[R] FW: New package apex 1.0.0 released on CRAN

== 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

[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-

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

[R] Sweave in PNG: driver online

gards, 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

Re: [R] Doubt about CCA and PCA

nent 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

Re: [R] problem whit Geneland

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 Outbre

Re: [R] How can i do an automatic upgrade of R 2.5.1 to R 2.7.1

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 Villeurba

[R] new mailing list: R-sig-genetics

-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

Re: [R] Research Notes

ve. 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 Villeur

Re: [R] representing binary data for Genetic Algorithm in R

anks, >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. -- #

Re: [R] CRAN packages hosting policy

ll 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 U

Re: [R] Fwd: time series regression

xt), 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:/

Re: [R] Spatially Lagged Predictor Variable Models

eto, 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. -- #

Re: [R] Plot Principal component analysis

lipses 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 - Laboratoi

Re: [R] How to include the documentation of a function in a Sweave document?

quot;) 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

Re: [R] How to include the documentation of a function in a Sweave document?

ase other attached packages: [1] phylobase_0.3 nlme_3.1-87 ape_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

Re: [R] Standard method for S4 object

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. Cheer

Re: [R] Standard method for S4 object

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 1

Re: [R] Accessing the elements of a list

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. -- ###

Re: [R] Which Linux OS on Athlon amd64, to comfortably run R?

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. -- ##

Re: [R] How can I use Adehabitat to obtain an .asc object with the predicted values of a niche model?

; 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 Evo

Re: [R] PCA with NA

f=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 Ev

Re: [R] shrink a dataframe for plotting

ing 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 Biolo

Re: [R] problem with nb2listw

icy=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 L

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 specif

Re: [R] Romoving elements from a vector. Looking for the opposite of c(), New user

PLEASE do read the posting guide http://www.R-project.org/posting-guide.html >and provide commented, minimal, self-contained, reproducible code. > > > > > 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 toremov

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 gene

Re: [R] vectorize a list

d, 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. -- ##

Re: [R] Sweave, and long lasting scripts

t; > 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.

Re: [R] how to split data.frame by row?

oked 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

Re: [R] PDF output

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 novembr

Re: [R] Can I create pdfs with dataframes instead of images?

/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/-

Re: [R] Help needed on calculation of Moran's I

tworks 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) Rega

Re: [R] grouping rows into bin ranges

rix,ncol=ncol(A)) > groupeA $`1` [,1] [,2] [,3] [1,]159 [2,]26 10 $`2` [,1] [,2] [,3] [1,]37 11 [2,]48 12 And then you can perform any action on these matrices using lapply or sapply. Regards, Thibaut. --

Re: [R] Spatial autocorrelation

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 Ville