Re: [R] Uncompressing data from read.socket
raje...@cse.iitm.ac.in wrote: Is it possible to uncompress gzipped data coming over a socket? As far I remember a message by Brian Ripley (I could not find it, though), it's not possible directly. You have to save as a file and read from disk; see docs on connection. Dieter -- View this message in context: http://r.789695.n4.nabble.com/Uncompressing-data-from-read-socket-tp2530790p2530829.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] choose.dir() gone?
Hi, I fail to find choose.dir() in my current R install (see below)? Didn't that exist at some point? How to achieve file.choose() equivalent functionality for directories? Thanks for any hints, Joh sessionInfo() R version 2.11.1 (2010-05-31) x86_64-pc-linux-gnu locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=en_US.UTF-8 [9] LC_ADDRESS=en_US.UTF-8LC_TELEPHONE=en_US.UTF-8 [11] LC_MEASUREMENT=en_US.UTF-8LC_IDENTIFICATION=en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] rkward_0.5.3 loaded via a namespace (and not attached): [1] tools_2.11.1 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] choose.dir() gone?
OK. Just checked and choose.file/choose.dir exists in the windows version - apparently not in the linux one ... does anybody have a nice platform-agnostic solution for this? Thanks, Joh Johannes Graumann wrote: Hi, I fail to find choose.dir() in my current R install (see below)? Didn't that exist at some point? How to achieve file.choose() equivalent functionality for directories? Thanks for any hints, Joh sessionInfo() R version 2.11.1 (2010-05-31) x86_64-pc-linux-gnu locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=en_US.UTF-8 [9] LC_ADDRESS=en_US.UTF-8LC_TELEPHONE=en_US.UTF-8 [11] LC_MEASUREMENT=en_US.UTF-8LC_IDENTIFICATION=en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] rkward_0.5.3 loaded via a namespace (and not attached): [1] tools_2.11.1 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Interactions in GAM
Thank you so much for your answer, it has been really useful. I have already included the interactions in the models and I have obtained better results. Best regards, Lucía Cañás Lucía Cañás Ferreiro Instituto Español de Oceanografía Centro Oceanográfico de A Coruña Paseo Marítimo Alcalde Francisco Vázquez, nº 10 15001 - A Coruña, SPAIN e-mail: lucia.ca...@co.ieo.es Tel: +34981205362; Fax: +34981229077 http://www.ieo.es [[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] Passing aruments with source
Hi. Im writing a small test program just to see how passing arguments work with R. From the command line everything works as expected but from inside R using source(test.R) i dont know where and how to send in the arguments did try source(test.R --test) but it just says that it cant find or open the file. (without the argument part it can). Anyone know how to make it work? //Joel Damberg -- View this message in context: http://r.789695.n4.nabble.com/Passing-aruments-with-source-tp2531012p2531012.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] Passing aruments with source
On Wed, Sep 8, 2010 at 10:11 AM, Joel joda2...@student.uu.se wrote: Hi. Im writing a small test program just to see how passing arguments work with R. From the command line everything works as expected but from inside R using source(test.R) i dont know where and how to send in the arguments did try source(test.R --test) but it just says that it cant find or open the file. (without the argument part it can). Anyone know how to make it work? source() runs the file in the context of the caller, so if you have an 'x' in the caller then the file sourced will see it. So here, where s.R is just: print(x) you can do: x=12 source(s.R) [1] 12 x=99 source(s.R) [1] 99 Barry __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] choose.dir() gone?
Dear Joh, On Wed, Sep 8, 2010 at 3:18 AM, Johannes Graumann johannes_graum...@web.de wrote: OK. Just checked and choose.file/choose.dir exists in the windows version - apparently not in the linux one ... does anybody have a nice platform-agnostic solution for this? Thanks, Joh [snip] Have a look at tk_choose.files in the tcltk package. library(tcltk) ?tk_choose.files Good luck, Jay *** G. Jay Kerns, Ph.D. Associate Professor Department of Mathematics Statistics Youngstown State University Youngstown, OH 44555-0002 USA Office: 1035 Cushwa Hall Phone: (330) 941-3310 Office (voice mail) -3302 Department -3170 FAX VoIP: gjke...@ekiga.net E-mail: gke...@ysu.edu http://people.ysu.edu/~gkerns/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Passing aruments with source
That is true but then I (or anyone else using the script) most know exactly what the name in the script is to be able to set it correctly and so on. Therefor it would be much better to be able to just send in the value and let the script handle the variable setting. But thx for the answer //Joel Damberg -- View this message in context: http://r.789695.n4.nabble.com/Passing-aruments-with-source-tp2531012p2531087.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] Uncompressing data from read.socket
Have a look at gzcon, for decompressing data as they arrive. From the help file: ‘gzcon’ provides a modified connection that wraps an existing connection, and decompresses reads or compresses writes through that connection. Standard ‘gzip’ headers are assumed. There is no indication in the gzcon help file that explicitly prohibits socketConnections. Also, see memDecompress for in-memory decompression of the entire object. -Matt On Wed, 2010-09-08 at 00:50 -0400, raje...@cse.iitm.ac.in wrote: Hi, Is it possible to uncompress gzipped data coming over a socket? [[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. -- Matthew S. Shotwell Graduate Student Division of Biostatistics and Epidemiology Medical University of South Carolina __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Passing aruments with source
On Wed, Sep 8, 2010 at 11:29 AM, Joel joda2...@student.uu.se wrote: That is true but then I (or anyone else using the script) most know exactly what the name in the script is to be able to set it correctly and so on. Therefor it would be much better to be able to just send in the value and let the script handle the variable setting. But thx for the answer Then what you really want to do is write a _function_ that takes arguments, and not a script. Tell your users something like: Do 'source(foo.R)' and then call the fnord function with your data set: fnord(x). Your foo.R file looks like this: fnord =function(x){ print(x) # etc } It's even possible to save functions to .RData files and then tell your users to attach() them, thus not putting objects in their working spaces. And the next step is to write a package for your function... Barry __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] likelyhood maximization problem with polr
Ok, thanks a lot ! I tried to compute the inverse of the variance covariance matrix of the estimators with vcov, which gave me this error : require(MASS) data(iris) model=polr(Species~Sepal.Length+Sepal.Width+Petal.Length+Petal.Width,iris,start = rep(1, 6),method= logistic) require(stats) vcov(model) Re-fitting to get Hessian Erreur dans optim(s0, fmin, gmin, method = BFGS, hessian = Hess, ...) : la valeur initiale dans 'vmin' n'est pas finie which means Error in optim(...) : the initial value in 'vmin' is not finite ... -- View this message in context: http://r.789695.n4.nabble.com/likelyhood-maximization-problem-with-polr-tp2528818p2531045.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] Saving/loading custom R scripts
Hi, How does R automatically load functions so that they are available from the workspace? Is it anything like Matlab - you just specify a directory path and it finds it? The reason I ask is because I found a really nice script that I would like to use on a regular basis, and it would be nice not to have to 'copy and paste' it into R on every startup: http://www.r-statistics.com/wp-content/uploads/2010/02/Friedman-Test-with-Post-Hoc.r.txt This would be for Ubuntu, if that makes any difference. Cheers -- View this message in context: http://r.789695.n4.nabble.com/Saving-loading-custom-R-scripts-tp2530924p2530924.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] Interpolation missing data
Hi R experts, I have set of data consists of 50 data. some of them are missing. I would need a function in R that can estimate missing data using interpolation methods. If you know this kind of function, write me the name of the function and its library. Thanks very much in advance! abotaha -- View this message in context: http://r.789695.n4.nabble.com/Interpolation-missing-data-tp2530871p2530871.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 list to data.frame iteratively
Hi, I have a preallocated dataframe to which I have to add a list whose vectors will become rows in the dataframe. This is done iteratively. How can I do this? I'm dealing with very large numbers...list of 1000 vectors to a dataframe of 20 iteratively for e.g. my list is as follows ll-list(c(1,2,3),c(2,3,4)) I have to add this to a dataframe dd-data.frame(matrix(nrow=10,ncol=3)) so that I get 1 2 3 2 3 4 etc. [[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] How to project a vector on a subspace?
Hi experts, I have a subspace represented as matrix of basic vectors and I want to project a vector on that subspace. Does R have any function that help me to do so? Thanks, James. -- View this message in context: http://r.789695.n4.nabble.com/How-to-project-a-vector-on-a-subspace-tp2530886p2530886.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] forecasting with non-linear models
Dear colleagues! Is it possible to make predictions in R? there is an exponential relationship detween y and x x-c(0.001,0.003,0.01,0.16,0.3,0.7,0.9) y-c(38.8,41.5,44.2,27,26.9,6.9,3) f-function(x,a,b){a*exp(b*x)} fm-nls(y~f(x,a,b), start=c(a=1,b=1)) How one can predict x when y=10 and is it possible to calculate standard error of x? The task is equal to function ED in drc package, but it use logistic regression only. Best regards, Elena. -- da...@rambler.ru. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] forecasting with non-linear models
Dear colleagues! Is it possible to make predictions in R? there is an exponential relationship detween y and x x-c(0.001,0.003,0.01,0.16,0.3,0.7,0.9) y-c(38.8,41.5,44.2,27,26.9,6.9,3) f-function(x,a,b){a*exp(b*x)} fm-nls(y~f(x,a,b), start=c(a=1,b=1)) How one can predict x when y=10 and is it possible to calculate standard error of x? The task is equal to function ED in drc package, but it use logistic regression only. Best regards, Elena. -- da...@rambler.ru. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] How to change font size in plot() function
Dear All, Could someone please advice me the way to change the size of the title and x and y-label in plot() function. I've tried to use 'font' and 'font.main' call in plot() function, but it didn't make any changes in terms of the size. Thanks Fir __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Failure to aggregate
Mnay thanks fr suggestions. I am afraid this is one tough daatframe... t = sqldf(select h, count(*) from x group by h) Error in sqliteExecStatement(con, statement, bind.data) : RS-DBI driver: (error in statement: no such table: x) In addition: Warning message: In value[[3L]](cond) : RAW() can only be applied to a 'raw', not a 'double' t = aggregate(x[price], by = x[h], FUN = NROW) Error in sort.list(y) : 'x' must be atomic for 'sort.list' Have you called 'sort' on a list? t = aggregate(x[price], by = x[h], FUN = length) Error in sort.list(y) : 'x' must be atomic for 'sort.list' Have you called 'sort' on a list? t = tapply(x$price, by = x$h, FUN = length) Error in is.list(INDEX) : 'INDEX' is missing class(x) [1] data.frame class(x$h) [1] POSIXt POSIXlt class(x$price) [1] integer -- View this message in context: http://r.789695.n4.nabble.com/Failure-to-aggregate-tp2528613p2530963.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] choose.dir() gone?
Maybe 'tk_choose.dir' in the tcltk package will do what you want. --- On Wed, 9/8/10, Johannes Graumann johannes_graum...@web.de wrote: From: Johannes Graumann johannes_graum...@web.de Subject: Re: [R] choose.dir() gone? To: r-h...@stat.math.ethz.ch Date: Wednesday, September 8, 2010, 3:18 AM OK. Just checked and choose.file/choose.dir exists in the windows version - apparently not in the linux one ... does anybody have a nice platform-agnostic solution for this? Thanks, Joh Johannes Graumann wrote: Hi, I fail to find choose.dir() in my current R install (see below)? Didn't that exist at some point? How to achieve file.choose() equivalent functionality for directories? Thanks for any hints, Joh sessionInfo() R version 2.11.1 (2010-05-31) x86_64-pc-linux-gnu locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=en_US.UTF-8 [9] LC_ADDRESS=en_US.UTF-8 LC_TELEPHONE=en_US.UTF-8 [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] rkward_0.5.3 loaded via a namespace (and not attached): [1] tools_2.11.1 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] (no subject)
Dear all, I need to estimate intensity and probability matrices by the continuous-time markov model... in a first time I used msm and it works perfectly. Nevertheless, I have to do other estimations that need programming the likelihood. Is it possible to see somewhere the likelihood used in the msm package? I have readen the papers about likelihood estimation of continuous-time markov models but and I tried to write the program but it does not work. Thank you very much Luis SAGAON TEYSSIER [[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] Failure to aggregate
I was able to aggregate (with sqldf, at least), after saving and re-loading the dataframe. My first guess was that h (and/or price?) now being a factor - stringsAsFactors = T by default - made the difference, and I tried to convert x$h to factor, but received an error. -- View this message in context: http://r.789695.n4.nabble.com/Failure-to-aggregate-tp2528613p2530989.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] big data
Hello, I searched the internet but i didn't find the answer for the next problem: I want to do a glm on a csv file consisting of 25 columns and 4 mln rows. Not all the columns are relevant. My problem is to read the data into R. Manipulate the data and then do a glm. I've tried with: dd-scan(myfile.csv,colClasses=classes) dat-as.data.frame(dd) My question is: what is the right way to do is? Can someone give me a hint? Thanks, Arend [[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] Saving/loading custom R scripts
You can create a .First function in your .Rprofile file (which will be in ~/.Rprofile). For example .First - function(){ source(Friedman-Test-with-Post-Hoc.r.txt) } You can also create your own package (mylibrary) down the line (see the R manual for creating extensions at http://cran.fhcrc.org/doc/manuals/R-exts.pdf) which will be a collection of your custom scripts that you have written, and then you can automatically load them using .First - function(){ library(mylibrary) } Hope this helps. Abhijit On 9/8/10 3:25 AM, DrCJones wrote: Hi, How does R automatically load functions so that they are available from the workspace? Is it anything like Matlab - you just specify a directory path and it finds it? The reason I ask is because I found a really nice script that I would like to use on a regular basis, and it would be nice not to have to 'copy and paste' it into R on every startup: http://www.r-statistics.com/wp-content/uploads/2010/02/Friedman-Test-with-Post-Hoc.r.txt This would be for Ubuntu, if that makes any difference. Cheers -- Abhijit Dasgupta, PhD Director and Principal Statistician ARAASTAT Ph: 301.385.3067 E: adasgu...@araastat.com W: http://www.araastat.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] programming continuous-time markov model likelihood
Dear all, I need to estimate intensity and probability matrices by the continuous-time markov model... in a first time I used msm and it works perfectly. Nevertheless, I have to do other estimations that need programming the likelihood. Is it possible to see somewhere the likelihood used in the msm package? I have readen the papers about likelihood estimation of continuous-time markov models but and I tried to write the program but it does not work. Thank you very much Luis SAGAON TEYSSIER [[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] Passing aruments with source
Thats an idea will try it out and see how it works Thanks a lot for your help. Joel -- View this message in context: http://r.789695.n4.nabble.com/Passing-aruments-with-source-tp2531012p2531138.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] Regression using mapply?
Hi, I have huge matrices in which the response variable is in the first column and the regressors are in the other columns. What I wanted to do now is something like this: #this is just to get an example-matrix DataMatrix - rep(1,1000); Disturbance - rnorm(900); DataMatrix[101:1000] - DataMatrix[101:1000]+Disturbance; DataMatrix - matrix(DataMatrix,ncol=10,nrow=100); #estimate univariate linear model with each regressor-column, response in the first column for(i in 2:10){ result - lm(DataMatrix[,1]~DataMatrix[,i]) } Is there any way to get rid of the for-loop using mapply (or some other function)? Thanks! Philipp __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to change font size in plot() function
try: ?title -- View this message in context: http://r.789695.n4.nabble.com/How-to-change-font-size-in-plot-function-tp2531127p2531161.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] bigmemory doubt
By far the easiest way to achieve this would be to use the bigmemory C++ structures in your program itself. However, if you do something on your own (but fundamentally have a column-major matrix in shared memory), it should be possible to play around with the pointer with R/bigmemory to accomplish this, yes. Feel free to email us directly for advice. Jay Message: 153 Date: Wed, 8 Sep 2010 10:52:19 +0530 (IST) From: raje...@cse.iitm.ac.in raje...@cse.iitm.ac.in To: r-help r-help@r-project.org Subject: [R] bigmemory doubt Message-ID: 1204692515.13855.1283923339865.javamail.r...@mail.cse.iitm.ac.in Content-Type: text/plain Hi, Is it possible for me to read data from shared memory created by a vc++ program into R using bigmemory? -- John W. Emerson (Jay) Associate Professor of Statistics Department of Statistics Yale University http://www.stat.yale.edu/~jay __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] forecasting with non-linear models
predict x for a given y(response)? If this is the case, you will have multiple x for a single y for this exponential model. In terms of logistic regression, If y =1, logit([P(Y=1)] = a + b*bx has infinite many x. The question seems not quite clear to me. -- View this message in context: http://r.789695.n4.nabble.com/forecasting-with-non-linear-models-tp2531125p2531186.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] Aggregating data from two data frames
Dear all, I'm working with two data frames. The first frame (agg_data) consists of two columns. agg_data[,1] is a unique ID for each row and agg_data[,2] contains a continuous variable. The second data frame (geo_data) consists of several columns. One of these columns (geo_data$ZCTA) corresponds to the unique ID in the first data frame. The problem is that only a subset of the unique ID present in the first data frame also appears in the second data fame. What I would like to do is to add another column to the second data frame (geo_data) that includes the value of the continuous variable from the first frame that corresponds to the unique ID. To put it differently, I want R to look at each row in the second data frame, look for the unique ID (geo_data$ZCTA), look for the same unique ID in the first data frame and then paste the value from the continous variable as a new column into the second data frame. I hope I'm somewhat clear here ... Is there a convenient way of doing this? Thanks very much in advance, Michael [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Aggregating data from two data frames
Have a look at match and merge. Hadley On Wednesday, September 8, 2010, Michael Haenlein haenl...@escpeurope.eu wrote: Dear all, I'm working with two data frames. The first frame (agg_data) consists of two columns. agg_data[,1] is a unique ID for each row and agg_data[,2] contains a continuous variable. The second data frame (geo_data) consists of several columns. One of these columns (geo_data$ZCTA) corresponds to the unique ID in the first data frame. The problem is that only a subset of the unique ID present in the first data frame also appears in the second data fame. What I would like to do is to add another column to the second data frame (geo_data) that includes the value of the continuous variable from the first frame that corresponds to the unique ID. To put it differently, I want R to look at each row in the second data frame, look for the unique ID (geo_data$ZCTA), look for the same unique ID in the first data frame and then paste the value from the continous variable as a new column into the second data frame. I hope I'm somewhat clear here ... Is there a convenient way of doing this? Thanks very much in advance, Michael [[alternative HTML version deleted]] __ r-h...@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Assistant Professor / Dobelman Family Junior Chair Department of Statistics / Rice University http://had.co.nz/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] big data
On 8 September 2010 at 13:26, André de Boer wrote: | I searched the internet but i didn't find the answer for the next problem: | I want to do a glm on a csv file consisting of 25 columns and 4 mln rows. | Not all the columns are relevant. My problem is to read the data into R. | Manipulate the data and then do a glm. | | I've tried with: | | dd-scan(myfile.csv,colClasses=classes) | dat-as.data.frame(dd) | | My question is: what is the right way to do is? | Can someone give me a hint? Look at the biglm package by Thomas Lumley which will allow you to fit glm models in chunks. Dirk -- Dirk Eddelbuettel | e...@debian.org | http://dirk.eddelbuettel.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] Extracting elements from list: Is [[ always faster than $ ??
Dear list It seems to me that extracting elements from a list using '[[' is somewhat faster than using '$'. For example: x- as.list(1:25) names(x) - letters[1:length(x)] dput(x) structure(list(a = 1L, b = 2L, c = 3L, d = 4L, e = 5L, f = 6L, g = 7L, h = 8L, i = 9L, j = 10L, k = 11L, l = 12L, m = 13L, n = 14L, o = 15L, p = 16L, q = 17L, r = 18L, s = 19L, t = 20L, u = 21L, v = 22L, w = 23L, x = 24L, y = 25L), .Names = c(a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w, x, y)) system.time({ for (ii in 1:100) x[[21]] }) user system elapsed 0.550.000.54 system.time({ for (ii in 1:100) x[[u]]}) user system elapsed 0.840.000.84 system.time({ for (ii in 1:100) x$u}) user system elapsed 1.120.001.13 Does anyone know if this is always the case? (I have not found anything about speed in this connection on the help pages, apologies if I have overlooked something). I use R.2.11.1 on Windows 7. 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.
Re: [R] Decision Tree in Python or C++?
For Python, check out the project orange: http://www.ailab.si/orange/doc/catalog/Classify/ClassificationTree.htm Not sure about C++, but OpenDT is in C: http://opendt.sourceforge.net/ Looks like OpenCV has both Python and C++ interface (didn't see Python interace to decision tree, though): http://opencv.willowgarage.com/documentation/cpp/decision_trees.html Andy -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Wensui Liu Sent: Saturday, September 04, 2010 5:14 PM To: noclue_ Cc: r-help@r-project.org Subject: Re: [R] Decision Tree in Python or C++? for python, please check http://onlamp.com/pub/a/python/2006/02/09/ai_decision_trees.html On Sat, Sep 4, 2010 at 11:21 AM, noclue_ tim@netzero.net wrote: Have anybody used Decision Tree in Python or C++? (or written their own decision tree implementation in Python or C++)? My goal is to run decision tree on 8 million obs as training set and score 7 million in test set. I am testing 'rpart' package on a 64-bit-Linux + 64-bit-R environment. But it seems that rpart is either not stable or running out of memory very quickly. (Is it because R is passing everything as copy instead of as object reference?) Any idea would be greatly appreciated! Have a nice weekend! -- View this message in context: http://r.789695.n4.nabble.com/Decision-Tree-in-Python-or-C-tp2 526810p2526810.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. -- == WenSui Liu wens...@paypal.com statcompute.spaces.live.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. Notice: This e-mail message, together with any attachme...{{dropped:11}} __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] lattice: layout and number of pages
Dear expeRts, ?xyplot says: In general, giving a high value of ‘layout[3]’ is not wasteful because blank pages are never created. But the following example does generate blank pages - well except for the ylab: data(barley) require(lattice) stripplot(yield~year|site, barley, layout=c(2,1,5)) Did I misinterpret the sentence from the help page or is this a bug? Yes - I know that his works fine: stripplot(yield~year|site, barley, layout=c(2,1)) Just curious... cu Philipp -- Dr. Philipp Pagel Lehrstuhl für Genomorientierte Bioinformatik Technische Universität München Wissenschaftszentrum Weihenstephan Maximus-von-Imhof-Forum 3 85354 Freising, Germany http://webclu.bio.wzw.tum.de/~pagel/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to project a vector on a subspace?
Can you be a little bit more specific? For example, the base vectors of the subspace and the vector you want to project. Specific artificial vectors/matrices are helpful. -- View this message in context: http://r.789695.n4.nabble.com/How-to-project-a-vector-on-a-subspace-tp2530886p2531245.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] How to project a vector on a subspace?
On Wed, Sep 8, 2010 at 2:52 AM, James vuda...@gmail.com wrote: Hi experts, I have a subspace represented as matrix of basic vectors and I want to project a vector on that subspace. Does R have any function that help me to do so? The projection of vector y onto the space spanned by the columns of X is fitted(lm.fit(X, y)) . Although not numerically optimal it can also be written: X %*% solve(crossprod(X, X), crossprod(X, y)) -- Statistics Software Consulting GKX Group, GKX Associates Inc. tel: 1-877-GKX-GROUP email: ggrothendieck at 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] Over lay 2 scale in same plot
Hi Peng, Thanks for your reply. I have tried it and it does work fine apart from one problem. Even though the second data set has same length as the first one, the point function seems to shit all the points towards left side. So the points are not in concordat co-ordinates as the bars. Any idea how this can be fixed ??? thanks in advace. regards, Mamun -- View this message in context: http://r.789695.n4.nabble.com/Over-lay-2-scale-in-same-plot-tp2528661p2531255.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] shared memory system for R windows
Hi, is there a shared memory implementation for R windows, preferably something that resembles the boost c++ libraries [[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] optimized value worse than starting Value
Dear all, I'm optimizing a relatively simple function. Using optimize the optimized parameter value is worse than the starting. why? f-function(delta,P,U){ minimiz-P+delta*U x-minimiz[1] y-minimiz[2] z-100*(y-x^2)^2+(1-x)^2 return(z) } result-optimize(f, interval=c(-10, 10), P=c(0.99,1.01), U=c(1,0)) result Output: result-optimize(f, interval=c(-10, 10), P=c(0.99,1.01), U=c(1,0)) result $minimum [1] -1.990015 $objective [1] 4.01 Function Value at Starting Point with free parameter=0: f(0,c(0.99,1.01),c(1,0)) [1] 0.089501 It seems as if optimize doesn't check the whole interval. result-optimize(f, interval=c(-1, 10), P=c(0.99,1.01), U=c(1,0)) result $minimum [1] 0.01497394 $objective [1] 2.481504e-05 Changing the lower interval value leads to the result I am looking for. How do I find this result when I have no idea where the optimal values lies and want to look in an interval that is as wide as possible? any ideas? Michael [[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] Uniform Distribution
Hello, I would like to uniformly distribute values from 0 to 200. Can someone help me find the appropriate uniform distribution generator? I would like to thank you in advance for your help. Best Regards Alex [[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] Uniform Distribution
Hi Alex, help.search(uniform) HTH, Stephan Am 08.09.2010 15:36, schrieb Alaios: Hello, I would like to uniformly distribute values from 0 to 200. Can someone help me find the appropriate uniform distribution generator? I would like to thank you in advance for your help. Best Regards Alex [[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] Interpolation missing data
try packages: {yaImpute}, {impute}, etc. -- View this message in context: http://r.789695.n4.nabble.com/Interpolation-missing-data-tp2530871p2531288.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] Uniform Distribution
?runif -- View this message in context: http://r.789695.n4.nabble.com/Uniform-Distribution-tp2531282p2531292.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] Uniform Distribution
On Wed, 2010-09-08 at 06:36 -0700, Alaios wrote: Hello, I would like to uniformly distribute values from 0 to 200. Can someone help me find the appropriate uniform distribution generator? I would like to thank you in advance for your help. Best Regards Alex ?runif runif(10, min = 0, max = 200) will give you 10 numbers uniformally distributed on the interval 0, 200. HTH G -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/ UK. WC1E 6BT. [w] http://www.freshwaters.org.uk %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Uniform Distribution
Thanks a lot. Tired the help.search(uniform) one other member of the list told me but the computer 10 minutes now it is scanning to infinity :) From: Gavin Simpson gavin.simp...@ucl.ac.uk Cc: r-help@r-project.org Sent: Wed, September 8, 2010 3:45:12 PM Subject: Re: [R] Uniform Distribution On Wed, 2010-09-08 at 06:36 -0700, Alaios wrote: Hello, I would like to uniformly distribute values from 0 to 200. Can someone help me find the appropriate uniform distribution generator? I would like to thank you in advance for your help. Best Regards Alex ?runif runif(10, min = 0, max = 200) will give you 10 numbers uniformally distributed on the interval 0, 200. HTH G -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/ UK. WC1E 6BT. [w] http://www.freshwaters.org.uk %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% [[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] circular data
Is there any package for clustering of circular data? karsar __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] question on optim
Hi Nan, You can take a look at the optimx package on CRAN. John Nash and I wrote this package to help lay and sophisticated users alike. This package unifies various optimization algorithms in R for smooth, box-constrained optimization. It has features for checking objective function, gradient (and hessian) specifications. It checks for potential problems due to poor scaling; checks feasibility of starting values. It provides diagnostics (KKT conditions) on whether or not a local optimum has been located. It also allows the user to run various optimization algorithms in one simple call, which is essentially identical to optim call. This feature can be especially useful for developers to benchmark different algorithms and choose the best one for their class of problems. http://cran.r-project.org/web/packages/optimx/index.html Ravi. -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Hey Sky Sent: Tuesday, September 07, 2010 2:48 PM To: Ben Bolker; r-h...@stat.math.ethz.ch Subject: Re: [R] question on optim thanks. Ben after read your email, I realized the initial value of w[5]=0 is a stupid mistake. and I have changed it. but I am sorry I cannot reproduce the result, convergence, as you get. the error message is non-finite finite difference value [12]. any suggestion about it? and could you plz recommend some R books on optimization, such as tips for setup gradient and others, or common mistakes? thanks Nan - Original Message From: Ben Bolker bbol...@gmail.com To: r-h...@stat.math.ethz.ch Sent: Tue, September 7, 2010 11:15:43 AM Subject: Re: [R] question on quot;optimquot; Hey Sky heyskywalker at yahoo.com writes: I do not know how to describe my question. I am a new user for R and write the following code for a dynamic labor economics model and use OPTIM to get optimizations and parameter values. the following code does not work due to the equation: wden[,i]-dnorm((1-regw[,i])/w[5])/w[5] where w[5] is one of the parameters (together with vector a, b and other elements in vector w) need to be estimated. if I delete the w[5] from the upper equation. that is: wden[,i]-dnorm(1-regw[,i]) optim will give me the estimated parameters. Thank you for the reproducible example! The problem is that you are setting the initial value of w[5] to zero, and then trying to divide by it ... I find that guess-rep(0,times=npar) guess[16] - 1 system.time(r1-optim(guess,myfunc1,data=mydata, method=BFGS,hessian=TRUE, control=list(trace=TRUE))) seems to work OK (I have no idea if the answers are sensible are not ...) If you're going to be doing a lot of this it might be wise to see if you can specify the gradient of your objective function for R -- it will speed up and stabilize the fitting considerably. By the way, you should be careful with this function: if we try this with Nelder-Mead instead, it appears to head to a set of parameters that lead to some sort of singularity in the objective function: system.time(r2-optim(guess,myfunc1,data=mydata, method=Nelder-Mead,hessian=FALSE, control=list(trace=TRUE,maxit=5000))) ## still thinks it hasn't converged, but objective function is ## much smaller ## plot 'slice' through objective space where 0 corresponds to ## fit-1 parameters and 1 corresponds to fit-2 parameters; ## adapted from emdbook::calcslice range - seq(-0.1,1.1,length=400) slicep - seq(range[1], range[2], length = 400) slicepars - t(sapply(slicep, function(x) (1 - x) * r1$par + x * r2$par)) v - apply(slicepars, 1, myfunc1) plot(range,v,type=l) Ideally, you should be able to look at the parameters of fit #2 and figure out (a) what the result means in terms of labor economics and (b) how to keep the objective function from going there, or at least identifying when it does. Ben Bolker __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] optimized value worse than starting Value
Dieter Menne had already told you what the problem is. You have 2 local minima. One is a global minimum. Depending on your starting interval, the optimizer can converge to one of the two local minima. If you want to be reasonably sure that you always find the global minimum, you either have to use problem-specific knowledge or try a sufficiently large number of starting values and pick the best solution. Here is one approach: require(BB) p0 - matrix(rnorm(20), 20, 1) # 20 random starting values ans - multiStart(par=p0, fn=f, action=optimize, P=c(0.99,1.01), U=c(1,0)) ans Hope this helps, Ravi. -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Michael Bernsteiner Sent: Wednesday, September 08, 2010 8:36 AM To: r-help@r-project.org Subject: [R] optimized value worse than starting Value Dear all, I'm optimizing a relatively simple function. Using optimize the optimized parameter value is worse than the starting. why? f-function(delta,P,U){ minimiz-P+delta*U x-minimiz[1] y-minimiz[2] z-100*(y-x^2)^2+(1-x)^2 return(z) } result-optimize(f, interval=c(-10, 10), P=c(0.99,1.01), U=c(1,0)) result Output: result-optimize(f, interval=c(-10, 10), P=c(0.99,1.01), U=c(1,0)) result $minimum [1] -1.990015 $objective [1] 4.01 Function Value at Starting Point with free parameter=0: f(0,c(0.99,1.01),c(1,0)) [1] 0.089501 It seems as if optimize doesn't check the whole interval. result-optimize(f, interval=c(-1, 10), P=c(0.99,1.01), U=c(1,0)) result $minimum [1] 0.01497394 $objective [1] 2.481504e-05 Changing the lower interval value leads to the result I am looking for. How do I find this result when I have no idea where the optimal values lies and want to look in an interval that is as wide as possible? any ideas? Michael [[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] How to project a vector on a subspace?
On Sep 8, 2010, at 15:22 , Gabor Grothendieck wrote: On Wed, Sep 8, 2010 at 2:52 AM, James vuda...@gmail.com wrote: Hi experts, I have a subspace represented as matrix of basic vectors and I want to project a vector on that subspace. Does R have any function that help me to do so? The projection of vector y onto the space spanned by the columns of X is fitted(lm.fit(X, y)) . Although not numerically optimal it can also be written: X %*% solve(crossprod(X, X), crossprod(X, y)) Perhaps qr.fitted(qr(X),y) is slightly faster than fitted(lm.fit(X,y)). Looks like it might be bypassing some red tape, and otherwise do the same. -- Peter Dalgaard 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] Regression using mapply?
On Sep 8, 2010, at 7:34 AM, Philipp Kunze wrote: Hi, I have huge matrices in which the response variable is in the first column and the regressors are in the other columns. What I wanted to do now is something like this: #this is just to get an example-matrix DataMatrix - rep(1,1000); Disturbance - rnorm(900); DataMatrix[101:1000] - DataMatrix[101:1000]+Disturbance; DataMatrix - matrix(DataMatrix,ncol=10,nrow=100); #estimate univariate linear model with each regressor-column, response in the first column for(i in 2:10){ result - lm(DataMatrix[,1]~DataMatrix[,i]) } result - apply(DataMatrix[,2:10], 2, function (x) lm(DataMatrix[, 1]~x) ) Which would have the added advantage that result would not be overwritten for iterations 3:10, which is what your code would have done. result will be a list of 9 models which might be a bit unweildy, so you might consider something like result - apply(DataMatrix[,2:10], 2, function (x) coef( lm(DataMatrix[,1]~x) ) ) result When you do so, you uncover a fatal flaw in your strategy, which suggests you have not even done this once on your data or simulations. -- David. Is there any way to get rid of the for-loop using mapply (or some other function)? -- 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] How to change font size in plot() function
That is one method, but he should also review: ?par where he will discover that cex.main is a parameter that could be used from within the plot function. FMH had written, by Peng, C had failed to include context: Could someone please advice me the way to change the size of the title and x and y-label in plot() function. I've tried to use 'font' and 'font.main' call in plot() function, but it didn't make any changes in terms of the size. On Sep 8, 2010, at 7:46 AM, Peng, C wrote: try: ?title -- View this message in context: http://r.789695.n4.nabble.com/How-to-change-font-size-in-plot-function-tp2531127p2531161.html Sent from the R help mailing list archive at Nabble.com. 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] optimized value worse than starting Value
On Wed, Sep 8, 2010 at 1:35 PM, Michael Bernsteiner dethl...@hotmail.com wrote: Dear all, I'm optimizing a relatively simple function. Using optimize the optimized parameter value is worse than the starting. why? f-function(delta,P,U){ minimiz-P+delta*U x-minimiz[1] y-minimiz[2] z-100*(y-x^2)^2+(1-x)^2 return(z) } This looks familiar. Is this some 1-d version of the Rosenbrock Banana Function? http://en.wikipedia.org/wiki/Rosenbrock_function It's designed to be hard to find the minimum. In the real world one would hope that things would not have such a pathological behaviour. Numerical optimisations are best done using as many methods as possible - see optimise, nlm, optim, nlminb and the whole shelf of library books devoted to it. Barry __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] pairs and panel.smooth for two groups
Hi, I have modified the USJudgeRatings data (available in R) to illustrate my question. # Use the first 4 variables of USJudgeRatings and add a group variable with two levels USJudgeRatings - USJudgeRatings[,1:4] USJudgeRatings$group - factor(c(rep(1, 22), rep(0, 21))) # I can draw a pairs graph where members of each group are drawn in different colors: pairs(USJudgeRatings[,1:4], col = c(2,3)[USJudgeRatings$group], pch = c(21,3)[USJudgeRatings$group]) # I would also like to add a smooth line to each subplot like pairs(USJudgeRatings[,1:4], panel=panel.smooth) # but I want the smooth to be done for each of the group, i.e. I want two smooths per subplot. # this creates only one smooth pairs(USJudgeRatings[,1:4], col = c(2,3)[USJudgeRatings$group], pch = c(21,3)[USJudgeRatings$group], panel = panel.smooth) # I understand that panel.smooth is a function that is called for each subplot. I don't know how to tell it to do a smooth for each of my group in each of the subplot. Any help would be appreciated! Best, Marie-Pierre __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Over lay 2 scale in same plot
Hi Mamum, The co-ordinates appear shifted because the bars are not centered at 1, 2, 3, etc. To give an example: # Create a barplot # of the numbers 1 through 10 barplot(1:10) # Now look at the x axis coordinates of these actual bars barplot(1:10, plot = FALSE) # One way to get these coordinates for yourself would be x - barplot(1:10) # this will plot AND save the object x # see the coordinates # This should have the points properly centered with the bars points(x = x, y = 10:1) HTH, Josh On Wed, Sep 8, 2010 at 6:14 AM, mamunbabu2001 mrashi...@hotmail.com wrote: Hi Peng, Thanks for your reply. I have tried it and it does work fine apart from one problem. Even though the second data set has same length as the first one, the point function seems to shit all the points towards left side. So the points are not in concordat co-ordinates as the bars. Any idea how this can be fixed ??? thanks in advace. regards, Mamun -- View this message in context: http://r.789695.n4.nabble.com/Over-lay-2-scale-in-same-plot-tp2528661p2531255.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 University of California, Los Angeles http://www.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.
[R] Checking if the distribution follow a power law
Dear all. I'm using igraph package, and do a research about network analysis. With power.law.fit from igraph package, it seems that we can fit a power law distribution to some data. But, I want to know how to judge whether the network distribution follows a power law or not. Does anyone know the way to do this? Thanks for any help. Daigo p.s. Also, I tried several ways such as http://www.mail-archive.com/r-h...@stat.math.ethz.ch/msg62520.html and I got results like this: Profiling... 2.5 % 97.5 % 2.393297 2.412650 What do these suggest? please tell me about this if someone knows. [[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] Matrixes inside matrixes
Hello everyone, Could you please help me find out if R supports matrixes inside matrixes? This is what I would like to do I have an area map of humidity per km. I would like at every cell to keep also information about the height of this area, the current temperature etc. Is something like that supported? I would like to thank you in advance for your help Best Regards Alex [[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] Matrixes inside matrixes
Hello, from ?array An array in R can have one, two or more dimensions. It is simply a vector which is stored with additional attributes giving the dimensions (attribute ‘dim’) and optionally names for those dimensions (attribute ‘dimnames’). A two-dimensional array is the same thing as a ‘matrix’. So, to answer your question, yes. Alaios wrote: Hello everyone, Could you please help me find out if R supports matrixes inside matrixes? This is what I would like to do I have an area map of humidity per km. I would like at every cell to keep also information about the height of this area, the current temperature etc. Is something like that supported? I would like to thank you in advance for your help Best Regards Alex [[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] Saving/loading custom R scripts
Hi, Just create a file called .Rprofile that is located in your working directory (this means you could actually have different ones in each working directory). In that file, you can put in code just like any other code that would be source()d in. For instance, all my .Rprofile files start with: r - getOption(repos) r[CRAN] - http://cran.stat.ucla.edu; options(repos = r) rm(r) So that I do not have to pick my CRAN mirror. Similarly you could merely add this line to the file: source(file = http://www.r-statistics.com/wp-content/uploads/2010/02/Friedman-Test-with-Post-Hoc.r.txt;) and R would go online, download that file and source it in (not that I am recommending re-downloading every time you start R). Then whatever names they used to define the functions, would be in your workspace. Note that in general, you will not get any output alerting you that it has worked; however, if you type ls() you should see those functions' names. Cheers, Josh On Wed, Sep 8, 2010 at 12:25 AM, DrCJones matthias.godd...@gmail.com wrote: Hi, How does R automatically load functions so that they are available from the workspace? Is it anything like Matlab - you just specify a directory path and it finds it? The reason I ask is because I found a really nice script that I would like to use on a regular basis, and it would be nice not to have to 'copy and paste' it into R on every startup: http://www.r-statistics.com/wp-content/uploads/2010/02/Friedman-Test-with-Post-Hoc.r.txt This would be for Ubuntu, if that makes any difference. Cheers -- View this message in context: http://r.789695.n4.nabble.com/Saving-loading-custom-R-scripts-tp2530924p2530924.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 University of California, Los Angeles http://www.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.
[R] saving heatmaps in graphical format that can be edited in graphic editor tools
I generated a heatmap in R using the following commands: mydata - read.csv(file=Data.csv, header=TRUE, sep=,) mydata - mydata[rowSums(mydata[,-1]^2) 0, ] rownames(mydata)=mydata$Name mydata - mydata[,2:253] mydatamatrix - data.matrix(mydata) mydatascale - t(scale(t(mydatamatrix))) hr - hclust(as.dist(1-cor(t(mydatascale), method=pearson)), method=complete) hc - hclust(as.dist(1-cor(mydatascale, method=spearman)), method=complete) myclhr - cutree(hr, h=max(hr$height)/2); mycolhr - sample(rainbow(256)); myclhc - cutree(hc, h=max(hc$height)/2); mycolhc - sample(rainbow(256)); mycolhr - mycolhr[as.vector(myclhr)]; mycolhc - mycolhc[as.vector(myclhc)]; library(gplots) library(RSvgDevice) jpeg(Heatmap.jpg, height=6+2/3, width=6+2/3, units=in, res=1200) heatmap.2(mydatamatrix, Rowv=as.dendrogram(hr), Colv=as.dendrogram(hc), dendrogram=both, scale=row, col=brewer.pal(3, YlOrRd), cexRow=0.01, cexCol=0.01, trace=none, density.info=none, key=TRUE, keysize=1.5, margin=c(5,8),RowSideColor=mycolhr, ColSideColor=mycolhc) dev.off() I would like to save the file in a graphical format that can be edited later in any image editing program (like corel). is there a way to do this in R? Its a lot of data I plotted on heatmap (~ 300*600). The x and y labels are difficult to read. I used cexRow = 0.01 and cexCol =0.01 with 1200 resolution to save as jpeg file. That helped but I can still hardly figure out the row labels. I want to be able to read them to interpret the results and also to edit them with different font/color in corel and may be add other things that could be relevant to my work. So, I guess my question here- is there a way I can make the labels readable in R itself or can I generate a list of the row and col labels (in the exact order as in figure) in a text file separately so I know the order and can try attaching it to heatmap in corel draw? any help will be appreciated! Thanks BD [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] saving heatmaps in graphical format that can be edited in graphic editor tool
I generated a heatmap in R using the following commands: mydata - read.csv(file=Data.csv, header=TRUE, sep=,) mydata - mydata[rowSums(mydata[,-1]^2) 0, ] rownames(mydata)=mydata$Name mydata - mydata[,2:253] mydatamatrix - data.matrix(mydata) mydatascale - t(scale(t(mydatamatrix))) hr - hclust(as.dist(1-cor(t(mydatascale), method=pearson)), method=complete) hc - hclust(as.dist(1-cor(mydatascale, method=spearman)), method=complete) myclhr - cutree(hr, h=max(hr$height)/2); mycolhr - sample(rainbow(256)); myclhc - cutree(hc, h=max(hc$height)/2); mycolhc - sample(rainbow(256)); mycolhr - mycolhr[as.vector(myclhr)]; mycolhc - mycolhc[as.vector(myclhc)]; library(gplots) library(RSvgDevice) jpeg(Heatmap.jpg, height=6+2/3, width=6+2/3, units=in, res=1200) heatmap.2(mydatamatrix, Rowv=as.dendrogram(hr), Colv=as.dendrogram(hc), dendrogram=both, scale=row, col=brewer.pal(3, YlOrRd), cexRow=0.01, cexCol=0.01, trace=none, density.info=none, key=TRUE, keysize=1.5, margin=c(5,8),RowSideColor=mycolhr, ColSideColor=mycolhc) dev.off() I would like to save the file in a graphical format that can be edited later in any image editing program (like corel). is there a way to do this in R? Its a lot of data I plotted on heatmap (~ 300*600). The x and y labels are difficult to read. I used cexRow = 0.01 and cexCol =0.01 with 1200 resolution to save as jpeg file. That helped but I can still hardly figure out the row labels. I want to be able to read them to interpret the results and also to edit them with different font/color in corel and may be add other things that could be relevant to my work. So, I guess my question here- is there a way I can make the labels readable in R itself or can I generate a list of the row and col labels (in the exact order as in figure) in a text file separately so I know the order and can try attaching it to heatmap in corel draw? any help will be appreciated! Thanks! BD -- View this message in context: http://r.789695.n4.nabble.com/saving-heatmaps-in-graphical-format-that-can-be-edited-in-graphic-editor-tool-tp2531512p2531512.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] saving heatmaps in graphical format that can be edited in graphic editor tools
Hi, Without your data, we cannot actually reproduce your plot; however, if you cannot read labels, there are generally three options. 1) Make the labels smaller (I have not used the function you used, so I'm not sure exactly how one would) 2) Use fewer labels (if you need them all, this is a particularly unattractive choice) 3) Make your graph bigger (this is the easiest though not always the best). Sometimes, simply rotating the labels can help them not overlap too. You can try changing the jpeg() line to: jpeg(Heatmap.jpg, height=10+2/3, width=10+2/3, units=in, res=1200) and keeping adding inches until things seem to work. The downside, of course, is that if it is every being printed, it may have to be shrunk, but as long as it is an image, that will just make everything smaller, not re-overlap the labels. HTH, Josh On Wed, Sep 8, 2010 at 8:29 AM, Bhakti Dwivedi bhakti.dwiv...@gmail.com wrote: I generated a heatmap in R using the following commands: mydata - read.csv(file=Data.csv, header=TRUE, sep=,) mydata - mydata[rowSums(mydata[,-1]^2) 0, ] rownames(mydata)=mydata$Name mydata - mydata[,2:253] mydatamatrix - data.matrix(mydata) mydatascale - t(scale(t(mydatamatrix))) hr - hclust(as.dist(1-cor(t(mydatascale), method=pearson)), method=complete) hc - hclust(as.dist(1-cor(mydatascale, method=spearman)), method=complete) myclhr - cutree(hr, h=max(hr$height)/2); mycolhr - sample(rainbow(256)); myclhc - cutree(hc, h=max(hc$height)/2); mycolhc - sample(rainbow(256)); mycolhr - mycolhr[as.vector(myclhr)]; mycolhc - mycolhc[as.vector(myclhc)]; library(gplots) library(RSvgDevice) jpeg(Heatmap.jpg, height=6+2/3, width=6+2/3, units=in, res=1200) heatmap.2(mydatamatrix, Rowv=as.dendrogram(hr), Colv=as.dendrogram(hc), dendrogram=both, scale=row, col=brewer.pal(3, YlOrRd), cexRow=0.01, cexCol=0.01, trace=none, density.info=none, key=TRUE, keysize=1.5, margin=c(5,8),RowSideColor=mycolhr, ColSideColor=mycolhc) dev.off() I would like to save the file in a graphical format that can be edited later in any image editing program (like corel). is there a way to do this in R? Its a lot of data I plotted on heatmap (~ 300*600). The x and y labels are difficult to read. I used cexRow = 0.01 and cexCol =0.01 with 1200 resolution to save as jpeg file. That helped but I can still hardly figure out the row labels. I want to be able to read them to interpret the results and also to edit them with different font/color in corel and may be add other things that could be relevant to my work. So, I guess my question here- is there a way I can make the labels readable in R itself or can I generate a list of the row and col labels (in the exact order as in figure) in a text file separately so I know the order and can try attaching it to heatmap in corel draw? any help will be appreciated! Thanks BD [[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. -- Joshua Wiley Ph.D. Student, Health Psychology University of California, Los Angeles http://www.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.
[R] How to get OR and CI from GEE R package
Hi, I am fitting a GEE model using gee R package, but I am not sure how to get OR and its CI? Could anyone give me some hints? Here are some output: gee.obj - gee(Affection~Sibsex+Probandsex,id = FAMID,family = binomial,corstr = independence,data =seldata) Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27 running glm to get initial regression estimate (Intercept) Sibsex2 Probandsex2 -1.6067213 0.3495830 0.5645009 summary(gee.obj) GEE: GENERALIZED LINEAR MODELS FOR DEPENDENT DATA gee S-function, version 4.13 modified 98/01/27 (1998) Model: Link: Logit Variance to Mean Relation: Binomial Correlation Structure: Independent Call: gee(formula = Affection ~ Sibsex + Probandsex, id = FAMID, data = seldata, family = binomial, corstr = independence) Summary of Residuals: Min 1Q Median 3QMax -0.3334466 -0.3334466 -0.2607218 0.6665534 0.8329557 Coefficients: Estimate Naive S.E.Naive z Robust S.E. Robust z (Intercept) -1.6067213 0.5265207 -3.0515824 0.5475068 -2.9346145 Sibsex2 0.3495830 0.4043623 0.8645293 0.4045141 0.8642049 Probandsex2 0.5645009 0.5543902 1.0182374 0.5580999 1.0114691 Estimated Scale Parameter: 1.027439 Number of Iterations: 1 Working Correlation [,1] [,2] [,3] [,4] [1,]1000 [2,]0100 [3,]0010 [4,]0001 exp(cbind(coef(gee.obj),confint(gee.obj,level = 0.9))) Waiting for profiling to be done... Error in profile.glm(object, which = parm, alpha = (1 - level)/4, trace = trace) : subscript out of bounds Error in exp(cbind(coef(gee.obj), confint(gee.obj, level = 0.9))) : Non-numeric argument to mathematical function exp(coef(gee.obj) + ) (Intercept) Sibsex2 Probandsex2 0.2005441 1.4184760 1.7585698 Thank you for your help, pingzhao [[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] Matrixes inside matrixes
Hi, You can have each cell of a matrix contain a matrix, but for a reason that is just not clear to me the matrices are wrapped in a list, m = matrix(replicate(4,matrix(1:9,3,3),simplify=FALSE), 2,2) m[1,2][[1]] str(m) and even more surprising to me, m itself has become a list for some reason. baptiste On 8 September 2010 17:22, Alaios ala...@yahoo.com wrote: Hello everyone, Could you please help me find out if R supports matrixes inside matrixes? This is what I would like to do I have an area map of humidity per km. I would like at every cell to keep also information about the height of this area, the current temperature etc. Is something like that supported? I would like to thank you in advance for your help Best Regards Alex [[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] saving heatmaps in graphical format that can be edited in graphic editor tools
Side note, since Nabble posts to R-help also, you only need to use Nabble or email, not both. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Change plot order in lattice xyplot
Greetings, I am writing with a question regarding plotting using the xyplot command in lattice. I currently have the commands shown below, but I need to produce a plot that orders the Month variable differently. I was told to use the lattice.options command (shown below) to change the plot order, and this helped by starting the plot at a point other than the bottom-left origin, but this did not transpose the plot in the way I need. I need the plot to begin with June, then July, August, September, October, beginning at the top left side of the plot area. Does anyone now how to make this happen? A section of my data and the commands I am currently using are shown below. Thank you for any assistance! Data: Month Log10_echo_integration_dens Log10_trawl_dens June -2.55876 -2.74726 June -2.24346 -3.7015 July -3.14616 -2.83227 July -2.69961 -3.7015 August -2.96135 -3.7015 August -2.29246 -2.29232 September -2.2096 -2.20181 September -1.80488 -1.81614 October -2.28896 -1.84266 October -2.4 -2.35319 #Commands lattice.options(default.args = list(as.table = TRUE)) xyplot(Log10_trawl_dens~Log10_echo_integration_dens | Month, data = (subset(T.A., Net_Type==T)),ylim=c(-4,0),xlim=c(-4,0),xlab=Log density from hydroacoustics (integration),ylab=Log density from Tucker trawl,main=Density estimates, Tucker Trawl, cex=1.5) Best, Paul S. [[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] Saving/loading custom R scripts
.. Not quite. ?Startup provides details, but note the comment about only the base package being loaded and the need to use somepackage::somefunction() or to explicitly first load a package whose functions are used in .Profile. Note also that .First could also be used instead of putting the code in a profile file. Cheers, Bert Gunter Genentech Nonclinical Statistics On Wed, Sep 8, 2010 at 8:20 AM, Joshua Wiley jwiley.ps...@gmail.com wrote: Hi, Just create a file called .Rprofile that is located in your working directory (this means you could actually have different ones in each working directory). In that file, you can put in code just like any other code that would be source()d in. For instance, all my .Rprofile files start with: r - getOption(repos) r[CRAN] - http://cran.stat.ucla.edu; options(repos = r) rm(r) So that I do not have to pick my CRAN mirror. Similarly you could merely add this line to the file: source(file = http://www.r-statistics.com/wp-content/uploads/2010/02/Friedman-Test-with-Post-Hoc.r.txt;) and R would go online, download that file and source it in (not that I am recommending re-downloading every time you start R). Then whatever names they used to define the functions, would be in your workspace. Note that in general, you will not get any output alerting you that it has worked; however, if you type ls() you should see those functions' names. Cheers, Josh On Wed, Sep 8, 2010 at 12:25 AM, DrCJones matthias.godd...@gmail.com wrote: Hi, How does R automatically load functions so that they are available from the workspace? Is it anything like Matlab - you just specify a directory path and it finds it? The reason I ask is because I found a really nice script that I would like to use on a regular basis, and it would be nice not to have to 'copy and paste' it into R on every startup: http://www.r-statistics.com/wp-content/uploads/2010/02/Friedman-Test-with-Post-Hoc.r.txt This would be for Ubuntu, if that makes any difference. Cheers -- View this message in context: http://r.789695.n4.nabble.com/Saving-loading-custom-R-scripts-tp2530924p2530924.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 University of California, Los Angeles http://www.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. -- Bert Gunter Genentech Nonclinical Biostatistics 467-7374 http://devo.gene.com/groups/devo/depts/ncb/home.shtml __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] saving heatmaps in graphical format that can be edited in graphic editor tool
On Wed, Sep 8, 2010 at 4:32 PM, BD bhakti.dwiv...@gmail.com wrote: I generated a heatmap in R using the following commands: mydata - read.csv(file=Data.csv, header=TRUE, sep=,) mydata - mydata[rowSums(mydata[,-1]^2) 0, ] rownames(mydata)=mydata$Name mydata - mydata[,2:253] mydatamatrix - data.matrix(mydata) mydatascale - t(scale(t(mydatamatrix))) hr - hclust(as.dist(1-cor(t(mydatascale), method=pearson)), method=complete) hc - hclust(as.dist(1-cor(mydatascale, method=spearman)), method=complete) myclhr - cutree(hr, h=max(hr$height)/2); mycolhr - sample(rainbow(256)); myclhc - cutree(hc, h=max(hc$height)/2); mycolhc - sample(rainbow(256)); mycolhr - mycolhr[as.vector(myclhr)]; mycolhc - mycolhc[as.vector(myclhc)]; library(gplots) library(RSvgDevice) jpeg(Heatmap.jpg, height=6+2/3, width=6+2/3, units=in, res=1200) heatmap.2(mydatamatrix, Rowv=as.dendrogram(hr), Colv=as.dendrogram(hc), dendrogram=both, scale=row, col=brewer.pal(3, YlOrRd), cexRow=0.01, cexCol=0.01, trace=none, density.info=none, key=TRUE, keysize=1.5, margin=c(5,8),RowSideColor=mycolhr, ColSideColor=mycolhc) dev.off() I would like to save the file in a graphical format that can be edited later in any image editing program (like corel). is there a way to do this in R? Its a lot of data I plotted on heatmap (~ 300*600). The x and y labels are difficult to read. I used cexRow = 0.01 and cexCol =0.01 with 1200 resolution to save as jpeg file. That helped but I can still hardly figure out the row labels. I want to be able to read them to interpret the results and also to edit them with different font/color in corel and may be add other things that could be relevant to my work. So, I guess my question here- is there a way I can make the labels readable in R itself or can I generate a list of the row and col labels (in the exact order as in figure) in a text file separately so I know the order and can try attaching it to heatmap in corel draw? any help will be appreciated! Thanks! I've been doing exactly this today. Use the svg() device driver to create an svg file. Then edit it with Inkscape, and open-source graphics layout and design program. For a demo, try: svg(foo.svg) plot(1:10) dev.off() Then open Inkscape and load foo.svg. You should be able to move all the bits of the plot around. It has saved me a ton of time today, since I wanted to move a legend on a ggplot graph to make room for another graphic. In Inkscape I can just select the elements of the legend and drag them around. Inkscape is cross-platform, so works on Windows/Mac/Linux I think (am using the Linux version). Barry __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] saving heatmaps in graphical format that can be edited in graphic editor tool
Thanks! I will try it now. I am using linux too! Bhakti On Wed, Sep 8, 2010 at 11:54 AM, Barry Rowlingson [via R] ml-node+2531559-939380251-160...@n4.nabble.comml-node%2b2531559-939380251-160...@n4.nabble.com wrote: On Wed, Sep 8, 2010 at 4:32 PM, BD [hidden email]http://user/SendEmail.jtp?type=nodenode=2531559i=0 wrote: I generated a heatmap in R using the following commands: mydata - read.csv(file=Data.csv, header=TRUE, sep=,) mydata - mydata[rowSums(mydata[,-1]^2) 0, ] rownames(mydata)=mydata$Name mydata - mydata[,2:253] mydatamatrix - data.matrix(mydata) mydatascale - t(scale(t(mydatamatrix))) hr - hclust(as.dist(1-cor(t(mydatascale), method=pearson)), method=complete) hc - hclust(as.dist(1-cor(mydatascale, method=spearman)), method=complete) myclhr - cutree(hr, h=max(hr$height)/2); mycolhr - sample(rainbow(256)); myclhc - cutree(hc, h=max(hc$height)/2); mycolhc - sample(rainbow(256)); mycolhr - mycolhr[as.vector(myclhr)]; mycolhc - mycolhc[as.vector(myclhc)]; library(gplots) library(RSvgDevice) jpeg(Heatmap.jpg, height=6+2/3, width=6+2/3, units=in, res=1200) heatmap.2(mydatamatrix, Rowv=as.dendrogram(hr), Colv=as.dendrogram(hc), dendrogram=both, scale=row, col=brewer.pal(3, YlOrRd), cexRow=0.01, cexCol=0.01, trace=none, density.info=none, key=TRUE, keysize=1.5, margin=c(5,8),RowSideColor=mycolhr, ColSideColor=mycolhc) dev.off() I would like to save the file in a graphical format that can be edited later in any image editing program (like corel). is there a way to do this in R? Its a lot of data I plotted on heatmap (~ 300*600). The x and y labels are difficult to read. I used cexRow = 0.01 and cexCol =0.01 with 1200 resolution to save as jpeg file. That helped but I can still hardly figure out the row labels. I want to be able to read them to interpret the results and also to edit them with different font/color in corel and may be add other things that could be relevant to my work. So, I guess my question here- is there a way I can make the labels readable in R itself or can I generate a list of the row and col labels (in the exact order as in figure) in a text file separately so I know the order and can try attaching it to heatmap in corel draw? any help will be appreciated! Thanks! I've been doing exactly this today. Use the svg() device driver to create an svg file. Then edit it with Inkscape, and open-source graphics layout and design program. For a demo, try: svg(foo.svg) plot(1:10) dev.off() Then open Inkscape and load foo.svg. You should be able to move all the bits of the plot around. It has saved me a ton of time today, since I wanted to move a legend on a ggplot graph to make room for another graphic. In Inkscape I can just select the elements of the legend and drag them around. Inkscape is cross-platform, so works on Windows/Mac/Linux I think (am using the Linux version). Barry __ [hidden email] http://user/SendEmail.jtp?type=nodenode=2531559i=1mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- View message @ http://r.789695.n4.nabble.com/saving-heatmaps-in-graphical-format-that-can-be-edited-in-graphic-editor-tool-tp2531512p2531559.html To unsubscribe from saving heatmaps in graphical format that can be edited in graphic editor tool, click herehttp://r.789695.n4.nabble.com/template/TplServlet.jtp?tpl=unsubscribe_by_codenode=2531512code=Ymhha3RpLmR3aXZlZGlAZ21haWwuY29tfDI1MzE1MTJ8LTE3NjEyNTUyNg==. -- View this message in context: http://r.789695.n4.nabble.com/saving-heatmaps-in-graphical-format-that-can-be-edited-in-graphic-editor-tool-tp2531512p2531575.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] optimized value worse than starting Value
Numerical optimisations are best done using as many methods as possible See the optimx package: http://cran.r-project.org/web/packages/optimx/index.html Ravi. -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Barry Rowlingson Sent: Wednesday, September 08, 2010 10:27 AM To: Michael Bernsteiner Cc: r-help@r-project.org Subject: Re: [R] optimized value worse than starting Value On Wed, Sep 8, 2010 at 1:35 PM, Michael Bernsteiner dethl...@hotmail.com wrote: Dear all, I'm optimizing a relatively simple function. Using optimize the optimized parameter value is worse than the starting. why? f-function(delta,P,U){ minimiz-P+delta*U x-minimiz[1] y-minimiz[2] z-100*(y-x^2)^2+(1-x)^2 return(z) } This looks familiar. Is this some 1-d version of the Rosenbrock Banana Function? http://en.wikipedia.org/wiki/Rosenbrock_function It's designed to be hard to find the minimum. In the real world one would hope that things would not have such a pathological behaviour. Numerical optimisations are best done using as many methods as possible - see optimise, nlm, optim, nlminb and the whole shelf of library books devoted to it. Barry __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] XML getNodeSet syntax for PUBMED XML export
I am looking for the syntax to capture XML tags marked with /DescriptorName MajorTopicYN=Y/ , but the combination of the internal space (between Name and Major and the embedded quote marks are defeating me. I can get all the DescriptorName tags, but these include both MajroTopicYN = Y and N variants. Any suggestions? Thanks in advance. Prototype text from PUBMED MeshHeadingList MeshHeading DescriptorName MajorTopicYN=YAntibodies, Monoclonal/DescriptorName /MeshHeading MeshHeading DescriptorName MajorTopicYN=NBlood Platelets/DescriptorName QualifierName MajorTopicYN=Nimmunology/QualifierName QualifierName MajorTopicYN=Yphysiology/QualifierName QualifierName MajorTopicYN=Nultrastructure/QualifierName /MeshHeading /MeshHeadingList [[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] Checking if the distribution follow a power law
On Sep 8, 2010, at 10:34 AM, NatsumiYotsumoto wrote: Dear all. I'm using igraph package, and do a research about network analysis. With power.law.fit from igraph package, it seems that we can fit a power law distribution to some data. But, I want to know how to judge whether the network distribution follows a power law or not. In order to determine whether something is from distribution A or not- A, one needs to have a sensible way of characterizing or considering what would be in the range of distributions in the not-A. Unfortunately for your question, the range of possible distributions is infinite. That means it would always be possible to have a better fitting distribution than what ever is distribution A. If you have alternatives to the power-law that you want to put to the test, then now is the time to offer them. My guess is that you do not, so I will offer alternatives: Alt A: a) read the citations in the email you cited, especially Newman then ... b) set up a histogram of your data using hist with logarithmic or geometric progression of the breaks argument. c) as a check on you exponent estimate, calculate alpha and se(alpha) as on pg 4-5 of that citation. Alt B: require(sos) ???fitting pareto ???fitting power network # and proceed from there -- David. Does anyone know the way to do this? Thanks for any help. Daigo p.s. Also, I tried several ways such as http://www.mail-archive.com/r-h...@stat.math.ethz.ch/msg62520.html and I got results like this: Profiling... 2.5 % 97.5 % 2.393297 2.412650 What do these suggest? please tell me about this if someone knows. -- 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] 3d plot layout?
Hello! I would like to ask if R can solve the following problem. I need to produce two 3d plots on a single page, that is to arrange them one above the other. Also, I need to visualize points by means of spheres, pyramids and cubes in the 3d space. Also, I would like to fill these symbols with colours. Is this possible to be done with R? In the two dimensional case the R plots are of excellent quality, I use the layout function to arrange the plots and the symbols from 20 to 25 that can be filled. So my question is can I produce an analogous 3d plot with R? Thank you in advance. Regards, Martin __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] two questions
Have you considered doing a permutation test on the interaction? Here is an article that gives the general procedure for a couple of algorithms and a comparison of how well they do: Anderson, Marti J and Legendre, Pierre; An Empirical Comparison of Permutation Methods for Tests of Partial Regression Coefficients in a Linear Model. J. Statist. Comput. Simul., 1999, vol 62, pp. 271-303. -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r- project.org] On Behalf Of Iasonas Lamprianou Sent: Tuesday, September 07, 2010 12:25 AM To: juan xiong; Dennis Murphy Cc: r-help@r-project.org Subject: Re: [R] two questions By the way, ordinal regression would require huge datasets because my dependent variable has around 20 different responses... but again, one might say that with so many ordinal responses, it is as if we have a linear/interval variable, right? I just hoped that there would be a two-way kruskal-wallis or something like that. On the other hand, what is going to happen if I (1) bootstrap data from all cells of my design and average the rank ordering of the data of every cell? And then (2) do the same but using data from a uniform/normal distribution so that I assume that there is no difference between the cells? From point (1) I will find the statistical value and from point (2) the expectation and then with a third step (3) I can run a chi-square on the observed/expected values. Would this be reasonable? But again, how can I distinguish between main and interaction effects? Dr. Iasonas Lamprianou Assistant Professor (Educational Research and Evaluation) Department of Education Sciences European University-Cyprus P.O. Box 22006 1516 Nicosia Cyprus Tel.: +357-22-713178 Fax: +357-22-590539 Honorary Research Fellow Department of Education The University of Manchester Oxford Road, Manchester M13 9PL, UK Tel. 0044 161 275 3485 iasonas.lampria...@manchester.ac.uk --- On Tue, 7/9/10, Dennis Murphy djmu...@gmail.com wrote: From: Dennis Murphy djmu...@gmail.com Subject: Re: [R] two questions To: juan xiong xiongjuan2...@gmail.com Cc: David Winsemius dwinsem...@comcast.net, r-help@r-project.org, Iasonas Lamprianou lampria...@yahoo.com Date: Tuesday, 7 September, 2010, 4:47 Hi: On Mon, Sep 6, 2010 at 5:26 PM, juan xiong xiongjuan2...@gmail.com wrote: Maybe Friedman test The Friedman test corresponds to randomized complete block designs, not general two-way classifications. David's advice is sound, but also investigate proportional odds models (e.g., lrm in Prof. Harrell's rms package) in case the 'usual' approach comes up short. It would be helpful to know the number of response categories and some idea of the number of cities-of-birth under study, though... HTH, Dennis On Mon, Sep 6, 2010 at 4:47 PM, David Winsemius dwinsem...@comcast.netwrote: The usual least-squares methods are fairly robust to departures from normality. Furthermore, it is the residuals that are assumed to be normally distributed (not the marginal distributions that you are probably looking at) , so it does not sound as though you have yet examined the data properly. Tell us what the descriptive stats (say the means, variance, 10th and 90th percentiles) are on the residuals within cells cross- classified by the gender and city-of-birth variables (say the means, variance, 10th and 90th percentiles). On Sep 6, 2010, at 4:34 PM, Iasonas Lamprianou wrote: Dear friends, two questions (1) does anyone know if there are any non-parametric equivalents of the two-way ANOVA in R? I have an ordinal non-normally distributed dependent variable and two factors (gender and city of birth). Normally, one would try a two-way anova, but if R has any non-parametric equivalents, that might be great. There is an entire task view page on robust methods if you decide to press on with this quest. (2) Also, if the interaction of gender and city of birth is statistically significant, which post-hoc tests should I run? How many cities are we talking about? Thanks Jason Dr. Iasonas Lamprianou -- 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. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list
Re: [R] Change plot order in lattice xyplot
Prior to creating a plot I usually just order the factor levels to the order I want them in. So for your example I would do: #Create some data library(lattice) x - runif(100, 0, 20) df - data.frame(x) df$y - (1:10) df$Month - c(October, September, August, July,June) #Plot the figure plt -xyplot(x~y | Month, data =df, layout=c(5,1), xlab=Log density from hydroacoustics (integration), ylab=Log density from Tucker trawl, main=Density estimates, Tucker Trawl, cex=1.5) #Factor levels aren't in the order you want them in. Reorder them how you want. df$Month - factor(df$Month, levels=c(June,July,August, September, October), order=TRUE) #Plot again. plt HTH, Sam -- View this message in context: http://r.789695.n4.nabble.com/Change-plot-order-in-lattice-xyplot-tp2531542p2531619.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] forecasting with non-linear models
Hi: You're fitting y as a function of x; as in any regression model, the x's are assumed to be conditionally fixed. If you want to model x as a function of y, that's a calibration problem. There are several issues at play: 1. In the model, you have assumed x is fixed, but afterward, you want to treat it as random. 2. You're implicitly assuming that the relationship between Y and X is invertible. If this were a math problem, you would be right: y = a exp(b * x) = x = (1/b) log(y/a). Unfortunately, this is a statistical problem, and several problems arise, among them: - the X and Y scales are very different, which suggests rather strongly that the distribution associated with random variation in Y is not the same as the distribution associated with random variation in X. - the distribution of random errors in Y is quite likely not going to have the same relationship to the distribution of random errors in X as the functional relationship between x and y above. More succinctly, the problem is a lack of invariance, so you can't simply invert the problem at the end. 3. Predictions are only as valid/reliable as the underlying model and its attendant assumptions. Your request to predict x as a function of y is essentially acknowledging that the prediction is useless before it is ever made, by point (1). Chemometrics deals with calibration problems regularly - I presume that many calibration functions are nonlinear, so you may find something useful by hunting in that area. In econometrics, a related (but not equivalent) problem is the so-called 'errors in variables', in which both y and x are assumed to be random. Of course, you could model the problem from a Bayesian perspective and hope that MCMC comes to the rescue :) The bottom line is that a statistical relationship between y and x does not translate to a corresponding relationship between x and y (through mathematical inversion). Basically, they are treated as separate problems, which makes sense because the conditional distribution of Y|X = x is not the same as that of X|Y = y. HTH, Dennis 2010/9/8 åÌÅÎÁ âÅÌÙÈ da...@rambler.ru Dear colleagues! Is it possible to make predictions in R? there is an exponential relationship detween y and x x-c(0.001,0.003,0.01,0.16,0.3,0.7,0.9) y-c(38.8,41.5,44.2,27,26.9,6.9,3) f-function(x,a,b){a*exp(b*x)} fm-nls(y~f(x,a,b), start=c(a=1,b=1)) How one can predict x when y=10 and is it possible to calculate standard error of x? The task is equal to function ED in drc package, but it use logistic regression only. Best regards, Elena. -- da...@rambler.ru. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] question on optim
Ben and Ravi have already pointed out that you have a problem with a non-computable (e.g., divide by zero or similar) objective function. This is common. optim() has mostly unconstrained optimizers. L-BFGS-B does handle box or bounds constraints. There is also Rvmmin, which is supposedly the same algorithm as optim's BFGS (I'm the author, but not the implementor of optim). However, Rvmmin has bounds constraints, so you could constrain the parameter going to zero to be .1 or something like that. You don't want to use a bound that would cause the computational failure, because the numerical gradient routine takes a step, essentially walking off the cliff. If you have analytic gradients, you can do much better usually. Note that bounds in Nelder-Mead are fairly awkward to use, and our codes are not very good for that. You might also try bobyqa from the minqa package, but be warned that it is an F1 race car relative to the Chevy of Rvmmin. Very good when set up right, but sometimes tricky to set up. John Nash Message: 33 Date: Tue, 7 Sep 2010 07:38:55 -0700 (PDT) From: Hey Sky heyskywal...@yahoo.com To: R r-help@r-project.org Subject: [R] question on optim Message-ID: 741050.53212...@web113920.mail.gq1.yahoo.com Content-Type: text/plain; charset=iso-8859-1 Hey, R users I do not know how to describe my question. I am a new user for R and write the following?code for a dynamic labor economics?model and use OPTIM to get optimizations and parameter values. the following code does not work due to the?equation: ?? wden[,i]-dnorm((1-regw[,i])/w[5])/w[5] where w[5]?is one of the parameters (together with vector a, b and other elements in vector w)?need to be estimated. if I delete the w[5] from the upper equation. that is: ?wden[,i]-dnorm(1-regw[,i]) optim will give me the estimated parameters. but the paramter w[5] is a key one for me. now my questions is: what reason lead to the first?equation does not work and the way to correct it to make it work? ?I wish I made the queston clear and thanks for any suggestion. Nan from Montreal __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] how to you output a vector to a column in excel?
If you have Excel running with the sheet that you want to use open, then in R you can just do: write.table( 1:10, 'clipboard', sep='\t', row.names=FALSE, col.names=FALSE ) (replace 1:10 with your vector) Then go to excel, right click on the cell where you want the first number to be, and select paste. -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r- project.org] On Behalf Of lord12 Sent: Tuesday, September 07, 2010 3:33 PM To: r-help@r-project.org Subject: [R] how to you output a vector to a column in excel? What is the syntax for this? If you have: vector = c(1,2,3,4), how would you output this to column A of an excel spreadsheet? -- View this message in context: http://r.789695.n4.nabble.com/how-to-you- output-a-vector-to-a-column-in-excel-tp2530470p2530470.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] Change plot order in lattice xyplot
-Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Sam Albers Sent: Wednesday, September 08, 2010 9:42 AM To: r-help@r-project.org Subject: Re: [R] Change plot order in lattice xyplot Prior to creating a plot I usually just order the factor levels to the order I want them in. So for your example I would do: #Create some data library(lattice) x - runif(100, 0, 20) df - data.frame(x) df$y - (1:10) df$Month - c(October, September, August, July,June) #Plot the figure plt -xyplot(x~y | Month, data =df, layout=c(5,1), xlab=Log density from hydroacoustics (integration), ylab=Log density from Tucker trawl, main=Density estimates, Tucker Trawl, cex=1.5) #Factor levels aren't in the order you want them in. Reorder them how you want. df$Month - factor(df$Month, levels=c(June,July,August, September, October), order=TRUE) You don't need to use the ordered=TRUE argument there and it may be mildly inappropriate. The command factor(theData, levels=theLevels) does not reorder theLevels. Using ordered=TRUE means to make an object of class ordered (a subclass of factor). Modelling functions like lm() deal with ordered factors a bit differently than unordered factors, but the ordered/factor distinction has no effect on how most graphics and data manipulation functions deal with them. Bill Dunlap Spotfire, TIBCO Software wdunlap tibco.com #Plot again. plt HTH, Sam -- View this message in context: http://r.789695.n4.nabble.com/Change-plot-order-in-lattice-xyp lot-tp2531542p2531619.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] Matrixes inside matrixes
To add to Erik's answer: You can use a three dimensional array if all of your data for one cell is the same type -- numeric presumably. If the data were different types (numeric and character, say), you could have a matrix of mode list to do that. However, that's unlikely to be worth the hassle. 'S Poetry' (found on www.burns-stat.com) has a chapter on arrays that might be of interest if you are using 3D arrays. I think all of that chapter should apply to R as well. On 08/09/2010 16:27, Erik Iverson wrote: Hello, from ?array An array in R can have one, two or more dimensions. It is simply a vector which is stored with additional attributes giving the dimensions (attribute ‘dim’) and optionally names for those dimensions (attribute ‘dimnames’). A two-dimensional array is the same thing as a ‘matrix’. So, to answer your question, yes. Alaios wrote: Hello everyone, Could you please help me find out if R supports matrixes inside matrixes? This is what I would like to do I have an area map of humidity per km. I would like at every cell to keep also information about the height of this area, the current temperature etc. Is something like that supported? I would like to thank you in advance for your help Best Regards Alex [[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. -- Patrick Burns pbu...@pburns.seanet.com http://www.burns-stat.com (home of 'Some hints for the R beginner' and 'The R Inferno') __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] big data
In addition to Dirks advice about the biglm package, you may also want to look at the RSQLite and SQLiteDF packages which may make dealing with the large dataset faster and easier, especially for passing the chunks to bigglm. -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r- project.org] On Behalf Of André de Boer Sent: Wednesday, September 08, 2010 5:27 AM To: r-help@r-project.org Subject: [R] big data Hello, I searched the internet but i didn't find the answer for the next problem: I want to do a glm on a csv file consisting of 25 columns and 4 mln rows. Not all the columns are relevant. My problem is to read the data into R. Manipulate the data and then do a glm. I've tried with: dd-scan(myfile.csv,colClasses=classes) dat-as.data.frame(dd) My question is: what is the right way to do is? Can someone give me a hint? Thanks, Arend [[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] XML getNodeSet syntax for PUBMED XML export
Hi Rob doc = xmlParse(url for document) dn = getNodeSet(doc, //descriptorna...@majortopic = 'Y']) will do what you want, I believe. XPath - a language for expressing such queries - is quite simple and based on a few simple primitive concepts from which one can create complex compound queries. The //DescriptorName is a node test. The [] is a predicate that includes/discards some of the resulting nodes. D. On 9/8/10 9:09 AM, Rob James wrote: I am looking for the syntax to capture XML tags marked with /DescriptorName MajorTopicYN=Y/ , but the combination of the internal space (between Name and Major and the embedded quote marks are defeating me. I can get all the DescriptorName tags, but these include both MajroTopicYN = Y and N variants. Any suggestions? Thanks in advance. Prototype text from PUBMED MeshHeadingList MeshHeading DescriptorName MajorTopicYN=YAntibodies, Monoclonal/DescriptorName /MeshHeading MeshHeading DescriptorName MajorTopicYN=NBlood Platelets/DescriptorName QualifierName MajorTopicYN=Nimmunology/QualifierName QualifierName MajorTopicYN=Yphysiology/QualifierName QualifierName MajorTopicYN=Nultrastructure/QualifierName /MeshHeading /MeshHeadingList [[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] try-error can not be test. Why?
Hi, I am having some strange problem with detecting try-error. From what I have read so far the following statement: try( log(a) ) == try-error should yield TRUE, however, it yields FALSE. I can not figure out why. Can someone help? Many thanks -- View this message in context: http://r.789695.n4.nabble.com/try-error-can-not-be-test-Why-tp2531675p2531675.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] try-error can not be test. Why?
On Sep 8, 2010, at 1:18 PM, telm8 wrote: Hi, I am having some strange problem with detecting try-error. From what I have read so far the following statement: try( log(a) ) == try-error should yield TRUE, however, it yields FALSE. I can not figure out why. Can someone help? class(try( log(a), silent=TRUE )) == try-error [1] TRUE Many thanks -- View this message in context: http://r.789695.n4.nabble.com/try-error-can-not-be-test-Why-tp2531675p2531675.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. 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] pairs and panel.smooth for two groups
This is fairly simple using lattice graphics: USJudgeRatings - USJudgeRatings[,1:4] USJudgeRatings$group - factor(c(rep(1, 22), rep(0, 21))) library(lattice) splom( ~USJudgeRatings[,1:4], groups=group, data=USJudgeRatings, type=c('p','smooth')) The ggplot2 package probably makes this easy as well (but I am still learning that). If you really need to use the pairs function then you will need to create your own panel function (which could call panel.smooth). -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r- project.org] On Behalf Of Marie-Pierre Sylvestre Sent: Wednesday, September 08, 2010 8:03 AM To: r-help@r-project.org Subject: [R] pairs and panel.smooth for two groups Hi, I have modified the USJudgeRatings data (available in R) to illustrate my question. # Use the first 4 variables of USJudgeRatings and add a group variable with two levels USJudgeRatings - USJudgeRatings[,1:4] USJudgeRatings$group - factor(c(rep(1, 22), rep(0, 21))) # I can draw a pairs graph where members of each group are drawn in different colors: pairs(USJudgeRatings[,1:4], col = c(2,3)[USJudgeRatings$group], pch = c(21,3)[USJudgeRatings$group]) # I would also like to add a smooth line to each subplot like pairs(USJudgeRatings[,1:4], panel=panel.smooth) # but I want the smooth to be done for each of the group, i.e. I want two smooths per subplot. # this creates only one smooth pairs(USJudgeRatings[,1:4], col = c(2,3)[USJudgeRatings$group], pch = c(21,3)[USJudgeRatings$group], panel = panel.smooth) # I understand that panel.smooth is a function that is called for each subplot. I don't know how to tell it to do a smooth for each of my group in each of the subplot. Any help would be appreciated! Best, Marie-Pierre __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] large files produced from image plots?
Hi list, I wonder if anyone has thoughts on making image plots in R [using image() or image.plot(), or filled.contour()]- I've made quite a bit now, but they seem quite large in size when exported to pdf file format (even after compressing with pdftk or ghostscript, which I regularly do). I know that for images, raster graphics output (png, tiff) may be the way to go, but often the ones I make are multi-panel plots with other graphics on them, and are usually included in a LaTeX document (PDFLaTeX does accept png) and require stretching/shrinking (and/or possibly editing with Adobe Illustrator). I have had some luck exporting image plots from Matlab (to postscript or pdf) before in the sense that the files seem smaller and less pixelated. Is this a difference in the way image() plots are produced, or with the way the image is written to the pdf() device (if anyone is familiar with other image-exporting programs...)? The other day I had a 13MB dataset, and probably plotted 3/4 of it! using image() and the compressed pdf output was about 8 MB (it contained other stuff but was an addition of a few KB). I tried filled.contour(), as I understand that it colors polygons to fill contours instead of coloring rectangles at each pixel - and it has saved me before - but this time the contours may have been too sharp as as its compressed pdf came out to be 62 MB... (ouch!). I have not tested this data set with other software programs so it may just have been a difficult data set. Is there a good solution to this (or is it simply not to use a vector-graphics format in these instances), and just for my curiosity, are you aware of any things that other software (data analysis) programs do uder the hood to make their exported images smaller/smoother? Thanks much! Stephen [[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] large files produced from image plots?
Hi, Have you tried the recent rasterImage() function? HTH, baptiste On Sep 8, 2010, at 7:30 PM, Stephen T. wrote: Hi list, I wonder if anyone has thoughts on making image plots in R [using image() or image.plot(), or filled.contour()]- I've made quite a bit now, but they seem quite large in size when exported to pdf file format (even after compressing with pdftk or ghostscript, which I regularly do). I know that for images, raster graphics output (png, tiff) may be the way to go, but often the ones I make are multi-panel plots with other graphics on them, and are usually included in a LaTeX document (PDFLaTeX does accept png) and require stretching/shrinking (and/or possibly editing with Adobe Illustrator). I have had some luck exporting image plots from Matlab (to postscript or pdf) before in the sense that the files seem smaller and less pixelated. Is this a difference in the way image() plots are produced, or with the way the image is written to the pdf() device (if anyone is familiar with other image-exporting programs...)? The other day I had a 13MB dataset, and probably plotted 3/4 of ! it! using image() and the compressed pdf output was about 8 MB (it contained other stuff but was an addition of a few KB). I tried filled.contour(), as I understand that it colors polygons to fill contours instead of coloring rectangles at each pixel - and it has saved me before - but this time the contours may have been too sharp as as its compressed pdf came out to be 62 MB... (ouch!). I have not tested this data set with other software programs so it may just have been a difficult data set. Is there a good solution to this (or is it simply not to use a vector-graphics format in these instances), and just for my curiosity, are you aware of any things that other software (data analysis) programs do uder the hood to make their exported images smaller/smoother? Thanks much! Stephen [[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] try-error can not be test. Why?
Thank worked! Thank you so much!!! -- View this message in context: http://r.789695.n4.nabble.com/try-error-can-not-be-test-Why-tp2531675p2531726.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] optimized value worse than starting Value
@Barry: Yes it is the Rosenbrock Function. I'm trying out some thing I found here: http://math.fullerton.edu/mathews/n2003/PowellMethodMod.html @Ravi: Thanks for your help. I will have a closer look at the BB package. Am I right, that the optimx package is ofline atm? (Windows) Michael From: rvarad...@jhmi.edu To: b.rowling...@lancaster.ac.uk; dethl...@hotmail.com CC: r-help@r-project.org Subject: RE: [R] optimized value worse than starting Value Date: Wed, 8 Sep 2010 12:09:31 -0400 Numerical optimisations are best done using as many methods as possible See the optimx package: http://cran.r-project.org/web/packages/optimx/index.html Ravi. -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Barry Rowlingson Sent: Wednesday, September 08, 2010 10:27 AM To: Michael Bernsteiner Cc: r-help@r-project.org Subject: Re: [R] optimized value worse than starting Value On Wed, Sep 8, 2010 at 1:35 PM, Michael Bernsteiner dethl...@hotmail.com wrote: Dear all, I'm optimizing a relatively simple function. Using optimize the optimized parameter value is worse than the starting. why? f-function(delta,P,U){ minimiz-P+delta*U x-minimiz[1] y-minimiz[2] z-100*(y-x^2)^2+(1-x)^2 return(z) } This looks familiar. Is this some 1-d version of the Rosenbrock Banana Function? http://en.wikipedia.org/wiki/Rosenbrock_function It's designed to be hard to find the minimum. In the real world one would hope that things would not have such a pathological behaviour. Numerical optimisations are best done using as many methods as possible - see optimise, nlm, optim, nlminb and the whole shelf of library books devoted to it. Barry __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] multiple graphs
Problem solved.. My bad. No prb with cdplot or graphics-part. The problem was the a-list.. command which resulted in all three levels of bar$h.r in a[[1]]. Skipping the list function sorted it out. par(mfrow=c(2,2)) a-levels(bar$h.r)[c(1,3,6)] print(a) lapply(a,function(x){ a-subset(bar,h.r==x) with(a, cdplot(wh~Age,ylab=x)) #plot.new() }) Regards, //M On 8. sep. 2010, at 03.37, David Winsemius wrote: On Sep 7, 2010, at 8:02 PM, moleps wrote: Dear all, I´m trying to create multiple graphs on the same page, but they are all stacked on top of each other. My code: par(mfrow=c(2,2)) a-list(levels(bar$h.r)[c(1,3,6)]) print(a) lapply(a,function(x){ a-subset(bar,h.r==x) with(a, cdplot(wh~Age,ylab=x)) #plot.new() }) The plot.new command doesnt help... Any ideas?? ?layout # assuming that the undescribed plotting function is base graphics. Some plotting functions are hard coded and are able to defeat the usual formatting options. -- 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] quot;try-errorquot; can not be test. Why?
telm8 chienlinterry.huang at postgrad.manchester.ac.uk writes: Thank worked! Thank you so much!!! in general it is safer (I think) to test inherits(try(log(a)),try-error) which takes care of the case when class(try(log(a))) has length 1 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Replace NAs in one column with data from another column
Hi list, I have a data frame (m) with 169221 rows and 10 columns and would like to make a new column containing the content of column 3 but replace the NAs in column 3 with the data in column 1 (from the same row as the NA in column 3). Column 1 has data in all rows. My first attempt was: for (i in 1:169221){ if (is.na(m[i,3])==TRUE){ m[i,11] - as.character(m[i,1])} else{ m[i,11] - as.character(m[i,3])} } Works - but takes too long time. I would appreciate alternative solutions. Best regards, Jakob __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Replace NAs in one column with data from another column
one way is the following: m - data.frame(x = rnorm(100), y = rnorm(100), z = rnorm(100)) m$z[sample(100, 20)] - NA m$z.new - ifelse(is.na(m$z), m$x, m$z) I hope it helps. Best, Dimitris On 9/8/2010 8:17 PM, Jakob Hedegaard wrote: Hi list, I have a data frame (m) with 169221 rows and 10 columns and would like to make a new column containing the content of column 3 but replace the NAs in column 3 with the data in column 1 (from the same row as the NA in column 3). Column 1 has data in all rows. My first attempt was: for (i in 1:169221){ if (is.na(m[i,3])==TRUE){ m[i,11]- as.character(m[i,1])} else{ m[i,11]- as.character(m[i,3])} } Works - but takes too long time. I would appreciate alternative solutions. Best regards, Jakob __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Dimitris Rizopoulos Assistant Professor Department of Biostatistics Erasmus University Medical Center Address: PO Box 2040, 3000 CA Rotterdam, the Netherlands Tel: +31/(0)10/7043478 Fax: +31/(0)10/7043014 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Replace NAs in one column with data from another column
?ifelse df$newCol - ifelse(is.na(df$col3), df$col1, df$col3) On Wed, Sep 8, 2010 at 2:17 PM, Jakob Hedegaard jakob.hedega...@agrsci.dk wrote: Hi list, I have a data frame (m) with 169221 rows and 10 columns and would like to make a new column containing the content of column 3 but replace the NAs in column 3 with the data in column 1 (from the same row as the NA in column 3). Column 1 has data in all rows. My first attempt was: for (i in 1:169221){ if (is.na(m[i,3])==TRUE){ m[i,11] - as.character(m[i,1])} else{ m[i,11] - as.character(m[i,3])} } Works - but takes too long time. I would appreciate alternative solutions. Best regards, Jakob __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem that you are trying to solve? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Replace NAs in one column with data from another column
Hi Jakob, You can use is.na() to create an index of which rows in column 3 are missing data, and then select these from column 1. Here is a simple example: dat - data.frame(V1 = 1:5, V3 = c(1, NA, 3, 4, NA)) dat$new - dat$V3 my.na - is.na(dat$V3) dat$new[my.na] - dat$V1[my.na] dat This should be quite fast. I broke the steps up to be explicit, but you can readily simplify them. HTH, Josh On Wed, Sep 8, 2010 at 11:17 AM, Jakob Hedegaard jakob.hedega...@agrsci.dk wrote: Hi list, I have a data frame (m) with 169221 rows and 10 columns and would like to make a new column containing the content of column 3 but replace the NAs in column 3 with the data in column 1 (from the same row as the NA in column 3). Column 1 has data in all rows. My first attempt was: for (i in 1:169221){ if (is.na(m[i,3])==TRUE){ m[i,11] - as.character(m[i,1])} else{ m[i,11] - as.character(m[i,3])} } Works - but takes too long time. I would appreciate alternative solutions. Best regards, Jakob __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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 University of California, Los Angeles http://www.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] circular data
Karen Sargsyan karsar at ibms.sinica.edu.tw writes: Is there any package for clustering of circular data? install.packages(sos) library(sos) findFn(circular clustering) See first row ... cheers Ben Bolker __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Saving/loading custom R scripts
One comment on the function: I see that it uses T/F instead of TRUE/FALSE in a number of places. You'll save yourself some headaches if you replace those 'T/F's. -Peter Ehlers On 2010-09-08 1:25, DrCJones wrote: Hi, How does R automatically load functions so that they are available from the workspace? Is it anything like Matlab - you just specify a directory path and it finds it? The reason I ask is because I found a really nice script that I would like to use on a regular basis, and it would be nice not to have to 'copy and paste' it into R on every startup: http://www.r-statistics.com/wp-content/uploads/2010/02/Friedman-Test-with-Post-Hoc.r.txt This would be for Ubuntu, if that makes any difference. 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] 'par mfrow' and not filling horizontally
Greetings, Folks. I'd appreciate being shown the way out of this one! I've been round the documentation in ever-drecreasing circles, and along other paths, without stumbling on the answer. The background to the question can be exemplified by the example (no graphics window open to start with): set.seed(54321) X0 - rnorm(50) ; Y0 - rnorm(50) par(mfrow=c(2,1),mfg=c(1,1),cex=0.5) plot(X0,Y0,pch=+,col=blue,xlim=c(-3,3),ylim=c(-3,3), xlab=X,ylab=Y,main=My Plot,asp=1) par(mfg=c(2,1)) plot(X0,Y0,pch=+,col=blue,xlim=c(-3,3),ylim=c(-3,3), xlab=X,ylab=Y,main=My Plot,asp=1) As you will see, both plots have been extended laterally to fill the plotting area horizontally, hence extend from approx X = -8 to approx X = +8 (on my X11 display), despite the xlim=c(-3,3); however, the ylim=c(-3,3) has been respected, as has asp=1. What I would like to see, independently of the shape of the graphics window, is a pair of square plots, each with X and Y ranging from -3 to 3, even if this leaves empty space in the graphics window on either side. Hints? With thanks, Ted. E-Mail: (Ted Harding) ted.hard...@manchester.ac.uk Fax-to-email: +44 (0)870 094 0861 Date: 08-Sep-10 Time: 20:01:19 -- XFMail -- __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Replace NAs in one column with data from another column
On Sep 8, 2010, at 2:24 PM, Joshua Wiley wrote: Hi Jakob, You can use is.na() to create an index of which rows in column 3 are missing data, and then select these from column 1. Here is a simple example: dat - data.frame(V1 = 1:5, V3 = c(1, NA, 3, 4, NA)) dat$new - dat$V3 my.na - is.na(dat$V3) dat$new[my.na] - dat$V1[my.na] dat This should be quite fast. I broke the steps up to be explicit, but you can readily simplify them. I was about to post something similar except I was going to avoid the $ operator thinking, incorrectly as it turned out, that it would be faster. I also include the Holtman/Rizopoulos suggestion of ifelse(). I was also surprised that ifelse is the winning strategy: dat[4] - dat[3]; idx -is.na(dat[, 3]) dat[is.na(dat[, 3]), 4] - dat[is.na(dat[, 3]), 1] benchmark(meth.ifelse = {dat$z.new - ifelse(is.na(dat$V3), dat$V1, dat$V3)}, + meth.dlr.sign={dat$new - dat$V3 + my.na - is.na(dat$V3) + dat$new[my.na] - dat$V1[my.na]}, + meth.index ={dat[4] - dat[3]; idx -is.na(dat[, 3]) + dat[idx, 4] - dat[idx, 1]}, + meth.forloop ={for (i in 1:nrow(dat)){ + if (is.na(dat[i,3])==TRUE){ + dat[i,4]- dat[i,1]} + else{ + dat[i,4]- dat[i,3]} } + }, + replications=5000, columns = c(test, replications, elapsed, + relative, user.self) ) test replications elapsed relative user.self 2 meth.dlr.sign 5000 0.502 1.081897 0.501 4 meth.forloop 5000 6.419 13.834052 6.409 1 meth.ifelse 5000 0.464 1.00 0.463 3meth.index 5000 2.908 6.267241 2.904 -- David. HTH, Josh On Wed, Sep 8, 2010 at 11:17 AM, Jakob Hedegaard jakob.hedega...@agrsci.dk wrote: Hi list, I have a data frame (m) with 169221 rows and 10 columns and would like to make a new column containing the content of column 3 but replace the NAs in column 3 with the data in column 1 (from the same row as the NA in column 3). Column 1 has data in all rows. My first attempt was: for (i in 1:169221){ if (is.na(m[i,3])==TRUE){ m[i,11] - as.character(m[i,1])} else{ m[i,11] - as.character(m[i,3])} } Works - but takes too long time. I would appreciate alternative solutions. Best regards, Jakob -- 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.