Re: [R] A question about is.interger function
Leon amstat2006 at gmail.com writes: Hi, All I am using is.integer function to examine whether an object is an integer or not, but I get such results, x-3 is.integer(x) [1] FALSE x - 3 typeof(3) [1] double This may not be a wise decision in hindsight, but probably was made to avoid conversion when in the next step you do x[2] = 1.5 y - as.integer(3) typeof(y) [1] integer x-3:4 x [1] 3 4 is.integer(x) [1] TRUE Here R seems to know that 3 is an integer, which I believe is a bit inconsistent, but wise, because mostly you use integers here. Mostly; because 1.5:3.5 gives a reasonable result [1] 1.5 2.5 3.5 Dieter __ 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] Help needed
Hi you experienced difference between matrix (cbind()) and data frame (data.frame(..)) or you have some NA value in your BMIGRP1 try: maxcls-max(dset[,2], na.rm=T) if you have some NA values or use str(dset) to look what types are your variables. HTH Petr On 25 Apr 2006 at 18:16, Anamika Chaudhuri wrote: Date sent: Tue, 25 Apr 2006 18:16:42 -0700 (PDT) From: Anamika Chaudhuri [EMAIL PROTECTED] To: Richard M. Heiberger [EMAIL PROTECTED], r-help@stat.math.ethz.ch Subject:Re: [R] Help needed As my earlier email said I am not getting the maxcls. I do get numbers coded as 1,2,3 for BMIGRP(when I print BMIGRP) but not getting the max of (1,2,3) which should be 3, I guess. Thanks for your help Anamika Anamika Chaudhuri [EMAIL PROTECTED] wrote: dset1-cbind(AGE,BMI,DEATH) BMIGRP-cut(BMI,breaks=c(14,20,25,57),right=TRUE) levels(BMIGRP) [1] (14,20] (20,25] (25,57] BMIGRP1-as.numeric(BMIGRP) AGEGRP-floor(AGE/10)-2 dset-cbind(AGEGRP,BMIGRP1,DEATH) maxage-max(dset[,1]) minage-min(dset[,1]) maxcls-max(dset[,2]) maxcls [1] NA Why doesnt it give me a no for maxcls then? Thanks. Richard M. Heiberger [EMAIL PROTECTED] wrote: x - rnorm(100) xx - cut(x,3) levels(xx) [1] (-2.37,-0.716] (-0.716,0.933] (0.933,2.58] as.numeric(xx) - - [[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 Petr Pikal [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] www.r-project.org
Hi, To sum up : * yes, the R website is operationnal. There is no reason whatsoever to change its content. * no javascript, no flash, no chartjunk !! * rework the style, start wih the css file(s) * stop with those frames, and use css to place some kind of fake frames * maybe store the name of your CRAN in a cookie What about - place somewhere a div called 'Focus on a package' where we could have a short presentation of a package, etc ... or for a CRAN task view (to do that, php would be great, but we can do I don't know perl scripts to generate static html pages) - a direct link to download R, which will redirect to the appropriate CRAN thanks to cookies - Propose the Table of Contents of the last volume of R news. - reduce the ratio (size of the head page graphic) / (information directly accesible) - move search, task views, and documentation from cran to www Romain From roger bos : After all, the r-help list doesn't even like HTML in email, so it may not like too many fancy stuff on their website either. html in email is evil. html in a website is normal. From Jon Baron : The only thing I might change is to replace the frames with some sort of CSS-based positioning. HOWEVER, the new version of Internet Explorer may totally destroy the usefulness of CSS, so maybe it is better to leave things as they are for now. What ! IE is not the only browser, and so not the better. Despite is dominant position, i don't think all website will abandon doing css because microsoft is not able to make its browser understand it. -- visit the R Graph Gallery : http://addictedtor.free.fr/graphiques mixmod 1.7 is released : http://www-math.univ-fcomte.fr/mixmod/index.php +---+ | Romain FRANCOIS - http://francoisromain.free.fr | | Doctorant INRIA Futurs / EDF | +---+ __ 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] Is there a way....
Hello, I would like to get rid of counting lines in fix() when i made a mistake in coding? Is there an easy way to an line numbers to editor? Thanks. Levent TERLEMEZ. __ 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] environment
Hi,
Consider the code :
g - function(){
print(.x)
.x - 3
}
f - function(){
environment(g) - environment()
.x - 2
g()
.x
}
f()
[1] 2
[1] 2
I would like f() to return 3. How can I do that ? Am I completely out of
place ?
Doing that, I want to avoid to pass .x as a parameter in f, because in
real life .x is pretty big and g() is called over and over in a loop.
Thanks
Romain
--
visit the R Graph Gallery : http://addictedtor.free.fr/graphiques
mixmod 1.7 is released : http://www-math.univ-fcomte.fr/mixmod/index.php
+---+
| Romain FRANCOIS - http://francoisromain.free.fr |
| Doctorant INRIA Futurs / EDF |
+---+
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[R] program and comment
Hi. I am a newbie to R. I need to do a courses projects with some manipulation lots of data record and some back-and-forth linear regression. I do not want to spend $100 for a SAS lincence, which professor used. So I decide to start to learn R to finish it. I am using R in Windows. I feel it is somehow works like mathemica. I try to write the work into a little program for future reference. (My data soon exceeds the workplace.) So that should be a script, right? Then I can load it in file/source R code. One thing puzzles me is that how to write comments in the script. I googled internet and the archive and did not find any clues. First, can anyone confirm that I took the correct approach for the problem? I understand R is quite different from program language like C/Pascal which I am familiar with and seems people write it with quite different style. Second, can anyone show me some idea about how to write the comment. Thanks. __ 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] program and comment
Guojun Zhu wrote: Hi. I am a newbie to R. I need to do a courses projects with some manipulation lots of data record and some back-and-forth linear regression. I do not want to spend $100 for a SAS lincence, which professor used. So I decide to start to learn R to finish it. I am using R in Windows. I feel it is somehow works like mathemica. I try to write the work into a little program for future reference. (My data soon exceeds the workplace.) So that should be a script, right? Then I can load it in file/source R code. One thing puzzles me is that how to write comments in the script. I googled internet and the archive and did not find any clues. First, can anyone confirm that I took the correct approach for the problem? I understand R is quite different from program language like C/Pascal which I am familiar with and seems people write it with quite different style. Second, can anyone show me some idea about how to write the comment. Thanks. It seems a good idea to me to add all your commands in a script and to source it in order to execute it. Comments can be added in R simply by starting a line with a # Greetz, Dirk -- Dirk De Becker Work: Kasteelpark Arenberg 30 3001 Heverlee phone: ++32(0)16/32.14.44 fax: ++32(0)16/32.85.90 Home: Waversebaan 90 3001 Heverlee phone: ++32(0)16/23.36.65 [EMAIL PROTECTED] mobile phone: ++32(0)498/51.19.86 Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm __ 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] program and comment
2006/4/26, Guojun Zhu [EMAIL PROTECTED]: Hi. I am a newbie to R. I need to do a courses *do* have a look at e.g.: - http://cran.r-project.org/manuals.html (An Introduction to R) - http://www.ms.unimelb.edu.au/~andrewpr/r-users/icebreakeR.pdf (contributed manual) - http://cran.r-project.org/doc/contrib/Short-refcard.pdf (reference-card) to search the archives you can use: - http://tolstoy.newcastle.edu.au/R/about.html - http://finzi.psych.upenn.edu/search.html I am using R in Windows. Have a look at Tinn-R (editor) like mathemica. I try to write the work into a little program for future reference. (My data soon exceeds the workplace.) So that should be a script, right? yes Then I can load it in file/source R code. source( yourScript.R ) check working path: getwd() if you don't know what this is: ?getwd ?source First, can anyone confirm that I took the correct approach for the problem? yes I understand R is quite different from program language like C/Pascal which I am familiar with and seems people write it with quite different style. it's a functional language and inherits from LISP (Scheme). You need to read the manual. Second, can anyone show me some idea about how to write the comment. Thanks. # this is a comment -- Regards, Hans-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
Re: [R] environment
Romain Francois [EMAIL PROTECTED] writes:
Hi,
Consider the code :
g - function(){
print(.x)
.x - 3
}
f - function(){
environment(g) - environment()
.x - 2
g()
.x
}
f()
[1] 2
[1] 2
I would like f() to return 3. How can I do that ? Am I completely out of
place ?
Doing that, I want to avoid to pass .x as a parameter in f, because in
real life .x is pretty big and g() is called over and over in a loop.
If you want to assign into the environment of g, you'll need - ,
otherwise you assign to a local variable.
Another possibility involves assign(..., parent.frame())
--
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
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[R] Minimum Volume Ellipsoid Estimator (cov.mve??)
Dear All, The Minimum Volume Ellipsoid estimator (cov.mve) was part of S+ but I cannot find it in R. Where can I find it? Why was it excluded? Cheers, Patrik Sweden __ 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] environment
Le 26.04.2006 11:02, Peter Dalgaard a écrit :
Romain Francois [EMAIL PROTECTED] writes:
Hi,
Consider the code :
g - function(){
print(.x)
.x - 3
}
f - function(){
environment(g) - environment()
.x - 2
g()
.x
}
f()
[1] 2
[1] 2
I would like f() to return 3. How can I do that ? Am I completely out of
place ?
Doing that, I want to avoid to pass .x as a parameter in f, because in
real life .x is pretty big and g() is called over and over in a loop.
If you want to assign into the environment of g, you'll need - ,
otherwise you assign to a local variable.
Another possibility involves assign(..., parent.frame())
Oh yes,
sorry for posting. I knew that.
--
visit the R Graph Gallery : http://addictedtor.free.fr/graphiques
mixmod 1.7 is released : http://www-math.univ-fcomte.fr/mixmod/index.php
+---+
| Romain FRANCOIS - http://francoisromain.free.fr |
| Doctorant INRIA Futurs / EDF |
+---+
__
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Re: [R] Generalized linear mixed models
On Tue, 25 Apr 2006, Peter Tait wrote: 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? Those are not GLMs, so the generalization would not be a glmm. It is not even clear what you would want to be random: just the intercepts? Perhaps you need to find literature discussing relevant models and see what software it proposes? -- 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 __ 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] Minimum Volume Ellipsoid Estimator (cov.mve??)
On Wed, 26 Apr 2006, Öhagen Patrik wrote: Dear All, The Minimum Volume Ellipsoid estimator (cov.mve) was part of S+ but I cannot find it in R. Where can I find it? help.search(cov.mve) gives cov.rob(MASS) Resistant Estimation of Multivariate Location and Scatter so you see not to know how to search. Why was it excluded? R is not a clone of S-PLUS (sic), but a different system based on the S language. Often there is better functionality in R (and indeed in this case there is later enhanced functionality in S-PLUS too). -- 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__ 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] Partially crossed and nested random factors in lme/lmer
1. Are you familiar with Pinheiro and Bates (2000) Mixed-Effects Models in S and S-Plus (Springer)? I've learned a lot from this book both about mixed models generally and about lme in particular -- and even indirectly about lmer. Examples in this book would, I believe, help you figure out how to get what you want from lme. Files containing virtually all the R commands in that book can be found in ~\library\nlme\scripts in your R installation directory. You can make a local copy and walk through the code line by line, trying various modifications as you go. 2. Are you familiar both with Doug Bates' recent article on mixed models in R News and with his mlmRev package and MlmSoftRev vignette? You can get an R script file of virtually all the R commands in the *.PDF file accompanying the vignette, which you can then modify as you wish to help you learn from the vignette. Examples in the vignette help file tell you how to do this. [If you use XEmacs, the edit(v1) line there may not work. Instead, try Stangle(v1$file) then look for a new *.R file in your working directory -- identified by getwd().] If you've spent some time with both of these and still would like further help from this group, please submit another post -- after first reading the posting guide! www.R-project.org/posting-guide.html, especially the bit about providing a self-contained example. Many different things might contribute to the problem you describe that the program terminates with the second lmer example. I tried copying your script into R and got, 'object duration.root.transf not found' from both lmer and lme. If your example had been self-contained -- and the simpler the better -- I might have been able to help more. hope this helps, spencer graves Corsin Müller, Zoologisches Inst. wrote: Hi all, I am not a very proficient R-user yet, so I hope I am not wasting people’s time. I want to run a linear mixed model with 3 random factors (A, B, C) where A and B are partially crossed and C is nested within B. I understand that this is not easily possible using lme but it might be using lmer. I encountered two problems when trying: Firstly, I can enter two random factors in lmer but I do not get complete outputs using both anova () and summary (). For instance, I only get df, SS, and MS using anova(). Even so the model runs without giving an error message. lmer.inspection - lmer( duration.root.transf~ sex*sample.sex+age+sample.age+sample.type+ first.bout+location+sample.source + (1|acceptor.grp) + (1|donor.grp)) anova (lmer.inspection) Analysis of Variance Table Df Sum Sq Mean Sq sex 1 0.06653 0.06653 sample.sex 1 0.60389 0.60389 … Running the same model in lme using only one random factor works fine. lme.inspection - lme( duration.root.transf~ sex*sample.sex+age+sample.age+sample.type+ first.bout+location+sample.source, random=~1|acceptor.grp) anova (lme.inspection) numDF denDF F-value p-value (Intercept)1 4427 47690.12 .0001 sex1 4427 7.93 0.0049 sample.sex 1 442765.71 .0001 … Running the example given in “?lmer” also does not give a complete anova table. However, the example discussed in the email by Jacob Michaelson on the 24th of April 2005 “[R] random interactions in lme” gives a complete output. So I seem to miss out on something. Secondly, I am at a loss with how I can enter the third random factor, which should be nested within acceptor.grp. When trying the to me intuitively sensible lmer.inspection - lmer(duration.root.transf~ … + (1|acceptor.grp/id) + (1|donor.grp)) the program terminates I am grateful for any suggestions. Version used: R 2.2.1 for Windows Thanks, Corsin Mueller Corsin Mueller Universität of Zuerich Zoological Institute Winterthurerstr. 190 8057 Zuerich Switzerland fon +41-(0)44-63 55277 fax +41-(0)44-63 55490 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 __ 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] www.r-project.org
The webmasters have not AFAICS replied in this thread, and perhaps you should wait for them. In particular, making cran.r-project.org an autodirector to the nearest mirror and replacing frames have I believe already been agreed and just need resources to implement (and first www. and cran.r-project.org are being moved to new hardware at a different physical site). Please remember that as always R has very limited human resources and is the web site a high priority within those resources? (I don't judge it so.) You will find discussion of frames vs css in the archives. On Wed, 26 Apr 2006, Romain Francois wrote: Hi, To sum up : * yes, the R website is operationnal. There is no reason whatsoever to change its content. * no javascript, no flash, no chartjunk !! * rework the style, start wih the css file(s) * stop with those frames, and use css to place some kind of fake frames * maybe store the name of your CRAN in a cookie What about - place somewhere a div called 'Focus on a package' where we could have a short presentation of a package, etc ... or for a CRAN task view (to do that, php would be great, but we can do I don't know perl scripts to generate static html pages) - a direct link to download R, which will redirect to the appropriate CRAN thanks to cookies - Propose the Table of Contents of the last volume of R news. - reduce the ratio (size of the head page graphic) / (information directly accesible) - move search, task views, and documentation from cran to www Romain From roger bos : After all, the r-help list doesn't even like HTML in email, so it may not like too many fancy stuff on their website either. html in email is evil. html in a website is normal. From Jon Baron : The only thing I might change is to replace the frames with some sort of CSS-based positioning. HOWEVER, the new version of Internet Explorer may totally destroy the usefulness of CSS, so maybe it is better to leave things as they are for now. What ! IE is not the only browser, and so not the better. Despite is dominant position, i don't think all website will abandon doing css because microsoft is not able to make its browser understand it. -- 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 __ 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] new.frame()
Hello, I would like to know whether R has a homogeneous function of S-plus's new.frame(), which create explicit frames in the evaluator and provide a locale for computations that can be shared among various functions. new.frame() in S-plus: http://www.uni-muenster.de/ZIV/Mitarbeiter/BennoSueselbeck/s-html/helpfiles/new.frame.html Thanks. __ 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] [O/T] undergrads and R
Dear John Fox, thank you for your reply. I appologize for not finding the sort.names option myself. As for the option of choosing several variables at a time, I would like to see this possibility everywhere where possible. Let me give a few examples: 1. Calculating the mean of several variables (for example, I often want to compute the mean of a set of variables measuring the same concept) 2. Recoding a set of variables with the same rule 3. Transforming a set of variables from factor to numeric or vice verse. (This would be especially useful when using data read from SPSS, as all variables with labels are converted to factors. These are often ordinal variables measured on 5 or more point scale, which are often as close as you can get in social sciences to interval variables. However for most of the analysis (like regression, factor analysis ...), they have to be treated as numeric.) As to how this should be done, I agree that a check-box to select all numeric variables might be to no thingking approach. I would just like to have an option to select several variables, the same way as is done now in for example factor analysis. I do understand that you want the students to think what they are doing. However I would like to present them the R commander as an alternative to SPSS also for doing their assignments for other courses and I do not believe they would be willing to make the change if they have to do so much clicks just to compute averages for let say 20 variables. I personally think that it is enough that the software does not allow you (or the students) to do wrong things (like computing a mean of the factor), especially not without thinking about it. Another option I would like are: 1. An option to save (or actually to not delete) the results of let say factor analysis, so I could use them for further analysis. 2. Currently, if I create a factor via command line, it is not recognized my the menus (for example, I can not do a frequency table). If I select a different data frame and then again the previous one as the active data frame, the new factor is now recognized in the menus. So I would also be satisfied by a refresh option for the active data frame. That would be all for now. Thanks again for the reply and for creating Rcmdr in the first place. Best regards, Ales John Fox pravi: Dear Ales, -Original Message- From: Ales Ziberna [mailto:[EMAIL PROTECTED] Sent: Tuesday, April 25, 2006 1:15 AM To: Richard M. Heiberger Cc: r-help@stat.math.ethz.ch; John Fox Subject: Re: [R] [O/T] undergrads and R I will be also using R commander with undergrad students, who actually already have some experience with R, however they have been using it more as programing language than a statistical tool and I want to get them more familiar with this aspect of R. First, when I had my first look at R commander, I really liked it, however, when I did a little more experiments, I found it quite frustrating at times, especially by the fact that when computing a certain statistics (for example mean), you can select only one variable at the time. Are there any plans to change this, so that a number of variables could be chosen? This was a deliberate choice, made to discourage students from computing statistics without thinking about them, but perhaps it's wrongheaded. I'd be interested to hear what people think. It would be very simple to change the Numerical Summaries dialog to permit more than one variable to be selected (in fact you could do it and recompile the package if you wished). Are you referring only to the Statistics - Summaries - Numerical summaries dialog, or are there other places where you'd like more than one variable to be selected? Would you like a check-box to select all numeric variables? More generally, I'm open to considering suggestions for improving the Rcmdr. I would also prefer to have the variables sorted the same way as they are in the data frame and and not alphabetically. See the sort.names Rcmdr option, described in ?Commander. Regards, John If this two (what I believe minor) things could be improved, I would find R commander much more usable. Otherwise, I find it a grate package, especially when working with social sciences students. Does anyone else have similar filings. Best regards, Ales Ziberna Richard M. Heiberger pravi: This semester for the first time I have been using the combination of R, R Commander (John Fox's package providing a menu-driven interface to R), and RExcel (Erich Neuwirth's package for interfacing R with Excel). The audience is the introductory Statistics class for Business undergradutes. The short summary is that I think the combination works well for this audience. I will be talking on my experience at the useR! conference in June. I added several additional menu items to Rcmdr for our group. I sent the January
Re: [R] new.frame()
?new.env ?local should help you. R works with environments, basically a frame plus an enclosure. On Wed, 26 Apr 2006, Anna Whitfield wrote: Hello, I would like to know whether R has a homogeneous function of S-plus's new.frame(), which create explicit frames in the evaluator and provide a locale for computations that can be shared among various functions. new.frame() in S-plus: http://www.uni-muenster.de/ZIV/Mitarbeiter/BennoSueselbeck/s-html/helpfiles/new.frame.html Thanks. __ 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 -- 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 __ 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] regression modeling
An interesting example of this is the forest cover data set that is available from http://www.ics.uci.edu/~mlearn The proportions of the different cover types change systematically as one moves through the file. It seems that distance through the file is a proxy for the geographical co-ordinates. Fitting a tree-based or suchlike model to the total data is not the way to go, unless one is going to model the pattern of change through the file as part of the modeling exercise. In any case, some preliminary exploration of the data is called for, so that such matters come to attention. For my money, the issue is not ease of performing regression with huge data sets, but ease of data exploration. John Maindonald email: [EMAIL PROTECTED] phone : +61 2 (6125)3473fax : +61 2(6125)5549 Mathematical Sciences Institute, Room 1194, John Dedman Mathematical Sciences Building (Building 27) Australian National University, Canberra ACT 0200. On 26 Apr 2006, at 8:00 PM, [EMAIL PROTECTED] wrote: From: Berton Gunter [EMAIL PROTECTED] Date: 26 April 2006 6:47:12 AM To: 'Weiwei Shi' [EMAIL PROTECTED], 'bogdan romocea' [EMAIL PROTECTED] Cc: 'r-help' R-help@stat.math.ethz.ch Subject: Re: [R] regression modeling May I offer a perhaps contrary perspective on this. Statistical **theory** tells us that the precision of estimates improves as sample size increases. However, in practice, this is not always the case. The reason is that it can take time to collect that extra data, and things change over time. So the very definition of what one is measuring, the measurement technology by which it is measured (think about estimating tumor size or disease incidence or underemployment, for example), the presence or absence of known or unknown large systematic effects, and so forth may change in unknown ways. This defeats, or at least complicates, the fundamental assumption that one is sampling from a (fixed) population or stable (e.g. homogeneous, stationary) process, so it's no wonder that all statistical bets are off. Of course, sometimes the necessary information to account for these issues is present, and appropriate (but often complex) statistical analyses can be performed. But not always. Thus, I am suspicious, cynical even, about those who advocate collecting all the data and subjecting the whole vast heterogeneous mess to arcane and ever more computer intensive (and adjustable parameter ridden) data mining algorithms to detect trends or discover knowledge. To me, it sounds like a prescription for turning on all the equipment and waiting to see what happens in the science lab instead of performing careful, well-designed experiments. I realize, of course, that there are many perfectly legitimate areas of scientific research, from geophysics to evolutionary biology to sociology, where one cannot (easily) perform planned experiments. But my point is that good science demands that in all circumstances, and especially when one accumulates and attempts to aggregata data taken over spans of time and space, one needs to beware of oversimplification, including statistical oversimplification. So interrogate the measurement, be skeptical of stability, expect inconsistency. While all models are wrong but some are useful (George Box), the second law tells us that entropy still rules. (Needless to say, public or private contrary views are welcome). -- Bert Gunter Genentech Non-Clinical Statistics South San Francisco, CA The business of the statistician is to catalyze the scientific learning process. - George E. P. Box __ 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] www.r-project.org
Romain Francois wrote: What about - place somewhere a div called 'Focus on a package' where we could have a short presentation of a package, etc ... or for a CRAN task view (to do that, php would be great, but we can do I don't know perl scripts to generate static html pages) - a direct link to download R, which will redirect to the appropriate CRAN thanks to cookies - Propose the Table of Contents of the last volume of R news. - reduce the ratio (size of the head page graphic) / (information directly accesible) - move search, task views, and documentation from cran to www Now maybe my original assessment that a CMS wasn't worth investing in needs a rethink. Suppose www.r-project.org was rebuilt with Plone: http://plone.org/ You'd get: * An easy-to-edit set of accessible web pages * A thorough search of site content * News and Events objects * Replace CRAN with Plone Software Center: http://plone.org/products/plonesoftwarecenter - as used to display plone Products here: http://plone.org/products * Use Plone Help Center for documentation, as used here: http://plone.org/documentation * Use poi to replace the R-bugs system: http://plone.org/products/poi - although plone itself has moved to using 'trac' http://www.edgewall.com/trac/ Of course, it requires time, hosting, and enthusiasm I'm currently lacking all three. Barry __ 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] lwd - Windows
On Wed, 26 Apr 2006, Francisco J. Zagmutt wrote: Dear all Is there a way or trick in windows to plot a line width that is not an integer i.e 1.5? I am aware that the documentation for window devices states Line widths as controlled by par(lwd=) are in multiples of the pixel size, and multiples 1 are silently converted to 1 but I was wondering if there is a workaround this. That's not what it says in R 2.3.0 (nor in my copy of 2.2.1)! ?windows says Line widths as controlled by 'par(lwd=)' are in multiples of 1/96inch. Multiples less than 1 are allowed, down to one pixel width. Also, IMHO the documentation for lwd in par may need some clarification since it states: The line width, a positive number, defaulting to 1. The interpretation is device-specific, and some devices do not implement line widths less than one. Perhaps it would be useful for the users to describe the behavior for the most important devices, and also to state that the number is an integer (at least for windows) and not just a positive number? False premise. Please don't ask for the documentation to be changed to your personal misreading of it. -- 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 __ 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] www.r-project.org
Le 26.04.2006 12:14, Prof Brian Ripley a écrit : The webmasters have not AFAICS replied in this thread, and perhaps you should wait for them. In particular, making cran.r-project.org an autodirector to the nearest mirror and replacing frames have I believe already been agreed and just need resources to implement (and first www. and cran.r-project.org are being moved to new hardware at a different physical site). Please remember that as always R has very limited human resources and is the web site a high priority within those resources? (I don't judge it so.) Absolutely. This is so not a priority for the core team. You are doing a wonderful job improving R, and I do not want in any case divert you from that. But, some people (like me) don't have the same abilities in R programming, but can (to some extent) contribute efforts in designing web pages. You will find discussion of frames vs css in the archives. I'm on my way ... -- visit the R Graph Gallery : http://addictedtor.free.fr/graphiques mixmod 1.7 is released : http://www-math.univ-fcomte.fr/mixmod/index.php +---+ | Romain FRANCOIS - http://francoisromain.free.fr | | Doctorant INRIA Futurs / EDF | +---+ __ 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] new.frame()
Also, the proto and R.oo packages provide object oriented ways of working with environments. On 4/26/06, Prof Brian Ripley [EMAIL PROTECTED] wrote: ?new.env ?local should help you. R works with environments, basically a frame plus an enclosure. On Wed, 26 Apr 2006, Anna Whitfield wrote: Hello, I would like to know whether R has a homogeneous function of S-plus's new.frame(), which create explicit frames in the evaluator and provide a locale for computations that can be shared among various functions. new.frame() in S-plus: http://www.uni-muenster.de/ZIV/Mitarbeiter/BennoSueselbeck/s-html/helpfiles/new.frame.html Thanks. __ 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 -- 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 __ 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] environment
A third possibility is to using the proto package and define
a proto object (an environment with special meaning for $)
containing the two components .x and g like this:
library(proto)
p - proto(.x = 2, g = function(.) { print(.$.x); .$.x - 3 })
p$.x # 2
print(p$g()) # 2, 3
p$.x # 3
or you can write the print statement as with(., print(.x))
On 26 Apr 2006 11:02:58 +0200, Peter Dalgaard [EMAIL PROTECTED] wrote:
Romain Francois [EMAIL PROTECTED] writes:
Hi,
Consider the code :
g - function(){
print(.x)
.x - 3
}
f - function(){
environment(g) - environment()
.x - 2
g()
.x
}
f()
[1] 2
[1] 2
I would like f() to return 3. How can I do that ? Am I completely out of
place ?
Doing that, I want to avoid to pass .x as a parameter in f, because in
real life .x is pretty big and g() is called over and over in a loop.
If you want to assign into the environment of g, you'll need - ,
otherwise you assign to a local variable.
Another possibility involves assign(..., parent.frame())
And a third possibility is:
library(proto)
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Re: [R] Partially crossed and nested random factors in lme/lmer
I do have Pinheiro and Bates 2000 and went through it several times – unfortunately without success for my particular issue. I was not aware of the article in R news or the mlmRev package you referred to, though. I will try with that. The example I gave was not self-contained. Sorry, my fault. Cheers, Corsin On Wed, 26 Apr 2006 03:11:52 -0700 Spencer Graves [EMAIL PROTECTED] wrote: 1. Are you familiar with Pinheiro and Bates (2000) Mixed-Effects Models in S and S-Plus (Springer)? I've learned a lot from this book both about mixed models generally and about lme in particular -- and even indirectly about lmer. Examples in this book would, I believe, help you figure out how to get what you want from lme. Files containing virtually all the R commands in that book can be found in ~\library\nlme\scripts in your R installation directory. You can make a local copy and walk through the code line by line, trying various modifications as you go. 2. Are you familiar both with Doug Bates' recent article on mixed models in R News and with his mlmRev package and MlmSoftRev vignette? You can get an R script file of virtually all the R commands in the *.PDF file accompanying the vignette, which you can then modify as you wish to help you learn from the vignette. Examples in the vignette help file tell you how to do this. [If you use XEmacs, the edit(v1) line there may not work. Instead, try Stangle(v1$file) then look for a new *.R file in your working directory -- identified by getwd().] If you've spent some time with both of these and still would like further help from this group, please submit another post -- after first reading the posting guide! www.R-project.org/posting-guide.html, especially the bit about providing a self-contained example. Many different things might contribute to the problem you describe that the program terminates with the second lmer example. I tried copying your script into R and got, 'object duration.root.transf not found' from both lmer and lme. If your example had been self-contained -- and the simpler the better -- I might have been able to help more. hope this helps, spencer graves Corsin Müller, Zoologisches Inst. wrote: Hi all, I am not a very proficient R-user yet, so I hope I am not wasting people’s time. I want to run a linear mixed model with 3 random factors (A, B, C) where A and B are partially crossed and C is nested within B. I understand that this is not easily possible using lme but it might be using lmer. I encountered two problems when trying: Firstly, I can enter two random factors in lmer but I do not get complete outputs using both anova () and summary (). For instance, I only get df, SS, and MS using anova(). Even so the model runs without giving an error message. lmer.inspection - lmer( duration.root.transf~ sex*sample.sex+age+sample.age+sample.type+ first.bout+location+sample.source + (1|acceptor.grp) + (1|donor.grp)) anova (lmer.inspection) Analysis of Variance Table Df Sum Sq Mean Sq sex 1 0.06653 0.06653 sample.sex 1 0.60389 0.60389 … Running the same model in lme using only one random factor works fine. lme.inspection - lme( duration.root.transf~ sex*sample.sex+age+sample.age+sample.type+ first.bout+location+sample.source, random=~1|acceptor.grp) anova (lme.inspection) numDF denDF F-value p-value (Intercept)1 4427 47690.12 .0001 sex1 4427 7.93 0.0049 sample.sex 1 442765.71 .0001 … Running the example given in “?lmer” also does not give a complete anova table. However, the example discussed in the email by Jacob Michaelson on the 24th of April 2005 “[R] random interactions in lme” gives a complete output. So I seem to miss out on something. Secondly, I am at a loss with how I can enter the third random factor, which should be nested within acceptor.grp. When trying the to me intuitively sensible lmer.inspection - lmer(duration.root.transf~ … + (1|acceptor.grp/id) + (1|donor.grp)) the program terminates I am grateful for any suggestions. Version used: R 2.2.1 for Windows Thanks, Corsin Mueller Corsin Mueller Universität of Zuerich Zoological Institute Winterthurerstr. 190 8057 Zuerich Switzerland fon +41-(0)44-63 55277 fax +41-(0)44-63 55490 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 Corsin Müller Universität Zürich Zoologisches Institut Winterthurerstr. 190 8057 Zürich Switzerland Tel +41-(0)44-63 55277 Fax +41-(0)44-63 55490 Email [EMAIL PROTECTED]
Re: [R] Is there a way....
Levent TERLEMEZ wrote: Hello, I would like to get rid of counting lines in fix() when i made a mistake in coding? Is there an easy way to an line numbers to editor? I think the feature you are requesting is not available. Beside, it is a good idea to use some appropriate editor and source() your function rather than using the fix() function. Uwe Ligges Thanks. Levent TERLEMEZ. __ 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] environment
Also, if you don;t need to create child objects which override .x,
and I don't think you do here, p could be further simplified to
this (only the print statement has been changed):
p - proto(.x = 2, g = function(.) { print(.x); .$.x - 3 })
On 4/26/06, Gabor Grothendieck [EMAIL PROTECTED] wrote:
A third possibility is to using the proto package and define
a proto object (an environment with special meaning for $)
containing the two components .x and g like this:
library(proto)
p - proto(.x = 2, g = function(.) { print(.$.x); .$.x - 3 })
p$.x # 2
print(p$g()) # 2, 3
p$.x # 3
or you can write the print statement as with(., print(.x))
On 26 Apr 2006 11:02:58 +0200, Peter Dalgaard [EMAIL PROTECTED] wrote:
Romain Francois [EMAIL PROTECTED] writes:
Hi,
Consider the code :
g - function(){
print(.x)
.x - 3
}
f - function(){
environment(g) - environment()
.x - 2
g()
.x
}
f()
[1] 2
[1] 2
I would like f() to return 3. How can I do that ? Am I completely out of
place ?
Doing that, I want to avoid to pass .x as a parameter in f, because in
real life .x is pretty big and g() is called over and over in a loop.
If you want to assign into the environment of g, you'll need - ,
otherwise you assign to a local variable.
Another possibility involves assign(..., parent.frame())
And a third possibility is:
library(proto)
__
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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 there a way....
Hello Levent,
there has recently been a thread on the ESS list by using setnu in EMACS:
https://stat.ethz.ch/pipermail/ess-help/2006-April/003450.html
Bernhard
-Ursprüngliche Nachricht-
Von: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Im Auftrag von Uwe Ligges
Gesendet: Mittwoch, 26. April 2006 13:38
An: Levent TERLEMEZ
Cc: r-help@stat.math.ethz.ch
Betreff: Re: [R] Is there a way
Levent TERLEMEZ wrote:
Hello,
I would like to get rid of counting lines in fix() when i made a
mistake in coding? Is there an easy way to an line numbers to editor?
I think the feature you are requesting is not available.
Beside, it is a good idea to use some appropriate editor and source()
your function rather than using the fix() function.
Uwe Ligges
Thanks.
Levent TERLEMEZ.
__
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*
Confidentiality Note: The information contained in this mess...{{dropped}}
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Re: [R] Is there a way....
[Levent TERLEMEZ] I would like to get rid of counting lines in fix() when i made a mistake in coding? Is there an easy way to an line numbers to editor? You may configure R to use the editor you want, the way you want. For example, if you want fix() to start Vim in graphical mode, highlighting file contents using R syntax, and numbering source lines, you might use the following R command: options(editor = gvim -c \set nu\ -c \set ft=r\) Of course, how to do this much depends on each editor. Some simpler editors may not have options for displaying the line number on each line. Yet, most keep the line counter for the cursor position updated in some mode or status bar, so if nothing better, you can learn to position the cursor while keeping an eye on that. :-) Once you find the proper incantation for your editor, and if you always want it activated, save the R command within your ~/.Rprofile file. P.S. - By the way, much congratulations and thanks to the R Core team for the recent publication of R 2.3.0. -- François Pinard http://pinard.progiciels-bpi.ca __ 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] The beautiful math plot
Dear R-help, How can I replicate the beautiful math plot found in the right-hand side of http://www.r-project.org/screenshots/desktop.jpg? I tried the following code but didn't obtain something as beautiful. r - seq(-10, 10, len=100) y - cos(r^2)*exp(-r/6) par(pty=s) plot(r,y,type=l) Thanks in advance! Yung-jui Yang [[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] The beautiful math plot
Dear R-help, How can I replicate the beautiful math plot found in the right-hand side of http://www.r-project.org/screenshots/desktop.jpg? I tried the following code but didn't obtain something as beautiful. r - seq(-10, 10, len=100) y - cos(r^2)*exp(-r/6) par(pty=s) plot(r,y,type=l) Thanks in advance! Yung-jui Yang [[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
Re: [R] The beautiful math plot
See:
?image
Markus Gesmann
FPMA
Lloyd's Market Analysis
Lloyd's * One Lime Street * London * EC3M 7HA
Telephone +44 (0)20 7327 6472
Facsimile +44 (0)20 7327 5718
http://www.lloyds.com
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Daniel Yang
Sent: 26 April 2006 13:39
To: R-help@stat.math.ethz.ch
Subject: [R] The beautiful math plot
Dear R-help,
How can I replicate the beautiful math plot found in the right-hand side
of http://www.r-project.org/screenshots/desktop.jpg? I tried the
following code but didn't obtain something as beautiful.
r - seq(-10, 10, len=100)
y - cos(r^2)*exp(-r/6)
par(pty=s)
plot(r,y,type=l)
Thanks in advance!
Yung-jui Yang
[[alternative HTML version deleted]]
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**
The information in this E-Mail and in any attachments is CON...{{dropped}}
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[R] About regression and plot
Dear R-help, This is my first R day. I want to ask some more beginner's questions. Q1. How can I obtain the covariance matrix for parameter estimates of a multiple regression? I checked ?lm but didn't get the information. Q2. How can I see the old graphs in the graph window? Q3. Can R plot animated graph? For example, I want to see the dynamic change of a 2D graph during a time period. Thanks in advance! Yung-jui Yang [[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] About regression and plot
--- I changed to format to text instead of html --- Dear R-help, This is my first R day. I want to ask some more beginner's questions. Q1. How can I obtain the covariance matrix for parameter estimates of a multiple regression? I checked ?lm but didn't get the information. Q2. How can I see the old graphs in the graph window? Q3. Can R plot animated graph? For example, I want to see the dynamic change of a 2D graph during a time period. Thanks in advance! Yung-jui Yang __ 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] About regression and plot
Le 26.04.2006 15:16, Daniel Yang a écrit :
Dear R-help,
This is my first R day. I want to ask some more beginner's questions.
Q1. How can I obtain the covariance matrix for parameter estimates of a
multiple regression? I checked ?lm but didn't get the information.
Q2. How can I see the old graphs in the graph window?
Q3. Can R plot animated graph? For example, I want to see the dynamic change
of a 2D graph during a time period.
Thanks in advance!
Yung-jui Yang
Welcome here,
You might want to learn R a few days, read the docs, etc .. and then
come back with questions.
That's how you will get the most of R.
R2 :
you can't, but you can open more than one graph at a time, with
?windows, or ?x11 or send a graphic to a file : ?pdf, ?png, ...
Or you reexecute the commands
R3 :
For a live animation :
x - rnorm(100)
for(i in 1:100){
plot(1:i, x[1:i], xlim=c(0,100), ylim=range(x), type=l)
Sys.sleep(.1)
}
You may want to save each graphic in a file and then build an animation
using convert (from ImageMagick) or whatever tools you have.
In R :
png('gr_%04d.png', width=600, height=400)
x - rnorm(100)
for(i in 1:100){
plot(1:i, x[1:i], xlim=c(0,100), ylim=range(x), type=l)
}
dev.off()
From a shell :
$ convert *.png out.gif
See also :
http://pinard.progiciels-bpi.ca/plaisirs/animations/index.html
http://dirk.eddelbuettel.com/code/rquantlib-rgl.html
Romain
--
visit the R Graph Gallery : http://addictedtor.free.fr/graphiques
mixmod 1.7 is released : http://www-math.univ-fcomte.fr/mixmod/index.php
+---+
| Romain FRANCOIS - http://francoisromain.free.fr |
| Doctorant INRIA Futurs / EDF |
+---+
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Re: [R] About regression and plot
On 4/26/06, Daniel Yang [EMAIL PROTECTED] wrote: --- I changed to format to text instead of html --- Dear R-help, This is my first R day. I want to ask some more beginner's questions. Read the posting guide at the bottom of each post to r-help. Q1. How can I obtain the covariance matrix for parameter estimates of a multiple regression? I checked ?lm but didn't get the information. ?vcov Q2. How can I see the old graphs in the graph window? Assuming you are using Windows, create a plot, e.g. plot(1), change focus to the plot, i.e. left click it, and choose Recording from the History menu. From that point on in the session (or until you turn it off), it will record your plots and you can change focus to the plot window and use PageUp and PageDn keys to move through them. Q3. Can R plot animated graph? For example, I want to see the dynamic change of a 2D graph during a time period. RSiteSearch(animation) __ 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] nls and factor
Hi Manuel,
an alternative to the approach pointed out by Prof. Ripley is to use
the package 'drc' which allows one or more parameters in a non-linear
regression model to depend on a factor.
You will need the latest version available at www.bioassay.dk (an older
version is available on CRAN).
Bconc - runif(30,0.1,10)
Aconc - runif(30,0.1,10)
At - runif(30,1,30)
Bt - runif(30,1,30)
BKm - 1
AKm - 0
EBoth - -0.41
yB - 100*exp(EBoth*Bt)*Bconc/(BKm+Bconc)+rnorm(30,0,1)
yA - 75*exp(EBoth*At)*Aconc/(AKm+Aconc)+rnorm(30,0,1)
## Constructing the dataset
tvalues - c(At, Bt)
conc - c(Aconc, Bconc)
yfactor - factor(rep(c(A, B), c(30, 30)))
y - c(yA, yB)
## Defining the non-linear function
twodimMM - function()
{
fct - function(x, parm)
{
parm[, 1]*exp(parm[, 2]*x[, 1])*x[, 2]/(parm[, 3] + x[, 2])
}
ssfct - function(dataset) # a very simple self starter function
{
return(c(90, -0.5, 0.8))
}
names - c(lev, Ev, km) # parameter names
return(list(fct=fct, ssfct=ssfct, names=names))
}
library(drc)
model1 - multdrc(y~cbind(tvalues,conc), yfactor, fct=twodimMM())
summary(model1)
## Collapsing the Ev parameters into a single parameter
model2 - multdrc(y~cbind(tvalues,conc), yfactor,
collapse=data.frame(yfactor,1,yfactor), fct=twodimMM())
anova(model2, model1) # model reduction is insignificant
summary(model2)
Christian
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Re: [R] Running R on Windows 2000 Terminal Services
Barry Rowlingson wrote: Gavin Simpson wrote: Dear list, My employer uses a Windows 2000 Terminal Server-based system for its college-wide managed computer service - computers connect directly to the WTS servers for their sessions, using a Citrix ICA client. When I asked them to install R (Windows) on an older version of this service the IT guys installed it but pulled it for performance issues. I am trying to get them to try again but receiving little encouragement from them. 'performance issues'? Well, if you have 100 students running MCMC simulations on one Windows 2000 TS box then you may well have 'performance issues'! Perhaps the TS service isn't intended for people to do real computer work on, but is just for Office apps. Then you come along and want your students to do serious number crunching. At that point the MS Word writers experience what we used to call 'lag'. Does anyone on the list have experience of a similar set-up? If you do, I could use that as part of my argument to invest some time in sorting these issues out. I really want to get the Windows version of R installed for teaching because at the moment I subject my students to the rather hostile world of an archaic UNIX session to run R - for them at least. We have a couple of labs that are similar - we use Wyse Thin Client Xterminals which boot Thinstation Linux from a server and then connect to Windows 2003 TS machines using RDP or Ubuntu Linux boxes using XDMCP. We dont use Citrix ICA. 'Performance issues' will depend very much on what you are doing. As a quick benchmark, last term we had 24 users in a lab all running Windows and running Matlab, Firefox, that kind of stuff. One dual 2.6GHz Xeon Dell with 4G Ram never went above 60% CPU usage. And we had another three similar Dells sitting idle waiting for installation. Sessions with R run regularly in these labs and we've never had 'performance issues'. Back in September there was some issue with your setup, but I forget the details. Do you remember? Is it something we ended up working around, or did the 2.2 release fix it? Duncan So possibly your IT support are stalling. Do they regularly say Have you tried switching it off and on again? in response to a support query [1]? Barry [1] Catchphrase of the tech support guys in comedy series 'The IT Crowd' __ 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] www.r-project.org
Romain Francois wrote: Dear R users and developpers, My question is adressed to both of you, so I choose R-help to post it. Are there any plans to jazz up the main R website : http://www.r-project.org The look it have now is the same for a long time and kind of sad compared to other statistical package's website. Of course, the comparison is not fair, since companies are paying web designers to draw lollipop websites ... There have been various suggestions along these lines (check the archives), but there are a number of constraints that make the problem difficult: - there are two web sites, www.r-project.org and cran.r-project.org with different needs. In particular, CRAN must be very low tech because it is mirrored on very diverse sites (including local copies, e.g. on a CDROM). - There are a lot of busy people who need to edit these pages occasionally, so a stable, standard, simple setup is extremely desirable. That means simple HTML to be edited in a text editor, no special CMS. These requirements are quite hard to meet, so expect changes to the web sites to be very time consuming, and possibly rejected en masse in the end. Duncan Murdoch My first idea was to organize some kind of web designing contest. But, I had a small talk with Friedrich Leisch about that, who said that I shouldn't expect too many competitors. So, what about creating a small team, create a home page project and then propose it to the core team. It goes without saying it : The core team has the final word. What do you think ? Who would like to play ? Romain __ 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] www.r-project.org
what about improving the Links page, with for instance a list of links - such as thoses in task views - grouped by theme, instead of modifying r-project site ? -- --- [EMAIL PROTECTED] CNRS UMR 8090 - http://www-good.ibl.fr Génomique et physiologie moléculaire des maladies métaboliques I.B.L 2eme etage - 1 rue du Pr Calmette, B.P.245, 59019 Lille Cedex Tel : 33 (0)3.20.87.10.44 Fax : 33 (0)3.20.87.10.31 __ 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] [Rd] R 2.3.0: Use of NULL as an environment is deprecated
2006/4/26, Uwe Ligges [EMAIL PROTECTED]: Pfaff, Bernhard Dr. wrote: BernPf == Pfaff, Bernhard Dr [EMAIL PROTECTED] on Wed, 26 Apr 2006 08:28:34 +0100 writes: BernPf Dear Andy, Uwe and remaining list subscribers, BernPf now, coming closer to the evil's root. Yesterday, I source compiled on a BernPf Linux box at home and the result is the same behaviour as pointed out BernPf below. This is regardless of the package version of 'urca'. Aside of BernPf 'urca', other packages that have Imports/Depends entries in the BernPf DESCRIPTION to packages that are shipped within the standard library of BernPf R show the warning too, e.g. fMultivar, VLMC, to name but a few. BernPf I do have set on both OS, i.e. Windows and Linux, a second library tree BernPf in Renviron.site with R-LIBS. If I comment this out and do a reinstall BernPf of the packages, i.e. the packages are now installed in the standard BernPf library, the warning does not show up any longer. Has something changed BernPf with regard to additional libraries that slipped my notice by upgrading BernPf to version 2.3.0? I don't think so. I ***NEVER*** install a package into the standard library. We have all CRAN packages in a different library, (and Bioconductor too) and I typically use about 6 library (paths), and I don't have your problem. I only get your warning if I get a version of a package that was installed previous to 2.3.0 (or it's alpha / beta / rc ) versions. BernPf Is it possible that during startup the environment is handeld/passed BernPf differently for standard and additional libraries? Would this odd BernPf behaviour qualify as a bug? If it was general, yes, but I think it's not. Hello Martin and all others involved in this thread, thank you very much for your time and patience. After having updated the packages in the standard library, too, the warning message does indeed not show up any longer by issuing the command library(urca) and similar with other packages. Just out of curiosity, I wonder what has changed in these packages (i.e. nlme, foreign, cluster and VR got updated) from downloading the '.exe' or the tarball in the official 2.3.0 release up to now? For sure you got (or still had in front of your R_LIBS path) packages that were compiled for R 2.3.0! That's it. Very simple. Uwe Ligges Best, Bernhard * Confidentiality Note: The information contained in this message, and any attachments, may contain confidential and/or privileged material. It is intended solely for the person(s) or entity to which it is addressed. Any review, retransmission, dissemination, or taking of any action in reliance upon this information by persons or entities other than the intended recipient(s) is prohibited. If you received this in error, please contact the sender and delete the material from any computer. * __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel I'm happy the problem was solved. I had the same problem with a package of mines (not on CRAN). The problem was an imported package that was compiled for R-2.2.0. Tnx all for solving my problem just before posting it on the list:D Antonio, Fabio Di Narzo. [[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] installation problem with 2.3.0
Hello,
I'm in the process of trying to upgrade our R software from version 2.2.3
to 2.3.0 on our Sun workstations. In the installation process I'm
encountering some puzzling errors whe I do the 'make install.' After
installing the doc files successfully the installation process crashes
while trying to install the etc files, with the following messages:
make[1]: Leaving directory `/usr/local/R-2.3.0/doc'
make[1]: Entering directory `/usr/local/R-2.3.0/etc'
installing etc ...
/bin/bash: -c: line 1: syntax error near unexpected token `;'
/bin/bash: -c: line 1: `for f in ; do ../tools/install-sh -c -m 644 ${f}
/usr/local/lib/R/etc; done'
make[1]: *** [install] Error 2
make[1]: Leaving directory `/usr/local/R-2.3.0/etc'
make: *** [install] Error 1
I've been studying the Makefile trying to figure out what would cause such
an error but so far I haven't been able to figure it out. We are using
Solaris 8 with GNU make version 3.79.1. I've also tried using the Sun
default make (i.e. /usr/ccs/bin/make) but I get the same result. I've
installed R (previous versions) many times on Solaris previously without
any problems and I'm puzzled as to why we're encountering this problem in
2.3.0. Does anybody have any suggestions for things I can try to remedy
this problem?
Thanks very much,
Eric
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Re: [R] lwd - Windows
Dear Prof Brian Ripley Thanks for replying to my question. I am sorry but it is still not clear to me if there is a way to handle an intermediate line width. In my windows system when I create a figure with 4 plots par(mfrow=c(2,2),lwd=1) the lines look a bit too thin and using lwd=2 makes them look a bit too thick, and if I use 1.5 it makes no difference. i.e par(mfrow=c(2,2)) plot(sin,lwd=1)#Too thin plot(sin,lwd=1.5)#Same as lwd=1 plot(sin,lwd=1.99)#Same as lwd=1 plot(sin,lwd=2)#Too thick Regards Francisco From: Prof Brian Ripley [EMAIL PROTECTED] To: Francisco J. Zagmutt [EMAIL PROTECTED] CC: R-help@stat.math.ethz.ch Subject: Re: [R] lwd - Windows Date: Wed, 26 Apr 2006 11:34:05 +0100 (BST) On Wed, 26 Apr 2006, Francisco J. Zagmutt wrote: Dear all Is there a way or trick in windows to plot a line width that is not an integer i.e 1.5? I am aware that the documentation for window devices states Line widths as controlled by par(lwd=) are in multiples of the pixel size, and multiples 1 are silently converted to 1 but I was wondering if there is a workaround this. That's not what it says in R 2.3.0 (nor in my copy of 2.2.1)! ?windows says Line widths as controlled by 'par(lwd=)' are in multiples of 1/96inch. Multiples less than 1 are allowed, down to one pixel width. Also, IMHO the documentation for lwd in par may need some clarification since it states: The line width, a positive number, defaulting to 1. The interpretation is device-specific, and some devices do not implement line widths less than one. Perhaps it would be useful for the users to describe the behavior for the most important devices, and also to state that the number is an integer (at least for windows) and not just a positive number? False premise. Please don't ask for the documentation to be changed to your personal misreading of it. -- 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 __ 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] environment
On Wed, 26 Apr 2006, Romain Francois wrote:
Hi,
Consider the code :
g - function(){
print(.x)
.x - 3
}
f - function(){
environment(g) - environment()
.x - 2
g()
.x
}
f()
[1] 2
[1] 2
I would like f() to return 3. How can I do that ? Am I completely out of
place ?
Doing that, I want to avoid to pass .x as a parameter in f, because in
real life .x is pretty big and g() is called over and over in a loop.
As long as .x doesn't get modified it probably won't be copied, so this is
unlikely to make any difference to memory use even if you work out how to
do it.
-thomas
Thomas Lumley Assoc. Professor, Biostatistics
[EMAIL PROTECTED] University of Washington, Seattle
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[R] cdf of weibull distribution
Hi, I have a data set which is assumed to follow weibull distr'. How can I find of cdf for this data. For example, for normal data I used (package - lmomco) cdfnor(15,parnor(lmom.ub(c(df$V1 Also, lmomco package does not have functions for finding cdf for some of the distributions like lognormal. Is there any other package, which can handle these distributions? Thanx in advance Sachin - [[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
Re: [R] cdf of weibull distribution
Sachin J [EMAIL PROTECTED] writes: Hi, I have a data set which is assumed to follow weibull distr'. How can I find of cdf for this data. For example, for normal data I used (package - lmomco) cdfnor(15,parnor(lmom.ub(c(df$V1 Also, lmomco package does not have functions for finding cdf for some of the distributions like lognormal. Is there any other package, which can handle these distributions? What's wrong with pweibull, plnorm, etc.? Or pnorm for that matter -- 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
Re: [R] [O/T] undergrads and R
Dear Ales, -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Ales Ziberna Sent: Wednesday, April 26, 2006 5:21 AM To: John Fox Cc: r-help@stat.math.ethz.ch Subject: Re: [R] [O/T] undergrads and R Dear John Fox, thank you for your reply. I appologize for not finding the sort.names option myself. As for the option of choosing several variables at a time, I would like to see this possibility everywhere where possible. Let me give a few examples: 1. Calculating the mean of several variables (for example, I often want to compute the mean of a set of variables measuring the same concept) 2. Recoding a set of variables with the same rule These would be useful and easy to do (though for 2. I'd have to provide a way to name the new variables). BTW, it would help to have a complete set of suggestions: I'd probably not have thought of 2. (You could send me your suggestions off-list.) I intend to work on a new version of the Rcmdr this summer, and, although I can't promise to incorporate all suggestions, I'll certainly consider them carefully. 3. Transforming a set of variables from factor to numeric or vice verse. This could get a bit convoluted, since the numeric-to-factor dialog asks you (optionally) to specify level names and rename the factor. I don't currently provide for converting factors to numeric, and would worry about misuse (though you can do this as a recode). (This would be especially useful when using data read from SPSS, as all variables with labels are converted to factors. These are often ordinal variables measured on 5 or more point scale, which are often as close as you can get in social sciences to interval variables. However for most of the analysis (like regression, factor analysis ...), they have to be treated as numeric.) Couldn't you do this with a redesigned Recode dialog? As to how this should be done, I agree that a check-box to select all numeric variables might be to no thingking approach. I would just like to have an option to select several variables, the same way as is done now in for example factor analysis. I do understand that you want the students to think what they are doing. However I would like to present them the R commander as an alternative to SPSS also for doing their assignments for other courses and I do not believe they would be willing to make the change if they have to do so much clicks just to compute averages for let say 20 variables. I personally think that it is enough that the software does not allow you (or the students) to do wrong things (like computing a mean of the factor), especially not without thinking about it. Another option I would like are: 1. An option to save (or actually to not delete) the results of let say factor analysis, so I could use them for further analysis. What would you like to save? Currently, you can save factor scores. The R Commander is designed around an active data set and an active statistical model. I'm open to incorporating other data structures, but suspect that in most instances that would lead me outside the boundaries of the R Commander or require a major redesign. Anyway, it's hard to tell without some more information about what you'd like. 2. Currently, if I create a factor via command line, it is not recognized my the menus (for example, I can not do a frequency table). If I select a different data frame and then again the previous one as the active data frame, the new factor is now recognized in the menus. So I would also be satisfied by a refresh option for the active data frame. If I follow this properly, then it doesn't seem to be correct. For example, if the data frame Data is the Rcmdr active data set then the command Data$new.variable - ... executed in the R console or in the Rcmdr Command window will immediately make the variable new.variable accessible in the Rcmdr. Regards, John That would be all for now. Thanks again for the reply and for creating Rcmdr in the first place. Best regards, Ales John Fox pravi: Dear Ales, -Original Message- From: Ales Ziberna [mailto:[EMAIL PROTECTED] Sent: Tuesday, April 25, 2006 1:15 AM To: Richard M. Heiberger Cc: r-help@stat.math.ethz.ch; John Fox Subject: Re: [R] [O/T] undergrads and R I will be also using R commander with undergrad students, who actually already have some experience with R, however they have been using it more as programing language than a statistical tool and I want to get them more familiar with this aspect of R. First, when I had my first look at R commander, I really liked it, however, when I did a little more experiments, I found it quite frustrating at times, especially by the fact that when computing a certain statistics (for example mean), you can select only one variable at the time. Are there any plans to change this,
[R] Were to find appropriate functions for a given task in R
This is a generic request concerning were to look for finding appropriate information on a precise procedure in R. Im using R for teaching introductory statistics and my students are learning how to deal with it. However, I find it difficult to locate some of the procedures. For instance, for basic crosstabulation, it is obvious that basic functions as table, ftable, and prop.table can be used. But there is a CrossTable function that is very useful. This is hidden in gmodels and gregmisc, as far as Ive been able to explore the packages. However, there is no way (unless I sit down to r-help for hours) to be sure if there is some other place in which a very useful function is hidden for table manipulation (for instance controlling for other variables). This is only an example. But there are many more. Were to look for CI for proportions? I can find it but it is not easy. I understand R is more appropriate for difficult statistical procedures (glm and similar), BUT students need to start somewhere . My specific claim is about the need for a sort of guide in which the different procedures could be classified (and some redundancies could be deleted ..by the way). Is there something similar around? Any project working on this? Any clue for? If not, I would suggest starting some kind of easy reference based on the problem to solve. This could indicate were to look for. Last day I find in package vcd that a function exist for testing the goodness-of-fit of a sample to binomial and other distributions .but this was VERY difficult to locate. Any way, as usual, any indication will be very useful (spaecially for my students!!!) Albert Sorribas Professor of Statistics and Operational Research Departament de Ciències Mèdiques Bàsiques Universitat de Lleida Montserrat Roig 2 25008-Lleida (Espanya) web.udl.es/Biomath/Group [[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
Re: [R] Were to find appropriate functions for a given task in R
you may find RSiteSearch() and help.search() functions useful for this purpose, considering usually different key words for the same topic. Best, Dimitris Dimitris Rizopoulos Ph.D. Student Biostatistical Centre School of Public Health Catholic University of Leuven Address: Kapucijnenvoer 35, Leuven, Belgium Tel: +32/(0)16/336899 Fax: +32/(0)16/337015 Web: http://www.med.kuleuven.be/biostat/ http://www.student.kuleuven.be/~m0390867/dimitris.htm - Original Message - From: Albert Sorribas [EMAIL PROTECTED] To: r-help@stat.math.ethz.ch Sent: Wednesday, April 26, 2006 5:31 PM Subject: [R] Were to find appropriate functions for a given task in R This is a generic request concerning were to look for finding appropriate information on a precise procedure in R. I'm using R for teaching introductory statistics and my students are learning how to deal with it. However, I find it difficult to locate some of the procedures. For instance, for basic crosstabulation, it is obvious that basic functions as table, ftable, and prop.table can be used. But there is a CrossTable function that is very useful. This is hidden in gmodels and gregmisc, as far as I've been able to explore the packages. However, there is no way (unless I sit down to r-help for hours) to be sure if there is some other place in which a very useful function is hidden for table manipulation (for instance controlling for other variables). This is only an example. But there are many more. Were to look for CI for proportions? I can find it but it is not easy. I understand R is more appropriate for difficult statistical procedures (glm and similar), BUT students need to start somewhere.. My specific claim is about the need for a sort of guide in which the different procedures could be classified (and some redundancies could be deleted...by the way). Is there something similar around? Any project working on this? Any clue for? If not, I would suggest starting some kind of easy reference based on the problem to solve. This could indicate were to look for. Last day I find in package vcd that a function exist for testing the goodness-of-fit of a sample to binomial and other distributions..but this was VERY difficult to locate. Any way, as usual, any indication will be very useful (spaecially for my students!!!) Albert Sorribas Professor of Statistics and Operational Research Departament de Ciències Mèdiques Bàsiques Universitat de Lleida Montserrat Roig 2 25008-Lleida (Espanya) web.udl.es/Biomath/Group [[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 Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm __ 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] Were to find appropriate functions for a given task in R
1. Check out the R reference card at http://www.rpad.org/Rpad/Rpad-refcard.pdf . There are also several others available from the CRAN website. 2. Check out TINN-R, a Windows text/R code editor that integrates the above and provides function tips inline to give the syntax of many R functions. 3. ?help.search 4. ?RSiteSearch (or search CRAN directly using Jon Baron's search engine). These do not eliminate the problem, but hopefully mitigate it. Given that there are several thousand R functions spread among hundreds of packages at at least three separate repositories (CRAN, BioConductor, and Omegahat), it's clearly a nontrivial issue. But that's why Google and other search services are multibillion dollar companies. HTH Cheers, Bert -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Albert Sorribas Sent: Wednesday, April 26, 2006 8:32 AM To: r-help@stat.math.ethz.ch Subject: [R] Were to find appropriate functions for a given task in R This is a generic request concerning were to look for finding appropriate information on a precise procedure in R. Im using R for teaching introductory statistics and my students are learning how to deal with it. However, I find it difficult to locate some of the procedures. For instance, for basic crosstabulation, it is obvious that basic functions as table, ftable, and prop.table can be used. But there is a CrossTable function that is very useful. This is hidden in gmodels and gregmisc, as far as Ive been able to explore the packages. However, there is no way (unless I sit down to r-help for hours) to be sure if there is some other place in which a very useful function is hidden for table manipulation (for instance controlling for other variables). This is only an example. But there are many more. Were to look for CI for proportions? I can find it but it is not easy. I understand R is more appropriate for difficult statistical procedures (glm and similar), BUT students need to start somewhere. My specific claim is about the need for a sort of guide in which the different procedures could be classified (and some redundancies could be deleted..by the way). Is there something similar around? Any project working on this? Any clue for? If not, I would suggest starting some kind of easy reference based on the problem to solve. This could indicate were to look for. Last day I find in package vcd that a function exist for testing the goodness-of-fit of a sample to binomial and other distributions.but this was VERY difficult to locate. Any way, as usual, any indication will be very useful (spaecially for my students!!!) Albert Sorribas Professor of Statistics and Operational Research Departament de Cihncies Mhdiques B`siques Universitat de Lleida Montserrat Roig 2 25008-Lleida (Espanya) web.udl.es/Biomath/Group [[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
Re: [R] Were to find appropriate functions for a given task in R
There is a reference sheet here: http://www.rpad.org/Rpad/R-refcard.pdf a function finder here: http://biostat.mc.vanderbilt.edu/s/finder/find.html and task views here: http://cran.r-project.org/src/contrib/Views/ Also use of RSiteSearch and help.search from within R can be helpful. On 4/26/06, Albert Sorribas [EMAIL PROTECTED] wrote: This is a generic request concerning were to look for finding appropriate information on a precise procedure in R. I'm using R for teaching introductory statistics and my students are learning how to deal with it. However, I find it difficult to locate some of the procedures. For instance, for basic crosstabulation, it is obvious that basic functions as table, ftable, and prop.table can be used. But there is a CrossTable function that is very useful. This is hidden in gmodels and gregmisc, as far as I've been able to explore the packages. However, there is no way (unless I sit down to r-help for hours) to be sure if there is some other place in which a very useful function is hidden for table manipulation (for instance controlling for other variables). This is only an example. But there are many more. Were to look for CI for proportions? I can find it but it is not easy. I understand R is more appropriate for difficult statistical procedures (glm and similar), BUT students need to start somewhere…. My specific claim is about the need for a sort of guide in which the different procedures could be classified (and some redundancies could be deleted…..by the way). Is there something similar around? Any project working on this? Any clue for? If not, I would suggest starting some kind of easy reference based on the problem to solve. This could indicate were to look for. Last day I find in package vcd that a function exist for testing the goodness-of-fit of a sample to binomial and other distributions….but this was VERY difficult to locate. Any way, as usual, any indication will be very useful (spaecially for my students!!!) Albert Sorribas Professor of Statistics and Operational Research Departament de Ciències Mèdiques Bàsiques Universitat de Lleida Montserrat Roig 2 25008-Lleida (Espanya) web.udl.es/Biomath/Group [[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 do read the posting guide! http://www.R-project.org/posting-guide.html
[R] garchFit from fSeries
Dear R People: I'm trying to use the garchFit function from the library(fSeries) However, R freezes every time that I use it. Is anyone else having this problem, please? Thanks in advance! R Version 2.2.1 Windows. Sincerely, Erin Hodgess Associate Professor Department of Computer and Mathematical Sciences University of Houston - Downtown mailto: [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] www.r-project.org
Maybe a separate web site that shows R off or maybe just a pointer to the R Graph Gallery. On 4/26/06, Duncan Murdoch [EMAIL PROTECTED] wrote: Romain Francois wrote: Dear R users and developpers, My question is adressed to both of you, so I choose R-help to post it. Are there any plans to jazz up the main R website : http://www.r-project.org The look it have now is the same for a long time and kind of sad compared to other statistical package's website. Of course, the comparison is not fair, since companies are paying web designers to draw lollipop websites ... There have been various suggestions along these lines (check the archives), but there are a number of constraints that make the problem difficult: - there are two web sites, www.r-project.org and cran.r-project.org with different needs. In particular, CRAN must be very low tech because it is mirrored on very diverse sites (including local copies, e.g. on a CDROM). - There are a lot of busy people who need to edit these pages occasionally, so a stable, standard, simple setup is extremely desirable. That means simple HTML to be edited in a text editor, no special CMS. These requirements are quite hard to meet, so expect changes to the web sites to be very time consuming, and possibly rejected en masse in the end. Duncan Murdoch My first idea was to organize some kind of web designing contest. But, I had a small talk with Friedrich Leisch about that, who said that I shouldn't expect too many competitors. So, what about creating a small team, create a home page project and then propose it to the core team. It goes without saying it : The core team has the final word. What do you think ? Who would like to play ? Romain __ 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] garch in tseries
Hello again! Is there a way to include a mean in the garch function in the library(tseries), please? I tried include.mean=T in the function statement but it didn't work thanks in advance! R Version 2.2.1 Windows Sincerely, Erin mailto: [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
[R] stl function
Hi, I have a monthly time series with missing values and I would use stl function to identify seasonality. I tried all settings of na.action but the result is the same: stl(tm245,s.window=11, na.action=na.pass) Error in stl(tm245, s.window = 11, na.action = na.pass) : NA/NaN/Inf in foreign function call (arg 1) Can you help me? Thanks Andrea Toreti [[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
Re: [R] Were to find appropriate functions for a given task in R
Thanks for the indications. All these suggestion will help a lot. The TINN-R application is impressive. However, I think something more PROBLEM directed is needed. I agree that Google and the ?RSiteSearch helps a lot, but yet the explanations (like this discussion) are not clear enough in many cases. Any way, this is my impression as a technical user. The R stuff is really good, but it is difficult to find what you need in many instances. Then, people tend to define its own functions (I'm doing this too), and a lack of standardization makes it difficult to keep everything into control. Albert Sorribas Professor of Statistics and Operational Research Departament de Ciències Mèdiques Bàsiques Universitat de Lleida Montserrat Roig 2 25008-Lleida (Espanya) web.udl.es/Biomath/Group -Mensaje original- De: Gabor Grothendieck [mailto:[EMAIL PROTECTED] Enviado el: miércoles, 26 de abril de 2006 17:47 Para: Albert Sorribas CC: r-help@stat.math.ethz.ch Asunto: Re: [R] Were to find appropriate functions for a given task in R There is a reference sheet here: http://www.rpad.org/Rpad/R-refcard.pdf a function finder here: http://biostat.mc.vanderbilt.edu/s/finder/find.html and task views here: http://cran.r-project.org/src/contrib/Views/ Also use of RSiteSearch and help.search from within R can be helpful. On 4/26/06, Albert Sorribas [EMAIL PROTECTED] wrote: This is a generic request concerning were to look for finding appropriate information on a precise procedure in R. I'm using R for teaching introductory statistics and my students are learning how to deal with it. However, I find it difficult to locate some of the procedures. For instance, for basic crosstabulation, it is obvious that basic functions as table, ftable, and prop.table can be used. But there is a CrossTable function that is very useful. This is hidden in gmodels and gregmisc, as far as I've been able to explore the packages. However, there is no way (unless I sit down to r-help for hours) to be sure if there is some other place in which a very useful function is hidden for table manipulation (for instance controlling for other variables). This is only an example. But there are many more. Were to look for CI for proportions? I can find it but it is not easy. I understand R is more appropriate for difficult statistical procedures (glm and similar), BUT students need to start somewhere . My specific claim is about the need for a sort of guide in which the different procedures could be classified (and some redundancies could be deleted ..by the way). Is there something similar around? Any project working on this? Any clue for? If not, I would suggest starting some kind of easy reference based on the problem to solve. This could indicate were to look for. Last day I find in package vcd that a function exist for testing the goodness-of-fit of a sample to binomial and other distributions .but this was VERY difficult to locate. Any way, as usual, any indication will be very useful (spaecially for my students!!!) Albert Sorribas Professor of Statistics and Operational Research Departament de Ciències Mèdiques Bàsiques Universitat de Lleida Montserrat Roig 2 25008-Lleida (Espanya) web.udl.es/Biomath/Group [[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 do read the posting guide! http://www.R-project.org/posting-guide.html
[R] help using tapply
Dear R-mates,
# Here's what I am trying to do. I have a dataset like this:
id = c(rep(1,8), rep(2,8))
dur1 - c( 17,18,19,18,24,19,24,24 )
est1 - c( rep(1,5), rep(2,3) )
dur2 - c(1,1,3,4,8,12,13,14)
est2 - rep(1,8)
mydata = data.frame(id,
estat=c(est1, est2),
durat=c(dur1, dur2))
# I want to one have this:
id = c(rep(1,8), rep(2,8))
dur1 - c( 17,18,19,20,28,1,2,3 )
est1 - c( rep(1,5), rep(2,3) )
dur2 - c(1,2,3,4,12,13,14,15)
est2 - rep(1,8)
mydata2 = = data.frame(id,
estat=c(est1, est2),
durat=c(dur1, dur2))
# What is happening here? I have a longitudinal dataset.
# Individuals are observed 8 times, and each time each of them are in a
certain state J (here, J={1,2}).
# Each observation is one unit of time away from the following one, except
observations 4 and 5, which are 8 units of time away from each other.
# So here we have individual 1 migrating from state 1 to state 2 at
observation #6,
# while individual 2 stays in state 1 as long as we can observe her.
# I am interested in the spell (duration) of each state.
# However, the durations are clearly mismesuared, and now I am trying to
give some consistency to the data.
# I am assuming that the first duration is correct. Departing from this, I
wrote the following function:
d - function(dur,est)
{
if ( sum( diff(est) )==0 ) # for those who didn't change state
{
for( i in c(2:4))
dur[i] - dur[i-1] + 1
dur[5] - dur[4] + 8
for( i in c(6:8) )
dur[i] - dur[i-1] + 1
}
if ( sum( diff(est) )!=0 ) # for those who changed state
{
j = which(diff(est)!=0) + 1# j is when the change occured
dur[j] = 1
k0 = which( c(1:8) j )[-c(1)]
k1 = which( c(1:8) j )
if(length(j) 1)
{
for( i in 1:(length(j)-1) )
k2 = c(1:8)[c(1:8) j[i] c(1:8) j[i+1]]
k = unique( c(k0,k1,k2) )
}
k = unique( c(k0,k1) )
k = k[!k%in%j]
if(5%in%k)
{
k = k[k != 5]
for(i in k[k5])
dur[i] = dur[i-1] + 1
dur[5] = dur[4] + 8
for(i in k[k5])
dur[i] = dur[i-1] + 1
} else
{
for(i in k)
dur[i] = dur[i-1] + 1
}
}
dur
}
# Now, if a do
d(dur1, est1)
# and
d(dur2,est2)
# I get what I want, except from the fact that I couldn't do this for a
large dataset.
# So I decide to use tapply. But this gives me
new.durat - tapply(mydata$durat, IND=mydata$id, FUN=d,
est=mydata$estat)
mydata$new.durat - unlist(new.durat)
mydata
id estat durat new.durat
1 1 11717
2 1 11818
3 1 11919
4 1 11820
5 1 12428
6 1 21929
7 1 22430
8 1 22431
9 2 1 1 1
10 2 1 1 2
11 2 1 3 3
12 2 1 4 4
13 2 1 812
14 2 11213
15 2 11314
16 2 11415
# what is not what I want. I can't figure it out why, but when I use tapply,
# the logical expression sum( diff(est) )==0 turns out to be true for both
individuals
# (whereas we know this is true only for individual #2).
# I am sorry for the long message. I will be very grateful for any help with
this problem.
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Re: [R] Were to find appropriate functions for a given task in R
Hi Albert, Maybe you can summarize what you find during your teaching and put them on one website. Everyone gives a piece of firewood, then we can build up a strong fire. Thanks Xiaohua On 4/26/06, Albert Sorribas [EMAIL PROTECTED] wrote: Thanks for the indications. All these suggestion will help a lot. The TINN-R application is impressive. However, I think something more PROBLEM directed is needed. I agree that Google and the ?RSiteSearch helps a lot, but yet the explanations (like this discussion) are not clear enough in many cases. Any way, this is my impression as a technical user. The R stuff is really good, but it is difficult to find what you need in many instances. Then, people tend to define its own functions (I'm doing this too), and a lack of standardization makes it difficult to keep everything into control. Albert Sorribas Professor of Statistics and Operational Research Departament de Ciències Mèdiques Bàsiques Universitat de Lleida Montserrat Roig 2 25008-Lleida (Espanya) web.udl.es/Biomath/Group -Mensaje original- De: Gabor Grothendieck [mailto:[EMAIL PROTECTED] Enviado el: miércoles, 26 de abril de 2006 17:47 Para: Albert Sorribas CC: r-help@stat.math.ethz.ch Asunto: Re: [R] Were to find appropriate functions for a given task in R There is a reference sheet here: http://www.rpad.org/Rpad/R-refcard.pdf a function finder here: http://biostat.mc.vanderbilt.edu/s/finder/find.html and task views here: http://cran.r-project.org/src/contrib/Views/ Also use of RSiteSearch and help.search from within R can be helpful. On 4/26/06, Albert Sorribas [EMAIL PROTECTED] wrote: This is a generic request concerning were to look for finding appropriate information on a precise procedure in R. I'm using R for teaching introductory statistics and my students are learning how to deal with it. However, I find it difficult to locate some of the procedures. For instance, for basic crosstabulation, it is obvious that basic functions as table, ftable, and prop.table can be used. But there is a CrossTable function that is very useful. This is hidden in gmodels and gregmisc, as far as I've been able to explore the packages. However, there is no way (unless I sit down to r-help for hours) to be sure if there is some other place in which a very useful function is hidden for table manipulation (for instance controlling for other variables). This is only an example. But there are many more. Were to look for CI for proportions? I can find it but it is not easy. I understand R is more appropriate for difficult statistical procedures (glm and similar), BUT students need to start somewhere . My specific claim is about the need for a sort of guide in which the different procedures could be classified (and some redundancies could be deleted ..by the way). Is there something similar around? Any project working on this? Any clue for? If not, I would suggest starting some kind of easy reference based on the problem to solve. This could indicate were to look for. Last day I find in package vcd that a function exist for testing the goodness-of-fit of a sample to binomial and other distributions .but this was VERY difficult to locate. Any way, as usual, any indication will be very useful (spaecially for my students!!!) Albert Sorribas Professor of Statistics and Operational Research Departament de Ciències Mèdiques Bàsiques Universitat de Lleida Montserrat Roig 2 25008-Lleida (Espanya) web.udl.es/Biomath/Group [[alternative HTML version deleted]] [[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
Re: [R] A question about is.interger function
Not to belabor the point, but if you really need to distinguish integers from other numerical constants, you could try something like this: x - as.integer(5) typeof(x) [1] integer is.integer(x) [1] TRUE on 4/26/2006 1:20 AM Leon said the following: Hi, All I am using is.integer function to examine whether an object is an integer or not, but I get such results, x-3 is.integer(x) [1] FALSE x-3:4 x [1] 3 4 is.integer(x) [1] TRUE Seems that the is.integer cannot handle scalers, is.integer(5) [1] FALSE is.integer(5:6) [1] TRUE Is this a bug in R or I made some mistakes? I am using R 2.2.1 under Windows XP Thanks a lot! Leon [[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 -- Michael Prager, Ph.D. Southeast Fisheries Science Center NOAA Center for Coastal Fisheries and Habitat Research Beaufort, North Carolina 28516 ** Opinions expressed are personal, not official. No ** official endorsement of any product is made or implied. __ 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] Polygon-like interactive selection of plotted points
[Please CC me for all replies, since I am not currently subscribed to the list.] Hi all, I have the following problem/question: Imagine you have a two- dimensional plot, and you want to select a number of points, around which you could draw a polygon. The points of the polygon are defined by clicking in the graphics window (locator()/identify()), all points inside the polygon are returned as an object. Is something like this already implemented? Thanks a lot in advance, Florian __ 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] www.r-project.org
Gabor Grothendieck ggrothendieck at gmail.com writes: Maybe a separate web site that shows R off or maybe just a pointer to the R Graph Gallery. I think the idea of a pointer to the R Graph Gallery is a better one than changing the current R website. I think that the main R web site should be accessible to as many users as possible, including those visually impaired. I hope EmacsSpeaks Statistics (ESS) people will appreciate this suggestion. I do like nice graphics and eye-candy. The other alternate could be an R-web site that is simple and easily accessible as simple mark-up text, which can be speech rendered. Anupam Tyagi. __ 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 beautiful math plot
Gesmann, Markus Markus.Gesmann at lloyds.com writes: See: ?image I would like to use this image in a publication. How do I get permission from the creater of this image? Anupam Tyagi. __ 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] Linker problem in installing 64-bit R
It turned out that I do not have the 64-bit readline library installed. After disabling it using the -without-readline option for ./configure, I successfully made a 64-bit build under Solaris 9. Thanks for your help. On 4/20/06, Prof Brian Ripley [EMAIL PROTECTED] wrote: Note: configure:4041: checking whether the C compiler works configure:4059: error: cannot run C compiled programs. so your compiler installation is broken, seriously enough that configure can make no progress. Also, gcc 3.4.2 is old and has a known bug that stops some R packages using Fortran working correctly, so please avoid it. Please seek local help with your OS. On Thu, 20 Apr 2006, Min Shao wrote: Hi, I am trying to compile R-2.2.1 on Solaris 2.9 with a 64-bit build. Following the instructions in R Installation and Adminstration, I changed the Note, those are example settings that have been tested, but not `instructions'. following settings in config.site: CC=gcc -m64 F77=g77 -64 CXX=g++ -m64 LDFLAGS=-L/usr/local/lib/sparcv9 -L/usr/local/lib But I got the following error messages: configure:3987: gcc -m64 -I/usr/local/include -L/usr/local/lib/sparcv9 -L/usr/local/lib conftest.c 5 /usr/ccs/bin/ld: skipping incompatible /work/net-local-b/sparc- sun-solaris2.9/bin/../lib/gcc/sparc-sun-solaris2.9 /3.4.2/sparcv9/libgcc.a when search ing for -lgcc /usr/ccs/bin/ld: skipping incompatible /work/net-local-b/sparc- sun-solaris2.9/bin/../lib/gcc/sparc-sun-solaris2.9 /3.4.2/sparcv9/libgcc_eh.a when sea rching for -lgcc_eh /usr/ccs/bin/ld: skipping incompatible /lib/sparcv9/libc.so when searching for -lc /usr/ccs/bin/ld: skipping incompatible /usr/lib/sparcv9/libc.so when searching for -lc /usr/ccs/bin/ld: skipping incompatible /usr/lib/sparcv9/libc.so when searching for -lc /usr/ccs/bin/ld: skipping incompatible /work/net-local-b/sparc- sun-solaris2.9/bin/../lib/gcc/sparc-sun-solaris2.9 /3.4.2/sparcv9/libgcc.a when search ing for -lgcc /usr/ccs/bin/ld: skipping incompatible /work/net-local-b/sparc- sun-solaris2.9/bin/../lib/gcc/sparc-sun-solaris2.9 /3.4.2/sparcv9/libgcc_eh.a when sea rching for -lgcc_eh /usr/ccs/bin/ld: skipping incompatible /lib/sparcv9/libc.so when searching for -lc /usr/ccs/bin/ld: skipping incompatible /usr/lib/sparcv9/libc.so when searching for -lc /usr/ccs/bin/ld: skipping incompatible /usr/lib/sparcv9/libc.so when searching for -lc /usr/ccs/bin/ld: warning: sparc:v9 architecture of input file `/work/net-local-b/sparc-sun-solaris2.9/bin/../lib/gcc/sparc- sun-solaris2.9 /3.4.2/spar cv9/crt1.o' is incompatible with sparc output /usr/ccs/bin/ld: warning: sparc:v9 architecture of input file `/work/net-local-b/sparc-sun-solaris2.9/bin/../lib/gcc/sparc- sun-solaris2.9 /3.4.2/spar cv9/crti.o' is incompatible with sparc output /usr/ccs/bin/ld: warning: sparc:v9 architecture of input file `/usr/ccs/lib/sparcv9/values-Xa.o' is incompatible with sparc output /usr/ccs/bin/ld: warning: sparc:v9 architecture of input file `/work/net-local-b/sparc-sun-solaris2.9/bin/../lib/gcc/sparc- sun-solaris2.9 /3.4.2/spar cv9/crtbegin.o' is incompatible with sparc output /usr/ccs/bin/ld: warning: sparc:v9 architecture of input file `/var/tmp//cckWp3Sb.o' is incompatible with sparc output /usr/ccs/bin/ld: warning: sparc:v9 architecture of input file `/work/net-local-b/sparc-sun-solaris2.9/bin/../lib/gcc/sparc- sun-solaris2.9 /3.4.2/spar cv9/crtend.o' is incompatible with sparc output /usr/ccs/bin/ld: warning: sparc:v9 architecture of input file `/work/net-local-b/sparc-sun-solaris2.9/bin/../lib/gcc/sparc- sun-solaris2.9 /3.4.2/spar cv9/crtn.o' is incompatible with sparc output configure:3990: $? = 0 configure:4036: result: a.out configure:4041: checking whether the C compiler works configure:4047: ./a.out configure: line 1: 25817 Bus Error (core dumped) ./$ac_file configure:4050: $? = 138 configure:4059: error: cannot run C compiled programs. I would appreciate any help with resolving the problem. Thanks, Min [[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 -- 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 [[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] Generalized SVD
Hi,
I need to computed the GSVD of two matrices. For doing so I used in my C
code the lapack routine dggsvd. But when I source my file gsvd.R I have
the following error:
Error in eval.with.vis(expr, envir, enclos) :
BLAS/LAPACK routine 'DGGSVD' gave error code -1
Is there a problem with the parameters passed through the gsvd.R script?
Is there a problem within the C script?
I will really appreciate your help.
Thanks,
Philippe
--
Philippe Hupé
Institut Curie, CNRS UMR 144 / Service Bioinformatique
Laboratoire de Transfert (4ème étage)
26 rue d'Ulm
75005 Paris - France
Email : [EMAIL PROTECTED]
Tél :+33 (0)1 44 32 42 75
Fax :+33 (0)1 42 34 65 28
website : http://bioinfo.curie.fr
vA - c(1.0, 2.0, 3.0,
3.0, 2.0, 1.0,
4.0, 5.0, 6.0,
7.0, 8.0, 8.0)
A - matrix(vA,4,3, byrow=TRUE)
vB - c(-2.0, -3.0, 3.0,
4.0, 6.0, 5.0)
B - matrix(vB,2,3, byrow=TRUE)
if(ncol(A)!=ncol(B))
{
stop(A and B matrix does not have the same column number)
}
gsvd - .C(GSVD,
JOBU = as.character('U'),
JOBV = as.character('V'),
JOBQ = as.character('Q'),
M = as.integer(nrow(A)),
N = as.integer(ncol(A)),
P = as.integer(nrow(B)),
K = integer(1),
L = integer(1),
A = as.double(A),
LDA = as.integer(nrow(A)),
B = as.double(B),
LDB = as.integer(nrow(B)),
ALPHA = double(ncol(A)),
BETA = double(ncol(A)),
U = double(nrow(A)*nrow(A)),
LDU = as.integer(nrow(A)),
V = double(nrow(B)*nrow(B)),
LDV = as.integer(nrow(B)),
Q = double(ncol(A)*ncol(A)),
LDQ = as.integer(ncol(A)),
WORK = double(max(c(3*ncol(A),nrow(A),nrow(B)))+ncol(A)),
IWORK = integer(ncol(A)),
INFO = integer(1),
PACKAGE=GSVD)
GSVD_1.0.tar.gz
Description: PostScript document
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[R] Code for Screenshots graphics (following on from ease-of-use issues on www.r-project.org)
Does anyone know where the code for the graphics on: http://www.r-project.org/screenshots/screenshots.html lives? - [[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
Re: [R] Polygon-like interactive selection of plotted points
On Wed, 2006-04-26 at 18:13 +0100, Florian Nigsch wrote: [Please CC me for all replies, since I am not currently subscribed to the list.] Hi all, I have the following problem/question: Imagine you have a two- dimensional plot, and you want to select a number of points, around which you could draw a polygon. The points of the polygon are defined by clicking in the graphics window (locator()/identify()), all points inside the polygon are returned as an object. Is something like this already implemented? Thanks a lot in advance, Florian I don't know if anyone has created a single function do to this (though it is always possible). However, using: RSiteSearch(points inside polygon) brings up several function hits that, if put together with the above interactive functions, could be used to do what you wish. That is, input the matrix of x,y coords of the interactively selected polygon and the x,y coords of the underlying points set to return the points inside or outside the polygon boundaries. Just as an FYI, you might also want to look at ?chull, which is in the base R distribution and returns the set of points on the convex hull of the underlying point set. This is to some extent, the inverse of what you wish to do. HTH, Marc Schwartz __ 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] help using tapply
On 4/26/06, Dimitri Szerman [EMAIL PROTECTED] wrote:
Dear R-mates,
# Here's what I am trying to do. I have a dataset like this:
id = c(rep(1,8), rep(2,8))
dur1 - c( 17,18,19,18,24,19,24,24 )
est1 - c( rep(1,5), rep(2,3) )
dur2 - c(1,1,3,4,8,12,13,14)
est2 - rep(1,8)
mydata = data.frame(id,
estat=c(est1, est2),
durat=c(dur1, dur2))
# I want to one have this:
id = c(rep(1,8), rep(2,8))
dur1 - c( 17,18,19,20,28,1,2,3 )
est1 - c( rep(1,5), rep(2,3) )
dur2 - c(1,2,3,4,12,13,14,15)
est2 - rep(1,8)
mydata2 = = data.frame(id,
estat=c(est1, est2),
durat=c(dur1, dur2))
# What is happening here? I have a longitudinal dataset.
# Individuals are observed 8 times, and each time each of them are in a
certain state J (here, J={1,2}).
# Each observation is one unit of time away from the following one, except
observations 4 and 5, which are 8 units of time away from each other.
# So here we have individual 1 migrating from state 1 to state 2 at
observation #6,
# while individual 2 stays in state 1 as long as we can observe her.
# I am interested in the spell (duration) of each state.
# However, the durations are clearly mismesuared, and now I am trying to
give some consistency to the data.
# I am assuming that the first duration is correct. Departing from this, I
wrote the following function:
d - function(dur,est)
{
if ( sum( diff(est) )==0 ) # for those who didn't change state
{
for( i in c(2:4))
dur[i] - dur[i-1] + 1
dur[5] - dur[4] + 8
for( i in c(6:8) )
dur[i] - dur[i-1] + 1
}
if ( sum( diff(est) )!=0 ) # for those who changed state
{
j = which(diff(est)!=0) + 1# j is when the change occured
dur[j] = 1
k0 = which( c(1:8) j )[-c(1)]
k1 = which( c(1:8) j )
if(length(j) 1)
{
for( i in 1:(length(j)-1) )
k2 = c(1:8)[c(1:8) j[i] c(1:8) j[i+1]]
k = unique( c(k0,k1,k2) )
}
k = unique( c(k0,k1) )
k = k[!k%in%j]
if(5%in%k)
{
k = k[k != 5]
for(i in k[k5])
dur[i] = dur[i-1] + 1
dur[5] = dur[4] + 8
for(i in k[k5])
dur[i] = dur[i-1] + 1
} else
{
for(i in k)
dur[i] = dur[i-1] + 1
}
}
dur
}
# Now, if a do
d(dur1, est1)
# and
d(dur2,est2)
# I get what I want, except from the fact that I couldn't do this for a
large dataset.
# So I decide to use tapply. But this gives me
new.durat - tapply(mydata$durat, IND=mydata$id, FUN=d,
est=mydata$estat)
mydata$new.durat - unlist(new.durat)
mydata
id estat durat new.durat
1 1 11717
2 1 11818
3 1 11919
4 1 11820
5 1 12428
6 1 21929
7 1 22430
8 1 22431
9 2 1 1 1
10 2 1 1 2
11 2 1 3 3
12 2 1 4 4
13 2 1 812
14 2 11213
15 2 11314
16 2 11415
# what is not what I want. I can't figure it out why, but when I use tapply,
# the logical expression sum( diff(est) )==0 turns out to be true for both
individuals
# (whereas we know this is true only for individual #2).
# I am sorry for the long message. I will be very grateful for any help with
this problem.
I didn't try to read all this carefully but I think you want to tapply
over the indices so you can use them in both columns:
with(mydata,
unlist(tapply(seq(id), id, function(i) d(durat[i], estat[i])))
)
or use by:
unlist(by(mydata, mydata$id, function(x) d(x$durat, x$estat)))
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Re: [R] Polygon-like interactive selection of plotted points
?in.convex.hull in the package tripack. url:www.econ.uiuc.edu/~rogerRoger Koenker email[EMAIL PROTECTED]Department of Economics vox: 217-333-4558University of Illinois fax: 217-244-6678Champaign, IL 61820 On Apr 26, 2006, at 1:25 PM, Marc Schwartz (via MN) wrote: On Wed, 2006-04-26 at 18:13 +0100, Florian Nigsch wrote: [Please CC me for all replies, since I am not currently subscribed to the list.] Hi all, I have the following problem/question: Imagine you have a two- dimensional plot, and you want to select a number of points, around which you could draw a polygon. The points of the polygon are defined by clicking in the graphics window (locator()/identify()), all points inside the polygon are returned as an object. Is something like this already implemented? Thanks a lot in advance, Florian I don't know if anyone has created a single function do to this (though it is always possible). However, using: RSiteSearch(points inside polygon) brings up several function hits that, if put together with the above interactive functions, could be used to do what you wish. That is, input the matrix of x,y coords of the interactively selected polygon and the x,y coords of the underlying points set to return the points inside or outside the polygon boundaries. Just as an FYI, you might also want to look at ?chull, which is in the base R distribution and returns the set of points on the convex hull of the underlying point set. This is to some extent, the inverse of what you wish to do. HTH, Marc Schwartz __ 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] accessing a SOAP based web service from R
Hi, I have a number of web services that run on a server and can be accessed via SOAP as well as by creating a specific URL. Now, for certain services, the argument that I need to send is about 10 to 20 characters and the URL approach works fine. However if the argument is a few kilobytes I would rather create a SOAP packet and send that off. So my first question is: is there a package that can create SOAP packets and communicate with a web service via SOAP? I have found the RSOAP package but that looks like it deals with accessing R via SOAP. I think my situation is simpler(?) Another approach I could use is to create a Java class that would do the communication and use SJava etc to use it. However that seems like overkill Now, if I use the URL approach I get back an XML document. I realize I could use the XML package for R to parse it. On the other hand if a SOAP package could decode the return document and simply hand back the result, that would make life easier. Any pointers would be greatly appreciated. Thanks, --- Rajarshi Guha [EMAIL PROTECTED] http://jijo.cjb.net GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE --- Q: What do you get when you cross a mosquito with a mountain climber? A: Nothing. You can't cross a vector with a scaler. __ 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] copying previously installed libraries to R 2.3.0
hi all, is there a new mechanism in R 2.3.0 for copying libraries from, say, R 2.2.1 to R 2.3.0? i ask because gabor grothendieck comments in his copydir.bat (from gabor's batchfiles at: http://cran.r-project.org/contrib/extra/batchfiles/batchfiles_0.2-5.zip ): ``:: I personally upgraded my 2.1.0 to 2.2.0 this way so it seems ok until :: R replaces this with something better which is expected for 2.3.0. ''' see also the posting below. cheers, thomas. [R] copy contributed packages from R 2.2.0 to 2.2.1 This message: [ Message body ] [ More options ] Related messages: [ Next message ] [ Previous message ] [ In reply to ] [ Next in thread ] From: Ronnie Babigumira rb.glists Date: Fri, 23 Dec 2005 15:58:36 +0100 Hi Helli, this came up last week, Here are some of the replys posted 1. In http://cran.r-project.org/contrib/extra/batchfiles/batchfiles_0.2-5.zip are two Windows XP batch files: movedir.bat copydir.bat which will move the packages (which is much faster and suitable if you don't need the old version of R any more) or copy the packages (which takes longer but preserves the old version). 2. x - installed.packages()[,1] install.packages(x) 3. This is one reason we normally recommend that you install into a separate library. Then update.packages(checkBuilt = TRUE) is all that is needed. However, foo - installed.packages() as.vector(foo[is.na(foo[, Priority]), 1]) will give you a character vector which you can feed to install.packages(), so it's not complex to do manually. 4. If the previous installation is still alive, fire it up and pS - packageStatus() pkgs - pS$inst$Package[!pS$inst$Priority %in% c(base, recommended)] save(pkgs, file = foo) In the new installation, load(foo) install.packages(pkgs) Helmut Kudrnovsky wrote: hi R-users, a few days ago R 2.2.1 came out. on my win xp i'installed R 2.2.0. along the time i've installed a lot of contributed packages. my internet-connection is not very fast. so my question: is it possible after installing R 2.2.1 to do copy/paste the contributed packages from the C:\Programme\R221 to the C:\Programme\R2.2.1- location in the files system? or have i to download and install the packages new? greetings from the snowy austria merry christmas helli system R.2.2.0 win xp __ R-help at 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 Received on Fri Dec 23 2005 - 15:58:36 EST This message: [ Message body ] Next message: Matthias Kohl: [R] convolution of the double exponential distribution Previous message: Helmut Kudrnovsky: [R] copy contributed packages from R 2.2.0 to 2.2.1 In reply to: Helmut Kudrnovsky: [R] copy contributed packages from R 2.2.0 to 2.2.1 Next in thread: Uwe Ligges: [R] copy contributed packages from R 2.2.0 to 2.2.1 Contemporary messages sorted: [ by date ] [ by thread ] [ by subject ] [ by author ] [ by messages with attachments ] This archive was generated by hypermail 2.2.0 : Sat Dec 31 2005 - 19:09:32 EST [[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
Re: [R] copying previously installed libraries to R 2.3.0
See Windows FAQ 2.8 - works well. -Christos -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Thomas Harte Sent: Wednesday, April 26, 2006 2:54 PM To: r-help@stat.math.ethz.ch Subject: [R] copying previously installed libraries to R 2.3.0 hi all, is there a new mechanism in R 2.3.0 for copying libraries from, say, R 2.2.1 to R 2.3.0? i ask because gabor grothendieck comments in his copydir.bat (from gabor's batchfiles at: http://cran.r-project.org/contrib/extra/batchfiles/batchfiles_0.2-5.zip ): ``:: I personally upgraded my 2.1.0 to 2.2.0 this way so it seems ok until :: R replaces this with something better which is expected for 2.3.0. ''' see also the posting below. cheers, thomas. [R] copy contributed packages from R 2.2.0 to 2.2.1 This message: [ Message body ] [ More options ] Related messages: [ Next message ] [ Previous message ] [ In reply to ] [ Next in thread ] From: Ronnie Babigumira rb.glists Date: Fri, 23 Dec 2005 15:58:36 +0100 Hi Helli, this came up last week, Here are some of the replys posted 1. In http://cran.r-project.org/contrib/extra/batchfiles/batchfiles_0.2-5.zip are two Windows XP batch files: movedir.bat copydir.bat which will move the packages (which is much faster and suitable if you don't need the old version of R any more) or copy the packages (which takes longer but preserves the old version). 2. x - installed.packages()[,1] install.packages(x) 3. This is one reason we normally recommend that you install into a separate library. Then update.packages(checkBuilt = TRUE) is all that is needed. However, foo - installed.packages() as.vector(foo[is.na(foo[, Priority]), 1]) will give you a character vector which you can feed to install.packages(), so it's not complex to do manually. 4. If the previous installation is still alive, fire it up and pS - packageStatus() pkgs - pS$inst$Package[!pS$inst$Priority %in% c(base, recommended)] save(pkgs, file = foo) In the new installation, load(foo) install.packages(pkgs) Helmut Kudrnovsky wrote: hi R-users, a few days ago R 2.2.1 came out. on my win xp i'installed R 2.2.0. along the time i've installed a lot of contributed packages. my internet-connection is not very fast. so my question: is it possible after installing R 2.2.1 to do copy/paste the contributed packages from the C:\Programme\R221 to the C:\Programme\R2.2.1- location in the files system? or have i to download and install the packages new? greetings from the snowy austria merry christmas helli system R.2.2.0 win xp __ R-help at 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 Received on Fri Dec 23 2005 - 15:58:36 EST This message: [ Message body ] Next message: Matthias Kohl: [R] convolution of the double exponential distribution Previous message: Helmut Kudrnovsky: [R] copy contributed packages from R 2.2.0 to 2.2.1 In reply to: Helmut Kudrnovsky: [R] copy contributed packages from R 2.2.0 to 2.2.1 Next in thread: Uwe Ligges: [R] copy contributed packages from R 2.2.0 to 2.2.1 Contemporary messages sorted: [ by date ] [ by thread ] [ by subject ] [ by author ] [ by messages with attachments ] This archive was generated by hypermail 2.2.0 : Sat Dec 31 2005 - 19:09:32 EST [[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 do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Code for Screenshots graphics (following on from ease-of-use issues on www.r-project.org)
On Wed, 2006-04-26 at 11:05 -0700, John McHenry wrote: Does anyone know where the code for the graphics on: http://www.r-project.org/screenshots/screenshots.html lives? demo(graphics) demo(image) demo(persp) These should cover each of the screen shots and then some. If you know how to navigate the R package subdirectories of your R installation, the R code files for the demos are located in the 'demo' subdir of the 'graphics' package. Typically this would be: $RHOME/library/graphics/demo HTH, Marc Schwartz __ 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] Polygon-like interactive selection of plotted points
On Wed, 26 Apr 2006, Marc Schwartz (via MN) wrote: On Wed, 2006-04-26 at 18:13 +0100, Florian Nigsch wrote: [Please CC me for all replies, since I am not currently subscribed to the list.] Hi all, I have the following problem/question: Imagine you have a two- dimensional plot, and you want to select a number of points, around which you could draw a polygon. The points of the polygon are defined by clicking in the graphics window (locator()/identify()), all points inside the polygon are returned as an object. Is something like this already implemented? Thanks a lot in advance, Florian I don't know if anyone has created a single function do to this (though it is always possible). However, using: RSiteSearch(points inside polygon) brings up several function hits that, if put together with the above interactive functions, could be used to do what you wish. That is, input the matrix of x,y coords of the interactively selected polygon and the x,y coords of the underlying points set to return the points inside or outside the polygon boundaries. This sequence from the splancs package should do it: library(splancs) set.seed(20060426) xy - cbind(x=runif(100), y=runif(100)) plot(xy) poly - getpoly() # this gets the polygon on-screen plot(xy) polygon(poly) io - inout(xy, poly) # this returns a logical vector for points in the polygon points(xy[io,], pch=16, col=blue) Roger Just as an FYI, you might also want to look at ?chull, which is in the base R distribution and returns the set of points on the convex hull of the underlying point set. This is to some extent, the inverse of what you wish to do. HTH, Marc Schwartz -- Roger Bivand Economic Geography Section, Department of Economics, Norwegian School of Economics and Business Administration, Helleveien 30, N-5045 Bergen, Norway. voice: +47 55 95 93 55; fax +47 55 95 95 43 e-mail: [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] accessing a SOAP based web service from R
Rajarshi Guha [EMAIL PROTECTED] writes: Hi, I have a number of web services that run on a server and can be accessed via SOAP as well as by creating a specific URL. Now, for certain services, the argument that I need to send is about 10 to 20 characters and the URL approach works fine. However if the argument is a few kilobytes I would rather create a SOAP packet and send that off. So my first question is: is there a package that can create SOAP packets and communicate with a web service via SOAP? SSOAP http://www.omegahat.org/SSOAP/ __ 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] Code for Screenshots graphics (following on from ease-of-use issues on www.r-project.org)
On Wed, 26 Apr 2006, Marc Schwartz (via MN) wrote: On Wed, 2006-04-26 at 11:05 -0700, John McHenry wrote: Does anyone know where the code for the graphics on: http://www.r-project.org/screenshots/screenshots.html lives? demo(graphics) demo(image) demo(persp) These should cover each of the screen shots and then some. At least three of them aren't there (though most of the necessary ideas are). The forest plot is example(catheter) in the rmeta package. The coplot with nice interactions is coplot(Ozone~Solar.R|Temp*Wind, number=4,pch=21,col=darkred,bg=darkred, data=airquality) and the code for the mathematical annotation example is in the archives at: http://finzi.psych.upenn.edu/R/Rhelp02a/archive/60471.html -thomas Thomas Lumley Assoc. Professor, Biostatistics [EMAIL PROTECTED] University of Washington, Seattle __ 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] copying previously installed libraries to R 2.3.0
the windoze faq that you refer to doesn't quite address the question that i asked, but thanks all the same. 2.8 What's the best way to upgrade? That's a matter of taste. For most people the best thing to do is to uninstall R (see the previous Q), install the new version, copy any installed packages to the library folder in the new installation, run update.packages() in the new R (`Update packages...' from the Packages menu, if you prefer) and then delete anything left of the old installation. Different versions of R are quite deliberately installed in parallel folders so you can keep old versions around if you wish. Upgrading from R 1.x.y to R 2.x.y is special as all the packages need to be reinstalled. Rather than copy them across, make a note of their names and re-install them from CRAN. Christos Hatzis [EMAIL PROTECTED] wrote: See Windows FAQ 2.8 - works well. -Christos -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Thomas Harte Sent: Wednesday, April 26, 2006 2:54 PM To: r-help@stat.math.ethz.ch Subject: [R] copying previously installed libraries to R 2.3.0 hi all, is there a new mechanism in R 2.3.0 for copying libraries from, say, R 2.2.1 to R 2.3.0? i ask because gabor grothendieck comments in his copydir.bat (from gabor's batchfiles at: http://cran.r-project.org/contrib/extra/batchfiles/batchfiles_0.2-5.zip ): ``:: I personally upgraded my 2.1.0 to 2.2.0 this way so it seems ok until :: R replaces this with something better which is expected for 2.3.0. ''' see also the posting below. cheers, thomas. [R] copy contributed packages from R 2.2.0 to 2.2.1 This message: [ Message body ] [ More options ] Related messages: [ Next message ] [ Previous message ] [ In reply to ] [ Next in thread ] From: Ronnie Babigumira Date: Fri, 23 Dec 2005 15:58:36 +0100 Hi Helli, this came up last week, Here are some of the replys posted 1. In http://cran.r-project.org/contrib/extra/batchfiles/batchfiles_0.2-5.zip are two Windows XP batch files: movedir.bat copydir.bat which will move the packages (which is much faster and suitable if you don't need the old version of R any more) or copy the packages (which takes longer but preserves the old version). 2. x - installed.packages()[,1] install.packages(x) 3. This is one reason we normally recommend that you install into a separate library. Then update.packages(checkBuilt = TRUE) is all that is needed. However, foo - installed.packages() as.vector(foo[is.na(foo[, Priority]), 1]) will give you a character vector which you can feed to install.packages(), so it's not complex to do manually. 4. If the previous installation is still alive, fire it up and pS - packageStatus() pkgs - pS$inst$Package[!pS$inst$Priority %in% c(base, recommended)] save(pkgs, file = foo) In the new installation, load(foo) install.packages(pkgs) Helmut Kudrnovsky wrote: hi R-users, a few days ago R 2.2.1 came out. on my win xp i'installed R 2.2.0. along the time i've installed a lot of contributed packages. my internet-connection is not very fast. so my question: is it possible after installing R 2.2.1 to do copy/paste the contributed packages from the C:\Programme\R221 to the C:\Programme\R2.2.1- location in the files system? or have i to download and install the packages new? greetings from the snowy austria merry christmas helli system R.2.2.0 win xp __ R-help at 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 Received on Fri Dec 23 2005 - 15:58:36 EST This message: [ Message body ] Next message: Matthias Kohl: [R] convolution of the double exponential distribution Previous message: Helmut Kudrnovsky: [R] copy contributed packages from R 2.2.0 to 2.2.1 In reply to: Helmut Kudrnovsky: [R] copy contributed packages from R 2.2.0 to 2.2.1 Next in thread: Uwe Ligges: [R] copy contributed packages from R 2.2.0 to 2.2.1 Contemporary messages sorted: [ by date ] [ by thread ] [ by subject ] [ by author ] [ by messages with attachments ] This archive was generated by hypermail 2.2.0 : Sat Dec 31 2005 - 19:09:32 EST [[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 [[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 in R
Hi, I cant understand where I am going wrong.Below is my code.I would really appreciate your help. Thanks. genfile-read.table(c:/tina/phd/bs871/hw/genfile.txt,skip=1) #read in SNP data snp.dat - as.matrix(genfile) snp.name - scan(c:/tina/phd/bs871/hw/genfile.txt,nline=1,what=character) Read 100 items n.snp - length(snp.name) n.id - 1 #number of fields for ids, sex and affection status ###form gntp using the two alleles of each SNP allele1 - snp.dat[,seq(1,2*n.snp,2)+n.id ] allele2 - snp.dat[,seq(2,2*n.snp,2)+n.id ] temp - matrix(paste(allele1,allele2,sep=|),dim(allele1)) temp - data.frame(temp) convt - function(x) x - factor(as.character(x),exclude=0|0) gntp - as.data.frame(lapply(temp,convt)) ###create new snp data with ids and gntp only names(gntp) - snp.name ids - as.data.frame(snp.dat[,1:n.id]) names(ids) - c(fid) snp.dat - cbind(ids,gntp) #read in phenotype data #-- phen.dat - read.table(c:/tina/phd/bs871/fram.csv,header=T,sep=,,na.string='') phen.name - scan(c:/tina/phd/bs871/fram.csv,nline=1,what=character) Read 1 item n.phen - length(phen.name) names(phen.dat) - c(id, phen.name) test.allsnp - function(phen) + + apply(phen.dat[,snp.name],glm.reg,phen=phen) ##Above:since snp gntp data are defined as factor, use lapply instead of apply(matrix only) #Below; apply() results in three dimensional list (phen,snp) #use unlist to convert the list into a vector, then use matrix to convert the vector #into a matrix of 15 columns, each row for a (phen,snp) combination with byrow=T final - matrix(unlist(apply(phen.dat[,phen.name],2,test.allsnp)),byrow=T,ncol=15) Error in apply(phen.dat[, phen.name], 2, test.allsnp) : dim(X) must have a positive length - [[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
Re: [R] cdf of weibull distribution
Peter Dalgaard wrote:
Sachin J [EMAIL PROTECTED] writes:
Hi,
I have a data set which is assumed to follow weibull distr'. How
can I find of cdf for this data. For example, for normal data I used
(package - lmomco)
cdfnor(15,parnor(lmom.ub(c(df$V1
If X is a Weibull random variable then -X has a generalized
extreme-value distribution. So something like
cdfgev(-15,pargev(lmom.ub(-c(df$V1
should do the trick.
Also, lmomco package does not have functions for finding cdf for
some of the distributions like lognormal. Is there any other package,
which can handle these distributions?
I recommend that you use the generalized normal distribution, a
reparametrized and extended version of the lognormal that accommodates
distributions with negative as well as positive skewness. See Hosking
Wallis, Regional Frequency Analysis, Cambridge Univ. Press, 1997,
p.198. The relevant routines in lmomco are cdfgno, lmomgno, pargno and
quagno.
What's wrong with pweibull, plnorm, etc.? Or pnorm for that matter
What's wrong, or at least what I often find somewhat incovenient, is
that R's distribution functions require the distribution parameters
to be supplied as separate arguments rather than as a single vector.
This complicates operations that involve passing parameters from one
function to another. For example, the OP's one-liner above would,
if pnorm were used, have to become something like
par - parnor(lmom.ub(c(df$V1)))
pnorm(15, par[1], par[2])
or, if we still want to do it in one line,
do.call('pnorm', as.list(c(15, parnor(lmom.ub(c(df$V1))
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Re: [R] www.r-project.org
I am coming late into the discussion, so apologies if the following points are redundant. 1) IMHO, the most important feature that would make life a lot easier for everyone is having search engines on the main webpage. I know you can click on the Search on the left hand side pane but putting it on the main webpage is much more useful. We can also have a targets section for the search (c.f. http://finzi.psych.upenn.edu/nmz.html) where one can search mailing list, html Manual, FAQ, user-inputted package name etc. 2) About having explicit URL print, may I suggest using http://maps.google.com approach of using the Link to this page (top right hand of the page) ? 3) I understand that R is restricted in terms of priority and human resources. But given that Asia (e.g. India, Singapore, China) has low labour costs and abundant computing personals, would it not make sense for some Asian research group to offer to spearhead and maintain the website ? From a marketing point of view some nice graphics, search functions and navigation etc would be useful to attract newcomers. There could be a simple version alternative (as it is now) for those who prefer or those who have trouble accessing the site. Just my £0.02. Regards, Adai On Tue, 2006-04-25 at 12:33 -0700, Spencer Graves wrote: Hi, Gabor: inline Gabor Grothendieck wrote: On Windows, right click the web page, choose Properties and copy the url there. That works, and I will use it in the future. Thanks. However, if the subject is not educating Spencer Graves but how to make www.r-project.org more user friendly, then it still might help to display as Address the actual web address of the archive page rather than www.r-project.org. It may not look as pretty, but I'm for function first and cosmetics only if they don't interfere with functionality. Best Wishes, spencer graves On 4/25/06, Spencer Graves [EMAIL PROTECTED] wrote: __ 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] Course - May 2006, R/Splus Fundamentals and Programming Techniques***San Francisco, Washington DC
XLSolutions Corporation (www.xlsolutions-corp.com) is proud to announce 2-day R/S-plus Fundamentals and Programming Techniques in San Francisco: www.xlsolutions-corp.com/Rfund.htm San Francisco *** May 25-26 Washington, DC *** May TBD Reserve your seat now at the early bird rates! Payment due AFTER the class Course Description: This two-day beginner to intermediate R/S-plus course focuses on a broad spectrum of topics, from reading raw data to a comparison of R and S. We will learn the essentials of data manipulation, graphical visualization and R/S-plus programming. We will explore statistical data analysis tools,including graphics with data sets. How to enhance your plots, build your own packages (librairies) and connect via ODBC,etc. We will perform some statistical modeling and fit linear regression models. Participants are encouraged to bring data for interactive sessions With the following outline: - An Overview of R and S - Data Manipulation and Graphics - Using Lattice Graphics - A Comparison of R and S-Plus - How can R Complement SAS? - Writing Functions - Avoiding Loops - Vectorization - Statistical Modeling - Project Management - Techniques for Effective use of R and S - Enhancing Plots - Using High-level Plotting Functions - Building and Distributing Packages (libraries) - Connecting; ODBC, Rweb, Orca via sockets and via Rjava Email us for group discounts. Email Sue Turner: [EMAIL PROTECTED] Phone: 206-686-1578 Visit us: www.xlsolutions-corp.com/training.htm Please let us know if you and your colleagues are interested in this classto take advantage of group discount. Register now to secure your seat! Interested in R/Splus Advanced course? email us. Cheers, Elvis Miller, PhD Manager Training. XLSolutions Corporation 206 686 1578 www.xlsolutions-corp.com [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
[R] Fwd: Re: Help needed
Note: forwarded message attached.
-
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Subject: Re: [R] Help needed
To: Petr Pikal [EMAIL PROTECTED]
In-Reply-To: [EMAIL PROTECTED]
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Thanks a lot.
How could I change the following code in SAS macro to R (the part marked in
red)?
Thanks so much!
attach(fram)
dset1-cbind(AGE,BMI,DEATH)
BMIGRP1-cut(BMI,breaks=c(14,20,25,57),right=TRUE)
levels(BMIGRP1)
BMIGRP-as.numeric(BMIGRP1)
AGEGRP-floor(AGE/10)-2
dset-cbind(AGEGRP,BMIGRP,DEATH)
maxage-max(dset[,1])
minage-min(dset[,1])
maxcls-max(dset[,2], na.rm=T)
mincls-min(dset[,2],na.rm=T)
nage-maxage-minage+1
nclass-maxcls-mincls+1
nsub-nrow(dset)
weight - matrix(,nage,1)
for ( i in minage:maxage )
{weight[i-minage+1,1] = sum(std = i)}
atrisk = matrix(,nclass,nage)
wevents = matrix(,nclass,nage)
#reduce data set to frequency table
for( i in (minage : maxage))
for( j in (mincls : maxcls))
#atrisk1-aggregate(dset[,c(AGEGRP,BMIGRP)],list(RANDID=dset1$RANDID,sum)
{atrisk[j-mincls+1,i-minage+1] =
sum((dset[,1]=i) (dset[,2]=j))
wevents[j-mincls+1,i-minage+1]=
sum((dset[,1]=i) (dset[,2]=j)(dset[,3]=1))}
vtit = char(t(mincls:maxcls),5,0) // {Total};
htit = {'at risk' 'events' 'rate/1000'};
*;
atrisk2 = atrisk // atrisk[+,1:nage];
event2 = wevents // wevents[+,1:nage];
atrisk3 = choose(atrisk2=0,1,atrisk2);
rate = event2/atrisk3;
Petr Pikal [EMAIL PROTECTED] wrote:
Hi
you experienced difference between matrix (cbind()) and data
frame (data.frame(..)) or you have some NA value in your BMIGRP1
try:
maxcls-max(dset[,2], na.rm=T)
if you have some NA values
or use
str(dset) to look what types are your variables.
HTH
Petr
On 25 Apr 2006 at 18:16, Anamika Chaudhuri wrote:
Date sent: Tue, 25 Apr 2006 18:16:42 -0700 (PDT)
From: Anamika Chaudhuri
To: Richard M. Heiberger , r-help@stat.math.ethz.ch
Subject: Re: [R] Help needed
As my earlier email said I am not getting the maxcls. I do get numbers
coded as 1,2,3 for BMIGRP(when I print BMIGRP) but not getting the max
of (1,2,3) which should be 3, I guess.
Thanks for your help
Anamika
Anamika Chaudhuri wrote:
dset1-cbind(AGE,BMI,DEATH)
BMIGRP-cut(BMI,breaks=c(14,20,25,57),right=TRUE)
levels(BMIGRP)
[1] (14,20] (20,25] (25,57]
BMIGRP1-as.numeric(BMIGRP)
AGEGRP-floor(AGE/10)-2
dset-cbind(AGEGRP,BMIGRP1,DEATH)
maxage-max(dset[,1])
minage-min(dset[,1])
maxcls-max(dset[,2])
maxcls
[1] NA
Why doesnt it give me a no for maxcls then?
Thanks.
Richard M. Heiberger wrote:
x - rnorm(100)
xx - cut(x,3)
levels(xx)
[1] (-2.37,-0.716] (-0.716,0.933] (0.933,2.58]
as.numeric(xx)
-
-
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Petr Pikal
[EMAIL PROTECTED]
-
Celebrate Earth Day everyday! Discover 10 things you can do to help slow
climate change. Yahoo! Earth Day
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divThanks a lot./div divHow could I change the following code in SAS
macro to R (the part marked in red)?/div divThanks so much!/div
divnbsp;/div
divattach(fram)BRdset1lt;-cbind(AGE,BMI,DEATH)BRBMIGRP1lt;-cut(BMI,breaks=c(14,20,25,57),right=TRUE)BRlevels(BMIGRP1)BRBMIGRPlt;-as.numeric(BMIGRP1)BRAGEGRPlt;-floor(AGE/10)-2BRdsetlt;-cbind(AGEGRP,BMIGRP,DEATH)BRmaxagelt;-max(dset[,1])BRminagelt;-min(dset[,1])BRmaxclslt;-max(dset[,2],
na.rm=T)BRminclslt;-min(dset[,2],na.rm=T)BRnagelt;-maxage-minage+1BRnclasslt;-maxcls-mincls+1BRnsublt;-nrow(dset)BRweight
lt;- matrix(,nage,1)BRfor ( i in minage:maxage )BRnbsp;
{weight[i-minage+1,1] = sum(std = i)}/div divnbsp; atrisk =
matrix(,nclass,nage)BRnbsp; wevents = matrix(,nclass,nage)BR#reduce data
set to frequency table BRnbsp;for( i in (minage : maxage))BRnbsp;for( j
in (mincls :
maxcls))BR#atrisk1lt;-aggregate(dset[,c(AGEGRP,BMIGRP)],list(RANDID=dset1$RANDID,sum)/div
divnbsp;nbsp;nbsp; {atrisk[j-mincls+1,i-minage+1]
=BRnbsp;nbsp;nbsp;nbsp; sum((dset[,1]=i)amp;
(dset[,2]=j))BRnbsp;nbsp;nbsp;
wevents[j-mincls+1,i-minage+1]=BRnbsp;nbsp;nbsp;nbsp;nbsp;
sum((dset[,1]=i)amp; (dset[,2]=j)amp;(dset[,3]=1))}/div divFONT
color=#ffvtit = char(t(mincls:maxcls),5,0) // {Total};BRhtit = {'at
risk' 'events' 'rate/1000'};BR*;BRatrisk2 = atrisk //
atrisk[+,1:nage];BRevent2 = wevents // wevents[+,1:nage];BRatrisk3 =
choose(atrisk2=0,1,atrisk2);BRrate =
[R] comparing mantel tests for three different species
Hi, I have calculated mantel statistics for three plant species to check for isolation by distance (thus, comparing genetic distance to geographic distance). Now, I would like to test whether the species have significantly different isolation by distance behaviour. Is there a R-function that allows me to do this? Cheers and thank for any comments Patrick -- Patrick Kuss PhD-student Institute of Botany University of Basel Schönbeinstr. 6 CH-4056 Basel +41 61 267 2976 __ 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] copying previously installed libraries to R 2.3.0
Note that the FAQ is really no different from batchfiles since the FAQ does not address how to move or copy the packages and the batchfiles scripts just do that (with the safeguard that they will not overwrite any packages that are already there so you could, for example, manually install a few packages and the move or copy the remaining ones over.) I think there was some discussion that 2.3.0 might have moving/copying capability built into the R installer but since it seems that that did not make it into 2.3.0 it should be possible to use the scripts, as before, or, alternatively, just re-install all your packages from scratch. By the way, there were some comments about the advantage of keeping your packages in a library so that you can just update the library. The problem with that is that if you want to keep multiple versions of R on the same system then you will want to make sure that each R version has packages that run with that version of R so if you clobber the ones that run with 2.2.0, say, by overwriting them with 2.3.0 packages then you can no longer use that library with 2.2.0. If you keep the packages in .../R/R-2/library then you can be sure that each R version has the right packages in its library without messing around. On 4/26/06, Thomas Harte [EMAIL PROTECTED] wrote: the windoze faq that you refer to doesn't quite address the question that i asked, but thanks all the same. 2.8 What's the best way to upgrade? That's a matter of taste. For most people the best thing to do is to uninstall R (see the previous Q), install the new version, copy any installed packages to the library folder in the new installation, run update.packages() in the new R (`Update packages...' from the Packages menu, if you prefer) and then delete anything left of the old installation. Different versions of R are quite deliberately installed in parallel folders so you can keep old versions around if you wish. Upgrading from R 1.x.y to R 2.x.y is special as all the packages need to be reinstalled. Rather than copy them across, make a note of their names and re-install them from CRAN. Christos Hatzis [EMAIL PROTECTED] wrote: See Windows FAQ 2.8 - works well. -Christos -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Thomas Harte Sent: Wednesday, April 26, 2006 2:54 PM To: r-help@stat.math.ethz.ch Subject: [R] copying previously installed libraries to R 2.3.0 hi all, is there a new mechanism in R 2.3.0 for copying libraries from, say, R 2.2.1 to R 2.3.0? i ask because gabor grothendieck comments in his copydir.bat (from gabor's batchfiles at: http://cran.r-project.org/contrib/extra/batchfiles/batchfiles_0.2-5.zip ): ``:: I personally upgraded my 2.1.0 to 2.2.0 this way so it seems ok until :: R replaces this with something better which is expected for 2.3.0. ''' see also the posting below. cheers, thomas. [R] copy contributed packages from R 2.2.0 to 2.2.1 This message: [ Message body ] [ More options ] Related messages: [ Next message ] [ Previous message ] [ In reply to ] [ Next in thread ] From: Ronnie Babigumira Date: Fri, 23 Dec 2005 15:58:36 +0100 Hi Helli, this came up last week, Here are some of the replys posted 1. In http://cran.r-project.org/contrib/extra/batchfiles/batchfiles_0.2-5.zip are two Windows XP batch files: movedir.bat copydir.bat which will move the packages (which is much faster and suitable if you don't need the old version of R any more) or copy the packages (which takes longer but preserves the old version). 2. x - installed.packages()[,1] install.packages(x) 3. This is one reason we normally recommend that you install into a separate library. Then update.packages(checkBuilt = TRUE) is all that is needed. However, foo - installed.packages() as.vector(foo[is.na(foo[, Priority]), 1]) will give you a character vector which you can feed to install.packages(), so it's not complex to do manually. 4. If the previous installation is still alive, fire it up and pS - packageStatus() pkgs - pS$inst$Package[!pS$inst$Priority %in% c(base, recommended)] save(pkgs, file = foo) In the new installation, load(foo) install.packages(pkgs) Helmut Kudrnovsky wrote: hi R-users, a few days ago R 2.2.1 came out. on my win xp i'installed R 2.2.0. along the time i've installed a lot of contributed packages. my internet-connection is not very fast. so my question: is it possible after installing R 2.2.1 to do copy/paste the contributed packages from the C:\Programme\R221 to the C:\Programme\R2.2.1- location in the files system? or have i to download and install the packages new? greetings from the snowy austria merry christmas helli system R.2.2.0 win xp __ R-help at stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE
Re: [R] Polygon-like interactive selection of plotted points
Roger, Just for fun I tried your script--nothing wrong with the script, but I created a seven sided polygon by clicking on seven points and letting getpoly complete the figure. At the end I notice that only three of the seven vertices are coded as being inside the ploygon (the blue points.) I'd send you a screen dump but I haven't gotten xwd to work with Exceed. Also I haven't checked any docs to see whether this is a known problem but suspect that Marc could be surprised by the behavior. Clint Clint BowmanINTERNET: [EMAIL PROTECTED] Air Dispersion Modeler INTERNET: [EMAIL PROTECTED] Air Quality Program VOICE: (360) 407-6815 Department of Ecology FAX:(360) 407-7534 USPS: PO Box 47600, Olympia, WA 98504-7600 Parcels:300 Desmond Drive, Lacey, WA 98503-1274 On Wed, 26 Apr 2006, Roger Bivand wrote: On Wed, 26 Apr 2006, Marc Schwartz (via MN) wrote: On Wed, 2006-04-26 at 18:13 +0100, Florian Nigsch wrote: [Please CC me for all replies, since I am not currently subscribed to the list.] Hi all, I have the following problem/question: Imagine you have a two- dimensional plot, and you want to select a number of points, around which you could draw a polygon. The points of the polygon are defined by clicking in the graphics window (locator()/identify()), all points inside the polygon are returned as an object. Is something like this already implemented? Thanks a lot in advance, Florian I don't know if anyone has created a single function do to this (though it is always possible). However, using: RSiteSearch(points inside polygon) brings up several function hits that, if put together with the above interactive functions, could be used to do what you wish. That is, input the matrix of x,y coords of the interactively selected polygon and the x,y coords of the underlying points set to return the points inside or outside the polygon boundaries. This sequence from the splancs package should do it: library(splancs) set.seed(20060426) xy - cbind(x=runif(100), y=runif(100)) plot(xy) poly - getpoly() # this gets the polygon on-screen plot(xy) polygon(poly) io - inout(xy, poly) # this returns a logical vector for points in the polygon points(xy[io,], pch=16, col=blue) Roger Just as an FYI, you might also want to look at ?chull, which is in the base R distribution and returns the set of points on the convex hull of the underlying point set. This is to some extent, the inverse of what you wish to do. HTH, Marc Schwartz -- Roger Bivand Economic Geography Section, Department of Economics, Norwegian School of Economics and Business Administration, Helleveien 30, N-5045 Bergen, Norway. voice: +47 55 95 93 55; fax +47 55 95 95 43 e-mail: [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 __ 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] Were to find appropriate functions for a given task in R
Then, people tend to define its own functions (I'm doing this too), and a lack of standardization makes it difficult to keep everything into control. If you think of R as more of a language rather than a pre-packaged statistical program, I feel that helps. In the C++ world, there are people all over writing classes and functions, and many of these have close or duplicate functionality. As a programmer, you can decide which one to use for your needs, or program your own, or extend someone else's, the choice is yours. The same in the R world, you have choices, and there does not have to be necessarily only method to do each task. I don't feel there needs to be 'control', everyone can implement what they want. If you think of R only as a prepacked statistical program however, I can see getting frustrated that there are usually many ways to do the same thing. R is much more than this though. That's how I see it anyway. __ 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] Polygon-like interactive selection of plotted points
On Wed, 26 Apr 2006, Clint Bowman wrote: Roger, Just for fun I tried your script--nothing wrong with the script, but I created a seven sided polygon by clicking on seven points and letting getpoly complete the figure. At the end I notice that only three of the seven vertices are coded as being inside the ploygon (the blue points.) Yes, whether a boundary vertex (or point exactly on a boundary line) is inside or outside is arbitrary, and the default algorithm isn't picky. Setting to bound= argument to TRUE or FALSE uses a different algorithm which does what you expect: inout(poly, poly, bound=NULL) [1] FALSE FALSE TRUE TRUE TRUE FALSE FALSE inout(poly, poly, bound=TRUE) [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE inout(poly, poly, bound=FALSE) [1] FALSE FALSE FALSE FALSE FALSE FALSE FALSE Computational geometry gets even more fun beyond 2D! Roger I'd send you a screen dump but I haven't gotten xwd to work with Exceed. Also I haven't checked any docs to see whether this is a known problem but suspect that Marc could be surprised by the behavior. Clint Clint Bowman INTERNET: [EMAIL PROTECTED] Air Dispersion ModelerINTERNET: [EMAIL PROTECTED] Air Quality Program VOICE: (360) 407-6815 Department of Ecology FAX:(360) 407-7534 USPS: PO Box 47600, Olympia, WA 98504-7600 Parcels:300 Desmond Drive, Lacey, WA 98503-1274 On Wed, 26 Apr 2006, Roger Bivand wrote: On Wed, 26 Apr 2006, Marc Schwartz (via MN) wrote: On Wed, 2006-04-26 at 18:13 +0100, Florian Nigsch wrote: [Please CC me for all replies, since I am not currently subscribed to the list.] Hi all, I have the following problem/question: Imagine you have a two- dimensional plot, and you want to select a number of points, around which you could draw a polygon. The points of the polygon are defined by clicking in the graphics window (locator()/identify()), all points inside the polygon are returned as an object. Is something like this already implemented? Thanks a lot in advance, Florian I don't know if anyone has created a single function do to this (though it is always possible). However, using: RSiteSearch(points inside polygon) brings up several function hits that, if put together with the above interactive functions, could be used to do what you wish. That is, input the matrix of x,y coords of the interactively selected polygon and the x,y coords of the underlying points set to return the points inside or outside the polygon boundaries. This sequence from the splancs package should do it: library(splancs) set.seed(20060426) xy - cbind(x=runif(100), y=runif(100)) plot(xy) poly - getpoly() # this gets the polygon on-screen plot(xy) polygon(poly) io - inout(xy, poly) # this returns a logical vector for points in the polygon points(xy[io,], pch=16, col=blue) Roger Just as an FYI, you might also want to look at ?chull, which is in the base R distribution and returns the set of points on the convex hull of the underlying point set. This is to some extent, the inverse of what you wish to do. HTH, Marc Schwartz -- Roger Bivand Economic Geography Section, Department of Economics, Norwegian School of Economics and Business Administration, Helleveien 30, N-5045 Bergen, Norway. voice: +47 55 95 93 55; fax +47 55 95 95 43 e-mail: [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 -- Roger Bivand Economic Geography Section, Department of Economics, Norwegian School of Economics and Business Administration, Helleveien 30, N-5045 Bergen, Norway. voice: +47 55 95 93 55; fax +47 55 95 95 43 e-mail: [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
[R] left-truncation in survreg
Dear R-users, I know that a few people have asked whether survreg handles left-truncation data and the reply that i have seen so far is that it does. However, when I try to use survreg on left-truncated data, I got the following error message. survcs3-survreg(Surv(start,end,status)~AG, data=DPONEcs3, dist=exponential) Error in survreg(Surv(start, end, status) ~ AG, data = DPONEcs3, dist = exponential) : Invalid survival type Then i tried cc-survreg(Surv(end,status)~AG, data=DPONEcs3, dist=exponential) and it works perfectly fine. May I know why survreg does not accept my left-truncated data? I used similar set of data on coxph and it works fine Many many thanks for your time and any comments given kind regards, sing yee [[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] Memory usage and limit
Hello everyone, I recently made a 64-bit build of R-2.2.1 under Solaris 9 using gcc v.3.4.2. The server has 12GB memory, 6 Sparc CPUs and plenty of swap space. I was the only user at the time of the following experiment. I wanted to benchmark R's capability to read large data files and used a data set consisting of 2MM records with 65 variables in each row. All but 2 of the variables are of the character type and the other two are numeric. The whole data set is about 600 MB when stored as plain ASCII file. The following code was used in the benchmarking runs: c = list(var1=0, var2=0, var3=, var4=, .var65=) A - scan(test.dat, skip = 1, sep = ,, what = c, nmax=X, quiet=FALSE) summary(A) where = 100 or 200 I made two runs with nmax=100 and nmax=200 respectively. The first run completed successfully, in about hour of CPU time. However, the actual memory usage exceeded 2.2GB, about 7 times of the acutal file size on disk. The second run aborted when the memory usage reached 4GB. The error messgae is vector memory exhausted (limit reached?). Three questions: 1) Why were so much memory and CPU consumed to read 300MB of data? Since almost all of the variables are character, I expected almost of 1-1 mapping between file size on disk and that in memory 2) Since this is a 64-bit build, I expected it could handle more than the 600MB of data I used. What does the error message mean? I don't beleive the vector length exceeded the theoretic limit of about 1 billion. 3) The original file was compressed and I had to uncompress it before the experiement. Is there a way to read compressed files directly in R Thanks so much for your help. Min [[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
Re: [R] Polygon-like interactive selection of plotted points
Clint, Not sure why I would be surprised (unless you meant Florian), as I have not actually used these functions. I simply referenced them as part of the search to assist Florian. :-) However, your reply did make me curious, so I installed the 'splancs' package along with 'sp' as a dependency. Just for reference, this is on R 2.3.0 under FC4 compiled from source. I did run Roger's code, the result of which is attached here as a PDF, which should come through the list. While my 7 sided polygon is likely different than yours, the result seems to be the same. That is, only 3 of the vertices are considered within the boundary and this is unaffected by the use of the 'bound' argument to input(). The 'bound' argument in inout() does need to be set to TRUE in order for the boundary points to be considered 'within' the polygon. Otherwise, with the default NULL, the assignment is arbitrary. Thus, Roger's code, which has the default NULL value in the call to inout(), could reasonably result in your/our finding. One quick guess here might be that the values returned by getpoly() are not the exact center points of the original dataset, but are the x,y coords of where the clicks occur. There is a hand-to-eyeball-coordination margin of error relative to the actual coords. Thus, the coordinate values returned by this approach are very slightly outside the polygon and not picked up by inout() as being on the boundary. I tried the followingm using identify() instead: library(splancs) set.seed(20060426) xy - cbind(x=runif(100), y=runif(100)) plot(xy) # Select the SAME 7 vertices here pts - identify(xy, n = 7) # These are the row indices into 'xy' # for the coords of the vertices pts [1] 18 44 51 61 73 89 91 io - inout(xy, xy[pts, ], bound = TRUE, quiet = FALSE) Points on boundary: [1] 18 44 51 61 73 89 91 Note that the same indices of the points are now returned by inout() as were selected when using identify(). Note also the setting of 'bound = TRUE'. You can now use: points(xy[io,], pch=16, col=blue) to draw BOTH the points inside the polygon and the boundary points as well. Thus, this would support my thoughts above, since identify() uses a 'tolerance' argument to identify the actual data points closest the mouse click, much like all.equal() does with respect to floating point comparisons. In a case like this, identify() would seem to be a better choice relative to selecting the polygon boundary if one wants the exact boundary points to be considered in or out of the polygon. HTH, Marc Schwartz On Wed, 2006-04-26 at 13:01 -0700, Clint Bowman wrote: Roger, Just for fun I tried your script--nothing wrong with the script, but I created a seven sided polygon by clicking on seven points and letting getpoly complete the figure. At the end I notice that only three of the seven vertices are coded as being inside the ploygon (the blue points.) I'd send you a screen dump but I haven't gotten xwd to work with Exceed. Also I haven't checked any docs to see whether this is a known problem but suspect that Marc could be surprised by the behavior. Clint On Wed, 26 Apr 2006, Roger Bivand wrote: On Wed, 26 Apr 2006, Marc Schwartz (via MN) wrote: On Wed, 2006-04-26 at 18:13 +0100, Florian Nigsch wrote: [Please CC me for all replies, since I am not currently subscribed to the list.] Hi all, I have the following problem/question: Imagine you have a two- dimensional plot, and you want to select a number of points, around which you could draw a polygon. The points of the polygon are defined by clicking in the graphics window (locator()/identify()), all points inside the polygon are returned as an object. Is something like this already implemented? Thanks a lot in advance, Florian I don't know if anyone has created a single function do to this (though it is always possible). However, using: RSiteSearch(points inside polygon) brings up several function hits that, if put together with the above interactive functions, could be used to do what you wish. That is, input the matrix of x,y coords of the interactively selected polygon and the x,y coords of the underlying points set to return the points inside or outside the polygon boundaries. This sequence from the splancs package should do it: library(splancs) set.seed(20060426) xy - cbind(x=runif(100), y=runif(100)) plot(xy) poly - getpoly() # this gets the polygon on-screen plot(xy) polygon(poly) io - inout(xy, poly) # this returns a logical vector for points in the polygon points(xy[io,], pch=16, col=blue) Roger Just as an FYI, you might also want to look at ?chull, which is in the base R distribution and returns the set of points on the convex hull of the underlying point set. This is to some extent, the inverse of what you wish to do. HTH, Marc
[R] Sign of loadings and scores from PCA in cross validation
Hi, The help file on princomp says that 'The signs of the columns of the loadings and scores are arbitrary, and so may differ between differnt programs for PCA, and even between different builds of R'. Does anyone know 1. Whether this applys to all functions like svd, eigen ... etc? 2. During a leave-one-out cross step, I notice the loadings also change sige when a different observation is held out. This causes the sign change of principal component score of the held-out observation. Since I use the same version of R, same procedure, and same program, to make the leave-one-out PC scores consistent, does that mean I have the take the absolute value of these scores before analyzing them? Thanks in advance for any help! Anne [[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] problem with get command
I don't understand what my error is in the following: I need to use the get command on a series of variables, but can't for some reason that I don't understand. Why am I told no such variable as ov$vn1 after getting a summary report on that very variable? summary(ov$vn1) Min. 1st Qu. Median Mean 3rd Qu. Max. NA's 1.0 25.0 81.0468.1450.0 159100.0 6050.0 dvars - paste(ov$dvn, 1:4, sep=) vars - c(ov$vn1,ov$vn2,ov$vn3,ov$vn4) summary(get(vars[1])) Error in get(x, envir, mode, inherits) : variable ov$vn1 was not found Execution halted Thomas Davidoff Assistant Professor Haas School of Business UC Berkeley Berkeley, CA 94618 Phone:(510) 643-1425 Fax:(510) 643-7357 email:[EMAIL PROTECTED] web:http://faculty.haas.berkeley.edu/davidoff/ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] help in R
Anamika Chaudhuri canamika16 at yahoo.com writes: Hi, I cant understand where I am going wrong.Below is my code.I would really appreciate your help. Dear Anamika, to improve your chances to get a response from this list, and to help in people responde quickly and accurately to you, please run through your code line-by-line and identify the line/lines where the problem is: even better if you can broadly identify what the problem is. It will be difficult for someone to replicate your programming problem, without having your dataset, and knowing it's contents. Anupam. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] problem with get command
ov$vn1 is not a variable. It is the result of applying the $ function to the ov and vn1 arguments. For example, using BOD which is a data frame that comes with R, rather than get(BOD$Time) use get(BOD)[[Time]] On 4/26/06, Thomas Davidoff [EMAIL PROTECTED] wrote: I don't understand what my error is in the following: I need to use the get command on a series of variables, but can't for some reason that I don't understand. Why am I told no such variable as ov$vn1 after getting a summary report on that very variable? summary(ov$vn1) Min. 1st Qu. Median Mean 3rd Qu. Max. NA's 1.0 25.0 81.0468.1450.0 159100.0 6050.0 dvars - paste(ov$dvn, 1:4, sep=) vars - c(ov$vn1,ov$vn2,ov$vn3,ov$vn4) summary(get(vars[1])) Error in get(x, envir, mode, inherits) : variable ov$vn1 was not found Execution halted Thomas Davidoff Assistant Professor Haas School of Business UC Berkeley Berkeley, CA 94618 Phone:(510) 643-1425 Fax:(510) 643-7357 email:[EMAIL PROTECTED] web:http://faculty.haas.berkeley.edu/davidoff/ __ 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] stl function
stl does this internally: x - na.action(as.ts(x)) so stl(x, s.window, na.action = f) is the same as stl(f(as.ts(x)), s.window) e.g. nottem[25] - NA # nottem is a built in data set in R stl(nottem, per) # error stl(nottem, per, na.action = na.contiguous) library(zoo) stl(nottem, per, na.action = na.locf) stl(nottem, per, na.action = na.approx) Whether any of these makes sense is another matter. On 4/26/06, Andrea Toreti [EMAIL PROTECTED] wrote: Hi, I have a monthly time series with missing values and I would use stl function to identify seasonality. I tried all settings of na.action but the result is the same: stl(tm245,s.window=11, na.action=na.pass) Error in stl(tm245, s.window = 11, na.action = na.pass) : NA/NaN/Inf in foreign function call (arg 1) Can you help me? Thanks Andrea Toreti [[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 do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Incomplete Trio in TDT analysis
I am involved in a study where, as in most of life, men demonstrate
themselves to be recalcitrant. So while we have many probands and most of
their mothers we only have about 50% of the trios being complete.
I have been running tdt and trio.types. It appears as if it is ignoring the
duos. Sometimes a duo can be informative. For instance
Father ..missing
Mother 1/2
Proband 1/1
This duo shows that for allele 2, this was clearly a case where 2 was
untransmitted.
Yet I do not think this family counts toward the output that is generated.
Am I correct? How do I use R to do TDT analysis where duo's are used if they
are informative?
If you want further details...
I made a subset that I called MessWith and it is made up of the first 24
probands and their parents. 2 probands had neither a mother nor a father. Of
the remaining, probands, 16 only had one parent.
summary(Genotype.914186)
Number of samples typed: 52 (72.2%)
Allele Frequency: (2 alleles)
Count Proportion
1 730.7
2 310.3
NA40 NA
Genotype Frequency:
Count Proportion
1/1260.5
1/2210.4
2/2 50.1
NA 20 NA
Heterozygosity (Hu) = 0.4225168
Poly. Inf. Content = 0.3309022
tdt(Genotype.914186, MessWith, famid, pid, fatid, motid, sex, affected )
Transmission/disequilibrium test
Data: Genotype.914186
Untransmitted allele frequencies, informative transmissions
and exact P-values
Allele Frequency Transmitted Untransmitted P-value
20. 3 2 1.000
trio.types(Genotype.914186, MessWith, famid, pid, fatid, motid, sex,
affected )
Farrel Buchinsky, MD
Pediatric Otolaryngologist
Allegheny General Hospital
Pittsburgh, PA
**
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[R] help
Hi,
I was trying to calculate an age adjusted rate for which we have the formula
as
sum(weight*rate)/sum(weight). I am using the framingham dataset called fram
here.I cant figure out how I could change the logical statement I have for the
standard dataset (in red) to calculate weight and calculating the wevents and
atrisk(in red)
Below is my code:
attach(fram)
dset1-cbind(AGE,BMI,DEATH)
BMIGRP1-cut(BMI,breaks=c(14,20,25,57),right=TRUE)
levels(BMIGRP1)
BMIGRP-as.numeric(BMIGRP1)
AGEGRP-floor(AGE/10)-2
dset-cbind(AGEGRP,BMIGRP,DEATH)
std-cbind(AGEGRP)
maxage-max(dset[,1])
minage-min(dset[,1])
maxcls-max(dset[,2], na.rm=T)
mincls-min(dset[,2],na.rm=T)
nage-maxage-minage+1
nclass-maxcls-mincls+1
nsub-nrow(dset)
weight - matrix(0,nage,1)
for ( i in minage:maxage )
weight[i-minage+1,1] = sum(std=i)
atrisk = matrix(0,nclass,nage)
wevents = matrix(0,nclass,nage)
for( i in minage : maxage)
for( j in mincls : maxcls)
atrisk[j-mincls+1,i-minage+1] =
sum((dset[,1]=i) (dset[,2]=j))
wevents[j-mincls+1,i-minage+1]=
sum((dset[,1]=i) (dset[,2]=j)(dset[,3]=1))
#vtit = char(t(mincls:maxcls),5,0) // {Total};
#htit = {'at risk' 'events' 'rate/1000'};
atrisk2 = atrisk // atrisk[+,1:nage];
event2 = wevents // wevents[+,1:nage];
atrisk3 = choose(atrisk2=0,1,atrisk2);
rate = event2/atrisk3;
this was done using sas macro.
Thanks so much!
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Re: [R] problem with get command [Broadcast]
Sorry, couldn't resist... From: Gabor Grothendieck ov$vn1 is not a variable. It is the result of applying the $ function to the ov and vn1 arguments. ... which would suggest: get($)(get(ov), vn1). 8-) Andy For example, using BOD which is a data frame that comes with R, rather than get(BOD$Time) use get(BOD)[[Time]] On 4/26/06, Thomas Davidoff [EMAIL PROTECTED] wrote: I don't understand what my error is in the following: I need to use the get command on a series of variables, but can't for some reason that I don't understand. Why am I told no such variable as ov$vn1 after getting a summary report on that very variable? summary(ov$vn1) Min. 1st Qu. Median Mean 3rd Qu. Max. NA's 1.0 25.0 81.0468.1450.0 159100.0 6050.0 dvars - paste(ov$dvn, 1:4, sep=) vars - c(ov$vn1,ov$vn2,ov$vn3,ov$vn4) summary(get(vars[1])) Error in get(x, envir, mode, inherits) : variable ov$vn1 was not found Execution halted Thomas Davidoff Assistant Professor Haas School of Business UC Berkeley Berkeley, CA 94618 Phone:(510) 643-1425 Fax:(510) 643-7357 email:[EMAIL PROTECTED] web:http://faculty.haas.berkeley.edu/davidoff/ __ 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] Incomplete Trio in TDT analysis
Using only informative incomplete trios and dropping others turns out
to bias the TDT (Curtis Sham 95). There are a variety of
modifications to handle case-parent trios, starting (I think) with
Weinberg's 1999 paper that uses the EM algorithm and a
likelihood-ratio test. I don't know of any of these methods that are
implemented in R. Perhaps they are in the package that you are using
but forgot to name.
Steve Buyske
At 8:26 PM -0400 4/26/06, Farrel Buchinsky wrote:
I am involved in a study where, as in most of life, men demonstrate
themselves to be recalcitrant. So while we have many probands and most of
their mothers we only have about 50% of the trios being complete.
I have been running tdt and trio.types. It appears as if it is ignoring the
duos. Sometimes a duo can be informative. For instance
Father ..missing
Mother 1/2
Proband 1/1
This duo shows that for allele 2, this was clearly a case where 2 was
untransmitted.
Yet I do not think this family counts toward the output that is generated.
Am I correct? How do I use R to do TDT analysis where duo's are used if they
are informative?
If you want further details...
I made a subset that I called MessWith and it is made up of the first 24
probands and their parents. 2 probands had neither a mother nor a father. Of
the remaining, probands, 16 only had one parent.
summary(Genotype.914186)
Number of samples typed: 52 (72.2%)
Allele Frequency: (2 alleles)
Count Proportion
1 730.7
2 310.3
NA40 NA
Genotype Frequency:
Count Proportion
1/1260.5
1/2210.4
2/2 50.1
NA 20 NA
Heterozygosity (Hu) = 0.4225168
Poly. Inf. Content = 0.3309022
tdt(Genotype.914186, MessWith, famid, pid, fatid, motid, sex, affected )
Transmission/disequilibrium test
Data: Genotype.914186
Untransmitted allele frequencies, informative transmissions
and exact P-values
Allele Frequency Transmitted Untransmitted P-value
20. 3 2 1.000
trio.types(Genotype.914186, MessWith, famid, pid, fatid, motid, sex,
affected )
Farrel Buchinsky, MD
Pediatric Otolaryngologist
Allegheny General Hospital
Pittsburgh, PA
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[R] What are the differences between ACF and PACF in time series analysis?
Hi all, I am desperately looking for answer to my previous question: what are the differences between ACF and PACF in time series and their applications? I got confused a lot by these two functions in R... Already having ACF, why do people decide to create PACF? Thanks a lot [[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
