Re: [R] Reshape a sparse matrix
Scott == Scott Hyde [EMAIL PROTECTED] on Tue, 15 May 2007 17:03:13 -1000 (HST) writes: Scott Hi, Scott I'd like to reshape a sparse matrix generated from the Matrix package. I can't seem to do it with the command Scott dim(A) - c(6,9) Scott which works perfectly with the base package matrices, but with the sparse matrices it errors with Scott Error in dim(A) = c(6, 9) : dim- : invalid first argument This *does* work in the current version of Matrix (0.99875-1), actually already in version 0.99875-0 . In the next version of Matrix, it will not only work, but also work sparsely internally via the new class sparseVector and its daughter classes, on which I've been working during the last 10 days or so... Interesting that you bring the topic up right now ... Scott Manipulating the Dim attribute of the sparse Matrix does not produce the desired effect. [EMAIL PROTECTED] - c(as.integer(9),as.integer(6)) does not produce a column ordering result, which I am assuming is because the data is stored in a row (i) and column (j) format instead (class dgTMatrix) You should not have manipulate slots of S4 classes in general. Some people say that you should not even access them directly. Scott Does a function for this exist? yes, as I said above dim(.) - .. works in the newest versions of Matrix. Regards, Martin Maechler, ETH Zurich __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] urca package - summary method -
Hi I am using the package urca and I am interested about the KPSS test. That works fine except the method summary did not work in the script, only when it is typed direct in the console the results are shown( not a source file). Is there any problem with these method ? __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] [R-pkgs] new packages 'ICS' and 'ICSNP'
Dear R useRs, The new contributed packages 'ICS' and 'ICSNP' are available on CRAN. Descriptions: The 'ICS' package implements the 2 scatter matrix transformation to obtain an invariant coordinate system or independent components, depending on the underlying assumptions. The result of the transformation is an object of the S4 class ics which is provided by this package. Besides generic functions to create and work with ics objects the package contains also some scatter matrices and two tests for multinormality. The 'ICSNP' package contains tools for nonparametric multivariate analysis, including the estimation of location and shape as well as some tests for location and independence. Shape matrices from this package can be used as one of the scatter matrices needed in the package ICS whereas the tests of this package can be used for testing in the framework of invariant coordinates or independent components obtained from the package ICS. The parametric Hotelling’s T test serves as a reference for the nonparametric location tests. Suggestions, bug reports and other comments are very welcome. Best wishes, Klaus, Seija, Hannu and Dave -- Klaus Nordhausen Researcher Tampere School of Public Health FIN-33014 University of Tampere phone: +358 3 3551 7086 fax:+358 3 3551 6057 e-mail: [EMAIL PROTECTED] ___ R-packages mailing list [EMAIL PROTECTED] https://stat.ethz.ch/mailman/listinfo/r-packages __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Reshape a sparse matrix
Thanks for the respons, Martin. The program I wrote works as well for doing the reshaping, but it is nice to have it built in. Is there a way to tell what version of Matrix is installed, and how do we know when new releases are issued? I installed Matrix fairly recently, and thought I was up to date. -Scott Original message Date: Wed, 16 May 2007 09:32:44 +0200 From: Martin Maechler [EMAIL PROTECTED] Subject: Re: [R] Reshape a sparse matrix To: Scott Hyde [EMAIL PROTECTED] Cc: r-help@stat.math.ethz.ch Scott == Scott Hyde [EMAIL PROTECTED] on Tue, 15 May 2007 17:03:13 -1000 (HST) writes: Scott Hi, Scott I'd like to reshape a sparse matrix generated from the Matrix package. I can't seem to do it with the command Scott dim(A) - c(6,9) Scott which works perfectly with the base package matrices, but with the sparse matrices it errors with Scott Error in dim(A) = c(6, 9) : dim- : invalid first argument This *does* work in the current version of Matrix (0.99875-1), actually already in version 0.99875-0 . In the next version of Matrix, it will not only work, but also work sparsely internally via the new class sparseVector and its daughter classes, on which I've been working during the last 10 days or so... Interesting that you bring the topic up right now ... Scott Manipulating the Dim attribute of the sparse Matrix does not produce the desired effect. [EMAIL PROTECTED] - c(as.integer(9),as.integer(6)) does not produce a column ordering result, which I am assuming is because the data is stored in a row (i) and column (j) format instead (class dgTMatrix) You should not have manipulate slots of S4 classes in general. Some people say that you should not even access them directly. Scott Does a function for this exist? yes, as I said above dim(.) - .. works in the newest versions of Matrix. Regards, Martin Maechler, ETH Zurich __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] how to reduce in a grid ?
hi dear R users, I'm a newbie with R and excuse me if my question is stupid ... but i've read lot of documentation and I don't know how to do. I have a dataset like xyvar1var2 241050 3 32070 325068 45 3442 531023 782342 7 32334 [...] And I need to produce grids like : y\x]0-2]]2-4]]4-6]]6-8] ]0-3] ]3-6]means of corresponding values for var1 (or var2) ]6-9] but I don't find any example in advance, lot of thanks for your help js _ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] use mathematics formula
hello, I wanna use some mathematics formula and to do this I tried several way in paricular using strsplit textconnection scan setdiff but I think that it's a lil hard the data frame that I'm working on is as follow donCalcara2 Id_Cara Form_C 1 743 if C325=. then C743=(C152/C103)*100| else C743=(C152/C325)*100 2 627 if C137=. Then C627=.| else do| if C109=. Then C627=(C138/S138)*(100-C137)| else C627=(C138/S138)*C109| end 3 638 C638 = C103 / S103 4 740 if C325=. then C740=(C346/C103)*100| else C740=(C346/C325)*100 5 739 if C155=. then C739=(C570/C103)*100| else C739=C155/(C155+C103)*100 6 628 if C325=. then C628=(C455/C103)*100| else C628=(C455/C325)*100 7 747if C325=. then C747=(C27/C103)*100| else C747=(C27/C325)*100 8 629 if C325=. then C629=(C454/C103)*100| else C629=(C454/C325)*100 9 737 if C325=. then C737=(C457/C103)*100| else C737=(C457/C325)*100 10 750 if C325=. then C750=(C431/C103)*100| else C750=(C431/C325)*100 11 754 if C325=. then C754=(C894/C103)*100| else C754=(C894/(C325+C894))*100 12 760 C760= C627 / 0.89 13 761 C761 = C177 * 0.89 14 586 if C325=. then C586=(C588/C103)*100 15 896 if C325=. then C896=(C895/C103)*100 16 751 if C325=. then C751=(C433/C103)*100| else C751=(C433/C325)*100 17 738 if C325=. then C738=(C151/C103)*100| else C738=(C151/C325)*100 18 744 C744=(C627*C177)/100 19 633 if C325=. then C633=(C130/C103)*100| else C633=(C130/C325)*100 20 732 if C325=. then C732=(C585/C103)*100| else C732=(C585/C325)*100 21 898 if C325=. then C898=(C897/C103)*100 Can you help me please? I'm French so if you can speak French it's better for me because of my English level _ [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Filled step-function?
Hello, I'd like to generate a filled step-function in R as you can see in the attachement (image is generated by grapher, but I need a freely available alternative). The problem is, that I don't know, how to fill it up. My code right now looks like this: pH - c(0,6.1,6.1,6.3,6.6,7.3,0) Tiefe - c(0,0,10,40,80,120,10) plot(pH,Tiefe,type=s,main=Tiefenfunktion pH,ylim=c(120,0),xlim=c(0,23)) Can someone give me an hint how to work on this? Thanks, Beate inline: pH.png__ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Package versions (was Reshape a sparse matrix)
On Tue, 15 May 2007, Scott Hyde wrote: Thanks for the respons, Martin. The program I wrote works as well for doing the reshaping, but it is nice to have it built in. Is there a way to tell what version of Matrix is installed, and how do we know when new releases are issued? I installed Matrix fairly recently, and thought I was up to date. library(help=Matrix) shows you the version. If you want it programmatically, one way is packageDescription(Matrix , fields=Version) update.packages() offers you updates. (It is possible that the mirror you use has not got 0.99875-1 yet, especially if this is a binary install, e.g, Windows or MacOS X. E.g. the Windows binary was only built yesterday afternoon.) -Scott Original message Date: Wed, 16 May 2007 09:32:44 +0200 From: Martin Maechler [EMAIL PROTECTED] Subject: Re: [R] Reshape a sparse matrix To: Scott Hyde [EMAIL PROTECTED] Cc: r-help@stat.math.ethz.ch Scott == Scott Hyde [EMAIL PROTECTED] on Tue, 15 May 2007 17:03:13 -1000 (HST) writes: Scott Hi, Scott I'd like to reshape a sparse matrix generated from the Matrix package. I can't seem to do it with the command Scott dim(A) - c(6,9) Scott which works perfectly with the base package matrices, but with the sparse matrices it errors with Scott Error in dim(A) = c(6, 9) : dim- : invalid first argument This *does* work in the current version of Matrix (0.99875-1), actually already in version 0.99875-0 . In the next version of Matrix, it will not only work, but also work sparsely internally via the new class sparseVector and its daughter classes, on which I've been working during the last 10 days or so... Interesting that you bring the topic up right now ... Scott Manipulating the Dim attribute of the sparse Matrix does not produce the desired effect. [EMAIL PROTECTED] - c(as.integer(9),as.integer(6)) does not produce a column ordering result, which I am assuming is because the data is stored in a row (i) and column (j) format instead (class dgTMatrix) You should not have manipulate slots of S4 classes in general. Some people say that you should not even access them directly. Scott Does a function for this exist? yes, as I said above dim(.) - .. works in the newest versions of Matrix. Regards, Martin Maechler, ETH Zurich __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] drop a letter
hello, how can I do to drop C from this character C325 ? _ [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Filled step-function?
Hi, I am not sure what exactly you would like to fill up and how, but take a look at ?polygon and the examples given there. hth Petr Beate Kowalczyk napsal(a): Hello, I'd like to generate a filled step-function in R as you can see in the attachement (image is generated by grapher, but I need a freely available alternative). The problem is, that I don't know, how to fill it up. My code right now looks like this: pH - c(0,6.1,6.1,6.3,6.6,7.3,0) Tiefe - c(0,0,10,40,80,120,10) plot(pH,Tiefe,type=s,main=Tiefenfunktion pH,ylim=c(120,0),xlim=c(0,23)) Can someone give me an hint how to work on this? Thanks, Beate __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Petr Klasterecky Dept. of Probability and Statistics Charles University in Prague Czech Republic __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] drop a letter
elyakhlifi mustapha wrote: hello, how can I do to drop C from this character C325 ? x - C325 substring(x, first=2) [1] 325 gsub(C, , x) [1] 325 gsub([A-Z], , x) [1] 325 ?substring ?gsub _ [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Chuck Cleland, Ph.D. NDRI, Inc. 71 West 23rd Street, 8th floor New York, NY 10010 tel: (212) 845-4495 (Tu, Th) tel: (732) 512-0171 (M, W, F) fax: (917) 438-0894 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] drop a letter
elyakhlifi mustapha wrote: hello, how can I do to drop C from this character C325 ? 1. if C is always single and always first: substring(C325,2) 2. more generic solution, drops all letters sp-unlist(strsplit(C325,split=[A-Z])) sp-sp[nchar(sp)0] sp -- View this message in context: http://www.nabble.com/drop-a-letter-tf3763392.html#a10638376 Sent from the R help mailing list archive at Nabble.com. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] lmer function
Dear all, the question was if lmer can estimate the variance components correctly, although my design is very UNbalanced. Also, how do I find the percentage of the variance from every component? Do I have to add all the varianc components and then divide each one by the total? Thanks P.S. lmer is excellent. It can estimate large datasets where SPSS gives me error messages and says it cannot estimate them. Keep on good work friends! Jason Dr. Iasonas Lamprianou Department of Education The University of Manchester Oxford Road, Manchester M13 9PL, UK Tel. 0044 161 275 3485 [EMAIL PROTECTED] - Original Message From: Douglas Bates [EMAIL PROTECTED] To: Steven McKinney [EMAIL PROTECTED] Cc: Iasonas Lamprianou [EMAIL PROTECTED]; r-help@stat.math.ethz.ch Sent: Tuesday, 15 May, 2007 2:17:34 AM Subject: Re: [R] lmer function On 5/14/07, Steven McKinney [EMAIL PROTECTED] wrote: Running lme4 0.9975-13 I'm still getting the warning $ operator not defined for this S4 class, returning NULL in: x$symbolic.cor It was my mistake. I fixed the problem in the development sources long ago but I haven't uploaded a new release since doing so. I'll upload a new release next week - this is finals week for us and they seem to expect that we will do things like grade exams rather than debugging code. :-) Is there a more recent version? Is there any known problem with this warning (incorrect results etc.) ? Not really. It is a benign cut-and-paste error. If you want to fix it now look for the function printMer in the source file lme4/R/lmer.R and change the default for the symbolic.cor argument to FALSE. sessionInfo() R version 2.5.0 (2007-04-23) powerpc-apple-darwin8.9.1 locale: C attached base packages: [1] stats graphics grDevices utils datasets methods [7] base other attached packages: lme4 Matrix lattice 0.9975-13 0.9975-110.15-4 Steven McKinney Statistician Molecular Oncology and Breast Cancer Program British Columbia Cancer Research Centre email: [EMAIL PROTECTED] tel: 604-675-8000 x7561 BCCRC Molecular Oncology 675 West 10th Ave, Floor 4 Vancouver B.C. V5Z 1L3 Canada -Original Message- From: [EMAIL PROTECTED] on behalf of Douglas Bates Sent: Mon 5/14/2007 12:43 PM To: Iasonas Lamprianou Cc: r-help@stat.math.ethz.ch Subject: Re: [R] lmer function On 5/14/07, Iasonas Lamprianou [EMAIL PROTECTED] wrote: Does anyone know if the lmer function of lme4 works fine for unbalanced designs? I have the examination results of 1000 pupils on three subjects, one score every term. So, I have three scores for English (one for every term), three scores for maths etc. However, not everybody was examined in maths, not everybody was examined in English etc, but everybody was in effect examined on four subjects. I also have information abouit the school. Would this model hive the right results for the variance components? mod_3_f - lmer(SCORE ~ GENDER + (1 |ID ) + (1 | TERM) + (1 | SUBJECT) , Dataset) Linear mixed-effects model fit by REML Formula: SCORE ~ GENDER + (1 | ID) + (1 | TERM) + (1 | SUBJECT) Data: Dataset AICBIC logLik MLdeviance REMLdeviance 247882 247926 -123936 247871 247872 Random effects: Groups NameVariance Std.Dev. ID (Intercept) 5.97288 2.44395 TERM (Intercept) 5.10307 2.25900 SUBJECT (Intercept) 0.25943 0.50934 Residual 4.41673 2.10160 number of obs: 53978, groups: ID, 5695; TERM, 4; SUBJECT, 4 Fixed effects: Estimate Std. Error t value (Intercept)14.303521.15870 12.34 GENDER[T.Male] -1.017760.06885 -14.78 Correlation of Fixed Effects: Warning in x$symbolic.cor : $ operator not defined for this S4 class, returning NULL What version of the lme4 package are you using? (Use sessionInfo() to check.) I think the bug that causes that warning has been fixed in the most recent version. (Intr) GENDER[T.M] -0.023 How do I interpert the results? Do you really want to treat SUBJECT as a random effect? I think it would be more common to treat it as a fixed effect. If I understand you correctly there are only two levels of SUBJECT and these are repeatable levels. If that is the case one could model SUBJECT as a fixed effect or consider its interaction within student with the term (SUBJECT|ID). It would make sense to regard the pair of responses in maths and English for each student in each term as a multivariate response but, at present, that model cannot be fit with lmer. I would also question whether you want the TERM to be modeled with a random effect. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained,
Re: [R] use mathematics formula
Perhaps you could step back and try and explain to the list what your overall goal is. From looking at your code, it looks like you are trying to take some SAS code and turn it in to the equivalent R code automatically. Is that correct? What is the problem you are trying to solve? Hadley On 5/16/07, elyakhlifi mustapha [EMAIL PROTECTED] wrote: hello, I wanna use some mathematics formula and to do this I tried several way in paricular using strsplit textconnection scan setdiff but I think that it's a lil hard the data frame that I'm working on is as follow donCalcara2 Id_Cara Form_C 1 743 if C325=. then C743=(C152/C103)*100| else C743=(C152/C325)*100 2 627 if C137=. Then C627=.| else do| if C109=. Then C627=(C138/S138)*(100-C137)| else C627=(C138/S138)*C109| end 3 638 C638 = C103 / S103 4 740 if C325=. then C740=(C346/C103)*100| else C740=(C346/C325)*100 5 739 if C155=. then C739=(C570/C103)*100| else C739=C155/(C155+C103)*100 6 628 if C325=. then C628=(C455/C103)*100| else C628=(C455/C325)*100 7 747if C325=. then C747=(C27/C103)*100| else C747=(C27/C325)*100 8 629 if C325=. then C629=(C454/C103)*100| else C629=(C454/C325)*100 9 737 if C325=. then C737=(C457/C103)*100| else C737=(C457/C325)*100 10 750 if C325=. then C750=(C431/C103)*100| else C750=(C431/C325)*100 11 754 if C325=. then C754=(C894/C103)*100| else C754=(C894/(C325+C894))*100 12 760 C760= C627 / 0.89 13 761 C761 = C177 * 0.89 14 586 if C325=. then C586=(C588/C103)*100 15 896 if C325=. then C896=(C895/C103)*100 16 751 if C325=. then C751=(C433/C103)*100| else C751=(C433/C325)*100 17 738 if C325=. then C738=(C151/C103)*100| else C738=(C151/C325)*100 18 744 C744=(C627*C177)/100 19 633 if C325=. then C633=(C130/C103)*100| else C633=(C130/C325)*100 20 732 if C325=. then C732=(C585/C103)*100| else C732=(C585/C325)*100 21 898 if C325=. then C898=(C897/C103)*100 Can you help me please? I'm French so if you can speak French it's better for me because of my English level _ [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] creating different strata
hie l would like to create about ten strata l have tried using sample(c(1,2),1,replace=TRUE) but all l get is a vector of 1 and 2 if i change it to sample(c(1,10),1,replace=TRUE) it gives me a vector of 1 and 10 how do l go about it - [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] converting a data frame to ts objects
Dear R-ians I have a data frame like Person_id Date/timeCount - -- --- 123 20 May 1999 1 123 21 May 1999 3 222 1 Feb 2000 2 222 3 Feb 2000 4 I want to create ts objects for each person_id (i.e. 123 and 222). Time series frequency can be in months and all starting from the same date (i.e. May 1999). Rather than manually creating sum of counts for each month and creating ts objects manually for each persons, Is there a function for creating ts objects automatically from such data? Thanks, Faith OZGUL __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Running R function as a Batch process
Hi, I am struggling with using R CMD BATCH command. Kindly suggest solution to the following problem. I have a function named CinC with accept two input parameters. This can be shown as: CinC - function(start, end) where start and end both are character strings. Please suggest me how can I run this function using command R CMD BATCH. Currently I am trying to do like this - R CMD BATCH c:/tt/CinC.r c:/tt/h.Rout -20070416 08:41 -20070416 10:33 What is wrong/incorrect with it? Your suggestions are important to me. Kindly reply. Thanks in advance. Regards Divya Sarthi [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] creating different strata
sorry all l got the answer thanks raymond chiruka [EMAIL PROTECTED] wrote: hie l would like to create about ten strata l have tried using sample(c(1,2),1,replace=TRUE) but all l get is a vector of 1 and 2 if i change it to sample(c(1,10),1,replace=TRUE) it gives me a vector of 1 and 10 how do l go about it - [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. - [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Filled step-function?
Hi Petr, polygon doesn't work very well, because I need a graphical display for the laboratory results of my institute. So I have a lot of data in .csv-format, and I don't really want to define a new polygon for each dataset, because then I have to do a lot of extra-work. I need a solution that works like the following, but with coloring the area under the function (like the image in my first posting): labdata - read.csv(labdata.csv, header=TRUE) attach(labdata) #for using column-names as variables plot(variable1,variable2,type=s,main=Title,ylim=c(120,0),xlim=c(0,10)) For each .csv-dataset I want to use this code with only slight adjustments... Tanks again, Beate Petr Klasterecky schrieb: Hi, I am not sure what exactly you would like to fill up and how, but take a look at ?polygon and the examples given there. hth Petr Beate Kowalczyk napsal(a): Hello, I'd like to generate a filled step-function in R as you can see in the attachement (image is generated by grapher, but I need a freely available alternative). The problem is, that I don't know, how to fill it up. My code right now looks like this: pH - c(0,6.1,6.1,6.3,6.6,7.3,0) Tiefe - c(0,0,10,40,80,120,10) plot(pH,Tiefe,type=s,main=Tiefenfunktion pH,ylim=c(120,0),xlim=c(0,23)) Can someone give me an hint how to work on this? Thanks, Beate __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] use mathematics formula
Explicez ce que vous voulez faire et donnez nous une petite example. Lisez et suivez les instuctions ici http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. On peut ecrire en anglais et francais. --- elyakhlifi mustapha [EMAIL PROTECTED] wrote: hello, I wanna use some mathematics formula and to do this I tried several way in paricular using strsplit textconnection scan setdiff but I think that it's a lil hard the data frame that I'm working on is as follow donCalcara2 Id_Cara Form_C 1 743 if C325=. then C743=(C152/C103)*100| else C743=(C152/C325)*100 2 627 if C137=. Then C627=.| else do| if C109=. Then C627=(C138/S138)*(100-C137)| else C627=(C138/S138)*C109| end 3 638 C638 = C103 / S103 4 740 if C325=. then C740=(C346/C103)*100| else C740=(C346/C325)*100 5 739 if C155=. then C739=(C570/C103)*100| else C739=C155/(C155+C103)*100 6 628 if C325=. then C628=(C455/C103)*100| else C628=(C455/C325)*100 7 747 if C325=. then C747=(C27/C103)*100| else C747=(C27/C325)*100 8 629 if C325=. then C629=(C454/C103)*100| else C629=(C454/C325)*100 9 737 if C325=. then C737=(C457/C103)*100| else C737=(C457/C325)*100 10 750 if C325=. then C750=(C431/C103)*100| else C750=(C431/C325)*100 11 754 if C325=. then C754=(C894/C103)*100| else C754=(C894/(C325+C894))*100 12 760 C760= C627 / 0.89 13 761 C761 = C177 * 0.89 14 586 if C325=. then C586=(C588/C103)*100 15 896 if C325=. then C896=(C895/C103)*100 16 751 if C325=. then C751=(C433/C103)*100| else C751=(C433/C325)*100 17 738 if C325=. then C738=(C151/C103)*100| else C738=(C151/C325)*100 18 744 C744=(C627*C177)/100 19 633 if C325=. then C633=(C130/C103)*100| else C633=(C130/C325)*100 20 732 if C325=. then C732=(C585/C103)*100| else C732=(C585/C325)*100 21 898 if C325=. then C898=(C897/C103)*100 Can you help me please? I'm French so if you can speak French it's better for me because of my English level _ [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] creating different strata
Something like this? sample((1:10),100,replace=TRUE) ?sample hth Petr raymond chiruka napsal(a): hie l would like to create about ten strata l have tried using sample(c(1,2),1,replace=TRUE) but all l get is a vector of 1 and 2 if i change it to sample(c(1,10),1,replace=TRUE) it gives me a vector of 1 and 10 how do l go about it - [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Petr Klasterecky Dept. of Probability and Statistics Charles University in Prague Czech Republic __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Running R function as a Batch process
d. sarthi maheshwari wrote: Hi, I am struggling with using R CMD BATCH command. Kindly suggest solution to the following problem. I have a function named CinC with accept two input parameters. This can be shown as: CinC - function(start, end) where start and end both are character strings. Please suggest me how can I run this function using command R CMD BATCH. Currently I am trying to do like this - R CMD BATCH c:/tt/CinC.r c:/tt/h.Rout -20070416 08:41 -20070416 10:33 What is wrong/incorrect with it? You should use the function commandArgs in your code to retrieve supplied arguments from the command line. Look at ?commandArgs ?Startup Your R invokation should look like this C:\ R CMD BATCH c:/tt/CinC.r c:/tt/h.Rout --args 20070416 08:41 20070416 10:33 And you should add something like this in your R code command.args-commandArgs(trailingOnly=TRUE) CinC(command.args[1],command.args[2]) -- View this message in context: http://www.nabble.com/Running-R-function-as-a-Batch-process-tf3764048.html#a10640433 Sent from the R help mailing list archive at Nabble.com. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] more woes trying to convert a data.frame to a numerical matrix
I have the following csv file: name,x,y,z category,delta,gamma,epsilon a,1,2,3 b,4,5,6 c,7,8,9 I'd like to create a numeric matrix of just the numbers in this csv dataset. I've tried the following program: sample.data - read.csv(sample.csv) numerical.data - as.matrix(sample.data[-1,-1]) However, print(numerical.data) returns what appears to be a matrix of characters: x y z 2 1 2 3 3 4 5 6 4 7 8 9 How do I force it to be numbers rather than characters? Thanks, Andrew [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Filled step-function?
Hi,
please reply to the entire list (as a carbon copy) - I do not always
read this list properly or may not know the solution.
I do not know your data, but there does not seem to be much more work.
This works well for me with your pH and Tiefe variables:
plot(pH,Tiefe,type=s,main=Tiefenfunktion pH,ylim=c(120,0),xlim=c(0,23))
for (i in (1:(length(pH)-2))){
polygon(x=c(pH[i], pH[i+1], pH[i+1], pH[i]), y=c(Tiefe[i], Tiefe[i],
max(Tiefe), max(Tiefe)), col=i)
}
or
plot(pH,Tiefe,type=s,main=Tiefenfunktion pH,ylim=c(120,0),xlim=c(0,23))
for (i in (1:(length(pH)-2))){
polygon(x=c(pH[i], pH[i+1], pH[i+1], pH[i]), y=c(Tiefe[i], Tiefe[i],
Tiefe[i+1], Tiefe[i+1]), col=i)
}
You just need to arrange your coordinates properly.
If your variables are not always named pH and Tiefe, just access them
directly from the labdata data.frame: you will have labdata[,1] for
variable1 (here pH) and labdata[,2] for variable2 (Tiefe).
hth
Petr
Beate Kowalczyk napsal(a):
Hi Peter,
polygon doesn't work very well, because I need a graphical display for
the laboratory results of my institute. So I have a lot of data in
.csv-format, and I don't really want to define a new polygon for each
dataset, because then I have to do a lot of extra-work. I need a
solution that works like the following, but with coloring the area under
the function (like the image in my first posting):
labdata - read.csv(labdata.csv, header=TRUE)
attach(labdata) #for using column-names as variables
plot(variable1,variable2,type=s,main=Title,ylim=c(120,0),xlim=c(0,10))
For each .csv-dataset I want to use this code with only slight
adjustments...
Tanks again, Beate
Petr Klasterecky schrieb:
Hi,
I am not sure what exactly you would like to fill up and how, but take
a look at
?polygon
and the examples given there.
hth
Petr
Beate Kowalczyk napsal(a):
Hello,
I'd like to generate a filled step-function in R as you can see in
the attachement (image is generated by grapher, but I need a freely
available alternative). The problem is, that I don't know, how to
fill it up. My code right now looks like this:
pH - c(0,6.1,6.1,6.3,6.6,7.3,0)
Tiefe - c(0,0,10,40,80,120,10)
plot(pH,Tiefe,type=s,main=Tiefenfunktion
pH,ylim=c(120,0),xlim=c(0,23))
Can someone give me an hint how to work on this?
Thanks, Beate
__
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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.
--
Petr Klasterecky
Dept. of Probability and Statistics
Charles University in Prague
Czech Republic
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Re: [R] more woes trying to convert a data.frame to a numerical matrix
?as.numeric ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Reseach 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 Andrew Yee Verzonden: woensdag 16 mei 2007 14:11 Aan: r-help@stat.math.ethz.ch Onderwerp: [R] more woes trying to convert a data.frame to a numerical matrix I have the following csv file: name,x,y,z category,delta,gamma,epsilon a,1,2,3 b,4,5,6 c,7,8,9 I'd like to create a numeric matrix of just the numbers in this csv dataset. I've tried the following program: sample.data - read.csv(sample.csv) numerical.data - as.matrix(sample.data[-1,-1]) However, print(numerical.data) returns what appears to be a matrix of characters: x y z 2 1 2 3 3 4 5 6 4 7 8 9 How do I force it to be numbers rather than characters? Thanks, Andrew [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Filled step-function?
Beate Kowalczyk wrote:
Hello,
I'd like to generate a filled step-function in R as you can see in the
attachement (image is generated by grapher, but I need a freely
available alternative). The problem is, that I don't know, how to fill
it up. My code right now looks like this:
pH - c(0,6.1,6.1,6.3,6.6,7.3,0)
Tiefe - c(0,0,10,40,80,120,10)
plot(pH,Tiefe,type=s,main=Tiefenfunktion pH,ylim=c(120,0),xlim=c(0,23))
Hi Beate,
If I understand this, you want the steps to be converted into a polygon
and displayed instead of the plot step display. You also want the y
axis reversed. This might do what you want:
stepfun.polygon-function(x,y,miny=min(y),col=NULL,...) {
plot(x,y,ylim=c(max(y),min(y)),type=n,...)
polyx-c(x[1],rep(x[2:length(x)],each=2),x[1])
polyy-c(rep(y,each=2))
polygon(polyx,polyy,col=col)
}
Note that you will probably only want the observed values of x and y, as
the zeros on the end produce an unwanted spike in the polygon.
Jim
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] more woes trying to convert a data.frame to a numerical matrix
On Wed, 2007-05-16 at 08:10 -0400, Andrew Yee wrote: I have the following csv file: name,x,y,z category,delta,gamma,epsilon a,1,2,3 b,4,5,6 c,7,8,9 I'd like to create a numeric matrix of just the numbers in this csv dataset. I've tried the following program: sample.data - read.csv(sample.csv) numerical.data - as.matrix(sample.data[-1,-1]) However, print(numerical.data) returns what appears to be a matrix of characters: x y z 2 1 2 3 3 4 5 6 4 7 8 9 How do I force it to be numbers rather than characters? Thanks, Andrew The problem is that you have two rows which contain alpha entries. The first row is treated as the header, but the second row is treated as actual data, thus overriding the numeric values in the subsequent rows. You could use: as.numeric(as.matrix(sample.data[-1, -1])) to coerce the matrix to numeric, or if you don't need the alpha entries, you could modify the read.csv() call to something like: read.csv(sample.csv, header = FALSE, skip = 2, row.names = 1, col.names = c(name, x, y, z) This will skip the first two rows, set the first column to the row names and give you a data frame with numeric columns, which in most cases can be treated as a numeric matrix and/or you could explicitly coerce it to one. HTH, Marc Schwartz __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] more woes trying to convert a data.frame to a numerical matrix
have a look at: ?as.numeric() and ?data.matrix(). 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 - Original Message - From: Andrew Yee [EMAIL PROTECTED] To: r-help@stat.math.ethz.ch Sent: Wednesday, May 16, 2007 2:10 PM Subject: [R] more woes trying to convert a data.frame to a numerical matrix I have the following csv file: name,x,y,z category,delta,gamma,epsilon a,1,2,3 b,4,5,6 c,7,8,9 I'd like to create a numeric matrix of just the numbers in this csv dataset. I've tried the following program: sample.data - read.csv(sample.csv) numerical.data - as.matrix(sample.data[-1,-1]) However, print(numerical.data) returns what appears to be a matrix of characters: x y z 2 1 2 3 3 4 5 6 4 7 8 9 How do I force it to be numbers rather than characters? Thanks, Andrew [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] more woes trying to convert a data.frame to a numerical matrix
Thanks for the suggestion and the explanation for why I was running into these troubles. I've tried: as.numeric(as.matrix(sample.data[-1, -1])) However, this creates another vector rather than a matrix. Is there a straight forward way to convert this directly into a numeric matrix rather than a vector? Additionally, I've also considered: data.matrix(sample.data[-1,-1] but bizarrely, it returns: x y z 2 1 1 1 3 2 2 2 4 3 3 3 Thanks, Andrew On 5/16/07, Marc Schwartz [EMAIL PROTECTED] wrote: On Wed, 2007-05-16 at 08:10 -0400, Andrew Yee wrote: I have the following csv file: name,x,y,z category,delta,gamma,epsilon a,1,2,3 b,4,5,6 c,7,8,9 I'd like to create a numeric matrix of just the numbers in this csv dataset. I've tried the following program: sample.data - read.csv(sample.csv) numerical.data - as.matrix(sample.data[-1,-1]) However, print(numerical.data) returns what appears to be a matrix of characters: x y z 2 1 2 3 3 4 5 6 4 7 8 9 How do I force it to be numbers rather than characters? Thanks, Andrew The problem is that you have two rows which contain alpha entries. The first row is treated as the header, but the second row is treated as actual data, thus overriding the numeric values in the subsequent rows. You could use: as.numeric(as.matrix(sample.data[-1, -1])) to coerce the matrix to numeric, or if you don't need the alpha entries, you could modify the read.csv() call to something like: read.csv(sample.csv, header = FALSE, skip = 2, row.names = 1, col.names = c(name, x, y, z) This will skip the first two rows, set the first column to the row names and give you a data frame with numeric columns, which in most cases can be treated as a numeric matrix and/or you could explicitly coerce it to one. HTH, Marc Schwartz [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Running R function as a Batch process
Hi,
There are many clues in the help.
First I created the file c:\sumfunction.R
x-as.numeric(commandArgs()[-1:-4] )
print(x)
addtogether-function(x,y){SUM-x+y;print(SUM)}
addtogether(x[1],x[2])
Then at the command line in Windows I enter
R --vanilla --slave --args 7 10 c:\sumfunction.R c:\logout.txt
Regards
Alex
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of d. sarthi
maheshwari
Sent: May 16, 2007 8:29 AM
To: r-help@stat.math.ethz.ch
Subject: [R] Running R function as a Batch process
Hi,
I am struggling with using R CMD BATCH command. Kindly suggest solution
to the following problem.
I have a function named CinC with accept two input parameters. This can
be shown as:
CinC - function(start, end)
where start and end both are character strings.
Please suggest me how can I run this function using command R CMD BATCH.
Currently I am trying to do like this - R CMD BATCH c:/tt/CinC.r
c:/tt/h.Rout -20070416 08:41 -20070416 10:33
What is wrong/incorrect with it?
Your suggestions are important to me. Kindly reply.
Thanks in advance.
Regards
Divya Sarthi
[[alternative HTML version deleted]]
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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] more woes trying to convert a data.frame to a numerical matrix
On Wed, 2007-05-16 at 08:40 -0400, Andrew Yee wrote: Thanks for the suggestion and the explanation for why I was running into these troubles. I've tried: as.numeric(as.matrix(sample.data[-1, -1])) However, this creates another vector rather than a matrix. Right. That's because I'm an idiot and need more caffeine... :-) Is there a straight forward way to convert this directly into a numeric matrix rather than a vector? Yeah, Dimitris' approach below of using data.matrix(). You could also use: mat - sapply(sample.data[-1, -1], as.numeric) rownames(mat) - rownames(sample.data[-1, -1]) mat x y z 2 1 1 1 3 2 2 2 4 3 3 3 Though, this is essentially what data.matrix() does internally. Additionally, I've also considered: data.matrix(sample.data[-1,-1] but bizarrely, it returns: x y z 2 1 1 1 3 2 2 2 4 3 3 3 That is a numeric matrix: str(data.matrix(sample.data[-1, -1])) int [1:3, 1:3] 1 2 3 1 2 3 1 2 3 - attr(*, dimnames)=List of 2 ..$ : chr [1:3] 2 3 4 ..$ : chr [1:3] x y z HTH, Marc Thanks, Andrew On 5/16/07, Marc Schwartz [EMAIL PROTECTED] wrote: On Wed, 2007-05-16 at 08:10 -0400, Andrew Yee wrote: I have the following csv file: name,x,y,z category,delta,gamma,epsilon a,1,2,3 b,4,5,6 c,7,8,9 I'd like to create a numeric matrix of just the numbers in this csv dataset. I've tried the following program: sample.data - read.csv(sample.csv) numerical.data - as.matrix(sample.data[-1,-1]) However, print(numerical.data ) returns what appears to be a matrix of characters: x y z 2 1 2 3 3 4 5 6 4 7 8 9 How do I force it to be numbers rather than characters? Thanks, Andrew The problem is that you have two rows which contain alpha entries. The first row is treated as the header, but the second row is treated as actual data, thus overriding the numeric values in the subsequent rows. You could use: as.numeric(as.matrix(sample.data[-1, -1])) to coerce the matrix to numeric, or if you don't need the alpha entries, you could modify the read.csv() call to something like: read.csv(sample.csv, header = FALSE, skip = 2, row.names = 1, col.names = c(name, x, y, z) This will skip the first two rows, set the first column to the row names and give you a data frame with numeric columns, which in most cases can be treated as a numeric matrix and/or you could explicitly coerce it to one. HTH, Marc Schwartz __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Is it possible to pass a Tcl/Tk component as argument to a function
hi! All: I wonder if someone has done this before... I am writing several functions that conduct statistical analysis using a GUI interface by Tcl/Tk, they share many identical GUI components. What I am trying to do now is to simplify the code by writing a GUI repository for all the components they use, thus save effort for code maintenance. Since they all use: mainFrame - tkcanvas(top) -- I wonder if I can write functions that take mainFrame as an argument, and call those functions from other place with initialized tkcanvas object. I did not see example like this and from my *limited* experience with tcltk, I found it always need something to be initialized before put to use, that makes me wonder if this idea will work... if it does not, any work arounds? like using Macro? Thanks Hao [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] converting a data frame to ts objects
On 5/16/07, fatih ozgul [EMAIL PROTECTED] wrote: Dear R-ians I have a data frame like Person_id Date/timeCount - -- --- 123 20 May 1999 1 123 21 May 1999 3 222 1 Feb 2000 2 222 3 Feb 2000 4 I want to create ts objects for each person_id (i.e. 123 and 222). Time series frequency can be in months and all starting from the same date (i.e. May 1999). Rather than manually creating sum of counts for each month and creating ts objects manually for each persons, Is there a function for creating ts objects automatically from such data? Try this: # read in as data frame and fix up date Lines.raw - Person_id Date/time Count 123 20 May 1999 1 123 21 May 1999 3 222 1 Feb 2000 2 222 3 Feb 2000 4 library(zoo) DF - read.table(textConnection(Lines.raw), skip = 1, col.names = c(Person_id, d, b, Y, Count)) DF$Date.time - as.Date(paste(DF$d, DF$b, DF$Y), %d %b %Y) # aggregate counts over months, series and convert to ts f - function(DF) aggregate(zoo(DF$Count), as.yearmon(DF$Date.time), sum) z - do.call(merge.zoo, lapply(split(DF, DF$Person_id), f)) frequency(z) - 12 as.ts(z) __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] more woes trying to convert a data.frame to a numerical matrix
Thanks for the suggestion. However, I've tried sapply and data.matrix. The problem is that it while it returns a numeric matrix, it gives back: 1 1 1 2 2 2 3 3 3 instead of 1 2 3 4 5 6 7 8 9 The latter matrix is the desired result Thanks, Andrew On 5/16/07, Marc Schwartz [EMAIL PROTECTED] wrote: On Wed, 2007-05-16 at 08:40 -0400, Andrew Yee wrote: Thanks for the suggestion and the explanation for why I was running into these troubles. I've tried: as.numeric(as.matrix(sample.data[-1, -1])) However, this creates another vector rather than a matrix. Right. That's because I'm an idiot and need more caffeine... :-) Is there a straight forward way to convert this directly into a numeric matrix rather than a vector? Yeah, Dimitris' approach below of using data.matrix(). You could also use: mat - sapply(sample.data[-1, -1], as.numeric) rownames(mat) - rownames(sample.data[-1, -1]) mat x y z 2 1 1 1 3 2 2 2 4 3 3 3 Though, this is essentially what data.matrix() does internally. Additionally, I've also considered: data.matrix(sample.data[-1,-1] but bizarrely, it returns: x y z 2 1 1 1 3 2 2 2 4 3 3 3 That is a numeric matrix: str(data.matrix(sample.data[-1, -1])) int [1:3, 1:3] 1 2 3 1 2 3 1 2 3 - attr(*, dimnames)=List of 2 ..$ : chr [1:3] 2 3 4 ..$ : chr [1:3] x y z HTH, Marc Thanks, Andrew On 5/16/07, Marc Schwartz [EMAIL PROTECTED] wrote: On Wed, 2007-05-16 at 08:10 -0400, Andrew Yee wrote: I have the following csv file: name,x,y,z category,delta,gamma,epsilon a,1,2,3 b,4,5,6 c,7,8,9 I'd like to create a numeric matrix of just the numbers in this csv dataset. I've tried the following program: sample.data - read.csv(sample.csv) numerical.data - as.matrix(sample.data[-1,-1]) However, print(numerical.data ) returns what appears to be a matrix of characters: x y z 2 1 2 3 3 4 5 6 4 7 8 9 How do I force it to be numbers rather than characters? Thanks, Andrew The problem is that you have two rows which contain alpha entries. The first row is treated as the header, but the second row is treated as actual data, thus overriding the numeric values in the subsequent rows. You could use: as.numeric(as.matrix(sample.data[-1, -1])) to coerce the matrix to numeric, or if you don't need the alpha entries, you could modify the read.csv() call to something like: read.csv(sample.csv, header = FALSE, skip = 2, row.names = 1, col.names = c(name, x, y, z) This will skip the first two rows, set the first column to the row names and give you a data frame with numeric columns, which in most cases can be treated as a numeric matrix and/or you could explicitly coerce it to one. HTH, Marc Schwartz [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] effective df in local polinomial regression
Hallo R-users, I would like to know if there is a way to get the effective degrees of freedom in local polinomial regression. At the moment, to carry out the local polinomial regression, I am using the function locpoly() in library KernSmooth (I need to estimate both the regression function and its derivatives, up to the 3rd one). Thanks, Simone -- Simone Vantini MOX - Modeling and Scientific Computing Dipartimento di Matematica F. Brioschi Politecnico di Milano Piazza Leonardo da Vinci, 32 I-20133 Milano (Italy) tel: +39 02 2399 4604 email: [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Is it possible to pass a Tcl/Tk component as argument to afunction
Dear Hao, You might take a look at how the Rcmdr package is implemented with many reusable elements. There is, for example, an initializeDialog function. I hope this helps, John John Fox, Professor Department of Sociology McMaster University Hamilton, Ontario Canada L8S 4M4 905-525-9140x23604 http://socserv.mcmaster.ca/jfox -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Hao Liu Sent: Wednesday, May 16, 2007 8:58 AM To: r-help@stat.math.ethz.ch Subject: [R] Is it possible to pass a Tcl/Tk component as argument to afunction hi! All: I wonder if someone has done this before... I am writing several functions that conduct statistical analysis using a GUI interface by Tcl/Tk, they share many identical GUI components. What I am trying to do now is to simplify the code by writing a GUI repository for all the components they use, thus save effort for code maintenance. Since they all use: mainFrame - tkcanvas(top) -- I wonder if I can write functions that take mainFrame as an argument, and call those functions from other place with initialized tkcanvas object. I did not see example like this and from my *limited* experience with tcltk, I found it always need something to be initialized before put to use, that makes me wonder if this idea will work... if it does not, any work arounds? like using Macro? Thanks Hao [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] log rank test p value
The best place to start is help(survdiff) That's right -- read the documentation! This tells you what is contained in the output to survdiff, namely objects n, obs, exp, chisq, and var, including descriptions of each. The number of degrees of freedom for the chisquare test is (#groups -1); both the obs and exp objects have one element per group. Terry Therneau __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] more woes trying to convert a data.frame to a numerical matrix
Thanks again to everyone for all your help. I think I've figured out the solution to my dilemma. Instead of using data.matrix or sapply, this works for me: sample.data-read.csv(sample.csv) sample.matrix.raw-as.matrix(sample.data[-1,-1]) sample.matrix - matrix(as.numeric(sample.matrix.raw), nrow=attributes(sample.matrix.raw)$dim[1], ncol=attributes( sample.matrix.raw)$dim[2]) With the above code, I get the desired matrix of: 1 2 3 4 5 6 7 8 9 (I'd like to be able to import the whole csv and then subset the relevant header and data sections (rather than creating a separate csv for the header and csv for the data) Of course, the above code seems kind of clunky, and welcome any suggestions for improvement. Thanks, Andrew On 5/16/07, Andrew Yee [EMAIL PROTECTED] wrote: Thanks for the suggestion. However, I've tried sapply and data.matrix. The problem is that it while it returns a numeric matrix, it gives back: 1 1 1 2 2 2 3 3 3 instead of 1 2 3 4 5 6 7 8 9 The latter matrix is the desired result Thanks, Andrew On 5/16/07, Marc Schwartz [EMAIL PROTECTED] wrote: On Wed, 2007-05-16 at 08:40 -0400, Andrew Yee wrote: Thanks for the suggestion and the explanation for why I was running into these troubles. I've tried: as.numeric(as.matrix(sample.data[-1, -1])) However, this creates another vector rather than a matrix. Right. That's because I'm an idiot and need more caffeine... :-) Is there a straight forward way to convert this directly into a numeric matrix rather than a vector? Yeah, Dimitris' approach below of using data.matrix(). You could also use: mat - sapply(sample.data[-1, -1], as.numeric) rownames(mat) - rownames(sample.data[-1, -1]) mat x y z 2 1 1 1 3 2 2 2 4 3 3 3 Though, this is essentially what data.matrix() does internally. Additionally, I've also considered: data.matrix(sample.data[-1,-1] but bizarrely, it returns: x y z 2 1 1 1 3 2 2 2 4 3 3 3 That is a numeric matrix: str(data.matrix(sample.data[-1, -1])) int [1:3, 1:3] 1 2 3 1 2 3 1 2 3 - attr(*, dimnames)=List of 2 ..$ : chr [1:3] 2 3 4 ..$ : chr [1:3] x y z HTH, Marc Thanks, Andrew On 5/16/07, Marc Schwartz [EMAIL PROTECTED] wrote: On Wed, 2007-05-16 at 08:10 -0400, Andrew Yee wrote: I have the following csv file: name,x,y,z category,delta,gamma,epsilon a,1,2,3 b,4,5,6 c,7,8,9 I'd like to create a numeric matrix of just the numbers in this csv dataset. I've tried the following program: sample.data - read.csv(sample.csv) numerical.data - as.matrix (sample.data[-1,-1]) However, print(numerical.data ) returns what appears to be a matrix of characters: x y z 2 1 2 3 3 4 5 6 4 7 8 9 How do I force it to be numbers rather than characters? Thanks, Andrew The problem is that you have two rows which contain alpha entries. The first row is treated as the header, but the second row is treated as actual data, thus overriding the numeric values in the subsequent rows. You could use: as.numeric(as.matrix(sample.data [-1, -1])) to coerce the matrix to numeric, or if you don't need the alpha entries, you could modify the read.csv() call to something like: read.csv(sample.csv, header = FALSE, skip = 2, row.names = 1, col.names = c(name, x, y, z) This will skip the first two rows, set the first column to the row names and give you a data frame with numeric columns, which in most cases can be treated as a numeric matrix and/or you could explicitly coerce it to one. HTH, Marc Schwartz [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Is it possible to pass a Tcl/Tk component as argument to a function
On 5/16/2007 8:58 AM, Hao Liu wrote: hi! All: I wonder if someone has done this before... I am writing several functions that conduct statistical analysis using a GUI interface by Tcl/Tk, they share many identical GUI components. What I am trying to do now is to simplify the code by writing a GUI repository for all the components they use, thus save effort for code maintenance. Since they all use: mainFrame - tkcanvas(top) -- I wonder if I can write functions that take mainFrame as an argument, and call those functions from other place with initialized tkcanvas object. I did not see example like this and from my *limited* experience with tcltk, I found it always need something to be initialized before put to use, that makes me wonder if this idea will work... if it does not, any work arounds? like using Macro? I think your question is too vague. Yes, you can pass your mainFrame object to a function. Will it work? Well, that depends on what you do with it. Could you put together a small example showing the sort of thing you want to do? If it works, then you probably don't need to post a question; if it doesn't, someone can probably point out what changes are necessary. Duncan Murdoch __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] more woes trying to convert a data.frame to a numerical matrix
On Wed, 2007-05-16 at 09:05 -0400, Andrew Yee wrote: Thanks for the suggestion. However, I've tried sapply and data.matrix. The problem is that it while it returns a numeric matrix, it gives back: 1 1 1 2 2 2 3 3 3 instead of 1 2 3 4 5 6 7 8 9 The latter matrix is the desired result Thanks, Andrew OK. One more time with gusto... We need to coerce the values to character first, since they are read in as factors and the results that we are seeing are the numeric values of the factor levels and not the numeric values themselves. Oy... mat - sapply(sample.data[-1, -1], function(x) as.numeric(as.character(x))) rownames(mat) - rownames(sample.data[-1, -1]) mat x y z 2 1 2 3 3 4 5 6 4 7 8 9 str(mat) num [1:3, 1:3] 1 4 7 2 5 8 3 6 9 - attr(*, dimnames)=List of 2 ..$ : chr [1:3] 2 3 4 ..$ : chr [1:3] x y z It looks like data.matrix() does not do the character coercion internally, so the above approach would seem to be better. Sorry about that. Another alternative would be to use the modifications to the read.csv() function call that I referenced initially and then use the result for your subsequent manipulations. Marc __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] partial least regression
hello r-helpers: there is a .txt file: x1 x2 x3 x4 x5 x6 x7 x8 x9 x10 x11 y1 17 5 77 18 19 24 7 24 24 72 52 100 2 6 72 18 17 15 4 12 18 35 42 97.2 17 2 58 10 5 3 4 3 3 40 28 98 17 2 69 14 13 12 4 6 6 50 37 93 2 3 75 20 38 18 6 12 18 73 67 99 14 4 59 16 18 9 4 3 15 47 40 99.95 17 4 87 18 17 12 4 15 12 69 46 100 14 3 74 15 9 12 1 15 12 44 35 98 17 6 76 15 33 21 15 9 18 46 41 100 17 5 76 17 22 18 1 15 9 54 38 100 20 16 98 23 43 27 27 24 27 87 67 99.9 20 6 110 25 36 18 7 18 12 99 88 90 20 6 100 20 19 18 4 15 21 84 60 99.2 17 6 72 13 31 18 5 21 12 52 43 95.6 20 15 104 25 53 30 31 30 30 100 90 99.93 17 13 68 21 42 24 14 18 12 75 69 99.1 17 8 63 14 18 9 10 15 25 39 38 95 20 7 88 19 28 18 7 15 24 61 49 100 20 14 61 18 48 15 11 21 18 48 48 99.91 20 9 94 22 38 21 13 31 12 84 80 99.43 17 7 70 16 28 12 18 12 12 52 38 100 17 6 80 17 46 18 18 24 18 70 69 99.2 and i write this program: library(pls) quality.data-read.table(d:\\work\\12.txt,col.names=c(x1,x2,x3,x4, x5,x6,x7,x8,x9,x10,x11,y1)) attach(quality.data) quality.data # pairs(cbind(x4,x5,y1)) X-data.frame(x1,x2,x3,x4,x5,x6,x7,x8,x9,x10,x11,y1) Y-data.frame(y1) quality.simpls-mvr(X,Y,1:11,method=simpls,validation=CV) #error happens in this row ,and the error information is about: error in :eval(expr, envir, enclos) :the length of number'envir' is not 1. i don't know how to solve this problem. who can help me make this program correct,please. thank you very much! kenneth __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] partial least regression
Your call to mvr does not correspond to the documentation. See ?mvr and try this: Lines - x1 x2 x3 x4 x5 x6 x7 x8 x9 x10 x11 y1 17 5 77 18 19 24 7 24 24 72 52 100 2 6 72 18 17 15 4 12 18 35 42 97.2 17 2 58 10 5 3 4 3 3 40 28 98 17 2 69 14 13 12 4 6 6 50 37 93 2 3 75 20 38 18 6 12 18 73 67 99 14 4 59 16 18 9 4 3 15 47 40 99.95 17 4 87 18 17 12 4 15 12 69 46 100 14 3 74 15 9 12 1 15 12 44 35 98 17 6 76 15 33 21 15 9 18 46 41 100 17 5 76 17 22 18 1 15 9 54 38 100 20 16 98 23 43 27 27 24 27 87 67 99.9 20 6 110 25 36 18 7 18 12 99 88 90 20 6 100 20 19 18 4 15 21 84 60 99.2 17 6 72 13 31 18 5 21 12 52 43 95.6 20 15 104 25 53 30 31 30 30 100 90 99.93 17 13 68 21 42 24 14 18 12 75 69 99.1 17 8 63 14 18 9 10 15 25 39 38 95 20 7 88 19 28 18 7 15 24 61 49 100 20 14 61 18 48 15 11 21 18 48 48 99.91 20 9 94 22 38 21 13 31 12 84 80 99.43 17 7 70 16 28 12 18 12 12 52 38 100 17 6 80 17 46 18 18 24 18 70 69 99.2 library(pls) quality.data - read.table(textConnection(Lines), header = TRUE) pairs(quality.data[c(x4, x5, y1)]) quality.simpls - mvr(y1 ~., ncomp = 6, quality.data, method = simpls, validation = CV) # replace 6 with whatever you want On 5/16/07, 赵玉忠 [EMAIL PROTECTED] wrote: hello r-helpers: there is a .txt file: x1 x2 x3 x4 x5 x6 x7 x8 x9 x10 x11 y1 17 5 77 18 19 24 7 24 24 72 52 100 2 6 72 18 17 15 4 12 18 35 42 97.2 17 2 58 10 5 3 4 3 3 40 28 98 17 2 69 14 13 12 4 6 6 50 37 93 2 3 75 20 38 18 6 12 18 73 67 99 14 4 59 16 18 9 4 3 15 47 40 99.95 17 4 87 18 17 12 4 15 12 69 46 100 14 3 74 15 9 12 1 15 12 44 35 98 17 6 76 15 33 21 15 9 18 46 41 100 17 5 76 17 22 18 1 15 9 54 38 100 20 16 98 23 43 27 27 24 27 87 67 99.9 20 6 110 25 36 18 7 18 12 99 88 90 20 6 100 20 19 18 4 15 21 84 60 99.2 17 6 72 13 31 18 5 21 12 52 43 95.6 20 15 104 25 53 30 31 30 30 100 90 99.93 17 13 68 21 42 24 14 18 12 75 69 99.1 17 8 63 14 18 9 10 15 25 39 38 95 20 7 88 19 28 18 7 15 24 61 49 100 20 14 61 18 48 15 11 21 18 48 48 99.91 20 9 94 22 38 21 13 31 12 84 80 99.43 17 7 70 16 28 12 18 12 12 52 38 100 17 6 80 17 46 18 18 24 18 70 69 99.2 and i write this program: library(pls) quality.data-read.table(d:\\work\\12.txt,col.names=c(x1,x2,x3,x4, x5,x6,x7,x8,x9,x10,x11,y1)) attach(quality.data) quality.data # pairs(cbind(x4,x5,y1)) X-data.frame(x1,x2,x3,x4,x5,x6,x7,x8,x9,x10,x11,y1) Y-data.frame(y1) quality.simpls-mvr(X,Y,1:11,method=simpls,validation=CV) #error happens in this row ,and the error information is about: error in :eval(expr, envir, enclos) :the length of number'envir' is not 1. i don't know how to solve this problem. who can help me make this program correct,please. thank you very much! kenneth __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Installing SJava - problem
Hi there. I am trying to install SJava on my windows xp machine. I downloaded the windows source file SJava_0.69-0.tar.gz from the web site http://www.omegahat.org/RSJava/ I have folloed the XP command line instructions as directed in the table underneath the download link: cd $RHOME/src/library unzip SJava_0.69-0.zip cd SJava ./configure.win $RHOME cd $RHOME/src/gnuwin32 make pkg-SJava I reconfigured the configure.win file so that the correct java sdk was referred to. Not a problem. However, when I try to type in make pkg-SJava i get the following error: C:\Program Files\R\R-2.5.0\src\gnuwin32make pkg-SJava 'make' is not recognized as an internal or external command, operable program or batch file. What do I need to do to rectify this? Thanks -- View this message in context: http://www.nabble.com/Installing-SJava---problem-tf3764923.html#a10642944 Sent from the R help mailing list archive at Nabble.com. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Installing SJava - problem
On Wed, 16 May 2007, mister_bluesman wrote: Hi there. I am trying to install SJava on my windows xp machine. I downloaded the windows source file SJava_0.69-0.tar.gz from the web site http://www.omegahat.org/RSJava/ I have folloed the XP command line instructions as directed in the table underneath the download link: cd $RHOME/src/library unzip SJava_0.69-0.zip cd SJava ./configure.win $RHOME cd $RHOME/src/gnuwin32 make pkg-SJava I reconfigured the configure.win file so that the correct java sdk was referred to. Not a problem. However, when I try to type in make pkg-SJava i get the following error: C:\Program Files\R\R-2.5.0\src\gnuwin32make pkg-SJava 'make' is not recognized as an internal or external command, operable program or batch file. What do I need to do to rectify this? Follow the instructions in 'R Installation and Administration' for building source packages on Windows. I don't know if SJava is currently buildable on Windows, not least because it requires an out-of-date Java (it objects to Java 6 aka 1.6.0), at least on Linux (and on x86_64 Linux no earlier Java is viable). -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] more woes trying to convert a data.frame to a numerical matrix
I think this might be a bit more straight forward: R mat - do.call(cbind, scan(clipboard, what=list(NULL, 0, 0, 0), sep=,, skip=2)) Read 3 records R mat [,1] [,2] [,3] [1,]123 [2,]456 [3,]789 Andy From: Andrew Yee Thanks again to everyone for all your help. I think I've figured out the solution to my dilemma. Instead of using data.matrix or sapply, this works for me: sample.data-read.csv(sample.csv) sample.matrix.raw-as.matrix(sample.data[-1,-1]) sample.matrix - matrix(as.numeric(sample.matrix.raw), nrow=attributes(sample.matrix.raw)$dim[1], ncol=attributes( sample.matrix.raw)$dim[2]) With the above code, I get the desired matrix of: 1 2 3 4 5 6 7 8 9 (I'd like to be able to import the whole csv and then subset the relevant header and data sections (rather than creating a separate csv for the header and csv for the data) Of course, the above code seems kind of clunky, and welcome any suggestions for improvement. Thanks, Andrew On 5/16/07, Andrew Yee [EMAIL PROTECTED] wrote: Thanks for the suggestion. However, I've tried sapply and data.matrix. The problem is that it while it returns a numeric matrix, it gives back: 1 1 1 2 2 2 3 3 3 instead of 1 2 3 4 5 6 7 8 9 The latter matrix is the desired result Thanks, Andrew On 5/16/07, Marc Schwartz [EMAIL PROTECTED] wrote: On Wed, 2007-05-16 at 08:40 -0400, Andrew Yee wrote: Thanks for the suggestion and the explanation for why I was running into these troubles. I've tried: as.numeric(as.matrix(sample.data[-1, -1])) However, this creates another vector rather than a matrix. Right. That's because I'm an idiot and need more caffeine... :-) Is there a straight forward way to convert this directly into a numeric matrix rather than a vector? Yeah, Dimitris' approach below of using data.matrix(). You could also use: mat - sapply(sample.data[-1, -1], as.numeric) rownames(mat) - rownames(sample.data[-1, -1]) mat x y z 2 1 1 1 3 2 2 2 4 3 3 3 Though, this is essentially what data.matrix() does internally. Additionally, I've also considered: data.matrix(sample.data[-1,-1] but bizarrely, it returns: x y z 2 1 1 1 3 2 2 2 4 3 3 3 That is a numeric matrix: str(data.matrix(sample.data[-1, -1])) int [1:3, 1:3] 1 2 3 1 2 3 1 2 3 - attr(*, dimnames)=List of 2 ..$ : chr [1:3] 2 3 4 ..$ : chr [1:3] x y z HTH, Marc Thanks, Andrew On 5/16/07, Marc Schwartz [EMAIL PROTECTED] wrote: On Wed, 2007-05-16 at 08:10 -0400, Andrew Yee wrote: I have the following csv file: name,x,y,z category,delta,gamma,epsilon a,1,2,3 b,4,5,6 c,7,8,9 I'd like to create a numeric matrix of just the numbers in this csv dataset. I've tried the following program: sample.data - read.csv(sample.csv) numerical.data - as.matrix (sample.data[-1,-1]) However, print(numerical.data ) returns what appears to be a matrix of characters: x y z 2 1 2 3 3 4 5 6 4 7 8 9 How do I force it to be numbers rather than characters? Thanks, Andrew The problem is that you have two rows which contain alpha entries. The first row is treated as the header, but the second row is treated as actual data, thus overriding the numeric values in the subsequent rows. You could use: as.numeric(as.matrix(sample.data [-1, -1])) to coerce the matrix to numeric, or if you don't need the alpha entries, you could modify the read.csv() call to something like: read.csv(sample.csv, header = FALSE, skip = 2, row.names = 1, col.names = c(name, x, y, z) This will skip the first two rows, set the first column to the row names and give you a data frame with numeric columns, which in most cases can be treated as a numeric matrix and/or you could explicitly coerce it to one. HTH, Marc Schwartz [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and
Re: [R] Installing SJava - problem
Thank you for your help. Does that mean I am unable to create a java program that runs on windows and evaluates R expressions within java code? Prof Brian Ripley wrote: On Wed, 16 May 2007, mister_bluesman wrote: Hi there. I am trying to install SJava on my windows xp machine. I downloaded the windows source file SJava_0.69-0.tar.gz from the web site http://www.omegahat.org/RSJava/ I have folloed the XP command line instructions as directed in the table underneath the download link: cd $RHOME/src/library unzip SJava_0.69-0.zip cd SJava ./configure.win $RHOME cd $RHOME/src/gnuwin32 make pkg-SJava I reconfigured the configure.win file so that the correct java sdk was referred to. Not a problem. However, when I try to type in make pkg-SJava i get the following error: C:\Program Files\R\R-2.5.0\src\gnuwin32make pkg-SJava 'make' is not recognized as an internal or external command, operable program or batch file. What do I need to do to rectify this? Follow the instructions in 'R Installation and Administration' for building source packages on Windows. I don't know if SJava is currently buildable on Windows, not least because it requires an out-of-date Java (it objects to Java 6 aka 1.6.0), at least on Linux (and on x86_64 Linux no earlier Java is viable). -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- View this message in context: http://www.nabble.com/Installing-SJava---problem-tf3764923.html#a10644239 Sent from the R help mailing list archive at Nabble.com. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] more woes trying to convert a data.frame to a numerical matrix
On Wed, 2007-05-16 at 11:29 -0400, Liaw, Andy wrote: I think this might be a bit more straight forward: R mat - do.call(cbind, scan(clipboard, what=list(NULL, 0, 0, 0), sep=,, skip=2)) Read 3 records R mat [,1] [,2] [,3] [1,]123 [2,]456 [3,]789 Andy snip Good approach Andy and with a large source file should also be faster I would think. Regards, Marc __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] urca package - summary method -
Hi
I am using the package urca and I am interested about the KPSS test.
That works fine except the method summary did not work in
the script,
only when it is typed direct in the console the results are
shown( not a
source file).
Hello,
which version of urca are using? The problem you mentioned has been
fixed in November last last year (see R-Help, there is an extensive
thread about the explicit loading of methods as well as the Changelog of
urca:
2006-11-04 Dr. Bernhard Pfaff [EMAIL PROTECTED]
* NAMESPACE: import(methods) inserted
).
I have checked again with:
file kpsstest.R
library(urca)
data(nporg)
gnp - na.omit(nporg[, gnp.r])
gnp.l - log(gnp)
kpss.gnp - ur.kpss(gnp.l, type=tau, lags=short)
summary(kpss.gnp)
summary(ur.kpss(gnp.l, type=tau, lags=short))
end file
and
R CMD BATCH --no-restore kpsstest.R
which runs flawlessly. Hence, a simple update of 'urca' should solve
your problem.
Best,
Bernhard
Is there any problem with these method ?
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*
Confidentiality Note: The information contained in this mess...{{dropped}}
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Re: [R] how to reduce in a grid ?
Try this: ## Dataset mydata - data.frame(x=sample(1:8,10,replace=T),y=sample(1:9,10,replace=T), var1=rnorm(10),var2=rnorm(10)) ## Put x and y in bins xcut - cut(mydata$x,seq(0,8,2)) ycut - cut(mydata$y,seq(0,9,3)) ## Create table tapply(mydata$var1,list(ycut,xcut),mean) - Norma On 5/16/07, Norbert [EMAIL PROTECTED] wrote: hi dear R users, I'm a newbie with R and excuse me if my question is stupid ... but i've read lot of documentation and I don't know how to do. I have a dataset like xyvar1var2 241050 3 32070 325068 45 3442 531023 782342 7 32334 [...] And I need to produce grids like : y\x]0-2]]2-4]]4-6]]6-8] ]0-3] ]3-6]means of corresponding values for var1 (or var2) ]6-9] but I don't find any example in advance, lot of thanks for your help js _ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Installing SJava - problem
On Wed, 16 May 2007, mister_bluesman wrote: Thank you for your help. Does that mean I am unable to create a java program that runs on windows and evaluates R expressions within java code? No, because a) I said 'I don't know': it might work but I thought you ought to be aware of the issue before doing a lot of work. b) there are other interfaces, e.g. rJava and friends. Prof Brian Ripley wrote: On Wed, 16 May 2007, mister_bluesman wrote: Hi there. I am trying to install SJava on my windows xp machine. I downloaded the windows source file SJava_0.69-0.tar.gz from the web site http://www.omegahat.org/RSJava/ I have folloed the XP command line instructions as directed in the table underneath the download link: cd $RHOME/src/library unzip SJava_0.69-0.zip cd SJava ./configure.win $RHOME cd $RHOME/src/gnuwin32 make pkg-SJava I reconfigured the configure.win file so that the correct java sdk was referred to. Not a problem. However, when I try to type in make pkg-SJava i get the following error: C:\Program Files\R\R-2.5.0\src\gnuwin32make pkg-SJava 'make' is not recognized as an internal or external command, operable program or batch file. What do I need to do to rectify this? Follow the instructions in 'R Installation and Administration' for building source packages on Windows. I don't know if SJava is currently buildable on Windows, not least because it requires an out-of-date Java (it objects to Java 6 aka 1.6.0), at least on Linux (and on x86_64 Linux no earlier Java is viable). -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html 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 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Installing SJava - problem
Thank you for your help. Does that mean I am unable to create a java program that runs on windows and evaluates R expressions within java code? mister_bluesman wrote: Hi there. I am trying to install SJava on my windows xp machine. I downloaded the windows source file SJava_0.69-0.tar.gz from the web site http://www.omegahat.org/RSJava/ I have folloed the XP command line instructions as directed in the table underneath the download link: cd $RHOME/src/library unzip SJava_0.69-0.zip cd SJava ./configure.win $RHOME cd $RHOME/src/gnuwin32 make pkg-SJava I reconfigured the configure.win file so that the correct java sdk was referred to. Not a problem. However, when I try to type in make pkg-SJava i get the following error: C:\Program Files\R\R-2.5.0\src\gnuwin32make pkg-SJava 'make' is not recognized as an internal or external command, operable program or batch file. What do I need to do to rectify this? Thanks -- View this message in context: http://www.nabble.com/Installing-SJava---problem-tf3764923.html#a10644264 Sent from the R help mailing list archive at Nabble.com. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] substitute x for pattern in a list, while preservign list structure. lapply, gsub, list...?
I am experimenting with some of the common r functions.
I had a question re:using gsub (or some similar functions) on the contents of
a list.
I want to design a function that looks at everything contained din a list,
and anytime it finds the text string pattern replace it with x. I also
wish to preserve the structure of the original list. What is a good way to
accomplish this?
I tried :
a = matrix(data=c(23,45,'red',78),nrow=2)
b = c('red','green',1,2,3)
d = data.frame( test1=c(223,445,'red',78,56) , test2= c('red',NA,NA,NA,NA) )
e= list(a,b,d)
list1 = list(a,b,d,e)
list2 = lapply(list1,function(list)(gsub(red,green,list)))
str(list1)
str(list2)
but the structue fo the list changed.
-
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[R] Unable to compile Matrix package
After upgrading to 2.5.0 under freebsd 6.2 I updated all the add-on packages in an R session via update.packages(...). R was unable to install the Matrix package because it couldn't find the package. Therefore I downloaded the *.tar.gz from the CRAN site and issued R CMD INSTALL Matrix_0.99875-1.tar.gz but the comilation ended in an error (see the complete attached r_log.tar.gz) cc -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/lib/R/include -I/usr/local/include -D__NO_MATH_INLINES -I../UFc cc -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/lib/R/include -I/usr/local/include -D__NO_MATH_INLINES -I../UFc ar -rucs ../COLAMD.a colamd.o colamd_global.oM ( cd Source ; make lib )M Error expanding embedded variable.M *** Error code 2M M Stop in /tmp/R.INSTALL.IuAhvE/Matrix/src/AMD.M *** Error code 1M M Stop in /tmp/R.INSTALL.IuAhvE/Matrix/src.M ERROR: compilation failed for package 'Matrix'M ** Removing '/usr/local/lib/R/library/Matrix'M NbBSD# exitMM exitM What shall I do? Ciao Vittorio __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] substitute x for pattern in a list, while preservign list structure. lapply, gsub, list...?
On Wed, 2007-05-16 at 09:25 -0700, new ruser wrote:
I am experimenting with some of the common r functions.
I had a question re:using gsub (or some similar functions) on the
contents of a list.
I want to design a function that looks at everything contained din a
list, and anytime it finds the text string pattern replace it with
x. I also wish to preserve the structure of the original list.
What is a good way to accomplish this?
I tried :
a = matrix(data=c(23,45,'red',78),nrow=2)
b = c('red','green',1,2,3)
d = data.frame( test1=c(223,445,'red',78,56) , test2=
c('red',NA,NA,NA,NA) )
e= list(a,b,d)
list1 = list(a,b,d,e)
list2 = lapply(list1,function(list)(gsub(red,green,list)))
str(list1)
str(list2)
but the structue fo the list changed.
I suspect that you will need to use rapply(), which is a recursive
version of lapply().
For example:
str(list1)
List of 4
$ : chr [1:2, 1:2] 23 45 red 78
$ : chr [1:5] red green 1 2 ...
$ :'data.frame': 5 obs. of 2 variables:
..$ test1: Factor w/ 5 levels 223,445,56,..: 1 2 5 4 3
..$ test2: Factor w/ 1 level red: 1 NA NA NA NA
$ :List of 3
..$ : chr [1:2, 1:2] 23 45 red 78
..$ : chr [1:5] red green 1 2 ...
..$ :'data.frame':5 obs. of 2 variables:
.. ..$ test1: Factor w/ 5 levels 223,445,56,..: 1 2 5 4 3
.. ..$ test2: Factor w/ 1 level red: 1 NA NA NA NA
list3 - rapply(list1, function(x) gsub(red, green, x),
how = replace)
str(list3)
List of 4
$ : chr [1:2, 1:2] 23 45 green 78
$ : chr [1:5] green green 1 2 ...
$ :List of 2
..$ test1: chr [1:5] 223 445 green 78 ...
..$ test2: chr [1:5] green NA NA NA ...
$ :List of 3
..$ : chr [1:2, 1:2] 23 45 green 78
..$ : chr [1:5] green green 1 2 ...
..$ :List of 2
.. ..$ test1: chr [1:5] 223 445 green 78 ...
.. ..$ test2: chr [1:5] green NA NA NA ...
Note however, the impact of using gsub(), which is that factors are
coerced to characters. So consider what you want the end game to be.
See ?rapply for more information.
HTH,
Marc Schwartz
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Re: [R] Unable to compile Matrix package
On 5/16/07, Vittorio De Martino [EMAIL PROTECTED] wrote: After upgrading to 2.5.0 under freebsd 6.2 I updated all the add-on packages in an R session via update.packages(...). R was unable to install the Matrix package because it couldn't find the package. Therefore I downloaded the *.tar.gz from the CRAN site and issued R CMD INSTALL Matrix_0.99875-1.tar.gz but the comilation ended in an error (see the complete attached r_log.tar.gz) cc -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/lib/R/include -I/usr/local/include -D__NO_MATH_INLINES -I../UFc cc -std=gnu99 -I/usr/local/lib/R/include -I/usr/local/lib/R/include -I/usr/local/include -D__NO_MATH_INLINES -I../UFc ar -rucs ../COLAMD.a colamd.o colamd_global.oM ( cd Source ; make lib )M Error expanding embedded variable.M *** Error code 2M M Stop in /tmp/R.INSTALL.IuAhvE/Matrix/src/AMD.M *** Error code 1M M Stop in /tmp/R.INSTALL.IuAhvE/Matrix/src.M ERROR: compilation failed for package 'Matrix'M ** Removing '/usr/local/lib/R/library/Matrix'M NbBSD# exitMM exitM What shall I do? As Duncan Murdoch once said, in extreme cases you could read the documentation. :-) The Matrix package requires that you use a version of `make' that is compatible with GNU make. Often this is called 'gmake' on BSD systems. If that is the case for you then setting the environment variable setenv MAKE gmake should work. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] read.table opening a website incl Password
Dear all, in the past I have been able to access websites with data directly. For example the following code works nicely mydata - read.table(http://www.lifetable.de/data/MPIDR/POL_2004.txt;, header=TRUE) But what happens if I need a username and password (a different site)? How do I do that? Or is it not possible to this in R? I tried something like this mydata.frame - read.table(myusr:[EMAIL PROTECTED]/adir/afile.txt) but it did not work. I'd appreciate any hints. My platform is Win32 (and I am actually running R 2.3.1, but I guess (hope!) this is not the reason. At least I checked the NEWS file whether any changes appeared since 2.3.1 which could affect this behavior). Thanks, Roland __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] lmer error confusion
Hi All. I'm trying to run a simple model from Baayan, Davidson, Bates and getting a confusing error message. Any ideas what I'm doing wrong here? # Here's the data. Subj- factor(rep(1:3,each=6)) Item- factor(rep(1:3,6)) SOA - factor(rep(0:1,3,each=3)) RT - c(466,520,502,475,494,490,516,566,577,491,544,526,484,529,539,470,511,528) priming - data.frame(cbind(Subj,Item,SOA,RT)) str(priming) 'data.frame': 18 obs. of 4 variables: $ Subj: num 1 1 1 1 1 1 2 2 2 2 ... $ Item: num 1 2 3 1 2 3 1 2 3 1 ... $ SOA : num 1 1 1 2 2 2 1 1 1 2 ... $ RT : num 466 520 502 475 494 490 516 566 577 491 ... #Here's the call taken directly from the paper priming.lmer1 - lmer(RT ~ SOA + (1 | Item) + (1 | Subj), data = priming) #Here's the error Error in rbind(Item = S4 object of class dgCMatrix, Subj = S4 object of class dgCMatrix) : cannot coerce type S4 to list vector Any idea what I'm doing wrong? sessionInfo() R version 2.5.0 (2007-04-23) i386-pc-mingw32 other attached packages: lme4 Matrix latticenlme 0.9975-13 0.99875-10.15-43.1-80 Rick DeShon [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] lmer function
On 5/16/07, Iasonas Lamprianou [EMAIL PROTECTED] wrote: Dear all, the question was if lmer can estimate the variance components correctly, although my design is very UNbalanced. Yes, lmer can handle unbalanced data and large data sets. Also, how do I find the percentage of the variance from every component? Do I have to add all the variance components and then divide each one by the total? Yes, that should do it. I enclose a short function to automate the process by extracting the information from the value of VarCorr. P.S. lmer is excellent. It can estimate large datasets where SPSS gives me error messages and says it cannot estimate them. Keep on good work friends! Thank you. It's wonderful to hear that it is helpful. The main objective in developing lmer was to be able to handle large data sets with crossed or partially crossed random effects. - Original Message From: Douglas Bates [EMAIL PROTECTED] To: Steven McKinney [EMAIL PROTECTED] Cc: Iasonas Lamprianou [EMAIL PROTECTED]; r-help@stat.math.ethz.ch Sent: Tuesday, 15 May, 2007 2:17:34 AM Subject: Re: [R] lmer function On 5/14/07, Steven McKinney [EMAIL PROTECTED] wrote: Running lme4 0.9975-13 I'm still getting the warning $ operator not defined for this S4 class, returning NULL in: x$symbolic.cor It was my mistake. I fixed the problem in the development sources long ago but I haven't uploaded a new release since doing so. I'll upload a new release next week - this is finals week for us and they seem to expect that we will do things like grade exams rather than debugging code. :-) Is there a more recent version? Is there any known problem with this warning (incorrect results etc.) ? Not really. It is a benign cut-and-paste error. If you want to fix it now look for the function printMer in the source file lme4/R/lmer.R and change the default for the symbolic.cor argument to FALSE. sessionInfo() R version 2.5.0 (2007-04-23) powerpc-apple-darwin8.9.1 locale: C attached base packages: [1] stats graphics grDevices utils datasets methods [7] base other attached packages: lme4 Matrix lattice 0.9975-13 0.9975-110.15-4 Steven McKinney Statistician Molecular Oncology and Breast Cancer Program British Columbia Cancer Research Centre email: [EMAIL PROTECTED] tel: 604-675-8000 x7561 BCCRC Molecular Oncology 675 West 10th Ave, Floor 4 Vancouver B.C. V5Z 1L3 Canada -Original Message- From: [EMAIL PROTECTED] on behalf of Douglas Bates Sent: Mon 5/14/2007 12:43 PM To: Iasonas Lamprianou Cc: r-help@stat.math.ethz.ch Subject: Re: [R] lmer function On 5/14/07, Iasonas Lamprianou [EMAIL PROTECTED] wrote: Does anyone know if the lmer function of lme4 works fine for unbalanced designs? I have the examination results of 1000 pupils on three subjects, one score every term. So, I have three scores for English (one for every term), three scores for maths etc. However, not everybody was examined in maths, not everybody was examined in English etc, but everybody was in effect examined on four subjects. I also have information abouit the school. Would this model hive the right results for the variance components? mod_3_f - lmer(SCORE ~ GENDER + (1 |ID ) + (1 | TERM) + (1 | SUBJECT) , Dataset) Linear mixed-effects model fit by REML Formula: SCORE ~ GENDER + (1 | ID) + (1 | TERM) + (1 | SUBJECT) Data: Dataset AICBIC logLik MLdeviance REMLdeviance 247882 247926 -123936 247871 247872 Random effects: Groups NameVariance Std.Dev. ID (Intercept) 5.97288 2.44395 TERM (Intercept) 5.10307 2.25900 SUBJECT (Intercept) 0.25943 0.50934 Residual 4.41673 2.10160 number of obs: 53978, groups: ID, 5695; TERM, 4; SUBJECT, 4 Fixed effects: Estimate Std. Error t value (Intercept)14.303521.15870 12.34 GENDER[T.Male] -1.017760.06885 -14.78 Correlation of Fixed Effects: Warning in x$symbolic.cor : $ operator not defined for this S4 class, returning NULL What version of the lme4 package are you using? (Use sessionInfo() to check.) I think the bug that causes that warning has been fixed in the most recent version. (Intr) GENDER[T.M] -0.023 How do I interpert the results? Do you really want to treat SUBJECT as a random effect? I think it would be more common to treat it as a fixed effect. If I understand you correctly there are only two levels of SUBJECT and these are repeatable levels. If that is the case one could model SUBJECT as a fixed effect or consider its interaction within student with the term (SUBJECT|ID). It would make sense to regard the pair of responses in maths and English for each student in each term as a multivariate response but, at present, that model cannot be fit with lmer. I would also question whether you want the TERM to be modeled with a random effect.
Re: [R] read.table opening a website incl Password
Roland Rau wrote: Dear all, in the past I have been able to access websites with data directly. For example the following code works nicely mydata - read.table(http://www.lifetable.de/data/MPIDR/POL_2004.txt;, header=TRUE) But what happens if I need a username and password (a different site)? How do I do that? Or is it not possible to this in R? I tried something like this mydata.frame - read.table(myusr:[EMAIL PROTECTED]/adir/afile.txt) but it did not work. I'd appreciate any hints. My platform is Win32 (and I am actually running R 2.3.1, but I guess (hope!) this is not the reason. At least I checked the NEWS file whether any changes appeared since 2.3.1 which could affect this behavior). In what way did it not work? The following seems to work for me: read.table(ftp://myusr:[EMAIL PROTECTED]/mydir/test.dat) Thanks, Roland __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Chuck Cleland, Ph.D. NDRI, Inc. 71 West 23rd Street, 8th floor New York, NY 10010 tel: (212) 845-4495 (Tu, Th) tel: (732) 512-0171 (M, W, F) fax: (917) 438-0894 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] lmer error confusion
On 5/16/07, Rick DeShon [EMAIL PROTECTED] wrote: Hi All. I'm trying to run a simple model from Baayan, Davidson, Bates and getting a confusing error message. Any ideas what I'm doing wrong here? # Here's the data. Subj- factor(rep(1:3,each=6)) Item- factor(rep(1:3,6)) SOA - factor(rep(0:1,3,each=3)) RT - c(466,520,502,475,494,490,516,566,577,491,544,526,484,529,539,470,511,528) priming - data.frame(cbind(Subj,Item,SOA,RT)) str(priming) 'data.frame': 18 obs. of 4 variables: $ Subj: num 1 1 1 1 1 1 2 2 2 2 ... $ Item: num 1 2 3 1 2 3 1 2 3 1 ... $ SOA : num 1 1 1 2 2 2 1 1 1 2 ... $ RT : num 466 520 502 475 494 490 516 566 577 491 ... #Here's the call taken directly from the paper priming.lmer1 - lmer(RT ~ SOA + (1 | Item) + (1 | Subj), data = priming) #Here's the error Error in rbind(Item = S4 object of class dgCMatrix, Subj = S4 object of class dgCMatrix) : cannot coerce type S4 to list vector Any idea what I'm doing wrong? sessionInfo() R version 2.5.0 (2007-04-23) i386-pc-mingw32 other attached packages: lme4 Matrix latticenlme 0.9975-13 0.99875-10.15-43.1-80 It's a version skew problem (and thanks for including the sessionInfo() output that makes it possible to detect this). Changes were made in version 0.99875-0 and later of the Matrix package that require a new version of the lme4 package. Please install version 0.99875-0 or later of lme4. However, while we are discussing this example, notice that using the cbind inside the call to data.frame causes the factors to become numeric variables. That is undesirable. In this case it is benign but it could be harmful. A better approach is simply to give the variables and their names in the call data.frame. Also, the sequence factor(rep(...)) can be written better as a call to the underutilized function gl. priming - data.frame(Subj = gl(3,6), Item = gl(3,1,18), SOA = gl(2,3,18,labels = 0:1), + RT = c(466,520,502,475,494,490,516,566,577,491,544,526,484,529,539,470,511,528)) str(priming) 'data.frame': 18 obs. of 4 variables: $ Subj: Factor w/ 3 levels 1,2,3: 1 1 1 1 1 1 2 2 2 2 ... $ Item: Factor w/ 3 levels 1,2,3: 1 2 3 1 2 3 1 2 3 1 ... $ SOA : Factor w/ 2 levels 0,1: 1 1 1 2 2 2 1 1 1 2 ... $ RT : num 466 520 502 475 494 490 516 566 577 491 ... lmer2(RT ~ SOA + (1|Subj) + (1|Item), priming) Linear mixed-effects model fit by REML Formula: RT ~ SOA + (1 | Subj) + (1 | Item) Data: priming AIC BIC logLik MLdeviance REMLdeviance 149.4 153 -70.72 154.4141.4 Random effects: Groups NameVariance Std.Dev. Subj (Intercept) 499.37 22.347 Item (Intercept) 607.80 24.654 Residual 137.35 11.719 Number of obs: 18, groups: Subj, 3; Item, 3 Fixed effects: Estimate Std. Error t value (Intercept) 522.111 19.604 26.633 SOA1 -18.889 5.525 -3.419 Correlation of Fixed Effects: (Intr) SOA1 -0.141 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] substitute x for pattern in a list, while preservign list structure. lapply, gsub, list...?
On 5/16/07, Marc Schwartz [EMAIL PROTECTED] wrote:
On Wed, 2007-05-16 at 09:25 -0700, new ruser wrote:
I am experimenting with some of the common r functions.
I had a question re:using gsub (or some similar functions) on the
contents of a list.
I want to design a function that looks at everything contained din a
list, and anytime it finds the text string pattern replace it with
x. I also wish to preserve the structure of the original list.
What is a good way to accomplish this?
I tried :
a = matrix(data=c(23,45,'red',78),nrow=2)
b = c('red','green',1,2,3)
d = data.frame( test1=c(223,445,'red',78,56) , test2=
c('red',NA,NA,NA,NA) )
e= list(a,b,d)
list1 = list(a,b,d,e)
list2 = lapply(list1,function(list)(gsub(red,green,list)))
str(list1)
str(list2)
but the structue fo the list changed.
I suspect that you will need to use rapply(), which is a recursive
version of lapply().
For example:
str(list1)
List of 4
$ : chr [1:2, 1:2] 23 45 red 78
$ : chr [1:5] red green 1 2 ...
$ :'data.frame': 5 obs. of 2 variables:
..$ test1: Factor w/ 5 levels 223,445,56,..: 1 2 5 4 3
..$ test2: Factor w/ 1 level red: 1 NA NA NA NA
$ :List of 3
..$ : chr [1:2, 1:2] 23 45 red 78
..$ : chr [1:5] red green 1 2 ...
..$ :'data.frame':5 obs. of 2 variables:
.. ..$ test1: Factor w/ 5 levels 223,445,56,..: 1 2 5 4 3
.. ..$ test2: Factor w/ 1 level red: 1 NA NA NA NA
list3 - rapply(list1, function(x) gsub(red, green, x),
how = replace)
str(list3)
List of 4
$ : chr [1:2, 1:2] 23 45 green 78
$ : chr [1:5] green green 1 2 ...
$ :List of 2
..$ test1: chr [1:5] 223 445 green 78 ...
..$ test2: chr [1:5] green NA NA NA ...
$ :List of 3
..$ : chr [1:2, 1:2] 23 45 green 78
..$ : chr [1:5] green green 1 2 ...
..$ :List of 2
.. ..$ test1: chr [1:5] 223 445 green 78 ...
.. ..$ test2: chr [1:5] green NA NA NA ...
Note however, the impact of using gsub(), which is that factors are
coerced to characters. So consider what you want the end game to be.
See ?rapply for more information.
Also note that from your str's above it appears that data.frames do not
survive rapply but rather are changed to plain lists. I don't know whether
that is intentional on the part of the developers or not.
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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] read.table opening a website incl Password
On Wed, 16 May 2007, Roland Rau wrote: Dear all, in the past I have been able to access websites with data directly. For example the following code works nicely mydata - read.table(http://www.lifetable.de/data/MPIDR/POL_2004.txt;, header=TRUE) But what happens if I need a username and password (a different site)? How do I do that? Or is it not possible to this in R? I tried something like this mydata.frame - read.table(myusr:[EMAIL PROTECTED]/adir/afile.txt) but it did not work. Well, it could not. You need ftp:// or http:// for this to be a URL. This ought to work for ftp:, but AFAIK not for http:. You could always try --internet2: if it works in IE, it will probably also work in R. I'd appreciate any hints. My platform is Win32 (and I am actually running R 2.3.1, but I guess (hope!) this is not the reason. At least I checked the NEWS file whether any changes appeared since 2.3.1 which could affect this behavior). Thanks, Roland __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] read.table opening a website incl Password
Chuck, Roland is trying to read from a web site instead of a ftp site. I have also gotten this to work: read.table(ftp://myusr:[EMAIL PROTECTED]/mydir/test.dat) But when I try to do the same thing from the SEC's ftp site I get an error, so beyond R, there may be some internet settings that need to be fiddled with. Maybe I can tag onto Roland's question and ask for hints on what configuration options are available? Thanks, Roger -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Chuck Cleland Sent: Wednesday, May 16, 2007 1:08 PM To: Roland Rau Cc: r-help@stat.math.ethz.ch Subject: Re: [R] read.table opening a website incl Password Roland Rau wrote: Dear all, in the past I have been able to access websites with data directly. For example the following code works nicely mydata - read.table(http://www.lifetable.de/data/MPIDR/POL_2004.txt;, header=TRUE) But what happens if I need a username and password (a different site)? How do I do that? Or is it not possible to this in R? I tried something like this mydata.frame - read.table(myusr:[EMAIL PROTECTED]/adir/afile.txt) but it did not work. I'd appreciate any hints. My platform is Win32 (and I am actually running R 2.3.1, but I guess (hope!) this is not the reason. At least I checked the NEWS file whether any changes appeared since 2.3.1 which could affect this behavior). In what way did it not work? The following seems to work for me: read.table(ftp://myusr:[EMAIL PROTECTED]/mydir/test.dat) Thanks, Roland __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Chuck Cleland, Ph.D. NDRI, Inc. 71 West 23rd Street, 8th floor New York, NY 10010 tel: (212) 845-4495 (Tu, Th) tel: (732) 512-0171 (M, W, F) fax: (917) 438-0894 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. ** * This message is for the named person's use only. It may contain confidential, proprietary or legally privileged information. No right to confidential or privileged treatment of this message is waived or lost by any error in transmission. If you have received this message in error, please immediately notify the sender by e-mail, delete the message and all copies from your system and destroy any hard copies. You must not, directly or indirectly, use, disclose, distribute, print or copy any part of this message if you are not the intended recipient. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] substitute x for pattern in a list, while preservign list structure. lapply, gsub, list...?
On Wed, 2007-05-16 at 13:18 -0400, Gabor Grothendieck wrote:
On 5/16/07, Marc Schwartz [EMAIL PROTECTED] wrote:
On Wed, 2007-05-16 at 09:25 -0700, new ruser wrote:
I am experimenting with some of the common r functions.
I had a question re:using gsub (or some similar functions) on the
contents of a list.
I want to design a function that looks at everything contained din a
list, and anytime it finds the text string pattern replace it with
x. I also wish to preserve the structure of the original list.
What is a good way to accomplish this?
I tried :
a = matrix(data=c(23,45,'red',78),nrow=2)
b = c('red','green',1,2,3)
d = data.frame( test1=c(223,445,'red',78,56) , test2=
c('red',NA,NA,NA,NA) )
e= list(a,b,d)
list1 = list(a,b,d,e)
list2 = lapply(list1,function(list)(gsub(red,green,list)))
str(list1)
str(list2)
but the structue fo the list changed.
I suspect that you will need to use rapply(), which is a recursive
version of lapply().
For example:
str(list1)
List of 4
$ : chr [1:2, 1:2] 23 45 red 78
$ : chr [1:5] red green 1 2 ...
$ :'data.frame': 5 obs. of 2 variables:
..$ test1: Factor w/ 5 levels 223,445,56,..: 1 2 5 4 3
..$ test2: Factor w/ 1 level red: 1 NA NA NA NA
$ :List of 3
..$ : chr [1:2, 1:2] 23 45 red 78
..$ : chr [1:5] red green 1 2 ...
..$ :'data.frame':5 obs. of 2 variables:
.. ..$ test1: Factor w/ 5 levels 223,445,56,..: 1 2 5 4 3
.. ..$ test2: Factor w/ 1 level red: 1 NA NA NA NA
list3 - rapply(list1, function(x) gsub(red, green, x),
how = replace)
str(list3)
List of 4
$ : chr [1:2, 1:2] 23 45 green 78
$ : chr [1:5] green green 1 2 ...
$ :List of 2
..$ test1: chr [1:5] 223 445 green 78 ...
..$ test2: chr [1:5] green NA NA NA ...
$ :List of 3
..$ : chr [1:2, 1:2] 23 45 green 78
..$ : chr [1:5] green green 1 2 ...
..$ :List of 2
.. ..$ test1: chr [1:5] 223 445 green 78 ...
.. ..$ test2: chr [1:5] green NA NA NA ...
Note however, the impact of using gsub(), which is that factors are
coerced to characters. So consider what you want the end game to be.
See ?rapply for more information.
Also note that from your str's above it appears that data.frames do not
survive rapply but rather are changed to plain lists. I don't know whether
that is intentional on the part of the developers or not.
Right, which I noted and would be consistent with the behavior of
lapply() on data frames, which also simplifies the result to a normal
list.
Since rapply() is documented to be recursive version of lapply(), the
result above would be expected, at least implicitly.
Thanks for raising the point Gabor.
Regards,
Marc
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Re: [R] read.table opening a website incl Password
Dear all, so far I tried various things but I did not really succeed: - starting R with --internet2 - using url() - using read.table(http://myusr:[EMAIL PROTECTED]/adir/afile.txt) I just have an idea what the problem could be for me: The username is actually an email address. So the '@'-character has some ambiguous meaning in my setting. Sorry that I did not think of that beforehand. Thank you very much for your help, Roland Prof Brian Ripley wrote: On Wed, 16 May 2007, Roland Rau wrote: Dear all, in the past I have been able to access websites with data directly. For example the following code works nicely mydata - read.table(http://www.lifetable.de/data/MPIDR/POL_2004.txt;, header=TRUE) But what happens if I need a username and password (a different site)? How do I do that? Or is it not possible to this in R? I tried something like this mydata.frame - read.table(myusr:[EMAIL PROTECTED]/adir/afile.txt) but it did not work. Well, it could not. You need ftp:// or http:// for this to be a URL. This ought to work for ftp:, but AFAIK not for http:. You could always try --internet2: if it works in IE, it will probably also work in R. I'd appreciate any hints. My platform is Win32 (and I am actually running R 2.3.1, but I guess (hope!) this is not the reason. At least I checked the NEWS file whether any changes appeared since 2.3.1 which could affect this behavior). Thanks, Roland __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] substitute x for pattern in a list, while preservign list structure. lapply, gsub, list...?
Here is a recursive function you could try. Here f has been defined only to
convert character variables. Modify to suit.
recurse - function(x, f) {
if (length(x) == 0) return(x)
if (is.list(x)) for(i in seq_along(x)) x[[i]] - recurse(x[[i]], f)
else x - f(x)
x
}
f - function(x) if (mode(x) == character) gsub(red, green, x) else x
list4 - recurse(list1, f)
On 5/16/07, new ruser [EMAIL PROTECTED] wrote:
I am experimenting with some of the common r functions.
I had a question re:using gsub (or some similar functions) on the contents
of a list.
I want to design a function that looks at everything contained din a list,
and anytime it finds the text string pattern replace it with x. I also
wish to preserve the structure of the original list. What is a good way to
accomplish this?
I tried :
a = matrix(data=c(23,45,'red',78),nrow=2)
b = c('red','green',1,2,3)
d = data.frame( test1=c(223,445,'red',78,56) , test2= c('red',NA,NA,NA,NA) )
e= list(a,b,d)
list1 = list(a,b,d,e)
list2 = lapply(list1,function(list)(gsub(red,green,list)))
str(list1)
str(list2)
but the structue fo the list changed.
-
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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.
[R] questions on package of KEGG
Dear list members: Once I know a KEGG pathway identifier, how can I check all its direct children identifiers? you know, I could use GOMFCHILDREN or GOCCCHILDREN to check the children terms for a specific GO term, but I don't know how to do it in the same way for KEGG in R? Many Thanks!! Hua __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Abline in dotplot
Hello, I have trouble adding an abline to a dotplot() from lattice package. For example, I would like to draw a line at x=3: library(lattice) x-1:5 names(x) - c(a, b, c, d, e) dotplot(sample(x)) panel.abline(v=3) Produces a line on the left hand side of the origin. What would be a correct way to do this? Thank you, Valeria V. Thompson Applied Statistics Group Mathematics Computing Technology The Boeing Company (425) 373-2740 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Abline in dotplot
Thompson, Valeria V said the following on 5/16/2007 12:04 PM:
Hello,
I have trouble adding an abline to a dotplot() from lattice package.
For example, I would like to draw a line at x=3:
library(lattice)
x-1:5
names(x) - c(a, b, c, d, e)
dotplot(sample(x))
panel.abline(v=3)
Produces a line on the left hand side of the origin. What would be a
correct way to do this?
Thank you,
Valeria V. Thompson
Applied Statistics Group
Mathematics Computing Technology
The Boeing Company
(425) 373-2740
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Try this instead:
library(lattice)
x-1:5
names(x) - c(a, b, c, d, e)
dotplot(sample(x),
panel = function(...) {
panel.dotplot(...)
panel.abline(v=3)
})
HTH,
--sundar
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Re: [R] Abline in dotplot
On 5/16/07, Thompson, Valeria V [EMAIL PROTECTED] wrote:
Hello,
I have trouble adding an abline to a dotplot() from lattice package.
For example, I would like to draw a line at x=3:
library(lattice)
x-1:5
names(x) - c(a, b, c, d, e)
dotplot(sample(x))
panel.abline(v=3)
Produces a line on the left hand side of the origin. What would be a
correct way to do this?
This would be one:
dotplot(sample(x),
panel = function(...) {
panel.abline(v=3)
panel.dotplot(...)
})
Your approach wouldn't generalize to the case where you have more than
one panel.
-Deepayan
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Re: [R] questions on package of KEGG
Li, Hua [EMAIL PROTECTED] writes: Dear list members: Once I know a KEGG pathway identifier, how can I check all its direct children identifiers? you know, I could use GOMFCHILDREN or GOCCCHILDREN to check the children terms for a specific GO term, but I don't know how to do it in the same way for KEGG in R? Many Thanks!! Hua I think you should ask this question on the bioconductor list. http://www.bioconductor.org/docs/postingGuide.html + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center http://bioconductor.org __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Best way to utilize R graphing capabilities from other program
I am working on an open source program to be used for model selection and evalution. I would like to utilize the graphical capabilities of R to generate plots that I would then display in my software program. What is the best way to go about this? I have looked at Rserve and also looked at re-compiling R as a shared library. I am looking for something that can be distributed internally with my program (so that the user does not need to install R separately) if possible, and also something relatively small. Any suggestions on how to proceed? Good tutorials on this subject? Thanks for any advice Take the Internet to Go: Yahoo!Go puts the Internet in your pocket: mail, news, photos more. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Re-sizing R graphics for Sweave
I am generating a single graphic containing about 31 Boxplots; the issue I am having is that not all the labels (3 characters each) are shown. Interactively, within a R session, I can simply re-size the graphics window and all the labels appear. But, what can I do non-interactively to have all the labels displayed when using Sweave? Can the labels be rotated 90-degrees; would this help? I guess one possibility would be to number the boxplots, but this may not help either. My thought would be to force the graphic to be a certain width, but I can't find how to do this. I have searched and can not find a way to do this automatically — I could not find anything in the R Graphics book by Paul Murrell that pointed me in the right direction either. Thank you, Tom -- Thomas E Adams National Weather Service Ohio River Forecast Center 1901 South State Route 134 Wilmington, OH 45177 EMAIL: [EMAIL PROTECTED] VOICE: 937-383-0528 FAX:937-383-0033 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] suppress plot w/ ewma function from qcc pkg
Hi, I've been searching for a solution to this but have come up empty. I would like to suppress the plot creation when using the ewma function in the qcc package. Normally it's just plot = FALSE, but the ewma function doesn't have this option. Anything I'm missing or a work around? Many thanks, Brian Francis Statistician II Charles River Laboratories __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Re-sizing R graphics for Sweave
On Wed, 2007-05-16 at 16:34 -0400, Thomas Adams wrote: I am generating a single graphic containing about 31 Boxplots; the issue I am having is that not all the labels (3 characters each) are shown. Interactively, within a R session, I can simply re-size the graphics window and all the labels appear. But, what can I do non-interactively to have all the labels displayed when using Sweave? Can the labels be rotated 90-degrees; would this help? I guess one possibility would be to number the boxplots, but this may not help either. My thought would be to force the graphic to be a certain width, but I can't find how to do this. I have searched and can not find a way to do this automatically — I could not find anything in the R Graphics book by Paul Murrell that pointed me in the right direction either. Thank you, Tom Presuming that you are using a 'figure' chunk in your .Rnw file, you can use: fig=TRUE,height=8,width=6.5= Your R code here... @ which will define the dimensions of your plot output file as 8 x 6.5. Adjust these as you require. See ?RweaveLatex You may also need to adjust the size of the titles, etc. in the plots, which you can do with the various 'cex' family of parameters. See ?par for more information there. HTH, Marc Schwartz __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Re-sizing R graphics for Sweave
Marc, That did it! Thank you so much for your help… Regards, Tom Marc Schwartz wrote: On Wed, 2007-05-16 at 16:34 -0400, Thomas Adams wrote: I am generating a single graphic containing about 31 Boxplots; the issue I am having is that not all the labels (3 characters each) are shown. Interactively, within a R session, I can simply re-size the graphics window and all the labels appear. But, what can I do non-interactively to have all the labels displayed when using Sweave? Can the labels be rotated 90-degrees; would this help? I guess one possibility would be to number the boxplots, but this may not help either. My thought would be to force the graphic to be a certain width, but I can't find how to do this. I have searched and can not find a way to do this automatically — I could not find anything in the R Graphics book by Paul Murrell that pointed me in the right direction either. Thank you, Tom Presuming that you are using a 'figure' chunk in your .Rnw file, you can use: fig=TRUE,height=8,width=6.5= Your R code here... @ which will define the dimensions of your plot output file as 8 x 6.5. Adjust these as you require. See ?RweaveLatex You may also need to adjust the size of the titles, etc. in the plots, which you can do with the various 'cex' family of parameters. See ?par for more information there. HTH, Marc Schwartz -- Thomas E Adams National Weather Service Ohio River Forecast Center 1901 South State Route 134 Wilmington, OH 45177 EMAIL: [EMAIL PROTECTED] VOICE: 937-383-0528 FAX:937-383-0033 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] converting a data frame to ts objects
On 5/16/07, Gabor Grothendieck [EMAIL PROTECTED] wrote: On 5/16/07, fatih ozgul [EMAIL PROTECTED] wrote: Dear R-ians I have a data frame like Person_id Date/timeCount - -- --- 123 20 May 1999 1 123 21 May 1999 3 222 1 Feb 2000 2 222 3 Feb 2000 4 I want to create ts objects for each person_id (i.e. 123 and 222). Time series frequency can be in months and all starting from the same date (i.e. May 1999). Rather than manually creating sum of counts for each month and creating ts objects manually for each persons, Is there a function for creating ts objects automatically from such data? Try this: # read in as data frame and fix up date Lines.raw - Person_id Date/time Count 123 20 May 1999 1 123 21 May 1999 3 222 1 Feb 2000 2 222 3 Feb 2000 4 library(zoo) DF - read.table(textConnection(Lines.raw), skip = 1, col.names = c(Person_id, d, b, Y, Count)) DF$Date.time - as.Date(paste(DF$d, DF$b, DF$Y), %d %b %Y) # aggregate counts over months, series and convert to ts f - function(DF) aggregate(zoo(DF$Count), as.yearmon(DF$Date.time), sum) z - do.call(merge.zoo, lapply(split(DF, DF$Person_id), f)) frequency(z) - 12 as.ts(z) A slight simplification based on zoo 1.3-1 (which just appeared on CRAN) is the following. It converts the month and year columns directly into class yearmon eliminating the intermediate step of going via Date class. Its the same number of lines but a couple of the lines are now simpler. # read in as data frame and fix up date Lines.raw - Person_id Date/time Count 123 20 May 1999 1 123 21 May 1999 3 222 1 Feb 2000 2 222 3 Feb 2000 4 library(zoo) DF - read.table(textConnection(Lines.raw), skip = 1, col.names = c(Person_id, d, b, Y, Count)) DF$yearmon - as.yearmon(paste(DF$b, DF$Y), %b %Y) # aggregate counts over months, merge series and convert to ts ag - function(DF) aggregate(zoo(DF$Count), DF$yearmon, sum) z - do.call(merge.zoo, lapply(split(DF, DF$Person_id), ag)) frequency(z) - 12 as.ts(z) __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] [R-pkgs] New version 0.9-7 of lars package
I uploaded a new version of the lars package to CRAN, which incorporates some nontrivial changes. 1) lars now has normalize and intercept options, both defaulted to TRUE, which means the variables are scaled to have unit euclidean norm, and an intercept is included in the model. Either or both can be set to FALSE. 2) lars has an additional type = stepwise option; now the list is type=c(lasso, lar, forward.stagewise,stepwise) This was included because it is trivial to implement, and useful for comparisons. Stepwise is a version of forward stepwise regression, where the variable to enter is the one most correlated with the residuals. This is not necessarily the same as the forward stepwise implemented as part of step() in R, where the variable entered is the one that, when included, reduces the RSS the most. 3) a method for summary() has been included, which gives an anova-type summary of the sequence of steps. 4) The plot method for lars defaults to plotting coefficients against the relative L1 norm of the coefficients. This was not done correctly in general for type lar and forward.stagewise, since the L1 norm does not change smoothly if coefficients pass through zero. This has been fixed. 5) A smalll number of of other changes have been made, some in response to email messages from users. Thanks to Yann-Ael Le Borgne for pointing out the problem in (4) and proposing a solution, and to Lukas Meier for reporting some bugs. Please let me know of any new problems, or old ones not yet repaired. Trevor Hastie Trevor Hastie [EMAIL PROTECTED] Professor Chair, Department of Statistics, Stanford University Phone: (650) 725-2231 (Statistics) Fax: (650) 725-8977 (650) 498-5233 (Biostatistics) Fax: (650) 725-6951 URL: http://www-stat.stanford.edu/~hastie address: room 104, Department of Statistics, Sequoia Hall 390 Serra Mall, Stanford University, CA 94305-4065 ___ R-packages mailing list [EMAIL PROTECTED] https://stat.ethz.ch/mailman/listinfo/r-packages __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Design matrix question
Hi useRs, Perhaps I am having a senior moment? I have a nested variable situation to model, toy example: df - data.frame(A = factor(c(a, a, x, x), levels = c(x, a)), + B = factor(c(b, x, x, x), levels = c(x, b))) df A B 1 a b 2 a x 3 x x 4 x x So of course the full design matrix is singular model.matrix(~ A * B, df) (Intercept) Aa Bb Aa:Bb 1 1 1 1 1 2 1 1 0 0 3 1 0 0 0 4 1 0 0 0 attr(,assign) [1] 0 1 2 3 attr(,contrasts) attr(,contrasts)$A [1] contr.treatment attr(,contrasts)$B [1] contr.treatment I'd like not to have the B term main effect in the model model.matrix(~ A * B - B, df) (Intercept) Aa Ax:Bb Aa:Bb 1 1 1 0 1 2 1 1 0 0 3 1 0 0 0 4 1 0 0 0 attr(,assign) [1] 0 1 2 2 attr(,contrasts) attr(,contrasts)$A [1] contr.treatment attr(,contrasts)$B [1] contr.treatment How do I get model.matrix to not add that column of zeroes? Why does model.matrix add that column of zeroes? Is this a bug, or a senior moment? Steven McKinney Statistician Molecular Oncology and Breast Cancer Program British Columbia Cancer Research Centre email: [EMAIL PROTECTED] tel: 604-675-8000 x7561 BCCRC Molecular Oncology 675 West 10th Ave, Floor 4 Vancouver B.C. V5Z 1L3 Canada __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Design matrix question
with(df, interaction(A, B)) [1] a.b a.x x.x x.x Levels: x.x a.x x.b a.b A.B - factor(with(df, interaction(A, B))) A.B [1] a.b a.x x.x x.x Levels: x.x a.x a.b model.matrix(~ A.B, df) (Intercept) A.B[T.a.x] A.B[T.a.b] 1 1 0 1 2 1 1 0 3 1 0 0 4 1 0 0 attr(,assign) [1] 0 1 1 attr(,contrasts) attr(,contrasts)$A.B [1] contr.Treatment __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] MICE for Cox model
R-helpers:
I have a dataset that has 168 subjects and 12 variables. Some of the
variables have missing data and I want to use the multiple imputation
capabilities of the mice package to address the missing data. Given
that mice only supports linear models and generalized linear models (via
the lm.mids and glm.mids functions) and that I need to fit Cox models, I
followed the previous suggestion of John Fox and have created my own
function cox.mids to use coxph to fit models to the imputed datasets.
(http://tolstoy.newcastle.edu.au/R/help/06/03/22295.html)
The function I created is:
cox.mids - function (formula, data, ...)
{
call - match.call()
if (!is.mids(data))
stop(The data must have class mids)
analyses - as.list(1:data$m)
for (i in 1:data$m) {
data.i - complete(data, i)
analyses[[i]] - coxph(formula, data = data.i, ...)
}
object - list(call = call, call1 = data$call, nmis = data$nmis,
analyses = analyses)
oldClass(object) - c(mira, coxph)
return(object)
}
The problem that I encounter occurs when I try to use the pool
function to pool the fitted models into one general model. Here is some
code that reproduces the error using the pbc dataset.
d - pbc[,c('time','status','age','sex','hepmeg','platelet', 'trt',
'trig')]
d[d==-9] - NA
d[,c(4,5,7)] - lapply(d[,c(4,5,7)], FUN=as.factor)
str(d)
imp - mice(d, m=10, maxit=10, diagnostics=T, seed=500,
defaultImputationMethod=c('norm', 'logreg', 'polyreg'))
fit - cox.mids(Surv(time,status) ~ age + sex + hepmeg + platelet + trt
+ trig, imp)
pool(fit)
I have looked at the pool function but cannot figure out what I have
done wrong. Would really appreciate any help with this.
Thanks,
Brant Inman
Mayo Clinic
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