[Rd] percent concordant function
Hi, I would like to compute ''SAS'' output statistic for logistic regression, namely the percent concordant, percent discordant, Sommer's D, Gamma, Tau-a...Actually, I'm very interested in percent concordant. Since the function 'cor' with method kendall compute the kendall's tau, I'm wondering how can I use this function to get back the percent concordant? Does anyone know if there is a package implementing those statistics? I look around on the web, but did not find anything useful. Thanks in advance Christophe [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] problems installing rJava with R-2.8.0
Dear R-developers,
I am having trouble installing rJava on R 2.8.0 / debian etch.
What goes wrong?
I am happy for every advice.
Best,
Christian
> install.packages("rJava")
Warning in install.packages("rJava") :
argument 'lib' is missing: using
'/nfs/compdiag/package/R/lib/bioconductor/release_2.3/x86_64'
--- Please select a CRAN mirror for use in this session ---
Loading Tcl/Tk interface ... done
trying URL 'http://cran.rakanu.com/src/contrib/rJava_0.6-0.tar.gz'
Content type 'application/x-gzip' length 234704 bytes (229 Kb)
opened URL
==
downloaded 229 Kb
* Installing *source* package 'rJava' ...
checking for gcc... gcc -std=gnu99
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -std=gnu99 -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/wait.h that is POSIX.1 compatible... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for string.h... (cached) yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking for unistd.h... (cached) yes
checking for an ANSI C-conforming const... yes
checking whether time.h and sys/time.h may both be included... yes
configure: checking whether gcc -std=gnu99 supports static inline...
yes
checking Java support in R... present:
interpreter : '/usr/lib/jvm/java-1.5.0-sun/jre/bin/java'
archiver: '/usr/lib/jvm/java-1.5.0-sun/bin/jar'
compiler: '/usr/lib/jvm/java-1.5.0-sun/bin/javac'
header prep.: '/usr/lib/jvm/java-1.5.0-sun/bin/javah'
cpp flags : '-I/usr/lib/jvm/java-1.5.0-sun/include
-I/usr/lib/jvm/java-1.5.0-sun/include/linux'
java libs :
'-L/usr/lib/jvm/java-1.5.0-sun-1.5.0.14/jre/lib/amd64/server
-L/usr/lib/jvm/java-1.5.0-sun-1.5.0.14/jre/lib/amd64
-L/usr/lib/jvm/java-1.5.0-sun-1.5.0.14/jre/../lib/amd64
-L/usr/local/lib64 -ljvm'
checking whether JNI programs can be compiled... yes
checking JNI data types... configure: error: One or more JNI types
differ from the corresponding native type. You may need to use
non-standard compiler flags or a different compiler in order to fix this.
ERROR: configuration failed for package 'rJava'
** Removing
'/nfs/compdiag/package/R/lib/bioconductor/release_2.3/x86_64/rJava'
The downloaded packages are in
/nfs/scratch/Rtmp/RtmpUMDzVa/downloaded_packages
Warning message:
In install.packages("rJava") :
installation of package 'rJava' had non-zero exit status
> sessionInfo()
R version 2.8.0 (2008-10-20)
x86_64-unknown-linux-gnu
locale:
C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] tcltk_2.8.0 tools_2.8.0
--
Christian Kohler
Institute of Functional Genomics
Computational Diagnostics
University of Regensburg (BioPark I)
D-93147 Regensburg (Germany)
Tel. +49 941 943 5055
Fax +49 941 943 5020
[EMAIL PROTECTED]
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[Rd] namespace import warning
When I require() some of my packages I am getting the warning
Warning message:
In namespaceImportFrom(self, asNamespace(ns)) :
replacing previous import: show
I think this is coming from a chain of dependencies that result in the
NAMESPACE from something (e.g. methods) being imported twice, but I
can't figure it out, and don't really even see how to debug it. (One of
my packages defines a method for show, but not a generic.)
Any suggestions?
Thanks,
Paul
La version française suit le texte anglais.
This email may contain privileged and/or confidential in...{{dropped:26}}
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Re: [Rd] problems installing rJava with R-2.8.0
On Oct 29, 2008, at 11:51 , Christian Kohler wrote:
Dear R-developers,
I am having trouble installing rJava on R 2.8.0 / debian etch.
What goes wrong?
Please send me the config.log. Also make sure you have configured R
with Java support (sudo R CMD javareconf).
Cheers,
S
install.packages("rJava")
Warning in install.packages("rJava") :
argument 'lib' is missing: using
'/nfs/compdiag/package/R/lib/bioconductor/release_2.3/x86_64'
--- Please select a CRAN mirror for use in this session ---
Loading Tcl/Tk interface ... done
trying URL 'http://cran.rakanu.com/src/contrib/rJava_0.6-0.tar.gz'
Content type 'application/x-gzip' length 234704 bytes (229 Kb)
opened URL
==
downloaded 229 Kb
* Installing *source* package 'rJava' ...
checking for gcc... gcc -std=gnu99
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -std=gnu99 -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/wait.h that is POSIX.1 compatible... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for string.h... (cached) yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking for unistd.h... (cached) yes
checking for an ANSI C-conforming const... yes
checking whether time.h and sys/time.h may both be included... yes
configure: checking whether gcc -std=gnu99 supports static inline...
yes
checking Java support in R... present:
interpreter : '/usr/lib/jvm/java-1.5.0-sun/jre/bin/java'
archiver: '/usr/lib/jvm/java-1.5.0-sun/bin/jar'
compiler: '/usr/lib/jvm/java-1.5.0-sun/bin/javac'
header prep.: '/usr/lib/jvm/java-1.5.0-sun/bin/javah'
cpp flags : '-I/usr/lib/jvm/java-1.5.0-sun/include
-I/usr/lib/jvm/java-1.5.0-sun/include/linux'
java libs :
'-L/usr/lib/jvm/java-1.5.0-sun-1.5.0.14/jre/lib/amd64/server
-L/usr/lib/jvm/java-1.5.0-sun-1.5.0.14/jre/lib/amd64
-L/usr/lib/jvm/java-1.5.0-sun-1.5.0.14/jre/../lib/amd64
-L/usr/local/lib64 -ljvm'
checking whether JNI programs can be compiled... yes
checking JNI data types... configure: error: One or more JNI types
differ from the corresponding native type. You may need to use
non-standard compiler flags or a different compiler in order to fix
this.
ERROR: configuration failed for package 'rJava'
** Removing
'/nfs/compdiag/package/R/lib/bioconductor/release_2.3/x86_64/rJava'
The downloaded packages are in
/nfs/scratch/Rtmp/RtmpUMDzVa/downloaded_packages
Warning message:
In install.packages("rJava") :
installation of package 'rJava' had non-zero exit status
sessionInfo()
R version 2.8.0 (2008-10-20)
x86_64-unknown-linux-gnu
locale:
C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] tcltk_2.8.0 tools_2.8.0
--
Christian Kohler
Institute of Functional Genomics
Computational Diagnostics
University of Regensburg (BioPark I)
D-93147 Regensburg (Germany)
Tel. +49 941 943 5055
Fax +49 941 943 5020
[EMAIL PROTECTED]
__
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[Rd] cochran.test {outliers} (PR#13227)
Full_Name: Katrina Chu Version: R 2.7.2 GUI 1.25 (5217) OS: Mac OS X Version 10.4.11 (Tiger) Submission from: (NULL) (131.202.107.54) I've been using Cochran's Test to check for outlying variance. I noticed that the degrees of freedom that are calculated and output are incorrect. The author has forgotten to take into account that df=n-1 and appears to have just left df=n. n=# samples per treatment and in the case where n is unequal across treatments, I believe that the average samples per treatment can be calculated, then minus 1. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] R books: self-serving question
thought someone here might know: how would I go about nominating my book (Ecological Models and Data in R, Princeton University Press 2008) for inclusion in the R books page ... ? I can supply bibliographic data, blurb etc. ... cheers Ben Bolker signature.asc Description: OpenPGP digital signature __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R books: self-serving question
Ben Bolker wrote: thought someone here might know: how would I go about nominating my book (Ecological Models and Data in R, Princeton University Press 2008) for inclusion in the R books page ... ? I can supply bibliographic data, blurb etc. ... cheers Ben Bolker I think you just fill in a BibTeX entry like this one http://www.r-project.org/doc/bib/R-books_bib.html#R:Dalgaard:2008 and send it off to ...er... well, I suppose anyone on the Core Team has write access, but some may be less liable to get it wrong than others. Most commits are by Kurt Hornik. -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R books: self-serving question
Dear Ben, Peter, et al: On Wed, Oct 29, 2008 at 6:56 PM, Peter Dalgaard <[EMAIL PROTECTED]> wrote: > Ben Bolker wrote: >> >> thought someone here might know: >> >> how would I go about nominating my book >> (Ecological Models and Data in R, Princeton >> University Press 2008) for inclusion >> in the R books page ... ? I can supply >> bibliographic data, blurb etc. ... >> >> cheers >>Ben Bolker > > I think you just fill in a BibTeX entry like this one > > http://www.r-project.org/doc/bib/R-books_bib.html#R:Dalgaard:2008 > > and send it off to ...er... well, I suppose anyone on the Core Team has > write access, but some may be less liable to get it wrong than others. Most > commits are by Kurt Hornik. > > -- > O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B > c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K > (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 > ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 > First: IMHO, there is nothing better than an *official* listing on the R-Project home page. At the same time, I got it in my mind a few months back (while working on a Teaching Task View) that an additional good place for such listings would be the R-Wiki: http://wiki.r-project.org/rwiki/doku.php?id=links:books There, books could be loosely organized by subject, author, ... whatever. Further, people could directly link from their book listing to CRAN package(s) associated with the book. The wiki is set up to do this easily. In this way, the responsibility for updates (new editions), listing in appropriate category, accuracy, etc would shift more to the author, and less to R-Core. (not that Kurt doesn't have enough to do.. :-) The R-Wiki syntax is easy, but not instantly obvious. I quickly threw together some instructions on how to add books to the Wiki: http://www.cc.ysu.edu/~gjkerns/addRbook.pdf I went to the link that Peter suggested above and tweaked the BibTeX to R-Wiki-speak (they are not identical). This is how far I got: http://www.cc.ysu.edu/~gjkerns/bibtexModified.txt At that point, I got busy with writing papers, new semester, new baby on the way; time disappears. In addition, I had some questions about linking to commercial sites from the wiki, how to organize the subjects, and who does(n't) want their book listed - although my guess is that authors have a vested interest in their book being listed, and accurately. Any suggestions? Good idea, bad idea? Full speed ahead or slam on the brakes? Best, Jay *** G. Jay Kerns, Ph.D. Associate Professor Department of Mathematics & Statistics Youngstown State University Youngstown, OH 44555-0002 USA Office: 1035 Cushwa Hall Phone: (330) 941-3310 Office (voice mail) -3302 Department -3170 FAX E-mail: [EMAIL PROTECTED] http://www.cc.ysu.edu/~gjkerns/ __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] row.names(data.frame(matrixWithDimnames)) depends on first rowname being "" or not. (PR#13230)
Full_Name: Bill Dunlap
Version: R version 2.9.0 Under development (unstable) (2008-10-29 r46795)
OS: Linux
Submission from: (NULL) (76.28.245.14)
When data.frame() is given a matrix with rownames, then the type of the output
row names depends on whether the first element of the input row names is "" or
not. The other elements of the input row names don't affect things. E.g.,
> data.frame(matrix(1:6, nrow=3, ncol=2, dimnames=list(c("","Row 2","Row 3"),
paste("Col",1:2
Col.1 Col.2
1 1 4
2 2 5
3 3 6
> data.frame(matrix(1:6, nrow=3, ncol=2, dimnames=list(c("Row 1","","Row 3"),
paste("Col",1:2
Col.1 Col.2
Row 1 1 4
2 5
Row 3 3 6
I noticed this when converting a table of word counts (by speaker) into a
data.frame and the word "" came first in the collating sequence so the words did
not become the row names of the output. If the "" was not first in the table
then the row names of the input were carried into the output.
I haven't had the time yet to make a fix for this, but the distinction between
row.names[1] != or == "" comes from code in data.frame() itself (not
as.data.frame.matrix):
81 if (missing(row.names) && nrows[i] > 0L) {
82 rowsi <- attr(xi, "row.names")
83 if (!(rowsi[[1L]] %in% ""))
84 row.names <- data.row.names(row.names, rowsi,
85 i)
86 }
Why is that check there?
Bill Dunlap
TIBCO Spotfire
wdunlap tibco.com
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[Rd] using yscrollcommand in tkcanvas crashes R (PR#13231)
Full_Name: Sundar Dorai-Raj Version: 2.8.0 OS: Windows Submission from: (NULL) (76.220.41.126) The following code crashes R: library(tcltk) tt <- tktoplevel() tc <- tkcanvas(tt, yscrollcommand = function(...) tkset(ts, ...)) > sessionInfo() R version 2.8.0 (2008-10-20) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] tcltk stats graphics grDevices utils datasets methods [8] base __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] conditionally import a namespace?
Dear R-devel, I have a problem defining the dependencies for a package. My package (latticist, not yet released) "Suggests" RGtk2, but specifically does not require it. If RGtk2 is available, the user can call a function that builds a GUI with RGtk2. However, I do not want to attach the RGtk2 namespace, because it is irrelevant to the user and exports about 7500 symbols. Last time I asked a similar question to this, Professor Ripley noted that the usual method to get around this situation is the use an explicit package prefix to function calls (the `::` operator). But this is not so easy with non-standard functions. Take this chunk of code: widg <- gtkComboBoxEntryNewText() widg$show() widg["width-request"] <- 100 The first call is easy to prefix, as RGtk2::gtkComboBoxEntryNewText() but the others, `$.RGtkObject` and `[<-.RGtkObject` are not. While I *could* rewrite all the code to use explicit functions, I think, the resulting code would be much less clear. Essentially what I want to do is conditionally import the RGtk2 namespace. Any suggestions? Thanks Felix -- Felix Andrews / 安福立 http://www.neurofractal.org/felix/ 3358 543D AAC6 22C2 D336 80D9 360B 72DD 3E4C F5D8 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
