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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,

I unintentionally missed to cc to r-devel. -------- Original Message -------- Subject: Re: [Rd] levels for list and data.frame Date: Tue, 21 Mar 2006 20:50:21 +0100 From: Gregor Gorjanc <gregor.gorjanc at gmail.com> Reply-To: gregor.gorjanc at gmail.com To: Martin Maechler <maechler at stat.math.ethz.ch> References: <441F2C49.8080703 at gmail.com> <17439.50351.172900.987055

Hello to everyone! I have built CRAN task view for genetics. For now I have not submit it to CRAN yet and it can be accessible from: http://www.bfro.uni-lj.si/MR/ggorjan/software/R/Genetics.html http://www.bfro.uni-lj.si/MR/ggorjan/software/R/Genetics.ctv I have not submitted it to CRAN, since I would like first some opinion about it. Genetics is really so broad field that I belive one person

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 am trying to plot a quadratcount object over a ppp object in the spatstat package. I ultimately want to get something like this http://bg9.imslab.co.jp/Rhelp/R-2.4.0/src/library/spatstat/man/images/big_quadratcount_001.png http://bg9.imslab.co.jp/Rhelp/R-2.4.0/src/library/spatstat/man/images/big_quadratcount_001.png See

On 12 October 2006 at 13:02, Gregor Gorjanc wrote: | Hello! | | I encounter the following problem when I try to load package foreign | | library(foreign) | Error in dyn.load(x, as.logical(local), as.logical(now)) : | unable to load shared library '/usr/lib/R/library/foreign/libs/foreign.so': | /usr/lib/R/library/foreign/libs/foreign.so: undefined symbol: | Rf_allocString | Error:

And a last post from Paul Gilbert. Thanks to all! This disscusion was really beneficial for me! -----Original Message----- From: Paul Gilbert [mailto:pgilbert at bank-banque-canada.ca] Sent: sre 2005-06-08 21:01 To: Gorjanc Gregor Subject: Re: [R] Random seed problem in MCMC coupling of chains Gorjanc Gregor wrote: > Thanks to Paul and Gabor for additional tips/examples. Actually, I find

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

Hello! Can someone provide me an estimate or relevant source of information on how long is command winepath available or from wich version of wine? I would need this as I work on some R[1] package R2WinBUGS[2] that calls a Windows program WinBUGS[3] and that program needs windows paths. Currently winepath or parsing of .wine/config is used and I wonder if I can remove fiddling with .wine/.config.

Hello R-users! I have tried to use Sweave within LyX* and found two ways to accomplish this. I have attached LyX source file for both ways. *<http://www.lyx.org> Lep pozdrav / With regards, Gregor Gorjanc ---------------------------------------------------------------------- University of Ljubljana Biotechnical Faculty URI: http://www.bfro.uni-lj.si/MR/ggorjan Zootechnical

Hello! I am writing some functions and I repeatedly acces internal factor codes. I figured out that internal codes are 1:n where 1 represents 1st level, 2 2nd level etc. This is not documented and I wonder if this is on purpose and subject to change or would be a good idea to add this to documentation for factor? I can prepair a pacth if this is accepted. -- Lep pozdrav / With regards,

Hello! Data.frames have new rownames funcionality, however in use of colnames<- in R-devel "changes" this. Here is the example: > df1 <- data.frame(letters[1:5]) > attributes(df1) $names [1] "letters.1.5." $row.names [1] 1 2 3 4 5 $class [1] "data.frame" > colnames(df1) <- "bla" > attributes(df1) $names [1] "bla"

Hello! I am trying to get specific fields from an XML document and I am totally puzzled. I hope someone can help me. # URL URL<-"http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=11877539,11822933,11871444&retmode=xml&rettype=citation" # download a XML file tmp <- xmlTreeParse(URL, isURL = TRUE) tmp <- xmlRoot(tmp) Now I want to extract only

Hello! Looking on how people use optim to get MLE I also noticed that one can use returned Hessian to get corresponding standard errors i.e. something like result <- optim(<< snip >>, hessian=T) result$par # point estimates vc <- solve(result$hessian) # var-cov matrix se <- sqrt(diag(vc)) # standard errors What is actually Hessian representing here?

Hello! I think that link to page of Duncan Murdoch (bellow) should be given http://www.murdoch-sutherland.com/Rtools/ at http://developer.r-project.org/. It's easy to launch Google and find mentioned page, but it took me quite some time to do this, because I was sure, that it is noted somewhere on {www,CRAN}.r-project.org. Maybe I didn't read carefully ... Lep pozdrav / With

Dear R core, influenced by recent panel discussion in Vienna I think that it would be nice to add package specific output of citation() function to package reference manuals. I think that apropriate place would be just after fields from DESCRIPTION file. This will be OK for CRAN, but not for locally installed packages as there is not reference manual there (at least on my linux box) - why is this

James, thanks for the response. I understand now my puzzle. tmp <- data.frame(y1=1:4, f1=factor(c("A", "B", "C", "D"))) tmp$y2 <- NA tmp[1:2, "y2"] <- 2 Does the job. I see that I should add a full column. In my case adding full column of NAs and then adding values, solves my problems. Thanks to all. james.holtman at convergys.com

Dear R developers, I noticed that core R distribution functions return NaN, when parameter values are out of parameter space. I have looked in source code and found that warnings and return of NaN are done internally in C code. For dgamma.c the line 49 is: if (shape <= 0 || scale <= 0) ML_ERR_return_NAN; OK. How should this be implemented if distribution functions are written

Hello! Does someone know how to produce L(y|mu) with plotmath? Some code with unsuccessfull results: plot(dnorm(x = seq(from = -4, to = 4, by = 0.1)), type = "l") ## Not what I want legend(legend = c(expression(L(y:mu))), x = "topright") ## Strange, is this a bug? legend(legend = c(expression(L(y|mu))), x = "top") ## Group produces an error legend(legend =

Hello! I use Sweave for a report and up to now I always copied Sweave.sty to a folder where I have the report. But this can be done better (or did I miss anything) with * extension of TEXMF variable in texmf/web2c/texmf.cnf or * linking /usr/lib/R/share/texmf to somewhere in /usr/share/texmf I tried with the following and I didn't need to put Sweave.sty in folder with a report: cd