Re: [R] testing independence of categorical variables
On Thu, 2007-11-22 at 16:16 +0500, Shoaaib Mehmood wrote: hi, is there a way of calculating of measuring dependence between two categorical variables. i tried using the chi square test to test for independence but i got error saying that the lengths of the two vectors don't match. Suppose X and Y are two factors. X has 5 levels and Y has 7 levels. This is what i tried doing temp-chisq.test(x,y) but got error the lengths of the two vectors don't match. any help will be appreciated Hi Shoaaib, Try using chisq.test(table(x,y)). If you using chisq.test(x,y) R will testing goodness-of-fit. -- Bernardo Rangel Tura, M.D,Ph.D National Institute of Cardiology Brazil __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] problem in closing R console
amna khan wrote: Dear Sir When I close R console then following message apear when I want to save the workspace. If I close the R console without saving workspace then R console is closed otherwise not. Error in gzfile(file, wb) : unable to open connection In addition: Warning message: In gzfile(file, wb) : cannot open compressed file '.RDataTmp' Regards You do not have write permissions in your working directory, I guess. Uwe Ligges __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] about Runtime Error
Xin Huang wrote: Hi, I wrote my own R program doing some MCMC simulation but I often got Runtime Error even the program only run for a couple of hundred times. The detail error message is as following: Runtime Error! Program: C:\Program Files\R\R-2.5.1\bin\Rgui.exe This application has requested the Runtime to terminate it in an unusual way. Please contact the application's support team for more information. When I turned off the program, there was another error message: RGui:Rgui.exe-Application Error The instruction at 0x5ad71531 referenced memory at 0x0014. The memory count not be read. Please let me know if there is anything I can do to solve the problem. Do you have own C code to do the MCMC steps or do you use some existing R package? In any case, solving the problem means fixing the code that causes the error, hence perhaps running it under some debugger. Best, Uwe Ligges Thank you very much. Xin __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] how to calculate the return?
Denver,
data is a matrix like this
AMR BS GE HR MO UK SP500
1974 -0.3505 -0.1154 -0.4246 -0.2107 -0.0758 0.2331 -0.2647
1975 0.7083 0.2472 0.3719 0.2227 0.0213 0.3569 0.3720
1976 0.7329 0.3665 0.2550 0.5815 0.1276 0.0781 0.2384
1977 -0.2034 -0.4271 -0.0490 -0.0938 0.0712 -0.2721 -0.0718
1978 0.1663 -0.0452 -0.0573 0.2751 0.1372 -0.1346 0.0656
1979 -0.2659 0.0158 0.0898 0.0793 0.0215 0.2254 0.1844
1980 0.0124 0.4751 0.3350 -0.1894 0.2002 0.3657 0.3242
1981 -0.0264 -0.2042 -0.0275 -0.7427 0.0913 0.0479 -0.0491
1982 1.0642 -0.1493 0.6968 -0.2615 0.2243 0.0456 0.2141
1983 0.1942 0.3680 0.3110 1.8682 0.2066 0.2640 0.2251
It is perhaps more natural to specify this information as a data frame.
I want to calculate the return say AMR,so I use
re=numeric(10)
for (i in 2:nrow(data))
re[1]=0
re[i]=log(data[i]/data[i-1])
to my surprise, the result is
re
[1] 0.0 0.0 0.0 0.0 0.0 0.0 0.0
0.0
[9] 0.0 -1.70109
A couple of things:
1. You don't need re[1]=0 inside the loop (or at all, in fact, since
numeric(10) will give a default value of 0).
2. It would be better to vectorise the code, to avoid the loop altogether.
3. You are looping over elements in the first column of data, which is why
the log values are zero.
Some better code:
re = c(0, diff(log(data[,AMR])))
Regards,
Richie.
Mathematical Sciences Unit
HSL
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Re: [R] CPCA?
Daniel Berner daniel.berner at mail.mcgill.ca writes: It would be great to know if and where an R code for Common Principal Component Analysis is available. The only code I know is in IMSL Fortran library, and that is proprietary, and that is expensive. After a quick look, it really appears that IMSL C library does not have the code, but you got to go to Fortran. Look for function DKPRIN (KPRIN). That code cannot be ported to R, naturally. Another issue is that the code obviously was written by Bernhard Flury, and he also has FORTRAN listing in his book Commaon Principal Components and Related Multivariate Models (J. Wiley Sons, 1988). I don't know of the licensing status of that code. I didn't find any explicit licensing information in the book (but may have overlooked something), apart from the usual book copyright that forbids everything. I assume it is the same code that is the base of DKPRIN in the IMSL FORTRAN library. Would mean a lot of typing at minimum, and for any sensible code, editing the code to use LAPACK where ever possible. Further, Flury descirbes the algorithm in his book, and it could be implemented independently in R. I think nobody has done that (yet). cheers, jari oksanen __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] help pleaseeeeeeeee
Hi Thank you very much for you interest and help in this mysterious problem. I am going to investigate the random numbers issue. Concerning the order.maxit helps but it is not what I have in mind. I think that in case order.max - if (is.null(order.max)) floor(10 * log10(n.)) else round(order.max) I am going to explain better what my procedure is J - I have developed a new approach to obtain forecast intervals. In this approach I select the order p of the autoregressive approximation by AIC criterion. - Until now I only test it in few time series - Now, I am using M1- competition data ( package: Mcomp) and for the *Yearly data* it is catastrophic L (error occurs) M1 M-Competition data: 1001 time series Type of data PeriodDEMOGR INDUST MACRO1 MACRO2 MICRO1 MICRO2 MICRO3 Total MONTHLY 75183 6492 10 89 104 617 QUARTERLY 39 18 45 59 5 2116 203 *YEARLY*3035 30 29 16 29 12 181 I am going to investigate deeper the order.max and the randomness. Thank you again for your time. Best, Clara sessionInfo() R version 2.6.0 (2007-10-03) i386-pc-mingw32 locale: LC_COLLATE=Portuguese_Portugal.1252;LC_CTYPE=Portuguese_Portugal.1252;LC_MONETARY=Portuguese_Portugal.1252;LC_NUMERIC=C;LC_TIME=Portuguese_Portugal.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] Mcomp_1.07 forecast_1.07 tseries_0.10-12 zoo_1.4-0 [5] quadprog_1.4-11 loaded via a namespace (and not attached): [1] grid_2.6.0 lattice_0.16-5 tools_2.6.0 2007/11/24, Steven McKinney [EMAIL PROTECTED]: Hi Clara, I suspect your error is happening because your input data is short (9 observations). In the help for ar() for argument order.max it states order.maxMaximum order (or order) of model to fit. Defaults to 10*log10(N) where N is the number of observations except for method=mle where it is the minimum of this quantity and 12. so perhaps the problem is 10*log10(9) is smaller than 1 and isn't being handled properly (this is just a guess). If I lengthen your data vector to be x-ts(c(-0.2052083,-0.3764986,-0.3762448,0.3740089 ,0.2737568,2.8235722,- 1.7783313,0.2728676,-0.3273164, -0.2052083,-0.3764986,-0.3762448,0.3740089,0.2737568,2.8235722,-1.7783313, 0.2728676,-0.3273164),start=c(1978,3),frequency=4,end=c(1982,3)) I can not trip the error. I filed a bug report. You might try specifying order.max in your function call. If I specify order.max = 1 I can not trip the error. res.ar-ar(x,aic=TRUE,demean=F) res.ar-ar(x,aic=TRUE,demean=F) Error in if (order 0) coefs[order, 1:order] else numeric(0) : missing value where TRUE/FALSE needed In addition: Warning message: In if (order 0) coefs[order, 1:order] else numeric(0) : the condition has length 1 and only the first element will be used res.ar-ar(x,aic=TRUE,demean=F) Error in if (order 0) coefs[order, 1:order] else numeric(0) : missing value where TRUE/FALSE needed In addition: Warning message: In if (order 0) coefs[order, 1:order] else numeric(0) : the condition has length 1 and only the first element will be used res.ar-ar(x,aic=TRUE,demean=F, order.max = 1) res.ar-ar(x,aic=TRUE,demean=F, order.max = 1) res.ar-ar(x,aic=TRUE,demean=F, order.max = 1) res.ar -ar(x,aic=TRUE,demean=F, order.max = 1) res.ar-ar(x,aic=TRUE,demean=F, order.max = 1) res.ar-ar(x,aic=TRUE,demean=F, order.max = 1) res.ar-ar(x,aic=TRUE,demean=F, order.max = 1) res.ar-ar(x,aic=TRUE,demean=F, order.max = 1) res.ar-ar(x,aic=TRUE,demean=F, order.max = 1) res.ar-ar(x,aic=TRUE,demean=F, order.max = 1) res.ar-ar(x,aic=TRUE,demean=F, order.max = 1) res.ar -ar(x,aic=TRUE,demean=F, order.max = 1) res.ar-ar(x,aic=TRUE,demean=F, order.max = 1) res.ar-ar(x,aic=TRUE,demean=F, order.max = 1) res.ar-ar(x,aic=TRUE,demean=F, order.max = 1) res.ar-ar(x,aic=TRUE,demean=F, order.max = 1) res.ar-ar(x,aic=TRUE,demean=F, order.max = 1) res.ar-ar(x,aic=TRUE,demean=F, order.max = 1) res.ar-ar(x,aic=TRUE,demean=F, order.max = 1) res.ar -ar(x,aic=TRUE,demean=F, order.max = 1) res.ar-ar(x,aic=TRUE,demean=F, order.max = 1) res.ar-ar(x,aic=TRUE,demean=F, order.max = 1) res.ar-ar(x,aic=TRUE,demean=F, order.max = 1) res.ar-ar(x,aic=TRUE,demean=F, order.max = 1) res.ar-ar(x,aic=TRUE,demean=F, order.max = 1) res.ar-ar(x,aic=TRUE,demean=F, order.max = 1) res.ar-ar(x,aic=TRUE,demean=F, order.max = 1) res.ar -ar(x,aic=TRUE,demean=F, order.max = 1) res.ar-ar(x,aic=TRUE,demean=F, order.max = 1) res.ar-ar(x,aic=TRUE,demean=F, order.max = 1) res.ar-ar(x,aic=TRUE,demean=F, order.max = 1)
[R] Unweighted meta-analysis
Hello I'm very much a beginner on meta-analysis, so apologies if this is a trivial posting. I've been sent a set data from separate experimental studies, Treatment and Control, but no measure of the variance of effect sizes, numbers of replicates etc. Instead, for each study, all I have is the mean value for the treatment and control (but not the SD). As far as I can tell, this forces me into an unweighted meta-analysis, with all the caveats and dangers associated with it. Two possible approaches might be: a) Take the ln(treatment/control) and perform a Fisher's randomisation test (and also calculate +/- CI). b) Regress the treatment vs control values, then randomise (with or without replacement?) individual values, comparing the true regression coefficient with the distribution of randomisation regression coefficients. Both approaches would appear to be fraught with risks; for example in the regression approach, it is probable that the error distribution of an individual randomised regression might not be normal - would this then invalidate the whole set of regressions? Many thanks for your advice. Roy -- Roy Sanderson Institute for Research on Environment and Sustainability (IRES) Devonshire Building Newcastle University Newcastle upon Tyne NE1 7RU [EMAIL PROTECTED] 0191 246 4835 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Dot plots in R
On Saturday 24 November 2007, Paul Smith wrote: Dear All, Can R produce dot plots like the one of the following picture: http://en.wikipedia.org/wiki/Image:Dotplot_of_random_values.png ? I have tried dotchart, but no success. I'm coming late to this thread, but I believe what Paul wants is better suited by the DOTplot() function from the UsingR package: it looks exactly the same as the web image and it has no axes, as Paul wants in a later message. x - sample(1:10, 30, replace=T) library(UsingR) DOTplot(x) Hth, Adrian -- Adrian Dusa Romanian Social Data Archive 1, Schitu Magureanu Bd 050025 Bucharest sector 5 Romania Tel./Fax: +40 21 3126618 \ +40 21 3120210 / int.101 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] help pleaseeeeeeeee
CCordeiro wrote: Hi Thank you very much for you interest and help in this mysterious problem. I am going to investigate the random numbers issue. Concerning the order.maxit helps but it is not what I have in mind. I think that in case Dear Clara, this did actually get investigated, but was continued in a thread on the R development list: http://www.nabble.com/Bug-in-package-stats-function-ar%28%29-%28PR-10459%29-tf4864536.html The problem is indeed with the order.max calculation, which should not allow order.max to equal the length of the data series (but does for very short time series). There are no random numbers involved in this calculation. Something like res.ar-ar(x,aic=TRUE,demean=F,order.max=length(x)-1) should prevent this particular problem from happening ... Ben Bolker PS: it was very good of you to give a reproducible example, and very helpful of you to point out this bug. In the future, the other helpful thing you could do is give your message an informative subject line (e.g. problem with ar() rather than help pleaseee) ... -- View this message in context: http://www.nabble.com/help-please-tf4862400.html#a13948775 Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] CPCA?
Jari Oksanen wrote: Daniel Berner daniel.berner at mail.mcgill.ca writes: It would be great to know if and where an R code for Common Principal Component Analysis is available. The only code I know is in IMSL Fortran library, and that is proprietary, and that is expensive. After a quick look, it really appears that IMSL C library does not have the code, but you got to go to Fortran. Look for function DKPRIN (KPRIN). That code cannot be ported to R, naturally. Another issue is that the code obviously was written by Bernhard Flury, and he also has FORTRAN listing in his book Commaon Principal Components and Related Multivariate Models (J. Wiley Sons, 1988). I don't know of the licensing status of that code. I didn't find any explicit licensing information in the book (but may have overlooked something), apart from the usual book copyright that forbids everything. I assume it is the same code that is the base of DKPRIN in the IMSL FORTRAN library. Would mean a lot of typing at minimum, and for any sensible code, editing the code to use LAPACK where ever possible. Further, Flury descirbes the algorithm in his book, and it could be implemented independently in R. I think nobody has done that (yet). cheers, jari oksanen I have a package that wraps some code Patrick Phillips wrote -- haven't put it on CRAN (yet) because of issues with including executable files in packages ... e-mail me if you want further info. Ben Bolker -- View this message in context: http://www.nabble.com/CPCA--tf4873113.html#a13948778 Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] pass lm( ) a char vector as the variables to be included
Dear Everyone in list: I am writing some codes to automate the process of fitting linear models where the names of variables of models are produced and stored in character vectors. But I have problems to pass the vectors to the lm( ) because I don't know how to strip the quotation marks automatically. Here are the codes of the example of lm( ): ## Annette Dobson (1990) An Introduction to Generalized Linear Models. ## Page 9: Plant Weight Data. ctl - (4.17,5.58,5.18,6.11,4.50,4.61,5.17,4.53,5.33,5.14) trt - (4.81,4.17,4.41,3.59,5.87,3.83,6.03,4.89,4.32,4.69) group - gl(2,10,20, labels=c(Ctl,Trt)) weight - c(ctl, trt) anova(lm.D9 - lm(weight ~ group)) lm.D90 - lm(weight ~ group - 1) # omitting intercept What I am doing is let the variable name group stored in a vector, say, g - group. The question is how to strip the quotation marks when we call lm( ) through g? Thank you all. Boshao Never miss a thing. Make Yahoo your home page. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] pass lm( ) a char vector as the variables to be included
Here are the codes of the example of lm( ):
## Annette Dobson (1990) An Introduction to
Generalized Linear Models.
## Page 9: Plant Weight Data.
ctl -
(4.17,5.58,5.18,6.11,4.50,4.61,5.17,4.53,5.33,5.14)
trt -
(4.81,4.17,4.41,3.59,5.87,3.83,6.03,4.89,4.32,4.69)
group - gl(2,10,20, labels=c(Ctl,Trt))
weight - c(ctl, trt)
anova(lm.D9 - lm(weight ~ group))
lm.D90 - lm(weight ~ group - 1) # omitting intercept
What I am doing is let the variable name group
stored in a vector, say, g - group. The question is
how to strip the quotation marks when we call lm( )
through g?
Try:
w = weight
g = group
form = as.formula(paste(w,g,sep=~))
lm(form)
Regards,
Richie.
Mathematical Sciences Unit
HSL
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Re: [R] testing independence of categorical variables
prettyR --- Shoaaib Mehmood [EMAIL PROTECTED] wrote: i cant find help for xtab. Which package contains this function On Nov 24, 2007 12:16 PM, G Ilhamto [EMAIL PROTECTED] wrote: hi shohaib, have you tried xtab instead of chisq.test? Ilham On Nov 22, 2007 6:16 AM, Shoaaib Mehmood [EMAIL PROTECTED] wrote: hi, is there a way of calculating of measuring dependence between two categorical variables. i tried using the chi square test to test for independence but i got error saying that the lengths of the two vectors don't match. Suppose X and Y are two factors. X has 5 levels and Y has 7 levels. This is what i tried doing temp-chisq.test(x,y) but got error the lengths of the two vectors don't match. any help will be appreciated -- Regards, Rana Shoaaib Mehmood __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Regards, Rana Shoaaib Mehmood (+92) 333 550 4531 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Instant Messaging, free SMS, sharing photos and more... Try the new Yahoo! Canada Messenger at http://ca.beta.messenger.yahoo.com/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] writing summary() to a text file
Hi All, I would like to output the results of a function into a text file, legible as a such. The function produces a summary quite like: summary(lm(x ~ y + w * z)) [for instance] and I am not clear how to save this summary into a text file 'automagically', because I need to be able to do it in a for() loop. Cheers, Federico -- Federico C. F. Calboli Department of Epidemiology and Public Health Imperial College, St. Mary's Campus Norfolk Place, London W2 1PG Tel +44 (0)20 75941602 Fax +44 (0)20 75943193 f.calboli [.a.t] imperial.ac.uk f.calboli [.a.t] gmail.com __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] help in md scaling
Dear list, I am starting a new project in cmdscale, and I have a question regarding distance matrix and covariance matrix. Can I use covariance as my distance matrix? Any good reference in this matter? Thank you, ilham [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] writing summary() to a text file
Would something like this do it? sink(file=reg.txt) summary(reg) sink() --- Federico Calboli [EMAIL PROTECTED] wrote: Hi All, I would like to output the results of a function into a text file, legible as a such. The function produces a summary quite like: summary(lm(x ~ y + w * z)) [for instance] and I am not clear how to save this summary into a text file 'automagically', because I need to be able to do it in a for() loop. Cheers, Federico -- Federico C. F. Calboli Department of Epidemiology and Public Health Imperial College, St. Mary's Campus Norfolk Place, London W2 1PG Tel +44 (0)20 75941602 Fax +44 (0)20 75943193 f.calboli [.a.t] imperial.ac.uk f.calboli [.a.t] gmail.com __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Looking for the perfect gift? Give the gift of Flickr! http://www.flickr.com/gift/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] R-2.6.1 is released
I've rolled up R-2.6.1.tar.gz a short while ago. This is a maintenance release and fixes a number of mostly minor bugs and platform issues, as well as a couple of major problems. Probably, the most important issues were - save-to-postscript on Windows - tcltk event loop with X11 - build issue on recent MacOSX See the full list of changes below. You can get it (in a short while) from http://cran.r-project.org/src/base/R-2/R-2.6.1.tar.gz or wait for it to be mirrored at a CRAN site nearer to you. Binaries for various platforms will appear in due course. For the R Core Team Peter Dalgaard These are the md5sums for the freshly created files, in case you wish to check that they are uncorrupted: 070cca21d9f8a6af15f992edb47a24d5 AUTHORS eb723b61539feef013de476e68b5c50a COPYING a6f89e2100d9b6cdffcea4f398e37343 COPYING.LIB 619aa712a6032fdbffd4f0c69d962859 FAQ 70447ae7f2c35233d3065b004aa4f331 INSTALL b6ed12e20f627a466378fc28006dc9c9 NEWS 88bbd6781faedc788a1cbd434194480c ONEWS 4f004de59e24a52d0f500063b4603bcb OONEWS 19c35a69e1afa73f5f70f91ff9939233 R-2.6.1.tar.gz 19c35a69e1afa73f5f70f91ff9939233 R-latest.tar.gz 433182754c05c2cf7a04ad0da474a1d0 README 020479f381d5f9038dcb18708997f5da RESOURCES 1ad28cbc84485ccdf4ce5721b34ed645 THANKS Here is the relevant bit of the NEWS file: CHANGES IN R VERSION 2.6.1 NEW FEATURES o The data.frame and factor methods for [[ now support the 'exact' argument introduced in 2.6.0. o plot.lm() gains a new argument 'cex.caption' to allow the size of the captions to be controlled. o A series of changes make the CHARSXP cache introduced in 2.6.0 faster (and in some cases many times faster) in sessions with a large number (e.g. a million) of unique character strings, and also if there are many empty strings. o embedFonts(), bitmap() and dev2bitmap() explicitly turn off auto-rotation in Ghostscript when generating PDF. o The canonical architecture is no longer checked when loading packages using a non-empty sub-architecture, since it is possible to (e.g.) build packages for i386-pc-linux-gnu on both that architecture and on x86_64-unknown-linux-gnu. o Deparsing will (if option warnIncomplete is set) warn on strings longer than the parser limit (8192 bytes). o url() now uses the UserAgent header in http transactions in the same way as download.file() (making use of option HTTPUserAgent). BUG FIXES o iconv() is again able to translate character strings with embedded nuls (such as those in UCS-2). o new.packages() and update.packages() failed when called on an empty library, since old.packages() threw an error. old.packages() now returns NULL (as documented) in that case. o Builds on Mac OS X 10.4 or higher now allocate enough space in the binary headers to relocate dependent libraries into the framework. o R CMD build now computes the exclusion list on the copy it makes: this avoids problems if the original sources contain symbolic links (which are resolved in the copy). Thanks to Michael Lawrence for diagnosis and patch. o object.size() had slightly too low a size for objects of type S4. o symbol() in plotmath expressions was only accepting valid character strings, which made it impossible to specify symbols such as aleph (obtained by symbol(\300)) in a UTF-8 locale. o An event handling issue caused autorepeat functions to misbehave with tcltk (notably scrollbars). o plot(sin, -5, 5) gives ylab 'sin(x)' again, where it resulted in 'x(x)' in 2.6.0. Further, plot(sin) again plots from [0,1] also in cases where a previously used coordinate system differs. o curve() with unspecified 'from', 'to' and 'xlim' now reuses the previous x limits, and not slightly larger ones. o It was intended that R code filenames in packages should start with an ASCII letter or digits (and R CMD INSTALL uses that), but the test used in R CMD build ([A-Za-z0-9]) was locale-specific (and excluded t to y in Estonian, for example). (PR#10351) o 'R CMD build' could misbehave when faced with files with CRLF line endings *and* no line ending on the final line of the file, removing the last byte of the file. o DF[i, j] failed in 2.6.0 if j was a logical vector selecting a single column. o Unix x11() would fail if a valid 'display' was specified but DISPLAY was unset. (PR#10379) o postscript() was not always ignoring .Postscript.Options in the workspace (where it should not have occurred). o help.search() would give an error if it found a badly installed package, even if 'package' was not specified. o tclServiceMode()
Re: [R] writing summary() to a text file
?capture.output On Nov 26, 2007 9:31 AM, Federico Calboli [EMAIL PROTECTED] wrote: Hi All, I would like to output the results of a function into a text file, legible as a such. The function produces a summary quite like: summary(lm(x ~ y + w * z)) [for instance] and I am not clear how to save this summary into a text file 'automagically', because I need to be able to do it in a for() loop. Cheers, Federico -- Federico C. F. Calboli Department of Epidemiology and Public Health Imperial College, St. Mary's Campus Norfolk Place, London W2 1PG Tel +44 (0)20 75941602 Fax +44 (0)20 75943193 f.calboli [.a.t] imperial.ac.uk f.calboli [.a.t] gmail.com __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem you are trying to solve? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] writing summary() to a text file
I would like to output the results of a function into a text file,
legible as a such. The function produces a summary quite like:
summary(lm(x ~ y + w * z))
You can either redirect output to a file using cat or sink; generate a
latex table using xtable (in the xtable package); or export the relevant
bits (e.g. the coefficients matrix) using write.csv.
Based upon your message, sink is probably your best bet/
sink(file=foo.txt)
summary(lm(x ~ y + w * z))
sink(NULL)
Regards,
Richie.
Mathematical Sciences Unit
HSL
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Re: [R] PCA with NA
The pcaMethods package offers a collection of different algorithms for PCA, some of which (NIPALS and others) can be used on data that have missing values. Kevin Wright On Nov 24, 2007 4:59 PM, Hartmut Oldenbürger [EMAIL PROTECTED] wrote: Hi Birgit, and All Possibly you should not consider the case completed ;-) There is an important alternative to imputing means, or estimates from first or second order regression (Frane, Psychometrica, BMDP): partial-least-squares (Wold), which uses as much information from the data as possible to estimate the principal components, or the missing data. Stephane Dray, also from Lyon, provides 'nipals' here: http://biomserv.univ-lyon1.fr/~dray/software.php There is also an interesting paper. - In case, you use PLS to estimate and impute, set the number of factors as high as reasonably possible, e.g. m-1, when m is the number of variables. best - Hartmut Oldenbürger --- [EMAIL PROTECTED] http://www.wipaed.wiso.uni-goettingen.de/~holdenb1 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] complex conjugates roots from polyroot?
Hi Spencer,
The default tolerance in your function might be a bit too conservative (i.e.
too small). Here is an example:
set.seed(123)
z - polyroot(sample(1:5, size=40, rep=T)) # polynomial of degree 39
zmat - which(outer(z, z, FUN=is.conj), arr.ind=T)
zmat[zmat[,1] zmat[,2], ]
row col
[1,] 3 5
[2,] 2 7
[3,] 6 10
[4,] 9 11
[5,] 13 15
[6,] 16 18
[7,] 1 22
[8,] 21 24
[9,] 17 25
[10,] 19 26
[11,] 23 29
[12,] 12 30
[13,] 20 32
[14,] 31 33
[15,] 8 34
[16,] 4 35
[17,] 28 36
[18,] 27 37
[19,] 38 39
findConjugates(z)
[1] -0.0168724+0.8593702i -0.4707594-0.7991353i -0.8955664-0.2000173i
[4] 0.1495329-0.9612410i 0.3762447-0.8971735i 0.5654040-0.7332919i
[7] 0.6648998-0.6811790i -0.9087387+0.3750093i -0.5663986-0.8890497i
[10] 0.7937910-0.6069981i 0.3565431-0.9877840i
You can see that your function finds only 11 conjugate pairs as opposed to
the correct 19 pairs (since there is only 1 real root, the rest must be
conjugate pairs). Increasing the tolerance to 1.e-10, gives all the 19
pairs. Therefore, I would suggest a default of 1.e-10 or even larger, say,
sqrt(.Machine$double.eps).
I wouldn't consider multiple real roots to be conjugates, since they are not
distinct points on the complex plane, as well as for the reason that you
have given.
Best,
Ravi.
---
Ravi Varadhan, Ph.D.
Assistant Professor, The Center on Aging and Health
Division of Geriatric Medicine and Gerontology
Johns Hopkins University
Ph: (410) 502-2619
Fax: (410) 614-9625
Email: [EMAIL PROTECTED]
Webpage: http://www.jhsph.edu/agingandhealth/People/Faculty/Varadhan.html
-Original Message-
From: Spencer Graves [mailto:[EMAIL PROTECTED]
Sent: Sunday, November 25, 2007 12:36 PM
To: Ravi Varadhan
Cc: r-help@r-project.org
Subject: Re: [R] complex conjugates roots from polyroot?
Hi, Ravi:
Question: Are duplicate real numbers complex conjugates? For
some purposes, perhaps. However, for identifying (damped) periodicity
on a difference or differential equation, we must exclude repeated real
roots.
In any event, your suggestion inspired me to create a function
findConjugates (see below), which I've added to the FinTS package
currently under development on R-Forge. The source code is currently
available via svn checkout
svn://svn.r-forge.r-project.org/svnroot/fints. In another day or so,
it should be available (with documentation) via
'install.packages(FinTS,repos=http://r-forge.r-project.org;)'. In
another couple of months, it should appear on CRAN.
Thanks again for your suggestion.
Best Wishes,
Spencer
##
findConjugates - function(x,
complex.eps=1000*.Machine[[double.neg.eps]]){
##
## 1. compute normalization
##
if(length(x)1)return(complex(0))
ax - abs(x)
m2 - outer(ax, ax, pmax)
##
## 2. Compute complex differences
##
c2 - (abs(outer(x, Conj(x), -) / m2) complex.eps)
c2[m2==0] - FALSE
c2 - (c2 lower.tri(c2))
##
## 3. Any differences exceed complex.eps?
##
if(any(c2)){
# check standard differences
d2 - (abs(outer(x, x, -) / m2) complex.eps)
d2[m2==0] - FALSE
#
cd2 - (c2 d2)
if(any(cd2)){
ic - sort(unique(row(cd2)[cd2]))
return(x[ic])
}
}
complex(0)
}
##
Ravi Varadhan wrote:
Hi Spencer,
Here is a simple approach to detect conjugate pairs:
is.conj - function(z1, z2, tol=1.e-10) {
# determine if two complex numbers are conjugates
cond1 - abs(Re(z1) - Re(z2)) tol
cond2 - abs(Im(z1) + Im(z2)) tol
cond1 cond2
}
set.seed(123)
z - polyroot(sample(1:5, size=8, rep=T))
zmat - which(outer(z, z, FUN=is.conj), arr.ind=T)
zmat[zmat[,1] zmat[,2], ]
# result
row col
[1,] 1 3
[2,] 5 6
[3,] 4 7
We see that (1,3), (4,7), and (5,6) are the conjugate pairs.
This doesn't address the issue of numerical round-off (there is no
argument
in polyroot that governs the accuracy of the roots).
Best,
Ravi.
---
Ravi Varadhan, Ph.D.
Assistant Professor, The Center on Aging and Health
Division of Geriatric Medicine and Gerontology
Johns Hopkins University
Ph: (410) 502-2619
Fax: (410) 614-9625
Email: [EMAIL PROTECTED]
Webpage: http://www.jhsph.edu/agingandhealth/People/Faculty/Varadhan.html
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
On
Behalf Of Spencer Graves
Sent: Friday, November 23, 2007 12:08 PM
To: r-help@r-project.org
Subject: [R] complex conjugates roots from polyroot?
Hi, All:
Is there a simple way to detect complex conjugates
Re: [R] writing summary() to a text file
Also, this works: s - summary(iris) capture.output(s, file = myfile.txt) and the Hmisc and xtable packages can output it in latex: library(xtable) print(xtable(s), file = myfile.tex) library(Hmisc) latex(s, file= myfile.tex) On Nov 26, 2007 9:59 AM, John Kane [EMAIL PROTECTED] wrote: Would something like this do it? sink(file=reg.txt) summary(reg) sink() --- Federico Calboli [EMAIL PROTECTED] wrote: Hi All, I would like to output the results of a function into a text file, legible as a such. The function produces a summary quite like: summary(lm(x ~ y + w * z)) [for instance] and I am not clear how to save this summary into a text file 'automagically', because I need to be able to do it in a for() loop. Cheers, Federico -- Federico C. F. Calboli Department of Epidemiology and Public Health Imperial College, St. Mary's Campus Norfolk Place, London W2 1PG Tel +44 (0)20 75941602 Fax +44 (0)20 75943193 f.calboli [.a.t] imperial.ac.uk f.calboli [.a.t] gmail.com __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Looking for the perfect gift? Give the gift of Flickr! http://www.flickr.com/gift/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Fwd: Empty list to use in a for cycle
Dear R-users,
I'm posting a problem I already asked help for some time ago, because I'm
facing that problem once again and even because now, reading that old
e-mail, and the answer recevied, I understand I've not made myself clear.
Here's the question: I need to create an empty list of a specific length to
fill it with a quite large amount of square matrices, which is 602. The
question is that these matrices are created inside a for cycle, and I do not
know how to recall all of them one by one, except by creating an empty list
before the cycle, than assigning for each value of the i index the amtrix
computed to the first element of the empty list.
The fact is that: i've trided to create an empty list with
vector(list,602)
and then putting it in a cycle, but it didn't work. This is the cycle I've
used. To prove it works (and then the cycle itself is not a problem) there's
also the output (i.e. the last square matrix computed).
for (i in unique(elio2$id)){
sub.mu - exp.mu[exp.mu$id==i,]
D - matrix(0,nrow( sub.mu),nrow(sub.mu))
diag(D) - sub.mu$deriv.link
A - mat.cov[1:nrow(D),1:nrow(D)]
R - corstr[1:nrow(D),1:nrow(D)]
W - solve(D)%*%solve(sqrt(A))%*%solve(R)%*%solve(sqrt(A))%*%solve(D)
}
W
[,1] [,2] [,3] [,4]
[1,] 3.492489e+02 -7.9324883721 0.0006286788 -0.0031046240
[2,] -7.932488e+00 17.4974625191 -1.7575467817 0.0001403319
[3,] 6.286788e-04 -1.7575467817 17.3227959738 -1.7529916860
[4,] -3.104624e-03 0.0001403319 -1.7529916860 17.2279244622
Does anyone knows how to insert each and every matrix like the one above in
a omnicomprehensive list? That's because I've to use a function requiring
me to have the matrices I need inside a list.
Thanks in advance, hope it's not a too much stupid problem!
niccolò
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Re: [R] writing summary() to a text file
Federico Calboli [EMAIL PROTECTED] wrote: I would like to output the results of a function into a text file, legible as a such. The function produces a summary quite like: Take a look at the sink() function. Does that do what you need? -- Mike Prager, NOAA, Beaufort, NC * Opinions expressed are personal and not represented otherwise. * Any use of tradenames does not constitute a NOAA endorsement. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Packages - a great resource, but hard to find the right one
hadley wickham [EMAIL PROTECTED] wrote: Which moves somewhat back towards my original suggestion of review articles. To me, an article which compared and contrasted four or five packages on a given topic would be much more useful than an article which reviewed only a single package. I think basing reviews around a specific topic/methodology would be more useful than basing them around a single package. I agree: Such articles would be welcome resources if published either in JSS or in R-News. -- Mike Prager, NOAA, Beaufort, NC * Opinions expressed are personal and not represented otherwise. * Any use of tradenames does not constitute a NOAA endorsement. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] limits on the length of the name of a script file in R 2.6.0.?
Hello! I posted earlier - about my problems with R 2.6 crashing (i.e., telling me it needs to shut down) every time I tried to open an R script. First, it looked like it was unhappy with my working outside of R folder (under Program Files). But not it looks like it was not really the problem. Now, it opens and works when I open scripts whose names are not very long (e.g., Selecting cases I need.R). But it does crash (gives me a message that R needs to shut down) when the script I am trying to open has a slightly longer file name (e.g, in my case: randforestImportanceExample with MR.r and longer). Is anyone aware of the limits the latest version of R imposes on script name length? I never experienced such a problem with R 2.5.0. Thank you! Dimitri Liakhovitski __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] pass lm( ) a char vector as the variables to be included
On Mon, 2007-11-26 at 14:17 +, [EMAIL PROTECTED] wrote:
Here are the codes of the example of lm( ):
## Annette Dobson (1990) An Introduction to
Generalized Linear Models.
## Page 9: Plant Weight Data.
ctl -
(4.17,5.58,5.18,6.11,4.50,4.61,5.17,4.53,5.33,5.14)
trt -
(4.81,4.17,4.41,3.59,5.87,3.83,6.03,4.89,4.32,4.69)
group - gl(2,10,20, labels=c(Ctl,Trt))
weight - c(ctl, trt)
anova(lm.D9 - lm(weight ~ group))
lm.D90 - lm(weight ~ group - 1) # omitting intercept
What I am doing is let the variable name group
stored in a vector, say, g - group. The question is
how to strip the quotation marks when we call lm( )
through g?
Try:
w = weight
g = group
form = as.formula(paste(w,g,sep=~))
lm(form)
Regards,
Richie.
For more complicated automation, the ideas and examples from Bill
Venables Programmer Niche article in the R newsletter from a few years
ago might be of use:
[39] Bill Venables. Programmer's niche. R News, 2(2):24-26, June 2002.
[ bib | PDF | http ]
The PDF is available here:
http://cran.r-project.org/doc/Rnews/Rnews_2002-2.pdf
HTH
G
Mathematical Sciences Unit
HSL
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Dr. Gavin Simpson [t] +44 (0)20 7679 0522
ECRC, UCL Geography, [f] +44 (0)20 7679 0565
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Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/
UK. WC1E 6BT. [w] http://www.freshwaters.org.uk
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Re: [R] limits on the length of the name of a script file in R 2.6.0.?
On 11/26/2007 11:03 AM, Dimitri Liakhovitski wrote: Hello! I posted earlier - about my problems with R 2.6 crashing (i.e., telling me it needs to shut down) every time I tried to open an R script. First, it looked like it was unhappy with my working outside of R folder (under Program Files). But not it looks like it was not really the problem. Now, it opens and works when I open scripts whose names are not very long (e.g., Selecting cases I need.R). But it does crash (gives me a message that R needs to shut down) when the script I am trying to open has a slightly longer file name (e.g, in my case: randforestImportanceExample with MR.r and longer). Is anyone aware of the limits the latest version of R imposes on script name length? I never experienced such a problem with R 2.5.0. The latest version of R is 2.6.1 (released today), but I doubt if you're using that yet. It has the same limit as Windows on filename length. 2.6.0 had a bug which meant long filenames could cause a crash. This was repaired a couple of weeks ago: http://developer.r-project.org/blosxom.cgi/R-2-6-branch/2007/11/10#c2007-11-10 Duncan Murdoch __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Problem installing R on Solaris 9
I've downloaded R-2.6.0 I want to install it on Solaris, so, I run the configure command, it to be fine, but once I run make it give me the following error: *ld: fatal : fichier Rmain.o : type de machine ELF erronV : EM_386 ld: fatal : Erreurs dans le traitement des fichiers. Aucun rVsultat n'a VtV Vcr it dans R.bin collect2: ld returned 1 exit status *** Error code 1 make: Fatal error: Command failed for target `R.bin' Current working directory /rgui-original/R-2.6.0/src/main *** Error code 1 make: Fatal error: Command failed for target `R' Current working directory /rgui-original/R-2.6.0/src/main *** Error code 1 make: Fatal error: Command failed for target `R' Current working directory /rgui-original/R-2.6.0/src *** Error code 1 make: Fatal error: Command failed for target `R' * Please have you any idea to solve this problem? Sincerely yours* * [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] All files inactive in installing R
Dear Sir I was facing various problems especially in making graphs. No graph file was displayed. I reinstall the R 2.6.0. During installation all files icon is inactive. It has not been marked. Which is creating many problems particularly grDevices are not responding. How to solve this problem Regards -- AMINA SHAHZADI Department of Statistics GC University Lahore, Pakistan. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Problem installing R on Solaris 9
On Mon, 26 Nov 2007, aziza belmaati wrote: I've downloaded R-2.6.0 I want to install it on Solaris, so, I run the configure command, it to be fine, but once I run make it give me the following error: *ld: fatal : fichier Rmain.o : type de machine ELF erronV : EM_386 ld: fatal : Erreurs dans le traitement des fichiers. Aucun rVsultat n'a VtV Vcr it dans R.bin collect2: ld returned 1 exit status *** Error code 1 make: Fatal error: Command failed for target `R.bin' Current working directory /rgui-original/R-2.6.0/src/main *** Error code 1 make: Fatal error: Command failed for target `R' Current working directory /rgui-original/R-2.6.0/src/main *** Error code 1 make: Fatal error: Command failed for target `R' Current working directory /rgui-original/R-2.6.0/src *** Error code 1 make: Fatal error: Command failed for target `R' * Please have you any idea to solve this problem? Yes, your compiler and your hardware/OS version differ. Since you haven't told us what either is, we can't even guess as to the difference. Please ask your local OS expertise for help (you also omitted to tell us who you work for). Sincerely yours* * [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. PLEASE do. -- 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@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Communicating from one function to another
My question is a seemingly simple one. I have a bunch of user-defined
functions which compute such-and-such objects. I want to be able to define a
variable in a particular function, then make use of it later, perhaps in a
different function, without necessarily having to move it around in argument
lists. In the C community, it would be called a global variable.
Question 1: Is this practical at all in the R language?
Suppose the variable is called x23. I want to assign a value to it, then use
it later. Seemingly, there are two cases:
Case I is if the variable is given its value at the top level.
Case II is if it is given its value inside a user-defined function. That I
do not know how to do.
Example:
func1 - function (){
x23 - 2.6
return ()
}
driver_func - function (){
func1 ()
print (x23)
return ()
}
However, when I call driver_func, it won't work. Beginning with the load
operation, I get:
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
func1 - function (){
+
+ x23 - 2.6
+
+ return ()
+
+ }
driver_func - function (){
+
+ func1 ()
+
+ print (x23)
+
+ return ()
+
+ }
driver_func ()
Error in print(x23) : object x23 not found
---
From Tom:
Clearly, the two functions cannot communicate. I am aware of the existence
of environments, but don't know much about them. Also, the attach function
and the get and set functions. Also, .GlobalEnv It might or might not make
sense to create a list of all of the variables, with two functions which
get all of them and set all of them. The function calls may be thought of as
an upside down tree. I want to be able to communicate from any node to any
other node.
Your advice?
Tom
Thomas L. Jones, PhD, Computer Science
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Re: [R] Problem installing R on Solaris 9
aziza belmaati wrote: I've downloaded R-2.6.0 I want to install it on Solaris, so, I run the configure command, it to be fine, but once I run make it give me the following error: *ld: fatal : fichier Rmain.o : type de machine ELF erronV : EM_386 ld: fatal : Erreurs dans le traitement des fichiers. Aucun rVsultat n'a VtV Vcr it dans R.bin collect2: ld returned 1 exit status *** Error code 1 make: Fatal error: Command failed for target `R.bin' Current working directory /rgui-original/R-2.6.0/src/main *** Error code 1 make: Fatal error: Command failed for target `R' Current working directory /rgui-original/R-2.6.0/src/main *** Error code 1 make: Fatal error: Command failed for target `R' Current working directory /rgui-original/R-2.6.0/src *** Error code 1 make: Fatal error: Command failed for target `R' * Please have you any idea to solve this problem? As far I gather, this error can occur if you accidentally mix machine types. Any chance that you have something remaining from an earlier build for (say) Linux in the source directory? Sincerely yours* * [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- 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@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] ftable as latex (with Hmisc?)
Dieter Menne wrote: Dear List, possibly called Frank, I tried to create an ftable lookalike of the following data set in LaTeX/Sweave with summary(formula,..), but I could not get it to work for count tables; numeric tables work fine. summary(formula,...,fun=table) does not give the full cross breakdown. See if fun=table (no quotes) or method='cross' work for you. Frank Other suggestions welcome. Note that in the output there should be empty fields on repeated column values like ftable produces. Dieter #--- library(Hmisc) df = data.frame(drug=sample(c(P,V),100,TRUE), Hist1=sample(c(Pos,Neg),100,TRUE), Hist2=sample(c(Pos,Neg),100,TRUE)) ftable(drug~Hist1+Hist2,data=df) __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Fwd: Empty list to use in a for cycle
On Mon, Nov 26, 2007 at 04:35:53PM +0100, Niccolò Bassani wrote:
Dear R-users,
I'm posting a problem I already asked help for some time ago, because I'm
facing that problem once again and even because now, reading that old
e-mail, and the answer recevied, I understand I've not made myself clear.
Here's the question: I need to create an empty list of a specific length to
fill it with a quite large amount of square matrices, which is 602. The
question is that these matrices are created inside a for cycle, and I do not
know how to recall all of them one by one, except by creating an empty list
before the cycle, than assigning for each value of the i index the amtrix
computed to the first element of the empty list.
The fact is that: i've trided to create an empty list with
vector(list,602)
and then putting it in a cycle, but it didn't work. This is the cycle I've
used. To prove it works (and then the cycle itself is not a problem) there's
also the output (i.e. the last square matrix computed).
for (i in unique(elio2$id)){
sub.mu - exp.mu[exp.mu$id==i,]
D - matrix(0,nrow( sub.mu),nrow(sub.mu))
diag(D) - sub.mu$deriv.link
A - mat.cov[1:nrow(D),1:nrow(D)]
R - corstr[1:nrow(D),1:nrow(D)]
W - solve(D)%*%solve(sqrt(A))%*%solve(R)%*%solve(sqrt(A))%*%solve(D)
}
W
[,1] [,2] [,3] [,4]
[1,] 3.492489e+02 -7.9324883721 0.0006286788 -0.0031046240
[2,] -7.932488e+00 17.4974625191 -1.7575467817 0.0001403319
[3,] 6.286788e-04 -1.7575467817 17.3227959738 -1.7529916860
[4,] -3.104624e-03 0.0001403319 -1.7529916860 17.2279244622
Does anyone knows how to insert each and every matrix like the one above in
a omnicomprehensive list? That's because I've to use a function requiring
me to have the matrices I need inside a list.
Thanks in advance, hope it's not a too much stupid problem!
niccol?
you seem to have all the ingredients, so where is the
problem? it's probably not really faster to preallocate this
(moderately long) list. so something like, e.g.
matlist - list()
for (i in 1:3) {
matlist[[i]] = matrix(i, 2, 2)
}
should do what you want: create a list of matrices.
joerg
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Re: [R] complex conjugates roots from polyroot?
Spencer,
I just observed that the polynomial root calculation in the package,
polynom, using the function solve() is more accurate than the polyroot()
function in the base package. Here is an example:
set.seed(1234)
p - polynomial(sample(1:10, size=45, rep=T)) # degree 44
z - solve(p)
findConjugates(z, complex.eps=.Machine$double.eps) # this identifies all 21
conjugate pairs
z1 - polyroot(p)
findConjugates(z1, complex.eps=.Machine$double.eps) # this only identifies
only 3 conjugate pairs
As, I had mentioned earlier, I can't tell what tolerances are used by these
algorithms. However, it appears that polynom is more accurate.
Best,
Ravi.
---
Ravi Varadhan, Ph.D.
Assistant Professor, The Center on Aging and Health
Division of Geriatric Medicine and Gerontology
Johns Hopkins University
Ph: (410) 502-2619
Fax: (410) 614-9625
Email: [EMAIL PROTECTED]
Webpage: http://www.jhsph.edu/agingandhealth/People/Faculty/Varadhan.html
-Original Message-
From: Spencer Graves [mailto:[EMAIL PROTECTED]
Sent: Sunday, November 25, 2007 12:36 PM
To: Ravi Varadhan
Cc: r-help@r-project.org
Subject: Re: [R] complex conjugates roots from polyroot?
Hi, Ravi:
Question: Are duplicate real numbers complex conjugates? For
some purposes, perhaps. However, for identifying (damped) periodicity
on a difference or differential equation, we must exclude repeated real
roots.
In any event, your suggestion inspired me to create a function
findConjugates (see below), which I've added to the FinTS package
currently under development on R-Forge. The source code is currently
available via svn checkout
svn://svn.r-forge.r-project.org/svnroot/fints. In another day or so,
it should be available (with documentation) via
'install.packages(FinTS,repos=http://r-forge.r-project.org;)'. In
another couple of months, it should appear on CRAN.
Thanks again for your suggestion.
Best Wishes,
Spencer
##
findConjugates - function(x,
complex.eps=1000*.Machine[[double.neg.eps]]){
##
## 1. compute normalization
##
if(length(x)1)return(complex(0))
ax - abs(x)
m2 - outer(ax, ax, pmax)
##
## 2. Compute complex differences
##
c2 - (abs(outer(x, Conj(x), -) / m2) complex.eps)
c2[m2==0] - FALSE
c2 - (c2 lower.tri(c2))
##
## 3. Any differences exceed complex.eps?
##
if(any(c2)){
# check standard differences
d2 - (abs(outer(x, x, -) / m2) complex.eps)
d2[m2==0] - FALSE
#
cd2 - (c2 d2)
if(any(cd2)){
ic - sort(unique(row(cd2)[cd2]))
return(x[ic])
}
}
complex(0)
}
##
Ravi Varadhan wrote:
Hi Spencer,
Here is a simple approach to detect conjugate pairs:
is.conj - function(z1, z2, tol=1.e-10) {
# determine if two complex numbers are conjugates
cond1 - abs(Re(z1) - Re(z2)) tol
cond2 - abs(Im(z1) + Im(z2)) tol
cond1 cond2
}
set.seed(123)
z - polyroot(sample(1:5, size=8, rep=T))
zmat - which(outer(z, z, FUN=is.conj), arr.ind=T)
zmat[zmat[,1] zmat[,2], ]
# result
row col
[1,] 1 3
[2,] 5 6
[3,] 4 7
We see that (1,3), (4,7), and (5,6) are the conjugate pairs.
This doesn't address the issue of numerical round-off (there is no
argument
in polyroot that governs the accuracy of the roots).
Best,
Ravi.
---
Ravi Varadhan, Ph.D.
Assistant Professor, The Center on Aging and Health
Division of Geriatric Medicine and Gerontology
Johns Hopkins University
Ph: (410) 502-2619
Fax: (410) 614-9625
Email: [EMAIL PROTECTED]
Webpage: http://www.jhsph.edu/agingandhealth/People/Faculty/Varadhan.html
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
On
Behalf Of Spencer Graves
Sent: Friday, November 23, 2007 12:08 PM
To: r-help@r-project.org
Subject: [R] complex conjugates roots from polyroot?
Hi, All:
Is there a simple way to detect complex conjugates in the roots
returned by 'polyroot'? The obvious comparison of each root with the
complex conjugate of the next sometimes produces roundoff error, and I
don't know how to bound its magnitude:
(tst - polyroot(c(1, -.6, .4)))
tst[-1]-Conj(tst[-2])
[1] 3.108624e-15+2.22045e-16i
abs(tst[-1]-Conj(tst[-2]))/abs(tst[-1])
1.971076e-15
.Machine$double.neg.eps
1.110223e-16
Testing (abs(tst[-1]-Conj(tst[-2]))/abs(tst[-1])
(20*.Machine$double.neg.eps)) would catch this example, but it might not
catch others.
The 'polyroot' help page says, See Also ... the 'zero' example in
the demos directory. Unfortunately, I've so far been unable to find
that.
[R] visualizing nucleotide sequence properties
Hi there, I am looking for R-packages that can help me visualize properties on nucleotide sequences. I want to display sequences in the 1-100K base range as lines and plot features above and below those lines. Any ideas would be welcome. Thanks, Bernd [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] mvr error in PLS package
On Mon, 2007-11-26 at 09:25 -0800, Bricklemyer, Ross S wrote: All, I have been using a data set to build pls models for three different soil properties. Two of the three models run fine; however I receive the following error for the final model. libs.IC.cal - mvr(libs.IC.fmla, data = libsdata.cond.cal, ncomp=20,validation = LOO, method = oscorespls) Error in colMeans(x, n, prod(dn), na.rm) : 'x' must be numeric There are many 0 for this soil property. Could this cause the error? Without having the data (or a small example therefore) it is impossible to tell. To start, try str(libsdata.cond.cal) and check that the variables referenced in your formula object (which is what I presume libs.IC.fmla is?) are all numeric and haven't got coded as factors or characters or something strange. G Best, Ross *** Ross Bricklemyer Dept. of Crop and Soil Sciences Washington State University 291D Johnson Hall PO Box 646420 Pullman, WA 99164-6420 Work: 509.335.3661 Cell/Home: 406.570.8576 Fax: 509.335.8674 Email: [EMAIL PROTECTED] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/ UK. WC1E 6BT. [w] http://www.freshwaters.org.uk %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Communicating from one function to another
Thomas L Jones wrote:
My question is a seemingly simple one. I have a bunch of user-
defined functions which compute such-and-such objects. I want to be
able to define a variable in a particular function, then make use of
it later, perhaps in a different function, without necessarily
having to move it around in argument lists. In the C community, it
would be called a global variable.
Global variables in R are used with - instead of -.
For example:
x - 1
y - 1
f - function() {
x - 2
y - 2
}
f()
will turn y to 2 but will not change x.
Alberto Monteiro
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Re: [R] Communicating from one function to another
On 11/26/2007 1:25 PM, Alberto Monteiro wrote:
Thomas L Jones wrote:
My question is a seemingly simple one. I have a bunch of user-
defined functions which compute such-and-such objects. I want to be
able to define a variable in a particular function, then make use of
it later, perhaps in a different function, without necessarily
having to move it around in argument lists. In the C community, it
would be called a global variable.
Global variables in R are used with - instead of -.
For example:
x - 1
y - 1
f - function() {
x - 2
y - 2
}
f()
will turn y to 2 but will not change x.
R doesn't really have global variables. - goes looking in parent
environments until it finds the target variable, and makes the
assignment there. If it never finds one, it makes the assignment in the
global environment, but the name is misleading: it should really be
called the user workspace.
Duncan Murdoch
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[R] looking for packages that visualize nucleotide sequence properties
Hi there, I am looking for R-packages that can help me visualize properties on nucleotide sequences. I want to display sequences in the 1-100K base range as lines and plot features above and below those lines. Any ideas would be welcome. Thanks, Bernd __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] ftable as latex (with Hmisc?)
Dieter Menne wrote: I tried to create an ftable lookalike of the following data set in LaTeX/Sweave with summary(formula,..), but I could not get it to work for count tables; numeric tables work fine. summary(formula,...,fun=table) does not give the full cross breakdown. Frank E Harrell Jr f.harrell at vanderbilt.edu writes: See if fun=table (no quotes) or method='cross' work for you. Frank No, it does not, that's why I asked. I had tried both, fun=table (with or without ) give a individual breakdown by factor, and method=cross an error message (works find with numerical data). Dieter df = data.frame(drug=sample(c(P,V),100,TRUE), + Hist1=sample(c(Pos,Neg),100,TRUE), + Hist2=sample(c(Pos,Neg),100,TRUE)) ftable(drug~Hist1+Hist2,data=df) drug P V Hist1 Hist2 Neg Neg14 6 Pos11 14 Pos Neg13 15 Pos14 13 summary(drug~Hist1+Hist2,data=df,fun=table) drugN=100 +---+---+---+--+--+ | | |N |P |V | +---+---+---+--+--+ |Hist1 |Neg| 45|25|20| | |Pos| 55|27|28| +---+---+---+--+--+ |Hist2 |Neg| 48|27|21| | |Pos| 52|25|27| +---+---+---+--+--+ |Overall| |100|52|48| +---+---+---+--+--+ summary(drug~Hist2+Hist2,data=df,method=cross) Error in Y %*% rep(1, ncol(Y)) : requires numeric matrix/vector arguments In addition: Warning message: In mean.default(newX[, i], ...) : argument is not numeric or logical: returning NA __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Communicating from one function to another
Duncan Murdoch wrote:
R doesn't really have global variables. - goes looking in parent
environments until it finds the target variable, and makes the
assignment there. If it never finds one, it makes the assignment in
the global environment, but the name is misleading: it should
really be called the user workspace.
Got it.
So, in this case:
x - 1
f - function() {
x - 2
g - function() {
x - 3
}
g()
x
}
f()
It's expected that f will return 3, but x would still be 1?
Alberto Monteiro
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[R] Preserving output of MCMC iterations
Dear colleagues,
I'm an epidemiologist with no background in programming and just
started using R a few weeks ago. I am working on the epidemiology of
African sleeping sickness, and am trying to use R to perform a Monte
Carlo Markov Chain analysis to estimate three unknown parameters within
a model of African sleeping sickness case detection that is mainly
informed by actual field programme data.
Basically, I have a set of four differential equations governing my
model, which I am implementing stochastically (small populations, low
transmission). I iterate the model a large number of times (10 000) for
each unique combination of plausible values of the three unknown
parameters a, b and c. After each iteration, I ask R to check whether
the output 'fits' the observed data: if it does, I ask R to add 1 to the
(i,j,k)th element of a 3-dimensional 'scores' array (3 unknown
parameters = 3 dimensions), where i,j, and k are the plausible values of
a,b and c that are currently being tested.
My intended output is in fact this 3-dimensional array, which is
essentially a likelihood surface wherein each (i,j,k)th element is the
likelihood of the corresponding combination of plausible parameter
values a, b and c.
The code I have written looks more or less like this:
FUN1(args) {
specify parameters based on arguments
replicate (10 000 times, {
{implement differential equations once}
if output fits data, scores[i,j,k]-scores[i,j,k]+1
})
}
FUN2(args) {
create 3-dim 'scores' array
apply FUN1 to each combination of a,b and c values, i.e. to each row of
a dataframe containing each combination
return(scores)
}
I've tested the various sub-routines within the code repeatedly and
everything seems to work fine with the exception of one problem: the
scores array that R returns when I call FUN2 is unchanged from its
initial specification within FUN2 (e.g. if I tell R the initial value of
the array elements should be 0, R returns an array with all 0s). The
scores array IS being updated with +1 after each data-fitting iteration
of the model (I checked this), but somehow these changes are not being
preserved outside of the replicate {} environment.
I've tried to look at the help archives and other help sources but
haven't been able to find or perhaps interpret solutions to my problem.
I've also looked at the contributed MCMC packages already available, but
for a variety of reasons these do not seem suitable for my purposes, and
I would prefer writing the full code myself.
Apologies if the explanation is not very clear - I'm still in the very
steep learning curve! I will be happy to clarify further.
Thanks in advance for your consideration.
Francesco
Francesco Checchi
Honorary Lecturer, Part-time PhD Student
Disease Control and Vector Biology Unit
Department of Infectious and Tropical Diseases
London School of Hygiene and Tropical Medicine
Room 51G6, 49-51 Bedford Square
London WC1B 3DP, United Kingdom
office +44 (0)20 7927 2336
mobile +44 (0)79 0671 9637
fax +44 (0)20 7927 2918
e-mail [EMAIL PROTECTED]
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[R] writing statistical function for boot
Hi everyone,
I need help in writing a statistical function for bootstrap. Suppose m is a
matrix with n cols and p rows, my original data. What I want to do is a
bootstrap (using boot from package boot) on eigenvectors from a PCA done on m
with a statistic function calculating the eigenvector bootstrap error ratio.
If R = number of bootstrap replicates, then my function should look something
like this where m.i is the ith bootstrap sample matrix (of course this is
wrong, but I wrote it to give an idea of what I am after)
pcasig - function(m) {
for (i in 1:R) {
pca.i - prcomp(m.i)
eigen.i - pca.i$rotation
estim - sum(eigen.1+
.+eigen.R) / R
a - matrix(estim, p, n)
se - ((sum((eigen.i-estim)^2))/(R-1))^0.5
t.i - a / se }
}
Thanks for your consideration,
Monica
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Re: [R] connection diagram
On Wed, 14 Nov 2007, Manal Helal wrote: Dimn Waves Tot. Parts In Wave Wave NoSerial Index W Order M Index DepTot. D1-Serial D1-IndexD1-OrderD1-M Index D2-Serial D2-IndexD2-OrderD2-M Index 2 7 1 0 1 0 0 0, 0 2 2 18 0 4, 4 3 2 1 2, 0 2 7 2 1 2 18 0 4, 4 2 4 20 0 2, 2 5 36 1 0, 4 following the tutorial on SNA, I see that I need to convert that into adjacency matrix to start plotting the graph, and I can not see how I can do that, Into one adjacency matrix -- you probably can't. [And, I think, probably don't really want to do that...] What you might be able to do is figure out what your actual actors are... the entities that are connected to each other... and use them (just them... or their relations...] to build your adjacency matrix. With your matrix in hand, you will want to keep track of those other variables... there are a lotta ways you could go about this, and there are a lot of decisions to affect your implementation. In the 'sna' package, look at the graph stack data structure. [m x N x N dimension -- an array of adjacency matrices which could be attributed values rather than 0/1 boolean is-connected assertions.] You might be best served by a series of plots, each taking into account a different combination of your available data variables. It almost sounds fun, doesn't it? :-) Not really familiar enough with your data to make many more suggestions. It sounds like your data structure is pretty nontrivial... maybe there are ways you can break it down into pieces that you can manage more easily, for your own sake? best, --elijah __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Plotting with R: setting the y axis
I have a series of numbers I'm wanting to plot. They come from a nanodrop machine, which graphs with a specific x and y indices. X goes from 220nm to 350nm, which I can set. But the y axis should go from -5 to 65, but I'm finding it impossible to hardcode that. I've looked. I've typed ?plot at the R prompt. Google has not been my friend. _R Graphics_, if it holds the key, has not presented it to me. Can anyone help? x - (220:350) z - c(21.56 , 21.12 , 20.44 , 19.83 , 19.35 , 18.53 , 18.01 , 17.78 , 17.51 , 17.34 , 17.26 , 17.18 , 17.18 , 17.23 , 17.36 , 17.65 , 17.95 , 18.57 , 19.42 , 20.14 , 21.22 , 22.1 , 22.64 , 23.56 , 24.66 , 25.32 , 26.2 , 27.02 , 27.61 , 28.45 , 29.15 , 29.57 , 30.34 , 31.2 , 31.67 , 32.25 , 32.64 , 32.8 , 32.88 , 32.87 , 32.8 , 32.61 , 32.32 , 32.05 , 31.49 , 30.7 , 29.76 , 29.13 , 28.1 , 27.06 , 26.44 , 25.51 , 24.56 , 23.9 , 22.88 , 21.86 , 21.15 , 19.96 , 18.72 , 17.89 , 16.73 , 15.64 , 14.53 , 13.8 , 12.8 , 11.9 , 11.32 , 10.4 , 9.49 , 8.95 , 8.19 , 7.41 , 6.63 , 6.15 , 5.48 , 4.88 , 4.53 , 4.06 , 3.67 , 3.43 , 3.09 , 2.81 , 2.53 , 2.36 , 2.15 , 1.97 , 1.86 , 1.71 , 1.6 , 1.5 , 1.45 , 1.4 , 1.34 , 1.31 , 1.28 , 1.25 , 1.23 , 1.21 , 1.18 , 1.14 , 1.12 , 1.09 , 1.06 , 1.02 , 1.01 , 1 , 0.98 , 0.97 , 0.96 , 0.95 , 0.94 , 0.94 , 0.93 , 0.92 , 0.92 , 0.9 , 0.89 , 0.88 , 0.87 , 0.84 , 0.82 , 0.81 , 0.8 , 0.79 , 0.78 , 0.77 , 0.76 , 0.76 , 0.75 , 0.73 , 0.71 ) jpeg(nano_WoloshukRIB401488.jpg) plot( x , z , type=l , cols=red , main=nanodrop - #012345 , xlab=Wavelength(nm) , ylab=10mm Absorbance ) dev.off() -- David Jacoby[EMAIL PROTECTED] Purdue Genomics Facility S049, WSLR building Phone: hah! __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Filling in a Zero Matrix
Hi Amy,
Many (perhaps most) of the people on the list do not receive emails with
html...so we can't see colored text. Also it would be helpfully to have
a bit of your data, so we can run your code (see the posting guide in
this regard,http://www.R-project.org/posting-guide.html).
Please explain what are the 'xlabel' and the 'ylabel' that you
mentioned. I don't see those variables in your code.
Julian
Amit Patel wrote:
Hi
I am very new to R and statistical programming in general. I am trying to
reorder data from a .csv file. I have managed to import the data and create a
zero matrix. I am now trying to fill the matrix. There seems to be some
problem with this section of my code. I have highlighted the dodgy code in
red. Please help if possible.
##
### Create matrix ###
##
#Open the csv file
OGSdata - read.table(MG3199.csv,sep=,,header=TRUE)
#creates 3 separate vectors
sample - OGSdata[,1]
mci - OGSdata[,2]
pct - OGSdata[,3]
#change mci range
offset - min(mci)-1
mci - (mci - offset)
#matrix sizes
mci_count - max(mci)
sample_count - max(sample)
#creates a zero matrix
OGS - mat.or.vec(mci_count,sample_count)
#Create labels
sample_lab - (A-9,B-9, C-9, D-9, E-9,A-12,B-12, C-12,
D-12, E-12)
#add data
for (i in 1:length(pct)) {
OGS(mci(i),sample(i))- pct(i);
}
What I want is to have colum1 from original data to be the xlabel, column 2
to be the ylabel and the 3rd colum to be the values in the matrix
Any help is appreciated.
Kind Regards
Amit Patel
___
now.
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Re: [R] question about extreme value distribution
As an alternative you could try quantile regression (find a regression line for the 95th percentile), if the relationship between max(y) and x is only due to more points (and therefore more oportunities for large values) then the estimated quantile lines should not differ significantly from 0. Try the following (where the truth is no relationship): set.seed(2) x - rep(1:10, 1:10) y - rexp(55, 1) plot(x,y) cor.test( 1:10, tapply( y, x, max ) ) library(quantreg) fit - rq( y ~ x, tau=c(0.5, 0.95) ) summary(fit) Notice that the cor.test is significant, but that the confidence intervals for the slopes both include 0. Hope this helps, -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare [EMAIL PROTECTED] (801) 408-8111 -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Avril Coghlan Sent: Thursday, November 22, 2007 5:46 AM To: [EMAIL PROTECTED] Cc: [EMAIL PROTECTED] Subject: [R] question about extreme value distribution Hello, I have a question about using extreme value distribution in R. I have two variables, X and Y, and have pairs of points (X1,Y1),(X2,Y2), (X3,Y3) etc. When I plot X against Y, it looks like the maximum value of Y (for a particular X) is correlated with X. Indeed, when I bin the data by X-value into equally sized bins, and test whether the maximum value of Y for a bin is correlated with the mean X for the bin, there is a significant correlation between max(Y) and X. However, I am not very happy with this because there is not an equal number of data points in each bin. I imagine that there is a better statistical test that I could use, if I could fit an extreme value distribution to the Y data. However, I'm not sure how to do this. I am wondering is there a way to use the extreme value distribution functions in R to test the hypothesis that the maximum of Y (for a particular X) is correlated with X? I would appreciate advice very much. regards Avril Coghlan -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Plotting with R: setting the y axis
On Monday 26 November 2007, Dave Jacoby wrote: I have a series of numbers I'm wanting to plot. They come from a nanodrop machine, which graphs with a specific x and y indices. X goes from 220nm to 350nm, which I can set. But the y axis should go from -5 to 65, but I'm finding it impossible to hardcode that. I've looked. I've typed ?plot at the R prompt. Google has not been my friend. _R Graphics_, if it holds the key, has not presented it to me. Can anyone help? x - (220:350) z - c(21.56 , 21.12 , 20.44 , 19.83 , 19.35 , 18.53 , 18.01 , 17.78 , 17.51 , 17.34 , 17.26 , 17.18 , 17.18 , 17.23 , 17.36 , 17.65 , 17.95 , 18.57 , 19.42 , 20.14 , 21.22 , 22.1 , 22.64 , 23.56 , 24.66 , 25.32 , 26.2 , 27.02 , 27.61 , 28.45 , 29.15 , 29.57 , 30.34 , 31.2 , 31.67 , 32.25 , 32.64 , 32.8 , 32.88 , 32.87 , 32.8 , 32.61 , 32.32 , 32.05 , 31.49 , 30.7 , 29.76 , 29.13 , 28.1 , 27.06 , 26.44 , 25.51 , 24.56 , 23.9 , 22.88 , 21.86 , 21.15 , 19.96 , 18.72 , 17.89 , 16.73 , 15.64 , 14.53 , 13.8 , 12.8 , 11.9 , 11.32 , 10.4 , 9.49 , 8.95 , 8.19 , 7.41 , 6.63 , 6.15 , 5.48 , 4.88 , 4.53 , 4.06 , 3.67 , 3.43 , 3.09 , 2.81 , 2.53 , 2.36 , 2.15 , 1.97 , 1.86 , 1.71 , 1.6 , 1.5 , 1.45 , 1.4 , 1.34 , 1.31 , 1.28 , 1.25 , 1.23 , 1.21 , 1.18 , 1.14 , 1.12 , 1.09 , 1.06 , 1.02 , 1.01 , 1 , 0.98 , 0.97 , 0.96 , 0.95 , 0.94 , 0.94 , 0.93 , 0.92 , 0.92 , 0.9 , 0.89 , 0.88 , 0.87 , 0.84 , 0.82 , 0.81 , 0.8 , 0.79 , 0.78 , 0.77 , 0.76 , 0.76 , 0.75 , 0.73 , 0.71 ) jpeg(nano_WoloshukRIB401488.jpg) plot( x , z , type=l , cols=red , main=nanodrop - #012345 , xlab=Wavelength(nm) , ylab=10mm Absorbance ) dev.off() see the arguments xlim and ylim in plot.default -- Dylan Beaudette Soil Resource Laboratory http://casoilresource.lawr.ucdavis.edu/ University of California at Davis 530.754.7341 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Specification Tests for Tobit Models
Dear R-List, I am using Tobit regression models to estimate censored dependent variables (using survreg in the survival package). I have 2 questions: 1) Is there any package providing specification tests for Tobit models (Hausman test proposed by Newey (1987), Journal of Econometrics, White Information Matrix test or any other test I do not know about so far)? 2) Are there any packages that implement SUR or simultaneous equations for censored regression? Thanks in advance, Malte Malte Brockmann [EMAIL PROTECTED] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Problem with avoiding rep
Dear All, Suppose that you have the following data: X Frequency 1 3 4 2 3 4 To get a vector with all observations, one could use data - c(rep(1,3),rep(4,2),rep(3,4)) I am wondering whether there exists an easier way of doing this. Any ideas? Thanks in advance, Paul __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] newbie polr() question
Hi everyone, I'm trying to understand some R output here for ordinal regression. I have some integer data called A split up into 3 ordinal categories, top, middle and bottom, T, M and B respectively. I have to explain this output to people who have a very poor idea about statistics and just need to make sure I know what I'm talking about first. Here's the output: Call: polr(formula = Factor ~ A, data = a, Hess = TRUE, method = logistic) Coefficients: ValueStd. Error t value A -0.1259028 0.04758539 -2.645829 Intercepts: Value Std. Error t value B|M -2.5872 0.5596 -4.6232 M|T 0.3044 0.4864 0.6258 Residual Deviance: 204.8798 AIC: 210.8798 I really am not sure what the intercepts mean at all. However, my understanding of the coefficient of A is that as the category increases, A decreases? If I have an A value of 10, how to I figure out the estimated probability that this score is in one of the three categories? thanks! __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] multiple comparisons/tukey kramer
On 2007-11-23, hadley wickham [EMAIL PROTECTED] wrote: What I need is a reference to the tests implemented in glht, so I can decide which one is appropriate for my data. Sequen, Changepoint et al. may be common terms in some fields, but not in the references I'm working from. Have you read the vignette: http://cran.r-project.org/doc/vignettes/multcomp/multcomp.pdf ? Thanks, I have, and I've now reread it, as well as looking at the examples in contrMat. I now understand that Tukey, Dunnett, Sequen et al. are 'convenience' terms, specifying all pair-wise, treatments vs control etc., contrasts. I worked through the numerical example in Dunnett's original paper, and also found a worked example of Tukey-Kramer contrasts, and reproduced the results using glht(LM, linfct = mcp(fac = 'Dunnett')) glht(LM, linfct = mcp(fac = 'Tukey')) I'm still finding the language very difficult. I was taught these methods using SS/MS language. Linear models were mentioned in passing, but the focus was on using (and hopefully understanding) the formulas for filling in the cells in an anova table. Has the linear model focus now replaced the 'traditional' approach I learned? It's been a very frustrating week or two as I try and come to terms with material I thought I already knew, so what I'm wondering is if I'm doomed to repeat this process with every variation on Anova designs I want to analyze in R unless I take the time to study linear models. Today's task, for example, is figuring out how to convert Sokal and Rohlf's two-level nested model II anova into R code, and it's not going well. Thanks, Tyler __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Problem with avoiding rep
x - c(1,4,3) freq - c(3,2,4) rep(x, freq) [1] 1 1 1 4 4 3 3 3 3 Gabor On Mon, Nov 26, 2007 at 07:34:36PM +, Paul Smith wrote: Dear All, Suppose that you have the following data: X Frequency 1 3 4 2 3 4 To get a vector with all observations, one could use data - c(rep(1,3),rep(4,2),rep(3,4)) I am wondering whether there exists an easier way of doing this. Any ideas? Thanks in advance, Paul __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Csardi Gabor [EMAIL PROTECTED]MTA RMKI, ELTE TTK __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Problem with avoiding rep
On Nov 26, 2007 7:45 PM, Gabor Csardi [EMAIL PROTECTED] wrote: x - c(1,4,3) freq - c(3,2,4) rep(x, freq) [1] 1 1 1 4 4 3 3 3 3 Thanks, Gabor. I had just tried rep(1:10,10:20) but should have tried rep(1:10,11:20) Paul On Mon, Nov 26, 2007 at 07:34:36PM +, Paul Smith wrote: Dear All, Suppose that you have the following data: X Frequency 1 3 4 2 3 4 To get a vector with all observations, one could use data - c(rep(1,3),rep(4,2),rep(3,4)) I am wondering whether there exists an easier way of doing this. Any ideas? Thanks in advance, Paul __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Csardi Gabor [EMAIL PROTECTED]MTA RMKI, ELTE TTK __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Filling in a Zero Matrix
My mistake, by xlabel and ylabel you are refering to the row and column
names of your matrix, right? To label a matrix you can simply use
colnames() and rownames().
Still its not clear to me what you are trying to do with your code.
Perhaps if you give us a sample of your data and explain clearly what
you are trying to achieve, we can help you to simplify your code.
Julian
Julian Burgos wrote:
Hi Amy,
Many (perhaps most) of the people on the list do not receive emails with
html...so we can't see colored text. Also it would be helpfully to have
a bit of your data, so we can run your code (see the posting guide in
this regard,http://www.R-project.org/posting-guide.html).
Please explain what are the 'xlabel' and the 'ylabel' that you
mentioned. I don't see those variables in your code.
Julian
Amit Patel wrote:
Hi
I am very new to R and statistical programming in general. I am trying to
reorder data from a .csv file. I have managed to import the data and create
a zero matrix. I am now trying to fill the matrix. There seems to be some
problem with this section of my code. I have highlighted the dodgy code in
red. Please help if possible.
##
### Create matrix ###
##
#Open the csv file
OGSdata - read.table(MG3199.csv,sep=,,header=TRUE)
#creates 3 separate vectors
sample - OGSdata[,1]
mci - OGSdata[,2]
pct - OGSdata[,3]
#change mci range
offset - min(mci)-1
mci - (mci - offset)
#matrix sizes
mci_count - max(mci)
sample_count - max(sample)
#creates a zero matrix
OGS - mat.or.vec(mci_count,sample_count)
#Create labels
sample_lab - (A-9,B-9, C-9, D-9, E-9,A-12,B-12, C-12,
D-12, E-12)
#add data
for (i in 1:length(pct)) {
OGS(mci(i),sample(i))- pct(i);
}
What I want is to have colum1 from original data to be the xlabel, column 2
to be the ylabel and the 3rd colum to be the values in the matrix
Any help is appreciated.
Kind Regards
Amit Patel
___
now.
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__
R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
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R-help@r-project.org mailing list
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Re: [R] Fwd: Empty list to use in a for cycle
You could try something like this (untested).
lapply(unique(elio2$id), function(i){
sub.mu - exp.mu[exp.mu$id==i, ]
n - nrow(sub.mu)
D - matrix(0, n, n)
diag(D) - sub.mu$deriv.link
A - mat.cov[seq_len(n), seq_len(n)]
R - corstr[seq_len(n), seq_len(n)]
SolveD - solve(D)
SolveA - solve(sqrt(A))
SolveD %*% SolveA %*% solve(R) %*% SolveA %*% SolveD
})
HTH,
Thierry
ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Research Institute for Nature and
Forest
Cel biometrie, methodologie en kwaliteitszorg / Section biometrics, methodology
and quality assurance
Gaverstraat 4
9500 Geraardsbergen
Belgium
tel. + 32 54/436 185
[EMAIL PROTECTED]
www.inbo.be
Do not put your faith in what statistics say until you have carefully
considered what they do not say. ~William W. Watt
A statistical analysis, properly conducted, is a delicate dissection of
uncertainties, a surgery of suppositions. ~M.J.Moroney
-Oorspronkelijk bericht-
Van: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Namens Niccolò Bassani
Verzonden: maandag 26 november 2007 16:36
Aan: [EMAIL PROTECTED]
Onderwerp: [R] Fwd: Empty list to use in a for cycle
Dear R-users,
I'm posting a problem I already asked help for some time ago, because I'm
facing that problem once again and even because now, reading that old e-mail,
and the answer recevied, I understand I've not made myself clear.
Here's the question: I need to create an empty list of a specific length to
fill it with a quite large amount of square matrices, which is 602. The
question is that these matrices are created inside a for cycle, and I do not
know how to recall all of them one by one, except by creating an empty list
before the cycle, than assigning for each value of the i index the amtrix
computed to the first element of the empty list.
The fact is that: i've trided to create an empty list with
vector(list,602)
and then putting it in a cycle, but it didn't work. This is the cycle I've
used. To prove it works (and then the cycle itself is not a problem) there's
also the output (i.e. the last square matrix computed).
for (i in unique(elio2$id)){
sub.mu - exp.mu[exp.mu$id==i,]
D - matrix(0,nrow( sub.mu),nrow(sub.mu))
diag(D) - sub.mu$deriv.link
A - mat.cov[1:nrow(D),1:nrow(D)]
R - corstr[1:nrow(D),1:nrow(D)]
W - solve(D)%*%solve(sqrt(A))%*%solve(R)%*%solve(sqrt(A))%*%solve(D)
}
W
[,1] [,2] [,3] [,4]
[1,] 3.492489e+02 -7.9324883721 0.0006286788 -0.0031046240 [2,] -7.932488e+00
17.4974625191 -1.7575467817 0.0001403319 [3,] 6.286788e-04 -1.7575467817
17.3227959738 -1.7529916860 [4,] -3.104624e-03 0.0001403319 -1.7529916860
17.2279244622
Does anyone knows how to insert each and every matrix like the one above in a
omnicomprehensive list? That's because I've to use a function requiring me to
have the matrices I need inside a list.
Thanks in advance, hope it's not a too much stupid problem!
niccolò
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] 'Split' character
One additionnal question about a problem that I just noticed in my script: the list created by my split function is sorted in the increasing order and not in the current order of the elements of the do.call argument (see the results of the two last lines of the following script). I was unsuccesful in tweaking my split function to have a proper order... If there is no way to do that, I guess it comes down to a very basic question: how can I reorder a list ? how can I reorder the list 'mydata.split' according to a-rep(1.5:10.5,each=2) b-rep(21:30,each=2) cd-101:120 mydata-data.frame(a,b,cd) mydata.split - split(mydata,do.call(paste,c(mydata[,1:2],sep = :)),drop=TRUE) names(mydata.split) unique(do.call(paste,c(mydata[,1:2],sep = :))) Sebastien Gabor Grothendieck a écrit : Try this using the BOD data frame that comes with R or try using interaction in place of paste: split(BOD, do.call(paste, c(BOD, sep = :)), drop=TRUE) On Nov 25, 2007 10:23 AM, [EMAIL PROTECTED] wrote: Thanks Jim and Herinque for you reply. The substitution you are both proposing works fine, except when a or b contains decimal numbers (which is mostly my case in a real dataset). In this case, there is no distinction between the decimal point and the one introduced by the split function. If the split function cannot be customized, then I guess I have to first substitute the decimal point in my dataset by e.g. a * sign and change it back to a . when the split is done... Sebastien jim holtman a écrit : Here is one way: a-1:10 b-21:30 mydata-data.frame(a,b) mydata.split-split(mydata,(mydata[,1:2]),drop=TRUE) x - mydata.split # customize the names names(x) - sapply(strsplit(names(x), \\.), paste, collapse=-my character-) x $`1-my character-21` a b 1 1 21 $`2-my character-22` a b 2 2 22 $`3-my character-23` a b 3 3 23 ... On Nov 24, 2007 6:15 PM, [EMAIL PROTECTED] wrote: Dear R-users, The following code splits a very simple dataframe into a list, each element of the list being one line of the dataframe. You will see that the split function names each element of the list by using uses the content of a and b and merging them with a . character. Is there a way to customize this character? a-1:10 b-21:30 mydata-data.frame(a,b) mydata.split-split(mydata,(mydata[,1:2]),drop=TRUE) mydata.split Thanks in advance for your help. Sebastien __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] spss, string factors, selecting
Hi, I am having trouble with a large dataset I am importing from SPSS. The problem is I have to merge two datasets (which seems to be working OK) then select rows based on attributes. I have a column with either blank cells, B or E entered. I want to select all rows with E. I have other columns with numerical data which I will then do analyses on. data[column== E] does not work. I use E not E, because levels (column) returns B E. Any help on what I am doing wrong is much appreciated. I'm getting quite stressed as I have 10 files with approx 100,000 records in each to analyse so manipulating data becomes a pain. Here is the code below, not sure it makes much sense without seeing the dataset:- chaff-read.spss(/Users/Kat/Desktop/papers in progress/btopaper/ edited BTO data/fatnewchaff.sav, to.data.frame=TRUE) chafffat-read.spss(/Users/Kat/Desktop/papers in progress/btopaper/ edited BTO data/fatmethods.sav) chaffmerge2-merge(chaff, chafffat, by.x=c(RINGNO, FAT, FATMTD), by.y=c(RINGNO, FAT, FATMTD), all=T) attach(chaffmerge2) chaffhabfactor-factor(chaffmerge2$HYBRID_A) levels(chaffhabfactor) Echaff-chaffmerge2[FATMTD== E,] attach(Echaff) names(Echaff) plotmeans(Echaff$FAT~Echaff$HYBRID_A) chaffFat-factor(Echaff$FAT) levels(chaffFat) chaffzeros-table(chaffFat, Echaff$HYBRID_A) chaffzeros chaffFat12345 0 261 354 345 1003 235 138 23 1762 2190420 3 70101 4 20000 5 145 34 123 100 60 8 00000 10 202 141 248 279 101 15 73 12 79 519 20 84 60 64 133 19 25 146 20 223 30 30 25 22 54 13 3530744 407 102 125 4520310 5010021 6001011 The 1,2,3,4,5, values of chaffFat above correspond to B which should have been removed [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Unweighted meta-analysis
Roy Sanderson a écrit : Hello I'm very much a beginner on meta-analysis, so apologies if this is a trivial posting. I've been sent a set data from separate experimental studies, Treatment and Control, but no measure of the variance of effect sizes, numbers of replicates etc. Instead, for each study, all I have is the mean value for the treatment and control (but not the SD). With possibly three very special kind of exceptions, what you've been sent is insufficient for any kind of analysis (meta- or otherwise) : no way to assess variability, hence no way to assess relative importance of noise to data or relative importance of different set of data. One possible exception is when the very nature of the experiment imply that your data come from a truly one-parameter distribution. I'm thinking, for example, of count data of rare events, which might, under not-so-unreasonable(-in-special-circumstances) conditions, come from a Poisson distribution. Another possible set of exception is that when the second (and following) parameter(s) can be deduced from obvious general knowledge. For example (set in a semi-imaginary setup), one may give you the number of people using a given service at least once during a specified period, *provided* that in order to use this service, people have to register with the service provider first. The data might be a simple number (no valid indication of variability, if service use is too ferquent to be modeled by a Poisson distribution), but looking up the number of registered users in some data bank might provide you with a valid proportion and population size, which is enough to meta-analyze. But the third possibility is of course that your means are indeed the result of experimenting on *ONE* experimental unit of each group. This is highly dependent of what is measured and how (an example of this might be industrial production per unit time with two different set of tools/machines in various industrial setups : here, the experimental unit is the industrial setup, and your mean is *one* measure of speed). Then, you have *individual* data, that you should analyze accordingly (e. g. t-test or Wilcoxon test if there is no relationship between treated and control experimental unit, paired t-test or paired Wilcoxon test if you are told that the means may be related, etc ...). This is not a meta-analysis, but an analysis. Outside these possibilities, I see no point of meta-analysing anything that isn't analysable by itself. As far as I can tell, this forces me into an unweighted meta-analysis, with all the caveats and dangers associated with it. As far as I can tell, you're forced to tell your sponsor/tutor/whatever either that he doesn't know what he asks for or that he's trying to fool you (and you saw it !) ; which might lead you to ask him to rethink his question, give you more informatin about the measumements and experimental setup, to provide you (or help you find) the missing data, to stop playing silly games or to go fly a kite... Two possible approaches might be: a) Take the ln(treatment/control) and perform a Fisher's randomisation test (and also calculate +/- CI). b) Regress the treatment vs control values, then randomise (with or without replacement?) individual values, comparing the true regression coefficient with the distribution of randomisation regression coefficients. I haven't the foggiest idea of what you're trying to do here : introducing artficial variability in order to separate it for variation between groups ? Unless you are in the case of one experiment = one experimental unit per group (see above) with no information about variability, the only information you can use is the *sign* of the difference Experimental-Control : if all or almost all of them go in the same direction, one might be tempted to conclude that this direction is not random (that's the sign test) . But this is only valid if the hypothesis Direction is 50/50 random under H0 has validity under the experimental setup, which your story doesn't tell... Both approaches would appear to be fraught with risks; for example in the regression approach, it is probable that the error distribution of an individual randomised regression might not be normal - would this then invalidate the whole set of regressions? Again, you'd work against an artificial variability that you'd have introduced yourself : what is the point ? HTH, Emmanuel Charpentier __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] pass lm( ) a char vector as the variables to be included
Gavin Simpson a écrit : On Mon, 2007-11-26 at 14:17 +, [EMAIL PROTECTED] wrote: Here are the codes of the example of lm( ): ## Annette Dobson (1990) An Introduction to Generalized Linear Models. ## Page 9: Plant Weight Data. ctl - (4.17,5.58,5.18,6.11,4.50,4.61,5.17,4.53,5.33,5.14) trt - (4.81,4.17,4.41,3.59,5.87,3.83,6.03,4.89,4.32,4.69) group - gl(2,10,20, labels=c(Ctl,Trt)) weight - c(ctl, trt) anova(lm.D9 - lm(weight ~ group)) lm.D90 - lm(weight ~ group - 1) # omitting intercept What I am doing is let the variable name group stored in a vector, say, g - group. The question is how to strip the quotation marks when we call lm( ) through g? Try: w = weight g = group form = as.formula(paste(w,g,sep=~)) lm(form) Regards, Richie. For more complicated automation, the ideas and examples from Bill Venables Programmer Niche article in the R newsletter from a few years ago might be of use: [39] Bill Venables. Programmer's niche. R News, 2(2):24-26, June 2002. [ bib | PDF | http ] The PDF is available here: http://cran.r-project.org/doc/Rnews/Rnews_2002-2.pdf Another possibility is to create macro (library(gtools) ; ? defmacro). See Thomas Lumley's paper in R News 2001-3 (Programmer’s Niche: Macros in R\n Overcoming R’s virtues). HTH, Emmanuel Charpentier __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Clean programming with R
Hmm - I looked for the codetools package on the UK(London) cran site and
couldn't find it - where can I find it please?
Martin
[EMAIL PROTECTED] wrote:
library(codetools)
findGlobals(power)
Thanks for your answer.
In addition, findGlobals(power,FALSE) gives the list of the globals
variables alone :
findGlobals(power,F)
$functions
[1] ^ { - return
$variables
[1] pp
Ce message a ete envoye par IMP, grace a l'Universite Paris 10 Nanterre
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
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[R] Odds Ratio calculation
Hello, I want to calculate Odds Ratio. I have a binary outcome and two groups of exposure: '1' are exposed, and '2' are not-exposed. I want '2' to be the reference group. By factor I get group '1' as a reference because it sorted in increasing order. How do I change it? Thank you, Sigalit. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Clean programming with R
Try some other mirror, or the main site:
http://cran.r-project.org/src/contrib/Descriptions/codetools.html
You can easily install it via
install.packages(codetools)
and then selecting an appropriate mirror.
Gabor
On Mon, Nov 26, 2007 at 08:19:39PM +, Martin Waller wrote:
Hmm - I looked for the codetools package on the UK(London) cran site and
couldn't find it - where can I find it please?
Martin
[EMAIL PROTECTED] wrote:
library(codetools)
findGlobals(power)
Thanks for your answer.
In addition, findGlobals(power,FALSE) gives the list of the globals
variables alone :
findGlobals(power,F)
$functions
[1] ^ { - return
$variables
[1] pp
Ce message a ete envoye par IMP, grace a l'Universite Paris 10 Nanterre
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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--
Csardi Gabor [EMAIL PROTECTED]MTA RMKI, ELTE TTK
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Re: [R] 'Split' character
one way is the following: vals - do.call(paste, c(mydata[1:2], sep = :)) fc - factor(vals, levels = unique(vals)) mydata.split - split(mydata, fc, drop = TRUE) names(mydata.split) I hope it helps. 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://med.kuleuven.be/biostat/ http://www.student.kuleuven.be/~m0390867/dimitris.htm Quoting Sébastien [EMAIL PROTECTED]: One additionnal question about a problem that I just noticed in my script: the list created by my split function is sorted in the increasing order and not in the current order of the elements of the do.call argument (see the results of the two last lines of the following script). I was unsuccesful in tweaking my split function to have a proper order... If there is no way to do that, I guess it comes down to a very basic question: how can I reorder a list ? how can I reorder the list 'mydata.split' according to a-rep(1.5:10.5,each=2) b-rep(21:30,each=2) cd-101:120 mydata-data.frame(a,b,cd) mydata.split - split(mydata,do.call(paste,c(mydata[,1:2],sep = :)),drop=TRUE) names(mydata.split) unique(do.call(paste,c(mydata[,1:2],sep = :))) Sebastien Gabor Grothendieck a écrit : Try this using the BOD data frame that comes with R or try using interaction in place of paste: split(BOD, do.call(paste, c(BOD, sep = :)), drop=TRUE) On Nov 25, 2007 10:23 AM, [EMAIL PROTECTED] wrote: Thanks Jim and Herinque for you reply. The substitution you are both proposing works fine, except when a or b contains decimal numbers (which is mostly my case in a real dataset). In this case, there is no distinction between the decimal point and the one introduced by the split function. If the split function cannot be customized, then I guess I have to first substitute the decimal point in my dataset by e.g. a * sign and change it back to a . when the split is done... Sebastien jim holtman a écrit : Here is one way: a-1:10 b-21:30 mydata-data.frame(a,b) mydata.split-split(mydata,(mydata[,1:2]),drop=TRUE) x - mydata.split # customize the names names(x) - sapply(strsplit(names(x), \\.), paste, collapse=-my character-) x $`1-my character-21` a b 1 1 21 $`2-my character-22` a b 2 2 22 $`3-my character-23` a b 3 3 23 ... On Nov 24, 2007 6:15 PM, [EMAIL PROTECTED] wrote: Dear R-users, The following code splits a very simple dataframe into a list, each element of the list being one line of the dataframe. You will see that the split function names each element of the list by using uses the content of a and b and merging them with a . character. Is there a way to customize this character? a-1:10 b-21:30 mydata-data.frame(a,b) mydata.split-split(mydata,(mydata[,1:2]),drop=TRUE) mydata.split Thanks in advance for your help. Sebastien __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] newbie polr() question
On Mon, 26 Nov 2007, Max wrote: Hi everyone, I'm trying to understand some R output here for ordinal regression. I have some integer data called A split up into 3 ordinal categories, top, middle and bottom, T, M and B respectively. I have to explain this output to people who have a very poor idea about statistics and just need to make sure I know what I'm talking about first. Here's the output: Call: polr(formula = Factor ~ A, data = a, Hess = TRUE, method = logistic) Coefficients: ValueStd. Error t value A -0.1259028 0.04758539 -2.645829 Intercepts: Value Std. Error t value B|M -2.5872 0.5596 -4.6232 M|T 0.3044 0.4864 0.6258 Residual Deviance: 204.8798 AIC: 210.8798 I really am not sure what the intercepts mean at all. However, my understanding of the coefficient of A is that as the category increases, A decreases? If I have an A value of 10, how to I figure out the estimated probability that this score is in one of the three categories? Use predict(): see the book polr supports for examples (and the theory). -- 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@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Clean programming with R
It is part of recent versions of R (a recommended package), so if Mr
Waller follows the advice of the posting guide, he will find it already
installed.
On Mon, 26 Nov 2007, Gabor Csardi wrote:
Try some other mirror, or the main site:
http://cran.r-project.org/src/contrib/Descriptions/codetools.html
You can easily install it via
install.packages(codetools)
and then selecting an appropriate mirror.
Gabor
On Mon, Nov 26, 2007 at 08:19:39PM +, Martin Waller wrote:
Hmm - I looked for the codetools package on the UK(London) cran site and
couldn't find it - where can I find it please?
Martin
[EMAIL PROTECTED] wrote:
library(codetools)
findGlobals(power)
Thanks for your answer.
In addition, findGlobals(power,FALSE) gives the list of the globals
variables alone :
findGlobals(power,F)
$functions
[1] ^ { - return
$variables
[1] pp
Ce message a ete envoye par IMP, grace a l'Universite Paris 10 Nanterre
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
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
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Filling in a Zero Matrix
You can use the reshape package:
x - read.table(textConnection(Samp MCI PCT
+ 11 2
+ 1 4 5
+ 1 7 8
+ 2 4 4
+ 2 7 5
+ 28 7), header=TRUE)
require(reshape)
x.m - melt(x, measure.var=PCT)
cast(x.m, MCI ~ Samp)
MCI 1 2
1 1 2 NA
2 4 5 4
3 7 8 5
4 8 NA 7
On Nov 26, 2007 11:50 AM, Amit Patel [EMAIL PROTECTED] wrote:
Hi
The data is in the format
Samp MCI PCT
11 2
1 4 5
1 7 8
2 4 4
2 7 5
28 7
I have split the columns into individual vectors
I would like the data in the format
MCI Samp1 Samp2
1 2 NA
4 5 4
7 8 5
8 NA 7
Kind Regards
Amit Patel
- Original Message
From: jim holtman [EMAIL PROTECTED]
To: Amit Patel [EMAIL PROTECTED]
Sent: Monday, 26 November, 2007 3:12:19 PM
Subject: Re: [R] Filling in a Zero Matrix
Could you please provide commented, minimal, self-contained,
reproducible code and an example of what you would like as output. We
don't have the test file that you are trying to read, nor really
understand what you would like as output.
On Nov 26, 2007 9:31 AM, Amit Patel [EMAIL PROTECTED] wrote:
Hi
I am very new to R and statistical programming in general. I am trying to
reorder data from a .csv file. I have managed to import the data and create
a zero matrix. I am now trying to fill the matrix. There seems to be some
problem with this section of my code. I have highlighted the dodgy code in
red. Please help if possible.
##
### Create matrix ###
##
#Open the csv file
OGSdata - read.table(MG3199.csv,sep=,,header=TRUE)
#creates 3 separate vectors
sample - OGSdata[,1]
mci - OGSdata[,2]
pct - OGSdata[,3]
#change mci range
offset - min(mci)-1
mci - (mci - offset)
#matrix sizes
mci_count - max(mci)
sample_count - max(sample)
#creates a zero matrix
OGS - mat.or.vec(mci_count,sample_count)
#Create labels
sample_lab - (A-9,B-9, C-9, D-9, E-9,A-12,B-12, C-12,
D-12, E-12)
#add data
for (i in 1:length(pct)) {
OGS(mci(i),sample(i))- pct(i);
}
What I want is to have colum1 from original data to be the xlabel, column
2 to be the ylabel and the 3rd colum to be the values in the matrix
Any help is appreciated.
Kind Regards
Amit Patel
___
now.
[[alternative HTML version deleted]]
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PLEASE do read the posting guide
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--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
What is the problem you are trying to solve?
Yahoo! Mail now has unlimited storage, which means you can have spam control
and more space for those important e-mails.
--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
What is the problem you are trying to solve?
__
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Re: [R] Communicating from one function to another
On 11/26/2007 1:46 PM, Alberto Monteiro wrote:
Duncan Murdoch wrote:
R doesn't really have global variables. - goes looking in parent
environments until it finds the target variable, and makes the
assignment there. If it never finds one, it makes the assignment in
the global environment, but the name is misleading: it should
really be called the user workspace.
Got it.
So, in this case:
x - 1
f - function() {
x - 2
g - function() {
x - 3
}
g()
x
}
f()
It's expected that f will return 3, but x would still be 1?
Yes, the one in the user workspace be unaffected.
Duncan Murdoch
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[R] Time Series Issues, Stationarity ..
Hello, I am very new to R and Time Series. I need some help including R codes about the following issues. I' ll really appreciate any number of answers... # I have a time series data composed of 24 values: myinput = c(n1,n2...,n24); # In order to make a forecasting a, I use the following codes result1 = arima(ts(myinput),order = c(p,d,q),seasonal = list(order=c(P,D,Q))) result2 = forecast(result1,12) plot(result2) Now, by using R code... 1) How can I determine if my data is statitonary or not ? (trend seasonal effects) 2) If not, how can I make it stationary ? 3) Is arima() function used only on STATIONARY data ? Or does it first determine if the data is stationary or not and makes it stationary ? (if it is non-stationary) 4) I tried different parameter values in arima() function, but every parameter gave very different results :(( . I even found tried best.arima() function but it also gave unsatisfactory result. So, how can I calculate the optimum arima() parameters (p,d,q,P,D,Q) that fit my data best ? Thanks in advance, best wishes.. Ozzy __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Odds Ratio calculation
sigalit mangut-leiba wrote: Hello, I want to calculate Odds Ratio. I have a binary outcome and two groups of exposure: '1' are exposed, and '2' are not-exposed. I want '2' to be the reference group. By factor I get group '1' as a reference because it sorted in increasing order. How do I change it? See ?factor and learn to use the levels argument of factor(). Uwe Ligges Thank you, Sigalit. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] ggplo2: fixed extent greater than data?
hadley wrote:
On 11/23/07, thegeologician [EMAIL PROTECTED] wrote:
I'd like to produce a series of maps with different data on, but exactly
the
same extent in each plot. Is there a way of switching the automatic
extent
(to the data of the last layer added) OFF? I'm trying something like:
I think this is a bug in coord_map, as the limits set on the scales
are basically ignored. However, I'm not completely sure how to fix
this, as simply subsetting the data to be contained within those
bounds may drop off points that are necessary to correctly draw
boundaries.
Essentially the problem is that the limits are specified on the
unprojected data, and I don't know how to apply them to the projected
data (and you might not want to do that anyway, given that it could
produce non-linear boundaries).
Yes, that's true, due to the projection. The coordinate grid will bulge in
or out of the (projected) rectangular area defined by its corners. But in my
case it doesn't matter, as long as I can get all maps to show the same
extent... Anyway, it might be a nice touch, if at some point you could get
that to work too - but we're talking GIS here, might be a bit far out of
what R is basically designed for... Surely not a top issue for ggplot2.
hadley wrote:
Additional question: is there a way of eliminating the extra spacing in a
map projection? The expand=c(0,0) parameter seems not to work...
This is a bug. The fix will be included in the next version of
ggplot, or you can fix the current version by running this code:
ScaleContinuous$new - function(., name=NULL, limits=c(NA,NA),
breaks=NULL, labels=NULL, variable, trans=identity, expand=c(0.05,
0)) {
if (is.null(breaks) !is.null(labels)) stop(Labels can only be
specified in conjunction with breaks)
.$proto(name=name, .input=variable, .output=variable,
limits=limits, .breaks = breaks, .labels = labels, .expand=expand)
}
Thanks, that did fix THAT particular problem, indeed. But I encountered a
few new ones..:
At the moment, I'm doing something like:
getOverviewMap-function(xmin=4,xmax=18,ymin=43,ymax=50,proj=,par=NULL){
p2-ggplot()
p2-p2+geom_path(data=wa,mapping=aes(x=x,y=y)) # political boundaries
p2-p2+geom_point(data=spts,mapping=aes(x=Lon,y=Lat,colour=red))
# sample
localities
# dummy points to fix extent:
xb-c(xmin,xmax,xmin,xmax)
yb-c(ymin,ymin,ymax,ymax)
bd-data.frame(xb,yb)
p2-p2+geom_point(data=bd,mapping=aes(x=xb,y=yb,plot=FALSE))
#axes:
p2-p2+scale_x_continuous(limits=c(xmin,xmax),expand=c(0,0),breaks=c(5,10,15,20))
p2-p2+scale_y_continuous(limits=c(ymin,ymax),expand=c(0,0),breaks=c(42,44,46,48,50))
p2$legend-FALSE
if(!(proj==none)) p2-p2+coord_map(project=proj,parameters=par)
return(p2)
}
I've fixed the extent-problem with some dummy points, outside of the area of
scope. The plot zooms to them, since I add them last.
wa is extracted from a call to map(), as shown on the ggplot2 site.
spts holds the sample localities.
Problem 1 (probably my stupidity): when I plot the sample localities without
colour=, they will be black and without Legend. When I give them colour,
as above, I can not get rid of the Legend! I tried to subset the plot and
gave the ..$legend-FALSE to different subsets and/or all layers, tried
the above statement at several places in the function... I didn't find the
trick. ;-(
Problem 2 (definitely my stupidity): I even couldn't find the right position
to place the plot=FALSE parameter, to suppress plotting of the dummy
points (corners). Or would ggplot2 notice and revert to the unwanted
smaller extent? Can I give them invisible colour?
Problem 3 (bug?): for testing, the function is designed to allow for the map
projection to be passed on. In cartesian coordinates (proj=none)
everything works fine. When I switch to - any, even rectangular - map
projection, I don't know how to override coord_map()s default behaviour to
omit the tick marks!?
Problem 4 (bug): As I said, cartesian coords are fine. In a map projection,
the country boundaries jump to the east by ~1 degree! It seems to me, wa -
but not the points? - might get projected twice, because of this strange
behaviour: when the function is run with proj=none it works fine
(default is cartesian). Any map projection set, the countries are offset.
BUT: When called with proj= after that, the map will also be fine (AND
projected)!! Since the parameter is passed through to mapproject, and there
it says an empty projection= defaults to the last projection used, I
assume no new calculation occurs in this case. The same happens even with
mercator projection (coord_map()s default) given as parameter.
Sorry for the lengthy post, but maybe my descriptions can help to track the
bugs... And of course I'd be thankful for any help! ;-)
--
View this message in context:
Re: [R] how to compute highest density interval?
The hpd function in the TeachingDemos package does this computation (for unimodal densities). -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare [EMAIL PROTECTED] (801) 408-8111 -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of gallon li Sent: Saturday, November 24, 2007 5:44 AM To: r-help Subject: [R] how to compute highest density interval? Suppose i want to compute a 95% highest density for a beta distribution beta(a,b) the two end points x1 and x2 shoudl satisfy the following two equations: pbeta(x1,a,b)-pbeta(x2,a,b)=95% dbeta(x1,a,b)=dbeta(x2,a,b) Is there any fast way to compute x1 and x2 in R? [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Time Series Issues, Stationarity ..
With 24 values you are asking the impossible from your data. If you use the standard Box Jenkins approach rather than an automatic ARIMA and using any prior knowledge of the data you might manage some form of forecast. Look at graphs of the data and their first differences. Look at graphs of the autocorrelation and partial autocorrelation functions. There are a range of text books that describe this kind of manual Box-Jenkins approach. There is an excellent account of stationarity and related matters in Pfaff, B (2006), Analysis of Integrated and Cointegrated Time Series with R, in the Springer USE R! series. This also contains an account of ARMA models. Best regards John On 26/11/2007, Ozcan Asilkan [EMAIL PROTECTED] wrote: Hello, I am very new to R and Time Series. I need some help including R codes about the following issues. I' ll really appreciate any number of answers... # I have a time series data composed of 24 values: myinput = c(n1,n2...,n24); # In order to make a forecasting a, I use the following codes result1 = arima(ts(myinput),order = c(p,d,q),seasonal = list(order=c(P,D,Q))) result2 = forecast(result1,12) plot(result2) Now, by using R code... 1) How can I determine if my data is statitonary or not ? (trend seasonal effects) 2) If not, how can I make it stationary ? 3) Is arima() function used only on STATIONARY data ? Or does it first determine if the data is stationary or not and makes it stationary ? (if it is non-stationary) 4) I tried different parameter values in arima() function, but every parameter gave very different results :(( . I even found tried best.arima() function but it also gave unsatisfactory result. So, how can I calculate the optimum arima() parameters (p,d,q,P,D,Q) that fit my data best ? Thanks in advance, best wishes.. Ozzy __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- John C Frain Trinity College Dublin Dublin 2 Ireland www.tcd.ie/Economics/staff/frainj/home.html mailto:[EMAIL PROTECTED] mailto:[EMAIL PROTECTED] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Time Series Issues, Stationarity ..
Ozcan Asilkan wrote: Hello, I am very new to R and Time Series. I need some help including R codes about the following issues. I' ll really appreciate any number of answers... # I have a time series data composed of 24 values: myinput = c(n1,n2...,n24); # In order to make a forecasting a, I use the following codes result1 = arima(ts(myinput),order = c(p,d,q),seasonal = list(order=c(P,D,Q))) result2 = forecast(result1,12) plot(result2) Now, by using R code... 1) How can I determine if my data is statitonary or not ? (trend seasonal effects) Look at the data and watch for different kinds of instationarity (or better, if the assumptions for stationarity are fulfilled). 2) If not, how can I make it stationary ? Depends on the kind of instationarity. Making it stationary might be impossible for the whole time series. 3) Is arima() function used only on STATIONARY data ? Or does it first determine if the data is stationary or not and makes it stationary ? (if it is non-stationary) No, R cannot think. It just does some calculations. 4) I tried different parameter values in arima() function, but every parameter gave very different results :(( . I even found tried best.arima() function but it also gave unsatisfactory result. So, how can I calculate the optimum arima() parameters (p,d,q,P,D,Q) that fit my data best ? You got to the right question. Unfortunately, we are all interested in its answer. It depends on your definition on best and is not that easy. You might want to start reading on the Box-Jenkins method to determine parameters and continue to read a good textbook on time series analysis. Or just ask the oracle. Best, Uwe Ligges Thanks in advance, best wishes.. Ozzy __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Install repeated library
It worked. The web page must have been down when I tried it the other day. Thank you, Becky On 11/26/07, Jonathan Baron [EMAIL PROTECTED] wrote: Try http://popgen.unimaas.nl/~jlindsey/rcode.html On 11/25/07 10:41, Becky Parker wrote: Hello - I cannot get to www.alpha.luc.ac.be/~jlindsey/rcode.html http://www.alpha.luc.ac.be/%7Ejlindsey/rcode .htmlto obtain and install the repeated library for use of glmm(). Is the web page not active? Can you give me an alternative location to obtain the repeated library? Thank you, Becky Parker [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Jonathan Baron, Professor of Psychology, University of Pennsylvania Home page: http://www.sas.upenn.edu/~baron Editor: Judgment and Decision Making (http://journal.sjdm.org) [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] spss, string factors, selecting
?subset subset(data, column == E) On Nov 26, 2007 3:07 PM, Katherine Jones [EMAIL PROTECTED] wrote: Hi, I am having trouble with a large dataset I am importing from SPSS. The problem is I have to merge two datasets (which seems to be working OK) then select rows based on attributes. I have a column with either blank cells, B or E entered. I want to select all rows with E. I have other columns with numerical data which I will then do analyses on. data[column== E] does not work. I use E not E, because levels (column) returns B E. Any help on what I am doing wrong is much appreciated. I'm getting quite stressed as I have 10 files with approx 100,000 records in each to analyse so manipulating data becomes a pain. Here is the code below, not sure it makes much sense without seeing the dataset:- chaff-read.spss(/Users/Kat/Desktop/papers in progress/btopaper/ edited BTO data/fatnewchaff.sav, to.data.frame=TRUE) chafffat-read.spss(/Users/Kat/Desktop/papers in progress/btopaper/ edited BTO data/fatmethods.sav) chaffmerge2-merge(chaff, chafffat, by.x=c(RINGNO, FAT, FATMTD), by.y=c(RINGNO, FAT, FATMTD), all=T) attach(chaffmerge2) chaffhabfactor-factor(chaffmerge2$HYBRID_A) levels(chaffhabfactor) Echaff-chaffmerge2[FATMTD== E,] attach(Echaff) names(Echaff) plotmeans(Echaff$FAT~Echaff$HYBRID_A) chaffFat-factor(Echaff$FAT) levels(chaffFat) chaffzeros-table(chaffFat, Echaff$HYBRID_A) chaffzeros chaffFat12345 0 261 354 345 1003 235 138 23 1762 2190420 3 70101 4 20000 5 145 34 123 100 60 8 00000 10 202 141 248 279 101 15 73 12 79 519 20 84 60 64 133 19 25 146 20 223 30 30 25 22 54 13 3530744 407 102 125 4520310 5010021 6001011 The 1,2,3,4,5, values of chaffFat above correspond to B which should have been removed [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem you are trying to solve? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Install repeated library
I was able to get the repeated library from http://popgen.unimaas.nl/~jlindsey/rcode.htmlhttp://popgen.unimaas.nl/%7Ejlindsey/rcode.html I still have not been able to find the repeated library on CRAN. It is not listed on http://cran.r-project.org/src/contrib/PACKAGES.html I also tried clicking on Packages Install packages in R 2.4.1. I selected a CRAN mirror [tried both USA (CA 1) and India] and 'repeated' is not in the list of packages. What am I doing wrong? Becky Parker On 11/25/07, Simon Blomberg [EMAIL PROTECTED] wrote: The repeated package is on CRAN. I installed it successfully from there. Simon. On Sun, 2007-11-25 at 10:41 -1200, Becky Parker wrote: Hello - I cannot get to www.alpha.luc.ac.be/~jlindsey/rcode.html http://www.alpha.luc.ac.be/%7Ejlindsey/rcode.htmlto obtain and install the repeated library for use of glmm(). Is the web page not active? Can you give me an alternative location to obtain the repeated library? Thank you, Becky Parker [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Simon Blomberg, BSc (Hons), PhD, MAppStat. Lecturer and Consultant Statistician Faculty of Biological and Chemical Sciences The University of Queensland St. Lucia Queensland 4072 Australia Room 320 Goddard Building (8) T: +61 7 3365 2506 email: S.Blomberg1_at_uq.edu.au Policies: 1. I will NOT analyse your data for you. 2. Your deadline is your problem. The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data. - John Tukey. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] spss, string factors, selecting
This sort of works. It does select the E data, but unfortunately it doesn't select the data from the other columns; I want to select data across about 5 columns by the factor E in one of the columns. It should be easy, but for some reason it is not working. The spaces being added don't help. It seems to work on my non-merged data files, although the merged file contains all the data I need. Thanks for the subset command though. Hadn't thought of using that. On 26-Nov-07, at 4:46 PM, jim holtman wrote: ?subset subset(data, column == E) [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Install repeated library
On Mon, 26 Nov 2007, Becky Parker wrote: I was able to get the repeated library from http://popgen.unimaas.nl/~jlindsey/rcode.htmlhttp://popgen.unimaas.nl/%7Ejlindsey/rcode.html I still have not been able to find the repeated library on CRAN. It is not listed on http://cran.r-project.org/src/contrib/PACKAGES.html I also tried clicking on Packages Install packages in R 2.4.1. I selected a CRAN mirror [tried both USA (CA 1) and India] and 'repeated' is not in the list of packages. What am I doing wrong? Nothing. AFAIK it has never been on CRAN. BTW, the correct address _is_ in the R FAQ, section 5.1.5. OTOH, expecting to use Windows binaries on such an old version of R will be a problem (many newer packages and many bug fixes are not available), as only 2.6.x is currently supported. Please update to R 2.6.1. Becky Parker On 11/25/07, Simon Blomberg [EMAIL PROTECTED] wrote: The repeated package is on CRAN. I installed it successfully from there. Simon. On Sun, 2007-11-25 at 10:41 -1200, Becky Parker wrote: Hello - I cannot get to www.alpha.luc.ac.be/~jlindsey/rcode.html http://www.alpha.luc.ac.be/%7Ejlindsey/rcode.htmlto obtain and install the repeated library for use of glmm(). Is the web page not active? Can you give me an alternative location to obtain the repeated library? Thank you, Becky Parker [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Simon Blomberg, BSc (Hons), PhD, MAppStat. Lecturer and Consultant Statistician Faculty of Biological and Chemical Sciences The University of Queensland St. Lucia Queensland 4072 Australia Room 320 Goddard Building (8) T: +61 7 3365 2506 email: S.Blomberg1_at_uq.edu.au Policies: 1. I will NOT analyse your data for you. 2. Your deadline is your problem. The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data. - John Tukey. -- 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@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] spss, string factors, selecting
That should give you back a subset of 'data' (with all its columns), for those with E in 'column'. Can you show an example of your data and what the desired output would be. The posting guide asks provide commented, minimal, self-contained, reproducible code so we don't have to speculate on what you want. On Nov 26, 2007 5:04 PM, Katherine Jones [EMAIL PROTECTED] wrote: This sort of works. It does select the E data, but unfortunately it doesn't select the data from the other columns; I want to select data across about 5 columns by the factor E in one of the columns. It should be easy, but for some reason it is not working. The spaces being added don't help. It seems to work on my non-merged data files, although the merged file contains all the data I need. Thanks for the subset command though. Hadn't thought of using that. On 26-Nov-07, at 4:46 PM, jim holtman wrote: ?subset subset(data, column == E) -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem you are trying to solve? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] 2d Joint Density Plot
Hi all, I'm fairly new to R, so I'm still trying to feel out what is available to me. I would like to be able to plot joint density in a two dimensional plot where density is indicated by color or darkness gradients, like a 2d color coded topographic map. Ideally, the output would be something I could then plot other points or lines on. Currently, I'm calculating joint density with the function kde2d(), and plotted with persp(). Thanks a bunch. -Joe [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] newbie polr() question
Prof Brian Ripley explained : On Mon, 26 Nov 2007, Max wrote: Hi everyone, I'm trying to understand some R output here for ordinal regression. I have some integer data called A split up into 3 ordinal categories, top, middle and bottom, T, M and B respectively. I have to explain this output to people who have a very poor idea about statistics and just need to make sure I know what I'm talking about first. Here's the output: Call: polr(formula = Factor ~ A, data = a, Hess = TRUE, method = logistic) Coefficients: ValueStd. Error t value A -0.1259028 0.04758539 -2.645829 Intercepts: Value Std. Error t value B|M -2.5872 0.5596 -4.6232 M|T 0.3044 0.4864 0.6258 Residual Deviance: 204.8798 AIC: 210.8798 I really am not sure what the intercepts mean at all. However, my understanding of the coefficient of A is that as the category increases, A decreases? If I have an A value of 10, how to I figure out the estimated probability that this score is in one of the three categories? Use predict(): see the book polr supports for examples (and the theory). I appreciate the reply, but have difficulty understanding what you mean by the book polr supports? :-? The manuals in R don't reference the polr() command, nor do they write about ordinal regression in R. (from what I can tell) The documentation of the polr() doesn't explain the output or the theory... I've done web searches on polr() and the MASS library and have found little of direct help to my question. Thanks, -Max __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] 2d Joint Density Plot
Look at levelplot in the lattice package. On Nov 26, 2007 5:19 PM, Josef Fruehwald [EMAIL PROTECTED] wrote: Hi all, I'm fairly new to R, so I'm still trying to feel out what is available to me. I would like to be able to plot joint density in a two dimensional plot where density is indicated by color or darkness gradients, like a 2d color coded topographic map. Ideally, the output would be something I could then plot other points or lines on. Currently, I'm calculating joint density with the function kde2d(), and plotted with persp(). Thanks a bunch. -Joe [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem you are trying to solve? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Communicating from one function to another
Global variables are strongly discouraged in R, but there are sometimes
when they may be needed and so are possible.
One example where they are used is in random number generation, every
time a random number function is called (rnorm for example) the global
variable .Random.seed is updated so that new random values will be
generated next time.
If you absolutely need a global variable, then use assign (or possibly
-) to do the assignment. Also choose a name such that your global
variable is unlikely to overwright or be overwritten (if you use x, then
both are likely to happen, preferable to use a name starting with '.').
A better approach is to use variables in a local environment such that
the 2 functions can both see the variable, but nothing outside of that
environment can. Here is a simple example:
tmp - local({
+ x23 - numeric(1)
+ func1 - function(){
+ x23 - 2.6
+ }
+ func2 - function(){
+ print(x23)
+ }
+ list(func1=func1,func2=func2)
+ })
func1 - tmp$func1
func2 - tmp$func2
func2()
[1] 0
func1()
func2()
[1] 2.6
tmp$func2()
[1] 2.6
The local function creates a new environment in which everything in the
{} is evaluated/created. This new environment then gets a variable
(x23) which starts off to be 0. The 2 functions defined in the same
environment can access x23. The list statement just combines the 2
functions into a single object to be returned.
So after running local, the variable tmp is a list with 2 elements each
being a function, we can run them as
tmp$func2() or copy them to easier to use functions. We run func2 and
see that x23 is currently 0, then run func1 to change the value (don't
see anything yet) then run func2 again to see the new value of x23.
This is a cleaner solution in that if we already have a variable called
x23, it does not get overwritten by the global and it is very
difficult to accidentally overwrite the x23 shared by the 2 functions.
Hope this helps,
--
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
[EMAIL PROTECTED]
(801) 408-8111
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Thomas L Jones, PhD
Sent: Monday, November 26, 2007 10:11 AM
To: R-project help
Subject: [R] Communicating from one function to another
My question is a seemingly simple one. I have a bunch of
user-defined functions which compute such-and-such objects. I
want to be able to define a variable in a particular
function, then make use of it later, perhaps in a different
function, without necessarily having to move it around in
argument lists. In the C community, it would be called a
global variable.
Question 1: Is this practical at all in the R language?
Suppose the variable is called x23. I want to assign a value
to it, then use it later. Seemingly, there are two cases:
Case I is if the variable is given its value at the top level.
Case II is if it is given its value inside a user-defined
function. That I do not know how to do.
Example:
func1 - function (){
x23 - 2.6
return ()
}
driver_func - function (){
func1 ()
print (x23)
return ()
}
However, when I call driver_func, it won't work. Beginning
with the load operation, I get:
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
func1 - function (){
+
+ x23 - 2.6
+
+ return ()
+
+ }
driver_func - function (){
+
+ func1 ()
+
+ print (x23)
+
+ return ()
+
+ }
driver_func ()
Error in print(x23) : object x23 not found
--
-
From Tom:
Clearly, the two functions cannot communicate. I am aware of
the existence of environments, but don't know much about
them. Also, the attach function and the get and set
functions. Also, .GlobalEnv It might or might not make sense
to create a list of all of the variables, with two
functions which get all of them and set all of them. The
function calls may be thought of as an upside down tree. I
want to be able to communicate from any node to any other node.
Your advice?
Tom
Thomas L. Jones, PhD, Computer Science
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PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] anyway to force rpart() to include a specific predictor
just my2cent: could you make a derived feature by including the desired predictor in each of features you use to present to rpart? (by the way, if I can understand your question right, I assume rpart picks only one predictor each time at each node) Best, Weiwei On 11/26/07, Wensui Liu [EMAIL PROTECTED] wrote: If I understand correctly, rpart() will pick predictor at each node automatically. I am wondering if there is a way to force rpart() including a specific predictor. The reason I am asking is that I'd like to use rpart() to detect interaction terms for some variables. Thanks. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. Did you always know? No, I did not. But I believed... ---Matrix III __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] anova planned comparisons/contrasts
Others have shown some approaches that work well for after you fit the
model. Here is another approach starting with the model fit itself:
tmp - c(control, glucose, fructose,
gluc+fruct, sucrose)
treatment - factor(rep( tmp, each=10 ), levels=tmp)
length - c(75, 67, 70, 75, 65, 71, 67, 67, 76, 68,
57, 58, 60, 59, 62, 60, 60, 57, 59, 61,
58, 61, 56, 58, 57, 56, 61, 60, 57, 58,
58, 59, 58, 61, 57, 56, 58, 57, 57, 59,
62, 66, 65, 63, 64, 62, 65, 65, 62, 67)
cm1 - rbind( int=1/5, cntrl = c(4, -1,-1,-1,-1)/4,
plus=c( 0, -1, -1, 3, -1 )/3,
sug1=c( 0, -1, 1, 0, 0),
sug2=c( 0, -1, -1, 0, 2)/2 )
cm2 - zapsmall(solve(cm1))
contrasts(treatment) - cm2[,-1]
treatment
sugars - data.frame( length=length, treatment=treatment )
fit - aov( length ~ treatment, data=sugars )
summary.lm(fit)
summary(fit)
summary(fit, split=list(treatment=list(
'Control vs. Sugars'=1, 'Gluc+Fruc vs. sugars'=2, 'Sugars'=3:4)))
Is this more what you were looking for?
--
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
[EMAIL PROTECTED]
(801) 408-8111
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Tyler Smith
Sent: Thursday, November 22, 2007 12:38 PM
To: [EMAIL PROTECTED]
Subject: [R] anova planned comparisons/contrasts
Hi,
I'm trying to figure out how anova works in R by translating
the examples in Sokal And Rohlf's (1995 3rd edition)
Biometry. I've hit a snag with planned comparisons, their box
9.4 and section 9.6. It's a basic anova design:
treatment - factor(rep(c(control, glucose, fructose,
gluc+fruct, sucrose), each = 10))
length - c(75, 67, 70, 75, 65, 71, 67, 67, 76, 68,
57, 58, 60, 59, 62, 60, 60, 57, 59, 61,
58, 61, 56, 58, 57, 56, 61, 60, 57, 58,
58, 59, 58, 61, 57, 56, 58, 57, 57, 59,
62, 66, 65, 63, 64, 62, 65, 65, 62, 67)
sugars - data.frame(treatment, length)
The basic analysis is easy enough:
anova(lm(length ~ treatment, sugars))
SR proceed to calculate planned comparisons between control
and all other groups, between gluc+fruct and the remaining
sugars, and among the three pure sugars. I can get the first
two comparisons using the
contrasts() function:
contrasts(sugars$treatment) - matrix(c(-4, 1, 1, 1, 1,
0, -1, 3, -1, -1), 5, 2)
summary(lm(length ~ treatment, sugars))
The results appear to be the same, excepting that the book
calculates an F value, whereas R produces an equivalent t
value. However, I can't figure out how to calculate a
contrast among three groups. For those without access to
Sokal and Rohlf, I've written an R function that performs the
analysis they use, copied below. Is there a better way to do
this in R?
Also, I don't know how to interpret the Estimate and Std.
Error columns from the summary of the lm with contrasts. It's
clear the intercept in this case is the grand mean, but what
are the other values? They appear to be the difference
between one of the contrast groups and the grand mean --
wouldn't an estimate of the differences between the
contrasted groups be more appropriate, or am I (likely)
misinterpreting this?
Thanks!
Tyler
MyContrast - function(Var, Group, G1, G2, G3=NULL) {
## Var == data vector, Group == factor
## G1, G2, G3 == character vectors of factor levels to contrast
nG1 = sum(Group %in% G1)
nG2 = sum(Group %in% G2)
GrandMean = mean(Var[Group %in% c(G1, G2, G3)])
G1Mean = mean(Var[Group %in% G1])
G2Mean = mean(Var[Group %in% G2])
if(is.null(G3))
MScontr = nG1 * ((G1Mean - GrandMean)^2) +
nG2 * ((G2Mean - GrandMean)^2)
else {
nG3 = sum(Group %in% G3)
G3Mean = mean(Var[Group %in% G3])
MScontr = (nG1 * ((G1Mean - GrandMean)^2) +
nG2 * ((G2Mean - GrandMean)^2) +
nG3 * ((G3Mean - GrandMean)^2))/2
}
An - anova(lm(Var ~ Group))
MSwithin = An[3]['Residuals',]
DegF = An$Df[length(An$Df)]
Fval = MScontr / MSwithin
Pval = 1 - pf(Fval, 1, DegF)
return (list(MS_contrasts = MScontr, MS_within = MSwithin,
F_value = Fval, P_value = Pval)) }
## The first two contrasts produce the same (+/- rounding
error) ## p-values as obtained using contrasts()
MyContrast(sugars$length, sugars$treatment, 'control',
c(fructose, gluc+fruct, glucose,
sucrose))
MyContrast(sugars$length, sugars$treatment, 'gluc+fruct',
c(fructose, glucose, sucrose))
## How do you do this in standard R?
MyContrast(sugars$length, sugars$treatment, fructose, glucose,
sucrose)
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Re: [R] newbie polr() question
Max a écrit : Prof Brian Ripley explained : On Mon, 26 Nov 2007, Max wrote: Hi everyone, I'm trying to understand some R output here for ordinal regression. I have some integer data called A split up into 3 ordinal categories, top, middle and bottom, T, M and B respectively. I have to explain this output to people who have a very poor idea about statistics and just need to make sure I know what I'm talking about first. Here's the output: Call: polr(formula = Factor ~ A, data = a, Hess = TRUE, method = logistic) Coefficients: ValueStd. Error t value A -0.1259028 0.04758539 -2.645829 Intercepts: Value Std. Error t value B|M -2.5872 0.5596 -4.6232 M|T 0.3044 0.4864 0.6258 Residual Deviance: 204.8798 AIC: 210.8798 I really am not sure what the intercepts mean at all. However, my understanding of the coefficient of A is that as the category increases, A decreases? If I have an A value of 10, how to I figure out the estimated probability that this score is in one of the three categories? Use predict(): see the book polr supports for examples (and the theory). I appreciate the reply, but have difficulty understanding what you mean by the book polr supports? :-? The manuals in R don't reference the polr() command, nor do they write about ordinal regression in R. (from what I can tell) The documentation of the polr() doesn't explain the output or the theory... I've done web searches on polr() and the MASS library and have found little of direct help to my question. Brian Ripley probably means Modern Applied Statistics with S, W Venables and B. Ripley (4th edn), Springer, 2002. I'd also add Categorical Data Analysis, Alan Agresti, Wiley (2000). HTH Emmanuel Charpentier __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] generating .Rd files
Hi R Gurus! I have a package that I am putting together. I waited until the end to do the documentation and would like to generate a set of empty .Rd files. Is there a quick way to do this, please? Thanks, Edna Bell PS I can't seem to access the Writing R Extensions manual from 2.6.1 on Windows. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Please ignore previous .Rd question
If the function is f, you can use prompt(f) Sorry thanks, Edna __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] generating .Rd files
Edna, maybe there is a way, but Rd files are not that difficult, writing an empty one requires less time than writing this email. Then just copy your empty file as many times as you want. Gabor ps. perhaps you didn't install the manuals. You can always read the up-to-date versions at the R homepage. On Mon, Nov 26, 2007 at 05:59:55PM -0600, Edna Bell wrote: Hi R Gurus! I have a package that I am putting together. I waited until the end to do the documentation and would like to generate a set of empty .Rd files. Is there a quick way to do this, please? Thanks, Edna Bell PS I can't seem to access the Writing R Extensions manual from 2.6.1 on Windows. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Csardi Gabor [EMAIL PROTECTED]MTA RMKI, ELTE TTK __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Problem with avoiding rep
Paul Smith [EMAIL PROTECTED] wrote in news:[EMAIL PROTECTED]: On Nov 26, 2007 7:45 PM, Gabor Csardi [EMAIL PROTECTED] wrote: x - c(1,4,3) freq - c(3,2,4) rep(x, freq) [1] 1 1 1 4 4 3 3 3 3 Thanks, Gabor. I had just tried rep(1:10,10:20) but should have tried rep(1:10,11:20) I am wondering it this worked example would be more scaleable? Assuming someone (me) has just copied your table to the clipboard: dt-read.table(clipboard,header=TRUE) dt X Frequency 1 1 3 2 4 2 3 3 4 dt.expand-rep(dt$X,dt$Frequency) dt.expand [1] 1 1 1 4 4 3 3 3 3 David Winsemius On Mon, Nov 26, 2007 at 07:34:36PM +, Paul Smith wrote: Dear All, Suppose that you have the following data: X Frequency 1 3 4 2 3 4 To get a vector with all observations, one could use data - c(rep(1,3),rep(4,2),rep(3,4)) I am wondering whether there exists an easier way of doing this. Any ideas? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] calculate column means when missing data is present
# Hello, # I have a matrix that contains some missing values denoted by NA. # I would like to calculate the mean for each column and not have the # NA values included. here is a sample matrix X below. c1 - c(1,4,3,2,NA,2,5,6,4,2) c2 - c(1,3,6,NA,NA,2,9,6,1,2) c3 - c(2,4,2,NA,4,2,NA,6,3,5) c4 - c(2,6,4,NA,4,2,NA,6,1,5) c5 - c(2,3,2,NA,4,2,9,6,NA,5) X-cbind(c1,c2,c3,c4,c5) X # I have tried a variety of methods to calculate the Column means but each time # i do not get the result i am looking for result-colMeans(X) # only returns a mean of NA X - X[!is.na(X)]# Effectively removes the NA values but now I cannot calculate Column Means # Below is the result of the column means I am looking for result c1 c2c3 c4c5 [1,] 3.22 3.75 3.5 3.75 4.125 # any help or ideas would be greatly appreciated # thanks in advance Luke Neraas [EMAIL PROTECTED] University of Alaska Fairbanks School of Fisheries and Ocean Sciences 11120 Glacier Highway UAF Fisheries Division Juneau, AK 99801 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] calculate column means when missing data is present
colMeans(X,na.rm=T) ?colMeans 2007/11/27, Luke Neraas [EMAIL PROTECTED]: # Hello, # I have a matrix that contains some missing values denoted by NA. # I would like to calculate the mean for each column and not have the # NA values included. here is a sample matrix X below. c1 - c(1,4,3,2,NA,2,5,6,4,2) c2 - c(1,3,6,NA,NA,2,9,6,1,2) c3 - c(2,4,2,NA,4,2,NA,6,3,5) c4 - c(2,6,4,NA,4,2,NA,6,1,5) c5 - c(2,3,2,NA,4,2,9,6,NA,5) X-cbind(c1,c2,c3,c4,c5) X # I have tried a variety of methods to calculate the Column means but each time # i do not get the result i am looking for result-colMeans(X) # only returns a mean of NA X - X[!is.na(X)]# Effectively removes the NA values but now I cannot calculate Column Means # Below is the result of the column means I am looking for result c1 c2c3 c4c5 [1,] 3.22 3.75 3.5 3.75 4.125 # any help or ideas would be greatly appreciated # thanks in advance Luke Neraas [EMAIL PROTECTED] University of Alaska Fairbanks School of Fisheries and Ocean Sciences 11120 Glacier Highway UAF Fisheries Division Juneau, AK 99801 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] calculate column means when missing data is present
Luke Check ?colMeans or help(colMeans) you will see there is an agrument, na.rm, which by default is FALSE - you need to set it to TRUE. Peter Alspach -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Luke Neraas Sent: Tuesday, 27 November 2007 1:59 p.m. To: r-help Subject: [R] calculate column means when missing data is present # Hello, # I have a matrix that contains some missing values denoted by NA. # I would like to calculate the mean for each column and not have the # NA values included. here is a sample matrix X below. c1 - c(1,4,3,2,NA,2,5,6,4,2) c2 - c(1,3,6,NA,NA,2,9,6,1,2) c3 - c(2,4,2,NA,4,2,NA,6,3,5) c4 - c(2,6,4,NA,4,2,NA,6,1,5) c5 - c(2,3,2,NA,4,2,9,6,NA,5) X-cbind(c1,c2,c3,c4,c5) X # I have tried a variety of methods to calculate the Column means but each time # i do not get the result i am looking for result-colMeans(X) # only returns a mean of NA X - X[!is.na(X)]# Effectively removes the NA values but now I cannot calculate Column Means # Below is the result of the column means I am looking for result c1 c2c3 c4c5 [1,] 3.22 3.75 3.5 3.75 4.125 # any help or ideas would be greatly appreciated # thanks in advance Luke Neraas [EMAIL PROTECTED] University of Alaska Fairbanks School of Fisheries and Ocean Sciences 11120 Glacier Highway UAF Fisheries Division Juneau, AK 99801 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. The contents of this e-mail are privileged and/or confidential to the named recipient and are not to be used by any other person and/or organisation. If you have received this e-mail in error, please notify the sender and delete all material pertaining to this e-mail. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] spss, string factors, selecting
Hi, This is probably a case where someone has to see what is happening on my computer and it is complicated by my data being from SPSS (not my choice). It is quite hard to give my data, because it is such a large dataset. I have analysed 9 other datasets that work fine, but this particular dataset was inputted wrong so requires merging of two datasets. This may be the problem. Example of data:- File 1. [1] Individual [2] Habitat type [3] Weight File 2. [1] Individual [2] Fat [3] Fat method. I merge the two files to create:- [1] Individual [2] Habitat type [3] Weight [4] Fat [5] Fat method My merging appears to work in the sense that I can plot Weight versus Fat and I get data, but if I ask to see the data file I see a sea of NAs. So I'm not sure how there can be data there to plot, see levels for and create tables for but I can't see it as a dataframe. I do get the plot I want. Fat method contains either blank cells, B or E. I wish to select all the rows in columns 1-4 which contain an E in Fat method. e.g. 120, 3, 20.2, 4, E 121, 4, 20.0, 5, B 132, 3, 21.2, 4, I want to select only the row containing E, so I can plot Fat vs Habitat and Weight vs. Fat. I have been doing this by using selectE-Data[Fatmethod== E,]. However, this does not work. It removes all of my data in the other columns to NA and I am left only with fatmethod and fat scores. It is odd it works with other datasets but not this one. Although with my other datasets when I ask to select E, I can still see B using levels(Fat method) but there is no data there, so my plots are correct. Sorry this is long. I'm having difficulty explaining it. Katherine On 26-Nov-07, at 5:09 PM, jim holtman wrote: That should give you back a subset of 'data' (with all its columns), for those with E in 'column'. Can you show an example of your data and what the desired output would be. The posting guide asks provide commented, minimal, self-contained, reproducible code so we don't have to speculate on what you want. On Nov 26, 2007 5:04 PM, Katherine Jones [EMAIL PROTECTED] wrote: This sort of works. It does select the E data, but unfortunately it doesn't select the data from the other columns; I want to select data across about 5 columns by the factor E in one of the columns. It should be easy, but for some reason it is not working. The spaces being added don't help. It seems to work on my non-merged data files, although the merged file contains all the data I need. Thanks for the subset command though. Hadn't thought of using that. On 26-Nov-07, at 4:46 PM, jim holtman wrote: ?subset subset(data, column == E) -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem you are trying to solve? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] lme object manipulation
Hello: I have an lme object, say lme_res2, which was generated using the varIdent. I'm trying to extract the double 1.532940 from the object, but I can't find it by attributes(lme_res2) or attributes(summary(lme_res2)). How can I pull it out (so that I can save it to another variable)? Thanks. Shin Linear mixed-effects model fit by REML Data: dat Log-restricted-likelihood: 22.3213 Fixed: express1 ~ race * thaps + race * tuni (Intercept)race thapstuni race:thaps race:tuni 7.00034057 -0.02675202 -0.05687972 0.01265845 -0.03859781 -0.11248439 Random effects: Formula: ~1 | fam (Intercept) StdDev: 0.1131353 Formula: ~1 | twin %in% fam (Intercept) StdDev: 0.1740635 Formula: ~1 | thaw %in% twin %in% fam (Intercept) Residual StdDev: 0.1177579 0.1182267 Variance function: Structure: Different standard deviations per stratum Formula: ~1 | race Parameter estimates: 01 1.00 1.532940 Number of Observations: 218 Number of Groups: fam twin %in% fam thaw %in% twin %in% fam 33 66 102 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] spss, string factors, selecting
Can you provide a small subset of the data that shows the problem. In a sense, what you are doing with: selectE-Data[Fatmethod== E,] should pull your rows of interest. What does 'str(Data)' show? What does 'str(selectE)' show? If you can at least include 10-20 rows of data that show what is happening, it would help. Here is an example using the data you sent and it seems to work just fine: x V1 V2 V3 V4 V5 1 120 3 20.2 4 E 2 121 4 20.0 5 B 3 132 3 21.2 4 str(x) 'data.frame': 3 obs. of 5 variables: $ V1: int 120 121 132 $ V2: int 3 4 3 $ V3: num 20.2 20 21.2 $ V4: int 4 5 4 $ V5: Factor w/ 3 levels , B, E: 3 2 1 x[x$V5 == E,] V1 V2 V3 V4 V5 1 120 3 20.2 4 E On Nov 26, 2007 8:31 PM, Katherine Jones [EMAIL PROTECTED] wrote: Hi, This is probably a case where someone has to see what is happening on my computer and it is complicated by my data being from SPSS (not my choice). It is quite hard to give my data, because it is such a large dataset. I have analysed 9 other datasets that work fine, but this particular dataset was inputted wrong so requires merging of two datasets. This may be the problem. Example of data:- File 1. [1] Individual [2] Habitat type [3] Weight File 2. [1] Individual [2] Fat [3] Fat method. I merge the two files to create:- [1] Individual [2] Habitat type [3] Weight [4] Fat [5] Fat method My merging appears to work in the sense that I can plot Weight versus Fat and I get data, but if I ask to see the data file I see a sea of NAs. So I'm not sure how there can be data there to plot, see levels for and create tables for but I can't see it as a dataframe. I do get the plot I want. Fat method contains either blank cells, B or E. I wish to select all the rows in columns 1-4 which contain an E in Fat method. e.g. 120, 3, 20.2, 4, E 121, 4, 20.0, 5, B 132, 3, 21.2, 4, I want to select only the row containing E, so I can plot Fat vs Habitat and Weight vs. Fat. I have been doing this by using selectE-Data[Fatmethod== E,]. However, this does not work. It removes all of my data in the other columns to NA and I am left only with fatmethod and fat scores. It is odd it works with other datasets but not this one. Although with my other datasets when I ask to select E, I can still see B using levels(Fat method) but there is no data there, so my plots are correct. Sorry this is long. I'm having difficulty explaining it. Katherine On 26-Nov-07, at 5:09 PM, jim holtman wrote: That should give you back a subset of 'data' (with all its columns), for those with E in 'column'. Can you show an example of your data and what the desired output would be. The posting guide asks provide commented, minimal, self-contained, reproducible code so we don't have to speculate on what you want. On Nov 26, 2007 5:04 PM, Katherine Jones [EMAIL PROTECTED] wrote: This sort of works. It does select the E data, but unfortunately it doesn't select the data from the other columns; I want to select data across about 5 columns by the factor E in one of the columns. It should be easy, but for some reason it is not working. The spaces being added don't help. It seems to work on my non-merged data files, although the merged file contains all the data I need. Thanks for the subset command though. Hadn't thought of using that. On 26-Nov-07, at 4:46 PM, jim holtman wrote: ?subset subset(data, column == E) -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem you are trying to solve? -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem you are trying to solve? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Packages - a great resource, but hard to find the right one
Loren Engrav wrote: It is clear that R and Bio are amazing resources and that many people invest lots of time in making them work, thank you Having said that From the point of view of an R/Bio novice an improved method to find packages would be very helpful as suggested by John Sorkin Three other things would also be helpful 1) a page titled for the newbie where the startup directions are clearly outlined, like print out the R Reference Index which can be found here and read it, etc It would be really helpful if a newbie (you?) started this by writing down at least the questions. The R Wiki might be a good place for this; check with the people who set it up. 2) the vignette's are quite terse and many assume the reader already knows something which may not be true, it would helpful if at the top of each there be a short paragraph saying before you read this, you must read this and this Documentation might be too terse; it happens. You need to tell this to each author in each specific instance. Authors of documentation don't always realize what's missing. (But see below: it might be that you aren't the intended audience for the documentation.) 3) old timers stop saying please read the documentation as I read that insatiably and if it fixed the problem I would not ask the next question, would be more helpful to say in vignette xyz at the bottom you will find abc which will show you what to do and would also follow the example of Bolker which educates and encourages the newbies Do remember that you aren't paying for the help you get. If some of it isn't very helpful, then just move on. Also remember that writing documentation for everyone is extremely difficult, so authors won't necessarily appreciate complaints that don't come with help for improvements. Maybe old timers shouldn't say please read the documentation and nothing else, but newbies shouldn't say please write better documentation and nothing else. Be specific and helpful about what is missing, and don't be upset when an author expects you to be experienced before using his package. There are more than 1000 packages on CRAN, but we don't need 1000 tutorials on R. Duncan Murdoch Thank you Loren Engrav Univ Wash Seattle __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
