[R] XML - ampersand escaped
Hi, I create some DOM with XML and would like to include cap; in the text of an element. The library automatically escapses it to amp;cap;. unescaping \\cap; does not help. any ideas? My current plan is to go through the output and replace it with gsub, but maybe there is a better way? thanks, ido library(XML) xml - xmlTree(tree) Warning message: In xmlRoot.XMLInternalDocument(currentNodes[[1]]) : empty XML document xml$addNode(test,a cap; b) xml$addNode(test,a \\cap; b) xml$value() ?xml version=1.0? tree testa amp;cap; b/test testa \amp;cap; b/test /tree __ 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] dev2bitmap: extra missing
Hi, I don't know if I am the first one to report the problem: in 2.8.0 dev2bitmap gained aa support, but extra is null if neither taa nor naa is specified. dev2bitmap(plot.pdf,type=pdfwrite) Error in paste(shQuote(gsexe), -dNOPAUSE -dBATCH -q -sDEVICE=, type, : object extra not found dev2bitmap(plot.pdf,type=pdfwrite,taa=4) I guess a useful default for extra is missing: if (!is.na(taa)) extra - paste( -dTextAlphaBits=, taa, sep = ) if (!is.na(gaa)) extra - paste(extra, -dGraphicsAlphaBits=, gaa, sep = ) cmd - paste(shQuote(gsexe), -dNOPAUSE -dBATCH -q -sDEVICE=, type, -r, res, -dAutoRotatePages=/None, -g, ceiling(res * width), x, ceiling(res * height), extra, -sOutputFile=, shQuote(file), , tmp, sep = ) best wishes, ido R.Version() $platform [1] x86_64-redhat-linux-gnu $arch [1] x86_64 $os [1] linux-gnu $system [1] x86_64, linux-gnu $status [1] $major [1] 2 $minor [1] 8.0 $year [1] 2008 $month [1] 10 $day [1] 20 $`svn rev` [1] 46754 $language [1] R $version.string [1] R version 2.8.0 (2008-10-20) __ 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] 2.7.0 breaks read.table
Hi, yes a bold statement, but I get different behaviour from 2.6.2 and 2.7.0 in read.table, and I don't find any documentation in http://cran.r-project.org/src/base/NEWS. A file like (space delimited): foo + . bar - . 2.7.0: tab - read.table(test.txt,as.is=TRUE) tab V1 V2 V3 1 foom 0 0 2 bar 0 0 while until now and on 2.6.2 tab - read.table(test.txt,as.is=TRUE) tab V1 V2 V3 1 foom + . 2 bar - . the really strange thing I just saw when preparing the simplified test case - I normally use tab delimited files (biological gff files by the way where +/- and . have some meaning). on 2.7.0: tab - read.table(test.txt,sep=\t, as.is=TRUE) tab V1 1 foom + . 2 bar - . so specifying the wrong separator brings up the old correct behaviour. best wishes, ido PS: I hope I cancelled the first non-member mailing list post in time - I forgot the system: R.Version() $platform [1] x86_64-redhat-linux-gnu $arch [1] x86_64 $os [1] linux-gnu $system [1] x86_64, linux-gnu $status [1] $major [1] 2 $minor [1] 7.0 $year [1] 2008 $month [1] 04 $day [1] 22 $`svn rev` [1] 45424 $language [1] R $version.string [1] R version 2.7.0 (2008-04-22) __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] paste data
I want to do very similar things with all the dataframes and their structure
is also the same.
Is there a way to write a loop? (so that I don't have to write the same 18
times)
I tried things like that:
for (x in 1:length(plot))
{
plot(paste(auto.,plot[x],sep=)[,1],
paste(auto.,plot[x],sep=)[,2],col=...)
}
you need to get() the data frames.
for (x in 1:length(plot))
{
df - get(plot[x])
plot(df[,1],df[,2],col=...)
}
HTH,
ido
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[R] Rscript on OSX
Hi, I directed somebody to install R (2.6.1) on his OSX computer, following instructions from http://cran.r-project.org/bin/macosx. She can run R from the console. But plot(1:10) doesn't produce any output or open a window (as I am used to from linux). More importantly: Rscript is not in the path (minor problem ln -s is hopefully doable). I tried to put a hardcoded path to Rscript into the shebang line but this fails. And when I try to invoke it directly: -bash: ./Rscript: cannot execute binary file On linux this works. I would like to send her some Rscripts, but how can we make them run on her system? thank you very much, ido imaclab3:/Library/Frameworks/R.framework/Resources/bin ru$ ls -l total 1008 -rwxrwxr-x 1 root admin 1654 Nov 26 17:36 BATCH -rwxrwxr-x 1 root admin 2188 Nov 26 17:36 COMPILE -rwxrwxr-x 1 root admin 34391 Nov 26 17:36 INSTALL -rwxrwxr-x 1 root admin 1593 Nov 26 17:36 LINK -rwxrwxr-x 1 root admin 7210 Nov 26 17:37 R -rwxrwxr-x 1 root admin 7210 Nov 26 17:37 R.orig -rw-rw-r-- 1 root admin 655 Nov 26 17:37 R.rej -rwxrwxr-x 1 root admin 2244 Nov 26 17:36 REMOVE -rwxrwxr-x 1 root admin 928 Nov 26 17:36 Rcmd -rwxrwxr-x 1 root admin 9523 Nov 26 17:36 Rd2dvi -rwxrwxr-x 1 root admin 842 Nov 26 17:36 Rd2txt -rwxrwxr-x 1 root admin 3237 Nov 26 17:36 Rdconv -rwxrwxr-x 1 root admin 1320 Nov 26 17:36 Rdiff -rwxrwxr-x 1 root admin 2854 Nov 26 17:36 Rprof -rwxrwxr-x 1 root admin 18084 Nov 26 17:36 Rscript -rwxrwxr-x 1 root admin 4656 Nov 26 17:36 SHLIB -rwxrwxr-x 1 root admin 16129 Nov 26 17:36 Sd2Rd -rwxrwxr-x 1 root admin 730 Nov 26 17:36 Stangle -rwxrwxr-x 1 root admin 726 Nov 26 17:36 Sweave -rwxrwxr-x 1 root admin 21715 Nov 26 17:36 build -rwxrwxr-x 1 root admin 78570 Nov 26 17:36 check -rwxrwxr-x 1 root admin 6927 Nov 26 17:36 config drwxrwxr-x 4 root admin 136 Nov 26 17:36 exec -rwxrwxr-x 1 root admin 3613 Nov 26 17:36 f77_f2c -rwxrwxr-x 1 root admin 10720 Nov 26 17:36 javareconf -rwxrwxr-x 1 root admin 215101 Nov 26 17:36 libtool -rwxrwxr-x 1 root admin 3495 Nov 26 17:36 mkinstalldirs -rwxrwxr-x 1 root admin 413 Nov 26 17:36 pager __ 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] Efficient way to substract all entries in two vectors from each other
Johannes Graumann wrote: Hi all, I'm to inexperienced to come up with the matrix solution elusively appearing on the horizon for the following problem and would appreciate if you could give me a nudge ... I have two vectors a, and b and need to find the closest match for each value of a in b. How to do that efficiently? I am not sure if I understood your problem correctly, but maybe this is of help. However its not memory efficient. a - c(3,10,50,100) b - c(7,8,300) b[apply(abs(outer(a,b,-)),1,which.min)] [1] 7 8 8 8 In Biobase there is the matchpt function doing this efficiently. best wishes, ido __ 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] get rid of format padding
Dear readers, I need to prevent the output of very large integers in scientific format. So I use format, but now the integers in the resulting tab delimited output file are padded. I tried justify=none or left, width=0 but nothing helps. 1\tA\t1\t1 2\ta\t1\t1 ^^^ thank you very much for your suggestions, ido vals - c(1,1) df - data.frame(c(A,b),format(vals),vals) write.table(df,test.tab,sep=\t,header=FALSE,quote=FALSE) df - data.frame(c(A,b),format(vals,just=none),vals) __ 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] Help with talking to R from Java (on Window)
Does anybody know any alternative ways to be able to call R from Java? JRI http://rosuda.org/JRI/ now contained in rJava http://www.rforge.net/rJava/ and new is this one which I think provides something on top of rJava maybe Rserve: http://www.ebi.ac.uk/microarray-srv/frontendapp/BIOCEP_README.txt best wishes ido __ 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.
