Re: [R] Problem using Tobit models in R (Testing and controlling for distributional assumptions and endogeneity)
Roger, thanks for your reply and especially for pointing out that quantreg does not calculate the SCLS estimator as I thought. You are also certainly right about the covariance matrices, I meant the difference to be psd. Nevertheless, my main questions remain open: How to I test distributional assumptions and endogeneity for Tobit models? In case I cannot reject endogeneity, how do I model structural equations with censored dependent variables? -Ursprüngliche Nachricht- Von: roger koenker [mailto:[EMAIL PROTECTED] Gesendet: Mittwoch, 28. November 2007 22:14 An: Malte Brockmann Cc: r-help@r-project.org Betreff: Re: [R] Problem using Tobit models in R (Testing and controlling for distributional assumptions and endogeneity) url:www.econ.uiuc.edu/~rogerRoger Koenker email[EMAIL PROTECTED]Department of Economics vox: 217-333-4558University of Illinois fax: 217-244-6678Champaign, IL 61820 On Nov 28, 2007, at 2:45 PM, Malte Brockmann wrote: Dear R-Community, I am currently using Tobit models (survreg in the survival package). 1a) Does R provide a straight-forward way to test distributional assumptions for tobit models? 1b) If not: I tried to apply the Hausman-test proposed in Newey (1987), Journal of Econometrics, on the Tobit estimator and the symmetrically censored least squares estimator proposed by Powell (1986) (quantreg package). This symmetrically censored least squares estimator is NOT what is computed by the quantreg package. What is computed is the Powell quantile regression estimator. Unfortunately, quantreg only provides covariance matrices based on the bootstrap which are not positive semi-definite, The bootstrapped covariance provided by quantreg is the usual sample covariance matrix of the bootstrapped realizations and is therefore necessarily positive semi-definite. Perhaps what you meant to say was that the difference between the two covariance matrices that you have computed was not psd; this could easily happen. Nothing ensures that the Powell QR estimate is less efficient than the usual (normal theory) tobit estimator, indeed there are very plausible conditions under which this is not the case. therefore the hausman test statistic based on the difference between both covariance matrices can be negative. Newey proposes 2 ways to calculate positive semi-definite covariance matrices: Is there a way to implement any of these without manually coding (or adapting) the tobit and SCLS estimation procedures to extract the necessary information needed for the estimation (first derivative of loglik w.r.t. theta, etc.)? 2) I apply the test for endogeneity proposed by Smith and Blundell (1986), Econometrica, and one of my variables turns out to be endogenous. Does R have a package for simultaneous equations with censored dependent variables? As far as I know, the sem package does estimate these types of equations. Thanks in advance Malte __ 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] Re placing values job
fyi On my machine match runs *much* faster...
t0 - Sys.time(); for (i in 1:reps) { match(Y,X) }; print(Sys.time() - t0)
Time difference of 0.1570001 secs
t0 - Sys.time(); for (i in 1:reps) { sapply(Y,function(Y){which(Y==X)})
}; print(Sys.time() - t0)
Time difference of 6.093 secs
6.09/.157
[1] 38.78981
Regards,
Sean
Peter Dalgaard wrote:
Ingmar Visser wrote:
does this do what you want?
sapply(y,function(y){which(y==x)})
Maybe, but match(Y,X) would be more to the point.
hth, Ingmar
On 28 Nov 2007, at 15:53, Serguei Kaniovski wrote:
Hallo,
I have two vectors of different lengths which contain the same set of
values:
X -c(2,6,1,7,4,3,5)
Y - c(1,1,6,4,6,1,4,1,2,3,6,6,1,2,4,4,5,4,1,7,6,6,4,4,7,1,2)
How can I replace the values in Y with the index (!) of the
corresponding
values in X. So 2 appears in X in the first coordinate, so all 2�s
in Y
should be replaced by 1, etc.
Thank you for your help,
Serguei
Austrian Institute of Economic Research (WIFO)
P.O.Box 91 Tel.: +43-1-7982601-231
1103 Vienna, AustriaFax: +43-1-7989386
Mail: [EMAIL PROTECTED]
http://www.wifo.ac.at/Serguei.Kaniovski
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Ingmar Visser
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The Netherlands
t: +31-20-5256723
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Re: [R] ftable as latex (with Hmisc?)
Richard M. Heiberger rmh at temple.edu writes: I think this does what you are asking for. It should be relatively easy to write a method latex.ftable() based on this. One or two row.vars and one or two col.vars should be straightforward (with n.rgroup and n.cgroup used for the second row and column). ... sample followed Thanks, this works for most cases. I feared I had missed something in summary(...,table). Dieter __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] R crashes using quantreg censored estimation (method fcen)
Dear List, my R session crashes if I repeatedly run the summary function on a quantreg object generated using the censored estimation method or if I set the number of bootstrap repititions reasonably high. Are there any known incompabilities between quantreg and Windows Vista AMD64? The error is reproducable using R 2.6.1 and R 2.5.1. sessionInfo() R version 2.6.1 (2007-11-26) i386-pc-mingw32 locale: LC_COLLATE=German_Germany.1252;LC_CTYPE=German_Germany.1252;LC_MONETARY=German_Germany.1252;LC_NUMERIC=C;LC_TIME=German_Germany.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] quantreg_4.10 SparseM_0.74 Thanks, Malte -Ursprüngliche Nachricht- Von: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Im Auftrag von Jared O'Connell Gesendet: Donnerstag, 29. November 2007 08:57 An: [EMAIL PROTECTED] Cc: [EMAIL PROTECTED] Betreff: Re: [R] Recommended textbooks for R? This page may be helpful :) http://www.r-project.org/doc/bib/R-books.html Modern Applied Statistics with S is quite broad and very good. On Nov 28, 2007 4:38 PM, Max [EMAIL PROTECTED] wrote: Hi everyone! I've recently begun to learn R for my job as the IT department suffers from lack of funding for new software. I was talking to the guy in charge of Requisitions and have found out the budget for books is in great shape. So, I'm curious what books people know of that have R examples and are good for: 1.) Uni and Multivariate Time Series Analysis/Forecasting 2.) GLMs (at this point it looks like I'll be focusing on nominal and ordinal regression models) 3.) Survival Models 4.) Multiple Regression Any suggestions would be awesome. :) thanks, -Max __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ 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] Clustering
Thank you very much! I had misunderstood it's true...
On Nov 28, 2007 6:28 PM, Birgit Lemcke [EMAIL PROTECTED] wrote:
Hello Eleni,
as far as I understood and used agnes() the method argument
determines only the clustering method.
If you use diss=TRUE the distances should be taken from the distance
matrix.
Birgit
Am 28.11.2007 um 12:18 schrieb Eleni Christodoulou:
Hello all!
I am performingsome clustering analysis on microarray data using
agnes{cluster} and I have created my own dissimilarity matrix
according to a
distance measure different from euclidean or manhattan etc. My
question
is, if I choose for example method=complete, how are the distances
between the elements calculated? Are they taken form the dissimilarity
matrix I have provided as the first argument?
clust.complete.agnes-agnes(as.dist(D),diss=TRUE,method=complete)
Thank you very much,
Eleni
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Birgit Lemcke
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Zollikerstrasse 107
CH-8008 Zürich
Switzerland
Ph: +41 (0)44 634 8351
[EMAIL PROTECTED]
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[R] Influence of subdataset
Dear r-helpers! Two closely related questions: 1) I would like to analyse the influence of a subdataset on the whole dataset (50 out of 350 datapoints) linear regression slope. I have read about influence.measures but this analyses only single datapoint. 2) I would like to compare the slope of the whole dataset with the slope of a subdataset consisting of the maximum values of 10 equal x-axis classes. any suggestions? Thanks Marcel __ Marcel Sandow Leibniz Institute of Marine Sciences - IFM-Geomar Experimental Ecology: Foodwebs Düsternbrooker Weg 20 24105 Kiel Germany Fon: +49-431-600-4404 Fax: +49-431-600-1515 Homepage: http://www.ifm-geomar.de E-mail: [EMAIL PROTECTED] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R crashes using quantreg censored estimation (method fcen)
On Thu, 2007-11-29 at 09:09 +0100, Malte Brockmann wrote: Dear List, my R session crashes if I repeatedly run the summary function on a quantreg object generated using the censored estimation method or if I set the number of bootstrap repititions reasonably high. Are there any known incompabilities between quantreg and Windows Vista AMD64? The error is reproducable using R 2.6.1 and R 2.5.1. Err, what does this have to do with Jared's reply to Max's posting about suitable textbooks and R? Please don't jump on a thread to ask your own question. Start your own thread. If you want people to help you with your problem, you are probably going to have to give a reproducible example - my R session crashes is way below what is requested in the posting guide. Even the statements about what you did are not enough - people need to be able to reproduce your problem on their machines. Read the posting guide (URL in the footer of this email) and resend a message to the list - a new one mind, so you start a new thread. And make sure you include a reproducible example. If you can't send your data, try it with one of the data sets that come with quantreg and if it fails with that also, use that data set in your example. You should also consider contacting the maintainer of quantreg. HTH G sessionInfo() R version 2.6.1 (2007-11-26) i386-pc-mingw32 locale: LC_COLLATE=German_Germany.1252;LC_CTYPE=German_Germany.1252;LC_MONETARY=German_Germany.1252;LC_NUMERIC=C;LC_TIME=German_Germany.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] quantreg_4.10 SparseM_0.74 Thanks, Malte -Ursprüngliche Nachricht- Von: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Im Auftrag von Jared O'Connell Gesendet: Donnerstag, 29. November 2007 08:57 An: [EMAIL PROTECTED] Cc: [EMAIL PROTECTED] Betreff: Re: [R] Recommended textbooks for R? This page may be helpful :) http://www.r-project.org/doc/bib/R-books.html Modern Applied Statistics with S is quite broad and very good. On Nov 28, 2007 4:38 PM, Max [EMAIL PROTECTED] wrote: Hi everyone! I've recently begun to learn R for my job as the IT department suffers from lack of funding for new software. I was talking to the guy in charge of Requisitions and have found out the budget for books is in great shape. So, I'm curious what books people know of that have R examples and are good for: 1.) Uni and Multivariate Time Series Analysis/Forecasting 2.) GLMs (at this point it looks like I'll be focusing on nominal and ordinal regression models) 3.) Survival Models 4.) Multiple Regression Any suggestions would be awesome. :) thanks, -Max __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ 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. -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/ UK. WC1E 6BT. [w] http://www.freshwaters.org.uk %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] library(RII)
Dear all I'm Manme from Spain. I could not solve one problem , so I still have to ask your help. I have a deaths and atrisk dataset. I would like to calculate IRR of the dataset but before I want to choose the smoothing parameter and I have the following error message: RII.CVplot(obs, pob, loglambda = seq(-2,18,len=21)) Error in plot.window(xlim, ylim, log, asp, ...) : need finites value de 'ylim' Moreover: Warning messages: 1: nothing argument finite for min; return Inf in: min(x) 2: nothing argument finite for max; return -Inf in: max(x) Do you have any idea what can be the problem? Thanks you __ ¿Chef por primera vez? Sé un mejor Cocinillas. [[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] R , Eclipse
Hi ! Everybody! I am learning R, and I installed R on my laptop(OpenSUSE). Because some my work was done under Eclipse , so I use the StatET plug-in for Eclipse. Most work well, but when I plot graphics, It can't display the picture. Why? How to start te graphic device? Any ideas on how to solve it was required. Thanks very much! boyang __ 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] Testing normality
Hi, I'm doing kolmogorv-smirnov test but I don't know what conclusions to take, I want to know if my data has a normal distribution: ks.test(dados1,pnorm) One-sample Kolmogorov-Smirnov test data: dados1 D = 0.972, p-value 2.2e-16 alternative hypothesis: two-sided Warning message: cannot compute correct p-values with ties in: ks.test(dados1, pnorm) Best regards, Pedro Marques __ 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] Testing normality
[EMAIL PROTECTED] schrieb: Hi, I'm doing kolmogorv-smirnov test but I don't know what conclusions to take, I want to know if my data has a normal distribution: ks.test(dados1,pnorm) One-sample Kolmogorov-Smirnov test data: dados1 D = 0.972, p-value 2.2e-16 alternative hypothesis: two-sided Warning message: cannot compute correct p-values with ties in: ks.test(dados1, pnorm) Best regards, Pedro Marques __ 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. Your approach amounts to testing if dados1 is a sample from a standard normal distribution. Is that what you want? Regards D. Trenkler -- Dietrich Trenkler c/o Universitaet Osnabrueck Rolandstr. 8; D-49069 Osnabrueck, Germany email: [EMAIL PROTECTED] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] How to perform Bayesian analysis in R?(corrected)
Dear Members i'm trying to access different packages used for Bayesian analysis, but failed to integrate after making the likelihood of the model the model like this a= exp(b)/summation(exp(b)) where 'b' = half of the natural log of 'a' please If some one knows about this type of integration for posterior distribution then pleae inform me SYED ADIL HUSSAIN MPHIL SCHOLER QAU, ISLAMABAD This is Virus Free Email Scanned by QAU's McAfee Virus Scanner THIS COMMUNICATION MAY CONTAIN CONFIDENTIAL AND/OR OTHERWISE PROPRIETARY MATERIAL and is thus for use only by the intended recipient. If you received this in error, please contact the sender and delete the e-mail and its attachments from all computers. www.qau.edu.pk __ 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] image() plot with z not in matrix format
Hello R cracks The image() function requires strictly increasing x and y values and z as a matrix. Actually, I don't have equally spaced variables, but anyway want to plot an colored image() (with z-information). An example of my problem is here: a-data.frame(rnorm(100), rnorm(100), runif(100)*100) How can I plot this data as an image (x=a[,1], y=a[,2] and z=a[,3])- according to ?image. It has to be possible to adapt the grid size so that every grid cell in the plot is coloured consequently. Thanks for your help Marc -- __ 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] sqlQuery of variable of type varchar - confusion with .
Dear list, I have a rather large dataset in SAS which I export to a SQLite database for subsequent use in R. One of the columns is cowidp 1881501224.2 1881501224.2 and the column is stored as a character in SAS. It becomes a varchar in the database (it should be - it is an identifier; not a number). Reading this into R gives cowidp 1 1881501224 2 1881501224 - i.e. the .2 is stripped off - and it becomes a numeric variable However, if I store replace . with _ in my SAS data then the column in my database is cowidp 1881501224_2 1881501224_2 Reading into R gives cowidp 1 1881501224_2 2 1881501224_2 as it should be - it becomes a factor Is the fact that the .-part does not seem to work a bug in sqlQuery (or somewhere else) or is it the intention that things containing a . are converted into numeric values if possible? Regards Søren __ 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] Odp: image() plot with z not in matrix format
Hi library(akima) a-data.frame(rnorm(100), rnorm(100), runif(100)*100) image(interp(a[,1], a[,2], a[,3])) Petr [EMAIL PROTECTED] [EMAIL PROTECTED] napsal dne 29.11.2007 12:52:32: Hello R cracks The image() function requires strictly increasing x and y values and z as a matrix. Actually, I don't have equally spaced variables, but anyway want to plot an colored image() (with z-information). An example of my problem is here: a-data.frame(rnorm(100), rnorm(100), runif(100)*100) How can I plot this data as an image (x=a[,1], y=a[,2] and z=a[,3])- according to ?image. It has to be possible to adapt the grid size so that every grid cell in the plot is coloured consequently. Thanks for your help Marc -- __ 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] R crashes using quantreg censored estimation (method fcen)
Thanks for your advice, Gavin. I hope to comply with the posting guide this time. With crashing I meant that the R-session is simply terminated without an error message (Vista, R2.6.1 and R2.5.1 with precompiled packages, sessionInfo see below). I could reproduce the error on a linux machine (R2.5.1-1 for which I have compiled the packages on my own). On the linux machine I at least get the following error message: *** caught segfault *** address (nil), cause 'unknown' Traceback: 1: .Fortran(xys, as.integer(m), as.integer(n), as.integer(p), as.integer(R), as.integer(m + 5), as.integer(p + 2), as.double(x), as.double(y), as.double(tau), as.double(tol), flag = integer(R), coef = double(p * R), resid = double(m), integer(m), double((m + 5) * (p + 2)), double(m), as.integer(1), sol = double((p + 2)), dsol = double(m), lsol = as.integer(0), xx = double(m * p), yy = double(m), as.integer(s), PACKAGE = quantreg) 2: boot.rq.xy(x, y, s, tau) 3: boot.rq(x[s, ], y[s], tau, ...) 4: summary.fcrq(model.powell, R = r) 5: summary(model.powell, R = 1e+06) I used the following command to generate the model: model.powell - rq(y ~ x1 + x2 + x3 + x4 + x5 + x6 + x7 + x8 + x9, method=fcen, data=data_test) summary(model.powell, R=100) I used 100 replications to make sure that the error is triggered I uploaded the data to www.esbf.de/quantreg/data_test.RData -Ursprüngliche Nachricht- Von: Gavin Simpson [mailto:[EMAIL PROTECTED] Gesendet: Donnerstag, 29. November 2007 11:45 An: Malte Brockmann Cc: [EMAIL PROTECTED] Betreff: Re: [R] R crashes using quantreg censored estimation (method fcen) On Thu, 2007-11-29 at 09:09 +0100, Malte Brockmann wrote: Dear List, my R session crashes if I repeatedly run the summary function on a quantreg object generated using the censored estimation method or if I set the number of bootstrap repititions reasonably high. Are there any known incompabilities between quantreg and Windows Vista AMD64? The error is reproducable using R 2.6.1 and R 2.5.1. Err, what does this have to do with Jared's reply to Max's posting about suitable textbooks and R? Please don't jump on a thread to ask your own question. Start your own thread. If you want people to help you with your problem, you are probably going to have to give a reproducible example - my R session crashes is way below what is requested in the posting guide. Even the statements about what you did are not enough - people need to be able to reproduce your problem on their machines. Read the posting guide (URL in the footer of this email) and resend a message to the list - a new one mind, so you start a new thread. And make sure you include a reproducible example. If you can't send your data, try it with one of the data sets that come with quantreg and if it fails with that also, use that data set in your example. You should also consider contacting the maintainer of quantreg. HTH G sessionInfo() R version 2.6.1 (2007-11-26) i386-pc-mingw32 locale: LC_COLLATE=German_Germany.1252;LC_CTYPE=German_Germany.1252;LC_MONETARY=German_Germany.1252;LC_NUMERIC=C;LC_TIME=German_Germany.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] quantreg_4.10 SparseM_0.74 Thanks, Malte __ 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. -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/ UK. WC1E 6BT. [w] http://www.freshwaters.org.uk %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] sqlQuery of variable of type varchar - confusion with .
On 11/29/2007 7:03 AM, Søren Højsgaard wrote: Dear list, I have a rather large dataset in SAS which I export to a SQLite database for subsequent use in R. One of the columns is cowidp 1881501224.2 1881501224.2 and the column is stored as a character in SAS. It becomes a varchar in the database (it should be - it is an identifier; not a number). Reading this into R gives cowidp 1 1881501224 2 1881501224 - i.e. the .2 is stripped off - and it becomes a numeric variable However, if I store replace . with _ in my SAS data then the column in my database is cowidp 1881501224_2 1881501224_2 Reading into R gives cowidp 1 1881501224_2 2 1881501224_2 as it should be - it becomes a factor Is the fact that the .-part does not seem to work a bug in sqlQuery (or somewhere else) or is it the intention that things containing a . are converted into numeric values if possible? If you're using sqlQuery from RODBC, then the as.is argument of sqlGetResults is relevant. It defaults to FALSE, and tries to convert things based on how they look. Duncan Murdoch __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] sqlQuery of variable of type varchar - confusion with .
On Thu, 29 Nov 2007, Søren Højsgaard wrote: Dear list, I have a rather large dataset in SAS which I export to a SQLite database for subsequent use in R. One of the columns is cowidp 1881501224.2 1881501224.2 and the column is stored as a character in SAS. It becomes a varchar in the database (it should be - it is an identifier; not a number). Reading this into R gives How? You haven't actually said, but I am surmising that you are using package RODBC with the default options, in which case this is exactly what the help page ?sqlQuery says should happen. cowidp 1 1881501224 2 1881501224 - i.e. the .2 is stripped off - and it becomes a numeric variable However, if I store replace . with _ in my SAS data then the column in my database is cowidp 1881501224_2 1881501224_2 Reading into R gives cowidp 1 1881501224_2 2 1881501224_2 as it should be - it becomes a factor Is the fact that the .-part does not seem to work a bug in sqlQuery (or somewhere else) or is it the intention that things containing a . are converted into numeric values if possible? See the 'as.is' argument to sqlGetResults(), which can be passed from sqlQuery(). It is exactly the same as read.table() in this respect. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595__ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] empty cells in ftable
hello when I enter: ftable(xtabs(cnt~jeo+slp+pcurv+asp+hey),data=dt) it gives a frequncy table. But some cells are empty. like this: 192 72 0 3 68 0 4 99 0 5 110 0 6 97 0 7 74 0 8 46 0 . . . (Those empty cells must have previous non empty values.) how can I get a table that does not contain empty cells ? Is this the proper table that will be used in logistic regression ? regards -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. __ 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] R crashes using quantreg censored estimation (method fcen)
1. As the posting guide advises, queries about packages should be sent in the first instance to the package author/maintainer before posting to the list. 2. As the posting guide also advises, a _minimal_ reproducible example is desirable not one that claims that somewhere in the middle of 1,000,000 bootstrap replications something goes wrong. I'll try to take a look at this with valgrind, but I can't promise any immediate resolution. url:www.econ.uiuc.edu/~rogerRoger Koenker email[EMAIL PROTECTED]Department of Economics vox: 217-333-4558University of Illinois fax: 217-244-6678Champaign, IL 61820 On Nov 29, 2007, at 6:32 AM, Malte Brockmann wrote: Thanks for your advice, Gavin. I hope to comply with the posting guide this time. With crashing I meant that the R-session is simply terminated without an error message (Vista, R2.6.1 and R2.5.1 with precompiled packages, sessionInfo see below). I could reproduce the error on a linux machine (R2.5.1-1 for which I have compiled the packages on my own). On the linux machine I at least get the following error message: *** caught segfault *** address (nil), cause 'unknown' Traceback: 1: .Fortran(xys, as.integer(m), as.integer(n), as.integer (p), as.integer(R), as.integer(m + 5), as.integer(p + 2), as.double(x), as.double(y), as.double(tau), as.double(tol), flag = integer(R), coef = double(p * R), resid = double(m), integer(m), double((m + 5) * (p + 2)), double(m), as.integer (1), sol = double((p + 2)), dsol = double(m), lsol = as.integer(0), xx = double(m * p), yy = double(m), as.integer(s), PACKAGE = quantreg) 2: boot.rq.xy(x, y, s, tau) 3: boot.rq(x[s, ], y[s], tau, ...) 4: summary.fcrq(model.powell, R = r) 5: summary(model.powell, R = 1e+06) I used the following command to generate the model: model.powell - rq(y ~ x1 + x2 + x3 + x4 + x5 + x6 + x7 + x8 + x9, method=fcen, data=data_test) summary(model.powell, R=100) I used 100 replications to make sure that the error is triggered I uploaded the data to www.esbf.de/quantreg/data_test.RData -Ursprüngliche Nachricht- Von: Gavin Simpson [mailto:[EMAIL PROTECTED] Gesendet: Donnerstag, 29. November 2007 11:45 An: Malte Brockmann Cc: [EMAIL PROTECTED] Betreff: Re: [R] R crashes using quantreg censored estimation (method fcen) On Thu, 2007-11-29 at 09:09 +0100, Malte Brockmann wrote: Dear List, my R session crashes if I repeatedly run the summary function on a quantreg object generated using the censored estimation method or if I set the number of bootstrap repititions reasonably high. Are there any known incompabilities between quantreg and Windows Vista AMD64? The error is reproducable using R 2.6.1 and R 2.5.1. Err, what does this have to do with Jared's reply to Max's posting about suitable textbooks and R? Please don't jump on a thread to ask your own question. Start your own thread. If you want people to help you with your problem, you are probably going to have to give a reproducible example - my R session crashes is way below what is requested in the posting guide. Even the statements about what you did are not enough - people need to be able to reproduce your problem on their machines. Read the posting guide (URL in the footer of this email) and resend a message to the list - a new one mind, so you start a new thread. And make sure you include a reproducible example. If you can't send your data, try it with one of the data sets that come with quantreg and if it fails with that also, use that data set in your example. You should also consider contacting the maintainer of quantreg. HTH G sessionInfo() R version 2.6.1 (2007-11-26) i386-pc-mingw32 locale: LC_COLLATE=German_Germany.1252;LC_CTYPE=German_Germany. 1252;LC_MONETARY=German_Germany. 1252;LC_NUMERIC=C;LC_TIME=German_Germany.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] quantreg_4.10 SparseM_0.74 Thanks, Malte __ 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. -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e]
Re: [R] How to perform Bayesian analysis in R?(corrected)
adilshah wrote: Dear Members i'm trying to access different packages used for Bayesian analysis, but failed to integrate after making the likelihood of the model the model like this a= exp(b)/summation(exp(b)) where 'b' = half of the natural log of 'a' please If some one knows about this type of integration for posterior distribution then pleae inform me SYED ADIL HUSSAIN MPHIL SCHOLER QAU, ISLAMABAD You haven't provided enough information for us to help you. PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. cheers Ben Bolker -- View this message in context: http://www.nabble.com/How-to-perform-Bayesian-analysis-in-R-%28corrected%29-tf4896524.html#a14025892 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] Boxplots from lme objects
Dear all!
W_XP, R 2.6.0
I am evaluating variety trails over several years, where the different
cultivars have not been present in the dataset the same number of years.
I use lme{nlme} to fit random effect models and estimable{gmodels} to
extract the fixed effects. The general model is:
lme(y ~ cultivar, data = data, na.action=na.omit,
random = ~ 1 | year/trial/rep)
The dataset is from six years and I only run the analyse on a subset
dataframe consisting the cultivars grown the last year (25 out of 82 for
the moment). All this runs well to produce tables, but what about
graphics?
How do I make boxplots from the lme objects? Producing the boxplots, I
want only 6 or 7 cultivars out of the 25 available in the object - so I
also need a way to subset the information in the lme objects.
Thank you
/CG
--
CG Pettersson, Ph.D.
Swedish University of Agricultural Sciences (SLU)
Dept. of Crop Production Ecology. Box 7043.
SE-750 07 Uppsala, Sweden
[EMAIL PROTECTED]
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Re: [R] ggplot2 melt function value
Hi:I recently started using the melt function and found that it is very useful and powerful,however I can't seem to find the way to change the default column header value to my custom column name. melted data are data frames. You can names[..]-myvalue for renaming, but make sure you don't need the column for reshaping afterwards. In the next version of reshape, cast will default (with a message) to using the last column of the data.frame if value and (all) columns are not available. This was a nice suggestion from Antony Unwin. Hadley -- http://had.co.nz/ __ 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] Question about using “par”
Hi, Sorry for bothering your guys again. I am trying to use par to put 6 figures into 3 rows and 2 columns. My code is: op - par(mfrow = c(1, 2)) xyplot(x1+x2+x3 ~ y, data=resulta, type=l, pch=LETTERS[1:3], lty=c(1:3), main=For k=3, theata1=1) xyplot(x1+x2+x3 ~ y, data=resultb, type=l, pch=LETTERS[1:3], lty=c(1:3), main=For k=3, theata1=5) xyplot(x1+x2+x3 ~ y, data=resultc, type=l, pch=LETTERS[1:3], lty=c(1:3), main=For k=5, theata1=1) xyplot(x1+x2+x3 ~ y, data=resultd, type=l, pch=LETTERS[1:3], lty=c(1:3), main=For k=5, theata1=5) xyplot(x1+x2+x3 ~ y, data=resulte, type=l, pch=LETTERS[1:3], lty=c(1:3), main=For k=10, theata1=1) xyplot(x1+x2+x3 ~ y, data=resultf, type=l, pch=LETTERS[1:3], lty=c(1:3), main=For k=10, theata1=5) par(op) But I can only get one figure in one page, not 6 figures in one page. Is there any other parameter I should specify? There is no error indicated. Thank you so much! Catherine -- View this message in context: http://www.nabble.com/Question-about-using-%E2%80%9Cpar%E2%80%9D-tf4894997.html#a14019058 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] LOCFIT:Automatic bandwidth selection for kernel regression
Hello all! I have recently started using the LOCFIT package, together with Clive Loader's book. I need to implement some method for automatic (plug-in) bandwidth selection in a multivariate kernel regression. From the book, and the LOCFIT documentation, it is not clear whether this is possible. As far as I can see, the only time the various automated procedures, e.g., SJPI, are used is in the kdeb function, which is for preparing a summary comparison of various selection methods, and only for a univariate kernel density. Does anyone here know of a way to implement automatic (plug-in) bandwidth selection for kernel regression, maybe with some R function that calls LOCFIT? Or can you suggest a good alternative package for this, either in R/Matlab or a stand-alone? Thanks a lot, and regards -- View this message in context: http://www.nabble.com/LOCFIT%3AAutomatic-bandwidth-selection-for-kernel-regression-tf4895390.html#a14020237 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] MS Excel Data
I am using MS Excel (Windos Operating system), how I import/export data between MS_Excel and R. Regds Faisal Afzal SIddiqui +92-300-9297089 [EMAIL PROTECTED] Never miss a thing. Make Yahoo your home page. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] MS Excel Data
On Wed, 28 Nov 2007, faisal afzal siddiqui wrote: I am using MS Excel (Windos Operating system), how I import/export data between MS_Excel and R. Why not read the 'R Data Import/Export' manual? It ships with R, or can be accessed from http://cran.r-project.org/manuals.html . -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@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] Doing PCA
Hi Fellow R enthusiasts I have managed to reshape my data using a much shorter script than before. Woohoo However now I have new problems. The code is below. There are no problems with the create matrix section. The problem code is highlighted in bold. I am trying to do PCA on the data. Here are the errors. Error1 code : OGSscaled = rangescale(OGS) error message : Error in dim(newX) - c(prod(d.call), d2) : dims [product 47960] do not match the length of object [43600] Error2 I tried to do PCA without rangescaling code :OGSpca - prcomp(OGS, center=FALSE) error message : Error in svd(x, nu = 0) : infinite or missing values in 'x' CODE ## ### Create matrix ### ## # load packages require(reshape) source(rangescale.r) #Open the csv file OGSdata - read.table(MG3199.csv,sep=,,header=TRUE) #create matrix x.m - melt(OGSdata, measure.var=pct) OGS - cast(x.m, mci ~ sample) ## ### PCA ## #scale profiles OGSscaled = rangescale(OGS) #do PCA result = prcomp(OGS, center=FALSE) #obtain scores matrix scores=result$rotation #PC1 vs PC2 plot plot(scores[,1], scores[,2], xlab=PC1, ylab=PC2) #add labels (0.005 and 0.003 offset to aviod obscuring points Kind Regards Amit Patel ___ now. [[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] Survreg(), Surv() and interval-censored data
The question (slightly rephrased) was Why does survreg(Surv(T.1, T.2, type='interval2') ~1, data=x) fail, when x is T.1 T.2 Status 1 0.000 0.62873036 1 2 0.000 2.07039068 1 3 0.000 1.40297214 1 4 0.000 0.09112871 1 5 0.000 0.75115280 1 6 0.000 2.36476839 1 ... The default model for survreg is a Weibull, for which a survival time of exactly zero is not a valid value. Your example triggers this error message. This is a bug in survreg. In the 10+ years the code has been available, no one has ever specified this particular data: a (0,x] interval for a Weibull. Congratulations! Fixing this will require some thought, however. To work around the problem, change 0 to NA, which marks the observation as left-censored. Terry Therneau (author of survreg) __ 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] Question about using “par”
cathelf cathelf at hotmail.com writes: Sorry for bothering your guys again. I am trying to use par to put 6 figures into 3 rows and 2 columns. My code is: op - par(mfrow = c(1, 2)) xyplot(x1+x2+x3 ~ y, data=resulta, type=l, pch=LETTERS[1:3], lty=c(1:3), main=For k=3, theata1=1) xyplot(x1+x2+x3 ~ y, data=resultb, type=l, pch=LETTERS[1:3], lty=c(1:3), main=For k=3, theata1=5) But I can only get one figure in one page, not 6 figures in one page. Is there any other parameter I should specify? There is no error indicated. Rule of thumb: what's documented under the header trellis or lattice does not use par. xyplot is a lattice/trellis function, which does not honor par(...) settings, but uses package grid for layout and everthing else. So either use standard plot plot(rnorm(100),rnorm(100)) or do something like: p = xyplot(whatever) print(p,split=c(1,1,2,2), more=TRUE) p = xyplot(whoever,... print(p,split=c(1,2,2,2), more=TRUE) See print.trellis for details. Dieter __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Time Series Issues, Stationarity ..
Look at the R help files for predict.Arima rather than using forecast to forecast an ARIMA model. You might plot your data and the first difference and you should be able to come to a conclusion about stationarity. With your very small data set you need a very parsimonious model. Knowledge about the nature of the data set would also be important. I see no seasonal effect in the data and wonder why you are proposing to allow two seasonal differences. Probably some form of smoothing would be more suitable in your case. Best Regards John On 29/11/2007, Ozcan Asilkan [EMAIL PROTECTED] wrote: Hi ohn, Thank you for your reply. I read in a few documents that if a Time Series data is NONStationary, ARIMA models must be used. So, if we suppose that my data is non-stationary, is it basically enough just to use the arima() function in R to make a future forecast ? Does arima function implicitly convert my data into stationary status by handling differencing, removing seasonality, etc. ? Or must I explicitly convert my data to stationary form in order to use arima() ? and here' s my code. I' ll appreciate your help making suggestions.. Thank you very much. Best regards.. Ozzy # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # Loading the library... library(forecast) # my input data having 3 years of monthly data (36 data) invec - c(15289,14282,16153,15885,15369,15488,15462,14697,15512,15506,15271,15111,14963,15150,15061,14896,15147,14967,15026,15102,14880,15181,14979,15300,15377,15323,15462,15422,15598,15518,15497,15593,15348,15453,15361,15361) # converting to TS invecTS - ts(invec, start = c(2005,1), frequency = 12) # using arima function invecTSAR = arima(invecTS, order = c(0,1,1), seasonal = list(order = c(0, 2, 0) ) ) # making a further 2 years forecasting (=24 months) invecTSARPR - forecast(invecTSAR,24) # and plotting plot(invecTSARPR,xlab=TIME, ylab=PRICE (€), fcol=red,plot.conf=F) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # On Nov 26, 2007 10:30 PM, Uwe Ligges [EMAIL PROTECTED] wrote: Ozcan Asilkan wrote: Hello, -- John C Frain Trinity College Dublin Dublin 2 Ireland www.tcd.ie/Economics/staff/frainj/home.html mailto:[EMAIL PROTECTED] mailto:[EMAIL PROTECTED] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] [R-pkgs] Package dlm version 0.8-1
I uploaded a new version of package dlm to CRAN. dlm provides functions for maximum likelihood, Kalman filtering and smoothing, and Bayesian analysis of Gaussian linear state space models, also known as Dynamic Linear Models. The most important visible changes from the previous version are the following. 1) Missing values are now allowed in the observations. 2) Extractor and replacement functions for the matrices defining a dlm are now available. 3) The function for Kalman smoothing, dlmSmooth, can take as arguments a data vector and a dlm object. Previously the argument had to be the output from dlmFilter. 4) In addition to the + method function for objects of class dlm, used to build complex models from simple components, all having the same dimensionality of the observation vector, there is now an outer sum, %+%, which creates a joint model from independent dlm's. This is useful to specify models for multivariate observations. 5) Minimal support for Markov chain Monte Carlo output analysis has been added, with functions mcmcSD, mcmcMean, ergMean. Thanks to Michael Lavine for suggesting the outer sum in (4). Please let me know of any problems. Comments and suggestions are very welcome. Giovanni Petris -- Giovanni Petris [EMAIL PROTECTED] Department of Mathematical Sciences University of Arkansas - Fayetteville http://definetti.uark.edu/~gpetris/ ___ R-packages mailing list [EMAIL PROTECTED] https://stat.ethz.ch/mailman/listinfo/r-packages __ 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] Odp: MS Excel Data
Hi [EMAIL PROTECTED] napsal dne 29.11.2007 04:54:18: I am using MS Excel (Windos Operating system), how I import/export data between MS_Excel and R. What data and how often. There are few options from add on packages through ODBC to copy and paste. If you bother to read any documentation about R you coud find it easily. Eg. if you know Google you can ask R export data excel and the first hit reveals you one possibility. Regards Petr Regds Faisal Afzal SIddiqui +92-300-9297089 [EMAIL PROTECTED] 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. __ 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] Re commended textbooks for R?
I am currently using: ---John Maindonald and John Braun. Data Analysis and Graphics Using R--- and find it very useful, note that there now is a 2007 edition. Most of the texts mentioned in the previous link have reviews on Amazon. Jared O'Connell-2 wrote: This page may be helpful :) http://www.r-project.org/doc/bib/R-books.html Modern Applied Statistics with S is quite broad and very good. On Nov 28, 2007 4:38 PM, Max [EMAIL PROTECTED] wrote: Hi everyone! I've recently begun to learn R for my job as the IT department suffers from lack of funding for new software. I was talking to the guy in charge of Requisitions and have found out the budget for books is in great shape. So, I'm curious what books people know of that have R examples and are good for: 1.) Uni and Multivariate Time Series Analysis/Forecasting 2.) GLMs (at this point it looks like I'll be focusing on nominal and ordinal regression models) 3.) Survival Models 4.) Multiple Regression Any suggestions would be awesome. :) thanks, -Max __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ 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. -- View this message in context: http://www.nabble.com/Recommended-textbooks-for-R--tf4895638.html#a14027317 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] rpvm error when loading
Hello, I get this error when issuing the library command (with rpvm) in R: = Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. library(rpvm) Error in dyn.load(x, as.logical(local), as.logical(now)) : unable to load shared library '/usr/local/lib/R/library/rpvm/libs/rpvm.so': /usr/local/lib/R/library/rpvm/libs/rpvm.so: cannot restore segment prot after reloc: Permission denied Error in library(rpvm) : .First.lib failed for 'rpvm' = I have successfully loaded R and PVM. Both of these are working for me. But I don't understand why I am getting the above-listed error. Can anyone provide some insight? Thanks! A Lenzo __ 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] Listing factor levels for elements of letters in an rpart plot
I would like to create a list of factor levels represented by elements of letters shown in an rpart plot. It seems that the order of levels for a factor are different than the alphabetized order returned a simple list command, e.g., rpartModel$factor_name. I was also wondering how best to model factors with many levels, or does the classification algorithm already subset these? I was thinking of thresholding observations on some minimum count for each level. __ 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] Recommended textbooks for R?
my favorite is MASS by B. Ripley. I bought it 6 yrs ago and am still browsing it when I have time. On Nov 28, 2007 10:38 AM, Max [EMAIL PROTECTED] wrote: Hi everyone! I've recently begun to learn R for my job as the IT department suffers from lack of funding for new software. I was talking to the guy in charge of Requisitions and have found out the budget for books is in great shape. So, I'm curious what books people know of that have R examples and are good for: 1.) Uni and Multivariate Time Series Analysis/Forecasting 2.) GLMs (at this point it looks like I'll be focusing on nominal and ordinal regression models) 3.) Survival Models 4.) Multiple Regression Any suggestions would be awesome. :) thanks, -Max __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- === 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] Re commended textbooks for R?
Thanks guys for the recomendations! :) aaront wrote on 11/29/2007 : I am currently using: ---John Maindonald and John Braun. Data Analysis and Graphics Using R--- and find it very useful, note that there now is a 2007 edition. Most of the texts mentioned in the previous link have reviews on Amazon. Jared O'Connell-2 wrote: This page may be helpful :) http://www.r-project.org/doc/bib/R-books.html Modern Applied Statistics with S is quite broad and very good. On Nov 28, 2007 4:38 PM, Max [EMAIL PROTECTED] wrote: Hi everyone! I've recently begun to learn R for my job as the IT department suffers from lack of funding for new software. I was talking to the guy in charge of Requisitions and have found out the budget for books is in great shape. So, I'm curious what books people know of that have R examples and are good for: 1.) Uni and Multivariate Time Series Analysis/Forecasting 2.) GLMs (at this point it looks like I'll be focusing on nominal and ordinal regression models) 3.) Survival Models 4.) Multiple Regression Any suggestions would be awesome. :) thanks, -Max __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ 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] How to manipulate a data frame
Dear list, I have a data frame like: log2.ratios[1:3,1:4] Clone a1 a2 a3 1 GS1-232B23 -0.0207500 0.17553833 0.21939333 2 RP11-82D16 -0.1896667 0.02645167 -0.03112333 3 RP11-62M23 -0.1761700 0.08214500 -0.04877000 how to make it to look like: log2.ratios[1:3,1:4] a1 a2 a3 a4 GS1-232B23 -0.0207500 0.17553833 0.21939333 0.0008 RP11-82D16 -0.1896667 0.02645167 -0.03112333 0.007 RP11-62M23 -0.1761700 0.08214500 -0.048770000.7666 I tried as.matrix(log2.ratios) and it seems it is not working. Thanks a lot! Allen [[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] R as server application
I found this link: http://jesus-loves-grass.blogspot.com/search/label/R%20server Which points to RSOAP and Rserver. __ 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 read in a txt file with some blanks
Hi Jim, Thanks! The pattern for blanks varies. It could be any of scenarios you outlined. Other folks pointed out the problem can be solved by specifying sep=\t in read.table(). Best, Allen On Nov 28, 2007 10:12 PM, jim holtman [EMAIL PROTECTED] wrote: The question is what do the 'blanks' mean? I assume that they are separating the variables since that is the default for read.table. So what is the difference between: 1) 1 2 one blank 2) 1 2 two blanks 3) 1 2 three blanks 4) How are these different conditions supposed to be interpreted? Now you replace the blanks with commas and that might do it for you. This would mean that 1 2 (which would be two variables where there are 2 blanks) would now be 1,,2 which would be three variables. So you need to define what is supposed to happen in these cases. On Nov 28, 2007 8:21 PM, affy snp [EMAIL PROTECTED] wrote: Hi Jim, Thanks a lot! I would like the blanks to be read as NAs. I tried cgh-read.table(file= WM115A.txt,header = TRUE,fill = TRUE,na.strings= NA) but the blanks were just filled by their flanking columns. Best, Allen On Nov 28, 2007 7:42 PM, jim holtman [EMAIL PROTECTED] wrote: If the data is fixed field, then read.fwf. Else blanks are normally allowed delimiters. How do you want to interprete blanks? There are number of ways, none of which you have specified. On Nov 28, 2007 6:46 PM, affy snp [EMAIL PROTECTED] wrote: Hi list, Is there a way to read in a txt file with some blanks? The ideal way could be to replace blanks with NAs. Thanks a lot! Allen [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem you are trying to solve? -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem you are trying to solve? [[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] re lative importance of predictors
Hi Robert, relaimpo does work with a (non-robust) linear model, i.e. calculations in relaimpo are using correlations between variables, and it is not possible to incorporate things like the Huber psi function. I am not an expert on robust regression, but I try to answer your question from the relaimpo point of view. If you run relaimpo on an rlm object, it will calculate relative importances based on the linear model with your prior weights (that you optionally specify with weights in rlm). I suppose it would be more appropriate to run relaimpo on your model with the weights as determined by rlm (stored in the w component of the output object, if I correctly interpret the help on rlm); you would have to do that explicitly, at least currently, since relaimpo uses the weights() function on the linear model object, and weights(rlm) returns the weights component of the output object. If a relative importance calculation within a linear model with modified weights (from w=) is a desirable solution for (at least special cases of) rlm objects, this can be incorporated into a future version of relaimpo as the default for these cases. I think it won't be possible to incorporate psi-functions. While I am at it: When trying out rlm, I was surprised that specifying w= without simultaneously using the weights=-option apparently interprets w= as weights=, i.e. the weights component of the resulting rlm object contains the initial w-values. On the other hand, when specifying both the weights and the w option, the weights component of the resulting rlm object contains the weights only and ignores the w-Option. This seems to me somewhat inconsistent. Regards, Ulrike robert.ptacnik wrote: Hei Group, I want to compare the relative importance of predictors in a multiple linear regression y~a+bx1+cx2... However, bptest indicates heteroskedasticity of my model. I therefore perform a robust regression (rlm), in combination with bootstrapping (as outlined in J. Fox, Bootstrapping Regression Models). Now I want to compare the relative importance of my predictors. Can I rely on the output of 'relaimpo' here? (which takes 'lm', not 'rlm' objects). Thanks, Robert -- NIVAs hovedkontor har flyttet til nye lokaler i CIENS - Forskningssenter for miljø og samfunn; Gaustadalléen 21, 0349 Oslo. Meld deg på vårt nyhetsbrev på www.niva.no __ 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. -- View this message in context: http://www.nabble.com/relative-importance-of-predictors-tf4897731.html#a14028871 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] str() options
Beautiful!
Exactly what I was looking for.
Thank you, Gabor
-Original Message-
From: Gabor Grothendieck [mailto:[EMAIL PROTECTED]
Sent: November 27, 2007 05:02 PM
To: Thompson, David (MNR)
Subject: Re: [R] str() options
On Nov 27, 2007 1:55 PM, Thompson, David (MNR)
[EMAIL PROTECTED] wrote:
Hello,
Is there a way to have str() and ls.str() return all factor levels?
str is an S3 generic so you can define your own str.factor. Here
we show the usual str and then show it again after we have
added our own str.factor:
str(iris)
'data.frame': 150 obs. of 5 variables:
$ Sepal.Length: num 5.1 4.9 4.7 4.6 5 5.4 4.6 5 4.4 4.9 ...
$ Sepal.Width : num 3.5 3 3.2 3.1 3.6 3.9 3.4 3.4 2.9 3.1 ...
$ Petal.Length: num 1.4 1.4 1.3 1.5 1.4 1.7 1.4 1.5 1.4 1.5 ...
$ Petal.Width : num 0.2 0.2 0.2 0.2 0.2 0.4 0.3 0.2 0.2 0.1 ...
$ Species : Factor w/ 3 levels setosa,versicolor,..: 1 1 1 1
1 1 1 1 1 1 ...
str.factor - function(object, ...) {
+ cat(factor w/, nlevels(object), levels, levels(object), \n)
+ }
str(iris)
'data.frame': 150 obs. of 5 variables:
$ Sepal.Length: num 5.1 4.9 4.7 4.6 5 5.4 4.6 5 4.4 4.9 ...
$ Sepal.Width : num 3.5 3 3.2 3.1 3.6 3.9 3.4 3.4 2.9 3.1 ...
$ Petal.Length: num 1.4 1.4 1.3 1.5 1.4 1.7 1.4 1.5 1.4 1.5 ...
$ Petal.Width : num 0.2 0.2 0.2 0.2 0.2 0.4 0.3 0.2 0.2 0.1 ...
$ Species :factor w/ 3 levels setosa versicolor virginica
*
Silviculture Data Analyst
Ontario Forest Research Institute
Ontario Ministry of Natural Resources
[EMAIL PROTECTED]
http://ofri.mnr.gov.on.ca
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to manipulate a data frame
affy snp wrote: Dear list, I have a data frame like: log2.ratios[1:3,1:4] Clone a1 a2 a3 1 GS1-232B23 -0.0207500 0.17553833 0.21939333 2 RP11-82D16 -0.1896667 0.02645167 -0.03112333 3 RP11-62M23 -0.1761700 0.08214500 -0.04877000 how to make it to look like: log2.ratios[1:3,1:4] a1 a2 a3 a4 GS1-232B23 -0.0207500 0.17553833 0.21939333 0.0008 RP11-82D16 -0.1896667 0.02645167 -0.03112333 0.007 RP11-62M23 -0.1761700 0.08214500 -0.048770000.7666 log2.ratios = data.frame( Clone=c(GS1-232B23, RP11-82D16, RP11-62M23), a1= c(-0.0207500,-0.1896667,-0.1761700), a2 = c(0.17553833,0.02645167,0.08214500), a3 = c(0.21939333,-0.03112333,-0.04877000), a4 = c(0.0008,0.007,0.7666)) log2.ratios[1:3,1:4] rownames(log2.ratios) - as.character(log2.ratios[,1]) log2.ratios - log2.ratios[,-1] -- View this message in context: http://www.nabble.com/How-to-manipulate-a-data-frame-tf4898180.html#a14030339 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] Question about using “par”
On top of which, you should expect a setting of mfrow=c(1,2) like you have to only allow you to put two figures in 1 row and 2 columns. Haris Skiadas Department of Mathematics and Computer Science Hanover College On Nov 29, 2007, at 9:35 AM, Dieter Menne wrote: cathelf cathelf at hotmail.com writes: Sorry for bothering your guys again. I am trying to use par to put 6 figures into 3 rows and 2 columns. My code is: op - par(mfrow = c(1, 2)) xyplot(x1+x2+x3 ~ y, data=resulta, type=l, pch=LETTERS[1:3], lty=c(1:3), main=For k=3, theata1=1) xyplot(x1+x2+x3 ~ y, data=resultb, type=l, pch=LETTERS[1:3], lty=c(1:3), main=For k=3, theata1=5) But I can only get one figure in one page, not 6 figures in one page. Is there any other parameter I should specify? There is no error indicated. Rule of thumb: what's documented under the header trellis or lattice does not use par. xyplot is a lattice/trellis function, which does not honor par(...) settings, but uses package grid for layout and everthing else. So either use standard plot plot(rnorm(100),rnorm(100)) or do something like: p = xyplot(whatever) print(p,split=c(1,1,2,2), more=TRUE) p = xyplot(whoever,... print(p,split=c(1,2,2,2), more=TRUE) See print.trellis for details. Dieter __ 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] Bootstrap Correlation Coefficient with Moving Block Bootstrap
Hello. I have got two problems in bootstrapping from dependent data sets. Given two time-series x and y. Both consisting of n observations with x consisting of dependent and y consisting of independent observations over time. Also assume, that the optimal block-length l is given. To obtain my bootstrap sample, I have to draw pairwise, but there is the problem of dependence of the x-observations and so if I draw the third observation of y, I cannot simply draw the third observation of x (to retain the serial correlation structure between x and y), because I devided x into blocks of length l and I have to draw blocks, then I draw from x. 1. How can I compute a bootstrap sample of the correlation coefficient between x and y with respect to the dependence in time-series of x? 2. How does it look like, if x and y both consist of dependent observations? I hope you can help me. I got really stuck with this problem. Sincerly Klein. __ 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] Data sets with usage in documentation object but not in code
On Thu, 29 Nov 2007, Jonathan Weeks wrote: All, I recently made some changes to my package and ran R CMD check, but I am getting a warning regarding my data sets. I am running R 2.6.1 I have an image (.RData) file containing five data sets in the data subdirectory and an .Rd file for each of the data sets in the man subdirectory. When I run the check I get the warning Data sets with usage in documentation object dataset name but not in code for each dataset. I did not get this warning with R 2.5 Does anyone have a suggestion for how to handle this? Show us a small reproducible example, or (failing that) make the package available for test? It's hard to guess at the cause, and hundreds of packages do similar things. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] How to align the text in the legend
Hello,
I tried to align lines of text in the legend of a plot. It always
defaults to the central alignment. How can I adjust it to be left
alignment?
Here is the code fragment written in python using Rpy module:
text = 'Quantiles #Loci\n'
text += '%s %6d\n' % (' 100',totalloci)
text += '%s %6d\n' % (' 95',per95cntloci)
text += '%s %6d\n' % (' 50',per50cntloci)
r.legend(20,30,text,cex=0.6,bty='n')
Thanks
Zhaoming
[[alternative HTML version deleted]]
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Re: [R] coloring leaves in clustering
EC == Eleni Christodoulou [EMAIL PROTECTED]
on Thu, 29 Nov 2007 18:25:46 +0200 writes:
EC Hello everyone,
EC I wanted to know if it was possible to change the color of certain
leaves in
EC a hclust object in order to make my graph more readable. I know I can
color
EC certain groups but I would like to enter a vector telling the plot
function
EC which leaves to color in which color.
Yes, you can do this.
Produce a dendrogram (S3 class) object from your hclust result
hc - hclust(...)
X - as.dendrogram(hc)
and then work with that (add 'nodePar' properties to certain nodes).
example(plot.dendrogram)
gives you a glimpse of the possibilities.
Someone else will have to give you details,
or provide you with utility functions maybe using
dendrapply() to achieve what you want.
Regards,
Martin Maechler, ETH Zurich
EC Thanks in advance,
EC Eleni
EC [[alternative HTML version deleted]]
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Please do avoid the above by *NOT* sending [text plus html] e-mails,
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EC
EC PLEASE do read the posting guide
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Re: [R] Data sets with usage in documentation object but not in code
Prof Brian Ripley wrote: On Thu, 29 Nov 2007, Jonathan Weeks wrote: All, I recently made some changes to my package and ran R CMD check, but I am getting a warning regarding my data sets. I am running R 2.6.1 I have an image (.RData) file containing five data sets in the data subdirectory and an .Rd file for each of the data sets in the man subdirectory. When I run the check I get the warning Data sets with usage in documentation object dataset name but not in code for each dataset. I did not get this warning with R 2.5 Does anyone have a suggestion for how to handle this? Show us a small reproducible example, or (failing that) make the package available for test? It's hard to guess at the cause, and hundreds of packages do similar things. You could also look at the output of tools:::list_data_in_pkg(yourPkg) and see if it makes you any wiser. (AFAICS, this is the list that the usage lines get compared to) -- 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] How to manipulate a data frame
Thanks a lot, Petr. Allen On Nov 29, 2007 12:12 PM, Petr PIKAL [EMAIL PROTECTED] wrote: Hi I just guess what you want but maybe rownames(log2.ratios) -log2ratios$Clone changes rownames and then you could get your output (after getting rid of first column). If you just want an output to spreadsheet without row names column, look at ?write.table especially row.names option. regards Petr [EMAIL PROTECTED] [EMAIL PROTECTED] napsal dne 29.11.2007 17:06:57: Dear list, I have a data frame like: log2.ratios[1:3,1:4] Clone a1 a2 a3 1 GS1-232B23 -0.0207500 0.17553833 0.21939333 2 RP11-82D16 -0.1896667 0.02645167 -0.03112333 3 RP11-62M23 -0.1761700 0.08214500 -0.04877000 how to make it to look like: log2.ratios[1:3,1:4] a1 a2 a3 a4 GS1-232B23 -0.0207500 0.17553833 0.21939333 0.0008 RP11-82D16 -0.1896667 0.02645167 -0.03112333 0.007 RP11-62M23 -0.1761700 0.08214500 -0.048770000.7666 I tried as.matrix(log2.ratios) and it seems it is not working. Thanks a lot! Allen [[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. [[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] Odp: How to align the text in the legend
Well, did you look at xjust, yjust options of legend?
And maybe it would be worth to check adj graphic parameter see ?par
Petr
[EMAIL PROTECTED] napsal dne 29.11.2007 18:14:55:
Hello,
I tried to align lines of text in the legend of a plot. It always
defaults to the central alignment. How can I adjust it to be left
alignment?
Here is the code fragment written in python using Rpy module:
text = 'Quantiles #Loci\n'
text += '%s %6d\n' % (' 100',totalloci)
text += '%s %6d\n' % (' 95',per95cntloci)
text += '%s %6d\n' % (' 50',per50cntloci)
r.legend(20,30,text,cex=0.6,bty='n')
Thanks
Zhaoming
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[R] Working with time series class object
Hi I have a daily time series dataset, witch is very irregular spaced. The data is stored in a text file with the fields; day;month;year;stock1 price; stock2 price;...;stockN price The problem is that a script like described below, will result in a not very useful time count in the object. For example, ts.plot does not produce a good time format in the horizontal axis. So, what is a correct way to work with irregular time series? Is there another class that work with irregular time series? script: Object -ts(data =dataset, start = 1, end = dim(dataset)[1],deltat = 1, ts.eps = getOption(ts.eps), class =mts) Where dataset is a numerical matrix with the data. __ 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] How to take the ave of two rows in a data frame
Dear list, I have a data frame like: log2.ratios[1:3,1:4] ID a1 a2 a3 1 GS1-232B23 -0.0207500 0.17553833 0.21939333 2 RP11-82D16 -0.1896667 0.02645167 -0.03112333 3 RP11-62M23 -0.1761700 0.08214500 -0.04877000 4 RP11-62M23 0.2761700 -0.15214500 -0.05877000 the 3rd and 4th rows are of the same ID, I would like to take the avarage of these two rows and get the data frame to: ID a1 a2 a3 1 GS1-232B23 -0.0207500 0.17553833 0.21939333 2 RP11-82D16 -0.1896667 0.02645167 -0.03112333 3 RP11-62M23 -0.05 -0.035 0.094135 Can anyone suggest how to deal with this (to take the ave of two rows of the same ID ) more quickly? Thanks a bunch! Allen [[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] Question on structuring variances using the lme4 package
I am modeling the effects of an environmental variable (X) on fish recruitment (Y) for several, ecologically related species (i) using a mixed-effects model. The linear relationship between X and Y includes a fixed effect that is common across all species and random effects that vary by species. In the lmer() notation from the package lme4: Model- lmer(Y ~ X +(X|i)) Because the residuals of the model are autocorrelated and the variances differ among species, I would like to include an AR(1) process, and species-specific variances. I have been unable to do this so far in lme4. In the older “nlme” package, this was possible using: Model-update (weights=varIdent(form= ~1|i), correlation = corAR1(form = ~ years|i) Is this possible in lme4, and if so, how? Any help would be much appreciated. Cheers, Carrie Holt, Ph.D., M.Sc., B.Sc.(Honours) University of Washington School of Aquatic Fishery Sciences Box 355020 Seattle, WA 98195 USA __ 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] MS Excel Data
The package RODBC by Pr. Ripley is very helpful for this (Thanks To B. Ripley). Also see the package xlsReadWrite (thanks to H.P Suter). The latter is maybe easier to use. Good luck AA. - Original Message - From: faisal afzal siddiqui [EMAIL PROTECTED] To: r-help@r-project.org Sent: Wednesday, November 28, 2007 10:54 PM Subject: [R] MS Excel Data I am using MS Excel (Windos Operating system), how I import/export data between MS_Excel and R. Regds Faisal Afzal SIddiqui +92-300-9297089 [EMAIL PROTECTED] 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. __ 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] image() plot with z not in matrix format
Hello Marc, Well, image() requires data values in a regular grid. So you need to interpolate your data to a regular grid before you do your plot. There are many interpolation methods, but a good place to start is to do linear interpolation. You should first use expand.grid() to create the regular grid where to interpolate your data. Then use the interp() function (in the akima package) to do the interpolation. Finally, to do the plot you can use image() or better yet, the plot.surface() function in the 'fields' package, which is an improved version of the image() function. I hope that helps, Julian [EMAIL PROTECTED] wrote: Hello R cracks The image() function requires strictly increasing x and y values and z as a matrix. Actually, I don't have equally spaced variables, but anyway want to plot an colored image() (with z-information). An example of my problem is here: a-data.frame(rnorm(100), rnorm(100), runif(100)*100) How can I plot this data as an image (x=a[,1], y=a[,2] and z=a[,3])- according to ?image. It has to be possible to adapt the grid size so that every grid cell in the plot is coloured consequently. Thanks for your help Marc -- __ 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] fatal error from R function gls
I would appreciate some help with the followiing error ... what did I do wrong and what is the woraroud. library(nlme) glmod - gls(A ~ T +cosP +cos2P +cos4P +cos5P +sin3P +sin5P +cosP2 +sinP3 +P2, correlation=corAR1(),method=ML) Error: cannot allocate vector of size 491.3 Mb I have a bunch of humans' breathing signals. The recording frequency was 30 samples per second. The only relevant variables are: amplitude, phase (inhale - exhale), timestamp (time at which each amplitude sample was recorded). I have to get rid of the time trend of the amplitude, and be left with the amplitude explained by the phase. Before devising a way to remove such a trend, it is necessary (I think) to figure out whether its nature that is whether such a time trend is linear or not. *General question: **Is there any technique and/or method to figure out the nature of the time trend in a series of data ?* Thank you in advance to anyone who provides any suggestion. Best, -- 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] Anova(car) SS digits
Hi,
When I use Anova(car) to produce type III SS, 'Sum Sq' is reported in
integers:
Anova(bot.lm3, type =III)
Anova Table (Type III tests)
Response: bottemp
Sum Sq DfF value Pr(F)
(Intercept) 45295 1 29436.4440 2e-16
fungroup 3 2 0.8259 0.44006
numsp.fun11 2 3.4503 0.03460
block 419 468.0017 2e-16
fungroup:numsp.fun6 4 1.0317 0.39340
fungroup:block9 8 0.7429 0.65346
numsp.fun:block 12 8 0.9501 0.47795
fungroup:numsp.fun:block 27 16 1.0920 0.36882
Residuals 205 133
I have tried specifying digits = 7 in the call to Anova, but that
doesn't change anything. The output from another stats program for the
same data confirms that the ouptut above is correct, but is rounded to
the nearest integer. The dataset is too large to post here, but I can
confirm that I get the expected results from the examples in ?Anova,
as well as for type = 'II' on my own data. This output, and relevant
options() and sessionInfo are pasted below. What am I doing wrong?
Thanks,
Tyler
mod - lm(conformity ~ fcategory*partner.status, data=Moore,
+contrasts=list(fcategory=contr.sum, partner.status=contr.sum))
Anova(mod)
Anova Table (Type II tests)
Response: conformity
Sum Sq Df F value Pr(F)
fcategory 11.61 2 0.2770 0.759564
partner.status 212.21 1 10.1207 0.002874
fcategory:partner.status 175.49 2 4.1846 0.022572
Residuals817.76 39
Anova(mod, type=III)
Anova Table (Type III tests)
Response: conformity
Sum Sq Df F valuePr(F)
(Intercept) 5752.8 1 274.3592 2.2e-16
fcategory 36.0 2 0.8589 0.431492
partner.status239.6 1 11.4250 0.001657
fcategory:partner.status 175.5 2 4.1846 0.022572
Residuals 817.8 39
Anova(bot.lm3, type =II)
Anova Table (Type II tests)
Response: bottemp
Sum Sq Df F value Pr(F)
fungroup 1.87 2 0.6069 0.54656
numsp.fun 11.14 2 3.6214 0.02942
block486.47 4 79.0379 2e-16
fungroup:numsp.fun 6.32 4 1.0275 0.39553
fungroup:block11.43 8 0.9283 0.49542
numsp.fun:block 11.29 8 0.9169 0.50473
fungroup:numsp.fun:block 26.89 16 1.0920 0.36882
Residuals204.65 133
options('digits')
$digits
[1] 7
options('contrasts')
$contrasts
[1] contr.sum contr.poly
sessionInfo()
R version 2.5.1 (2007-06-27)
i486-pc-linux-gnu
locale:
LC_CTYPE=en_CA.UTF-8;LC_NUMERIC=C;LC_TIME=en_CA.UTF-8;LC_COLLATE=en_CA.UTF-8;
LC_MONETARY=en_CA.UTF-8;LC_MESSAGES=en_CA.UTF-8;LC_PAPER=en_CA.UTF-8;LC_NAME=C;
LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_CA.UTF-8;LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods
[7] base
other attached packages:
car
1.2-7
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[R] error in utils:::menuInstallPkgs() for R 2.6.1
Hi, I have upgraded on Windows from R 2.5.1 to R2.6.1 and when i've tried to install packages with utils:::menuInstallPkgs() i've got the following error (which i never got before) Warning: unable to access index for repository http://cran.hostingzero.com/bin/windows/contrib/2.6 Do you have any idea why? Sys.info() sysname release version nodename Windows NT 5.1 (build 2600) Service Pack 2 machine x86 Thanks, Monica _ Your smile counts. The more smiles you share, the more we donate. Join in. www.windowslive.com/smile?ocid=TXT_TAGLM_Wave2_oprsmilewlhmtagline [[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] Wireframe graph: black and white shading instead of color
All, The code below produces a color 3D graph. I'd like to make it black and white shading. I tried setting col.regions to FALSE but this just made it completely white. I want the graph to look exactly as is, except black (or grey) and white shading. Is this possible? Cheers, David p.list = c(.01, .1, .25, .5, .75, .9) cov.list = c(.2, .1, .05) ### leave out .01 X = rep(p.list, 3) Y = rep(cov.list, 1, each=6) Z = c(2475.00, 225.00,75.00,25.00, 8.33, 2.78, 9900.00, 900.00, 300.00, 100.00, 33.33,11.11, 39600.00, 3600.00, 1200.00, 400.00, 133.33,44.4) lattice.options(default.theme = col.whitebg) wireframe(Z ~ X * Y, scales = list(arrows = FALSE), bg = white, drape = TRUE, shade = FALSE, colorkey = FALSE, xlab = p, ylab = C.O.V., zlab =n) __ 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] extracting items from R objects and using them in \Sexpr with Sweave--problem with $
Running R 2.5.1 on WinXP with Tinn-R, and using Sweave via MikTex.
I am having trouble with the code below:
---
lowerCI95=
lowerCI95713 - t.test(data713, alternative=greater)
lowerCI95713.bound - lowerCI95713$conf.int[1]
@
Thus a lower 95\% confidence bound on the mean octane concentration is
\Sexpr{lowerCI95713.bound}.
ttest=
t.test713 - t.test(data713, mu=87, alternative=greater)
p.value - t.test713$p.value
@
-
When I Sweave and then pdflatex the files, the output pdf file contains
the verbatim text:
Thus a lower 95% confidence bound on the mean octane concentration is
lowerCI95713.bound.
That is, LaTeX is not recognizing and processing \Sexpr. When I look at
my .tex file in an editor with LaTeX syntax highlighting, I see that
LaTeX is interpreting everything between the two $ in the original code
(one before conf.int and one before p.value) as a math environment. I
think that's why the \Sexpr is not getting processed into the single
number as it should.
Any ideas how to make this work? The $ is the only way I know how to
access components of R objects.
Thank you.
--Chris
--
Christopher W. Ryan, MD
SUNY Upstate Medical University Clinical Campus at Binghamton
40 Arch Street, Johnson City, NY 13790
cryanatbinghamtondotedu
PGP public keys available at http://home.stny.rr.com/ryancw/
If you want to build a ship, don't drum up the men to gather wood,
divide the work and give orders. Instead, teach them to yearn for the
vast and endless sea. [Antoine de St. Exupery]
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Re: [R] Question on structuring variances using the lme4 package
Catherine A. Holt caholt at u.washington.edu writes: I am modeling the effects of an environmental variable (X) on fish recruitment (Y) for several, ecologically related species (i) using a mixed-effects model. The linear relationship between X and Y includes a fixed effect that is common across all species and random effects that vary by species. In the lmer() notation from the package lme4: Model- lmer(Y ~ X +(X|i)) Because the residuals of the model are autocorrelated and the variances differ among species, I would like to include an AR(1) process, and species-specific variances. I have been unable to do this so far in lme4. In the older “nlme” package, this was possible using: Model-update (weights=varIdent(form= ~1|i), correlation = corAR1(form = ~ years|i) Is this possible in lme4, and if so, how? Any help would be much appreciated. Cheers, No, it is not (yet) possible. Any reason not use lme? It works, and it is stable, and well documented (Pinheiro/Bates)? lmer is a package in development, it has been made public mainly to provide feedback to the author, Douglas Bates. See also the special list http://news.gmane.org/gmane.comp.lang.r.lme4.devel Dieter __ 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 in utils:::menuInstallPkgs() for R 2.6.1
Monica Pisica wrote: Hi, I have upgraded on Windows from R 2.5.1 to R2.6.1 and when i've tried to install packages with utils:::menuInstallPkgs() i've got the following error (which i never got before) Warning: unable to access index for repository http://cran.hostingzero.com/bin/windows/contrib/2.6 This CRAN mirror seems to be offline. Just choose another one. Uwe Do you have any idea why? Sys.info() sysname release version nodename Windows NT 5.1 (build 2600) Service Pack 2 machine x86 Thanks, Monica _ Your smile counts. The more smiles you share, the more we donate. Join in. www.windowslive.com/smile?ocid=TXT_TAGLM_Wave2_oprsmilewlhmtagline [[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] MS Excel Data
On Nov 29, 2007 3:01 PM, Bert Gunter [EMAIL PROTECTED] wrote: This has been discussed on this list many times before. Google on Import Excel R. Note also that there are potential problems (loss of digits) due to Excel idiosyncracies depending on what you do. http://www.burns-stat.com/pages/Tutor/spreadsheet_addiction.html provides some details. Finally, I have found that for rectangular data sets with no missing fields in Excel (tables), cutting and read.tabling **the data only ** is a simple(but probably not without risk) way to do it: (after cutting the data only in Excel to the clipboard) in R: newdat - read.table(clipboard, head=FALSE, row.names=NULL) The columns can then be named via names(newdat) - ... I omit column headers because in most of the Excel data I get the column names have spaces and other non-alphanumeric characters which R cannot easily digest. One could separately scan() just the vector of column headers and use regular expressions to extract the names. But for small tables, I find it easier just to create the names manually. You can include headers with spaces in the copy with: DF - read.delim(clipboard) __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Anova(car) SS digits
On 2007-11-29, John Fox [EMAIL PROTECTED] wrote: Anova() creates an object of class anova which then gets printed by the print method for anova objects. The reason that the sums of squares for the type II tests are rounded like this is because of the large value for the intercept. Although Anova() doesn't take a digits argument, print.anova() does, and so, e.g., you could use the command print(Anova(bot.lm3, type =III), digits=7) I hope this helps, John Very much. Thanks! Tyler __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Wireframe graph: black and white shading instead of color
On 11/29/07, David Afshartous [EMAIL PROTECTED] wrote: All, The code below produces a color 3D graph. I'd like to make it black and white shading. I tried setting col.regions to FALSE but this just made it completely white. I want the graph to look exactly as is, except black (or grey) and white shading. Is this possible? Perhaps you want something like wireframe(Z ~ X * Y, drape = TRUE, par.settings = standard.theme(color = FALSE)) Generally, for black and white output, the recommended approach is to start a device using trellis.device(..., color = FALSE) The call above attaches the resulting settings to the particular object rather than the device. -Deepayan Cheers, David p.list = c(.01, .1, .25, .5, .75, .9) cov.list = c(.2, .1, .05) ### leave out .01 X = rep(p.list, 3) Y = rep(cov.list, 1, each=6) Z = c(2475.00, 225.00,75.00,25.00, 8.33, 2.78, 9900.00, 900.00, 300.00, 100.00, 33.33,11.11, 39600.00, 3600.00, 1200.00, 400.00, 133.33,44.4) lattice.options(default.theme = col.whitebg) wireframe(Z ~ X * Y, scales = list(arrows = FALSE), bg = white, drape = TRUE, shade = FALSE, colorkey = FALSE, xlab = p, ylab = C.O.V., zlab =n) __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to align the text in the legend
Thanks Petr!
I checked both of your suggestions and nothing seems working for me.
I don't understand why the well-formatted text string got re-aligned in
the legend of plot.
This is what I got:
Quantitles #Samples
1002759
95 121
50 0
And here is what I'm looking for:
Quantitles #Samples
100 2759
95 121
500
-Original Message-
From: Petr PIKAL [mailto:[EMAIL PROTECTED]
Sent: Thursday, November 29, 2007 12:35 PM
To: Wang, Zhaoming (NIH/NCI) [C]
Cc: r-help@r-project.org
Subject: Odp: [R] How to align the text in the legend
Well, did you look at xjust, yjust options of legend?
And maybe it would be worth to check adj graphic parameter see ?par
Petr
[EMAIL PROTECTED] napsal dne 29.11.2007 18:14:55:
Hello,
I tried to align lines of text in the legend of a plot. It always
defaults to the central alignment. How can I adjust it to be left
alignment?
Here is the code fragment written in python using Rpy module:
text = 'Quantiles #Loci\n'
text += '%s %6d\n' % (' 100',totalloci)
text += '%s %6d\n' % (' 95',per95cntloci)
text += '%s %6d\n' % (' 50',per50cntloci)
r.legend(20,30,text,cex=0.6,bty='n')
Thanks
Zhaoming
[[alternative HTML version deleted]]
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Re: [R] How to align the text in the legend
Have you tried a non-proportional font like Courier?
On Nov 29, 2007 12:14 PM, Wang, Zhaoming (NIH/NCI) [C]
[EMAIL PROTECTED] wrote:
Hello,
I tried to align lines of text in the legend of a plot. It always
defaults to the central alignment. How can I adjust it to be left
alignment?
Here is the code fragment written in python using Rpy module:
text = 'Quantiles #Loci\n'
text += '%s %6d\n' % (' 100',totalloci)
text += '%s %6d\n' % (' 95',per95cntloci)
text += '%s %6d\n' % (' 50',per50cntloci)
r.legend(20,30,text,cex=0.6,bty='n')
Thanks
Zhaoming
[[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.
--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
What is the problem you are trying to solve?
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Re: [R] How to align the text in the legend
Can you give me a little more in detail? I'm new to this.
Thanks
Zhaoming
-Original Message-
From: jim holtman [mailto:[EMAIL PROTECTED]
Sent: Thursday, November 29, 2007 4:05 PM
To: Wang, Zhaoming (NIH/NCI) [C]
Cc: r-help@r-project.org
Subject: Re: [R] How to align the text in the legend
Have you tried a non-proportional font like Courier?
On Nov 29, 2007 12:14 PM, Wang, Zhaoming (NIH/NCI) [C]
[EMAIL PROTECTED] wrote:
Hello,
I tried to align lines of text in the legend of a plot. It always
defaults to the central alignment. How can I adjust it to be left
alignment?
Here is the code fragment written in python using Rpy module:
text = 'Quantiles #Loci\n'
text += '%s %6d\n' % (' 100',totalloci)
text += '%s %6d\n' % (' 95',per95cntloci)
text += '%s %6d\n' % (' 50',per50cntloci)
r.legend(20,30,text,cex=0.6,bty='n')
Thanks
Zhaoming
[[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.
--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
What is the problem you are trying to solve?
__
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Re: [R] extracting items from R objects and using them in \Sexpr with Sweave--problem with $
On Thu, 29 Nov 2007, Christopher W. Ryan wrote:
Running R 2.5.1 on WinXP with Tinn-R, and using Sweave via MikTex.
I am having trouble with the code below:
---
lowerCI95=
lowerCI95713 - t.test(data713, alternative=greater)
lowerCI95713.bound - lowerCI95713$conf.int[1]
@
Thus a lower 95\% confidence bound on the mean octane concentration is
\Sexpr{lowerCI95713.bound}.
ttest=
t.test713 - t.test(data713, mu=87, alternative=greater)
p.value - t.test713$p.value
@
-
When I Sweave and then pdflatex the files, the output pdf file contains
the verbatim text:
Thus a lower 95% confidence bound on the mean octane concentration is
lowerCI95713.bound.
Adding
data713 - rnorm(10)
at the start of the first chunk (provide commented, minimal,
self-contained, reproducible code), and running this as
sessionInfo()
R version 2.6.0 (2007-10-03)
i386-pc-mingw32
locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
States.1252;LC_MONETARY=English_United
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
attached base packages:
[1] tools stats graphics grDevices utils datasets methods
[8] base
I got
Thus a lower 95\% confidence bound on the mean octane concentration is
-0.204003137749730.
That is, LaTeX is not recognizing and processing \Sexpr.
Nor should it. That is Sweave's job.
When I look at
my .tex file in an editor with LaTeX syntax highlighting, I see that
LaTeX is interpreting everything between the two $ in the original code
(one before conf.int and one before p.value) as a math environment. I
think that's why the \Sexpr is not getting processed into the single
number as it should.
Any ideas how to make this work? The $ is the only way I know how to
access components of R objects.
First, give us commented, minimal, self-contained, reproducible code.
I suspect there is something upstream of what you provided that
caused the problem. Perhaps narrowing your focus will reveal what it is,
but in any case we must guess what your problem is without reproducible
code.
HTH,
Chuck
p.s. Time for you and me both to upgrade to R-2.6.1
Thank you.
--Chris
--
Christopher W. Ryan, MD
SUNY Upstate Medical University Clinical Campus at Binghamton
40 Arch Street, Johnson City, NY 13790
cryanatbinghamtondotedu
PGP public keys available at http://home.stny.rr.com/ryancw/
If you want to build a ship, don't drum up the men to gather wood,
divide the work and give orders. Instead, teach them to yearn for the
vast and endless sea. [Antoine de St. Exupery]
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Charles C. Berry(858) 534-2098
Dept of Family/Preventive Medicine
E mailto:[EMAIL PROTECTED] UC San Diego
http://famprevmed.ucsd.edu/faculty/cberry/ La Jolla, San Diego 92093-0901
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Re: [R] How can R be used to solve algebra equations?
The Ryacas package might be able to do it... Søren Fra: [EMAIL PROTECTED] på vegne af francogrex Sendt: to 29-11-2007 22:00 Til: r-help@r-project.org Emne: [R] How can R be used to solve algebra equations? suppose I have this equation: (x^2+y^2+3z^3)/(5*z^2*x^3)=0 and I want to find x in relation to the other variables which actually is: x=sqrt(-3*z^3-y^2) or x=-sqrt(-3*z^3-y^2) Can R give me this expression solution? I know there is uniroot, but here I want the expression not the value, because I do not have values for y and z. Thanks -- View this message in context: http://www.nabble.com/How-can-R-be-used-to-solve-algebra-equations--tf4899794.html#a14034422 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.
Re: [R] How can R be used to solve algebra equations?
Yes, try this: library(Ryacas) Loading required package: XML x - Sym(x) y - Sym(y) z - Sym(z) Solve((x^2+y^2+3*z^3)/(5*z^2*x^3)==0, x) [1] Starting Yacas! expression(list(x == root(-(4 * (y^2 + 3 * z^3)), 2)/2, x == -root(-(4 * (y^2 + 3 * z^3)), 2)/2)) On Nov 29, 2007 5:06 PM, Søren Højsgaard [EMAIL PROTECTED] wrote: The Ryacas package might be able to do it... Søren Fra: [EMAIL PROTECTED] på vegne af francogrex Sendt: to 29-11-2007 22:00 Til: r-help@r-project.org Emne: [R] How can R be used to solve algebra equations? suppose I have this equation: (x^2+y^2+3z^3)/(5*z^2*x^3)=0 and I want to find x in relation to the other variables which actually is: x=sqrt(-3*z^3-y^2) or x=-sqrt(-3*z^3-y^2) Can R give me this expression solution? I know there is uniroot, but here I want the expression not the value, because I do not have values for y and z. Thanks -- View this message in context: http://www.nabble.com/How-can-R-be-used-to-solve-algebra-equations--tf4899794.html#a14034422 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-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 align the text in the legend
try this when plotting the legend:
plot(...)
par(family='mono')
legend('topright', legend=)
This should use fixed width fonts for your legend.
On Nov 29, 2007 4:20 PM, Wang, Zhaoming (NIH/NCI) [C]
[EMAIL PROTECTED] wrote:
Can you give me a little more in detail? I'm new to this.
Thanks
Zhaoming
-Original Message-
From: jim holtman [mailto:[EMAIL PROTECTED]
Sent: Thursday, November 29, 2007 4:05 PM
To: Wang, Zhaoming (NIH/NCI) [C]
Cc: r-help@r-project.org
Subject: Re: [R] How to align the text in the legend
Have you tried a non-proportional font like Courier?
On Nov 29, 2007 12:14 PM, Wang, Zhaoming (NIH/NCI) [C]
[EMAIL PROTECTED] wrote:
Hello,
I tried to align lines of text in the legend of a plot. It always
defaults to the central alignment. How can I adjust it to be left
alignment?
Here is the code fragment written in python using Rpy module:
text = 'Quantiles #Loci\n'
text += '%s %6d\n' % (' 100',totalloci)
text += '%s %6d\n' % (' 95',per95cntloci)
text += '%s %6d\n' % (' 50',per50cntloci)
r.legend(20,30,text,cex=0.6,bty='n')
Thanks
Zhaoming
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
What is the problem you are trying to solve?
--
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] How can R be used to solve algebra equations?
On Thu, Nov 29, 2007 at 01:00:59PM -0800, francogrex wrote: suppose I have this equation: (x^2+y^2+3z^3)/(5*z^2*x^3)=0 and I want to find x in relation to the other variables which actually is: x=sqrt(-3*z^3-y^2) or x=-sqrt(-3*z^3-y^2) Can R give me this expression solution? I know there is uniroot, but here I want the expression not the value, because I do not have values for y and z. I suggest the use of maxima rather than R. The two complement each other very nicely: http://maxima.sf.net -- Daniel Lakeland [EMAIL PROTECTED] http://www.street-artists.org/~dlakelan __ 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 align the text in the legend
Thanks Jim! And it does work!!
Zhaoming
-Original Message-
From: jim holtman [mailto:[EMAIL PROTECTED]
Sent: Thursday, November 29, 2007 5:26 PM
To: Wang, Zhaoming (NIH/NCI) [C]
Cc: r-help@r-project.org
Subject: Re: [R] How to align the text in the legend
try this when plotting the legend:
plot(...)
par(family='mono')
legend('topright', legend=)
This should use fixed width fonts for your legend.
On Nov 29, 2007 4:20 PM, Wang, Zhaoming (NIH/NCI) [C]
[EMAIL PROTECTED] wrote:
Can you give me a little more in detail? I'm new to this.
Thanks
Zhaoming
-Original Message-
From: jim holtman [mailto:[EMAIL PROTECTED]
Sent: Thursday, November 29, 2007 4:05 PM
To: Wang, Zhaoming (NIH/NCI) [C]
Cc: r-help@r-project.org
Subject: Re: [R] How to align the text in the legend
Have you tried a non-proportional font like Courier?
On Nov 29, 2007 12:14 PM, Wang, Zhaoming (NIH/NCI) [C]
[EMAIL PROTECTED] wrote:
Hello,
I tried to align lines of text in the legend of a plot. It always
defaults to the central alignment. How can I adjust it to be left
alignment?
Here is the code fragment written in python using Rpy module:
text = 'Quantiles #Loci\n'
text += '%s %6d\n' % (' 100',totalloci)
text += '%s %6d\n' % (' 95',per95cntloci)
text += '%s %6d\n' % (' 50',per50cntloci)
r.legend(20,30,text,cex=0.6,bty='n')
Thanks
Zhaoming
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
What is the problem you are trying to solve?
--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
What is the problem you are trying to solve?
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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Re: [R] How can R be used to solve algebra equations?
francogrex said the following on 11/29/2007 1:00 PM: suppose I have this equation: (x^2+y^2+3z^3)/(5*z^2*x^3)=0 and I want to find x in relation to the other variables which actually is: x=sqrt(-3*z^3-y^2) or x=-sqrt(-3*z^3-y^2) Can R give me this expression solution? I know there is uniroot, but here I want the expression not the value, because I do not have values for y and z. Thanks Try: library(Ryacas) yacas(Solve((x^2+y^2+3*z^3)/(5*z^2*x^3)==0, x)) expression(list(x == root(-(4 * (y^2 + 3 * z^3)), 2)/2, x == -root(-(4 * (y^2 + 3 * z^3)), 2)/2)) HTH, --sundar __ 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] configure the margin of the plot
I'm trying to put two plots side-by-side in two panels. Since the y-axis of the two plots is the same, I want to leave out the y-axis of the second plot. And the two plots look quite separate from each other. Is there any way to have them stay closer to each other? I've tried to adjust mar option of par but it has a global effect as I see the left margin of the first plot will be adjusted as well. Below is the code fragment: r.par(mfrow=[1,2],mar=[5,4,1,1]) r.plot(x,hets,xlim=[0,105],xlab='Samples(%)',ylab='Heterozygosity(%)',co l=colors,cex=0.6) ... plot(completion,hets,xlim=[40,100],xlab=Sample Completion(%),ylab=,col=colors,axes=False,cex=0.6) Thanks Zhaoming [[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] List operations in R
hello:
I am very confused when it comes to list operations in
R.
I seek help in the following problem.
I have two different vectors
myIDs - a character vector with no names to their
elements
x2 - another character vector derived from unlisting a
list where an element has both a name and value.
I am not happy the way x2 is with names and values to
every element.
myIDs[1:10]
[1] 54898 7083 7031 7083 4175 4605
7494 5111 960 990
class(myIDs)
[1] character
Similarly x2 objects is
x2[1:4]
1000_at 1001_at 1002_f_at 1003_s_at
559570751557 643
class(x2)
[1] character
I am not happy the way x2 is right now. I do not want
names of the elements. I want to write to another
object x3 that has only values of the elements and not
their names.
How can I do that?
I can give a [[]] to get the value of element.
x2[[1]]
[1] 5595
When I try to give a range of numbers:
x2[[1:4]]
Error in x2[[1:4]] : attempt to select more than one
element
Frustrated, I wanted to create another object z, and
append all values of x2 to z.
z = c()
for(i in 1:length(x2)){
+ append(z,x2[[i]],after=length(z))}
length(z)
[1] 0
now z is empty. this is really frustrating. Can
someone help me please how to deal in this situation.
Thanks
Sri
Be a better pen pal.
__
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
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Re: [R] configure the margin of the plot
try this: layout(cbind(1,2)) par(mar=c(4,4,2,0)) plot(0) par(mar=c(4,0,2,0)) plot(0, yaxt='n', ylab='') On Nov 29, 2007 5:41 PM, Wang, Zhaoming (NIH/NCI) [C] [EMAIL PROTECTED] wrote: I'm trying to put two plots side-by-side in two panels. Since the y-axis of the two plots is the same, I want to leave out the y-axis of the second plot. And the two plots look quite separate from each other. Is there any way to have them stay closer to each other? I've tried to adjust mar option of par but it has a global effect as I see the left margin of the first plot will be adjusted as well. Below is the code fragment: r.par(mfrow=[1,2],mar=[5,4,1,1]) r.plot(x,hets,xlim=[0,105],xlab='Samples(%)',ylab='Heterozygosity(%)',co l=colors,cex=0.6) ... plot(completion,hets,xlim=[40,100],xlab=Sample Completion(%),ylab=,col=colors,axes=False,cex=0.6) Thanks Zhaoming [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem you are trying to solve? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] List operations in R
?unname
?unlist
cheers,
Rolf Turner
On 30/11/2007, at 1:07 PM, Srinivas Iyyer wrote:
hello:
I am very confused when it comes to list operations in
R.
I seek help in the following problem.
I have two different vectors
myIDs - a character vector with no names to their
elements
x2 - another character vector derived from unlisting a
list where an element has both a name and value.
I am not happy the way x2 is with names and values to
every element.
myIDs[1:10]
[1] 54898 7083 7031 7083 4175 4605
7494 5111 960 990
class(myIDs)
[1] character
Similarly x2 objects is
x2[1:4]
1000_at 1001_at 1002_f_at 1003_s_at
559570751557 643
class(x2)
[1] character
I am not happy the way x2 is right now. I do not want
names of the elements. I want to write to another
object x3 that has only values of the elements and not
their names.
How can I do that?
I can give a [[]] to get the value of element.
x2[[1]]
[1] 5595
When I try to give a range of numbers:
x2[[1:4]]
Error in x2[[1:4]] : attempt to select more than one
element
Frustrated, I wanted to create another object z, and
append all values of x2 to z.
z = c()
for(i in 1:length(x2)){
+ append(z,x2[[i]],after=length(z))}
length(z)
[1] 0
now z is empty. this is really frustrating. Can
someone help me please how to deal in this situation.
Thanks
Sri
__
__
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guide.html
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##
Attention:\ This e-mail message is privileged and confid...{{dropped:9}}
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Re: [R] MS Excel Data
Here is a very crude function I use quite often. It tries to recognize
whether you have headers or not by checking the very first character. If
it is numeric, it assumes that there are no headers. The suppressWarnings
gets rid of a warning one gets when trying to coerce a character to
numeric. The main advantage of the function is that you do not have to
type too much :-)
clip - function(){
if(is.na(suppressWarnings(as.numeric(scan(clipboard, what=,
nmax=1)
read.delim(clipboard)
else
read.delim(clipboard, header=FALSE)
Cheers,
Andy
__
Andy Jaworski
518-1-01
Process Laboratory
3M Corporate Research Laboratory
-
E-mail: [EMAIL PROTECTED]
Tel: (651) 733-6092
Fax: (651) 736-3122
Bert Gunter
[EMAIL PROTECTED]
ne.comTo
Sent by: 'Gabor Grothendieck'
[EMAIL PROTECTED] [EMAIL PROTECTED]
project.orgcc
r-help@r-project.org
Subject
11/29/2007 06:39 Re: [R] MS Excel Data
PM
Better yet! Thanks Gabor.
-- Bert
-Original Message-
From: Gabor Grothendieck [mailto:[EMAIL PROTECTED]
Sent: Thursday, November 29, 2007 12:10 PM
To: Bert Gunter
Cc: r-help@r-project.org
Subject: Re: [R] MS Excel Data
On Nov 29, 2007 3:01 PM, Bert Gunter [EMAIL PROTECTED] wrote:
This has been discussed on this list many times before. Google on Import
Excel R. Note also that there are potential problems (loss of digits)
due
to Excel idiosyncracies depending on what you do.
http://www.burns-stat.com/pages/Tutor/spreadsheet_addiction.html
provides
some details.
Finally, I have found that for rectangular data sets with no missing
fields
in Excel (tables), cutting and read.tabling **the data only ** is a
simple(but probably not without risk) way to do it:
(after cutting the data only in Excel to the clipboard) in R:
newdat - read.table(clipboard, head=FALSE, row.names=NULL)
The columns can then be named via names(newdat) - ...
I omit column headers because in most of the Excel data I get the column
names have spaces and other non-alphanumeric characters which R cannot
easily digest. One could separately scan() just the vector of column
headers
and use regular expressions to extract the names. But for small tables, I
find it easier just to create the names manually.
You can include headers with spaces in the copy with:
DF - read.delim(clipboard)
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PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] MS Excel Data
Better yet! Thanks Gabor. -- Bert -Original Message- From: Gabor Grothendieck [mailto:[EMAIL PROTECTED] Sent: Thursday, November 29, 2007 12:10 PM To: Bert Gunter Cc: r-help@r-project.org Subject: Re: [R] MS Excel Data On Nov 29, 2007 3:01 PM, Bert Gunter [EMAIL PROTECTED] wrote: This has been discussed on this list many times before. Google on Import Excel R. Note also that there are potential problems (loss of digits) due to Excel idiosyncracies depending on what you do. http://www.burns-stat.com/pages/Tutor/spreadsheet_addiction.html provides some details. Finally, I have found that for rectangular data sets with no missing fields in Excel (tables), cutting and read.tabling **the data only ** is a simple(but probably not without risk) way to do it: (after cutting the data only in Excel to the clipboard) in R: newdat - read.table(clipboard, head=FALSE, row.names=NULL) The columns can then be named via names(newdat) - ... I omit column headers because in most of the Excel data I get the column names have spaces and other non-alphanumeric characters which R cannot easily digest. One could separately scan() just the vector of column headers and use regular expressions to extract the names. But for small tables, I find it easier just to create the names manually. You can include headers with spaces in the copy with: DF - read.delim(clipboard) __ 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] Controlling Postscript output, size and orientation
I'm trying to get my graphics so that I can use them in LaTeX to create (via ) a pdf presentation. I've tried controlling inner and outer margins and figure size using par(), to no avail. The ps output keeps appearing as a portrait page with a centered figure. Nothing I have been able to do so far has changed that. Below is the code: par(bg=yellow, lab=c(10,5,7) #mai=c(1.25, 1, 0.2, 0.2), #pin=c(6,4) ) curve(20-(40*(exp(-.4*x)-1)), from=0, to=9, n=1000, add=F, type= l, lwd=2, xlab=Ocassion of Measurement, ylab=y, ) I had the same issue with a trellis plot: obs.plot- xyplot(msen~Age, data=obs.msen, groups=ID2, type=l, lwd=2, col=1, xlab=Age, ylab=Maternal Sensitivity, ylim=c(-.5,4.5),xlim=c(0,5), panel=panel.superpose, par.settings=list(background=list(col=white)) ) obs.plot - --- Project Scientist University of California, Irvine -- View this message in context: http://www.nabble.com/Controlling-Postscript-output%2C-size-and-orientation-tf4899986.html#a14035096 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] The R Book - great resource for R beginners
Hi all, I've recently discovered The R Book by Micheal J. Crawley. I am new to R and I am finding it incredibly useful. With my background in math and programming, I expected that I would be able to pick it up quickly, but even after reading several other intro books, I found it was still hard to figure out how to get data into R and how dataframes relate to vectors and actually doing statistics with R. But, The R Book is well written and gives plenty of examples and explains many of the often used tools within R. It's both a tutorial and a relatively advanced reference book for R, very accessible to a beginner like me. Just curious: What have been the experiences of others who have used The R Book? Thanks, Bob Harris - [[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] List operations in R
To remove the 'names':
x2 - c('1001_a'='123', '1002_b'='345')
x2
1001_a 1002_b
123 345
names(x2) - NULL
x2
[1] 123 345
To append:
z - letters[1:4]
z
[1] a b c d
z - c(z,x2)
z
[1] a b c d 123 345
On Nov 29, 2007 7:07 PM, Srinivas Iyyer [EMAIL PROTECTED] wrote:
hello:
I am very confused when it comes to list operations in
R.
I seek help in the following problem.
I have two different vectors
myIDs - a character vector with no names to their
elements
x2 - another character vector derived from unlisting a
list where an element has both a name and value.
I am not happy the way x2 is with names and values to
every element.
myIDs[1:10]
[1] 54898 7083 7031 7083 4175 4605
7494 5111 960 990
class(myIDs)
[1] character
Similarly x2 objects is
x2[1:4]
1000_at 1001_at 1002_f_at 1003_s_at
559570751557 643
class(x2)
[1] character
I am not happy the way x2 is right now. I do not want
names of the elements. I want to write to another
object x3 that has only values of the elements and not
their names.
How can I do that?
I can give a [[]] to get the value of element.
x2[[1]]
[1] 5595
When I try to give a range of numbers:
x2[[1:4]]
Error in x2[[1:4]] : attempt to select more than one
element
Frustrated, I wanted to create another object z, and
append all values of x2 to z.
z = c()
for(i in 1:length(x2)){
+ append(z,x2[[i]],after=length(z))}
length(z)
[1] 0
now z is empty. this is really frustrating. Can
someone help me please how to deal in this situation.
Thanks
Sri
Be a better pen pal.
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+1 513 646 9390
What is the problem you are trying to solve?
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Re: [R] main plot title
On 30/11/2007, at 3:53 PM, marciarr wrote:
Hi Jim,
Thanks for your answer.
Unfortunately, because the x of my plot function is not actually
waht I need
on my graph's title, your advice does not work. Thanks anyway,
Marcia
Jim answered the question you asked. If his advice didn't work, then
you
asked the wrong question. It pays to do a little thinking about a
problem
before asking the list for help.
What are you expecting anyway? That R should be able to read your mind?
cheers,
Rolf Turner
##
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Re: [R] vector sprintf argument [SEC=UNCLASSIFIED]
Hi Tom, Try this: G - Number: %s sprintf(G, toString(A)) [1] Number: 3, 4, 5 Cheers Joe Joe Crombie Biosecurity and Information Sciences Bureau of Rural Science Canberra Australia p: +61 2 6272 5906 e: [EMAIL PROTECTED] -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Tom Sgouros Sent: Friday, 30 November 2007 12:43 PM To: r-help@r-project.org Subject: [R] vector sprintf argument Hello all: If I have a vector and a format, I want to do this: A - c(3,4,5) F - Number: %d, %d, %d sprintf(F,A) This doesn't work because A isn't three arguments, it's just one. Is there a way to peel the vector members out of A so that sprintf can get at them? I would like to do this because I have a large set of variable-length data that I'd like to print out in fancy formatted form. The vectors range in length from 2 to 7. Each row is different, so I had been hoping to do this with an array of formats, too. I feel like I'm either overlooking something obvious, or have determined to do this in an un-R fashion. Any advice is welcome. (On this topic, that is.) Many thanks, -tom -- tomfool at as220 dot org http://sgouros.com http://whatcheer.net __ 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. --IMPORTANT - This message has been issued by The Department of Agriculture, Fisheries and Forestry (DAFF). The information transmitted is for the use of the intended recipient only and may contain confidential and/or legally privileged material. It is your responsibility to check any attachments for viruses and defects before opening or sending them on. Any reproduction, publication, communication, re-transmission, disclosure, dissemination or other use of the information contained in this e-mail by persons or entities other than the intended recipient is prohibited. The taking of any action in reliance upon this information by persons or entities other than the intended recipient is prohibited. If you have received this e-mail in error please notify the sender and delete all copies of this transmission together with any attachments. If you have received this e-mail as part of a valid mailing list and no longer want to receive a message such as this one advise the sender by return e-mail accordingly. Only e-mail correspondence which includes this footer, has been authorised by DAFF -- __ 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] MS Excel Data
Or even:
clip - function() read.delim(clipboard, header =
is.na(suppressWarnings(as.numeric(scan(clipboard, , 1)
On Nov 29, 2007 7:51 PM, [EMAIL PROTECTED] wrote:
Here is a very crude function I use quite often. It tries to recognize
whether you have headers or not by checking the very first character. If
it is numeric, it assumes that there are no headers. The suppressWarnings
gets rid of a warning one gets when trying to coerce a character to
numeric. The main advantage of the function is that you do not have to
type too much :-)
clip - function(){
if(is.na(suppressWarnings(as.numeric(scan(clipboard, what=,
nmax=1)
read.delim(clipboard)
else
read.delim(clipboard, header=FALSE)
Cheers,
Andy
__
Andy Jaworski
518-1-01
Process Laboratory
3M Corporate Research Laboratory
-
E-mail: [EMAIL PROTECTED]
Tel: (651) 733-6092
Fax: (651) 736-3122
Bert Gunter
[EMAIL PROTECTED]
ne.comTo
Sent by: 'Gabor Grothendieck'
[EMAIL PROTECTED] [EMAIL PROTECTED]
project.orgcc
r-help@r-project.org
Subject
11/29/2007 06:39 Re: [R] MS Excel Data
PM
Better yet! Thanks Gabor.
-- Bert
-Original Message-
From: Gabor Grothendieck [mailto:[EMAIL PROTECTED]
Sent: Thursday, November 29, 2007 12:10 PM
To: Bert Gunter
Cc: r-help@r-project.org
Subject: Re: [R] MS Excel Data
On Nov 29, 2007 3:01 PM, Bert Gunter [EMAIL PROTECTED] wrote:
This has been discussed on this list many times before. Google on Import
Excel R. Note also that there are potential problems (loss of digits)
due
to Excel idiosyncracies depending on what you do.
http://www.burns-stat.com/pages/Tutor/spreadsheet_addiction.html
provides
some details.
Finally, I have found that for rectangular data sets with no missing
fields
in Excel (tables), cutting and read.tabling **the data only ** is a
simple(but probably not without risk) way to do it:
(after cutting the data only in Excel to the clipboard) in R:
newdat - read.table(clipboard, head=FALSE, row.names=NULL)
The columns can then be named via names(newdat) - ...
I omit column headers because in most of the Excel data I get the column
names have spaces and other non-alphanumeric characters which R cannot
easily digest. One could separately scan() just the vector of column
headers
and use regular expressions to extract the names. But for small tables, I
find it easier just to create the names manually.
You can include headers with spaces in the copy with:
DF - read.delim(clipboard)
__
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https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] configure the margin of the plot
It looks much better now! Thanks Jim!! -Original Message- From: jim holtman [mailto:[EMAIL PROTECTED] Sent: Thursday, November 29, 2007 7:29 PM To: Wang, Zhaoming (NIH/NCI) [C] Cc: r-help@r-project.org Subject: Re: [R] configure the margin of the plot try this: layout(cbind(1,2)) par(mar=c(4,4,2,0)) plot(0) par(mar=c(4,0,2,0)) plot(0, yaxt='n', ylab='') On Nov 29, 2007 5:41 PM, Wang, Zhaoming (NIH/NCI) [C] [EMAIL PROTECTED] wrote: I'm trying to put two plots side-by-side in two panels. Since the y-axis of the two plots is the same, I want to leave out the y-axis of the second plot. And the two plots look quite separate from each other. Is there any way to have them stay closer to each other? I've tried to adjust mar option of par but it has a global effect as I see the left margin of the first plot will be adjusted as well. Below is the code fragment: r.par(mfrow=[1,2],mar=[5,4,1,1]) r.plot(x,hets,xlim=[0,105],xlab='Samples(%)',ylab='Heterozygosity(%)', co l=colors,cex=0.6) ... plot(completion,hets,xlim=[40,100],xlab=Sample Completion(%),ylab=,col=colors,axes=False,cex=0.6) Thanks Zhaoming [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem you are trying to solve? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] main plot title
Hello Rolf,
I am sorry for the incovenience. Well, here it goes again!
Let's say, I have a time series for the variable Chl. I wrote a function
pgram that gives me the raw periodogram of the time series. So, this
function uses the values of my time series in an algorithm that gives me new
x and y values. And those are the coordinates that I am actually using on
the final plot function inside pgram (Chl is actually not an argument of
my plot function...). I am interested that the title of the original dataset
I used appears on my plot. Because I will use this function several time
series (let's say Chl and A, with different data sets), I would like to
obtain each time on the title of my plot for pgram(x), Raw periodogram of
x or for pgram(A), Raw periodogram of A.
Hope it is clearer now,
Cheers,
Marcia Rocha
Rolf Turner-3 wrote:
On 30/11/2007, at 3:53 PM, marciarr wrote:
Hi Jim,
Thanks for your answer.
Unfortunately, because the x of my plot function is not actually
waht I need
on my graph's title, your advice does not work. Thanks anyway,
Marcia
Jim answered the question you asked. If his advice didn't work, then
you
asked the wrong question. It pays to do a little thinking about a
problem
before asking the list for help.
What are you expecting anyway? That R should be able to read your mind?
cheers,
Rolf Turner
##
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and provide commented, minimal, self-contained, reproducible code.
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[R] using color coded colorbars for bar plots
Hello R Fundi, The poetic title of this post is a request for help in regard to a simple plotting question. I have displayed the mean observations of a series variables using barplot(). On the same figure I have colored the bars to represent the Standard deviation of each variable using color.scale(). Now I wish to add a graduated colorbar (legend) that corresponds to the colors representing the standard devitation. Simple. Or so it seemed. Has anyone attempted to do this before? Thanks for your time. Jim Dell __ 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] vector sprintf argument
The only thing I can think of is: a - c(1,2.7,5.19) F-c(numeric: %d ,%g ,%8.3f) x-sapply(1:length(a),function(i) sprintf(F[i],a[i])) y-paste(x,sep=,collapse=) But I am sure that you will get a better advice elsewhere. --- Tom Sgouros [EMAIL PROTECTED] wrote: Hello all: If I have a vector and a format, I want to do this: A - c(3,4,5) F - Number: %d, %d, %d sprintf(F,A) This doesn't work because A isn't three arguments, it's just one. Is there a way to peel the vector members out of A so that sprintf can get at them? I would like to do this because I have a large set of variable-length data that I'd like to print out in fancy formatted form. The vectors range in length from 2 to 7. Each row is different, so I had been hoping to do this with an array of formats, too. I feel like I'm either overlooking something obvious, or have determined to do this in an un-R fashion. Any advice is welcome. (On this topic, that is.) Many thanks, -tom -- tomfool at as220 dot org http://sgouros.com http://whatcheer.net __ 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] main plot title
The answer is exactly the same: deparse(substitute(x))
go to the help page on 'deparse'
On Nov 29, 2007 10:53 PM, marciarr [EMAIL PROTECTED] wrote:
Hello Rolf,
I am sorry for the incovenience. Well, here it goes again!
Let's say, I have a time series for the variable Chl. I wrote a function
pgram that gives me the raw periodogram of the time series. So, this
function uses the values of my time series in an algorithm that gives me new
x and y values. And those are the coordinates that I am actually using on
the final plot function inside pgram (Chl is actually not an argument of
my plot function...). I am interested that the title of the original dataset
I used appears on my plot. Because I will use this function several time
series (let's say Chl and A, with different data sets), I would like to
obtain each time on the title of my plot for pgram(x), Raw periodogram of
x or for pgram(A), Raw periodogram of A.
Hope it is clearer now,
Cheers,
Marcia Rocha
Rolf Turner-3 wrote:
On 30/11/2007, at 3:53 PM, marciarr wrote:
Hi Jim,
Thanks for your answer.
Unfortunately, because the x of my plot function is not actually
waht I need
on my graph's title, your advice does not work. Thanks anyway,
Marcia
Jim answered the question you asked. If his advice didn't work, then
you
asked the wrong question. It pays to do a little thinking about a
problem
before asking the list for help.
What are you expecting anyway? That R should be able to read your mind?
cheers,
Rolf Turner
##
Attention:\ This e-mail message is privileged and confid...{{dropped:9}}
__
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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.
--
View this message in context:
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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.
--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
What is the problem you are trying to solve?
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and provide commented, minimal, self-contained, reproducible code.
[R] what to do if residuals produced by lm() have long tails?
Hi, I am using lm() for regression analysis of my data set. My regression results look pretty good, i.e., the coefficient is significant and the p value is much less than 0.05. But when I checked the residuals, both using qqnorm() and hist(), the distribution does not look normal. It looks like the residuals have long tails. I assume that lm() uses OLS, and since one of the assumptions of OLS is that the residuals has to be normally distributed, I am wondering if this means I should reject my regression results all together. If so, then what should I use instead? Are there ways to deal with distributions with long tails using lm() or OLS, or entirely different models are needed instead? Thanks, -- Tom [[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] vector sprintf argument
According to the help page sprintf will recycle its arguments: The arguments (including fmt) are recycled if possible a whole number of times to the length of the longest, and then the formatting is done in parallel. Therefore the following works: sprintf(Number: %d, A) [1] Number: 3 Number: 4 Number: 5 Another option is to create a character string from A and then print it: sprintf(Number: %s, paste(A, collapse= )) [1] Number: 3 4 5 -Christos -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Moshe Olshansky Sent: Thursday, November 29, 2007 11:45 PM To: Tom Sgouros; r-help@r-project.org Subject: Re: [R] vector sprintf argument The only thing I can think of is: a - c(1,2.7,5.19) F-c(numeric: %d ,%g ,%8.3f) x-sapply(1:length(a),function(i) sprintf(F[i],a[i])) y-paste(x,sep=,collapse=) But I am sure that you will get a better advice elsewhere. --- Tom Sgouros [EMAIL PROTECTED] wrote: Hello all: If I have a vector and a format, I want to do this: A - c(3,4,5) F - Number: %d, %d, %d sprintf(F,A) This doesn't work because A isn't three arguments, it's just one. Is there a way to peel the vector members out of A so that sprintf can get at them? I would like to do this because I have a large set of variable-length data that I'd like to print out in fancy formatted form. The vectors range in length from 2 to 7. Each row is different, so I had been hoping to do this with an array of formats, too. I feel like I'm either overlooking something obvious, or have determined to do this in an un-R fashion. Any advice is welcome. (On this topic, that is.) Many thanks, -tom -- tomfool at as220 dot org http://sgouros.com http://whatcheer.net __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] main plot title
Hi Jim,
Thanks for your answer.
Unfortunately, because the x of my plot function is not actually waht I need
on my graph's title, your advice does not work. Thanks anyway,
Marcia
jholtman wrote:
hopefully this will help you:
mydata - 1:10
my.plot - function(x) plot(x, main=paste('dataset =',
deparse(substitute(x
my.plot(mydata)
On Nov 29, 2007 9:05 PM, marciarr [EMAIL PROTECTED] wrote:
Dear R users,
I am having a problem with the main title of a plot. I have written a
function returning a plot and I would like that the main title of this
plot
shows actually the name of the dataset I have used. So, for instance: if
my
dataset is called Chl, I would like that my plot to be entitled : Raw
periodogram of Chl. I know the function paste. I suppose I would be
looking for something like: plot(main=paste(Raw periodogram of, ...).
How can the program understand that the name of the data set is supposed
to
go there?
Thank you very much for your answers!!!
Marcia
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Re: [R] The R Book - great resource for R beginners
IMHO The R Book is far better than indicated in that review and should be near the top of the list for beginners looking for a manual for R. Tom Katharine Mullen wrote: It was reviewed in the most recent R News (http://www.r-project.org/doc/Rnews/Rnews_2007-2.pdf). On Thu, 29 Nov 2007, Robert Harris wrote: Hi all, I've recently discovered The R Book by Micheal J. Crawley. I am new to R and I am finding it incredibly useful. With my background in math and programming, I expected that I would be able to pick it up quickly, but even after reading several other intro books, I found it was still hard to figure out how to get data into R and how dataframes relate to vectors and actually doing statistics with R. But, The R Book is well written and gives plenty of examples and explains many of the often used tools within R. It's both a tutorial and a relatively advanced reference book for R, very accessible to a beginner like me. Just curious: What have been the experiences of others who have used The R Book? Thanks, Bob Harris - [[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. -- View this message in context: http://www.nabble.com/Recommended-textbooks-for-R--tf4895638.html#a14039487 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] main plot title
hopefully this will help you:
mydata - 1:10
my.plot - function(x) plot(x, main=paste('dataset =', deparse(substitute(x
my.plot(mydata)
On Nov 29, 2007 9:05 PM, marciarr [EMAIL PROTECTED] wrote:
Dear R users,
I am having a problem with the main title of a plot. I have written a
function returning a plot and I would like that the main title of this plot
shows actually the name of the dataset I have used. So, for instance: if my
dataset is called Chl, I would like that my plot to be entitled : Raw
periodogram of Chl. I know the function paste. I suppose I would be
looking for something like: plot(main=paste(Raw periodogram of, ...).
How can the program understand that the name of the data set is supposed to
go there?
Thank you very much for your answers!!!
Marcia
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Jim Holtman
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+1 513 646 9390
What is the problem you are trying to solve?
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Re: [R] main plot title
On 30/11/2007, at 4:53 PM, marciarr wrote:
Hello Rolf,
I am sorry for the incovenience. Well, here it goes again!
Let's say, I have a time series for the variable Chl. I wrote a
function
pgram that gives me the raw periodogram of the time series. So, this
function uses the values of my time series in an algorithm that
gives me new
x and y values. And those are the coordinates that I am actually
using on
the final plot function inside pgram (Chl is actually not an
argument of
my plot function...). I am interested that the title of the
original dataset
I used appears on my plot. Because I will use this function several
time
series (let's say Chl and A, with different data sets), I would
like to
obtain each time on the title of my plot for pgram(x), Raw
periodogram of
x or for pgram(A), Raw periodogram of A.
Hope it is clearer now,
Not a lot, I'm afraid. But I think I may be getting the idea
Here's an outline of my understanding of the situation:
o you have a time series ``Chl''
o you apply your home-grown function pgram() to it,
pg.Chl - pgram(Chl)
o the result ``pg.Chl'' is a list with components ``x'' and ``y''
(x being frequency and y being ``power'')
o you now want to plot pg.Chl with another home-grown function,
say my.pgram.plot(), and you want the name ``Chl'' to appear in
the title of the plot.
Well --- for goodness sake! --- my.pgram.plot() has to be able to get
the
information about that name from *somewhere*! R, wonderful as it is, is
not psychic.
There are two obvious ways of doing this: They have (obviously!) to be
effected back in the function pgram() which *does* have access to the
name ``Chl''. If this information is not somehow enclosed in the object
pg.Chl, then there is no way for my.pgram.plot() to obtain this
information.
Method 1: Make the name of the ``power'' equal to ``Chl'' rather
than ``y''.
You can do this making use of the deparse(substitute(whatever))
technique
that Jim Holtman told you about. There are various elaborations to this
idea --- e.g. you could make the name ``power.Chl'', and then extract
the
``Chl'' bit by using gsub() or str.split() or substr() or ..
Method 2: Give the object returned by pgram() a component or
(probably better)
an attribute, called say ``dataname'' equal to the name of the time
series
to which pgram() was applied. Again, this name can be obtained via the
deparse(substitute(...)) technique. You then write my.plot.pgram()
so that
it extracts ``dataname'' from the object fed to it, and then uses
dataname
to form the title.
The important thing to remember is that R has endless ways to store,
manipulate,
and process information that is available to it, but it CANNOT magically
produce information that is not available to it.
cheers,
Rolf Turner
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