[R] R 2.14.0 Design library
Dear all, I have recently upgraded to R 2.14.0 with Windows 7. I wish to use the command 'cph' but the Design library is no longer on the list of installable packages. How can I install Design so that I may use the 'cph' function? Many thanks, Laura [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R 2.14.0 Design library
Le mercredi 04 janvier 2012 à 09:04 +, Bonnett, Laura a écrit : Dear all, I have recently upgraded to R 2.14.0 with Windows 7. I wish to use the command 'cph' but the Design library is no longer on the list of installable packages. How can I install Design so that I may use the 'cph' function? Design has been replaced with rms for some time, with (AFAIK) the same functions. http://cran.r-project.org/web/packages/rms/index.html Cheers __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R 2.14.0 Design library
Thank you! -Original Message- From: Milan Bouchet-Valat [mailto:nalimi...@club.fr] Sent: 04 January 2012 09:23 To: Bonnett, Laura Cc: 'r-help@r-project.org' Subject: Re: [R] R 2.14.0 Design library Le mercredi 04 janvier 2012 à 09:04 +, Bonnett, Laura a écrit : Dear all, I have recently upgraded to R 2.14.0 with Windows 7. I wish to use the command 'cph' but the Design library is no longer on the list of installable packages. How can I install Design so that I may use the 'cph' function? Design has been replaced with rms for some time, with (AFAIK) the same functions. http://cran.r-project.org/web/packages/rms/index.html Cheers __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Extract concordance from coxph.object
Dear all, As I said in my previous email I have just upgraded to R 2.14.0 on Windows 7. I have just run the 'coxph' function and notice that a Concordance statistic is produced. Is there any way to extract this information from the output? E.g. can I call the concordance value independently of calling the output? Many thanks, Laura [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] About source()
On 03.01.2012 21:22, Li SUN wrote: Thanks, Rolf, Justin and Uwe! Actually I wanted to run .R file as a script, just like what people do for bash scripts or python scripts. It seems to me that adding #!/usr/bin/R -f at the first line is what I need. Is this true? Perhaps even Rscript rather than R. Uwe Ligges Li Sun 2012/1/2 Rolf Turnerrolf.tur...@xtra.co.nz: On 03/01/12 17:02, Li SUN wrote: Hello, I am a beginner to the R language and find it fantastic and well-designed, quite different from other programming languages. What a refreshingly sensible attitude!!! :-) This is the first time I post on the r-help mailing list. In invoking the function source(filename), it seems that the filename has to exist in the current working directory, otherwise it has to be specified in full path. So is there any mechanism(such as environment variable) to specify an additional directory of .R files that source() could search in? I'm no expert on this, and others may correct me, but (1) I don't believe any such mechanism exists. (2) It's probably not a good idea, even if such a mechanism were to exist. Directories have a tree structure, rather than being linearly ordered in the way that data bases on your R search path are ordered. I believe you would run all sorts of risks of confusion and of getting the wrong file were you to invoke such a mechanism. It is ``good practice'' to have separate directories associated with different projects and to situate all files, that you might wish to source in respect of a given project, in the directory associated with that project. I know that this is an irritating sort of response --- ``No, you can't do that, and you shouldn't do it anyway!'' --- but I sincerely believe this to be true. That being said, I also believe that you could program up such a mechanism yourself. I.e. build a function source2() which would have a hard coded list of directories to search, and would make use of the try() function. Might be a good exercise for you, given that you are starting out in R and looking to upgrade your skills! :-) cheers, Rolf Turner __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] tcltk on linux/rhel6
On 04/01/2012 01:52, Peter Langfelder wrote: On Tue, Jan 3, 2012 at 4:03 PM, Carl Baribaultcrlbr...@gmail.com wrote: Dear All, I've seen posts to the effect that.. 1) choose.dir is only available for windows, and 2) tk_choose.dir would be the linux equivalent. I'm still having trouble with the subject package on linux/rhel6. I've specified --with-tcltk during ./configure, and I still get the response... install.packages(tcltk) My understanding is that tcltk is included in the base installation now. You should be able to load it using library(tcltk) without explicitly installing it. You can install tcltk2 as an add-on package. Yes, but you need OS support (for both). Whoever installed this R needs to read the R-admin manual and note the need for -devel RPMs for Tcl and Tk. Then study the configure messages which tell you if tcltk was built. -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] About source()
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On 04/01/12 10:39, Uwe Ligges wrote: On 03.01.2012 21:22, Li SUN wrote: Thanks, Rolf, Justin and Uwe! Actually I wanted to run .R file as a script, just like what people do for bash scripts or python scripts. It seems to me that adding #!/usr/bin/R -f at the first line is what I need. Is this true? Perhaps even Rscript rather than R. And there is also littler from Dirk Eddelbüttel: http://dirk.eddelbuettel.com/code/littler.html - From the description: littler provides hash-bang (i.e. script starting with #!/some/path) capability for GNU R, as well as simple command-line and piping use. Similar to Rscript, but with some differences. I used both, and in most cases they are equivalent. Rainer Uwe Ligges Li Sun 2012/1/2 Rolf Turnerrolf.tur...@xtra.co.nz: On 03/01/12 17:02, Li SUN wrote: Hello, I am a beginner to the R language and find it fantastic and well-designed, quite different from other programming languages. What a refreshingly sensible attitude!!! :-) This is the first time I post on the r-help mailing list. In invoking the function source(filename), it seems that the filename has to exist in the current working directory, otherwise it has to be specified in full path. So is there any mechanism(such as environment variable) to specify an additional directory of .R files that source() could search in? I'm no expert on this, and others may correct me, but (1) I don't believe any such mechanism exists. (2) It's probably not a good idea, even if such a mechanism were to exist. Directories have a tree structure, rather than being linearly ordered in the way that data bases on your R search path are ordered. I believe you would run all sorts of risks of confusion and of getting the wrong file were you to invoke such a mechanism. It is ``good practice'' to have separate directories associated with different projects and to situate all files, that you might wish to source in respect of a given project, in the directory associated with that project. I know that this is an irritating sort of response --- ``No, you can't do that, and you shouldn't do it anyway!'' --- but I sincerely believe this to be true. That being said, I also believe that you could program up such a mechanism yourself. I.e. build a function source2() which would have a hard coded list of directories to search, and would make use of the try() function. Might be a good exercise for you, given that you are starting out in R and looking to upgrade your skills! :-) cheers, Rolf Turner __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. - -- Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany) Centre of Excellence for Invasion Biology Stellenbosch University South Africa Tel : +33 - (0)9 53 10 27 44 Cell: +33 - (0)6 85 62 59 98 Fax : +33 - (0)9 58 10 27 44 Fax (D):+49 - (0)3 21 21 25 22 44 email: rai...@krugs.de Skype: RMkrug -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.11 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iEYEARECAAYFAk8EIs4ACgkQoYgNqgF2egpF+QCeObN8q+U6HHlM/Tsls/wF+VoH /twAn2zaTzVrCdTxvENSK2buPlFsjlnC =tEkV -END PGP SIGNATURE- __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Extract concordance from coxph.object
Le mercredi 04 janvier 2012 à 09:27 +, Bonnett, Laura a écrit : Dear all, As I said in my previous email I have just upgraded to R 2.14.0 on Windows 7. I have just run the 'coxph' function and notice that a Concordance statistic is produced. Is there any way to extract this information from the output? E.g. can I call the concordance value independently of calling the output? If you have a look at str(coxmodel) (assuming coxmodel holds the object) then you'll see that there's a concordance member. You can use coxmodel$concordance to get it. Cheers __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] KS and AD test for Generalized PAreto and Generalized Extreme value
Dear R helpers, I need to use KS and AD test for Generalized Pareto and Generalized extreme value. E.g. if I need to use KS for Weibull, I have teh syntax ks.test(x.wei,pweibull, shape=2,scale=1) Similarly, for AD I use ad.test(x, distr.fun, ...) My problem is fir given data, I have estimated the parameters of GPD and GEV using lmom. But I am not able to find out the distribution name I should be use for these distributions if I wish to use these tests. E.g, for gamma, I can use pgamma etc. What distribution name I should use for GPD and GEV and for that matter where can I find the distribution names I can use for KS and AD test. Thanks in advance Regards Vincy [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] An R interface to Model Building
Brett, Spencer, I replied to Brett on the R-SIG-GUI mailing list, suggesting to use the proto package. I found it most useful to structure the code when developing my R2STATS interface. 2. Have you reviewed the other R projects with a graphical user interface for R? Several are listed at http://sciviews.org/_rgui http://sciviews.org/_rgui/. Is this page still maintained? I wrote to Philippe Grosjean months ago but received no reply. 3. If you would like to collaborate on a project with others, r-forge.r-project.org is a standard place for hosting collaborative projects relating to R. I looked for a few of the projects listed at http://sciviews.org/_rgui http://sciviews.org/_rgui/ and couldn't find any on R-Forge. The R2STATS and the AtelieR packages are on R-Forge and provide GUIs for fitting and comparing various models (GLM and GLMM), both in a frequentist and a Bayesian approach. Best, Yvonnick Noel University of Brittany at Rennes Department of Psychology France __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] A problem of meta analysis based on metafor package
I would like to make a meta analysis based on metafor package. If I only have the data of RR, 95%CI of every study, could I finish the meta analysis? If possible, how to do it? Millions of thanks! -- View this message in context: http://r.789695.n4.nabble.com/A-problem-of-meta-analysis-based-on-metafor-package-tp4260896p4260896.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Linear regression using matrices
I'm new to R and I'm not a Statistician I'm an Accountant, but I'm finding it an excellent tool for the business analysis work I do. I need to run LM() where both response and predictor are held in matrices. The model follows the form:- regression1 = matrix1.col1 - matrix2.col1 regression2 = matrix1.col2-matrix2.col2 and so on.. I have no problem with the multivariate response but I can't get the function to recognise a tabular predictor. Is this possible without using a loop ? -- View this message in context: http://r.789695.n4.nabble.com/Linear-regression-using-matrices-tp4260945p4260945.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] problem in R
data-matrix(rnorm(10)) data[c(1,4,6)]-NA print(data) data-matrix(data[!is.na(data)]) print(data) - Isaac Research Assistant Quantitative Finance Faculty, UTS -- View this message in context: http://r.789695.n4.nabble.com/problem-in-R-tp4260254p4260976.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Error formal argument softmax matched by multiple actual arguments
I am running the nnet package as neural.soft-nnet(custcat~region+ed+marital+tenure+age+address+income,size=3,softmax=TRUE) This returns the error message : formal argument softmax matched by multiple actual arguments Here the dependent variable custcat is a factor with 4-levels. This error does not crop up for any other arguments of nnet(), including entropy=TRUE, linout=TRUE and censored=TRUE This post : http://userprimary.net/posts/2010/03/16/reentrant-bugs-without-concurrency/ http://userprimary.net/posts/2010/03/16/reentrant-bugs-without-concurrency/ identifies the error message formal argument matched by multiple actual arguments as a bug arising out of the R-internals function matchArgs Is there a work-around to this problem? I am using R version 2.12.2 (2011-02-25) Regards, Yashwanth -- View this message in context: http://r.789695.n4.nabble.com/Error-formal-argument-softmax-matched-by-multiple-actual-arguments-tp4260949p4260949.html Sent from the R help mailing list archive at Nabble.com. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Linear regression using matrices
I've done a lot of research on this very topic and found a few solutions. But
all the ways I've discovered involve loops.
Applying it to what you want, the best way I've found is to do (stolen from
an experienced R user, of course):
y-array(rnorm(100),dim=c(10,10))
x-array(rnorm(100),dim=c(10,10))
regg-list()
for(i in 1:ncol(y))
{
regg[[i]]-lm(y[,i]~x[,i])
}
Now the reason I've stuck onto the list() method is because the output is
still in lm() format. So you can write neat functions to extract every
statistic you want off summary(regg[[N]]).
-
Isaac
Research Assistant
Quantitative Finance Faculty, UTS
--
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Re: [R] RODBC installation: error message
On 12-01-03 2:39 PM, gregory benison wrote:
If one attempts to install RODBC (via install.packages('RODBC'))
without having an ODBC driver installed, this error message results:
checking sqlext.h presence... no
checking for sqlext.h... no
configure: error: ODBC headers sql.h and sqlext.h not found
ERROR: configuration failed for package 'RODBC'
* removing '/usr/lib/R/library/RODBC'
Yes, the RODBC README describes the needed prerequisites, but for
someone who just wants to use RODBC and tries to install it in the
most natural way, i.e. from R Installation and Administration:
For most users it suffices to call ‘install.packages(pkgname)’
the result is the above error message, which could be more informative.
RODBC is not my package, but I can say from experience that it's hard to
put together error messages that satisfy everyone. Here, the problem is
that configuration couldn't find the files sql.h and sqlext.h, and
that's what the error says. Not installing ODBC is one reason that
might happen; another is installing it improperly, and there are
probably others, too. I think it's best if the error messages describe
the problems; trying to diagnose the solution is something that needs
human intervention.
One thing R could do better is to provide a standard way to view README
and similar files before installing a package. That might have helped here.
Duncan Murdoch
Greg Benison
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Re: [R] R 2.14.0 Design library
See http://biostat.mc.vanderbilt.edu/Rrms for a list of changes that the user needs to deal with, especially with respect to plotting predicted values. Frank Bonnett, Laura wrote Thank you! -Original Message- From: Milan Bouchet-Valat [mailto:nalimilan@] Sent: 04 January 2012 09:23 To: Bonnett, Laura Cc: 'r-help@' Subject: Re: [R] R 2.14.0 Design library Le mercredi 04 janvier 2012 à 09:04 +, Bonnett, Laura a écrit : Dear all, I have recently upgraded to R 2.14.0 with Windows 7. I wish to use the command 'cph' but the Design library is no longer on the list of installable packages. How can I install Design so that I may use the 'cph' function? Design has been replaced with rms for some time, with (AFAIK) the same functions. http://cran.r-project.org/web/packages/rms/index.html Cheers __ R-help@ mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. - Frank Harrell Department of Biostatistics, Vanderbilt University -- View this message in context: http://r.789695.n4.nabble.com/R-2-14-0-Design-library-tp4260537p4261125.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Using a mathematical expression in sapply() XXXX
Hello everyone, I have the following call to sapply() and error message. Is the most efficient way to deal with this to make sum(!is.na(x)) a function in a separate line prior to this call? If not, please advise. N.Valid=sapply(x,sum(!is.na(x))) Error in match.fun(FUN) : 'sum(!is.na(x))' is not a function, character or symbol Thanks! Dan [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Using a mathematical expression in sapply() XXXX
Le mercredi 04 janvier 2012 à 08:41 -0500, Dan Abner a écrit : Hello everyone, I have the following call to sapply() and error message. Is the most efficient way to deal with this to make sum(!is.na(x)) a function in a separate line prior to this call? If not, please advise. N.Valid=sapply(x,sum(!is.na(x))) Error in match.fun(FUN) : 'sum(!is.na(x))' is not a function, character or symbol You can use this: sapply(x, function(x) sum(!is.na(x))) But, if you can convert x to a matrix, it would be faster and shorter to check for NAs beforehand, and use apply(): x - matrix(c(1, 2, NA, 3, NA, 4), 2) apply(!is.na(x), 2, sum) Regards __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] simulating stable VAR process
Hello all, I looking at package dse or vars or mAr I know how to simulate a VAR(p) process, my problem is that most of those processes are unstable (not weakly stationary). Do anybody know how to generate a random VAR (or VARMA even better) process that is weakly stationary? Thanks -- View this message in context: http://r.789695.n4.nabble.com/simulating-stable-VAR-process-tp4261177p4261177.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] simulating stable VAR process
More specifically. I know that a condition for a VAR(p) process to be stable (weakly stationary) is that the companion form of the equation (see AWESOME Pfaff book analysis of integrated and cointegrated time series in R) as eigenvalues of modulus 1. My problem is that I want to generate such processes... When I try to generate random VAR(p) processes they seems to explode (clearly they are not weakly stationary...) Is there a way somebody know? -- View this message in context: http://r.789695.n4.nabble.com/simulating-stable-VAR-process-tp4261177p4261210.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Using a mathematical expression in sapply() XXXX
On Jan 4, 2012, at 7:41 AM, Dan Abner dan.abne...@gmail.com wrote: Hello everyone, I have the following call to sapply() and error message. Is the most efficient way to deal with this to make sum(!is.na(x)) a function in a separate line prior to this call? Yes or inline using an anonymous/lambda function: sapply(XX, function(x) sum(!is.na(x))) If not, please advise. N.Valid=sapply(x,sum(!is.na(x))) Error in match.fun(FUN) : 'sum(!is.na(x))' is not a function, character or symbol Thanks! Dan [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] RODBC installation: error message
Le mardi 03 janvier 2012 à 11:39 -0800, gregory benison a écrit :
If one attempts to install RODBC (via install.packages('RODBC'))
without having an ODBC driver installed, this error message results:
checking sqlext.h presence... no
checking for sqlext.h... no
configure: error: ODBC headers sql.h and sqlext.h not found
ERROR: configuration failed for package 'RODBC'
* removing '/usr/lib/R/library/RODBC'
Yes, the RODBC README describes the needed prerequisites, but for
someone who just wants to use RODBC and tries to install it in the
most natural way, i.e. from R Installation and Administration:
For most users it suffices to call ‘install.packages(pkgname)’
I guess this applies only to users installing binary packages. If you
build packages from source, the build system runs ./configure, which
returns this automated message.
Ideally, you shouldn't need to build packages from source when all you
want is use them... (Distributions could ship binary packages that R
would detect and install automatically?)
Cheers
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[R] Update method on existing reference class object
Hi
Being able to do object oriented programming in R is really good. I now
started using the Reference Classes and really like it.
Though, I have one problem: I cannot find a way to update a method on an
existing object.
The flexibility that scripting gives (really needed for interactive data
analysis) is lost if everything have to be recalculated all the time.
For example:
cl1 - setRefClass(cl1,
fields=list(x=data.frame),
methods=list(
init=function(){Read and process data},
fitModel=function(){Fit different kind of models and keep the results
in x and other fields}
)
)
tmp - cl1$new()
tmp$x - 5
tmp$fun()
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] Using a mathematical expression in sapply() XXXX
Dan, It depends on what you want to achieve. I suspect you just want to remove missing values before summing; if so, consider sapply(x, sum, na.rm=TRUE) instead. To make your code running, try sapply(x, function(x) sum(!is.na(x))) However, this would just count the number of non-missing values per subgroup, not the sum of the values. Similarly, sapply(x, function(x) sum(x, na.rm=TRUE)) would follow the same rationale but give the sums (with missing values removed), i.e. the same results as the first line of code. I'd rather choose the first option than this one, though. Of course, you could also define a new function sum1 - function(x) sum(!is.na(x)) # or probably rather sum(x, na.rm=TRUE), depending on your needs and then use sapply(x, sum1) but that seems a bit overkill, I'd say... HTH, Michael -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-bounces@r- project.org] On Behalf Of Dan Abner Sent: Wednesday, January 04, 2012 14:41 To: r-help@r-project.org Subject: [R] Using a mathematical expression in sapply() Hello everyone, I have the following call to sapply() and error message. Is the most efficient way to deal with this to make sum(!is.na(x)) a function in a separate line prior to this call? If not, please advise. N.Valid=sapply(x,sum(!is.na(x))) Error in match.fun(FUN) : 'sum(!is.na(x))' is not a function, character or symbol Thanks! Dan [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting- guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Linear regression using matrices
OK thanks. In my case I think it might be possible to work around this by reshaping my data and then using lmlist() to run separate regressions for each data group. lmlist() is new to me but it looks like it will do the job. -- View this message in context: http://r.789695.n4.nabble.com/Linear-regression-using-matrices-tp4260945p4261368.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Getting Sphericity Tests for Within Subject Repeated Measure Anova (using car package)
On 1/3/2012 9:36 PM, maximilian.mueller wrote: Here is the syntax: options(contrasts=c(contr.sum, contr.poly)) read.csv2(test21.csv) - dat3 mod3 - lm(cbind(umsatz_t1, umsatz_t2, umsatz_t3, umsatz_t4) + cbind(ebitda_t1, ebitda_t2, ebitda_t3, ebitda_t4) + ~ 1, data=dat3) idata3 - data.frame(Umsatz=factor(1:4), EBITDA=factor(1:4)) aov3 - Anova(mod3, idata=idata3, idesign= ~Umsatz+EBITDA, type=III) Fehler in check.imatrix(X.design) : Terms in the intra-subject model matrix are not orthogonal. summary(aov3, multivariate=F) That's because you've defined two identical factor variables. idata3- data.frame(Umsatz=factor(1:4), EBITDA=factor(1:4)) idata3 - data.frame(Umsatz=factor(1:4), EBITDA=factor(1:4)) idata3 Umsatz EBITDA 1 1 1 2 2 2 3 3 3 4 4 4 If your data is a doubly-multivariate design with two repeated variables Umsatz and EBIDTA crossed with 4 time points each, you might want to look at the vignette HE Plots for Repeated Measures Designs in the heplots package for theory and examples vignette(repeated, package=heplots) -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. York University Voice: 416 736-5115 x66249 Fax: 416 736-5814 4700 Keele StreetWeb: http://www.datavis.ca Toronto, ONT M3J 1P3 CANADA __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Using a mathematical expression in sapply() XXXX
On Jan 4, 2012, at 14:57 , Milan Bouchet-Valat wrote: Le mercredi 04 janvier 2012 à 08:41 -0500, Dan Abner a écrit : Hello everyone, I have the following call to sapply() and error message. Is the most efficient way to deal with this to make sum(!is.na(x)) a function in a separate line prior to this call? If not, please advise. N.Valid=sapply(x,sum(!is.na(x))) Error in match.fun(FUN) : 'sum(!is.na(x))' is not a function, character or symbol You can use this: sapply(x, function(x) sum(!is.na(x))) But, if you can convert x to a matrix, it would be faster and shorter to check for NAs beforehand, and use apply(): x - matrix(c(1, 2, NA, 3, NA, 4), 2) apply(!is.na(x), 2, sum) Just for completeness: You might also do sapply(lapply(x, is.na), sum) I suspect that the anonymous function approach is more efficient, though (if you really need those extra milliseconds of your life). Regards __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Peter Dalgaard, Professor Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Email: pd@cbs.dk Priv: pda...@gmail.com __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] KS and AD test for Generalized PAreto and Generalized Extreme value
On Jan 4, 2012, at 5:49 AM, Vincy Pyne wrote: Dear R helpers, I need to use KS and AD test for Generalized Pareto and Generalized extreme value. When I searched on these names Generalized Pareto and Generalized extreme value I got plenty of hits (over 90 in one case and over 100 in another) You should learn to search with either sos::findFn or with RSiteSearch, -- David. E.g. if I need to use KS for Weibull, I have teh syntax ks.test(x.wei,pweibull, shape=2,scale=1) Similarly, for AD I use ad.test(x, distr.fun, ...) My problem is fir given data, I have estimated the parameters of GPD and GEV using lmom. But I am not able to find out the distribution name I should be use for these distributions if I wish to use these tests. E.g, for gamma, I can use pgamma etc. What distribution name I should use for GPD and GEV and for that matter where can I find the distribution names I can use for KS and AD test. Thanks in advance Regards Vincy [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. David Winsemius, MD West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] RODBC installation: error message
On Jan 4, 2012, at 8:02 AM, Milan Bouchet-Valat wrote:
Le mardi 03 janvier 2012 à 11:39 -0800, gregory benison a écrit :
If one attempts to install RODBC (via install.packages('RODBC'))
without having an ODBC driver installed, this error message results:
checking sqlext.h presence... no
checking for sqlext.h... no
configure: error: ODBC headers sql.h and sqlext.h not found
ERROR: configuration failed for package 'RODBC'
* removing '/usr/lib/R/library/RODBC'
Yes, the RODBC README describes the needed prerequisites, but for
someone who just wants to use RODBC and tries to install it in the
most natural way, i.e. from R Installation and Administration:
For most users it suffices to call ‘install.packages(pkgname)’
I guess this applies only to users installing binary packages. If you
build packages from source, the build system runs ./configure, which
returns this automated message.
Ideally, you shouldn't need to build packages from source when all you
want is use them... (Distributions could ship binary packages that R
would detect and install automatically?)
That is up to the resources available for each Linux distribution. Debian based
distributions have done a better job of this for R than most, largely due to
Dirk et al making the commitment and taking the time over the years to support
a large number of CRAN packages via apt.
However, there is not the same level of commitment for others (eg. Fedora,
RHEL/CentOS, etc.), leaving most others to install from source, thus requiring
users to manually satisfy pre-requisites for installation. R itself is
available for installation via binary, but the selection of CRAN packages is
much more limited.
As Duncan noted, the message is pretty clear in that the ODBC header files are
missing, which are required to compile RODBC from source. On RH based Linuxen,
this requires the installation of the unixODBC-devel RPM, much as one would
need to have other *-devel RPMs (eg. readline-devel) installed for compiling
many applications from source.
In years past, the *-devel RPMs were frequently installed by default, but as
the Linux community has evolved, current defaults tend to not install
'development' related packages, which include compilers and related tools. This
allows for smaller footprints for the installed OS for non-technical end users.
If you are going to use R on Linux, you need to be prepared to get your hands
dirty under the hood at a lower level than if you are using Windows or OSX.
In this particular case, Prof. Ripley has taken great pains to provide
documents to guide the user on the installation of not only RODBC itself, but
other components of the ODBC ecosystem to get things working.
Regards,
Marc Schwartz
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[R] Warning message about closing a connection XXXX
Hello everyone, After running the following code, I obtain this error message. mydata - read.table(textConnection(mystring), +header=TRUE, sep=,, +row.names=id, na.strings= ) mydata Warning message: closing unused connection 3 (mystring) = However, when I attempt to run read.table() again and immediately submit the close() function (below), I obtain this message: close(mystring) Error in UseMethod(close) : no applicable method for 'close' applied to an object of class character = How can I avoid the warning message altogether? Thank you, Dan [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Warning message about closing a connection XXXX
On Jan 4, 2012, at 9:53 AM, Dan Abner wrote: Hello everyone, After running the following code, I obtain this error message. mydata - read.table(textConnection(mystring), +header=TRUE, sep=,, +row.names=id, na.strings= ) mydata Warning message: closing unused connection 3 (mystring) = However, when I attempt to run read.table() again and immediately submit the close() function (below), I obtain this message: close(mystring) Error in UseMethod(close) : no applicable method for 'close' applied to an object of class character = How can I avoid the warning message altogether? ?closeAllConnections The error message occurs because mystring was never the connection name. -- David Winsemius, MD West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Getting Sphericity Tests for Within Subject Repeated Measure Anova (using car package)
Dear Max, I'm having a little trouble following what you did and am also confused by the subject of your posting. Is this a response to another message? Is it really about getting sphericity tests? In addition: (1) Why are you adding together the response matrices cbind(umsatz_t1, umsatz_t2, umsatz_t3, umsatz_t4) and cbind(ebitda_t1, ebitda_t2, ebitda_t3, ebitda_t4)? (2) From the names of the responses, I imagine that you have two, crossed, repeated-measures factors: umsatz vs. ebita, and times 1 through 4. If that's correct, then the intra-subject data should look like idata3 - data.frame( condition=rep(c(umsatz, ebita), each=5), time=ordered(rep(1:5, 2))) and the intra-subject design should be ~condition*time. Best, John John Fox Senator William McMaster Professor of Social Statistics Department of Sociology McMaster University Hamilton, Ontario, Canada http://socserv.mcmaster.ca/jfox -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-bounces@r- project.org] On Behalf Of maximilian.mueller Sent: January-03-12 9:36 PM To: r-help@r-project.org Subject: Re: [R] Getting Sphericity Tests for Within Subject Repeated Measure Anova (using car package) Hello everyone, I am also trying to do within subjects repeated measures anova followed by the test of sphericity (see sample dataset attached below) and I am facing some problems. I tried to assign the example to my research question, but could not really solve it. Here is the syntax: options(contrasts=c(contr.sum, contr.poly)) read.csv2(test21.csv) - dat3 mod3 - lm(cbind(umsatz_t1, umsatz_t2, umsatz_t3, umsatz_t4) + cbind(ebitda_t1, ebitda_t2, ebitda_t3, ebitda_t4) + ~ 1, data=dat3) idata3 - data.frame(Umsatz=factor(1:4), EBITDA=factor(1:4)) aov3 - Anova(mod3, idata=idata3, idesign= ~Umsatz+EBITDA, type=III) Fehler in check.imatrix(X.design) : Terms in the intra-subject model matrix are not orthogonal. summary(aov3, multivariate=F) with the data set dat3 dat3 umsatz_t1 umsatz_t2 umsatz_t3 umsatz_t4 ebitda_t1 ebitda_t2 ebitda_t3 1 0.10239021 0.18241379 0.28875806 0.28875806 0.07622154 0.05543311 0.06776469 2 0.10239021 1.21769038 0.05840222 0.05840222 0.04794192 0.04642960 0.03727069 3 0.05124775 0.65373713 0.25976771 0.25976771 0.04794192 0.04435191 0.03167950 4 0.10239021 0.18241379 0.28875806 0.28875806 0.07622154 0.05543311 0.06776469 5 0.10239021 1.21769038 0.05840222 1.21769038 0.04794192 0.04642960 0.03727069 6 0.06776469 0.28875806 0.06776469 0.65373713 0.07622154 0.18241379 0.10239021 7 0.03727069 0.05840222 0.03727069 0.18241379 0.04794192 0.25976771 0.04794192 8 0.03727069 0.25976771 0.06776469 1.21769038 0.04557920 0.65373713 0.07622154 9 0.06776469 0.28875806 0.06776469 0.28875806 0.07622154 0.18241379 0.04794192 10 0.03727069 0.05840222 0.03727069 0.05840222 0.04794192 0.04642960 0.04557920 11 0.25976771 0.05543311 0.03727069 0.05543311 0.07622154 0.06776469 0.03167950 12 0.28875806 0.04642960 0.07622154 0.04642960 0.04794192 0.03727069 0.06776469 13 0.05840222 0.18241379 0.04794192 0.25976771 0.07622154 0.03167950 0.03727069 14 0.06776469 1.21769038 0.07622154 0.28875806 0.04794192 0.06776469 0.04642960 15 0.03727069 0.28875806 0.03727069 0.03727069 0.06776469 0.03727069 0.04435191 16 0.04794192 0.04642960 0.04557920 0.04557920 0.06776469 0.28875806 0.06776469 17 0.07622154 0.06776469 0.03167950 0.07622154 0.03727069 0.05840222 0.03727069 18 0.04794192 0.04642960 0.03727069 0.04435191 0.07622154 0.03167950 0.03727069 19 0.04794192 0.04435191 0.03167950 0.05543311 0.04794192 0.06776469 0.04642960 ebitda_t4 1 0.04642960 2 0.04435191 3 0.05543311 4 0.04642960 5 0.18241379 6 0.25976771 7 0.04794192 8 0.07622154 9 0.04794192 10 0.04557920 11 0.07622154 12 0.04794192 13 0.04557920 14 0.03167950 15 0.03167950 16 0.65373713 17 0.18241379 18 0.04557920 19 0.03167950 Thanks four your help... Sincerely, Max - M a x i m i l i a n M ue l l e r PhD-Student Department of Business Studies Leuphana Universität Lüneburg -- View this message in context: http://r.789695.n4.nabble.com/Getting- Sphericity-Tests-for-Within-Subject-Repeated-Measure-Anova-using-car- package-tp841030p4259642.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting- guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Is there a way to update a method on an existing Reference Class object?
Hi
Being able to do object oriented programming in R is really good. I
now started using the Reference Classes and really like it.
Though, I have one problem: I cannot find a way to update a method on
an existing object.
The flexibility that scripting gives (really needed for interactive
data analysis) is lost if everything have to be recalculated all the
time.
For example I would normally work something like this:
cl1 - setRefClass(cl1,
fields=list(x=data.frame),
methods=list(
init=function(){Read and process data},
fitModel=function(){Fit different kind of models and keep the
results in x and other fields},
plotFit1=function(){Plot the fit one way},
plotFit2=function(){Plot the fit in another way way})
)
I would then initialize it and run the functions on it:
cl1Object - cl1$new()
...
The problem then comes if I need to change something in one of the
methods, because I then have to run all the initialization and fitting
again, since the change is done to cl1 and not cl1Object, of
course.
The reference class documentation states that it is not possible since
this would give problems with inheritance etc. Is there a workaround
to this?
The very best
Peder
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[R] [Matlab] Need help on ARIMA and Matlab
Hi, I have to forecast some value of a time series using an ARIMA(5,1,3) model. I saw in Matlab there isn't a function for ARIMA models because ARIMA models are a type of Box-Jenkins models. But how to set parameters? In the Box-Jenkins models m = bj(data,[nb nc nd nf nk]) How to set nb, nc, nd, nf and nk in order to have an ARIMA(p,d,q) model? Thanks [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] subscript with comma
Hi, I want to write a word with subscript in a graph. Unfortunately, the subscript contains a comma, so all my trials didn't work and I didn't find how to do it. I want to write sm as normal text and w,grass in the subscript. Can anybody help me? And a more general question: I read the help to plotmath, but I still didn't understand, how it works. Is there a good documentation, book,... which explains all this stuff? Thanks in advance! -- View this message in context: http://r.789695.n4.nabble.com/subscript-with-comma-tp4261579p4261579.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Adding a vertical line to plot with two overlapping density plots
Hi, A simple question I hope. I wish to add a single vertical line to a plot with several density plots. Here is a simplified example. thedata - data.frame(x1=rnorm(100,1,1),x2=rnorm(100,3,1)) #create data thedata.m-melt(thedata) densityplot(~value, thedata.m, groups=variable,auto.key=list(columns=2)) #this gives the two density plots # what I wish now is to add a vertical line, for example v=2. Many thanks, Josh. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] [Matlab] Need help on ARIMA and Matlab
Perhaps you are confusedthis is R-help that said, it's very easy with forecast:::forecast.Arima in R Michael On Wed, Jan 4, 2012 at 8:38 AM, Antonio Tirri antonio.ti...@gmail.com wrote: Hi, I have to forecast some value of a time series using an ARIMA(5,1,3) model. I saw in Matlab there isn't a function for ARIMA models because ARIMA models are a type of Box-Jenkins models. But how to set parameters? In the Box-Jenkins models m = bj(data,[nb nc nd nf nk]) How to set nb, nc, nd, nf and nk in order to have an ARIMA(p,d,q) model? Thanks [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Using a mathematical expression in sapply() XXXX
On Jan 4, 2012, at 9:17 AM, peter dalgaard wrote: On Jan 4, 2012, at 14:57 , Milan Bouchet-Valat wrote: Le mercredi 04 janvier 2012 à 08:41 -0500, Dan Abner a écrit : Hello everyone, I have the following call to sapply() and error message. Is the most efficient way to deal with this to make sum(!is.na(x)) a function in a separate line prior to this call? If not, please advise. N.Valid=sapply(x,sum(!is.na(x))) Error in match.fun(FUN) : 'sum(!is.na(x))' is not a function, character or symbol You can use this: sapply(x, function(x) sum(!is.na(x))) But, if you can convert x to a matrix, it would be faster and shorter to check for NAs beforehand, and use apply(): x - matrix(c(1, 2, NA, 3, NA, 4), 2) apply(!is.na(x), 2, sum) Just for completeness: You might also do sapply(lapply(x, is.na), sum) I thought from context that the sum of negation of is.na was what was desired, since the negation operator was used and the name of the results was N.Valid. So consider substituting the existing function, complete.cases in place of is.na: sapply(lapply(x, complete.cases), sum) Or use the existing function na.omit with length: sapply(lapply(x, na.omit), length) I suspect that the anonymous function approach is more efficient, though (if you really need those extra milliseconds of your life). -- David Winsemius, MD West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] quadratic programming-maximization instead of
Maximizing f(x) = x'Ax makes sense only when A is negative-definite. Therefore, this is the same as minimizing x'Bx, where B = -A, and B is positive-definite. In other words, you should be able to simply flip the sign of the original matrix . This should yield a positive-definite matrix since the original matrix ought to be negative-definite. Ravi --- Ravi Varadhan, Ph.D. Assistant Professor, Division of Geriatric Medicine and Gerontology School of Medicine Johns Hopkins University Ph. (410) 502-2619 email: rvarad...@jhmi.edumailto:rvarad...@jhmi.edu [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] subscript with comma
On 04.01.2012 16:12, suse wrote: Hi, I want to write a word with subscript in a graph. Unfortunately, the subscript contains a comma, so all my trials didn't work and I didn't find how to do it. I want to write sm as normal text and w,grass in the subscript. Can anybody help me? And a more general question: I read the help to plotmath, but I still didn't understand, how it works. Is there a good documentation, book,... which explains all this stuff? ?plotmath suggests to use a comma separated list as in: plot(1, main=expression(sm[list(w,grass)])) Uwe Ligges Thanks in advance! -- View this message in context: http://r.789695.n4.nabble.com/subscript-with-comma-tp4261579p4261579.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Merging and subsetting with row names XXXX
Hello everyone, I have two questions: 1) I want to create a subset of a data frame column-wise and simultaneously extract the row names into a proper variable. I tried this, but received an error: myleft-mydata[c(id=row.names(mydata),workshop,gender,q1,q2)] Error in `[.data.frame`(mydata, c(id = row.names(mydata), workshop, : undefined columns selected Is the following the best way to go about this: myleft-data.frame(id=row.names(mydata),mydata)[c(id,workshop,gender,q1,q2)] myleft 2) Is it possible to merge data using merge() with a by variable that is the row names? I tried this: both-merge(myleft,myright,by=row.names(myleft)) Error in fix.by(by.x, x) : 'by' must specify valid column(s) both Suggestions? Thanks! Dan [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Adding a vertical line to plot with two overlapping density plots
Hi
Hi,
A simple question I hope. I wish to add a single vertical line to a plot
with several density plots.
Here is a simplified example.
thedata - data.frame(x1=rnorm(100,1,1),x2=rnorm(100,3,1)) #create data
thedata.m-melt(thedata)
densityplot(~value, thedata.m, groups=variable,auto.key=list(columns=2))
#this gives the two density plots
#
what I wish now is to add a vertical line, for example v=2.
If you mean densityplot from lattice here is a function (addapted from
Gabor Grothendieck's code] which adds arbitrary line(s) into panels. Is
options are similar to abline and once=TRUE means you want different lines
to different panels.
addLine
function (a = NULL, b = NULL, v = NULL, h = NULL, ..., once = FALSE)
{
tcL - trellis.currentLayout()
k - 0
for (i in 1:nrow(tcL)) for (j in 1:ncol(tcL)) if (tcL[i,
j] 0) {
k - k + 1
trellis.focus(panel, j, i, highlight = FALSE)
if (once)
panel.abline(a = a[k], b = b[k], v = v[k], h = h[k],
...)
else panel.abline(a = a, b = b, v = v, h = h, ...)
trellis.unfocus()
}
}
Regards
Petr
Many thanks,
Josh.
[[alternative HTML version deleted]]
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Re: [R] Merging and subsetting with row names XXXX
Hi As you did not provide any data you probably can not get canned solution Hello everyone, I have two questions: 1) I want to create a subset of a data frame column-wise and simultaneously extract the row names into a proper variable. I tried this, but received an error: myleft-mydata[c(id=row.names(mydata),workshop,gender,q1,q2)] Error in `[.data.frame`(mydata, c(id = row.names(mydata), workshop, : undefined columns selected Is the following the best way to go about this: myleft-data.frame(id=row.names(mydata),mydata)[c (id,workshop,gender,q1,q2)] myleft If I understand correctly you want only some columns, all rows and make also new column identical with row names. either cbind(id=row.names(mydata),mydata[, c(2,4,5,6)]) or data.frame(id=row.names(mydata),mydata[, c(2,4,5,6)]) can do it. 2) Is it possible to merge data using merge() with a by variable that is the AFAI no. row names? I tried this: both-merge(myleft,myright,by=row.names(myleft)) Error in fix.by(by.x, x) : 'by' must specify valid column(s) both Suggestions? Regards Petr Thanks! Dan [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] function in R for my exercise
Hi R helpers!
I have a question. I'm trying to create a function for an exercise. Here are
the arguments I should include:
x and y are numeric
z is a name (plus,minus,multiply,divide)
and swap is logical.
Here is what the function should do:
When z=plus, then x+y is performed and so on for the other z names. It
should give a NA when the z argument doesn't correspond to something mention
before.
When swap =TRUE, then y must be on the left side of the equation (y/x
instead of x/y).
So far, I managed to get something worked for the first part of the body
function (typing plus performes indeed an addition...) but I couldn't get
how to make the second part working. Any suggestion?
Here is the code I have so far:
myFunc- function(x,y,z,swap)
{ res= NULL
if(z ==plus) res=x+y
else if(z==minus) res=x-y
else if(z== multiply) res=x*y
else if(z==divide) res=x/y
else res-NA
return(res)}
Then, I tried to include some lines to take this swap function into
account by splitting somehow my function in 2:
myFunc- function(x,y,z,swap)
{ res1= NULL
res2=NULL
if(z ==plus) res1=x+y
else if(z==minus) res1=x-y
else if(z== multiply) res1=x*y
else if(z==divide) res1=x/y
else res1-NA
if(z ==plus) res2=y+x
else if(z==minus) res2=y-x
else if(z== multiply) res2=y*x
else if(z==divide) res2=y/x
else res2-NA
if (swap-T) return(res2)
else return(res1)
}
Any suggestions would be more than appreciated! I already thank you!
And happy new year! (that may be redundant to most of you I know ^^)
Thomas
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] Adding a vertical line to plot with two overlapping density plots
thank you very much Petr. Yes, I meant densityplot form lattice.
The code I gave plots the densities of both x1 and x2 in one panel.
Could you show me how to integrate the function addline into the code so
that a vertical line v=0 is added?
On 4 January 2012 15:55, Petr PIKAL petr.pi...@precheza.cz wrote:
Hi
Hi,
A simple question I hope. I wish to add a single vertical line to a plot
with several density plots.
Here is a simplified example.
thedata - data.frame(x1=rnorm(100,1,1),x2=rnorm(100,3,1)) #create data
thedata.m-melt(thedata)
densityplot(~value, thedata.m, groups=variable,auto.key=list(columns=2))
#this gives the two density plots
#
what I wish now is to add a vertical line, for example v=2.
If you mean densityplot from lattice here is a function (addapted from
Gabor Grothendieck's code] which adds arbitrary line(s) into panels. Is
options are similar to abline and once=TRUE means you want different lines
to different panels.
addLine
function (a = NULL, b = NULL, v = NULL, h = NULL, ..., once = FALSE)
{
tcL - trellis.currentLayout()
k - 0
for (i in 1:nrow(tcL)) for (j in 1:ncol(tcL)) if (tcL[i,
j] 0) {
k - k + 1
trellis.focus(panel, j, i, highlight = FALSE)
if (once)
panel.abline(a = a[k], b = b[k], v = v[k], h = h[k],
...)
else panel.abline(a = a, b = b, v = v, h = h, ...)
trellis.unfocus()
}
}
Regards
Petr
Many thanks,
Josh.
[[alternative HTML version deleted]]
__
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https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[[alternative HTML version deleted]]
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] problem in R
I'm not a huge fan of this sort of solution because it doesn't make
sense for non-vector-shaped (i.e., matrix or data.frame) data. It only
works here because the matrix produced is a special 1xN case.
E.g.,
# Set up some data (and yes, I realize I'm using the trick I'm
speaking out against, but c'est la vie)
testData - matrix(rnorm(20), 5)
testData[c(3,6,7)] - NA
testData[!is.na(testData)] # No longer a matrix so any information
stored in the shape is lost
# I'd prefer something like
testData[complete.cases(testData), ]
or perhaps these sorts of helper functions:
completeRows - function(x){
x[rowSums(is.na(x)) == 0L, ]
}
completeCols - function(x){
x[, colSums(is.na(x)) == 0L]
}
both of which I believe will work for matrices data.frames. With a
little work, one could make them work for regular vectors as well to
have a general solution.
In general, however, you'll need to figure out what the correct
treatment of NA's for your problem is: some functions like lm(), sum()
etc. can deal with NAs so you don't need to pre-change your input.
(Protip: with lm(), I find people almost always prefer na.exclude to
the default na.omit)
Michael
On Wed, Jan 4, 2012 at 6:01 AM, iliketurtles isaacm...@gmail.com wrote:
data-matrix(rnorm(10))
data[c(1,4,6)]-NA
print(data)
data-matrix(data[!is.na(data)])
print(data)
-
Isaac
Research Assistant
Quantitative Finance Faculty, UTS
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and provide commented, minimal, self-contained, reproducible code.
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Adding a vertical line to plot with two overlapping density plots
thank you very much Petr. Yes, I meant densityplot form lattice.
The code I gave plots the densities of both x1 and x2 in one panel.
Could you show me how to integrate the function addline into the code so
that a vertical line v=0 is added?
The function is used after you make a plot.
addLine(v=2)
shall be OK
before you of course need to define the function
addLine - function (a = NULL, b = NULL, v = NULL, h = NULL, ..., once =
FALSE)
{
tcL - trellis.currentLayout()
k - 0
for (i in 1:nrow(tcL)) for (j in 1:ncol(tcL)) if (tcL[i,
j] 0) {
k - k + 1
trellis.focus(panel, j, i, highlight = FALSE)
if (once)
panel.abline(a = a[k], b = b[k], v = v[k], h = h[k],
...)
else panel.abline(a = a, b = b, v = v, h = h, ...)
trellis.unfocus()
}
}
Regards
Petr
On 4 January 2012 15:55, Petr PIKAL petr.pi...@precheza.cz wrote:
Hi
Hi,
A simple question I hope. I wish to add a single vertical line to a
plot
with several density plots.
Here is a simplified example.
thedata - data.frame(x1=rnorm(100,1,1),x2=rnorm(100,3,1)) #create
data
thedata.m-melt(thedata)
densityplot(~value, thedata.m,
groups=variable,auto.key=list(columns=2))
#this gives the two density plots
#
what I wish now is to add a vertical line, for example v=2.
If you mean densityplot from lattice here is a function (addapted from
Gabor Grothendieck's code] which adds arbitrary line(s) into panels. Is
options are similar to abline and once=TRUE means you want different
lines
to different panels.
addLine
function (a = NULL, b = NULL, v = NULL, h = NULL, ..., once = FALSE)
{
tcL - trellis.currentLayout()
k - 0
for (i in 1:nrow(tcL)) for (j in 1:ncol(tcL)) if (tcL[i,
j] 0) {
k - k + 1
trellis.focus(panel, j, i, highlight = FALSE)
if (once)
panel.abline(a = a[k], b = b[k], v = v[k], h = h[k],
...)
else panel.abline(a = a, b = b, v = v, h = h, ...)
trellis.unfocus()
}
}
Regards
Petr
Many thanks,
Josh.
[[alternative HTML version deleted]]
__
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https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] function in R for my exercise
Unfortunately, there's a general no-homework rule because we never
know what your instructor wants you to figure out on your own (though,
a sincere thanks for admitting this was hw rather than trying to trick
us like so many). That said, I think your second function, while a
little clumsy, does work but for one little error near the end. It's
very obvious when you see it so don't overthink it, but look closely
at the lines that involve swap.
If you want to make it more elegant, I'd suggest you look at the
?switch construct: also, to make the swap bit more elegant, think
about how one exchanges variable values in a language like C and put
some construct like that within an if statement near the top. If you
want to get real elegant, note that after you figure out switch,
constructs like `+`(3, 4) are valid in R (though certainly beyond the
scope of your exercise)
Hope this helps,
Michael
On Wed, Jan 4, 2012 at 9:45 AM, Thomthom rime.tho...@gmail.com wrote:
Hi R helpers!
I have a question. I'm trying to create a function for an exercise. Here are
the arguments I should include:
x and y are numeric
z is a name (plus,minus,multiply,divide)
and swap is logical.
Here is what the function should do:
When z=plus, then x+y is performed and so on for the other z names. It
should give a NA when the z argument doesn't correspond to something mention
before.
When swap =TRUE, then y must be on the left side of the equation (y/x
instead of x/y).
So far, I managed to get something worked for the first part of the body
function (typing plus performes indeed an addition...) but I couldn't get
how to make the second part working. Any suggestion?
Here is the code I have so far:
myFunc- function(x,y,z,swap)
{ res= NULL
if(z ==plus) res=x+y
else if(z==minus) res=x-y
else if(z== multiply) res=x*y
else if(z==divide) res=x/y
else res-NA
return(res)}
Then, I tried to include some lines to take this swap function into
account by splitting somehow my function in 2:
myFunc- function(x,y,z,swap)
{ res1= NULL
res2=NULL
if(z ==plus) res1=x+y
else if(z==minus) res1=x-y
else if(z== multiply) res1=x*y
else if(z==divide) res1=x/y
else res1-NA
if(z ==plus) res2=y+x
else if(z==minus) res2=y-x
else if(z== multiply) res2=y*x
else if(z==divide) res2=y/x
else res2-NA
if (swap-T) return(res2)
else return(res1)
}
Any suggestions would be more than appreciated! I already thank you!
And happy new year! (that may be redundant to most of you I know ^^)
Thomas
--
View this message in context:
http://r.789695.n4.nabble.com/function-in-R-for-my-exercise-tp4261710p4261710.html
Sent from the R help mailing list archive at Nabble.com.
__
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and provide commented, minimal, self-contained, reproducible code.
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and provide commented, minimal, self-contained, reproducible code.
[R] putting regression output right on a plot
hi: does anyone know if it's possible and, if so, where there's an example, of putting the output of summary(lm) right on the plot of the data itself. If the answer is to use capture.output and then text, I'll try that but I was thinking there might be an example somewhere ? thanks. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] interaction plot and x axis
Dear all I am trying to make an interaction plot among 6 variables; e.g. PH to be in the x axis and the rest 5 variables in the y axis. The code that I am using is the below: The name of my file is e.g. spec so spec-read.csv(spec.csv) head (spec) str(spec) names-names(spec)[2:6] speclong - reshape(spec, idvar = id, varying = list(names), v.names=outcome,direction = long) speclong$time2-factor(speclong$time,labels=rep( ,5)) interaction.plot(speclong$PH,speclong$time2,speclong$outcome, xaxt=n, type=l, log=y, trace.label=,col=rainbow(8)) what I want is to change the labels of the x axis. If for example I don't use xaxt=n, by default it shows some values of PH e.g. 4.93, 5.97, 6.23, 6.47, 6.59, 6.77, 6.89, 7.35 but it don't show the ticks in each value. However I would like to define the x values e.g. 5.0, 5.5, 6.0, 6.5, 7.0. I used the xlim but it says error as well axis(1, at=c(5.0, 5.5, 6.0, 6.5, 7.0)) but still there is a problem. Does anyone know how I can define that? Thank you in advance. Kind regards Maria [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] KS and AD test for Generalized PAreto and Generalized Extreme value
fExtremes::pgpd pgev have always worked for me. Though, if I remember right, the physical sciences and finance tend to use reciprocal definitions for one of the parameters (can't remember which -- xi in gpd perhaps?) so tread lightly. Michael On Wed, Jan 4, 2012 at 8:21 AM, David Winsemius dwinsem...@comcast.net wrote: On Jan 4, 2012, at 5:49 AM, Vincy Pyne wrote: Dear R helpers, I need to use KS and AD test for Generalized Pareto and Generalized extreme value. When I searched on these names Generalized Pareto and Generalized extreme value I got plenty of hits (over 90 in one case and over 100 in another) You should learn to search with either sos::findFn or with RSiteSearch, -- David. E.g. if I need to use KS for Weibull, I have teh syntax ks.test(x.wei,pweibull, shape=2,scale=1) Similarly, for AD I use ad.test(x, distr.fun, ...) My problem is fir given data, I have estimated the parameters of GPD and GEV using lmom. But I am not able to find out the distribution name I should be use for these distributions if I wish to use these tests. E.g, for gamma, I can use pgamma etc. What distribution name I should use for GPD and GEV and for that matter where can I find the distribution names I can use for KS and AD test. Thanks in advance Regards Vincy [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. David Winsemius, MD West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Warning message about closing a connection XXXX
Re How can I avoid the warning message altogether? ?closeAllConnections I think of calls to closeAllConnections() in the same way that I think of calls to rm(list=objects()): they both can remove things that are not theirs to remove. Calling gc() will close all unused connections, so no damage can be done. (I thought that the warning about closing unused text connections was dropped in a recent release of R so neither is really needed.) Bill Dunlap Spotfire, TIBCO Software wdunlap tibco.com -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of David Winsemius Sent: Wednesday, January 04, 2012 7:10 AM To: Dan Abner Cc: r-help@r-project.org Subject: Re: [R] Warning message about closing a connection On Jan 4, 2012, at 9:53 AM, Dan Abner wrote: Hello everyone, After running the following code, I obtain this error message. mydata - read.table(textConnection(mystring), +header=TRUE, sep=,, +row.names=id, na.strings= ) mydata Warning message: closing unused connection 3 (mystring) = However, when I attempt to run read.table() again and immediately submit the close() function (below), I obtain this message: close(mystring) Error in UseMethod(close) : no applicable method for 'close' applied to an object of class character = How can I avoid the warning message altogether? ?closeAllConnections The error message occurs because mystring was never the connection name. -- David Winsemius, MD West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Finding Source of Error Message of 'Non-Unique Index Entries'
On Tue, 3 Jan 2012, David Winsemius wrote: burns.tds[ !duplicated(burns.tds) , ] Apparently it does not matter if the site column in the data frame is a factor or a character, read.zoo() generates the same error. Applying the above produces a long list starting with: burns.tds[!duplicated(burns.tds), ] site sampdatequant 599 BC-3 1992-03-270.100 600 BC-3 1992-04-300.100 601 BC-3 1992-05-300.100 603 BC-3 1992-06-190.100 1214BC-3 1992-07-200.100 1215BC-3 1992-08-100.100 1216BC-3 1992-09-300.100 1217BC-3 1992-10-290.100 1218BC-3 1992-11-190.100 1929BC-3 1995-03-238.080 I don't know how to interpret this. I don't see two rows with the same values, but ~ 500 rows each with a different value. What is duplicated? The entire row? The site ID? ?duplicated has some examples, but those do not show the output of the function nor explain what's duplicated. I need to get past this blockage and appreciate your help in determining why read.zoo() sees duplicates when the database table has none, and how to resolve this issue. TIA, Rich __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Warning message about closing a connection XXXX
On 04/01/2012 17:12, William Dunlap wrote: Re How can I avoid the warning message altogether? ?closeAllConnections I think of calls to closeAllConnections() in the same way that I think of calls to rm(list=objects()): they both can remove things that are not theirs to remove. Calling gc() will close all unused connections, so no damage can be done. (I thought that the warning about closing unused text connections was dropped in a recent release of R so neither is really needed.) Yes, it was. The warning is there because the user may need to do something about the 'other end' of the now-closed connection, which R manages for textConnections. There is however one circumstance where gc() does not close all unused connections, and that is when gzcon() is used (because that involves two connections and it is not clear when the inner one is 'in use': and we used to guess wrong). Rather than using a sledgehammer, use showConnections(all=TRUE) to see all connections, and close the ones you want to (and its help page shows you how). Bill Dunlap Spotfire, TIBCO Software wdunlap tibco.com -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of David Winsemius Sent: Wednesday, January 04, 2012 7:10 AM To: Dan Abner Cc: r-help@r-project.org Subject: Re: [R] Warning message about closing a connection On Jan 4, 2012, at 9:53 AM, Dan Abner wrote: Hello everyone, After running the following code, I obtain this error message. mydata- read.table(textConnection(mystring), +header=TRUE, sep=,, +row.names=id, na.strings= ) mydata Warning message: closing unused connection 3 (mystring) = However, when I attempt to run read.table() again and immediately submit the close() function (below), I obtain this message: close(mystring) Error in UseMethod(close) : no applicable method for 'close' applied to an object of class character = How can I avoid the warning message altogether? ?closeAllConnections The error message occurs because mystring was never the connection name. -- David Winsemius, MD West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] subscript with comma
On Jan 4, 2012, at 10:51 AM, Uwe Ligges wrote: On 04.01.2012 16:12, suse wrote: Hi, I want to write a word with subscript in a graph. Unfortunately, the subscript contains a comma, so all my trials didn't work and I didn't find how to do it. I want to write sm as normal text and w,grass in the subscript. Can anybody help me? And a more general question: I read the help to plotmath, but I still didn't understand, how it works. Is there a good documentation, book,... which explains all this stuff? I've wondered about that, too. Murrell's text, R Graphics, doesn't even have plotmath in its function list or Index. The insight that allowed me to get a significantly higher frequency of success was realizing that the correct separators between separate expressions were * and ~ rather than space or comma. Inside an expression a comma will signal a new expression element. A space without a plotmath operator intervening just throws an error plot(1, main=expression(sm[w grass])) Error: unexpected symbol in plot(1, main=expression(sm[w grass My suggestion is to search the archive for answers from Ligges, Dalgaard, Lumley and Grothendeick that involve expression or plotmath. (Apologies to any other plotmath-meisters). I still get surprises such as with these: plot(1, main=expression(sm[w|grass])) plot(1, main=expression(sm[w%|%grass])) ?plotmath suggests to use a comma separated list as in: plot(1, main=expression(sm[list(w,grass)])) The other approach that succeeds it just to use a quoted comma connected by valid separators. plot(1, main=expression(sm[w*,~grass])) -- David Winsemius, MD West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Finding Source of Error Message of 'Non-Unique Index Entries'
On Jan 4, 2012, at 12:21 PM, Rich Shepard wrote: On Tue, 3 Jan 2012, David Winsemius wrote: burns.tds[ !duplicated(burns.tds) , ] Apparently it does not matter if the site column in the data frame is a factor or a character, read.zoo() generates the same error. Applying the above produces a long list starting with: burns.tds[!duplicated(burns.tds), ] site sampdatequant 599 BC-3 1992-03-270.100 600 BC-3 1992-04-300.100 601 BC-3 1992-05-300.100 603 BC-3 1992-06-190.100 1214BC-3 1992-07-200.100 1215BC-3 1992-08-100.100 1216BC-3 1992-09-300.100 1217BC-3 1992-10-290.100 1218BC-3 1992-11-190.100 1929BC-3 1995-03-238.080 I don't know how to interpret this. I don't see two rows with the same values, but ~ 500 rows each with a different value. What is duplicated? The entire row? The site ID? You didn't ask for what was duplicated, but rather what was NOT duplicated with that code. In the case of a dataframe it is the entire row that is tested. ?duplicated has some examples, but those do not show the output of the function nor explain what's duplicated. I need to get past this blockage and appreciate your help in determining why read.zoo() sees duplicates when the database table has none, and how to resolve this issue. I think you need to reduce this problem to a dataframe that you either post an access method for or use dput() to include. Then you need to say what you goals are and what code is not working on that example. TIA, Rich __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. David Winsemius, MD West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Warning message about closing a connection XXXX
On 12-01-04 12:25 PM, Prof Brian Ripley wrote: On 04/01/2012 17:12, William Dunlap wrote: Re How can I avoid the warning message altogether? ?closeAllConnections I think of calls to closeAllConnections() in the same way that I think of calls to rm(list=objects()): they both can remove things that are not theirs to remove. Calling gc() will close all unused connections, so no damage can be done. (I thought that the warning about closing unused text connections was dropped in a recent release of R so neither is really needed.) Yes, it was. The warning is there because the user may need to do something about the 'other end' of the now-closed connection, which R manages for textConnections. There is however one circumstance where gc() does not close all unused connections, and that is when gzcon() is used (because that involves two connections and it is not clear when the inner one is 'in use': and we used to guess wrong). Rather than using a sledgehammer, use showConnections(all=TRUE) to see all connections, and close the ones you want to (and its help page shows you how). In older versions that do give the warning, wouldn't it be sufficient to name the textConnection, and close it explicitly? E.g. mydata- read.table(con - textConnection(mystring), header=TRUE, sep=,, row.names=id, na.strings= ) close(con) Duncan Murdoch Bill Dunlap Spotfire, TIBCO Software wdunlap tibco.com -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of David Winsemius Sent: Wednesday, January 04, 2012 7:10 AM To: Dan Abner Cc: r-help@r-project.org Subject: Re: [R] Warning message about closing a connection On Jan 4, 2012, at 9:53 AM, Dan Abner wrote: Hello everyone, After running the following code, I obtain this error message. mydata- read.table(textConnection(mystring), +header=TRUE, sep=,, +row.names=id, na.strings= ) mydata Warning message: closing unused connection 3 (mystring) = However, when I attempt to run read.table() again and immediately submit the close() function (below), I obtain this message: close(mystring) Error in UseMethod(close) : no applicable method for 'close' applied to an object of class character = How can I avoid the warning message altogether? ?closeAllConnections The error message occurs because mystring was never the connection name. -- David Winsemius, MD West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] subscript with comma
-Original Message- From: r-help-boun...@r-project.org [mailto:r-help-bounces@r- project.org] On Behalf Of David Winsemius Sent: Wednesday, January 04, 2012 9:53 AM To: Uwe Ligges Cc: r-help@r-project.org; suse Subject: Re: [R] subscript with comma On Jan 4, 2012, at 10:51 AM, Uwe Ligges wrote: On 04.01.2012 16:12, suse wrote: Hi, I want to write a word with subscript in a graph. Unfortunately, the subscript contains a comma, so all my trials didn't work and I didn't find how to do it. I want to write sm as normal text and w,grass in the subscript. Can anybody help me? And a more general question: I read the help to plotmath, but I still didn't understand, how it works. Is there a good documentation, book,... which explains all this stuff? I've wondered about that, too. Murrell's text, R Graphics, doesn't even have plotmath in its function list or Index. The insight that allowed me to get a significantly higher frequency of success was realizing that the correct separators between separate expressions were * and ~ rather than space or comma. Inside an expression a comma will signal a new expression element. A space without a plotmath operator intervening just throws an error plot(1, main=expression(sm[w grass])) Error: unexpected symbol in plot(1, main=expression(sm[w grass My suggestion is to search the archive for answers from Ligges, Dalgaard, Lumley and Grothendeick that involve expression or plotmath. (Apologies to any other plotmath-meisters). I still get surprises such as with these: plot(1, main=expression(sm[w|grass])) plot(1, main=expression(sm[w%|%grass])) ?plotmath suggests to use a comma separated list as in: plot(1, main=expression(sm[list(w,grass)])) The other approach that succeeds it just to use a quoted comma connected by valid separators. plot(1, main=expression(sm[w*,~grass])) -- David Winsemius, MD West Hartford, CT I haven't followed this whole thread and may have missed some requirement, but what about just using the text string that you want in the subscript? E.g. plot(1, main=expression(sm['w,grass'])) Hope this is helpful, Dan Daniel J. Nordlund Washington State Department of Social and Health Services Planning, Performance, and Accountability Research and Data Analysis Division Olympia, WA 98504-5204 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Warning message about closing a connection XXXX
On 04/01/2012 18:21, Duncan Murdoch wrote: On 12-01-04 12:25 PM, Prof Brian Ripley wrote: On 04/01/2012 17:12, William Dunlap wrote: Re How can I avoid the warning message altogether? ?closeAllConnections I think of calls to closeAllConnections() in the same way that I think of calls to rm(list=objects()): they both can remove things that are not theirs to remove. Calling gc() will close all unused connections, so no damage can be done. (I thought that the warning about closing unused text connections was dropped in a recent release of R so neither is really needed.) Yes, it was. The warning is there because the user may need to do something about the 'other end' of the now-closed connection, which R manages for textConnections. There is however one circumstance where gc() does not close all unused connections, and that is when gzcon() is used (because that involves two connections and it is not clear when the inner one is 'in use': and we used to guess wrong). Rather than using a sledgehammer, use showConnections(all=TRUE) to see all connections, and close the ones you want to (and its help page shows you how). In older versions that do give the warning, wouldn't it be sufficient to name the textConnection, and close it explicitly? E.g. mydata- read.table(con - textConnection(mystring), header=TRUE, sep=,, row.names=id, na.strings= ) close(con) Yes, but you cannot do that retrospectively. I would say this is still good practice. Duncan Murdoch Bill Dunlap Spotfire, TIBCO Software wdunlap tibco.com -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of David Winsemius Sent: Wednesday, January 04, 2012 7:10 AM To: Dan Abner Cc: r-help@r-project.org Subject: Re: [R] Warning message about closing a connection On Jan 4, 2012, at 9:53 AM, Dan Abner wrote: Hello everyone, After running the following code, I obtain this error message. mydata- read.table(textConnection(mystring), + header=TRUE, sep=,, + row.names=id, na.strings= ) mydata Warning message: closing unused connection 3 (mystring) = However, when I attempt to run read.table() again and immediately submit the close() function (below), I obtain this message: close(mystring) Error in UseMethod(close) : no applicable method for 'close' applied to an object of class character = How can I avoid the warning message altogether? ?closeAllConnections The error message occurs because mystring was never the connection name. -- David Winsemius, MD West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Is using glht with Tukey for lme post-hoc comparisons an appropriate substitute to TukeyHSD?
Anne,
Thank you for writing back, and for including your data.
I have two things here. First, I ran an a analysis of your data and have
my observations
on interpretation. Second, I answer your general question about glht and
TukeyHSD when there are interactions.
I illustrate how to get the same answer from glht with an example from your
data.
## install.packages(HH) ## if you do not already have it
library(HH)
Active - read.table(textConnection(
Treatment HabitatpActive
1G E 0.18541667
1G E 0.0250
1G E 0.04208333
1G E 0.14847222
1G E 0.0806
1G E 0.1678
1G S 0.0511
1G S 0.1908
1G S 0.1233
1G S 0.3572
1G S 0.4375
1G S 0.02638889
1R E 0.38736111
1R E 0.51180556
1R E 0.14916667
1R E 0.61041667
1R E 0.36013889
1R E 0.11347222
1R S 0.10805556
1R S 0.1872
1R S 0.27625000
1R S 0.25236111
1R S 0.18208333
1R S 0.16152778
2G E 0.25916667
2G E 0.3719
2G E 0.02263889
2G E 0.18402778
2G E 0.4575
2G E 0.0225
2G S 0.02958333
2G S 0.10069444
2G S 0.12875000
2G S 0.1136
2G S 0.13680556
2G S 0.07875000
2R E 0.57513889
2R E 0.1289
2R E 0.3200
2R E 0.55736111
2R E 0.7889
2R E 0.6506
2R S 0.35527778
2R S 0.4836
2R S 0.2136
2R S 0.3528
2R S 0.5261
2R S 0.29416667
R+G E 0.37027778
R+G E 0.20263889
R+G E 0.0719
R+G E 0.49041667
R+G E 0.21847222
R+G E 0.1356
R+G S 0.2086
R+G S 0.23986111
R+G S 0.02180556
R+G S 0.2325
R+G S 0.28916667
R+G S 0.50208333
), header=TRUE)
## close.connection()
closeAllConnections()
logitAct - logit(Active$pActive)
model3 - aov(logitAct ~ Treatment*Habitat, data=Active)
summary(model3)
summary(glht(model3, focus=Treatment, linfct=mcp(Treatment=Tukey)))
TukeyHSD(model3)
with(Active, table(Treatment, Habitat))
par(omd=c(0, .95, 0, 1))
model3.mmc - glht.mmc(model3, linfct=mcp(Treatment=Tukey))
plot(model3.mmc, ry=c(-2.75, 0.25), x.offset=.8)
plot.matchMMC(model3.mmc$mca)
## 1G 1R 2G 2R R+G
R.linear - c(-1, 0, -1, 2, 0 )
names(R.linear) - c('1G', '1R', '2G', '2R', 'R+G')
lmat.R - orthog.complete(as.matrix(R.linear))
dimnames(lmat.R)[[2]][1] - R.linear
model3.mmc - glht.mmc(model3, linfct=mcp(Treatment=Tukey),
focus.lmat=lmat.R)
plot(model3.mmc, ry=c(-2.75, 0.25), x.offset=.8)
plot.matchMMC(model3.mmc$lmat, col.signif=blue)
Active$Treatment - factor(Active$Treatment, levels=c('1G', '2G', 'R+G',
'1R', '2R'))
contrasts(Active$Treatment) - lmat.R[c('1G', '2G', 'R+G', '1R', '2R'),]
model3g - aov(logitAct ~ Treatment*Habitat, data=Active)
summary(model3g, split=list(Treatment=list(R.linear=1, rest=2:4)),
expand.split=FALSE)
position(Active$Habitat) - c(2, 4)
interaction2wt(logitAct ~ Treatment*Habitat, data=Active)
## from the above tables and graphs, it looks like the only thing
## going on in the data you posted is the linear effect of R.
## On your questions on glht and TukeyHSD.
## Without interactions or covariates they give the same answer.
## With interactions or covariates the default for glht is to give
different answers.
## The output from glht includes a warning to that effect.
##
## From ?glht
## Warning message:
## In mcp2matrix(model, linfct = linfct) :
## covariate interactions found -- default contrast might be inappropriate
##
## From ?glht, read about the interaction_average argument.
## With the glht argument interaction_average=TRUE, they give the same
answer
## With your example,
summary(glht(model3, linfct=mcp(Treatment=Tukey,
interaction_average=TRUE)))
TukeyHSD(model3, which=Treatment)
Rich
On Tue, Jan 3, 2012 at 7:26 PM, Anne Aubut an438...@dal.ca wrote:
Hello Richard,
Thank you so much for getting back to me. In the ?glht example, the
confidence intervals are the same and the p-values are very similar. I ran
a 2-way ANOVA and compared the results for the glht code with Tukey and
TukeyHSD for Treatment, which was a significant main effect (output is
below). I found that the p-values for glht and TukeyHSD differed quite a
bit. If glht with Tukey is just another method to run Tukey HSD, I don't
understand why the two methods yeilded different results. If they are not
equivalent, how is glht calculating the p-values? I also ran my 2-way
ANOVA without the Treatment*Habitat interaction and I found that the glht
and TukeyHSD methods did
Re: [R] Finding Source of Error Message of 'Non-Unique Index Entries'
On Wed, 4 Jan 2012, David Winsemius wrote: You didn't ask for what was duplicated, but rather what was NOT duplicated with that code. In the case of a dataframe it is the entire row that is tested. My original question was what was duplicated, but ... I changed the function by dropping the 'not'. There's something seriously wrong here and I need help from R gurus to tell me why. Example: burns.tds[duplicated(burns.tds), ] ... 25760 BC-1.5 1996-09-19 NA 25761 BC-1.5 1996-09-19 0.010 ... But, when I query the database table I see this: select * from chemistry where site = 'BC-1.5' and sampdate = '1996-09-19' and param = 'TDS'; site | sampdate | param | quant | units | qual | easting | northing | stream | basin ++---+---+---+--+-+--+- -+ BC-1.5 | 1996-09-19 | TDS | 935 | mg/L | | | | BurnsCrk | (1 row) There is only a single row for that site, sampdate, and parameter and the quantity is different from those in the R data frame. I think you need to reduce this problem to a dataframe that you either post an access method for or use dput() to include. Then you need to say what you goals are and what code is not working on that example. I'll gladly do this. Which data frame should I make available: the original chemdata or the subset burns.tds? I'll start with the latter. Compressed dput() output attached. My goal is to produce time series plots of TDS, by site, on several streams over the period for which that component was measured. Lattice lets me superpose multiple lines on the same axis set with different color lines and a legend. What's not working is something in the workflow of subsettiong chemdata to extract all TDS data for a named stream (e.g., burns.tds and winters.tds), then convert them to zoo objects using read.zoo(). Somewhere along this process my data are being mangled. It's not in the source data frame, chemdata: chemdata[duplicated(chemdata), ] [1] site sampdate paramquantunitsqual easting northing [9] stream basin 0 rows (or 0-length row.names) The command I used to subset burns.tds from chemdata was: burns.tds - subset(chemdata, stream == 'BurnsCrk', select = c(site, sampdate, param == 'TDS', quant), drop = T) Thanks, David, Rich __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Adding a vertical line to plot with two overlapping density plots
That works, but if all you want is one vertical line at 0, this will work
densityplot(~value, thedata.m, groups=variable,auto.key=list(columns=2),
panel = function(x, y, ...) {
panel.densityplot(x, ...)
panel.abline(v=0)
}
)
--
David L Carlson
Associate Professor of Anthropology
Texas AM University
College Station, TX 77843-4352
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf Of Petr PIKAL
Sent: Wednesday, January 04, 2012 10:27 AM
To: josh rosen
Cc: r-help@r-project.org
Subject: Re: [R] Adding a vertical line to plot with two overlapping density
plots
thank you very much Petr. Yes, I meant densityplot form lattice.
The code I gave plots the densities of both x1 and x2 in one panel.
Could you show me how to integrate the function addline into the code so
that a vertical line v=0 is added?
The function is used after you make a plot.
addLine(v=2)
shall be OK
before you of course need to define the function
addLine - function (a = NULL, b = NULL, v = NULL, h = NULL, ..., once =
FALSE)
{
tcL - trellis.currentLayout()
k - 0
for (i in 1:nrow(tcL)) for (j in 1:ncol(tcL)) if (tcL[i,
j] 0) {
k - k + 1
trellis.focus(panel, j, i, highlight = FALSE)
if (once)
panel.abline(a = a[k], b = b[k], v = v[k], h = h[k],
...)
else panel.abline(a = a, b = b, v = v, h = h, ...)
trellis.unfocus()
}
}
Regards
Petr
On 4 January 2012 15:55, Petr PIKAL petr.pi...@precheza.cz wrote:
Hi
Hi,
A simple question I hope. I wish to add a single vertical line to a
plot
with several density plots.
Here is a simplified example.
thedata - data.frame(x1=rnorm(100,1,1),x2=rnorm(100,3,1)) #create
data
thedata.m-melt(thedata)
densityplot(~value, thedata.m,
groups=variable,auto.key=list(columns=2))
#this gives the two density plots
#
what I wish now is to add a vertical line, for example v=2.
If you mean densityplot from lattice here is a function (addapted from
Gabor Grothendieck's code] which adds arbitrary line(s) into panels. Is
options are similar to abline and once=TRUE means you want different
lines
to different panels.
addLine
function (a = NULL, b = NULL, v = NULL, h = NULL, ..., once = FALSE)
{
tcL - trellis.currentLayout()
k - 0
for (i in 1:nrow(tcL)) for (j in 1:ncol(tcL)) if (tcL[i,
j] 0) {
k - k + 1
trellis.focus(panel, j, i, highlight = FALSE)
if (once)
panel.abline(a = a[k], b = b[k], v = v[k], h = h[k],
...)
else panel.abline(a = a, b = b, v = v, h = h, ...)
trellis.unfocus()
}
}
Regards
Petr
Many thanks,
Josh.
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http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Warning message about closing a connection XXXX
On Jan 4, 2012, at 19:21 , Duncan Murdoch wrote: On 12-01-04 12:25 PM, Prof Brian Ripley wrote: Rather than using a sledgehammer, use showConnections(all=TRUE) to see all connections, and close the ones you want to (and its help page shows you how). In older versions that do give the warning, wouldn't it be sufficient to name the textConnection, and close it explicitly? E.g. mydata- read.table(con - textConnection(mystring), header=TRUE, sep=,, row.names=id, na.strings= ) close(con) Or, in recent versions, use the tools designed for the purpose and do mydata - read.table(text=mystring, ) -- Peter Dalgaard, Professor, Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Email: pd@cbs.dk Priv: pda...@gmail.com __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Finding Source of Error Message of 'Non-Unique Index Entries'
Nothing attached. I don't know what you entitled teh compressed dput output but it did not pass the filters of the mailserver and you did not copy me. If chemdata is available as a text file, hten make sure its extension is .txt and then attach it. -- David. On Jan 4, 2012, at 1:31 PM, Rich Shepard wrote: On Wed, 4 Jan 2012, David Winsemius wrote: You didn't ask for what was duplicated, but rather what was NOT duplicated with that code. In the case of a dataframe it is the entire row that is tested. My original question was what was duplicated, but ... I changed the function by dropping the 'not'. There's something seriously wrong here and I need help from R gurus to tell me why. Example: burns.tds[duplicated(burns.tds), ] ... 25760 BC-1.5 1996-09-19 NA 25761 BC-1.5 1996-09-19 0.010 ... But, when I query the database table I see this: select * from chemistry where site = 'BC-1.5' and sampdate = '1996-09-19' and param = 'TDS'; site | sampdate | param | quant | units | qual | easting | northing | stream | basin ++---+---+---+-- +-+--+- -+ BC-1.5 | 1996-09-19 | TDS | 935 | mg/L | | | | BurnsCrk | (1 row) There is only a single row for that site, sampdate, and parameter and the quantity is different from those in the R data frame. I think you need to reduce this problem to a dataframe that you either post an access method for or use dput() to include. Then you need to say what you goals are and what code is not working on that example. I'll gladly do this. Which data frame should I make available: the original chemdata or the subset burns.tds? I'll start with the latter. Compressed dput() output attached. My goal is to produce time series plots of TDS, by site, on several streams over the period for which that component was measured. Lattice lets me superpose multiple lines on the same axis set with different color lines and a legend. What's not working is something in the workflow of subsettiong chemdata to extract all TDS data for a named stream (e.g., burns.tds and winters.tds), then convert them to zoo objects using read.zoo(). Somewhere along this process my data are being mangled. It's not in the source data frame, chemdata: chemdata[duplicated(chemdata), ] [1] site sampdate paramquantunitsqual easting northing [9] stream basin 0 rows (or 0-length row.names) The command I used to subset burns.tds from chemdata was: burns.tds - subset(chemdata, stream == 'BurnsCrk', select = c(site, sampdate, param == 'TDS', quant), drop = T) Thanks, David, Rich __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. David Winsemius, MD West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Using a mathematical expression in sapply() XXXX
On Jan 4, 2012, at 16:32 , David Winsemius wrote: On Jan 4, 2012, at 9:17 AM, peter dalgaard wrote: On Jan 4, 2012, at 14:57 , Milan Bouchet-Valat wrote: Le mercredi 04 janvier 2012 à 08:41 -0500, Dan Abner a écrit : Hello everyone, I have the following call to sapply() and error message. Is the most efficient way to deal with this to make sum(!is.na(x)) a function in a separate line prior to this call? If not, please advise. N.Valid=sapply(x,sum(!is.na(x))) Error in match.fun(FUN) : 'sum(!is.na(x))' is not a function, character or symbol You can use this: sapply(x, function(x) sum(!is.na(x))) But, if you can convert x to a matrix, it would be faster and shorter to check for NAs beforehand, and use apply(): x - matrix(c(1, 2, NA, 3, NA, 4), 2) apply(!is.na(x), 2, sum) Just for completeness: You might also do sapply(lapply(x, is.na), sum) I thought from context that the sum of negation of is.na was what was desired, since the negation operator was used and the name of the results was N.Valid. Oops. Yes. So consider substituting the existing function, complete.cases in place of is.na: sapply(lapply(x, complete.cases), sum) Yes. I suppose Negate(is.na) would just be being silly. Unless x is a list of data frames or something... Picking up on Milan's note, notice that if x is a data frame, then conversion to matrix is automatic and, e.g. apply(!is.na(airquality), 2, sum) Ozone Solar.RWindTemp Month Day 116 146 153 153 153 153 works fine. -- Peter Dalgaard, Professor, Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Email: pd@cbs.dk Priv: pda...@gmail.com __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Finding Source of Error Message of 'Non-Unique Index Entries' [FIXED]
On Wed, 4 Jan 2012, David Winsemius wrote: Nothing attached. I don't know what you entitled teh compressed dput output but it did not pass the filters of the mailserver and you did not copy me. David, It must have been stripped off as too large (14K). Regardless, I solved the problem: The examples in the subset help page show only a single row criterion being used, but does not explicitly note that rows can be selected only one criterion at a time. Because the issue showed up only with the subset() function to extract rows with the parameter TDS, the problem had to be in that syntax. By changing the data frame argument to subset() from the overall chemdata to that of only a single stream, creation of the zoo object threw no errors and duplicated() returned zero rows. Wow! And I thought I understood the subset() syntax. I now do! Thanks to you, Gabor, and everyone else who responded to this thread, Rich __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Finding Source of Error Message of 'Non-Unique Index Entries' [FIXED]
On Jan 4, 2012, at 3:21 PM, Rich Shepard wrote: On Wed, 4 Jan 2012, David Winsemius wrote: Nothing attached. I don't know what you entitled teh compressed dput output but it did not pass the filters of the mailserver and you did not copy me. David, It must have been stripped off as too large (14K). Regardless, I solved the problem: The examples in the subset help page show only a single row criterion being used, but does not explicitly note that rows can be selected only one criterion at a time. Because that is simply not true. Connect your criteria with ampersands and you can have as many as you want. The only requirement is that the logical vector that results be exactly the number of rows in the dataframe as described in the help page. Because the issue showed up only with the subset() function to extract rows with the parameter TDS, the problem had to be in that syntax. By changing the data frame argument to subset() from the overall chemdata to that of only a single stream, creation of the zoo object threw no errors and duplicated() returned zero rows. Wow! And I thought I understood the subset() syntax. I now do! Thanks to you, Gabor, and everyone else who responded to this thread, Rich __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. David Winsemius, MD West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Passing multiple arguments to a function through sapply() XXXX
Hello everyone,
How does one pass multiple arguments of a user defined function to that
function when called within sapply()?
I have the following:
myna-function(x,miss.val) {x[x %in% miss.val]-NA;x}
mydataNA3-sapply(mydataNA,c(x=myna,miss.val=c(9,99)))
Error in match.fun(FUN) :
'c(x = myna, miss.val = c(9, 99))' is not a function, character or symbol
mydataNA3
Thanks!
Dan
[[alternative HTML version deleted]]
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Re: [R] Passing multiple arguments to a function through sapply() XXXX
On Jan 4, 2012, at 3:47 PM, Dan Abner wrote:
Hello everyone,
How does one pass multiple arguments of a user defined function to
that
function when called within sapply()?
I have the following:
myna-function(x,miss.val) {x[x %in% miss.val]-NA;x}
mydataNA3-sapply(mydataNA,c(x=myna,miss.val=c(9,99)))
Error in match.fun(FUN) :
'c(x = myna, miss.val = c(9, 99))' is not a function, character or
symbol
mydataNA3
In the absence of test data this is a guess:
mydataNA3-sapply(mydataNA, myna, miss.val=c(9,99) )
--
David Winsemius, MD
West Hartford, CT
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Re: [R] putting regression output right on a plot
On Jan 4, 2012, at 11:30 AM, Mark Leeds wrote: hi: does anyone know if it's possible and, if so, where there's an example, of putting the output of summary(lm) right on the plot of the data itself. If the answer is to use capture.output and then text, I'll try that but I was thinking there might be an example somewhere ? thanks. http://finzi.psych.upenn.edu/R/library/gplots/html/sinkplot.html http://finzi.psych.upenn.edu/R/library/gtools/html/capture.html [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. David Winsemius, MD West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Warning message about closing a connection XXXX
On 01/04/2012 09:25 AM, Prof Brian Ripley wrote:
On 04/01/2012 17:12, William Dunlap wrote:
Re
How can I avoid the warning message altogether?
?closeAllConnections
I think of calls to closeAllConnections() in the same
way that I think of calls to rm(list=objects()):
they both can remove things that are not theirs to remove.
Calling gc() will close all unused connections, so
no damage can be done. (I thought that the warning
about closing unused text connections was dropped in
a recent release of R so neither is really needed.)
Yes, it was. The warning is there because the user may need to do
something about the 'other end' of the now-closed connection, which R
manages for textConnections.
There is however one circumstance where gc() does not close all unused
connections, and that is when gzcon() is used (because that involves two
connections and it is not clear when the inner one is 'in use': and we
used to guess wrong).
Rather than using a sledgehammer, use showConnections(all=TRUE) to see
all connections, and close the ones you want to (and its help page shows
you how).
Since connections are using R's finalizers, and order of evaluation of
finalizers are not reliable, it is not always possible to get in front
of the automatic close, e.g., when a reference class relies on a
finalize method to tidy up after itself (perhaps this was also the case
with gzcon?).
setOldClass(c(file, connection))
setRefClass(A, fields=list(x=file),
methods=list(initialize=function(fname, ...) {
callSuper(x=file(fname, r))
}, finalize=function() {
## This sometimes provokes an error
close(.self$x)
}))
getRefClass(A)$new(/tmp)
A desirable feature would allow the message or automatic close to be
silenced, or the potentially closed connection to be queried for its
validity.
Martin
Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com
-Original Message-
From: r-help-boun...@r-project.org
[mailto:r-help-boun...@r-project.org] On Behalf Of David Winsemius
Sent: Wednesday, January 04, 2012 7:10 AM
To: Dan Abner
Cc: r-help@r-project.org
Subject: Re: [R] Warning message about closing a connection
On Jan 4, 2012, at 9:53 AM, Dan Abner wrote:
Hello everyone,
After running the following code, I obtain this error message.
mydata- read.table(textConnection(mystring),
+ header=TRUE, sep=,,
+ row.names=id, na.strings= )
mydata
Warning message:
closing unused connection 3 (mystring)
=
However, when I attempt to run read.table() again and immediately
submit
the close() function (below), I obtain this message:
close(mystring)
Error in UseMethod(close) :
no applicable method for 'close' applied to an object of class
character
=
How can I avoid the warning message altogether?
?closeAllConnections
The error message occurs because mystring was never the connection
name.
--
David Winsemius, MD
West Hartford, CT
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--
Computational Biology
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
Location: M1-B861
Telephone: 206 667-2793
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[R] [newbie] stack operations, or functions with side effects (or both)
summary: Specifically, how does one do stack/FIFO operations in R?
Generally, how does one code functions with side effects in R?
details:
I have been a coder for years, mostly using C-like semantics (e.g.,
Java). I am now trying to become a scientist, and to use R, but I don't
yet have the sense of good R and R idiom (i.e., expressions that are
to R what (e.g.) the Schwartzian transform is to Perl).
I have a data-assimilation problem for which I see a solution that
wants a stack--or, really, just a pop(...) such that
* s - c(1:5)
* print(s)
[1] 1 2 3 4 5
* pop(s)
[1] 1
* print(s)
[1] 2 3 4 5
but in fact I get
pop(s)
Error: could not find function pop
and Rseek'ing finds me nothing. When I try to write pop(...) I get
pop1 - function(vector_arg) {
+ length(vector_arg) - lv
+ vector_arg[1] - ret
+ vector_arg - vector_arg[2:lv]
+ ret
+ }
pop1(s)
[1] 1
print(s)
[1] 1 2 3 4 5
i.e., no side effect on the argument
pop2 - function(vector_arg) {
+ length(vector_arg) - lv
+ vector_arg[1] - ret
+ assign(vector_arg, vector_arg[2:lv])
+ return(ret)
+ }
pop2(s)
[1] 1
print(s)
[1] 1 2 3 4 5
ditto :-( What am I missing?
* Is there already a stack API for R (which I would expect)? If so, where?
* How to cause the desired side effect to the argument in the code above?
TIA, Tom Roche tom_ro...@pobox.com
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Re: [R] [newbie] stack operations, or functions with side effects (or both)
do s[1] and s[-1] do what you're looking for?
those are just to display... if you want to change s, you need to reassign
it or fiddle with namespacing. however, I'd say it is better to write R
code as though data structures are immutable until you explicitly re-assign
them rather than trying to deal with side effects and state...
pop - function(vec){
+ print(vec[1])
+ print(vec[-1])
+ return(vec[-1])
+}
s - 1:5
s - pop(s)
[1] 1
[1] 2 3 4 5
s
[1] 2 3 4 5
On Wed, Jan 4, 2012 at 1:22 PM, Tom Roche tom_ro...@pobox.com wrote:
summary: Specifically, how does one do stack/FIFO operations in R?
Generally, how does one code functions with side effects in R?
details:
I have been a coder for years, mostly using C-like semantics (e.g.,
Java). I am now trying to become a scientist, and to use R, but I don't
yet have the sense of good R and R idiom (i.e., expressions that are
to R what (e.g.) the Schwartzian transform is to Perl).
I have a data-assimilation problem for which I see a solution that
wants a stack--or, really, just a pop(...) such that
* s - c(1:5)
* print(s)
[1] 1 2 3 4 5
* pop(s)
[1] 1
* print(s)
[1] 2 3 4 5
but in fact I get
pop(s)
Error: could not find function pop
and Rseek'ing finds me nothing. When I try to write pop(...) I get
pop1 - function(vector_arg) {
+ length(vector_arg) - lv
+ vector_arg[1] - ret
+ vector_arg - vector_arg[2:lv]
+ ret
+ }
pop1(s)
[1] 1
print(s)
[1] 1 2 3 4 5
i.e., no side effect on the argument
pop2 - function(vector_arg) {
+ length(vector_arg) - lv
+ vector_arg[1] - ret
+ assign(vector_arg, vector_arg[2:lv])
+ return(ret)
+ }
pop2(s)
[1] 1
print(s)
[1] 1 2 3 4 5
ditto :-( What am I missing?
* Is there already a stack API for R (which I would expect)? If so, where?
* How to cause the desired side effect to the argument in the code above?
TIA, Tom Roche tom_ro...@pobox.com
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Re: [R] tcltk on linux/rhel6
Brian, FYI, I had previously installed tcl-devel but had overlooked tk-devel on the OS. Now that I've installed tk-devel on the OS, the following sequence of commands has succeeded: sudo ./configure --with-tcltk sudo make sudo make check sudo make install R ... library(tcltk) Loading Tcl/Tk interface ... done Thanks for your suggestions. Best, CB On Wed, Jan 4, 2012 at 3:40 AM, Prof Brian Ripley rip...@stats.ox.ac.uk wrote: On 04/01/2012 01:52, Peter Langfelder wrote: On Tue, Jan 3, 2012 at 4:03 PM, Carl Baribaultcrlbr...@gmail.com wrote: Dear All, I've seen posts to the effect that.. 1) choose.dir is only available for windows, and 2) tk_choose.dir would be the linux equivalent. I'm still having trouble with the subject package on linux/rhel6. I've specified --with-tcltk during ./configure, and I still get the response... install.packages(tcltk) My understanding is that tcltk is included in the base installation now. You should be able to load it using library(tcltk) without explicitly installing it. You can install tcltk2 as an add-on package. Yes, but you need OS support (for both). Whoever installed this R needs to read the R-admin manual and note the need for -devel RPMs for Tcl and Tk. Then study the configure messages which tell you if tcltk was built. -- Brian D. Ripley, rip...@stats.ox.ac.uk 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, UK Fax: +44 1865 272595 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] calculate quantiles of a custom function
Am Dienstag, 3. Januar 2012, 19:51:36 schrieb Prof. Dr. Matthias Kohl:
D - AbscontDistribution(d = function(x) dbeta(x, 2, 6) + dbeta(x,6,2),
low = 0, up = 1, withStand = TRUE)
Dear all,
thank you all again for your help.
So, summing up, (in case this might be useful to other beginners - like me)
this is how it can be done:
library(distr)
dcustom - function(x) {
(dbeta(x,2,6) + dbeta(x,6,2))/2# I need to divide by 2 to get 1 as
# result of
integration;
}
pcustom - function(x) {
integrate(dmyspeaker,0,x)$value
}
D - AbscontDistribution(d = dcustom, low = 0, up = 1, withStand = TRUE)
qcustom - function(x){
q(D)(x)
}
Best,
Gerhard
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[R] problem on plotting ts data
Hi, i try to plot ts data on x-y coordiante I want my data to be points, but somehow it always comes out with lines and # linked bwtween data, i used plot(lag(x,-9),y,type=p), x and y are time series data is there anyway to remove those lines? Thanks a lot -- View this message in context: http://r.789695.n4.nabble.com/problem-on-plotting-ts-data-tp4261865p4261865.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Combining characters
Hi all, I'm trying to combine exhaustively several character arrays in R like: x=c(one,two,three) y=c(yellow,blue,green) z=c(apple,cheese) in order to get concatenation of x[1] y[1] z[1] (one yellow apple) x[1] y[1] z[2] (one yellow cheese) x[1] y[2] z[1](one blue apple) ... x[length(x)] y[length(y)] z[length(z)] (three green cheese) Anyone has a solution ? Thank in advance -- View this message in context: http://r.789695.n4.nabble.com/Combining-characters-tp4261888p4261888.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Symbols in graph
Hi, Is there an easy way to add symbols to a line in a scatter plot, so that only a few symbols are added per line (a line drawn based on a large set of data points) , in order to distinguish several lines in one graph (not a symbol for each data point as is the default in plot()). Thanks a lot! Rgds, Yvonne [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] subscript with comma
Thank you! It works now. But I still don't understand, how all these expressions, , paste, group, eval... have to be used together. (For example, I first tried expression(sm[w,grass]) but it didn't work, and I couldn't find, why (and when) commas are interpreted here differently). So: Is there somewhere an introduction (rather than examples) to this? Books, documents etc. -- View this message in context: http://r.789695.n4.nabble.com/subscript-with-comma-tp4261579p4261931.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] problem on plotting ts data
thanks, it works! -- View this message in context: http://r.789695.n4.nabble.com/problem-on-plotting-ts-data-tp4261865p4262179.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] problem on plotting ts data
Hello, Try 'as.vector' or 'as.numeric' x - as.ts(rnorm(20)) y - as.ts(rnorm(20)) plot(x) plot(as.vector(lag(x,-9)),as.vector(y),type=p) # works plot(as.numeric(lag(x,-9)),as.numeric(y),type=p) # also works Rui Barradas -- View this message in context: http://r.789695.n4.nabble.com/problem-on-plotting-ts-data-tp4261865p4262106.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] function in R for my exercise
Hi Michael,
Thanks for your answer! sorry I didn't see this rule... No problem,
I'll try to figure it out by myself.
Thanks for your indication though!
Thomas
2012/1/4, Michael Weylandt [via R] ml-node+s789695n4261894...@n4.nabble.com:
Unfortunately, there's a general no-homework rule because we never
know what your instructor wants you to figure out on your own (though,
a sincere thanks for admitting this was hw rather than trying to trick
us like so many). That said, I think your second function, while a
little clumsy, does work but for one little error near the end. It's
very obvious when you see it so don't overthink it, but look closely
at the lines that involve swap.
If you want to make it more elegant, I'd suggest you look at the
?switch construct: also, to make the swap bit more elegant, think
about how one exchanges variable values in a language like C and put
some construct like that within an if statement near the top. If you
want to get real elegant, note that after you figure out switch,
constructs like `+`(3, 4) are valid in R (though certainly beyond the
scope of your exercise)
Hope this helps,
Michael
On Wed, Jan 4, 2012 at 9:45 AM, Thomthom rime.tho...@gmail.com wrote:
Hi R helpers!
I have a question. I'm trying to create a function for an exercise. Here
are
the arguments I should include:
x and y are numeric
z is a name (plus,minus,multiply,divide)
and swap is logical.
Here is what the function should do:
When z=plus, then x+y is performed and so on for the other z names. It
should give a NA when the z argument doesn't correspond to something
mention
before.
When swap =TRUE, then y must be on the left side of the equation (y/x
instead of x/y).
So far, I managed to get something worked for the first part of the body
function (typing plus performes indeed an addition...) but I couldn't
get
how to make the second part working. Any suggestion?
Here is the code I have so far:
myFunc- function(x,y,z,swap)
        { res= NULL
         if(z ==plus) res=x+y
         else if(z==minus) res=x-y
         else if(z== multiply) res=x*y
         else if(z==divide) res=x/y
         else res-NA
         return(res)}
Then, I tried to include some lines to take this swap function into
account by splitting somehow my function in 2:
myFunc- function(x,y,z,swap)
        { res1= NULL
         res2=NULL
         if(z ==plus) res1=x+y
         else if(z==minus) res1=x-y
         else if(z== multiply) res1=x*y
         else if(z==divide) res1=x/y
         else res1-NA
         if(z ==plus) res2=y+x
         else if(z==minus) res2=y-x
         else if(z== multiply) res2=y*x
         else if(z==divide) res2=y/x
         else res2-NA
         if (swap-T) return(res2)
         else return(res1)
       }
Any suggestions would be more than appreciated! I already thank you!
And happy new year! (that may be redundant to most of you I know ^^)
Thomas
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[R] plot rq lm
Dear Community, I'd like to plot an rq object the same way I do with a lm one, is it possible? Something like this plot(rqmodel , 1:4, id.labels=rownames(pga1)); where rqmodel - rq(log(vd) ~ v1 + log(v2) +log(v3) + v4 + v5 ,data =dat) Thanks in advance and apologies, I'm pretty newbie with this, u...@host.com -- View this message in context: http://r.789695.n4.nabble.com/plot-rq-lm-tp4262170p4262170.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Options for generating editable figures?
Thank you for the advice; this is very helpful. I will see how they feel about installing Inkscape. I'll also work on getting R installed in a Windows environment so I can produce .emf and .wmf files. I found one old message on this list from someone who had luck doing this by running R with Wine. (When you say you mostly give them graphs in .wmf or .emf, I'm assuming you have a Windows machine? If I'm wrong and you have some other way of producing these files, please let me know. I almost got pstoedit/libemf working through MacPorts, but it messes up the line widths and characters pretty bad.) Thanks, --Allen On 1/3/12 12:47 PM, Greg Snow wrote: I have had clients who also wanted to make little changes to the graphs (mostly changing colors or line widths). Most after doing this a couple of times have been happy to give be better descriptions of what they want so I can just do it correctly the first time. I mostly give them the graphs in .wmf or .emf format, however I have found that if I create the file and send it to them, most have problems getting it into word or power point, instead I usually copy and paste it into a word document and send the word document to them, they can then copy and paste from there to their presentation or report. Of course this is only an option if you have MS word on the same computer as you are working on. With those files double clicking takes the user into a basic editor where they can change colors, line widths, etc. However, sometimes opening that editor will redo all the text, so what started as changing one line color also requires them to re orient all the axis and tick labels. Inkscape is a much more capable program for doing these kinds of edits, and for basic editing it is fairly straight forward, so for your description of options below, I would suggest that you make them learn Inkscape if they really want to edit the graphs themselves. Inkscape can also import pdf files (though it is an import rather than a simple open and you often need to ungroup a bunch of objects before editing them) so that may be another option for you. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Combining characters
Hello, If you want to apply the same procedure to all elements of an object, check out the '*apply' functions. In this case, x=c(one,two,three) y=c(yellow,blue,green) z=c(apple,cheese) lapply(x, function(x) paste(x, y)) gives a good picture of what you want to do, just transform it into a function and use the function: f - function(x, y) unlist(lapply(x, function(x) paste(x,y))) f(x, f(y, z)) With more than 3 vectors, you could try a recursive version. I hope this helps. Rui Barradas -- View this message in context: http://r.789695.n4.nabble.com/Combining-characters-tp4261888p4262632.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] using var from bash in R script
Dear R users, This probably a really noob question, but I'm stuck. I'd like to pass some variables from bash to R as strings. I can successfully pass variables using commandArgs(), the problem is that I end up with an array. So, for example: Args - commandArgs(TRUE) Args [1] one two three Now, it just so happens that one, two, three are names of columns that I'd like to work with. I'd like to do something like this: print(summary(lm(Args[1] ~ Args[2]))) But, this doesn't work. The alternative would be to let bash write a number of R-scripts and then rm them when done, but that seems like an unnecessary step. Can this be done? Thanks -- View this message in context: http://r.789695.n4.nabble.com/using-var-from-bash-in-R-script-tp4262857p4262857.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] RODBC installation: error message
One thing R could do better is to provide a standard way to view README and similar files before installing a package. That might have helped here. Agreed... right now, the R documentation points to a straightforward, one-line way to download and install packages from the R command line, but not to a similarly straightforward way to view a package's README content (as far as I can tell). __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Combining characters
Hi. You can use expand.grid here expand.grid(x,y,z) Andrija On Wed, Jan 4, 2012 at 5:32 PM, jeremy jeremynamer...@gmail.com wrote: Hi all, I'm trying to combine exhaustively several character arrays in R like: x=c(one,two,three) y=c(yellow,blue,green) z=c(apple,cheese) in order to get concatenation of x[1] y[1] z[1] (one yellow apple) x[1] y[1] z[2] (one yellow cheese) x[1] y[2] z[1](one blue apple) ... x[length(x)] y[length(y)] z[length(z)] (three green cheese) Anyone has a solution ? Thank in advance -- View this message in context: http://r.789695.n4.nabble.com/Combining-characters-tp4261888p4261888.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Combining characters
? expand.grid Michael On Wed, Jan 4, 2012 at 10:32 AM, jeremy jeremynamer...@gmail.com wrote: Hi all, I'm trying to combine exhaustively several character arrays in R like: x=c(one,two,three) y=c(yellow,blue,green) z=c(apple,cheese) in order to get concatenation of x[1] y[1] z[1] (one yellow apple) x[1] y[1] z[2] (one yellow cheese) x[1] y[2] z[1](one blue apple) ... x[length(x)] y[length(y)] z[length(z)] (three green cheese) Anyone has a solution ? Thank in advance -- View this message in context: http://r.789695.n4.nabble.com/Combining-characters-tp4261888p4261888.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Combining characters
On Jan 4, 2012, at 10:32 AM, jeremy wrote: Hi all, I'm trying to combine exhaustively several character arrays in R like: x=c(one,two,three) y=c(yellow,blue,green) z=c(apple,cheese) in order to get concatenation of x[1] y[1] z[1] (one yellow apple) x[1] y[1] z[2] (one yellow cheese) x[1] y[2] z[1](one blue apple) ... x[length(x)] y[length(y)] z[length(z)] (three green cheese) Anyone has a solution ? Thank in advance See ?expand.grid and ?paste DF - expand.grid(x, y, z) DF Var1 Var2 Var3 1one yellow apple 2two yellow apple 3 three yellow apple 4one blue apple 5two blue apple 6 three blue apple 7one green apple 8two green apple 9 three green apple 10 one yellow cheese 11 two yellow cheese 12 three yellow cheese 13 one blue cheese 14 two blue cheese 15 three blue cheese 16 one green cheese 17 two green cheese 18 three green cheese with(DF, paste(Var1, Var2, Var3)) [1] one yellow appletwo yellow applethree yellow apple [4] one blue apple two blue apple three blue apple [7] one green apple two green apple three green apple [10] one yellow cheese two yellow cheese three yellow cheese [13] one blue cheese two blue cheese three blue cheese [16] one green cheesetwo green cheesethree green cheese HTH, Marc Schwartz __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Combining characters
Try expand.grid() to create all the combinations. Then just collapse them with paste(): apply(expand.grid(x, y, z), 1, paste, collapse = ) Cheers, Josh On Wed, Jan 4, 2012 at 8:32 AM, jeremy jeremynamer...@gmail.com wrote: Hi all, I'm trying to combine exhaustively several character arrays in R like: x=c(one,two,three) y=c(yellow,blue,green) z=c(apple,cheese) in order to get concatenation of x[1] y[1] z[1] (one yellow apple) x[1] y[1] z[2] (one yellow cheese) x[1] y[2] z[1](one blue apple) ... x[length(x)] y[length(y)] z[length(z)] (three green cheese) Anyone has a solution ? Thank in advance -- View this message in context: http://r.789695.n4.nabble.com/Combining-characters-tp4261888p4261888.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Joshua Wiley Ph.D. Student, Health Psychology Programmer Analyst II, Statistical Consulting Group University of California, Los Angeles https://joshuawiley.com/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Combining characters
apply(expand.grid(x, y, z, stringsAsFactors=F), 1, paste, collapse=' ') On Wed, Jan 4, 2012 at 8:32 AM, jeremy jeremynamer...@gmail.com wrote: Hi all, I'm trying to combine exhaustively several character arrays in R like: x=c(one,two,three) y=c(yellow,blue,green) z=c(apple,cheese) in order to get concatenation of x[1] y[1] z[1] (one yellow apple) x[1] y[1] z[2] (one yellow cheese) x[1] y[2] z[1](one blue apple) ... x[length(x)] y[length(y)] z[length(z)] (three green cheese) Anyone has a solution ? Thank in advance -- View this message in context: http://r.789695.n4.nabble.com/Combining-characters-tp4261888p4261888.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] using var from bash in R script
On Jan 4, 2012, at 3:08 PM, dood wrote: Dear R users, This probably a really noob question, but I'm stuck. I'd like to pass some variables from bash to R as strings. I can successfully pass variables using commandArgs(), the problem is that I end up with an array. So, for example: Args - commandArgs(TRUE) Args [1] one two three Now, it just so happens that one, two, three are names of columns that I'd like to work with. I'd like to do something like this: print(summary(lm(Args[1] ~ Args[2]))) But, this doesn't work. The alternative would be to let bash write a number of R-scripts and then rm them when done, but that seems like an unnecessary step. Can this be done? Thanks See ?as.formula and ?paste Something along the lines of the following should work: Args - c(one, two, three) Args [1] one two three paste(Args[1], ~, Args[2]) [1] one ~ two as.formula(paste(Args[1], ~, Args[2])) one ~ two Then use: summary(lm(as.formula(paste(Args[1], ~, Args[2] If 'one', 'two' and 'three' are columns in a data frame (say 'DF'), you will want to use the data argument in the call to lm(): summary(lm(as.formula(paste(Args[1], ~, Args[2])), data = DF)) HTH, Marc Schwartz __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Symbols in graph
Hi, Is there an easy way to add symbols to a line in a scatter plot, so that only a few symbols are added per line (a line drawn based on a large set of data points) , in order to distinguish several lines in one graph (not a symbol for each data point as is the default in plot()). Hi Yvonne, You can use the points function to plot every 10th point (or other sequence). points(x[seq(1,length(x),by=10)],y[seq(1,length(y),by=10)],...) Jim __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] a quick question about rbinom
Hello, I have the following code using rbinom, but I don't understand what *+1* means in the code. Could someone help? Thanks so much, X1-c(A,B)[rbinom(n,1,0.6)+1] X2-c(C,D)[rbinom(n,1,0.1)+1] -- View this message in context: http://r.789695.n4.nabble.com/a-quick-question-about-rbinom-tp4262977p4262977.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] a quick question about rbinom
Homework? If not, context? -- Bert On Wed, Jan 4, 2012 at 1:38 PM, lynn.tsai vernal@gmail.com wrote: Hello, I have the following code using rbinom, but I don't understand what *+1* means in the code. Could someone help? Thanks so much, X1-c(A,B)[rbinom(n,1,0.6)+1] X2-c(C,D)[rbinom(n,1,0.1)+1] -- View this message in context: http://r.789695.n4.nabble.com/a-quick-question-about-rbinom-tp4262977p4262977.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Bert Gunter Genentech Nonclinical Biostatistics Internal Contact Info: Phone: 467-7374 Website: http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] a quick question about rbinom
homework or not, ?rbinom should be plenty. On Wed, Jan 4, 2012 at 1:38 PM, lynn.tsai vernal@gmail.com wrote: Hello, I have the following code using rbinom, but I don't understand what *+1* means in the code. Could someone help? Thanks so much, X1-c(A,B)[rbinom(n,1,0.6)+1] X2-c(C,D)[rbinom(n,1,0.1)+1] -- View this message in context: http://r.789695.n4.nabble.com/a-quick-question-about-rbinom-tp4262977p4262977.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] subscript with comma
On 12-01-04 11:41 AM, suse wrote: Thank you! It works now. But I still don't understand, how all these expressions, , paste, group, eval... have to be used together. (For example, I first tried expression(sm[w,grass]) but it didn't work, and I couldn't find, why (and when) commas are interpreted here differently). So: Is there somewhere an introduction (rather than examples) to this? Books, documents etc. You could try the reference from the ?plotmath page, but I don't think it is a tutorial, which seems to be what you want. Basically the examples are how to do it. Learn what expressions are like in R, then put together the pieces from demo(plotmath) by building expressions containing those pieces. I don't see anything like sm[w,grass] in the demos, so I would just try it to see what happens: and as you found, it doesn't work. But there is an example with commas (list(x,y,z)) and an example with subscript (x[i]), so you should be able to guess that sm[list(w,grass)] would work, and it does! Duncan Murdoch -- View this message in context: http://r.789695.n4.nabble.com/subscript-with-comma-tp4261579p4261931.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] About source()
Thanks, guys! I am using Rscript at the moment and will definitely try littler. Li Sun 2012/1/4 Rainer M Krug r.m.k...@gmail.com: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On 04/01/12 10:39, Uwe Ligges wrote: On 03.01.2012 21:22, Li SUN wrote: Thanks, Rolf, Justin and Uwe! Actually I wanted to run .R file as a script, just like what people do for bash scripts or python scripts. It seems to me that adding #!/usr/bin/R -f at the first line is what I need. Is this true? Perhaps even Rscript rather than R. And there is also littler from Dirk Eddelbüttel: http://dirk.eddelbuettel.com/code/littler.html - From the description: littler provides hash-bang (i.e. script starting with #!/some/path) capability for GNU R, as well as simple command-line and piping use. Similar to Rscript, but with some differences. I used both, and in most cases they are equivalent. Rainer Uwe Ligges Li Sun 2012/1/2 Rolf Turnerrolf.tur...@xtra.co.nz: On 03/01/12 17:02, Li SUN wrote: Hello, I am a beginner to the R language and find it fantastic and well-designed, quite different from other programming languages. What a refreshingly sensible attitude!!! :-) This is the first time I post on the r-help mailing list. In invoking the function source(filename), it seems that the filename has to exist in the current working directory, otherwise it has to be specified in full path. So is there any mechanism(such as environment variable) to specify an additional directory of .R files that source() could search in? I'm no expert on this, and others may correct me, but (1) I don't believe any such mechanism exists. (2) It's probably not a good idea, even if such a mechanism were to exist. Directories have a tree structure, rather than being linearly ordered in the way that data bases on your R search path are ordered. I believe you would run all sorts of risks of confusion and of getting the wrong file were you to invoke such a mechanism. It is ``good practice'' to have separate directories associated with different projects and to situate all files, that you might wish to source in respect of a given project, in the directory associated with that project. I know that this is an irritating sort of response --- ``No, you can't do that, and you shouldn't do it anyway!'' --- but I sincerely believe this to be true. That being said, I also believe that you could program up such a mechanism yourself. I.e. build a function source2() which would have a hard coded list of directories to search, and would make use of the try() function. Might be a good exercise for you, given that you are starting out in R and looking to upgrade your skills! :-) cheers, Rolf Turner __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. - -- Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany) Centre of Excellence for Invasion Biology Stellenbosch University South Africa Tel : +33 - (0)9 53 10 27 44 Cell: +33 - (0)6 85 62 59 98 Fax : +33 - (0)9 58 10 27 44 Fax (D): +49 - (0)3 21 21 25 22 44 email: rai...@krugs.de Skype: RMkrug -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.11 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iEYEARECAAYFAk8EIs4ACgkQoYgNqgF2egpF+QCeObN8q+U6HHlM/Tsls/wF+VoH /twAn2zaTzVrCdTxvENSK2buPlFsjlnC =tEkV -END PGP SIGNATURE- __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
