[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 probability:
+ order(lpd,decreasing=TRUE)
+
+ #pdf(Number of pops.pdf,((210-10)/25.4),((297-10)/25.4))
+ #theWd-getwd()
+ ##setwd(theWd)
+ #par(mfrow = c(5, 2),cex=0.25)
+ #for(irun in 1:nrun)
+ #
+ #{
+ #
+ ###Below is code form the Geneland Plotnpop function
+ #fileparam - paste(path.mcmc, parameters.txt, sep = )
+ #param - as.matrix(read.table(fileparam))
+ #thinning - as.numeric(param[param[, 1] == thinning, 3
[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 np, 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.
Re: [R] How can i do an automatic upgrade of R 2.5.1 to R 2.7.1
Dear Jason,
I don't know if this interests you, but one thing you might want to do
while 'upgrading' (in fact it is just a new installation) is re-install
all the packages that were installed on your previous R version.
I made a small script to do so:
###
reinst.pack - function(pathToOldR){
instDir - paste(pathToOldR,/library/,sep=)
pack - dir(instDir)
basePack - sub(/base,, system.file())
basePack - dir(basePack)
pack - setdiff(pack,basePack)
pack
install.packages(pkg=pack)
}
###
You just have to launch the script from your new R version, giving it
the path to the old version of R.
For instance I had to do:
###
reinst.pack(/usr/local/lib64/R-2.6.0/)
also installing the dependency ‘spam’
essai de l'URL
'http://cran.univ-lyon1.fr/src/contrib/spam_0.13-1.tar.gz'
http://cran.univ-lyon1.fr/src/contrib/spam_0.13-1.tar.gz%27
Content type 'application/x-tar' length 212961 bytes (207 Kb)
URL ouverte
==
downloaded 207 Kb
[...]
###
It should work if you packages where installed at the default place.
Cheers,
Thibaut.
Jason Lee schreef:
Hi,
I am aware this is somehow FAQ question but I ve been searching from
R-cran
archive about the related matter and could not find anything closer
to this.
I want to upgrade my R version from 2.5.1. to 2.7.1. What is the best
way to
load the latest one apart from installing the packages (tar.gz) from
http://cran.ms.unimelb.edu.au/?
Please help.
Thanks..
[[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.
--
##
Thibaut JOMBART
CNRS UMR 5558 - Laboratoire de Biométrie et Biologie Evolutive
Universite Lyon 1
43 bd du 11 novembre 1918
69622 Villeurbanne Cedex
Tél. : 04.72.43.29.35
Fax : 04.72.43.13.88
[EMAIL PROTECTED]
http://biomserv.univ-lyon1.fr/%7Ejombart/
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.
[R] new mailing list: R-sig-genetics
Dear list, A new mailing list *R-sig-genetics* has just been created (thanks to Martin Maechler). This list is dedicated to discussions about the *analysis of genetic markers* using the R software. The covered topics, along with various information about the list, are available from the R-sig-genetics homepage: https://stat.ethz.ch/mailman/listinfo/r-sig-genetics Best regards, Thibaut Jombart. -- ## Thibaut JOMBART CNRS UMR 5558 - Laboratoire de Biométrie et Biologie Evolutive Universite Lyon 1 43 bd du 11 novembre 1918 69622 Villeurbanne Cedex Tél. : 04.72.43.29.35 Fax : 04.72.43.13.88 [EMAIL PROTECTED] http://biomserv.univ-lyon1.fr/%7Ejombart/ 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] Research Notes
Barry Rowlingson wrote: I use a thing called 'Plain Text File'... Basically I keep a file called 'NOTES.txt' in each project directory I work in and keep it updated as I work. I keep note of where data comes from, what I do to it, what various functions do and so on. Then I can use Unix command-line tools such as 'grep' and 'find' to search them. I wouldn't dream of using a proprietary tool with a proprietary and closed format for this kind of thing EVER. If you want something more sophisticated than my Plain Text File solution then keep a 'NOTES.tex' file then you can include equations and graphics. Plus it's then trivial to cut things out of it into your final reports and papers. And for a small amount of additional pain, one can use Sweave. It is much more powerful than tex alone and this assures a perfect match between commands and outputs. Best, Thibaut. -- ## Thibaut JOMBART CNRS UMR 5558 - Laboratoire de Biométrie et Biologie Evolutive Universite Lyon 1 43 bd du 11 novembre 1918 69622 Villeurbanne Cedex Tél. : 04.72.43.29.35 Fax : 04.72.43.13.88 [EMAIL PROTECTED] http://biomserv.univ-lyon1.fr/%7Ejombart/ 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] representing binary data for Genetic Algorithm in R
Dear Esmail, you really have to have a look at some introduction to R (e.g. http://cran.r-project.org/doc/manuals/R-intro.pdf), but see the Manual section in R website (http://www.r-project.org/). That would answer many of your questions. Hello all, I am trying to implement a simple Genetic Algorithm. I am doing this in R since I want access to the statistical functions (eg lm) it provides. I'm not new to programming, or GAs, but I am totally new to R (the package and the language), and I am hoping someone could help with these questions: 1. I am going to use a binary representation, it seems that vectors of Factors would be what I should use? I would specify values of TRUE/FALSE instead? Or is there a better choice for manipulating binary strings? Does this seem like a legitimate way to create a random one: sample(0:1, vec_size, replace=T) Factors are nice to manipulate binary strings (they use integers as internal representation). 2. Am I correct in assuming that R is interpreted (and hence is going to be noticeably slower than compiled languages)? Yep. But you can have R call C and Fortran code as well. 3. Is there some sort of debugging facility? ?debug 4. Does anyone know how to do an effective search for R in google (or other search engines). The fact that this is a single letters seems to have most applications ignore this input. This might help me in finding answers to some other basic questions I have (such as is there an equivalent function to printf in R? cat and print are not quite working right for me -- but I need to dig deeper into the documentation) Functions: ?, help.search, apropos, RSiteSearch. See also http://www.rseek.org/. I am not sure if this belongs into the help or development group, so I'm giving this a try. If this is the wrong group to post in, please let me know and I'll repost. Instructions and posting guide are there: http://www.r-project.org/mail.html There will probably be more elementary questions (I am reading the various manuals too .. but if anyone has some other favorite sites they want to recommend please do so) Thanks, Esmail ps: I there a USENET group dedicated to R? pps: I am also exploring ways of calling R functions from Java, if anyone has any comments regarding that please share. See the rJava package. Regards, Thibaut. -- ## Thibaut JOMBART CNRS UMR 5558 - Laboratoire de Biométrie et Biologie Evolutive Universite Lyon 1 43 bd du 11 novembre 1918 69622 Villeurbanne Cedex Tél. : 04.72.43.29.35 Fax : 04.72.43.13.88 [EMAIL PROTECTED] http://lbbe.univ-lyon1.fr/-Jombart-Thibaut-.html?lang=en 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] CRAN packages hosting policy
Julien Barnier wrote: Hi to all, I recently created a small package which contains some simple R functions in order to help students in my research unit to use R. The package is pure R, it passes R CMD check, but it is really designed for internal use and, moreover, it is entirely documented in french. Is it possible to upload and to host this kind of package to CRAN ? Or is it better, as it is quite a private tool and not really designed for widespread adoption, to set up my own repository ? Thanks in advance, Hi Julien, I would not pretend that I know anything about the hosting policy on CRAN. However, another place where you could try and host your package is R-Forge (though you might have to ask them the same question): https://r-forge.r-project.org/ Among other things, you can manage your sources via svn, and install the package directly from their server. And do many other terrific things, like bug-tracking, mailing-lists, forums, etc. Hope this will help. Best regards, Thibaut. -- ## Thibaut JOMBART CNRS UMR 5558 - Laboratoire de Biométrie et Biologie Evolutive Universite Lyon 1 43 bd du 11 novembre 1918 69622 Villeurbanne Cedex Tél. : 04.72.43.29.35 Fax : 04.72.43.13.88 [EMAIL PROTECTED] http://lbbe.univ-lyon1.fr/-Jombart-Thibaut-.html?lang=en 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] Fwd: time series regression
bereket weldeslassie wrote: Hi Everyone, One more information to my question. I am trying to do a time series regression using the lm function. *My intention is to investigate the relationship between a dependent time series variable and several independent time series variables.* According to the durbin watson test the errors are autocorrelated. And then I tried to use the gls function to accomodate for the autocorrelated errors. My question is how do I know what ARMA process (order) to use in the gls function? Or is there any other way to do the time series regression in R? I highly appreciate your help. Thanks, Bereket [[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. Hi, Temporal autocorrelation seems to be a contagious process... even for emails. I received yours three times in 5 minutes. Concerning your question, I am no expert in time series, but you may also try ordinary least squares after 'removing' autocorrelation. This can be achieved by regression onto a lagged variable (see lag.listw in spdep, which can also be applied to temporal context), or onto eigenvectors of a temporal proximity matrix. Cheers, Thibaut. -- ## Thibaut JOMBART CNRS UMR 5558 - Laboratoire de Biométrie et Biologie Evolutive Universite Lyon 1 43 bd du 11 novembre 1918 69622 Villeurbanne Cedex Tél. : 04.72.43.29.35 Fax : 04.72.43.13.88 [EMAIL PROTECTED] http://lbbe.univ-lyon1.fr/-Jombart-Thibaut-.html?lang=en 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] Spatially Lagged Predictor Variable Models
ArunPrasad wrote: Hi Everyone, I am doing a project based on Spatially Lagged Predictor Variable Models, I would like to know which package in R would execute this model. Also, I am new to this field of spatial statistics. Any suggestions for a good book on spatial regression analysis would be appreciated. Thanks Again. Cheers Arun Hi, you may have a look at lag.listw in the package 'spdep' by R Bivand, which computes a lag vector given a variable and a list of spatial weights. There is a nice review of spatial methods in ecology, already mentioned on this list I think: Carsten F. Dormann, Jana M. McPherson, Miguel B. Araújo, Roger Bivand, Janine Bolliger, Gudrun Carl, Richard G. Davies, Alexandre Hirzel, Walter Jetz, W. Daniel Kissling, Ingolf Kühn, Ralf Ohlemüller, Pedro R. Peres-Neto, Björn Reineking, Boris Schröder, Frank M. Schurr and Robert Wilson,. (2007) Methods to account for spatial autocorrelation in the analysis of species distributional data: a review. /Ecography/ 30:5, 609–628 This may be a good starting point. Cheers, Thibaut. -- ## Thibaut JOMBART CNRS UMR 5558 - Laboratoire de Biométrie et Biologie Evolutive Universite Lyon 1 43 bd du 11 novembre 1918 69622 Villeurbanne Cedex Tél. : 04.72.43.29.35 Fax : 04.72.43.13.88 [EMAIL PROTECTED] http://lbbe.univ-lyon1.fr/-Jombart-Thibaut-.html?lang=en 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] Plot Principal component analysis
Jim Lemon wrote: SNN wrote: Hi, I have matrix of 300,000*115 (snps*individual). I ran the PCA on the covariance matrix which has a dimention oof 115*115. I have the first 100 individuals from group A and the rest of 15 individuals from group B. I need to plot the data in two and 3 dimentions with respect to PC1 and PC2 and (in 3D with respect to PC1, PC2 and PC3). I do not know how to have the plot ploting the first 100 points corresponding to group A in red (for example) and the rest of the 15 points in Blue? i.e I want the each group in a diffrent color in the same plot. I appreciate if someone can help. Hi Nancy, (if indeed you are a Nancy and that is not a webnym) Say that your groups really are coded A and B, the group coding variable is called group. You can define a color vector like this: colorvector-ifelse(group==A,red,blue) Jim __ 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. Hi Nancy, in your case you may also use inertia ellipses to represent your groups, in addition to different colors. Here is an example using a microsatellite dataset from adegenet (but valid for SNPs of course): # library(ade4) library(adegenet) data(microbov) # dataset # replace missing values obj=na.replace(microbov,method=mean) # perform your pca, keep 3 axes pca1=dudi.pca(obj$tab,scannf=FALSE,nf=3,scale=FALSE) # plot the result s.class(pca1$li,obj$pop) s.class(pca1$li,obj$pop,col=sample(colors(),15)) # here, replace col by the appropriate vector of colors. # The resulting graphic represents each genotype by a point, and adds ellipses of different color for each group; each ellipse represents 95 % of the inertia of the corresponding group. The more ellipses overlap, the less your groups are differentiated on the factorial plane. Cheers, Thibaut. -- ## Thibaut JOMBART CNRS UMR 5558 - Laboratoire de Biométrie et Biologie Evolutive Universite Lyon 1 43 bd du 11 novembre 1918 69622 Villeurbanne Cedex Tél. : 04.72.43.29.35 Fax : 04.72.43.13.88 [EMAIL PROTECTED] http://lbbe.univ-lyon1.fr/-Jombart-Thibaut-.html?lang=en http://pbil.univ-lyon1.fr/software/adegenet/ __ 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] How to include the documentation of a function in a Sweave document?
Jean lobry wrote:
Dear R-help,
I would like to include the documentation of an R function in an
*.rnw document processed by Sweave. Because I'm sharing my *.rnw
files with colleagues under Linux and Windows (I'm on Mac OS X),
I would like a pure R solution.
The naive approach doesn't work, because Sweaving this *.rnw
file:
tmp.rnw
\documentclass{article}
\begin{document}
=
?plot
@
\end{document}
tmp.rnw
yields the following LaTeX file on my platform (session info at the end):
tmp.tex
\documentclass{article}
\usepackage{/Library/Frameworks/R.framework/Resources/share/texmf/Sweave}
\begin{document}
\begin{Schunk}
\begin{Sinput}
`?`(plot)
\end{Sinput}
\end{Schunk}
\end{document}
tmp.tex ---
-
in which no Soutput has been generated. Is it possible to redirect the
help output, in a platform-independent way, so that it is included in
the Soutput environment of the LaTeX file?
Best,
Jean
sessionInfo()
R version 2.6.2 (2008-02-08)
i386-apple-darwin8.10.1
locale:
C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] rcompgen_0.1-17
Maybe a clue: we can use
cat(readLines(as.character(?plot)),sep=\n)
to display the help (here, of plot) directly to the screen. So we could
use something like:
echo=TRUE,print=FALSE,eval=FALSE=
?plot
@
echo=FALSE,print=TRUE,eval=TRUE=
cat(readLines(as.character(?plot)),sep=\n)
@
But this doesn't work (latex compilation error) as weird characters
appear in the produced tex, at some places (tabulations?), like:
_T_h_e _D_e_f_a_
(not sure what it will look like in this email, but emacs reads things
like _^HT_^HH_^He...).
Maybe an encoding problem? I tried specifying different encoding to
readLines, with no luck (latin1, UTF-8). Otherwise, the help appears in
the .tex.
Cheers,
Thibaut.
sessionInfo()
R version 2.6.2 (2008-02-08)
i686-pc-linux-gnu
locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
attached base packages:
[1] datasets utils stats graphics grDevices methods base
other attached packages:
[1] phylobase_0.3 nlme_3.1-87ape_2.1-1 adegenet_1.1-0
pixmap_0.4-7
[6] ade4_1.4-5 MASS_7.2-41
loaded via a namespace (and not attached):
[1] grid_2.6.2 lattice_0.17-6 rcompgen_0.1-17 tcltk_2.6.2
[5] tools_2.6.2
--
##
Thibaut JOMBART
CNRS UMR 5558 - Laboratoire de Biométrie et Biologie Evolutive
Universite Lyon 1
43 bd du 11 novembre 1918
69622 Villeurbanne Cedex
Tél. : 04.72.43.29.35
Fax : 04.72.43.13.88
[EMAIL PROTECTED]
http://lbbe.univ-lyon1.fr/-Jombart-Thibaut-.html?lang=en
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] How to include the documentation of a function in a Sweave document?
Duncan Murdoch wrote:
Maybe a clue: we can use
cat(readLines(as.character(?plot)),sep=\n)
to display the help (here, of plot) directly to the screen. So we could
use something like:
echo=TRUE,print=FALSE,eval=FALSE=
?plot
@
echo=FALSE,print=TRUE,eval=TRUE=
cat(readLines(as.character(?plot)),sep=\n)
@
But this doesn't work (latex compilation error) as weird characters
appear in the produced tex, at some places (tabulations?), like:
_T_h_e _D_e_f_a_
(not sure what it will look like in this email, but emacs reads things
like _^HT_^HH_^He...).
Maybe an encoding problem? I tried specifying different encoding to
readLines, with no luck (latin1, UTF-8). Otherwise, the help appears
in the .tex.
Those are backspaces: it's trying to underline the title. You'd get
a better display if you read the latex version instead. I think you
need to construct the path to it yourself (using system.file() etc.)
Duncan Murdoch
Thanks for the hint !
So, the code below roughly works:
###
\documentclass{article}
\usepackage{verbatim}
\begin{document}
echo=TRUE,print=FALSE,eval=FALSE=
?plot
@
echo=FALSE,print=FALSE,results=tex=
path - sub(help,latex,as.character(?plot))
path - paste(path,'tex',sep=.)
cat(readLines(path),sep=\n)
@
\end{document}
###
The document compiles with pdflatex but still complains about a bunch of
unknown latex instructions (like \HeaderA, used at the begining of the
included (plot.tex) tex file. The resulting pdf indeed looks a bit nasty.
What command shall we include in the header to have it work?
Best,
Thibaut.
--
##
Thibaut JOMBART
CNRS UMR 5558 - Laboratoire de Biométrie et Biologie Evolutive
Universite Lyon 1
43 bd du 11 novembre 1918
69622 Villeurbanne Cedex
Tél. : 04.72.43.29.35
Fax : 04.72.43.13.88
[EMAIL PROTECTED]
http://lbbe.univ-lyon1.fr/-Jombart-Thibaut-.html?lang=en
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] Standard method for S4 object
Martin Morgan wrote: Christophe Genolini wrote: Personnally I would find stuff like names, $, $-, or [ useful as these are usual operation with S3 objects. Is it possible in S4 to define $- ? If there is a slot name 'a' in Possible yes, see below. Usual? It implies to the user that this is a list- or data.frame-like object (where $ is used most commonly). Maybe your object is not like that? It also seems like a short step from direct slot access (although it doesn't have to be), which might be breaking the abstraction layer that object orientation provides. And it shifts the responsibility for confirming that 'name' is a slot, and dispatching on different values of 'name' (e.g. for some slots perhaps one doesn't want to allow access, and then the code inside the '$' method has to check that), back to the developer (instead of allowing the method definition and dispatch to do its work). Generally these seem like backward steps to me. Yes, to me too. But it is nonetheless useful when you convert an 'old' S3 class to S4 and want to re-use your old code as much as possible (or want users to be able to do so). I don't know if this is the case here. Plus, as $ and $- are just wrappers for @ and @-, the procedure checking the validity of a value assigned to a slot is still called when using $-. Another, maybe interesting option is to use accessors to change the values of the slots. This might be more object-oriented, and would allow for more control on the content of the object. Cheers, Thibaut. -- ## Thibaut JOMBART CNRS UMR 5558 - Laboratoire de Biométrie et Biologie Evolutive Universite Lyon 1 43 bd du 11 novembre 1918 69622 Villeurbanne Cedex Tél. : 04.72.43.29.35 Fax : 04.72.43.13.88 [EMAIL PROTECTED] http://lbbe.univ-lyon1.fr/-Jombart-Thibaut-.html?lang=en http://pbil.univ-lyon1.fr/software/adegenet/ __ 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] Standard method for S4 object
Christophe Genolini wrote: Hi the list, I am defining a new class MyClass. Shortly, I will submit a package with it. Before, I would like to know if there is a kind of non official list of what method a new S4 object have. More precisely, personnaly, I use 'print', 'summary' and 'plot' a lot. So for my new class, I define these 3 methods. Is there some other method that a R user can raisonnably expect ? Some minimum basic tools... Thanks Christophe Hi, /I think your question should be more relevant on Rdev./ I am not sure that 'print' is called when printing an S4 object. I think 'show' is used instead. You might find which methods are usual: http://wiki.r-project.org/rwiki/doku.php?id=tips:classes-s4 may help. Personnally I would find stuff like names, $, $-, or [ useful as these are usual operation with S3 objects. Regards, Thibaut. -- ## Thibaut JOMBART CNRS UMR 5558 - Laboratoire de Biométrie et Biologie Evolutive Universite Lyon 1 43 bd du 11 novembre 1918 69622 Villeurbanne Cedex Tél. : 04.72.43.29.35 Fax : 04.72.43.13.88 [EMAIL PROTECTED] http://lbbe.univ-lyon1.fr/-Jombart-Thibaut-.html?lang=en http://pbil.univ-lyon1.fr/software/adegenet/ __ 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] Accessing the elements of a list
Shubha Vishwanath Karanth wrote: Hi R, I wanted to know how do we access the elements of a list. In particular, v=list(c(1,2,3,4,5),c(1,2,33,4,5),c(1,2,333,4,5),c(1,2,,4,5)) I want to access all the thirds items of the elements of the list. i.e., I want to access the elements, 3,33,333,. This can be done through sapply as: sapply(v,function(x) x[3]) But I need to access this without using 'sapply'. Like in a data frame, we do df[2,3] etc Any ideas? Hi, not the most elegant, but this works: cmd unlist(as.data.frame(v)[3,]) c.1..2..3..4..5. c.1..2..33..4..5. c.1..2..333..4..5. c.1..2....4..5. 3 33 333 Cheers, Thibaut. -- ## Thibaut JOMBART CNRS UMR 5558 - Laboratoire de Biométrie et Biologie Evolutive Universite Lyon 1 43 bd du 11 novembre 1918 69622 Villeurbanne Cedex Tél. : 04.72.43.29.35 Fax : 04.72.43.13.88 [EMAIL PROTECTED] http://lbbe.univ-lyon1.fr/-Jombart-Thibaut-.html?lang=en http://pbil.univ-lyon1.fr/software/adegenet/ __ 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] Which Linux OS on Athlon amd64, to comfortably run R?
8rino-Luca Pantani wrote: Dear R-users. I eventually bought myself a new computer with the following characteristics: Processor AMD ATHLON 64 DUAL CORE 4000+ (socket AM2) Mother board ASR SK-AM2 2 Ram Corsair Value 1 GB DDR2 800 Mhz Hard Disk WESTERN DIGITAL 160 GB SATA2 8MB I'm a newcomer to the Linux world. I started using it (Ubuntu 7.10 at work and FC4 on laptop) on a regular basis on May. I must say I'm quite comfortable with it, even if I have to re-learn a lot of things. But this is not a problem, I will improve my knowledge with time. My main problem now, is that I installed Ubuntu 7.10 Gutsy Gibbon on the new one amd64. To install R on it i followed the directions found here http://help.nceas.ucsb.edu/index.php/Installing_R_on_Ubuntu but unfortunately it did not work. After reading some posts on the R-SIG-debian list, such as https://stat.ethz.ch/pipermail/r-sig-debian/2007-October/000253.html I immediately realize that an amd64 is not the right processor to make life easy. Therefore I would like to know from you, how can I solve this problem: Should I install the i386 version of R ? Should I install another flavour of Linux ? Which one ? Fedora Core 7 ? Debian ? Thanks a lot, for any suggestion Hi, I've got an Athlon 64bits 3000+ processor and Ubuntu LTS (dapper) installed (64 bits version) on my laptop. I do not have any problem to install R from the sources, as long as the correct libraries/compilers/etc. are installed. But it is no pain if you just follow what the configure script tells you (and use apt-get to install missing packages). I guess a common mistake is to forget to install -dev versions of packages, which sometimes contain required headers. However, you should not have troubles installing R on different R distributions, 64bits or not. Hope this help. Thibaut, 64bit-linux-Ruser and still alive. -- ## Thibaut JOMBART CNRS UMR 5558 - Laboratoire de Biométrie et Biologie Evolutive Universite Lyon 1 43 bd du 11 novembre 1918 69622 Villeurbanne Cedex Tél. : 04.72.43.29.35 Fax : 04.72.43.13.88 [EMAIL PROTECTED] http://lbbe.univ-lyon1.fr/-Jombart-Thibaut-.html?lang=en http://pbil.univ-lyon1.fr/software/adegenet/ __ 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] How can I use Adehabitat to obtain an .asc object with the predicted values of a niche model?
Núria Roura wrote: Dear all, I'm using the package adehabitat in R to import several .asc files(=matrix), and also create a kasc object (=dataframe) with all of them. The main idea is to use this kasc object to map the predicted values ofclimate-matching model for an overall area. However, I don't know how toproceed: Do I have to project the model (already stored in R) onto the kascobject directly, or convert the kasc object to a data frame where each rowrefers to a pixel? On the other hand, I would also like to know how to obtain the XYcoordinates for each row of the kasc object. Thank you very much. Cheers, Núria Roura -- View this message in context: http://www.nabble.com/How-can-I-use-Adehabitat-to-obtain-an-.asc-object-with-the-predicted-values-of-a-niche-model--tf4944431.html#a14155047Sent from the R help mailing list archive at Nabble.com. [EMAIL PROTECTED] mailing listhttps://stat.ethz.ch/mailman/listinfo/r-helpPLEASE do read the posting guide http://www.R-project.org/posting-guide.htmland provide commented, minimal, self-contained, reproducible code. Dear Nuria, The mailing list devoted to adehabitat may be a better place for your post. See: http://www.faunalia.com/cgi-bin/mailman/listinfo/animov Regards, Thibaut. -- ## Thibaut JOMBART CNRS UMR 5558 - Laboratoire de Biométrie et Biologie Evolutive Universite Lyon 1 43 bd du 11 novembre 1918 69622 Villeurbanne Cedex Tél. : 04.72.43.29.35 Fax : 04.72.43.13.88 [EMAIL PROTECTED] http://lbbe.univ-lyon1.fr/-Jombart-Thibaut-.html?lang=en http://pbil.univ-lyon1.fr/software/adegenet/ __ 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] PCA with NA
Birgit Lemcke wrote:
Dear all,
(Mac OS X 10.4.11, R 2.6.0)
I have a quantitative dataset with a lot of Na´s in it. So many, that
it is not possible to delete all rows with NA´s and also not
possible, to delete all variables with NA´s.
Is there a function for a principal component analysis, that can deal
with so many NA´s.
Thanks in advance
Birgit
Birgit Lemcke
Institut für Systematische Botanik
Zollikerstrasse 107
CH-8008 Zürich
Switzerland
Ph: +41 (0)44 634 8351
[EMAIL PROTECTED]
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Hi,
in centred PCA, missing data should be replaced by the mean of available
data.
Let X be your analyzed matrix (variables in columns).
##
X = matrix(runif(300),ncol=10)
idx = sample(1:nrow(X),5)
X[idx,] = NA
sum(is.na(X))
[1] 95
library(ade4)
dudi.pca(X,center=TRUE,scale=FALSE)
Erreur dans dudi.pca(X, center = TRUE, scale = FALSE) : na entries in table
##
Now we replace missing values :
##
f1 - function(vec) {
m - mean(vec, na.rm = TRUE)
vec[is.na(vec)] - m
return(vec)
}
Y = apply(X,2,f1)
pcaY = dudi.pca(Y,center=TRUE,scale=FALSE,nf=2,scannf=FALSE)
s.label(pcaY$li)
sunflowerplot(pcaY$li[idx,1:2], add=TRUE)
##
All missing values are placed at the non-informative point, i.e. at the
origin.
Regards,
Thibaut.
--
##
Thibaut JOMBART
CNRS UMR 5558 - Laboratoire de Biométrie et Biologie Evolutive
Universite Lyon 1
43 bd du 11 novembre 1918
69622 Villeurbanne Cedex
Tél. : 04.72.43.29.35
Fax : 04.72.43.13.88
[EMAIL PROTECTED]
http://lbbe.univ-lyon1.fr/-Jombart-Thibaut-.html?lang=en
http://pbil.univ-lyon1.fr/software/adegenet/
__
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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 with nb2listw
[EMAIL PROTECTED] wrote: Hi, I am a new student to R and I was hoping someone could help me with the error message I keep getting when I try to use the nb2listw() function. I have 45 sites and I want to get an autocorrelation value for sites within 1000m of each other. coords-cbind(EAST,NORTH) coords-as.matrix(coords) nb1000-dnearneigh(coords,0,1000,longlat=TRUE) then when I try to run the nb2listw(nb1000, style=W) I get an error message of Empty neighbour sets found. Can someone tell me what this means and how to possible fix it. Thanks Lynnette ~ Lynnette Dagenais M.Sc. Candidate Department of Renewable Resources University of Alberta Edmonton, AB __ 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. Hi, this means that at least on site has no neighbours. Set zero.policy=TRUE (you may read ?nb2listw) to avoid getting an error. chooseCN (pack. adegenet) could help you choose your connection network interactively. Cheers, Thibaut. -- ## Thibaut JOMBART CNRS UMR 5558 - Laboratoire de Biométrie et Biologie Evolutive Universite Lyon 1 43 bd du 11 novembre 1918 69622 Villeurbanne Cedex Tél. : 04.72.43.29.35 Fax : 04.72.43.13.88 [EMAIL PROTECTED] http://lbbe.univ-lyon1.fr/-Jombart-Thibaut-.html?lang=en http://pbil.univ-lyon1.fr/software/adegenet/ __ 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] shrink a dataframe for plotting
Alexy Khrabrov wrote: I get tables with millions of rows. For plotting to a screen-size jpg, obviously just about 1000 points are enough. Instead of feeding plot() the original millions of rows, I'd rather shrink the original dataframe, using some kind of the following interpolation: -- split dataframe into chunks of N rows each, e.g. 1000 rows each -- compute average for each column -- issue one new row of those averages into the shrunk result Is there any existing package to do that in R? Otherwise, which R idioms are most effective to achieve that? Cheers, Alexy Hi, if you want to extract relevant information from such a table, splitting rows in arbitrary chuncks may not solve your problem. Ordinations in reduced space are designed for that kind of task, but hierachical clustering may also help. See Legendre Legendre (1998, Numerical Ecology, Elsevier) for examples of such methods in Ecology, and the R packages ade4, vegan and hclust. Regards, Thibaut. -- ## Thibaut JOMBART CNRS UMR 5558 - Laboratoire de Biométrie et Biologie Evolutive Universite Lyon 1 43 bd du 11 novembre 1918 69622 Villeurbanne Cedex Tél. : 04.72.43.29.35 Fax : 04.72.43.13.88 [EMAIL PROTECTED] http://lbbe.univ-lyon1.fr/-Jombart-Thibaut-.html?lang=en http://pbil.univ-lyon1.fr/software/adegenet/ __ 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] adding an image to a plot
Selon Rajarshi Guha [EMAIL PROTECTED]: Hi, I'm writing code to generate a plot, in which I draw a series of rectangles. So my code is of the form plot.new() plot.window( ... ) draw rectangle draw rectangle ... Is there a way for me to insert a PNG or PDF graphic at a specific position in the plot (ideally in plot coordinates)? I realize that this might probably be better done in a separate image editor, but if it could be done programmatically that would be very handy Thanks, Hi, you can insert pixmaps at specified coordinates using s.logo in the ade4 package. Regards, Thibaut. __ 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] Romoving elements from a vector. Looking for the opposite of c(), New user
Thomas Frööjd wrote:
Not sure i explained it good enough. Ill try with an example
say
x=[3,3,4,4,4,4,5,5,6,8]
z=[3,4,4,5,5]
what i want to get after removing z from x is something like
x=[3,4,4,6,8]
On Nov 15, 2007 3:29 PM, Charilaos Skiadas [EMAIL PROTECTED] wrote:
On Nov 15, 2007, at 9:15 AM, Thomas Frööjd wrote:
Hi
I have three vectors say x, y, z. One of them, x contains observations
on a variable. To x I want to append all observations from y and
remove all from z. For appending c() is easily used
x - c(x,y)
But how do I remove all observations in z from x? You can say I am
looking for the opposite of c().
If you are looking for the opposite of c, provided you want to remove
the first part of things, then perhaps this would work:
z-c(x,y)
z[-(1:length(x))]
However, if you wanted to remove all appearances of elements of x
from c(x,y), regardless of whether those elements appear in the x
part of in the y part, I think you would want:
z[!z %in% x]
Probably there are other ways.
Welcome to R!
Best regards
Haris Skiadas
Department of Mathematics and Computer Science
Hanover College
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Hi,
you may try this :
x=[3,3,4,4,4,4,5,5,6,8]
z=c(3,4,4,5,5)
f1 - function(vec,toremove){
+
+ for(elem in toremove){
+ temp - grep(elem,vec)[1]
+ if(!is.na(temp)) vec - vec[-temp]
+ }
+
+ return(vec)
+ }
f1(x,z)
[1] 3 4 4 6 8
Regards,
Thibaut.
--
##
Thibaut JOMBART
CNRS UMR 5558 - Laboratoire de Biométrie et Biologie Evolutive
Universite Lyon 1
43 bd du 11 novembre 1918
69622 Villeurbanne Cedex
Tél. : 04.72.43.29.35
Fax : 04.72.43.13.88
[EMAIL PROTECTED]
http://lbbe.univ-lyon1.fr/-Jombart-Thibaut-.html?lang=en
http://pbil.univ-lyon1.fr/software/adegenet/
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Re: [R] factors levels ?
Hi, see ?cut ?pretty can also help to define boundaries. Regards, Thibaut. Hi, It's just some example code.. The application is uninteresting. I am searching for some functionality. X - rnorm(100) //my data Y - seq(-3,3,by=0.1) // bin boundaries. Now I would like to generate a - list of factors, length as X... i.e.: all values in the range [-3,-2.9) have the same factor... [-3,-2.9) etc. I would assume R has such a function but I cant recall which one it is. -- W. Eryk Wolski __ 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] vectorize a list
Frank Schmid wrote: Dear R user Suppose I have the following list: f - rnorm(2) s - rnorm(3) l - list(f,s) l [[1]] [1] 0.31784399 0.08575421 [[2]] [1] -0.6191679 0.7615479 -1.0087659 Can I stack the entries of this list in 1 vector with the first list entry followed by the second? The reference manual says that I can use the command /stack/, which can take as arguments either a list or a data frame. But taking simply /stack(l)/ does not work, although it is a list. Many thanks for your hint Frank Schmid __ 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. Hi, no need to use stack here: l=list(a=1:4,b=5:8) l $a [1] 1 2 3 4 $b [1] 5 6 7 8 unlist(l) a1 a2 a3 a4 b1 b2 b3 b4 1 2 3 4 5 6 7 8 Regards, Thibaut. -- ## Thibaut JOMBART CNRS UMR 5558 - Laboratoire de Biométrie et Biologie Evolutive Universite Lyon 1 43 bd du 11 novembre 1918 69622 Villeurbanne Cedex Tél. : 04.72.43.29.35 Fax : 04.72.43.13.88 [EMAIL PROTECTED] http://lbbe.univ-lyon1.fr/-Jombart-Thibaut-.html?lang=en http://pbil.univ-lyon1.fr/software/adegenet/ __ 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] Sweave, and long lasting scripts
John Lande wrote: Dear R user, I am using Sweave to write my reports with R code. Unlucly my code take a lot of time to run, and I don't want to run it multiple time, if possible, as I am still developping the tools. It seems that a sweave run does not save the enviroment at the end of the process, is there a way to avoid to lunch multiple time the same commands? maybe it could be possible to store chunck of code results, and only call them in the next runs. thank you [[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. Hi, the package 'cacheSweave' seems to fulfil your needs. Regards, Thibaut. -- ## Thibaut JOMBART CNRS UMR 5558 - Laboratoire de Biométrie et Biologie Evolutive Universite Lyon 1 43 bd du 11 novembre 1918 69622 Villeurbanne Cedex Tél. : 04.72.43.29.35 Fax : 04.72.43.13.88 [EMAIL PROTECTED] http://lbbe.univ-lyon1.fr/-Jombart-Thibaut-.html?lang=en http://pbil.univ-lyon1.fr/software/adegenet/ __ 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] Can I create pdfs with dataframes instead of images?
Tom.O wrote: Hi I am doing some correlation analysis where I graphically display the results by using image() and then exporting the results in a PDF. I also use the par(mfrow=c(2,2)) to fit 4 images on the same sheet. But I wonder if it possible to use the some methodology to export the 4 matrixes on a PDF with the raw data an getting them in a nice 2*2 pattern with col row names. Thanks Regards Tom Hi, plotting text is a documented topic. See for instance: http://tolstoy.newcastle.edu.au/R/e2/help/07/10/27432.html Regards, Thibaut. -- ## Thibaut JOMBART CNRS UMR 5558 - Laboratoire de Biométrie et Biologie Evolutive Universite Lyon 1 43 bd du 11 novembre 1918 69622 Villeurbanne Cedex Tél. : 04.72.43.29.35 Fax : 04.72.43.13.88 [EMAIL PROTECTED] http://lbbe.univ-lyon1.fr/-Jombart-Thibaut-.html?lang=en http://pbil.univ-lyon1.fr/software/adegenet/ __ 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] PDF output
Pedro de Barros wrote: Dear All, I am trying to save a plot made with ggplot as pdf. I just created the plot, then printed it to the default graphics device (screen). I then tried to create a pdf file choosing (from the menus) File-Save As-PDF file. However, I get an error as Error: Invalid font type In addition: Warning messages: 1: font family not found in PostScript font database 2: font family not found in PostScript font database I am using R2.6.0 on Windows. I would appreciate any help about how to solve this Thanks, Pedro Hi, may you provide a code sample (commands producing the figure) to try and reproduce this error ? Thibaut. -- ## Thibaut JOMBART CNRS UMR 5558 - Laboratoire de Biométrie et Biologie Evolutive Universite Lyon 1 43 bd du 11 novembre 1918 69622 Villeurbanne Cedex Tél. : 04.72.43.29.35 Fax : 04.72.43.13.88 [EMAIL PROTECTED] http://lbbe.univ-lyon1.fr/-Jombart-Thibaut-.html?lang=en http://pbil.univ-lyon1.fr/software/adegenet/ __ 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] how to split data.frame by row?
Henrique Dallazuanna wrote: If I understand your question: df - data.frame(x=rnorm(20), y=rnorm(20), z=rnorm(20)) df - as.matrix(df) dim(df) dim(df) - c(10,6) dim(df) - c(5,12) On 29/10/2007, Weiwei Shi [EMAIL PROTECTED] wrote: hi, if I have 20 x 3 data.frame, how to split it into 10 x 6 (moving the lower part of 10x3 to column) or 5 x 12 thanks Hi, I am not sure that the produced result is what is looked for; however the question is not clear to me either. The indicated code gives: df=data.frame(x=1:4,y=5:8) df=as.matrix(df) df newdf=df dim(newdf) = c(2,4) newdf while I would have thought that : newdf=cbind(df[1:2,], df[3:4,]) newdf was what was looked for. But there may be a quicker way. Regards, Thibaut. -- ## Thibaut JOMBART CNRS UMR 5558 - Laboratoire de Biométrie et Biologie Evolutive Universite Lyon 1 43 bd du 11 novembre 1918 69622 Villeurbanne Cedex Tél. : 04.72.43.29.35 Fax : 04.72.43.13.88 [EMAIL PROTECTED] http://lbbe.univ-lyon1.fr/-Jombart-Thibaut-.html?lang=en http://pbil.univ-lyon1.fr/software/adegenet/ __ 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] Help needed on calculation of Moran's I
Geertje Van der Heijden wrote: Hi, I am trying to calculate Moran's I test for the residuals for a regression equation, but I have trouble converting my coordinates into nb format. I have used the dnearneigh() funtion now with an arbitrarily high upper distance to make it include all plots. However, when I do the lm.morantest() I get a Moran's I value which is the same as the expected value and a P-value of 1. I have used the following code: attach(lowland) coords - as.matrix(cbind(long, $lat)) coord.nb - dnearneigh(coords, 0, 1 longlat=TRUE) coord.list - nb2listw(coord.nb, style=W) lianasp.lm - lm(lianasprich ~ log(averdist) + dsl + lianadens + wooddens) lm.morantest(lianasp.lm, coord.list, alternative=two.sided) And get the following result Global Moran's I for regression residuals data: model: lm(formula = lianasprich ~ log(averdist) + dsl + lianadens + wooddens) weights: coord.list Moran I statistic standard deviate = 0, p-value = 1 alternative hypothesis: two.sided sample estimates: Observed Moran's IExpectation Variance -1.754386e-02 -1.754386e-02 2.125706e-16 Can anyone tell me where I went wrong or if there is another way to generate a nb list? Many thanks, Geertje Hi, did you have a look at the graph you produced (using plot.nb)? Maybe the maximum distance between any two neighbours is too high. What does max(dist(coords)) say ? Anyway, there are many different connection networks available in several R packages, some being more appropriate than others to model paticular spatial distributions. The package adegenet proposes a small tool to choose among several graphs interactively: library(adegenet) xy = matrix(runif(100),ncol=2) yourcn = chooseCN(xy) Regards, Thibaut. -- ## Thibaut JOMBART CNRS UMR 5558 - Laboratoire de Biométrie et Biologie Evolutive Universite Lyon 1 43 bd du 11 novembre 1918 69622 Villeurbanne Cedex Tél. : 04.72.43.29.35 Fax : 04.72.43.13.88 [EMAIL PROTECTED] http://lbbe.univ-lyon1.fr/-Jombart-Thibaut-.html?lang=en http://pbil.univ-lyon1.fr/software/adegenet/ __ 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] Spatial autocorrelation
Geertje Van der Heijden wrote: Hi, I have collected data on trees from 5 forest plots located within the same landscape. Data within the plots are spatially autocorrelated (calculated using Moran's I). I would like to do a ANCOVA type of analysis combining these five plots, but the assumption that there is no autocorrelation in the residuals is obviously violated. Does anyone have any ideas how to incorporate these spatial effects in my analysis? I have been reading up on autoregressive techniques, but I am not sure if it works with more than one plot. All help is greatly appreciated! Many thanks, Geertje van der Heijden Hi, one way to remove spatial autocorrelation is to use Moran's Eigenvectors as predictors in multiple regression. But as there are always n-1 vectors for n points, you will have to choose the predictors to be retained (using standard model selection procedures). Here is an example of how to get the eigenvectors using the ade4 and spdep packages. library(ade4) library(spdep) library(adegenet) xy = matrix(rnorm(100),ncol=2) plot(xy) # get a connection network (here, Delaunay triangulation) cn = chooseCN(xy,ask=FALSE,res=listw)$cn # get Moran's Eigenvectors U = orthobasis.listw(cn) # visualize the first 9 vectors par(mfrow=c(3,3)) for(i in 1:9) s.value(xy,U[,i],addaxes=FALSE, include.ori=FALSE) And then you can use the columns of U as spatial predictors in your model. A few vectors should be able to remove the autocorrelation among residuals. Regards, Thibaut. -- ## Thibaut JOMBART CNRS UMR 5558 - Laboratoire de Biométrie et Biologie Evolutive Universite Lyon 1 43 bd du 11 novembre 1918 69622 Villeurbanne Cedex Tél. : 04.72.43.29.35 Fax : 04.72.43.13.88 [EMAIL PROTECTED] http://lbbe.univ-lyon1.fr/-Jombart-Thibault-.html?lang=en http://pbil.univ-lyon1.fr/software/adegenet/ __ 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.
