[R] import data from splus
Dear Sir, I am using R for the first time and I am looking for a function or a command that allows to import Splus data into R. I have already heard about functions called readSdata and readSfiles in the Rstreams package. I did not find the last new version of this package on the CRAN and its old one did not work on R 1.8.0 (the vesrion that I am using). Would you please mention me the updated package that I should install and possibly the suitable function to apply. Thanks in adavance. M.S. __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Time zones
It depends on your OS, which you haven't told us. And OSes tend to hide the information quite effectively. On a Unix/Linux system, try 'man tzset'. That reads named timeszones from a directory, nowadays /usr/share/zoneinfo or /usr/share/lib/zoneinfo or something like that. On Windows, the C runtime has rules like (from the _tzset entry in MSDN) TZ=tzn[+|-]hh[:mm[:ss] ][dzn] tzn Three-letter time-zone name, such as PST. You must specify the correct offset from local time to UTC. hh Difference in hours between UTC and local time. Optionally signed. mm Minutes. Separated from hh by a colon (:). ss Seconds. Separated from mm by a colon (:). dzn Three-letter daylight-saving-time zone such as PDT. If daylight saving time is never in effect in the locality, set TZ without a value for dzn. The C run-time library assumes the United States's rules for implementing the calculation of Daylight Saving Time (DST). so it seems EST5EDT would be correct (but I didn't find a list of names). Did you try EST5EDT to see if it seemed to work? On Mon, 9 Aug 2004, David Scott wrote: I am analysing some data collected over a number of months from Allentown, PA, which is just north of Philadelphia. I am using as.POSIXct for dates and times, and I need to get the timezone specification correct. Going on the documentation for DateTimeClasses, I believe one way to specify the correct time zone is tz=EST5EDT I would be grateful for any advice on this. I ask because I haven't been able to find a list of all the possible time zones or formats that can be used. I have done a bit of googling without to much success. -- 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 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] returns the value of a polynomial of degree n evaluated at x.
See package polynom on CRAN. On Mon, 9 Aug 2004, McClatchie, Sam (PIRSA-SARDI) wrote: Is there a function in R that is similar to polyval in matlab? (y = polyval(p,x) returns the value of a polynomial of degree n evaluated at x. The input argument p is a vector of length n+1 whose elements are the coefficients in descending powers of the polynomial to be evaluated). http://www.mathworks.com/access/helpdesk/help/techdoc/ref/polyval.html I have possibly missed it in the R help files, so please excuse me if I have. Polynomial evaluation yielded no result in a search of help, and the functions poly() and locpoly() don't seem to be what I am after. -- 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 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] import data from splus
Please read the `R Data Import/Export' Manual that ships with R. You are looking for package foreign. On Mon, 9 Aug 2004, Mehrez Samaali wrote: I am using R for the first time and I am looking for a function or a command that allows to import Splus data into R. I have already heard about functions called readSdata and readSfiles in the Rstreams package. Those functions were made obselete by package foreign in April 2001. However did a first-time user hear about them? I did not find the last new version of this package on the CRAN It's in the Archive. and its old one did not work on R 1.8.0 (the vesrion that I am using). That's already rather old, but does have package foreign. Would you please mention me the updated package that I should install and possibly the suitable function to apply. -- 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 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] ess settings
Dear R users, I downloaded an ess-5.2.2 package and hope to use emacs as front to work with R. I modified ~/.emacs and start R by M-x R. But I found when I quited the R session, it still asked me to save the work space or not. I added inferior-R-args with --save args. But it seemed that it had no effect. Can you tell me how to pass the arguments other than --no-readline to R. Thanks a lot. Below is the part for ess settings. (setq load-path (cons ~/.emacs.d/lisp/ess-5.2.2/lisp load-path)) (require 'ess-site) (setq ess-default-style GNU) (setq inferior-ess-program R) (setq inferior-R-program-name ~/.local/bin/R) ; unix systems (setq inferior-R-args --save --no-readline) (setq ess-pre-run-hook '((lambda () (setq ess-directory ~/study/R/) (setq ess-ask-for-ess-directory nil) ))) -- Yours Sincerely Jin __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] displaying computation outputs inside for loops
Dear R-users,
I am puzzled by for loops and am kind of ashamed to ask because it is so
simple. There must be something I am missing in the way they are executed.
Basically, I would like to iterate a given number of time and generate a
bunch of stats (that's what loops are designed for, right?). Before doing
this I simply want to test simple procedure and see if they work (ie got the
syntax right - my main problem as I am new to R - and produce expected
results).
Even for something as basic as
for (i in 1:3) {i}
I get no screen output. Shouldn't R systematically display i for every loop
just like I am requesting with invoking i? When checking at the end of the
looping, i is indeed assigned to 5 but I cannot get intermediate values.
Further testing shows that i takes all the values in turn.
for (i in 1:3) {str(i)}
int 1
int 2
int 3
but summary(i) doesn't display anything. Isn't there something weird with
this? Am I expecting something wrong and for loops just don't work that way,
unless using str() command? I tried print() and other descriptive commands
but to no avail.
A quick explanation would be grately appreciated
Thomas
***
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Re: [R] displaying computation outputs inside for loops
Hi Thomas,
is this what you would like to get,
for(i in 1:3){
x - rnorm(5)
cat(the values of `x' are:, format(x), \n)
cat(computation, i, finished\n\n)
}
for(i in 1:3) print(i)
I hope this helps.
Best,
Dimitris
Dimitris Rizopoulos
Doctoral Student
Biostatistical Centre
School of Public Health
Catholic University of Leuven
Address: Kapucijnenvoer 35, Leuven, Belgium
Tel: +32/16/396887
Fax: +32/16/337015
Web: http://www.med.kuleuven.ac.be/biostat/
http://www.student.kuleuven.ac.be/~m0390867/dimitris.htm
- Original Message -
From: Dewez Thomas [EMAIL PROTECTED]
To: 'R mailing list' [EMAIL PROTECTED]
Sent: Monday, August 09, 2004 11:15 AM
Subject: [R] displaying computation outputs inside for loops
Dear R-users,
I am puzzled by for loops and am kind of ashamed to ask because it
is so
simple. There must be something I am missing in the way they are
executed.
Basically, I would like to iterate a given number of time and
generate a
bunch of stats (that's what loops are designed for, right?). Before
doing
this I simply want to test simple procedure and see if they work (ie
got the
syntax right - my main problem as I am new to R - and produce
expected
results).
Even for something as basic as
for (i in 1:3) {i}
I get no screen output. Shouldn't R systematically display i for
every loop
just like I am requesting with invoking i? When checking at the
end of the
looping, i is indeed assigned to 5 but I cannot get intermediate
values.
Further testing shows that i takes all the values in turn.
for (i in 1:3) {str(i)}
int 1
int 2
int 3
but summary(i) doesn't display anything. Isn't there something weird
with
this? Am I expecting something wrong and for loops just don't work
that way,
unless using str() command? I tried print() and other descriptive
commands
but to no avail.
A quick explanation would be grately appreciated
Thomas
***
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destin...{{dropped}}
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[R] Installing RMySQL on Windows XP for R 1.9.1
Hi, I'm thankful for any help on installing RMySQL on Windows XP for R 1.9.1 The thread http://tolstoy.newcastle.edu.au/R/help/04/01/1021.html already tried to discuss the matter. It concludes that Windows Sources for Packages are alike the Linux ones. So I extracted the files from the RMySQL_*.tar.gz from http://stat.bell-labs.com/RS-DBI/download/index.html and stuffed them into a zip-file which was willingly taken by the install routine of my RGui. It said the well known updating HTML package descriptions but when using library(RMySQL) the error Error in testRversion(descfields) : This package has not been installed properly. See the Note in ?library. Obviously the note wasn't very helpful and so I ask you for any help. Regards Robert __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] linear regression
Dear Consultant I've done linear regression successfully on R a few times before. But this time it keeps telling me:- Error in lm.fit(x, y, offset = offset, singular.ok = singular.ok, ...) : 0 (non-NA) cases The model is:- fm1 - lm(TS.CM ~ AGE + SEX + HFE.Y.01 + TFC2B.01 + HFE.Y.01*TFC2B.01, data = IRONresults, subset = DIAG2.1D == 0) summary (fm1) TS.CM is a continuous variable (%s), sex is coded 0 = women, 1 = men, DIAG2.1D is coded 0 = non-demented, 1 = ALzheimer's disease and the genes, HFE.Y.01 TFC2B.01, are coded 0 = non-carrier and 1 = carrier I've tried recoding the data to use 1 2, instead of 0 1, and I've removed the rows with missing data. I've also tried putting ...lm(formula = TS.CM ~ ... But I always get the same error message What am I doing wrong? A related question: what's the minimum no of data points for regression analysis to work? We have only 23 cases carrying both genes out of 447 and only 8 out of 264 in the above subset (ie non-demented). I seem to remember hearing somewhere that you needed a minimum of ~30 (?), so probably this wouldn't work anyway. Still, I'd like to know what I was doing wrong! Many thanks Donald (Lehmann) __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] Installing RMySQL on Windows XP for R 1.9.1
Hi, I cannot help you install RMySQL on Windows, but most likely RMySQL contains non-R code too, such as C code, that requires compilation and then your gunzip-untar-rezip approach will not work. For your information, you can use the RODBC package instead. I recently downloaded and installed a MySQL server on my Windows XP *Pro* machine. Then I use the RODBC package (on CRAN and installs directly on Windows) to connect to it. In order for this to work you have to have an ODBC service running on your machine. You will find one for most Windows versions called MyODBC on the mysql.com download pages (links at the right margin). When it works you will be connected to you db from R by library(RODBC) channel - odbcConnect(MyDatabase, uid=root) # or some other username df - sqlQuery(select * from myTable) See also ?RODBC. I just did the above two days ago from scratch and it was pretty easy. I won't time to help you more now since I'm writing up my thesis... Cheers Henrik Bengtsson -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Robert Wania Sent: Monday, August 09, 2004 11:34 AM To: [EMAIL PROTECTED] Subject: [R] Installing RMySQL on Windows XP for R 1.9.1 Hi, I'm thankful for any help on installing RMySQL on Windows XP for R 1.9.1 The thread http://tolstoy.newcastle.edu.au/R/help/04/01/1021.html already tried to discuss the matter. It concludes that Windows Sources for Packages are alike the Linux ones. So I extracted the files from the RMySQL_*.tar.gz from http://stat.bell-labs.com/RS-DBI/download/index.html and stuffed them into a zip-file which was willingly taken by the install routine of my RGui. It said the well known updating HTML package descriptions but when using library(RMySQL) the error Error in testRversion(descfields) : This package has not been installed properly. See the Note in ?library. Obviously the note wasn't very helpful and so I ask you for any help. Regards Robert __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] Installing RMySQL on Windows XP for R 1.9.1
The code snippet was incorrect; here the correct one (I hope) library(RODBC) channel - odbcConnect(MyDatabase, uid=root) # or some other username df - sqlQuery(channel, select * from myTable) /Henrik -Original Message- From: Henrik Bengtsson [mailto:[EMAIL PROTECTED] Sent: Monday, August 09, 2004 11:59 AM To: 'Robert Wania'; '[EMAIL PROTECTED]' Subject: RE: [R] Installing RMySQL on Windows XP for R 1.9.1 Hi, I cannot help you install RMySQL on Windows, but most likely RMySQL contains non-R code too, such as C code, that requires compilation and then your gunzip-untar-rezip approach will not work. For your information, you can use the RODBC package instead. I recently downloaded and installed a MySQL server on my Windows XP *Pro* machine. Then I use the RODBC package (on CRAN and installs directly on Windows) to connect to it. In order for this to work you have to have an ODBC service running on your machine. You will find one for most Windows versions called MyODBC on the mysql.com download pages (links at the right margin). When it works you will be connected to you db from R by library(RODBC) channel - odbcConnect(MyDatabase, uid=root) # or some other username df - sqlQuery(select * from myTable) See also ?RODBC. I just did the above two days ago from scratch and it was pretty easy. I won't time to help you more now since I'm writing up my thesis... Cheers Henrik Bengtsson -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Robert Wania Sent: Monday, August 09, 2004 11:34 AM To: [EMAIL PROTECTED] Subject: [R] Installing RMySQL on Windows XP for R 1.9.1 Hi, I'm thankful for any help on installing RMySQL on Windows XP for R 1.9.1 The thread http://tolstoy.newcastle.edu.au/R/help/04/01/1021.html already tried to discuss the matter. It concludes that Windows Sources for Packages are alike the Linux ones. So I extracted the files from the RMySQL_*.tar.gz from http://stat.bell-labs.com/RS-DBI/download/index.html and stuffed them into a zip-file which was willingly taken by the install routine of my RGui. It said the well known updating HTML package descriptions but when using library(RMySQL) the error Error in testRversion(descfields) : This package has not been installed properly. See the Note in ?library. Obviously the note wasn't very helpful and so I ask you for any help. Regards Robert __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] /minus or /hyphen in PS output
Dear R devolepers! Wouldn't you change src/main/devPS.c file (patch will follow). Problem is with minus sign in ps output. The original code forces the name /minus to the character number 45 (-). But /minus symbol is not defined in standard Adobe encoding and (even worse) is not defined in most type1 fonts (where the name /hyphen is used instead), in this case you will have an empty space instead of -. Redefining encoding for this fonts does not help because encoding vector in ps output got corrected and /hyphen (or any other name I have selected for 45'th character) is replaced with /minus. I have tried this patch and it works for me. 449,450c449 // if(c == 45) strcpy(dest, /minus); else strcpy(dest, state-p0); --- if(c == 45) strcpy(dest, /minus); else strcpy(dest, state-p0); __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] Installing RMySQL on Windows XP for R 1.9.1
You do need a binary version of RMySQL. See http://cran.r-project.org/bin/windows/contrib/1.9/@ReadMe which tells you to get it from http://stat.bell-labs.com/RS-DBI/download the very page you got the sources from. I do think you should read all of the pages you look at, as in both cases you have ignored crucial information. On Mon, 9 Aug 2004, Henrik Bengtsson wrote: Hi, I cannot help you install RMySQL on Windows, but most likely RMySQL contains non-R code too, such as C code, that requires compilation and then your gunzip-untar-rezip approach will not work. It never works, and no one said it did. The rw-FAQ answers this question, and the message in the archives said Please consult the rw-FAQ for how to install packages. For your information, you can use the RODBC package instead. I recently downloaded and installed a MySQL server on my Windows XP *Pro* machine. Then I use the RODBC package (on CRAN and installs directly on Windows) to connect to it. In order for this to work you have to have an ODBC service running on your machine. You will find one for most Windows versions called MyODBC on the mysql.com download pages (links at the right margin). When it works you will be connected to you db from R by library(RODBC) channel - odbcConnect(MyDatabase, uid=root) # or some other username df - sqlQuery(select * from myTable) See also ?RODBC. I just did the above two days ago from scratch and it was pretty easy. I won't time to help you more now since I'm writing up my thesis... Cheers Henrik Bengtsson -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Robert Wania Sent: Monday, August 09, 2004 11:34 AM To: [EMAIL PROTECTED] Subject: [R] Installing RMySQL on Windows XP for R 1.9.1 Hi, I'm thankful for any help on installing RMySQL on Windows XP for R 1.9.1 The thread http://tolstoy.newcastle.edu.au/R/help/04/01/1021.html already tried to discuss the matter. It concludes that Windows Sources for Packages are alike the Linux ones. So I extracted the files from the RMySQL_*.tar.gz from http://stat.bell-labs.com/RS-DBI/download/index.html and stuffed them into a zip-file which was willingly taken by the install routine of my RGui. It said the well known updating HTML package descriptions but when using library(RMySQL) the error Error in testRversion(descfields) : This package has not been installed properly. See the Note in ?library. Obviously the note wasn't very helpful and so I ask you for any help. It was *very* helpful. Your failure to read the rw-FAQ was unhelpful. -- 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 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] linear regression
Donald Lehmann [EMAIL PROTECTED] writes: Dear Consultant I've done linear regression successfully on R a few times before. But this time it keeps telling me:- Error in lm.fit(x, y, offset = offset, singular.ok = singular.ok, ...) : 0 (non-NA) cases The model is:- fm1 - lm(TS.CM ~ AGE + SEX + HFE.Y.01 + TFC2B.01 + HFE.Y.01*TFC2B.01, data = IRONresults, subset = DIAG2.1D == 0) summary (fm1) TS.CM is a continuous variable (%s), sex is coded 0 = women, 1 = men, DIAG2.1D is coded 0 = non-demented, 1 = ALzheimer's disease and the genes, HFE.Y.01 TFC2B.01, are coded 0 = non-carrier and 1 = carrier I've tried recoding the data to use 1 2, instead of 0 1, and I've removed the rows with missing data. I've also tried putting ...lm(formula = TS.CM ~ ... But I always get the same error message What am I doing wrong? You don't need to give the main effects when there's a * term (that's a SASism, the R equivalent is : and a*b == a+b+a:b by definition), but that is hardly the main problem. Could you have a look at this? : with(IRONresults, complete.cases(TS.CM, AGE, SEX, HFE.Y.01, TFC2B.01)) If you get all FALSE, you'll know what hit you... A related question: what's the minimum no of data points for regression analysis to work? We have only 23 cases carrying both genes out of 447 and only 8 out of 264 in the above subset (ie non-demented). I seem to remember hearing somewhere that you needed a minimum of ~30 (?), so probably this wouldn't work anyway. Still, I'd like to know what I was doing wrong! Technically, you just need linearly independent predictors and more observations than parameters (incl. the intercept). Other bounds get bandied about on what should be required for a *meaningful* analysis (like 10 observations per parameter), but these are quite heuristic and empirical in nature. -- O__ Peter Dalgaard Blegdamsvej 3 c/ /'_ --- Dept. of Biostatistics 2200 Cph. N (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] ess settings
Dear Jin, First, we have a mailing list for ESS questions; this is probably more relevant than r-help for these questions. https://stat.ethz.ch/mailman/listinfo/ess-help Just last week this came up, and although the ESS documentation suggests setting inferior-R-args, it doesn't seem to be used. I will look into solutions for this. IN the meantime, there is a temporary workaround mentioned in the mailing lists; see thread starting https://stat.ethz.ch/pipermail/ess-help/2004-August/002031.html Best wishes, Stephen Jin Shusong writes: Dear R users, I downloaded an ess-5.2.2 package and hope to use emacs as front to work with R. I modified ~/.emacs and start R by M-x R. But I found when I quited the R session, it still asked me to save the work space or not. I added inferior-R-args with --save args. But it seemed that it had no effect. Can you tell me how to pass the arguments other than --no-readline to R. Thanks a lot. Below is the part for ess settings. (setq load-path (cons ~/.emacs.d/lisp/ess-5.2.2/lisp load-path)) (require 'ess-site) (setq ess-default-style GNU) (setq inferior-ess-program R) (setq inferior-R-program-name ~/.local/bin/R); unix systems (setq inferior-R-args --save --no-readline) (setq ess-pre-run-hook '((lambda () (setq ess-directory ~/study/R/) (setq ess-ask-for-ess-directory nil) ))) -- Yours Sincerely Jin __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] GLS with binomial errors ?
Hi R-users: I want to model deforestation using GLS in order to handle spatial autocorrelation. My response variables is binary data (Yes or Not) and my explanatory variables are categorical (1, 2, 3). I have only been able to find code which handles normally distributed data, whereas I have binary data. Anyone know how apply GLS modelling with a binary response variable? Many thanks in advance! Cristian Echeverria [[alternative HTML version deleted]] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Memory failure!!!!
Hi, I am trying to increase the memory R can use. I am running R under Windows on a machine with 2 GB of physical RAM and 4GB of paged memory. I wrote in the R property windows --sdi --max-mem-size=4094M, but the R itself when it is doing a bayesian modelling (geoR) it stops at 1,096K and i get memory errors because it cannot allocate a new segment of about 500K of memory. I don't have Visual Basic so i cannot use the other commands suggested in Help. Also, if i am using memory.size(max=TRUE) i get a value corresponding to about 1024K, and if i am using memory.limit(size=NA) i get a value of about 4000K. How can i force R to use more memory? thank you for any suggestion, Monica Monica Palaseanu-Lovejoy University of Manchester School of Geography Mansfield Cooper Bld. 3.21 Oxford Road Manchester M13 9PL England, UK Tel: +44 (0) 275 8689 Email: [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] (no subject)
Hi ! mu name is Paolo and I teach statistic in a small college in Brazil and we use Linux. We started to use R as our statitical software. I,ve been trying to use some commands I see in the documentation online but i doesn not work. Commands like simple.hist.and.boxplot and others related with graphing. Do I need a special ppackage ? how do I load it ? Thanks __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Memory failure!!!!
Monica Palaseanu-Lovejoy wrote: Hi, I am trying to increase the memory R can use. I am running R under Windows on a machine with 2 GB of physical RAM and 4GB of paged memory. I wrote in the R property windows --sdi --max-mem-size=4094M, but the R itself when it is doing a bayesian modelling (geoR) it stops at 1,096K and i get memory errors because it cannot allocate a new segment of about 500K of memory. In that case either a) your memory is too fragmented and you should start a new R session or b) or you need much more than 500K, and you are just getting the error from one allocation (out of many) that fails. The next question is which version of Windows this is. Some versions do not support that much memory, others have a hole of 512M (???, PCI address space is within the 4GB address space, AFAIR)... I don't have Visual Basic so i cannot use the other commands suggested in Help. Also, if i am using memory.size(max=TRUE) i get a value corresponding to about 1024K, and if i am using memory.limit(size=NA) i get a value of about 4000K. I hope you mean about 4000*M*... Or more precisely, what you get is: 4094*1024*1024 [1] 4292870144 Uwe Ligges How can i force R to use more memory? thank you for any suggestion, Monica Monica Palaseanu-Lovejoy University of Manchester School of Geography Mansfield Cooper Bld. 3.21 Oxford Road Manchester M13 9PL England, UK Tel: +44 (0) 275 8689 Email: [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] Installing RMySQL on Windows XP for R 1.9.1
I apologize for mixing the source and binary packages. (Although R didn't complain? Nevertheless this is no excuse) After installing the binary package the only problem was the libmysql.dll, which was not found by R (but it was within the package). I put it in the windows/system32 directory and everything works find. Thanks for the instant help Robert -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Behalf Of Prof Brian Ripley Sent: Monday, August 09, 2004 12:22 PM To: Henrik Bengtsson Cc: [EMAIL PROTECTED]; 'Robert Wania' Subject: RE: [R] Installing RMySQL on Windows XP for R 1.9.1 You do need a binary version of RMySQL. See http://cran.r-project.org/bin/windows/contrib/1.9/@ReadMe which tells you to get it from http://stat.bell-labs.com/RS-DBI/download the very page you got the sources from. I do think you should read all of the pages you look at, as in both cases you have ignored crucial information. On Mon, 9 Aug 2004, Henrik Bengtsson wrote: Hi, I cannot help you install RMySQL on Windows, but most likely RMySQL contains non-R code too, such as C code, that requires compilation and then your gunzip-untar-rezip approach will not work. It never works, and no one said it did. The rw-FAQ answers this question, and the message in the archives said Please consult the rw-FAQ for how to install packages. For your information, you can use the RODBC package instead. I recently downloaded and installed a MySQL server on my Windows XP *Pro* machine. Then I use the RODBC package (on CRAN and installs directly on Windows) to connect to it. In order for this to work you have to have an ODBC service running on your machine. You will find one for most Windows versions called MyODBC on the mysql.com download pages (links at the right margin). When it works you will be connected to you db from R by library(RODBC) channel - odbcConnect(MyDatabase, uid=root) # or some other username df - sqlQuery(select * from myTable) See also ?RODBC. I just did the above two days ago from scratch and it was pretty easy. I won't time to help you more now since I'm writing up my thesis... Cheers Henrik Bengtsson -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Robert Wania Sent: Monday, August 09, 2004 11:34 AM To: [EMAIL PROTECTED] Subject: [R] Installing RMySQL on Windows XP for R 1.9.1 Hi, I'm thankful for any help on installing RMySQL on Windows XP for R 1.9.1 The thread http://tolstoy.newcastle.edu.au/R/help/04/01/1021.html already tried to discuss the matter. It concludes that Windows Sources for Packages are alike the Linux ones. So I extracted the files from the RMySQL_*.tar.gz from http://stat.bell-labs.com/RS-DBI/download/index.html and stuffed them into a zip-file which was willingly taken by the install routine of my RGui. It said the well known updating HTML package descriptions but when using library(RMySQL) the error Error in testRversion(descfields) : This package has not been installed properly. See the Note in ?library. Obviously the note wasn't very helpful and so I ask you for any help. It was *very* helpful. Your failure to read the rw-FAQ was unhelpful. -- 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 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Memory failure!!!!
On Mon, 9 Aug 2004, Monica Palaseanu-Lovejoy wrote: I am trying to increase the memory R can use. I am running R under Windows on a machine with 2 GB of physical RAM and 4GB of paged memory. I wrote in the R property windows --sdi --max-mem-size=4094M, but the R itself when it is doing a bayesian modelling (geoR) it stops at 1,096K and i get memory errors because it cannot allocate a new segment of about 500K of memory. Please read the rw-FAQ. Windows cannot allocate 4Gb to a user process, and unless you have followed the instructions there you are limited to 2Gb (and probably a bit less). Also please read the posting guide and report the exact message you got, as it requests. Unless it says something about memory limits, it is because the memory could not be obtained from the OS. I don't have Visual Basic so i cannot use the other commands suggested in Help. What has Visual Basic to do with this? Also, if i am using memory.size(max=TRUE) i get a value corresponding to about 1024K, and if i am using memory.limit(size=NA) i get a value of about 4000K. How can i force R to use more memory? By making it available to R. Try rebooting your machine before running R, to reduce memory fragmentation. -- 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 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] (no subject)
On Mon, 09 Aug 2004 08:01:55 -0300 Paolo Tommasini [EMAIL PROTECTED] wrote: Hi ! mu name is Paolo and I teach statistic in a small college in Brazil and we use Linux. We started to use R as our statitical software. I,ve been trying to use some commands I see in the documentation online but i doesn not work. Commands like simple.hist.and.boxplot and others related with graphing. Do I need a special ppackage ? how do I load it ? This function is probably a function of the package Simple that accompanies the user-contributed introduction to R simpleR http://www.math.csi.cuny.edu/Statistics/R/simpleR/index.html Download the tarball on this webpage http://www.math.csi.cuny.edu/Statistics/R/simpleR/Simple_0.4.tar.gz and install it (as root) as follows: # R CMD INSTALL Simple_0.4.tar.gz Then (as a normal user) you can load the package (from within R using the library() command) library(Simple) to see an example of this simple.hist.and.boxplot() function do example(simple.hist.and.boxplot) to see the help for it, use ?simple.hist.and.boxplot For graphics commands you do not need to use contributed packages. On a standard R installation, a lot is already available. See ?hist, ?boxplot, ?plot etc. or the Graphics section of the R manual An Introduction to R. HTH, Tobias __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] looking for graphic functions; was: (no subject)
Paolo Tommasini wrote: Hi ! mu name is Paolo and I teach statistic in a small college in Brazil and we use Linux. We started to use R as our statitical software. I,ve been trying to use some commands I see in the documentation online but i doesn not work. Commands like simple.hist.and.boxplot and others related with graphing. Do I need a special ppackage ? how do I load it ? Please use a sensible subject line (and see the posting guide mentioned below). Where did you find anything about a function simple.hist.and.boxplot? If you are talking about the online document simpleR by John Verzani, I'd suggest to look at the corresponding R package mentioned in that document. If it is not in there, either hack it yourself or ask the author. Have you already looked at ?hist and ?boxplot? Uwe Ligges Thanks __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] linear constraint optim with bounds/reparametrization
Hello All, I would like to optimize a (log-)likelihood function subject to a number of linear constraints between parameters. These constraints are equality constraints of the form A%*%theta=c, ie (1,1) %*% 0.8,0.2)^t = 1 meaning that these parameters should sum to one. Moreover, there are bounds on the individual parameters, in most cases that I am considering parameters are bound between zero and one because they are probabilities. My problems/questions are the following: 1) constrOptim does not work in this case because it only fits inequality constraints, ie A%*%theta = c --- As a result when providing starting values constrOptim exits with an error saying that the initial point is not feasible, which it isn't because it is not in the interior of the constraint space. Is there an alternative to constrOptim that can handle such strict (equality) linear constraints? 2) Another option of course would be to reparametrize the problem as follows. I will illustrate with an example: I have parameters: p [,1] [1,] 0.8 [2,] 0.2 [3,] 0.2 [4,] 0.8 [5,] 0.6 [6,] 0.1 [7,] 0.3 [8,] 0.1 [9,] 0.3 [10,] 0.6 [11,] 0.5 [12,] 0.5 and the following constraints (all these constraint amount to certain probabilities summing to one, ie the first two parameters sum to one, the second pair of parameters sum to one etc): A [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [1,]110000000 0 0 0 [2,]001100000 0 0 0 [3,]000011100 0 0 0 [4,]000000011 1 0 0 [5,]000000000 0 1 1 and the bounds on the constraints are: ci [,1] [1,]1 [2,]1 [3,]1 [4,]1 [5,]1 The bounds on the parameters are all zero and one. In order to reparametrize I could use z=ginv(b)%*%(p-ginv(A)%*%cc) with b=Null(t(A)) and optimize z instead of p using p=ginv(a)%*%ci + b%*%z My question is however what the bounds on z are? In the above example z is: z [,1] [1,] -0.2333 [2,] -0.0333 [3,] -0.57974349 [4,] -0.37974349 [5,] -0.07974349 [6,] -0.18856181 [7,] -0.18856181 which conforms to the constraints, so these values can be used as an intial estimate. If I knew the bounds on z I could use optim with method=L-BFGS. I hope this problem is sufficiently clear to elicit response, if not please let me know. ingmar ps: to reproduce above example use the following: p=matrix(c(0.8, 0.2, 0.20, 0.8, 0.6, 0.1, 0.3, 0.1, 0.3, 0.6, 0.5, 0.5),nc=1) A = matrix(c(1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 , 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0 , 0, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0 , 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 0, 0 , 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1),nc=12,byrow=T) ci=matrix(rep(1,5),nc=1) b=Null(t(A)) z=ginv(b)%*%(p-ginv(A)%*%cc) pp=ginv(a)%*%ci + b%*%z __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] URL change for Statistik ETH and web interface to mailing lists.
[exceptional cross-posting on purpose]
Dear users/readers of our mailing lists,
The following ONLY affects the web interface to our mailing lists.
This is both for subscription changes and the mailing list archives.
For a long time, our Statistics ETHZ home page has been
available both as
http://www.stat.math.ethz.ch/ [old default]
and http://stat.ethz.ch/[new default]
For several reasons however, the longer URL above has been the
``default'', or the one to which stat.ethz.ch was automagically converted.
This now has finally been switched two hours ago, such that
http://stat.ethz.ch/ is now the official URL in all respects and
http://www.stat.math.ethz.ch/ is just an alias to the new URL
(and it seems to behave strangely just now for me, but that
should be very temporary).
For existing mailing lists and their web interface, the change
change has to happen ``inside mailman'' (by calling the correct
python script and changing the lists URL explictly)
once for each list.
I wanted to first announce this widely and do the change in
about 24 hours or so.
You may have to accept the SSL certificate again {and it's not
from a so called trusted agency since that would cost us lots
of money we rather spend differently}.
Regards,
Martin Maechler [EMAIL PROTECTED] http://stat.ethz.ch/~maechler/
Seminar fuer Statistik, ETH Zurich, Switzerland
__
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PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] R packages install problems linux - X not found (WhiteBoxEL 3)
I am concerned by your indications of previously having had RH9 on the same box and that you had to force an update of the XFree Devel RPM. Forcing the installation of an RPM is almost always a bad thing. When you installed WB on the system, did you do a clean installation or some type of upgrade? If the latter, it is reasonable to consider that there may be some level of mixing and matching of RPMS from the two distributions going on. This could result in a level of marginally or wholly incompatible versions of RPMS being installed. Could you clarify that point? Also, be sure that you have the same versions of the XFree series RPMS installed. Use: rpm -qa | grep XFree in a console and be sure that the RPMS return the same version schema. If not, it is possible that one of your problems is the mixing of versions. Take note of the output of the above and be sure that the XFree86-Mesa-libGL and XFree86-Mesa-libGLU RPMS are installed as well. Some of the messages above would also suggest a problem finding R related headers. How did you install R? This may be a red herring of sorts, given the other problems, but may be helpful. Marc __ Marc, Sorry for the confusion yesterday - in my defence, it was very hot and humid here in Hampshire (31 Celsius at 15:00hrs and still 25 at 20:00hrs). What had happened was that I had done a clean install of WB Linux, including the XFree86 and other developer packages. However, the on-line updating system updated the XFree86 packages to a newer sub version. It seems that it didn't do this correctly for the XFree86 developer package, which was missing vital files. However it showed up in the rpm database as being installed (i.e. rpm -qa | grep XFree showed it thus). I downloaded another rpm for this manually and I only forced the upgrade because it was the same version as already 'installed' (as far as the rpm database was concerned). I assumed that all dependencies were sorted out through the install in the first place. I only mentioned RH9 to show that I had some familiarity with the RedHat policy of separating out the 'includes' etc into a separate developer package. Once all this had been sorted out, I was then left with a compilation error which pointed to a missing dependency or similar, which was not due to missing developer packages, but, as you and Prof Ripley correctly point out, from the R installation itself. Having grown fat and lazy on using R under the MS Windows environment, I was struggling to identify the precise nature of this remaining problem. As regards the R installation, I did this from the RH9 binary for version 1.9.1, as I did not think that the Fedora Core 2 binary would be appropriate here. Perhaps I should now compile from the source instead? Regards M __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R Matrix package solve
torsten, thanks for the mail. I have reinstalled the Matrix package, but still get the same problems. Any ideas? matt nunes. --On 04 August 2004 3:26pm +0200 Torsten Hothorn [EMAIL PROTECTED] wrote: On Wed, 4 Aug 2004, Matt Nunes wrote: hello. I have a query about the Matrix package for R. I wrote some code a while ago using the Matrix package version 1.6.2 with an early version of R, to do some linear least squares for regression: xn [,1] [,2] [,3] [,4] [1,]1 0.7429352 0.5519528 0.4100652 [2,]1 0.7443713 0.5540886 0.4124477 [3,]1 0.7447385 0.5546355 0.4130584 [4,]1 0.7459597 0.5564558 0.4150936 temp-crossprod(xn) temp [,1] [,2] [,3] [,4] [1,] 4.00 2.978005 2.2171327 1.6506648 [2,] 2.978005 2.217133 1.6506648 1.2289297 [3,] 2.217133 1.650665 1.2289297 0.9149473 [4,] 1.650665 1.228930 0.9149473 0.6811865 solve.Matrix(temp,t(xn)) [,1] [,2] [,3] [,4] [1,] 33397.34 122081.7 -241005.4 85527.48 [2,] 21063.72 -664920.2 812316.0 -168459.99 [3,] -236935.74 1125548.2 -86.2 -10835.64 [4,] 199314.69 -608045.8 297509.1 111221.72 (Note: here I used solve.Matrix since the generic solve said the matrix is singular). I recently updated my versions of R to 1.9.1 and also the Matrix package, but I can't seem to get any similar equivalent matrix calculations to work (I get error messages like .Call function name not in DLL for package Matrix this very much looks like a corrupted package installation. Try to reinstall `Matrix' Torsten or Lapack routine dpotrf returned error code 4). I have also tried using symmetric matrix commands, but to no avail. Can anyone help me out? many thanks Matt Nunes __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] linear constraint optim with bounds/reparametrization
from Ingmar Visser:
I would like to optimize a (log-)likelihood function subject to a number of
linear constraints between parameters. These constraints are equality
constraints of the form A%*%theta=c, ie (1,1) %*% 0.8,0.2)^t = 1 meaning
that these parameters should sum to one. Moreover, there are bounds on the
individual parameters, in most cases that I am considering parameters are
bound between zero and one because they are probabilities.
My problems/questions are the following:
1) constrOptim does not work in this case because it only fits inequality
constraints, ie A%*%theta = c
---
I was struggling with the same problem a few weeks ago in the portfolio optimization
context. You can impose equality constraints by using inequality constraints = and =
simultaneously. See the example bellow.
As a result when providing starting values constrOptim exits with an error
saying that the initial point is not feasible, which it isn't because it is
not in the interior of the constraint space.
In constrOptim the feasible region is defined by ui%*%theta-ci =0. My first attempt
to obtain feasible starting values was based on solving for theta from ui%*%theta =
ci. Some of the items in the right hand side of the feasible region are, however, very
often very small negative numbers, and hence, theta is not feasible. Next, I started
to increase ci by epsilon (a slack variable) and checked if the result was feasible.
The code is in the example bellow. If ui is not a square matrix, theta is obtained by
simulation. It is helpfull to know the upper and lower limits of the theta vector. In
my case they are often [0,1]. Usually only 2-3 simulations are required.
In the example, the weights (parameters) have limits [0,1] such that their sum is
limited to unity, as in your case. See, how Amat and b0 are defined.
V - matrix(c(0.12,0,0,0,0.21,0,0,0,0.28),3,3) # variances
Cor - matrix(c(1,0.25,0.25,0.25,1,0.45,0.05,0.45,1),3,3) # correlations
sigma - t(V)%*%Cor%*%V # covariance matrix
ER - c(0.07,0.12,0.18) # expected returns
Dmat - sigma # adopted from solve.QP
dvec - rep(0,3)#
k - 3 # number of assets
reslow - rep(0,k) # lower limits for
portfolio weights
reshigh - rep(1,k) # upper limits for
portfolio weights
pm - 0.10 # target return
rfree - 0.05 # risk-free return
risk.aversion - 2.5# risk aversion parameter
### RISKLESS = FALSE; SHORTS = TRUE ; CONSTRAINTS = TRUE
a1 - rep(1, k)
a2 - as.vector(ER)+rfree
a3 - matrix(0,k,k)
diag(a3) - 1
Amat - t(rbind(a1, a2, a3, -a3))
b0 - c(1,pm,reslow, -reshigh)
objectf.mean - function(x) # object
function
{
return(sum(t(x)%*%ER-1/2*risk.aversion*t(x)%*%sigma%*%x)-(t(x)%*%ER-pm))
}
# Getting starting values for constrOptim
ui - t(Amat)
ci - b0
if (dim(ui)[1] == dim(ui)[2])
{
test - F
cieps - ci
while(test==F)
{
theta - qr.solve(ui,cieps)
foo - (ui%*%theta-ci) # check if the initial values are in
the feasible area
test - all(foo 0)
if(test==T) initial - theta# initial values for portfolio weights
cieps - cieps+0.1
}
}
if (dim(ui)[1] != dim(ui)[2]) # if Amat is not square, simulate the
starting values
{
test - F
i - 1
while(test==F)
{
theta - runif(k, min = 0, max = 1)
foo - (ui%*%theta-ci)
test - all(foo 0)# and check that theta is feasible
if (test == T) initial - theta
i - i+1
}
}
initial
res - constrOptim(initial, objectf.mean, NULL, ui=t(Amat), ci=b0, control =
list(fnscale=-1))
res$par # portfolio weights (parameters)
y - t(res$par)%*%ER# return on the portfolio
y
I hope this helps.
Hannu Kahra
Progetti Speciali
Monte Paschi Asset Management SGR S.p.A.
Via San Vittore, 37 - 20123 Milano, Italia
Tel.: +39 02 43828 754
Mobile: +39 333 876 1558
Fax: +39 02 43828 247
E-mail: [EMAIL PROTECTED]
Web: www.mpsam.it
Le informazioni trasmesse sono da intendersi per esclusivo uso del destinatario e
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RE: [R] R packages install problems linux - X not found (WhiteBoxEL 3)
On Mon, 2004-08-09 at 08:13, Dr Mike Waters wrote: snip Marc, Sorry for the confusion yesterday - in my defence, it was very hot and humid here in Hampshire (31 Celsius at 15:00hrs and still 25 at 20:00hrs). What had happened was that I had done a clean install of WB Linux, including the XFree86 and other developer packages. However, the on-line updating system updated the XFree86 packages to a newer sub version. It seems that it didn't do this correctly for the XFree86 developer package, which was missing vital files. However it showed up in the rpm database as being installed (i.e. rpm -qa | grep XFree showed it thus). I downloaded another rpm for this manually and I only forced the upgrade because it was the same version as already 'installed' (as far as the rpm database was concerned). I assumed that all dependencies were sorted out through the install in the first place. OK, that helps. I still have a lingering concern that, given the facts above, there may be other integrity issues in the RPM database, if not elsewhere. From reading the WB web site FAQ's (http://www.whiteboxlinux.org/faq.html) , it appears that they are using up2date/yum for system updates. Depending upon the version in use, there have been issues especially with up2date (hangs, incomplete updates, etc.) which could result in other problems. I use yum via the console here (under FC2), though I note that a GUI version of yum has been created, including replacing the RHN/up2date system tray alert icon. A thought relative to this specifically: If there is or may be an integrity problem related to the rpm database, you should review the information here: http://www.rpm.org/hintskinks/repairdb/ which provides instructions on repairing the database. Note the important caveats regarding backups, etc. The two key steps there are to remove any residual lock files using (as root): rm -f /var/lib/rpm/__* and then rebuilding the rpm database using (also as root): rpm -vv --rebuilddb I think that there needs to be some level of comfort that this basic foundation for the system is intact and correct. I only mentioned RH9 to show that I had some familiarity with the RedHat policy of separating out the 'includes' etc into a separate developer package. Once all this had been sorted out, I was then left with a compilation error which pointed to a missing dependency or similar, which was not due to missing developer packages, but, as you and Prof Ripley correctly point out, from the R installation itself. Having grown fat and lazy on using R under the MS Windows environment, I was struggling to identify the precise nature of this remaining problem. As regards the R installation, I did this from the RH9 binary for version 1.9.1, as I did not think that the Fedora Core 2 binary would be appropriate here. Perhaps I should now compile from the source instead? I would not use the FC2 RPM, since FC2 has many underlying changes not the least of which includes the use of the 2.6 kernel series and the change from XFree86 to x.org. Both changes resulted in significant havoc during the FC2 testing phases and there was at least one issue here with R due to the change in X. According to the WB FAQs: If you cannot find a package built specifically for RHEL3 or WBEL3 you can try a package for RH9 since many of the packages in RHEL3 are the exact same packages as appeared in RH9. Thus, it would seem reasonable to use the RH9 RPM that Martyn has created. An alternative would certainly be to compile R from the source tarball. In either case, I would remove the current installation of R and after achieving a level of comfort that your RPM database is OK, reinstall R using one of the above methods. Pay close attention to any output during the installation process, noting any error or warning messages that may occur. If you go the RPM route, be sure that the MD5SUM of the RPM file matches the value that Martyn has listed on CRAN to ensure that the file has been downloaded in an intact fashion. These are my thoughts at this point. You need to get to a point where the underlying system is stable and intact, then get R to the same state before attempting to install new packages. HTH, Marc __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] displaying computation outputs inside for loops
On Mon, 9 Aug 2004, Dewez Thomas wrote: Dear R-users, I am puzzled by for loops and am kind of ashamed to ask because it is so simple. There must be something I am missing in the way they are executed. If you want an explanation, rather than just a way to get printing, look at FAQ 7.18. -thomas __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] hclust-segmentation fault
I am getting the Segmentation fault when using hclust in R-1.9.1 running under SuSe 9.0 64-bit kernel on a dual opteron system with 8G of RAM. I was wandering if anybody could offer any insight? Thanks, mario. __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] built-in Sweave-like documentation in R-2.x
Hi devels, i did not find at this page: http://developer.r-project.org/ideas.txt any ideas concerning incorporating documentation possibilities (say, Sweave-based) into R-scripts. Was it discussed already? (If discussed, then what is the decision/conclusion then?) thanks, Valery __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] linear constraint optim with bounds/reparametrization
On Mon, 9 Aug 2004, Kahra Hannu wrote: 1) constrOptim does not work in this case because it only fits inequality constraints, ie A%*%theta = c --- I was struggling with the same problem a few weeks ago in the portfolio optimization context. You can impose equality constraints by using inequality constraints = and = simultaneously. See the example bellow. Ick. You do not want to use constrOptim for equality constraints. constrOptim is a log-barrier interior-point method, meaning that it adds a multiple of log(A%*%theta-c) to the objective function. This is a really bad idea as a way of faking equality constraints. Use Lagrange multipliers and optim. -thomas __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] log-linear contrasts
Dear list members, suppose I have a one-way ANOVA where the explanatory variable is of class ordered(). How can I define, instead of the default linear, quadratic, cubic contrasts, a set of log-linear contrasts corresponding to logb(c(1,2,4,8,16,60)+1,2) ? Regards, Christoph __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] built-in Sweave-like documentation in R-2.x
On Monday 09 August 2004 09:52, Khamenia, Valery wrote: Hi devels, i did not find at this page: http://developer.r-project.org/ideas.txt any ideas concerning incorporating documentation possibilities (say, Sweave-based) into R-scripts. Was it discussed already? (If discussed, then what is the decision/conclusion then?) See the 'Writing R Extensions' manual, specifically Creating R Packages - Writing package vignettes HTH, Deepayan __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] R packages install problems linux - X not found (WhiteBoxEL 3)
On Sun, 2004-08-08 at 22:22, Prof Brian Ripley wrote: On Sun, 8 Aug 2004, Marc Schwartz wrote: On Sun, 2004-08-08 at 14:10, Dr Mike Waters wrote: snip Thanks for the responses guys. I used to have RH9 installed on this machine and I found out about the separate developer packages then. I thought that I had got the relevant XFree devel package installed, but although it showed up in the rpm database as being present, the required files were not present. I did a forced rpm upgrade from the WhiteBox updates directory and that problem is now fixed, at least for car. Marc, thanks for the pointer on the rgl problem. However, I have a slightly different problem with the install of this package. It gets through to the point where it tries to make the rgl.so from the various .o files and fails then, as follows: g++ -I/usr/lib/R/include -I/usr/X11R6/include -DHAVE_PNG_H -I/usr/include -I/usr/local/include -Wall -pedantic -fno-exceptions -fno-rtti -fPIC -O2 -g -march=i386 -mcpu=i686 -c glgui.cpp -o glgui.o g++ -L/usr/local/lib -o rgl.so x11lib.o x11gui.o types.o math.o fps.o pixmap.o gui.o api.o device.o devicemanager.o rglview.o scene.o glgui.o -L/usr/X11R6/lib -L/usr/lib -lstdc++ -lX11 -lXext -lGL -lGLU -lpng /usr/lib/gcc-lib/i386-redhat-linux/3.2.3/../../../crt1.o(.text+0x18): In function `_start': : undefined reference to `main' x11lib.o(.text+0x84): In function `set_R_handler': /tmp/R.INSTALL.13414/rgl/src/x11gui.h:33: undefined reference to `R_InputHandlers' x11lib.o(.text+0x92):/tmp/R.INSTALL.13414/rgl/src/x11gui.h:33: undefined reference to `addInputHandler' x11lib.o(.text+0xfb): In function `unset_R_handler': /tmp/R.INSTALL.13414/rgl/src/x11lib.cpp:52: undefined reference to `R_InputHandlers' x11lib.o(.text+0x103):/tmp/R.INSTALL.13414/rgl/src/x11lib.cpp:52: undefined reference to `removeInputHandler' collect2: ld returned 1 exit status make: *** [rgl.so] Error 1 ERROR: compilation failed for package 'rgl' ** Removing '/usr/lib/R/library/rgl' - No doubt another failed dependency... DOH! Regards I am concerned by your indications of previously having had RH9 on the same box and that you had to force an update of the XFree Devel RPM. Forcing the installation of an RPM is almost always a bad thing. When you installed WB on the system, did you do a clean installation or some type of upgrade? If the latter, it is reasonable to consider that there may be some level of mixing and matching of RPMS from the two distributions going on. This could result in a level of marginally or wholly incompatible versions of RPMS being installed. Could you clarify that point? Also, be sure that you have the same versions of the XFree series RPMS installed. Use: rpm -qa | grep XFree in a console and be sure that the RPMS return the same version schema. If not, it is possible that one of your problems is the mixing of versions. Take note of the output of the above and be sure that the XFree86-Mesa-libGL and XFree86-Mesa-libGLU RPMS are installed as well. Some of the messages above would also suggest a problem finding R related headers. How did you install R? This may be a red herring of sorts, given the other problems, but may be helpful. I think it is the exact point. Those entry points are in R.bin, so should be missing. The g++ line is missing `-shared', which is picked up from R_HOME/etc/Makeconf, specifically from SHLIB_CXXLDFLAGS = -shared So the R installation doesn't have the right flags. This could be my fault. It transpires that this is not set correctly in the RPMs for RH9 and 8.x. I will look into it (this is most probably due to a missing BuildRequires). This isn't the first time someone has had this problem. I apologize for not fixing it, but at the time I was convinced the RPMS were OK. Martyn __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] hclust-segmentation fault
MarioM == Medvedovic, Mario (medvedm) [EMAIL PROTECTED]
on Mon, 9 Aug 2004 10:47:16 -0400 writes:
MarioM I am getting the Segmentation fault when using
MarioM hclust in R-1.9.1 running under SuSe 9.0 64-bit
MarioM kernel on a dual opteron system with 8G of RAM. I
MarioM was wandering if anybody could offer any insight?
{ where will you get when wandering around? :-) }
I have seen other problematic behavior on a 64-bit kernel Linux
on the Opteron though not with SuSE and only with R-devel (R-2.0.0-unstable)
Can you give a reproducible example please
(as the posting guide asks you to)?
Martin Maechler
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Re: [R] hclust-segmentation fault
On Mon, 9 Aug 2004, Medvedovic, Mario (medvedm) wrote: I am getting the Segmentation fault when using hclust in R-1.9.1 running under SuSe 9.0 64-bit kernel on a dual opteron system with 8G of RAM. I was wandering if anybody could offer any insight? Please try to use the debugger to supply more information, or give us some code we can reproduce on a similar system to see if we can reproduce the segfault. -- 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 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] built-in Sweave-like documentation in R-2.x
Hi! I'm not a developer, but you can take a look at the article Sweave, Part II: Package Vignettes in R-news Vol. 3/2, October 2003. Regards. On Mon, 9 Aug 2004, Khamenia, Valery wrote: Hi devels, i did not find at this page: http://developer.r-project.org/ideas.txt any ideas concerning incorporating documentation possibilities (say, Sweave-based) into R-scripts. Was it discussed already? (If discussed, then what is the decision/conclusion then?) thanks, Valery __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Ulises M. Alvarez LAB. DE ONDAS DE CHOQUE FISICA APLICADA Y TECNOLOGIA AVANZADA UNAM -u-m-a-l-v-a-r-e-z- at -f-a-t-a- dot -u-n-a-m- dot -m-x- __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] (REPOST) Simple main effects in 2-way repeated measure ANOVA
Dear Prof. Ripley I am sorry that reposting the mail was perceived as not complying to the correct list etiquette: I do not usually frequent the list and I just thought that the message went unnoticed. I apologize for the insistence. On the subject matter of the e-mail, yes, there was a typo, the error term was indeed Error(Subj/Time). But I am still interested in examining the simple main effects, when the interaction of Time and Group is significant: Time: -- ControlGroup: before vs after TreatmentGroup: before vs after Group: -- Before: ControlGroup vs TreatmentGroup After: ControlGroup vs TreatmentGroup Is this incorrect statistical praxis? Other software packages display the results for the above tests after the ANOVA. However, I couldn't find a simple way to extract this information in R. Also, I am not sure how to include a confounding variable, like Age, in the formulation of the model. Thanks for your help giuseppe Prof Brian Ripley wrote: Why has this been REPOSTed? It was delivered last Thursday. On Sun, 8 Aug 2004, Giuseppe Pagnoni wrote: I am running a 2-way repeated measure anova with 1 between-subjects factor (Group=treatment, control), and 1 within-subject factor (Time of measurement: time1, time2). I extract the results of the anova with: summary(aov(effect ~ Group*Time + Error=Subj/Time, data=mydata)) That's not valid syntax for an R formula. Did you mean Error(Subj/Time)? Now, this must be clearly a dumb question, but how can I quickly extract in R all the post-hoc t-tests for the simple main effects? I very much hope you cannot, as you have specified an interaction, and you should not want t-tests for main effects in the presence of an interaction, and certainly not with the default R coding. Did you mean Group + Time? Also, while I am at it, how do I enter in the model a counfounding covariate (e.g., Age)? And on a different matter, is there a way to receive interactive user input in an R script? Something like Enter the name of the factor: , or even more simply Press Enter to see the result of the next analysis ?readline, or cat + scan or ... using connections. -- Giuseppe Pagnoni, Ph.D. Dept. of Psychiatry and Behavioral Sciences 1639 Pierce Drive, Suite 4000 WMB Bldg., Atlanta, GA 30322, U.S. phone: 404-712-8431 fax: 404-727-3233 e-mail: [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
AW: [R] built-in Sweave-like documentation in R-2.x
See the 'Writing R Extensions' manual, specifically Creating R Packages - Writing package vignettes thank you, i saw this entry. However, this entry is rather about how to include documents (in particular Sweave-based) into a package. But I have meant smth else. Let me explain in example. Today I use emacs as environment for my R-sessions. I am quite happy to use Sweave, but not happy, that there is no good possibility to run some selected *part* of the R-code. Indeed, the R-chunks are alternated with Latex-chunks in Sweave. So, if one would like to execute, say, three consequent R-chunks (C-c C-r in ESS-mode), then the corresponding Latex-chunks between the R-chunks will cause side-effects. Actually, it is because neither ESS nor R could accept Latex-chunks and the markup symbols of Sweave. This makes interactive work in .Rnw files not fully convenient. Making the above short: would it be a bad idea to allow Latex-friendly documentation chunks in R-language? Thank you. P.S. I am sorry if i missed something well-known concerning the subj. -- Valery. __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] hclust-segmentation fault
Well, the use of debugger will take some time, but here is a simple code that invariably causes the fault. Mario. indata-matrix(rnorm(1000,0,1),ncol=10) ed-dist(indata) hc.e-hclust(ed,average) -Original Message- From: Prof Brian Ripley [mailto:[EMAIL PROTECTED] Sent: Monday, August 09, 2004 11:14 AM To: Medvedovic, Mario (medvedm) Cc: '[EMAIL PROTECTED]' Subject: Re: [R] hclust-segmentation fault On Mon, 9 Aug 2004, Medvedovic, Mario (medvedm) wrote: I am getting the Segmentation fault when using hclust in R-1.9.1 running under SuSe 9.0 64-bit kernel on a dual opteron system with 8G of RAM. I was wandering if anybody could offer any insight? Please try to use the debugger to supply more information, or give us some code we can reproduce on a similar system to see if we can reproduce the segfault. -- 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 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] built-in Sweave-like documentation in R-2.x
What exactly do you mean by this?
1. generation of Sweave-style docs from R programs or interaction? A
related approach is the reviveable statistical analysis (the
authors/researchers will have to forgive me for not recalling the WWW
site or their Uni!)
2. tools for doing docs and analysis at the same time? Emacs Speaks
Statistics has supported this with R since last century (1997 or so).
3. the vignettes of Bioconductor?
4. a text book in line with the above?
best,
-tony
Khamenia, Valery [EMAIL PROTECTED] writes:
Hi devels,
i did not find at this page:
http://developer.r-project.org/ideas.txt
any ideas concerning incorporating documentation
possibilities (say, Sweave-based) into R-scripts.
Was it discussed already?
(If discussed, then what is the decision/conclusion then?)
thanks,
Valery
__
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PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
--
Anthony Rossini Research Associate Professor
[EMAIL PROTECTED]http://www.analytics.washington.edu/
Biomedical and Health Informatics University of Washington
Biostatistics, SCHARP/HVTN Fred Hutchinson Cancer Research Center
UW (Tu/Th/F): 206-616-7630 FAX=206-543-3461 | Voicemail is unreliable
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Re: AW: [R] built-in Sweave-like documentation in R-2.x
On Monday 09 August 2004 10:23, Khamenia, Valery wrote: See the 'Writing R Extensions' manual, specifically Creating R Packages - Writing package vignettes thank you, i saw this entry. However, this entry is rather about how to include documents (in particular Sweave-based) into a package. But I have meant smth else. Let me explain in example. Today I use emacs as environment for my R-sessions. I am quite happy to use Sweave, but not happy, that there is no good possibility to run some selected *part* of the R-code. Indeed, the R-chunks are alternated with Latex-chunks in Sweave. So, if one would like to execute, say, three consequent R-chunks (C-c C-r in ESS-mode), then the corresponding Latex-chunks between the R-chunks will cause side-effects. Actually, it is because neither ESS nor R could accept Latex-chunks and the markup symbols of Sweave. This makes interactive work in .Rnw files not fully convenient. Is selecting and 'C-c C-r'-ing the 3 chunks separately that bad? The pieces for what you want are there. You can use Stangle() on a Sweave format file to extract the R code chunks. In your usage, a crude implementation would involve writing your selection to a file, running Stangle on it, and source()-ing the resulting .R file. Others may have better suggestions. Deepayan __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] hclust-segmentation fault
On Mon, 9 Aug 2004, Medvedovic, Mario (medvedm) wrote: Well, the use of debugger will take some time, but here is a simple code that invariably causes the fault. Mario. indata-matrix(rnorm(1000,0,1),ncol=10) ed-dist(indata) hc.e-hclust(ed,average) Works fine on R 1.9.1 on our dual Opteron 248 under FC2. We know of some pertinent compiler bugs on x86_64, so is this gcc 3.3.3 or later? -Original Message- From: Prof Brian Ripley [mailto:[EMAIL PROTECTED] Sent: Monday, August 09, 2004 11:14 AM To: Medvedovic, Mario (medvedm) Cc: '[EMAIL PROTECTED]' Subject: Re: [R] hclust-segmentation fault On Mon, 9 Aug 2004, Medvedovic, Mario (medvedm) wrote: I am getting the Segmentation fault when using hclust in R-1.9.1 running under SuSe 9.0 64-bit kernel on a dual opteron system with 8G of RAM. I was wandering if anybody could offer any insight? Please try to use the debugger to supply more information, or give us some code we can reproduce on a similar system to see if we can reproduce the segfault. -- 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 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R packages install problems linux - X not found (WhiteBoxEL 3)
Maybe you can try with the other RHEL clone like CentOS-3: http://install.linux.duke.edu/pub/linux/add-on/distrib/centos-3.1/i386/rpms/R-1.9.0-0.duke.1.el3.i386.rpm http://install.linux.duke.edu/pub/linux/add-on/distrib/centos-3.1/i386/srpms/R-1.9.0-0.duke.1.el3.src.rpm Best wishes, Muhammad Subianto On this day 09/08/2004 04:12 PM, Marc Schwartz wrote: On Mon, 2004-08-09 at 08:13, Dr Mike Waters wrote: snip Marc, Sorry for the confusion yesterday - in my defence, it was very hot and humid here in Hampshire (31 Celsius at 15:00hrs and still 25 at 20:00hrs). What had happened was that I had done a clean install of WB Linux, including the XFree86 and other developer packages. However, the on-line updating system updated the XFree86 packages to a newer sub version. It seems that it didn't do this correctly for the XFree86 developer package, which was missing vital files. However it showed up in the rpm database as being installed (i.e. rpm -qa | grep XFree showed it thus). I downloaded another rpm for this manually and I only forced the upgrade because it was the same version as already 'installed' (as far as the rpm database was concerned). I assumed that all dependencies were sorted out through the install in the first place. OK, that helps. I still have a lingering concern that, given the facts above, there may be other integrity issues in the RPM database, if not elsewhere. From reading the WB web site FAQ's (http://www.whiteboxlinux.org/faq.html) , it appears that they are using up2date/yum for system updates. Depending upon the version in use, there have been issues especially with up2date (hangs, incomplete updates, etc.) which could result in other problems. I use yum via the console here (under FC2), though I note that a GUI version of yum has been created, including replacing the RHN/up2date system tray alert icon. A thought relative to this specifically: If there is or may be an integrity problem related to the rpm database, you should review the information here: http://www.rpm.org/hintskinks/repairdb/ which provides instructions on repairing the database. Note the important caveats regarding backups, etc. The two key steps there are to remove any residual lock files using (as root): rm -f /var/lib/rpm/__* and then rebuilding the rpm database using (also as root): rpm -vv --rebuilddb I think that there needs to be some level of comfort that this basic foundation for the system is intact and correct. I only mentioned RH9 to show that I had some familiarity with the RedHat policy of separating out the 'includes' etc into a separate developer package. Once all this had been sorted out, I was then left with a compilation error which pointed to a missing dependency or similar, which was not due to missing developer packages, but, as you and Prof Ripley correctly point out, from the R installation itself. Having grown fat and lazy on using R under the MS Windows environment, I was struggling to identify the precise nature of this remaining problem. As regards the R installation, I did this from the RH9 binary for version 1.9.1, as I did not think that the Fedora Core 2 binary would be appropriate here. Perhaps I should now compile from the source instead? I would not use the FC2 RPM, since FC2 has many underlying changes not the least of which includes the use of the 2.6 kernel series and the change from XFree86 to x.org. Both changes resulted in significant havoc during the FC2 testing phases and there was at least one issue here with R due to the change in X. According to the WB FAQs: If you cannot find a package built specifically for RHEL3 or WBEL3 you can try a package for RH9 since many of the packages in RHEL3 are the exact same packages as appeared in RH9. Thus, it would seem reasonable to use the RH9 RPM that Martyn has created. An alternative would certainly be to compile R from the source tarball. In either case, I would remove the current installation of R and after achieving a level of comfort that your RPM database is OK, reinstall R using one of the above methods. Pay close attention to any output during the installation process, noting any error or warning messages that may occur. If you go the RPM route, be sure that the MD5SUM of the RPM file matches the value that Martyn has listed on CRAN to ensure that the file has been downloaded in an intact fashion. These are my thoughts at this point. You need to get to a point where the underlying system is stable and intact, then get R to the same state before attempting to install new packages. HTH, Marc __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: AW: [R] built-in Sweave-like documentation in R-2.x
If you name chunks that should be run together the same thing
(i.e. similar to how Noweb suggests that you should create documents),
then ess-eval-thread will evaluate all chunks in the thread
(i.e. that noweb would have sent to the same file upon tangling).
This is similar to the ess-eval-chunk ESS function.
Khamenia, Valery [EMAIL PROTECTED] writes:
See the 'Writing R Extensions' manual, specifically
Creating R Packages - Writing package vignettes
thank you, i saw this entry. However, this entry is rather
about how to include documents (in particular Sweave-based)
into a package. But I have meant smth else.
Let me explain in example. Today I use emacs as
environment for my R-sessions. I am quite happy to
use Sweave, but not happy, that there is no good
possibility to run some selected *part* of the R-code.
Indeed, the R-chunks are alternated with
Latex-chunks in Sweave. So, if one would like to
execute, say, three consequent R-chunks (C-c C-r in ESS-mode),
then the corresponding Latex-chunks between the
R-chunks will cause side-effects. Actually, it is
because neither ESS nor R could accept Latex-chunks
and the markup symbols of Sweave. This makes interactive
work in .Rnw files not fully convenient.
Making the above short: would it be a bad idea to
allow Latex-friendly documentation chunks in
R-language?
Thank you.
P.S. I am sorry if i missed something well-known
concerning the subj.
--
Valery.
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Anthony Rossini Research Associate Professor
[EMAIL PROTECTED]http://www.analytics.washington.edu/
Biomedical and Health Informatics University of Washington
Biostatistics, SCHARP/HVTN Fred Hutchinson Cancer Research Center
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Re: AW: [R] built-in Sweave-like documentation in R-2.x
Deepayan Sarkar [EMAIL PROTECTED] writes:
Is selecting and 'C-c C-r'-ing the 3 chunks separately that bad?
Yes. The UI should take care of it for him.
Others may have better suggestions.
A bit more work on the chunk evaluation approach within Emacs is one;
it almost does what is needed, but not quite.
best,
-tony
--
Anthony Rossini Research Associate Professor
[EMAIL PROTECTED]http://www.analytics.washington.edu/
Biomedical and Health Informatics University of Washington
Biostatistics, SCHARP/HVTN Fred Hutchinson Cancer Research Center
UW (Tu/Th/F): 206-616-7630 FAX=206-543-3461 | Voicemail is unreliable
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Follow-up Q Re: [R] displaying computation outputs inside for loops
I have a somewhat related question. A while back I was doing some simulations
using for() loops, and I wanted to keep track of the iterations using a line of
code quite similar to what Dimitris presented below. Instead of printing the
iteration message at the end of each iteration (actually, at the end of every
100th), nothing was printed until the for() loop was complete, and *then* all
the iteration messages were reported. Extending Dimitris' example:
for(i in 1:1){
x - rnorm(5)
cat(the values of `x' are:, format(x), \n)
cat(computation, i, finished\n\n)
}
demonstrates what I'm referring to (using R v1.9.1 with Windows XP): Iterations
are not printed as they occur, only at the end of the for() loop computation.
An interesting wrinkle is that I sometimes use Emacs (and ESS). Running the
code from within Emacs prints the iterations as they occur; also, if I switch to
other programs and then back to R, iterations have been printed.
Can anybody help me out with what's going on (and how to print iterations from
within a for() loop as they occur)?
Thanks, Dave
Dave Atkins, PhD
University of Washington
Message: 28
Date: Mon, 9 Aug 2004 11:26:08 +0200
From: Dimitris Rizopoulos [EMAIL PROTECTED]
Subject: Re: [R] displaying computation outputs inside for loops
To: Dewez Thomas [EMAIL PROTECTED]
Cc: [EMAIL PROTECTED]
Message-ID: [EMAIL PROTECTED]
Content-Type: text/plain; charset=iso-8859-1
Hi Thomas,
is this what you would like to get,
for(i in 1:3){
x - rnorm(5)
cat(the values of `x' are:, format(x), \n)
cat(computation, i, finished\n\n)
}
for(i in 1:3) print(i)
I hope this helps.
Best,
Dimitris
Dimitris Rizopoulos
Doctoral Student
Biostatistical Centre
School of Public Health
Catholic University of Leuven
Address: Kapucijnenvoer 35, Leuven, Belgium
Tel: +32/16/396887
Fax: +32/16/337015
Web: http://www.med.kuleuven.ac.be/biostat/
http://www.student.kuleuven.ac.be/~m0390867/dimitris.htm
- Original Message -
From: Dewez Thomas [EMAIL PROTECTED]
To: 'R mailing list' [EMAIL PROTECTED]
Sent: Monday, August 09, 2004 11:15 AM
Subject: [R] displaying computation outputs inside for loops
Dear R-users,
I am puzzled by for loops and am kind of ashamed to ask because it
is so
simple. There must be something I am missing in the way they are
executed.
Basically, I would like to iterate a given number of time and
generate a
bunch of stats (that's what loops are designed for, right?). Before
doing
this I simply want to test simple procedure and see if they work (ie
got the
syntax right - my main problem as I am new to R - and produce
expected
results).
Even for something as basic as
for (i in 1:3) {i}
I get no screen output. Shouldn't R systematically display i for
every loop
just like I am requesting with invoking i? When checking at the
end of the
looping, i is indeed assigned to 5 but I cannot get intermediate
values.
Further testing shows that i takes all the values in turn.
for (i in 1:3) {str(i)}
int 1
int 2
int 3
but summary(i) doesn't display anything. Isn't there something weird
with
this? Am I expecting something wrong and for loops just don't work
that way,
unless using str() command? I tried print() and other descriptive
commands
but to no avail.
A quick explanation would be grately appreciated
Thomas
***
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[R] Approaches to using RUnit
Having used JUnit and PyUnit, I was pleased to see the release of the RUnit package on CRAN. I'm wondering if there are any RUnit users out there that would be willing to share some tips on how they organize their code to work with RUnit. Specifically, I'm wondering about the best way to load/import/source the functions to be tested. I would like to end up with a script, testall or some such, that allows me to run all the unit tests in a given directory. One way I've thought about looks like: myfunc.R -- # some functions here -- runit_myfunc.R -- source(myfunc.R) # test function here -- + seth __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] hclust-segmentation fault
MarioM == Medvedovic, Mario (medvedm) [EMAIL PROTECTED]
on Mon, 9 Aug 2004 11:31:45 -0400 writes:
MarioM Well, the use of debugger will take some time
well
did you try
R -d gdb
... GDB welcome messages
... GDB welcome messages
run
and then the R commands and after the segmentation fault, simply
bt
{ = 'backtrace' =^= traceback() in R }
?
MarioM but here is a simple code that invariably causes the
MarioM fault. Mario.
indata - matrix(rnorm(1000,0,1),ncol=10)
ed - dist(indata)
hc.e - hclust(ed,average)
to make this really reproducible you'd have to give a
set.seed(n)
at the beginning. But since you say it's invariably, that's ok.
As for Prof Ripley's, these R calls also work here on our Opteron
machine w/o a problem.
Martin Maechler
-Original Message- From: Prof Brian Ripley
[mailto:[EMAIL PROTECTED] Sent: Monday, August 09,
2004 11:14 AM To: Medvedovic, Mario (medvedm) Cc:
'[EMAIL PROTECTED]' Subject: Re: [R]
hclust-segmentation fault
On Mon, 9 Aug 2004, Medvedovic, Mario (medvedm) wrote:
I am getting the Segmentation fault when using hclust
in
R-1.9.1 running
under SuSe 9.0 64-bit kernel on a dual opteron system
with
8G of RAM.
I was wandering if anybody could offer any insight?
Please try to use the debugger to supply more
information, or give us some code we can reproduce on a
similar system to see if we can reproduce the segfault.
--
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, UK Fax:
+44 1865 272595
MarioM __
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MarioM http://www.R-project.org/posting-guide.html
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Re: Follow-up Q Re: [R] displaying computation outputs inside for loops
On Mon, 9 Aug 2004, Dave Atkins wrote:
I have a somewhat related question. A while back I was doing some simulations
using for() loops, and I wanted to keep track of the iterations using a line of
code quite similar to what Dimitris presented below. Instead of printing the
iteration message at the end of each iteration (actually, at the end of every
100th), nothing was printed until the for() loop was complete, and *then* all
the iteration messages were reported. Extending Dimitris' example:
for(i in 1:1){
x - rnorm(5)
cat(the values of `x' are:, format(x), \n)
cat(computation, i, finished\n\n)
}
demonstrates what I'm referring to (using R v1.9.1 with Windows XP): Iterations
are not printed as they occur, only at the end of the for() loop computation.
This *is* in the rw-FAQ. Please see the posting guide.
An interesting wrinkle is that I sometimes use Emacs (and ESS). Running the
code from within Emacs prints the iterations as they occur; also, if I switch to
other programs and then back to R, iterations have been printed.
--
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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Re: [R] Approaches to using RUnit
Seth Falcon [EMAIL PROTECTED] writes:
Having used JUnit and PyUnit, I was pleased to see the release of the
RUnit package on CRAN.
I'm wondering if there are any RUnit users out there that would be
willing to share some tips on how they organize their code to work with
RUnit.
Specifically, I'm wondering about the best way to load/import/source the
functions to be tested. I would like to end up with a script, testall
or some such, that allows me to run all the unit tests in a given
directory.
Hi Seth -
The version that I was working on (before the other folks released a
less eclectic and more functional/general package) had a
testrunner(test=c(list,of,functions),testall=FALSE)
API, along with a preliminary tcltk
GUIrunner()
with a similar intended API. I've been trying to find the initiative
to integrate (overlay) those tools with the current RUnit as an
add-on, but the difference is that I attached tests as S4 object
instantiations.
Stop by if you want to chat a bit about it.
best,
-tony
--
Anthony Rossini Research Associate Professor
[EMAIL PROTECTED]http://www.analytics.washington.edu/
Biomedical and Health Informatics University of Washington
Biostatistics, SCHARP/HVTN Fred Hutchinson Cancer Research Center
UW (Tu/Th/F): 206-616-7630 FAX=206-543-3461 | Voicemail is unreliable
FHCRC (M/W): 206-667-7025 FAX=206-667-4812 | use Email
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Re: [R] linear constraint optim with bounds/reparametrization
Hi, Tom: Why is adding a multiple of log(A*theta-c) to the objective function ... a really bad idea as a way of faking equality constraints? I've used Lagrange multipliers on other occasions, but if computer time is cheaper than the time to work out the Lagrange multiplier approach, why is it a bad idea to add violation of constraints to the objective function? I've done it myself in the past and have gotten what looked like sensible results. Best Wishes, spencer graves Thomas Lumley wrote: On Mon, 9 Aug 2004, Kahra Hannu wrote: 1) constrOptim does not work in this case because it only fits inequality constraints, ie A%*%theta = c --- I was struggling with the same problem a few weeks ago in the portfolio optimization context. You can impose equality constraints by using inequality constraints = and = simultaneously. See the example bellow. Ick. You do not want to use constrOptim for equality constraints. constrOptim is a log-barrier interior-point method, meaning that it adds a multiple of log(A%*%theta-c) to the objective function. This is a really bad idea as a way of faking equality constraints. Use Lagrange multipliers and optim. -thomas __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] R packages install problems linux - X not found (WhiteBoxEL 3)
On Mon, 2004-08-09 at 15:13, Dr Mike Waters wrote: [SNIP] Once all this had been sorted out, I was then left with a compilation error which pointed to a missing dependency or similar, which was not due to missing developer packages, but, as you and Prof Ripley correctly point out, from the R installation itself. Having grown fat and lazy on using R under the MS Windows environment, I was struggling to identify the precise nature of this remaining problem. As regards the R installation, I did this from the RH9 binary for version 1.9.1, as I did not think that the Fedora Core 2 binary would be appropriate here. Perhaps I should now compile from the source instead? The Red Hat 9 RPM is appropriate for you, but it is currently buggy, so you are best compiling from source. I need to add gcc-g++ to the list of BuildRequires (packages that must be installed at build time). This isn't strictly necessary to build R, but if R is configured without a C++ compiler, of course it does not know how to build packages with C++ code in them. Martyn __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: Follow-up Q Re: [R] displaying computation outputs inside for loops
I have now been enlightened via Windows FAQ 6.2 on When using Rgui the output
to the console seems to be delayed. Ctrl-W toggles whether console output is
buffered.
[As a side note: Damn! I was hoping to avoid that response (i.e., having my
ignorance pointed out), but all my searches of R-help and FAQs had focused on
for() and iteration, which didn't find the right answer. Knowing the
right question to ask goes a long way...]
Thanks, Dave
Prof Brian Ripley wrote:
On Mon, 9 Aug 2004, Dave Atkins wrote:
I have a somewhat related question. A while back I was doing some simulations
using for() loops, and I wanted to keep track of the iterations using a line of
code quite similar to what Dimitris presented below. Instead of printing the
iteration message at the end of each iteration (actually, at the end of every
100th), nothing was printed until the for() loop was complete, and *then* all
the iteration messages were reported. Extending Dimitris' example:
for(i in 1:1){
x - rnorm(5)
cat(the values of `x' are:, format(x), \n)
cat(computation, i, finished\n\n)
}
demonstrates what I'm referring to (using R v1.9.1 with Windows XP): Iterations
are not printed as they occur, only at the end of the for() loop computation.
This *is* in the rw-FAQ. Please see the posting guide.
An interesting wrinkle is that I sometimes use Emacs (and ESS). Running the
code from within Emacs prints the iterations as they occur; also, if I switch to
other programs and then back to R, iterations have been printed.
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[R] FAQs (was: displaying computation outputs inside for loops)
On Mon, 9 Aug 2004, Dave Atkins wrote: [As a side note: Damn! I was hoping to avoid that response (i.e., having my ignorance pointed out), but all my searches of R-help and FAQs had focused on for() and iteration, which didn't find the right answer. Knowing the right question to ask goes a long way...] This illustrates why reading the FAQs is a useful thing to do. You can find these things out before they cause problems for you (that is, you all, not specifically Dave). With help pages and the email archives it can be difficult to find the right index terms. The FAQs are short enough that you can just read the whole thing, and the answer is likely to be clearer and more detailed than you will get from asking the question again. (If it isn't, then asking can someone clear up this question about FAQ 7.13? is likely to get useful help). -thomas __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Simultaneous subscripts and superscripts
Dear List,
I'd like to add text to a plot where a text symbol has both a
superscript and subscript. For example, the variable S with a
superscript 2 and a subscript t. I have been able to accomplish this
using either
expression( paste(S,atop(scriptstyle(2),scriptstyle(t))) )
or
expression( {S[t]}^2 )
but the spacing isn't quite right (or rather what I'd like) using
either of these. By 'right' I mean the placement and spacing don't
quite coincide with what I'd expect if I superimposed S^2 with S[t].
Is there a way to place BOTH a subscript and superscript so that they
are placed identically as if I had overlayed S^2 and S[t]?
I'm using R 1.9.0 on Mac OSX.
Thanks,
Brian
--
*
Brian Beckage
Department of Botany
University of Vermont
Marsh Life Science Building
Burlington, VT 05405
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RE: [R] Simultaneous subscripts and superscripts
expression(S[t]^2) looks pretty good for me (on windows()).
Andy
From: Brian Beckage
Dear List,
I'd like to add text to a plot where a text symbol has both a
superscript and subscript. For example, the variable S with a
superscript 2 and a subscript t. I have been able to accomplish this
using either
expression( paste(S,atop(scriptstyle(2),scriptstyle(t))) )
or
expression( {S[t]}^2 )
but the spacing isn't quite right (or rather what I'd like) using
either of these. By 'right' I mean the placement and spacing don't
quite coincide with what I'd expect if I superimposed S^2 with S[t].
Is there a way to place BOTH a subscript and superscript so that they
are placed identically as if I had overlayed S^2 and S[t]?
I'm using R 1.9.0 on Mac OSX.
Thanks,
Brian
--
*
Brian Beckage
Department of Botany
University of Vermont
Marsh Life Science Building
Burlington, VT 05405
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Re: [R] Simultaneous subscripts and superscripts
Brian Beckage wrote:
Dear List,
I'd like to add text to a plot where a text symbol has both a
superscript and subscript. For example, the variable S with a
superscript 2 and a subscript t. I have been able to accomplish this
using either
expression( paste(S,atop(scriptstyle(2),scriptstyle(t))) )
or
expression( {S[t]}^2 )
but the spacing isn't quite right (or rather what I'd like) using either
of these. By 'right' I mean the placement and spacing don't quite
coincide with what I'd expect if I superimposed S^2 with S[t]. Is there
a way to place BOTH a subscript and superscript so that they are placed
identically as if I had overlayed S^2 and S[t]?
I'm using R 1.9.0 on Mac OSX.
Thanks,
Brian
I think that depends on the font in use. If letters don't have the same
width, it is difficult to calculate pretty bounding boxes ... and the
expected behaviour is to left-align. Hence it's as expected.
Are you volunteering to add some fuzz to plotmath.c? I guess you will
have to add quite a lot of code for this tiny step... (and R is not TeX,
BTW).
Uwe Ligges
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RE: [R] Simultaneous subscripts and superscripts
Yep, it looks good on my system as well. I had tried
expression(S^2[t]) but not expression(S[t]^2) and the order matters.
Thanks for the help.
Brian
Brian
At 1:44 PM -0400 8/9/04, Liaw, Andy wrote:
expression(S[t]^2) looks pretty good for me (on windows()).
Andy
From: Brian Beckage
Dear List,
I'd like to add text to a plot where a text symbol has both a
superscript and subscript. For example, the variable S with a
superscript 2 and a subscript t. I have been able to accomplish this
using either
expression( paste(S,atop(scriptstyle(2),scriptstyle(t))) )
or
expression( {S[t]}^2 )
but the spacing isn't quite right (or rather what I'd like) using
either of these. By 'right' I mean the placement and spacing don't
quite coincide with what I'd expect if I superimposed S^2 with S[t].
Is there a way to place BOTH a subscript and superscript so that they
are placed identically as if I had overlayed S^2 and S[t]?
I'm using R 1.9.0 on Mac OSX.
Thanks,
Brian
--
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Brian Beckage
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University of Vermont
Marsh Life Science Building
Burlington, VT 05405
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Brian Beckage
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University of Vermont
Marsh Life Science Building
Burlington, VT 05405
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Fax : 802 656-0440
email: [EMAIL PROTECTED]
web : www.uvm.edu/~bbeckage
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RE: [R] Simultaneous subscripts and superscripts
Andy Liaw wrote expression(S[t]^2) looks pretty good to me (on windows()). And to me too (sparc-sun-solaris2.9; R version 1.9.1). cheers, Rolf Turner __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] Simultaneous subscripts and superscripts
Yes, I agree. I thought I had tried it both way, but I guess I was
too quick to look for more complicated solutions.
Brian
At 2:10 PM -0400 8/9/04, Liaw, Andy wrote:
I guess it's good to type what makes sense: I can understand squaring S[t],
but it's hard for me to fathom subscripting S^2...
-Original Message-
From: Brian Beckage [mailto:[EMAIL PROTECTED]
Sent: Monday, August 09, 2004 1:55 PM
To: Liaw, Andy; [EMAIL PROTECTED]
Subject: RE: [R] Simultaneous subscripts and superscripts
Yep, it looks good on my system as well. I had tried
expression(S^2[t]) but not expression(S[t]^2) and the order matters.
Thanks for the help.
Brian
Brian
At 1:44 PM -0400 8/9/04, Liaw, Andy wrote:
expression(S[t]^2) looks pretty good for me (on windows()).
Andy
From: Brian Beckage
Dear List,
I'd like to add text to a plot where a text symbol has both a
superscript and subscript. For example, the variable S with a
superscript 2 and a subscript t. I have been able to
accomplish this
using either
expression( paste(S,atop(scriptstyle(2),scriptstyle(t))) )
or
expression( {S[t]}^2 )
but the spacing isn't quite right (or rather what I'd like) using
either of these. By 'right' I mean the placement and
spacing don't
quite coincide with what I'd expect if I superimposed S^2
with S[t].
Is there a way to place BOTH a subscript and superscript
so that they
are placed identically as if I had overlayed S^2 and S[t]?
I'm using R 1.9.0 on Mac OSX.
Thanks,
Brian
--
*
Brian Beckage
Department of Botany
University of Vermont
Marsh Life Science Building
Burlington, VT 05405
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University of Vermont
Marsh Life Science Building
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Fax : 802 656-0440
email: [EMAIL PROTECTED]
web : www.uvm.edu/~bbeckage
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University of Vermont
Marsh Life Science Building
Burlington, VT 05405
Phone: 802 656-0197
Fax : 802 656-0440
email: [EMAIL PROTECTED]
web : www.uvm.edu/~bbeckage
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[R] Need help on this problem!
Hi everyone, I have posted a similar question to this list, but I don't get a reply. I really want to solve this problem, so I post it again... I am trying to use R to fit some mixed-effects models for a nested data. The data is a simulated data with 111 subjects. Each subject has 6 waves' data. Below are the first two subjects' data : simu1[1:12,] Grouped Data: gf ~ age | id id occasion age gf tau b0 b1b2 1 11 4.056714 35.08943 14.8 14.502078 5.209333 -5.199452 2 12 14.056714 87.18276 14.8 14.502078 5.209333 -5.199452 3 13 29.056714 91.19566 14.8 14.502078 5.209333 -5.199452 4 14 42.056714 91.32411 14.8 14.502078 5.209333 -5.199452 5 15 57.056714 91.47233 14.8 14.502078 5.209333 -5.199452 6 16 65.056714 91.55138 14.8 14.502078 5.209333 -5.199452 7 21 3.353627 16.94166 14.8 -0.331536 5.293478 -5.392813 8 22 13.353627 69.87644 14.8 -0.331536 5.293478 -5.392813 9 23 28.353627 76.18644 14.8 -0.331536 5.293478 -5.392813 10 24 41.353627 74.89508 14.8 -0.331536 5.293478 -5.392813 11 25 56.353627 73.40505 14.8 -0.331536 5.293478 -5.392813 12 26 64.353627 72.61037 14.8 -0.331536 5.293478 -5.392813 Firstly, I used lme to fit a mixed effects model with quadratic curve. simu1$age2-simu1$age^2 mm.lme.2-lme(gf~age+age2,random=~age+age2|id,data=simu1) It works well: summary(mm.lme.2) Linear mixed-effects model fit by REML Data: simu1 AIC BIClogLik 5222.225 5267.193 -2601.113 Random effects: Formula: ~age + age2 | id Structure: General positive-definite, Log-Cholesky parametrization StdDev Corr (Intercept) 2.729384e+00 (Intr) age age 1.068434e-01 0.648 age28.285027e-34 0.000 0.000 Residual1.082344e+01 Fixed effects: gf ~ age + age2 Value Std.Error DF t-value p-value (Intercept) 23.902926 1.1606163 553 20.59503 .0001 age 3.046429 0.0815675 553 37.34854 .0001 age2-0.034015 0.0011395 553 -29.85176 .0001 Correlation: (Intr) age age -0.790 age2 0.697 -0.964 Standardized Within-Group Residuals: Min Q1Med Q3Max -2.5233682 -0.6801665 -0.1735055 0.5243569 2.7772921 Number of Observations: 666 Number of Groups: 111 However, when I tried to fit the following model and the starting value is very close to the true value: simu.nlme-nlme(gf~b00 + b10 * age + b20 * max(0,(age-tau0)),data=simu1,fixed=b00+b10+b20+tau0~1,random=b00+b10+b20+tau0~1,group=~id, start=c(b00=4.08,b10=5.32,b20=-5.29,tau0=14.8),method=REML) It shows following error: ** Error in MEEM(object, conLin, control$niterEM) : Singularity in backsolve at level 0, block 1 ** I also fitted the same model by using SAS and winBUGS. They all worked well... Do you have any suggestions on this problem? Any reply will be appreciated! Lijuan __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] error when calling debugger()
Hi,
I am getting an error message when I am trying to run the debugger() on
the last.dump. The debugger() stops after I make a selection. Could
someone please suggest what it might mean? The R log is included below.
This is R-1.8.1 on RH 7.3.
Thanks, Vadim
load(last.dump.rda)
debugger(last.dump)
Message: Error in split(x, f) : Group length is 0 but data length 0
Available environments had calls:
1: try({
2: local(for (ticker in univ$ticker) {
3: eval.parent(substitute(eval(quote(expr), envir)))
4: eval(expr, p)
5: eval(expr, envir, enclos)
6: eval(quote(for (ticker in univ$ticker) {
7: eval(expr, envir, enclos)
8: local(for (i in l) {
9: eval.parent(substitute(eval(quote(expr), envir)))
10: eval(expr, p)
11: eval(expr, envir, enclos)
12: eval(quote(for (i in l) {
13: eval(expr, envir, enclos)
14: accumulate(accu, lapply(split(seq(length(key)), key), function(i) {
15: lapply(split(seq(length(key)), key), function(i) {
16: split(seq(length(key)), key)
17: split.default(seq(length(key)), key)
Enter an environment number, or 0 to exit Selection: 1
Error in get(.obj, envir = dump[[.selection]]) :
recursive default argument reference
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[R] Easy acf and pacf for irregular time series in R
R: Is there an easy way to get the acf and pacf for an irregular times series? That is, the acf and pacf with lag lengths that are in units of time, not observation number. Thanks, Jason Higbee Research Associate Federal Reserve Bank of St. Louis The views expressed in this email are the author's and not necessarily those of the Federal Reserve Bank of St. Louis or the Federal Reserve System [[alternative HTML version deleted]] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] error when calling debugger()
I ran across this behavior in debugger a while ago -- it is R Problem 2656.
As far as I know, no one has made any sense of what is happening in
debugger, but the bug that was the cause of debugger being called was
trying to subscript columns of a matrix that didn't exist. (You can see the
example in the bug report.) That doesn't seem like much of a hint in this
case, however.
Patrick Burns
Burns Statistics
[EMAIL PROTECTED]
+44 (0)20 8525 0696
http://www.burns-stat.com
(home of S Poetry and A Guide for the Unwilling S User)
Vadim Ogranovich wrote:
Hi,
I am getting an error message when I am trying to run the debugger() on
the last.dump. The debugger() stops after I make a selection. Could
someone please suggest what it might mean? The R log is included below.
This is R-1.8.1 on RH 7.3.
Thanks, Vadim
load(last.dump.rda)
debugger(last.dump)
Message: Error in split(x, f) : Group length is 0 but data length 0
Available environments had calls:
1: try({
2: local(for (ticker in univ$ticker) {
3: eval.parent(substitute(eval(quote(expr), envir)))
4: eval(expr, p)
5: eval(expr, envir, enclos)
6: eval(quote(for (ticker in univ$ticker) {
7: eval(expr, envir, enclos)
8: local(for (i in l) {
9: eval.parent(substitute(eval(quote(expr), envir)))
10: eval(expr, p)
11: eval(expr, envir, enclos)
12: eval(quote(for (i in l) {
13: eval(expr, envir, enclos)
14: accumulate(accu, lapply(split(seq(length(key)), key), function(i) {
15: lapply(split(seq(length(key)), key), function(i) {
16: split(seq(length(key)), key)
17: split.default(seq(length(key)), key)
Enter an environment number, or 0 to exit Selection: 1
Error in get(.obj, envir = dump[[.selection]]) :
recursive default argument reference
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[R] The sm Package - axis limit values and axis removal
Hi there, I am trying to place axis limit values on plots generated using the sm.density(x) function as in figure 1.6 (page 8) of Bowman Azzalini (1997). I realize The sm Package does not apply the x, y or zlim values in 3D plots, is there a way to add this information after the fact? Also, can one remove the upper plot axis; apparently this and addition of xlim values can be accomplished in S-Plus. Thanks in advance, Bruce _ Bruce Catton MSc Candidate Forest Sciences University of British Columbia email: [EMAIL PROTECTED] [[alternative HTML version deleted]] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] How to import specific column(s) using read.table?
Dear R people, I have a very big tab-delim txt file with header and I only want to import several columns into R. I checked the options for read.table and only found nrows which lets you specify the maximum number of rows to read in. Although I can use some text editors (e.g., wordpad) to edit the txt file first before running R, I feel its not very convenient. The reason for me to do this is that if I import the whole file into R, it will eat up too much of my systems memory. Even after I remove it later, I still cant release the memory. Anyone has any suggestions? Thank you very much, Frank __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] How to import specific column(s) using read.table?
On Mon, 9 Aug 2004, F Duan wrote:
Dear R people,
I have a very big tab-delim txt file with header and I only want to import
several columns into R. I checked the options for read.table and only
found nrows which lets you specify the maximum number of rows to read in.
Although I can use some text editors (e.g., wordpad) to edit the txt file first
before running R, I feel its not very convenient. The reason for me to do this
is that if I import the whole file into R, it will eat up too much of my
systems memory. Even after I remove it later, I still cant release the memory.
You can't avoid reading the whole file, but you can avoid having it in
memory.
I'll assume you know how many lines are in the file, call it N. (this
isn't necessary but it is tidier) and that you are interested in columns
10 and 110, both numeric
If you do something like
inputfile-file(inputfile.txt,open=r)
result-data.frame(col10=numeric(N), col110=numeric(N))
chunksize-1000
nchunks- ceiling(N/1000)
for(i in 1:nchunks){
chunk-read.table(inputfile,nrows=chunksize)
result[ (i-1)*chunksize+ (1:chunksize),]-chunk[,c(10,110)]
}
close(inputfile)
you can choose the chunk size so that the memory use is not too bad.
There are also more efficient ways that make you do more of the work (eg
read in lines of text with readLines and use regular expressions to
extract the columns you need)
-thomas
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Re: [R] How to import specific column(s) using read.table?
If you've got access to unix tools (i.e. linux or cygwin), consider
the cut command. Great for column selection.
Thomas Lumley [EMAIL PROTECTED] writes:
On Mon, 9 Aug 2004, F Duan wrote:
Dear R people,
I have a very big tab-delim txt file with header and I only want to import
several columns into R. I checked the options for read.table and only
found nrows which lets you specify the maximum number of rows to read in.
Although I can use some text editors (e.g., wordpad) to edit the txt file first
before running R, I feel its not very convenient. The reason for me to do this
is that if I import the whole file into R, it will eat up too much of my
systems memory. Even after I remove it later, I still cant release the memory.
You can't avoid reading the whole file, but you can avoid having it in
memory.
I'll assume you know how many lines are in the file, call it N. (this
isn't necessary but it is tidier) and that you are interested in columns
10 and 110, both numeric
If you do something like
inputfile-file(inputfile.txt,open=r)
result-data.frame(col10=numeric(N), col110=numeric(N))
chunksize-1000
nchunks- ceiling(N/1000)
for(i in 1:nchunks){
chunk-read.table(inputfile,nrows=chunksize)
result[ (i-1)*chunksize+ (1:chunksize),]-chunk[,c(10,110)]
}
close(inputfile)
you can choose the chunk size so that the memory use is not too bad.
There are also more efficient ways that make you do more of the work (eg
read in lines of text with readLines and use regular expressions to
extract the columns you need)
-thomas
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Re: [R] How to import specific column(s) using read.table?
There is no way for read.table to skip columns. It is however very easy to do this with a preprocessing of the table: cut, awk and perl all come to mind, and you could do it in R too, reading a block of rows at a time and writing them back out. scan() can skip columns, but I would still use preprocessing with scan. On Mon, 9 Aug 2004, F Duan wrote: I have a very big tab-delim txt file with header and I only want to import several columns into R. I checked the options for read.table and only found nrows which lets you specify the maximum number of rows to read in. Although I can use some text editors (e.g., wordpad) to edit the txt file first before running R, I feel its not very convenient. The reason for me to do this is that if I import the whole file into R, it will eat up too much of my systems memory. Even after I remove it later, I still cant release the memory. The peculiar quotes suggest this is Windows -- the Rtools we use to build R there contain a cut.exe. -- 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 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Using R boxplot function in Excel
Hi, I have downloaded the R-Com and I was able to run Interactive Graphics Demo 2 in excel. However, I couldn't create my own boxplot. Whenever I tried to run any code, it always say Error in loading DLL, even =rput(A1,A2:A20). Any idea about what's going wrong? A detailed explaination about how to use R-Excel tool would be greatly appreciated. Thanks a lot in advance! PS: I would like you to use the following data as an example. AB C 12.5186182 7.394714354 6.58360308 11.37597453 16.66820087 3.900166247 7.059103407 9.696804606 3.738396698 13.80587153 21.95622475 5.365668029 7.933769009 9.572635842 4.195704277 14.80409653 12.39208079 6.883236109 8.974253685 12.02387754 5.842696863 7.6083609 18.08369863 4.75223318 10.01654143 10.61151753 4.940416728 10.22753966 7.59634933 5.150066626 9.638591817 17.68393592 5.427933173 12.9405328 17.35731932 5.079704705 7.758718564 14.28801913 5.319497531 9.873025445 16.89445473 5.044402668 8.023517946 16.28102329 5.637006679 7.214663381 24.19544618 5.083052782 11.82039457 5.482319845 5.26250973 8.432808752 14.50188112 7.040906111 10.41255589 8.92899781 3.335806595 14.0030136 18.31841647 3.26446583 9.75501396 18.97398026 6.075650289 11.25837687 16.9443803 5.077193363 13.51650669 22.33716661 2.850945874 stationery, fonts and colors. Start enjoying all the benefits of MSN® Premium right now and get the first two months FREE*. __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] on.exit() inside local()
Hi,
Since I routinely open files in a loop I've developed a habit of using
on.exit() to close them. Since on.exit() needs to be called within a
function I use eval() as a surrogate. For example:
for (fileName in c(a, b)) eval({
con - file(fileName);
on.exit(close(con))
})
and con will be closed no matter what.
However it stopped working once I wrapped the loop in local():
local(
+ for (foo in seq(2)) eval({
+ on.exit(cat(foo, \n))
+ })
+ )
Error in cat(foo, \n) : Object foo not found
W/o local()it works just fine
for (foo in seq(2)) eval({
+ on.exit(cat(foo, \n))
+ })
1
2
The reason I wanted the local() is to keep 'foo' from interfering with
the existing environments, but somehow this breaks the thing.
At this point I am stuck. Could someone please tell what's going on?
Thanks,
Vadim
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[R] Enduring LME confusion or Psychologists and Mixed-Effects
Dear ExpeRts, Suppose I have a typical psychological experiment that is a within-subjects design with multiple crossed variables and a continuous response variable. Subjects are considered a random effect. So I could model aov1 - aov(resp~fact1*fact2+Error(subj/(fact1*fact2)) However, this only holds for orthogonal designs with equal numbers of observation and no missing values. These assumptions are easily violated so I seek refuge in fitting a mixed-effects model with the nlme library. lme1 - lme(resp~fact1*fact2, random=~1|subj) When testing the significance of the effects of my factors, with anova(lme1), the degrees of freedom that lme uses in the denominator spans all observations and is identical for all factors and their interaction. I read in a previous post on the list ([R] Help with lme basics) that this is inherent to lme. I studied the instructive book of Pinheiro Bates and I understand why the degrees of freedom are assigned as they are, but think it may not be appropriate in this case. Used in this way it seems that lme is more prone to type 1 errors than aov. To get more conservative degrees of freedom one could model lme2 - lme(resp~fact1*fact2, random=~1|subj/fact1/fact2) But this is not a correct model because it assumes the factors to be hierarchically ordered, which they are not. Another alternative is to model the random effect using a matrix, as seen in [R] lme and mixed effects on this list. lme3 - (resp~fact1*fact2, random=list(subj=pdIdent(form=~fact1-1), subj=~1, fact2=~1) This provides correct degrees of freedom for fact1, but not for the other effects and I must confess that I don't understand this use of matrices, Im not a statistician. My questions thus come down to this: 1. When aovs assumptions are violated, can lme provide the right model for within-subjects designs where multiple fixed effects are NOT hierarchically ordered? 2. Are the degrees of freedom in anova(lme1) the right ones to report? If so, how do I convince a reviewer that, despite the large number of degrees of freedom, lme does provide a conservative evaluation of the effects? If not, how does one get the right denDf in a way that can be easily understood? I hope that my confusion is all due to an ignorance of statistics and that someone on this list will kindly point that out to me. I do realize that this type of question has been asked before, but think that an illuminating answer can help R spread into the psychological community. __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
