Re: [R] Magnitude of trend in time series
Rand Wilcox has produced a set of functions for S-Plus and (IIRC) R, which includes Theil-Sen regression. The following url gives a pdf to the workshop that they were designed to accompany, along with instructions on how to source and use them. http://psychology.usc.edu/rwilcox/workshop.pdf The following url is to his homepage which gives the above link plus those to the function files themselves. http://psychology.usc.edu/faculty_homepage.php?id=43 HTH Regards Mike -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Barry Baker Sent: 12 January 2007 23:48 To: r-help@stat.math.ethz.ch Subject: [R] Magnitude of trend in time series Hello, I am analyzing some climate time series data using the Mann Kendall package and was wondering if there was a way to calculate the trend using Sen's nonparametric estimator slope in R? Thank you in advance, Barry _ Barry Baker, Ph.D. Global Climate Change Initiative The Nature Conservancy 2424 Spruce St., Suite 100 Boulder, CO 80302 Tel: (303)-541-0322 Fax: (303)-449-4328 http://nature.org/tncscience/scientists/misc/baker.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 and provide commented, minimal, self-contained, reproducible code. __ 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] if statement error
Jenny,
are there any missing values in your vectors? If so, what effect do you
think this will have on an expression like that required by the if statement
that must resolve fully to either true or false?
Regards,
Mike
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Jenny Stadt
Sent: 17 October 2006 18:19
To: r-help@stat.math.ethz.ch
Subject: [R] if statement error
Hi List,
I was not able to make this work. I know it is a simple one, sorry to
bother. Give me some hints pls. Thanks!
Jen
if(length(real.d)=30 length(real.b)=30 beta1*beta2*theta1*theta20 )
{ r - 1; corr - 1; }
real.d and real.b are two vectors, beta1,beta2,theta1,and theta2 are
constants. The error occurred like this:
Error in if (length(real.d) = 30 length(real.b) = 30 beta1 * beta2 *
:
missing value where TRUE/FALSE needed
[[alternative HTML version deleted]]
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Re: [R] how do I tell configure where to find Java?
I'm not familiar with gcj, but my initial reaction would be a ln -s for the
relevant compiler executable from /usr/java into /usr/bin.
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Liaw, Andy
Sent: 03 October 2006 19:40
To: r-help
Subject: [R] how do I tell configure where to find Java?
Dear R-help,
I'm trying to build R-2.4.0 on our Opteron-based Scyld cluster. The system
has gcj (the GNU Java compiler, part of GCC) stuff in /usr/bin. When I
installed jdk 1.5.08, the install script placed it in /usr/java (I didn't
have a choice, as the script didn't offer that option). Now when I run
configure in R-2.4.0, it finds gcj, which is not what I want to use. Is
there a way to tell configure where to look for Java? I tried configure
--help but didn't see anything related to Java.
Best,
Andy
Andy Liaw, PhD
Biometrics ResearchPO Box 2000 RY33-300
Merck Research LabsRahway, NJ 07065
andy_liaw(a)merck.com 732-594-0820
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and provide commented, minimal, self-contained, reproducible code.
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Re: [R] how do I tell configure where to find Java? [Broadcast]
For a jre you could create a file called /etc/profile.d/java.sh containing
the following (JAVA_HOME path will need to point to the correct directory
for your particular Java version):
#!/bin/sh
JAVA_HOME=/usr/java/jre1.5.0_08
export JAVA_HOME
JAVA_BIN=$JAVA_HOME/bin
CLASSPATH=$CLASSPATH:$JAVA_HOME:$JAVA_HOME/lib
PATH=$JAVA_BIN:$PATH
export JAVA_BIN CLASSPATH PATH
-Original Message-
From: Liaw, Andy [mailto:[EMAIL PROTECTED]
Sent: 03 October 2006 20:31
To: mike waters
Cc: 'r-help'
Subject: RE: [R] how do I tell configure where to find Java? [Broadcast]
Before I do that, I would need to remove the gcj stuff that are in /usr/bin.
If I know how to remove gcj, I'd gladly do that. However, for the
particular version of the OS, the entire GCC seems to be bundled into one
rpm, and I could not remove just the gcj component. Neither do I wish to
mess with files that are part of some RPMs--- in my experience that's
invitation for trouble later.
Best,
Andy
From: mike waters
I'm not familiar with gcj, but my initial reaction would be a ln -s
for the relevant compiler executable from /usr/java into /usr/bin.
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Liaw, Andy
Sent: 03 October 2006 19:40
To: r-help
Subject: [R] how do I tell configure where to find Java?
Dear R-help,
I'm trying to build R-2.4.0 on our Opteron-based Scyld cluster. The
system has gcj (the GNU Java compiler, part of
GCC) stuff in /usr/bin. When I installed jdk 1.5.08, the install
script placed it in /usr/java (I didn't have a choice, as the script
didn't offer that option). Now when I run configure in R-2.4.0, it
finds gcj, which is not what I want to use. Is there a way to tell
configure where to look for Java? I tried configure --help but didn't
see anything related to Java.
Best,
Andy
Andy Liaw, PhD
Biometrics ResearchPO Box 2000 RY33-300
Merck Research LabsRahway, NJ 07065
andy_liaw(a)merck.com 732-594-0820
--
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and provide commented, minimal, self-contained, reproducible code.
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[R] Looking for an unequal variances equivalent of the Kruskal Wallis nonparametric one way ANOVA
Well fellow R users, I throw myself on your mercy. Help me, the unworthy, satisfy my employer, the ungrateful. My feeble ramblings follow... I've searched R-Help, the R Website and done a GOOGLE without success for a one way ANOVA procedure to analyse data that are both non-normal in nature and which exhibit unequal variances and unequal sample sizes across the 4 treatment levels. My particular concern is to be able to discrimintate between the 4 different treatments (as per the Tukey HSD in happier times). To be precise, the data exhibit negative skew and platykurtosis and I was unable to obtain a sensible transformation to normalise them (obviously trying subtracting the value from range maximum plus one in this process). Hence, the usual Welch variance-weighted one way ANOVA needs to be replaced by a nonparametric alternative, Kruskal-Wallis being ruled out for obvious reasons. I have read that, if the treatment with the fewest sample numbers has the smallest variance (true here) the parametric tests are conservative and safe to use, but I would like to do this 'by the book'. TVMIA, Regards, Mike __ 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] Looking for an unequal variances equivalent of the KruskalWallis nonparametric one way ANOVA
Peter, Thank you for your prompt response. The degrees of freedom for the 6 treatment means range from 33 to 48, so are relatively large. The Levene test for homogeneity of variance is giving values of 13 to 14 for each of the 5 subjective measures being analysed (i.e. highly significant for thos d.o.f.), with skewness significant at p0.0001 and kurtosis generally around p0.01 to p0.02. I have run Bonferroni adjusted pairwise comparisons of the means, which give approximately the same levels of significance as for the straightforward Welch comparisons. Regards, Mike -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Peter Dalgaard Sent: 27 April 2006 16:39 To: Mike Waters Cc: R-help@stat.math.ethz.ch Subject: Re: [R] Looking for an unequal variances equivalent of the KruskalWallis nonparametric one way ANOVA Mike Waters [EMAIL PROTECTED] writes: Well fellow R users, I throw myself on your mercy. Help me, the unworthy, satisfy my employer, the ungrateful. My feeble ramblings follow... I've searched R-Help, the R Website and done a GOOGLE without success for a one way ANOVA procedure to analyse data that are both non-normal in nature and which exhibit unequal variances and unequal sample sizes across the 4 treatment levels. My particular concern is to be able to discrimintate between the 4 different treatments (as per the Tukey HSD in happier times). To be precise, the data exhibit negative skew and platykurtosis and I was unable to obtain a sensible transformation to normalise them (obviously trying subtracting the value from range maximum plus one in this process). Hence, the usual Welch variance-weighted one way ANOVA needs to be replaced by a nonparametric alternative, Kruskal-Wallis being ruled out for obvious reasons. I have read that, if the treatment with the fewest sample numbers has the smallest variance (true here) the parametric tests are conservative and safe to use, but I would like to do this 'by the book'. What are the sample sizes like? Which assumptions are you willing to make _under the null hypothesis_? If it makes sense to compare means (even if nonnormal), then a Welch-type procedure might suffice if the DF are large. pairwise.wilcox.test() might also be a viable alternative, with a suitably p-adjustment. This would make sense if you believe that the relevant null for comparison between any two treatments is that they have identical distributions. (With only four groups, I'd be inclined to use the Bonferroni adjustment, since it is known to be conservative, but not badly so.) -- 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-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] Generalized linear mixed models
Peter, The types of model you are looking to fit are *nonlinear* models. In fact, to be more precise, they are examples of nonlinear ordinal regression models. Check out the nordr package in R. a link to documentation is: http://rss.acs.unt.edu/Rdoc/library/gnlm/html/nordr.html Regards, Mike -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Peter Tait Sent: 26 April 2006 03:28 To: r-help@stat.math.ethz.ch Subject: [R] Generalized linear mixed models Hi, I would like to fit a generalized linear mixed model (glmm) with a 3 level response. My data is from a longitudinal study with multiple observations/patient and multiple patients / country. Is there an R package that will fit a proportional odds, continuation ratio, or adjacent categories glmm? Thanks Peter __ 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] message posting
This can be checked/set from the toolbar at the top via the drop-down box next to the Compose in this mail format section displayed using: Tools-Options-Mail Format HTH Regards Mike A picture may be worth a thousand words, but HTML adds far more than a thousand bytes to an email. -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Gavin Simpson Sent: 21 April 2006 14:32 To: Steven Lacey Cc: r-help@stat.math.ethz.ch Subject: Re: [R] message posting On Fri, 2006-04-21 at 09:22 -0400, Steven Lacey wrote: Hi, I sent two emails to the R help list and got no reply. While this may be my question, it is unlike the users of this list not to reply (thankfully!). I checked for my message using the archive for April 2006 and found the following where the text of message should have been: An embedded and charset-unspecified text was scrubbed... Does this message mean that my message wasn't posted or couldn't be viewed? If so, what did I do wrong? The only thing that comes to mind is that I set the font in outlook to courrier new so that the columns in a table would line up. Thanks for any advice, Steve Hi Steve [[alternative HTML version deleted]] No idea if this has anything to do with it or not, but you are asked to configure your emailer to *not* send html mail. Configure Outlook to send plain text only (generally) or set it up to send plain text only to r-help if you really want to send html-mail to others. It's been a long while since I used Outlook/Windows, but IIRC you can set this up somewhere amongst the myriad of prefs in Outlook. G -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% * Note new Address, Telephone Fax numbers from 6th April 2006 * %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Gavin Simpson ECRC ENSIS [t] +44 (0)20 7679 0522 UCL Department of Geography [f] +44 (0)20 7679 0565 Pearson Building [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street [w] http://www.ucl.ac.uk/~ucfagls/cv/ London, UK. [w] http://www.ucl.ac.uk/~ucfagls/ WC1E 6BT. %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% __ 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] R crashes during 'eigen'
Taking that matrix, stripping out the quoted row and column i.d.s and entering it into MATLAB R14 (7.01) as M, I get from the eig(M) operation: E = eig(M) E = -0. -0. -0. -0. -0. -0. -0. -0. -0. -0. -0. -0. -0. -0. -0. -0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 0. 7.4486 7.4486 7.4486 7.4486 7.4486 7.4486 7.4486 7.4486 7.4486 7.4486 7.4486 7.4486 7.4486 7.4486 7.4486 7.4486 7.4486 7.4486 7.4486 7.4486 7.4486 7.4486 7.4486 7.4486 7.4486 7.4486 7.4486 7.4486 7.4486 7.4486 7.4486 7.4486 7.4486 7.4486 7.4486 7.4486 7.4486 7.4486 7.4486 7.4486 7.4486 7.4486 I presume this is the expected output (i.e. all non-zero eigenvalues the same, 7.4486). Regards, Mike -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Martin Maechler Sent: 29 March 2006 17:02 To: Simon Wood Cc: r-help@stat.math.ethz.ch; [EMAIL PROTECTED] Subject: Re: [R] R crashes during 'eigen' Simon == Simon Wood [EMAIL PROTECTED] on Wed, 29 Mar 2006 16:14:14 +0100 (BST) writes: It looks like there might be a bug in the symmetry detection routine of eigen. When I do eigen(M, symmetric=FALSE) it works fine. Simon - but the matrix is symmetric, which seems to be correctly detected Simon (since eigen() hangs whether symmetric=TRUE is supplied or not). Eigenvalues (after omitting their imaginary parts, which are essentially zeros) are the same as the ones obtained with EISPACK to within a small multiple of machine epsilon. However, the eigenvector matrices seem different ! This happens on R-2.2.1-patched and R-2.3.0 (both compiled from daily snapshots). Simon - This is OK isn't it? All the non-zero eigenvalues are the same for this Simon matrix, so the eigenvectors can't be uniquely defined, can they? Indeed, you are right, Simon. But anyway the fact is that the LAPACK based eigen seems to end in an infinite loop, and I can confirm the behavior for at least R 2.2.1, R-patched and R-devel (aka 2.3.0 alpha) with the R builtin versions of BLAS and LAPACK and also with Atlas. Seems quite a bad story to me at the moment. I assume that octave (or matlab) which are also based on BLAS + LAPACK internally can eigen-decompose the matrix correctly? Could anyone check this (without much effort) for us? Thanks in advance, Martin Maechler, ETH Zurich Simon best, Simon Simon - Simon Wood, Mathematical Sciences, University of Bath, Bath BA2 7AY - +44 (0)1225 386603 www.maths.bath.ac.uk/~sw283/ Andy PS. My system is Windows 2000 on a Xeon CPU. I use precompiled Pentium 4 Rblas DLL from CRAN, but the same thing happens with standard Rblas. __ Andy Jaworski 518-1-01 Process Laboratory 3M Corporate Research Laboratory - E-mail: [EMAIL PROTECTED] Tel: (651) 733-6092 Fax: (651) 736-3122 C.J.Albers [EMAIL PROTECTED] ac.uk To Sent by: r-help@stat.math.ethz.ch [EMAIL PROTECTED] cc at.math.ethz.ch Subject [R] R crashes during 'eigen' 03/28/2006 10:01 AM Hi all, Hi, When I want to compute the eigenvalues eigenvectors of a specific matrix, R crashes (i.e. it stops responding to any input). I've tried it with different versions of R (2.1.1, 2.2.0, 2.2.1) - all with crashing as result. What I did before the crash was: M - as.matrix(read.table(thematrix,header=T)) eigen(M) If, instead of eigen(M), I use eigen(M, EISPACK=T), R doesn't crash. So, I know a workaround my problem, but still don't understand why R crashes. Could anyone explain this? In case someone wants to download my matrix to see where it goes wrong, it can be downloaded from http://mcs.open.ac.uk/cja235/thematrix (warning: obviously, R might crash so save your unsaved work first). thanks, Casper Albers [[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 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE
Re: [R] binomial models with too many 1s???
I take it that a zero inflated negative binomial (i.e. Poisson) regression model is what you are trying to fit, aka ZIP? If so try looking at the documentation for the zicounts package for R, for one. Of course, you can also search on these keywords yourself, to find exactly what you want Regards, Mike -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of I.Szentirmai Sent: 23 February 2006 17:24 To: R-help@stat.math.ethz.ch Subject: [R] binomial models with too many 1s??? Dear R users, Does anyone know a solution for the problem when there are too many ones or zeros in the respons of a binomial model? I think this means that the data are over/under despersed and the result is very bad model fit. I'm using glmmPQL(family=quasibinomial) to fit a model to my data, but the model estimates are not in the range they should be due to overdispersion (or under?) What shall I do? Is there a model type for this kind of data? I would prefer to keep all may data, otherwise I could also select some of the ones so that their number will be equal to the number of zeros. But I don't thik this is the right way... Any help would be appreciated. Thanks, Istvan __ 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] The Perils of PowerPoint
And thus to that 'New Age' Management Role, that of the Professional PowePoint Ranger. He (invariably he) who culls the fruits of the labours of others to present in ever more slick PowerPoint compendia, whilst never sullying their hands with 'real' work. 8¬ Mike -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of bogdan romocea Sent: 06 September 2005 18:43 To: R-help@stat.math.ethz.ch Subject: Re: [R] The Perils of PowerPoint I don't understand why there's so much discussion on PowerPoint. IMHO, that can only obscure the real thing: - The Perils of Miscommunication - The Perils of Not Taking Responsibility (if PowerPoint is to blame for X, then who's to blame for choosing and using PowerPoint in the first place?) - The Perils of Being an Idiot - and so on. (I'm in grave danger here, and also responsible for using R.) -Original Message- From: Mulholland, Tom [mailto:[EMAIL PROTECTED] Sent: Tuesday, September 06, 2005 2:27 AM Cc: Achim Zeileis; r-help@stat.math.ethz.ch Subject: Re: [R] The Perils of PowerPoint For some reason (probably that our organisation has blocked the site) I could not see the original articles that prompted the post. I however immediately assumed that this was precipitated by Tufte and his comments about PowerPoint (I recall seeing a good example of PowerPoint on his site) http://www.edwardtufte.com/tufte/powerpoint When this first came up I recall some dispute about the comments www.sociablemedia.com/articles_dispute.htm and that John Fox did something http://ils.unc.edu/~jfox/powerpoint/introduction.html that I enjoyed reading. Other links that are lying on my computer are In defense of PowerPoint http://www.jnd.org/dn.mss/in_defense_of_powerp.html and Does PowerPoint make you stupid? at http://www.presentations.com/presentations/delivery/article_di splay.jsp?vnu_content_id=1000482464 Tom -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Behalf Of Tim Churches Sent: Saturday, 3 September 2005 10:08 AM To: [EMAIL PROTECTED] Cc: Achim Zeileis; r-help@stat.math.ethz.ch Subject: Re: [R] The Perils of PowerPoint (Ted Harding) wrote: By the way, the Washington Post/Minneapolis Star Tribune article is somewhat reminiscent of a short (15 min) broadcast on BBC Radio 4 back on October 18 2004 15:45-16:00 called Microsoft Powerpoint and the Decline of Civilisation which explores similar themes and also frequently quotes Tufte. Unfortunately it lapsed for ever from Listen Again after the statutory week, so I can't point you to a replay. (However, I have carefully preserved the cassette recording I made). Try http://sooper.org/misc/powerpoint.mp3 (copyright law notwithstanding...) Tim C __ 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 __ 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] R-help
Diego, Have you checked out the home site for nls2? Specifically the system requirements page? http://www.inra.fr/miaj/public/AB/nls2/available.html That says that nls2 requires a Unix-like operating system. Basically, the script for building the library is for such systems only, it also depends upon a lex (flex) library being available. Regards, Mike -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of HM Diego Hernán Sent: 22 August 2005 18:47 To: r-help@stat.math.ethz.ch Subject: [R] R-help Hello I need help with the way to install nls2 library for windows, or the script that can be used for install the nls2 library. Do you know if this library works in windows? Best regards. Diego Rojas Cali-Colombia __ 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] Running Internet Explorer from Withing R
Walt, As Peter said - browsURL(), which does work on Windows (well XP SP2 for definite). For example, to open a google search window: browseURL(http://www.google.co.uk;) Regards, Mike -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Walter R. Paczkowski Sent: 28 July 2005 17:08 To: r-help@stat.math.ethz.ch Subject: [R] Running Internet Explorer from Withing R Good morning, Is it possible to open an html file using IE but from within R? I wrote a small function to generate tables in html but I'd like to write another function to call IE and open the html file. Thanks, Walt Paczkowski Walter R. Paczkowski, Ph.D. Data Analytics Corp. 44 Hamilton Lane Plainsboro, NJ 08536 (V) 609-936-8999 (F) 609-936-3733 __ 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] deal package
-Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Uwe Ligges Sent: 30 June 2005 10:44 To: Weiwei Shi Cc: R-help@stat.math.ethz.ch Subject: Re: [R] deal package Weiwei Shi wrote: Hi, I am wondering if anyone here used deal package in R to do the bayesian network. I am curious about its scalability: how many variables and how many observations can it handle in a reasonable time. If you have some good experience, please share your data configurations. Questions like this should better be sent to the package mainatiner or author of the corresponding function, who probably has more experiences and background knowledge on the code than (almost?) all other readers of this list. Uwe Ligges thanks, There are resources and a link to subscribe to the mailing list for DEAL at the following URL: http://www.math.aau.dk/novo/deal/ That's the best place for you to go for help here. Regards, Mike _ 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] Job Opportunity: Statistical Guru CC 083
Wow, Cutting edge to bleeding heart - and all in one day! 8¬ Mike P.s. Uwe - start with an easy one, like a Unicorn. -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Uwe Ligges Sent: 15 May 2005 12:00 To: Don Alexander Cc: r-help@stat.math.ethz.ch Subject: Re: [R] Job Opportunity: Statistical Guru CC 083 BTW: I am looking for a wife that is very intelligent, earns at least 300,000$ a year, is less than 25 years old, is a real beauty, happily cooks, cleans, and works in the garden, and is never moody, of course. She would have the great opportunity to solve one of the most complex challenges facing human life today: Marrying me, a guy working 12 hours a day, only talking about statistics and alike, looking tired, frequently beeing ill, a couple of years older, always moody, not even remembering his own birthday. Of course, I will not send any answers on your inquiries if I like your photo and you have sent me at least 10,000$. Uwe Ligges Don Alexander wrote: Do you consider yourself a cutting edge statistical expert with a penchant for applying your broad theoretical background to solving some of the most complex statistical challenges facing human health today? Does the idea of working for an emerging company who has a strong management team, financial backing and world class scientific advisors appeal to you? If so, read on... Our client is a drug development platform technology company whose patent pending intellectual property is poised to dramatically impact both drug discovery and development processes. The ultimate benefit to the drug development process will be to identify safer compounds for development, shorten the time for drugs to get to market and identify diagnostic markers for earlier disease detection. This technology will increase the success rate, decrease the time to market and stopdevelopment of products before critical investments are lost. Responsibilities: Independently develop novel statistical approaches to a variety of data types. Provide statistical support for all data-mining efforts, platform Quality Control, and data monitoring. Produce statistical programs as needed. Qualifications: Ph.D. or Masters in Statistics At least 8 years of experience Prior experience in R, S, SAS and/or S-plus and Design of Experiments (DOE) Prior Data Mining knowledge (PLS, neural networks, OLAP, etc.) Breadth of statistical approaches (Q Value/false discovery rate, P Value, Bayesian, Frequentist, Monte Carlo Methods, multivariate data analysis, logistic regression, chi-squared, Random Forest (RF) predictors) Prior experience in a Life Sciences research and development environment Bioinformatics knowledge preferable Ability to lead or direct the work of others Characteristics: Naturally creative, with a broad background Self starter Assertive with a positive outlook and performance oriented attitude Passion, energy, personal drive and motivation Outstanding communication skills, a strategic mindset, an ability to interface at an executive level and a polished presence are required As a professional search firm, we will only be responding to those inquiries that most closely align with the stated requirements. Moreover, our client employer can only review candidates with valid US work authorization at this time. Please include the position ID (CC 083) in the subject line of your correspondence to ensure review and forward your credentials (* Word/PDF/HTML or Text format please), in confidence, to: [EMAIL PROTECTED] General CV/resume submissions for inclusion in our knowledgebase of future opportunities can be made to: [EMAIL PROTECTED] For our most recent searches, please review our web site at: www.ccesearch.com. Kind regards, Don Alexander Director of Biz Dev Life Sciences Carlyle Conlan (919) 474-0771x105 [EMAIL PROTECTED] http://www.ccesearch.com __ 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
FW: [R] distance between distributions
Sorry, forgot to send this to the list originally. -Original Message- From: Mike Waters [mailto:[EMAIL PROTECTED] Sent: 06 May 2005 18:40 To: 'Campbell' Subject: RE: [R] distance between distributions -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Campbell Sent: 06 May 2005 11:19 To: vograno; r-help Subject: Re: [R] distance between distributions I may have missed the point here but isn't this an obvious case for using the bootstrap. A paper by Mallows, the exact reference escapes me, establishes the conditions under which asymtotics of the marginal distribution imply a well behaved limit. Perhaps a better discussion of the issues can be found and a pair of papers by Bickel and Freedman, see Annals Of Statistics Vol 9, Number 6. HTH Phineas Campbell Vadim Ogranovich [EMAIL PROTECTED] 05/06/05 1:36 AM Hi, This is more of a general stat question. I am looking for a easily computable measure of a distance between two empirical distributions. Say I have two samples x and y drawn from X and Y. I want to compute a statistics rho(x,y) which is zero if X = Y and grows as X and Y become less similar. Kullback-Leibler distance is the most official choice, however it needs estimation of the density. The estimation of the density requires one to choose a family of the distributions to fit from or to use some sort of non-parametric estimation. I have no intuition whether the resulting KL distance will be sensitive to the choice of the family of the distribution or of the fitting method. Any suggestion of an alternative measure or insight into sensitivity of the KL distance will be highly appreciated. The distributions I deal with are those of stock returns and qualitatively close to the normal dist with much fatter tails. The tails in general should be modeled non-parametrically. Thanks, Vadim [[alternative HTML version deleted]] _ Was this the reference you were thinking of? C. L. Mallows. A note on asymptotic joint normality. Annals of Mathematical Statistics,43(2):508-515, 1972 Another reference that might be of relevance is: Bootstrap Methods for the Nonparametric Assessment of Population Bioequivelance and Similarity of Distributions. Czado C. and Munk A. ; this can be obtained as a postscript document from: http://www-m4.ma.tum.de/Papers/Czado/simrev.ps HTH Mike __ 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] Searching for a string in RSQLite
-Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Duncan Murdoch Sent: 25 November 2004 15:38 To: [EMAIL PROTECTED] Subject: [R] Searching for a string in RSQLite I'd like to search for a particular string in an SQLite database using RSQLite, but I'm running into problems constructing the query properly, because of embedded quotes and parens in the string. Is there a function that escapes these for me, or some other fixup that would let me do the queries below? In the real situation I don't have control over what strings get searched for. Example based on ?SQLite: library(RSQLite) m - dbDriver(SQLite) con - dbConnect(m, dbname = base.dbms) data(USArrests) dbWriteTable(con, USArrests, USArrests, overwrite = T) [1] TRUE state - Wyoming # this works fine: dbGetQuery(con, paste(SELECT * from USArrests where row_names=',state,',sep=)) row_names Murder Assault UrbanPop Rape 1 Wyoming6.8 161 60 15.6 # Buf if the search string contains characters that SQL interprets, I # get an error state - messy: ' ( dbGetQuery(con, paste(SELECT * from USArrests where row_names=',state,',sep=)) Error in sqliteExecStatement(con, statement) : RS-DBI driver: (error in statement: near (: syntax error) Duncan Murdoch __ [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 The normal character for escaping the next character to prevent it being interpreted in SQL (including SQLite) is the backslash (i.e. \). Unless, of course, I'm not understanding the precise nature of your request. Regards Mike __ [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 packages install problems linux - X not found (WhiteBoxEL 3)
-Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Marc Schwartz Sent: 09 August 2004 15:13 To: Dr Mike Waters Cc: R-Help Subject: RE: [R] R packages install problems linux - X not found (WhiteBoxEL 3) On Mon, 2004-08-09 at 08:13, Dr Mike Waters wrote: snip Marc, Sorry for the confusion yesterday - in my defence, it was very hot and humid here in Hampshire (31 Celsius at 15:00hrs and still 25 at 20:00hrs). What had happened was that I had done a clean install of WB Linux, including the XFree86 and other developer packages. However, the on-line updating system updated the XFree86 packages to a newer sub version. It seems that it didn't do this correctly for the XFree86 developer package, which was missing vital files. However it showed up in the rpm database as being installed (i.e. rpm -qa | grep XFree showed it thus). I downloaded another rpm for this manually and I only forced the upgrade because it was the same version as already 'installed' (as far as the rpm database was concerned). I assumed that all dependencies were sorted out through the install in the first place. OK, that helps. I still have a lingering concern that, given the facts above, there may be other integrity issues in the RPM database, if not elsewhere. From reading the WB web site FAQ's (http://www.whiteboxlinux.org/faq.html) , it appears that they are using up2date/yum for system updates. Depending upon the version in use, there have been issues especially with up2date (hangs, incomplete updates, etc.) which could result in other problems. I use yum via the console here (under FC2), though I note that a GUI version of yum has been created, including replacing the RHN/up2date system tray alert icon. A thought relative to this specifically: If there is or may be an integrity problem related to the rpm database, you should review the information here: http://www.rpm.org/hintskinks/repairdb/ which provides instructions on repairing the database. Note the important caveats regarding backups, etc. The two key steps there are to remove any residual lock files using (as root): rm -f /var/lib/rpm/__* and then rebuilding the rpm database using (also as root): rpm -vv --rebuilddb I think that there needs to be some level of comfort that this basic foundation for the system is intact and correct. I only mentioned RH9 to show that I had some familiarity with the RedHat policy of separating out the 'includes' etc into a separate developer package. Once all this had been sorted out, I was then left with a compilation error which pointed to a missing dependency or similar, which was not due to missing developer packages, but, as you and Prof Ripley correctly point out, from the R installation itself. Having grown fat and lazy on using R under the MS Windows environment, I was struggling to identify the precise nature of this remaining problem. As regards the R installation, I did this from the RH9 binary for version 1.9.1, as I did not think that the Fedora Core 2 binary would be appropriate here. Perhaps I should now compile from the source instead? I would not use the FC2 RPM, since FC2 has many underlying changes not the least of which includes the use of the 2.6 kernel series and the change from XFree86 to x.org. Both changes resulted in significant havoc during the FC2 testing phases and there was at least one issue here with R due to the change in X. According to the WB FAQs: If you cannot find a package built specifically for RHEL3 or WBEL3 you can try a package for RH9 since many of the packages in RHEL3 are the exact same packages as appeared in RH9. Thus, it would seem reasonable to use the RH9 RPM that Martyn has created. An alternative would certainly be to compile R from the source tarball. In either case, I would remove the current installation of R and after achieving a level of comfort that your RPM database is OK, reinstall R using one of the above methods. Pay close attention to any output during the installation process, noting any error or warning messages that may occur. If you go the RPM route, be sure that the MD5SUM of the RPM file matches the value that Martyn has listed on CRAN to ensure that the file has been downloaded in an intact fashion. These are my thoughts at this point. You need to get to a point where the underlying system is stable and intact, then get R to the same state before attempting to install new packages. HTH, Marc From unpacking the tarball and running ./configure in the R source directory, I obtain the fact that crti.o is needed by ld.so and was not found. This file is not present on the system. This file, along with crtn.o is usually installed by the gnu libc packages, I believe. However, I know that not all *nix
RE: [R] R packages install problems linux - X not found(WhiteBoxEL 3)
Marc, Yes - the glibc-devel package was shown to be installed using rpm -qa. It is also one of the packages upgraded by up2date from the original version supplied with the WhiteBox distribution. I concluded that there were probably more such improperly/incompletely upgraded packages and cut my losses. Everything seems to be fine second time around. I must have been unlucky. Regards Mike -Original Message- From: Marc Schwartz [mailto:[EMAIL PROTECTED] Sent: 10 August 2004 15:30 To: Dr Mike Waters Cc: R-Help Subject: RE: [R] R packages install problems linux - X not found(WhiteBoxEL 3) On Tue, 2004-08-10 at 08:15, Dr Mike Waters wrote: snip From unpacking the tarball and running ./configure in the R source directory, I obtain the fact that crti.o is needed by ld.so and was not found. This file is not present on the system. This file, along with crtn.o is usually installed by the gnu libc packages, I believe. However, I know that not all *nix distributions include these files among their packages. From a web search, I have not been able to ascertain whether this lack of a crti.o is due to there not being one in the distribution, or to another incomplete package install. So, I did a completely fresh installation of WhiteBox, followed by R built from source, checked that it ran and then installed the R packages. Only then did I run up2date. At least crti.o and crtn.o are still there this time, along with the XFree86 includes. A bit of a cautionary tale, all in all. Thanks for all the help and support. Regards M Mike, From my FC2 system: $ rpm -qf /usr/lib/crti.o glibc-devel-2.3.3-27 $ rpm -qf /usr/lib/crtn.o glibc-devel-2.3.3-27 So, you are correct relative to the source of these two files. A follow up question might be, did you include the devel packages during your initial install? If not, that would explain the lack of these files. if you did, then it would add another data point to support the notion that your system was, to some level, compromised and a clean install was probably needed, rather than just trying to re-create the RPM database. Glad that you are up and running at this point. Given Martyn's follow up messages, it looks like there may be an issue with the RH9 RPM, so for the time being using the source tarball would be appropriate. Best regards, Marc __ [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 packages install problems linux - X not found (WhiteBoxEL 3)
I am concerned by your indications of previously having had RH9 on the same box and that you had to force an update of the XFree Devel RPM. Forcing the installation of an RPM is almost always a bad thing. When you installed WB on the system, did you do a clean installation or some type of upgrade? If the latter, it is reasonable to consider that there may be some level of mixing and matching of RPMS from the two distributions going on. This could result in a level of marginally or wholly incompatible versions of RPMS being installed. Could you clarify that point? Also, be sure that you have the same versions of the XFree series RPMS installed. Use: rpm -qa | grep XFree in a console and be sure that the RPMS return the same version schema. If not, it is possible that one of your problems is the mixing of versions. Take note of the output of the above and be sure that the XFree86-Mesa-libGL and XFree86-Mesa-libGLU RPMS are installed as well. Some of the messages above would also suggest a problem finding R related headers. How did you install R? This may be a red herring of sorts, given the other problems, but may be helpful. Marc __ Marc, Sorry for the confusion yesterday - in my defence, it was very hot and humid here in Hampshire (31 Celsius at 15:00hrs and still 25 at 20:00hrs). What had happened was that I had done a clean install of WB Linux, including the XFree86 and other developer packages. However, the on-line updating system updated the XFree86 packages to a newer sub version. It seems that it didn't do this correctly for the XFree86 developer package, which was missing vital files. However it showed up in the rpm database as being installed (i.e. rpm -qa | grep XFree showed it thus). I downloaded another rpm for this manually and I only forced the upgrade because it was the same version as already 'installed' (as far as the rpm database was concerned). I assumed that all dependencies were sorted out through the install in the first place. I only mentioned RH9 to show that I had some familiarity with the RedHat policy of separating out the 'includes' etc into a separate developer package. Once all this had been sorted out, I was then left with a compilation error which pointed to a missing dependency or similar, which was not due to missing developer packages, but, as you and Prof Ripley correctly point out, from the R installation itself. Having grown fat and lazy on using R under the MS Windows environment, I was struggling to identify the precise nature of this remaining problem. As regards the R installation, I did this from the RH9 binary for version 1.9.1, as I did not think that the Fedora Core 2 binary would be appropriate here. Perhaps I should now compile from the source instead? Regards M __ [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
[R] R packages install problems linux - X not found (WhiteBox EL 3)
Good evening everyone, I am used to using R under Windows, but have done an install of 1.9.1 under WhiteBox linux 3 (based on RHEL 3). This all went without a hitch, along with most of the additional package installs. However, while trying to install car and rgl I hit a problem regarding the X environment not being found. As I was doing the install from a console *within* the X environment, this is obviously down to a missing environment variable or link. The X11 directories all seem to be in the usual places. I've checked as much as I can through the archives and googled around, but to no avail. Any help appreciated. Thanks for taking the time to read this. Regards M [[alternative HTML version deleted]] __ [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
FW: [R] R packages install problems linux - X not found (WhiteBoxEL 3)
-Original Message- From: Dr Mike Waters [mailto:[EMAIL PROTECTED] Sent: 08 August 2004 20:11 To: '[EMAIL PROTECTED]' Subject: RE: [R] R packages install problems linux - X not found (WhiteBoxEL 3) -Original Message- Correction on the above URL. I pasted the wrong one here. It should be: https://www.stat.math.ethz.ch/pipermail/r-help/2004-August/053994.html Marc Thanks for the responses guys. I used to have RH9 installed on this machine and I found out about the separate developer packages then. I thought that I had got the relevant XFree devel package installed, but although it showed up in the rpm database as being present, the required files were not present. I did a forced rpm upgrade from the WhiteBox updates directory and that problem is now fixed, at least for car. Marc, thanks for the pointer on the rgl problem. However, I have a slightly different problem with the install of this package. It gets through to the point where it tries to make the rgl.so from the various .o files and fails then, as follows: g++ -I/usr/lib/R/include -I/usr/X11R6/include -DHAVE_PNG_H -I/usr/include -I/usr/local/include -Wall -pedantic -fno-exceptions -fno-rtti -fPIC -O2 -g -march=i386 -mcpu=i686 -c glgui.cpp -o glgui.o g++ -L/usr/local/lib -o rgl.so x11lib.o x11gui.o types.o math.o fps.o pixmap.o gui.o api.o device.o devicemanager.o rglview.o scene.o glgui.o -L/usr/X11R6/lib -L/usr/lib -lstdc++ -lX11 -lXext -lGL -lGLU -lpng /usr/lib/gcc-lib/i386-redhat-linux/3.2.3/../../../crt1.o(.text+0x18): In function `_start': : undefined reference to `main' x11lib.o(.text+0x84): In function `set_R_handler': /tmp/R.INSTALL.13414/rgl/src/x11gui.h:33: undefined reference to `R_InputHandlers' x11lib.o(.text+0x92):/tmp/R.INSTALL.13414/rgl/src/x11gui.h:33: undefined reference to `addInputHandler' x11lib.o(.text+0xfb): In function `unset_R_handler': /tmp/R.INSTALL.13414/rgl/src/x11lib.cpp:52: undefined reference to `R_InputHandlers' x11lib.o(.text+0x103):/tmp/R.INSTALL.13414/rgl/src/x11lib.cpp:52: undefined reference to `removeInputHandler' collect2: ld returned 1 exit status make: *** [rgl.so] Error 1 ERROR: compilation failed for package 'rgl' ** Removing '/usr/lib/R/library/rgl' - No doubt another failed dependency... DOH! Regards M __ [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
