Re: [R] creating a database
Can a simple matrix be used for this or would it be better and more efficient to create an external database to hold the data. If so, should the database be created using C and how would I do this (seeing as that I have never programmed in C)? You don't want to be down at the C level, most likely: it would be much more straightforward and programmer-efficient to use one of the available bindings to one of the available open-source databases. R has useful / usable bindings to postgresql, sqlite, and mysql, among many others. These are, however, more generally useful when you reach the point that you simply can't manage the volume of your data in R objects or in data frames. [And, well, you can go a LONG way with intelligently named R objects. :-)] --elijah __ 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] connection diagram
On Wed, 14 Nov 2007, Manal Helal wrote: Dimn Waves Tot. Parts In Wave Wave NoSerial Index W Order M Index DepTot. D1-Serial D1-IndexD1-OrderD1-M Index D2-Serial D2-IndexD2-OrderD2-M Index 2 7 1 0 1 0 0 0, 0 2 2 18 0 4, 4 3 2 1 2, 0 2 7 2 1 2 18 0 4, 4 2 4 20 0 2, 2 5 36 1 0, 4 following the tutorial on SNA, I see that I need to convert that into adjacency matrix to start plotting the graph, and I can not see how I can do that, Into one adjacency matrix -- you probably can't. [And, I think, probably don't really want to do that...] What you might be able to do is figure out what your actual actors are... the entities that are connected to each other... and use them (just them... or their relations...] to build your adjacency matrix. With your matrix in hand, you will want to keep track of those other variables... there are a lotta ways you could go about this, and there are a lot of decisions to affect your implementation. In the 'sna' package, look at the graph stack data structure. [m x N x N dimension -- an array of adjacency matrices which could be attributed values rather than 0/1 boolean is-connected assertions.] You might be best served by a series of plots, each taking into account a different combination of your available data variables. It almost sounds fun, doesn't it? :-) Not really familiar enough with your data to make many more suggestions. It sounds like your data structure is pretty nontrivial... maybe there are ways you can break it down into pieces that you can manage more easily, for your own sake? best, --elijah __ 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] Any useR conference in US in YR2008
Something like this - alternating among continents - happens with AoIR, the Association for Internet Research. A real effort has been made to make sure that the conference is in North America no more than every other year, with alternating slots going to Europe and (once so far..) to Australia. There is quite a lot of discussion of how to get that particular conference (and research-base) spun up in South America, as well - and I think that eventually we'll see a conference hosted there. A good model to follow, I think; AoIR is, like useR, a relatively young and savvy conference/group, pretty close to the bleeding edge. --elijah On Fri, 23 Nov 2007, [EMAIL PROTECTED] wrote: Date: Fri, 23 Nov 2007 11:13:53 +1000 From: [EMAIL PROTECTED] To: [EMAIL PROTECTED], [EMAIL PROTECTED] Cc: R-help@r-project.org Subject: Re: [R] Any useR conference in US in YR2008 Apropos this issue, the R Foundation has had an offer to host useR 2009 from a European based group rather than a North American based one. My understanding is that no decision has yet been taken, though. If other groups had an interest in hosting useR 2009, it might not be a bad idea to register that interest fairly soon. There was a suggestion that alternating between the North America and Europe would be a good idea, but I don't know if this is a cosy understanding of what would be nice, or a reasonably firm policy decision. (I'm also not sure in which camp little places like Brazil, New Zealand, Australia, Japan, China, India, ..., would fit in this rather occidental view of the world, too. :-) Bill Venables. Bill Venables CSIRO Laboratories PO Box 120, Cleveland, 4163 AUSTRALIA Office Phone (email preferred): +61 7 3826 7251 Fax (if absolutely necessary): +61 7 3826 7304 Mobile: +61 4 8819 4402 Home Phone: +61 7 3286 7700 mailto:[EMAIL PROTECTED] http://www.cmis.csiro.au/bill.venables/ -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Marc Schwartz Sent: Friday, 23 November 2007 3:54 AM To: Wensui Liu Cc: r-help@r-project.org Subject: Re: [R] Any useR conference in US in YR2008 None sponsored by the R Foundation. There may be others, offered by the various companies who offer R/S-PLUS training. They do periodically post e-mails about them on these lists. Regards, Marc On Thu, 2007-11-22 at 12:44 -0500, Wensui Liu wrote: Thank you so much, Marc! So if I understand correctly, there is no conference related to R in US in the coming yr2008. Am I correct? On 11/22/07, Marc Schwartz [EMAIL PROTECTED] wrote: On Thu, 2007-11-22 at 11:58 -0500, Wensui Liu wrote: Dear usRs, Is there any conference for usR in US next year? Happy Turkey day! wensui R related conferences, at least those officially related to the R Foundation, are listed here: http://www.r-project.org/conferences.html This past August, the useR! conference was at Iowa State University. Next year's useR! conference is in Dortmund, Germany. If the pattern holds, the useR! conference in 2009 will be back in the U.S. HTH, Marc Schwartz __ 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. __ 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] biocep project (R for the Web and the Virtual R Workbench)
Some of the bits and pieces in this look like very strong candidates for breaking off into CRAN packages, if you haven't done so already. This looks like very nice work - you should be proud! :-) --elijah On Mon, 19 Nov 2007, Karim Chine wrote: Date: Mon, 19 Nov 2007 19:44:51 + From: Karim Chine [EMAIL PROTECTED] To: R-help@r-project.org Subject: [R] biocep project (R for the Web and the Virtual R Workbench) Dear all, I have been writing during last year at the European Bioinformatics Institute a general unified open source solution for R integration. This work is now available via this link: http://www.ebi.ac.uk/microarray-srv/frontendapp/ The different frameworks and tools of the biocep project are now robust enough for production use. The different APIs are finalized but the documentation is incomplete. the last version of the biocep README file can be found here : http://www.ebi.ac.uk/microarray-srv/frontendapp/BIOCEP_README.txt Here are the major use cases I dealt with : - Generate java mappings for R Objects (Standard/S4). - Generate java mappings for selected packages' functions (Generic/TypeInfoed). - Use R and the R packages as a Java Toolkit via a Rich, High level, Object-Oriented API. - Deploy and use R as a remote component. - Expose automatically R packages and the R API as JAX-WS stateless or statefull Web Services. - Use R within a resource pooling infrastructure for scalable, web oriented, data analysis applications. - Use the Remote Resources Pooling framework (RPF) to deploy and use distributed computational resources (non R based, native libraries with JNI support or java code) - Use R for parallel computing via a Java API or Web Services. - Create and use Remote R Instances from within R (snow' like fucntions : makeCluster, clusterEvalQ, clusterExport, clusterApply, stopCluster ..) - Use the R API from within an applet (book, use and release a Remote R Instance via HTTP Tunneling) - Use R to generate Graphics on the fly for thin web clients - Use R from within a Workbench that includes an advanced script editor, a Spreadsheet View fully connected to R data and functions, an R Object Inspector, composable and dockable Views, interactive R devices, clonable R Graphics.. - Use the Workbench from within a browser or via Java Web Start to access a pool of Remote R Instances - Use the Workbench to control on demand any Remote R Instance - Provide a packaging for R Based Desktop applications that enables Web based, one click installation (Embedded R for Windows, detected R for other operating systems) This work uses extensively a large number of existing open source projects as is or patched. The public SVN url/login/pasword for the biocep project are in the README file You may want to try the Virtual R Workbench on your local machine, use the following link : http://www.ebi.ac.uk/microarray-srv/frontendapp/rworkbench.jnlp or type 'javaws http://www.ebi.ac.uk/microarray-srv/frontendapp/rworkbench.jnlp' from the command line. This is a one click installation process for Windows and Mac OS X. (You need to preinstall R on Mac OS X while on Widows an embedded R 2.6 can be deployed and used) The Java Web Start installer creates an RWorkbench directory in your home dir with all the files required. You may continue launching the application via the url (good for fetching updates automatically) or use the RWorkbench/VRWorkbench.txt to Run the application off line. rename it to VRWorkbench.bat on Windows or type 'source VRWorkbench.txt' on Mac OS X command line. use the sources of biocep to run the R Workbench on Unix-like operating systems. Best wishes, Karim __ 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] connection diagram
hi, You should probably be looking at the functions in the following packages: sna network(s) graph dynamicgraph mathgraph igraph Matrix and a few others ;) what you're describing sounds like, to my ear, a restricted social network diagram; many of the problems you describe are typical of such problems, and are accounted for in the packages described above. The most difficult part is likely to be the plots; handling an annotated, weighted, complex network is fairly straightforward in terms of data handling and analytic tools (e.g. regressions on networks are common...). --elijah On Tue, 13 Nov 2007, Manal Helal wrote: Date: Tue, 13 Nov 2007 12:44:16 +1100 From: Manal Helal [EMAIL PROTECTED] To: r-help@r-project.org Subject: [R] connection diagram Hi I am practically new to R, and need to construct connection diagrams, I have a table of data, of nodes in vertical rows, and horizontally the number of outgoing connections to other nodes, and the indices of these nodes, each in a column, so some columns are used, and some are not, based on how many connections I have the node is identified by these variables (dimension, wave number, partition number, index) the number of incoming and outgoing connections to each nodes varies, but obviously there is a relationship First: I need to draw diagrams of these connections Second: I need to apply regression analysis on this data, to predict a closed formula of how the 4 variables above decide how many incoming connections, and outgoing connections, and from/to which node(s) Am I making sense? if so, is this doable in R? or do I need to use other tools? If R can do it, I really need to find a tutorial or a starting link that I can follow to learn more how I can do these, sorry for being that ignorant about R, but I think I will need it a lot if it does what I need, thank you very much for your help in advance, __ 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] PVM error message
I am working with a Fedora Core 6 OS and R 2.5. I have just finished I am using PVM3.4.5+6-WIN32.tar.gz Isn't that supposed to be the wad of files for Windows machines? there's a different link on the PVM homepage to the source for unices... --elijah __ 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] Implementing R through Oracle
I have looked through all the ROracle documentation, R-help, R-dev, Googled the world and still cannot figure out this issue. Everything I read it is about connecting to an Oracle database and pulling data, processing it, and then pushing it back to Oracle. I am running in pl/sql code so I already have a Oracle session open. What I want to do is from Oracle call R. I am having a mental challenge in seeing how this can be done. Any words of wisdon? EXTPROC in Oracle, calling an R CMD BATCH session? Dirty but workable. [p.s. I don't normally do Oracle but the stuff at http://www.idevelopment.info/data/Oracle/DBA_tips/PL_SQL/PLSQL_1.shtml shows basically how to do it...] --elijah __ 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] DBI Package
I have some problems with DBI package, I want to connect to PostgreSQL database but I don't know the way to do it. pg - dbDriver(PostgreSQL) ... nope. That won't work. you need the RdbiPgSQL package from Bioconductor. Along with DBI, as I recall. --elijah__ 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] Cluster Analysis
Subject: [R] Cluster Analysis Dear all, I would like to know if I can do a hierarchical cluster analysis in R using my own similarity matrix and how. Thanks. Katia Freire. Yes. ;) Reading the help for dist() and hclust() should make the procedure for doing this appear fairly straightforward. For interpreting the results, cutree() should be helpful.. --elijah __ 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] Cannot install 'rgl'
Do you have the X11 devel packages installed? You probably do not.
--elijah
On Mon, 29 Oct 2007, Metaxab wrote:
Date: Mon, 29 Oct 2007 05:45:33 -0700 (PDT)
From: Metaxab [EMAIL PROTECTED]
To: r-help@r-project.org
Subject: [R] Cannot install 'rgl'
Hello I have the following problem:
I am trying to install the 'rgl' package by:
sudo R
install.packages('rgl',dependencies=TRUE)
I get the following message
checking for X... no
configure: error: X11 not found but required, configure aborted.
ERROR: configuration failed for package 'rgl'
** Removing '/usr/local/lib/R/site-library/rgl'
How can I resolve this issue
I run Ubuntu 7.10
Thank you in advance
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Re: [R] pseudo code
Requires: T = cluster(X): A hierarchical clustering algorithm L = cut-tree(T; k): produces a partition with k non-singleton clusters The functions you'll want to read the documentation to, here, are hclust() and cutree(). They're fairly straightforward and nicely documented. It looks like you are running cutree at multiple heights of the hclust object to get different numbers of clusters; am I interpreting that correctly? --elijah s(L1;L2): a similarity between two partitions 1: f = 0:8 2: T =cluster(X) fthe reference clustering 3: for i = 1 to num subsamples do 4: subi =subsamp(X; f) fsub-sample a fraction f of the datag 5: Ti=cluster(subi) 6: end for 7: for k = 2 to kmax do 8: L1=cut-tree(T; k) fpartition the reference clusteringg 9: for i = 1 to maximum iterations do 10: L2 =cut-tree(Ti; k) 11: S(i; k) = s(L2;L1) computed only on the patterns of subi. 12: end for 13: end for I am glad about any help, don't really know what to do! thanks, regards Julia -- __ 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] igraph and plotting connected components
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? Edge-crossing minimization is a research topic all in itself, for folks who deal with graph-style data on a regular basis. ;-) It is *hard* to construct sane graphs automatically, which is why software in this area so frequently produces what appear to be sub-par results. [And it is difficult for human beings to evaluate the 'quality' of such graphs, comparatively - we just aren't good at this task.] Rgraphviz in Bioconductor does a great job of this. It's a wrapper for the Graphviz library, so the R docs are a little sparse, but there's a tremendous amount of flexibility there. Seconded - graphviz in general is quite good; getting your data into dot-file format is often a productive step in the viz process. Dot-file format is also *ridiculously simple* to generate , which I think of as a factor well in its favor. :-) the dynamicGraph package (which I think lives in bioconductor as well) is reasonably useful for smallish graphs. I hear that there's a tk-based interactive graph layouter available with graphviz's source - you might look there, too. There's also Pajek, which is pretty and interactive but not R, for-Windows, and not even very compatible with the data formats usually used by folks with R. ;) There's also the pixelglow build of graphviz on OSX, which is beautiful and fun to mess with. There are a couple other graph packages as well... most not interactive, which sounds like what you're likely wanting. [With some of the iterative graph rendering algorithms - particularly the ones that deal with energy minimization algorithms and the like - nondeterministic mostly - you can sometimes re-run the layout function and get wildly different results, particularly for complex graphs. You might try this.] --elijah wright school of library and information science indiana university, bloomington __ 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] curvilinear grid
The idea is that you're modeling an irregular shaped object, a body of water, a river or estuary, say. It's fairly common practice to use a grid squished and rotated so that the main flow is along one axis, and the other axis spans the flow in most spots. So there is a single transformation that gets you from a rectangular grid to the shape of your estuary, but there isn't a tidy analytical way to describe it, like there is with a map projection. Instead there is an x and y for each grid point, and the cell dimensions vary all over the place. spplot, in the sp package seems almost to do what I'm after, but I can't figure out if there is a way to invoke it that does what I want, or if I'm barking up the wrong tree. Ask on R-sig-geo? I haven't seen a query from you come through over there... and that would be the logical place to ask questions about the sp package and similar bits... --e __ 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] sprucing up the R homepage
http://www.broad.mit.edu/~finnyk/Rhome.jpg If you run Eric Lecoutre's code to produce the graphic, available at http://www.r-project.org/misc/acpclust.R, unchanged except for the addition of these lines: library(Cairo) Cairo(600,400,file=Rlogo_swiss.png,type=png,bg=white) then you get this: http://members.optusnet.com.au/tchur/Rlogo_swiss.png which I think looks even better. Kudos to Simon Urbanek and Jeffrey Horner for the excellent Cairo device driver for R (and which works even without an X server, which makes it great for web server applications). It seems to have lost labels on the left, though... and there is some oddness on the right edge, too, where the number 45 found in the other two plot versions has been replaced with V. De Gen... - what looks like part of someone's name or some other descriptor. The (1-3) 60% under the PCA 5 Vars section also intersects with part of a plot. Overall the effect is better, but the fine details could use some tweaking. --elijah __ 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] sprucing up the R homepage
So I applied my corrected margins to Tim's Cairo trick and voila: http://www.broad.mit.edu/~finnyk/Rlogo_swiss.png This is hands-down the best version, in my opinion! Yes, it is definitely much nicer than the version on www.r-project.org now. :-) --e __ 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] Connecting R to PostgreSQL via RODBC, on Windows
I feel like I must be missing something rather plain, but I don't get it. how is one supposed to use R as a PgSQL client on Windows? Assume my windows desktop is on the same network as a PgSQL server, and I just need to use R to connect and pull down some data. The thing that is confusing me is that RODBC doesn't seem to know anything about PgSQL, in that odbcDataSources(type = all) only returns info about MS/Excell/Access/dBase stuff. What does it take to get RODBC to deal with PgSQL? There's an odbc-to-pgsql driver for windows that will need to be installed. You can find that here: http://www.postgresql.org/ftp/odbc/versions/ Then, you set up your connection to postgresql via the Control Panel, under Administrative Tools, then Data Sources. Then connect to that with R. [I have mostly done this under Linux - it has been quite a while since I've needed to do it on Windows, but this is a broadly correct outline of the necessary steps.] --e __ 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.
