Re: [R] NAs introduced by coercion in dist()
[EMAIL PROTECTED] napsal dne 02.05.2007 16:47:55: It was suggested that the 'NAs introduced by coercion' message might be warning me that my data are not what they should be. I checked this using str(PeaksMatrix), as suggested, and the data seem to be what I thought they were: 'data.frame': 335 obs. of 127 variables: $ Code : Factor w/ 335 levels A1MR,A1MU,..: 1 2 3 4 5 6 7 8 9 10 ... $ P3.70 : num 0 0 0 0 0 0 0 0 0 0 ... $ P3.97 : num 0 0 0 0 0 0 0 0 0 0 ... $ P4.29 : num 0 0 0 0 0 0 0 0 0 0 ... $ P4.90 : num 0 0 0 0 0 0 0 0 0 0 ... $ P6.30 : num 0 0 0 0 0 0 0 0 0 0 ... $ P6.45 : num 7.73 0 0 0 0 0 4.03 0 0 0 ... $ P6.55 : num 0 0 0 0 0 0 0 0 0 0 ... ... I do have 335 observations, 127 variables that are named P3.70, 3.97, P4.29, etc.. This was a relief, but I still don't know whether the distance matrix is what it should be. I tried 'str(dist.PxMx)', which is the name of my distance matrix, but I get something that has not much meaning to me, an unexperienced R user: Class 'dist' atomic [1:55945] 329.6 194.9 130.1 70.7 116.9 ... ..- attr(*, Size)= int 335 ..- attr(*, Labels)= chr [1:335] 1 2 3 4 ... ..- attr(*, Diag)= logi FALSE ..- attr(*, Upper)= logi FALSE ..- attr(*, method)= chr euclidean ..- attr(*, call)= language dist(x = PeaksMatrix, method = euclidean, diag = FALSE, upper = FALSE, p = 2) Any more suggestions, please? Well, it seems that you have the data which you want but why you do not see them is not clear for me. I tried: x-sample(0:2, 100, replace=T) dim(x)-c(10,10) x [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [1,]010011110 1 [2,]010210200 2 [3,]020001101 2 ... [10,]120012021 0 xx-data.frame(var=c(a, b),x) xx var X1 X2 X3 X4 X5 X6 X7 X8 X9 X10 1a 0 1 0 0 1 1 1 1 0 1 2b 0 1 0 2 1 0 2 0 0 2 9a 1 1 0 1 1 0 0 2 2 0 10 b 1 2 0 0 1 2 0 2 1 0 dist(xx, method='euclidean', diag=F,upper=F) 12345678 9 2 2.966479 3 2.345208 3.146427 4 3.633180 3.633180 4.571652 5 4.195235 5.549775 4.571652 4.195235 6 4.195235 4.195235 4.062019 3.924283 3.924283 7 1.816590 3.781534 3.316625 3.781534 3.781534 4.806246 8 2.774887 4.571652 3.633180 4.062019 4.062019 4.806246 3.316625 9 3.316625 4.449719 4.062019 4.449719 3.316625 4.449719 2.774887 3.146427 10 2.774887 5.029911 3.633180 4.324350 3.146427 4.324350 2.569047 2.966479 2.774887 xxx-dist(xx, method='euclidean', diag=F,upper=F) Warning message: NAs introduced by coercion str(xxx) Class 'dist' atomic [1:45] 2.97 2.35 3.63 4.20 4.20 ... ..- attr(*, Size)= int 10 ..- attr(*, Diag)= logi FALSE ..- attr(*, Upper)= logi FALSE ..- attr(*, method)= chr euclidean ..- attr(*, call)= language dist(x = xx, method = euclidean, diag = F, upper = F) seems to be similar to what you get. So I wonder why you do not see you matrix. Try dist.PxMx[1:50] or head(dist.PxMx) to see if you can get something from it. Regards Petr Silvia Lomascolo wrote: I work with Windows and use R version 2.4.1. I am JUST starting to learn this program... I get this warning message 'NAs introduced by coercion' while trying to build a distance matrix (to be analyzed with NMDS later) from a 336 x 100 data matrix. The original matrix has lots of zeros and no missing values, but I don't think this should matter. I searched this forum and people have suggested that the warning should be ignored but when I try to print the distance matrix I only get the row numbers (the matrix seems to be 'empty') and I'm not being able to judge whether the matrix worked or not. To get the distance matrix I wrote: dist.PxMx - dist (PeaksMatrix, method='euclidean', diag=FALSE, upper=FALSE) I tried including the p argument (included in the help for dist()) and leaving it out, but that didn't seem to change anything. I think that's required for one distance measure though, not for euclidean dist. Should I really ignore this warning? If so, why am I not being able to see the distance matrix? -- View this message in context: http://www.nabble.com/NAs-introduced-by- coercion-in-dist%28%29-tf3680727.html#a10286882 Sent from the R help mailing list archive at Nabble.com. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the
[R] Odp: about using read.table
Hi Did you see FAQ 2.16? Try file.choose() Regards Petr [EMAIL PROTECTED] [EMAIL PROTECTED] napsal dne 03.05.2007 02:26:27: Hi,Dear R users, I have a file text nommed chif which contains 16 lines and 4 columns in the disc dur. I have a difficulty to read this file in R console I have used the following command chif - read.table(c:/chif.txt, header=T, sep= ) I have obtained from R console:undefined file! Can you please help me.Thank you in advance. [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Problem with the installation of install R on Sun Solaris
Hi All, First we install sun studio 11 on the server and then tried to install R This time I am getting the different errors. Please find attached the config.log files 1. old_config: before installation of sun studio 2. new_config: after installation of sun studio Thanks, Vipin From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Sent: Tuesday, May 01, 2007 8:27 PM To: Vipin Singhal Subject: Re: [R] Problem with the installation of install R on Sun Solaris Here is my config.site file that I used to compile R-2.4.1 on Solaris 10 for amd64 arch. You will need to install sun studio 11 which you can get at http://developers.sun.com/sunstudio/. For building documentation I used tetex but the guy who developed it has decided to call it quits so you may want to go with a different tex implementation. I am not sure what architecture you are using so you will need to vary your -xarch flag accordingly. You can find more information on xarch at http://docs.sun.com/source/819-3688/cc_ops.app.html Good luck! #!/bin/sh PATH=/opt/SUNWspro/bin:/usr/ccs/bin:/usr/bin:/usr/ucb:/usr/local/teTeX/ bin/i386-pc-solaris2.10 #Assembler and archiver AR=/usr/ccs/bin/ar AS=/usr/ccs/bin/as #Tools for building documentation TEX=/usr/local/teTeX/bin/i386-pc-solaris2.10/tex LATEX=/usr/local/teTeX/bin/i386-pc-solaris2.10/latex PDFTEX=/usr/local/teTeX/bin/i386-pc-solaris2.10/pdftex PDFLATEX=/usr/local/teTeX/bin/i386-pc-solaris2.10/pdflatex DVIPS=/usr/local/teTeX/bin/i386-pc-solaris2.10/dvips MAKEINFO=/usr/local/teTeX/bin/i386-pc-solaris2.10/makeinfo #Compiler commands CC=/opt/SUNWspro/bin/cc CXX=/opt/SUNWspro/bin/CC F77=/opt/SUNWspro/bin/f95 FC=/opt/SUNWspro/bin/f95 #Compiler flags (if you do not what to build in 64 bit then remove -xarch=amd64) CFLAGS=-xO5 -xlibmil -xarch=amd64 -xmodel=medium -xlibmieee -xc99=%all CXXFLAGS=-xO5 -xlibmil -xarch=amd64 -xmodel=medium -xlibmieee xlang=f95 FCFLAGS=-xO5 -xlibmil -xarch=amd64 -xmodel=medium -fsimple=0 -ftrap=%all FFLAGS=-xO5 -xlibmil -xarch=amd64 -xmodel=medium -fsimple=0 -ftrap=%all #Linker (if you do not want to build in 64 bit then use /usr/ccs/bin/ld and remove the 64 off the end of each linked pat) LD=/usr/ccs/bin/amd64/ld LDFLAGS=-xarch=amd64 -xmodel=medium -L/usr/local/lib/64 -L/usr/sfw/lib/64 -L/lib/amd64 -L/opt/SUNWspro/lib/amd64 -L/usr/openwin/lib/64 -R/usr/local/lib/64 -R/usr/sfw/lib/64 -R/lib/amd64 -R/opt/SUNWspro/lib/amd64 R_BROWSER=/usr/sfw/bin/mozilla MAKE=/usr/local/bin/make ##LIBnn=amd64 ##r_arch=amd64 MAIN_LD=/opt/SUNWspro/bin/cc -xarch=amd64 Vipin Singhal [EMAIL PROTECTED] Sent by: [EMAIL PROTECTED] 05/01/2007 06:09 AM To R-help@stat.math.ethz.ch cc Subject [R] Problem with the installation of install R on Sun Solaris __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. “This email and any files transmitted with it contain confidential, proprietary, privileged information of Symphony Services Corp (India) Pvt. Ltd. and are intended solely for the use of the recipient/s to whom it is addressed. Any unauthorized notifying, copying or distributing of this e-mail, directly or indirectly, and the contents therein in full or part is prohibited by any entity who is not a recipient. Any email received inadvertently or by mistake should be deleted by the entity who is not a recipient thereof. You may be pleased to notify the sender immediately by email and the email should be deleted from your system”. This file contains any messages produced by compilers while running configure, to aid debugging if configure makes a mistake. It was created by R configure 2.4.1, which was generated by GNU Autoconf 2.59. Invocation command line was $ ./configure ## - ## ## Platform. ## ## - ## hostname = ardsass1d uname -m = i86pc uname -r = 5.10 uname -s = SunOS uname -v = Generic_118855-36 /usr/bin/uname -p = i386 /bin/uname -X = System = SunOS Node = ardsass1d Release = 5.10 KernelID = Generic_118855-36 Machine = i86pc BusType = unknown Serial = unknown Users = unknown OEM# = 0 Origin# = 1 NumCPU = 3 /bin/arch = i86pc /usr/bin/arch -k = i86pc /usr/convex/getsysinfo = unknown hostinfo = unknown /bin/machine = unknown /usr/bin/oslevel = unknown /bin/universe = unknown PATH: /usr/sbin PATH: /usr/bin PATH: /opt/sfw/bin PATH: /usr/openwin/bin ## --- ## ## Core tests. ## ## --- ## configure:1805: checking build system type configure:1823: result: i386-pc-solaris2.10 configure:1831: checking host system type configure:1845: result: i386-pc-solaris2.10 configure:2397: checking for pwd configure:2415: found /usr/bin/pwd configure:2428:
[R] Sharpe-Ratio
Hello, Is there any possibility how i can calculate the Sharpe Ratio of a ts? KR, Alin Soare [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Bayesian logistic regression with a beta prior (MCMClogit)
Dear all,
I am trying to use the logistic regression with MCMClogit (package:
MCMCpack/Coda) and I want to put a beta prior on the parameters, but it's
giving me error message (please see output below) no matter what shape 1 or
2 I use. It works perfect with the cauchy or normal priors. Do you know if
there is a catch there somewhere? Thanks
logpriorfun - function(beta,shape1,shape2){
sum(dbeta(beta,shape1,shape2, log=T)) }
posterior - MCMClogit(nausea~nsaid*diuretic, data=w,
verbose=2000,burnin = 1000, mcmc = 1,
user.prior.density=logpriorfun,shape1=1,shape2=1)
user.prior.density(beta.start) == -Inf.
Error in MCMClogit(nausea ~ nsaid * diuretic, data = w, verbose = 2000, :
Respecify and call MCMClogit() again.
--
View this message in context:
http://www.nabble.com/Bayesian-logistic-regression-with-a-beta-prior-%28MCMClogit%29-tf3684970.html#a10300145
Sent from the R help mailing list archive at Nabble.com.
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[R] Single Title for the Multiple plot page
Dear List, In R we can plot multiple graphs in same page using par(mfrow = c(*,*)). In each plot we can set title using main and sub commands. However, is there any way that we can place an universal title above the set of plots placed in the same page (not individual plot titles, all i need is a title of the whole graph page) as well as sib-titles? Do I need any package to do so? Thank you for your time. Mohammad Ehsanul Karim (R - 2.3.1 on windows) Institute of Statistical Research and Training University of Dhaka __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] searching for special variables
Dear R-Experts, in my program I have a big workspace. Now I want to look for all variables which have the letters 777 in their name (e.g. ask777first) and afterwards I need to delete those variables. How can I reach this aim? Any ideas, Corinna __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Query about RODBC to access MySQL from Windows
First, try this kind of connection string channel - odbcConnect(mysqldsn,uname;Password=pwd;Database=default_db) If it doesn't work, in order to understand if it's a permission issue, try to connect with another client (still using the RODBC!!if you use the mysql client, you will not use ODBC but the mysql driver!!!). If it dooesn't solve the problem, give us more details on how you retrieve the data... Hi I am trying to use RODBC in R installed on Windows to access MySQL database (on a linux box). I set up a DSN and specified this DSN in R as follows library(RODBC); channel - odbcConnect(mysqldsn); RODB Connection 5 Details: case=nochange PORT=3306 Although this seems to connect properly, running any command yields NO results. i.e. sqlQuery(channel, show tables) yields 0 rows when there are close to 500 tables in the database. Ditto with any other query. It does not cause an error, but it returns 0 rows. The USER DSN mysqldsn is set up as follows :- host : zion.xxx.xxx.xxx default database : default_db port : 3306 username : uname password : pwd Running use default_db; show tables; command from the command prompt on the db server returns 500 rows. I find this problem while running any query. Running select * from tname limit 100 returns 0 rows whereas tname has around a million records. In the past, I have used MySQL clients for Windows to access the database without encountering any such problem I even tried setting up the mysqldsn DSN as a system DSN instead of a user DSN. I would like to know a) whether this is a permissions issue at some level b) whether there is any solution for this problem in R Thanks Lalitha __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Passa a Infostrada. ADSL e Telefono senza limiti e senza canone Telecom http://click.libero.it/infostrada __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] searching for special variables
one option is use something like the following: a - 1:10 b777 - rnorm(10) c777 - letters[1:6] fit - lm(b777 ~ a) a777d777 - 5 ## lis - ls() rm(list = c(lis[grep(777, lis)], lis)) ls() I hope it helps. Best, Dimitris Dimitris Rizopoulos Ph.D. Student Biostatistical Centre School of Public Health Catholic University of Leuven Address: Kapucijnenvoer 35, Leuven, Belgium Tel: +32/(0)16/336899 Fax: +32/(0)16/337015 Web: http://med.kuleuven.be/biostat/ http://www.student.kuleuven.be/~m0390867/dimitris.htm - Original Message - From: Schmitt, Corinna [EMAIL PROTECTED] To: r-help@stat.math.ethz.ch Cc: Schmitt, Corinna [EMAIL PROTECTED] Sent: Thursday, May 03, 2007 9:58 AM Subject: [R] searching for special variables Dear R-Experts, in my program I have a big workspace. Now I want to look for all variables which have the letters 777 in their name (e.g. ask777first) and afterwards I need to delete those variables. How can I reach this aim? Any ideas, Corinna __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] help with plot axis
Hello
i have a plot, and want the axis too be with larger writing, i found some
functions but they didnt work
this is my plot, and if the axis can be with bigger writing can the legend
inside the plot be in same the size??
plot(femsplot, xlab='Indeks',ylab='Kødprocent', pch=22)
abline(lm(femsplot), lwd=1)
points(firsplot, col='green', pch=2)
abline(lm(firsplot), lwd=1, col='green')
points(fjersplot, col='red', pch=8)
abline(lm(fjersplot), lwd=1, col='red')
legend(locator(1),legend=c('90 kg','80 kg','70 kg'),pch=c(22,2,8),lwd=1,
col=c('black','green','red'))
i have attached the plot, so you can se it...
Thank you
Rina
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Re: [R] searching for special variables
ls(pattern=.*777.*) Schmitt, Corinna wrote: Dear R-Experts, in my program I have a big workspace. Now I want to look for all variables which have the letters 777 in their name (e.g. ask777first) and afterwards I need to delete those variables. How can I reach this aim? -- View this message in context: http://www.nabble.com/searching-for-special-variables-tf3685103.html#a10300943 Sent from the R help mailing list archive at Nabble.com. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Single Title for the Multiple plot page
Mohammad Ehsanul Karim wrote: Dear List, In R we can plot multiple graphs in same page using par(mfrow = c(*,*)). In each plot we can set title using main and sub commands. However, is there any way that we can place an universal title above the set of plots placed in the same page (not individual plot titles, all i need is a title of the whole graph page) as well as sib-titles? Do I need any package to do so? Thank you for your time. This is covered in a number of places in the archives and RSiteSearch(Overall Title) points you to relevant posts. I'm not sure there is an example of having both a title and subtitle, but that is easy enough: par(mfrow=c(1,2), oma=c(2,0,2,0)) plot(1:10) plot(1:10) title(Centered Overall Title, outer=TRUE) mtext(side=1, Centered Subtitle, outer=TRUE) You might consider upgrading to a more recent version of R. Mohammad Ehsanul Karim (R - 2.3.1 on windows) Institute of Statistical Research and Training University of Dhaka __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Chuck Cleland, Ph.D. NDRI, Inc. 71 West 23rd Street, 8th floor New York, NY 10010 tel: (212) 845-4495 (Tu, Th) tel: (732) 512-0171 (M, W, F) fax: (917) 438-0894 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Query about RODBC to access MySQL from Windows
On Thu, 3 May 2007, Bruno C. wrote: First, try this kind of connection string channel - odbcConnect(mysqldsn,uname;Password=pwd;Database=default_db) I presume the DSN was set up in a dialog box under Windows, and tested there (which provides a different client). This makes me suspect the DSN is valid, but pointing at the wrong database. I noticed (s)he did not use 'use default_db; show tables; when running from RODBC, which would have been a fairer test. Simple diagnostic output like that from odbcGetInfo() is missing from the report. If it doesn't work, in order to understand if it's a permission issue, try to connect with another client (still using the RODBC!!if you use the mysql client, you will not use ODBC but the mysql driver!!!). If it dooesn't solve the problem, give us more details on how you retrieve the data... (And read the posting guide and try to ask a question that we have some hope of answering, for example, one about R!) Hi I am trying to use RODBC in R installed on Windows to access MySQL database (on a linux box). I set up a DSN and specified this DSN in R as follows library(RODBC); channel - odbcConnect(mysqldsn); RODB Connection 5 Details: case=nochange PORT=3306 Although this seems to connect properly, running any command yields NO results. i.e. sqlQuery(channel, show tables) yields 0 rows when there are close to 500 tables in the database. Ditto with any other query. It does not cause an error, but it returns 0 rows. The USER DSN mysqldsn is set up as follows :- host : zion.xxx.xxx.xxx default database : default_db port : 3306 username : uname password : pwd Running use default_db; show tables; command from the command prompt on the db server returns 500 rows. I find this problem while running any query. Running select * from tname limit 100 returns 0 rows whereas tname has around a million records. In the past, I have used MySQL clients for Windows to access the database without encountering any such problem I even tried setting up the mysqldsn DSN as a system DSN instead of a user DSN. I would like to know a) whether this is a permissions issue at some level b) whether there is any solution for this problem in R Thanks Lalitha -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Odp: help with plot axis
Hi
[EMAIL PROTECTED] napsal dne 03.05.2007 10:33:22:
Hello
i have a plot, and want the axis too be with larger writing, i found
some
functions but they didnt work
this is my plot, and if the axis can be with bigger writing can the
legend
inside the plot be in same the size??
plot(femsplot, xlab='Indeks',ylab='Kødprocent', pch=22)
abline(lm(femsplot), lwd=1)
points(firsplot, col='green', pch=2)
abline(lm(firsplot), lwd=1, col='green')
points(fjersplot, col='red', pch=8)
abline(lm(fjersplot), lwd=1, col='red')
legend(locator(1),legend=c('90 kg','80 kg','70
kg'),pch=c(22,2,8),lwd=1,
col=c('black','green','red'))
i have attached the plot, so you can se it...
I would recommend you to:
read help pages
?plot
?axis
?par
?legend
with special attention to cex and its companion parameters
Regards
Petr
Thank you
Rina
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Re: [R] Install SciView under Windows Vista
I guess you have an outdated version of R2HTML. Please run
update.packages(checkBuilt=TRUE) and try again. If it still does not
work, please notify its package maintainer and tell him the package's
version number.
Uwe Ligges
Tim Sippel wrote:
Hello-
I have been trying to install SciView under Windows Vista (Home Premium
version,
32 bit OS, Intel Core Duo 2.13GHz, 2Gig RAM).
I am getting an error, apparently related to the R2HTML package (version
1.54)
as you will see in the R information below my signature.
I have tried to email directly to [EMAIL PROTECTED] for support but have
had my message returned as undeliverable.
Your help is very much appreciated!
Tim
R version 2.5.0 (2007-04-23)
Copyright (C) 2007 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
[Previously saved workspace restored]
Loading required package: datasets
Loading required package: utils
Loading required package: grDevices
Loading required package: graphics
Loading required package: stats
Loading required package: tcltk
Loading Tcl/Tk interface ... done
Loading required package: R2HTML
Error in `parent.env-`(`*tmp*`, value = NULL) :
use of NULL environment is defunct
In addition: Warning message:
'Sys.putenv' is deprecated.
Use 'Sys.setenv' instead.
See help(Deprecated)
Error: package 'R2HTML' could not be loaded
local({pkg - select.list(sort(.packages(all.available = TRUE)))
+ if(nchar(pkg)) library(pkg, character.only=TRUE)})
Error in `parent.env-`(`*tmp*`, value = NULL) :
use of NULL environment is defunct
Error: package/namespace load failed for 'R2HTML'
R.Version()
$platform
[1] i386-pc-mingw32
$arch
[1] i386
$os
[1] mingw32
$system
[1] i386, mingw32
$status
[1]
$major
[1] 2
$minor
[1] 5.0
$year
[1] 2007
$month
[1] 04
$day
[1] 23
$`svn rev`
[1] 41293
$language
[1] R
$version.string
[1] R version 2.5.0 (2007-04-23)
search()
[1] .GlobalEnvpackage:tcltk package:stats
[4] package:graphics package:grDevices package:utils
[7] package:datasets package:methods Autoloads
[10] package:base
capabilities(tcltk)
tcltk
TRUE
[[alternative HTML version deleted]]
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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[R] Nested ANOVA in R
Dear R users, I installed an experiment as following setup: - Four plant species - Seed addition as main factor with two levels: control and seed addition. - Four replicates (sites) - 8 plots in each site arranged as two rows (each rows 4 plots) one meter far from each other - Four sub-plots in each plot (therefore 32 sub-plots in each site) - In the four plots in each site (first row of plots) seeds of each of four plant species were sowed onto one sub-plot by random (therefore 4 sub-plots sown by a plant species in four different plots in each site). In the other four plots (second row of plots) one sub-plot selected by random as control for each of four plant species (therefore 4 sub-plots in four different plots in each site as control for a plant species). Now, my first question is about the name of this design. I thought this is a 3-factor split-plot arrangement. My second question is about data analysis for this experiment in R. I would like to test the effect of seed addition and sites on the seedling emergence of each plant species separately using a three- way ANOVA (??). Because of the hierarchical experimental design, the experiment must be analyzed by nested ANOVA but I do not know how I must arrange dataset and then how to write ANOVA model in R. I would greatly appreciate if somebody gives me some comments on these cases Thank you very much in advance, Majid Majid Iravani PhD Student Swiss Federal Research Institute WSL Research Group of Vegetation Ecology Zürcherstrasse 111 CH-8903 Birmensdorf Switzerland Phone: +41-1-739-2693 Fax: +41-1-739-2215 Email: [EMAIL PROTECTED] http://www.wsl.ch/staff/majid.iravani/ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Install SciView under Windows Vista
Are you sure your version of R2HTML is up-to-date and built under R 2.5.0?
Use update.packages(checkBuilt=TRUE) if you have not already done so.
That got me R2HTML 1.58, not 1.54.
On Thu, 3 May 2007, Tim Sippel wrote:
Hello-
I have been trying to install SciView under Windows Vista (Home Premium
version,
32 bit OS, Intel Core Duo 2.13GHz, 2Gig RAM).
I am getting an error, apparently related to the R2HTML package (version
1.54)
as you will see in the R information below my signature.
I have tried to email directly to [EMAIL PROTECTED] for support but have
() had my message returned as undeliverable.
Your help is very much appreciated!
Tim
R version 2.5.0 (2007-04-23)
Copyright (C) 2007 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
[Previously saved workspace restored]
Loading required package: datasets
Loading required package: utils
Loading required package: grDevices
Loading required package: graphics
Loading required package: stats
Loading required package: tcltk
Loading Tcl/Tk interface ... done
Loading required package: R2HTML
Error in `parent.env-`(`*tmp*`, value = NULL) :
use of NULL environment is defunct
In addition: Warning message:
'Sys.putenv' is deprecated.
Use 'Sys.setenv' instead.
See help(Deprecated)
Error: package 'R2HTML' could not be loaded
local({pkg - select.list(sort(.packages(all.available = TRUE)))
+ if(nchar(pkg)) library(pkg, character.only=TRUE)})
Error in `parent.env-`(`*tmp*`, value = NULL) :
use of NULL environment is defunct
Error: package/namespace load failed for 'R2HTML'
R.Version()
$platform
[1] i386-pc-mingw32
$arch
[1] i386
$os
[1] mingw32
$system
[1] i386, mingw32
$status
[1]
$major
[1] 2
$minor
[1] 5.0
$year
[1] 2007
$month
[1] 04
$day
[1] 23
$`svn rev`
[1] 41293
$language
[1] R
$version.string
[1] R version 2.5.0 (2007-04-23)
search()
[1] .GlobalEnvpackage:tcltk package:stats
[4] package:graphics package:grDevices package:utils
[7] package:datasets package:methods Autoloads
[10] package:base
capabilities(tcltk)
tcltk
TRUE
[[alternative HTML version deleted]]
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Brian D. Ripley, [EMAIL PROTECTED]
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax: +44 1865 272595
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[R] Filling array: No recycling
Hello, is it possible to fill an array with no using of the recycling rule? My problem. I want to fill an array but my values have not always the same length. My aim. I want to fill the array only ONE TIME. All vacent places should be written with NA. Thank's a lot. Felix Example: #Write 1 to 3 only one time. The last #5 place should be NA. dim(as.array(letters)) array(1:3, c(2,4) ) #na.strings = NA __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Filling array: No recycling
First make your vectors to have the same length and then put them to the array. x - c(1,2) x [1] 1 2 length(x) - 5 x [1] 1 2 NA NA NA Petr Felix Wave napsal(a): Hello, is it possible to fill an array with no using of the recycling rule? My problem. I want to fill an array but my values have not always the same length. My aim. I want to fill the array only ONE TIME. All vacent places should be written with NA. Thank's a lot. Felix Example: #Write 1 to 3 only one time. The last #5 place should be NA. dim(as.array(letters)) array(1:3, c(2,4) ) #na.strings = NA __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Petr Klasterecky Dept. of Probability and Statistics Charles University in Prague Czech Republic __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Problem with the installation of install R on Sun Solaris
*** Error code 1
make: Fatal error: Command failed for target `R.bin'
Current working directory /opt/dev/R/R-2.4.1/src/main
*** Error code 1
The following command caused the error:
make install-bin-local
make: Fatal error: Command failed for target `R'
Current working directory /opt/dev/R/R-2.4.1/src/main
*** Error code 1
The following command caused the error:
for d in scripts include extra appl nmath unix main modules library; do \
(cd ${d} make R) || exit 1; \
done
make: Fatal error: Command failed for target `R'
Current working directory /opt/dev/R/R-2.4.1/src
*** Error code 1
The following command caused the error:
for d in m4 tools doc etc share src tests po; do \
(cd ${d} make R) || exit 1; \
done
make: Fatal error: Command failed for target `R'
[[alternative HTML version deleted]]
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Re: [R] Filling array: No recycling
How about A - array(NA, c(2,4) ) x - 1:3 A[seq_along(x)] - x ? On Thu, 3 May 2007, Felix Wave wrote: Hello, is it possible to fill an array with no using of the recycling rule? My problem. I want to fill an array but my values have not always the same length. My aim. I want to fill the array only ONE TIME. All vacent places should be written with NA. Thank's a lot. Felix Example: #Write 1 to 3 only one time. The last #5 place should be NA. dim(as.array(letters)) array(1:3, c(2,4) ) #na.strings = NA __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Filling array: No recycling
Felix I'm not quite sure I understand your example, but try: a - array(NA,c(2,2,3)) jj - c(12,33,22) a[1:length(jj)] - jj a which will fill only the first three elemens of array a HTH rksh On 3 May 2007, at 10:41, Felix Wave wrote: Hello, is it possible to fill an array with no using of the recycling rule? My problem. I want to fill an array but my values have not always the same length. My aim. I want to fill the array only ONE TIME. All vacent places should be written with NA. Thank's a lot. Felix Example: #Write 1 to 3 only one time. The last #5 place should be NA. dim(as.array(letters)) array(1:3, c(2,4) ) #na.strings = NA __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting- guide.html and provide commented, minimal, self-contained, reproducible code. -- Robin Hankin Uncertainty Analyst National Oceanography Centre, Southampton European Way, Southampton SO14 3ZH, UK tel 023-8059-7743 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] searching for special variables
sorry, forgot to delete objects. rm(list=ls(pattern=.*777.*)) Vladimir Eremeev wrote: ls(pattern=.*777.*) Schmitt, Corinna wrote: in my program I have a big workspace. Now I want to look for all variables which have the letters 777 in their name (e.g. ask777first) and afterwards I need to delete those variables. How can I reach this aim? -- View this message in context: http://www.nabble.com/searching-for-special-variables-tf3685103.html#a10302565 Sent from the R help mailing list archive at Nabble.com. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Plotting more errorbar-functions in one plot
Hello, it´s new for me tu use R for my statistics analysis, so I need some help. The problem is: I want to plot errorbar-functions from two measurements in one coordinate-system. For that I use the following code: library(sfsmisc) errbar(XAchse,Means,Mins,Maxs,xlab=,ylab=,xlim=range(0,100)) lines(XAchse,Means) par(new=TRUE) errbar(XAchse,MeansN,MinsN,MaxsN,xlab=,ylab=,xlim=range(0,100)) lines(XAchse,MeansN) My problem is, that I want to have the same scaling on the x-axis, but I don´t know, what I have to do for that. If I say: errbar(XAchse,MeansN,MinsN,MaxsN,xlab=,ylab=,xlim=range(0,100), ylim= yrange(0,1)) I get the following error: Error in plot.default(x, y, ylim = range(y, yplus, yminus), xlab = xlab, : formal argument ylim matched by multiple actual arguments I tried a lot of things, but nothing helped. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] searching for special variables
Try: rm(list = ls(patt = 777)) On 5/3/07, Schmitt, Corinna [EMAIL PROTECTED] wrote: Dear R-Experts, in my program I have a big workspace. Now I want to look for all variables which have the letters 777 in their name (e.g. ask777first) and afterwards I need to delete those variables. How can I reach this aim? Any ideas, Corinna __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Single Title for the Multiple plot page
Sometimes I just overlay a blank plot and annotate with text. par(mfrow=c(1,2), oma=c(2,0,2,0)) plot(1:10) plot(1:10) oldpar - par() par(mfrow=c(1,1),new=TRUE,mar=rep(0,4),oma=rep(0,4)) plot.window(xlim=c(0,1),ylim=c(0,1),mar=rep(0,4)) text(0.5,c(0.98,0.02),c(Centered Overall Title,Centered Subtitle), cex=c(1.4,1)) par(oldpar) --- Chuck Cleland [EMAIL PROTECTED] wrote: Mohammad Ehsanul Karim wrote: Dear List, In R we can plot multiple graphs in same page using par(mfrow = c(*,*)). In each plot we can set title using main and sub commands. However, is there any way that we can place an universal title above the set of plots placed in the same page (not individual plot titles, all i need is a title of the whole graph page) as well as sib-titles? Do I need any package to do so? Thank you for your time. This is covered in a number of places in the archives and RSiteSearch(Overall Title) points you to relevant posts. I'm not sure there is an example of having both a title and subtitle, but that is easy enough: par(mfrow=c(1,2), oma=c(2,0,2,0)) plot(1:10) plot(1:10) title(Centered Overall Title, outer=TRUE) mtext(side=1, Centered Subtitle, outer=TRUE) You might consider upgrading to a more recent version of R. Mohammad Ehsanul Karim (R - 2.3.1 on windows) Institute of Statistical Research and Training University of Dhaka __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Chuck Cleland, Ph.D. NDRI, Inc. 71 West 23rd Street, 8th floor New York, NY 10010 tel: (212) 845-4495 (Tu, Th) tel: (732) 512-0171 (M, W, F) fax: (917) 438-0894 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Single Title for the Multiple plot page
Here is a way of putting a title in the outer margin:
par(mfrow=c(2,2), oma=c(0,0,3,0)) # leave space in outer margin
plot(1)
plot(2)
plot(3)
plot(4)
mtext('Outer Title', adj=0.5, side=3, outer=TRUE)
On 5/3/07, Mohammad Ehsanul Karim [EMAIL PROTECTED] wrote:
Dear List,
In R we can plot multiple graphs in same page using
par(mfrow = c(*,*)). In each plot we can set title
using main and sub commands.
However, is there any way that we can place an
universal title above the set of plots placed in the
same page (not individual plot titles, all i need is a
title of the whole graph page) as well as sib-titles?
Do I need any package to do so?
Thank you for your time.
Mohammad Ehsanul Karim (R - 2.3.1 on windows)
Institute of Statistical Research and Training
University of Dhaka
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and provide commented, minimal, self-contained, reproducible code.
--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
What is the problem you are trying to solve?
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[R] hi
hi,
I have a problem to use union function because one of the elements is a
character and the others are numeric
for(j in 1:length(I)) {
+ C1 - levels(factor(subset(donParEssai, Id_Essai == 1006961 Id_Cara ==
I[j], select = Date_O)[,1]))
+ C2 - as.numeric(levels(factor(subset(donParEssai, Id_Essai == 1006961
Id_Cara == I[j], select = Stade_O)[,1])))
+ C3 - length(as.numeric(levels(factor(subset(donParEssai, Id_Essai == 1006961
Id_Cara == I[j], select = Id_Geno)[,1]
+ C4 - length(levels(factor(subset(donParEssai, Id_Essai == 1006961 Id_Cara
== I[j], select = Id_Rep)[,1])))
+ C5 - mean(as.numeric(as.character(subset(donParEssai, Id_Essai == 1006961
Id_Cara == I[j], select = Val_O)[,1])))
+ C6 - range(as.numeric(as.character(subset(donParEssai, Id_Essai == 1006961
Id_Cara == I[j], select = Val_O)[,1])))
+ C7 - sd(as.numeric(as.character(subset(donParEssai, Id_Essai == 1006961
Id_Cara == I[j], select = Val_O)[,1])))
+ RecapCara[j,] -
union(C1,union(C2,union(C3,union(C4,union(C5,union(C6,C7))
+ }
Erreur dans RecapCara[j, ] - union(C1, union(C2, union(C3, union(C4, union(C5,
:
le nombre d'objets à remplacer n'est pas multiple de la taille du
remplacement
print(RecapCara)
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
[1,] NA 213 7.66129 5.2 17.1 2.318801
[2,] NA 213 50.56774 47.3 53.9 1.469222
C1
[1] 29/08/2005
I can't paste C1 with others values how could I do to paste C1 with others
please?
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Re: [R] Odp: about using read.table
I believe you mean R for Windows 2.16 ? --- Petr PIKAL [EMAIL PROTECTED] wrote: Hi Did you see FAQ 2.16? Try file.choose() Regards Petr [EMAIL PROTECTED] [EMAIL PROTECTED] napsal dne 03.05.2007 02:26:27: Hi,Dear R users, I have a file text nommed chif which contains 16 lines and 4 columns in the disc dur. I have a difficulty to read this file in R console I have used the following command chif - read.table(c:/chif.txt, header=T, sep= ) I have obtained from R console:undefined file! Can you please help me.Thank you in advance. [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Multiple scatterplots
--- Bert Gunter [EMAIL PROTECTED] wrote: Please note: in R you can specify (some of the) graphics parameters as the appropriate length vectors. So your plot example below can also be done as, for example: plot( rep.int(aa,3),c(cc,bb,dd),col=rep(c(red,blue,green),e=length(aa))) However, this doesn't seem to fit the posted request, where maybe something like a trellis plot of the different distributions is what is wanted?? -- but I may well misunderstand. Thanks, that's a nice way to do things. I, too, am not sure what the OP wanted. The subject and the text differed so I went with the text. You may well be right or simple par(mfrow=3) might do it. Bert Gunter Genentech Nonclinical Statistics -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of John Kane Sent: Wednesday, May 02, 2007 11:06 AM To: Kostadin Cholakov; r-help@stat.math.ethz.ch Subject: Re: [R] Multiple scatterplots Your title and your posting do not say the same thing. Assuming you want all three distributions on one scatter plot does this help? aa - 1:10 bb - 11:2 cc - bb^2 dd - c(3,4,7,9,11,32,11,14,5,9) plot(aa,cc, col=red) points(aa,bb, col=blue) points(aa,dd, col=green) Also in plotting it is a good idea to look at all the variations etc that you can get with par() Type ?par --- Kostadin Cholakov [EMAIL PROTECTED] wrote: Hi, I have to plot three Ziph distributions for three languages where the x value represents the rank of a given word and the y value represents the relative frequency of this word in the corpus. Is there some way so that I can plot all three distributions on a single scatterplot, preferably with different colours :) I tried to find something in the R manual but there are no such examples :( Thank you! __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Odp: hi
Hi
[EMAIL PROTECTED] napsal dne 03.05.2007 14:01:27:
hi,
I have a problem to use union function because one of the elements is a
character and the others are numeric
for(j in 1:length(I)) {
+ C1 - levels(factor(subset(donParEssai, Id_Essai == 1006961 Id_Cara
==
I[j], select = Date_O)[,1]))
+ C2 - as.numeric(levels(factor(subset(donParEssai, Id_Essai == 1006961
Id_Cara == I[j], select = Stade_O)[,1])))
+ C3 - length(as.numeric(levels(factor(subset(donParEssai, Id_Essai ==
1006961 Id_Cara == I[j], select = Id_Geno)[,1]
+ C4 - length(levels(factor(subset(donParEssai, Id_Essai == 1006961
Id_Cara
== I[j], select = Id_Rep)[,1])))
+ C5 - mean(as.numeric(as.character(subset(donParEssai, Id_Essai ==
1006961
Id_Cara == I[j], select = Val_O)[,1])))
+ C6 - range(as.numeric(as.character(subset(donParEssai, Id_Essai ==
1006961
Id_Cara == I[j], select = Val_O)[,1])))
+ C7 - sd(as.numeric(as.character(subset(donParEssai, Id_Essai ==
1006961
Id_Cara == I[j], select = Val_O)[,1])))
+ RecapCara[j,] -
union(C1,union(C2,union(C3,union(C4,union(C5,union(C6,C7))
+ }
Erreur dans RecapCara[j, ] - union(C1, union(C2, union(C3, union(C4,
union(C5, :
le nombre d'objets ŕ remplacer n'est pas multiple de la taille
du remplacement
print(RecapCara)
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
[1,] NA 213 7.66129 5.2 17.1 2.318801
[2,] NA 213 50.56774 47.3 53.9 1.469222
C1
[1] 29/08/2005
I can't paste C1 with others values how could I do to paste C1 with
others please?
Change it to numeric?
Regards
Petr
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Re: [R] upgrade to 2.5
I find it easier to install all the packages again: #---run in previous version packages - installed.packages()[,Package] save(packages, file=Rpackages) #---run in new version load(Rpackages) for (p in setdiff(packages, installed.packages()[,Package])) install.packages(p) -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Robert A LaBudde Sent: Wednesday, May 02, 2007 5:39 PM To: R-help@stat.math.ethz.ch Subject: Re: [R] upgrade to 2.5 At 01:41 PM 5/2/2007, you wrote: On 5/2/07, Sundar Dorai-Raj [EMAIL PROTECTED] wrote: Iasonas Lamprianou said the following on 5/2/2007 8:25 AM: Hi I am using R version 2.4.1. How can I upgrade to version 2.5 without having to install all the packages again? Thanks Jason You may find the following link relevant. http://finzi.psych.upenn.edu/R/Rhelp02a/archive/75359.html if you use Windows XP. This link was useful to me, as I am new to R. (Win2000, R-2.5.0) What I have been doing is using a file compare utility (Beyond Compare in my case) to move files in the old library directory to the new one, if the files are missing in the new one. Then I perform an update.packages command. This procedure appears to work without problem. It would seem much preferable to have all packages saved in an installation-independent directory, instead of a library directory under R's installation directory. Then, of course, no update would be necessary. I can't find how this option is settable in R, other than a direct argument to library() or install.package(). How does one shift the R default libraries location to a particular directory? Thanks. Robert A. LaBudde, PhD, PAS, Dpl. ACAFS e-mail: [EMAIL PROTECTED] Least Cost Formulations, Ltd.URL: http://lcfltd.com/ 824 Timberlake Drive Tel: 757-467-0954 Virginia Beach, VA 23464-3239Fax: 757-467-2947 Vere scire est per causas scire __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] convert text to exprission good for lm arguments
Hi, I ran into a problem of converting a text representation of an expression into parsed expression to be further evaluated inside lm (). n - 100 data - data.frame(x= rnorm (n), y= rnorm (n)) data. lm - lm (y ~ x, data=data) ## this works update(data. lm , subset=x0) Call: lm (formula = y ~ x, data = data, subset = x 0) Coefficients: (Intercept) x -0.07864094193322170023 -0.14596982635007796358 ## this doesn't work ## text representation of subset subset - x0 update(data. lm , subset=parse(text=subset)) Error in `[.data.frame`(list(y = c(-0.601925958140825, -0.111931189071517, : invalid subscript type What is the correct way to convert x0 into a valid subset argument? Thanks, Vadim [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Sharpe-Ratio
http://finzi.psych.upenn.edu/R/library/tseries/html/sharpe.html --- Soare Marcian-Alin [EMAIL PROTECTED] wrote: Hello, Is there any possibility how i can calculate the Sharpe Ratio of a ts? KR, Alin Soare [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] adding a column to a matrix
Hello, Please, consider the functions pmin and pmax. Tuesday, May 1, 2007, 3:29:54 PM, you wrote: rc thanks for the previous advice it seems to have worked what about the following rc l have the following dataset and would like to calculate the actual survival time by rc if censoring time survival time then actual survival time rc =survival time else its= censoring time. rc treatmentgrp strata censoringTime survivalTime censoring actualsurvivaltim rc [1,] 1 1 1.012159 1137.80922 0 rc [2,] 2 2 32.971439 247.21786 0 rc [3,] 2 1 85.758253 797.04949 0 rc [4,] 1 1 16.999171 78.92309 0 rc l used matrix to genarate the data rc thanks in advance rc Vladimir Eremeev [EMAIL PROTECTED] wrote: rc m-cbind(m,0) m[m[,3]m[,4],5]-1 rc colnames(m)[5]-censoring rc raymond chiruka wrote: i would like to add a variable to an existing matrix by manipulating 2 previous variables eg for the data m treat strata censti survTime [1,] 1 2 284.684074 690.4961005 [2,] 1 1 172.764515 32.3990335 [3,] 1 1 2393.195400 24.6145279 [4,] 2 1 30.3647718.0272267 [5,] 1 1 523.182282 554.7659501 l would want to add a new column censoring by comparing ( if censti survtime then censoring=1) how do l go about it thanks the code l used to generate the data is n=100 m=matrix(nrow=n,ncol=4) colnames(m)=c(treat, strata, censti, survTime) for(i in 1:100) m[i,]=c(sample(c(1,2),1,replace=TRUE),sample(c(1,2),1,replace=TRUE),rexp(1,.002),rexp(1,.005)) m l know its ugly but it seems to work any suggestions l still new at this thanks -- Best regards, Vladimirmailto:[EMAIL PROTECTED] --SevinMail-- __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] convert text to exprission good for lm arguments
Try: do.call(update, list(data.lm, subset = parse(text = subset))) On 5/3/07, Vadim Ogranovich [EMAIL PROTECTED] wrote: Hi, I ran into a problem of converting a text representation of an expression into parsed expression to be further evaluated inside lm (). n - 100 data - data.frame(x= rnorm (n), y= rnorm (n)) data. lm - lm (y ~ x, data=data) ## this works update(data. lm , subset=x0) Call: lm (formula = y ~ x, data = data, subset = x 0) Coefficients: (Intercept) x -0.07864094193322170023 -0.14596982635007796358 ## this doesn't work ## text representation of subset subset - x0 update(data. lm , subset=parse(text=subset)) Error in `[.data.frame`(list(y = c(-0.601925958140825, -0.111931189071517, : invalid subscript type What is the correct way to convert x0 into a valid subset argument? Thanks, Vadim [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] convert text to exprission good for lm arguments
Vadim Ogranovich wrote: Hi, I ran into a problem of converting a text representation of an expression into parsed expression to be further evaluated inside lm (). n - 100 data - data.frame(x= rnorm (n), y= rnorm (n)) data. lm - lm (y ~ x, data=data) ## this works update(data. lm , subset=x0) Call: lm (formula = y ~ x, data = data, subset = x 0) Coefficients: (Intercept) x -0.07864094193322170023 -0.14596982635007796358 ## this doesn't work ## text representation of subset subset - x0 update(data. lm , subset=parse(text=subset)) Error in `[.data.frame`(list(y = c(-0.601925958140825, -0.111931189071517, : invalid subscript type What is the correct way to convert x0 into a valid subset argument? update(data.lm,subset=eval(parse(text=subset))) -- View this message in context: http://www.nabble.com/convert-text-to-exprission-good-for-lm-arguments-tf3686309.html#a10304608 Sent from the R help mailing list archive at Nabble.com. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] factanal AIC?
Dear list members,
Could any expert on factor analysis be so kind to explain how to calculate AIC
on the output of factanal. Do I calculate AIC wrong or is
factanal$criteria[objective] not a negative log-likelihood?
Best regards
Jens Oehlschlägel
The AIC calculated using summary.factanal below don't appear correct to me:
n items factors total.df rest.df model.df LL AIC
AICc BIC
1 100020 1 210 170 40 -5.192975386 90.38595
93.80618 286.6962
2 100020 2 210 151 59 -3.474172303 124.94834
132.48026 414.5059
3 100020 3 210 133 77 -1.745821627 157.49164
170.51984 535.3888
4 100020 4 210 116 94 -0.120505369 188.24101
207.97582 649.5700
5 100020 5 210 100 110 -0.099209921 220.19842
247.66749 760.0515
6 100020 6 210 85 125 -0.072272695 250.14455
286.18574 863.6140
7 100020 7 210 71 139 -0.054668588 278.10934
323.36515 960.2873
8 100020 8 210 58 152 -0.041708051 304.08342
358.99723 1050.0622
9 100020 9 210 46 164 -0.028686298 328.05737
392.87174 1132.9292
10 100020 10 210 35 175 -0.015742783 350.03149
424.78877 1208.8887
11 100020 11 210 25 185 -0.007007901 370.01402
454.55947 1277.9487
12 100020 12 210 16 194 -0.005090725 388.01018
481.99776 1340.1147
summary.factanal - function(object, ...){
if (inherits(object, try-error)){
c(n=NA, items=NA, factors=NA, total.df=NA, rest.df=NA, model.df=NA, LL=NA,
AIC=NA, AICc=NA, BIC=NA)
}else{
n - object$n.obs
p - length(object$uniquenesses)
m - object$factors
model.df - (p*m) + (m*(m+1))/2 + p - m^2
total.df - p*(p+1)/2
rest.df - total.df - model.df # = object$dof
LL - -as.vector(object$criteria[objective])
k - model.df
aic - 2*k - 2*LL
aicc - aic + (2*k*(k+1))/(n-k-1)
bic - k*log(n) - 2*LL
c(n=n, items=p, factors=m, total.df=total.df, rest.df=rest.df,
model.df=model.df, LL=LL, AIC=aic, AICc=aicc, BIC=bic)
}
}
multifactanal - function(factors=1:3, ...){
names(factors) - factors
ret - lapply(factors, function(factors){
try(factanal(factors=factors, ...))
})
class(ret) - multifactanal
ret
}
summary.multifactanal - function(object,...){
do.call(rbind, lapply(object, summary.factanal))
}
print.multifactanal - function(x,...){
ret - summary.multifactanal(x)
print(ret, ...)
invisible(ret)
}
# simulate a true 4-factor model
n - 1000
ktrue - 4
kfac - 5
true - matrix(rnorm(n*ktrue), ncol=ktrue)
x - matrix(rep(true, kfac)+rnorm(n*ktrue*kfac), ncol=ktrue*kfac)
dimnames(x) - list(NULL, paste(rep(letters[1:ktrue], kfac), rep(1:kfac,
rep(ktrue, kfac)), sep=))
covmat - cov.wt(x)
# run factanal for several numbers of factors
mf - multifactanal(factors=1:12, covmat=covmat)
mf
version
_
platform i386-pc-mingw32
arch i386
os mingw32
system i386, mingw32
status
major 2
minor 5.0
year 2007
month 04
day23
svn rev41293
language R
version.string R version 2.5.0 (2007-04-23)
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Re: [R] upgrade to 2.5
I usually install a new version over the old one (in the same directory). I did this since R 1.xx, using windows 2000 and then windows XP. No bugs were found, everything always works fine. Iasonas Lamprianou wrote: Hi I am using R version 2.4.1. How can I upgrade to version 2.5 without having to install all the packages again? Thanks Jason -- View this message in context: http://www.nabble.com/upgrade-to-2.5-tf3681336.html#a10304613 Sent from the R help mailing list archive at Nabble.com. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Problem with GARCH models in R compared to S-PLUS
Hi R, I have three queries regarding handling GARCH functions in R. Below I document the same: Unlike S-Plus, R doesn't handle Multivariate GARCH models. R has a package for BEKK GARCH model but not for DVEC GARCH models. The GARCH function in S-PLUS has the capability of fixing some model parameters at certain values to evaluate the fit of a particular model. But the same optionality is not provided by the GARCH models in R. So, how can I overcome these difficulties which I am facing in R? Are these procedures in the development stage of R? (I mean the packages are yet to be built?)..Any developmental work going on with this? Thank a lot for your help, Shubha [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] convert text to exprission good for lm arguments
On 5/3/07, Vladimir Eremeev [EMAIL PROTECTED] wrote: Vadim Ogranovich wrote: Hi, I ran into a problem of converting a text representation of an expression into parsed expression to be further evaluated inside lm (). n - 100 data - data.frame(x= rnorm (n), y= rnorm (n)) data. lm - lm (y ~ x, data=data) ## this works update(data. lm , subset=x0) Call: lm (formula = y ~ x, data = data, subset = x 0) Coefficients: (Intercept) x -0.07864094193322170023 -0.14596982635007796358 ## this doesn't work ## text representation of subset subset - x0 update(data. lm , subset=parse(text=subset)) Error in `[.data.frame`(list(y = c(-0.601925958140825, -0.111931189071517, : invalid subscript type What is the correct way to convert x0 into a valid subset argument? update(data.lm,subset=eval(parse(text=subset))) Just wanted to point out one difference. Using eval is not quite the same as using do.call since the Call: part does not come out as desired if you use eval but if you use do.call it comes out good enough that you can tell what was intended to be subset from the output: update(data.lm,subset=eval(parse(text=subset))) Call: lm(formula = y ~ x, data = data, subset = eval(parse(text = subset))) Coefficients: (Intercept)x -0.1335 -0.1248 do.call(update, list(data.lm, subset = parse(text = subset))) Call: lm(formula = y ~ x, data = data, subset = expression(x 0)) Coefficients: (Intercept)x -0.1335 -0.1248 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Sharpe-Ratio
have a look at Rmetrics www.rmetrics.org for R in finance in general and the taskview http://cran.r-project.org/src/contrib/Views/ I hope that helps. AA. - Original Message - From: Soare Marcian-Alin [EMAIL PROTECTED] To: R-help@stat.math.ethz.ch Sent: Wednesday, May 02, 2007 6:32 PM Subject: [R] Sharpe-Ratio Hello, Is there any possibility how i can calculate the Sharpe Ratio of a ts? KR, Alin Soare [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to install previous packages after upgrading to R 2.5.0?
I use a script, i.e., place a few lines of R code in a file:
## create a vector of package names
my.packages - c('pkgname1','pkgname2','pkgname3')
## install them (check whether other args to install.packages() need
to be specified)
install.packages(pkgs=my.packages)
and then source the script. Keep the script around, then on every
upgrade to R, just source it again.
-Don
At 2:12 PM -0700 5/2/07, Jeffrey Wood wrote:
Hello,
I have just upgraded from R-2.4.1 to R-2.5.0 for Windows.
I had installed a large number of add-on packages under 2.4.1. Is
there an easy way to install (or load, if that's the easier way)
those packages under 2.5.0, without having to install each package
by hand?
Thanks,
Jeff
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--
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Environmental Protection Department
Lawrence Livermore National Laboratory
Livermore, CA, USA
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[R] [R-pkgs] randomSurvivalForest 2.1.0 now available
Dear useRs: Release 2.1.0 of the randomSurvivalForest package is now available. -- CHANGES TO RELEASE 2.1.0 Release 2.1.0 represents a minor upgrade of the product, and will not affect most users of the prior version of the product. Key changes are as follows: o R 2.5.0 compliance issues and necessitated modifications. o Modification of PMML representation of RSF forest output. The RSF custom extension has been moved from the DataDictionary node to a new MiningBuildTask node. Note that forests produced with Release 2.0.0 will have to be regenerated using Release 2.1.0. We apologize for the inconvenience. o Fast processing of data involving large numbers of predictors (as in many genomic examples) by using the option big.data=TRUE. This option bypasses the huge overhead needed by R in creating design matrices and parsing formula. However, users should be aware of some side effects. See the RSF help file for more details. Thanks to Steven (Xi) Chen for pointing out the problem. o Only the top 100 predictors are now printed to the terminal when calling plot.error(). This deals with settings as above when one might have thousands of predictors. o Introduced a new wrapper find.interaction() for testing for pairwise interactions between predictors. - [EMAIL PROTECTED] Udaya B. Kogalur, Ph.D. Kogalur Shear Corporation 5425 Nestleway Drive, Suite L1 Clemmons, NC 27012 ___ R-packages mailing list [EMAIL PROTECTED] https://stat.ethz.ch/mailman/listinfo/r-packages __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] reshape question
Hello all, A quick question concerning a behavior of reshape I fail tu understand, probably something obvious but I just can't see it. With the following data frame further referred to as tab : Variete;Semis.Date;Date_Mesure.1;Variable_Mesure.1;Valeur_Mesure.1;Date_Mesure.2;Variable_Mesure.2;Valeur_Mesure.2;Date_Mesure.3;Variable_Mesure.3;Valeur_Mesure.3;Date_Mesure.4;Variable_Mesure.4;Valeur_Mesure.4;Date_Mesure.5;Variable_Mesure.5;Valeur_Mesure.5;Date_Mesure.6;Variable_Mesure.6;Valeur_Mesure.6;Date_Mesure.7;Variable_Mesure.7;Valeur_Mesure.7;Date_Mesure.8;Variable_Mesure.8;Valeur_Mesure.8;Date_Mesure.9;Variable_Mesure.9;Valeur_Mesure.9;Date_Mesure.10;Variable_Mesure.10;Valeur_Mesure.10 A;22/10/2004;38527;Partie aérienne.Verse;3.23;38516;Grain.Humidité;0.71;38523;Grain.Humidité;0.67;38526;Grain.Humidité;0.61;38530;Grain.Humidité;0.56;38532;Grain.Humidité;0.53;38537;Grain.Humidité;0.47;38539;Grain.Humidité;0.45;38544;Grain.Humidité;0.44;38551;Grain.Humidité;0.17 B;22/10/2004;38527;Partie aérienne.Verse;3.45;38516;Grain.Humidité;0.76;38523;Grain.Humidité;0.68;38526;Grain.Humidité;0.63;38530;Grain.Humidité;0.59;38532;Grain.Humidité;0.54;38537;Grain.Humidité;0.49;38539;Grain.Humidité;0.48;38544;Grain.Humidité;0.46;38551;Grain.Humidité;0.15 I execute the following command : reshape(tab,direction=long,varying=grep(Mesure,colnames(tab))) This gives me what I need except for a small glitch : I end up with the column Variable_Mesure containing the numerical values which were contained in the Valeur_Mesure.number columns of the wide data frame and conversely I have in the column Valeurs_Mesure column of my long dataframe the factor levels contained in the Variable_Mesure.number columns of the original wide dataframe. What is this inversion due to ? If it is an error on my part, which I suppose it is, how do I correct this ? Thanls in advance. PS - I am running R 2.3.1 on a Windows platform David Gouache Arvalis - Institut du Végétal Station de La Minière 78280 Guyancourt Tel: 01.30.12.96.22 / Port: 06.86.08.94.32 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] [R-pkgs] Ryacas now on CRAN
Ryacas is now available on CRAN. (Previously it was
available on the Omegahat repository.)
Ryacas is an R package that provides an interface from R to
the yacas computer algebra system. It can be used for
computer algebra, exact arithmetic, ASCII pretty printing
and R to TeX output. R, yacas and Ryacas are all free
software packages distributed under the GPL version 2.
Ryacas is written in R. It uses a recursive decent
R-to-yacas translator and an XML-based OpenMath yacas-to-R
translator. yacas is run as a second process to which
R communicates via a socket interface.
There are 8 different user level interfaces
(yacas.character, yacas.expression, yacas.function,
yacas.formula, Sym objects, Expr objects, yacmode and
runYacas). Most users will primarily use Sym objects.
NEW INSTALLATION FOR WINDOWS USERS
A key change in moving to CRAN is that yacas.exe is no longer
part of the Ryacas distribution so that Windows users must
separately install yacas 1.0.63. :( Non-windows users always
had to separately install yacas. To simplify this somewhat
the yacasInstall() R command will download and install yacas from
within R on Windows:
# Windows installation procedure
install.packages(Ryacas, dep = TRUE)
library(Ryacas)
yacasInstall()
For non-windows users the installation procedure is the same as
before; namely, install yacas and then install the Ryacas R package.
yacasInstall is not available on non-Windows systems. More
installation information is available on the Ryacas home page.
LINKS
Home Page (Overview, News, Installation, Sample Session, Links, SVN)
http://code.google.com/p/ryacas/
News (on source changes; not entirely same as home page news)
http://ryacas.googlecode.com/svn/trunk/inst/NEWS
Vignette (includes many examples)
http://ryacas.googlecode.com/svn/trunk/inst/doc/Ryacas.pdf
SAMPLE SESSION
(need fixed font email viewer to view correctly)
library(Ryacas)
# algebra
library(Ryacas)
x - Sym('x')
(x+1) * (x-1)
expression((x + 1) * (x - 1))
Simplify(%)
expression(x^2 - 1)
PrettyForm(%)
2
x - 1
# calculus
Integrate(x+tan(x), x)
expression(x^2/2 - log(cos(x)))
# exact arithmetic
yacas('12/24')
expression(1/2)
# ASCII pretty printing
exp(-x^2)/(cos(x)+exp(x))
expression(exp(-x^2)/(cos(x) + exp(x)))
PrettyForm(%)
/ / 2 \ \
Exp\ -\ x / /
---
Cos( x ) + Exp( x )
# matrix - yacas matrices are row-wise
List(List(1,2),List(x,6))
expression(list(list(1, 2), list(x, 6)))
PrettyForm(%)
/ \
| ( 1 ) ( 2 ) |
| |
| ( x ) ( 6 ) |
\ /
# output TeX
k - Sym('k')
yacas(TeXForm((x+1)^2 + k^3), retclass = 'unquote')
$\left( x + 1\right) ^{2} + k ^{3}$
detach()
yacas was developed by Ayal Pinkus and other contributors.
Ryacas was developed by Rob Goedman, Gabor Grothendieck,
Søren Højsgaard and Ayal Pinkus. Contact Rob for Mac
issues and Gabor for all other issues.
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[R] R Wiki down?
Hi. I can't access the site http://wiki.r-project.org/. I didn't find any notice about this on http://www.r-project.org/. Does anyone have any more information about the R Wiki status? Thanks! -- TMK -- 212-460-5430home 917-656-5351cell __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] reshape question
Try this: cn - names(tab) nm - list(Date = grep(Date_, cn, value = TRUE), Variable = grep(Variable, cn, value = TRUE), Valeur = grep(Valeur, cn, value = TRUE) ) reshape(tab, direction = long, varying = nm) On 5/3/07, GOUACHE David [EMAIL PROTECTED] wrote: Hello all, A quick question concerning a behavior of reshape I fail tu understand, probably something obvious but I just can't see it. With the following data frame further referred to as tab : Variete;Semis.Date;Date_Mesure.1;Variable_Mesure.1;Valeur_Mesure.1;Date_Mesure.2;Variable_Mesure.2;Valeur_Mesure.2;Date_Mesure.3;Variable_Mesure.3;Valeur_Mesure.3;Date_Mesure.4;Variable_Mesure.4;Valeur_Mesure.4;Date_Mesure.5;Variable_Mesure.5;Valeur_Mesure.5;Date_Mesure.6;Variable_Mesure.6;Valeur_Mesure.6;Date_Mesure.7;Variable_Mesure.7;Valeur_Mesure.7;Date_Mesure.8;Variable_Mesure.8;Valeur_Mesure.8;Date_Mesure.9;Variable_Mesure.9;Valeur_Mesure.9;Date_Mesure.10;Variable_Mesure.10;Valeur_Mesure.10 A;22/10/2004;38527;Partie aérienne.Verse;3.23;38516;Grain.Humidité;0.71;38523;Grain.Humidité;0.67;38526;Grain.Humidité;0.61;38530;Grain.Humidité;0.56;38532;Grain.Humidité;0.53;38537;Grain.Humidité;0.47;38539;Grain.Humidité;0.45;38544;Grain.Humidité;0.44;38551;Grain.Humidité;0.17 B;22/10/2004;38527;Partie aérienne.Verse;3.45;38516;Grain.Humidité;0.76;38523;Grain.Humidité;0.68;38526;Grain.Humidité;0.63;38530;Grain.Humidité;0.59;38532;Grain.Humidité;0.54;38537;Grain.Humidité;0.49;38539;Grain.Humidité;0.48;38544;Grain.Humidité;0.46;38551;Grain.Humidité;0.15 I execute the following command : reshape(tab,direction=long,varying=grep(Mesure,colnames(tab))) This gives me what I need except for a small glitch : I end up with the column Variable_Mesure containing the numerical values which were contained in the Valeur_Mesure.number columns of the wide data frame and conversely I have in the column Valeurs_Mesure column of my long dataframe the factor levels contained in the Variable_Mesure.number columns of the original wide dataframe. What is this inversion due to ? If it is an error on my part, which I suppose it is, how do I correct this ? Thanls in advance. PS - I am running R 2.3.1 on a Windows platform David Gouache Arvalis - Institut du Végétal Station de La Minière 78280 Guyancourt Tel: 01.30.12.96.22 / Port: 06.86.08.94.32 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] the Surv function
2007/5/2, Jennifer Dillon [EMAIL PROTECTED]: Hi, I'm trying to do a simple survival analysis on some data, and I'm having the following problem (here's my code and the error message): out - Surv(fup,event=status) Error in Surv(fup, event = status) : argument time2 is missing, with no default I am not very familiar with this, but shouldn' t it be: out - Surv(fup, status==1) where fup is your vector of time differences and status your vector to denote censored events (e.g. 1 is an uncensored event and 2 for a censored events). Have a look at section 12.2 of introductory statistics with R by P. Dalgaard -- A. Goralczyk Göttingen, Ger. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Off topic? Geographic data
Sorry if this is off-topic, but since there are so many data sets in R, I wonder if there is any data set with Geographic data, like (latitude,longitude) lists of the contour of the continents and countries. Alberto Monteiro __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Package contrast error
Trying to use contrast to look at differences within an lme lme.fnl.REML - lme(Max ~ S + Tr + Yr + Tr:Yr, random = ~1 |TID, method = REML) I have three levels of Tr I'm trying to contrast among different years (R, T97, T98), years = 1997-1999, so I'm interested in contrasts of the interaction term. anova(lme.fnl.REML) numDF denDF F-value p-value (Intercept) 1 168 19255.389 .0001 S 1 168 5.912 0.0161 Tr 2 11615.919 .0001 Yr 1 16877.837 .0001 Tr:Yr 2 16847.584 .0001 summary(lme.fnl.REML) Linear mixed-effects model fit by REML Data: NULL AIC BIClogLik 580.6991 613.5399 -281.3496 Random effects: Formula: ~1 | TID (Intercept) Residual StdDev: 0.3697006 0.5316062 Fixed effects: Max ~ S + Tr + Yr + Tr:Yr Value Std.Error DF t-value p-value (Intercept) -13.5681 113.2623 168 -0.119793 0.9048 SM 0.21870.0957 168 2.284605 0.0236 TrT97 1375.5897 164.0060 116 8.387434 0. TrT98 2890.9462 455.3497 116 6.348848 0. Yr 0.00990.0567 168 0.174005 0.8621 TrT97:Yr -0.68830.0821 168 -8.384798 0. TrT98:Yr -1.44630.2279 168 -6.347310 0. Correlation: (Intr) SM TrT97 TrT98 Yr TT97:Y SM0.067 TrT97-0.691 -0.049 TrT98-0.248 -0.001 0.171 Yr -1.000 -0.067 0.691 0.248 TrT97:Yr 0.691 0.048 -1.000 -0.171 -0.691 TrT98:Yr 0.248 0.001 -0.171 -1.000 -0.248 0.171 Standardized Within-Group Residuals: Min Q1 Med Q3 Max -2.19017911 -0.58108001 -0.04983642 0.57323031 2.39811353 Number of Observations: 291 Number of Groups: 119 When I try to get the contrast I get one of two errors each time. Trying for a paired contrast... tst - contrast(lme.fnl.REML, a=list(Yr=levels(Yr), Tr=R), b=list (Yr=levels(Yr, Tr=T97))) Error in gendata.default(fit = list(modelStruct = list(reStruct = list ( : not enough factors Trying to include the other factor to make R happy tst - contrast(lme.fnl.REML, a=list(Yr=levels(Yr), Tr=R), b=list (Yr=levels(Yr, Tr=T97)), c=list(Yr=levels(Yr, Tr=T98)) + ) Error in contrastCalc(fit, ...) : argument 4 matches multiple formal arguments Can anyone help with the syntax here? Thanks Ken [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] reshape question
Here is a minor improvement (cn and nm as before): reshape(tab, direction = long, varying = nm, v.names = names(nm)) On 5/3/07, Gabor Grothendieck [EMAIL PROTECTED] wrote: Try this: cn - names(tab) nm - list(Date = grep(Date_, cn, value = TRUE), Variable = grep(Variable, cn, value = TRUE), Valeur = grep(Valeur, cn, value = TRUE) ) reshape(tab, direction = long, varying = nm) On 5/3/07, GOUACHE David [EMAIL PROTECTED] wrote: Hello all, A quick question concerning a behavior of reshape I fail tu understand, probably something obvious but I just can't see it. With the following data frame further referred to as tab : Variete;Semis.Date;Date_Mesure.1;Variable_Mesure.1;Valeur_Mesure.1;Date_Mesure.2;Variable_Mesure.2;Valeur_Mesure.2;Date_Mesure.3;Variable_Mesure.3;Valeur_Mesure.3;Date_Mesure.4;Variable_Mesure.4;Valeur_Mesure.4;Date_Mesure.5;Variable_Mesure.5;Valeur_Mesure.5;Date_Mesure.6;Variable_Mesure.6;Valeur_Mesure.6;Date_Mesure.7;Variable_Mesure.7;Valeur_Mesure.7;Date_Mesure.8;Variable_Mesure.8;Valeur_Mesure.8;Date_Mesure.9;Variable_Mesure.9;Valeur_Mesure.9;Date_Mesure.10;Variable_Mesure.10;Valeur_Mesure.10 A;22/10/2004;38527;Partie aérienne.Verse;3.23;38516;Grain.Humidité;0.71;38523;Grain.Humidité;0.67;38526;Grain.Humidité;0.61;38530;Grain.Humidité;0.56;38532;Grain.Humidité;0.53;38537;Grain.Humidité;0.47;38539;Grain.Humidité;0.45;38544;Grain.Humidité;0.44;38551;Grain.Humidité;0.17 B;22/10/2004;38527;Partie aérienne.Verse;3.45;38516;Grain.Humidité;0.76;38523;Grain.Humidité;0.68;38526;Grain.Humidité;0.63;38530;Grain.Humidité;0.59;38532;Grain.Humidité;0.54;38537;Grain.Humidité;0.49;38539;Grain.Humidité;0.48;38544;Grain.Humidité;0.46;38551;Grain.Humidité;0.15 I execute the following command : reshape(tab,direction=long,varying=grep(Mesure,colnames(tab))) This gives me what I need except for a small glitch : I end up with the column Variable_Mesure containing the numerical values which were contained in the Valeur_Mesure.number columns of the wide data frame and conversely I have in the column Valeurs_Mesure column of my long dataframe the factor levels contained in the Variable_Mesure.number columns of the original wide dataframe. What is this inversion due to ? If it is an error on my part, which I suppose it is, how do I correct this ? Thanls in advance. PS - I am running R 2.3.1 on a Windows platform David Gouache Arvalis - Institut du Végétal Station de La Minière 78280 Guyancourt Tel: 01.30.12.96.22 / Port: 06.86.08.94.32 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] nlme fixed effects specification
dear R experts: sorry, I have to ask this again. I know that the answer is in section 7.2 of S Programming, but I don't have the book (and I plan to buy the next edition---which I hope will be titled S/R programming ;-) ). I believe the following yields a standard fixed-effects estimation: fixed.effects = as.factor( as.integer( runif(100)*10 ) ) y=rnorm(100); x=rnorm(100); print(summary(lm( Y ~ X + fe))) I would like to know how to get the same coefficient on X using nlme. (I cannot use this ordinary lm method in my real application, simply because I have 10,000 fixed effects.) I tried a variety of arguments to the fixed nlme parameter (e.g., fixed=list(fmid)), but did not get the syntax right. could someone please tell me the magic spell? may I also suggest that such an example be added to the nlme examples documentation, too, please? help appreciated. regards, /ivo __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Package contrast error
Ken Nussear wrote: Trying to use contrast to look at differences within an lme lme.fnl.REML - lme(Max ~ S + Tr + Yr + Tr:Yr, random = ~1 |TID, method = REML) I have three levels of Tr I'm trying to contrast among different years (R, T97, T98), years = 1997-1999, so I'm interested in contrasts of the interaction term. anova(lme.fnl.REML) numDF denDF F-value p-value (Intercept) 1 168 19255.389 .0001 S 1 168 5.912 0.0161 Tr 2 11615.919 .0001 Yr 1 16877.837 .0001 Tr:Yr 2 16847.584 .0001 summary(lme.fnl.REML) Linear mixed-effects model fit by REML Data: NULL AIC BIClogLik 580.6991 613.5399 -281.3496 Random effects: Formula: ~1 | TID (Intercept) Residual StdDev: 0.3697006 0.5316062 Fixed effects: Max ~ S + Tr + Yr + Tr:Yr Value Std.Error DF t-value p-value (Intercept) -13.5681 113.2623 168 -0.119793 0.9048 SM 0.21870.0957 168 2.284605 0.0236 TrT97 1375.5897 164.0060 116 8.387434 0. TrT98 2890.9462 455.3497 116 6.348848 0. Yr 0.00990.0567 168 0.174005 0.8621 TrT97:Yr -0.68830.0821 168 -8.384798 0. TrT98:Yr -1.44630.2279 168 -6.347310 0. Correlation: (Intr) SM TrT97 TrT98 Yr TT97:Y SM0.067 TrT97-0.691 -0.049 TrT98-0.248 -0.001 0.171 Yr -1.000 -0.067 0.691 0.248 TrT97:Yr 0.691 0.048 -1.000 -0.171 -0.691 TrT98:Yr 0.248 0.001 -0.171 -1.000 -0.248 0.171 Standardized Within-Group Residuals: Min Q1 Med Q3 Max -2.19017911 -0.58108001 -0.04983642 0.57323031 2.39811353 Number of Observations: 291 Number of Groups: 119 When I try to get the contrast I get one of two errors each time. Trying for a paired contrast... tst - contrast(lme.fnl.REML, a=list(Yr=levels(Yr), Tr=R), b=list (Yr=levels(Yr, Tr=T97))) Error in gendata.default(fit = list(modelStruct = list(reStruct = list ( : not enough factors Trying to include the other factor to make R happy tst - contrast(lme.fnl.REML, a=list(Yr=levels(Yr), Tr=R), b=list (Yr=levels(Yr, Tr=T97)), c=list(Yr=levels(Yr, Tr=T98)) + ) Error in contrastCalc(fit, ...) : argument 4 matches multiple formal arguments Can anyone help with the syntax here? I believe you need to include one or more values S at which to contrast the treatments in each of the lists. So you might try something like this: contrast(lme.fnl.REML, a=list(Yr=levels(Yr), Tr=R, S=M), b=list(Yr=levels(Yr), Tr=T97, S=M)) or contrast(lme.fnl.REML, a=list(Yr=levels(Yr), Tr=R, S=levels(S)), b=list(Yr=levels(Yr), Tr=T97, S=levels(S))) Thanks Ken [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Chuck Cleland, Ph.D. NDRI, Inc. 71 West 23rd Street, 8th floor New York, NY 10010 tel: (212) 845-4495 (Tu, Th) tel: (732) 512-0171 (M, W, F) fax: (917) 438-0894 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Bayesian logistic regression with a beta prior (MCMClogit)
Dear Franco,
Have you tried using the beta.start option in MCMClogit? (The problem may
be where you are starting your chain.)
Regards,
-Cody
francogrex
[EMAIL PROTECTED]
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Subject
[R] Bayesian logistic regression
05/03/2007 12:21 with a beta prior (MCMClogit)
AM
Dear all,
I am trying to use the logistic regression with MCMClogit (package:
MCMCpack/Coda) and I want to put a beta prior on the parameters, but it's
giving me error message (please see output below) no matter what shape 1 or
2 I use. It works perfect with the cauchy or normal priors. Do you know if
there is a catch there somewhere? Thanks
logpriorfun - function(beta,shape1,shape2){
sum(dbeta(beta,shape1,shape2, log=T)) }
posterior - MCMClogit(nausea~nsaid*diuretic, data=w,
verbose=2000,burnin = 1000, mcmc = 1,
user.prior.density=logpriorfun,shape1=1,shape2=1)
user.prior.density(beta.start) == -Inf.
Error in MCMClogit(nausea ~ nsaid * diuretic, data = w, verbose = 2000, :
Respecify and call MCMClogit() again.
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Re: [R] Off topic? Geographic data
On 5/3/2007 1:19 PM, Alberto Vieira Ferreira Monteiro wrote: Sorry if this is off-topic, but since there are so many data sets in R, I wonder if there is any data set with Geographic data, like (latitude,longitude) lists of the contour of the continents and countries. The maps and mapdata packages have this. (They work together; mapdata has more detail than maps). Duncan Murdoch __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] R package development in windows
I'm attempting to build an R package for distribution and am working from the directions found at http://www.maths.bris.ac.uk/~maman/computerstuff/Rhelp/Rpackages.html#Wi n-Win I've read through Writing R Extensions and various other helpful web sites. I've installed all relevant software (perl, cygwin, mingwin, hhc.exe). Here is what I have done so far: 1) Sourced data and functions into R 2) Used package.skeleton 3) Edited Description file 4) Edited my windows path to ensure the new programs (e.g., perl) are in the path 5) Then, I open DOS and do the following in the script below C:\Program Files\R\R-2.4.1\binRcmd build --force --binary g:\foo * checking for file 'g:\foo/DESCRIPTION' ... OK * preparing 'g:\foo': * checking DESCRIPTION meta-information ...'sh' is not recognized as an internal or external command, operable program or batch file. OK * removing junk files 'sh' is not recognized as an internal or external command, operable program or batch file. 'sh' is not recognized as an internal or external command, operable program or batch file. 'sh' is not recognized as an internal or external command, operable program or batch file. Error: cannot open file 'foo/DESCRIPTION' for reading I'ver read through about as much documentation as I can find, and I'm just not sure what I should do from here. I admit that I have reached a point of frustration and must apologize if the problem would be evident if I read documentation further, but I'm about tapped out after a few days of experimentation. Can anyone suggest how I could resolve this and what the next steps would be? Thanks: I'm using Windows XP and R 2.4.1 Harold [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Package contrast error
Ken,
lme.fnl.REML - lme(Max ~ S + Tr + Yr + Tr:Yr, random = ~1 |TID,
method = REML)
You have three variables in the model: S, Tr and Yr.
tst - contrast(lme.fnl.REML, a=list(Yr=levels(Yr), Tr=R), b=list
(Yr=levels(Yr, Tr=T97)))
Error in gendata.default(fit = list(modelStruct = list(reStruct = list
( :
not enough factors
I think that you need to specify a value for S in the lists for a and b.
Also, I think that there is a typo:
b=list(Yr=levels(Yr), Tr=T97)
instead of
b=list(Yr=levels(Yr, Tr=T97))
Trying to include the other factor to make R happy
tst - contrast(lme.fnl.REML, a=list(Yr=levels(Yr), Tr=R), b=list
(Yr=levels(Yr, Tr=T97)), c=list(Yr=levels(Yr, Tr=T98))
+ )
Error in contrastCalc(fit, ...) : argument 4 matches multiple formal
arguments
Max
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Re: [R] R package development in windows
Doran, Harold said the following on 5/3/2007 11:32 AM: I'm attempting to build an R package for distribution and am working from the directions found at http://www.maths.bris.ac.uk/~maman/computerstuff/Rhelp/Rpackages.html#Wi n-Win I've read through Writing R Extensions and various other helpful web sites. I've installed all relevant software (perl, cygwin, mingwin, hhc.exe). Here is what I have done so far: 1) Sourced data and functions into R 2) Used package.skeleton 3) Edited Description file 4) Edited my windows path to ensure the new programs (e.g., perl) are in the path 5) Then, I open DOS and do the following in the script below C:\Program Files\R\R-2.4.1\binRcmd build --force --binary g:\foo * checking for file 'g:\foo/DESCRIPTION' ... OK * preparing 'g:\foo': * checking DESCRIPTION meta-information ...'sh' is not recognized as an internal or external command, operable program or batch file. OK * removing junk files 'sh' is not recognized as an internal or external command, operable program or batch file. 'sh' is not recognized as an internal or external command, operable program or batch file. 'sh' is not recognized as an internal or external command, operable program or batch file. Error: cannot open file 'foo/DESCRIPTION' for reading I'ver read through about as much documentation as I can find, and I'm just not sure what I should do from here. I admit that I have reached a point of frustration and must apologize if the problem would be evident if I read documentation further, but I'm about tapped out after a few days of experimentation. Can anyone suggest how I could resolve this and what the next steps would be? Thanks: I'm using Windows XP and R 2.4.1 Harold Do you have Rtools installed and in your system path? You should read all the documentation on that page. http://www.murdoch-sutherland.com/Rtools/ HTH, --sundar __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R package development in windows
It can find sh.exe so you haven't installed Rtools. There are several HowTo's listed in the links section here that include pointers to R manuals and other step by step instructions: http://code.google.com/p/batchfiles/ On 5/3/07, Doran, Harold [EMAIL PROTECTED] wrote: I'm attempting to build an R package for distribution and am working from the directions found at http://www.maths.bris.ac.uk/~maman/computerstuff/Rhelp/Rpackages.html#Wi n-Win I've read through Writing R Extensions and various other helpful web sites. I've installed all relevant software (perl, cygwin, mingwin, hhc.exe). Here is what I have done so far: 1) Sourced data and functions into R 2) Used package.skeleton 3) Edited Description file 4) Edited my windows path to ensure the new programs (e.g., perl) are in the path 5) Then, I open DOS and do the following in the script below C:\Program Files\R\R-2.4.1\binRcmd build --force --binary g:\foo * checking for file 'g:\foo/DESCRIPTION' ... OK * preparing 'g:\foo': * checking DESCRIPTION meta-information ...'sh' is not recognized as an internal or external command, operable program or batch file. OK * removing junk files 'sh' is not recognized as an internal or external command, operable program or batch file. 'sh' is not recognized as an internal or external command, operable program or batch file. 'sh' is not recognized as an internal or external command, operable program or batch file. Error: cannot open file 'foo/DESCRIPTION' for reading I'ver read through about as much documentation as I can find, and I'm just not sure what I should do from here. I admit that I have reached a point of frustration and must apologize if the problem would be evident if I read documentation further, but I'm about tapped out after a few days of experimentation. Can anyone suggest how I could resolve this and what the next steps would be? Thanks: I'm using Windows XP and R 2.4.1 Harold [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Truncating trailing digits
Hello, I am relatively new to R and have a rudimentary question, I think. How does one truncate the number of digits displayed after the decimal when viewing the results of analyses? My apologies if this question has been answered previously, I was not able to find references very easily. Thank you in advance, Matt [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R package development in windows
Thanks Gabor, Sundar, and Tony. Indeed, Rtools was missing from the
path. With that resolved, and another 10 minute windows restart, I get
the following below. The log suggests that hhc is not installed. It is,
and, according to the directions I am following, I have placed it in the
c:\cygwin directory.
BTW, package.skeleton() doesn't seem to create the correct DESCRIPTION
template. I had to add the DEPENDS line. Without this, I get another
error.
C:\Program Files\R\R-2.4.1\binRcmd build --force --binary g:\foo
* checking for file 'g:\foo/DESCRIPTION' ... OK
* preparing 'g:\foo':
* checking DESCRIPTION meta-information ... OK
* removing junk files
* checking for LF line-endings in source files
* checking for empty or unneeded directories
* building binary distribution
WARNING
* some HTML links may not be found
installing R.css in c:/TEMP/Rinst40061099
Using auto-selected zip options ''
latex: not found
latex: not found
latex: not found
-- Making package foo
latex: not found
adding build stamp to DESCRIPTION
latex: not found
latex: not found
latex: not found
installing R files
latex: not found
installing data files
latex: not found
installing man source files
installing indices
latex: not found
not zipping data
installing help
Warning: \alias{foo} already in foo-package.Rd -- skipping the one in
foo.Rd
Building/Updating help pages for package 'foo'
Formats: text html latex example chm
foo-package texthtmllatex example chm
foo texthtmllatex example chm
mydatatexthtmllatex example chm
hhc: not found
cp: cannot stat `c:/TEMP/Rbuild40048815/foo/chm/foo.chm': No such file
or direct
ory
make[1]: *** [chm-foo] Error 1
make: *** [pkg-foo] Error 2
*** Installation of foo failed ***
Removing 'c:/TEMP/Rinst40061099/foo'
ERROR
* installation failed
C:\Program Files\R\R-2.4.1\bin
-Original Message-
From: Gabor Grothendieck [mailto:[EMAIL PROTECTED]
Sent: Thursday, May 03, 2007 2:50 PM
To: Doran, Harold
Cc: r-help@stat.math.ethz.ch
Subject: Re: [R] R package development in windows
It can find sh.exe so you haven't installed Rtools.
There are several HowTo's listed in the links section here
that include pointers to R manuals and other step by step
instructions:
http://code.google.com/p/batchfiles/
On 5/3/07, Doran, Harold [EMAIL PROTECTED] wrote:
I'm attempting to build an R package for distribution and
am working
from the directions found at
http://www.maths.bris.ac.uk/~maman/computerstuff/Rhelp/Rpackages.html#
Wi
n-Win
I've read through Writing R Extensions and various other
helpful web
sites. I've installed all relevant software (perl, cygwin, mingwin,
hhc.exe). Here is what I have done so far:
1) Sourced data and functions into R
2) Used package.skeleton
3) Edited Description file
4) Edited my windows path to ensure the new programs (e.g.,
perl) are
in the path
5) Then, I open DOS and do the following in the script below
C:\Program Files\R\R-2.4.1\binRcmd build --force --binary g:\foo
* checking for file 'g:\foo/DESCRIPTION' ... OK
* preparing 'g:\foo':
* checking DESCRIPTION meta-information ...'sh' is not
recognized as
an internal or external command, operable program or batch file.
OK
* removing junk files
'sh' is not recognized as an internal or external command, operable
program or batch file.
'sh' is not recognized as an internal or external command, operable
program or batch file.
'sh' is not recognized as an internal or external command, operable
program or batch file.
Error: cannot open file 'foo/DESCRIPTION' for reading
I'ver read through about as much documentation as I can
find, and I'm
just not sure what I should do from here. I admit that I
have reached
a point of frustration and must apologize if the problem would be
evident if I read documentation further, but I'm about tapped out
after a few days of experimentation.
Can anyone suggest how I could resolve this and what the next steps
would be?
Thanks:
I'm using Windows XP and R 2.4.1
Harold
[[alternative HTML version deleted]]
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] Parsing data with an uneven number of delimiters
I have a list of data that is delimited by a / and, as long as there is an equal number of delimiters, I can parse the data and put it into a data frame: t1-c(a/a/a,b/bb/bbb,ccc/cc/c) t2-strsplit(t1,/) t3-data.frame(t2) t3 c..aaa.. c..bbbbbb.. c..cccccc.. 1a b ccc 2a bb cc 3a bbb c However, if I don't have an equal number of delimiters, this technique doesn't work: l1-c(a/a/a,b/bb/bbb,cc/c) l2-strsplit(l1,/) l3-data.frame(l2) Error in data.frame(c(a, a, a), c(b, bb, bbb), c(cc, c : arguments imply differing number of rows: 3, 2 Is there an easy way to get this into a data frame with NA's (or something else) where the missing data would be? Thanks in advance. Kevin Burke __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Off topic? Geographic data
On Thu, 3 May 2007, Alberto Vieira Ferreira Monteiro wrote: Sorry if this is off-topic, but since there are so many data sets in R, I wonder if there is any data set with Geographic data, like (latitude,longitude) lists of the contour of the continents and countries. Please see the Spatial Task View on CRAN. In general, position data is heavily protected outside the US, so that existing and available data is limited for other countries. The maps and mapdata packages have some databases, some of which are also up to date, but others still feature the Soviet Union and Yugoslavia, which is only of historical interest. There is an interface to more recent shorelines in the maptools package, which will handle all the levels of detail in GSHHS. The CDC has a set of shapefiles covering many countries with borders from about 1997, but sadly these are restricted. Some enlightened countries are releasing data; Canada has recently decided to do so: http://www.geogratis.gc.ca/, an initiative other countries could with benefit follow. The US has by far the most developed geographical data service sector, because the data are free like beer but hard to use, creating opportunties for service providers. Most of these data formats can be read by functions in maptools or rgdal. Roger Alberto Monteiro -- Roger Bivand Economic Geography Section, Department of Economics, Norwegian School of Economics and Business Administration, Helleveien 30, N-5045 Bergen, Norway. voice: +47 55 95 93 55; fax +47 55 95 95 43 e-mail: [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R package development in windows
On 5/3/2007 3:04 PM, Doran, Harold wrote:
Thanks Gabor, Sundar, and Tony. Indeed, Rtools was missing from the
path. With that resolved, and another 10 minute windows restart, I get
the following below. The log suggests that hhc is not installed. It is,
and, according to the directions I am following, I have placed it in the
c:\cygwin directory.
I think the problem is that you are following a real mix of
instructions, and they don't make sense.
It would be nice if folks would submit patches to the R Admin manual (or
to the Rtools web site) rather than putting together web sites with
advice that is bad from day one, and quickly gets worse when it is not
updated.
BTW, package.skeleton() doesn't seem to create the correct DESCRIPTION
template. I had to add the DEPENDS line. Without this, I get another
error.
C:\Program Files\R\R-2.4.1\binRcmd build --force --binary g:\foo
R 2.4.1 is no longer current; the package building instructions in R
2.5.0 have been simplified a bit. You might want to try those.
Duncan Murdoch
* checking for file 'g:\foo/DESCRIPTION' ... OK
* preparing 'g:\foo':
* checking DESCRIPTION meta-information ... OK
* removing junk files
* checking for LF line-endings in source files
* checking for empty or unneeded directories
* building binary distribution
WARNING
* some HTML links may not be found
installing R.css in c:/TEMP/Rinst40061099
Using auto-selected zip options ''
latex: not found
latex: not found
latex: not found
-- Making package foo
latex: not found
adding build stamp to DESCRIPTION
latex: not found
latex: not found
latex: not found
installing R files
latex: not found
installing data files
latex: not found
installing man source files
installing indices
latex: not found
not zipping data
installing help
Warning: \alias{foo} already in foo-package.Rd -- skipping the one in
foo.Rd
Building/Updating help pages for package 'foo'
Formats: text html latex example chm
foo-package texthtmllatex example chm
foo texthtmllatex example chm
mydatatexthtmllatex example chm
hhc: not found
cp: cannot stat `c:/TEMP/Rbuild40048815/foo/chm/foo.chm': No such file
or direct
ory
make[1]: *** [chm-foo] Error 1
make: *** [pkg-foo] Error 2
*** Installation of foo failed ***
Removing 'c:/TEMP/Rinst40061099/foo'
ERROR
* installation failed
C:\Program Files\R\R-2.4.1\bin
-Original Message-
From: Gabor Grothendieck [mailto:[EMAIL PROTECTED]
Sent: Thursday, May 03, 2007 2:50 PM
To: Doran, Harold
Cc: r-help@stat.math.ethz.ch
Subject: Re: [R] R package development in windows
It can find sh.exe so you haven't installed Rtools.
There are several HowTo's listed in the links section here
that include pointers to R manuals and other step by step
instructions:
http://code.google.com/p/batchfiles/
On 5/3/07, Doran, Harold [EMAIL PROTECTED] wrote:
I'm attempting to build an R package for distribution and
am working
from the directions found at
http://www.maths.bris.ac.uk/~maman/computerstuff/Rhelp/Rpackages.html#
Wi
n-Win
I've read through Writing R Extensions and various other
helpful web
sites. I've installed all relevant software (perl, cygwin, mingwin,
hhc.exe). Here is what I have done so far:
1) Sourced data and functions into R
2) Used package.skeleton
3) Edited Description file
4) Edited my windows path to ensure the new programs (e.g.,
perl) are
in the path
5) Then, I open DOS and do the following in the script below
C:\Program Files\R\R-2.4.1\binRcmd build --force --binary g:\foo
* checking for file 'g:\foo/DESCRIPTION' ... OK
* preparing 'g:\foo':
* checking DESCRIPTION meta-information ...'sh' is not
recognized as
an internal or external command, operable program or batch file.
OK
* removing junk files
'sh' is not recognized as an internal or external command, operable
program or batch file.
'sh' is not recognized as an internal or external command, operable
program or batch file.
'sh' is not recognized as an internal or external command, operable
program or batch file.
Error: cannot open file 'foo/DESCRIPTION' for reading
I'ver read through about as much documentation as I can
find, and I'm
just not sure what I should do from here. I admit that I
have reached
a point of frustration and must apologize if the problem would be
evident if I read documentation further, but I'm about tapped out
after a few days of experimentation.
Can anyone suggest how I could resolve this and what the next steps
would be?
Thanks:
I'm using Windows XP and R 2.4.1
Harold
[[alternative HTML version deleted]]
__
R-help@stat.math.ethz.ch mailing list
Re: [R] [SPAM] - Re: R package development in windows - Bayesian Filter detected spam
Thanks, Duncan. I'll look into that. Is there an authoritative document
that codifies the new package development procedures for 2.5.0
(windows-specific), or is that Writing R Extensions? In this thread
alone I've received multiple emails pointing to multiple web sites with
instructions for windows. Inasmuch as its appreciated, I'm a bit
confused as to which I should consider authoritative.
I do hope I can resolve this and appreciate the help I've received.
However, I feel a bit compelled to note how very difficult this process
is.
Harold
-Original Message-
From: Duncan Murdoch [mailto:[EMAIL PROTECTED]
Sent: Thursday, May 03, 2007 3:24 PM
To: Doran, Harold
Cc: Gabor Grothendieck; r-help@stat.math.ethz.ch
Subject: [SPAM] - Re: [R] R package development in windows -
Bayesian Filter detected spam
On 5/3/2007 3:04 PM, Doran, Harold wrote:
Thanks Gabor, Sundar, and Tony. Indeed, Rtools was missing from the
path. With that resolved, and another 10 minute windows
restart, I get
the following below. The log suggests that hhc is not installed. It
is, and, according to the directions I am following, I have
placed it
in the c:\cygwin directory.
I think the problem is that you are following a real mix of
instructions, and they don't make sense.
It would be nice if folks would submit patches to the R Admin
manual (or to the Rtools web site) rather than putting
together web sites with advice that is bad from day one, and
quickly gets worse when it is not updated.
BTW, package.skeleton() doesn't seem to create the correct
DESCRIPTION
template. I had to add the DEPENDS line. Without this, I
get another
error.
C:\Program Files\R\R-2.4.1\binRcmd build --force --binary g:\foo
R 2.4.1 is no longer current; the package building
instructions in R 2.5.0 have been simplified a bit. You
might want to try those.
Duncan Murdoch
* checking for file 'g:\foo/DESCRIPTION' ... OK
* preparing 'g:\foo':
* checking DESCRIPTION meta-information ... OK
* removing junk files
* checking for LF line-endings in source files
* checking for empty or unneeded directories
* building binary distribution
WARNING
* some HTML links may not be found
installing R.css in c:/TEMP/Rinst40061099
Using auto-selected zip options ''
latex: not found
latex: not found
latex: not found
-- Making package foo
latex: not found
adding build stamp to DESCRIPTION
latex: not found
latex: not found
latex: not found
installing R files
latex: not found
installing data files
latex: not found
installing man source files
installing indices
latex: not found
not zipping data
installing help
Warning: \alias{foo} already in foo-package.Rd -- skipping
the one in
foo.Rd Building/Updating help pages for package 'foo'
Formats: text html latex example chm
foo-package texthtmllatex
example chm
foo texthtmllatex
example chm
mydatatexthtmllatex
example chm
hhc: not found
cp: cannot stat `c:/TEMP/Rbuild40048815/foo/chm/foo.chm':
No such file
or direct ory
make[1]: *** [chm-foo] Error 1
make: *** [pkg-foo] Error 2
*** Installation of foo failed ***
Removing 'c:/TEMP/Rinst40061099/foo'
ERROR
* installation failed
C:\Program Files\R\R-2.4.1\bin
-Original Message-
From: Gabor Grothendieck [mailto:[EMAIL PROTECTED]
Sent: Thursday, May 03, 2007 2:50 PM
To: Doran, Harold
Cc: r-help@stat.math.ethz.ch
Subject: Re: [R] R package development in windows
It can find sh.exe so you haven't installed Rtools.
There are several HowTo's listed in the links section here that
include pointers to R manuals and other step by step
instructions:
http://code.google.com/p/batchfiles/
On 5/3/07, Doran, Harold [EMAIL PROTECTED] wrote:
I'm attempting to build an R package for distribution and
am working
from the directions found at
http://www.maths.bris.ac.uk/~maman/computerstuff/Rhelp/Rpackages.html
#
Wi
n-Win
I've read through Writing R Extensions and various other
helpful web
sites. I've installed all relevant software (perl,
cygwin, mingwin,
hhc.exe). Here is what I have done so far:
1) Sourced data and functions into R
2) Used package.skeleton
3) Edited Description file
4) Edited my windows path to ensure the new programs (e.g.,
perl) are
in the path
5) Then, I open DOS and do the following in the script below
C:\Program Files\R\R-2.4.1\binRcmd build --force
--binary g:\foo
* checking for file 'g:\foo/DESCRIPTION' ... OK
* preparing 'g:\foo':
* checking DESCRIPTION meta-information ...'sh' is not
recognized as
an internal or external command, operable program or batch file.
OK
* removing junk files
'sh' is
Re: [R] Truncating trailing digits
On Thu, 2007-05-03 at 12:14 -0400, Pietrzykowski, Matthew (GE, Research) wrote: Hello, I am relatively new to R and have a rudimentary question, I think. How does one truncate the number of digits displayed after the decimal when viewing the results of analyses? My apologies if this question has been answered previously, I was not able to find references very easily. Thank you in advance, Matt The answer is it depends. There are user configurable options in R that determine how default output is displayed, relative to the number of significant digits and the use of scientific notation. See ?options for more information, specifically 'digits' and 'scipen'. These don't necessarily guarantee a fixed number of digits after the decimal however. If you are creating your own output functions and want greater control over the formatting (ie. column alignment, etc.), including specifically the number of digits after the decimal, then see ?formatC and ?sprintf which allow for this. Also see ?cat which is how much of standard R console output is generated. HTH, Marc Schwartz __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Truncating trailing digits
Perhaps format is what you are looking for: ?format Charles Annis, P.E. [EMAIL PROTECTED] phone: 561-352-9699 eFax: 614-455-3265 http://www.StatisticalEngineering.com -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Pietrzykowski, Matthew (GE, Research) Sent: Thursday, May 03, 2007 12:14 PM To: r-help@stat.math.ethz.ch Subject: [R] Truncating trailing digits Hello, I am relatively new to R and have a rudimentary question, I think. How does one truncate the number of digits displayed after the decimal when viewing the results of analyses? My apologies if this question has been answered previously, I was not able to find references very easily. Thank you in advance, Matt [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] [SPAM] - Re: R package development in windows - Bayesian Filter detected spam
On 5/3/2007 3:33 PM, Doran, Harold wrote:
Thanks, Duncan. I'll look into that. Is there an authoritative document
that codifies the new package development procedures for 2.5.0
(windows-specific), or is that Writing R Extensions? In this thread
alone I've received multiple emails pointing to multiple web sites with
instructions for windows. Inasmuch as its appreciated, I'm a bit
confused as to which I should consider authoritative.
I do hope I can resolve this and appreciate the help I've received.
However, I feel a bit compelled to note how very difficult this process
is.
The manuals are the authoritative reference. Writing R Extensions tells
you what to do to set up a package. The R Administration and
Installation manual tells you how to set up your system so those
instructions will work. On Windows, you want to pay particular
attention to the appendix of the Admin manual called The Windows
Toolset. This is Appendix E in the distributed .pdf; an HTML version is
available here:
http://cran.r-project.org/doc/manuals/R-admin.html#The-Windows-toolset
We realize that these instructions are not easy to follow, there's no
need to tell us that. However, specific corrections or improvements
would be welcome.
Duncan Murdoch
Harold
-Original Message-
From: Duncan Murdoch [mailto:[EMAIL PROTECTED]
Sent: Thursday, May 03, 2007 3:24 PM
To: Doran, Harold
Cc: Gabor Grothendieck; r-help@stat.math.ethz.ch
Subject: [SPAM] - Re: [R] R package development in windows -
Bayesian Filter detected spam
On 5/3/2007 3:04 PM, Doran, Harold wrote:
Thanks Gabor, Sundar, and Tony. Indeed, Rtools was missing from the
path. With that resolved, and another 10 minute windows
restart, I get
the following below. The log suggests that hhc is not installed. It
is, and, according to the directions I am following, I have
placed it
in the c:\cygwin directory.
I think the problem is that you are following a real mix of
instructions, and they don't make sense.
It would be nice if folks would submit patches to the R Admin
manual (or to the Rtools web site) rather than putting
together web sites with advice that is bad from day one, and
quickly gets worse when it is not updated.
BTW, package.skeleton() doesn't seem to create the correct
DESCRIPTION
template. I had to add the DEPENDS line. Without this, I
get another
error.
C:\Program Files\R\R-2.4.1\binRcmd build --force --binary g:\foo
R 2.4.1 is no longer current; the package building
instructions in R 2.5.0 have been simplified a bit. You
might want to try those.
Duncan Murdoch
* checking for file 'g:\foo/DESCRIPTION' ... OK
* preparing 'g:\foo':
* checking DESCRIPTION meta-information ... OK
* removing junk files
* checking for LF line-endings in source files
* checking for empty or unneeded directories
* building binary distribution
WARNING
* some HTML links may not be found
installing R.css in c:/TEMP/Rinst40061099
Using auto-selected zip options ''
latex: not found
latex: not found
latex: not found
-- Making package foo
latex: not found
adding build stamp to DESCRIPTION
latex: not found
latex: not found
latex: not found
installing R files
latex: not found
installing data files
latex: not found
installing man source files
installing indices
latex: not found
not zipping data
installing help
Warning: \alias{foo} already in foo-package.Rd -- skipping
the one in
foo.Rd Building/Updating help pages for package 'foo'
Formats: text html latex example chm
foo-package texthtmllatex
example chm
foo texthtmllatex
example chm
mydatatexthtmllatex
example chm
hhc: not found
cp: cannot stat `c:/TEMP/Rbuild40048815/foo/chm/foo.chm':
No such file
or direct ory
make[1]: *** [chm-foo] Error 1
make: *** [pkg-foo] Error 2
*** Installation of foo failed ***
Removing 'c:/TEMP/Rinst40061099/foo'
ERROR
* installation failed
C:\Program Files\R\R-2.4.1\bin
-Original Message-
From: Gabor Grothendieck [mailto:[EMAIL PROTECTED]
Sent: Thursday, May 03, 2007 2:50 PM
To: Doran, Harold
Cc: r-help@stat.math.ethz.ch
Subject: Re: [R] R package development in windows
It can find sh.exe so you haven't installed Rtools.
There are several HowTo's listed in the links section here that
include pointers to R manuals and other step by step
instructions:
http://code.google.com/p/batchfiles/
On 5/3/07, Doran, Harold [EMAIL PROTECTED] wrote:
I'm attempting to build an R package for distribution and
am working
from the directions found at
http://www.maths.bris.ac.uk/~maman/computerstuff/Rhelp/Rpackages.html
#
Wi
n-Win
I've read through Writing R Extensions and various
Re: [R] [SPAM] - Re: R package development in windows - BayesianFilter detected spam
Harold,
I totally echo your sentiments on the difficulty of creating an R package in
Windows. I really wish that this process could be made a bit less painful.
Ravi.
---
Ravi Varadhan, Ph.D.
Assistant Professor, The Center on Aging and Health
Division of Geriatric Medicine and Gerontology
Johns Hopkins University
Ph: (410) 502-2619
Fax: (410) 614-9625
Email: [EMAIL PROTECTED]
Webpage: http://www.jhsph.edu/agingandhealth/People/Faculty/Varadhan.html
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Doran, Harold
Sent: Thursday, May 03, 2007 3:33 PM
To: Duncan Murdoch
Cc: r-help@stat.math.ethz.ch
Subject: Re: [R] [SPAM] - Re: R package development in windows -
BayesianFilter detected spam
Thanks, Duncan. I'll look into that. Is there an authoritative document
that codifies the new package development procedures for 2.5.0
(windows-specific), or is that Writing R Extensions? In this thread
alone I've received multiple emails pointing to multiple web sites with
instructions for windows. Inasmuch as its appreciated, I'm a bit
confused as to which I should consider authoritative.
I do hope I can resolve this and appreciate the help I've received.
However, I feel a bit compelled to note how very difficult this process
is.
Harold
-Original Message-
From: Duncan Murdoch [mailto:[EMAIL PROTECTED]
Sent: Thursday, May 03, 2007 3:24 PM
To: Doran, Harold
Cc: Gabor Grothendieck; r-help@stat.math.ethz.ch
Subject: [SPAM] - Re: [R] R package development in windows -
Bayesian Filter detected spam
On 5/3/2007 3:04 PM, Doran, Harold wrote:
Thanks Gabor, Sundar, and Tony. Indeed, Rtools was missing from the
path. With that resolved, and another 10 minute windows
restart, I get
the following below. The log suggests that hhc is not installed. It
is, and, according to the directions I am following, I have
placed it
in the c:\cygwin directory.
I think the problem is that you are following a real mix of
instructions, and they don't make sense.
It would be nice if folks would submit patches to the R Admin
manual (or to the Rtools web site) rather than putting
together web sites with advice that is bad from day one, and
quickly gets worse when it is not updated.
BTW, package.skeleton() doesn't seem to create the correct
DESCRIPTION
template. I had to add the DEPENDS line. Without this, I
get another
error.
C:\Program Files\R\R-2.4.1\binRcmd build --force --binary g:\foo
R 2.4.1 is no longer current; the package building
instructions in R 2.5.0 have been simplified a bit. You
might want to try those.
Duncan Murdoch
* checking for file 'g:\foo/DESCRIPTION' ... OK
* preparing 'g:\foo':
* checking DESCRIPTION meta-information ... OK
* removing junk files
* checking for LF line-endings in source files
* checking for empty or unneeded directories
* building binary distribution
WARNING
* some HTML links may not be found
installing R.css in c:/TEMP/Rinst40061099
Using auto-selected zip options ''
latex: not found
latex: not found
latex: not found
-- Making package foo
latex: not found
adding build stamp to DESCRIPTION
latex: not found
latex: not found
latex: not found
installing R files
latex: not found
installing data files
latex: not found
installing man source files
installing indices
latex: not found
not zipping data
installing help
Warning: \alias{foo} already in foo-package.Rd -- skipping
the one in
foo.Rd Building/Updating help pages for package 'foo'
Formats: text html latex example chm
foo-package texthtmllatex
example chm
foo texthtmllatex
example chm
mydatatexthtmllatex
example chm
hhc: not found
cp: cannot stat `c:/TEMP/Rbuild40048815/foo/chm/foo.chm':
No such file
or direct ory
make[1]: *** [chm-foo] Error 1
make: *** [pkg-foo] Error 2
*** Installation of foo failed ***
Removing 'c:/TEMP/Rinst40061099/foo'
ERROR
* installation failed
C:\Program Files\R\R-2.4.1\bin
-Original Message-
From: Gabor Grothendieck [mailto:[EMAIL PROTECTED]
Sent: Thursday, May 03, 2007 2:50 PM
To: Doran, Harold
Cc: r-help@stat.math.ethz.ch
Subject: Re: [R] R package development in windows
It can find sh.exe so you haven't installed Rtools.
There are several HowTo's listed in the links section here that
include pointers to R manuals and other step by step
instructions:
http://code.google.com/p/batchfiles/
On 5/3/07, Doran, Harold [EMAIL PROTECTED] wrote:
I'm attempting to build an R package for distribution and
am
Re: [R] Parsing data with an uneven number of delimiters
Try this:
l1-c(a/a/a,b/bb/bbb,cc/c)
l2-strsplit(l1,/)
# determine maximum length
maxLen - max(sapply(l2, length))
# pad to maximum length
do.call('data.frame', lapply(l2, function(x)c(x, rep(NA, maxLen-length(x)
c..aaa.. c..bbbbbb.. c..ccc...NA.
1a b cc
2a bbc
3a bbb NA
On 5/3/07, Kevin Burke [EMAIL PROTECTED] wrote:
I have a list of data that is delimited by a / and, as long as there is an
equal number of delimiters, I can parse the data and put it into a data frame:
t1-c(a/a/a,b/bb/bbb,ccc/cc/c)
t2-strsplit(t1,/)
t3-data.frame(t2)
t3
c..aaa.. c..bbbbbb.. c..cccccc..
1a b ccc
2a bb cc
3a bbb c
However, if I don't have an equal number of delimiters, this technique
doesn't work:
l1-c(a/a/a,b/bb/bbb,cc/c)
l2-strsplit(l1,/)
l3-data.frame(l2)
Error in data.frame(c(a, a, a), c(b, bb, bbb), c(cc, c :
arguments imply differing number of rows: 3, 2
Is there an easy way to get this into a data frame with NA's (or something
else) where the missing data would be?
Thanks in advance.
Kevin Burke
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
What is the problem you are trying to solve?
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Parsing data with an uneven number of delimiters
Try: read.table(textConnection(l1), sep = /, fill = TRUE) On 5/3/07, Kevin Burke [EMAIL PROTECTED] wrote: I have a list of data that is delimited by a / and, as long as there is an equal number of delimiters, I can parse the data and put it into a data frame: t1-c(a/a/a,b/bb/bbb,ccc/cc/c) t2-strsplit(t1,/) t3-data.frame(t2) t3 c..aaa.. c..bbbbbb.. c..cccccc.. 1a b ccc 2a bb cc 3a bbb c However, if I don't have an equal number of delimiters, this technique doesn't work: l1-c(a/a/a,b/bb/bbb,cc/c) l2-strsplit(l1,/) l3-data.frame(l2) Error in data.frame(c(a, a, a), c(b, bb, bbb), c(cc, c : arguments imply differing number of rows: 3, 2 Is there an easy way to get this into a data frame with NA's (or something else) where the missing data would be? Thanks in advance. Kevin Burke __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] [SPAM] - Re: R package development in windows - BayesianFilter detected spam
Suggest you try following the advice I already gave, viz. reading the
relevant HowTo links on the batchfiles home page.
One gives pointers to the authoritative sources (the manuals)
and the other gives step by step instructions. These do answer
both of the subsequent questions the poster had.
On 5/3/07, Ravi Varadhan [EMAIL PROTECTED] wrote:
Harold,
I totally echo your sentiments on the difficulty of creating an R package in
Windows. I really wish that this process could be made a bit less painful.
Ravi.
---
Ravi Varadhan, Ph.D.
Assistant Professor, The Center on Aging and Health
Division of Geriatric Medicine and Gerontology
Johns Hopkins University
Ph: (410) 502-2619
Fax: (410) 614-9625
Email: [EMAIL PROTECTED]
Webpage: http://www.jhsph.edu/agingandhealth/People/Faculty/Varadhan.html
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Doran, Harold
Sent: Thursday, May 03, 2007 3:33 PM
To: Duncan Murdoch
Cc: r-help@stat.math.ethz.ch
Subject: Re: [R] [SPAM] - Re: R package development in windows -
BayesianFilter detected spam
Thanks, Duncan. I'll look into that. Is there an authoritative document
that codifies the new package development procedures for 2.5.0
(windows-specific), or is that Writing R Extensions? In this thread
alone I've received multiple emails pointing to multiple web sites with
instructions for windows. Inasmuch as its appreciated, I'm a bit
confused as to which I should consider authoritative.
I do hope I can resolve this and appreciate the help I've received.
However, I feel a bit compelled to note how very difficult this process
is.
Harold
-Original Message-
From: Duncan Murdoch [mailto:[EMAIL PROTECTED]
Sent: Thursday, May 03, 2007 3:24 PM
To: Doran, Harold
Cc: Gabor Grothendieck; r-help@stat.math.ethz.ch
Subject: [SPAM] - Re: [R] R package development in windows -
Bayesian Filter detected spam
On 5/3/2007 3:04 PM, Doran, Harold wrote:
Thanks Gabor, Sundar, and Tony. Indeed, Rtools was missing from the
path. With that resolved, and another 10 minute windows
restart, I get
the following below. The log suggests that hhc is not installed. It
is, and, according to the directions I am following, I have
placed it
in the c:\cygwin directory.
I think the problem is that you are following a real mix of
instructions, and they don't make sense.
It would be nice if folks would submit patches to the R Admin
manual (or to the Rtools web site) rather than putting
together web sites with advice that is bad from day one, and
quickly gets worse when it is not updated.
BTW, package.skeleton() doesn't seem to create the correct
DESCRIPTION
template. I had to add the DEPENDS line. Without this, I
get another
error.
C:\Program Files\R\R-2.4.1\binRcmd build --force --binary g:\foo
R 2.4.1 is no longer current; the package building
instructions in R 2.5.0 have been simplified a bit. You
might want to try those.
Duncan Murdoch
* checking for file 'g:\foo/DESCRIPTION' ... OK
* preparing 'g:\foo':
* checking DESCRIPTION meta-information ... OK
* removing junk files
* checking for LF line-endings in source files
* checking for empty or unneeded directories
* building binary distribution
WARNING
* some HTML links may not be found
installing R.css in c:/TEMP/Rinst40061099
Using auto-selected zip options ''
latex: not found
latex: not found
latex: not found
-- Making package foo
latex: not found
adding build stamp to DESCRIPTION
latex: not found
latex: not found
latex: not found
installing R files
latex: not found
installing data files
latex: not found
installing man source files
installing indices
latex: not found
not zipping data
installing help
Warning: \alias{foo} already in foo-package.Rd -- skipping
the one in
foo.Rd Building/Updating help pages for package 'foo'
Formats: text html latex example chm
foo-package texthtmllatex
example chm
foo texthtmllatex
example chm
mydatatexthtmllatex
example chm
hhc: not found
cp: cannot stat `c:/TEMP/Rbuild40048815/foo/chm/foo.chm':
No such file
or direct ory
make[1]: *** [chm-foo] Error 1
make: *** [pkg-foo] Error 2
*** Installation of foo failed ***
Removing 'c:/TEMP/Rinst40061099/foo'
ERROR
* installation failed
C:\Program Files\R\R-2.4.1\bin
-Original Message-
From: Gabor Grothendieck [mailto:[EMAIL PROTECTED]
Sent: Thursday, May 03, 2007 2:50 PM
To: Doran, Harold
Cc:
[R] Calculate sums in Matrixes
Dear R-users, The data that I want to treat refer to claims and a glm have been adjusted to the it. Now there are some calculations that I wanrt to do with the residuals and estimations from the model. The glm model has variables that refer to the fleet to wich the vehicle refers to and variables that refer to the vehicle (CC, type of vehicle, weight, etc). In that sense I need to calculate sums, like the ones that I attached again. I am following the paper:* Experience Rating Schemes for Fleets of Vehicles from Denise Desjardins, Georges Dionne and Jean Pinquet * Thanks Pedro sums[1].pdf Description: Adobe PDF document __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] the Surv function
2007/5/2, Jennifer Dillon [EMAIL PROTECTED]: Hi, I'm trying to do a simple survival analysis on some data, and I'm having the following problem (here's my code and the error message): out - Surv(fup,event=status) Error in Surv(fup, event = status) : argument time2 is missing, with no default From reading the documentation, it seems that I should be able to simply write: Surv(time1, event) if my data is right-censored, which it is. Help! Thanks a million, Jen -- Jennifer Dillon Doctoral Student Harvard Biostatistics Room 414B, Building 1 [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Read this page about Applied Survival Analysis: http://www.ats.ucla.edu/stat/r/examples/asa/default.htm Rod. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R Wiki down?
Talbot == Talbot Katz [EMAIL PROTECTED] on Thu, 03 May 2007 12:35:27 -0400 writes: Talbot Hi. I can't access the site Talbot http://wiki.r-project.org/. I didn't find any Talbot notice about this on http://www.r-project.org/. Talbot Does anyone have any more information about the R Talbot Wiki status? Thanks! Yes, it is currently down. Thanks for the note. It's maintainer has hereby __ CC __ be notified as well. Regards, Martin Maechler ETH Zurich __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] A question about POSIXct
Dear List: I have a simple two-column data set in .csv format, with the first column being the date and second column being some value. I use read.csv() to import the data as follows: x - read.csv(myfile.csv,header=T, dec=., colClasses=c(Date=POSIXct)) The structure of x is: str(x) `data.frame': 2959 obs. of 2 variables: $ Date:'POSIXct', format: chr 1998-01-01 1998-01-01 1998-01-01 1998-01-01 ... $ Value: num 0.07379 0.07181 0.01555 0.00630 0.00688 ... This is not what I want. Instead, I want the structure to be the same as that of the following data set: str(danish) atomic [1:2167] 1.68 2.09 1.73 1.78 4.61 ... - attr(*, times)='POSIXct', format: chr [1:2167] 1980-01-02 18:00:00 1980-01-03 18:00:00 1980-01-04 18:00:00 1980-01-06 18:00:00 ... danish is a data set that the package evir comes with. Any help would be appreciated. [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] [SPAM] - Re: R package development in windows - BayesianFilter detected spam
On 5/3/2007 3:51 PM, Ravi Varadhan wrote:
Harold,
I totally echo your sentiments on the difficulty of creating an R package in
Windows. I really wish that this process could be made a bit less painful.
As mentioned below, version 2.5.0 makes it a bit less painful. Your
wish has come true!
The only problem is that there are a lot more bits still to go...
Duncan Murdoch
Ravi.
---
Ravi Varadhan, Ph.D.
Assistant Professor, The Center on Aging and Health
Division of Geriatric Medicine and Gerontology
Johns Hopkins University
Ph: (410) 502-2619
Fax: (410) 614-9625
Email: [EMAIL PROTECTED]
Webpage: http://www.jhsph.edu/agingandhealth/People/Faculty/Varadhan.html
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Doran, Harold
Sent: Thursday, May 03, 2007 3:33 PM
To: Duncan Murdoch
Cc: r-help@stat.math.ethz.ch
Subject: Re: [R] [SPAM] - Re: R package development in windows -
BayesianFilter detected spam
Thanks, Duncan. I'll look into that. Is there an authoritative document
that codifies the new package development procedures for 2.5.0
(windows-specific), or is that Writing R Extensions? In this thread
alone I've received multiple emails pointing to multiple web sites with
instructions for windows. Inasmuch as its appreciated, I'm a bit
confused as to which I should consider authoritative.
I do hope I can resolve this and appreciate the help I've received.
However, I feel a bit compelled to note how very difficult this process
is.
Harold
-Original Message-
From: Duncan Murdoch [mailto:[EMAIL PROTECTED]
Sent: Thursday, May 03, 2007 3:24 PM
To: Doran, Harold
Cc: Gabor Grothendieck; r-help@stat.math.ethz.ch
Subject: [SPAM] - Re: [R] R package development in windows -
Bayesian Filter detected spam
On 5/3/2007 3:04 PM, Doran, Harold wrote:
Thanks Gabor, Sundar, and Tony. Indeed, Rtools was missing from the
path. With that resolved, and another 10 minute windows
restart, I get
the following below. The log suggests that hhc is not installed. It
is, and, according to the directions I am following, I have
placed it
in the c:\cygwin directory.
I think the problem is that you are following a real mix of
instructions, and they don't make sense.
It would be nice if folks would submit patches to the R Admin
manual (or to the Rtools web site) rather than putting
together web sites with advice that is bad from day one, and
quickly gets worse when it is not updated.
BTW, package.skeleton() doesn't seem to create the correct
DESCRIPTION
template. I had to add the DEPENDS line. Without this, I
get another
error.
C:\Program Files\R\R-2.4.1\binRcmd build --force --binary g:\foo
R 2.4.1 is no longer current; the package building
instructions in R 2.5.0 have been simplified a bit. You
might want to try those.
Duncan Murdoch
* checking for file 'g:\foo/DESCRIPTION' ... OK
* preparing 'g:\foo':
* checking DESCRIPTION meta-information ... OK
* removing junk files
* checking for LF line-endings in source files
* checking for empty or unneeded directories
* building binary distribution
WARNING
* some HTML links may not be found
installing R.css in c:/TEMP/Rinst40061099
Using auto-selected zip options ''
latex: not found
latex: not found
latex: not found
-- Making package foo
latex: not found
adding build stamp to DESCRIPTION
latex: not found
latex: not found
latex: not found
installing R files
latex: not found
installing data files
latex: not found
installing man source files
installing indices
latex: not found
not zipping data
installing help
Warning: \alias{foo} already in foo-package.Rd -- skipping
the one in
foo.Rd Building/Updating help pages for package 'foo'
Formats: text html latex example chm
foo-package texthtmllatex
example chm
foo texthtmllatex
example chm
mydatatexthtmllatex
example chm
hhc: not found
cp: cannot stat `c:/TEMP/Rbuild40048815/foo/chm/foo.chm':
No such file
or direct ory
make[1]: *** [chm-foo] Error 1
make: *** [pkg-foo] Error 2
*** Installation of foo failed ***
Removing 'c:/TEMP/Rinst40061099/foo'
ERROR
* installation failed
C:\Program Files\R\R-2.4.1\bin
-Original Message-
From: Gabor Grothendieck [mailto:[EMAIL PROTECTED]
Sent: Thursday, May 03, 2007 2:50 PM
To: Doran, Harold
Cc: r-help@stat.math.ethz.ch
Subject: Re: [R] R package development in windows
It can find sh.exe so you haven't installed Rtools.
There are several HowTo's
Re: [R] A question about POSIXct
A follow-up question: The example in ?attr uses a character string of dim. Besides dim and times, what other character strings are available or can be used? On 5/3/07, Michael Sumner [EMAIL PROTECTED] wrote: Hello, It seems that danish is a numeric vector with attributes attached - the attribute vector is POSIXct and is the same length as danish. You can create this from a data frame like this: x - data.frame(Date = ISOdate(2007, 5, 1:10), Value = rnorm(10)) str(x) 'data.frame': 10 obs. of 2 variables: $ Date :'POSIXct', format: chr 2007-05-01 12:00:00 2007-05-02 12:00:00 2007-05-03 12:00:00 2007-05-04 12:00:00 ... $ Value: num 1.891 0.741 -0.368 1.701 -0.660 ... xx - x$Value attr(xx, times) - x$Date str(xx) atomic [1:10] 0.0414 -0.7124 -1.2976 0.3101 0.4343 ... - attr(*, times)='POSIXct', format: chr [1:10] 2007-05-01 12:00:00 2007-05-02 12:00:00 2007-05-03 12:00:00 2007-05-04 12:00:00 ... HTH Cheers, Mike. Dear List: I have a simple two-column data set in .csv format, with the first column being the date and second column being some value. I use read.csv() to import the data as follows: x - read.csv(myfile.csv,header=T, dec=., colClasses=c(Date=POSIXct)) The structure of x is: str(x) `data.frame': 2959 obs. of 2 variables: $ Date:'POSIXct', format: chr 1998-01-01 1998-01-01 1998-01-01 1998-01-01 ... $ Value: num 0.07379 0.07181 0.01555 0.00630 0.00688 ... This is not what I want. Instead, I want the structure to be the same as that of the following data set: str(danish) atomic [1:2167] 1.68 2.09 1.73 1.78 4.61 ... - attr(*, times)='POSIXct', format: chr [1:2167] 1980-01-02 18:00:00 1980-01-03 18:00:00 1980-01-04 18:00:00 1980-01-06 18:00:00 ... danish is a data set that the package evir comes with. Any help would be appreciated. [[alternative HTML version deleted]] [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] A question about POSIXct
Hello, It seems that danish is a numeric vector with attributes attached - the attribute vector is POSIXct and is the same length as danish. You can create this from a data frame like this: x - data.frame(Date = ISOdate(2007, 5, 1:10), Value = rnorm(10)) str(x) 'data.frame': 10 obs. of 2 variables: $ Date :'POSIXct', format: chr 2007-05-01 12:00:00 2007-05-02 12:00:00 2007-05-03 12:00:00 2007-05-04 12:00:00 ... $ Value: num 1.891 0.741 -0.368 1.701 -0.660 ... xx - x$Value attr(xx, times) - x$Date str(xx) atomic [1:10] 0.0414 -0.7124 -1.2976 0.3101 0.4343 ... - attr(*, times)='POSIXct', format: chr [1:10] 2007-05-01 12:00:00 2007-05-02 12:00:00 2007-05-03 12:00:00 2007-05-04 12:00:00 ... HTH Cheers, Mike. Dear List: I have a simple two-column data set in .csv format, with the first column being the date and second column being some value. I use read.csv() to import the data as follows: x - read.csv(myfile.csv,header=T, dec=., colClasses=c(Date=POSIXct)) The structure of x is: str(x) `data.frame': 2959 obs. of 2 variables: $ Date:'POSIXct', format: chr 1998-01-01 1998-01-01 1998-01-01 1998-01-01 ... $ Value: num 0.07379 0.07181 0.01555 0.00630 0.00688 ... This is not what I want. Instead, I want the structure to be the same as that of the following data set: str(danish) atomic [1:2167] 1.68 2.09 1.73 1.78 4.61 ... - attr(*, times)='POSIXct', format: chr [1:2167] 1980-01-02 18:00:00 1980-01-03 18:00:00 1980-01-04 18:00:00 1980-01-06 18:00:00 ... danish is a data set that the package evir comes with. Any help would be appreciated. [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Bayesian logistic regression with a beta prior (MCMClogit)
Hi, yes but I realized afterwards that it's the logfun argument that had to
be put to logfun=F and the logpriorfun function had to be log=F
logpriorfun - function(beta,shape1,shape2){
sum(dbeta(beta,shape1,shape2,log=F)) }
But that's just for that particular example. I find I am having problems
still even after adjusting for that. Using other data it is not accepting
the estimation of beta.start with maximum likelihood
(user.prior.density(beta.start) = 0) and it is obliging me to specify it
giving me a very narrow range, and hence the acceptance rate of the output
is very mediocre (0.01)... I don't know I am missing something here maybe.
As much as I was excited about the MCMCpack, I am finding that it is no
substitute for BUGS/Brugs.
Cody_Hamilton wrote:
Dear Franco,
Have you tried using the beta.start option in MCMClogit? (The problem may
be where you are starting your chain.)
Regards,
-Cody
--
View this message in context:
http://www.nabble.com/Bayesian-logistic-regression-with-a-beta-prior-%28MCMClogit%29-tf3684970.html#a10312824
Sent from the R help mailing list archive at Nabble.com.
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] A question about POSIXct
Thank you, Mike! On 5/3/07, Michael Sumner [EMAIL PROTECTED] wrote: Hello, It seems that danish is a numeric vector with attributes attached - the attribute vector is POSIXct and is the same length as danish. You can create this from a data frame like this: x - data.frame(Date = ISOdate(2007, 5, 1:10), Value = rnorm(10)) str(x) 'data.frame': 10 obs. of 2 variables: $ Date :'POSIXct', format: chr 2007-05-01 12:00:00 2007-05-02 12:00:00 2007-05-03 12:00:00 2007-05-04 12:00:00 ... $ Value: num 1.891 0.741 -0.368 1.701 -0.660 ... xx - x$Value attr(xx, times) - x$Date str(xx) atomic [1:10] 0.0414 -0.7124 -1.2976 0.3101 0.4343 ... - attr(*, times)='POSIXct', format: chr [1:10] 2007-05-01 12:00:00 2007-05-02 12:00:00 2007-05-03 12:00:00 2007-05-04 12:00:00 ... HTH Cheers, Mike. Dear List: I have a simple two-column data set in .csv format, with the first column being the date and second column being some value. I use read.csv() to import the data as follows: x - read.csv(myfile.csv,header=T, dec=., colClasses=c(Date=POSIXct)) The structure of x is: str(x) `data.frame': 2959 obs. of 2 variables: $ Date:'POSIXct', format: chr 1998-01-01 1998-01-01 1998-01-01 1998-01-01 ... $ Value: num 0.07379 0.07181 0.01555 0.00630 0.00688 ... This is not what I want. Instead, I want the structure to be the same as that of the following data set: str(danish) atomic [1:2167] 1.68 2.09 1.73 1.78 4.61 ... - attr(*, times)='POSIXct', format: chr [1:2167] 1980-01-02 18:00:00 1980-01-03 18:00:00 1980-01-04 18:00:00 1980-01-06 18:00:00 ... danish is a data set that the package evir comes with. Any help would be appreciated. [[alternative HTML version deleted]] [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Install SciView under Windows Vista
Thanks for your advice. Seems to have been a quirk in the installation of
R2HTML which is now resolved.
Tim
-Original Message-
From: Prof Brian Ripley [mailto:[EMAIL PROTECTED]
Sent: 03 May 2007 21:29
To: Tim Sippel
Cc: r-help@stat.math.ethz.ch
Subject: Re: [R] Install SciView under Windows Vista
Are you sure your version of R2HTML is up-to-date and built under R 2.5.0?
Use update.packages(checkBuilt=TRUE) if you have not already done so.
That got me R2HTML 1.58, not 1.54.
On Thu, 3 May 2007, Tim Sippel wrote:
Hello-
I have been trying to install SciView under Windows Vista (Home Premium
version,
32 bit OS, Intel Core Duo 2.13GHz, 2Gig RAM).
I am getting an error, apparently related to the R2HTML package (version
1.54)
as you will see in the R information below my signature.
I have tried to email directly to [EMAIL PROTECTED] for support but
have
() had my message returned as undeliverable.
Your help is very much appreciated!
Tim
R version 2.5.0 (2007-04-23)
Copyright (C) 2007 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
[Previously saved workspace restored]
Loading required package: datasets
Loading required package: utils
Loading required package: grDevices
Loading required package: graphics
Loading required package: stats
Loading required package: tcltk
Loading Tcl/Tk interface ... done
Loading required package: R2HTML
Error in `parent.env-`(`*tmp*`, value = NULL) :
use of NULL environment is defunct
In addition: Warning message:
'Sys.putenv' is deprecated.
Use 'Sys.setenv' instead.
See help(Deprecated)
Error: package 'R2HTML' could not be loaded
local({pkg - select.list(sort(.packages(all.available = TRUE)))
+ if(nchar(pkg)) library(pkg, character.only=TRUE)})
Error in `parent.env-`(`*tmp*`, value = NULL) :
use of NULL environment is defunct
Error: package/namespace load failed for 'R2HTML'
R.Version()
$platform
[1] i386-pc-mingw32
$arch
[1] i386
$os
[1] mingw32
$system
[1] i386, mingw32
$status
[1]
$major
[1] 2
$minor
[1] 5.0
$year
[1] 2007
$month
[1] 04
$day
[1] 23
$`svn rev`
[1] 41293
$language
[1] R
$version.string
[1] R version 2.5.0 (2007-04-23)
search()
[1] .GlobalEnvpackage:tcltk package:stats
[4] package:graphics package:grDevices package:utils
[7] package:datasets package:methods Autoloads
[10] package:base
capabilities(tcltk)
tcltk
TRUE
[[alternative HTML version deleted]]
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PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Brian D. Ripley, [EMAIL PROTECTED]
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax: +44 1865 272595
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] Issue with the Matrix package
Hi all, I am wondering if this is a bug in the Matrix package or if it something that I am just getting wrong...here is an example: m = matrix(0,4,4) dimnames(m) = list(letters[1:4], letters[5:8]) r = c(a,b,a,d) m[r,2] = 1 m e f g h a 0 1 0 0 b 0 1 0 0 c 0 0 0 0 d 0 1 0 0 M = Matrix(0,4,4) dimnames(M) = list(letters[1:4], letters[5:8]) M[r,2] = 1 M 4 x 4 sparse Matrix of class dgCMatrix a . 2 . . b . 1 . . c . . . . d . 1 . . The documentation reads: Most of the time, the function works via a traditional (_full_) 'matrix'. However, 'Matrix(0, nrow,ncol)' directly constructs an empty sparseMatrix, as does 'Matrix(FALSE, *)'. So is this when an exception comes, and if so can someone explain to me why we get the 2? It would seem that it should just reassign the 1 to a 1 not add the number of times it is assigning a 1. Cheers, --Tony [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] A question about POSIXct
Jacques Wagnor wrote: A follow-up question: The example in ?attr uses a character string of dim. Besides dim and times, what other character strings are available or can be used? Ah, it's not limited to those. Any character string would do (guru caveats aside). I suspect my narrow answer to your question might lead you astray, perhaps you should cut to the chase and ask how to get your data file into which function in evir . . . Cheers, Mike. On 5/3/07, Michael Sumner [EMAIL PROTECTED] wrote: Hello, It seems that danish is a numeric vector with attributes attached - the attribute vector is POSIXct and is the same length as danish. You can create this from a data frame like this: x - data.frame(Date = ISOdate(2007, 5, 1:10), Value = rnorm(10)) str(x) 'data.frame': 10 obs. of 2 variables: $ Date :'POSIXct', format: chr 2007-05-01 12:00:00 2007-05-02 12:00:00 2007-05-03 12:00:00 2007-05-04 12:00:00 ... $ Value: num 1.891 0.741 -0.368 1.701 -0.660 ... xx - x$Value attr(xx, times) - x$Date str(xx) atomic [1:10] 0.0414 -0.7124 -1.2976 0.3101 0.4343 ... - attr(*, times)='POSIXct', format: chr [1:10] 2007-05-01 12:00:00 2007-05-02 12:00:00 2007-05-03 12:00:00 2007-05-04 12:00:00 ... HTH Cheers, Mike. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Library Package for Tobit regression
Hello R-Users: I am want to use tobit regression for left censored panel/longitudinal data. Could you please provide me the name of library and/or package that will give me option of fitting tobit regression model for longitudinal data? Thank you. Sattar __ [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] reodering factor
R 2.4.1
Windows XP
How does one reorder a factor?
I have the following data:
factor(data$Group)
[1] ZZ ZT ZT ZZ ZZ ZT ZZ ZZ ZT ZT ZT ZT ZZ ZT ZT ZZ ZT ZZ ZT ZZ ZT ZT ZZ ZZ ZT
ZZ ZT ZZ ZT ZZ ZZ ZT ZZ ZT
Levels: ZT ZZ
In my regression (i.e. lm(y~data$Group) ZT is taken as the reference category
and I get an estimate for ZZ. I would like ZZ to be the reference category and
obtain an estimate for ZT.
Thank,
John
John Sorkin M.D., Ph.D.
Chief, Biostatistics and Informatics
University of Maryland School of Medicine Division of Gerontology
Baltimore VA Medical Center
10 North Greene Street
GRECC (BT/18/GR)
Baltimore, MD 21201-1524
(Phone) 410-605-7119
(Fax) 410-605-7913 (Please call phone number above prior to faxing)
Confidentiality Statement:
This email message, including any attachments, is for the so...{{dropped}}
__
R-help@stat.math.ethz.ch mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] [R-pkgs] new package: RSVGTipsDevice: create SVG plots with tooltips hyperlinks
the DESCRIPTION file: Package: RSVGTipsDevice Version: 0.7.0 Date:04/30/2007 Title: An R SVG graphics device with dynamic tips and hyperlinks Author: Tony Plate [EMAIL PROTECTED], based on RSvgDevice by T Jake Luciani [EMAIL PROTECTED] Maintainer: Tony Plate [EMAIL PROTECTED] Depends: R (= 1.4) Description: A graphics device for R that uses the w3.org xml standard for Scalable Vector Graphics. This version supports tooltips with 1 to 3 lines, hyperlinks, and line styles. License: GPL version 2 or newer. http://www.gnu.org/copyleft/gpl.html ___ R-packages mailing list [EMAIL PROTECTED] https://stat.ethz.ch/mailman/listinfo/r-packages __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] reodering factor
One way to reorder a factor is to define a new
factor and specify the order of levels using
the levels argument of the factor() function.
The first category specified for the levels
argument will be the reference category in
model fits such as with lm().
mydata - data.frame(y = c(runif(10), runif(10) + 10), grp = c(rep(A, 10),
rep(B, 10)))
mydata
y grp
1 0.0808684 A
2 0.2930649 A
3 0.4671063 A
4 0.7815386 A
5 0.5360262 A
6 0.8092338 A
7 0.9965648 A
8 0.3549031 A
9 0.3426956 A
10 0.2988377 A
11 10.6528479 B
12 10.7118101 B
13 10.4484731 B
14 10.9638309 B
15 10.7650812 B
16 10.6355089 B
17 10.7003755 B
18 10.2147930 B
19 10.8901356 B
20 10.6319798 B
lm(y ~ grp, data = mydata)
Call:
lm(formula = y ~ grp, data = mydata)
Coefficients:
(Intercept) grpB
0.4961 10.1654
mydata$grp2 - factor(mydata$grp, levels = c(B, A))
mydata
y grp grp2
1 0.0808684 AA
2 0.2930649 AA
3 0.4671063 AA
4 0.7815386 AA
5 0.5360262 AA
6 0.8092338 AA
7 0.9965648 AA
8 0.3549031 AA
9 0.3426956 AA
10 0.2988377 AA
11 10.6528479 BB
12 10.7118101 BB
13 10.4484731 BB
14 10.9638309 BB
15 10.7650812 BB
16 10.6355089 BB
17 10.7003755 BB
18 10.2147930 BB
19 10.8901356 BB
20 10.6319798 BB
lm(y ~ grp2, data = mydata)
Call:
lm(formula = y ~ grp2, data = mydata)
Coefficients:
(Intercept)grp2A
10.66 -10.17
Steven McKinney
Statistician
Molecular Oncology and Breast Cancer Program
British Columbia Cancer Research Centre
email: [EMAIL PROTECTED]
tel: 604-675-8000 x7561
BCCRC
Molecular Oncology
675 West 10th Ave, Floor 4
Vancouver B.C.
V5Z 1L3
Canada
-Original Message-
From: [EMAIL PROTECTED] on behalf of John Sorkin
Sent: Thu 5/3/2007 7:10 PM
To: r-help@stat.math.ethz.ch
Subject: [R] reodering factor
R 2.4.1
Windows XP
How does one reorder a factor?
I have the following data:
factor(data$Group)
[1] ZZ ZT ZT ZZ ZZ ZT ZZ ZZ ZT ZT ZT ZT ZZ ZT ZT ZZ ZT ZZ ZT ZZ ZT ZT ZZ ZZ ZT
ZZ ZT ZZ ZT ZZ ZZ ZT ZZ ZT
Levels: ZT ZZ
In my regression (i.e. lm(y~data$Group) ZT is taken as the reference category
and I get an estimate for ZZ. I would like ZZ to be the reference category and
obtain an estimate for ZT.
Thank,
John
John Sorkin M.D., Ph.D.
Chief, Biostatistics and Informatics
University of Maryland School of Medicine Division of Gerontology
Baltimore VA Medical Center
10 North Greene Street
GRECC (BT/18/GR)
Baltimore, MD 21201-1524
(Phone) 410-605-7119
(Fax) 410-605-7913 (Please call phone number above prior to faxing)
Confidentiality Statement:
This email message, including any attachments, is for the so...{{dropped}}
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] reodering factor
Hi John,
You should use (http://rweb.stat.umn.edu/R/library/stats/html/relevel.html), so
newGroup - relevel (data$Group, ref = ZZ)
Reza
On 5/3/07, John Sorkin [EMAIL PROTECTED] wrote:
R 2.4.1
Windows XP
How does one reorder a factor?
I have the following data:
factor(data$Group)
[1] ZZ ZT ZT ZZ ZZ ZT ZZ ZZ ZT ZT ZT ZT ZZ ZT ZT ZZ ZT ZZ ZT ZZ ZT ZT ZZ ZZ
ZT ZZ ZT ZZ ZT ZZ ZZ ZT ZZ ZT
Levels: ZT ZZ
In my regression (i.e. lm(y~data$Group) ZT is taken as the reference category
and I get an estimate for ZZ. I would like ZZ to be the reference category
and obtain an estimate for ZT.
Thank,
John
John Sorkin M.D., Ph.D.
Chief, Biostatistics and Informatics
University of Maryland School of Medicine Division of Gerontology
Baltimore VA Medical Center
10 North Greene Street
GRECC (BT/18/GR)
Baltimore, MD 21201-1524
(Phone) 410-605-7119
(Fax) 410-605-7913 (Please call phone number above prior to faxing)
Confidentiality Statement:
This email message, including any attachments, is for the so...{{dropped}}
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] Problem with the installation of install R on Sun Solaris
./configure hecking whether stripping libraries is possible... no configure: WARNING: you cannot build info or html versions of the R manuals checking for cos in -lm... yes checking for sin in -lm... yes checking for dlopen in -ldl... yes checking readline/history.h usability... no checking readline/history.h presence... no checking for readline/history.h... no checking readline/readline.h usability... no checking readline/readline.h presence... no checking for readline/readline.h... no checking for rl_callback_read_char in -lreadline... no checking for main in -lncurses... no checking for main in -ltermcap... yes checking for rl_callback_read_char in -lreadline... no checking for history_truncate_file... no configure: error: --with-readline=yes (default) and headers/libs are not available Plase help me for the same Regards Jomy [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Problem with the installation of install R on Sun Solaris
Please do read the 'R Installation and Administration' manual, which answers this and all your other questions. I make this your sixth post on the subject line (and someone using a different address has posted with the identical line). You are still sending HTML, so please do study the posting guide (as mentioned in the only reply to those posts I see in the list archives). As it says If it is clear that you have done basic background research, you are far more likely to get an informative response. On Fri, 4 May 2007, Jomy Jose wrote: ./configure hecking whether stripping libraries is possible... no configure: WARNING: you cannot build info or html versions of the R manuals checking for cos in -lm... yes checking for sin in -lm... yes checking for dlopen in -ldl... yes checking readline/history.h usability... no checking readline/history.h presence... no checking for readline/history.h... no checking readline/readline.h usability... no checking readline/readline.h presence... no checking for readline/readline.h... no checking for rl_callback_read_char in -lreadline... no checking for main in -lncurses... no checking for main in -ltermcap... yes checking for rl_callback_read_char in -lreadline... no checking for history_truncate_file... no configure: error: --with-readline=yes (default) and headers/libs are not available Plase help me for the same Regards Jomy [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
