Re: [R] Matlab inv() and R solve() differences
Joseph P Gray wrote: I submit the following matrix to both MATLAB and R x= 0.133 0.254 -0.214 0.116 0.254 0.623 -0.674 0.139 -0.214 -0.674 0.910 0.011 0.116 0.139 0.011 0.180 MATLAB's inv(x) provides the following 137.21 -50.68 -4.70 -46.42 -120.71 27.28 -8.94 62.19 -58.15 6.93 -7.89 36.94 8.35 11.17 10.42 -14.82 R's solve(x) provides: 261.94 116.22 150.92 -267.78 116.22 344.30 286.68 -358.30 150.92 286.68 252.96 -334.09 -267.78 =358.30 -334.09 475.22 inv(x)*x = I(4) and solve(x)%*%x = I(4) Is there a way to obtain the MATLAB result in R? Multiply x[3,4] by 10: xx - x xx[3,4]-0.11 solve(xx) [,1] [,2] [,3] [,4] [1,] 137.20892 -50.67500 -4.705127 -46.41581 [2,] -120.71445 27.27570 -8.937571 62.19270 [3,] -58.15073 6.93474 -7.886343 36.93919 [4,]8.34851 11.17053 10.415928 -14.81602 -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - (p.dalga...@biostat.ku.dk) FAX: (+45) 35327907 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How do I get my IT department to bless R?
2009/1/29 Daniel Viar dan.v...@gmail.com: How does one get an all Microsoft shop on board with allowing users to user R? An 'all Microsoft shop' is what exactly? There is nothing on your PC that isn't from Microsoft? That makes me think that you're either going to be forced to do your statistics in Excel or you're going to have to write everything from scratch in MS Visual Basic/C#/ASP/Bandwagon-of-the-month Language. $Deity have mercy upon your soul. MS don't make anything even *remotely* like R, and if your IT dept don't see that then get them fixed or fired. Now the argument between R and other proprietary stats packages (SPSS, SAS, Stata) is something completely different. But if the powers that be won't allow non-MS software, then those options are as closed off as R is to you. 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] R DCOMServer Manager 2.0
Smita.KUMAR at rbs.com writes: We use R DCOMServer Manager 2.0, this application uses RGUI 2.3.0 as one of its components. We are planning to upgrade to the latest version of RGUI 2.8.0 but found that R DCOMServer manager is not compatible with the latest version. Check the messages at: http://www.mail-archive.com/rco...@mailman.csd.univie.ac.at/ You can download the latest (working) version from http://rcom.univie.ac.at/download/devel/ And better don't post RDCOM questions here, there is a danger of being rippled by higher authorities on this list when you do. The mailing list above is for RCOM related questions. Dieter __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] ERROR: compilation failed for package 'RdbiPgSQL'
Dear Srinivas Iyyer, I know you wrote this error statement nearly two year ago. But yesterday night I had the same problem. So here is the solution. If you use debian distribution (I use sage) you have to install the following packages to compile RdbiPgSQL: postgresql-8.1 and libpq-dev. You had not installed libpq-dev. That caused the error. So long, Elmar __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Equivalent of Hold On MatLab Command
Does R have a graphic command equivalent of MatLab Hold On ? I am trying to sabve on a pdf file a composite drawing. I first declare the canvas size, then I define the layout, finally I generate the 4 plots according to layout order. Eventually I close the pdf file (dev.off()). The resulting PDF file contains 2 pages. The first one shows only the layout. The second one shows the whole composite drawing. MatLab has the command Hold On to work around similar synchronization problems. Does R have have an equivalent command ? Thank you so much, Maura tutti i telefonini TIM! [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Matlab inv() and R solve() differences
Hello, is there a upper limit to kappa value where I can consider a matrix well-conditioned? Cleber Kingsford Jones wrote: I suppose the solution is unstable because x is ill-conditioned: x [,1] [,2] [,3] [,4] [1,] 0.133 0.254 -0.214 0.116 [2,] 0.254 0.623 -0.674 0.139 [3,] -0.214 -0.674 0.910 0.011 [4,] 0.116 0.139 0.011 0.180 cor(x) [,1] [,2] [,3] [,4] [1,] 1.000 0.9963557 -0.9883690 0.8548065 [2,] 0.9963557 1.000 -0.9976663 0.8084090 [3,] -0.9883690 -0.9976663 1.000 -0.7663847 [4,] 0.8548065 0.8084090 -0.7663847 1.000 kappa(x) [1] 2813.326 hth, Kingsford Jones On Thu, Jan 29, 2009 at 7:00 PM, Joseph P Gray jpg...@uwm.edu wrote: I submit the following matrix to both MATLAB and R x= 0.133 0.254 -0.214 0.116 0.254 0.623 -0.674 0.139 -0.214 -0.674 0.910 0.011 0.116 0.139 0.011 0.180 MATLAB's inv(x) provides the following 137.21 -50.68 -4.70 -46.42 -120.71 27.28 -8.94 62.19 -58.15 6.93 -7.89 36.94 8.35 11.17 10.42 -14.82 R's solve(x) provides: 261.94 116.22 150.92 -267.78 116.22 344.30 286.68 -358.30 150.92 286.68 252.96 -334.09 -267.78 =358.30 -334.09 475.22 inv(x)*x = I(4) and solve(x)%*%x = I(4) Is there a way to obtain the MATLAB result in R? Thanks for any help. Pat Gray __ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] error message with roxygen
Hello useRs, I'm trying to use the Roxygen package. Here my code file : #' A packge to check Roxygen's sanity #' @name helloRoxygen-package #' @docType package NA And my R code to generate the package : library(roxygen) package.skeleton(helloRoxygen, code_files = roxy.r, force = T) roxygenize(helloRoxygen, helloRoxygen, copy.package = F, unlink.target = F, overwrite = T) I obtain this error message : Writing helloRoxygen-package to helloRoxygen/man/helloRoxygen-package.Rd Writing namespace directives to helloRoxygen/NAMESPACE Merging collate directive with helloRoxygen/DESCRIPTION to helloRoxygen/DESCRIPTION *Avis dans load.dependencies() : Package(s) 'helloRoxygen' wouldn't load; callgraphs might be incomplete.* I don't understand what this means. I'm doing something wrong? Thank you for your help. Best regards, david [[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] plotting lines with missing data for x values
Gareth Campbell wrote: I have some data (REE plots - geochemistry) where I have values 1:14 for the x axis, but have no data for some x values. Here for example, let's say that I don't have data for x=2,5,8. So x-1:14 y-c(4, NA, 5, 9, NA, 3.4, 8, NA, 19, 22, 12, 14, 15.3, 15) if I plot the data plot(x,y) and then I want to join with lines lines(x,y) How do I get it so the points join across the missing x-values? So the line joins, for example, point 1,4 with point 3,5 (i.e across point 2,NA)? By convention, NA's say to break the lines, so remove the NA's. okay - !is.na(x) !is.na(y) lines(x[okay], y[okay]) Duncan Murdoch Thanks in advance. Gareth Campbell PhD Candidate The University of Auckland P+649 815 3670 M+6421 256 3511 E gareth.campb...@esr.cri.nz gcam...@gmail.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. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] scoping rules for 'for' [was - Re: for/if loop ]
'The R Inferno' page 36. Patrick Burns patr...@burns-stat.com +44 (0)20 8525 0696 http://www.burns-stat.com (home of The R Inferno and A Guide for the Unwilling S User) SnowManPaddington wrote: Hi ya, thanks a lot everyone!! I changed rr:ii-1 to rr:(ii-1) and the code works!!! I finally get some estimates from the optimization function (i am doing a logit model with 2 segments). Thanks thanks!!! I didn't realize rr:(ii-1) and rr:ii-1 would make such a big difference, especially because the professor used rr:ii-1 in his Gauss code. I didn't realize it means so much different in R! davidr-2 wrote: The lines below made me understand clearly. Maybe they are already in some documentation, but if not, it might help others to avoid my misunderstanding. Thanks to all for the clarifications. -- David -Original Message- From: Duncan Murdoch [mailto:murd...@stats.uwo.ca] Sent: Thursday, January 29, 2009 9:54 AM To: David Reiner dav...@rhotrading.com Cc: Henrik Bengtsson; r-help@r-project.org; SnowManPaddington Subject: [SPAM] - Re: [R] scoping rules for 'for' [was - Re: for/if loop ] - Found word(s) list error in the Text body snip Feel free to do what you like to the variable within the loop (though you might cause Luke to grind his teeth when it messes up his compiler). It will be set to the next value in the 1:10 vector the next time it comes back to the top. snip Duncan Murdoch __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Factor Analysis-factanal function
Dear friends, I'm using R to produce the following Factor Analysis: matriz.cor-hetcor(matrix(as.factor(data), ncol=variables, byrow=T))$correlations factanal(x=data, factors=2, covmat=matriz.cor, scores='regression') Then the screen output shows the following message: Error en factanal(x = data, factors = 2, covmat = matrix, : requested scores without an 'x' matrix Do you know some additional function in order to produce a matrix of scores when 'covmat' parameter is used?. Thank you. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Matlab inv() and R solve() differences
Joseph P Gray wrote: I submit the following matrix to both MATLAB and R x= 0.133 0.254 -0.214 0.116 0.254 0.623 -0.674 0.139 -0.214 -0.674 0.910 0.011 0.116 0.139 0.011 0.180 MATLAB's inv(x) provides the following 137.21 -50.68 -4.70 -46.42 -120.71 27.28 -8.94 62.19 -58.15 6.93 -7.89 36.94 8.35 11.17 10.42 -14.82 R's solve(x) provides: 261.94 116.22 150.92 -267.78 116.22 344.30 286.68 -358.30 150.92 286.68 252.96 -334.09 -267.78 =358.30 -334.09 475.22 The matrix x is clearly symmetric. Therefore I expect a symmetric inverse of x. The result of Matlab's inv(x) is clearly not symmetric. R's result is symmetric. I find what is shown as Matlab's result difficult to believe. Berend -- View this message in context: http://www.nabble.com/Matlab-inv%28%29-and-R-solve%28%29-differences-tp21740213p21745164.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] Problem installing RMySQL (S4R.h:40:17: error: S.h: No such file or directory?)
Hi, I'm trying to install RMySQL and I keep hitting errors. My computer is: uname -a Linux cricket 2.6.18-92.1.22.el5PAE #1 SMP Tue Dec 16 12:36:25 EST 2008 i686 i686 i386 GNU/Linux I have set the following environment settings: export PKG_LIBS=-L/usr/lib/mysql -lmysqlclient export PKG_CPPFLAGS=-I/usr/include/mysql I run the following command: R CMD INSTALL --library $HOME/R/i386-redhat-linux-gnu-library/2.7 RMySQL_0.7-2.tar.gz And I get the output below. Can anyone help me with this? What additional system details can I send? Thanks very much for any tips. Dan. R CMD INSTALL --library $HOME/R/i386-redhat-linux-gnu-library/2.7 RMySQL_0.7-2.tar.gz * Installing *source* package 'RMySQL' ... checking for gcc... gcc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ANSI C... none needed checking how to run the C preprocessor... gcc -E checking for compress in -lz... yes checking for getopt_long in -lc... yes checking for mysql_init in -lmysqlclient... no checking for egrep... grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking mysql.h usability... no checking mysql.h presence... no checking for mysql.h... no configure: creating ./config.status config.status: creating src/Makevars ** libs gcc -m32 -std=gnu99 -I/usr/include/R -I/usr/include/mysql -I/usr/local/include-fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic -fasynchronous-unwind-tables -c RS-DBI.c -o RS-DBI.o In file included from RS-DBI.h:32, from RS-DBI.c:22: S4R.h:40:17: error: S.h: No such file or directory S4R.h:53:24: error: Rversion.h: No such file or directory S4R.h:54:51: error: missing binary operator before token ( S4R.h:62:26: error: Rdefines.h: No such file or directory S4R.h:154:49: error: missing binary operator before token ( S4R.h:176:49: error: missing binary operator before token ( In file included from RS-DBI.c:22: RS-DBI.h:100: error: expected specifier-qualifier-list before 'SEXPTYPE' RS-DBI.h:170: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token RS-DBI.h:173: error: expected ')' before '*' token RS-DBI.h:174: error: expected ')' before '*' token RS-DBI.h:175: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token RS-DBI.h:176: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token RS-DBI.h:179: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token RS-DBI.h:181: error: expected ')' before '*' token RS-DBI.h:182: error: expected ')' before '*' token RS-DBI.h:183: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token RS-DBI.h:184: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token RS-DBI.h:187: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token RS-DBI.h:188: error: expected ')' before '*' token RS-DBI.h:189: error: expected ')' before '*' token RS-DBI.h:190: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token RS-DBI.h:191: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token RS-DBI.h:194: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token RS-DBI.h:195: error: expected ')' before '*' token RS-DBI.h:213: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token RS-DBI.h:220: error: expected ')' before '*' token RS-DBI.h:224: error: expected ')' before '*' token RS-DBI.h:231: error: expected ')' before '*' token RS-DBI.h:251: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token RS-DBI.h:253: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token RS-DBI.h:257: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token RS-DBI.h:259: error: expected declaration specifiers or '...' before 'SEXPTYPE' RS-DBI.h:260: error: expected declaration specifiers or '...' before 'SEXPTYPE' RS-DBI.c:36: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token RS-DBI.c:109: error: expected ')' before '*' token RS-DBI.c:137: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token RS-DBI.c:207: error: expected ')' before '*' token RS-DBI.c:261: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token RS-DBI.c:309: error: expected ')' before '*' token RS-DBI.c: In function 'RS_DBI_allocFields': RS-DBI.c:350: warning: implicit declaration of function
Re: [R] Accessing R as a Web service (UNCLASSIFIED)
Google for R and soap to get information on running R on webserver using soap. cheers, Paul Neiderer, Andrew (Civ, ARL/CISD) wrote: Classification: UNCLASSIFIED Caveats: NONE I am new to R and somewhat to Web server programming. I am a Java programmer, however, and have done quite a bit with X3D (extensible 3D) computer graphics. A statistician that I work with is doing multidimensional scaling (MDS) and provides some x,y,z's which I display using X3D. Currently he is using Permap which more than gets the job done but is written in Visual Basic (I believe). I think it would be a big job to use Permap as a Web service. So I am looking at R (for other reasons as well). My question is - Can I access R via SOAP, e.g., running on a server. Assuming I worded my question correctly and someone understands my question, please provide URLs . so I can get knowledgeable. Thank you. - Andrew M. Neiderer Classification: UNCLASSIFIED Caveats: NONE __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Drs. Paul Hiemstra Department of Physical Geography Faculty of Geosciences University of Utrecht Heidelberglaan 2 P.O. Box 80.115 3508 TC Utrecht Phone: +31302535773 Fax:+31302531145 http://intamap.geo.uu.nl/~paul __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] tab characters
I see 'The R Inferno' being refered quiet often recently. But it was now pointed by Duncan Murdoch that for example the statement concerning variables in a for loop is not correct in there (page 62). As I can not find any information about the book been reviewed by anyone I have a question: is it reliable resource for learning about R? What is the authority of Patrick Burns? I would like to avoid spending much time on learning from 'The R Inferno' to only later discover that it was wrong. Mvh. Marie On Fri, Jan 30, 2009 at 11:13 AM, Patrick Burns pbu...@pburns.seanet.comwrote: 'The R Inferno' pages 45-46. Patrick Burns patr...@burns-stat.com +44 (0)20 8525 0696 http://www.burns-stat.com (home of The R Inferno and A Guide for the Unwilling S User) Nick Matzke wrote: Hi all, Working at the R command line, how do I get strings to display e.g. tab or newline characters as they should be displayed, rather than as e.g. \n or \t? e.g.: x=\t x=\t x [1] \t print(x) [1] \t __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] How do I get my IT department to bless R?
Daniel Viar wrote: I currently use R at work under the radar, but there's a chance I could loose that access. I'd like to get our company to feel comfortable with open source and R in particular. Does anyone have any experience with their company's IT department and management that they would be willing to share? How does one get an all Microsoft shop on board with allowing users to user R? I know about the recent NY Times article and recent news. I'm afraid I may need some case studies or examples of what other companies have done. Any help would be greatly appreciated. What alternative do they expect you to use? If they expect you to use Excel for statistics then its worth letting them know that this would be a very bad idea as there are many short-comings, some of which I've referenced at.. http://slack.ser.man.ac.uk/progs/stata/avoid_excel.html Neil -- View this message in context: http://www.nabble.com/How-do-I-get-my-IT-department-to-%22bless%22-R--tp21739359p21746356.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Problem installing RMySQL (S4R.h:40:17: error: S.h: No such file or directory?)
Dan Bolser wrote: Hi, I'm trying to install RMySQL and I keep hitting errors. My computer is: uname -a Linux cricket 2.6.18-92.1.22.el5PAE #1 SMP Tue Dec 16 12:36:25 EST 2008 i686 i686 i386 GNU/Linux I have set the following environment settings: export PKG_LIBS=-L/usr/lib/mysql -lmysqlclient export PKG_CPPFLAGS=-I/usr/include/mysql I run the following command: R CMD INSTALL --library $HOME/R/i386-redhat-linux-gnu-library/2.7 RMySQL_0.7-2.tar.gz Hi Dan, You will certainly want to upgrade R first. The latest version is R 2.8.1. Jeff And I get the output below. Can anyone help me with this? What additional system details can I send? Thanks very much for any tips. Dan. R CMD INSTALL --library $HOME/R/i386-redhat-linux-gnu-library/2.7 RMySQL_0.7-2.tar.gz * Installing *source* package 'RMySQL' ... checking for gcc... gcc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ANSI C... none needed checking how to run the C preprocessor... gcc -E checking for compress in -lz... yes checking for getopt_long in -lc... yes checking for mysql_init in -lmysqlclient... no checking for egrep... grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking mysql.h usability... no checking mysql.h presence... no checking for mysql.h... no configure: creating ./config.status config.status: creating src/Makevars ** libs gcc -m32 -std=gnu99 -I/usr/include/R -I/usr/include/mysql -I/usr/local/include-fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic -fasynchronous-unwind-tables -c RS-DBI.c -o RS-DBI.o In file included from RS-DBI.h:32, from RS-DBI.c:22: S4R.h:40:17: error: S.h: No such file or directory S4R.h:53:24: error: Rversion.h: No such file or directory S4R.h:54:51: error: missing binary operator before token ( S4R.h:62:26: error: Rdefines.h: No such file or directory S4R.h:154:49: error: missing binary operator before token ( S4R.h:176:49: error: missing binary operator before token ( In file included from RS-DBI.c:22: RS-DBI.h:100: error: expected specifier-qualifier-list before 'SEXPTYPE' RS-DBI.h:170: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token RS-DBI.h:173: error: expected ')' before '*' token RS-DBI.h:174: error: expected ')' before '*' token RS-DBI.h:175: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token RS-DBI.h:176: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token RS-DBI.h:179: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token RS-DBI.h:181: error: expected ')' before '*' token RS-DBI.h:182: error: expected ')' before '*' token RS-DBI.h:183: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token RS-DBI.h:184: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token RS-DBI.h:187: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token RS-DBI.h:188: error: expected ')' before '*' token RS-DBI.h:189: error: expected ')' before '*' token RS-DBI.h:190: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token RS-DBI.h:191: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token RS-DBI.h:194: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token RS-DBI.h:195: error: expected ')' before '*' token RS-DBI.h:213: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token RS-DBI.h:220: error: expected ')' before '*' token RS-DBI.h:224: error: expected ')' before '*' token RS-DBI.h:231: error: expected ')' before '*' token RS-DBI.h:251: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token RS-DBI.h:253: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token RS-DBI.h:257: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token RS-DBI.h:259: error: expected declaration specifiers or '...' before 'SEXPTYPE' RS-DBI.h:260: error: expected declaration specifiers or '...' before 'SEXPTYPE' RS-DBI.c:36: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token RS-DBI.c:109: error: expected ')' before '*' token RS-DBI.c:137: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token RS-DBI.c:207: error: expected ')' before '*' token RS-DBI.c:261: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token RS-DBI.c:309: error: expected ')'
Re: [R] Matlab inv() and R solve() differences
Berend Hasselman wrote: Joseph P Gray wrote: I submit the following matrix to both MATLAB and R x= 0.133 0.254 -0.214 0.116 0.254 0.623 -0.674 0.139 -0.214 -0.674 0.910 0.011 0.116 0.139 0.011 0.180 MATLAB's inv(x) provides the following 137.21 -50.68 -4.70 -46.42 -120.71 27.28 -8.94 62.19 -58.15 6.93 -7.89 36.94 8.35 11.17 10.42 -14.82 R's solve(x) provides: 261.94 116.22 150.92 -267.78 116.22 344.30 286.68 -358.30 150.92 286.68 252.96 -334.09 -267.78 =358.30 -334.09 475.22 The matrix x is clearly symmetric. Therefore I expect a symmetric inverse of x. The result of Matlab's inv(x) is clearly not symmetric. R's result is symmetric. I find what is shown as Matlab's result difficult to believe. Yes. See my earlier post. (Well. I believe it, but not with the same input!) -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - (p.dalga...@biostat.ku.dk) FAX: (+45) 35327907 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Q about how to use Anova.mlm
Dear Paul, -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of pgseye Sent: January-29-09 10:07 PM To: r-help@r-project.org Subject: Re: [R] Q about how to use Anova.mlm Thanks a lot for that John - really helpful. I generated some random numbers and seem to be able to get it to work, so that's great. One thing - it's come up with a 'Type III' test and given me a few warnings. What's the difference between Type II and Type III tests (if there's some basic guide you can point me to). The default for Anova() is type-II tests, but the computational approach taken doesn't provide a test for the intercept, which is the only between-subject term in the model; thus, a type-III test is substituted. In a model with only an intercept, there is no distinction between the two types of tests. More generally, types II and III tests address different hypotheses in models in which some terms are marginal to others. There's a brief explanation in my R and S-PLUS Companion to Applied Regression (Wiley, 2002), which is the book associated with the car package in which Anova() resides. There's a more complete discussion in my Applied Regression Analysis and Generalized Linear Models, Second Edition (Sage, 2008). Neither book, BTW, discusses repeated-measures models. I hope this helps, John Thank you again. Best, Paul -- View this message in context: http://www.nabble.com/Q-about-how-to-use- Anova.mlm-tp21739443p21740704.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] From z to Rho
Hi, when performing a spearman_test stratified by a given factor in package coin, how is it possible to obtain the value of Rho, the Spearman correlation coefficient ? Thanks in advance Gilles (F) [[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] Factor Analysis-factanal function
Dear Ricardo, Factor scores are linear combinations of the original variables and therefore to get factor scores, factanal() needs the data, not just the correlation matrix among the variables. Perhaps what you want is the factor-score coefficient matrix. Since you're apparently using a varimax rotation, which is orthogonal, you could compute the factor-score coefficients from the correlation matrix among variables and the factor loadings. To do this for an oblique rotation, you'd need the factor-correlation matrix, which factanal() sadly and inexplicably doesn't report. All this is academic, however, because if you don't have the original data from which to compute factor scores, what use are the factor-score coefficients? I hope this helps, John -- John Fox, Professor Department of Sociology McMaster University Hamilton, Ontario, Canada web: socserv.mcmaster.ca/jfox -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Ocaña Riola, Ricardo Sent: January-30-09 5:30 AM To: r-help@r-project.org Subject: [R] Factor Analysis-factanal function Dear friends, I'm using R to produce the following Factor Analysis: matriz.cor-hetcor(matrix(as.factor(data), ncol=variables, byrow=T))$correlations factanal(x=data, factors=2, covmat=matriz.cor, scores='regression') Then the screen output shows the following message: Error en factanal(x = data, factors = 2, covmat = matrix, : requested scores without an 'x' matrix Do you know some additional function in order to produce a matrix of scores when 'covmat' parameter is used?. Thank you. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Problem installing RMySQL (S4R.h:40:17: error: S.h: No such file or directory?)
Looks like you installed R from an RPM and missed the R-devel RPM. On Fri, 30 Jan 2009, Dan Bolser wrote: Hi, I'm trying to install RMySQL and I keep hitting errors. My computer is: uname -a Linux cricket 2.6.18-92.1.22.el5PAE #1 SMP Tue Dec 16 12:36:25 EST 2008 i686 i686 i386 GNU/Linux I have set the following environment settings: export PKG_LIBS=-L/usr/lib/mysql -lmysqlclient export PKG_CPPFLAGS=-I/usr/include/mysql I run the following command: R CMD INSTALL --library $HOME/R/i386-redhat-linux-gnu-library/2.7 RMySQL_0.7-2.tar.gz And I get the output below. Can anyone help me with this? What additional system details can I send? Well, what your OS is is often helpful, and how you installed R, and of course the 'at a minimum' information asked for in the posting guide. Thanks very much for any tips. Dan. R CMD INSTALL --library $HOME/R/i386-redhat-linux-gnu-library/2.7 RMySQL_0.7-2.tar.gz * Installing *source* package 'RMySQL' ... checking for gcc... gcc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ANSI C... none needed checking how to run the C preprocessor... gcc -E checking for compress in -lz... yes checking for getopt_long in -lc... yes checking for mysql_init in -lmysqlclient... no checking for egrep... grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking mysql.h usability... no checking mysql.h presence... no checking for mysql.h... no configure: creating ./config.status config.status: creating src/Makevars ** libs gcc -m32 -std=gnu99 -I/usr/include/R -I/usr/include/mysql -I/usr/local/include-fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic -fasynchronous-unwind-tables -c RS-DBI.c -o RS-DBI.o In file included from RS-DBI.h:32, from RS-DBI.c:22: S4R.h:40:17: error: S.h: No such file or directory S4R.h:53:24: error: Rversion.h: No such file or directory S4R.h:54:51: error: missing binary operator before token ( S4R.h:62:26: error: Rdefines.h: No such file or directory S4R.h:154:49: error: missing binary operator before token ( S4R.h:176:49: error: missing binary operator before token ( In file included from RS-DBI.c:22: RS-DBI.h:100: error: expected specifier-qualifier-list before 'SEXPTYPE' RS-DBI.h:170: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token RS-DBI.h:173: error: expected ')' before '*' token RS-DBI.h:174: error: expected ')' before '*' token RS-DBI.h:175: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token RS-DBI.h:176: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token RS-DBI.h:179: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token RS-DBI.h:181: error: expected ')' before '*' token RS-DBI.h:182: error: expected ')' before '*' token RS-DBI.h:183: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token RS-DBI.h:184: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token RS-DBI.h:187: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token RS-DBI.h:188: error: expected ')' before '*' token RS-DBI.h:189: error: expected ')' before '*' token RS-DBI.h:190: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token RS-DBI.h:191: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token RS-DBI.h:194: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token RS-DBI.h:195: error: expected ')' before '*' token RS-DBI.h:213: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token RS-DBI.h:220: error: expected ')' before '*' token RS-DBI.h:224: error: expected ')' before '*' token RS-DBI.h:231: error: expected ')' before '*' token RS-DBI.h:251: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token RS-DBI.h:253: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token RS-DBI.h:257: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token RS-DBI.h:259: error: expected declaration specifiers or '...' before 'SEXPTYPE' RS-DBI.h:260: error: expected declaration specifiers or '...' before 'SEXPTYPE' RS-DBI.c:36: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token RS-DBI.c:109: error: expected ')' before '*' token RS-DBI.c:137: error: expected '=', ',', ';', 'asm' or '__attribute__' before '*' token RS-DBI.c:207: error: expected
Re: [R] tab characters
On 1/30/2009 7:19 AM, Marie Sivertsen wrote: I see 'The R Inferno' being refered quiet often recently. But it was now pointed by Duncan Murdoch that for example the statement concerning variables in a for loop is not correct in there (page 62). As I can not find any information about the book been reviewed by anyone I have a question: is it reliable resource for learning about R? What is the authority of Patrick Burns? I would like to avoid spending much time on learning from 'The R Inferno' to only later discover that it was wrong. That's the first error I've seen in it. In my opinion, it's a very useful reference. Duncan Murdoch Mvh. Marie On Fri, Jan 30, 2009 at 11:13 AM, Patrick Burns pbu...@pburns.seanet.comwrote: 'The R Inferno' pages 45-46. Patrick Burns patr...@burns-stat.com +44 (0)20 8525 0696 http://www.burns-stat.com (home of The R Inferno and A Guide for the Unwilling S User) Nick Matzke wrote: Hi all, Working at the R command line, how do I get strings to display e.g. tab or newline characters as they should be displayed, rather than as e.g. \n or \t? e.g.: x=\t x=\t x [1] \t print(x) [1] \t __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] princomp - varimax - factanal
Hi! I am trying to analyse with R a database that I have previously analysed with SPSS. Steps with SPSS: Factorial analysis Extraction options : I select = Principal component analysis Rotation: varimax Steps with R: I have tried it with varimax function with factanal or with princomp...and the results are different of what I have with SPSS. I think that varimax function is incorporated in factanal function. Does anybody know which are the instructions into R to do exactly the same of what I have done with SPSS??? Thank you very much! [[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] tab characters
Marie Sivertsen wrote: I see 'The R Inferno' being refered quiet often recently. But it was now pointed by Duncan Murdoch that for example the statement concerning variables in a for loop is not correct in there (page 62). As I can not find any information about the book been reviewed by anyone I have a question: is it reliable resource for learning about R? What is the authority of Patrick Burns? I would like to avoid spending much time on learning from 'The R Inferno' to only later discover that it was wrong. In short: Don't worry too much. Pat is an experienced S and R user. In fact, he's been around since R was little but a gleam in its fathers' eyes. He has a record of writing stuff and publishing on the web, in a style somewhat different from what the publishing companies seem to want. The R Inferno is his latest addition, so he's liable to make a few Hey, I wrote about that kind of posts. A quick look suggest that this should be quite an amusing read, but it isn't a textbook for beginners learning R. Rather, it is assumed that you already know the basics, and now need to read about the pitfalls. There could be inaccuracies (the for loop description is indeed mildly off-base), but the intended audience can reasonably be assumed to possess a critical mind. And the nice thing about web publications is that mistakes can be fixed quickly. -pd -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - (p.dalga...@biostat.ku.dk) FAX: (+45) 35327907 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Equivalent of Hold On MatLab Command
Does R have a graphic command equivalent of MatLab Hold On ?
I am trying to sabve on a pdf file a composite drawing. I first
declare the canvas size, then I define the layout, finally I
generate the 4 plots according to layout order. Eventually I close
the pdf file (dev.off()).
The resulting PDF file contains 2 pages. The first one shows only
the layout. The second one shows the whole
composite drawing.
MatLab has the command Hold On to work around similar
synchronization problems.
Does R have have an equivalent command ?
If you are using base graphics (i.e. not lattice/ grid graphics), then you
can mimic MATLAB's hold on feature by using the points/lines/polygons
functions to add additional details to your plots without starting a new
plot. In the case of a multiplot layout, you can use par(mfg=...) to pick
which plot you add things to.
#open the pdf device
pdf(test.pdf)
#setup the layout
par(mfrow=c(2,2))
#plot at each location
for(i in 1:4) plot(runif(1:10))
#return to the first plot
par(mfg=c(1,1))
#add a line to this plot (without replacing anything)
lines(seq(0.1,1,0.1))
#close the device to complete the plot
dev.off()
If you have an extra page in you PDF file, it's probably because you've
called plot.new() somewhere where you didn't mean to (either explicitly or
implicitly). Without a reproducible example, it's hard to help further.
Regards,
Richie.
Mathematical Sciences Unit
HSL
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[R] Rgraphviz install
Hi I've tried several times and followed what others suggest in installing Rgraphviz (https://stat.ethz.ch/pipermail/bioconductor/2008-June/022838.html) But I could not load library(Rgraphviz). There's a message that 'This application has failed to start because libcdt-4.dll was not found' Could anyone suggest me how to make it work? june _ ore_012009 [[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] lmer and weights
I'm using R2.8.1 and trying to do some nested modelling using lmer and weights. When I multiply/divide weights with a constant, variance of groups intercept changes, but variance of the residual doesn't (using unconditional model). Shouldn't they change equally? Are there any specifications on how to set weights properly? Thanks for reply, ___ Gasper Cankar. PhD researcher National Examinations Centre (Ric) gasper.can...@ric.si tel. +386 1 54 84 682 fax. +386 1 54 84 601 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] OO programming S3/S4 paradigm - General question
Hi, Being relatively new to OO programming and not so old on R, I noticed the possibility to do OO programming in R. But it seems there is two paradigms S3 that seems the old one but is the one used in the R.oo package and S4 which seems more recent As a starting point, which one is best to use? Is R.oo useful? what are the main difference between the two? Any feedback helpful. Many thanks in advance have a nice weekend! Julien _ charlas. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] [R-pkgs] np 0.30-1 (nonparametric kernel smoothing methods for mixed data types) is available on CRAN...
Dear R users, Version 0.30-1 of the np package has been released and uploaded to CRAN. The np package provides nonparametric kernel smoothing methods for mixed data types. We encourage anyone using the package to upgrade to the latest version. Description: This package provides a variety of nonparametric (and semiparametric) kernel methods that seamlessly handle a mix of continuous, unordered, and ordered factor data types. We would like to gratefully acknowledge support from the Natural Sciences and Engineering Research Council of Canada (NSERC:www.nserc.ca), the Social Sciences and Humanities Research Council of Canada (SSHRC:www.sshrc.ca), and the Shared Hierarchical Academic Research Computing Network (SHARCNET:www.sharcnet.ca). License: GPL Note that version 0.30-0 and 0.30-1 provide some much needed functionality and bug fixes to the package. Changes from Version 0.30-0 to 0.30-1 [29-Jan-2009] * predict now supports bandwidth, density, distribution, conbandwidth, condensity, and condistribution objects * Consistently allow predictions for categorical values outside of support of training data Note that predictions based upon unconditional density objects defined over categorical variables that lie outside the support of the training data may no longer be true probabilities (i.e., as defined over the training data and the extended/augmented support -- their sum may exceed one) and may therefore require renormalization by the user * Fixed a numerical issue which could hinder npregbw()'s cross validation with higher-order kernels * Default nmulti in npplregbw() is now set correctly * Fixed a bug with the ridging routine in npscoefbw(), added ridging to npscoef * Fixed trivial i/o issue with Multistart 1 of using npscoefbw() Changes from Version 0.20-4 to 0.30-0 [15-Jan-2009] * Added basic user-interrupt checking for all underlying C code so that either Ctrl-C (Rterm) or the `STOP' icon (Rgui) will interrupt all running processes. This has a number of desirable side effects in addition to being able to interrupt C-based processes including i) R no longer showing up as `not responding' under the task manager (Windows) or the activity monitor (Mac OS X) and ii) buffered output now being correctly displayed when using Rgui under Windows and Mac OS X Note that repeated interruption of large jobs can reduce available memory under R - if this becomes an issue (i.e., you get a `cannot allocate...' error under R) simply restart R (i.e., exit then run a fresh R session) * Added a function npseed() that allows the user to set/reset the random seed for all underlying C routines * Fixed a bug that caused npplregbw() to ignore any kernel options for the regression of y on z * Refined certain constants used in the normal-reference density bandwidth rule for increased accuracy * Moved from using the maximum likelihood estimate of variance throughout to the degrees of freedom corrected estimate (all variance estimates now change by the factor (n-1)/n) Feedback, comments, bug reports, and suggestions for improvement are always welcome. Best regards, Jeff Racine Tristen Hayfield -- Professor J. S. Racine Phone: (905) 525 9140 x 23825 Department of EconomicsFAX:(905) 521-8232 McMaster Universitye-mail: raci...@mcmaster.ca 1280 Main St. W.,Hamilton, URL: http://www.economics.mcmaster.ca/racine/ Ontario, Canada. L8S 4M4 `The generation of random numbers is too important to be left to chance.' ___ R-packages mailing list r-packa...@r-project.org https://stat.ethz.ch/mailman/listinfo/r-packages __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Subsetting without partial matches
I have a list of observations of individuals. I would like to make a
list of individuals, with a data frame of observations for each individual.
The following code usually works, but not always
--
# Make a list of empty data frames
animals = list()
indivs = levels(Z$individual_id)
donotprint - sapply(indivs, function(i){
animals[[i]] = data.frame()
})
# Add observations of each animal to the appropriate frame
donotprint - apply(Z, 1, function(r){
ind = r[[individual_id]]
bind = ind # Use different names to confirm that the partial matching
is being done on the left
animals[[bind]]$sighting_number -
c(animals[[ind, exact=TRUE]]$sighting_number, r[[sighting_number]])
animals[[bind]]$date-
c(animals[[ind, exact=TRUE]]$date, r[[date]])
animals[[bind]]$age -
c(animals[[ind, exact=TRUE]]$age, r[[age_num]])
})
--
The problem is partial matching. When it gives the wrong answer, it
gives partial match warnings. Adding exact=TRUE to the left, the way
that I added it to the right, simply produces an argument error.
Changing to single brackets produces other errors.
I read the help, and the Language Definition (not the whole thing), but
could not find clear documentation of what single brackets with
character variable arguments are supposed to do in lists, nor of how
partial matching is handled on the left side of an assignment, nor of
whether R is supposed to do partial-match indexing when an exact match
is available (I would have thought not, and it's documented that it's
not supposed to for function arguments).
I am interested in how the subsetting is supposed to work, but even more
in what might be the best way to code this sort of thing in R.
I am using R 2.6.2 on Mandriva linux.
Thanks for any help,
JD
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Re: [R] OO programming S3/S4 paradigm - General questio
S3 is the original OO approach in R. It is the predominant one and the simplest one. That's the one to use if you are starting out. You may never, in fact, need to go beyond that. S4 builds on S3 so learning S3 won't be a waste of time even if you decide to use S4 later. S4 is substantially more complex than S3. There are also a number of packages that implement alternative OO models. R.oo implements a model closer to the conventional model that other languages use. proto implements the prototype model, particularly applicable to user interface work. On Fri, Jan 30, 2009 at 8:47 AM, julien cuisinier j_cuisin...@hotmail.com wrote: Hi, Being relatively new to OO programming and not so old on R, I noticed the possibility to do OO programming in R. But it seems there is two paradigms S3 that seems the old one but is the one used in the R.oo package and S4 which seems more recent As a starting point, which one is best to use? Is R.oo useful? what are the main difference between the two? Any feedback helpful. Many thanks in advance have a nice weekend! Julien _ charlas. [[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] tab characters
Thank you both Peter and Duncan for explanations. 'The R Inferno' is indeed not so much introduction but I find it useful to know about how I can go wrong in simple things before I do. Mvh. Marie On Fri, Jan 30, 2009 at 3:03 PM, Peter Dalgaard p.dalga...@biostat.ku.dkwrote: Marie Sivertsen wrote: I see 'The R Inferno' being refered quiet often recently. But it was now pointed by Duncan Murdoch that for example the statement concerning variables in a for loop is not correct in there (page 62). As I can not find any information about the book been reviewed by anyone I have a question: is it reliable resource for learning about R? What is the authority of Patrick Burns? I would like to avoid spending much time on learning from 'The R Inferno' to only later discover that it was wrong. In short: Don't worry too much. Pat is an experienced S and R user. In fact, he's been around since R was little but a gleam in its fathers' eyes. He has a record of writing stuff and publishing on the web, in a style somewhat different from what the publishing companies seem to want. The R Inferno is his latest addition, so he's liable to make a few Hey, I wrote about that kind of posts. A quick look suggest that this should be quite an amusing read, but it isn't a textbook for beginners learning R. Rather, it is assumed that you already know the basics, and now need to read about the pitfalls. There could be inaccuracies (the for loop description is indeed mildly off-base), but the intended audience can reasonably be assumed to possess a critical mind. And the nice thing about web publications is that mistakes can be fixed quickly. -pd [[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] princomp - varimax - factanal
Maybe look into vegan - although this is not my area of specialty (assuming I have one at all). good luck On Fri, Jan 30, 2009 at 9:00 AM, Alberto Maceda Veiga amac...@ub.edu wrote: Hi! I am trying to analyse with R a database that I have previously analysed with SPSS. Steps with SPSS: Factorial analysis Extraction options : I select = Principal component analysis Rotation: varimax Steps with R: I have tried it with varimax function with factanal or with princomp...and the results are different of what I have with SPSS. I think that varimax function is incorporated in factanal function. Does anybody know which are the instructions into R to do exactly the same of what I have done with SPSS??? Thank you very much! [[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. -- Stephen Sefick Let's not spend our time and resources thinking about things that are so little or so large that all they really do for us is puff us up and make us feel like gods. We are mammals, and have not exhausted the annoying little problems of being mammals. -K. Mullis __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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 collect arrays in an array?
Dear R-Experts, Seek your help. Please let me know how arrays of different sizes can be collected in one array. suppose I want to collect following arrays in one array. How can I do so? array(1): #row=3, #col=4(these columns store data of different types) array(2): #row=6, #col=4 array(3): #row=3, #col=4 want to store in Main_array How to define dimensions of Main_array? Thank you. Regards, Suresh -- View this message in context: http://www.nabble.com/How-to-collect-arrays-in-an-array--tp21748883p21748883.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] From z to Rho
Do these functions help? #Fisher's r-to-z: fr2z - function(r) atanh(r) #Fisher's z-to-r: fz2r - function(z) tanh(z) On Fri, Jan 30, 2009 at 9:29 AM, LE PAPE Gilles lepape.gil...@neuf.fr wrote: Hi, when performing a spearman_test stratified by a given factor in package coin, how is it possible to obtain the value of Rho, the Spearman correlation coefficient ? Thanks in advance Gilles (F) [[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. -- Mike Lawrence Graduate Student Department of Psychology Dalhousie University www.thatmike.com Looking to arrange a meeting? Check my public calendar: http://www.thatmike.com/mikes-public-calendar ~ Certainty is folly... I think. ~ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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 collect arrays in an array?
why not a list? On Fri, Jan 30, 2009 at 10:10 AM, Suresh_FSFM suresh.ghals...@gmail.com wrote: Dear R-Experts, Seek your help. Please let me know how arrays of different sizes can be collected in one array. suppose I want to collect following arrays in one array. How can I do so? array(1): #row=3, #col=4(these columns store data of different types) array(2): #row=6, #col=4 array(3): #row=3, #col=4 want to store in Main_array How to define dimensions of Main_array? Thank you. Regards, Suresh -- View this message in context: http://www.nabble.com/How-to-collect-arrays-in-an-array--tp21748883p21748883.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. -- Stephen Sefick Let's not spend our time and resources thinking about things that are so little or so large that all they really do for us is puff us up and make us feel like gods. We are mammals, and have not exhausted the annoying little problems of being mammals. -K. Mullis __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Date functions
Hi there, I am completely new to R and would like to do two things with date functions: 1. Compute any date from a specified starting point, e.g. x - 2 months 2. How do I determine the weekday of any given date? Thanks in advance -- View this message in context: http://www.nabble.com/Date-functions-tp21748580p21748580.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] Date functions
# 1 d - Sys.Date() seq(d, len = 2, by = 2 months)[2] # 2 as.numeric(format(d, %w)) # 0 = Sunday # or format(d, %a) See R News 4/1 for more info and the table at the end of it in particular. On Fri, Jan 30, 2009 at 9:54 AM, ehxpieterse eduard.piete...@macquarie.com wrote: Hi there, I am completely new to R and would like to do two things with date functions: 1. Compute any date from a specified starting point, e.g. x - 2 months 2. How do I determine the weekday of any given date? Thanks in advance -- View this message in context: http://www.nabble.com/Date-functions-tp21748580p21748580.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] How to collect arrays in an array?
Thanks for a prompt response. Ok. I see your point. However, then next silly question is how to access these elements of list dynamically? suppose I want to access 3rd item or 3rd element of the list (which would be my array-3 stored at 3rd position in the list). Thank you. Regards, Suresh stephen sefick wrote: why not a list? On Fri, Jan 30, 2009 at 10:10 AM, Suresh_FSFM suresh.ghals...@gmail.com wrote: Dear R-Experts, Seek your help. Please let me know how arrays of different sizes can be collected in one array. suppose I want to collect following arrays in one array. How can I do so? array(1): #row=3, #col=4(these columns store data of different types) array(2): #row=6, #col=4 array(3): #row=3, #col=4 want to store in Main_array How to define dimensions of Main_array? Thank you. Regards, Suresh -- View this message in context: http://www.nabble.com/How-to-collect-arrays-in-an-array--tp21748883p21748883.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. -- Stephen Sefick Let's not spend our time and resources thinking about things that are so little or so large that all they really do for us is puff us up and make us feel like gods. We are mammals, and have not exhausted the annoying little problems of being mammals. -K. Mullis __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- View this message in context: http://www.nabble.com/How-to-collect-arrays-in-an-array--tp21748883p21749677.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] simulating outcomes - categorical distribution (?)
Hi, I am simulating an event that has 15 possible outcomes and I have a vector 'pout' that gives me the probability of each outcome - different outcomes have different probabilities. Does anyone know a simple way of simulating the outcome of my event? If my event had only two possible outcomes (0/1) I would pick a uniform random number between 0 and 1 and use it to choose between the two possible outcomes given a certain probability of outcome 0 or failure 1. Now, since I have 15 possible outcomes, I guess that this should be done with some form of a categorical distribution but I couldn't find a function for the categorical distribution yet. Thanks for any suggestions! Gonçalo __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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 collect arrays in an array?
You'll need the [[ operator. Your.list.name[[3]] gives the third element. ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest Cel biometrie, methodologie en kwaliteitszorg / Section biometrics, methodology and quality assurance Gaverstraat 4 9500 Geraardsbergen Belgium tel. + 32 54/436 185 thierry.onkel...@inbo.be www.inbo.be To call in the statistician after the experiment is done may be no more than asking him to perform a post-mortem examination: he may be able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher The plural of anecdote is not data. ~ Roger Brinner The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data. ~ John Tukey -Oorspronkelijk bericht- Van: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] Namens Suresh_FSFM Verzonden: vrijdag 30 januari 2009 16:45 Aan: r-help@r-project.org Onderwerp: Re: [R] How to collect arrays in an array? Thanks for a prompt response. Ok. I see your point. However, then next silly question is how to access these elements of list dynamically? suppose I want to access 3rd item or 3rd element of the list (which would be my array-3 stored at 3rd position in the list). Thank you. Regards, Suresh stephen sefick wrote: why not a list? On Fri, Jan 30, 2009 at 10:10 AM, Suresh_FSFM suresh.ghals...@gmail.com wrote: Dear R-Experts, Seek your help. Please let me know how arrays of different sizes can be collected in one array. suppose I want to collect following arrays in one array. How can I do so? array(1): #row=3, #col=4(these columns store data of different types) array(2): #row=6, #col=4 array(3): #row=3, #col=4 want to store in Main_array How to define dimensions of Main_array? Thank you. Regards, Suresh -- View this message in context: http://www.nabble.com/How-to-collect-arrays-in-an-array--tp21748883p2174 8883.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. -- Stephen Sefick Let's not spend our time and resources thinking about things that are so little or so large that all they really do for us is puff us up and make us feel like gods. We are mammals, and have not exhausted the annoying little problems of being mammals. -K. Mullis __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- View this message in context: http://www.nabble.com/How-to-collect-arrays-in-an-array--tp21748883p2174 9677.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. Dit bericht en eventuele bijlagen geven enkel de visie van de schrijver weer en binden het INBO onder geen enkel beding, zolang dit bericht niet bevestigd is door een geldig ondertekend document. The views expressed in this message and any annex are purely those of the writer and may not be regarded as stating an official position of INBO, as long as the message is not confirmed by a duly signed document. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Rgraphviz install
June Wong wrote: Hi I've tried several times and followed what others suggest in installing Rgraphviz (https://stat.ethz.ch/pipermail/bioconductor/2008-June/022838.html) But I could not load library(Rgraphviz). There's a message that 'This application has failed to start because libcdt-4.dll was not found' Could anyone suggest me how to make it work? Yes, install the latest graphviz from the installer graphviz-2.20.3.msi. Note that it install under a directory called .2.21 So no idea which version it is (and hard to find out). Best, Uwe Ligges june _ ore_012009 [[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 collect arrays in an array?
Thanks a lot ! :-) Regards, Suresh ONKELINX, Thierry wrote: You'll need the [[ operator. Your.list.name[[3]] gives the third element. ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest Cel biometrie, methodologie en kwaliteitszorg / Section biometrics, methodology and quality assurance Gaverstraat 4 9500 Geraardsbergen Belgium tel. + 32 54/436 185 thierry.onkel...@inbo.be www.inbo.be To call in the statistician after the experiment is done may be no more than asking him to perform a post-mortem examination: he may be able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher The plural of anecdote is not data. ~ Roger Brinner The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data. ~ John Tukey -Oorspronkelijk bericht- Van: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] Namens Suresh_FSFM Verzonden: vrijdag 30 januari 2009 16:45 Aan: r-help@r-project.org Onderwerp: Re: [R] How to collect arrays in an array? Thanks for a prompt response. Ok. I see your point. However, then next silly question is how to access these elements of list dynamically? suppose I want to access 3rd item or 3rd element of the list (which would be my array-3 stored at 3rd position in the list). Thank you. Regards, Suresh stephen sefick wrote: why not a list? On Fri, Jan 30, 2009 at 10:10 AM, Suresh_FSFM suresh.ghals...@gmail.com wrote: Dear R-Experts, Seek your help. Please let me know how arrays of different sizes can be collected in one array. suppose I want to collect following arrays in one array. How can I do so? array(1): #row=3, #col=4(these columns store data of different types) array(2): #row=6, #col=4 array(3): #row=3, #col=4 want to store in Main_array How to define dimensions of Main_array? Thank you. Regards, Suresh -- View this message in context: http://www.nabble.com/How-to-collect-arrays-in-an-array--tp21748883p2174 8883.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. -- Stephen Sefick Let's not spend our time and resources thinking about things that are so little or so large that all they really do for us is puff us up and make us feel like gods. We are mammals, and have not exhausted the annoying little problems of being mammals. -K. Mullis __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- View this message in context: http://www.nabble.com/How-to-collect-arrays-in-an-array--tp21748883p2174 9677.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. Dit bericht en eventuele bijlagen geven enkel de visie van de schrijver weer en binden het INBO onder geen enkel beding, zolang dit bericht niet bevestigd is door een geldig ondertekend document. The views expressed in this message and any annex are purely those of the writer and may not be regarded as stating an official position of INBO, as long as the message is not confirmed by a duly signed document. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- View this message in context: http://www.nabble.com/How-to-collect-arrays-in-an-array--tp21748883p21750072.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] Analytics Training Institute launches course on R
Hi All, Now you can join for R course offered by G K Analytics Training Institute Pvt Ltd. We also provide online training Program for those who are willing to take up this course. To know more about the courses offered visit www.analyticstraining.in You can also mail us your queries at i...@analyticstraining.in. Regards ATI Team [[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] simulating outcomes - categorical distribution (?)
on 01/30/2009 09:46 AM Gonçalo Ferraz wrote: Hi, I am simulating an event that has 15 possible outcomes and I have a vector 'pout' that gives me the probability of each outcome - different outcomes have different probabilities. Does anyone know a simple way of simulating the outcome of my event? If my event had only two possible outcomes (0/1) I would pick a uniform random number between 0 and 1 and use it to choose between the two possible outcomes given a certain probability of outcome 0 or failure 1. Now, since I have 15 possible outcomes, I guess that this should be done with some form of a categorical distribution but I couldn't find a function for the categorical distribution yet. Thanks for any suggestions! Gonçalo See ?sample sample(OutcomeVector, NumberOfOutcomesToGenerate, prob = pout, replace = TRUE) where OutcomeVector and pout contain a 1:1 pairing of each event to its respective probability. pout - 1:15 / 100 pout [1] 0.01 0.02 0.03 0.04 0.05 0.06 0.07 0.08 0.09 0.10 0.11 0.12 0.13 [14] 0.14 0.15 # Set seed for reproducibility set.seed(1) # Generate 1000 replicates using the target probability distribution Outcomes - sample(1:15, 1000, prob = pout, replace = TRUE) table(Outcomes) Outcomes 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 11 15 27 43 34 48 53 73 70 65 102 112 109 120 118 # Note that the random sample will approach the desired distribution # in large samples, not be exact prop.table(table(Outcomes)) Outcomes 1 2 3 4 5 6 7 8 9101112 0.011 0.015 0.027 0.043 0.034 0.048 0.053 0.073 0.070 0.065 0.102 0.112 131415 0.109 0.120 0.118 BTW, you could use sample() to do this for binary outcomes as well, or use rbinom() to generate replicates from a binomial distribution. Using: help.search(distribution) will lead you to additional information on other distributions available. HTH, Marc Schwartz __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Subsetting without partial matches
I have not seen you describe the value of doing partial matching in
this application, so pardon this perhaps non-responsive reply:
Wouldn't it have been much, much simpler to have used the subset
function (which returns a dataframe object) at the first assignment to
donotprint?
Something along the lines of (untested) :
donotprint - sapply(indivs, function(i){
animals[[i]] = subset(Z, individual_id == i, select =
c(sighting_number, date, age_num) ) } # reconsider naming variable
date
)
--
David Winsemius
On Jan 30, 2009, at 7:46 AM, Jonathan Dushoff wrote:
I have a list of observations of individuals. I would like to make
a list of individuals, with a data frame of observations for each
individual.
The following code usually works, but not always
--
# Make a list of empty data frames
animals = list()
indivs = levels(Z$individual_id)
donotprint - sapply(indivs, function(i){
animals[[i]] = data.frame()
})
# Add observations of each animal to the appropriate frame
donotprint - apply(Z, 1, function(r){
ind = r[[individual_id]]
bind = ind # Use different names to confirm that the partial
matching is being done on the left
animals[[bind]]$sighting_number -
c(animals[[ind, exact=TRUE]]$sighting_number,
r[[sighting_number]])
animals[[bind]]$date-
c(animals[[ind, exact=TRUE]]$date, r[[date]])
animals[[bind]]$age -
c(animals[[ind, exact=TRUE]]$age, r[[age_num]])
})
--
The problem is partial matching. When it gives the wrong answer, it
gives partial match warnings. Adding exact=TRUE to the left, the
way that I added it to the right, simply produces an argument
error. Changing to single brackets produces other errors.
I read the help, and the Language Definition (not the whole thing),
but could not find clear documentation of what single brackets with
character variable arguments are supposed to do in lists, nor of how
partial matching is handled on the left side of an assignment, nor
of whether R is supposed to do partial-match indexing when an exact
match is available (I would have thought not, and it's documented
that it's not supposed to for function arguments).
I am interested in how the subsetting is supposed to work, but even
more in what might be the best way to code this sort of thing in R.
I am using R 2.6.2 on Mandriva linux.
Thanks for any help,
JD
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[R] identifying what labels have been created in a plot
Colleagues R 2.8.0; OS X, Vista, Ubuntu Linux In some instances, when I create a graphic using plot(XVAR, YVAR), it would be valuable to know the values that R will display on the y-axis (e.g., if the range of data is 0-70, it might display 0, 10, 30, 50, 70). Is there a simple means to access these values? Also, in some instances, additional ticks appear between the displayed values (in this case, at 20, 40, 60). Can I obtain the list of the positions of all ticks? Access to this information permits me to tailor the ticks and labels in a particular manner. Thanks for any suggestions. Dennis Dennis Fisher MD P (The P Less Than Company) Phone: 1-866-PLessThan (1-866-753-7784) Fax: 1-415-564-2220 www.PLessThan.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] paste together object names to pass it on to a function
Hello, I have a maybe trivial question, but I simply don't understand well enought how to work with text/strings: I have a rather compelx data structure, a big list with several sub-lists/dataframes and for certain calculations (which I do in loops), I only need a certain group of sub-lists/dataframes, which I want to specify with a name vector and paste together the object name and pass it on to a function. Here an (hopefully) instructive example #Data Example gnuff-list() gnuff$IHD$LE-66 gnuff$LUNG$LE -55 #This is the list, where I collect data for different diseases at the second level of the list #Now I want to do calcualtions just for these two diseases and the sub-list LE within these diseases nam - c(LUNG,IHD) for(i in 1:2) x[i] - paste(gnuff,nam[i],LE,sep=$) /2 x #So I try to paste the name of the object which I mean (gnuff$IHD$LEand gnuff$LUNG$LE, respectivly), but R treats them as a string and not as the name of an object. # I tried seveal commands to make it treat like an object name (the get() looked most promising), but so far to no avail #commands I have tried j - eval(paste(gnuff,nam[i],LE,sep=$)) parse(paste(gnuff,nam[i],sep=$)) quote(paste(gnuff,nam[i],sep=$)) get(paste(gnuff,nam[i],sep=$)) Anybody any hints where to look? Thanks and have a great weekend! Best, Stefan __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] identifying what labels have been created in a plot
It might be easier to generate the plot without the y-axis and then add you data with 'axis' using whatever tick marks you want. On Fri, Jan 30, 2009 at 11:51 AM, Dennis Fisher fis...@plessthan.com wrote: Colleagues R 2.8.0; OS X, Vista, Ubuntu Linux In some instances, when I create a graphic using plot(XVAR, YVAR), it would be valuable to know the values that R will display on the y-axis (e.g., if the range of data is 0-70, it might display 0, 10, 30, 50, 70). Is there a simple means to access these values? Also, in some instances, additional ticks appear between the displayed values (in this case, at 20, 40, 60). Can I obtain the list of the positions of all ticks? Access to this information permits me to tailor the ticks and labels in a particular manner. Thanks for any suggestions. Dennis Dennis Fisher MD P (The P Less Than Company) Phone: 1-866-PLessThan (1-866-753-7784) Fax: 1-415-564-2220 www.PLessThan.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. -- 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.
[R] sub question
Hello R users, I have a string, for example: x - \t\tabc\t def This string can contain any number of tabulations. I want to replace each tabulation of the begining of the string by the same number of space: abc\t def I'm trying to do this with gsub : gsub(\t, , x) # replace every \t [1] abc def sub(^\t, , x) # replace only the first \t [1] \tabc\t def sub(^\t*, , x) # replace all beginning \t, but only one space [1] abc\t def How can I do this ? Thank you very much. david [[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] run query using rexcel runrfile and rodbc sql query
Hi,
I'm using R-2.8.1 for windows. I wrote a script calls the RODBC
package to run sql queries against an oracle database. It runs fine
when run from the rconsole and returns a data.frame with a summary for
a set of experiments. I want to run this script using the
rinterface.RunRFile command in an excel plugin, using the rexcel
package. When I run the code from my excel plugin I get an error:
Error -2147220502 in Module RExcel.RServer Error running expression
eval(parse(text=source(.rexcel..hzpouai)))
Here is my excel plugin code:
rinterface.StartRServer
rinterface.RRun setwd(C:/Documents and Settings/bbolt/
Desktop)
ChDir C:/Documents and Settings/bbolt/Desktop
rinterface.RunRFile Script.r
It works fine if Script.r is something simple like:
Text - data.frame(Hello=Hello)
But will give me the error when Script.R is something like:
inSet - TEST853
library(RODBC)
query - function(qu){
con -
odbcConnect
(Development
,uid=username,pwd=password,believeNRows=FALSE,rows_at_time=50)
sqlQuery(con,qu)
}
qu - paste(m.parentid as SET from setmap m where m.childid in
(select t.experiment from experimentsets t where
t.setname=',inSET,'),sep=)
ExperimentSet - as.character(query(qu)[,1])
The error only occurs when I call my query function. Does anyone
know if there is a way to run sql queries in this manner?
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Re: [R] identifying what labels have been created in a plot
on 01/30/2009 10:51 AM Dennis Fisher wrote: Colleagues R 2.8.0; OS X, Vista, Ubuntu Linux In some instances, when I create a graphic using plot(XVAR, YVAR), it would be valuable to know the values that R will display on the y-axis (e.g., if the range of data is 0-70, it might display 0, 10, 30, 50, 70). Is there a simple means to access these values? Also, in some instances, additional ticks appear between the displayed values (in this case, at 20, 40, 60). Can I obtain the list of the positions of all ticks? Access to this information permits me to tailor the ticks and labels in a particular manner. Thanks for any suggestions. Dennis See ?axis, where in the Details, it will lead you to ?axTicks plot(c(0, 70), c(0, 70)) # Y axis tick marks axTicks(2) [1] 0 10 20 30 40 50 60 70 pretty() will also get you similar information, save when using log scaling: pretty(c(0, 70)) [1] 0 10 20 30 40 50 60 70 Keep in mind that you can always explicitly call axis() using the 'at' argument to specify the locations of the tick marks and labels, after plotting something without the axes being drawn by default. HTH, Marc Schwartz __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] paste together object names to pass it on to a function
This should do it: ?[[ gnuff-list() gnuff$IHD$LE-66 gnuff$LUNG$LE -55 nam - c(LUNG,IHD) x - numeric(2) # allocate for(i in 1:2) + x[i] - gnuff[[nam[i]]]$LE / 2 x [1] 27.5 33.0 On Fri, Jan 30, 2009 at 12:06 PM, stefan.d...@gmail.com stefan.d...@gmail.com wrote: Hello, I have a maybe trivial question, but I simply don't understand well enought how to work with text/strings: I have a rather compelx data structure, a big list with several sub-lists/dataframes and for certain calculations (which I do in loops), I only need a certain group of sub-lists/dataframes, which I want to specify with a name vector and paste together the object name and pass it on to a function. Here an (hopefully) instructive example #Data Example gnuff-list() gnuff$IHD$LE-66 gnuff$LUNG$LE -55 #This is the list, where I collect data for different diseases at the second level of the list #Now I want to do calcualtions just for these two diseases and the sub-list LE within these diseases nam - c(LUNG,IHD) for(i in 1:2) x[i] - paste(gnuff,nam[i],LE,sep=$) /2 x #So I try to paste the name of the object which I mean (gnuff$IHD$LEand gnuff$LUNG$LE, respectivly), but R treats them as a string and not as the name of an object. # I tried seveal commands to make it treat like an object name (the get() looked most promising), but so far to no avail #commands I have tried j - eval(paste(gnuff,nam[i],LE,sep=$)) parse(paste(gnuff,nam[i],sep=$)) quote(paste(gnuff,nam[i],sep=$)) get(paste(gnuff,nam[i],sep=$)) Anybody any hints where to look? Thanks and have a great weekend! Best, Stefan __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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.
[R] Using Rscript
Dear List, Hopefully someone will point me to a piece of documentation that I have overlooked. I am running Rscript successfully to read and execute an R program, but have failed to find the correct syntax to route the output to a file using the Rscript command that invokes the job. I tried Rscript -e 'sink(outputfile)' script.R , but it then ignored the scriptfile. I know that pipes would solve the problem in unix, but I have no idea how the windows equivalent works. I am running R.2.8.0 on windows, Many thanks, Philip This message should be regarded as confidential. If you have received this email in error please notify the sender and destroy it immediately. Statements of intent shall only become binding when confirmed in hard copy by an authorised signatory. The contents of this email may relate to dealings with other companies within the Detica Group plc group of companies. Detica Limited is registered in England under No: 1337451. Registered offices: Surrey Research Park, Guildford, Surrey, GU2 7YP, England. [[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] paste together object names to pass it on to a function
A rule of thumb is that if the solution seems a lot harder than the task, there is probably a better approach. I think you want something like: lapply(gnuff[nam], function(x) x$LE) Patrick Burns patr...@burns-stat.com +44 (0)20 8525 0696 http://www.burns-stat.com (home of The R Inferno and A Guide for the Unwilling S User) stefan.d...@gmail.com wrote: Hello, I have a maybe trivial question, but I simply don't understand well enought how to work with text/strings: I have a rather compelx data structure, a big list with several sub-lists/dataframes and for certain calculations (which I do in loops), I only need a certain group of sub-lists/dataframes, which I want to specify with a name vector and paste together the object name and pass it on to a function. Here an (hopefully) instructive example #Data Example gnuff-list() gnuff$IHD$LE-66 gnuff$LUNG$LE -55 #This is the list, where I collect data for different diseases at the second level of the list #Now I want to do calcualtions just for these two diseases and the sub-list LE within these diseases nam - c(LUNG,IHD) for(i in 1:2) x[i] - paste(gnuff,nam[i],LE,sep=$) /2 x #So I try to paste the name of the object which I mean (gnuff$IHD$LEand gnuff$LUNG$LE, respectivly), but R treats them as a string and not as the name of an object. # I tried seveal commands to make it treat like an object name (the get() looked most promising), but so far to no avail #commands I have tried j - eval(paste(gnuff,nam[i],LE,sep=$)) parse(paste(gnuff,nam[i],sep=$)) quote(paste(gnuff,nam[i],sep=$)) get(paste(gnuff,nam[i],sep=$)) Anybody any hints where to look? Thanks and have a great weekend! Best, Stefan __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Analytics Training Institute launches course on R
Cool nice initiative. Regards, Ajay Rodney Dangerfield - My marriage is on the rocks again, yeah, my wife just broke up with her boyfriend. On Fri, Jan 30, 2009 at 9:46 PM, Analytics Training analyticstraining...@gmail.com wrote: Hi All, Now you can join for R course offered by G K Analytics Training Institute Pvt Ltd. We also provide online training Program for those who are willing to take up this course. To know more about the courses offered visit www.analyticstraining.in You can also mail us your queries at i...@analyticstraining.in. Regards ATI Team [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] paste together object names to pass it on to a function
Or perhaps: lapply(gnuff, [[, LE) On Fri, Jan 30, 2009 at 12:35 PM, Patrick Burns pbu...@pburns.seanet.com wrote: A rule of thumb is that if the solution seems a lot harder than the task, there is probably a better approach. I think you want something like: lapply(gnuff[nam], function(x) x$LE) Patrick Burns patr...@burns-stat.com +44 (0)20 8525 0696 http://www.burns-stat.com (home of The R Inferno and A Guide for the Unwilling S User) stefan.d...@gmail.com wrote: Hello, I have a maybe trivial question, but I simply don't understand well enought how to work with text/strings: I have a rather compelx data structure, a big list with several sub-lists/dataframes and for certain calculations (which I do in loops), I only need a certain group of sub-lists/dataframes, which I want to specify with a name vector and paste together the object name and pass it on to a function. Here an (hopefully) instructive example #Data Example gnuff-list() gnuff$IHD$LE-66 gnuff$LUNG$LE -55 #This is the list, where I collect data for different diseases at the second level of the list #Now I want to do calcualtions just for these two diseases and the sub-list LE within these diseases nam - c(LUNG,IHD) for(i in 1:2) x[i] - paste(gnuff,nam[i],LE,sep=$) /2 x #So I try to paste the name of the object which I mean (gnuff$IHD$LEand gnuff$LUNG$LE, respectivly), but R treats them as a string and not as the name of an object. # I tried seveal commands to make it treat like an object name (the get() looked most promising), but so far to no avail #commands I have tried j - eval(paste(gnuff,nam[i],LE,sep=$)) parse(paste(gnuff,nam[i],sep=$)) quote(paste(gnuff,nam[i],sep=$)) get(paste(gnuff,nam[i],sep=$)) Anybody any hints where to look? Thanks and have a great weekend! Best, Stefan __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] princomp - varimax - factanal
At 3:00 PM +0100 1/30/09, Alberto Maceda Veiga wrote: Hi! I am trying to analyse with R a database that I have previously analysed with SPSS. Steps with SPSS: Factorial analysis Extraction options : I select = Principal component analysis Rotation: varimax Unfortunately, SPSS labels principal components as a factor model. It is not. So, extracting the first n factors by using factanal will give you a very different solution than the first n principal components. Steps with R: I have tried it with varimax function with factanal or with princomp...and the results are different of what I have with SPSS. I think that varimax function is incorporated in factanal function. Does anybody know which are the instructions into R to do exactly the same of what I have done with SPSS??? To duplicate the SPSS analysis try using the psych package. The principal function in the psych package will extract the first n components (defaults to 1) and then by default rotate using varimax. library(psych) pc - principal(my.data,n) #where n is the number components you want to extract Let me know if this matches the SPSS output. Bill Thank you very much! [[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. -- William Revelle http://personality-project.org/revelle.html Professor http://personality-project.org/personality.html Department of Psychology http://www.wcas.northwestern.edu/psych/ Northwestern University http://www.northwestern.edu/ Attend ISSID/ARP:2009 http://issid.org/issid.2009/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] bootstrapping in regression
Hi Thomas, Thomas Mang schrieb: I have a question here: I am not sure if I understand your 'fit the full model ... to the permuted data set'. Am I correct to suppose that once the residuals of the reduced-model fit have been permuted and added back to the fitted values, the values obtained this way (fitted + permuted residuals) now constitute the new y-values to which the full model is fitted? Is that correct ? It is. Look at section 2.2, Permutation of Residuals under the Reduced Model here: Anderson, M. J. Legendre, P. An empirical comparison of permutation methods for tests of partial regression coefficients in a linear model. Journal of Statistical Computation and Simulation, 1999, 62, 271-303 Do you know if this procedure is also valid for a mixed-effects model ? That's a good question... if you find out anything about this, please let me know. HTH, Stephan __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Matlab inv() and R solve() differences
Hi Cleber, there is no hard-and-fast magic number here. Ill-conditioning also depends on what you are trying to do (inference? prediction?). The condition number is only one of a number of conditioning/collinearity diagnostics commonly used. Take a look at: Golub, G. H., Van Loan, C. F. (1996). Matrix Computations (3rd ed.). Baltimore: Johns Hopkins University Press. Belsley, D. A. (1991a). Conditioning Diagnostics: Collinearity and Weak Data in Regression. New York, NY: Wiley. Hill, R. C., Adkins, L. C. (2001). Collinearity. In B. H. Baltagi (Ed.), A Companion to Theoretical Econometrics (p. 256-278). Oxford: Blackwell HTH, Stephan Cleber Nogueira Borges schrieb: Hello, is there a upper limit to kappa value where I can consider a matrix well-conditioned? Cleber Kingsford Jones wrote: I suppose the solution is unstable because x is ill-conditioned: x [,1] [,2] [,3] [,4] [1,] 0.133 0.254 -0.214 0.116 [2,] 0.254 0.623 -0.674 0.139 [3,] -0.214 -0.674 0.910 0.011 [4,] 0.116 0.139 0.011 0.180 cor(x) [,1] [,2] [,3] [,4] [1,] 1.000 0.9963557 -0.9883690 0.8548065 [2,] 0.9963557 1.000 -0.9976663 0.8084090 [3,] -0.9883690 -0.9976663 1.000 -0.7663847 [4,] 0.8548065 0.8084090 -0.7663847 1.000 kappa(x) [1] 2813.326 hth, Kingsford Jones On Thu, Jan 29, 2009 at 7:00 PM, Joseph P Gray jpg...@uwm.edu wrote: I submit the following matrix to both MATLAB and R x= 0.133 0.254 -0.214 0.116 0.254 0.623 -0.674 0.139 -0.214 -0.674 0.910 0.011 0.116 0.139 0.011 0.180 MATLAB's inv(x) provides the following 137.21 -50.68 -4.70 -46.42 -120.71 27.28 -8.94 62.19 -58.15 6.93 -7.89 36.94 8.35 11.17 10.42 -14.82 R's solve(x) provides: 261.94 116.22 150.92 -267.78 116.22 344.30 286.68 -358.30 150.92 286.68 252.96 -334.09 -267.78 =358.30 -334.09 475.22 inv(x)*x = I(4) and solve(x)%*%x = I(4) Is there a way to obtain the MATLAB result in R? Thanks for any help. Pat Gray __ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] princomp - varimax - factanal
Thank you very much Bill!!! We get it. The results are the same. Best wishes, Alberto 2009/1/30 William Revelle li...@revelle.net At 3:00 PM +0100 1/30/09, Alberto Maceda Veiga wrote: Hi! I am trying to analyse with R a database that I have previously analysed with SPSS. Steps with SPSS: Factorial analysis Extraction options : I select = Principal component analysis Rotation: varimax Unfortunately, SPSS labels principal components as a factor model. It is not. So, extracting the first n factors by using factanal will give you a very different solution than the first n principal components. Steps with R: I have tried it with varimax function with factanal or with princomp...and the results are different of what I have with SPSS. I think that varimax function is incorporated in factanal function. Does anybody know which are the instructions into R to do exactly the same of what I have done with SPSS??? To duplicate the SPSS analysis try using the psych package. The principal function in the psych package will extract the first n components (defaults to 1) and then by default rotate using varimax. library(psych) pc - principal(my.data,n) #where n is the number components you want to extract Let me know if this matches the SPSS output. Bill Thank you very much! [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.htmlhttp://www.r-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- William Revelle http://personality-project.org/revelle.html Professor http://personality-project.org/personality.html Department of Psychology http://www.wcas.northwestern.edu/psych/ Northwestern University http://www.northwestern.edu/ Attend ISSID/ARP:2009 http://issid.org/issid.2009/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.htmlhttp://www.r-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Alberto Maceda Veiga Departamento de Biología Animal Vertebrados. 1ª Planta. Despacho 151. Facultad de Biología Universidad de Barcelona Av. Diagonal, 645 08028 Barcelona Spain Tel: 93 4021041 Fax: 93 4034426 Email: albertomac...@gmail.com º º º [[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] paste together object names to pass it on to a function
Perhaps this will help: #Data Example gnuff-list() gnuff$IHD$LE-66 gnuff$LUNG$LE -55 #This is the list, where I collect data for different diseases at the #second level of the list #Now I want to do calcualtions just for these two diseases and the #sub-list LE within these diseases nam - c(LUNG,IHD) for(i in nam) print(gnuff[[i]]) # use the elements of nam as the index values # the lack of output from an evaluation done within the for-loop might be one of Burns' Infernal examples. # here's see one of my mistakes: for(i in nam) (gnuff[[i]]) #---returns a list--- #$LE #[1] 55 #$LE #[1] 66 #--- for(i in nam) print(gnuff[[i]]$LE) #use list extraction to get the values #[1] 55 #[1] 66 On Jan 30, 2009, at 12:06 PM, stefan.d...@gmail.com wrote: Hello, I have a maybe trivial question, but I simply don't understand well enought how to work with text/strings: I have a rather compelx data structure, a big list with several sub-lists/dataframes and for certain calculations (which I do in loops), I only need a certain group of sub-lists/dataframes, which I want to specify with a name vector and paste together the object name and pass it on to a function. Here an (hopefully) instructive example #Data Example gnuff-list() gnuff$IHD$LE-66 gnuff$LUNG$LE -55 #This is the list, where I collect data for different diseases at the second level of the list #Now I want to do calcualtions just for these two diseases and the sub-list LE within these diseases nam - c(LUNG,IHD) for(i in 1:2) x[i] - paste(gnuff,nam[i],LE,sep=$) /2 x #So I try to paste the name of the object which I mean (gnuff$IHD$LEand gnuff$LUNG$LE, respectivly), but R treats them as a string and not as the name of an object. # I tried seveal commands to make it treat like an object name (the get() looked most promising), but so far to no avail #commands I have tried j - eval(paste(gnuff,nam[i],LE,sep=$)) parse(paste(gnuff,nam[i],sep=$)) quote(paste(gnuff,nam[i],sep=$)) get(paste(gnuff,nam[i],sep=$)) Anybody any hints where to look? Thanks and have a great weekend! Best, Stefan __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Fitted values and residuals from glmmPQL (MASS package)
Dear All, I would like to analyse the residuals from a generalized linear mixed model (GLMM) that I estimated, with random effects, by means of the command glmmPQL, from the MASS package. It is not very clear to me what the actual residuals to analyse are (Y - Yhat): I obtain two columns of residuals, of which the first are population residuals, and the second refer to the grouping used in the random effects. Which of the two (or which combination of the two) are my actual errors? Working the problem through the fitted values creates the same confusion to me, as I also have two columns of fitted values. There's probably something about the way mixed models are treated in R that I'm not catching here... Can someone help me? Thanks and best regards, Roberto Patuelli Roberto Patuelli, Ph.D. Post-doc researcher Institute for Economic Research (IRE) University of Lugano via Maderno 24, CP 4361 CH-6904 Lugano Switzerland Phone: +41-(0)58-666-4166 Fax: +39-02-700419665 Email: roberto.patue...@lu.unisi.ch Homepage: http://www.people.lu.unisi.ch/patuellr [[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] identifying what labels have been created in a plot
You might want to look at the pretty function. The code that I have seen often calls that function for the creation of axis tick levels with min and max as arguments. And its help page suggests that axTicks may give you exactly what you were seeking. -- David Winsemius On Jan 30, 2009, at 11:51 AM, Dennis Fisher wrote: Colleagues R 2.8.0; OS X, Vista, Ubuntu Linux In some instances, when I create a graphic using plot(XVAR, YVAR), it would be valuable to know the values that R will display on the y- axis (e.g., if the range of data is 0-70, it might display 0, 10, 30, 50, 70). Is there a simple means to access these values? Also, in some instances, additional ticks appear between the displayed values (in this case, at 20, 40, 60). Can I obtain the list of the positions of all ticks? Access to this information permits me to tailor the ticks and labels in a particular manner. Thanks for any suggestions. Dennis Dennis Fisher MD P (The P Less Than Company) Phone: 1-866-PLessThan (1-866-753-7784) Fax: 1-415-564-2220 www.PLessThan.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] sub question
David Hajage wrote:
Hello R users,
I have a string, for example:
x - \t\tabc\t def
This string can contain any number of tabulations. I want to replace each
tabulation of the begining of the string by the same number of space:
abc\t def
I'm trying to do this with gsub :
gsub(\t, , x) # replace every \t
[1] abc def
sub(^\t, , x) # replace only the first \t
[1] \tabc\t def
sub(^\t*, , x) # replace all beginning \t, but only one space
[1] abc\t def
How can I do this ?
there may be better solutions, but this should do:
strings = c('pure', '\t- 1 removed', '\t\t- 2 removed, 1 left -\t')
gsub('\t|(*COMMIT)(*FAIL)', ' ', strings, perl=TRUE)
# pure - 1 removed - 2 removed, 1 left -\t
vQ
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Re: [R] Fitted values and residuals from glmmPQL (MASS package)
glmmPQL is a wrapper for lme, so look at its documentation (and the especially the Pinheiro-Bates book). On Fri, 30 Jan 2009, Roberto Patuelli wrote: Dear All, I would like to analyse the residuals from a generalized linear mixed model (GLMM) that I estimated, with random effects, by means of the command glmmPQL, from the MASS package. It is not very clear to me what the actual residuals to analyse are (Y - Yhat): I obtain two columns of residuals, of which the first are population residuals, and the second refer to the grouping used in the random effects. Which of the two (or which combination of the two) are my actual errors? Working the problem through the fitted values creates the same confusion to me, as I also have two columns of fitted values. There's probably something about the way mixed models are treated in R that I'm not catching here... Can someone help me? Thanks and best regards, Roberto Patuelli Roberto Patuelli, Ph.D. Post-doc researcher Institute for Economic Research (IRE) University of Lugano via Maderno 24, CP 4361 CH-6904 Lugano Switzerland Phone: +41-(0)58-666-4166 Fax: +39-02-700419665 Email: roberto.patue...@lu.unisi.ch Homepage: http://www.people.lu.unisi.ch/patuellr [[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. -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Using Rscript
You use the facilities of your command-line shell. Rscript infile.R outfile works in every one I have seen in recent years, including Windows' cmd.exe (although many people prefer more capable shells on that platform such as tcsh or bash). On Fri, 30 Jan 2009, Philip Whittall wrote: Dear List, Hopefully someone will point me to a piece of documentation that I have overlooked. I am running Rscript successfully to read and execute an R program, but have failed to find the correct syntax to route the output to a file using the Rscript command that invokes the job. I tried Rscript -e 'sink(outputfile)' script.R , but it then ignored the scriptfile. I know that pipes would solve the problem in unix, but I have no idea how the windows equivalent works. I am running R.2.8.0 on windows, Many thanks, Philip This message should be regarded as confidential. If you have received this email in error please notify the sender and destroy it immediately. Statements of intent shall only become binding when confirmed in hard copy by an authorised signatory. The contents of this email may relate to dealings with other companies within the Detica Group plc group of companies. Detica Limited is registered in England under No: 1337451. Registered offices: Surrey Research Park, Guildford, Surrey, GU2 7YP, England. [[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. -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] help with time series
Hello everyone I'm working with R 2.8.1 on a windows machine I have a question regarding time series analysis The first question is how does R expect the input file to be structured? I'm working with a *.txt file similar to the abbreviated one here: Date,stage 4/2/1953,7.56 4/3/1953,7.56 4/4/1953,7.54 4/5/1953,7.53 4/6/1953,7.5 4/7/1953,7.47 4/8/1953,7.44 4/9/1953,7.41 4/10/1953,7.37 4/11/1953,7.33 4/12/1953,7.3 4/13/1953,7.26 4/14/1953,7.28 4/15/1953,7.28 4/16/1953,7.23 4/17/1953,7.47 4/18/1953,7.59 4/19/1953,7.58 4/20/1953,7.57 4/21/1953,7.56 4/22/1953,7.55 4/23/1953,7.53 4/24/1953,7.51 4/25/1953,7.48 4/26/1953,7.46 4/27/1953,7.5 4/28/1953,7.56 The data record is substantially longer - 50 years worth of daily hydrologic water stage data (column 2). R seems to get confused by the format of this input not knowing what to do with the date field, and also deciding to treat everything as a level. I'm reading the data as follows: mystage - read.table(C:\\Documents and Settings\\skfriedman\\Desktop\\R-scripts\\stage.txt, header = TRUE) looking at the data I get the following: mystage[1:4,] [1] 4/2/1953,7.56 4/3/1953,7.56 4/4/1953,7.54 4/5/1953,7.53 20195 Levels: 1/1/1954,8.72 1/1/1955,8.48 1/1/1956,7.94 1/1/1957,7.88 1/1/1958,8.5 ... 9/9/2007,8.84 What I'd like is a time series with a starting data of April 21, 1953. ending December 30, 2008. data are daily records, so the frequency should be 365 (?) not counting leap year nuisances. So the first question is how should I build the input file to correctly import it to a time series with an odd beginning date? The analysis I'm really trying to get to will involve calculating the mean monthly stage, the mean seasonal (aggregated over several months) stage, the annual maximum period with a continuous stage greater than 0. Thanks in advance I will summary solutions. Much appreciated Steve Steve Friedman Ph. D. Spatial Statistical Analyst Everglades and Dry Tortugas National Park 950 N Krome Ave (3rd Floor) Homestead, Florida 33034 steve_fried...@nps.gov Office (305) 224 - 4282 Fax (305) 224 - 4147 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] help with time series
To seperate the columns, use the sep argument in read.table() mystage - read.table(C:\\Documents and Settings\\skfriedman\\Desktop\\R-scripts\\stage.txt, header = TRUE,sep=',') On Fri, Jan 30, 2009 at 4:17 PM, steve_fried...@nps.gov wrote: Hello everyone I'm working with R 2.8.1 on a windows machine I have a question regarding time series analysis The first question is how does R expect the input file to be structured? I'm working with a *.txt file similar to the abbreviated one here: Date,stage 4/2/1953,7.56 4/3/1953,7.56 4/4/1953,7.54 4/5/1953,7.53 4/6/1953,7.5 4/7/1953,7.47 4/8/1953,7.44 4/9/1953,7.41 4/10/1953,7.37 4/11/1953,7.33 4/12/1953,7.3 4/13/1953,7.26 4/14/1953,7.28 4/15/1953,7.28 4/16/1953,7.23 4/17/1953,7.47 4/18/1953,7.59 4/19/1953,7.58 4/20/1953,7.57 4/21/1953,7.56 4/22/1953,7.55 4/23/1953,7.53 4/24/1953,7.51 4/25/1953,7.48 4/26/1953,7.46 4/27/1953,7.5 4/28/1953,7.56 The data record is substantially longer - 50 years worth of daily hydrologic water stage data (column 2). R seems to get confused by the format of this input not knowing what to do with the date field, and also deciding to treat everything as a level. I'm reading the data as follows: mystage - read.table(C:\\Documents and Settings\\skfriedman\\Desktop\\R-scripts\\stage.txt, header = TRUE) looking at the data I get the following: mystage[1:4,] [1] 4/2/1953,7.56 4/3/1953,7.56 4/4/1953,7.54 4/5/1953,7.53 20195 Levels: 1/1/1954,8.72 1/1/1955,8.48 1/1/1956,7.94 1/1/1957,7.88 1/1/1958,8.5 ... 9/9/2007,8.84 What I'd like is a time series with a starting data of April 21, 1953. ending December 30, 2008. data are daily records, so the frequency should be 365 (?) not counting leap year nuisances. So the first question is how should I build the input file to correctly import it to a time series with an odd beginning date? The analysis I'm really trying to get to will involve calculating the mean monthly stage, the mean seasonal (aggregated over several months) stage, the annual maximum period with a continuous stage greater than 0. Thanks in advance I will summary solutions. Much appreciated Steve Steve Friedman Ph. D. Spatial Statistical Analyst Everglades and Dry Tortugas National Park 950 N Krome Ave (3rd Floor) Homestead, Florida 33034 steve_fried...@nps.gov Office (305) 224 - 4282 Fax (305) 224 - 4147 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Mike Lawrence Graduate Student Department of Psychology Dalhousie University www.thatmike.com Looking to arrange a meeting? Check my public calendar: http://www.thatmike.com/mikes-public-calendar ~ Certainty is folly... I think. ~ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] help with time series
Copy and paste this into an R session: Lines - Date,stage 4/2/1953,7.56 4/3/1953,7.56 4/4/1953,7.54 4/5/1953,7.53 4/6/1953,7.5 4/7/1953,7.47 4/8/1953,7.44 4/9/1953,7.41 4/10/1953,7.37 4/11/1953,7.33 4/12/1953,7.3 4/13/1953,7.26 4/14/1953,7.28 4/15/1953,7.28 4/16/1953,7.23 4/17/1953,7.47 4/18/1953,7.59 4/19/1953,7.58 4/20/1953,7.57 4/21/1953,7.56 4/22/1953,7.55 4/23/1953,7.53 4/24/1953,7.51 4/25/1953,7.48 4/26/1953,7.46 4/27/1953,7.5 4/28/1953,7.56 library(zoo) library(chron) # z - read.zoo(myfile.csv, header = TRUE, sep = ,, FUN = as.chron) z - read.zoo(textConnection(Lines), header = TRUE, sep = ,, FUN = as.chron) plot(z) On Fri, Jan 30, 2009 at 3:17 PM, steve_fried...@nps.gov wrote: Hello everyone I'm working with R 2.8.1 on a windows machine I have a question regarding time series analysis The first question is how does R expect the input file to be structured? I'm working with a *.txt file similar to the abbreviated one here: Date,stage 4/2/1953,7.56 4/3/1953,7.56 4/4/1953,7.54 4/5/1953,7.53 4/6/1953,7.5 4/7/1953,7.47 4/8/1953,7.44 4/9/1953,7.41 4/10/1953,7.37 4/11/1953,7.33 4/12/1953,7.3 4/13/1953,7.26 4/14/1953,7.28 4/15/1953,7.28 4/16/1953,7.23 4/17/1953,7.47 4/18/1953,7.59 4/19/1953,7.58 4/20/1953,7.57 4/21/1953,7.56 4/22/1953,7.55 4/23/1953,7.53 4/24/1953,7.51 4/25/1953,7.48 4/26/1953,7.46 4/27/1953,7.5 4/28/1953,7.56 The data record is substantially longer - 50 years worth of daily hydrologic water stage data (column 2). R seems to get confused by the format of this input not knowing what to do with the date field, and also deciding to treat everything as a level. I'm reading the data as follows: mystage - read.table(C:\\Documents and Settings\\skfriedman\\Desktop\\R-scripts\\stage.txt, header = TRUE) looking at the data I get the following: mystage[1:4,] [1] 4/2/1953,7.56 4/3/1953,7.56 4/4/1953,7.54 4/5/1953,7.53 20195 Levels: 1/1/1954,8.72 1/1/1955,8.48 1/1/1956,7.94 1/1/1957,7.88 1/1/1958,8.5 ... 9/9/2007,8.84 What I'd like is a time series with a starting data of April 21, 1953. ending December 30, 2008. data are daily records, so the frequency should be 365 (?) not counting leap year nuisances. So the first question is how should I build the input file to correctly import it to a time series with an odd beginning date? The analysis I'm really trying to get to will involve calculating the mean monthly stage, the mean seasonal (aggregated over several months) stage, the annual maximum period with a continuous stage greater than 0. Thanks in advance I will summary solutions. Much appreciated Steve Steve Friedman Ph. D. Spatial Statistical Analyst Everglades and Dry Tortugas National Park 950 N Krome Ave (3rd Floor) Homestead, Florida 33034 steve_fried...@nps.gov Office (305) 224 - 4282 Fax (305) 224 - 4147 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Anova and a covariate of no interest
Hi, I have a design with 1 group and repeated measures and a covariate whose effects I¹d like to remove from the data. I tried different models with aov but am not sure if I did it correctly. The design is thus 4 blocks and n=15 and a covariate ³cov² 1- aov.m = aov(da~block+cov+Error(subj),data=d); summary(aov.m) Error: subj Df Sum Sq Mean Sq F value Pr(F) cov1 0.37859 0.37859 2.709 0.1237 Residuals 13 1.81677 0.13975 Error: Within Df Sum Sq Mean Sq F valuePr(F) block 3 0.89600 0.29867 10.7536 2.413e-05 *** cov1 0.00030 0.00030 0.01090.9173 Residuals 41 1.13872 0.02777 Did I did set it up right?? Could I use lm and /or lme to get the covariate out. What would be the formula?? Thanks for your help __ Patrick Bédard Ph.D. Dept. of Neuroscience Brown University [[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] problem using identify() after plot()
I can't seem to use the point-and-click identify() function properly. I'm running R 2.5.1 (I know, I need to get around to upgrading) under Win XP. The problem is, when I click on a point on the graph, I get an error, no point within 0.25 inches. But in some areas, I can click where there is no visible point anywhere close, and an identify() label will pop up. The troublesome code is shown below. I've posted an example graph here: http://bingweb.binghamton.edu/~cryan/junkidentify2.pdf I'd be grateful if anyone could take a look at it. The text() labels are in red, and the results of pointing-and-clicking are shown in black. Notice point 4, for example: near the origin in black, but upper center in red (which is where the real data point should be: point 4 is (11,16) Any chance all the NA's are the problem? plot(V2,mean.barr, type=n) text(V2, mean.barr, label=rownames(temp), col=red) identify(rownames(temp)) # here's the gist of the data str(temp) summary(temp) rownames(temp) temp mean.barr V2 1 NA 6 2 NA 1 3 12.5 6 4 16.0 11 5 11.0 4 6 12.0 0 7 NA 4 8 NA 5 9 NA 2 10NA 3 11 16.5 11 12 14.5 8 13NA 1 14 7.5 4 15 12.5 1 16 20.0 0 17NA 10 18 17.0 11 19NA 0 20 8.5 5 21 10.5 8 22 12.0 5 23 5.0 1 24 8.5 7 25NA 19 26 12.0 0 27NA 2 28NA 0 29 12.5 5 30 18.0 10 31 16.5 20 32 16.5 19 33 9.0 4 34 9.5 4 35 7.0 1 36 8.0 4 37 8.5 13 38 18.5 13 39 9.0 9 40 11.0 1 41 4.0 7 42 11.5 26 43 3.5 12 44 8.5 12 45 10.0 15 46 11.0 5 Thanks --Chris -- Christopher W. Ryan, MD SUNY Upstate Medical University Clinical Campus at Binghamton 40 Arch Street, Johnson City, NY 13790 cryanatbinghamtondotedu PGP public keys available at http://home.stny.rr.com/ryancw/ If you want to build a ship, don't drum up the men to gather wood, divide the work and give orders. Instead, teach them to yearn for the vast and endless sea. [Antoine de St. Exupery] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Ancova
Hello, I have the following ancova: my_ancova = aov(x~a+b) How do I obtain the means of b once the covariate a has been removed? thanks __ Patrick Bédard Ph.D. Dept. of Neuroscience Brown University [[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] reshape with two time variables
I have a data frame in wide format that I'd like to convert to long format. For example, in wide format I have: id A1B1A1B2A2B1A2B2 1 1 400 475 420 510 2 2 390 500 470 472 3 3 428 512 555 610 4 4 703 787 801 822 5 5 611 634 721 705 6 6 543 522 612 788 7 7 411 488 506 623 8 8 654 644 711 795 A is one repeated-measures variable with levels 1 and 2. B is a second repeated-measures variable also with levels 1 and 2. I'd like to end up with: id A B value 1 1 1 1 400 2 2 1 1 390 3 3 1 1 428 4 4 1 1 703 5 5 1 1 611 6 6 1 1 543 7 7 1 1 411 8 8 1 1 654 9 1 1 2 475 10 2 1 2 500 11 3 1 2 512 12 4 1 2 787 13 5 1 2 634 14 6 1 2 522 15 7 1 2 488 16 8 1 2 644 17 1 2 1 420 18 2 2 1 470 19 3 2 1 555 20 4 2 1 801 21 5 2 1 721 22 6 2 1 612 23 7 2 1 506 24 8 2 1 711 25 1 2 2 510 26 2 2 2 472 27 3 2 2 610 28 4 2 2 822 29 5 2 2 705 30 6 2 2 788 31 7 2 2 623 32 8 2 2 795 I've been working with reshape and with the reshape package, but with no success for the two-time-variable case. Can anyone help please? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Ancova
Dear Patrick, -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Patrick B é dard Sent: January-30-09 6:31 PM To: r-help@r-project.org Subject: [R] Ancova Hello, I have the following ancova: my_ancova = aov(x~a+b) How do I obtain the means of b once the covariate a has been removed? One way is to use the function effect() in the effects package: effect(b, my_ancova) which will give you the adjusted means for x at the levels of b with a set to its overall mean. I hope this helps, John thanks __ Patrick Bidard Ph.D. Dept. of Neuroscience Brown University [[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] non-interactive connection to SQL Server
Moshe, Thanks so much for the added comment, I had fallen into the exact same little syntax pitfall. Your clarification really helped! Jack Moshe Olshansky-2 wrote: Yes, it does - thank you! The only thing I forgot (and it took me a while to find this out) was to separate the fields by semicolon, i.e. the correct command is: odbcDriverConnect(driver=SQL Server; database=dataBaseName; wsid=myComputer; server=dataBaseServer; uid=moshe; pwd=moshe) --- Prof Brian Ripley rip...@stats.ox.ac.uk wrote: On Wed, 13 Feb 2008, Moshe Olshansky wrote: Hi everyone, I am afraid that I have already asked this question in the past (or at least I knew an answer to it) but I am unable to do it now. I have an SQL Server data base. I used the GUI interface of odbcDriverConnect to create a .dsn file for this data base and every time I want to connect I invoke odbcDriverConnect() which opens GUI from which I choose my .dsn file and the connection is established. Now I want to do this automatically (without GUI) and all my attempts fail. If I remember correctly the dsn must be a string containing all the connection details but it does not work for me. Clearly it does, as you did that via odbcDriverConnect. Look at the object it returns: it contains the string it used. You can use that directly. Could anybody help, please! Thank you! Moshe. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- View this message in context: http://www.nabble.com/non-interactive-connection-to-SQL-Server-tp15474256p21758234.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] reshape with two time variables
On Fri, Jan 30, 2009 at 5:57 PM, Neil Stewart neil.stew...@warwick.ac.uk wrote: I have a data frame in wide format that I'd like to convert to long format. For example, in wide format I have: id A1B1A1B2A2B1A2B2 1 1 400 475 420 510 2 2 390 500 470 472 3 3 428 512 555 610 4 4 703 787 801 822 5 5 611 634 721 705 6 6 543 522 612 788 7 7 411 488 506 623 8 8 654 644 711 795 A is one repeated-measures variable with levels 1 and 2. B is a second repeated-measures variable also with levels 1 and 2. I'd like to end up with: id A B value 1 1 1 1 400 2 2 1 1 390 3 3 1 1 428 4 4 1 1 703 5 5 1 1 611 6 6 1 1 543 7 7 1 1 411 8 8 1 1 654 9 1 1 2 475 10 2 1 2 500 11 3 1 2 512 12 4 1 2 787 13 5 1 2 634 14 6 1 2 522 15 7 1 2 488 16 8 1 2 644 17 1 2 1 420 18 2 2 1 470 19 3 2 1 555 20 4 2 1 801 21 5 2 1 721 22 6 2 1 612 23 7 2 1 506 24 8 2 1 711 25 1 2 2 510 26 2 2 2 472 27 3 2 2 610 28 4 2 2 822 29 5 2 2 705 30 6 2 2 788 31 7 2 2 623 32 8 2 2 795 I've been working with reshape and with the reshape package, but with no success for the two-time-variable case. Can anyone help please? If you're using melt from the reshape package, once you've melted the data, you'll need to do something like: m$a - as.numeric(substr(m$variable, 1, 1)) m$b - as.numeric(substr(m$variable, 3, 3)) m$variable - NULL Hadley -- http://had.co.nz/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] reshape with two time variables
This will work: x - read.table(textConnection( id A1B1A1B2A2B1A2B2 + 1 1 400 475 420 510 + 2 2 390 500 470 472 + 3 3 428 512 555 610 + 4 4 703 787 801 822 + 5 5 611 634 721 705 + 6 6 543 522 612 788 + 7 7 411 488 506 623 + 8 8 654 644 711 795), header=TRUE) closeAllConnections() require(reshape) x.m - melt(x, id='id') x.m$A - sub(A(\\d+).*, \\1, x.m$variable, perl=TRUE) x.m$B - sub(.*B(\\d+), \\1, x.m$variable, perl=TRUE) x.m$variable - NULL x.m id value A B 1 1 400 1 1 2 2 390 1 1 3 3 428 1 1 4 4 703 1 1 5 5 611 1 1 6 6 543 1 1 7 7 411 1 1 8 8 654 1 1 9 1 475 1 2 10 2 500 1 2 11 3 512 1 2 12 4 787 1 2 13 5 634 1 2 14 6 522 1 2 15 7 488 1 2 16 8 644 1 2 17 1 420 2 1 18 2 470 2 1 19 3 555 2 1 20 4 801 2 1 21 5 721 2 1 22 6 612 2 1 23 7 506 2 1 24 8 711 2 1 25 1 510 2 2 26 2 472 2 2 27 3 610 2 2 28 4 822 2 2 29 5 705 2 2 30 6 788 2 2 31 7 623 2 2 32 8 795 2 2 On Fri, Jan 30, 2009 at 6:57 PM, Neil Stewart neil.stew...@warwick.ac.uk wrote: I have a data frame in wide format that I'd like to convert to long format. For example, in wide format I have: id A1B1A1B2A2B1A2B2 1 1 400 475 420 510 2 2 390 500 470 472 3 3 428 512 555 610 4 4 703 787 801 822 5 5 611 634 721 705 6 6 543 522 612 788 7 7 411 488 506 623 8 8 654 644 711 795 A is one repeated-measures variable with levels 1 and 2. B is a second repeated-measures variable also with levels 1 and 2. I'd like to end up with: id A B value 1 1 1 1 400 2 2 1 1 390 3 3 1 1 428 4 4 1 1 703 5 5 1 1 611 6 6 1 1 543 7 7 1 1 411 8 8 1 1 654 9 1 1 2 475 10 2 1 2 500 11 3 1 2 512 12 4 1 2 787 13 5 1 2 634 14 6 1 2 522 15 7 1 2 488 16 8 1 2 644 17 1 2 1 420 18 2 2 1 470 19 3 2 1 555 20 4 2 1 801 21 5 2 1 721 22 6 2 1 612 23 7 2 1 506 24 8 2 1 711 25 1 2 2 510 26 2 2 2 472 27 3 2 2 610 28 4 2 2 822 29 5 2 2 705 30 6 2 2 788 31 7 2 2 623 32 8 2 2 795 I've been working with reshape and with the reshape package, but with no success for the two-time-variable case. Can anyone help please? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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.
[R] Extracting coordinates for cluster::clusplot()
Dear Friends, require(cluster) x - rbind(cbind(rnorm(10, 0, 0.5), rnorm(10, 0, 0.5)), cbind(rnorm(15, 5, 0.5), rnorm(15, 5, 0.5))) plot(pp - pam(x, 2), which.plots = 1) How can I extract the coordinates used in the plot? _ Professor Michael Kubovy University of Virginia Department of Psychology Postal Address: P.O.Box 400400, Charlottesville, VA 22904-4400 Express Parcels Address: Gilmer Hall, Room 102, McCormick Road, Charlottesville, VA 22903 Office:B011;Phone: +1-434-982-4729 Lab:B019; Phone: +1-434-982-4751 WWW:http://www.people.virginia.edu/~mk9y/ Skype name: polyurinsane [[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] OT :Interview with the CEO , REvolution Computing : Commercial R launched
Dear List, Please find an interview with Richard Schultz, CEO REvolution Computing. REvolution Computing just launched their latest product, commercial as well as enterprise versions of R which include service contracts and tech support. The interview is viewable at http://www.decisionstats.com/2009/01/interviewrichard-schultz-ceo-revolution-computing/( and if site is slow..it is :) also at www.smartdatacollective.com Best Wishes, Ajay Delhi,India www.decisionstats.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.
[R] Corrected Links: OT :Interview with the CEO , REvolution Computing : Commercial R launched
Corrected Links Dear List, Please find an interview with Richard Schultz, CEO REvolution Computing. REvolution Computing just launched their latest product, commercial as well as enterprise versions of R which include service contracts and tech support. The interview is viewable at http://www.decisionstats.com/2009/01/interviewrichard-schultz-ceo-revolution-computing/ Best Wishes, Ajay Delhi,India www.decisionstats.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] Accessing R as a Web service (UNCLASSIFIED)
Neiderer, Andrew (Civ, ARL/CISD) neide...@arl.army.mil writes: Classification: UNCLASSIFIED Caveats: NONE I am new to R and somewhat to Web server programming. I am a Java programmer, however, and have done quite a bit with X3D (extensible 3D) computer graphics. A statistician that I work with is doing multidimensional scaling (MDS) and provides some x,y,z's which I display using X3D. Currently he is using Permap which more than gets the job done but is written in Visual Basic (I believe). I think it would be a big job to use Permap as a Web service. So I am looking at R (for other reasons as well). My question is - Can I access R via SOAP, e.g., running on a server. Assuming I worded my question correctly and someone understands my question, please provide URLs . so I can get knowledgeable. See RWebServices, which allows construction of SOAP-based web service wrappers around R. Martin Thank you. - Andrew M. Neiderer Classification: UNCLASSIFIED Caveats: NONE __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M2 B169 Phone: (206) 667-2793 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Accessing R as a Web service (UNCLASSIFIED)
Also look at biocep - http://biocep-distrib.r-forge.r-project.org/ -Roy M. On Jan 30, 2009, at 8:52 PM, Martin Morgan wrote: Neiderer, Andrew (Civ, ARL/CISD) neide...@arl.army.mil writes: Classification: UNCLASSIFIED Caveats: NONE I am new to R and somewhat to Web server programming. I am a Java programmer, however, and have done quite a bit with X3D (extensible 3D) computer graphics. A statistician that I work with is doing multidimensional scaling (MDS) and provides some x,y,z's which I display using X3D. Currently he is using Permap which more than gets the job done but is written in Visual Basic (I believe). I think it would be a big job to use Permap as a Web service. So I am looking at R (for other reasons as well). My question is - Can I access R via SOAP, e.g., running on a server. Assuming I worded my question correctly and someone understands my question, please provide URLs . so I can get knowledgeable. See RWebServices, which allows construction of SOAP-based web service wrappers around R. Martin Thank you. - Andrew M. Neiderer Classification: UNCLASSIFIED Caveats: NONE __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M2 B169 Phone: (206) 667-2793 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. ** The contents of this message do not reflect any position of the U.S. Government or NOAA. ** Roy Mendelssohn Supervisory Operations Research Analyst NOAA/NMFS Environmental Research Division Southwest Fisheries Science Center 1352 Lighthouse Avenue Pacific Grove, CA 93950-2097 e-mail: roy.mendelss...@noaa.gov (Note new e-mail address) voice: (831)-648-9029 fax: (831)-648-8440 www: http://www.pfeg.noaa.gov/ Old age and treachery will overcome youth and skill. From those who have been given much, much will be expected __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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 do I get my IT department to bless R?
On 1/30/09, Warren Young war...@etr-usa.com wrote: Could you please share a link to the NY Times article? http://www.nytimes.com/2009/01/07/technology/business-computing/07program.html Also do not miss the follow-up blog from the author, plus the the related comments [1]. Liviu [1] http://bits.blogs.nytimes.com/2009/01/08/r-you-ready-for-r/ . -- Do you know how to read? http://www.alienetworks.com/srtest.cfm Do you know how to write? http://garbl.home.comcast.net/~garbl/stylemanual/e.htm#e-mail __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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 do I get my IT department to bless R?
On 1/30/09, Neil Shephard nsheph...@gmail.com wrote: If they expect you to use Excel for statistics then its worth letting them know that this would be a very bad idea as there are many short-comings, some of which I've referenced at.. http://slack.ser.man.ac.uk/progs/stata/avoid_excel.html Very neat resource; thanks. Liviu PS [hijack] Would it make sense to have it (or similar information) assembled in a .pdf documentation file and made available on the Contributed documentation section of R's web site? -- Do you know how to read? http://www.alienetworks.com/srtest.cfm Do you know how to write? http://garbl.home.comcast.net/~garbl/stylemanual/e.htm#e-mail __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] need a help with dealing XML
Hi all, I am trying to read data from a XML file but the thing is when I am trying to read data from XML it is not allowing me to read and store nodes in objects can any one suggest how can i solve this problem. thanks in advance [[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.
