similar to: Extract just some fields from XML

Duncan, you are a king! Thanks a lot for this cookie. It really helped me. Thanks for the code as well as detailed explanation at the end. >Hi Gregor. > >Here is a function that will collect all of the nodes in the >XML document whose names are in the vector elementNames > >getElements = >function(elementNames) >{ > els = list() > > startElement = function(node,

Hello! I am crossposting this to R-help and BioC, since it is relevant to both groups. I wrote a wrapper for Entrez search utility (link for this is provided bellow), which can add some new search functionality to existing code in Bioconductor's package 'annotate'*. http://eutils.ncbi.nlm.nih.gov/entrez/query/static/esearch_help.html Entrez search utuility returns a XML document

Hello R users! I just found out that I have 49 invitations for Gmail (gmail.google.com). I have been using it now for a while and is really nice. Don't forget 1 GB for free. I will invite those who respond to this mail by FIFO. -- Lep pozdrav / With regards, Gregor Gorjanc ------------------------------------------------------------------------ University of Ljubljana Biotechnical

Hello! Those of you, who use Sweave a lot, will probably find my shell script usable. You can get it at: http://www.bfro.uni-lj.si/MR/ggorjan/programs/shell/Sweave.sh No warranty, however don't hesitate to contact me if you find an error or have a patch! -- Lep pozdrav / With regards, Gregor GORJANC --------------------------------------------------------------- University of

Hello! Say I have a function foo1, which has argument ... to pass various arguments to foo2 i.e. foo1 <- function(x, ...) { foo2(x, ...) } Say that foo2 accepts argument arg1 and I would like to do the following: - if foo1 is called as foo1(x) then I would like to assign some value to arg1 inside foo1 before calling foo2 arg1 <- "some value" foo2(x, arg1=arg1) - if foo1 is

Hello! I was just wondering if Sweave can work with \input or \include LaTeX commands. So, is it aware of such a possible hierarchy in documents. I would test that, but I don't have such a report available at the moment. I thought of that when I was writting shell script for Sweave from command line and I have solved that part there. -- Lep pozdrav / With regards, Gregor GORJANC

Hello! I was reading R-intro and I have some suggestions: R-intro.html#A-sample-session rm(fm, fm1, lrf, x, dummy) suggestion rm(fm, fm1, lrf, x, y, w, dummy) The next section will look at data from the classical experiment of Michaelson and Morley to measure the speed of light. file.show("morley.tab") mm <- read.table("morley.tab") suggestion mm <- data(morley)

Hello! Has anyone successfully compiled F90 sources in R-package? I found the same question on r-devel list from 2002 and I wonder if there is any progress. I heard that g95 and gfortran can be usable. And one more thing. I have a program written in F90 and lets suppose that compiler is not a problem. I've read manual 'Writing R Extensions' and successfully loaded one F77 subroutine

Hello! Has anyone successfully compiled F90 sources in R-package? I found the same question on r-devel list from 2002 and I wonder if there is any progress. I heard that g95 and gfortran can be usable. And one more thing. I have a program written in F90 and lets suppose that compiler is not a problem. I've read manual 'Writing R Extensions' and successfully loaded one F77 subroutine

Hello! I have a continous distribution and would like to get mode (the most frequent value in distribution). I easily found mean, median and other basic thing but not mode function. Can anyone help? I know there my might be problems with multiple modes, but still I think that there should be a mode function in R. Please send mail to R-help list and me, so I can get response faster. Thank

Hello! New version of R has came out and I would like to thank to all developers on this matter. So I should probably upgrade. Fine and no problem. For windows I just grab the latest precompiled binnaries and install them. Then I see a report on a bug, which is or will be fixed in pacthed version. So I need to get binnaries from patched build and install them, right? How often do you people

Hello! New version of R has came out and I would like to thank to all developers on this matter. So I should probably upgrade. Fine and no problem. For windows I just grab the latest precompiled binnaries and install them. Then I see a report on a bug, which is or will be fixed in pacthed version. So I need to get binnaries from patched build and install them, right? How often do you people

Hello! I am performing coupling of chains in MCMC and I need the same value of seed for two chains. I will show demo of what I want: R code, which might show my example is: niter <- 3 nchain <- 2 tmpSeed <- 123 for (i in 1:niter) { # iterations for (j in 1:nchain) { # chains set.seed(tmpSeed) a <- runif(1) cat("iter:", i, "chain:", j,

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("

Hello! I would like to get MLE for parameter lambda of Poisson distribution. I can use fitdistr() for this. After looking a bit into the code of this function I can see that value for lambda and its standard error is estimated via estimate <- mean(x) sds <- sqrt(estimate/n) Is this MLE? With my poor math/stat knowledge I thought that MLE for Poisson parameter is (in mixture of LaTeX

Hello to Rusers! I am puzzled with R and I really do not know where to look in for my problem. I am moving from SAS and I have difficulties in translating SAS to R world. I hope I will get some hints or pointers so I can study from there on. I would like to do something like this. In SAS I can write a macro as example bellow, which is afcourse a silly one but shows what I don't know how

Hi! Is anyone experiencing the following: $ gpg --keyserver subkeys.pgp.net --recv-key E2A11821 gpg: requesting key E2A11821 from hkp server subkeys.pgp.net gpg: keyserver timed out gpg: keyserver receive failed: keyserver error Regards, Gregor

Hi I get the following warings on my ubuntu (gutsy) machine > library(matrix) > data.frame(x=1:5, z=5)[1:5, ] x z 1 1 5 2 2 5 3 3 5 4 4 5 5 5 5 Warning message: ':::' is deprecated. 'methods' is deprecated. 'seemsS4Object' is deprecated. Use 'isS4' instead. See help("Deprecated") It is quite annoying since I often subset the data.frames. Will

Hello! Is it possible to set na.rm=TRUE in a global way? I'am constantly forgeting on this when performing analyses. I agree that one should be carefull with this when developing some code, but not necesarilly so in data analysis. Lep pozdrav / With regards, Gregor Gorjanc ---------------------------------------------------------------------- University of Ljubljana PhD student

Hello! I would like to use constrain to sum coeficients of a factor to 0 instead of classical corner contraint i.e. I would like to fit a model like lm(y ~ 1 + effectA + effectB) and say get parameters intercept effectA_1 effectA_2 effectB_1 effectB_2 effectB_3 where effectA_1 represents deviation of level A_1 from intercept and sum(effectA_1, effectA_2) = 0 and the same for factor B. Is