Re: [R] Flow Cytometry Standard, fcs format in R.
there is rflowcyt (older and on its way out) and flowCore, which contains a newer tool set available at www.bioconductor.org Horacio Castellini wrote: Hi all. How do I extract date from fcs format file with R. I.e I'd like make statistical analysis using R-program, but I don't know if there are R-packets for fcs format file, and using examples. Thanks. Pta: In Linux SO exist any program that transform from fcs format to ASCII text file? __ R-help@stat.math.ethz.ch 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. -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch 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] Vignettes menu
Hi, I don't think that advice given was quite correct. The addition of the menu is not a misfeature of Bioconductor packages, but rather an intentional act, I appreciate points of view differ, but there are times when you might choose slightly less pejorative language. As for the question, it seems to me to be entirely an R question, if someone wants to know how to remove a menu item from the windows version, that seems to be a pretty general question about manipulating R, and has nothing to do with any specific package. Robert Prof Brian Ripley wrote: Please ask questions about Bioconductor packages of the maintainer or or the Bioconductor list. This is not a (mis-)feature of R, and does not happen with most packages. On Wed, 9 May 2007, Alejandro wrote: Hello, when i try to load a library with library command (for example library(Biobase)) a new menu appears on R command console (Vignettes) with links to the help documents. Is it possible to eliminate this menu or avoid the appearance of this menu? Thanks in advance, Alejandro -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch 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] Gentleman and Ihaka , 2000 paper question
not sure just what you want, but here are some snippets
newton -
function(lfun, est, tol = 1e-7, niter = 500) {
cscore - lfun$score(est)
if (abs(cscore) tol)
return(est)
for (i in 1:niter) {
new - est - cscore / lfun$d2(est)
cscore - lfun$score(new)
if (abs(cscore) tol)
return(new)
est - new
}
stop(exceeded allowed number of iterations)
}
with the likelihood function
Rmklike -
function(data) {
n - length(data)
sumx - sum(data)
lfun - function(mu) n * log(mu) - mu * sumx
score - function(mu) n / mu - sumx
d2 - function(mu) -n / mu^2
list(lfun = lfun, score = score, d2 = d2)
}
Leeds, Mark (IED) wrote:
In their paper, Lexical Scope and Statistical Computing, the authors (
Gentleman and Ihaka ) go to great length explaining why R's use of
lexical scoping creates advantages when doing statistical computations.
If anyone has or is familiar with this paper, could they provide the
main program code for how the newton function would be called in their
example on page 500 of the paper. The authors are extremely clear in
their writing and the paper is quite an eye opener for me but it seems
like lfun somehow needs to be initialized so that it grabs the
environment of Rmklike.
Rmlike is called to create the likelihood function, and since that
function is defined in the body of Rmlike, it has the evaluation
environment by default. And any return value will have the correct
environment.
I'm not sure how one would go about doing this so I am wondering what
the main program that calls newton would be
if there was one. Thanks.
So,
data=rexp(10, rate=.3)
lf = Rmklike(data)
newton(lf, .1)
seems to do the trick (and surprisingly still works, as written some
unbelievably long time ago)
Robert
Mark
This is not an offer (or solicitation of an offer) to buy/se...{{dropped}}
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
206-667-7700
[EMAIL PROTECTED]
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Problems with 'delay'/'delayedAssign' when installing data package
Or you could check and see that this is several versions of Bioconductor in the past and rather than using the well documented and advertised method for obtaining data that are consistent with your version of R you have chosen to completely circumvent that procedure and loaded a package for some obsolete version of R. So, if you have newer R there are newer versions of this data from Bioconductor, http://bioconductor.org/packages/1.9/data/annotation/html/hgu95av2.html shows that for a current R, we are at version 1.14.0 for this package. Duncan Murdoch wrote: On 2/15/2007 3:57 AM, Wolfram Fischer wrote: I downloaded: http://www.bioconductor.org/data/metaData/hgu95av2_1.7.0.tar.gz described as: Package: hgu95av2 Title: A data package containing annotation data for hgu95av2 Version: 1.7.0 Created: Wed Jan 12 16:57:23 2005 Author: Lin,Chenwei Description: Annotation data file for hgu95av2 assembled using data from public data repositories Maintainer: Lin,Chenwei [EMAIL PROTECTED] LazyLoad: yes Depends: R(= 2.0.0) License: LGPL Packaged: Thu Mar 3 15:43:00 2005; biocbuild It is an example database of the geneplotter library. Trying to install, I got: $ R CMD INSTALL hgu95av2_1.7.0.tar.gz * Installing *source* package 'hgu95av2' ... ** R ** data ** preparing package for lazy loading Error: 'delay' is defunct. Use 'delayedAssign' instead. See help(Defunct) Execution halted ERROR: lazy loading failed for package 'hgu95av2' ** Removing '/usr/local/lib64/R-2.4.1/library/hgu95av2' How to by-pass this problem? There are two possibilities: update the package to follow current R usage (which is something the maintainer should do, but if the maintainer is not active you may have to do it yourself), or run in an old version of R (pre-2.2.0) from before delay() was made defunct. You may also use this as a sign that the package is not being actively maintained, since this change happened in R 2.2.0 in 2005. I don't know if that's reasonable for a collection of annotation data or not. Duncan Murdoch __ R-help@stat.math.ethz.ch 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. -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch 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] Correlation to a Single Gene
In the package genefilter, from www.bioconductor.org there is a function to do this (genefinder, if I recall correctly) best wishes Robert Charles C. Berry wrote: On Wed, 17 Jan 2007, Damion Colin Nero wrote: I am trying to find a way to perform pairwise correlations against one gene in a matrix rather than computing every pairwise correlation. I am interested in how 1 transcription factor correlates to every gene in a matrix of 55 experiments (columns) by 23,000 genes (rows), performing the correlation by rows. Trying to perform every pairwise correlation in this fashion is too memory intensive for any computer I am currently using so I am wondering if anyone had a method for doing pairwise correlations to a single gene or if there is a preexisting package in R that might address this. You measure the transcription factor once in each of 55 experiments and you measure gene *expression* (or some other quantity) on each of 23000 genes? cor.vec - cor (transfac, t( gene.mat ) ) will do. Questions like this might best be posted to the bioconductor mail list. Damion Nero Plant Molecular Biology Lab Department of Biology New York University __ R-help@stat.math.ethz.ch 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. Charles C. Berry(858) 534-2098 Dept of Family/Preventive Medicine E mailto:[EMAIL PROTECTED] UC San Diego http://biostat.ucsd.edu/~cberry/ La Jolla, San Diego 92093-0901 __ R-help@stat.math.ethz.ch 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. -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch 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] problem installing RdbiPgSQL for 2.4
Oleg Bartunov wrote: I just upgraded R to version 2.4.0 and now I can't install packages RdbiPgSQL. I used the same procedure I did for previous versions of R ! Actually, last time I installed RdbiPgSQL day before upgrading but now I got: downloaded 27Kb * Installing *source* package 'RdbiPgSQL' ... creating cache ./config.cache checking for PQconnectdb in -lpq... no I could not find your PostgreSQL client libraries! Well it looks like you might have done more than that since the error is saying that the package cannot find your postgres client libraries and note in the text right below this are some suggestions on how to specify non-standard locations. I have tried on two systems with postgres in its standard location and observed no such problem. Use --with-pgsql-libraries=PATH; if running R's INSTALL, use --configure-args='--with-pgsql-libraries=PATH'; or set PG_LIB_DIR in your environment to the library path, and rerun the configure/install. ERROR: configuration failed for package 'RdbiPgSQL' ** Removing '/usr/local/lib/R/library/RdbiPgSQL' The downloaded packages are in /tmp/RtmpA3Mdb4/downloaded_packages Warning message: installation of package 'RdbiPgSQL' had non-zero exit status in: install.packages(RdbiPgSQL, repos = rS, configure.args = c(PGSQL = --with-pgsql-libraries=/usr/local/pgsql/lib --with-pgsql-includes=/usr/local/pgsql/include)) Looks like install.packages doesn't pass configure.args to the package. Regards, Oleg _ Oleg Bartunov, Research Scientist, Head of AstroNet (www.astronet.ru), Sternberg Astronomical Institute, Moscow University, Russia Internet: oleg@sai.msu.su, http://www.sai.msu.su/~megera/ phone: +007(495)939-16-83, +007(495)939-23-83 __ R-help@stat.math.ethz.ch 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. -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch 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] Reserve and biobase
You should ask questions about Bioconductor software on the Bioconductor
list, you might also read the posting guide and provide version numbers
for all packages you are using (the output of sessionInfo is useful).
Biobase does not do any plotting, so where ever the action is coming
from it is unlikely to be Biobase that is doing it. I don't use Rserve
so I cannot comment on how that might interact with other software. I
have no idea what you are trying to do, but somehow you seem to be doing
a lot more than just loading Biobase - so why not try just doing that
and leave out all the other code opening devices (and why open two
postscript devices and then close them?).
Robert
saeedeh maleki wrote:
Hi
I am using Rserve for R2.3.1.
every time after I load Biobase library, a new Graphics window frame pops
up. Could any onw know how can avoid it.
Best
Saeede
class testReserve {
public static void main(String[] args) {
RServeConnection rsCon = null;
Rconnection c = null;
Process proc = null;
try {
Runtime rt = Runtime.getRuntime();
proc = rt.exec(generalMetaData.rserveDir);
try {
c = new Rconnection();
c.eval(library(grDevices));
//c.eval(graphics.off());
c.eval(postscript());
//load library
c.eval(library(tools));
System.out.println( load library tools);
c.eval( postscript('foo2.ps'));
c.eval( library(Biobase));
c.eval(graphics.off());
System.out.println( load library Biobase);
}
catch (RSrvException ex1) {
System.out.println(ex1.getMessage());
}
}
catch (Exception e) {
System.out.print(cannot run rserve);
}
//end of testing
}
}
-
[[alternative HTML version deleted]]
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R-help@stat.math.ethz.ch mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
206-667-7700
[EMAIL PROTECTED]
__
R-help@stat.math.ethz.ch 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] Bug/problem reporting: Possible to modify posting guide FAQ?
Hi, I guess the question often comes down to whether it is a bug report, or a question. If you know it is a bug, and have a complete and correct example where the obviously incorrect behavior occurs and you are positive that the problem is the package then sending it to the maintainer is appropriate. When I get these I try to deal with them. Real bug reports that go to the mailing list may be missed so in my opinion it would be best to cc the maintainer and we will amend the FAQ in that direction. If instead you are asking a question, of the form, is this a bug, or why is this happening, then for BioC at least, it is better to post directly to the list, as there are many folks who can help and you are more likely to get an answer. When I get one of these emails I always refer the person to the mailing lists. I see little problem with being redirected by a maintainer to the mailing list if they feel that the question is better asked there. Bioconductor is different from R, clearly our mailing list has to be more about the constituent packages, since we will direct questions about R to the appropriate R mailing lists. R mailing lists tend to be about R, so asking about a specific package there (among the 1000 or so) often does not get you very far, but sometimes it does. best wishes Robert Steven McKinney wrote: If users post a bug or problem issue to an R-based news group (R-devel, R-help, BioC - though BioC is far more forgiving) they get yelled at for not reading the posting guide and FAQ. Please *_do_* read the FAQ, the posting guide, ... the yellers do say. So I read the BioC FAQ and it says... http://www.bioconductor.org/docs/faq/ Bug reports on packages should perhaps be sent to the package maintainer rather than to r-bugs. So I send email to a maintainer, who I believe rightly points out best to send this kind of questions to the bioc mailing list, rather than to myself privately, because other people might (a) also have answers or (b) benefit from the questions answers. Could the FAQ possibly be revised to some sensible combination that generates less finger pointing, such as Bug reports on packages should be sent to the Bioconductor mailing list, and sent or copied to the package maintainer, rather than to r-bugs. or Bug reports on packages should be sent to the package maintainer, and copied to the Bioconductor mailing list, rather than to r-bugs. Could the posting guides to R-help and R-devel do something similar? Sign me Tired of all the finger pointing http://www.r-project.org/posting-guide.html If the question relates to a contributed package , e.g., one downloaded from CRAN, try contacting the package maintainer first. You can also use find(functionname) and packageDescription(packagename) to find this information. Only send such questions to R-help or R-devel if you get no reply or need further assistance. This applies to both requests for help and to bug reports. How about If the question relates to a contributed package , e.g., one downloaded from CRAN, email the list and be sure to additionally send to or copy to the package maintainer as well. You can use find(functionname) and packageDescription(packagename) to find this information. Only send such questions to one of R-help or R-devel. This applies to both requests for help and to bug reports. __ R-help@stat.math.ethz.ch 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. -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch 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] Clique technique-Package
the graph, RBGL and Rgraphviz packages at www.bioconductor.org have a fairly substantial implementation of many different graph representations, algorithms (including clique finding) and layout algorithms j.joshua thomas wrote: Dear R Users, I am looking clique a graph technique, to identify the values from the dataset. I tried with help.search(graph) it show's the graphics related stuff Is there any package that i can use to find Clique in a dataset? Thanks in Advance JJ -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch 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] deal with R.package panel
Hi, There should be a 20 page pdf document in the doc directory, distributed with the package. That answers most of these questions. Also, please read the posting guide so that you give enough information to actually have some chance of answering your questions, best wishes Robert Pavel Khomski wrote: hello! my question conserns with use of panel package (written by R.C.Gentlman) (unfortunately the manual and help sites are very short) 1. is it possible to do analysis just without a(ny) covariate? i suggest do it by introducing a covariate with level=0 in all obervations, this because of Q(z)=Q_o exp(beta*z), but it seemingly doesn't work meaning what? 2. in the option gamma in the call of panel function: do you mean an initial value for parameter vector gamma? say if i have 3 theta-parameters, so i have to initialize gamma=c(xxx,xxx,xxx), correct? yes 3. are the (first ) observed times =0 allowed (in $time vectors) or schould in such a case begin with =1, if there are any? I suspect 0, but since you have said nothing about what you are actually trying to do, it is entirely a guess on my part best wishes Robert thanks for your response __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] deal with R.package panel
I just realized that the pdf on CRAN is corrupt, a new package has been uploaded and will percolate through over the next few days, one supposes. Robert Gentleman wrote: Hi, There should be a 20 page pdf document in the doc directory, distributed with the package. That answers most of these questions. Also, please read the posting guide so that you give enough information to actually have some chance of answering your questions, best wishes Robert Pavel Khomski wrote: hello! my question conserns with use of panel package (written by R.C.Gentlman) (unfortunately the manual and help sites are very short) 1. is it possible to do analysis just without a(ny) covariate? i suggest do it by introducing a covariate with level=0 in all obervations, this because of Q(z)=Q_o exp(beta*z), but it seemingly doesn't work meaning what? 2. in the option gamma in the call of panel function: do you mean an initial value for parameter vector gamma? say if i have 3 theta-parameters, so i have to initialize gamma=c(xxx,xxx,xxx), correct? yes 3. are the (first ) observed times =0 allowed (in $time vectors) or schould in such a case begin with =1, if there are any? I suspect 0, but since you have said nothing about what you are actually trying to do, it is entirely a guess on my part best wishes Robert thanks for your response __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Weighted networks and multigraphs
Hi, Some implementations are available in the packages graph and RBGL from Bioconductor (www.bioconductor.org). I think you will find that they do what you would like, but let the maintainers know if not. best wishes Robert Wilson, Andrew wrote: I would like to apply network measures (such as betweenness centrality, upper boundedness, etc.) to a weighted graph with non-integer weights, defined by a euclidean distance matrix. The package sna provides the measures that I want to use, but seems only to operate on binary graphs. I have read work by Mark Newman (http://aps.arxiv.org/abs/cond-mat/0407503/), who suggests that a weighted graph can be transformed into an unweighted multigraph, to which such measures can be applied. It seems that the package giRaph contains a function to handle multigraphs, but there is no example in the manual to show how it is used. I am also not sure whether this multigraph structure can be used as input into the relevant functions in the sna package. Can anyone advise? Many thanks, Andrew Wilson __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] is library loaded
Hi, Almost surely this is a bad name. With the advent of name spaces it is important to distinguish between loading and attaching. This function tests for attached packages. To test for loaded packages we already have loadedNamespaces. Best wishes, Robert John Fox wrote: Dear Omar, The following function tests whether a package is in the search path (with the package name given in quotes): packageLoaded - function(name) 0 != length(grep(paste(^package:, name, $, sep=), search())) I hope this helps, John John Fox Department of Sociology McMaster University Hamilton, Ontario Canada L8S 4M4 905-525-9140x23604 http://socserv.mcmaster.ca/jfox -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Omar Lakkis Sent: Tuesday, September 13, 2005 2:09 PM To: r-help@stat.math.ethz.ch Subject: [R] is library loaded Is there a way to test if a library has been loaded? is.loaded does not give me what I want, I am looking to say: if loaded(Rdbi) dbSendQuery(conn, q) if loaded(RODBC) sqlQuery(conn, q) I need this to support both unix and windows platforms as I could not find a windows distribution for RdbiPgSQL. I am using R 2.1.0 and postgresql. I will be connecting to the database using Rdbi and RdbiPgSQL and have other developers using windows connect with RODBC, unless someone can suggest a better solution. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Drawing a graph with vertices and edges using tcl/tk
Rgraphviz is a fairly complete interface that works on all systems now, including Windows. http://www.bioconductor.org/packages/bioc/devel/src/contrib/html/Rgraphviz.html but not the absolute latest Graphviz (2.4) as it has gone through pretty extensive code rearrangements. We should have a version for Graphviz 2.4 in the next few weeks. Robert Gabor Grothendieck wrote: Another approach is the Bell Labs graphviz system. See http://www.graphviz.com For an example of using it from R, see the dot.proto function in the 'proto' package. dot.proto generates dot language output to draw a graphviz graph of the objects in any R program written using 'proto'. library(proto) example(dot.proto) # see ?dot.proto for instructions on displaying graph The above approach should work on any OS supported by R (since graphviz works on all of them); however, on UNIX one could also use the Rgraphviz package that specifically interfaces R with graphviz: http://www.bioconductor.org/repository/release1.4/package/html/Rgraphviz.html On 7/31/05, Søren Højsgaard [EMAIL PROTECTED] wrote: Dear all; I would like to draw a graph with vertices and edges, and I guess tcl/tk would be appropriate. I don't know tcl/tk but have googled for a 10-page (or so) introduction to 'getting started with tcl/tk in R' but without any luck. - Does anyone know of the existence of such a document or any other web-based material on the subject? - Does anyone have an (informative) piece of code which does something similar to what I want? Thanks in advance Søren __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Re: S4 method inheritance
Duncan Murdoch wrote: Ross Boylan wrote: On Mon, 2005-05-23 at 14:41 -0700, Ross Boylan wrote: Finally, I'm a bit concerned that one article mentioned that S4 inheritance, in practice, is used mostly for data, not methods (Thomas Lumley, R News 4(1), June 2004: p. 36). Am I going down a road I shouldn't travel? Hmm, maybe I just found out. If B is an S4 subclass of A (aka extends A), how does B's method foo invoke A's foo? Your question doesn't make sense in S4. In S4, classes don't have methods, generics have methods. There's no such thing as B's method or A's method. You might get what you want with foo(as(bObject, A)) if bObject is an instance of class B. The question assumes that A's foo was defined as an in place function, so there's no (obvious) named object for it, i.e, setMethod(A, signature(blah=numeric), function(x) something) In general it may be best to think of a generic function as a dispatching mechanism. For S4 methods are associated with a specific generic function. A generic knows about all methods that are associated with it, and about no others. Thus in S4, the little tiff over who owns label goes away - they both do - different packages can define generic functions for label, or anything else they care to, and users can write methods for specific generic functions and associate them with a generic. [Note that in the S3 system there is no real mechanism for saying that foo.bar is a method for one generic named foo, and not for another - but the language does allow for multiple generics named foo - one of the very many reasons that S3 does not really do what you want it to, but many seem convinced otherwise]. The class hierarchy of the actual supplied arguments, is used to determine the dispatch order (a linearization of the available methods) once the generic is invoked. The most specific method is used first. It may intiate a call to callNextMethod (S4) or NextMethod (S3) to transfer control to the next most specific method - the manual pages provide more specific details. As Duncan said - classes do not own methods in this paradigm. Generic functions do. HTH Robert I don't know what you mean by in place function, but I hope my answer helps anyway. Duncan Murdoch __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Re: S4 method inheritance
Ross Boylan wrote: On Tue, May 24, 2005 at 06:27:56AM -0700, Robert Gentleman wrote: Duncan Murdoch wrote: Ross Boylan wrote: On Mon, 2005-05-23 at 14:41 -0700, Ross Boylan wrote: Finally, I'm a bit concerned that one article mentioned that S4 inheritance, in practice, is used mostly for data, not methods (Thomas Lumley, R News 4(1), June 2004: p. 36). Am I going down a road I shouldn't travel? Hmm, maybe I just found out. If B is an S4 subclass of A (aka extends A), how does B's method foo invoke A's foo? Your question doesn't make sense in S4. In S4, classes don't have methods, generics have methods. There's no such thing as B's method or A's method. You might get what you want with foo(as(bObject, A)) if bObject is an instance of class B. The question assumes that A's foo was defined as an in place function, so there's no (obvious) named object for it, i.e, setMethod(A, signature(blah=numeric), function(x) something) In general it may be best to think of a generic function as a dispatching mechanism. For S4 methods are associated with a specific generic function. specific generic is a reference to the ability to define generics within the context of a particular package? Well, more that you can identify one (either explicitly by its package [ie. fully-qualified name], or implicitly by the fact that it is first on the search path - the former being prefered). But the notion is that there is one and you have asked that your method be made available to that one generic function for dispatch. This is in contrast to S3 - where no such functionality exists - that I know of; under S3 any method is a method for all generic functions of the correct name and the programmer has no (easy) control. Under S4 methods are not really ordinary functions, should not be called directly and are invoked only via calls to the generic (you can of course break all of those rules). A generic knows about all methods that are associated with it, and about no others. Presumably setMethod does the association. Is the where argument intended to identify which generic method to pick? The fact that there is not a package argument to setMethod, as there is to setGeneric, is a little confusing to me. I believe that is the documented behavior. Yes the where argument should allow you complete specificity. I will leave it to the auther to clarify differences between the where and package arguments in the call to setGeneric (or you, if you care to explore the code). Thus in S4, the little tiff over who owns label goes away - they both do - different packages can define generic They is two different packages? Or is this a reference to my original confusion about class vs generic ownership of a method? It is the two packages. The S langauge allows for the same symbol to be bound to different values in different namespaces (in R that is becoming explicit, in SPlus it is less so, but still generally true). I can think of no good reason to treat generic functions, or any other first class object, differently. HTH, Robert functions for label, or anything else they care to, and users can write methods for specific generic functions and associate them with a generic. ... HTH Robert __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] string syntactic sugar in R? - long post
Hi,
In Bioconductor, we have something called copySubstitute, which does
what you want, I believe,
x=select @var1@ from @tab1@
copySubstitute(textConnection(x), symbolValues= list(var1=Race,
tab1=ReallyBigTable), dest=stdout())
yields
select Race from ReallyBigTable
you can read in from any connection and write out to any connection,
change the delimiter, etc.
We use it to autogenerate manual pages and other documentation for
packages that have lots of similar structure, as well as for things
like what you want to do.
Best wishes,
Robert
On May 7, 2005, at 1:36 AM, charles loboz wrote:
Currently in R, constructing a string containing
values of variables is done using 'paste' and can be
an error-prone and traumatic experience. For example,
when constructing a db query we have to write,
paste(SELECT value FROM table where
date =',cdate,')
we are getting null result from it, because without
(forgotten...) sep= we get
SELECT value FROM table where date='
2005-05-05 '
instead of
SELECT value FROM table where date='2005-05-05'
Adding sep= as a habit results in other errors, like
column names joined with keywords - because of
forgotten spaces. Not to mention mixing up or
unbalancing quote marks etc. The approach used by
paste is similar to that of many other languages (like
early Java, VB etc) and is inherently error-prone
because of poor visualization. There is a way to
improve it.
In the Java world gstrings were introduced
specifically for this purpose. A gstring is a string
with variable names embedded and replaced by values
(converted to strings, lazy eval) before use. An
example in R-syntax would be:
alpha - 8; beta=xyz
gstr - the result is ${alpha} with the comment
${beta}
cat(gstr)
the result is 8 with the comment xyz
This syntactic sugar reduces significantly the number
of mistakes made with normal string concatenations.
Gstrings are used in ant and groovy - (for details see
http://groovy.codehaus.org/Strings, jump to GStrings).
They are particularly useful for creating readable and
error-free SQL statements, but obviously the simplify
'normal' string+value handling in all situations. [ps:
gstrings are not nestable]
I was wondering how difficult it would be to add such
syntactic sugar to R and would that create some
language problems? May be it is possible that it could
be done as some gpaste function, parsing the argument
for ${var}, extracting variables from the environment,
evaluating them and producing the final string?
I admit my bias - using ant for years and groovy for
months and having to do a lot of SQL queries does not
put me in the mainstream of R users - so it may be
that this idea is not usable to a wider group of
users.
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+---
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| Robert Gentleman phone: (206) 667-7700
|
| Head, Program in Computational Biology fax: (206) 667-1319 |
| Division of Public Health Sciences office: M2-B865
|
| Fred Hutchinson Cancer Research Center
|
| email: [EMAIL PROTECTED]
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Re: [R] Windows List of Folders?
Hi, We have some documentation of the file handling capabilities, among other things, at http://www.bioconductor.org/develPage/develPage.html comments, improvements etc welcome. Best wishes, Robert On Apr 29, 2005, at 4:01 PM, Henrik Bengtsson wrote: Example: path - system.file(package=base) pathnames - list.files(path, full.names=TRUE) isDir - file.info(pathnames)$isdir dirs - pathnames[isDir] files - pathnames[!isDir] If you don't get the 'isDir' line, think of it as infos - file.info(pathnames) isDir - infos$isdir /Henrik [EMAIL PROTECTED] wrote: For windows, how can I list only the folders in some folder? I was thinking that dir() and file.info() with isdir==TRUE being something that might work. These folders or directories are numerically named with no dot extension names or other characters. Typically, these are 3132, 3334, ... Here is what I tried. The last line is where I need more work. pData=C:/Myfiles/R/Data/ setwd (pData) x - dir(pData, all.files=F) y - file.info(x, x$isdir==T) TIA Kenneth Ray Hobson, P.E. Oklahoma DOT - QA IAS Manager 200 N.E. 21st Street Oklahoma City, OK 73105-3204 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html +--- + | Robert Gentleman phone: (206) 667-7700 | | Head, Program in Computational Biology fax: (206) 667-1319 | | Division of Public Health Sciences office: M2-B865 | | Fred Hutchinson Cancer Research Center | | email: [EMAIL PROTECTED] | +--- + __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] interval censoring case 1 or current status data
Yes, the Icens package handles all forms of censored data (1-dim) On Apr 27, 2005, at 11:59 AM, Chao Zhu wrote: Dear all, Is there a function in R dealing with the NPMLE for current status data or interval censored case 1 data? Thanks, Jimmy [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html +--- + | Robert Gentleman phone: (206) 667-7700 | | Head, Program in Computational Biology fax: (206) 667-1319 | | Division of Public Health Sciences office: M2-B865 | | Fred Hutchinson Cancer Research Center | | email: [EMAIL PROTECTED] | +--- + __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Developing R classes
And some notes on the Bioconductor developer page. On Dec 28, 2004, at 9:38 AM, Thomas Lumley wrote: On Tue, 28 Dec 2004, Gilvan Justino wrote: Hi, I´m trying to write some R classes but I din´t find documentation enought to develop them. I read there is 2 ways to write classes, using S3 ou S4 models. And it seems that S4 is the best model, so I thing I should use this one. There's a small example in the R Newsletter, Volume 1, 2004. -thomas__ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html +--- + | Robert Gentleman phone: (206) 667-7700 | | Head, Program in Computational Biology fax: (206) 667-1319 | | Division of Public Health Sciences office: M2-B865 | | Fred Hutchinson Cancer Research Center | | email: [EMAIL PROTECTED] | +--- + __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] How about a mascot for R?
On Dec 6, 2004, at 3:15 PM, Richard A. O'Keefe wrote: Thomas Yee [EMAIL PROTECTED] wrote: ps. Ross has Maori origins, so a native NZ animal is a better idea than usual. The native animals of New Zealand include no mammals except for - marine mammals in the coastal waters, such as the Hector's dolphin - a few species of bat which got blown over from Australia. Otherwise, there are birds, reptiles, insects, and a few oddballs. The most notable oddballs would be Tuataras, famous for their third eye. We have some onychophorans, of which it has been said that Contemporary Onychophorans are able to predate organisms several times larger than themselves (take _that_, SAS!) Wetas are quite interesting; they are basically grasshoppers some of which played the ecological role of (and are about the same size as) mice. Hi, We had a brief discussion and narrowed it to two, coincidentally among those named by Richard. The tuatara (there is some charm in associating a software product with what is essentially a slow moving dinosaur) and the weta (for those unaware, one might also describe it as a grasshopper designed by the Pentagon - these have some serious armor plating and a ferocious grip). Of course this is one of many views, kiwis, kokakos etc have lots of charm as well - and I think New Zealand might lay some claim to the giant squid. No need to stick with non-extinct things either - I suspect the dodo is up for grabs. And on the NZ front the Moa or the Haast eagle. Ross and Robert I suspect that only birds have the cuddly appeal required of a mascot. Perhaps it's worth pointing out that Kiwis are a kind of Ratite. __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html +--- + | Robert Gentleman phone: (206) 667-7700| | Head, Program in Computational Biology fax: | | Division of Public Health Sciences office: M2-B865 | | Fred Hutchinson Cancer Research Center email: [EMAIL PROTECTED] | +--- + __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R Graphs
From Bioconductor: graph, Rgraphviz, and RBGL.. On Wed, Oct 20, 2004 at 06:17:22PM +0200, Vito Ricci wrote: Dear R-users, I'm finding for a R-package concerning graphs. Is there some kind of that package? I've a set of correlation coeffients between several variable and I wish to built a graph to link variables correlated. Many thanks. Best, Vito = Diventare costruttori di soluzioni The business of the statistician is to catalyze the scientific learning process. George E. P. Box Visitate il portale http://www.modugno.it/ e in particolare la sezione su Palese http://www.modugno.it/archivio/cat_palese.shtml __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- +---+ | Robert Gentleman phone : (617) 632-5250 | | Associate Professor fax: (617) 632-2444 | | Department of Biostatistics office: M1B20| | Harvard School of Public Health email: [EMAIL PROTECTED]| +---+ __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Error Using pm.getabst()
You will almost surely do better to ask about Bioconductor packages on the Bioconductor mailing list. Next, it is helpful to know what versions of things you are using. As for your problem, did you look to see what kind of object absts is? There seems to be no default method for xmlRoot, and it is likely that the call to create the absts object failed (prior to this). You might want to try stepping through the commands, one at a time and checking each step. Often, the problem arises because you have not properly set up your connection to the internet and so none of the querying software will work. Robert On Thu, Aug 12, 2004 at 08:20:10PM +, [EMAIL PROTECTED] wrote: R Users: After installing Bioconductor, RSXML and all the relevant Win32 DLLs (libxml2, zlib, iconv), I receive the following error message when using pm.getabst() Error in xmlRoot(absts) : no applicable method for xmlRoot I receive this when using the example from help(pm.getabst). Downloading the target XML file, parsing it with xmlTreeParse and applying xmlRoot returns no error. Your thoughts/suggestions are appreciated. Mark Larsen __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- +---+ | Robert Gentleman phone : (617) 632-5250 | | Associate Professor fax: (617) 632-2444 | | Department of Biostatistics office: M1B20| | Harvard School of Public Health email: [EMAIL PROTECTED]| +---+ __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Using permax with Data Frame Containing Missing Values
There is currently no handling of NAs in permax. Your only simple option is to drop those rows with NA's in them, or to perform some sort of imputation. I will mention it to the package's author, Robert On Wed, Jul 07, 2004 at 12:47:05PM +0100, Brian Lane wrote: I'm new to this site so I hope this isn't too naive a problem. I'm trying to use the permax function with a data frame containing gene expression measurements taken from 79 microarray experiments with 3000 genes per array. The data contains missing values and every time I use permax with the data frame I get the error: NA/NaN/Inf in foreign function call (arg 1) Could anyone suggest how I might get round this problem? Regards, Brian Lane Dept of Haematology University of Liverpool __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- +---+ | Robert Gentleman phone : (617) 632-5250 | | Associate Professor fax: (617) 632-2444 | | Department of Biostatistics office: M1B20| | Harvard School of Public Health email: [EMAIL PROTECTED]| +---+ __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Creating and editing networks
Or graph, RBGL and Rgraphviz from www.bioconductor.org On Sun, May 09, 2004 at 02:35:02PM +0200, Uwe Ligges wrote: Gabor Grothendieck wrote: I want to draw and edit networks. Currently I will do something like this -- my actual networks are larger and more complex: 1. Plot network # use polygon with nodes as example network N - 20 t. - 2*pi*seq(N+1)/N plot(cos(t.), sin(t.), type=b, pch=19, cex=5, col=blue, axes=F, ann=F) 2. copy and paste the graphic as a metafile into Word. 3. edit the network there. The editing typically just involves moving nodes and the attached edges. Of course, Word does not know the edges are attached to the nodes so I have to move the nodes and then move the attached edges, as well. The networks are too complex to create the diagrams by hand which is why I want to create them in R and then edit them by hand. The above strategy is marginally acceptable but I was wondering if anyone had a better strategy which retains the simplicity of the present approach but gives me the capability to have the edges move along with attached nodes when editing them. (Note that the strategy must consist of generating the network under program control, preferably in R, and then editing it afterwards. I am not looking to create the entire network by hand since the networks are too complex for that. I had tried specifying the networks in dot from Bell Labs but 1. its still more work than generating the network in R 2. the automatic layout it chooses is so far from what I need that its a lot of work to fix it up by hand in dotty and 3. I could never get them to look just how I like. I have also tried Excel and Powerpoint, both of which support connectors, which are edges that move along with attached nodes, but to use them I have to create the entire network by hand and the networks have grown too complex to do that.) __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Have you tried the CRAN package dynamicGraph by Jens Henrik Badsberg? Uwe Ligges __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- +---+ | Robert Gentleman phone : (617) 632-5250 | | Associate Professor fax: (617) 632-2444 | | Department of Biostatistics office: M1B20| | Harvard School of Public Health email: [EMAIL PROTECTED]| +---+ __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Different missing links on Windows in 'check' vs. 'install'
On Tue, Mar 09, 2004 at 12:38:33PM +, Prof Brian Ripley wrote: On Tue, 9 Mar 2004, Duncan Murdoch wrote: On Tue, 9 Mar 2004 08:03:44 + (GMT), you wrote: No, both will find links in the same library as installing into (plus those which are fixed up on installation, e.g. to the base package). Several of us have looked for years for a fix, and this is the best scheme we have come up with. You can't put in absolute paths in the HTML as e.g. a private library may be used with more than one version of R (or R may be updated later). Short of adding symbolic links to Windows (and getting browsers to follow them), how do you propose `we should fix' it? Here's a proposal: All of check and build and install should default to the same library location. Check and build aren't meant to be permanent installs, so if the package already exists there, it'll have to be temporarily moved out of the way. You may not own the main library and so not have permission to install/check/build there. If you do, you can use check on an installed copy of the package. As for build, this is one of the reasons why Rcmd INSTALL --build was needed, as that installs in the standard place and then wraps up the installed copy. Yes, but for automated checking of many packages (60+ in Bioconductor and over 200 in CRAN) it would be nice to be able to separate out the real issues from the supposed ones. Perhaps we need a mechanism to generate some sort of database of these (which is updated/modified by R INSTALL, for example). Then R CMD check could generate an index file of resolved/supplied links for the library path that R is using, generally $R_HOME/library, and then we simply compare against that. It seems that we are currently making the wrong comparison. What might make more sense (it seems to me) is to check and see if the links are resolved only against base R + any packages in the depends/suggests field of the package being checked. Since these are the ones that we will try to ensure are available at run time. References outside of that set could be warnings. Here we are not trying to physically resolve the links, just make sure that they are resolvable given the version of R and the package dependencies. Robert -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- +---+ | Robert Gentleman phone : (617) 632-5250 | | Associate Professor fax: (617) 632-2444 | | Department of Biostatistics office: M1B20| | Harvard School of Public Health email: [EMAIL PROTECTED]| +---+ __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Object validation and formal classes
On Thu, Jan 29, 2004 at 09:30:19PM +0100, Torsten Steuernagel wrote: I'm using R 1.8.1 (Win32, Linux) and have some difficulties using validation functions for S4 classes. The problem is if I specify a validation function with setValidity(myclass, validate.myclass) object validation is only performed when I create an instance using new(myclass), or when I explicitly call validObject(x) where x is of class myclass, of course. According to the reference docs, I would expect that validation always takes place implicitly when I manipulate an object of myclass. This especially includes implicit validation if I change slots directly, i.e. [EMAIL PROTECTED] - 1:50 should call my validation function. Unfortunately, it isn't called and instead of raising an error and leaving the object unchanged in case validation fails, the object is always changed no matter what I assign to the slot. There are some efficiency issues that prevent constant checking (at least at the present time). There are also some other issues that need to be adequately addressed too. For example, suppose I had an object with two slots a - a character string b - the number of characters and I set my validity checker to make sure that the length of the string is the number in b. Now that basically means that I can never change the string (except to other strings of the same length) if validity checking happened after every change. I somehow need changing both a and b to be instantaneous (which they currently are not). We have not really gone far enough down that path yet to know what the right thing is, but we are working on it. So for now validity checking occurs at a few specific points and if/when you ask for it. Robert I'm not sure if I'm missing something here or if I just didn't get the point of validation functions, but I believe there must be a way to assure that an object is in a consistent state. Thanks for your help, Torsten __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- +---+ | Robert Gentleman phone : (617) 632-5250 | | Associate Professor fax: (617) 632-2444 | | Department of Biostatistics office: M1B20| | Harvard School of Public Health email: [EMAIL PROTECTED]| +---+ __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] OO programming in R
I have some notes and examples using S4 (for want of a better name) at http://biosun1.harvard.edu/courses/individual/bio271/ lectures 12 and 13 -- Robert On Thu, Feb 13, 2003 at 08:34:35AM -0800, Roger Peng wrote: You may want to look at the book Programming with Data by John Chambers, which describes the new-style classes. It has yet to fail me. Also the Bioconductor packages (http://www.bioconductor.org) use the new-style class system and provide a good source of code examples (even if you're not interested in bioinformatics). -roger ___ UCLA Department of Statistics [EMAIL PROTECTED] http://www.stat.ucla.edu/~rpeng On Thu, 13 Feb 2003, Kris Nackaerts wrote: Dear, I'm looking for some examples on OO programming in R. I have the programming manual with explanation on UseMethod and NextMethod but I miss some practical examples to get me going (I hope). I searched the web but could not find a good independent tutorial on this. Any suggestions are welcome, Kris -- http://perswww.kuleuven.ac.be/~u0027178/VCard/mycard.php?name=krisn Minds are like parachutes, they only work when open __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help -- +---+ | Robert Gentleman phone : (617) 632-5250 | | Associate Professor fax: (617) 632-2444 | | Department of Biostatistics office: M1B20| | Harvard School of Public Health email: [EMAIL PROTECTED] | +---+ __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] Bus error with xyplot
On Mon, Feb 03, 2003 at 10:00:46AM -0500, Liaw, Andy wrote: From: Martin Maechler [mailto:[EMAIL PROTECTED]] Giovanni == Giovanni Petris [EMAIL PROTECTED] on Mon, 3 Feb 2003 08:36:06 -0600 (CST) writes: Giovanni Has anybody else experienced something like the example below? not recently. Could it be that your version of the `grid' package (which is loaded by `lattice') or `lattice' are incompatible (i.e. older than) to your R version? After library(lattice), use .path.package() to see where it was loaded from. This brings up (IIRC) a topic that was discussed on R-devel a while ago: Version checks for required packages. Is this feasible? Seems quite worthwhile to me... And there has been some work on it (reposTools, under www.bioconductor.org), however, getting this right is not a small thing and has some fairly large implications that we are looking at. We too would like to be able to do this reliably. Robert [...] Cheers, Andy -- __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help -- +---+ | Robert Gentleman phone : (617) 632-5250 | | Associate Professor fax: (617) 632-2444 | | Department of Biostatistics office: M1B20 | Harvard School of Public Health email: [EMAIL PROTECTED] | +---+ __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] substitute, eval and hastables
On Wed, Jan 29, 2003 at 01:07:52PM +0100, Serge Boiko wrote: I have the following problem. I have an automatically generated named list with stringified names: a - list(A=..., B=..., C=..., ) then I want to refer to the elements of the list, stored as an vector of names: nn - c(A, B, C), so that I could get list elements like a$nn[1], a$nn[2], etc. Obviously it doesn't work. Instead I do: nn.Exp - substitute(expression(a$b), list(b=nn[1])) eval(nn.Exp) in a result I get expession(a$A) but not the value stored in the list. Meanwhile if I manually construct expression as expression(a$A) and then evaluate it, it works fine. How do I solve that problem? Perhaps using such a list with stringified names are not very good programming style, but this is convenient to store and retrieve elements if list should be filled automatically from numerous sources. In this way I'm trying to emulate a hash-table behavior. Perhaps there is a better way? If you want hash table behavior you could try using environments (as that is really about all that they are). I have been spending some time thinking (and a little coding) about a hash table class but it is unlikely to appear before the summer. Robert Any help is highly appreciated Thanks, -Serge __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help -- +---+ | Robert Gentleman phone : (617) 632-5250 | | Associate Professor fax: (617) 632-2444 | | Department of Biostatistics office: M1B20 | Harvard School of Public Health email: [EMAIL PROTECTED] | +---+ __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help
