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All, Recently I ran across a URL documenting published research using R: http://www.cgd.ucar.edu/ccr/ammann/millennium/CODES_MBH.html A note on the site indicates that the code is being revised. The code and data are provided, so that one could reproduce the results without having to buy a proprietary software program. In poking around the R website it is clear that a lot of thought has gone

Dear R users, seqinR 1.0-5 has been released yesterday on CRAN, so that the source code of the package should be available on all CRAN mirrors within the next 24h. The updated package vignette is here: http://pbil.univ-lyon1.fr/software/SeqinR/seqinr_1_0-5.pdf User level visible changes are: o A new function dotPlot() is now available. http://pbil.univ-lyon1.fr/software/SeqinR/SEQINR_CRAN/DOC/html/dotPlot.html o A new function crelistfromclientdata() is now available to create a list on the ser...

Dear R users, seqinR 1.0-5 has been released yesterday on CRAN, so that the source code of the package should be available on all CRAN mirrors within the next 24h. The updated package vignette is here: http://pbil.univ-lyon1.fr/software/SeqinR/seqinr_1_0-5.pdf User level visible changes are: o A new function dotPlot() is now available. http://pbil.univ-lyon1.fr/software/SeqinR/SEQINR_CRAN/DOC/html/dotPlot.html o A new function crelistfromclientdata() is now available to create a list on the ser...

...nterface (GUI) for the ade4 package. Only the most basic functions of ade4 have a GUI in this first version : classical one-table data analysis methods (PCA, COA, MCA, PCO, etc.), one table with groups of rows (BGA, WGA, DA), and two-tables analysis methods (Coinertia analysis, CCA, PCAIV). http://pbil.univ-lyon1.fr/JTHome/ade4TkGUI.jpg One of the benefits of using ade4TkGUI is the centralized graphical display of the dudi objects created by ade4. A dudi is a list with many components http://pbil.univ-lyon1.fr/ade4html/dudi.html The GUI presents a window in which the user can click on dudi compo...

...nterface (GUI) for the ade4 package. Only the most basic functions of ade4 have a GUI in this first version : classical one-table data analysis methods (PCA, COA, MCA, PCO, etc.), one table with groups of rows (BGA, WGA, DA), and two-tables analysis methods (Coinertia analysis, CCA, PCAIV). http://pbil.univ-lyon1.fr/JTHome/ade4TkGUI.jpg One of the benefits of using ade4TkGUI is the centralized graphical display of the dudi objects created by ade4. A dudi is a list with many components http://pbil.univ-lyon1.fr/ade4html/dudi.html The GUI presents a window in which the user can click on dudi compo...

...itle \section{Introduction to \Rlogo:} This is about the \Rlogo~sofware suite\footnote{ \Rlogo~is available at...}. % include source in final document \myinput{tex.tex} \end{document} ---------------------------------------------------------- with: unix$ pdflatex tex.tex this is what I get: http://pbil.univ-lyon1.fr/members/lobry/tmp/tex.pdf The PDF version of the R-Logo I'm using is here: http://pbil.univ-lyon1.fr/members/lobry/tmp/Rlogo.pdf HTH, Jean -- Jean R. Lobry (lobry at biomserv.univ-lyon1.fr) Laboratoire BBE-CNRS-UMR-5558, Univ. C. Bernard - LYON I, 43 Bd 11/11/1918,...

...itle \section{Introduction to \Rlogo:} This is about the \Rlogo~sofware suite\footnote{ \Rlogo~is available at...}. % include source in final document \myinput{tex.tex} \end{document} ---------------------------------------------------------- with: unix$ pdflatex tex.tex this is what I get: http://pbil.univ-lyon1.fr/members/lobry/tmp/tex.pdf The PDF version of the R-Logo I'm using is here: http://pbil.univ-lyon1.fr/members/lobry/tmp/Rlogo.pdf HTH, Jean -- Jean R. Lobry (lobry at biomserv.univ-lyon1.fr) Laboratoire BBE-CNRS-UMR-5558, Univ. C. Bernard - LYON I, 43 Bd 11/11/1918,...

...w = c(1, 2), cex = 0.7) for(i in 1:2) dotchart(1:10) @ <<fig=T,width=8,height=4>>= par(mfrow = c(1, 2), cex = 0.7) for(i in 1:2) hist(1:10) @ <<fig=T,width=8,height=4>>= par(mfrow = c(1, 2), cex = 0.7) for(i in 1:2) plot(1:10) @ \end{document} I obtain the following: http://pbil.univ-lyon1.fr/members/lobry/mini.pdf that is with the second dotchart (on the right) smaller than the one on the left. I do not have the same problem with hist() or plot(). Any idea of what should I do for my two dotcharts to be of the same size? Best, > sessionInfo() R version 2.4.0 (2006-1...

Hallo everyone, excuse me if this is not a genuine R question but I do not know where to ask else. Referring to e.g. https://stat.ethz.ch/pipermail/r-help/2004-December/062114.html I wonder if these measurements of 3000 criminals (raw data) are available anywhere. At least I didn't find them in the R datasets package or by means of Google. What I did find was a table of frequencies of

...unction - the presentation of the "explore" function had been improved - the "ordiCLust" function has been added, to do cluster analysis on multivariate analysis row scores, with several dynamic graphic help tools (a help page is also available). See these screenshots : http://pbil.univ-lyon1.fr/JTHome/ordiClust1.png http://pbil.univ-lyon1.fr/JTHome/ordiClust2.png http://pbil.univ-lyon1.fr/JTHome/ordiClust3.png Thanks you to all the people who sent me remarks, advice, and bug reports. Comments are still (and always) welcome. Jean -- Jean Thioulouse - Labo Biometrie et Biol...

...unction - the presentation of the "explore" function had been improved - the "ordiCLust" function has been added, to do cluster analysis on multivariate analysis row scores, with several dynamic graphic help tools (a help page is also available). See these screenshots : http://pbil.univ-lyon1.fr/JTHome/ordiClust1.png http://pbil.univ-lyon1.fr/JTHome/ordiClust2.png http://pbil.univ-lyon1.fr/JTHome/ordiClust3.png Thanks you to all the people who sent me remarks, advice, and bug reports. Comments are still (and always) welcome. Jean -- Jean Thioulouse - Labo Biometrie et Biol...

Dear list, I'm trying to understand the graphical parameters by a systematic exploration of the par() function (if you are interested by the result it's here http://pbil.univ-lyon1.fr/R/fichestd/tdr75.pdf, the comments are all in french but it's pure R code under Sweave). I have a problem with par(tmag) illustrated by the following code: ################################################### par(mfrow = c(2, 2)) for(tmag in seq(from = 0.5, to = 2, length = 4)){...

Hi, All i want is to export my list into c: drive and save it as csv file and manually import into Excel. I have the read the article but i am having issues http://pbil.univ-lyon1.fr/library/base/html/write.table.html > excel<-write.table(probe_gene, file = "c:\foo.csv", sep = ",", col.names = > NA) Error in file(file, ifelse(append, "a", "w")) : unable to open connection In addition: Warning message: ca...

...gt; > So, I'm just curious: how do you refer in your own language to > this kind of graphic? How do you call it? > > Best, > > Jean Thanks to all who replied either privately or on the list. I have summarized the answers at the beginning of the following document: http://pbil.univ-lyon1.fr/members/lobry/R/diaposcam.pdf Let me know if you have more eatable examples. Best, Jean -- Jean R. Lobry (lobry at biomserv.univ-lyon1.fr) Laboratoire BBE-CNRS-UMR-5558, Univ. C. Bernard - LYON I, 43 Bd 11/11/1918, F-69622 VILLEURBANNE CEDEX, FRANCE allo : +33 472 43 2...

How does one tell Sweave() to include analysis warning messages in the verbatim output? _____________________________ Professor Michael Kubovy University of Virginia Department of Psychology USPS: P.O.Box 400400 Charlottesville, VA 22904-4400 Parcels: Room 102 Gilmer Hall McCormick Road Charlottesville, VA 22903 Office: B011 +1-434-982-4729 Lab: B019

Please could someone point me in the right direction as I appear to be having a total mental block with fairly basic PCA problem! I have a large dataframe where rows represent independent observations and columns are variables. I am wanting to perform PCA sequentially on blocks of nrows at a time and produce a graphical output of the loadings for the first 2 EOFs for each variable. I'm sure

Dear list, I would like to make a Sweave document that, for a given package, automatically inserts the graphical outputs obtained when runing the example code of high level plot functions. That is, for the "graphics" base package, something like this: http://pbil.univ-lyon1.fr/R/fichestd/tdr79.pdf For this, I need the list of high level plot functions of a given package. I have encountered a problem when calling twice the help.search() function which is illustrated bellow: [rufus:~] lobry% R --vanilla --quiet > sessionInfo() Version 2.3.0 (2006-04-24)...

Dear useRs, the seqinR package contains utilities to import and analyze biological sequence data. For a general introduction see this document: http://pbil.univ-lyon1.fr/software/SeqinR//vignette.pdf Please do not use r-help for questions about seqinR or r-bugs for bug report about seqinR. Use instead the seqinR diffusion list: http://pbil.univ-lyon1.fr/software/SeqinR//mailing.php?lang=eng A new version of seqinR, seqinR 1.1-4, has been released on...

Dear useRs, the seqinR package contains utilities to import and analyze biological sequence data. For a general introduction see this document: http://pbil.univ-lyon1.fr/software/SeqinR//vignette.pdf Please do not use r-help for questions about seqinR or r-bugs for bug report about seqinR. Use instead the seqinR diffusion list: http://pbil.univ-lyon1.fr/software/SeqinR//mailing.php?lang=eng A new version of seqinR, seqinR 1.1-4, has been released on...

...of changes: o A new *experimental* function extractseqs() to download sequences thru zlib compressed sockets from an ACNUC server is released. Preliminary tests suggest that working with about 100,000 CDS is possible with a home ADSL connection. See the manual chapter 3 page 44 at http://pbil.univ-lyon1.fr/software/SeqinR/seqinr_1_0-7.pdf for some system.time() examples. o As pointed by Emmanuel Prestat the URL used in dia.bactgensize() was no more available, this has been fixed in the current version. o As pointed by Guy Perriere, the function oriloc() was no more compatible wi...