[R] Sample size calculations for one sided binomial exact test
I'm trying to compute sample size requirements for a binomial exact test. we want to show that the proportion is at least 90% assuming that it is 95%, with 80% power so any asymptotic approximations are out of the questions. I was planning on using binom.test to perform the simple test against a prespecified value, but cannot find any functions for computing sample size. do any exist? Thanks, Andrew [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Dragging an .RData file into R on win-7 doesn't work?
NppToR is not guaranteed to work when ran as Administrator. This is due to the different permissions that is running. NppToR without admin privileges should not be able to find the running R process, or should not be able to control it. Although If you run NppToR as Admin it should be able to control it, but there is no reason to except to install the R auto completion files. My Suggestion, create a local library to keep your packages in. Save the location in your Rprofile file. Then there is no reason to ever run R as admin. -Andrew On Fri, Oct 22, 2010 at 3:16 AM, Tal Galili tal.gal...@gmail.com wrote: Hi all, I sometimes drag an .RData file into an open R console so to load that data into the file. I use windows 7, and it works fine. But, if I open R by using: right click on icon - properties - compatibility - (mark the box) run this program as an administrator Then I can no longer drag the .RData into the R console. (also, the nppToR extension for notepadd++ stops sending the R script to R...) You probably wonder, why might I be interested in running R with administrator privileges - the reason is that if R is installed under c: directory, I will be blocked from installing new packages to R (unless I either install R on d: drive, or enable admin privileges). I know many people here prefer linux (gnu/linux), but still some of us (for example, me) use windows, so help here will be valuable. Thanks, Tal Contact Details:--- Contact me: tal.gal...@gmail.com | 972-52-7275845 Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) | www.r-statistics.com (English) -- [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Help request: highlighting R code on WordPress.com blogs
The question would be performance issues for having too many functions. We could just limit it to the reserved keywords. Another option for the functions is to highlight anything that looks like a function with the regular expression /[\w._]+(?=\()/ that is any function name with periods and underscores that is immediately followed by an open parentheses, or optionally by any number of spaces then an open parentheses /[\w._]+[ \t]*(?=\()/ -Andrew On Thu, Sep 9, 2010 at 1:01 PM, Yihui Xie x...@yihui.name wrote: Thanks, Tal. It does not look too difficult to write such a brush, which is actually a JS file. However, I have a concern that R has thousands of functions (in base R only), so it might not worth including all of them in the brush, which is the way that they implemented the highlighting script for Java and VB (they didn't define the list of functions because there are too many). Then what we need to do is just to insert a few keywords like TRUE/FALSE/for/while in the JS. I would like to contribute 10 minutes on this if nobody will pick up this job. Regards, Yihui -- Yihui Xie xieyi...@gmail.com Phone: 515-294-2465 Web: http://yihui.name Department of Statistics, Iowa State University 2215 Snedecor Hall, Ames, IA On Thu, Sep 9, 2010 at 3:02 AM, Tal Galili tal.gal...@gmail.com wrote: Hello dear R help members (and also Yihui and Romain), There are currently 28 R bloggers (out of the 117 R-bloggers I know of) that are using wordpress.com for publishing their R code (and I suspect this number will increase with time). WordPress.com doesn't support R syntax highlighting, nor can it be embedded from other services (like gist git) After contacting the WordPress.com vip manager, he instructed me that they will add R support if a relevant brush will be created according to this document: http://alexgorbatchev.com/SyntaxHighlighter/manual/brushes/custom.html Since this is what they use on wordpress.com (see: http://en.support.wordpress.com/code/posting-source-code/). Creating this brush is beyond my ability at this point, I am writing to ask if any of you can/wishes to make this brush for the community. Something I thought might be relevant is the code Yihui Xie recently wrote for creating a NPPtoR code brush (http://yihui.name/en/wp-content/uploads/2010/08/Npp_R_Auto_Completion.r) If such a brush will be created, I'll push to have it included in wordpress.com and to try and inform the current R bloggers using it. Best, Tal Contact Details:--- Contact me: tal.gal...@gmail.com | 972-52-7275845 Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) | www.r-statistics.com (English) -- __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] predict.lda breaks when priors are specified
Dear R help, What am I doing wrong here? when I don't specify the priors it works just fine but when I specify the priors it breaks. Does anyone know why and how I can fix it? N=2 ncontrol=ncases=50 X - as.matrix(rnorm(N,0,1)) eta - -5.3 + X * 1.7 p - exp(eta)/(1+exp(eta)) Y - rbinom(N,1,p) controls - sample(seq_len(N), ncontrol, prob=!Y) cases - sample(seq_len(N), ncases, prob=Y) data-rbind( + data.frame(Y = 0, X = cbind(1,X[controls,])), + data.frame(Y = 1, X = cbind(1,X[cases,]))) head(data) Y X.1 X.2 1 0 1 0.6965323 2 0 1 -0.0817520 3 0 1 2.8673412 4 0 1 -0.2351386 5 0 1 0.2653452 6 0 1 -1.2437612 m - lda(Y~X,subset=c(controls,cases),priors=c(.95,.05)) predict(m) Error in model.frame.default(formula = Y ~ X, priors = c(0.95, 0.05), : variable lengths differ (found for '(priors)') predict(m,prior=c(.95,0.05)) Error in model.frame.default(formula = Y ~ X, priors = c(0.95, 0.05), : variable lengths differ (found for '(priors)') --- Thanks, Andrew __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] predict.lda breaks when priors are specified
Never mind. Stupid misplaced 's'. -Andrew On Sun, May 16, 2010 at 5:39 PM, Andrew Redd ar...@stat.tamu.edu wrote: Dear R help, What am I doing wrong here? when I don't specify the priors it works just fine but when I specify the priors it breaks. Does anyone know why and how I can fix it? N=2 ncontrol=ncases=50 X - as.matrix(rnorm(N,0,1)) eta - -5.3 + X * 1.7 p - exp(eta)/(1+exp(eta)) Y - rbinom(N,1,p) controls - sample(seq_len(N), ncontrol, prob=!Y) cases - sample(seq_len(N), ncases, prob=Y) data-rbind( + data.frame(Y = 0, X = cbind(1,X[controls,])), + data.frame(Y = 1, X = cbind(1,X[cases,]))) head(data) Y X.1 X.2 1 0 1 0.6965323 2 0 1 -0.0817520 3 0 1 2.8673412 4 0 1 -0.2351386 5 0 1 0.2653452 6 0 1 -1.2437612 m - lda(Y~X,subset=c(controls,cases),priors=c(.95,.05)) predict(m) Error in model.frame.default(formula = Y ~ X, priors = c(0.95, 0.05), : variable lengths differ (found for '(priors)') predict(m,prior=c(.95,0.05)) Error in model.frame.default(formula = Y ~ X, priors = c(0.95, 0.05), : variable lengths differ (found for '(priors)') --- Thanks, Andrew __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Derivative of the probit
Is there a function to compute the derivative of the probit (qnorm) function in R, or in any of the packages? Thanks, -Andrew [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Changing the Prompt for browser()
Is there a way that I can change the prompt for within a browser() call. I
often use use code like
with(obj1,browser())
Browse[1]
Is there a way that I can set it so that I can get something like
with(obj1,browser(prompt=obj1))
obj1[1]
I know that prompt is not a valid option for browser, but it would be nice
if it were. There is an option('prompt) but that does not affect the
prompt for browser. Can I change this and how?
Thanks,
Andrew
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Re: [R] R user defined language file for NotePad++
HI there. nice discussion. I'm the developer for NppToR. First NppToR should not make any changes to your workflow in Notepad++. It should be as unobtrusive as possible. In fact I use it with several languages daily with no problems. If is does get in the way I need to know about it, and please post on the forums on sourceforge. If you only want the syntax highlighting I recommend downloading the executable version and run the generateSyntaxFiles.exe. The advantage there is that it will automatically integrate the R syntax XML with any other languages that you might have. If you insist on having a useDefineLang.xml file here is a direct link to one of my early versions before I created the syntax generator, which also extracts keywords from a packages in your library. http://www.stat.tamu.edu/~aredd/site/sites/default/files/userDefineLang_R.xml -Andrew Redd On Thu, Oct 8, 2009 at 8:20 PM, Jason Rupert jasonkrup...@yahoo.com wrote: Unfortunately, I need the ability to switch between languages within one editor and I like the flexibility and simplicity offered via the NotePad++ to support other key languages within my current workflow. Thus, I am attempting to limit editor switching and build up skills within one editor. ...I suppose the search will need to continue... Thank you again for your feedback and suggestions on tracking down previously mentioned R Language definition file for NotePad++ under my current operating constrains. Thanks again. --- On Thu, 10/8/09, Remko Duursma remkoduur...@gmail.com wrote: From: Remko Duursma remkoduur...@gmail.com Subject: Re: [R] R user defined language file for NotePad++ To: Jason Rupert jasonkrup...@yahoo.com Cc: R-help@r-project.org Date: Thursday, October 8, 2009, 8:15 PM Jason, if you install NppToR, it generates the XML file for you, I think. That is one way to get it. Or, you could use Npptor as is, it not only gives R syntax highlighting, but can also send commands to the Rgui (simply by pressing F8). I have been using it for quite a while and I really like it. Remko - Remko Duursma Post-Doctoral Fellow Centre for Plants and the Environment University of Western Sydney Hawkesbury Campus Richmond NSW 2753 Dept of Biological Science Macquarie University North Ryde NSW 2109 Australia Mobile: +61 (0)422 096908 www.remkoduursma.com On Fri, Oct 9, 2009 at 12:07 PM, Jason Rupert jasonkrup...@yahoo.com wrote: Thank you very much for the reply, but this doesn't appear to be the XML file to load into NotePad++ to use as a User Defined Language. It appears to be an stand-alone executable that interacts with NotePad++ and the R GUI. I guess I will keep looking for a bit and maybe breakdown and build the XML and then end up posting it for others. Thanks again. --- On Wed, 10/7/09, Gabor Grothendieck ggrothendi...@gmail.com wrote: From: Gabor Grothendieck ggrothendi...@gmail.com Subject: Re: [R] R user defined language file for NotePad++ To: Jason Rupert jasonkrup...@yahoo.com Cc: R-help@r-project.org Date: Wednesday, October 7, 2009, 10:08 PM Check out: http://sourceforge.net/projects/npptor/ On Wed, Oct 7, 2009 at 11:04 PM, Jason Rupert jasonkrup...@yahoo.com wrote: I am a big fan of NotePad++ ( http://notepad-plus.sourceforge.net/uk/site.htm), which allows users to develop an XML schema that allows NotePad++ to be more Language aware. Thus, I'm curious if there are any R users out there that may have developed the XML user defined language for NotePad++. Just curious if there is already one out there. Thanks again for any feedback. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented
Re: [R] portable R editor
Thanks for the plug on NppToR. Yes it is portable, but a few of the features don't work. I have it on my plan to have a launcher for the portable apps menu. Also the website for NppToR is now https://sourceforge.net/projects/npptor/ On my personal website I also keep, semi-up-to-date a portableapps.comcompatible launcher for R. http://www.stat.tamu.edu/~aredd/site/?q=node/2. There is a full installation and just the launcher. If you download just the launcher you can install the latest version of R into the bin directory and It will work. I think it is version 2.8.0 in the installer. I'll update that soon. Andrew Redd On Mon, Mar 2, 2009 at 8:13 PM, Michael Bibo michael_b...@health.qld.gov.au wrote: Werner Wernersen pensterfuzzer at yahoo.de writes: Hi, I have been dreaming about a complete R environment on my USB stick for a long time. Now I finally want to realize it but what I am missing is a good, portable editor for R which has tabs and syntax highlighting, can execute code, has bookmarks and a little project file management facility pretty much like Tinn-R has those. I like Tinn-R but it seems like there is only a very old version of Tinn-R which works standalone. Hi Werner, Three options: I have previously posted about using Emacs + ESS on a USB stick: http://finzi.psych.upenn.edu/R/Rhelp02/archive/107419.html Tinn-R will work portably. I have simply copied the installed Tinn-R folder from one machine to another on which I do not have administrator privileges and therefore cannot do a normal install. Another option is Notepad++ (http://notepad- plus.sourceforge.net/uk/site.htm). There is even a portable version available fom www.portableapps.com. Andrew Redd has created (and is continuing to develop) NppToR (http://www.stat.tamu.edu/~aredd/site/?q=node/37http://www.stat.tamu.edu/%7Earedd/site/?q=node/37) which provides syntax highlighting, code folding and code passing to R. Notepad++ has a tabbed interface as well as add-ons including a file explorer, windows manager and multiclipboard manager. It also allows for the recording of macros, and the instructions found at this blog (http://aztecpassage.blogspot.com/2007/11/load-new-file-from-template-in- notepad.htmlhttp://aztecpassage.blogspot.com/2007/11/load-new-file-from-template-in-%0Anotepad.html) use Notepad++'s built-in capacity to run external tools to create new files from templates. Michael Bibo Queensland Health __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Rf_error crashes entire program.
I'm having a problem with the error and warning functions. I've tried this
on multiple machine so I'm fairly sure it's not machine dependent and I've
tried it on the latest versions 2.6.0-2.7.1. Whenever my program gets to an
error or warning it crashes the entire program rather than throwing the
error like it should.
Here are the relevant bits.
...
char const * const ExeedsMinVarianceError = PFDA ERR: Near zero
variance encountered. Estimation Unstable. Terminating Estimation.;
if(debug){printf(Da:\n);printmat(DaOld,1,*ka);fflush(stdout);}
daxpy_(ka, mOne, Da, one, DaOld, one);
for(i=0;i*ka;i++)convergenceCriteria+=fabs(DaOld[i]);
if(Da[*ka] MinVariance){
printf(PING);fflush(stdout);
warning(ExeedsMinVarianceError);
break;
}
and the output from running in batch mode that I get is this:
Da:
0.18034.988e-017
PING
and here the program crashes. I've tried this in multiple places and
sometimes the error is thrown sometimes not. Does anyone have an idea of
what is going on. I could not find any discussion of this error yet.
Thank you,
Andrew Redd
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Re: [R] Rf_error crashes entire program.
Switching all of my printfs to Rprintf fixed the problem the errors now proceed correctly. I was unable to reproduce the error, but now that is irrelevant, at least to me. Thanks for the help. -Andrew [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
