Re: [R] edit.data.frame
That changes the object if you make a change in the editor, so definitely NOT to be recommended. On Fri, 13 Jan 2006, ronggui wrote: I think fix(data.frame.name) is the best way . 2006/1/13, Prof Brian Ripley [EMAIL PROTECTED]: On Thu, 12 Jan 2006, Fredrik Lundgren wrote: Sometimes I have huge data.frames and the small spreadsheetlike edit.data.frame is quite handy to get an overview of the data. However, when I close the editor all data are rolled over the console window, which takes time and clutters the window. Is there a way to avoid this? If you mean printed to the R terminal/console, assign the result or use invisible(edit(object)). -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-p! roject.org/posting-guide.html --黄荣贵Deparment of SociologyFudan University -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595__ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Curve fitting
I made a mistake in my equations : all the logarithms are neperian! - Réacheminé par Nadege ND Durand/RD/abx/FR le 01/13/2006 09:15 - Nadege ND Durand 01/12/2006 19:11 Pour : [EMAIL PROTECTED] cc : Objet : Curve fitting Hi! I have a problem of curve fitting. I use the following data : - vector of predictor data : 0 0.4 0.8 1.2 1.6 - vector of response data : 0.81954 0.64592 0.51247 0.42831 0.35371 I perform parametric fits using custom equations when I use this equation : y = yo + K *(1/(1+exp(-(a+b*ln(x) the fitting result is OK but when I use this more general equation :y = yo + K *(1/(1+exp(-(a+b*log(x)+c*x , then I get an aberrant curve! I don't understand that... The second fitting should be at least as good as the first one because when taking c=0, both equations are identical! There is here a mathematical phenomenon that I don't understand!could someone help me Thanks a lot in advance! Nadège [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] edit.data.frame
On 12 Jan 2006, at 22:17, Fredrik Lundgren wrote: Dear list, Sometimes I have huge data.frames and the small spreadsheetlike edit.data.frame is quite handy to get an overview of the data. However, when I close the editor all data are rolled over the console window, which takes time and clutters the window. Is there a way to avoid this? An alternative to the editor is showData() from the relimp package. It is modeless, meaning that your data window can be left open/ minimized while you work in R. I haven't tested it with _very_ large data frames though. David -- Professor David Firth http://www.warwick.ac.uk/go/dfirth __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Basis of fisher.test
On 13-Jan-06 Prof Brian Ripley wrote: On Thu, 12 Jan 2006 [EMAIL PROTECTED] wrote: [...] ?fisher.test says only: [That following is not a quote from a current version of R.] In the one-sided 2 by 2 cases, p-values are obtained directly using the hypergeometric distribution. Otherwise, computations are based on a C version of the FORTRAN subroutine FEXACT which implements the network developed by Mehta and Patel (1986) and improved by Clarkson, Fan Joe (1993). The FORTRAN code can be obtained from URL: http://www.netlib.org/toms/643. No, it *also* says Two-sided tests are based on the probabilities of the tables, and take as 'more extreme' all tables with probabilities less than or equal to that of the observed table, the p-value being the sum of such probabilities. which answers the question (there are only two-sided tests for such tables). Thanks for the above information, which is indeed the definitive straightforward answer to my question! (Not sure that I quite agree with the two-sided terminology, though, since the ranking is unidirectional based on decreasing probability, and the P-value is that of the least-probability tail -- i.e. analagous to the large (-2*loglik) tail of a likelihood-ratio test -- which I've always visualised as a 1-tailed test (depite the fact that the other tail can on occasion be indicative of a fit too good to be true). Now, what does the posting guide say about stating the R version and updating before posting? Well, I plead that in practice there is necessarily a grey area here! My quotation was from ?fisher.test in R-2.1.0beta of 2004/04/08, the most recent version installed on any of my machines. Admittedly a bit behind the times, but not grossly; and that help page has not changed in this respect since the earliest version I have installed, which is R-1.2.3 of 2001/04/26. Contents of help pages can change overnight as R evolves. While it is better to be up-to-date than behind the times (even slightly), there is a compromise to be struck between upgrading to the latest R every time one has a question which might be answered thereby, or going on-line to read the latest PDF documentation from CRAN, on the one hand, and on the other asking a straightforward question to the list. Thanks again, and best wishes, Ted. E-Mail: (Ted Harding) [EMAIL PROTECTED] Fax-to-email: +44 (0)870 094 0861 Date: 13-Jan-06 Time: 08:55:11 -- XFMail -- __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Basis of fisher.test
On Fri, 13 Jan 2006 [EMAIL PROTECTED] wrote: On 13-Jan-06 Prof Brian Ripley wrote: On Thu, 12 Jan 2006 [EMAIL PROTECTED] wrote: [...] ?fisher.test says only: [That following is not a quote from a current version of R.] In the one-sided 2 by 2 cases, p-values are obtained directly using the hypergeometric distribution. Otherwise, computations are based on a C version of the FORTRAN subroutine FEXACT which implements the network developed by Mehta and Patel (1986) and improved by Clarkson, Fan Joe (1993). The FORTRAN code can be obtained from URL: http://www.netlib.org/toms/643. No, it *also* says Two-sided tests are based on the probabilities of the tables, and take as 'more extreme' all tables with probabilities less than or equal to that of the observed table, the p-value being the sum of such probabilities. which answers the question (there are only two-sided tests for such tables). Thanks for the above information, which is indeed the definitive straightforward answer to my question! (Not sure that I quite agree with the two-sided terminology, though, since the ranking is unidirectional based on decreasing probability, and the P-value is that of the least-probability tail -- i.e. analagous to the large (-2*loglik) tail of a likelihood-ratio test -- which I've always visualised as a 1-tailed test (depite the fact that the other tail can on occasion be indicative of a fit too good to be true). As statistics is usually taught, significance tests are always one-tailed. The two-sided t-test is one-tailed, the test statistic being |T|. In any case, the `two-sided' is part of the arguments given to the function, so this para is just using the already-established terminology. Now, what does the posting guide say about stating the R version and updating before posting? Well, I plead that in practice there is necessarily a grey area here! My quotation was from ?fisher.test in R-2.1.0beta of 2004/04/08, the most recent version installed on any of my machines. Admittedly a bit behind the times, but not grossly; and that help page has not changed in this respect since the earliest version I have installed, which is R-1.2.3 of 2001/04/26. Contents of help pages can change overnight as R evolves. While it is better to be up-to-date than behind the times (even slightly), there is a compromise to be struck between upgrading to the latest R every time one has a question which might be answered thereby, or going on-line to read the latest PDF documentation from CRAN, on the one hand, and on the other asking a straightforward question to the list. Well, if you had given the R version number the problem would have been much more obvious. Thanks again, and best wishes, Ted. E-Mail: (Ted Harding) [EMAIL PROTECTED] Fax-to-email: +44 (0)870 094 0861 Date: 13-Jan-06 Time: 08:55:11 -- XFMail -- __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] edit.data.frame - summary
Thanks to David Firth Brian Ripley ronggui jim holtman who help with this question. showData() from the relimp package works and shows the dataframe as.is but scrolls rather weak with huge data.frames (15 000 x 120) fix(...) is somewhat dangerous as you usually don't want to correct individual data but get an overview invisible(edit(...)) does the trick and scrolls with excellent speed even with huge dataframes but not exactly as.is (dates as negative or positive integer, minor problem). Fredrik - Original Message - From: David Firth [EMAIL PROTECTED] To: Fredrik Lundgren [EMAIL PROTECTED] Cc: R-help r-help@stat.math.ethz.ch Sent: Friday, January 13, 2006 9:21 AM Subject: Re: [R] edit.data.frame On 12 Jan 2006, at 22:17, Fredrik Lundgren wrote: Dear list, Sometimes I have huge data.frames and the small spreadsheetlike edit.data.frame is quite handy to get an overview of the data. However, when I close the editor all data are rolled over the console window, which takes time and clutters the window. Is there a way to avoid this? An alternative to the editor is showData() from the relimp package. It is modeless, meaning that your data window can be left open/ minimized while you work in R. I haven't tested it with _very_ large data frames though. David -- Professor David Firth http://www.warwick.ac.uk/go/dfirth __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] first derivative of a time series
Hi, I need to derive a time series that represents the first derivative of an original time series. The function coefDeriv in the cyclones package seemed to be the ticket, but I'm not sure if I am interpreting the output of the function correctly...or even using the function correctly. This is a snipbit of what I've been trying: library(cyclones) ## read in my 1-column of values, each line is a different time step ts.table - read.table(timeseries.1d) ts.values - ts.table[,1] ## first calculate coefficients to pass to coefDeriv ts.coef - coefFit(ts.values) d.ts - coefDeriv(ts.coef) --- However, when I try to look at d.ts$y.deriv, assumning that this will plot the derivative I want, all the numbers are huge (on the order of e+02 to e+08) when my original time series ranged from 0 to 970. Am I going about this the wrong way? Or are there other tools that would lead me to estimating the derivative of a time series? Thanks in advance for any help! g __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] help with gepRglm::likfit.glsm
Hi,
I'm exploring likfit.glsm and I need some help. I have to say that I'm
not an MCMC expert ...
I did a first run of likfit.glsm with S.scale=0.002 and it worked
whithout problems but there was strong autocorrelation and the chain
convergence for the ramdom effects was quite poor, so I changed S.scale
to 0.4, which gave acceptance rates close to 0.6 as proposed on the
documentation, and the autocorrelation and chain convergence was ok.
However when I tried to run likfit.glsm it gave the following error:
gdn.glsm2.lf - likfit.glsm(gdn.glsm2.prelf, cov.model =
exponential, ini.phi=26, lambda=0)
likfit.glsm: likelihood maximisation using the function optim.
phi = 26 tausq.rel = 0
Error in if (det(Delta2) != 0) { : missing value where TRUE/FALSE needed
In addition: Warning message:
cannot use argument lambda with the given objects in mcmc.obj in:
likfit.glsm(gdn.glsm2.prelf, cov.model = exponential, ini.phi = 26,
below is the code for both runs.
Thanks
EJ
# first run
mod - list(beta=gdn.lf$beta, cov.pars=gdn.lf$cov.pars,
cov.model=gdn.lf$cov.model, nugget=gdn.lf$nugget,
aniso.pars=gdn.lf$aniso.pars, family=poisson, lambda=gdn.lf$lambda)
mcc - mcmc.control(S.scale=0.002)
gdn.glsm1 - glsm.mcmc(gdn, model=mod, mcmc.input=mcc)
gdn.glsm1.prelf - prepare.likfit.glsm(gdn.glsm1)
gdn.glsm1.lf - likfit.glsm(gdn.glsm1.prelf, cov.model = exponential,
ini.phi=26, lambda = 0)
# second run
mcc - mcmc.control(S.scale=0.4)
gdn.glsm2 - glsm.mcmc(gdn, model=mod, mcmc.input=mcc)
gdn.glsm2.prelf - prepare.likfit.glsm(gdn.glsm2)
gdn.glsm2.lf - likfit.glsm(gdn.glsm2.prelf, cov.model = exponential,
ini.phi=26, lambda=0)
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Re: [R] infinite recursion in do.call when lme4 loaded only
Dieter == Dieter Menne [EMAIL PROTECTED] on Thu, 12 Jan 2006 18:14:32 + (UTC) writes: Dieter Peter Dalgaard p.dalgaard at biostat.ku.dk writes: A larg program which worked with lme4/R about a year ago failed when I re-run it today. I reproduced the problem with the program below. -- When lme4 is loaded (but never used), the do.call fails with infinite recursion after 60 seconds. Memory used increases beyond bonds in task manager. However, it surely has to do with methods dispatch: system.time(do.call(rbind.data.frame,caScore)) [1] 0.99 0.00 0.99 0.00 0.00 which provides you with another workaround. Dieter Peter, I had increased the optional value already, but I still don't understand Dieter what this recursion overflow has to do with the lm4 loading. Aahh, you've hit a secret ;-) no, but a semi-hidden feature: lme4 loads Matrix and Matrix activates versions of rbind() and cbind() which use rbind2/cbind2 which are S4 generics and default methods that are slightly different than then the original base rbind() and cbind(). This was a necessity since the original rbind(), cbind() have first argument ..., i.e. an invalid signature for S4 method dispatch. This was in NEWS for R 2.2.0 : o Experimental versions of cbind() and rbind() in methods package, based on new generic function cbind2(x,y) and rbind2(). This will allow the equivalent of S4 methods for cbind() and rbind() --- currently only after an explicit activation call, see ?cbind2. And 'Matrix' uses the activation call in its .OnLoad hook. This is now getting much too technical to explain for R-help, so if we want to go there, we should move this topic to R-devel, and I'd like to do so, and will be glad if you can provide more details on how exactly you're using rbind. Martin Maechler, ETH Zurich __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] infinite recursion in do.call when lme4 loaded only
MM == Martin Maechler [EMAIL PROTECTED] on Fri, 13 Jan 2006 12:24:51 +0100 writes: Dieter == Dieter Menne [EMAIL PROTECTED] on Thu, 12 Jan 2006 18:14:32 + (UTC) writes: Dieter Peter Dalgaard p.dalgaard at biostat.ku.dk writes: A larg program which worked with lme4/R about a year ago failed when I re-run it today. I reproduced the problem with the program below. -- When lme4 is loaded (but never used), the do.call fails with infinite recursion after 60 seconds. Memory used increases beyond bonds in task manager. However, it surely has to do with methods dispatch: system.time(do.call(rbind.data.frame,caScore)) [1] 0.99 0.00 0.99 0.00 0.00 which provides you with another workaround. Dieter Peter, I had increased the optional value already, but I still don't understand Dieter what this recursion overflow has to do with the lm4 loading. MM Aahh, you've hit a secret ;-) no, but a semi-hidden feature: MM lme4 loads Matrix and Matrix activates versions of rbind() and MM cbind() which use rbind2/cbind2 which are S4 generics and MM default methods that are slightly different than then the MM original base rbind() and cbind(). MM This was a necessity since the original rbind(), cbind() have MM first argument ..., i.e. an invalid signature for S4 method MM dispatch. MM This was in NEWS for R 2.2.0 : MM o Experimental versions of cbind() and rbind() in methods package, MM based on new generic function cbind2(x,y) and rbind2(). This will MM allow the equivalent of S4 methods for cbind() and rbind() --- MM currently only after an explicit activation call, see ?cbind2. MM And 'Matrix' uses the activation call in its .OnLoad hook. MM This is now getting much too technical to explain for R-help, so MM if we want to go there, we should move this topic to R-devel, MM and I'd like to do so, and will be glad if you can provide more MM details on how exactly you're using rbind. One thing -- very useful for you -- I forgot to add: You can easily quickly revert the other cbind/rbind activation by using methods:::bind_activation(FALSE) so you don't need to unload lme4 or Matrix, and you can reactivate them again after your special computation by methods:::bind_activation(on = TRUE) Martin __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Scientific notation in plots
Is it possible to use scientific notation of numbers on the axis of plots without using the xEy notation. That means: a beatiful 1x10^3 instead of 1E3. Logarithmic scale, in my case. Thank you very much! Oddmund ** Oddmund Nordgård Department of Haematology and Oncology Stavanger University Hospital P.O. Box 8100 4068 STAVANGER Phone: 51 51 89 34 Email: [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] edit.data.frame - summary
On Fri, 13 Jan 2006, Fredrik Lundgren wrote: Thanks to David Firth Brian Ripley ronggui jim holtman who help with this question. showData() from the relimp package works and shows the dataframe as.is but scrolls rather weak with huge data.frames (15 000 x 120) fix(...) is somewhat dangerous as you usually don't want to correct individual data but get an overview invisible(edit(...)) does the trick and scrolls with excellent speed even with huge dataframes It has been tested on tens of thousands of columns. but not exactly as.is (dates as negative or positive integer, minor problem). Well, actually this is `as.is' and showData is not (and that _is_ documented on the help page). If you want to see the printed representation, call invisible(edit(format(your_df))) A non-modal read-only version of the dataeditors would be a nice programming exercise. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] help with gepRglm::likfit.glsm
-Original Message-
From: [EMAIL PROTECTED] [SMTP:[EMAIL PROTECTED] On Behalf Of ernesto
Sent: Friday, January 13, 2006 9:25 AM
To: Mailing List R
Subject: [R] help with gepRglm::likfit.glsm
Hi,
I'm exploring likfit.glsm and I need some help. I have to say that I'm
not an MCMC expert ...
I did a first run of likfit.glsm with S.scale=0.002 and it worked
whithout problems but there was strong autocorrelation and the chain
convergence for the ramdom effects was quite poor, so I changed S.scale
to 0.4, which gave acceptance rates close to 0.6 as proposed on the
documentation, and the autocorrelation and chain convergence was ok.
However when I tried to run likfit.glsm it gave the following error:
gdn.glsm2.lf - likfit.glsm(gdn.glsm2.prelf, cov.model =
exponential, ini.phi=26, lambda=0)
likfit.glsm: likelihood maximisation using the function optim.
phi = 26 tausq.rel = 0
Error in if (det(Delta2) != 0) { : missing value where TRUE/FALSE needed
In addition: Warning message:
cannot use argument lambda with the given objects in mcmc.obj in:
likfit.glsm(gdn.glsm2.prelf, cov.model = exponential, ini.phi = 26,
-
Regarding the warning: the argument 'lambda' corresponds to the model for
continuous variables (used in geoR) whereas you seem to have counts.
The error has occurred to me when i try to fit a spatial correlation function
that the data does not support. For example when i try to fit the matern model
with too few observations. Then i fall back into exponential or gaussian and
then the error disappears. Try fitting the gaussian. Also try changing the
initial
values for the correlation distance.
Ruben
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[R] R and filemaker pro DB
I have been looking for a database application to use in conjunction with R (on a Windows network). When I approached my organization's IT department to ask about using MySQL, they made a counter-offer of Filemaker Pro (v8). It is not specifically mentioned in 'R Data Import/Export', nor do searches of the archives turn up much information. Does anyone have any experience using Filemaker Pro with R? Should package RODBC work with Filemaker, as it is odbc-compliant? (I will be doing some trials anyway). Any other relevant advice welcome. Michael Bibo Queensland Health [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Taking code from packages
On 1/13/2006 2:04 AM, Ales Ziberna wrote: Hello! I am currently in the process of creating (my first) package, which (when ready) I intend to publish to CRAN. In the process of creating this package I have taken some code form existing packages. I have actually copied parts of functions in to new functions. This code is usually something very basic such as Rand index. What is the proper procedure for this? Since most of R (and also the packages I have taken code form) is published under GPL, I think this should be OK. However I do not know if: 1.I should still ask authors of the packages for permission or at least notify them. It is polite to notify them. 2.Ad references to the functions (and packages) from which I had taken the code or only to the references they use. The GPL requires that you maintain their copyright notices. You have the right to use their work, the GPL doesn't give you ownership of it. The usual way to do this is to leave their copyright notice intact, and add your own if you have made modifications. An alternative which is usually (but not always) better is to say that your package depends on theirs, and then just use their functions. The advantage is that it avoids any of the above mixed copyright issues, and it makes sure that when the author fixes a bug, you benefit too. The disadvantage is that it makes your package dependent on theirs, so if changes are needed in it for some future version of R, you'll have to wait for the other maintainer to do them (or copy their code at that point). (I'm a little sensitive about dependencies now, since the LaTeX seminar template I've used a few times no longer works. It depends on too many LaTeX packages, and someone, somewhere has introduced incompatibilities in them. Seems like I'll be forced to use Powerpoint or Impress.) Duncan Murdoch What about regarding code that was sent to the list, usually as a response to one of my problems. I assume that in this case it is best to consult the author? Any comments and opinions are very welcomed! Best regards, Ales Ziberna __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] multivariate markov switching
Dear helpers, Does anyone know about a package or a function that allows to estimate Multivariate Markov-Switching Models, like MS-VAR as introduced by Krolzig(1997) with R ? Thanks a lot!! Carlo __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Getting the numeric value of difftime
Hi folks, I have a small, maybe newbie, question concerning date operations. The follwing snippet date1 = 2005-11-20; date2 = 2005-11-17; difftime(date1, date2) results in Time difference of 3 days. How can I extract just the numerical value 3? As a workaround I apply mean() on the result which gives me just a numerical value. Thanks a lot, Christian __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Scientific notation in plots
try something like this: axis(side=2, at=c(0, 5e+5, 1.5e+6, 2.5e+6), labels=expression(0, 5%*%10^5, 1.5%*%10^6, 2.5%*%10^6) it will place your 5e+5, 1.5e+6, 2.5e+6 as scientific notation at the correct positions on the y axis. the key is the labels=expression part. Cheers iain --- Oddmund NordgÃ¥rd [EMAIL PROTECTED] wrote: Is it possible to use scientific notation of numbers on the axis of plots without using the xEy notation. That means: a beatiful 1x10^3 instead of 1E3. Logarithmic scale, in my case. Thank you very much! Oddmund ** Oddmund Nordgård Department of Haematology and Oncology Stavanger University Hospital P.O. Box 8100 4068 STAVANGER Phone: 51 51 89 34 Email: [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] multivariate markov switching
I don't know the MS-VAR model. The graphical models page on the r-project site refers to a number of packages that deal with these types of models of which I don't know the specifics. The depmix package does multivariate hidden markov models. best, ingmar From: Carlo Fezzi [EMAIL PROTECTED] Organization: Dip. Scienze Statistiche - Univ. di Bologna Date: Fri, 13 Jan 2006 13:50:04 +0100 (CET) To: r-help@stat.math.ethz.ch Subject: [R] multivariate markov switching Dear helpers, Does anyone know about a package or a function that allows to estimate Multivariate Markov-Switching Models, like MS-VAR as introduced by Krolzig(1997) with R ? Thanks a lot!! Carlo __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Getting the numeric value of difftime
Christian Neumann wrote: Hi folks, I have a small, maybe newbie, question concerning date operations. The follwing snippet date1 = 2005-11-20; date2 = 2005-11-17; difftime(date1, date2) results in Time difference of 3 days. How can I extract just the numerical value 3? As a workaround I apply mean() on the result which gives me just a numerical value. If you want to get one thing _as_ another the R-ish solution is nearly always to do as.another(oneThing). You want it numeric? You got it! date1 = 2005-11-20; date2 = 2005-11-17; difftime(date1, date2) Time difference of 3 days as.numeric(difftime(date1, date2)) [1] 3 Barry __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Getting the numeric value of difftime
This was just discussed two days ago: https://www.stat.math.ethz.ch/pipermail/r-help/2006-January/084453.html On 1/13/06, Christian Neumann [EMAIL PROTECTED] wrote: Hi folks, I have a small, maybe newbie, question concerning date operations. The follwing snippet date1 = 2005-11-20; date2 = 2005-11-17; difftime(date1, date2) results in Time difference of 3 days. How can I extract just the numerical value 3? As a workaround I apply mean() on the result which gives me just a numerical value. Thanks a lot, Christian __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] CRAN versions of lme4/Matrix don't appear to work with R 2.1.1
After downloading from the WA mirror, the lme4 related packages appear to run fine . Thanks for everyone's help. Chuck __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] CRAN versions of lme4/Matrix don't appear to work with R 2.1.1
On 12 January 2006 at 17:42, White, Charles E WRAIR-Wash DC wrote: | 1) It was the Statlib mirror from which I was downloading. If I don't get any more interesting messages before I return to work in the morning, I'll try installing off of a different mirror. IIRC we had repeated 'bug reports' from users of Statlib. That mirror seems to not value internal consistency too highly. Maybe it is aiming to become a 'randomized mirror' ? Just kidding... Dirk -- Hell, there are no rules here - we're trying to accomplish something. -- Thomas A. Edison __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] [Rd] infinite recursion in do.call when lme4 loaded only
Martin Maechler maechler at stat.math.ethz.ch writes: One thing -- very useful for you -- I forgot to add: You can easily quickly revert the other cbind/rbind activation by using methods:::bind_activation(FALSE) so you don't need to unload lme4 or Matrix, and you can reactivate them again after your special computation by methods:::bind_activation(on = TRUE) Do haut's di hi... Looks like we need a non-recursive replacement for the elegant do.call(rbind..) constructs. Dieter __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Getting the numeric value of difftime
just try as.numeric(difftime(date1, date2)) Best, Dimitris Dimitris Rizopoulos Ph.D. Student Biostatistical Centre School of Public Health Catholic University of Leuven Address: Kapucijnenvoer 35, Leuven, Belgium Tel: +32/(0)16/336899 Fax: +32/(0)16/337015 Web: http://www.med.kuleuven.be/biostat/ http://www.student.kuleuven.be/~m0390867/dimitris.htm - Original Message - From: Christian Neumann [EMAIL PROTECTED] To: r-help@stat.math.ethz.ch Sent: Friday, January 13, 2006 2:05 PM Subject: [R] Getting the numeric value of difftime Hi folks, I have a small, maybe newbie, question concerning date operations. The follwing snippet date1 = 2005-11-20; date2 = 2005-11-17; difftime(date1, date2) results in Time difference of 3 days. How can I extract just the numerical value 3? As a workaround I apply mean() on the result which gives me just a numerical value. Thanks a lot, Christian __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Scientific notation in plots
Just what I needed! Thank you very much! Oddmund On Fri, 13 Jan 2006, IAIN GALLAGHER wrote: try something like this: axis(side=2, at=c(0, 5e+5, 1.5e+6, 2.5e+6), labels=expression(0, 5%*%10^5, 1.5%*%10^6, 2.5%*%10^6) it will place your 5e+5, 1.5e+6, 2.5e+6 as scientific notation at the correct positions on the y axis. the key is the labels=expression part. Cheers iain --- Oddmund NordgÃ¥rd [EMAIL PROTECTED] wrote: Is it possible to use scientific notation of numbers on the axis of plots without using the xEy notation. That means: a beatiful 1x10^3 instead of 1E3. Logarithmic scale, in my case. Thank you very much! Oddmund ** Oddmund Nordgård Department of Haematology and Oncology Stavanger University Hospital P.O. Box 8100 4068 STAVANGER Phone: 51 51 89 34 Email: [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Taking code from packages
I usually place in my mypackage-package.Rd file a pointer to the existence of a THANKS file and then put the THANKS file in the inst directory (which gets copied to the top level directory by the build tools during the build). For example, after installing dyn try: library(dyn) package?dyn for instructions on accessing the THANKS file from within R. On 1/13/06, Ales Ziberna [EMAIL PROTECTED] wrote: Hello! I am currently in the process of creating (my first) package, which (when ready) I intend to publish to CRAN. In the process of creating this package I have taken some code form existing packages. I have actually copied parts of functions in to new functions. This code is usually something very basic such as Rand index. What is the proper procedure for this? Since most of R (and also the packages I have taken code form) is published under GPL, I think this should be OK. However I do not know if: 1. I should still ask authors of the packages for permission or at least notify them. 2. Ad references to the functions (and packages) from which I had taken the code or only to the references they use. What about regarding code that was sent to the list, usually as a response to one of my problems. I assume that in this case it is best to consult the author? Any comments and opinions are very welcomed! Best regards, Ales Ziberna __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Course in Statistical Practise in Epidemiology using R
Course in STATISTICAL PRACTICE IN EPIDEMIOLOGY USING R Tartu, Estonia, Thursday 8 - Tuesday 13 June 2006 The course is aimed at epidemiologists and statisticians who wish to use R for statistical modelling and analysis of epidemiological data. The course requires basic knowledge of epidemiological concepts and study types. These will only be briefly reviewed, whereas the more advanced epidemiological and statistical concepts will be treated in depth. Contents: - History of R. Language. Objects. Functions. Interface to other dataformats. Dataframes. Classical methods: Mantel-Haenszel etc. Tabulation of data. Logistic regression for case-control-studies. Poisson regression for follow-up studies. Parametrization of models. Causal inference. Graphics in R. Graphical reporting of results. Time-splitting SMR. Survival analysis in continuous time. Parametric survival models. Interval censoring. Nested and matched case-control studies. Case-cohort studies. Competing risk models. Multistage models. Bootstrap and simulation. The methods will be illustrated using R in practical exercises. The Epi package for epidemiological analysis in R will be introduced. Participants are required to have a fairly good understanding of statistical principles and some familiarity with epidemiological concepts. The course will be mainly practically oriented with more than half the time at the computer. Price: 500 EUR. (250 EUR for cuntries outside EU-2003 and the like). Application deadline: 15 April 2006. Further information at: www.biostat.ku.dk/~bxc/SPE -- Krista Fischer, University of Tartu, Estonia Esa Läärä, University of Oulu, Finland Bendix Carstensen, Steno Diabetes Center, Denmark Organizers __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Data with no separator
Perhaps read.fwf() can be of use... Andy From: Jeffrey T. Steedle I have data in which each row consists of a long string of number, letters, symbols, and blank spaces. I would like to simply scan in strings of length 426, but R takes the spaces that occur in the data as separators. Is there any way around this? Thanks, Jeff Steedle -- Jeffrey T. Steedle ([EMAIL PROTECTED]) Psychological Studies in Education Stanford University School of Education __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Curve fitting
ndurand at fr.abx.fr writes: I made a mistake in my equations : all the logarithms are neperian! - Réacheminé par Nadege ND Durand/RD/abx/FR le 01/13/2006 09:15 - it doesn't matter; all the basic issues raised by me and by Albyn Jones still apply. If we are going to help you, you need to provide more detail about what you tried in R and more background on what you're trying to achieve in general. As we both said, fitting a 5-parameter model to 5 data points is nearly impossible. If you provide more detail about your data and your broader goal, we might be able to help. Ben Bolker __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Scientific notation in plots
You could also use a function like this to transform a number x into your
beautiful notation, where x is the number and digits is the number of digits
you would like to see after the decimal. Then you could use the axis and labels
syntax suggested by Iain, as such:
sciNotation - function(x, digits = 1) {
if (length(x) 1) {
return(append(sciNotation(x[1]), sciNotation(x[-1])))
}
if (!x) return(0)
exponent - floor(log10(x))
base - round(x / 10^exponent, digits)
as.expression(substitute(base %*% 10^exponent,
list(base = base, exponent = exponent)))
}
plot(1:1000, axes = FALSE, type = l, frame.plot = TRUE)
axis(1, at = axTicks(1), label = sciNotation(axTicks(1), 1))
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of IAIN GALLAGHER
Sent: Friday, January 13, 2006 8:09 AM
To: Oddmund Nordgård
Cc: r-help@stat.math.ethz.ch
Subject: Re: [R] Scientific notation in plots
try something like this:
axis(side=2, at=c(0, 5e+5, 1.5e+6, 2.5e+6),
labels=expression(0, 5%*%10^5, 1.5%*%10^6, 2.5%*%10^6)
it will place your 5e+5, 1.5e+6, 2.5e+6 as scientific
notation at the correct positions on the y axis. the
key is the labels=expression part.
Cheers
iain
--- Oddmund Nordgård [EMAIL PROTECTED] wrote:
Is it possible to use scientific notation of numbers
on the axis of plots
without using the xEy notation. That means: a
beatiful 1x10^3 instead of 1E3.
Logarithmic scale, in my case.
Thank you very much!
Oddmund
**
Oddmund Nordgård
Department of Haematology and Oncology
Stavanger University Hospital
P.O. Box 8100
4068 STAVANGER
Phone: 51 51 89 34
Email: [EMAIL PROTECTED]
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[R] Problems installing R 2.2.1
We are trying to install R2.2.1 on a IBM P655 Cluster, SuSE LE 9.1 We are using gcc v 3.3.3 and we are getting this error on make g77 -fPIC -g -O2 -ffloat-store -c dlamc.f -o dlamc.lo g77 -fPIC -g -O2 -c dlapack0.f -o dlapack0.lo g77 -fPIC -g -O2 -c dlapack1.f -o dlapack1.lo g77 -fPIC -g -O2 -c dlapack2.f -o dlapack2.lo g77 -fPIC -g -O2 -c dlapack3.f -o dlapack3.lo g77 -fPIC -g -O2 -c cmplx.f -o cmplx.lo gcc -shared -L/usr/local/lib -o libRlapack.so dlamc.lo dlapack0.lo dlapack1.lo dlapack2.lo dlapack3.lo cmplx.lo -lf77blas -latlas -lg2c -lm -lgcc_s /usr/lib/gcc-lib/powerpc-suse-linux/3.3.3/../../../../powerpc-suse-linux /bin/ld: Error: The symbol `s_wsfe' has a R_PPC_REL24 relocation, that means '/usr/local/lib/libf77blas.a(xerbla.o)' was compiled without -fPIC. /usr/lib/gcc-lib/powerpc-suse-linux/3.3.3/../../../../powerpc-suse-linux /bin/ld: Error: The symbol `do_fio' has a R_PPC_REL24 relocation, that means '/usr/local/lib/libf77blas.a(xerbla.o)' was compiled without -fPIC. /usr/lib/gcc-lib/powerpc-suse-linux/3.3.3/../../../../powerpc-suse-linux /bin/ld: Error: The symbol `do_fio' has a R_PPC_REL24 relocation, that means '/usr/local/lib/libf77blas.a(xerbla.o)' was compiled without -fPIC. /usr/lib/gcc-lib/powerpc-suse-linux/3.3.3/../../../../powerpc-suse-linux /bin/ld: Error: The symbol `e_wsfe' has a R_PPC_REL24 relocation, that means '/usr/local/lib/libf77blas.a(xerbla.o)' was compiled without -fPIC. /usr/lib/gcc-lib/powerpc-suse-linux/3.3.3/../../../../powerpc-suse-linux /bin/ld: Error: The symbol `s_stop' has a R_PPC_REL24 relocation, that means '/usr/local/lib/libf77blas.a(xerbla.o)' was compiled without -fPIC. collect2: ld returned 1 exit status make[4]: *** [libRlapack.so] Error 1 make[4]: Leaving directory `/opt/devel/POWER/R/R-2.2.1/src/modules/lapack' make[3]: *** [R] Error 2 make[3]: Leaving directory `/opt/devel/POWER/R/R-2.2.1/src/modules/lapack' make[2]: *** [R] Error 1 make[2]: Leaving directory `/opt/devel/POWER/R/R-2.2.1/src/modules' make[1]: *** [R] Error 1 make[1]: Leaving directory `/opt/devel/POWER/R/R-2.2.1/src' make: *** [R] Error 1 Any ideas would be appreciated. I will continue reading the documentation. Anne Shelton ITS Research IT Group University at Albany 1400 Washington Ave. - MSC-100 Albany, NY 1 Office: 437-4525 Cell: 788-8634 [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Taking code from packages
On Fri, 13 Jan 2006, Ales Ziberna wrote: I am currently in the process of creating (my first) package, which (when ready) I intend to publish to CRAN. In the process of creating this package I have taken some code form existing packages. I have actually copied parts of functions in to new functions. This code is usually something very basic such as Rand index. What is the proper procedure for this? Why not simply specify that their package is a dependency and use their code directly? __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R newbie example code question
Ted:
Your .xthelp is extremely useful, help on Linux being otherwise
quite awkward to use since a pager in the same window make it hard
to cut/paste examples --- where 'more' or 'less' really means
'instead of' :-)
Suggestion: include -title
cat(cat $HLPFIL\nxterm -title 'R-help' -e less $HLPFIL \n,
file=con)
hintIt would be nice if this solution made it into the R-FAQ or R-Admin
manual./hint
Failing that, it is a good example of something that would
work well in a wiki. But, thankfully, you included the subject line
from the original thread to make it searchable in the news archives.
(Ted Harding) wrote:
[R] help output paged in separate window
The solution I finally opted for, and still use,
is based (in a Linux environment) on including
the following code in your .Rprofile file:
.xthelp - function() {
tdir - tempdir()
pgr - paste(tdir, /pgr, sep=)
con - file(pgr, w)
cat(#! /bin/bash\n, file=con)
cat(export HLPFIL=`mktemp , tdir, /R_hlp.XX`\n,
sep=, file=con)
cat(cat $HLPFIL\nxterm -e less $HLPFIL \n, file=con)
close(con)
system(paste(chmod 755 , pgr, sep=))
options(pager=pgr)
}
.xthelp()
rm(.xthelp)
(and it's also specific to the 'bash' shell because
of the #! /bin/bash\n, but you should be able to
change this appropriately). The above was posted by
Roger Bivand on 27 May.
When you start an R session, this code is executed as
part of sourcing your .Rprofile, and it has the effect that
any output from R which would be paged is stored in a
temporary file which is then read by 'less' in a
separate X window which is detached from your R session
(i.e. your command interface will not hang while it is
being displayed). You can close the X window displaying
the 'less' output by closing 'less' (e.g. type q), or
you can leave it open and any new paged output will go
into a new window -- so you can for instance do
?glm
?family
?binomial
and you will have three mutually relevant help windows
open at once between which you can cross-reference.
As to extracting the code for examples, this is easy
in X windows since you just use your mouse: left-button
drag to hghlight a block of text, middle-button click
to paste the block into another window (of course the
mouse must be over the correct window!)
So you can use the mouse to copy code from the help
pages to the command window.
As I say, this is a Linux-oriented solution, and I don't
know what details would be required for anything similar
in a Windows environment.
It is also worth reading the various contributions to
the above thread, since several suggestions were made.
Hoping this helps,
Ted.
E-Mail: (Ted Harding) [EMAIL PROTECTED]
Fax-to-email: +44 (0)870 094 0861
Date: 10-Jan-06 Time: 13:30:35
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Michael Friendly Email: friendly AT yorku DOT ca
Professor, Psychology Dept.
York University Voice: 416 736-5115 x66249 Fax: 416 736-5814
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Re: [R] Taking code from packages
First thank you for you reply! First let me assure you that I did not think or intent to just use their code and use GPL as an excuse. Although I would like to just make my package dependant on theirs and use their functions that is not possible. The main reason is that I do not want to use the whole functions, but just parts of it. For example, I only need one statistics, while their function computes several. Since I call my function several thousand times, I want to make it as fast as possible. I am also modified (although only slightly) the functions, I am a little worried about naming them as sole authors of the function, since I do not want to make them responsible for any mistakes I have made. What I was thinking of doing is: 1.. Notify the original authors! 2.. In the Author (s) section of the function help, I would write Their name (Modifications made by My Name). 3.. Use the same license (GPL 2) as they do. I did not intent to write them as the package authors, since their code represent a very small part of the whole package. How does that sound? Best regards, Ales Ziberna P.S.: I did not find any other special copyright notices. - Original Message - From: Duncan Murdoch [EMAIL PROTECTED] To: Ales Ziberna [EMAIL PROTECTED] Cc: r-help@stat.math.ethz.ch Sent: Friday, January 13, 2006 1:46 PM Subject: Re: [R] Taking code from packages On 1/13/2006 2:04 AM, Ales Ziberna wrote: Hello! I am currently in the process of creating (my first) package, which (when ready) I intend to publish to CRAN. In the process of creating this package I have taken some code form existing packages. I have actually copied parts of functions in to new functions. This code is usually something very basic such as Rand index. What is the proper procedure for this? Since most of R (and also the packages I have taken code form) is published under GPL, I think this should be OK. However I do not know if: 1. I should still ask authors of the packages for permission or at least notify them. It is polite to notify them. 2. Ad references to the functions (and packages) from which I had taken the code or only to the references they use. The GPL requires that you maintain their copyright notices. You have the right to use their work, the GPL doesn't give you ownership of it. The usual way to do this is to leave their copyright notice intact, and add your own if you have made modifications. An alternative which is usually (but not always) better is to say that your package depends on theirs, and then just use their functions. The advantage is that it avoids any of the above mixed copyright issues, and it makes sure that when the author fixes a bug, you benefit too. The disadvantage is that it makes your package dependent on theirs, so if changes are needed in it for some future version of R, you'll have to wait for the other maintainer to do them (or copy their code at that point). (I'm a little sensitive about dependencies now, since the LaTeX seminar template I've used a few times no longer works. It depends on too many LaTeX packages, and someone, somewhere has introduced incompatibilities in them. Seems like I'll be forced to use Powerpoint or Impress.) Duncan Murdoch What about regarding code that was sent to the list, usually as a response to one of my problems. I assume that in this case it is best to consult the author? Any comments and opinions are very welcomed! Best regards, Ales Ziberna __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Problems installing R 2.2.1
Anne P Shelton [EMAIL PROTECTED] writes: We are trying to install R2.2.1 on a IBM P655 Cluster, SuSE LE 9.1 We are using gcc v 3.3.3 and we are getting this error on make g77 -fPIC -g -O2 -ffloat-store -c dlamc.f -o dlamc.lo g77 -fPIC -g -O2 -c dlapack0.f -o dlapack0.lo g77 -fPIC -g -O2 -c dlapack1.f -o dlapack1.lo g77 -fPIC -g -O2 -c dlapack2.f -o dlapack2.lo g77 -fPIC -g -O2 -c dlapack3.f -o dlapack3.lo g77 -fPIC -g -O2 -c cmplx.f -o cmplx.lo gcc -shared -L/usr/local/lib -o libRlapack.so dlamc.lo dlapack0.lo dlapack1.lo dlapack2.lo dlapack3.lo cmplx.lo -lf77blas -latlas -lg2c -lm -lgcc_s /usr/lib/gcc-lib/powerpc-suse-linux/3.3.3/../../../../powerpc-suse-linux /bin/ld: Error: The symbol `s_wsfe' has a R_PPC_REL24 relocation, that means '/usr/local/lib/libf77blas.a(xerbla.o)' was compiled without -fPIC. /usr/lib/gcc-lib/powerpc-suse-linux/3.3.3/../../../../powerpc-suse-linux /bin/ld: Error: The symbol `do_fio' has a R_PPC_REL24 relocation, that means '/usr/local/lib/libf77blas.a(xerbla.o)' was compiled without -fPIC. /usr/lib/gcc-lib/powerpc-suse-linux/3.3.3/../../../../powerpc-suse-linux /bin/ld: Error: The symbol `do_fio' has a R_PPC_REL24 relocation, that means '/usr/local/lib/libf77blas.a(xerbla.o)' was compiled without -fPIC. /usr/lib/gcc-lib/powerpc-suse-linux/3.3.3/../../../../powerpc-suse-linux /bin/ld: Error: The symbol `e_wsfe' has a R_PPC_REL24 relocation, that means '/usr/local/lib/libf77blas.a(xerbla.o)' was compiled without -fPIC. /usr/lib/gcc-lib/powerpc-suse-linux/3.3.3/../../../../powerpc-suse-linux /bin/ld: Error: The symbol `s_stop' has a R_PPC_REL24 relocation, that means '/usr/local/lib/libf77blas.a(xerbla.o)' was compiled without -fPIC. collect2: ld returned 1 exit status make[4]: *** [libRlapack.so] Error 1 make[4]: Leaving directory `/opt/devel/POWER/R/R-2.2.1/src/modules/lapack' make[3]: *** [R] Error 2 make[3]: Leaving directory `/opt/devel/POWER/R/R-2.2.1/src/modules/lapack' make[2]: *** [R] Error 1 make[2]: Leaving directory `/opt/devel/POWER/R/R-2.2.1/src/modules' make[1]: *** [R] Error 1 make[1]: Leaving directory `/opt/devel/POWER/R/R-2.2.1/src' make: *** [R] Error 1 Any ideas would be appreciated. I will continue reading the documentation. Looks like you need to recompile ATLAS (or stop trying to link against it). This is slightly tricky because ATLAS is not too keen on making PIC code. AFAIR (it's been a while) you may or may not be given the choice of modifying flags during the configuration phase (where need to stick in -fPIC all over the place). Alternatively, you can just let it run and diddle the Make.Linux_* file afterwards. -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Taking code from packages
On 1/13/06, Ales Ziberna [EMAIL PROTECTED] wrote: First thank you for you reply! First let me assure you that I did not think or intent to just use their code and use GPL as an excuse. Although I would like to just make my package dependant on theirs and use their functions that is not possible. The main reason is that I do not want to use the whole functions, but just parts of it. For example, I only need one statistics, while their function computes several. Since I call my function several thousand times, I want to make it as fast as possible. You might want to time the difference just in case.Predicting performance is notoriously difficult to do. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R newbie example code question
On 13-Jan-06 Michael Friendly wrote:
Ted:
Your .xthelp is extremely useful, help on Linux being otherwise
quite awkward to use since a pager in the same window make it hard
to cut/paste examples --- where 'more' or 'less' really means
'instead of' :-)
Glad you found it useful. I find it indispensable!
For the record: this is not my code but Roger Bivand's,
it being the one out of several suggestions on that thread
which I decided to adopt. I still admire the neat way he
wrapped it all up.
One of the beautiful features is that *anything* which would
be paged comes up in the separate window, so for instance
you could execute in R
page(glm)
and you can then scan up and down, and cutpaste chunks if
you want, etc., and in several different windows for different
things at once (or even the same thing several times over if
you want to see different parts at the same time). Great for
playing with variants.
Suggestion: include -title
cat(cat $HLPFIL\nxterm -title 'R-help' -e less $HLPFIL \n,
file=con)
hintIt would be nice if this solution made it into the R-FAQ
or R-Admin manual./hint Failing that, it is a good example of
something that would work well in a wiki. But, thankfully, you
included the subject line from the original thread to make it
searchable in the news archives.
A good hint! In fact a good place for it (or for a URL to it)
could be the help file for help and friends. In the circumstances,
this is where I would have looked first./hint
Best wishes,
Ted.
(Ted Harding) wrote:
[R] help output paged in separate window
The solution I finally opted for, and still use,
is based (in a Linux environment) on including
the following code in your .Rprofile file:
.xthelp - function() {
tdir - tempdir()
pgr - paste(tdir, /pgr, sep=)
con - file(pgr, w)
cat(#! /bin/bash\n, file=con)
cat(export HLPFIL=`mktemp , tdir, /R_hlp.XX`\n,
sep=, file=con)
cat(cat $HLPFIL\nxterm -e less $HLPFIL \n, file=con)
close(con)
system(paste(chmod 755 , pgr, sep=))
options(pager=pgr)
}
.xthelp()
rm(.xthelp)
(and it's also specific to the 'bash' shell because
of the #! /bin/bash\n, but you should be able to
change this appropriately). The above was posted by
Roger Bivand on 27 May.
When you start an R session, this code is executed as
part of sourcing your .Rprofile, and it has the effect that
any output from R which would be paged is stored in a
temporary file which is then read by 'less' in a
separate X window which is detached from your R session
(i.e. your command interface will not hang while it is
being displayed). You can close the X window displaying
the 'less' output by closing 'less' (e.g. type q), or
you can leave it open and any new paged output will go
into a new window -- so you can for instance do
?glm
?family
?binomial
and you will have three mutually relevant help windows
open at once between which you can cross-reference.
As to extracting the code for examples, this is easy
in X windows since you just use your mouse: left-button
drag to hghlight a block of text, middle-button click
to paste the block into another window (of course the
mouse must be over the correct window!)
So you can use the mouse to copy code from the help
pages to the command window.
As I say, this is a Linux-oriented solution, and I don't
know what details would be required for anything similar
in a Windows environment.
It is also worth reading the various contributions to
the above thread, since several suggestions were made.
Hoping this helps,
Ted.
E-Mail: (Ted Harding) [EMAIL PROTECTED]
Fax-to-email: +44 (0)870 094 0861
Date: 10-Jan-06 Time: 13:30:35
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--
Michael Friendly Email: friendly AT yorku DOT ca
Professor, Psychology Dept.
York University Voice: 416 736-5115 x66249 Fax: 416 736-5814
4700 Keele Streethttp://www.math.yorku.ca/SCS/friendly.html
Toronto, ONT M3J 1P3 CANADA
E-Mail: (Ted Harding) [EMAIL PROTECTED]
Fax-to-email: +44 (0)870 094 0861
Date: 13-Jan-06 Time: 15:45:47
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[R] Can I ask for the C code inside an R function using .C?
Hello, all,
It is a general question, but I couldn't find the answer elsewhere.
I am using an R function using .C but don't understand one of its
behaviors without the C code. I am wondering the so-called 'open
source'. It doesn't include the C code together with the R function,
does it? So what I want to ask is whether it is justified, possible or
polite to ask for the C code behind the R function.
Sorry if I miss anything! Thank you as always!
Regards,
Yingfu
###
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Re: [R] Taking code from packages
The thing that is most important and has not been mentioned is to ensure that modified functions have a changed name. People have taken my code without consulting me, changed what it did and put it up in a package with the original name (and no indication that I was the author), and then quoted GPL at me when I complained. So this may perhaps help you understand where some of your answers are coming from. I would suggest adding to your suggested documentation the exact source you used (it makes it easier to find out if that had been updated later). R itself borrows software from other packages, and you will see some examples of how it is referenced in various places including COPYRIGHTS. In retrospect we should have been more careful to rename things, e.g. entry points in conpiled code, even if we made no changes as the original author might want to use his current versions with R. On Fri, 13 Jan 2006, Ales Ziberna wrote: First thank you for you reply! First let me assure you that I did not think or intent to just use their code and use GPL as an excuse. Although I would like to just make my package dependant on theirs and use their functions that is not possible. The main reason is that I do not want to use the whole functions, but just parts of it. For example, I only need one statistics, while their function computes several. Since I call my function several thousand times, I want to make it as fast as possible. I am also modified (although only slightly) the functions, I am a little worried about naming them as sole authors of the function, since I do not want to make them responsible for any mistakes I have made. What I was thinking of doing is: 1.. Notify the original authors! 2.. In the Author (s) section of the function help, I would write Their name (Modifications made by My Name). 3.. Use the same license (GPL 2) as they do. I did not intent to write them as the package authors, since their code represent a very small part of the whole package. How does that sound? Best regards, Ales Ziberna P.S.: I did not find any other special copyright notices. - Original Message - From: Duncan Murdoch [EMAIL PROTECTED] To: Ales Ziberna [EMAIL PROTECTED] Cc: r-help@stat.math.ethz.ch Sent: Friday, January 13, 2006 1:46 PM Subject: Re: [R] Taking code from packages On 1/13/2006 2:04 AM, Ales Ziberna wrote: Hello! I am currently in the process of creating (my first) package, which (when ready) I intend to publish to CRAN. In the process of creating this package I have taken some code form existing packages. I have actually copied parts of functions in to new functions. This code is usually something very basic such as Rand index. What is the proper procedure for this? Since most of R (and also the packages I have taken code form) is published under GPL, I think this should be OK. However I do not know if: 1. I should still ask authors of the packages for permission or at least notify them. It is polite to notify them. 2. Ad references to the functions (and packages) from which I had taken the code or only to the references they use. The GPL requires that you maintain their copyright notices. You have the right to use their work, the GPL doesn't give you ownership of it. The usual way to do this is to leave their copyright notice intact, and add your own if you have made modifications. An alternative which is usually (but not always) better is to say that your package depends on theirs, and then just use their functions. The advantage is that it avoids any of the above mixed copyright issues, and it makes sure that when the author fixes a bug, you benefit too. The disadvantage is that it makes your package dependent on theirs, so if changes are needed in it for some future version of R, you'll have to wait for the other maintainer to do them (or copy their code at that point). (I'm a little sensitive about dependencies now, since the LaTeX seminar template I've used a few times no longer works. It depends on too many LaTeX packages, and someone, somewhere has introduced incompatibilities in them. Seems like I'll be forced to use Powerpoint or Impress.) Duncan Murdoch What about regarding code that was sent to the list, usually as a response to one of my problems. I assume that in this case it is best to consult the author? Any comments and opinions are very welcomed! Best regards, Ales Ziberna __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Brian D. Ripley, [EMAIL PROTECTED]
Re: [R] Can I ask for the C code inside an R function using .C?
Source code for R and all CRAN packages are on CRAN. If you want the C or
Fortran code used in R or add-on packages, you need to download the source
(the .tar.gz files). You won't see the code if you just install the binary.
Andy
From: Yingfu Xie
Hello, all,
It is a general question, but I couldn't find the answer elsewhere.
I am using an R function using .C but don't understand one of its
behaviors without the C code. I am wondering the so-called 'open
source'. It doesn't include the C code together with the R function,
does it? So what I want to ask is whether it is justified, possible or
polite to ask for the C code behind the R function.
Sorry if I miss anything! Thank you as always!
Regards,
Yingfu
###
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Mic...{{dropped}}
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R-help@stat.math.ethz.ch mailing list
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PLEASE do read the posting guide!
http://www.R-project.org/posting-guide.html
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PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Can I ask for the C code inside an R function using .C?
You can download the source from any package from a CRAN mirror near you and
the src directory will contain the source code of the included C and fortran
functions.
hth, ingmar
From: Yingfu Xie [EMAIL PROTECTED]
Date: Fri, 13 Jan 2006 17:04:43 +0100
To: r-help@stat.math.ethz.ch
Subject: [R] Can I ask for the C code inside an R function using .C?
Hello, all,
It is a general question, but I couldn't find the answer elsewhere.
I am using an R function using .C but don't understand one of its
behaviors without the C code. I am wondering the so-called 'open
source'. It doesn't include the C code together with the R function,
does it? So what I want to ask is whether it is justified, possible or
polite to ask for the C code behind the R function.
Sorry if I miss anything! Thank you as always!
Regards,
Yingfu
###
This message has been scanned by F-Secure Anti-Virus for Mic...{{dropped}}
__
R-help@stat.math.ethz.ch mailing list
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[R] Saving data in an R package - how to maintain that t avariable is a 'factor' when it is coded as 1, 2, 3...
I have a .txt file obtained by saving a data frame in which the first four columns are factors (but represented as 1,2,3 etc). The first four lines are Pig Evit Cu Litter Start Weight Feed Time 4601 1 1 1 26.5 26.5 NA 1 4601 1 1 1 26.5 27.5 5.25 2 4601 1 1 1 26.5 36.5 17.6 3 4601 1 1 1 26.5 40.2 28.5 4 I would like to include that data set in an R-package. When I load the data from the package the first four columns are read in as numeric variables. This is consistent with the documentation of read.table - but it is not what I want! I can of course change the coding of the variables, but there ought to be another way. Can anyone help me on that? Best regards Søren Højsgaard __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] CRAN versions of lme4/Matrix don't appear to work with R 2.1.1
Are you familiar with sessionInfo(), e.g.: sessionInfo() R version 2.2.1, 2005-12-20, i386-pc-mingw32 attached base packages: [1] methods stats graphics grDevices utils datasets [7] base other attached packages: lme4 latticeMatrix 0.98-1 0.12-11 0.99-6 This can almost eliminate the possibilities for typographical errors in specifying the version name. The posting guide (www.R-project.org/posting-guide.html) also asks posters to mention mention the platform (Windows2000, Linux, MacOS X). Best Wishes, spencer graves White, Charles E WRAIR-Wash DC wrote: After downloading from the WA mirror, the lme4 related packages appear to run fine . Thanks for everyone's help. Chuck __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Saving data in an R package - how to maintain that t avariable is a 'factor' when it is coded as 1, 2, 3...
colClasses
x - read.table('clipboard', header=T,
colClasses=c(rep('factor',4),rep('numeric',4)))
x
Pig Evit Cu Litter Start Weight Feed Time
1 46011 1 1 26.5 26.5NA1
2 46011 1 1 26.5 27.5 5.252
3 46011 1 1 26.5 36.5 17.603
4 46011 1 1 26.5 40.2 28.504
str(x)
`data.frame': 4 obs. of 8 variables:
$ Pig : Factor w/ 1 level 4601: 1 1 1 1
$ Evit : Factor w/ 1 level 1: 1 1 1 1
$ Cu: Factor w/ 1 level 1: 1 1 1 1
$ Litter: Factor w/ 1 level 1: 1 1 1 1
$ Start : num 26.5 26.5 26.5 26.5
$ Weight: num 26.5 27.6 36.5 40.3
$ Feed : numNA 5.2 17.6 28.5
$ Time : num 1 2 3 4
On 1/13/06, Søren Højsgaard [EMAIL PROTECTED] wrote:
I have a .txt file obtained by saving a data frame in which the first four
columns are factors (but represented as 1,2,3 etc). The first four lines are
Pig Evit Cu Litter Start Weight Feed Time
4601 1 1 1 26.5 26.5 NA 1
4601 1 1 1 26.5 27.5 5.25 2
4601 1 1 1 26.5 36.5 17.6 3
4601 1 1 1 26.5 40.2 28.5 4
I would like to include that data set in an R-package. When I load the
data from the package the first four columns are read in as numeric
variables. This is consistent with the documentation of read.table - but
it is not what I want! I can of course change the coding of the variables,
but there ought to be another way. Can anyone help me on that?
Best regards
Søren Højsgaard
__
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Jim Holtman
Cincinnati, OH
+1 513 247 0281
What the problem you are trying to solve?
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Re: [R] Saving data in an R package - how to maintain that t avariable is a 'factor' when it is coded as 1, 2, 3...
?read.table, see argument colClasses. You can use a .R wrapper to a .tab file in the data directory of a package. Or, perhaps better, include it as a .rda file. On Fri, 13 Jan 2006, Søren Højsgaard wrote: I have a .txt file obtained by saving a data frame in which the first four columns are factors (but represented as 1,2,3 etc). The first four lines are Pig Evit Cu Litter Start Weight Feed Time 4601 1 1 1 26.5 26.5 NA 1 4601 1 1 1 26.5 27.5 5.25 2 4601 1 1 1 26.5 36.5 17.6 3 4601 1 1 1 26.5 40.2 28.5 4 I would like to include that data set in an R-package. When I load the data from the package the first four columns are read in as numeric variables. This is consistent with the documentation of read.table - but it is not what I want! I can of course change the coding of the variables, but there ought to be another way. Can anyone help me on that? Best regards Søren Højsgaard __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595__ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] glmmPQL: Na/NaN/Inf in foreign function call
I'm using glmmPQL, and I still have a few problems with it. In addition to the issue reported earlier, I'm getting the following error and I was wondering if there's something I can do about it. Error in logLik.reStruct(object, conLin) : Na/NaN/Inf in foreign function call (arg 3) ... Warnings: 1: Singular precistion matrix in level -1, block 4 (...) 4: The interaction terms are primed ~ log(dist) * role random = ~ dist | target.utt / prime.utt The family is binomial (logit). I ensured that log(dist) is always [0; 1]. Role is a factor (binary). target.utt and prime.utt are categories as well. This is version 2.1.1 - is the latest version more reliable? Thanks for any help you can give me. Dave __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Can I ask for the C code inside an R function using .C?
If you have a slow connection and/or you don't want to download the entire
source code you can find the sources for R on this site
https://svn.r-project.org/R/trunk/
Francisco
From: Liaw, Andy [EMAIL PROTECTED]
To: 'Yingfu Xie' [EMAIL PROTECTED], r-help@stat.math.ethz.ch
Subject: Re: [R] Can I ask for the C code inside an R function using .C?
Date: Fri, 13 Jan 2006 11:13:51 -0500
Source code for R and all CRAN packages are on CRAN. If you want the C or
Fortran code used in R or add-on packages, you need to download the source
(the .tar.gz files). You won't see the code if you just install the
binary.
Andy
From: Yingfu Xie
Hello, all,
It is a general question, but I couldn't find the answer elsewhere.
I am using an R function using .C but don't understand one of its
behaviors without the C code. I am wondering the so-called 'open
source'. It doesn't include the C code together with the R function,
does it? So what I want to ask is whether it is justified, possible or
polite to ask for the C code behind the R function.
Sorry if I miss anything! Thank you as always!
Regards,
Yingfu
###
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[R] better way to replace missing values with zero
I would like to replace all missing values (NAs) with zero like below--where
ever they may be--but some of the column classes are non-numeric so I get an
error:
dim(temp)
[1] 699 313
temp[is.na(temp)] - 0
Error in as.Date.default(value) : do not know how to convert 'value' to
class Date
So I have to use more conveluted code:
for (k in c(1:ncol(temp))) {
if (class(temp[, k])==numeric) {
temp[, k][is.na(temp[, k])] - 0
}
}
This is much more code and requires a for loop. Can anyone please show me a
better way?
Thanks,
Roger
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Re: [R] Can I ask for the C code inside an R function using .C?
Just wondering: How do people with slow connections get R? The Windows
binary is about 25MB, while the source .tar.gz is only 13.7MB.
Andy
From: Francisco J. Zagmutt
If you have a slow connection and/or you don't want to
download the entire
source code you can find the sources for R on this site
https://svn.r-project.org/R/trunk/
Francisco
From: Liaw, Andy [EMAIL PROTECTED]
To: 'Yingfu Xie' [EMAIL PROTECTED],
r-help@stat.math.ethz.ch
Subject: Re: [R] Can I ask for the C code inside an R
function using .C?
Date: Fri, 13 Jan 2006 11:13:51 -0500
Source code for R and all CRAN packages are on CRAN. If you
want the C or
Fortran code used in R or add-on packages, you need to
download the source
(the .tar.gz files). You won't see the code if you just install the
binary.
Andy
From: Yingfu Xie
Hello, all,
It is a general question, but I couldn't find the answer
elsewhere.
I am using an R function using .C but don't understand one of its
behaviors without the C code. I am wondering the so-called 'open
source'. It doesn't include the C code together with the
R function,
does it? So what I want to ask is whether it is
justified, possible or
polite to ask for the C code behind the R function.
Sorry if I miss anything! Thank you as always!
Regards,
Yingfu
###
This message has been scanned by F-Secure Anti-Virus for
Mic...{{dropped}}
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[R] Variance-covariance by factor
Dear all, I have a data frame with one factor and four numeric variables and wish to obtain the var-cor matrix separately by factor. I tried by() and sapply() but getting nowhere. I understand this can be done by subsetting the dataframe, but there should have some sleek ways of doing it. Here is a simulated dataframe; s - rep(c(A,B,C), c(25,22,18)) d - c(rnorm(25,14,2.6),rnorm(22,15.2,2.8),rnorm(18,16.4,3.0)) h - c(rnorm(25,10,1.4),rnorm(22,11.2,1.8),rnorm(18,12.3,2.0)) l - c(rnorm(25,6.8,1.6), rnorm(22,7.0,1.7),rnorm(18,7.3,1.8)) w - c(rnorm(25,2.5,0.65),rnorm(22,2.6,0.7),rnorm(18,2.8,0.71)) sim - data.frame(cbind(S = s, D= d, H=h,L=l,W=w)) sim.var - sapply(split(sim, sim$S), function(z) var(z)) Error in var(z) : missing observations in cov/cor In addition: Warning message: NAs introduced by coercion sim.var - by(sim, sim$S, function(z) var(z)) Error in var(z) : missing observations in cov/cor In addition: Warning message: NAs introduced by coercion Debug() and trac() the function got no further info. Because the error suggested missing data, I looked at the data frame and was surprised str(sim) `data.frame': 65 obs. of 5 variables: $ S: Factor w/ 3 levels A,B,C: 1 1 1 1 1 1 1 1 1 1 ... $ D: Factor w/ 65 levels 10.0860856437045,..: 51 12 21 11 8 15 57 44 19 60 ... $ H: Factor w/ 65 levels 10.0345903489406,..: 17 2 4 52 6 21 29 9 62 10 ... $ L: Factor w/ 65 levels 10.3854663209663,..: 10 6 23 55 60 8 58 65 11 2 ... $ W: Factor w/ 65 levels 0.93902749732563,..: 38 13 33 12 22 39 47 31 36 53 ... Why the data.frame() converts numeric vectors d, h, l, w into factors? Any suggestions for 1) how to compute var-cor by factor in a data frame, and 2) why data.frame converts numeric variables into factors ? sessionInfo() R version 2.2.0, 2005-10-06, i386-pc-mingw32 attached base packages: [1] methods stats graphics grDevices utils datasets base Thanks, Richard Yang Northern Forestry Centre /Centre de foresterie du Nord Canadian Forest Service/Service canadien des forêts Natural Resources Canada /Ressources naturelles Canada 5320-122 Street/5320, rue 122 Edmonton Alberta Canada T6H 3S5 [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] apply
Hello,
I have a dataset d which is
d
pop catch
1 66462.01 10807.757
2 87486.73 46257.885
3 57211.64 9345.058
4 71321.62 4892.868
5 100024.89 27334.248
6 104504.91 48535.092
7 95295.51 39348.195
8 93737.35 34343.489
9 89375.05 28750.743
10 95312.65 30755.064
11 100888.17 55404.370
12 84790.23 37751.074
13 81129.82 29277.443
14 69797.09 21500.398
15 61690.34 18199.664
16 60671.08 19349.051
17 62852.57 16300.982
18 90646.32 34793.148
And a function opt1:
opt1 - function (x) {
Z - x + M
c.hat - (x/Z)*pop*(1-exp(-Z))
y - (catch - c.hat)^2
return(y)
}
And define M = 0.25
For each row I want to return a value F that is a minimization of the
opt1 function
I have tried many variations of:
d$F-apply(d,2,optim(0.3,opt1,method=BFGS)
and even:
For (I in 1:length(pop))apply(d,2,optim(0.3,opt1,method=BFGS))
Every time I get the same error message
Error in optim(0.3, opt1, method = BFGS) :
objective function in optim evaluates to length 18 not 1
So the apply function is returning 18 values of F which I want but the
function only wants to return 1 value.
Any Suggestions.
Thanks,
Cam
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Re: [R] find mean of a list of timeseries
Try:
(a+b+c)/3
On 1/13/06, tom wright [EMAIL PROTECTED] wrote:
Can someone please give me a clue how to 're'write this so I dont need
to use loops.
a-ts(matrix(c(1,1,1,10,10,10,20,20,20),nrow=3),names=c('var1','var2','var3'))
b-ts(matrix(c(2,2,2,11,11,11,21,21,21),nrow=3),names=c('var1','var2','var3'))
c-ts(matrix(c(3,3,3,12,12,12,22,22,22),nrow=3),names=c('var1','var2','var3'))
data-list(a,b,c)
I now want to find the means of all vectors var1,var2 and var3
i.e. I need to end up with a new time series with three data vectors
(var1, var2 and var3)
result-ts(matrix(c(2,2,2,11,11,11,21,21,21),nrow=3),names=c('var1','var2','var3))
I think its the list thats throwing my use of apply, I might be wrong
but what other data structure could I use?
Many thanks
Tom
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[R] update 'groupedData' and 'lme' objects
Dear R users, I have the following code:
require(nlme)
myfunc - function(data, n, m, maxIter = 3){
working - groupedData(formula = y~x|id, data=data)
val - NULL
r - 0
while(r maxIter){
new.data - data.frame(x=rnorm(n),y=rnorm(n),id=rep(1:n,each=m))
working - update(working, data = new.data)
# val - some results
r - r + 1
}
val
}
n - 10
m - 2
foo - data.frame(x=rnorm(n),y=rnorm(n),id=rep(1:n,each=m))
myfunc(foo, n=n, m=m)
-
I get this error message:
myfunc(foo, n=n, m=m)
Error in inherits(data, data.frame) : object new.data not found
I believe the error is generated within the evaluation of the function
'update'.
The real code I used is more complicated but basically I got a similar error
message when using 'update' for an object 'lme', e.g.
function(...){
fit.lme - lme(...)
while(...){
create newdata
fit.lme - update(fit.lme, newdata)
}
}
Everything works fine when using an object 'lm'
function(...){
fit.lm - lm(...)
while(...){
create newdata
fit.lm - update(fit.lm, newdata)
}
}
I might be wrong, but I guess that this problem is related to different
evaluation
frames, the one invoked by 'myfunc' and the one invoked by 'update'
(both for 'lme' and 'groupedData' objects).
Any suggestion to overcome this problem would be greatly appreciated
Marco Geraci
R version: 2.2.1
nlme version: 3.1-68.1
OS: Window XP
-
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Re: [R] Can I ask for the C code inside an R function using .C?
Well, if you have a slow modem connection and you are an average user that
doesn't want (or doesn't know how) to compile the source code, you may spend
half an hour or more downloading the windows binary. Then you realize you
want to see a .C function and you will have to spend another 15 to 20
minutes downloading the source tar.gz...OR you can lookup the specific
function in the mentioned website in a fraction of the time. Off course,
overall if you check C or Fortran functions all the time you may want to
have a local copy of the source. I think is great that users have that
flexibility, hence they should be aware of both options.
Cheers
Francisco
,
you may prefer just to visit a web site and see the specific function that
you want to learn about, rather than waiting another 15 to 20 minutes to
download the source tar.gz.
From: Liaw, Andy [EMAIL PROTECTED]
To: 'Francisco J. Zagmutt'
[EMAIL PROTECTED],[EMAIL PROTECTED],r-help@stat.math.ethz.ch
Subject: RE: [R] Can I ask for the C code inside an R function using .C?
Date: Fri, 13 Jan 2006 13:26:02 -0500
Just wondering: How do people with slow connections get R? The Windows
binary is about 25MB, while the source .tar.gz is only 13.7MB.
Andy
From: Francisco J. Zagmutt
If you have a slow connection and/or you don't want to
download the entire
source code you can find the sources for R on this site
https://svn.r-project.org/R/trunk/
Francisco
From: Liaw, Andy [EMAIL PROTECTED]
To: 'Yingfu Xie' [EMAIL PROTECTED],
r-help@stat.math.ethz.ch
Subject: Re: [R] Can I ask for the C code inside an R
function using .C?
Date: Fri, 13 Jan 2006 11:13:51 -0500
Source code for R and all CRAN packages are on CRAN. If you
want the C or
Fortran code used in R or add-on packages, you need to
download the source
(the .tar.gz files). You won't see the code if you just install the
binary.
Andy
From: Yingfu Xie
Hello, all,
It is a general question, but I couldn't find the answer
elsewhere.
I am using an R function using .C but don't understand one of its
behaviors without the C code. I am wondering the so-called 'open
source'. It doesn't include the C code together with the
R function,
does it? So what I want to ask is whether it is
justified, possible or
polite to ask for the C code behind the R function.
Sorry if I miss anything! Thank you as always!
Regards,
Yingfu
###
This message has been scanned by F-Secure Anti-Virus for
Mic...{{dropped}}
__
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Re: [R] apply
You are not calling apply() properly. Please read relevant reference
material carefully. You might also wish to pick up one of the several good
books on R (check CRAN website) -- I like VR's S PROGRAMMING.
I did not go through your example in detail, but your apply() call should be
of the form
apply(d,2,function(x)optim(x,...))
You may or may not get into scoping problems with the opt1 argument and have
to pass it in explicitly -- I can't remember how things work with optim.
-- Bert Gunter
Genentech Non-Clinical Statistics
South San Francisco, CA
The business of the statistician is to catalyze the scientific learning
process. - George E. P. Box
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of
Guenther, Cameron
Sent: Friday, January 13, 2006 11:03 AM
To: [EMAIL PROTECTED]
Subject: [R] apply
Hello,
I have a dataset d which is
d
pop catch
1 66462.01 10807.757
2 87486.73 46257.885
3 57211.64 9345.058
4 71321.62 4892.868
5 100024.89 27334.248
6 104504.91 48535.092
7 95295.51 39348.195
8 93737.35 34343.489
9 89375.05 28750.743
10 95312.65 30755.064
11 100888.17 55404.370
12 84790.23 37751.074
13 81129.82 29277.443
14 69797.09 21500.398
15 61690.34 18199.664
16 60671.08 19349.051
17 62852.57 16300.982
18 90646.32 34793.148
And a function opt1:
opt1 - function (x) {
Z - x + M
c.hat - (x/Z)*pop*(1-exp(-Z))
y - (catch - c.hat)^2
return(y)
}
And define M = 0.25
For each row I want to return a value F that is a minimization of the
opt1 function
I have tried many variations of:
d$F-apply(d,2,optim(0.3,opt1,method=BFGS)
and even:
For (I in 1:length(pop))apply(d,2,optim(0.3,opt1,method=BFGS))
Every time I get the same error message
Error in optim(0.3, opt1, method = BFGS) :
objective function in optim evaluates to length 18 not 1
So the apply function is returning 18 values of F which I want but the
function only wants to return 1 value.
Any Suggestions.
Thanks,
Cam
__
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Re: [R] R and filemaker pro DB
On 1/13/06 7:08 AM, Michael Bibo [EMAIL PROTECTED] wrote: I have been looking for a database application to use in conjunction with R (on a Windows network). When I approached my organization's IT department to ask about using MySQL, they made a counter-offer of Filemaker Pro (v8). It is not specifically mentioned in 'R Data Import/Export', nor do searches of the archives turn up much information. Does anyone have any experience using Filemaker Pro with R? Should package RODBC work with Filemaker, as it is odbc-compliant? (I will be doing some trials anyway). Any other relevant advice welcome. I have used Fmpro via RODBC a bit. I also use MySQL and PostgreSQL quite a bit with R. For smaller datasets, Fmpro is probably fine, but for larger datasets (more than a few thousand rows), fmpro is pretty slow compared to a dedicated SQL server. Also, there is a great deal of flexibility in database design, tuning, backup, and enterpriseness. However, note that SQL servers do not come with GUI front ends like fmpro, so if you are building a database for use other than data management, fmpro is a good quick solution. So, I would do what you suggest you are going to do and set up both MySQL or PostgreSQL and fmpro and see which better meets your needs. They are quite different in many ways, though. Sean __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] for loop should check the looping index !!
Hello , a-c(1) for(i in 2:length(a)) do.something with a[[i]] I get : Error in a[[i]] : subscript out of bounds Am I missing something here? Doesnt R check the value of i inside for and if the condition is not tru, dont do anything thanks, johan - Got holiday prints? See all the ways to get quality prints in your hands ASAP. [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Idempotent apply
One small problem with apply is that it is not idempotent - it always
puts the result vector in the first dimension of the result array. For
example:
a - array(1:24, c(2,3,4))
dim(apply(a, c(1,2), I))
dim(apply(a, c(1,2), diff))
I've written a wrapper around apply that rearranges the dimensions
into the original order.
# Idempotent apply
iapply - function (X, MARGIN, FUN, ...) {
dims - c((1:length(dim(X)))[!(1:length(dim(X)) %in% MARGIN)], MARGIN)
res - apply(X, MARGIN, FUN)
if (length(dim(res)) == length(dims)) {
aperm(res, order(dims))
} else {
res
}
}
dim(iapply(a, c(1,2), I))
dim(iapply(a, c(1,2), diff))
Hopefully this may be of use to someone else. The function isn't
completely satisfying as apply doesn't deal nicely with functions that
return higher-dimensional arrays (eg. apply(a, 1, I)) and reduces 1-D
arrays to vectors (eg. apply(a,3,sum)). Any comments on the code
would be greatfully appreciated.
Hadley
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[R] Syntax for linear mixed model
The syntax below works, and gives the expected results, in R version 2.0.0, provided that I have loaded packages Matrix, latticeExtra and lme4. However, I cannot get it to work in version 2.2.1. Can anyone tell me how to fit this model in the more recent version? Thanks in anticipation, Nick Galwey barleyprogeny.model1lme - lme(yield_g_m2 ~ 1, data = barleyprogeny.unbalanced, random = ~ 1|fline + fblock) [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] for loop should check the looping index !!
Yep, you missed the fact that 2:1 generates the sequence c(2,1). Personally, I'd excuse you for missing this, as the documentation for seq says: The operator ':' and the 'seq(from, to)' form generate the sequence 'from, from+1, ..., to'. Maybe I'm missing something, but I don't see anywhere on the help page for seq and : any mention of the fact the seq() generates a descending sequence if 'to' is less than 'from'. In programming, *never* use a construct like 1:length(x) or 2:length(x), always using something like seq(1,len=length(x)) (or simply seq(len=length(x)), or seq(2, len=length(x)-1) or seq(along=x)[-1]. -- Tony Plate johan Faux wrote: Hello , a-c(1) for(i in 2:length(a)) do.something with a[[i]] I get : Error in a[[i]] : subscript out of bounds Am I missing something here? Doesnt R check the value of i inside for and if the condition is not tru, dont do anything thanks, johan - Got holiday prints? See all the ways to get quality prints in your hands ASAP. [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] for loop should check the looping index !!
johan Faux [EMAIL PROTECTED] writes: Hello , a-c(1) for(i in 2:length(a)) do.something with a[[i]] I get : Error in a[[i]] : subscript out of bounds Am I missing something here? Doesnt R check the value of i inside for and if the condition is not tru, dont do anything Well, 2:1 [1] 2 1 The for loop as such has no idea what you're going to do with the index variable, so will faithfully try to do.something with a[[2]] -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] apply
In addition the error message explicitly says:
Error in optim(0.3, opt1, method = BFGS) :
objective function in optim evaluates to length 18 not 1
And from the objective function we see
opt1 - function (x) {
Z - x + M
c.hat - (x/Z)*pop*(1-exp(-Z))
y - (catch - c.hat)^2
return(y)
}
The last line should be replaced by:
sum(y)
rather than return(y). See ?optim, ?apply, and the reference Bert
gives below.
HTH,
--sundar
Berton Gunter wrote:
You are not calling apply() properly. Please read relevant reference
material carefully. You might also wish to pick up one of the several good
books on R (check CRAN website) -- I like VR's S PROGRAMMING.
I did not go through your example in detail, but your apply() call should be
of the form
apply(d,2,function(x)optim(x,...))
You may or may not get into scoping problems with the opt1 argument and have
to pass it in explicitly -- I can't remember how things work with optim.
-- Bert Gunter
Genentech Non-Clinical Statistics
South San Francisco, CA
The business of the statistician is to catalyze the scientific learning
process. - George E. P. Box
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of
Guenther, Cameron
Sent: Friday, January 13, 2006 11:03 AM
To: [EMAIL PROTECTED]
Subject: [R] apply
Hello,
I have a dataset d which is
d
pop catch
1 66462.01 10807.757
2 87486.73 46257.885
3 57211.64 9345.058
4 71321.62 4892.868
5 100024.89 27334.248
6 104504.91 48535.092
7 95295.51 39348.195
8 93737.35 34343.489
9 89375.05 28750.743
10 95312.65 30755.064
11 100888.17 55404.370
12 84790.23 37751.074
13 81129.82 29277.443
14 69797.09 21500.398
15 61690.34 18199.664
16 60671.08 19349.051
17 62852.57 16300.982
18 90646.32 34793.148
And a function opt1:
opt1 - function (x) {
Z - x + M
c.hat - (x/Z)*pop*(1-exp(-Z))
y - (catch - c.hat)^2
return(y)
}
And define M = 0.25
For each row I want to return a value F that is a minimization of the
opt1 function
I have tried many variations of:
d$F-apply(d,2,optim(0.3,opt1,method=BFGS)
and even:
For (I in 1:length(pop))apply(d,2,optim(0.3,opt1,method=BFGS))
Every time I get the same error message
Error in optim(0.3, opt1, method = BFGS) :
objective function in optim evaluates to length 18 not 1
So the apply function is returning 18 values of F which I want but the
function only wants to return 1 value.
Any Suggestions.
Thanks,
Cam
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Re: [R] Variance-covariance by factor
The cbind should be removed: sim - data.frame(S = s, D= d, H=h, L=l, W=w) by(sim[,-1], sim$S, var) On 1/13/06, Yang, Richard [EMAIL PROTECTED] wrote: Dear all, I have a data frame with one factor and four numeric variables and wish to obtain the var-cor matrix separately by factor. I tried by() and sapply() but getting nowhere. I understand this can be done by subsetting the dataframe, but there should have some sleek ways of doing it. Here is a simulated dataframe; s - rep(c(A,B,C), c(25,22,18)) d - c(rnorm(25,14,2.6),rnorm(22,15.2,2.8),rnorm(18,16.4,3.0)) h - c(rnorm(25,10,1.4),rnorm(22,11.2,1.8),rnorm(18,12.3,2.0)) l - c(rnorm(25,6.8,1.6), rnorm(22,7.0,1.7),rnorm(18,7.3,1.8)) w - c(rnorm(25,2.5,0.65),rnorm(22,2.6,0.7),rnorm(18,2.8,0.71)) sim - data.frame(cbind(S = s, D= d, H=h,L=l,W=w)) sim.var - sapply(split(sim, sim$S), function(z) var(z)) Error in var(z) : missing observations in cov/cor In addition: Warning message: NAs introduced by coercion sim.var - by(sim, sim$S, function(z) var(z)) Error in var(z) : missing observations in cov/cor In addition: Warning message: NAs introduced by coercion Debug() and trac() the function got no further info. Because the error suggested missing data, I looked at the data frame and was surprised str(sim) `data.frame': 65 obs. of 5 variables: $ S: Factor w/ 3 levels A,B,C: 1 1 1 1 1 1 1 1 1 1 ... $ D: Factor w/ 65 levels 10.0860856437045,..: 51 12 21 11 8 15 57 44 19 60 ... $ H: Factor w/ 65 levels 10.0345903489406,..: 17 2 4 52 6 21 29 9 62 10 ... $ L: Factor w/ 65 levels 10.3854663209663,..: 10 6 23 55 60 8 58 65 11 2 ... $ W: Factor w/ 65 levels 0.93902749732563,..: 38 13 33 12 22 39 47 31 36 53 ... Why the data.frame() converts numeric vectors d, h, l, w into factors? Any suggestions for 1) how to compute var-cor by factor in a data frame, and 2) why data.frame converts numeric variables into factors ? sessionInfo() R version 2.2.0, 2005-10-06, i386-pc-mingw32 attached base packages: [1] methods stats graphics grDevices utils datasets base Thanks, Richard Yang Northern Forestry Centre /Centre de foresterie du Nord Canadian Forest Service/Service canadien des forêts Natural Resources Canada /Ressources naturelles Canada 5320-122 Street/5320, rue 122 Edmonton Alberta Canada T6H 3S5 [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] panel data unit root tests
If replies to this post will no longer be useful for you, then please
discregard this comment. If not, I will start by saying that I could
not understand enough of your question to respond directly.
RSiteSearch(panel unit root) led me to an exchange we had following a
related question you posted last October
(ttp://finzi.psych.upenn.edu/R/Rhelp02a/archive/63545.html). Did you
try the nlme package as suggested there? I've just now looked at that,
and I confess I could not figure out how to do it in a few minutes.
Do you want to perform a unit root test for a particular panel data
set you have? Or do you want to develop software for a particular panel
unit root test? If the former, I suggest you prepare a very simple toy
example trying to do something like this using lme with perhaps corAR1,
then send this list a question on whether it is possible to do what you
want with lme, asking how to take the next step with the toy example.
If rather you want to develop software for a particular unit root test,
then I suggest you at least provide a more complete citation than just
a la Arellano Bond. In either case, I also suggest you review the
posting guide! www.R-project.org/posting-guide.html and try to make
your post as easily understood as possible. In general, I think that
posts that are clear and succinct tend to get quicker, more useful
answers. Maybe I'm just dense, but I don't understand what you are
asking. For example, your code includes print(levinlin(ws, year, id,
lags = 3)). What is the levinlin function? RSiteSearch(levinlin)
produced zero hits.
hope this helps.
spencer graves
jukka ruohonen wrote:
When finally got some time to do some coding, I started and stopped right
after. The stationary test is a good starting point because it demonstrates
how we should be able to move the very basic R matrices. I have a real-
world small N data set with
rows:
id(n=1)---t1---variable1
...
id=(N=20)---T=21---variable1
Thus, a good test case. For first id I was considering something like this:
lag - as.integer(lags)
lags.p - lags + 1
id - unique(group)
id.l - length(id)
y.l - length(y)
yid.l - length(y)/id.l
if (lag yid.l -2)
stop(\nlag too long for defined cross-sections.\n)
#for (i in id) {
lagy - y[2:yid.l]
lagy.em - embed(lagy, lags)
id.l - length(id)
dy - diff(y)[1:yid.l-1]
dy.em - embed(dy, lags)
# }
print(levinlin(ws, year, id, lags = 3))
Couldn't figure the loop over units out but with N = 1 the data
transformation seemed to work just fine. Now we should pool the new
variables within the panel and regress y over yt-1 and dy-t1 ++ dy-t-j
with, say, BIC doing the job for d's (H0: y-1 ~ 0) for each in the panel.
Now the above example puts the right-hand on columns, and if we are dealing
with panel models in general, we should store the new variables together
with dX's, which should then give clues to IV estimator with e.g.
orthogonal deviations, e.g. k - y ~ yt-1 + x + as.factor(id)). So one
confusing part is the requirement of some big storage base for different
matrices doing the IV business with lags/levels - the amount of instruments
can be enormous with possibly calculation problems in a GMM dynamic panel
estimator a la Arellano Bond. Therefore one should code the theoretically
relevant instruments beforehand with various transformation matrices. Thus,
should I start to study something that can be done with the newly added
SparseM package?
Regards,
Jukka Ruohonen.
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[R] Rd file--latex {array} help
I am trying to build the notation for combination as the function
\code{choose} in a *.Rd file; but it is not working.
To reduce to essence
\deqn{ \left( \begin{array}{c}
r-1 \\
n
\end{array} \right)
}
I have double checked the latex logic (without \deqn{}) in LaTexIT on
MacOSX so it seems fine.
I've read the R-ext.pdf and down some searching in the
archives--stumped.
R CMD Rd2dvi --pdf
renders something like this
( r-1\n )
Advice?
Thanks.
Wil
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[R] change lattice panel background color
I can't find a way to change just the panel background color in lattice. I would like NA regions in levelplot() to appear black. I've tried the trellis.par.set() stuff, but it it makes the background of the whole graphic black. Thanks, Scott Waichler Pacific Northwest National Laboratory scott.waichler _at _ pnl.gov __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] LaTeX slide show (Was: Re: Taking code from packages)
Duncan Murdoch wrote: On 1/13/2006 2:04 AM, Ales Ziberna wrote: Hello! [snip] (I'm a little sensitive about dependencies now, since the LaTeX seminar template I've used a few times no longer works. It depends on too many LaTeX packages, and someone, somewhere has introduced incompatibilities in them. Seems like I'll be forced to use Powerpoint or Impress.) Try LaTeX Beamer! It is the best thing that happend to LaTeX in a long time. Simply beautiful, intuitive and very easy to use, and it's not yet another 'seminar' or 'prosper'. Part of MikTeX now. See http://latex-beamer.sourceforge.net/ for documentation, examples etc. Cheers Henrik Duncan Murdoch [snip] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
