geno), delta.coord=100,
path.mcmc=path.mcmc)
+ ## MCMC postprocessing
+ PostProcessChain(coordinates=coord,path.mcmc=path.mcmc,genotypes=geno,
nxdom=50,nydom=50,burnin=burnin)
+ }
+ ## Computing average posterior probability
+
+ lpd <- rep(NA,nrun)
+ for(irun in 1:nrun)
+ {
+ path.lpd <- paste(path.mcmc,"log.posterior.density.txt",sep="")
+ lpd[irun] <- mean(scan(path.lpd)[-(1:burnin)])
+ }
+ ## Runs sorted by decreasing average posterior prob
[R] Sweave in PNG: driver online
Dear R addicts, Back in 2006, I posted the proposition for a tweak of the Sweave driver so that PNG figures can be produced instead of eps/pdf : https://stat.ethz.ch/pipermail/r-help/2006-March/102122.html The amount of code modified is tiny (it was designed to induce minimal changes to the official code), but so far the driver seems to have been useful to a number of users. From 2006 on, successive versions of the code were supposed to incorporate the official driver. My current understanding is that this tweak won't incorporate the official release, although an alternative approach is still supposed to take place eventually. Meanwhile, a fairly recent update of the alternative driver can be found online from my website: http://sites.google.com/site/thibautjombart/r-packages A vignette describes briefly the new features and how the driver can be used. Best regards, Thibaut. -- ## Dr Thibaut JOMBART MRC Centre for Outbreak Analysis and Modelling Department of Infectious Disease Epidemiology Imperial College - Faculty of Medicine St Mary’s Campus Norfolk Place London W2 1PG United Kingdom Tel. : 0044 (0)20 7594 3658 t.jomb...@imperial.ac.uk http://sites.google.com/site/thibautjombart/ http://adegenet.r-forge.r-project.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.
Re: [R] Doubt about CCA and PCA
Dear Francisco, CCA and PCA are quite different methods. CCA regresses your 'response' data onto a set of explanatory variables. This needs to invert the matrix of covariances of the predictors, which is only possible if n>p, where n is the number of observations and p the number of explanatory variables. PCA is defined in any case. The ratio between n and p is then relevant only if you intend to infer principal axes / component of the population (as opposed to using the PA/PC as mere descriptors of the sample). I would recommend reading : Joliffe, I. T. Principal Component Analysis Springer, 2004 which tackles the latter point very clearly. Best regards, Thibaut. -- ## Dr Thibaut JOMBART MRC Centre for Outbreak Analysis and Modelling Department of Infectious Disease Epidemiology Imperial College - Faculty of Medicine St Mary’s Campus Norfolk Place London W2 1PG United Kingdom Tel. : 0044 (0)20 7594 3658 t.jomb...@imperial.ac.uk http://www1.imperial.ac.uk/medicine/people/t.jombart/ http://adegenet.r-forge.r-project.org/ From: r-help-boun...@r-project.org [r-help-boun...@r-project.org] On Behalf Of Francisco Javier Santos Alamillos [fsan...@ujaen.es] Sent: 23 November 2009 21:43 To: r-help@r-project.org Subject: [R] Doubt about CCA and PCA Dear R community, I'm working with PCA and CCA methods, and I have a theoretical question. Why is it necesary to have more temporal values than variables when the CCA O PCA are going to be used? Could you advise to me some any paper about it? Thanks in advance, [[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. __ 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.
Re: [R] problem whit Geneland
David Winsemius wrote: > help.search did not offer any clues. Using Baron's search page, I got > reference to r-help entries from 2004, but looking at the current > documentation , I see no such function. I am wondering if the name of the > function was changed in later versions of the package and you are mixing old > documentation or examples with a newer installation of that package? > > Here is a 2005 version of the package documentation and it does have that > function: > http://phase.hpcc.jp/mirrors/stat/R/CRAN/doc/packages/Geneland.pdf > > Perhaps you want the MCMC function? > > Description > Markov Chain Monte-Carlo inference under various models > > Usage > MCMC( coordinates=NULL, genotypes,## ploidy=2, dominance="Codominant", > allele.numbers, > path.mcmc, # path to output directory > # hyper-prior parameters > rate.max,delta.coord=0,shape1=2,shape2=20, npopmin=1,npopinit,npopmax, > # dimensions > nb.nuclei.max, > # options in mcmc computations > nit,thinning=1,freq.model="Uncorrelated", varnpop=TRUE, spatial=TRUE, > jcf=TRUE, filter.null.alleles=TRUE, prop.update.cell=0.1, > write.rate.Poisson.process=FALSE, write.number.nuclei=TRUE, > write.number.pop=TRUE, write.coord.nuclei=TRUE, write.color.nuclei=TRUE, > write.freq=TRUE, write.ancestral.freq=TRUE, write.drifts=TRUE, > write.logposterior=TRUE, write.loglikelihood=TRUE, write.true.coord=TRUE, > write.size.pop=FALSE, miss.loc) Hello, You might reach a broader range of Geneland users by sending your post to R-sig-genetics: https://stat.ethz.ch/mailman/listinfo/r-sig-genetics Cheers, Thibaut. -- ## Dr Thibaut JOMBART MRC Centre for Outbreak Analysis and Modelling Department of Infectious Disease Epidemiology Imperial College - Faculty of Medicine St Marys Campus Norfolk Place London W2 1PG United Kingdom Tel. : 0044 (0)20 7594 3658 jomb...@biomserv.univ-lyon1.fr http://biomserv.univ-lyon1.fr/%7Ejombart/ http://adegenet.r-forge.r-project.org/ [[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.
