[R] Updates to R Core and R Foundation Membership
Hi all, It is my pleasure to announce new members to R Core and to the R Foundation whose efforts will be most appreciated as R continues to evolve and advance. There are 2 new R core members: Martin Morgan and Michael Lawrence. In addition Stefano Iacus has decided to step down from R Core. There are 7 new R foundation members: Dirk Eddelbuettel, Torsten Hothorn, Marc Schwartz, Hadley Wickham, and Achim Zeileis, Martin Morgan and Michael Lawrence. The R Foundation now has 29 ordinary members. Please join me in welcoming them to their new roles and especially in thanking Stefano for his many years of contributions. best wishes Robert for the R Foundation -- Robert Gentleman rgent...@gmail.com [[alternative HTML version deleted]] ___ r-annou...@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-announce __ 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] step by step debugger in R?
Hi, Romain Francois wrote: Duncan Murdoch wrote: On 5/22/2009 10:59 AM, Michael wrote: Really I think if there is a Visual Studio strength debugger, our collective time spent in developing R code will be greatly reduced. If someone who knows how to write a debugger plugin for Eclipse wants to help, we could have that fairly easily. All the infrastructure is there; it's the UI part that's missing. Duncan Murdoch [I've copied Mark Bravington and Robert Gentleman to the list as they are likely to have views here, and I am not sure they monitor R-help] Hello, Making a front-end to debugging was one of the proposed google summer of code for this year [1], it was not retained eventually, but I am still motivated. Pretty much all infrastructure is there, and some work has been done __very recently__ in R's debugging internals (ability to step up). As I see it, the ability to call some sort of hook each time the debugger waits for input would make it much easier for someone to write I have still not come to an understanding of what this is supposed to do? When you have the browser prompt you can call any function or code you want to. There is no need for something special to allow you to do that. front-ends. A recent post of mine (patch included) [2] on R-devel suggested a custom prompt for browser which would do the trick, but I now think that a hook would be more appropriate. Without something similar to that, there is no way that I know of for making a front-end, unless maybe if you embed R ... (please let me know how I am wrong) I think you are wrong. I can't see why it is needed. The external debugger has lots of options for handling debugging. It can rewrite code (see examples in trace for how John Chambers has done this to support tracing at a location), which is AFAIK a pretty standard approach to writing debuggers. It can figure out where the break point is (made a bit easier by allowing it to put in pieces of text in the call to browser). These are things the internal debugger can't do. There is also the debug package [3,4] which does __not__ work with R internals but rather works with instrumenting tricks at the R level. debug provides a tcl/tk front-end. It is my understanding that it does not work using R internals (do_browser, ...) because it was not possible at the time, and I believe this is still not possible today, but I might be wrong. I'd prefer to be wrong actually. I don't understand this statement. It has always been possible to work with the internal version - but one can also take the approach of rewriting code. There are some difficulties supporting all the operations that one would like by rewriting code and I think a combination of external controls and the internal debugger will get most of the functionality that anyone wants. There are somethings that are hard and once I have a more complete list I will be adding this to the appropriate manual. I will also be documenting the changes that I have been making, but that project is in flux and won't be done until the end of August, so people who want to look at it are welcome (it is in R-devel), but it is in development and could change pretty much without notice. Romain noted that we now support stepping out from one place to another function. We also have a debugonce flag that lets you get close to step in, but step in is very hard in R. I am mostly interested in writing tools in R that can be used by anyone that wants to write an external debugger and am not that interested in any particular external debugger. I would be happy to listen to feature requests or issues that arise - but the discussion should probably be on R-devel mailing list. best wishes Robert Romain [1] : http://www.r-project.org/soc09/ideas.html#p5 [2] : https://stat.ethz.ch/pipermail/r-devel/2009-April/053128.html [3] : http://cran.r-project.org/web/packages/debug/index.html [4] : http://cran.r-project.org/doc/Rnews/Rnews_2003-3.pdf -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 rgent...@fhcrc.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] Plink bed files
Hi Frederico, You will likely have more luck asking about Bioinformatics related questions on the Bioconductor list, you might look at the rtracklayer package which can import bed files, if they really are bed files, and otherwise you would have to get the file format and write your own parser. Robert Federico Calboli wrote: Hi All, does anyone know how to import binary .bed files generated by Plink (http://pngu.mgh.harvard.edu/~purcell/plink/ ) into R? the Plink FAQ explains how to conver other types of files, not the .bed. Cheers, Federico -- Federico C. F. Calboli Department of Epidemiology and Public Health Imperial College, St. Mary's Campus Norfolk Place, London W2 1PG Tel +44 (0)20 75941602 Fax +44 (0)20 75943193 f.calboli [.a.t] imperial.ac.uk f.calboli [.a.t] gmail.com [[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. -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 [EMAIL PROTECTED] __ 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] Finding a path using the Graph package
Have a look at the RBGL package (but you probably want to update your R etc to something more recent) [EMAIL PROTECTED] wrote: Hello, Does anyone know of a way of finding all the nodes that are between a pair of specified nodes in the excellent graph package (R vers 2.5.0). I have a class(graphAM) object and need to determine all possible pathways in this object. Here's an example: In the simple case of a--b--c (where -- denotes conected to) the list of all pathways would be: ab ba abc cba cb bc. Thanks in advance, Dan __ 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. -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 [EMAIL PROTECTED] __ 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] KM estimation for interval censoring?
The Icens package implements a number of different estimation paradigms. Briefly, for interval censored data, the KM does not apply, but Turnbull's method does. Relevant citations for Icens are in it. For a Cox model approach, there was at one time a package, not at CRAN, by Commenges (and a Biometrics paper, I believe), Google suggests that Dr. Commenges is pretty active in this area. David Winsemius wrote: gallon li [EMAIL PROTECTED] wrote in news:[EMAIL PROTECTED]: Does anybody know if there is such a function to estimate the distribution for interval censored data? survfit doesn't work for this type of data as I tried various references. My reading of R-help posts by Therneau and Lumley is that interval censoring is only available for parametric estimates in the survival package. It's not KM, but perhaps this will be of interest: Turnbull's Nonparametric Estimator for Interval-Censored Data Suely Ruiz Giolo http://www.est.ufpr.br/rt/suely04a.pdf Giolo cites KLEIN, J. P, MOESCHBERGER, M. Survival Analysis. New York: Springer Verlag, 1997, for the algorithm. This MIT-CSAIL report says they have an available R package that handles interval censoring and time-dependent covariates: http://dspace.mit.edu/bitstream/1721.1/33957/1/MIT-CSAIL-TR-2006-055.pdf -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 [EMAIL PROTECTED] __ 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] Analyzing Publications from Pubmed via XML
or just try looking in the annotate package from Bioconductor Gabor Grothendieck wrote: On Dec 13, 2007 9:03 PM, Farrel Buchinsky [EMAIL PROTECTED] wrote: I would like to track in which journals articles about a particular disease are being published. Creating a pubmed search is trivial. The search provides data but obviously not as an R dataframe. I can get the search to export the data as an xml feed and the xml package seems to be able to read it. xmlTreeParse( http://eutils.ncbi.nlm.nih.gov/entrez/eutils/erss.cgi?rss_guid=0_JYbpsax0ZAAPnOd7nFAX-29fXDpTk5t8M4hx9ytT- ,isURL=TRUE) But getting from there to a dataframe in which one column would be the name of the journal and another column would be the year (to keep things simple) seems to be beyond my capabilities. Has anyone ever done this and could you share your script? Are there any published examples where the end result is a dataframe. I guess what I am looking for is an easy and simple way to parse the feed and extract the data. Alternatively how does one turn an RSS feed into a CSV file? Try this: library(XML) doc - xmlTreeParse(http://eutils.ncbi.nlm.nih.gov/entrez/eutils/erss.cgi?rss_guid=0_JYbpsax0ZAAPnOd7nFAX-29fXDpTk5t8M4hx9ytT-;, isURL = TRUE, useInternalNodes = TRUE) sapply(c(//author, //category), xpathApply, doc = doc, fun = xmlValue) __ 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. -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 [EMAIL PROTECTED] __ 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] Rgraphviz
Hi, Most likely you are mixing and matching things that do not play nicely together. Since you did not give us details on just what you did (I have re-installed, is so vague as to be of no value, please provide accurate and complete descriptions of what you did when asking for help) You can either choose to use the OS X binaries, in which case you must also use the binary version of graphviz (available here: http://r.research.att.com/#pkg) or you can choose to install from source, in which case you must install both graphviz and Rgraphviz from source (and that means you will need to have the appropriate tools installed). Loren Engrav wrote: Rgraphviz I cannot load it I have re-installed etc etc etc etc And cannot load it Message is 6): Library not loaded: /usr/local/lib/libgvc.3.dylib Referenced from: /Library/Frameworks/R.framework/Versions/2.6/Resources/library/Rgraphviz/lib s/ppc/Rgraphviz.so Reason: image not found Error : .onLoad failed in 'loadNamespace' for 'Rgraphviz' Error: package/namespace load failed for 'Rgraphviz' MacOS10.4.10 What am I doing wrong? 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. -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 [EMAIL PROTECTED] __ 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] igraph and plotting connected components
graph, RBGL and Rgraphviz, all available at www.bioconductor.org Dieter Best wrote: Hello there, I am using the igraph package to build graphs from my data. If I plot a graph though, it's not easy for me to see what's going on. Does anybody know how to rearrange a graph to get a plot without too many crossing lines? Maybe other packages? Thanks a lot in advance for any pointers, -- D - [[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. -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 [EMAIL PROTECTED] __ 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] linewidth in Rgraphviz
Hi Ben, Sorry for the slow reply, but something like this works, library(Rgraphviz) example(randomEGraph) x = plot(g1) xx = sapply(AgEdge(x), lines, lwd=2, len=1) there are other ways too - but this might be the easiest let me know if that does what you want... Robert Ben Bolker wrote: I'm an Rgraphviz newbie trying to figure out how to do some things/whether they are possible. Apparently graphviz does allow you to modify line widths of edges: see https://mailman.research.att.com/pipermail/graphviz-interest/2001q2/51.html (although it looks a little obscure even in graphviz). [As discussed in the thread above, the weight parameter in Rgraphviz sets the parameters of the graph layout algorithm, NOT the linewidth of the edge itself.] I can probably figure this out given enough hours, but if someone were able to put together an example in a few minutes (or know that it's impossible or very difficult) I would be grateful ... cheers Ben Bolker -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 [EMAIL PROTECTED] __ 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] Network Construction in R
there are several packages that can be used: the graph, RBGL and Rgraphviz packages, provide data structures, algorithms, and layout/plotting tools for graphs/networks. There are quite a few more specialized packages at Bioconductor (typically more related to biological problems). There, you can use biocViews to see what is available. best wishes Robert Johannes Urpelainen wrote: Hi, I am trying to construct a social network from a data frame with rows acra numa acrb numb yearexpab eaboimpab iabo 10 USA2 CAN 20 1957 4017.000 0.0 3187.000 0.0 91 USA2 CUB 40 1957 628.000 0.0 526.000 0.0 144 USA2 HAI 41 1957 25.000 0.0 20.000 0.0 and so on. I want the network to have directed edges from node acra to node acrb weighted by expab. What is the most convenient way to construct this network object? Thank you very much! Best, -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 [EMAIL PROTECTED] __ 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.
