[R] Problem of lmer under FreeBSD
I encounter such problem with lmer under FreeBSD, but not under Windows. Anyone knows why? Thanks. example(lmer) lmer (fm1 - lmer(Reaction ~ Days + (Days|Subject), sleepstudy)) Error in UseMethod(as.logical) : no applicable method for as.logical traceback() 9: as.logical(EMverbose) 8: as.logical(EMverbose) 7: lmerControl() 6: do.call(lmerControl, control) 5: lmer(Reaction ~ Days + (Days | Subject), sleepstudy) 4: eval.with.vis(expr, envir, enclos) 3: eval.with.vis(ei, envir) 2: source(zfile, local, echo = echo, prompt.echo = paste(prompt.prefix, getOption(prompt), sep = ), continue.echo = paste(prompt.prefix, getOption(continue), sep = ), verbose = verbose, max.deparse.length = Inf, encoding = encoding, skip.echo = skips) 1: example(lmer) sessionInfo() R version 2.6.0 (2007-10-03) i386-portbld-freebsd6.3 locale: C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] lme4_0.99875-9Matrix_0.999375-2 lattice_0.16-5 loaded via a namespace (and not attached): [1] grid_2.6.0 rcompgen_0.1-15 tools_2.6.0 -- Ronggui Huang Department of Sociology, Fudan University, Shanghai, China Department of Public and Social Administration, CityU, HK __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Error: cannot allocate vector of size ... Bcc: Add Cc | Add Bcc
I read the subject message in a number of R archived emails. Since I am experiencing the same problem: upfmla A ~ T + cosP + cos2P + cos4P + cos5P + sin3P + sin5P + cosP2 + sinP3 + P2 glmod - gls(upfmla,correlation=corAR1(),method=ML) Error: cannot allocate vector of size 491.3 Mb dim(xx) [1] 8025 14 and since I'm running R on a 64-bit Linux platform ... I wonder whether this problem has been solved or I'm better off giving up the Generalized Least Squares models. Would it make sense to break the data into two halves and fit one half at a time ? Thank you . Happy new year, -- Maura E.M [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] (package e1071) SVM tune for best parameters: why they are different everytime i run?
Hi, I run the following tuning function for svm. It's very strange that every time i run this function, the best.parameters give different values. [A] svm.tune - tune(svm, train.x, train.y, validation.x=train.x, validation.y=train.y, ranges = list(gamma = 2^(-1:2), cost = 2^(-3:2))) # where train.x and train.y are matrix specified. # output command: svm.tune$best.parameters$cost svm.tune$best.parameters$gamma result: cost gamma 0.25 4.00 run A again: cost gamma 1 4 again: cost gamma 0.25 4.00 The result is so unstable, if it varies so much, why do we need to tune? Do you know if this behavior is normal? Can we trust the best.parameters for prediction? Thank you so much to help out!! Best Regards, Maggie [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] nlme package
AGAIN, please do not crosspost!
Vallejo, Roger wrote:
In using the NLME package (R 2.6.1 for Windows),
Which version of nlme? nlme is a contributed package that can be updated
independently of R releases.
I am having a problem in running an R script that used to run with no
problems using a Linux OS in 2004. So I am wondering if during these last ~3
yrs we had major changes in the syntax of the NLME package that I am not
aware.
For sure you are not aware. And which version of nlme have you used in 2004?
This is the R script:
library(nlme)
treat=as.factor(c(1,2,1,2,1,2,1,2))
mouse=as.factor(c(1,1,2,2,3,3,4,4))
time=as.factor(c(1,1,1,1,2,2,2,2))
mouse.anova=function(vec){lme(vec~treat+time+treat*time,random=~1|mouse/time)}
lme.out=apply(exprmat,1,mouse.anova)
Well, out error message is:
Error in apply(exprmat, 1, mouse.anova) : object exprmat not found
Guess why ... and re-read the posting guide, please.
Uwe Ligges
This is the ERROR message:
Error in lme.formula(vec ~ treat + time + treat * time, random = ~1 | :
nlminb problem, convergence error code = 1
message = singular convergence (7)
I will appreciate your help in pointing mistakes in this R script.
Thank you very much.
Roger
Roger L. Vallejo, Ph.D.
Computational Biologist Geneticist
U.S. Department of Agriculture, ARS
National Center for Cool Cold Water Aquaculture
11861 Leetown Road
Kearneysville, WV 25430
Voice: (304) 724-8340 Ext. 2141
Email: [EMAIL PROTECTED]
http://www.ars.usda.gov/pandp/people/people.htm?personid=37662
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
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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] data.frame - how to calculate the number of rows
Try this: summaryBy(B+C~ A+D, data=daten,FUN=c(mean, var, length)) On 26/12/2007, Agrarimmobilien [EMAIL PROTECTED] wrote: this works now, cbind(summaryBy(B+C~ A, data=df, FUN=c(mean, var)), 'numrows'=as.numeric(table(df$A))) but now, I cannot add another column D beside A, as I do before, like cbind(summaryBy(B+C~ A+D, data=df,FUN=c(mean, var)), 'numrows'=as.numeric(table(df$A))) because of this D, I got the following error message in german: Fehler in data.frame(..., check.names = FALSE) : Argumente implizieren unterschiedliche Anzahl Zeilen: 21, 18 error in data.frame(, check.names = FALSE): arguments has differents counts of rows: 21, 18 has anybody an idea, what I can do ? On 26/12/2007, Agrarimmobilien [EMAIL PROTECTED] wrote: Hello, I had to give some more information to my posting: as ouput there are more than one row, depending on the values of column A (transformierung to distinct values, here 3 and 4, but there are much more) ABC 1 3 6 5 2 3 4 20 3 3 8 2 4 4 8 3 5 4 2 6 Output: ABC num rows 1 36 6.16 3 2 45 4.00 3 B is mean and C variance. thank you Macki Hello, it seems to be a simple problem, but I couldn't find an answer in the archiv. (I think, it must has something to do with the group-select, like in php) I've the following data.frame: ABC 1 3 6 5 2 4 4 20 3 5 8 2 I want to get the number of the rows in the 4th column, like: ABC num rows 1 36 6.16 3 (B is mean, C is variance by using summaryBy(B+C~ A, data=daten, FUN=c(mean,var)) from the doBy-package) But, how can I add the column 'numrow' and count the number of the rows? Thanks! Macki __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] how to remove paths from where library() looks for packages
Perhaps this: .libPaths(unique(installed.packages()[,2])) On 25/12/2007, Lynd Bacon [EMAIL PROTECTED] wrote: Greetings. My current installation of R 2.6.1 on Unbuntu 7.10 (Gutsy) is looking for packages in a directory that doesn't contain any: library() Warning message: In library() : library /usr/lib/R/site-library contains no packages .libPaths() [1] /usr/local/lib/R/site-library /usr/lib/R/site-library [3] /usr/lib/R/library I'd like to eliminate the path to the empty directory so I don't get this vexsome warning message. Any and all suggestions will be greatly appreciated! Cheers, Lynd -- _ Lynd Bacon Woodside CA USA GMT-08:00 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] (package e1071) SVM tune for best parameters: why they are different everytime i run?
Maggie Wang wrote: Hi, I run the following tuning function for svm. It's very strange that every time i run this function, the best.parameters give different values. [A] svm.tune - tune(svm, train.x, train.y, validation.x=train.x, validation.y=train.y, ranges = list(gamma = 2^(-1:2), cost = 2^(-3:2))) # where train.x and train.y are matrix specified. # output command: svm.tune$best.parameters$cost svm.tune$best.parameters$gamma result: cost gamma 0.25 4.00 run A again: cost gamma 1 4 again: cost gamma 0.25 4.00 The result is so unstable, if it varies so much, why do we need to tune? Do you know if this behavior is normal? Can we trust the best.parameters for prediction? I guess you do not have really many observations in your dataset. Then it highly depends ion the cross validation sets which parameter is best. And therefore you get quite different results. Uwe Ligges Thank you so much to help out!! Best Regards, Maggie [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] (package e1071) SVM tune for best parameters: why they are different everytime i run?
Thank you so much! I will have a try!! ~ maggie On Dec 27, 2007 6:43 PM, Uwe Ligges [EMAIL PROTECTED] wrote: Maggie Wang wrote: Hi, Uwe, Thanks for the reply!! I have 87 observations in total. If this amount causes the different best.parameters, is there a better way than cross validation to tune them? In order to get stable (I do not say best) results, you could try some bootstrap with many replications or leave-one-out crossvalidation. Uwe Thank you so much for the help! Best Regards, Maggie On Dec 27, 2007 6:17 PM, Uwe Ligges [EMAIL PROTECTED] wrote: Maggie Wang wrote: Hi, I run the following tuning function for svm. It's very strange that every time i run this function, the best.parameters give different values. [A] svm.tune - tune(svm, train.x, train.y, validation.x=train.x, validation.y=train.y, ranges = list(gamma = 2^(-1:2), cost = 2^(-3:2))) # where train.x and train.y are matrix specified. # output command: svm.tune$best.parameters$cost svm.tune$best.parameters$gamma result: cost gamma 0.25 4.00 run A again: cost gamma 1 4 again: cost gamma 0.25 4.00 The result is so unstable, if it varies so much, why do we need to tune? Do you know if this behavior is normal? Can we trust the best.parametersfor prediction? I guess you do not have really many observations in your dataset. Then it highly depends ion the cross validation sets which parameter is best. And therefore you get quite different results. Uwe Ligges Thank you so much to help out!! Best Regards, Maggie [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.htmlhttp://www.r-project.org/posting-guide.html http://www.r-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Affy Package
Damn, this was a cross-post (and I replied to all), apologies for my re-cross-posting. To Roger, the original poster: PLEASE do read the posting guide of R-help before posting and NEVER EVER do crossposting again. Thanks, Uwe Ligges Uwe Ligges wrote: Vallejo, Roger wrote: Dear R Users, In the expresso function, which combination of these methods for data pre-processing (when using affymetrix oligo arrays) is the best: bgcorrect.metod = rma rma2 mas normalize.method = qspline quantiles loess pmcorrect.method = pmonly subtractmm mas summary.method = liwong avgdiff medianpolish mas There are many options within each method. I would appreciate a hint on the best combination. There is more than one implemented, hence we can guess that there is no generally best one among these, i.e. it depends on your data what to use. Uwe Ligges Thank you very much in advance. Roger Roger L. Vallejo, Ph.D. Computational Biologist Geneticist U.S. Department of Agriculture, ARS National Center for Cool Cold Water Aquaculture 11861 Leetown Road Kearneysville, WV 25430 Voice: (304) 724-8340 Ext. 2141 Email: [EMAIL PROTECTED] http://www.ars.usda.gov/pandp/people/people.htm?personid=37662 [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] (package e1071) SVM tune for best parameters: why they are different everytime i run?
Maggie Wang wrote: Hi, Uwe, Thanks for the reply!! I have 87 observations in total. If this amount causes the different best.parameters, is there a better way than cross validation to tune them? In order to get stable (I do not say best) results, you could try some bootstrap with many replications or leave-one-out crossvalidation. Uwe Thank you so much for the help! Best Regards, Maggie On Dec 27, 2007 6:17 PM, Uwe Ligges [EMAIL PROTECTED] wrote: Maggie Wang wrote: Hi, I run the following tuning function for svm. It's very strange that every time i run this function, the best.parameters give different values. [A] svm.tune - tune(svm, train.x, train.y, validation.x=train.x, validation.y=train.y, ranges = list(gamma = 2^(-1:2), cost = 2^(-3:2))) # where train.x and train.y are matrix specified. # output command: svm.tune$best.parameters$cost svm.tune$best.parameters$gamma result: cost gamma 0.25 4.00 run A again: cost gamma 1 4 again: cost gamma 0.25 4.00 The result is so unstable, if it varies so much, why do we need to tune? Do you know if this behavior is normal? Can we trust the best.parametersfor prediction? I guess you do not have really many observations in your dataset. Then it highly depends ion the cross validation sets which parameter is best. And therefore you get quite different results. Uwe Ligges Thank you so much to help out!! Best Regards, Maggie [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.htmlhttp://www.r-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] (package e1071) SVM tune for best parameters: why they are different everytime i run?
Hi, Uwe, Thanks for the reply!! I have 87 observations in total. If this amount causes the different best.parameters, is there a better way than cross validation to tune them? Thank you so much for the help! Best Regards, Maggie On Dec 27, 2007 6:17 PM, Uwe Ligges [EMAIL PROTECTED] wrote: Maggie Wang wrote: Hi, I run the following tuning function for svm. It's very strange that every time i run this function, the best.parameters give different values. [A] svm.tune - tune(svm, train.x, train.y, validation.x=train.x, validation.y=train.y, ranges = list(gamma = 2^(-1:2), cost = 2^(-3:2))) # where train.x and train.y are matrix specified. # output command: svm.tune$best.parameters$cost svm.tune$best.parameters$gamma result: cost gamma 0.25 4.00 run A again: cost gamma 1 4 again: cost gamma 0.25 4.00 The result is so unstable, if it varies so much, why do we need to tune? Do you know if this behavior is normal? Can we trust the best.parametersfor prediction? I guess you do not have really many observations in your dataset. Then it highly depends ion the cross validation sets which parameter is best. And therefore you get quite different results. Uwe Ligges Thank you so much to help out!! Best Regards, Maggie [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.htmlhttp://www.r-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Error: cannot allocate vector of size ...
Maura E Monville wrote: I read the subject message in a number of R archived emails. Since I am experiencing the same problem: upfmla A ~ T + cosP + cos2P + cos4P + cos5P + sin3P + sin5P + cosP2 + sinP3 + P2 glmod - gls(upfmla,correlation=corAR1(),method=ML) Error: cannot allocate vector of size 491.3 Mb dim(xx) [1] 8025 14 How much memory is consumed in your workspace? If so, remove huge objects from your workspace How big is upfmla? Are there factors in it? If so, how many levels? Then you can calculate the size of your design matrix. 64-bit is nice, but how much RAM is in your machine? Uwe Ligges and since I'm running R on a 64-bit Linux platform ... I wonder whether this problem has been solved or I'm better off giving up the Generalized Least Squares models. Would it make sense to break the data into two halves and fit one half at a time ? Thank you . Happy new year, __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Affy Package
Vallejo, Roger wrote: Dear R Users, In the expresso function, which combination of these methods for data pre-processing (when using affymetrix oligo arrays) is the best: bgcorrect.metod = rma rma2 mas normalize.method = qspline quantiles loess pmcorrect.method = pmonly subtractmm mas summary.method = liwong avgdiff medianpolish mas There are many options within each method. I would appreciate a hint on the best combination. There is more than one implemented, hence we can guess that there is no generally best one among these, i.e. it depends on your data what to use. Uwe Ligges Thank you very much in advance. Roger Roger L. Vallejo, Ph.D. Computational Biologist Geneticist U.S. Department of Agriculture, ARS National Center for Cool Cold Water Aquaculture 11861 Leetown Road Kearneysville, WV 25430 Voice: (304) 724-8340 Ext. 2141 Email: [EMAIL PROTECTED] http://www.ars.usda.gov/pandp/people/people.htm?personid=37662 [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Problem of lmer under FreeBSD
Hello Ronggui Huang, I am working with FreeBSD 8.0-CURRENT (i386) and R-2.6.1 (not built from ports). After loading version 0.99875-9 of lme4 and then executing the example library(lme4) example(lmer) all works fine for me. On 27.12.2007 09:19 (UTC+1), Ronggui wrote: I encounter such problem with lmer under FreeBSD, but not under Windows. Anyone knows why? Thanks. Assuming, that your R installation is correct (from math/R ?), you should consider to reinstall lme4 and its dependencies. It is possible that these package have been built on a prior version of R. For installing the package 'Matrix' on FreeBSD you have to use gmake instead of make. The following example will do it setenv MAKE gmake R CMD INSTALL Matrix_0.999375-3.tar.gz unsetenv MAKE If reinstalling packages not solves your problem, please try if reinstalling R does. (Under FreeBSD the R sources build and install fine, so there is no need to use the port at math/R ...) Hope this helps, Rainer example(lmer) lmer (fm1 - lmer(Reaction ~ Days + (Days|Subject), sleepstudy)) Error in UseMethod(as.logical) : no applicable method for as.logical traceback() 9: as.logical(EMverbose) 8: as.logical(EMverbose) 7: lmerControl() 6: do.call(lmerControl, control) 5: lmer(Reaction ~ Days + (Days | Subject), sleepstudy) 4: eval.with.vis(expr, envir, enclos) 3: eval.with.vis(ei, envir) 2: source(zfile, local, echo = echo, prompt.echo = paste(prompt.prefix, getOption(prompt), sep = ), continue.echo = paste(prompt.prefix, getOption(continue), sep = ), verbose = verbose, max.deparse.length = Inf, encoding = encoding, skip.echo = skips) 1: example(lmer) sessionInfo() R version 2.6.0 (2007-10-03) i386-portbld-freebsd6.3 locale: C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] lme4_0.99875-9Matrix_0.999375-2 lattice_0.16-5 loaded via a namespace (and not attached): [1] grid_2.6.0 rcompgen_0.1-15 tools_2.6.0 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Problem of lmer under FreeBSD
Dear Rainer, Thanks for your suggestion. The problem lies in the Matrix package. I installed it under R-2.5.0. When I upgraded R to R-2.6.0, I didn't upgrade all the add-on packages. I reinstall Matrix and lme4 packages, things are going fine. Regards Ronggui HUANG 2007/12/27, Rainer Hurling [EMAIL PROTECTED]: Hello Ronggui Huang, I am working with FreeBSD 8.0-CURRENT (i386) and R-2.6.1 (not built from ports). After loading version 0.99875-9 of lme4 and then executing the example library(lme4) example(lmer) all works fine for me. On 27.12.2007 09:19 (UTC+1), Ronggui wrote: I encounter such problem with lmer under FreeBSD, but not under Windows. Anyone knows why? Thanks. Assuming, that your R installation is correct (from math/R ?), you should consider to reinstall lme4 and its dependencies. It is possible that these package have been built on a prior version of R. For installing the package 'Matrix' on FreeBSD you have to use gmake instead of make. The following example will do it setenv MAKE gmake R CMD INSTALL Matrix_0.999375-3.tar.gz unsetenv MAKE If reinstalling packages not solves your problem, please try if reinstalling R does. (Under FreeBSD the R sources build and install fine, so there is no need to use the port at math/R ...) Hope this helps, Rainer example(lmer) lmer (fm1 - lmer(Reaction ~ Days + (Days|Subject), sleepstudy)) Error in UseMethod(as.logical) : no applicable method for as.logical traceback() 9: as.logical(EMverbose) 8: as.logical(EMverbose) 7: lmerControl() 6: do.call(lmerControl, control) 5: lmer(Reaction ~ Days + (Days | Subject), sleepstudy) 4: eval.with.vis(expr, envir, enclos) 3: eval.with.vis(ei, envir) 2: source(zfile, local, echo = echo, prompt.echo = paste(prompt.prefix, getOption(prompt), sep = ), continue.echo = paste(prompt.prefix, getOption(continue), sep = ), verbose = verbose, max.deparse.length = Inf, encoding = encoding, skip.echo = skips) 1: example(lmer) sessionInfo() R version 2.6.0 (2007-10-03) i386-portbld-freebsd6.3 locale: C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] lme4_0.99875-9Matrix_0.999375-2 lattice_0.16-5 loaded via a namespace (and not attached): [1] grid_2.6.0 rcompgen_0.1-15 tools_2.6.0 -- Ronggui Huang Department of Sociology, Fudan University, Shanghai, China Department of Public and Social Administration, CityU, HK __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] probability from different values
one addition ...
Hello Ricardo,
another solution could be using package distr:
library(distr)
A - c(18,18,18,19,20,21,22,23,24,25,26,27,28)
DA - DiscreteDistribution(A)
# maybe
# support(DA)
# plot (DA)
B - c(82,83,84,85,85,86,87,88,89,90,91,91,92)
DB - DiscreteDistribution(B)
# support(DB)
# plot(DB)
DC - DB - DA# convolution with of DB with (-DA)
# support(DC)
# plot(DC)
to get the probabilities for the C-values:
p(DC)(support(DC))
hth,
Matthias
[EMAIL PROTECTED] wrote:
i have two vectors (A and B) and i need create another vector (C)
from the subtraction of A's values with the B's values. How can i
estimate the probability of C's values if i have differents values
combinations of A and B that can result in the same value? like 90
-20 = 70 and 91 - 21 = 70.
example:
B = {18 1818 19 20 21 22 23 24
25 26 27 28}
A = {82 83 84 85 85 86 87 88 89
90 91 9192 }
Try this:
A = c(18,18,18,19,20,21,22,23,24,25,26,27,28)
B = c(82,83,84,85,85,86,87,88,89,90,91,91,92)
lenA = length(A)
lenB = length(B)
AA = rep(A, lenB)
BB = rep(B, each=lenA)
table(AA-BB)/(lenA*lenB)
Regards,
Richie.
Mathematical Sciences Unit
HSL
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Re: [R] probability from different values
Hello Ricardo,
another solution could be using package distr:
library(distr)
A - c(18,18,18,19,20,21,22,23,24,25,26,27,28)
DA - DiscreteDistribution(A)
# maybe
# support(DA)
# plot (DA)
B - c(82,83,84,85,85,86,87,88,89,90,91,91,92)
DB - DiscreteDistribution(B)
# support(DB)
# plot(DB)
DC - DB - DA# convolution with of DB with (-DA)
# support(DC)
# plot(DC)
hth,
Matthias
[EMAIL PROTECTED] wrote:
i have two vectors (A and B) and i need create another vector (C)
from the subtraction of A's values with the B's values. How can i
estimate the probability of C's values if i have differents values
combinations of A and B that can result in the same value? like 90
-20 = 70 and 91 - 21 = 70.
example:
B = {18 1818 19 20 21 22 23 24
25 26 27 28}
A = {82 83 84 85 85 86 87 88 89
90 91 9192 }
Try this:
A = c(18,18,18,19,20,21,22,23,24,25,26,27,28)
B = c(82,83,84,85,85,86,87,88,89,90,91,91,92)
lenA = length(A)
lenB = length(B)
AA = rep(A, lenB)
BB = rep(B, each=lenA)
table(AA-BB)/(lenA*lenB)
Regards,
Richie.
Mathematical Sciences Unit
HSL
ATTENTION:
This message contains privileged and confidential inform...{{dropped:20}}
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Re: [R] R Compilation error on Ubuntu
On Tue, Dec 25, 2007 at 01:35:19AM -0800, Satoshi Takahama wrote: Hi Taka, I was just trying to do this yesterday and ran into the same problem (compiling R 2.6.1 on Gutsy Gibbon). Apparently this happens on Debian/Ubuntu distributions because the developer install is separate from the user install. Basically, to address the configure error: --with-readline=yes (default) and headers/libs are not available you need the development version of readline: sudo apt-get install libreadline5-dev (see http://cran.r-project.org/doc/manuals/R-admin.html) Later, I ran into another configure error: --with-x=yes (default) and X11 headers/libs are not available so I installed xorg-dev: sudo apt-get install xorg-dev (see http://tolstoy.newcastle.edu.au/R/e2/help/06/11/5193.html) At the end, I also got a configure WARNING: you cannot build info or HTML versions of the R manuals so then I installed texinfo: sudo apt-get install texinfo (see http://tolstoy.newcastle.edu.au/R/e2/help/07/04/15498.html) If you do sudo apt-get build-dep r-base you get all build-dependencies automatically filled in by the system. Dirk Hope this helps, ST - Original Message From: Takatsugu Kobayashi [EMAIL PROTECTED] To: [EMAIL PROTECTED] Sent: Monday, December 24, 2007 10:52:11 AM Subject: Re: [R] R Compilation error on Ubuntu Hi I bought a new laptop HP dv9500 just a week ago and installed a Ubuntu gutsy ribbon on this laptop. I wanted to install Fedora but there are more threads on Ubuntu, so I decided to install Ubuntu. After hours of struggle in configuring x server/graphic card stuff, I installed R for Gutsy ribbon using sudo apt-get install g77 r-core'. Now when I tried to install 'sp' package I got this error message: Warning in install.packages(sp) : argument 'lib' is missing: using '/usr/local/lib/R/site-library' --- Please select a CRAN mirror for use in this session --- Loading Tcl/Tk interface ... done trying URL 'http://cran.mtu.edu/src/contrib/sp_0.9-17.tar.gz' Content type 'application/x-gzip' length 359194 bytes opened URL == downloaded 350Kb * Installing *source* package 'sp' ... ** libs gcc-4.2 -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include -fpic -g -O2 -c gcdist.c -o gcdist.o /bin/bash: gcc-4.2: command not found make: *** [gcdist.o] Error 127 ERROR: compilation failed for package 'sp' ** Removing '/usr/local/lib/R/site-library/sp' The downloaded packages are in /tmp/RtmpfOk3H7/downloaded_packages Warning message: installation of package 'sp' had non-zero exit status in: install.packages(sp) Then, I removed this gutsy ribbon version of R and attempted to install fresh R-2.6.1.tar.gz. When I tried to build it, I got this error message: configure: error: --with-readline=yes (default) and headers/libs are not available I installed xserver-xorg-dev ok. I am using Fedora 6 on my desktop and have never seen these above error messages. Should I install a Fedora and R on it? Or should I just create a link using 'ln -s'? I appreciate your help. [[replacing trailing spam]] taka __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Never miss a thing. Make Yahoo your home page. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Three out of two people have difficulties with fractions. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] probability from different values
Hi all,
i'm new R user and i need some help:
i have two vectors (A and B) and i need create another vector (C) from the
subtraction of A's values with the B's values. How can i estimate the
probability of C's values if i have differents values combinations of A and B
that can result in the same value? like 90 -20 = 70 and 91 - 21 = 70.
example:
B = {18 1818 19 20 21 22 23 24 25
26 27 28}
A = {82 83 84 85 85 86 87 88 89 90
91 9192 }
Considering C's values that were computed from different frequencies of the A
and B, is it necessary any mathematical convolution to estimated the
probability more precisely?
Thanks a lot
Ricardo
Be a better friend, newshound, and
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[R] Too many open files
Dear all,
Did this problem that was posted in 2006 (see below) ever got fully resolved
?
I am encountering the exact same issue
; I have executed get.hist.quote() in a loop and now R not only refuses to
establish any further connections to yahoo, but, worse, it will not open any
files either. For example, I cannot even save my current workspace for that
reason.
I tried
closeAllConnections()
As well as
showConnections()
But I do not see any open connections.
Also, does get.hist.quote() not close its connection internally once it is
done ?
Any help would be immensely useful as I am quite stuck.
Thanks!
Markus
Re: [R] Too many open files
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From: Seth Falcon sfalcon_at_fhcrc.org
Date: Sat 27 May 2006 - 09:21:36 EST
Omar Lakkis [EMAIL PROTECTED] writes:
This may be more of an OS question ...
I have this call
r = get.hist.quote(symbol, start= format(start, %Y-%m-%d), end=
format(end, %Y-%m-%d))
which does a url request
in a loop and my program runs out of file handlers after few hundred
rotations. The error message is: 'Too many open files'. Other than
increasing the file handlers assigned to my process, is there a way to
cleanly release and reuse these connections?
Inside your loop you need to close the connection object created by url().
for (i in 1:500) {
con - url(urls[i])
## ... stuff here ...
close(con)
}
R only allows you to have a fixed number of open connections at one time,
and they do not get closed automatically when they go out of scope. These
commands may help make clear how things work...
showConnections()
description class mode text isopen can read can write
f = url(http://www.r-project.org;, open=r)
showConnections()
From: Gabor Grothendieck ggrothendieck_at_gmail.com
Date: Sat 27 May 2006 - 09:47:20 EST
Try closeAllConnections()
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Re: [R] probability from different values
i have two vectors (A and B) and i need create another vector (C)
from the subtraction of A's values with the B's values. How can i
estimate the probability of C's values if i have differents values
combinations of A and B that can result in the same value? like 90
-20 = 70 and 91 - 21 = 70.
example:
B = {18 1818 19 20 21 22 23 24
25 26 27 28}
A = {82 83 84 85 85 86 87 88 89
90 91 9192 }
Try this:
A = c(18,18,18,19,20,21,22,23,24,25,26,27,28)
B = c(82,83,84,85,85,86,87,88,89,90,91,91,92)
lenA = length(A)
lenB = length(B)
AA = rep(A, lenB)
BB = rep(B, each=lenA)
table(AA-BB)/(lenA*lenB)
Regards,
Richie.
Mathematical Sciences Unit
HSL
ATTENTION:
This message contains privileged and confidential inform...{{dropped:20}}
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[R] A function for random test based on longest run (UNCLASSIFIED)
Classification: UNCLASSIFIED Caveats: NONE Hello, R users, Has anybody written a function for random test based on the length of longest run of same events. I really appreciate your help. Kyong Park Classification: UNCLASSIFIED Caveats: NONE [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] A function for random test based on longest run of same events (U NCLASSIFIED)
Classification: UNCLASSIFIED Caveats: NONE Hello, R users, Has anybody written a function for random test based on the length of longest run of same events. I really appreciate your help. Kyong Park Classification: UNCLASSIFIED Caveats: NONE [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] how to remove paths from where library() looks for packages
Thanks, Henrique! I'm not sure this will help since the paths are
already unique.
Phil Spector wrote separately(Phil, I hope it's ok that I quote you here
for the list):
Lynd -
If the message bothers you, look at /etc/R/Renviron and modify
the line that defines R_LIBS . However, note that these are set
up for you so that if you install packages through either Ubuntu's
repositories or the install.package() function, everything should
just work, so you might want to leave things as they are.
This line in this particular installation of R 2.6.1 on my Ubuntu 7.10
workstation reads:
R_LIBS=${R_LIBS-'/usr/local/lib/R/site-library:/usr/lib/R/site-library:/usr/lib/R/library'}
One question (for me, at least), is why did I start to get this warning
message, to begin with? I wasn't getting it with an earlier version of R.
The warning I'm getting started to appear after I updated from 2.5.1 to
2.6.1. I did this using the procedure described on:
http://cran.cnr.berkeley.edu/bin/linux/ubuntu/
I used Ubuntu's Synaptic Package Manager to install R initially on this
particular machine, from what I can recall. After updating to 2.6.1,
the packages I had previously installed with 2.5.1 were in the directory
/usr/local/lib/R/site-library. When I now install additional packages
in 2.6.1, they are installed to this directory, and not to
/usr/lib/R/site-library, the directory library() gives warnings about.
My hypothesis is that the default library configurations for the two
versions were different for some reason.
Thanks, Henrique and Phil, for your help!
Cheers,
Lynd
Henrique Dallazuanna wrote:
Perhaps this:
.libPaths(unique(installed.packages()[,2]))
On 25/12/2007, Lynd Bacon [EMAIL PROTECTED] wrote:
Greetings. My current installation of R 2.6.1 on Unbuntu 7.10 (Gutsy)
is looking for packages in a directory that doesn't contain any:
library()
Warning message:
In library() : library /usr/lib/R/site-library contains no packages
.libPaths()
[1] /usr/local/lib/R/site-library /usr/lib/R/site-library
[3] /usr/lib/R/library
I'd like to eliminate the path to the empty directory so I don't get
this vexsome warning message. Any and all suggestions will be greatly
appreciated!
Cheers,
Lynd
--
_
Lynd Bacon
Woodside CA USA GMT-08:00
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--
_
Lynd Bacon
Woodside CA USA GMT-08:00
+1 650.593.2198 (home office)
+1 650.462.8015 (YouGov/Polimetrix Inc.)
+1 650.863.1959 (mobile)
[EMAIL PROTECTED]
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Re: [R] Principal Components Analysis
On Wed, 26 Dec 2007, SNN wrote: Hi, I do have a file that has 50 columns and 40 rows. I want to apply PCA on that data and this is what I did h1-read.table(Ccode.txt, sep='\t', header=F) # reads the data from the file Ccode.txt h2-prcomp(na.omit(h1),center=T) but I am getting the following error Error in svd(x, nu = 0) : 0 extent dimensions I appreciate if someone can help You probably have a missing value in every row. But does PCA with 50 columns make sense: 461 of the PCs are constant and arbitrary? It is possible you meant PC on the transpose (sometimes called Q-mode) -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Problem of lmer under FreeBSD
On Thu, 27 Dec 2007, ronggui wrote: I encounter such problem with lmer under FreeBSD, but not under Windows. Anyone knows why? Thanks. Most likely you have a mixed-up system, with some packages installed under an earlier version of R. Please use update.packages(checkBuilt=TRUE) to fix this. (The culprit is probably Matrix.) Searching the archives just after the releases of R 2.6.0 will find quite a few postings from people who had made the same mistake. example(lmer) lmer (fm1 - lmer(Reaction ~ Days + (Days|Subject), sleepstudy)) Error in UseMethod(as.logical) : no applicable method for as.logical traceback() 9: as.logical(EMverbose) 8: as.logical(EMverbose) 7: lmerControl() 6: do.call(lmerControl, control) 5: lmer(Reaction ~ Days + (Days | Subject), sleepstudy) 4: eval.with.vis(expr, envir, enclos) 3: eval.with.vis(ei, envir) 2: source(zfile, local, echo = echo, prompt.echo = paste(prompt.prefix, getOption(prompt), sep = ), continue.echo = paste(prompt.prefix, getOption(continue), sep = ), verbose = verbose, max.deparse.length = Inf, encoding = encoding, skip.echo = skips) 1: example(lmer) sessionInfo() R version 2.6.0 (2007-10-03) i386-portbld-freebsd6.3 locale: C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] lme4_0.99875-9Matrix_0.999375-2 lattice_0.16-5 loaded via a namespace (and not attached): [1] grid_2.6.0 rcompgen_0.1-15 tools_2.6.0 -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] A function for random test based on longest run (UNCLASSIFIED)
require(tseries) ?runs.test Also, take a look at dieharder, it implements a large number of randomness tests: http://www.phy.duke.edu/~rgb/General/dieharder.php -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Park, Kyong H Mr ECBC Sent: Thursday, December 27, 2007 11:05 AM To: 'r-help@r-project.org' Subject: [R] A function for random test based on longest run (UNCLASSIFIED) Classification: UNCLASSIFIED Caveats: NONE Hello, R users, Has anybody written a function for random test based on the length of longest run of same events. I really appreciate your help. Kyong Park Classification: UNCLASSIFIED Caveats: NONE [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Principal Components Analysis
Are there lots of missing values in the data? If so, my guess would be that na.omit(h1) leaves you with no data. Have you checked this? Bert Gunter Genentech -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of SNN Sent: Wednesday, December 26, 2007 2:49 PM To: r-help@r-project.org Subject: [R] Principal Components Analysis Hi, I do have a file that has 50 columns and 40 rows. I want to apply PCA on that data and this is what I did h1-read.table(Ccode.txt, sep='\t', header=F) # reads the data from the file Ccode.txt h2-prcomp(na.omit(h1),center=T) but I am getting the following error Error in svd(x, nu = 0) : 0 extent dimensions I appreciate if someone can help Thanks -- View this message in context: http://www.nabble.com/Principal--Components-Analysis-tp14507365p14507365.htm l Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Apresentação Evangelismcenter
Prezados Cybernautas: Em fase de crescimento, a Evangelismcenter apresenta agora um sistema mais acessível a todos os visitantes e com mais conteúdos para consulta. Destacamos entre outros, um sistema de Bíblia On-line, Vídeos, Notícias, Links, Fórum, Chat, etc etc... http://www.evangelismcenter.org/ Desejamos a todos umas Boas Festas e umas Boas Entradas em 2008 com muita Paz e Amor Evangelismcenter Modificar Dados ( http://www.evangelismcenter.org/eva/index.php?option=com_acajoomact=changesubscriber=6436cle=d2f731f3e7a962b2b0aa7e9be6bc9b8elistid=1 ) Remover E-mail ( http://www.evangelismcenter.org/eva/index.php?option=com_acajoomact=unsubscribesubscriber=6436cle=d2f731f3e7a962b2b0aa7e9be6bc9b8elistid=1 ) [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Apresentação Evangelismcenter
Prezados Cybernautas: Em fase de crescimento, a Evangelismcenter apresenta agora um sistema mais acessível a todos os visitantes e com mais conteúdos para consulta. Destacamos entre outros, um sistema de Bíblia On-line, Vídeos, Notícias, Links, Fórum, Chat, etc etc... http://www.evangelismcenter.org/ Desejamos a todos umas Boas Festas e umas Boas Entradas em 2008 com muita Paz e Amor Evangelismcenter Modificar Dados ( http://www.evangelismcenter.org/eva/index.php?option=com_acajoomact=changesubscriber=6435cle=db8cf5b0beb7e55ada18179dd273listid=1 ) Remover E-mail ( http://www.evangelismcenter.org/eva/index.php?option=com_acajoomact=unsubscribesubscriber=6435cle=db8cf5b0beb7e55ada18179dd273listid=1 ) [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] A function for random test based on longest run (UNCLASSI FIED)
Classification: UNCLASSIFIED Caveats: NONE Thanks for your quick response. The program you mentioned below available from R is based on number of runs (up or down) not based on a longest length of runs of same events. To be more specific, for example, from a series, HHTHHHH, the number of runs are 5, and the longest length of runs of the same events is 4. I'll check for the website you mentioned below. Kyong -Original Message- From: bogdan romocea [mailto:[EMAIL PROTECTED] Sent: Thursday, December 27, 2007 12:08 PM To: [EMAIL PROTECTED] Cc: r-help Subject: RE: [R] A function for random test based on longest run (UNCLASSIFIED) require(tseries) ?runs.test Also, take a look at dieharder, it implements a large number of randomness tests: http://www.phy.duke.edu/~rgb/General/dieharder.php -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Park, Kyong H Mr ECBC Sent: Thursday, December 27, 2007 11:05 AM To: 'r-help@r-project.org' Subject: [R] A function for random test based on longest run (UNCLASSIFIED) Classification: UNCLASSIFIED Caveats: NONE Hello, R users, Has anybody written a function for random test based on the length of longest run of same events. I really appreciate your help. Kyong Park Classification: UNCLASSIFIED Caveats: NONE [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Classification: UNCLASSIFIED Caveats: NONE [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] getting a string output from str
I would like to use the output from str() in a homemade function but str does not return a value! eg: list(x=str(1:20),y=str(1:15)) returns odd output... Thanks - Kevin. -- View this message in context: http://www.nabble.com/getting-a-string-output-from-str-tp14517059p14517059.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] getting a string output from str
If you want to capture the output of the str function in a vector of character strings, try the capture.output function. From: [EMAIL PROTECTED] on behalf of eggsbrown Sent: Thu 12/27/2007 11:51 AM To: r-help@r-project.org Subject: [R] getting a string output from str I would like to use the output from str() in a homemade function but str does not return a value! eg: list(x=str(1:20),y=str(1:15)) returns odd output... Thanks - Kevin. -- View this message in context: http://www.nabble.com/getting-a-string-output-from-str-tp14517059p14517059.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Odd time conversion glitch
Hello, all. I ran across an odd problem while working in R 2.6.0. The command line text follows. Basically, I attempted to convert a character vector of length 13 (in a data frame with 13 rows) from a character representation of dates to a POSIX representation using strptime. strptime returned a vector of length 9, which appears to contain 13 values (!) in the appropriate format. I can't find any way to convince the strptime output that it has 13 values . . . even though (for example) posixvector[1:13] returns 13 values, anothervectorof length13-posixvector[1:13] produces a length mismatch error. Can anyone help diagnose this, or work around it? Many thanks, ~Pat Carroll. Dataset$DateFilled [1] 10/20/2005 11/4/2005 11/18/2005 12/2/2005 4/3/2006 6/5/2006 7/14/2006 4/27/2007 5/7/2007 7/17/2007 2/14/2005 [12] 2/14/2005 2/21/2005 datefilledpos-strptime(Dataset$DateFilled,format=%m/%d/%Y) datefilledpos [1] 2005-10-20 2005-11-04 2005-11-18 2005-12-02 2006-04-03 2006-06-05 2006-07-14 2007-04-27 2007-05-07 2007-07-17 2005-02-14 [12] 2005-02-14 2005-02-21 length(datefilledpos) [1] 9 length(Dataset$DateFilled) [1] 13 datefilledpos[1:13] [1] 2005-10-20 2005-11-04 2005-11-18 2005-12-02 2006-04-03 2006-06-05 2006-07-14 2007-04-27 2007-05-07 2007-07-17 2005-02-14 [12] 2005-02-14 2005-02-21 Dataset$DateFilled-datefilledpos Error in `$-.data.frame`(`*tmp*`, DateFilled, value = list(sec = c(0, : replacement has 9 rows, data has 13 Dataset$DateFilled-datefilledpos[1:13] Error in `$-.data.frame`(`*tmp*`, DateFilled, value = list(sec = c(0, : replacement has 9 rows, data has 13 Pat Carroll. what matters most is how well you walk through the fire. bukowski. Be a better friend, newshound, and __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Running R from a CD on Windows?
Greetings, R-ians: Yes it's easy to run R from a CD: I copied my windows installation folder to the CD, then copied my R working directory to the CD. To run from the CD, I copy the working directory from the CD to the desktop, and then create an R desktop icon that points to Rgui.exe on the CD, and starts in the working directory folder I just copied to the desktop. The problem is that to create the desktop R icon you need to know that Rgui.exe is on the CD in the bin subfolder of the R-2.6.1 folder, which I know but the person being introduced to R for the first time does not. And creating a desktop icon is busywork that some find annoying. And then the user needs to copy the basic working directory folder to the desktop, since R needs to be able to write to it and writing to the CD can't work with a write-once CD. Alas, my uses just want to put the CD in the drive and have the autorun facility take care all this: 1) If there isn't a folder named R-project on the desktop, copy the one on the CD to the desktop. 2) Create a desktop icon for R that points to Rgui.exe on the CD. The installation must determine what drive is currently being accessed, since D:\R-2.6.1\bin\Rgui.exe would only work if the CD was running from drive D. 3) Have the icon Start in desktop\R-project which is legal if you create the icon yourself, but apparently not legal to put on the CD since the windows are erased and cannot be filled in if the icon is copied back from the CD to the desktop. Since the basic R installation on Windows can create a desktop icon, I know this must be possible. I would be grateful for any help. Thanks Charles Annis, P.E. [EMAIL PROTECTED] phone: 561-352-9699 eFax: 614-455-3265 http://www.StatisticalEngineering.com __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Running R from a CD on Windows?
There is a batch script, rgui.bat, in batchfiles, see home page at batchfiles.googlecode.com, that will search the registry and a few other places for R and start up R if it can find it. It does not search CD's automatically but that would be simple to add. On Dec 27, 2007 3:25 PM, Charles Annis, P.E. [EMAIL PROTECTED] wrote: Greetings, R-ians: Yes it's easy to run R from a CD: I copied my windows installation folder to the CD, then copied my R working directory to the CD. To run from the CD, I copy the working directory from the CD to the desktop, and then create an R desktop icon that points to Rgui.exe on the CD, and starts in the working directory folder I just copied to the desktop. The problem is that to create the desktop R icon you need to know that Rgui.exe is on the CD in the bin subfolder of the R-2.6.1 folder, which I know but the person being introduced to R for the first time does not. And creating a desktop icon is busywork that some find annoying. And then the user needs to copy the basic working directory folder to the desktop, since R needs to be able to write to it and writing to the CD can't work with a write-once CD. Alas, my uses just want to put the CD in the drive and have the autorun facility take care all this: 1) If there isn't a folder named R-project on the desktop, copy the one on the CD to the desktop. 2) Create a desktop icon for R that points to Rgui.exe on the CD. The installation must determine what drive is currently being accessed, since D:\R-2.6.1\bin\Rgui.exe would only work if the CD was running from drive D. 3) Have the icon Start in desktop\R-project which is legal if you create the icon yourself, but apparently not legal to put on the CD since the windows are erased and cannot be filled in if the icon is copied back from the CD to the desktop. Since the basic R installation on Windows can create a desktop icon, I know this must be possible. I would be grateful for any help. Thanks Charles Annis, P.E. [EMAIL PROTECTED] phone: 561-352-9699 eFax: 614-455-3265 http://www.StatisticalEngineering.com __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Running R from a CD on Windows?
Sounds like you want to write some VisualBasic script that sets up the link etc., started by the autorun.inf facility. In any case, many virus and/or behavior checkers will shout when you implement things like that ... - and I have disabled auto-anything for CD/USB devices not only form security reasons. Uwe Ligges Charles Annis, P.E. wrote: Greetings, R-ians: Yes it's easy to run R from a CD: I copied my windows installation folder to the CD, then copied my R working directory to the CD. To run from the CD, I copy the working directory from the CD to the desktop, and then create an R desktop icon that points to Rgui.exe on the CD, and starts in the working directory folder I just copied to the desktop. The problem is that to create the desktop R icon you need to know that Rgui.exe is on the CD in the bin subfolder of the R-2.6.1 folder, which I know but the person being introduced to R for the first time does not. And creating a desktop icon is busywork that some find annoying. And then the user needs to copy the basic working directory folder to the desktop, since R needs to be able to write to it and writing to the CD can't work with a write-once CD. Alas, my uses just want to put the CD in the drive and have the autorun facility take care all this: 1) If there isn't a folder named R-project on the desktop, copy the one on the CD to the desktop. 2) Create a desktop icon for R that points to Rgui.exe on the CD. The installation must determine what drive is currently being accessed, since D:\R-2.6.1\bin\Rgui.exe would only work if the CD was running from drive D. 3) Have the icon Start in desktop\R-project which is legal if you create the icon yourself, but apparently not legal to put on the CD since the windows are erased and cannot be filled in if the icon is copied back from the CD to the desktop. Since the basic R installation on Windows can create a desktop icon, I know this must be possible. I would be grateful for any help. Thanks Charles Annis, P.E. [EMAIL PROTECTED] phone: 561-352-9699 eFax: 614-455-3265 http://www.StatisticalEngineering.com __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Conditionally incrementing a loop counter
Hi, I am trying a for loop from 1 to 100 by 1. However, if a condition does not get met, I want to throw away that iteration. So if my loop is for (i in 1:100) and i is say, 25 and the condition is not met then I don't want i to go up to 26. Is there a way to do that? I can't seem to manually adjust i because from what I understand, R creates 100 long vector and uses that to loops thru and I'm not sure how to get at the index of that vector. Any suggestions? Thanks in advance. Mike Jones Westat 1650 Research Blvd. RE401 Rockville, MD 20850 Ph: 240.314.2312 [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Conditionally incrementing a loop counter
Mike Jones wrote: Hi, I am trying a for loop from 1 to 100 by 1. However, if a condition does not get met, I want to throw away that iteration. So if my loop is for (i in 1:100) and i is say, 25 and the condition is not met then I don't want i to go up to 26. Is there a way to do that? I can't seem to manually adjust i because from what I understand, R creates 100 long vector and uses that to loops thru and I'm not sure how to get at the index of that vector. Any suggestions? Thanks in advance. You're not being entirely clear. If you don't increment the loop counter, you generally get stuck in an infinite loop. That is, unless you rely on external input somehow, which you never told us about. You can easily do a while()-type loop in R, but whether that solves your problem is hard to tell. Often the solution lies in whole-object thinking, and can end up quite different from index-fiddling, so it might help if you said what the actual problem is. -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Reminiscing on 20 years using S
My first exposure to S was on an ATT 3B2 (a 3B2/100, I think), at the Auckland (Mt Albert) Applied Mathematics Division Station of the NZ Dept of Scientific and Industrial Research. The AMD Head Office in Wellington had one also. There may have been one or more others; I cannot remember. This would have been in 1983, maybe. It was a superbly engineered machine, but the sofware (System V, version 3.2) had its problems. If you back deleted too far along the command line, something unpleasant (losing the line? or worse?) happened. On typing 1+1 at the S command line, it took a second to get an answer. John Maindonald email: [EMAIL PROTECTED] phone : +61 2 (6125)3473fax : +61 2(6125)5549 Centre for Mathematics Its Applications, Room 1194, John Dedman Mathematical Sciences Building (Building 27) Australian National University, Canberra ACT 0200. On 27 Dec 2007, at 10:00 PM, [EMAIL PROTECTED] wrote: From: roger koenker [EMAIL PROTECTED] Date: 27 December 2007 9:56:45 AM To: Greg Snow [EMAIL PROTECTED] Cc: R-help list [EMAIL PROTECTED] Subject: Re: [R] Reminiscing on 20 years using S On Dec 26, 2007, at 2:05 PM, Greg Snow wrote: I realized earlier this year (2007) that it was in 1987 that I first started using an early version of S (it was ported to VMS and was called success). That means that I have been using some variant of S (to various degrees) for over 20 years now (I don't feel that old). Boxing day somehow seems appropriate for this thread. R.I.P. to all those old boxes of yesteryore and the software that ran on them -- and yet there is always a residual archaeological curiosity. I discovered recently that the MIT athena network contains a circa 1989 version of S: http://stuff.mit.edu/afs/athena/astaff/project/Sdev/S/ which made me wonder whether there was any likelihood that one could recreate S Thu Dec 7 16:49:47 EST 1989. Curiosity is one thing, time to dig through the layers of ancient civilizations is quite another. But if anyone would like to offer a (preferably educated) guess about the feasibility of such a project, like I said, I would be curious. url:www.econ.uiuc.edu/~rogerRoger Koenker email [EMAIL PROTECTED] Department of Economics vox:217-333-4558University of Illinois fax:217-244-6678Champaign, IL 61820 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] warning on gamma option in par(args) or calling par(= new)?
Dear All,
I have the following function
tstpar -
function(n = 200, want.pdf = FALSE, pdfFileName = NULL){
oldpar - par(no.readonly = TRUE)
on.exit(par(oldpar))
steps - seq(from = 1, to = 8, by = 1)
h - 10; w - 6
if(want.pdf){pdf(file = pdfFileName, onefile = TRUE,
paper = letter, width = w, height = h)}
par(mfrow = c(4,2))
for(i in steps){
txt - paste(i = , i)
hist(rnorm(n), main = txt)
}
if(want.pdf){dev.off()}
}
when called with default values tstpar() every thing works fine.
However I get 2 sorts of warnings
1- if I call the function to generate a pdf as
tstpar(want.pdf = TRUE, pdfFilename = jj.pdf)
I get the following warning msg:
calling par(new=) with no plot in: par(oldpar)
with an empty device which I don not understand since I close
the device in the function.
2- If I comment the line
if (want.pdf){dev.off()}
I get the following warning
'gamma' cannot be modified on this device in: par(args)
with 2 empty devices.
I do not understand why I get those warnings and why I get those empty devices.
I looked up in RSiteSearch and I found the 2 following posts
http://finzi.psych.upenn.edu/R/Rhelp02a/archive/38553.html
In this post M. Schwarz explains that there is not a plot created that's why R
generates the
warning. In the case of tstpar, I generate the hist plots and should not be
getting the warning.
And in the following post Prof Ripley refers to an old R warning for pdf()
devices
Which is not the case here.
http://finzi.psych.upenn.edu/R/Rhelp02a/archive/23215.html
I do not see what I am missing. Thanks for any hint.
I use R 2.5.1 under Win XP.
I apologize if the question is related to my older R version which I will
upgrade.
AA.
[[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] Conditionally incrementing a loop counter
Please read the posting guide and provide a simple reproducible example as it asks you to. Very likely a loop is not even needed. -- Bert Gunter Genentech, Inc. -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Mike Jones Sent: Thursday, December 27, 2007 1:35 PM To: [EMAIL PROTECTED] Subject: [R] Conditionally incrementing a loop counter Hi, I am trying a for loop from 1 to 100 by 1. However, if a condition does not get met, I want to throw away that iteration. So if my loop is for (i in 1:100) and i is say, 25 and the condition is not met then I don't want i to go up to 26. Is there a way to do that? I can't seem to manually adjust i because from what I understand, R creates 100 long vector and uses that to loops thru and I'm not sure how to get at the index of that vector. Any suggestions? Thanks in advance. Mike Jones Westat 1650 Research Blvd. RE401 Rockville, MD 20850 Ph: 240.314.2312 [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] groupedData function not found
Hello, I'm trying to use the groupedData function and R is giving me the message: Error: can not find function groupedData The code is coming from a textbook so I think it should be correct: pigs-data.frame(cbind(pig.time,pig.id,pig.wt)) pig.growth-groupedData(pig.wt~pig.time|pig.id,data=pigs) I have added the package nlme and to confirm that it was installed correctly I requested the list of functions included in the package (library(help=nlme)) and I do see groupData in the list. I am using R 2.6.1 in Windows XP. I'll appreciate your help. Thanks, Andrea Previtali Post-doc fellow Dept. of Biology, Univ. of Utah, SLC, UT. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Conditionally incrementing a loop counter: Take 2
My apologies for not including a working example.
Here it is:
for (i in 1:10){
cat(initial i = ,i,\n)
x - runif(1)
if (x 0.7){
i - i-1
}
cat(second i = ,i,\n)
}
When I ran this i got what follows, so there were four cases where I
wanted the i not to increment.
initial i = 1
second i = 1
initial i = 2
second i = 1
initial i = 3
second i = 3
initial i = 4
second i = 3
initial i = 5
second i = 4
initial i = 6
second i = 6
initial i = 7
second i = 7
initial i = 8
second i = 7
initial i = 9
second i = 9
initial i = 10
second i = 10
-Original Message-
From: Mike Jones
Sent: Thursday, December 27, 2007 4:35 PM
To: '[EMAIL PROTECTED]'
Subject: Conditionally incrementing a loop counter
Hi,
I am trying a for loop from 1 to 10 by 1. However, if a condition does
not get met, I want to throw away that iteration. So if my loop is
for (i in 1:10)
and i is say, 4 and the condition is not met then I don't want i to go
up to 5. Is there a way to do that? I can't seem to manually adjust i
because from what I understand, R creates 10 long vector and uses that
to loops thru and I'm not sure how to get at the index of that
vector. Any suggestions? Thanks in advance.
Mike Jones
Westat
1650 Research Blvd. RE401
Rockville, MD 20850
Ph: 240.314.2312
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Conditionally incrementing a loop counter: Take 2
Mike Jones wrote:
My apologies for not including a working example.
Here it is:
for (i in 1:10){
cat(initial i = ,i,\n)
x - runif(1)
if (x 0.7){
i - i-1
}
cat(second i = ,i,\n)
}
When I ran this i got what follows, so there were four cases where I
wanted the i not to increment.
initial i = 1
second i = 1
initial i = 2
second i = 1
initial i = 3
second i = 3
initial i = 4
second i = 3
initial i = 5
second i = 4
initial i = 6
second i = 6
initial i = 7
second i = 7
initial i = 8
second i = 7
initial i = 9
second i = 9
initial i = 10
second i = 10
Is this the kind of effect you want?
x - runif(10)
cbind(x, 1:10, cumsum(x .7))
x
[1,] 0.384165631 1 1
[2,] 0.392715845 2 2
[3,] 0.895936431 3 2
[4,] 0.910242185 4 2
[5,] 0.689987301 5 3
[6,] 0.237071326 6 4
[7,] 0.225032680 7 5
[8,] 0.001856286 8 6
[9,] 0.392034868 9 7
[10,] 0.655076045 10 8
If you insist on using a loop, you need to separate the loop control
from the manipulation of i, as in (e.g.)
i - 0
for (j in 1:10){
i - i + 1
cat(initial i = ,i,\n)
x - runif(1)
if (x 0.7){
i - i-1
}
cat(second i = ,i,\n)
}
-Original Message-
From:Mike Jones
Sent:Thursday, December 27, 2007 4:35 PM
To: '[EMAIL PROTECTED]'
Subject: Conditionally incrementing a loop counter
Hi,
I am trying a for loop from 1 to 10 by 1. However, if a condition does
not get met, I want to throw away that iteration. So if my loop is
for (i in 1:10)
and i is say, 4 and the condition is not met then I don't want i to go
up to 5. Is there a way to do that? I can't seem to manually adjust i
because from what I understand, R creates 10 long vector and uses that
to loops thru and I'm not sure how to get at the index of that
vector. Any suggestions? Thanks in advance.
Mike Jones
Westat
1650 Research Blvd. RE401
Rockville, MD 20850
Ph: 240.314.2312
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B
c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K
(*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918
~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Odd time conversion glitch
Read RNews 4/1 and follow the advice there. On Dec 27, 2007 2:31 PM, Pat Carroll [EMAIL PROTECTED] wrote: Hello, all. I ran across an odd problem while working in R 2.6.0. The command line text follows. Basically, I attempted to convert a character vector of length 13 (in a data frame with 13 rows) from a character representation of dates to a POSIX representation using strptime. strptime returned a vector of length 9, which appears to contain 13 values (!) in the appropriate format. I can't find any way to convince the strptime output that it has 13 values . . . even though (for example) posixvector[1:13] returns 13 values, anothervectorof length13-posixvector[1:13] produces a length mismatch error. Can anyone help diagnose this, or work around it? Many thanks, ~Pat Carroll. Dataset$DateFilled [1] 10/20/2005 11/4/2005 11/18/2005 12/2/2005 4/3/2006 6/5/2006 7/14/2006 4/27/2007 5/7/2007 7/17/2007 2/14/2005 [12] 2/14/2005 2/21/2005 datefilledpos-strptime(Dataset$DateFilled,format=%m/%d/%Y) datefilledpos [1] 2005-10-20 2005-11-04 2005-11-18 2005-12-02 2006-04-03 2006-06-05 2006-07-14 2007-04-27 2007-05-07 2007-07-17 2005-02-14 [12] 2005-02-14 2005-02-21 length(datefilledpos) [1] 9 length(Dataset$DateFilled) [1] 13 datefilledpos[1:13] [1] 2005-10-20 2005-11-04 2005-11-18 2005-12-02 2006-04-03 2006-06-05 2006-07-14 2007-04-27 2007-05-07 2007-07-17 2005-02-14 [12] 2005-02-14 2005-02-21 Dataset$DateFilled-datefilledpos Error in `$-.data.frame`(`*tmp*`, DateFilled, value = list(sec = c(0, : replacement has 9 rows, data has 13 Dataset$DateFilled-datefilledpos[1:13] Error in `$-.data.frame`(`*tmp*`, DateFilled, value = list(sec = c(0, : replacement has 9 rows, data has 13 Pat Carroll. what matters most is how well you walk through the fire. bukowski. Be a better friend, newshound, and __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Lda and Qda
Hi all,
I'm working with some data: 54 variables and a column of classes, each
observation as one of a possible seven different classes:
var.can3-lda(x=dados[,c(1:28,30:54)],grouping=dados[,55],CV=TRUE)
Warning message:
In lda.default(x, grouping, ...) : variables are collinear
summary(var.can3)
Length Class Mode
class 3 factor numeric ### why?? I don't understand it
posterior 21 -none- numeric
call 4 -none- call## what's this?
var.can-lda(dados[,c(1:28,30:54)],dados[,55])#porque a variavel 29 é
constante
Warning message:
In lda.default(x, grouping, ...) : variables are collinear
summary(var.can)
Length Class Mode
prior 7-none- numeric
counts7-none- numeric
means 371-none- numeric
scaling 318-none- numeric
lev 7-none- character
svd 6-none- numeric
N 1-none- numeric
call 3-none- call
(normalizar-function(matriz){ n-dim(matriz)[1]; m-dim(matriz)[2];
normas-sqrt(colSums(matriz*matriz));
matriz.normalizada-matriz/t(matrix(rep(normas,n),m,n));return(matriz.normalizada)})
function(matriz){ n-dim(matriz)[1]; m-dim(matriz)[2];
normas-sqrt(colSums(matriz*matriz));
matriz.normalizada-matriz/t(matrix(rep(normas,n),m,n));return(matriz.normalizada)}
var.canonicas-as.matrix(dados[,c(1:28,30:54)])%*%(normalizar(var.can$scaling))
summary(var.canonicas)
LD1 LD2 LD3 LD4
Min. :-21.942 Min. :-6.820 Min. :-10.138 Min. :-6.584
1st Qu.:-20.014 1st Qu.:-5.480 1st Qu.: -8.280 1st Qu.: 0.872
Median :-19.495 Median :-5.007 Median : -7.800 Median : 1.083
Mean :-18.827 Mean :-4.760 Mean : -7.803 Mean : 1.134
3rd Qu.:-18.975 3rd Qu.:-4.456 3rd Qu.: -7.278 3rd Qu.: 1.311
Max. : -7.886 Max. : 3.116 Max. : -1.619 Max. : 5.556
LD5 LD6
Min. :-11.083 Min. :-4.4972
1st Qu.: -1.237 1st Qu.:-1.6497
Median : -1.100 Median :-1.0909
Mean : -1.100 Mean :-0.9808
3rd Qu.: -0.957 3rd Qu.:-0.4598
Max. : 4.712 Max. : 7.5356
I don't know wether I need to specify a training set and a testing set, I also
don't know the error nor the classifier; shouldn't the lenght of class of
var.can3 be 7 since I only have 7 different classes?
Best regards,
Pedro Marques
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[R] Help with lm and multiple linear regression?
Hello, I'm new to R, but I've read the intro to R and successfully connected it to an instance of mysql. I'm trying to perform multiple linear regression, but I'm having trouble using the lm function. To start, I have read in a simply y matrix of values(dependent variable) and x matrix of independent variables. It says both are data frames, but lm is giving me an error that my y variable is a list. Any suggestions on how to do this? It's not clear to me what the problem is as they're both data frames. My actual problem will use a much wider matrix of coefficients, I've only included two for illustration. Additionally, I'd actually like to weight the observations. How would I go about doing that? I also have that as a separate column vector. Thanks, Aaron Here's my session: margin margin 166.67 2 -58.33 3 100.00 4 -33.33 5 200.00 6 -83.33 7 -100.00 8 0.00 9 100.00 10 -18.18 11 -55.36 12 -125.00 13 -33.33 14 -200.00 150.00 16 -100.00 17 75.00 180.00 19 -200.00 20 35.71 21 100.00 22 50.00 23 -86.67 24 165.00 personcoeff Person1 Person2 1 -1 1 2 -1 1 3 -1 1 4 -1 1 5 -1 1 6 -1 1 70 0 80 0 90 1 10 -1 1 11 -1 1 12 -1 1 13 -1 1 14 -1 0 15 0 0 16 0 0 17 0 1 18 -1 1 19 -1 1 20 -1 1 21 -1 1 22 -1 1 23 -1 1 24 -1 1 class(margin) [1] data.frame class(personcoeff) [1] data.frame lm(margin~personcoeff) Error in model.frame(formula, rownames, variables, varnames, extras, extranames, : invalid type (list) for variable 'margin' Be a better friend, newshound, and [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Conditionally incrementing a loop counter: Take 2
Since I didn't want the i to increment in the loop when the condition is not
met, then in my example I wanted the loop to actually run 14 times instead of
the 10 since I wanted 4 of the iterations to be thrown away, or ignored. I
still haven't been able to figure this out. Going the while route doesn't
seem to work for me either.
nums - numeric(10)
i - 1
garbage - 0
while (i = 10){
x - runif(1)
cat(x = ,x,\n)
if (x 0.1){
nums[i] - x
i - i + 1
}
else{
garbage - garbage+1
}
cat(i = ,i,garbage = ,garbage,\n)
}
-Original Message-
From: Peter Dalgaard [mailto:[EMAIL PROTECTED]
Sent: Thursday, December 27, 2007 5:36 PM
To: Mike Jones
Cc: [EMAIL PROTECTED]
Subject: Re: [R] Conditionally incrementing a loop counter: Take 2
Mike Jones wrote:
My apologies for not including a working example.
Here it is:
for (i in 1:10){
cat(initial i = ,i,\n)
x - runif(1)
if (x 0.7){
i - i-1
}
cat(second i = ,i,\n)
}
When I ran this i got what follows, so there were four cases where I
wanted the i not to increment.
initial i = 1
second i = 1
initial i = 2
second i = 1
initial i = 3
second i = 3
initial i = 4
second i = 3
initial i = 5
second i = 4
initial i = 6
second i = 6
initial i = 7
second i = 7
initial i = 8
second i = 7
initial i = 9
second i = 9
initial i = 10
second i = 10
Is this the kind of effect you want?
x - runif(10)
cbind(x, 1:10, cumsum(x .7))
x
[1,] 0.384165631 1 1
[2,] 0.392715845 2 2
[3,] 0.895936431 3 2
[4,] 0.910242185 4 2
[5,] 0.689987301 5 3
[6,] 0.237071326 6 4
[7,] 0.225032680 7 5
[8,] 0.001856286 8 6
[9,] 0.392034868 9 7
[10,] 0.655076045 10 8
If you insist on using a loop, you need to separate the loop control
from the manipulation of i, as in (e.g.)
i - 0
for (j in 1:10){
i - i + 1
cat(initial i = ,i,\n)
x - runif(1)
if (x 0.7){
i - i-1
}
cat(second i = ,i,\n)
}
-Original Message-
From:Mike Jones
Sent:Thursday, December 27, 2007 4:35 PM
To: '[EMAIL PROTECTED]'
Subject: Conditionally incrementing a loop counter
Hi,
I am trying a for loop from 1 to 10 by 1. However, if a condition
does not get met, I want to throw away that iteration. So if my
loop is for (i in 1:10) and i is say, 4 and the condition is not met
then I don't want i to go up to 5. Is there a way to do that? I
can't seem to manually adjust i because from what I understand, R
creates 10 long vector and uses that to loops thru and I'm not sure
how to get at the index of that vector. Any suggestions? Thanks in
advance.
Mike Jones
Westat
1650 Research Blvd. RE401
Rockville, MD 20850
Ph: 240.314.2312
[[alternative HTML version deleted]]
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--
O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B
c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K
(*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918
~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907
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[R] SAS to R - if you don't have a SAS license
Hi all, if you do not have a SAS license but want to convert native SAS data files, the solution below will work. # read SAS data without SAS # 1. Download free SAS System Viewer from either of the sites below: # http://www.sas.com/apps/demosdownloads/setupcat.jsp?cat=SAS+System+Viewer (requires registration) # http://www.umass.edu/statdata/software/downloads/SASViewer/index.html # 2. Open SAS data in the SAS System Viewer # 3. View-Formatted sets the data in formatted view # 4. Save As File...csv file - this is your SAS data file # 5. View-Variables (now showing the variable names and formats) # 6. Save As File...csv file - this is your SAS variable definition file # run code below wrkdir-getwd() # save working directory to reset later # Select the SAS data file... sas.data-read.table(file.choose(),header=T, sep=,, na.strings=.) # Select SAS variable definition file... sas.def-read.csv(file.choose()) # str(sas.def) # sas.def$SASFORMAT[sas.def$Type==Char]-character # sas.def$SASFORMAT[sas.def$Type==Num]-numeric sas.def$SASFORMAT[substr(sas.def$Format,1,4)==DATE]-date sas.def-sas.def[,length(names(sas.def))] # pick last column tmp-which(sas.def==date) sas.data[,tmp] - as.data.frame(strptime(sas.data[,tmp], %d%b%Y:%H:%M:%S)) str(sas.data) print(head(sas.data)) setwd(wrkdir) # reset working directory rm(wrkdir,tmp,sas.def) # the end Be a better friend, newshound, and __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Efficiency of for-loop in R
Hi, I just realized that in Matlab, as long as memory is pre-allocated, doing for-loop doesn't cost more time than doing things in vector form. But it seems in R, it still cost a lot to do for-loop. Is there any improvement in R that I missed. Thanks a lot. Merry Xmas Everyone ! __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] SAS to R - if you don't have a SAS license
while I move data between SAS and R all the time, personally I don't think your recommendation is very practical. Instead, I feel SAS transport file is much better than csv. Plus, the sas dataset created on unix can't be opened by sas viewer on windows. It is even undoable if the dataset is large. Just my $0.02. On Dec 27, 2007 6:33 PM, Gyula Gulyas [EMAIL PROTECTED] wrote: Hi all, if you do not have a SAS license but want to convert native SAS data files, the solution below will work. # read SAS data without SAS # 1. Download free SAS System Viewer from either of the sites below: # http://www.sas.com/apps/demosdownloads/setupcat.jsp?cat=SAS+System+Viewer (requires registration) # http://www.umass.edu/statdata/software/downloads/SASViewer/index.html # 2. Open SAS data in the SAS System Viewer # 3. View-Formatted sets the data in formatted view # 4. Save As File...csv file - this is your SAS data file # 5. View-Variables (now showing the variable names and formats) # 6. Save As File...csv file - this is your SAS variable definition file # run code below wrkdir-getwd() # save working directory to reset later # Select the SAS data file... sas.data-read.table(file.choose(),header=T, sep=,, na.strings=.) # Select SAS variable definition file... sas.def-read.csv(file.choose()) # str(sas.def) # sas.def$SASFORMAT[sas.def$Type==Char]-character # sas.def$SASFORMAT[sas.def$Type==Num]-numeric sas.def$SASFORMAT[substr(sas.def$Format,1,4)==DATE]-date sas.def-sas.def[,length(names(sas.def))] # pick last column tmp-which(sas.def==date) sas.data[,tmp] - as.data.frame(strptime(sas.data[,tmp], %d%b%Y:%H:%M:%S)) str(sas.data) print(head(sas.data)) setwd(wrkdir) # reset working directory rm(wrkdir,tmp,sas.def) # the end Be a better friend, newshound, and __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- === WenSui Liu Statistical Project Manager ChoicePoint Precision Marketing (http://spaces.msn.com/statcompute/blog) __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Help with lm and multiple linear regression? (Plain Text version)
consider merging everything into a singe dataframe. i haven't tried
it, but something like the following could work:
reg.data - cbind(margin, personcoeff)
names(reg.data) - c('margin', 'p1', 'p2')
lm(margin~p1+p2, data = reg.data)
the idea here is that by specifying the data frame with the data
argument in lm, R looks for the columns of the names specified in the
formula.
for weights, see ?lm and look for the weights argument.
cheers,
tc
On Dec 28, 2007 10:22 AM, Aaron Barzilai [EMAIL PROTECTED] wrote:
(Apologies the previous version was sent as rich text)
Hello,
I'm new to R, but I've read the intro to R and successfully connected it to
an instance of mysql. I'm trying to perform multiple linear regression, but
I'm having trouble using the lm function. To start, I have read in a simply
y matrix of values(dependent variable) and x matrix of independent variables.
It says both are data frames, but lm is giving me an error that my y
variable is a list.
Any suggestions on how to do this? It's not clear to me what the problem is
as they're both data frames. My actual problem will use a much wider matrix
of coefficients, I've only included two for illustration.
Additionally, I'd actually like to weight the observations. How would I go
about doing that? I also have that as a separate column vector.
Thanks,
Aaron
Here's my session:
margin
margin
166.67
2 -58.33
3 100.00
4 -33.33
5 200.00
6 -83.33
7 -100.00
8 0.00
9 100.00
10 -18.18
11 -55.36
12 -125.00
13 -33.33
14 -200.00
150.00
16 -100.00
17 75.00
180.00
19 -200.00
20 35.71
21 100.00
22 50.00
23 -86.67
24 165.00
personcoeff
Person1 Person2
1 -1 1
2 -1 1
3 -1 1
4 -1 1
5 -1 1
6 -1 1
70 0
80 0
90 1
10 -1 1
11 -1 1
12 -1 1
13 -1 1
14 -1 0
15 0 0
16 0 0
17 0 1
18 -1 1
19 -1 1
20 -1 1
21 -1 1
22 -1 1
23 -1 1
24 -1 1
class(margin)
[1] data.frame
class(personcoeff)
[1] data.frame
lm(margin~personcoeff)
Error in model.frame(formula, rownames, variables, varnames, extras,
extranames, :
invalid type (list) for variable 'margin'
Be a better friend, newshound, and
__
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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.
--
Tim Calkins
0406 753 997
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[R] Help with lm and multiple linear regression? (Plain Text version)
(Apologies the previous version was sent as rich text) Hello, I'm new to R, but I've read the intro to R and successfully connected it to an instance of mysql. I'm trying to perform multiple linear regression, but I'm having trouble using the lm function. To start, I have read in a simply y matrix of values(dependent variable) and x matrix of independent variables. It says both are data frames, but lm is giving me an error that my y variable is a list. Any suggestions on how to do this? It's not clear to me what the problem is as they're both data frames. My actual problem will use a much wider matrix of coefficients, I've only included two for illustration. Additionally, I'd actually like to weight the observations. How would I go about doing that? I also have that as a separate column vector. Thanks, Aaron Here's my session: margin margin 166.67 2 -58.33 3 100.00 4 -33.33 5 200.00 6 -83.33 7 -100.00 8 0.00 9 100.00 10 -18.18 11 -55.36 12 -125.00 13 -33.33 14 -200.00 150.00 16 -100.00 17 75.00 180.00 19 -200.00 20 35.71 21 100.00 22 50.00 23 -86.67 24 165.00 personcoeff Person1 Person2 1 -1 1 2 -1 1 3 -1 1 4 -1 1 5 -1 1 6 -1 1 70 0 80 0 90 1 10 -1 1 11 -1 1 12 -1 1 13 -1 1 14 -1 0 15 0 0 16 0 0 17 0 1 18 -1 1 19 -1 1 20 -1 1 21 -1 1 22 -1 1 23 -1 1 24 -1 1 class(margin) [1] data.frame class(personcoeff) [1] data.frame lm(margin~personcoeff) Error in model.frame(formula, rownames, variables, varnames, extras, extranames, : invalid type (list) for variable 'margin' Be a better friend, newshound, and __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Efficiency of for-loop in R
Exactly what is the problem you are trying to solve? Could you provide commented, minimal, self-contained, reproducible code? A lot depends on what you are trying to do, There might be other ways, in R, than a 'for' loop to solve your problems. On Dec 27, 2007 6:44 PM, Tong Wang [EMAIL PROTECTED] wrote: Hi, I just realized that in Matlab, as long as memory is pre-allocated, doing for-loop doesn't cost more time than doing things in vector form. But it seems in R, it still cost a lot to do for-loop. Is there any improvement in R that I missed. Thanks a lot. Merry Xmas Everyone ! __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem you are trying to solve? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Reminiscing on 20 years using S
My introduction to S was around 1984 on a 3B20 and VAX systems at Bell Labs. I still have a copy of the brown book written by Becker and Chambers on the S Interactive Language (copyright 1984). I remember the graphical output on a daisy-wheel printer and using the HP plotter that was connected in serial with the terminal you were using. When you wanted to plot, escape sequences were sent so the plotter interpreted the output and plotted on paper that it moved back and forth as the pens went horizontal. It has changed a lot, but has also stayed the same in a number of ways. On Dec 27, 2007 5:12 PM, John Maindonald [EMAIL PROTECTED] wrote: My first exposure to S was on an ATT 3B2 (a 3B2/100, I think), at the Auckland (Mt Albert) Applied Mathematics Division Station of the NZ Dept of Scientific and Industrial Research. The AMD Head Office in Wellington had one also. There may have been one or more others; I cannot remember. This would have been in 1983, maybe. It was a superbly engineered machine, but the sofware (System V, version 3.2) had its problems. If you back deleted too far along the command line, something unpleasant (losing the line? or worse?) happened. On typing 1+1 at the S command line, it took a second to get an answer. John Maindonald email: [EMAIL PROTECTED] phone : +61 2 (6125)3473fax : +61 2(6125)5549 Centre for Mathematics Its Applications, Room 1194, John Dedman Mathematical Sciences Building (Building 27) Australian National University, Canberra ACT 0200. On 27 Dec 2007, at 10:00 PM, [EMAIL PROTECTED] wrote: From: roger koenker [EMAIL PROTECTED] Date: 27 December 2007 9:56:45 AM To: Greg Snow [EMAIL PROTECTED] Cc: R-help list [EMAIL PROTECTED] Subject: Re: [R] Reminiscing on 20 years using S On Dec 26, 2007, at 2:05 PM, Greg Snow wrote: I realized earlier this year (2007) that it was in 1987 that I first started using an early version of S (it was ported to VMS and was called success). That means that I have been using some variant of S (to various degrees) for over 20 years now (I don't feel that old). Boxing day somehow seems appropriate for this thread. R.I.P. to all those old boxes of yesteryore and the software that ran on them -- and yet there is always a residual archaeological curiosity. I discovered recently that the MIT athena network contains a circa 1989 version of S: http://stuff.mit.edu/afs/athena/astaff/project/Sdev/S/ which made me wonder whether there was any likelihood that one could recreate S Thu Dec 7 16:49:47 EST 1989. Curiosity is one thing, time to dig through the layers of ancient civilizations is quite another. But if anyone would like to offer a (preferably educated) guess about the feasibility of such a project, like I said, I would be curious. url:www.econ.uiuc.edu/~rogerRoger Koenker email [EMAIL PROTECTED] Department of Economics vox:217-333-4558University of Illinois fax:217-244-6678Champaign, IL 61820 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem you are trying to solve? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Conditionally incrementing a loop counter: Take 2
John Fox wrote:
Dear Mike,
You could use a repeat loop and manage the index yourself:
i - 0
repeat{
x - runif(1)
if (x .1){
i - i + 1
cat(x = , x, \n)
}
if (i == 10) break
}
But if your example problem reflects your actual application, why not just
generate uniform random numbers on the interval (0, .1)?
As I read it, it is the sequence of i's not the x's that are sought. The
example suddenly skipped from something with x .7 to something with x
.1, but it might be that Mike's while loop just needed to print i at
the top of the loop rather than at the bottom. The result should
(AFAICS) be equivalent to
rep(1:10, 1+rgeom(10, .7))
[1] 1 1 2 3 4 5 6 7 8 8 9 10 10
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]
project.org] On Behalf Of Mike Jones
Sent: December-27-07 6:08 PM
To: Peter Dalgaard
Cc: [EMAIL PROTECTED]
Subject: Re: [R] Conditionally incrementing a loop counter: Take 2
Since I didn't want the i to increment in the loop when the condition
is not met, then in my example I wanted the loop to actually run 14
times instead of the 10 since I wanted 4 of the iterations to be thrown
away, or ignored. I still haven't been able to figure this out. Going
the while route doesn't seem to work for me either.
nums - numeric(10)
i - 1
garbage - 0
while (i = 10){
x - runif(1)
cat(x = ,x,\n)
if (x 0.1){
nums[i] - x
i - i + 1
}
else{
garbage - garbage+1
}
cat(i = ,i,garbage = ,garbage,\n)
}
-Original Message-
From: Peter Dalgaard [mailto:[EMAIL PROTECTED]
Sent: Thursday, December 27, 2007 5:36 PM
To: Mike Jones
Cc: [EMAIL PROTECTED]
Subject: Re: [R] Conditionally incrementing a loop counter: Take 2
Mike Jones wrote:
My apologies for not including a working example.
Here it is:
for (i in 1:10){
cat(initial i = ,i,\n)
x - runif(1)
if (x 0.7){
i - i-1
}
cat(second i = ,i,\n)
}
When I ran this i got what follows, so there were four cases where I
wanted the i not to increment.
initial i = 1
second i = 1
initial i = 2
second i = 1
initial i = 3
second i = 3
initial i = 4
second i = 3
initial i = 5
second i = 4
initial i = 6
second i = 6
initial i = 7
second i = 7
initial i = 8
second i = 7
initial i = 9
second i = 9
initial i = 10
second i = 10
Is this the kind of effect you want?
x - runif(10)
cbind(x, 1:10, cumsum(x .7))
x
[1,] 0.384165631 1 1
[2,] 0.392715845 2 2
[3,] 0.895936431 3 2
[4,] 0.910242185 4 2
[5,] 0.689987301 5 3
[6,] 0.237071326 6 4
[7,] 0.225032680 7 5
[8,] 0.001856286 8 6
[9,] 0.392034868 9 7
[10,] 0.655076045 10 8
If you insist on using a loop, you need to separate the loop control
from the manipulation of i, as in (e.g.)
i - 0
for (j in 1:10){
i - i + 1
cat(initial i = ,i,\n)
x - runif(1)
if (x 0.7){
i - i-1
}
cat(second i = ,i,\n)
}
-Original Message-
From: Mike Jones
Sent: Thursday, December 27, 2007 4:35 PM
To:'[EMAIL PROTECTED]'
Subject: Conditionally incrementing a loop counter
Hi,
I am trying a for loop from 1 to 10 by 1. However, if a condition
does not get met, I want to throw away that iteration. So if my
loop is for (i in 1:10) and i is say, 4 and the condition is not met
then I don't want i to go up to 5. Is there a way to do that? I
can't seem to manually adjust i because from what I understand, R
creates 10 long vector and uses that to loops thru and I'm not
sure
how to get at the index of that vector. Any suggestions? Thanks in
advance.
Mike Jones
Westat
1650 Research Blvd. RE401
Rockville, MD 20850
Ph: 240.314.2312
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Re: [R] Efficiency of for-loop in R
HI, The question is meant to be a general one, I am trying to find out if there is new development in R that I might have missed. but here's a trivial example, To compute y=sin(x) , x = 1,2,... 10 x=1:10, 1. y =sin(x) 2. for(i in 1:10) y=sin(x[i]) 1 is much faster than 2. Old Matlab also had this problem, but in new versions, 1 and 2 are mostly the same. I am just wondering if the same improvement has happened or will happen to R. Thanks . - Original Message - From: jim holtman [EMAIL PROTECTED] Date: Thursday, December 27, 2007 4:39 pm Subject: Re: [R] Efficiency of for-loop in R To: Tong Wang [EMAIL PROTECTED] Cc: R help [EMAIL PROTECTED] Exactly what is the problem you are trying to solve? Could you provide commented, minimal, self-contained, reproducible code? A lot depends on what you are trying to do, There might be other ways, in R, than a 'for' loop to solve your problems. On Dec 27, 2007 6:44 PM, Tong Wang [EMAIL PROTECTED] wrote: Hi, I just realized that in Matlab, as long as memory is pre- allocated, doing for-loop doesn't cost more time than doing things in vector form. But it seems in R, it still cost a lot to do for-loop. Is there any improvement in R that I missed. Thanks a lot. Merry Xmas Everyone ! __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting- guide.html and provide commented, minimal, self-contained, reproducible code. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem you are trying to solve? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Efficiency of for-loop in R
I will venture a guess in that in the case of the 'for' loop, you are calling 'sin' 100,000 times incurring the cost of individual function calls at the interpreter level plus evaluating 'for' loop. In the vectorized case, you are only interpreting a single 'sin' call and then internally evaluating the 'sin' function, which is a lot faster. Also the results are different in the two cases. In case 1) you get 10 values back in 'y' and in 2) you only get the value of the last loop through the 'for' loop. system.time(for (i in 1:10) y - sin(i)) user system elapsed 0.170.000.28 str(y) num 0.0357 system.time(y - sin(1:10)) user system elapsed 0.010.000.02 str(y) num [1:10] 0.841 0.909 0.141 -0.757 -0.959 ... R is typically optimized for vector type operations. On Dec 27, 2007 8:39 PM, Tong Wang [EMAIL PROTECTED] wrote: HI, The question is meant to be a general one, I am trying to find out if there is new development in R that I might have missed. but here's a trivial example, To compute y=sin(x) , x = 1,2,... 10 x=1:10, 1. y =sin(x) 2. for(i in 1:10) y=sin(x[i]) 1 is much faster than 2. Old Matlab also had this problem, but in new versions, 1 and 2 are mostly the same. I am just wondering if the same improvement has happened or will happen to R. Thanks . - Original Message - From: jim holtman [EMAIL PROTECTED] Date: Thursday, December 27, 2007 4:39 pm Subject: Re: [R] Efficiency of for-loop in R To: Tong Wang [EMAIL PROTECTED] Cc: R help [EMAIL PROTECTED] Exactly what is the problem you are trying to solve? Could you provide commented, minimal, self-contained, reproducible code? A lot depends on what you are trying to do, There might be other ways, in R, than a 'for' loop to solve your problems. On Dec 27, 2007 6:44 PM, Tong Wang [EMAIL PROTECTED] wrote: Hi, I just realized that in Matlab, as long as memory is pre- allocated, doing for-loop doesn't cost more time than doing things in vector form. But it seems in R, it still cost a lot to do for-loop. Is there any improvement in R that I missed. Thanks a lot. Merry Xmas Everyone ! __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting- guide.html and provide commented, minimal, self-contained, reproducible code. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem you are trying to solve? -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem you are trying to solve? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Help with lm and multiple linear regression? (Plain Text version)
Tim (and others who responded privately),
Thanks for the help, this approach did work. I have also reread ?lm a little
more closely, I do see the weights functionality.
I have one last question: Now that I understand how to call this function and
review the results, I want to extend it to my much larger real problem, with
100s of columns. Is there a way to call the function in more of a matrix
algebra syntax, where I would list the matrix(e.g. personcoeff) rather than the
individual column names? It seems like I might need to use lm.wfit, but per
the help I'd rather use lm.
Thanks,
Aaron
- Original Message
From: Tim Calkins [EMAIL PROTECTED]
To: Aaron Barzilai [EMAIL PROTECTED]
Cc: r-help@r-project.org
Sent: Thursday, December 27, 2007 6:55:57 PM
Subject: Re: [R] Help with lm and multiple linear regression? (Plain Text
version)
consider merging everything into a singe dataframe. i haven't tried
it, but something like the following could work:
reg.data - cbind(margin, personcoeff)
names(reg.data) - c('margin', 'p1', 'p2')
lm(margin~p1+p2, data = reg.data)
the idea here is that by specifying the data frame with the data
argument in lm, R looks for the columns of the names specified in the
formula.
for weights, see ?lm and look for the weights argument.
cheers,
tc
On Dec 28, 2007 10:22 AM, Aaron Barzilai [EMAIL PROTECTED] wrote:
(Apologies the previous version was sent as rich text)
Hello,
I'm new to R, but I've read the intro to R and successfully connected it to
an instance of mysql. I'm trying to perform multiple linear regression, but
I'm having trouble using the lm function. To start, I have read in a simply
y matrix of values(dependent variable) and x matrix of independent variables.
It says both are data frames, but lm is giving me an error that my y
variable is a list.
Any suggestions on how to do this? It's not clear to me what the problem is
as they're both data frames. My actual problem will use a much wider matrix
of coefficients, I've only included two for illustration.
Additionally, I'd actually like to weight the observations. How would I go
about doing that? I also have that as a separate column vector.
Thanks,
Aaron
Here's my session:
margin
margin
166.67
2 -58.33
3 100.00
4 -33.33
5 200.00
6 -83.33
7 -100.00
80.00
9 100.00
10 -18.18
11 -55.36
12 -125.00
13 -33.33
14 -200.00
150.00
16 -100.00
17 75.00
180.00
19 -200.00
20 35.71
21 100.00
22 50.00
23 -86.67
24 165.00
personcoeff
Person1 Person2
1 -1 1
2 -1 1
3 -1 1
4 -1 1
5 -1 1
6 -1 1
70 0
80 0
90 1
10 -1 1
11 -1 1
12 -1 1
13 -1 1
14 -1 0
15 0 0
16 0 0
17 0 1
18 -1 1
19 -1 1
20 -1 1
21 -1 1
22 -1 1
23 -1 1
24 -1 1
class(margin)
[1] data.frame
class(personcoeff)
[1] data.frame
lm(margin~personcoeff)
Error in model.frame(formula, rownames, variables, varnames, extras,
extranames, :
invalid type (list) for variable 'margin'
Be a better friend, newshound, and
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Tim Calkins
0406 753 997
Be a better friend, newshound, and
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[R] How to catch data from the different dataframes and lm problem?
Dear all:
I am a new R-user and I have 2 questions
about it.
1) I have a dataframe. Based on “formulation” and “subject”, a
dataframe is split into 4 dataframes. The
example is as follows. Moreover, I want
to calculate “test” value for these 4 dataframes. My question is that the
“test” values not
correct and I do not know where the problem is.
2) There are 12 “test” (y) values from 1). Then, I want to model the
relationship
between “concentration” (X) and “test” (Y) by fitting the linear regression,
such lm(Y~X) and this is my target. I
think that if I can catch “test” (Y) values and “concentration” (X) values into
a dataframe, then I can carry out regression. So, how to catch all “test”
values from
different dataframes? Or does anyone
have better way to get this target?
Example:
w-(c(1,1,1,2,2,2,1,1,1,2,2,2))
y-(c(1,1,1,1,1,1,2,2,2,2,2,2))
z-(c(1,2,3,1,2,3,1,2,3,1,2,3))
c-(c(0.1,10,20,0.3,2.5,6,20,25,60,35,40,45))
df-data.frame(formulation=y, subject=w,
time=z, concentration=c)
A.split-split(df, list(df$formulation,
df$subject) )
for (j in 1:length(A.split)){
test - 0
for(i in
2:length(A.split[[j]][[time]])){
test[i] - (A.split[[1]][[time]][i] -
A.split[[1]][[time]][i-1]) *
(A.split[[1]][[concentration]][i] -
A.split[[1]][[concentration]][i-1])* 0.5
test[i]-test[i]+test[i-1]
}
output-data.frame(A.split[[j]][[subject]],A.split[[j]][[formulation]],A.split[[j]][[time]],A.split[[j]][[concentration]],test)
colnames(output)-list(subject,formulation,time,concentration,test)
show(output)
}
Best regards,
Hsin-Ya Lee
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Re: [R] Help with lm and multiple linear regression? (Plain Text version)
Hi Aaron,
if I understand your question correctly, you can use the . in the
formula, like so:
dat - data.frame(x=1:10,y=rnorm(10),z=10:1)
lm(x~., data=dat)
The dot there stands for everything not already specified, so in this
case that would be y and z (since x is already on the lhs). You can
even omit things from . with the minus operator:
lm(x~.-y, data=dat)
This will do a regression of x on z only (and a constant of course).
You can see another approach in the examples section of the help
entry on ?formula (I was led to that entry from reading the Details
section of ?lm).
Haris Skiadas
Department of Mathematics and Computer Science
Hanover College
On Dec 27, 2007, at 9:20 PM, Aaron Barzilai wrote:
Tim (and others who responded privately),
Thanks for the help, this approach did work. I have also reread ?
lm a little more closely, I do see the weights functionality.
I have one last question: Now that I understand how to call this
function and review the results, I want to extend it to my much
larger real problem, with 100s of columns. Is there a way to call
the function in more of a matrix algebra syntax, where I would list
the matrix(e.g. personcoeff) rather than the individual column
names? It seems like I might need to use lm.wfit, but per the help
I'd rather use lm.
Thanks,
Aaron
- Original Message
From: Tim Calkins [EMAIL PROTECTED]
To: Aaron Barzilai [EMAIL PROTECTED]
Cc: r-help@r-project.org
Sent: Thursday, December 27, 2007 6:55:57 PM
Subject: Re: [R] Help with lm and multiple linear regression?
(Plain Text version)
consider merging everything into a singe dataframe. i haven't tried
it, but something like the following could work:
reg.data - cbind(margin, personcoeff)
names(reg.data) - c('margin', 'p1', 'p2')
lm(margin~p1+p2, data = reg.data)
the idea here is that by specifying the data frame with the data
argument in lm, R looks for the columns of the names specified in the
formula.
for weights, see ?lm and look for the weights argument.
cheers,
tc
On Dec 28, 2007 10:22 AM, Aaron Barzilai [EMAIL PROTECTED]
wrote:
(Apologies the previous version was sent as rich text)
Hello,
I'm new to R, but I've read the intro to R and successfully
connected it to an instance of mysql. I'm trying to perform
multiple linear regression, but I'm having trouble using the lm
function. To start, I have read in a simply y matrix of values
(dependent variable) and x matrix of independent variables. It
says both are data frames, but lm is giving me an error that my y
variable is a list.
Any suggestions on how to do this? It's not clear to me what the
problem is as they're both data frames. My actual problem will
use a much wider matrix of coefficients, I've only included two
for illustration.
Additionally, I'd actually like to weight the observations. How
would I go about doing that? I also have that as a separate
column vector.
Thanks,
Aaron
Here's my session:
margin
margin
166.67
2 -58.33
3 100.00
4 -33.33
5 200.00
6 -83.33
7 -100.00
80.00
9 100.00
10 -18.18
11 -55.36
12 -125.00
13 -33.33
14 -200.00
150.00
16 -100.00
17 75.00
180.00
19 -200.00
20 35.71
21 100.00
22 50.00
23 -86.67
24 165.00
personcoeff
Person1 Person2
1 -1 1
2 -1 1
3 -1 1
4 -1 1
5 -1 1
6 -1 1
70 0
80 0
90 1
10 -1 1
11 -1 1
12 -1 1
13 -1 1
14 -1 0
15 0 0
16 0 0
17 0 1
18 -1 1
19 -1 1
20 -1 1
21 -1 1
22 -1 1
23 -1 1
24 -1 1
class(margin)
[1] data.frame
class(personcoeff)
[1] data.frame
lm(margin~personcoeff)
Error in model.frame(formula, rownames, variables, varnames,
extras, extranames, :
invalid type (list) for variable 'margin'
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