Re: [R] how to make a data file
Hi well probably the best approach for you is to read some introductory documents. I would recommend this sequence R-intro R-lang R-data Posting guide or you can try to go through some documents from CRAN, in many of them you can find introductory chapters. And leas but not last when starting with R I found usefull Paul Johnson's Rtips (StatsRUs). At least for more concise help you need to provide R version, OS, and what exactly you did and how you failed - as recommended in posting guide ;-) HTH Petr On 31 Oct 2006 at 11:31, amna khan wrote: Date sent: Tue, 31 Oct 2006 11:31:08 +0500 From: amna khan [EMAIL PROTECTED] To: R-help@stat.math.ethz.ch Subject:[R] how to make a data file Sir after importing data from excel to R, I am not understanding how to make this data file. So that I can use it in extRemeToolkit and other packages. Thank you -- AMINA SHAHZADI Department of Statistics GC University Lahore, Pakistan. Email: [EMAIL PROTECTED] [EMAIL PROTECTED] [EMAIL PROTECTED] [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Petr Pikal [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] problem in intallasation
Hi you are Windows user? I guess yes. So you probably downloaded file for compilation or for other OSses. You need to download R-2.4.0- win32.exe. HTH Petr On 31 Oct 2006 at 11:19, amna khan wrote: Date sent: Tue, 31 Oct 2006 11:19:29 +0500 From: amna khan [EMAIL PROTECTED] To: R-help@stat.math.ethz.ch Subject:[R] problem in intallasation Sir I have downloaded new release of R 2.4.0. But there is no R.2.4.0.exefile for installing it. I request you to please guid me. Regards -- AMINA SHAHZADI Department of Statistics GC University Lahore, Pakistan. Email: [EMAIL PROTECTED] [EMAIL PROTECTED] [EMAIL PROTECTED] [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Petr Pikal [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Problem mit den Spracheinstellungen nach Installation von R
Dirk Hüser wrote: Hallo, ich habe ein Problem mit R. Ich hoffe hier auf die freundliche Hilfe der Community. Schilderung des Problems: Ich habe R 2.4.0 auf einem Rechner (1) installiert. - Am Anfang der Installation klickte ich auf Setup Deutsch. - Dann führte ich die Installation weiter mit den Grundeinstellungen fort. - Das Ergebnis: Nach der Installation hatte ich wie erhofft eine deutschsprachige Bedienoberfläche. Ich habe R 2.4.0. auf einem weiteren Rechner (2) installiert. - Am Anfang der Installation klickte ich auf Setup Deutsch. - Dann führte ich die Installation weiter mit den Grundeinstellungen fort. - Das Ergebnis: Nach der Installation hatte ich eine englischsprachige Bedienoberfläche. [This mailing list is in English.] Selecting the language in the installer only applies to the installer itself, not to the R GUI nor the error messages. Ich hätte jetzt gerne auf Rechner (2) gerne eine deutschsprachige Bedienoberfläche. Wie kann ich das bewerkstelligen? Ich habe bisher für dieses Problem kein Lösung gefunden. Zusatz: Auf Rechner (2) war vorher R 2.3.0. mit englischer Bedienoberfläche installiert. Es wurde vor der Installation komplett deinstallier und auch der Programmordner gelöscht. This depends on the locales for that machine. Probably, your second machine is configured for some different locale. You can set the environment variable LANGUAGE=de in order to get messages in german language. Uwe Ligges Ich hoffe, dass mir irgendjemand helfen kann. Über hilfreiche Tipps per Mail würde ich mich sehr freuen. MfG DIRK __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Which executable is associated with R CMD INSTALL?
On Mon, 30-Oct-2006 at 04:44PM -0500, Duncan Murdoch wrote:
| Try R CMD printenv R_HOME and you'll find which R home directory it is
| using. You can see a lot more with R CMD printenv or various options
| to R CMD config.
Thanks for that information. It knocks my theory on the head. Pity
that, because I might have been able to do something about it if that
was the problem. Now I'm at a loss to work out why lme4 installation
cannot find Matrix, and more strangely, why nothing else gave a
similar problem. I think I've tried every version of lme4 and Matrix
that has emerged since R-2.4.0 has been released.
The fact that no other Red hat user has a problem indicates the
problem is this end; but I'm short of ideas about where to look.
Looks like it's back to versions 6 months old -- like proprietary
software users have to put up with. :-(
(This is not a complaint)
--
~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.
___Patrick Connolly
{~._.~} Great minds discuss ideas
_( Y )_Middle minds discuss events
(:_~*~_:)Small minds discuss people
(_)-(_) . Anon
~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] POSIXct time zone and daylight savings issues
On Mon, 30 Oct 2006, Sebastian P. Luque wrote: Hi again, A related issue I can't quite understand is: R tt - as.POSIXct(2006-05-24, tz=EEST) R tt [1] 2006-05-24 EEST R seq(tt, length=12, by=months) [1] 2006-05-24 EEST 2006-06-24 EEST 2006-07-24 EEST 2006-08-24 EEST [5] 2006-09-24 EEST 2006-10-24 EEST 2006-11-24 EEST 2006-12-24 EEST [9] 2007-01-24 EEST 2007-02-24 EEST 2007-03-24 EEST 2007-04-24 EEST R tt - as.POSIXct(2006-05-24, tz=EET) R seq(tt, length=12, by=months) [1] 2006-05-24 EEST 2006-06-24 EEST 2006-07-24 EEST 2006-08-24 EEST [5] 2006-09-24 EEST 2006-10-24 EEST 2006-11-24 EET 2006-12-24 EET [9] 2007-01-24 EET 2007-02-24 EET 2007-03-24 EET 2007-04-24 EEST R sessionInfo() R version 2.4.0 (2006-10-03) x86_64-pc-linux-gnu locale: LC_CTYPE=en_CA.UTF-8;LC_NUMERIC=C;LC_TIME=en_CA.UTF-8;LC_COLLATE=en_CA.UTF-8;LC_MONETARY=en_CA.UTF-8;LC_MESSAGES=en_CA.UTF-8;LC_PAPER=en_CA.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_CA.UTF-8;LC_IDENTIFICATION=C attached base packages: [1] methods stats graphics grDevices utils datasets [7] base other attached packages: lattice 0.14-9 i.e. daylight savings 'tzone' attribute gets adjusted automatically when providing the standard time attribute, but not when providing the daylight savings time. Does this behaviour depend on the OS/locale? Should the 'tz' argument supplied when creating POSIXct objects always be the standard time version? No, it should be a timezone, and the timezone specification includes when DST is in effect. See ?as.POSIXct for details and references of timezones. For example, EST is a timezone without DST and EST5EDT is a timezone with DST (and they agree in winter). It looks like Linux is interpreting EEST as UTC+3 throughout the year (which appears not to be used anywhere as an actual timezone). So the behaviour is clear: EEST does not have DST, and $isdst == 0 in that 'timezone', whereas EET does have DST. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] match lists
Try this: A - list(matrix(c(2,3,3,1,2,2), 3, dimnames = list(NULL, letters[1:2])), matrix(c(3,3,2,5,1,3), 3, dimnames = list(NULL, letters[3:4]))) B - list(matrix(c(1:5, 20*(1:5), 10+20*(1:5)), 5, dimnames = list(NULL, letters[5:7])), matrix(c(1:5, 10*(1:5), 10+10*(1:5)), 5, dimnames = list(NULL, letters[8:10]))) lapply(1:2, function(i) lapply(1:2, function(j) B[[i]][A[[i]][,j],])) On 10/29/06, Heymans, MW [EMAIL PROTECTED] wrote: Dear list, I have this problem, please your advice. I have list A that contains two matrix elements: [[1]] a b [1,] 2 1 [2,] 3 2 [3,] 3 2 [[2]] c d [1,] 3 5 [2,] 3 1 [3,] 2 3 and list B, that also contains 2 matrices: [[1]] e f g [1,] 1 20 30 [2,] 2 40 50 [3,] 3 60 70 [4,] 4 80 90 [5,] 5 100 110 [[2]] h i j [1,] 1 10 20 [2,] 2 20 30 [3,] 3 30 40 [4,] 4 40 50 [5,] 5 50 60 Now I want to match each column of list A with each row of list B in such a way that element 1 of list A corresponds to element 1 of list B (and element 2 of A with 2 of B). So, in total there will be 4 new matrices, 1 for each column of list A. For example, for column a of list A the new matrix will be: 2 40 50 3 60 70 3 60 70 thanks, Martijn VUmc Amsterdam [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] [ggplot] controlling axis and major/minor tick marks
Hello there! I'm starting with ggplot and was wondering how I could control the axis of a plot. I would like the axis of the plot to be drawn black which I thought to acheive with the option axis.colour=black. However, this had no real effect on the plot. Then I found grid.colour which I changed to black as well. Now I got my axis as I wanted them, but ggplot now draws the grid inside the plot with black lines as well, which definetly do not want to appear. So how can I get a black border around my plots? Furthermore, I would like to indicate positions of major and minor ticks in my plots. Where can I do this? Thanks in advance. Greetings, Sebastian Ah, I use R 2.3.1 and ggplot 0.4.0, if that is important ... __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] read.fwf and header
Martin Maechler wrote: Gregor == Gregor Gorjanc [EMAIL PROTECTED] on Mon, 30 Oct 2006 23:33:21 +0100 writes: Gregor Daniel Nordlund wrote: Gregor, According to the help for read.fwf, sep needs to be set to a value that occurs only in the header record. I changed the spaces to commas in the header record of your example and used the following syntax and was able to read the file just fine. new.data-read.fwf(file=test.txt, widths=c(3, 4, 10, 3, 2, 2, 2, 2, 11, 19), header=TRUE, sep=',') Hope this is helpful, Dan Gregor Thanks Dan! But I have to modfy file first. Not that Gregor much of work but still. Yes, but I think it shows read.fwf() should not be extended for even more special cases: In my (and probably R-core's) view, read.fwf() should only have to be used for ``legacy data files'' (those times when people used *no* separators in order to save disk space), since nowadays, such data files should automatically have correct separators. -- Fix the file producing process rather than make read.fwf() unnecessarily more complicated. Thank you for this explanation of your (and probably R-core's) view! I really appreciate such feedback. I do agree that read.fwf is a bit archaic way to import data, but sometimes you can not fix file producing process. Perhaps above explanation and code examples from this thread could be added to read.fwf help page. I can provide a patch if my proposal is sane. Regards, Gregor __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Problem setting TMPDIR on the fly
Sorted - sort of... I've simply wrapped the invocation of R in a shell script along with the necessary environment variables. However, this is precisely the solution that I was hoping to avoid! I can see why it would be inadvisable to switch TMPDIR mid way through a session, but wouldn't it be useful to able switch it on the way in? As ever thanks for the help, cheers, Ben -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Peter Dalgaard Sent: 30 October 2006 17:08 To: Benjamin Lloyd-Hughes Cc: Peter Dalgaard Subject: Re: [R] Problem setting TMPDIR on the fly Benjamin Lloyd-Hughes [EMAIL PROTECTED] writes: Hi Peter, Thanks for the swift response! The problem is arising because I'm running R in batch mode through cron. As such I'd rather set all such environment variables explicitly and not make any assumptions about what variables maybe getting set on the way in. A typical call looks like this /usr/bin/R CMD BATCH --vanilla foo.R bar.Rout The first few lines of foo.R might run .libPaths(c(/usr/lib/R/library, /eurotempest/software/src/R/packages)) Sys.putenv(TMPDIR = /eurotempest/tmp/R/) Hence the problem. Is there a more sensible way to go? I'd just set it on the command line, as in TMPDIR=/eurotempest/tmp/R/ R -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Peter Dalgaard Sent: 30 October 2006 16:33 To: Benjamin Lloyd-Hughes Cc: r-help@stat.math.ethz.ch Subject: Re: [R] Problem setting TMPDIR on the fly Benjamin Lloyd-Hughes [EMAIL PROTECTED] writes: Hi folks, I'm having a spot of bother with tempdir(). If I set the environment variable TMPDIR in my shell prior to invoking R it works as expected: Sys.getenv(TMPDIR) TMPDIR /eurotempest/tmp/R tempdir() [1] /eurotempest/tmp/R/Rtmp0xY4XD However if I don't set it prior to entry, but attempt to set it from within the current session, the change is not detected/respected: Sys.getenv(TMPDIR) TMPDIR Sys.putenv(TMPDIR = /eurotempest/tmp/R/) Sys.getenv(TMPDIR) TMPDIR /eurotempest/tmp/R/ tempdir() [1] /tmp/Rtmp9chsNX Any ideas? You're not supposed to do that. There is one and only one tempdir per R session. This is used for storing stuff which R expects to be able to find again later, so it would be a bad thing just to switch it out. -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 -- This e-mail and its contents are intended for the use of the addressee(s) and may be confidential/privileged. No-one else may review, copy, disclose or otherwise use it or its contents. If you receive this e-mail in error, please contact the originator and delete it as soon as possible. Benfield Limited is authorised by the Financial Services Authority under the reference number 311884. Registered in England no 1170753. Registered office 55 Bishopsgate. Please refer to Benfield Limited's terms and conditions (www.benfieldgroup.com/terms) for a description of our services, duties and points of contact. Please review these terms and conditions at inception and renewal of all reinsurance and insurance contracts. Please note that our terms and conditions and interests in other companies may change over time and these changes will be reflected on the Benfield Limited website. The latest version of our terms and conditions supersedes all previous versions. == -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 -- This e-mail and its contents are intended for the use of the addressee(s) and may be confidential/privileged. No-one else may review, copy, disclose or otherwise use it or its contents. If you receive this e-mail in error, please contact the originator and delete it as soon as possible. Benfield Limited is authorised by the Financial Services Authority under the reference number 311884. Registered in England no 1170753. Registered office 55 Bishopsgate. Please refer to Benfield Limited's terms and conditions (www.benfieldgroup.com/terms) for a description of our services, duties and points of contact. Please review these
[R] generic pasting of strings
Hi there, is there a way to make the following code generic, so that i can paste() the columns in tmp1 depending on the dimensions given in embed()? tmp1 - embed(as.vector(shrinkTable$AOIname), dimension = 2); tmp1 [,1] [,2] [1,] AOI4 AOI1 [2,] AOI6 AOI4 [3,] AOI4 AOI6 tmp2 - paste(tmp1[, 2], tmp1[, 1], sep = ); tmp2 [1] AOI1AOI4 AOI4AOI6 AOI6AOI4 for dimension = 3 this would look like this: tmp1 - embed(as.vector(shrinkTable$AOIname), dimension = 3); tmp1 [,1] [,2] [,3] [1,] AOI6 AOI4 AOI1 [2,] AOI4 AOI6 AOI4 tmp2 - paste(tmp1[ ,3], tmp1[, 2], tmp1[, 1], sep = ); tmp2 [1] AOI1AOI4AOI6 AOI4AOI6AOI4 Any ideas? Thanks for your help, Robert Lischke __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] R crashing during batch file formatting
Hi R users:
I have the British Household Panel Survey (BHPS) in .tab format. I want to
feed it through the Amelia package (which will be an interesting job in
itself)..
But first I need to convert the various types of missing value (from about
-9 to -1) to a more generic NA code.
Ive written the following function to do this:
BHPS.converter - function(from=D:/Data/BHPS/UKDA-5151-tab/tab/,
to=D:/BHPS/NA/, ext=tab ) {
from.files - dir(from, pattern=paste(.,ext,$,sep=) )
existing.to.files - dir(to,
pattern=paste(.,ext,$,sep=) )
still.to.do.index - 1:length(from.files)
still.to.do.index -
still.to.do.index[-match(existing.to.files, from.files)]
obs.to.do - length(still.to.do.index)
for (i in 1:obs.to.do){
temp.table -
read.delim(paste(from,from.files[still.to.do.index[i]], sep=))
print(paste(read:,
from.files[still.to.do.index[i]]))
temp.table[temp.table 0 ] - NA
write.table(temp.table,
file=paste(to,from.files[still.to.do.index[i]], sep=))
print(paste(written:,
from.files[still.to.do.index[i]]))
}
rm(i, from.files, existing.to.files, still.to.do.index,
obs.to.do, temp.table)
}
It checks for existing files in the to directory (where files which have
been modified with R- - NA) because when I tried to do this conversion
operation previously it got about ½ way through then crashed.
The problem is that it crashes *this time* too, without displaying a prompt
to say its read a single file.
The file it gets stuck on is about 75mb in size.
I am using a dual-core 3.2Ghz Pentium D processor with 2 Gb memory ( 2Gb
virtual memory), and (unfortunately) Windows XP.
Questions:
1) Any general tips on how to increase the amount of memory available to
process the file?
2) Can you see a more efficient way of doing what Im doing?
3) Whats the best way of coding for multiple forms of NA? the BHPS code
-8 (meaning inapplicable, not routed for this respondent) should really
be distinguished from other forms of nonresponse...
Thanks,
Jon
p.s. Apologies if this is slightly too vague/long winded...
Jon Minton
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] generic pasting of strings
try something like: apply(tmp1[, ncol(tmp1):1], 1, paste, sep = ) I hope it helps. Best, Dimitris Dimitris Rizopoulos Ph.D. Student Biostatistical Centre School of Public Health Catholic University of Leuven Address: Kapucijnenvoer 35, Leuven, Belgium Tel: +32/(0)16/336899 Fax: +32/(0)16/337015 Web: http://med.kuleuven.be/biostat/ http://www.student.kuleuven.be/~m0390867/dimitris.htm - Original Message - From: Robert Lischke [EMAIL PROTECTED] To: r-help@stat.math.ethz.ch Sent: Tuesday, October 31, 2006 12:36 PM Subject: [R] generic pasting of strings Hi there, is there a way to make the following code generic, so that i can paste() the columns in tmp1 depending on the dimensions given in embed()? tmp1 - embed(as.vector(shrinkTable$AOIname), dimension = 2); tmp1 [,1] [,2] [1,] AOI4 AOI1 [2,] AOI6 AOI4 [3,] AOI4 AOI6 tmp2 - paste(tmp1[, 2], tmp1[, 1], sep = ); tmp2 [1] AOI1AOI4 AOI4AOI6 AOI6AOI4 for dimension = 3 this would look like this: tmp1 - embed(as.vector(shrinkTable$AOIname), dimension = 3); tmp1 [,1] [,2] [,3] [1,] AOI6 AOI4 AOI1 [2,] AOI4 AOI6 AOI4 tmp2 - paste(tmp1[ ,3], tmp1[, 2], tmp1[, 1], sep = ); tmp2 [1] AOI1AOI4AOI6 AOI4AOI6AOI4 Any ideas? Thanks for your help, Robert Lischke __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R crashing during batch file formatting
On 10/31/2006 6:43 AM, Jon Minton wrote: It checks for existing files in the ‘to’ directory (where files which have been modified with R- - NA) because when I tried to do this conversion operation previously it got about ½ way through then crashed. The problem is that it crashes *this time* too, without displaying a prompt to say it’s read a single file. When you say crash, do you mean it displays an R error (like unable to allocate vector of length ) or a real crash with a Windows popup? Which version are you using? There were some fixes to the memory management after the 2.3.1 release, but I haven't heard of any problems in 2.4.0 before this. Duncan Murdoch __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R crashing during batch file formatting
Hi
you shall probably provide more information (OS, R version).
I cannot help you much with crash but here is some opinion.
I would try to do conversion interactively before I transferred it to
a function.
However, if you want different types of NA and your data is numeric,
you probably could make a distinction by using -Inf, Inf, NaN and NA,
but then you need to be careful when doing analysis, as these values
can be treated differently.
HTH
Petr
On 31 Oct 2006 at 11:43, Jon Minton wrote:
From: Jon Minton [EMAIL PROTECTED]
To: r-help@stat.math.ethz.ch
Date sent: Tue, 31 Oct 2006 11:43:22 -
Subject:[R] R crashing during batch file formatting
Hi R users:
I have the British Household Panel Survey (BHPS) in .tab format. I
want to feed it through the Amelia package (which will be an
interesting job in itself)..
But first I need to convert the various types of missing value (from
about -9 to -1) to a more generic NA code.
Ive written the following function to do this:
BHPS.converter - function(from=D:/Data/BHPS/UKDA-5151-tab/tab/,
to=D:/BHPS/NA/, ext=tab ) {
from.files - dir(from,
pattern=paste(.,ext,$,sep=) )
existing.to.files - dir(to,
pattern=paste(.,ext,$,sep=) )
still.to.do.index - 1:length(from.files)
still.to.do.index -
still.to.do.index[-match(existing.to.files, from.files)]
obs.to.do - length(still.to.do.index)
for (i in 1:obs.to.do){
temp.table -
read.delim(paste(from,from.files[still.to.do.index[i]], sep=))
print(paste(read:,
from.files[still.to.do.index[i]]))
temp.table[temp.table 0 ] - NA
write.table(temp.table,
file=paste(to,from.files[still.to.do.index[i]], sep=))
print(paste(written:,
from.files[still.to.do.index[i]]))
}
rm(i, from.files, existing.to.files,
still.to.do.index,
obs.to.do, temp.table)
}
It checks for existing files in the to directory (where files which
have been modified with R- - NA) because when I tried to do this
conversion operation previously it got about ˝ way through then
crashed.
The problem is that it crashes *this time* too, without displaying a
prompt to say its read a single file.
The file it gets stuck on is about 75mb in size.
I am using a dual-core 3.2Ghz Pentium D processor with 2 Gb memory (
2Gb virtual memory), and (unfortunately) Windows XP.
Questions:
1) Any general tips on how to increase the amount of memory available
to
process the file?
2) Can you see a more efficient way of doing what Im doing?
3) Whats the best way of coding for multiple forms of NA? the BHPS
code -8 (meaning inapplicable, not routed for this respondent)
should really be distinguished from other forms of nonresponse...
Thanks,
Jon
p.s. Apologies if this is slightly too vague/long winded...
Jon Minton
[[alternative HTML version deleted]]
Petr Pikal
[EMAIL PROTECTED]
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Re: [R] R crashing during batch file formatting
Hi - i mean a 'real crash' (out of the R application) rather than an error. I'm using 2.3.1: is it worth upgrading? Jon -Original Message- From: Duncan Murdoch [mailto:[EMAIL PROTECTED] Sent: 31 October 2006 12:05 To: Jon Minton Cc: r-help@stat.math.ethz.ch Subject: Re: [R] R crashing during batch file formatting On 10/31/2006 6:43 AM, Jon Minton wrote: It checks for existing files in the to directory (where files which have been modified with R- - NA) because when I tried to do this conversion operation previously it got about ½ way through then crashed. The problem is that it crashes *this time* too, without displaying a prompt to say its read a single file. When you say crash, do you mean it displays an R error (like unable to allocate vector of length ) or a real crash with a Windows popup? Which version are you using? There were some fixes to the memory management after the 2.3.1 release, but I haven't heard of any problems in 2.4.0 before this. Duncan Murdoch __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R crashing during batch file formatting
Thanks,
Windows XP Media Centre Edition (!) Version 2002 Service Pack 2
R version 2.3.1 (already heard that 2.4.0 has better memory handling?)
I think I'll use NaN for 'not applicable' and NA for 'missing': does anyone
know how Amelia handles and distinguishes between these two (only the
latter, of course, need imputing), and so if this can be done without
further formatting?
Jon
-Original Message-
From: Petr Pikal [mailto:[EMAIL PROTECTED]
Sent: 31 October 2006 12:15
To: Jon Minton; r-help@stat.math.ethz.ch
Subject: Re: [R] R crashing during batch file formatting
Hi
you shall probably provide more information (OS, R version).
I cannot help you much with crash but here is some opinion.
I would try to do conversion interactively before I transferred it to
a function.
However, if you want different types of NA and your data is numeric,
you probably could make a distinction by using -Inf, Inf, NaN and NA,
but then you need to be careful when doing analysis, as these values
can be treated differently.
HTH
Petr
On 31 Oct 2006 at 11:43, Jon Minton wrote:
From: Jon Minton [EMAIL PROTECTED]
To: r-help@stat.math.ethz.ch
Date sent: Tue, 31 Oct 2006 11:43:22 -
Subject:[R] R crashing during batch file formatting
Hi R users:
I have the British Household Panel Survey (BHPS) in .tab format. I
want to feed it through the Amelia package (which will be an
'interesting' job in itself)..
But first I need to convert the various types of missing value (from
about -9 to -1) to a more generic 'NA' code.
I've written the following function to do this:
BHPS.converter - function(from=D:/Data/BHPS/UKDA-5151-tab/tab/,
to=D:/BHPS/NA/, ext=tab ) {
from.files - dir(from,
pattern=paste(.,ext,$,sep=) )
existing.to.files - dir(to,
pattern=paste(.,ext,$,sep=) )
still.to.do.index - 1:length(from.files)
still.to.do.index -
still.to.do.index[-match(existing.to.files, from.files)]
obs.to.do - length(still.to.do.index)
for (i in 1:obs.to.do){
temp.table -
read.delim(paste(from,from.files[still.to.do.index[i]], sep=))
print(paste(read:,
from.files[still.to.do.index[i]]))
temp.table[temp.table 0 ] - NA
write.table(temp.table,
file=paste(to,from.files[still.to.do.index[i]], sep=))
print(paste(written:,
from.files[still.to.do.index[i]]))
}
rm(i, from.files, existing.to.files,
still.to.do.index,
obs.to.do, temp.table)
}
It checks for existing files in the 'to' directory (where files which
have been modified with R- - NA) because when I tried to do this
conversion operation previously it got about ˝ way through then
crashed.
The problem is that it crashes *this time* too, without displaying a
prompt to say it's read a single file.
The file it gets stuck on is about 75mb in size.
I am using a dual-core 3.2Ghz Pentium D processor with 2 Gb memory (
2Gb virtual memory), and (unfortunately) Windows XP.
Questions:
1) Any general tips on how to increase the amount of memory available
to
process the file?
2) Can you see a more efficient way of doing what I'm doing?
3) What's the best way of coding for multiple forms of NA? - the BHPS
code '-8' (meaning 'inapplicable', not routed for this respondent)
should really be distinguished from other forms of nonresponse...
Thanks,
Jon
p.s. Apologies if this is slightly too vague/long winded...
Jon Minton
[[alternative HTML version deleted]]
Petr Pikal
[EMAIL PROTECTED]
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] [ggplot] controlling axis and major/minor tick marks
Hi Sebastian, axis.colour should control the colour of the tickmarks, the axis labels, and the line which the ticks attach to. What is not working in your case? grid.colour only effects the grid lines inside the plot. Currently, ggplot has no notion of major and minor tick marks (mainly because I don't have a good algorithim to generate them), but it is on my to do list. Regards, Hadley On 10/31/06, Sebastian Weber [EMAIL PROTECTED] wrote: Hello there! I'm starting with ggplot and was wondering how I could control the axis of a plot. I would like the axis of the plot to be drawn black which I thought to acheive with the option axis.colour=black. However, this had no real effect on the plot. Then I found grid.colour which I changed to black as well. Now I got my axis as I wanted them, but ggplot now draws the grid inside the plot with black lines as well, which definetly do not want to appear. So how can I get a black border around my plots? Furthermore, I would like to indicate positions of major and minor ticks in my plots. Where can I do this? Thanks in advance. Greetings, Sebastian Ah, I use R 2.3.1 and ggplot 0.4.0, if that is important ... __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Compiling R packages on Ubuntu
I am unable to compile R packages from source on Ubuntu dapper/edgy. Does anybody have an experience? When I do install.packages(nlme,depend=TRUE), I get following error messages. Can someone help? I get similar messages for any package I try to compile. VR - * Installing *source* package 'nlme' ... ** libs gcc -I/usr/share/R/include -I/usr/share/R/include-fvisibility=hidden -fpic -g -O2 -std=gnu99 -c corStruct.c -o corStruct.o In file included from base.h:29, from matrix.h:27, from corStruct.c:27: /usr/share/R/include/S.h:37:20: error: stdlib.h: No such file or directory /usr/share/R/include/S.h:38:19: error: stdio.h: No such file or directory In file included from /usr/lib/gcc/i486-linux-gnu/4.1.2/include/syslimits.h:7, from /usr/lib/gcc/i486-linux-gnu/4.1.2/include/limits.h:11, from /usr/share/R/include/S.h:39, from base.h:29, from matrix.h:27, from corStruct.c:27: /usr/lib/gcc/i486-linux-gnu/4.1.2/include/limits.h:122:61: error: limits.h: No such file or directory In file included from base.h:29, from matrix.h:27, from corStruct.c:27: /usr/share/R/include/S.h:41:19: error: math.h: No such file or directory In file included from /usr/share/R/include/S.h:55, from base.h:29, from matrix.h:27, from corStruct.c:27: /usr/share/R/include/R_ext/RS.h:23:38: error: string.h: No such file or directory In file included from base.h:34, from matrix.h:27, from corStruct.c:27: /usr/share/R/include/Rinternals.h:36:19: error: errno.h: No such file or directory /usr/share/R/include/Rinternals.h:44:19: error: ctype.h: No such file or directory In file included from base.h:34, from matrix.h:27, from corStruct.c:27: /usr/share/R/include/Rinternals.h:767: error: expected declaration specifiers or $(B!F(B...$(B!G(B before $(B!F(BFILE$(B!G (B/usr/share/R/include/Rinternals.h:770: error: expected declaration specifiers or $(B!F(B...$(B!G(B before $(B!F(BFILE$(B!G (BIn file included from matrix.h:27, from corStruct.c:27: base.h:38:21: error: libintl.h: No such file or directory corStruct.c: In function $(B!F(BcorStruct_factList$(B!G(B: corStruct.c:58: warning: implicit declaration of function $(B!F(Blog$(B!G (BcorStruct.c:58: warning: incompatible implicit declaration of built-in function $(B!F(Blog$(B!G (BcorStruct.c:58: warning: implicit declaration of function $(B!F(Bfabs$(B!G (BcorStruct.c:58: warning: incompatible implicit declaration of built-in function $(B!F(Bfabs$(B!G (BcorStruct.c:60: warning: implicit declaration of function $(B!F(Bmemcpy$(B!G (BcorStruct.c:60: warning: incompatible implicit declaration of built-in function $(B!F(Bmemcpy$(B!G (BcorStruct.c: In function $(B!F(Bsymm_fullCorr$(B!G(B: corStruct.c:93: warning: implicit declaration of function $(B!F(Bexp$(B!G (BcorStruct.c:93: warning: incompatible implicit declaration of built-in function $(B!F(Bexp$(B!G (BcorStruct.c:95: warning: implicit declaration of function $(B!F(Bcos$(B!G (BcorStruct.c:95: warning: incompatible implicit declaration of built-in function $(B!F(Bcos$(B!G (BcorStruct.c:96: warning: implicit declaration of function $(B!F(Bsin$(B!G (BcorStruct.c:96: warning: incompatible implicit declaration of built-in function $(B!F(Bsin$(B!G (BcorStruct.c: In function $(B!F(Bsymm_fact$(B!G(B: corStruct.c:166: warning: incompatible implicit declaration of built-in function $(B!F(Blog$(B!G (BcorStruct.c:166: warning: incompatible implicit declaration of built-in function $(B!F(Bfabs$(B!G (BcorStruct.c:168: warning: incompatible implicit declaration of built-in function $(B!F(Bmemcpy$(B!G (BcorStruct.c: In function $(B!F(Bnat_fullCorr$(B!G(B: corStruct.c:216: warning: incompatible implicit declaration of built-in function $(B!F(Bexp$(B!G (BcorStruct.c: In function $(B!F(BAR1_mat$(B!G(B: corStruct.c:281: warning: implicit declaration of function $(B!F(Bpow$(B!G (BcorStruct.c:281: warning: incompatible implicit declaration of built-in function $(B!F(Bpow$(B!G (BcorStruct.c: In function $(B!F(Bsafe_phi$(B!G(B: corStruct.c:292: warning: incompatible implicit declaration of built-in function $(B!F(Bexp$(B!G (BcorStruct.c:295: warning: incompatible implicit declaration of built-in function $(B!F(Bexp$(B!G (BcorStruct.c: In function $(B!F(BAR1_fact$(B!G(B: corStruct.c:316: warning: implicit declaration of function $(B!F(Bsqrt$(B!G (BcorStruct.c:316: warning: incompatible implicit declaration of built-in function $(B!F(Bsqrt$(B!G (BcorStruct.c:318: warning: incompatible implicit declaration of built-in function $(B!F(Blog$(B!G (BcorStruct.c: In function $(B!F(BCAR1_mat$(B!G(B: corStruct.c:369:
Re: [R] plotting multiple groups (newbie Q)
Now I want to do some plotting: plot(kSum$F2[group==N],kSum$DP_Level.mean[group==N],type=l) # This works fine plot(kSum$F2[group==SN],kSum$DP_Level.mean[group==SN],type=l) # This plots both N and SN in one line sequentially plot(kSum$F2[group==Y],kSum$DP_Level.mean[group==Y],type=l) # This gives the following error messages. What is group? I suspect it is not the kSum$group that you think it is. Hadley __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R crashing during batch file formatting
On 10/31/2006 7:29 AM, Jon Minton wrote: Hi - i mean a 'real crash' (out of the R application) rather than an error. I'm using 2.3.1: is it worth upgrading? Yes, though it might just convert that crash into an R error. Duncan Murdoch Jon -Original Message- From: Duncan Murdoch [mailto:[EMAIL PROTECTED] Sent: 31 October 2006 12:05 To: Jon Minton Cc: r-help@stat.math.ethz.ch Subject: Re: [R] R crashing during batch file formatting On 10/31/2006 6:43 AM, Jon Minton wrote: It checks for existing files in the ‘to’ directory (where files which have been modified with R- - NA) because when I tried to do this conversion operation previously it got about ½ way through then crashed. The problem is that it crashes *this time* too, without displaying a prompt to say it’s read a single file. When you say crash, do you mean it displays an R error (like unable to allocate vector of length ) or a real crash with a Windows popup? Which version are you using? There were some fixes to the memory management after the 2.3.1 release, but I haven't heard of any problems in 2.4.0 before this. Duncan Murdoch __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] write to clipboard under Linux
On Sun, 29 Oct 2006, Johannes Hüsing wrote: Dear all, I am trying to use the clipboard when writing a table. Typing: write.table(object, file=clipboard) leads to the message: Fehler in file(file, ifelse(append, a, w)) : 'mode' für die Zwischenablage muss unter Unix 'r' sein My interpretation is that I am not allowed to write into the clipboard from a program called from R. Is there a way to change this behaviour? Linux does not have a clipboard but an X11 session has primary and secondary selections. ?file says Clipboard: 'file' can also be used with 'description = clipboard' in mode 'r' only. It reads the X11 primary selection, which can also be specified as 'X11_primary' and the secondary selection as 'X11_secondary'. When the clipboard is opened for reading, the contents are immediately copied to internal storage in the connection. Unix users wishing to _write_ to the primary selection may be able to do so via 'xclip' (URL: http://people.debian.org/~kims/xclip/), for example by 'pipe(xclip -i, w)'. so RTFM applied. Writing to an X11 selection needs multiple threads and I did not think it worth the very considerable effort of implementing (unlike for Windows). Note that window managers may have other clipboards, and for example the RGtk2 package has interfaces to gtk clipboards. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595__ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] one problem about how to hold graphic with R
Sorry to disturb you, but can you help me to solve one little problem? I want to draw a graphic after another with R but I cannot find the first one after that. Do you know the command to hold the graphic with R? I remember with Matlab you may use hold on. Thanks. -- Baohua Yang Email:[EMAIL PROTECTED] [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Odd behaviour of removing 'nothing' from an array or data frame
I've just found some behaviour which strikes me as odd, but I'm not sure
whether it's a bug or a feature. If you don't mind, I'd like to explain
via a couple of examples.
Let x = 1:10.
Then intuitively, to me at least, the command x[-integer(0)] should leave
x untouched. However the actual output under R2.4.0 is integer(0).
A slightly more involved example demonstrates why I think this behaviour
is back to front.
First we define a data frame, in this case some people, with their
heights.
peoples.heights = data.frame(names = c(Alice, Bob, Carol), heights =
c(1.67, 1.85, 175))
To make sure the heights are sensible, we define a filter out impossibly
tall people.
dubious.records = which(peoples.heights$heights 2.5) #3
peoples.heights = peoples.heights[-dubious.records,]
This all works fine since dubious.records is not empty. However, if all
the records had been entered properly, then we would get
#dubious.records = integer(0)
Then the command peoples.heights = peoples.heights[-dubious.records,]
strips all the rows to give
#[1] names heights
#0 rows (or 0-length row.names)
i.e. instead of removing the bad records, I've lost everything.
I know that it's possible to recode this so problems don't occur, but the
point is that the answer is unexpected.
Can anybody explain if this behaviour is intentional or useful in some
way, or is it an oversight?
Regards,
Richie.
Mathematical Sciences Unit
HSL
Buxton
SK17 9JN
01298 21(x8672)
ATTENTION:
This message contains privileged and confidential informatio...{{dropped}}
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Re: [R] Odd behaviour of removing 'nothing' from an array or data frame
Thanks for the reply Peter, though I'm not quite convinced.
#dubious.records = integer(0)
identical(dubious.records, -dubious.records)
[1] TRUE
how can peoples.heights[-dubious.records,] be different from
peoples.heights[dubious.records,]?
Tell me if I'm being willfully ignorant here, but I'm sure they should be
different. In the first case, the minus sign represents subtraction, so
it is correct that dubious.records and -dubious.records are identical.
However, in the second case, inside the square brackets, the minus sign
represents set complement, not subtraction, so dubious.records and -
dubious.records are not the same.
If x = runif(10), then x[-c(2,3,5)] means remove from x the values at the
second, third and fifth position.
By extension x[-integer(0)] should mean remove from x no values, and not
remove from x all values, which is the current behaviour.
Regards,
Richie.
Mathematical Sciences Unit
HSL
Buxton
SK17 9JN
01298 21(x8672)
[EMAIL PROTECTED] wrote on 31/10/2006 14:27:05:
[EMAIL PROTECTED] writes:
I've just found some behaviour which strikes me as odd, but I'm not
sure
whether it's a bug or a feature. If you don't mind, I'd like to
explain
via a couple of examples.
Let x = 1:10.
Then intuitively, to me at least, the command x[-integer(0)] should
leave
x untouched. However the actual output under R2.4.0 is integer(0).
A slightly more involved example demonstrates why I think this
behaviour
is back to front.
First we define a data frame, in this case some people, with their
heights.
peoples.heights = data.frame(names = c(Alice, Bob, Carol),
heights =
c(1.67, 1.85, 175))
To make sure the heights are sensible, we define a filter out
impossibly
tall people.
dubious.records = which(peoples.heights$heights 2.5) #3
peoples.heights = peoples.heights[-dubious.records,]
This all works fine since dubious.records is not empty. However, if
all
the records had been entered properly, then we would get
#dubious.records = integer(0)
Then the command peoples.heights = peoples.heights[-dubious.records,]
strips all the rows to give
#[1] names heights
#0 rows (or 0-length row.names)
i.e. instead of removing the bad records, I've lost everything.
I know that it's possible to recode this so problems don't occur, but
the
point is that the answer is unexpected.
Can anybody explain if this behaviour is intentional or useful in some
way, or is it an oversight?
Consistency! It's not particularly useful, but it follows from general
principles, which it in the long run doesn't pay to depart from.
The issue is that the result of using an indexing operator ([)
should depend only on the _value_ of its argument, not the expression
used to compute it. Just like you most likely expect log(2+2) not to be
different from log(4). And since
dubious.records - integer(0)
identical(dubious.records, -dubious.records)
[1] TRUE
how can peoples.heights[-dubious.records,] be different from
peoples.heights[dubious.records,]?
R could actually look at the expression and act on the minus sign, but
that way lies madness. Consider
keep - -dubious.records
drop - dubious.records
peoples.heights[keep,]
peoples.heights[-dubious.records,]
peoples.heights[-keep,]
etc... I think you'll get the picture.
--
O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B
c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K
(*) \(*) -- University of Copenhagen Denmark Ph: (+45)
35327918
~~ - ([EMAIL PROTECTED]) FAX: (+45)
35327907
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[R] getMethod(s) and var.test
Hi, How do I retrieve the var.test() function code? I had a similar problem once before with another function but getMethods() solved the problem then. Now I tried several combinations for var.test() without success. Regards benjamin -- Benjamin Otto Universitaetsklinikum Eppendorf Hamburg Institut fuer Klinische Chemie Martinistrasse 52 20246 Hamburg [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] getMethod(s) and var.test
On second thought, sometimes you need the .default (as in your case and for t.test) but not always...for aov you just need getAnywhere(aov) Not sure why... It seems the best choices to get package code are 1. body() 2. methods() 3. methods(packagename,default) 4. methods(packagename,mod) 5. getAnywhere(packagename) 6. getAnywhere(packagename.default) Jeff -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Benjamin Otto Sent: Tuesday, October 31, 2006 10:15 AM To: R-Help Subject: [R] getMethod(s) and var.test Hi, How do I retrieve the var.test() function code? I had a similar problem once before with another function but getMethods() solved the problem then. Now I tried several combinations for var.test() without success. Regards benjamin -- Benjamin Otto Universitaetsklinikum Eppendorf Hamburg Institut fuer Klinische Chemie Martinistrasse 52 20246 Hamburg [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] [ggplot] controlling axis and major/minor tick marks
Hi Sebastian, Then I plot my stuff with p2 - ggplot(knn, . ~ power , aes=list(y=log10(k2m/(degree*kSize)), x=log10(degree), shape=alpha)) p2 - ggpoint(p2) p2 and I do not see any axis at all. The tick marks are there, they are black as they should. I don't think I understand what you mean by axis - do you mean you want a line running along side the plot next to the tick marks? By the way, I already wondered why I can not change the shapes of the symbols in use. I figured that they are set statically in map_shapes. How about introducing an option for this somewhere? I mean to overhaul the options system to provide a lot more flexibility, but I have yet to get around to this unfortunately. I definetly need minor tick marks and will hack my way through ggplot to acheive this if it does not seem to difficult to me. May you give me a tip where to start / where should I have to modify things. I am planning on rewriting a lot of the scales system, but again, when I have time. It would be useful if you could provide a specification of what minor tickmarks are: how are they different from major tick marks? what do they look like? when do you want to see them? do you generate them using the same principle as major tick marks? Hadley __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] ANNOUNCEMENT: 20% Discount on the Latest R Books from Chapman Hall/CRC Press
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Re: [R] read.fwf and header
Archaic it may be, but I still have to deal with fixed format data files on a daily basis. David L. Reiner Rho Trading Securities, LLC Chicago IL 60605 312-362-4963 -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Martin Maechler Sent: Tuesday, October 31, 2006 1:52 AM To: [EMAIL PROTECTED] Cc: r-help@stat.math.ethz.ch Subject: Re: [R] read.fwf and header snip In my (and probably R-core's) view, read.fwf() should only have to be used for ``legacy data files'' (those times when people used *no* separators in order to save disk space), since nowadays, such data files should automatically have correct separators. -- Fix the file producing process rather than make read.fwf() unnecessarily more complicated. Martin Maechler, ETH Zurich __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Convert Lift Tables to Gain Tables
Hello All, I wonder is there any existing R routine to convert a lift table (say from the object of class performance) into a gain table through a profit / loss missclassification matrix. Thanks! marco __ [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] 2.4.0 and lattice 0.14-9: Changed behaviour of scales-argumenttck
On 10/31/06, Gerrit Eichner [EMAIL PROTECTED] wrote: Dear list, I have observed a change in the behaviour of the scales-argument tck of xyplot() after having installed R 2.4.0 (for version info see below). The help page of xyplot() says about the scales-argument tck: 'tck' numeric to control length of tick marks. Can be a vector of length 2, to control left/bottom and right/top separately. But if I issue xyplot( y ~ x, scales= list( tck= c( 1, 0))) (with suitable numeric vectors x and y, of course) the plot shows alternating tick mark lengths *on every side* of the plot (i.e., the length of every second tick mark is zero). I wanted to see tick marks only on the left and bottom side of the coordinate system (as I did see before with R 2.2.0 and lattice version 0.12-9). It's a bug that I had a fix for but forgot to include in the last update. A new version of lattice should be available in a day or two. Has anybody a workaround to get back the original (documented) behaviour? Since you are on linux, you could simply check out the svn version from https://svn.r-project.org/R-packages/trunk/lattice and compile it. -Deepayan Thanks a lot! Best regards -- Gerrit PS: My system: version _ platform x86_64-unknown-linux-gnu arch x86_64 os linux-gnu system x86_64, linux-gnu status major 2 minor 4.0 year 2006 month 10 day03 svn rev39566 language R version.string R version 2.4.0 (2006-10-03) __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Confidence interval calculation in prop.test
On 10/30/06, Richard Johnston [EMAIL PROTECTED] wrote: The confidence interval calculation in prop.test appears to be incorrect when alternative=greater. The upper limit is always set to 1.000. Am I missing something? Like the t.test function the prop.test function returns a one-sided interval when the alternative is greater or less. The output indicates that the 95% lower confidence bound on the proportion is 0.0369. If you choose alternative = less you will get a 95% upper confidence bound (and the lower bound will always be given as 0). Only when you use the default value, two-sided, for the alternative parameter will you get both the upper and lower bounds calculated. total=c(250,250) success=c(55,31) prop.test(success,total,alternative=greater,correct=TRUE) 2-sample test for equality of proportions with continuity correction data: success out of total X-squared = 7.4289, df = 1, p-value = 0.003209 alternative hypothesis: greater 95 percent confidence interval: 0.03693065 1. sample estimates: prop 1 prop 2 0.220 0.124 [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] getMethod(s) and var.test
I have found that you need this to see the stats package code getAnywhere(var.test.default) Jeff -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Benjamin Otto Sent: Tuesday, October 31, 2006 10:15 AM To: R-Help Subject: [R] getMethod(s) and var.test Hi, How do I retrieve the var.test() function code? I had a similar problem once before with another function but getMethods() solved the problem then. Now I tried several combinations for var.test() without success. Regards benjamin -- Benjamin Otto Universitaetsklinikum Eppendorf Hamburg Institut fuer Klinische Chemie Martinistrasse 52 20246 Hamburg [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Odd behaviour of removing 'nothing' from an array or data frame
[EMAIL PROTECTED] writes: Thanks for the reply Peter, though I'm not quite convinced. #dubious.records = integer(0) identical(dubious.records, -dubious.records) [1] TRUE how can peoples.heights[-dubious.records,] be different from peoples.heights[dubious.records,]? Tell me if I'm being willfully ignorant here, but I'm sure they should be different. In the first case, the minus sign represents subtraction, so it is correct that dubious.records and -dubious.records are identical. However, in the second case, inside the square brackets, the minus sign represents set complement, not subtraction, so dubious.records and - dubious.records are not the same. Nono, that is the point: Minus is minus, no matter where it occurs. Changing what it means depending on context leads to inconsistent behaviour. E.g., you shouldn't get different behaviour from assigning an index expression to an intermediate variable, as in peoples.heights[-dubious.records,] keep - -dubious.records peoples.heights[keep,] However, that would happen if the minus was interpreted differently within []: There is no way for R to realize that the sign change in the assignment has anything to do with indexing (OK, there is, but then the value of keep later on would depend on what it had been used for! Things quickly get really nasty). -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] generic pasting of strings
On 10/31/06, Robert Lischke [EMAIL PROTECTED] wrote: Hi there, is there a way to make the following code generic, so that i can paste() the columns in tmp1 depending on the dimensions given in embed()? tmp1 - embed(as.vector(shrinkTable$AOIname), dimension = 2); tmp1 [,1] [,2] [1,] AOI4 AOI1 [2,] AOI6 AOI4 [3,] AOI4 AOI6 tmp2 - paste(tmp1[, 2], tmp1[, 1], sep = ); tmp2 [1] AOI1AOI4 AOI4AOI6 AOI6AOI4 for dimension = 3 this would look like this: tmp1 - embed(as.vector(shrinkTable$AOIname), dimension = 3); tmp1 [,1] [,2] [,3] [1,] AOI6 AOI4 AOI1 [2,] AOI4 AOI6 AOI4 tmp2 - paste(tmp1[ ,3], tmp1[, 2], tmp1[, 1], sep = ); tmp2 [1] AOI1AOI4AOI6 AOI4AOI6AOI4 Try do.call like this: do.call(paste, c(as.data.frame(tmp1), sep = )) __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] plotting question
i have the following code below and at the end there are some plotting statements. it actualy looks quite nice when you run it but there is just one strange thing happening that don't know how to fix. the three things being plotted are aggfxdata[,logbidask] which has its own set of times ( it's a zoo object ). rollmeanlogbidask which has a subset of the times that aggfxdata has. basically it starts later than aggfxdata[,logbidask] and when the plot is done, it works in the sense that rollmeanlogbidask gets plotted later. then, i plot the variable lt on the same plot witrh it's vertical axis on the right side and this works nicely also. the only that doesn't quite work is that lt, time wise, lt, starting at the same time as the aggfxdata[,logbidask] when it should be starting a few minutes after rollmeanlogbidask. the times in it are correct and i don't think it has to do with the fact that things are zoo ( but i could be wrong ? ). i must be doing something wrong in my commands. the weird thing is that rollmeanlogbidask starts at the appropriate place ? maybe i have to give lt a different frequency but when i do the dput , i don'ts ee freequency as part of it ? this probably sounds way more confusing than it actually is but, if you run below, you will see exactly what io mean. thanks a lot to anyone who can be bothered pasitng below. as usual, you would need zoo and chron. aggfxdata-structure(c(114.834516129032, 114.7922, 114.820808080808, 114.838260869565, 114.837560975610, 114.776697247706, 114.7969, 114.745714285714, 114.734923076923, 114.661939393939, 114.646574074074, 114.703486238532, 114.646453900709, 114.651948051948, 114.742671755725, 114.721132075472, 114.828647058824, 114.885978260870, 114.936860465116, 114.94, 114.967763157895, 114.935107526882, 114.92225, 115.015606060606, 115.077261146497, 115.034248366013, 114.961923076923, 114.976463414634, 115.063468208092, 115.085882352941, 115.166847826087, 115.153306451613, 115.137719298246, 115.080735294118, 115.074090909091, 115.021134751773, 114.903450292398, 114.916153846154, 114.888306451613, 114.937469879518, 114.890943396226, 114.849747899160, 114.926912751678, 114.874567901235, 114.837980769231, 114.797538461538, 114.746707317073, 114.696013071895, 114.67645833, 114.852184466019, 114.848548387097, 114.8078, 114.835050505051, 114.851304347826, 114.852439024390, 114.792844036697, 114.8117, 114.759206349206, 114.748307692308, 114.675939393939, 114.661296296296, 114.717889908257, 114.660921985816, 114.665779220779, 114.756870229008, 114.735471698113, 114.841941176471, 114.899184782609, 114.949186046512, 114.953990384615, 114.982280701754, 114.948924731183, 114.9368, 115.028863636364, 115.091592356688, 115.0478, 114.975576923077, 114.990365853659, 115.078381502890, 115.099705882353, 115.180326086957, 115.166370967742, 115.151052631579, 115.095147058824, 115.088522727273, 115.035390070922, 114.917894736842, 114.930128205128, 114.903790322581, 114.952409638554, 114.906226415094, 114.863865546218, 114.940939597315, 114.890370370370, 114.852211538462, 114.812307692308, 114.760548780488, 114.710326797386, 114.69020833, 114.866213592233, 4.74355319771057, 4.74319148388547, 4.74343474081987, 4.74358150022944, 4.74358339314172, 4.74305881517423, 4.74322922997911, 4.74277728938584, 4.7426822736, 4.74204918880485, 4.7419183321792, 4.74241320264843, 4.74191617575789, 4.74196131670693, 4.74275385322944, 4.74256674074965, 4.74349887668465, 4.74399761812053, 4.74443655563793, 4.74447111073972, 4.74471490416156, 4.74442779363424, 4.74431911442163, 4.74512545618279, 4.74566600467616, 4.74528870019174, 4.74466035230505, 4.74478789738982, 4.74554867613244, 4.74573870836097, 4.74644044208183, 4.74632106516708, 4.74618687097407, 4.74569654200703, 4.74563889435559, 4.74517785826786, 4.74415506578588, 4.74426356601777, 4.74402779250609, 4.74445322900522, 4.74404986890124, 4.74368619357562, 4.7443574082389, 4.74390959824271, 4.74358423039023, 4.7432343669113, 4.74278746542368, 4.74234766049834, 4.74217470698038, 4.7437070219583), .Dim = c(50, 3), .Dimnames = list( NULL, c(bid, ask, logbidask)), index = structure(c(1152058200, 1152058800, 1152059400, 115206, 1152060600, 1152061200, 1152061800, 1152062400, 1152063000, 1152063600, 1152064200, 1152064800, 1152065400, 1152066000, 1152066600, 1152067200, 1152067800, 1152068400, 1152069000, 1152069600, 1152070200, 1152070800, 1152071400, 1152072000, 1152072600, 1152073200, 1152073800, 1152074400, 1152075000, 1152075600, 1152076200, 1152076800, 1152077400, 1152078000, 1152078600, 1152079200, 1152079800, 1152080400, 1152081000, 1152081600, 1152082200, 1152082800, 1152083400, 1152084000, 1152084600, 1152085200, 1152085800, 1152086400, 1152087000, 1152087600), class = c(POSIXt, POSIXct)), class = zoo) rollmeanlogbidask-structure(c(4.74371176689231, 4.74380800837135, 4.7439123277474, 4.74400406541921, 4.7440745668118,
Re: [R] plotting question
I think you will have to ensure that lt has the same set of times as the prior plot to do it that way. Since time(lt) is a subset of time(aggfxdata) it would be good enough to do this: par(new = TRUE) lt2 - merge(zoo(, time(aggfxdata)), lt) plot(lt2, type = l, lty = 2) On 10/31/06, Leeds, Mark (IED) [EMAIL PROTECTED] wrote: i have the following code below and at the end there are some plotting statements. it actualy looks quite nice when you run it but there is just one strange thing happening that don't know how to fix. the three things being plotted are aggfxdata[,logbidask] which has its own set of times ( it's a zoo object ). rollmeanlogbidask which has a subset of the times that aggfxdata has. basically it starts later than aggfxdata[,logbidask] and when the plot is done, it works in the sense that rollmeanlogbidask gets plotted later. then, i plot the variable lt on the same plot witrh it's vertical axis on the right side and this works nicely also. the only that doesn't quite work is that lt, time wise, lt, starting at the same time as the aggfxdata[,logbidask] when it should be starting a few minutes after rollmeanlogbidask. the times in it are correct and i don't think it has to do with the fact that things are zoo ( but i could be wrong ? ). i must be doing something wrong in my commands. the weird thing is that rollmeanlogbidask starts at the appropriate place ? maybe i have to give lt a different frequency but when i do the dput , i don'ts ee freequency as part of it ? this probably sounds way more confusing than it actually is but, if you run below, you will see exactly what io mean. thanks a lot to anyone who can be bothered pasitng below. as usual, you would need zoo and chron. aggfxdata-structure(c(114.834516129032, 114.7922, 114.820808080808, 114.838260869565, 114.837560975610, 114.776697247706, 114.7969, 114.745714285714, 114.734923076923, 114.661939393939, 114.646574074074, 114.703486238532, 114.646453900709, 114.651948051948, 114.742671755725, 114.721132075472, 114.828647058824, 114.885978260870, 114.936860465116, 114.94, 114.967763157895, 114.935107526882, 114.92225, 115.015606060606, 115.077261146497, 115.034248366013, 114.961923076923, 114.976463414634, 115.063468208092, 115.085882352941, 115.166847826087, 115.153306451613, 115.137719298246, 115.080735294118, 115.074090909091, 115.021134751773, 114.903450292398, 114.916153846154, 114.888306451613, 114.937469879518, 114.890943396226, 114.849747899160, 114.926912751678, 114.874567901235, 114.837980769231, 114.797538461538, 114.746707317073, 114.696013071895, 114.67645833, 114.852184466019, 114.848548387097, 114.8078, 114.835050505051, 114.851304347826, 114.852439024390, 114.792844036697, 114.8117, 114.759206349206, 114.748307692308, 114.675939393939, 114.661296296296, 114.717889908257, 114.660921985816, 114.665779220779, 114.756870229008, 114.735471698113, 114.841941176471, 114.899184782609, 114.949186046512, 114.953990384615, 114.982280701754, 114.948924731183, 114.9368, 115.028863636364, 115.091592356688, 115.0478, 114.975576923077, 114.990365853659, 115.078381502890, 115.099705882353, 115.180326086957, 115.166370967742, 115.151052631579, 115.095147058824, 115.088522727273, 115.035390070922, 114.917894736842, 114.930128205128, 114.903790322581, 114.952409638554, 114.906226415094, 114.863865546218, 114.940939597315, 114.890370370370, 114.852211538462, 114.812307692308, 114.760548780488, 114.710326797386, 114.69020833, 114.866213592233, 4.74355319771057, 4.74319148388547, 4.74343474081987, 4.74358150022944, 4.74358339314172, 4.74305881517423, 4.74322922997911, 4.74277728938584, 4.7426822736, 4.74204918880485, 4.7419183321792, 4.74241320264843, 4.74191617575789, 4.74196131670693, 4.74275385322944, 4.74256674074965, 4.74349887668465, 4.74399761812053, 4.74443655563793, 4.74447111073972, 4.74471490416156, 4.74442779363424, 4.74431911442163, 4.74512545618279, 4.74566600467616, 4.74528870019174, 4.74466035230505, 4.74478789738982, 4.74554867613244, 4.74573870836097, 4.74644044208183, 4.74632106516708, 4.74618687097407, 4.74569654200703, 4.74563889435559, 4.74517785826786, 4.74415506578588, 4.74426356601777, 4.74402779250609, 4.74445322900522, 4.74404986890124, 4.74368619357562, 4.7443574082389, 4.74390959824271, 4.74358423039023, 4.7432343669113, 4.74278746542368, 4.74234766049834, 4.74217470698038, 4.7437070219583), .Dim = c(50, 3), .Dimnames = list( NULL, c(bid, ask, logbidask)), index = structure(c(1152058200, 1152058800, 1152059400, 115206, 1152060600, 1152061200, 1152061800, 1152062400, 1152063000, 1152063600, 1152064200, 1152064800, 1152065400, 1152066000, 1152066600, 1152067200, 1152067800, 1152068400, 1152069000, 1152069600, 1152070200, 1152070800, 1152071400, 1152072000, 1152072600, 1152073200, 1152073800, 1152074400, 1152075000, 1152075600, 1152076200, 1152076800, 1152077400, 1152078000, 1152078600,
Re: [R] Missing data analysis in R
there is a green book by joe shafer ( I forget the name but it's
probsably on amazon ). I also
Can't say it's in the same format as faraday's book but I think it's
fairly popular for multiple
Imputation techniques etc.
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Inman, Brant A.
M.D.
Sent: Tuesday, October 31, 2006 12:18 PM
To: r-help@stat.math.ethz.ch
Subject: [R] Missing data analysis in R
I am looking for a book that discusses the theory of multiple imputation
(and other methods of dealing with missing data) and, just as
importantly, how to implement these methods in R or S-Plus. Ideally,
the book would have a structure similar to Faraway (Regression),
PinheiroBates (Mixed Effects) and Wood (GAMs) and would be very modern
(i.e. published within the last couple of years).
Any ideas? If such a book does not exist, one of the experts on this
help list should write it! (I will gladly buy the first copy.)
Brant Inman
Mayo Clinic
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This is not an offer (or solicitation of an offer) to buy/se...{{dropped}}
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Re: [R] Missing data analysis in R
Have a look at J.L Schafer: ANALYSIS OF INCOMPLETE MULTIVARIATE DATA (1997). R already has several packages that deal with missing data imputation, I believe. Search around (please excuse my laziness). Don't know if you can get exactly what you want (an R/S -centric text), though. Bert Gunter Nonclinical Statistics 7-7374 -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Inman, Brant A. M.D. Sent: Tuesday, October 31, 2006 9:18 AM To: r-help@stat.math.ethz.ch Subject: [R] Missing data analysis in R I am looking for a book that discusses the theory of multiple imputation (and other methods of dealing with missing data) and, just as importantly, how to implement these methods in R or S-Plus. Ideally, the book would have a structure similar to Faraway (Regression), PinheiroBates (Mixed Effects) and Wood (GAMs) and would be very modern (i.e. published within the last couple of years). Any ideas? If such a book does not exist, one of the experts on this help list should write it! (I will gladly buy the first copy.) Brant Inman Mayo Clinic [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Hmisc or Lattice plot with error bars, Depth (independent variable) on Y axis
I just discovered that using the xYplot (Hmisc) and rotating the grid
viewport (and the labels etc) given me exactly what I need. I wish I had
thought of that much sooner
-Original Message-
From: Deepayan Sarkar [mailto:[EMAIL PROTECTED]
Sent: Monday, October 30, 2006 6:04 PM
To: Mike Bock
Cc: r-help@stat.math.ethz.ch
Subject: Re: [R] Hmisc or Lattice plot with error bars, Depth
(independent variable) on Y axis
On 10/30/06, Mike Bock [EMAIL PROTECTED] wrote:
I am trying to create some plots of concentration versus depth. I
want Depth on the Y axis and the concentrations on the X axis. I also
need to plot error bars.
The xYplot function in Hmisc is very nearly ideal but I have to put
depth on the x-axis to get it to work. When I transpose the X and Y
axes in the xYplot command, the error bars disappear (no surprise given
the help file). It there a way to get the plot command to flip the
axes? That would be ideal as I could use the grouping functions in
xYplot and save a bunch of work.
If no such command exists any other ideas?
See
demo(intervals)
The untruncated code can be seen with
file.show(system.file(demo/intervals.R, package = lattice))
There was a recent thread dealing with extensions (grouping and
switching axes):
[1] https://stat.ethz.ch/pipermail/r-help/2006-October/114883.html
-Deepayan
This message contains information that may be confidential, ...{{dropped}}
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Re: [R] getMethod(s) and var.test
you may try something like this: body.fun - lapply(methods(var.test), get, envir = environment(var.test), mode = function) names(body.fun) - methods(var.test) body.fun I hope it helps. Best, Dimitris Dimitris Rizopoulos Ph.D. Student Biostatistical Centre School of Public Health Catholic University of Leuven Address: Kapucijnenvoer 35, Leuven, Belgium Tel: +32/(0)16/336899 Fax: +32/(0)16/337015 Web: http://med.kuleuven.be/biostat/ http://www.student.kuleuven.be/~m0390867/dimitris.htm - Original Message - From: Benjamin Otto [EMAIL PROTECTED] To: R-Help r-help@stat.math.ethz.ch Sent: Tuesday, October 31, 2006 4:15 PM Subject: [R] getMethod(s) and var.test Hi, How do I retrieve the var.test() function code? I had a similar problem once before with another function but getMethods() solved the problem then. Now I tried several combinations for var.test() without success. Regards benjamin -- Benjamin Otto Universitaetsklinikum Eppendorf Hamburg Institut fuer Klinische Chemie Martinistrasse 52 20246 Hamburg [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] information about sna packages
I don't think so, but you should email the package's author, Carter Butts for help on this package. His email is [EMAIL PROTECTED] On 31/10/06, Bagatti Davide [EMAIL PROTECTED] wrote: Hello, I'm a student who want to use the R social network analysis package. I have a question: can this package analyse dynamical networks (network changing over time)? I didn't find this functionality in the package's user manual. Thank you Davide [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- = David Barron Said Business School University of Oxford Park End Street Oxford OX1 1HP __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Put a normal curve on plot
I would like to be able to place a normal distribution surrounding the
predicted values at various places on a plot. Below is some toy code
that creates a scatterplot and plots a regression line through the data.
library(MASS)
mu - c(0,1)
Sigma - matrix(c(1,.8,.8,1), ncol=2)
set.seed(123)
x - mvrnorm(50,mu,Sigma)
plot(x)
abline(lm(x[,2] ~ x[,1]))
Say I want to add a normal distribution surrounding the predicted values
at the x-values of -1, 0, and 1. That is, at the points
\hat{y} = \mu + \beta_1(-1)
\hat{y} = \mu + \beta_1(0)
\hat{y} = \mu + \beta_1(1)
How might I go about doing this?
Harold
version
_
platform i386-pc-mingw32
arch i386
os mingw32
system i386, mingw32
status
major 2
minor 4.0
year 2006
month 10
day03
svn rev39566
language R
version.string R version 2.4.0 (2006-10-03)
[[alternative HTML version deleted]]
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Re: [R] read.fwf and header
I also have to deal with fixed format files from time to time. Generally I have no control over the format in those cases. On 10/31/06, [EMAIL PROTECTED] [EMAIL PROTECTED] wrote: Archaic it may be, but I still have to deal with fixed format data files on a daily basis. David L. Reiner Rho Trading Securities, LLC Chicago IL 60605 312-362-4963 -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Martin Maechler Sent: Tuesday, October 31, 2006 1:52 AM To: [EMAIL PROTECTED] Cc: r-help@stat.math.ethz.ch Subject: Re: [R] read.fwf and header snip In my (and probably R-core's) view, read.fwf() should only have to be used for ``legacy data files'' (those times when people used *no* separators in order to save disk space), since nowadays, such data files should automatically have correct separators. -- Fix the file producing process rather than make read.fwf() unnecessarily more complicated. Martin Maechler, ETH Zurich __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Odd behaviour of removing 'nothing' from an array or data frame
As Peter said, it's the value that counts, not the way you calculated it. If you print -c(2,3,5) you get three negative numbers. If you print -integer(0), you don't get any. The first case is asking for elements to be left out, the second isn't. The moral of the story is to use logical indices rather than negative ones: dubious.records - peoples.heights$heights 2.5 peoples.heights = peoples.heights[!dubious.records,] Unfortunately, there are some matching functions that return numeric indices, not logical vectors (eg. grep). For this case I created an unwhich function - but is there a better way to proceed? Hadley __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Compiling R packages on Ubuntu
On 31 October 2006 at 18:30, Vikas Rawal wrote: | I am unable to compile R packages from source on Ubuntu | dapper/edgy. Does anybody have an experience? Please note that CRAN actually pre-builds binaries of R 2.4.0 thanks to untiring efforts of Christian Steigies. This *is* mentioned in the R FAQ. | When I do install.packages(nlme,depend=TRUE), I get following error messages. Can someone help? | | I get similar messages for any package I try to compile. Yo do no seem to have a development environment installed. Please do $ sudo apt-get install r-base-dev and try again. Longer term, consider investing in one of the books discussing the GNU compiler toolchain as the compiler was fairly explicit in its eror message, and it pays off to listen to the compiler. r-base-dev is also mentioned in the R FAQ. Dirk -- Hell, there are no rules here - we're trying to accomplish something. -- Thomas A. Edison __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] one problem about how to hold graphic with R
Gavin Simpson gavin.simpson at ucl.ac.uk writes: On Tue, 2006-10-31 at 21:36 +0800, yang baohua wrote: Sorry to disturb you, but can you help me to solve one little problem? I want to draw a graphic after another with R but I cannot find the first one after that. Do you know the command to hold the graphic with R? I remember with Matlab you may use hold on. Thanks. [snip] Is this what you were looking for? HTH G Actually, it sounds more like what yang wants is par(new=TRUE) Ben Bolker __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Missing data analysis in R
I am looking for a book that discusses the theory of multiple imputation (and other methods of dealing with missing data) and, just as importantly, how to implement these methods in R or S-Plus. Ideally, the book would have a structure similar to Faraway (Regression), PinheiroBates (Mixed Effects) and Wood (GAMs) and would be very modern (i.e. published within the last couple of years). Any ideas? If such a book does not exist, one of the experts on this help list should write it! (I will gladly buy the first copy.) Brant Inman Mayo Clinic [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] graphics ignore tabs in text
Dear R-help,
I seem to recall that I can use \t to get tab in a string on a
graphics device, but it doesn't seem to work. Try:
lab - a\tb\tc
cat(lab, \n) # works in the console output
plot(1:5, main=lab) # no tabs in the title
text(3, 3, lab) # no tabs in the text
I get the same result both in the windows() and pdf() devices. Any
ideas?
This is R-patched Windows binary just downloaded from CRAN.
R version 2.4.0 Patched (2006-10-29 r39744)
Best,
Andy
Andy Liaw, PhD
Biometrics ResearchPO Box 2000 RY33-300
Merck Research LabsRahway, NJ 07065
andy_liaw(a)merck.com 732-594-0820
--
Notice: This e-mail message, together with any attachments,...{{dropped}}
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Re: [R] Put a normal curve on plot
Something like this?
library(MASS)
mu - c(0,1)
Sigma - matrix(c(1,.8,.8,1), ncol=2)
set.seed(123)
x - mvrnorm(50,mu,Sigma)
dta - data.frame(x=x[,1],y=x[,2])
plot(x)
fit - lm(y~x, data=dta)
sfit - summary(fit)
se - sfit$sigma
abline(fit)
yhat - predict(fit,data.frame(x=c(-1,0,1)),se.fit=TRUE)
x1 - seq(-2,0,length=50)
x2 - x1 + 1
x3 - x2 + 1
lines(x1,yhat$fit[1]+dnorm(x1,-1,se))
lines(x2,yhat$fit[2]+dnorm(x2,0,se))
lines(x3,yhat$fit[3]+dnorm(x3,1,se))
On 31/10/06, Doran, Harold [EMAIL PROTECTED] wrote:
I would like to be able to place a normal distribution surrounding the
predicted values at various places on a plot. Below is some toy code
that creates a scatterplot and plots a regression line through the data.
library(MASS)
mu - c(0,1)
Sigma - matrix(c(1,.8,.8,1), ncol=2)
set.seed(123)
x - mvrnorm(50,mu,Sigma)
plot(x)
abline(lm(x[,2] ~ x[,1]))
Say I want to add a normal distribution surrounding the predicted values
at the x-values of -1, 0, and 1. That is, at the points
\hat{y} = \mu + \beta_1(-1)
\hat{y} = \mu + \beta_1(0)
\hat{y} = \mu + \beta_1(1)
How might I go about doing this?
Harold
version
_
platform i386-pc-mingw32
arch i386
os mingw32
system i386, mingw32
status
major 2
minor 4.0
year 2006
month 10
day03
svn rev39566
language R
version.string R version 2.4.0 (2006-10-03)
[[alternative HTML version deleted]]
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
=
David Barron
Said Business School
University of Oxford
Park End Street
Oxford OX1 1HP
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] [ggplot] controlling axis and major/minor tick marks
If you are willing to use grid you can set the color of the tick marks, labels and place a box around the chart like this: x - 1:10 y - x*x # create box around plot library(ggplot) qplot(x, y) # black border around plot grid.edit(grill-border, height = unit(.99, npc), width = unit(.99, npc), gp = gpar(col = black)) # black tick marks and labels grid.edit(yaxis1, gp = gpar(col = black)) If you play around with str(grid.get(grill-border)) and the other names on this list: plot-surrounds background plot grid1-1 grill-background grill-vertical grill-horizontal grill-border xaxis1 axis-ticks axis-labels yaxis1 border1-1 border ylabel xlabel title and use grid.edit to make changes as in the examples above you can change quite a bit. On 10/31/06, Sebastian Weber [EMAIL PROTECTED] wrote: Hi Hadley! axis.colour should control the colour of the tickmarks, the axis labels, and the line which the ticks attach to. What is not working in your case? grid.colour only effects the grid lines inside the plot. Well, I used gopt to set the following global defaults for my plots: ggopt() List of 11 $ aspect.ratio : num 0.618 $ axis.colour : chr black $ background.colour: chr black $ background.fill : chr white $ grid.colour : chr white $ grid.fill: chr white $ legend.position : chr right $ save : logi FALSE $ strip.gp :List of 3 ..$ col : chr white ..$ fill: chr grey80 ..$ lwd : num 3 ..- attr(*, class)= chr gpar $ strip.text :function (variable, value) $ strip.text.gp: list() ..- attr(*, class)= chr gpar - attr(*, class)= chr options Then I plot my stuff with p2 - ggplot(knn, . ~ power , aes=list(y=log10(k2m/(degree*kSize)), x=log10(degree), shape=alpha)) p2 - ggpoint(p2) p2 and I do not see any axis at all. The tick marks are there, they are black as they should. By the way, I already wondered why I can not change the shapes of the symbols in use. I figured that they are set statically in map_shapes. How about introducing an option for this somewhere? Currently, ggplot has no notion of major and minor tick marks (mainly because I don't have a good algorithim to generate them), but it is on my to do list. I definetly need minor tick marks and will hack my way through ggplot to acheive this if it does not seem to difficult to me. May you give me a tip where to start / where should I have to modify things. Regards, Sebastian Regards, Hadley On 10/31/06, Sebastian Weber [EMAIL PROTECTED] wrote: Hello there! I'm starting with ggplot and was wondering how I could control the axis of a plot. I would like the axis of the plot to be drawn black which I thought to acheive with the option axis.colour=black. However, this had no real effect on the plot. Then I found grid.colour which I changed to black as well. Now I got my axis as I wanted them, but ggplot now draws the grid inside the plot with black lines as well, which definetly do not want to appear. So how can I get a black border around my plots? Furthermore, I would like to indicate positions of major and minor ticks in my plots. Where can I do this? Thanks in advance. Greetings, Sebastian Ah, I use R 2.3.1 and ggplot 0.4.0, if that is important ... __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] POSIXct time zone and daylight savings issues
On Tue, 31 Oct 2006 09:24:02 + (GMT), Prof Brian Ripley [EMAIL PROTECTED] wrote: [...] No, it should be a timezone, and the timezone specification includes when DST is in effect. See ?as.POSIXct for details and references of timezones. For example, EST is a timezone without DST and EST5EDT is a timezone with DST (and they agree in winter). It looks like Linux is interpreting EEST as UTC+3 throughout the year (which appears not to be used anywhere as an actual timezone). So the behaviour is clear: EEST does not have DST, and $isdst == 0 in that 'timezone', whereas EET does have DST. Thanks for this explanation. Very important to check whether the supplied 'tz' is really interpreted as a valid time zone by the OS! Cheers, -- Seb __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] getMethod(s) and var.test
Dimitris, I like your version better than the one-line commands such as methods(). It appears that your version gives ALL of the code. Jeff -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Dimitris Rizopoulos Sent: Tuesday, October 31, 2006 11:12 AM To: Benjamin Otto Cc: r-help@stat.math.ethz.ch Subject: Re: [R] getMethod(s) and var.test you may try something like this: body.fun - lapply(methods(var.test), get, envir = environment(var.test), mode = function) names(body.fun) - methods(var.test) body.fun I hope it helps. Best, Dimitris Dimitris Rizopoulos Ph.D. Student Biostatistical Centre School of Public Health Catholic University of Leuven Address: Kapucijnenvoer 35, Leuven, Belgium Tel: +32/(0)16/336899 Fax: +32/(0)16/337015 Web: http://med.kuleuven.be/biostat/ http://www.student.kuleuven.be/~m0390867/dimitris.htm - Original Message - From: Benjamin Otto [EMAIL PROTECTED] To: R-Help r-help@stat.math.ethz.ch Sent: Tuesday, October 31, 2006 4:15 PM Subject: [R] getMethod(s) and var.test Hi, How do I retrieve the var.test() function code? I had a similar problem once before with another function but getMethods() solved the problem then. Now I tried several combinations for var.test() without success. Regards benjamin -- Benjamin Otto Universitaetsklinikum Eppendorf Hamburg Institut fuer Klinische Chemie Martinistrasse 52 20246 Hamburg [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] margins in heatmap.2 and fond size for x-axis
Hi, I am using heatmap.2 and have this problem now: heatmap.2(as.matrix(t7[,4:8]), col=c(green, yellow, red), margins=c(35,10)+0.1, RowSideColors=class.colors, trace=none, ylab=drugs, xlab=network signatures, scale=none)# I put the following line into a function and call that function (i.heatmap.1) and R complains: Error in plot.new() : figure margins too large I have to manually enlarge this empty one and re-call that function so I can get result. I tried to use par(mar) but it seems it does not help: par(mar=c(25,4,4,4)+0.1) Warning message: calling par(new=) with no plot i.heatmap.1(t7, non-ox) Error in plot.new() : figure margins too large Error in par(op) : invalid value specified for graphical parameter pin In addition: Warning message: calling par(new=) with no plot The reason I need a large margin is my xaxis font is too long, like ng_sodium_transport. I googled the r-help and found there is no way to make it smaller since I am using the smallest = 1. Is there other way around? Thanks -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. Did you always know? No, I did not. But I believed... ---Matrix III __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Odd behaviour of removing 'nothing' from an array or data frame
hadley wickham [EMAIL PROTECTED] writes: As Peter said, it's the value that counts, not the way you calculated it. If you print -c(2,3,5) you get three negative numbers. If you print -integer(0), you don't get any. The first case is asking for elements to be left out, the second isn't. The moral of the story is to use logical indices rather than negative ones: dubious.records - peoples.heights$heights 2.5 peoples.heights = peoples.heights[!dubious.records,] Unfortunately, there are some matching functions that return numeric indices, not logical vectors (eg. grep). For this case I created an unwhich function - but is there a better way to proceed? How about negIndex - function(x) if (length(x)) -x else TRUE x - 1:10 x[negIndex(which(x4))] [1] 1 2 3 4 x[negIndex(which(x11))] [1] 1 2 3 4 5 6 7 8 9 10 Of course in this case, you can just avoid the which() bit entirely and do x[!(x4)] [1] 1 2 3 4 x[!(x11)] [1] 1 2 3 4 5 6 7 8 9 10 -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Odd behaviour of removing 'nothing' from an array or data frame
I think I had that similar problem at some point in the way past and got
around it by checking the length of dubious records before I
Sent it into the expression. If the length is zero don't send it into
the expression.
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of
[EMAIL PROTECTED]
Sent: Tuesday, October 31, 2006 9:02 AM
To: r-help@stat.math.ethz.ch
Subject: [R] Odd behaviour of removing 'nothing' from an array or data
frame
I've just found some behaviour which strikes me as odd, but I'm not sure
whether it's a bug or a feature. If you don't mind, I'd like to explain
via a couple of examples.
Let x = 1:10.
Then intuitively, to me at least, the command x[-integer(0)] should
leave x untouched. However the actual output under R2.4.0 is
integer(0).
A slightly more involved example demonstrates why I think this behaviour
is back to front.
First we define a data frame, in this case some people, with their
heights.
peoples.heights = data.frame(names = c(Alice, Bob, Carol), heights
= c(1.67, 1.85, 175))
To make sure the heights are sensible, we define a filter out impossibly
tall people.
dubious.records = which(peoples.heights$heights 2.5) #3
peoples.heights = peoples.heights[-dubious.records,]
This all works fine since dubious.records is not empty. However, if all
the records had been entered properly, then we would get
#dubious.records = integer(0)
Then the command peoples.heights = peoples.heights[-dubious.records,]
strips all the rows to give
#[1] names heights
#0 rows (or 0-length row.names)
i.e. instead of removing the bad records, I've lost everything.
I know that it's possible to recode this so problems don't occur, but
the point is that the answer is unexpected.
Can anybody explain if this behaviour is intentional or useful in some
way, or is it an oversight?
Regards,
Richie.
Mathematical Sciences Unit
HSL
Buxton
SK17 9JN
01298 21(x8672)
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Re: [R] Measurements of 3000 criminals
Jean == Jean lobry [EMAIL PROTECTED] on Sat, 28 Oct 2006 13:07:04 +0200 writes: Hallo everyone, excuse me if this is not a genuine R question but I do not know where to ask else. Referring to e.g. https://stat.ethz.ch/pipermail/r-help/2004-December/062114.html I wonder if these measurements of 3000 criminals (raw data) are available anywhere. At least I didn't find them in the R datasets package or by means of Google. What I did find was a table of frequencies of the central values for *grouped* classifications (finger lenghts) in the Handbook of Small Data Sets. Thank you in advance. D. Trenkler Jean Dietrich, Jean I'm not sure, but this is perhaps what you want: Jean crim - Jean read.table(http://pbil.univ-lyon1.fr/R/donnees/criminals1902.txt;) May I propose to enhance this to cfile - http://pbil.univ-lyon1.fr/R/donnees/criminals1902.txt; crimtab - as.table(data.matrix(read.table(cfile, check.names=FALSE))) ## and e.g., print(crimtab, zero=.) Jean, this is really very nice, and given the historic importance of the data, I'd like to add this to the official R 'datasets' (the standard data set package), with tribute to you and Anne-Béatrice, and the references. If you agree, I'd be happy if you could help me (in private e-mail exchanges) to easily complete the relevant help page. Martin Maechler, ETH Zurich Jean For some R code playing with this dataset, open this Jean (draft) document: Jean http://pbil.univ-lyon1.fr/members/lobry/R/convergencet.pdf Jean and jump to section 4. Jean HTH, Jean Jean -- Jean R. Lobry ([EMAIL PROTECTED]) Jean Laboratoire BBE-CNRS-UMR-5558, Univ. C. Bernard - LYON Jean I, 43 Bd 11/11/1918, F-69622 VILLEURBANNE CEDEX, Jean FRANCE allo : +33 472 43 27 56 fax : +33 472 43 13 88 Jean http://pbil.univ-lyon1.fr/members/lobry/ Jean __ Jean R-help@stat.math.ethz.ch mailing list Jean https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do Jean read the posting guide Jean http://www.R-project.org/posting-guide.html and Jean provide commented, minimal, self-contained, Jean reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] graphics ignore tabs in text
On Tue, 2006-10-31 at 09:13 -0500, Liaw, Andy wrote: Dear R-help, I seem to recall that I can use \t to get tab in a string on a graphics device, but it doesn't seem to work. Try: lab - a\tb\tc cat(lab, \n) # works in the console output plot(1:5, main=lab) # no tabs in the title text(3, 3, lab) # no tabs in the text I get the same result both in the windows() and pdf() devices. Any ideas? This is R-patched Windows binary just downloaded from CRAN. R version 2.4.0 Patched (2006-10-29 r39744) Best, Andy Andy, I don't believe that tab expansion works in plots, though I will stand to be corrected on that. Using the X11() device on FC5 (which I recreated using png() and attached here), you can clearly see the dashed boxes where the tab character (non-printable 0x9) is being drawn. However, it is one character, not expanded as is the case in a textual console/GUI. What are you trying to accomplish? Perhaps there is a better way (ie. to do column alignments, etc.) such as textplot() in the gplots package. HTH, Marc Schwartz Rplot001.png Description: PNG image __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Odd behaviour of removing 'nothing' from an array or data frame
On 10/31/2006 9:50 AM, [EMAIL PROTECTED] wrote: Thanks for the reply Peter, though I'm not quite convinced. #dubious.records = integer(0) identical(dubious.records, -dubious.records) [1] TRUE how can peoples.heights[-dubious.records,] be different from peoples.heights[dubious.records,]? Tell me if I'm being willfully ignorant here, but I'm sure they should be different. In the first case, the minus sign represents subtraction, so it is correct that dubious.records and -dubious.records are identical. However, in the second case, inside the square brackets, the minus sign represents set complement, not subtraction, so dubious.records and - dubious.records are not the same. If x = runif(10), then x[-c(2,3,5)] means remove from x the values at the second, third and fifth position. By extension x[-integer(0)] should mean remove from x no values, and not remove from x all values, which is the current behaviour. As Peter said, it's the value that counts, not the way you calculated it. If you print -c(2,3,5) you get three negative numbers. If you print -integer(0), you don't get any. The first case is asking for elements to be left out, the second isn't. The moral of the story is to use logical indices rather than negative ones: dubious.records - peoples.heights$heights 2.5 peoples.heights = peoples.heights[!dubious.records,] works for any number of dubious records, including zero. Duncan Murdoch __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Missing data analysis in R
On Tue, 2006-10-31 at 11:17 -0600, Inman, Brant A. M.D. wrote: I am looking for a book that discusses the theory of multiple imputation (and other methods of dealing with missing data) and, just as importantly, how to implement these methods in R or S-Plus. Ideally, the book would have a structure similar to Faraway (Regression), PinheiroBates (Mixed Effects) and Wood (GAMs) and would be very modern (i.e. published within the last couple of years). Any ideas? If such a book does not exist, one of the experts on this help list should write it! (I will gladly buy the first copy.) Brant Inman Mayo Clinic One of the better references is: Statistical Analysis with Missing Data, Second Edition by Roderick J. A. Little, Donald B. Rubin Wiley-Interscience; 2nd edition (September 9, 2002) ISBN: 0471183865 http://www.amazon.com/Statistical-Analysis-Missing-Data-Second/dp/0471183865 In addition, see Frank Harrell's book Regression Modeling Strategies, Chapter 3 on Missing Data. More information here: http://biostat.mc.vanderbilt.edu/twiki/bin/view/Main/RmS and see Frank's function 'aregImpute' in the Hmisc package. More information is here: http://biostat.mc.vanderbilt.edu/twiki/bin/view/Main/Hmisc with function specific help here: http://biostat.mc.vanderbilt.edu/s/Hmisc/html/aregImpute.html Within R, if you use: RSiteSearch(Missing Data) you will also get many hits. Finally, the Multivariate task view on CRAN has a Missing Data section about half way down the page: http://cran.r-project.org/src/contrib/Views/Multivariate.html HTH, Marc Schwartz __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] plotting question
On Tue, 2006-10-31 at 12:08 -0500, Leeds, Mark (IED) wrote: i have the following code below and at the end there are some plotting statements. it actualy looks quite nice when you run it but there is just one strange thing happening that don't know how to fix. The problem you had, was that par(new = TRUE) # not T! resets the plotting coordinate system, so even though the axis looks like it extends the full range of the first data series, it covers the range of lt, e.g.: plot(aggfxdata[,logbidask],main=,col=4) lines(rollmeanlogbidask,col=2) par(new=T) plot(lt,axes=F,type=l,lty=2) axis(side = 3) # new coords system This works: plot(aggfxdata[,logbidask], main = , col = 4) lines(rollmeanlogbidask, col = 2) usr - par(usr) par(usr = c(usr[1:2], 0.76, 7.24)) lines(lt, lty = 2) axis(4, at = pretty(range(lt)), tck = -0.02) ..., I think. But I cheat, because, here: par(usr = c(usr[1:2], 0.76, 7.24)) I got the last two numbers by doing the following plot(lt) par(usr)[3:4] [1] 0.76 7.24 A question then arises, how to process lt such that we end up with the same numbers that R would have used to plot lt, i.e. which function or bit of code will give: what.R.would.give(lt) [1] 1.152076e+09 1.152088e+09 7.60e-01 7.24e+00 Without doing the plotting? HTH G the three things being plotted are aggfxdata[,logbidask] which has its own set of times ( it's a zoo object ). rollmeanlogbidask which has a subset of the times that aggfxdata has. basically it starts later than aggfxdata[,logbidask] and when the plot is done, it works in the sense that rollmeanlogbidask gets plotted later. then, i plot the variable lt on the same plot witrh it's vertical axis on the right side and this works nicely also. the only that doesn't quite work is that lt, time wise, lt, starting at the same time as the aggfxdata[,logbidask] when it should be starting a few minutes after rollmeanlogbidask. the times in it are correct and i don't think it has to do with the fact that things are zoo ( but i could be wrong ? ). i must be doing something wrong in my commands. the weird thing is that rollmeanlogbidask starts at the appropriate place ? maybe i have to give lt a different frequency but when i do the dput , i don'ts ee freequency as part of it ? this probably sounds way more confusing than it actually is but, if you run below, you will see exactly what io mean. thanks a lot to anyone who can be bothered pasitng below. as usual, you would need zoo and chron. aggfxdata-structure(c(114.834516129032, 114.7922, 114.820808080808, 114.838260869565, 114.837560975610, 114.776697247706, 114.7969, 114.745714285714, 114.734923076923, 114.661939393939, 114.646574074074, 114.703486238532, 114.646453900709, 114.651948051948, 114.742671755725, 114.721132075472, 114.828647058824, 114.885978260870, 114.936860465116, 114.94, 114.967763157895, 114.935107526882, 114.92225, 115.015606060606, 115.077261146497, 115.034248366013, 114.961923076923, 114.976463414634, 115.063468208092, 115.085882352941, 115.166847826087, 115.153306451613, 115.137719298246, 115.080735294118, 115.074090909091, 115.021134751773, 114.903450292398, 114.916153846154, 114.888306451613, 114.937469879518, 114.890943396226, 114.849747899160, 114.926912751678, 114.874567901235, 114.837980769231, 114.797538461538, 114.746707317073, 114.696013071895, 114.67645833, 114.852184466019, 114.848548387097, 114.8078, 114.835050505051, 114.851304347826, 114.852439024390, 114.792844036697, 114.8117, 114.759206349206, 114.748307692308, 114.675939393939, 114.661296296296, 114.717889908257, 114.660921985816, 114.665779220779, 114.756870229008, 114.735471698113, 114.841941176471, 114.899184782609, 114.949186046512, 114.953990384615, 114.982280701754, 114.948924731183, 114.9368, 115.028863636364, 115.091592356688, 115.0478, 114.975576923077, 114.990365853659, 115.078381502890, 115.099705882353, 115.180326086957, 115.166370967742, 115.151052631579, 115.095147058824, 115.088522727273, 115.035390070922, 114.917894736842, 114.930128205128, 114.903790322581, 114.952409638554, 114.906226415094, 114.863865546218, 114.940939597315, 114.890370370370, 114.852211538462, 114.812307692308, 114.760548780488, 114.710326797386, 114.69020833, 114.866213592233, 4.74355319771057, 4.74319148388547, 4.74343474081987, 4.74358150022944, 4.74358339314172, 4.74305881517423, 4.74322922997911, 4.74277728938584, 4.7426822736, 4.74204918880485, 4.7419183321792, 4.74241320264843, 4.74191617575789, 4.74196131670693, 4.74275385322944, 4.74256674074965, 4.74349887668465, 4.74399761812053, 4.74443655563793, 4.74447111073972, 4.74471490416156, 4.74442779363424, 4.74431911442163, 4.74512545618279, 4.74566600467616, 4.74528870019174, 4.74466035230505, 4.74478789738982, 4.74554867613244, 4.74573870836097, 4.74644044208183, 4.74632106516708, 4.74618687097407, 4.74569654200703,
Re: [R] one problem about how to hold graphic with R
On Tue, 2006-10-31 at 21:36 +0800, yang baohua wrote: Sorry to disturb you, but can you help me to solve one little problem? I want to draw a graphic after another with R but I cannot find the first one after that. Do you know the command to hold the graphic with R? I remember with Matlab you may use hold on. Thanks. You don't say which OS. On MS Windows one can turn on a history of plots to the graphics device and replay your plots - it is in the menu bar for example. In all OSes, you can start up a new device to take the plot - which is what Matlab does IIRC, so you have two or more plot windows on screen at any one time. This is done like this: plot(1:10) x11() plot(1:20) x11() plot(rnorm(100)) see ?Devices You can set a device to be active, i.e. switch around between plotting windows using dev.set(), e.g.: dev.cur() # example from above leaves device 4 active X11 4 dev.set(3) # switch to device dev.cur() # check X11 3 plot(sort(rnorm(100))) # plot something new on this device Is this what you were looking for? HTH G -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Gavin Simpson [t] +44 (0)20 7679 0522 ECRC ENSIS, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/ UK. WC1E 6BT. [w] http://www.freshwaters.org.uk %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] information about sna packages
Davide, sna uses adjacency matrices, so one (crude) solution would be to store the dynamical network as a list of matrices. This is of course not very space efficient. Gabor On Tue, Oct 31, 2006 at 02:28:28PM +0100, Bagatti Davide wrote: Hello, I'm a student who want to use the R social network analysis package. I have a question: can this package analyse dynamical networks (network changing over time)? I didn't find this functionality in the package's user manual. Thank you Davide [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Csardi Gabor [EMAIL PROTECTED]MTA RMKI, ELTE TTK __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] R News, volume 6, issue 4 is now available
Hi The October 2006 issue of R News is now available on CRAN under the Documentation/Newsletter link. Paul (on behalf of the R News Editorial Board) -- Dr Paul Murrell Department of Statistics The University of Auckland Private Bag 92019 Auckland New Zealand 64 9 3737599 x85392 [EMAIL PROTECTED] http://www.stat.auckland.ac.nz/~paul/ ___ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-announce __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] 2.4.0 and lattice 0.14-9: Changed behaviour of scales-argumenttck
Dear list, I have observed a change in the behaviour of the scales-argument tck of xyplot() after having installed R 2.4.0 (for version info see below). The help page of xyplot() says about the scales-argument tck: 'tck' numeric to control length of tick marks. Can be a vector of length 2, to control left/bottom and right/top separately. But if I issue xyplot( y ~ x, scales= list( tck= c( 1, 0))) (with suitable numeric vectors x and y, of course) the plot shows alternating tick mark lengths *on every side* of the plot (i.e., the length of every second tick mark is zero). I wanted to see tick marks only on the left and bottom side of the coordinate system (as I did see before with R 2.2.0 and lattice version 0.12-9). Has anybody a workaround to get back the original (documented) behaviour? Thanks a lot! Best regards -- Gerrit PS: My system: version _ platform x86_64-unknown-linux-gnu arch x86_64 os linux-gnu system x86_64, linux-gnu status major 2 minor 4.0 year 2006 month 10 day03 svn rev39566 language R version.string R version 2.4.0 (2006-10-03) - AR Dr. Gerrit Eichner Mathematical Institute [EMAIL PROTECTED] Justus-Liebig-University Giessen Tel: +49-(0)641-99-32104 Arndtstr. 2, 35392 Giessen, Germany Fax: +49-(0)641-99-32029 http://www.math.uni-giessen.de __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] plotting question
On Tue, 2006-10-31 at 18:11 +, Gavin Simpson wrote: On Tue, 2006-10-31 at 12:08 -0500, Leeds, Mark (IED) wrote: i have the following code below and at the end there are some plotting statements. it actualy looks quite nice when you run it but there is just one strange thing happening that don't know how to fix. The problem you had, was that par(new = TRUE) # not T! resets the plotting coordinate system, so even though the axis looks like it extends the full range of the first data series, it covers the range of lt, e.g.: plot(aggfxdata[,logbidask],main=,col=4) lines(rollmeanlogbidask,col=2) par(new=T) plot(lt,axes=F,type=l,lty=2) axis(side = 3) # new coords system This works: plot(aggfxdata[,logbidask], main = , col = 4) lines(rollmeanlogbidask, col = 2) usr - par(usr) par(usr = c(usr[1:2], 0.76, 7.24)) lines(lt, lty = 2) axis(4, at = pretty(range(lt)), tck = -0.02) Following off-list emails with Mark, I tracked down how to do this automatically, for the thread... It is document in ?par in the section on xaxs and yaxs (x and y axis styles). This defaults to r, which adds/subtracts 4% to the x/ylims, so, plot(aggfxdata[,logbidask], main = , col = 4) lines(rollmeanlogbidask, col = 2) usr - par(usr) # extend range of data by 4% rany - (max(lt) - min(lt)) * 0.04 par(usr = c(usr[1:2], min(lt) - rany, max(lt) + rany)) lines(lt, lty = 2) axis(4, at = pretty(range(lt)), tck = -0.02) the above does exactly as I'd done before, but automagically. G ..., I think. But I cheat, because, here: par(usr = c(usr[1:2], 0.76, 7.24)) I got the last two numbers by doing the following plot(lt) par(usr)[3:4] [1] 0.76 7.24 A question then arises, how to process lt such that we end up with the same numbers that R would have used to plot lt, i.e. which function or bit of code will give: what.R.would.give(lt) [1] 1.152076e+09 1.152088e+09 7.60e-01 7.24e+00 Without doing the plotting? HTH G the three things being plotted are aggfxdata[,logbidask] which has its own set of times ( it's a zoo object ). rollmeanlogbidask which has a subset of the times that aggfxdata has. basically it starts later than aggfxdata[,logbidask] and when the plot is done, it works in the sense that rollmeanlogbidask gets plotted later. then, i plot the variable lt on the same plot witrh it's vertical axis on the right side and this works nicely also. the only that doesn't quite work is that lt, time wise, lt, starting at the same time as the aggfxdata[,logbidask] when it should be starting a few minutes after rollmeanlogbidask. the times in it are correct and i don't think it has to do with the fact that things are zoo ( but i could be wrong ? ). i must be doing something wrong in my commands. the weird thing is that rollmeanlogbidask starts at the appropriate place ? maybe i have to give lt a different frequency but when i do the dput , i don'ts ee freequency as part of it ? this probably sounds way more confusing than it actually is but, if you run below, you will see exactly what io mean. thanks a lot to anyone who can be bothered pasitng below. as usual, you would need zoo and chron. aggfxdata-structure(c(114.834516129032, 114.7922, 114.820808080808, 114.838260869565, 114.837560975610, 114.776697247706, 114.7969, 114.745714285714, 114.734923076923, 114.661939393939, 114.646574074074, 114.703486238532, 114.646453900709, 114.651948051948, 114.742671755725, 114.721132075472, 114.828647058824, 114.885978260870, 114.936860465116, 114.94, 114.967763157895, 114.935107526882, 114.92225, 115.015606060606, 115.077261146497, 115.034248366013, 114.961923076923, 114.976463414634, 115.063468208092, 115.085882352941, 115.166847826087, 115.153306451613, 115.137719298246, 115.080735294118, 115.074090909091, 115.021134751773, 114.903450292398, 114.916153846154, 114.888306451613, 114.937469879518, 114.890943396226, 114.849747899160, 114.926912751678, 114.874567901235, 114.837980769231, 114.797538461538, 114.746707317073, 114.696013071895, 114.67645833, 114.852184466019, 114.848548387097, 114.8078, 114.835050505051, 114.851304347826, 114.852439024390, 114.792844036697, 114.8117, 114.759206349206, 114.748307692308, 114.675939393939, 114.661296296296, 114.717889908257, 114.660921985816, 114.665779220779, 114.756870229008, 114.735471698113, 114.841941176471, 114.899184782609, 114.949186046512, 114.953990384615, 114.982280701754, 114.948924731183, 114.9368, 115.028863636364, 115.091592356688, 115.0478, 114.975576923077, 114.990365853659, 115.078381502890, 115.099705882353, 115.180326086957, 115.166370967742, 115.151052631579, 115.095147058824, 115.088522727273, 115.035390070922, 114.917894736842, 114.930128205128, 114.903790322581, 114.952409638554, 114.906226415094, 114.863865546218, 114.940939597315,
[R] savePlot and dev.copy
Dear R gurus, R 2.4.0 under Windows XP. We have developed several dozen R functions to make and save specialized plots. These use savePlot() to optionally save the plot to files (eps, jpg, png, ...). The thought has come up of putting the functions into an R package. Because savePlot is available only on Windows, we would instead detect the OS and use dev.copy in place of savePlot when not running under Windows. My question is, if this code is rewritten anyway, what are the pros and cons of using dev.copy under *all* operating systems vs. using savePlot on Windows and dev.copy on other platforms? Thanks! -- Mike Prager, NOAA, Beaufort, NC * Opinions expressed are personal and not represented otherwise. * Any use of tradenames does not constitute a NOAA endorsement. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] graphics ignore tabs in text
Hi Marc Schwartz wrote: On Tue, 2006-10-31 at 09:13 -0500, Liaw, Andy wrote: Dear R-help, I seem to recall that I can use \t to get tab in a string on a graphics device, but it doesn't seem to work. Try: lab - a\tb\tc cat(lab, \n) # works in the console output plot(1:5, main=lab) # no tabs in the title text(3, 3, lab) # no tabs in the text I get the same result both in the windows() and pdf() devices. Any ideas? This is R-patched Windows binary just downloaded from CRAN. R version 2.4.0 Patched (2006-10-29 r39744) Best, Andy Andy, I don't believe that tab expansion works in plots, though I will stand to be corrected on that. I'm surprised that this has never come up before, but I know of no special handling of tabs in the graphics code. I suspect if we wanted to do something we would have to add code to detect '\t' and replace it with a number of spaces (maybe based on a user-settable option). Paul Using the X11() device on FC5 (which I recreated using png() and attached here), you can clearly see the dashed boxes where the tab character (non-printable 0x9) is being drawn. However, it is one character, not expanded as is the case in a textual console/GUI. What are you trying to accomplish? Perhaps there is a better way (ie. to do column alignments, etc.) such as textplot() in the gplots package. HTH, Marc Schwartz __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Dr Paul Murrell Department of Statistics The University of Auckland Private Bag 92019 Auckland New Zealand 64 9 3737599 x85392 [EMAIL PROTECTED] http://www.stat.auckland.ac.nz/~paul/ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Multivariate regression
Thank you Robin (also thanks to Andris and Bernhard). I did get answers to
my problem using lm as you had suggested. But my main concern is about
getting the appropriate standard errors for \hat{beta}.
My response is actually preference data, where each individual ranks a list
of k items, assigning them unique ranks from 1 to k. Since the ranks for
each item are negatively-correlated within an individual, I would like to
take this into consideration. Although lm gives me correct parameter
estimates, I think that the standard errors are overestimated.
Best,
Ravi.
---
Ravi Varadhan, Ph.D.
Assistant Professor, The Center on Aging and Health
Division of Geriatric Medicine and Gerontology
Johns Hopkins University
Ph: (410) 502-2619
Fax: (410) 614-9625
Email: [EMAIL PROTECTED]
Webpage: http://www.jhsph.edu/agingandhealth/People/Faculty/Varadhan.html
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Robin Hankin
Sent: Monday, October 30, 2006 4:17 AM
To: Andris Jankevics
Cc: r-help@stat.math.ethz.ch
Subject: Re: [R] Multivariate regression
Hi
I discovered the other day that lm() does some of the work for
you:
library(mvtnorm)
X - matrix(rnorm(60),ncol=3)
beta - matrix(1:6,ncol=2)
sig - matrix(c(1,0.7,0.7,1),2,2)
Y - X %*% beta + rmvnorm(n=20,sigma=sig)
lm(Y ~ X-1)
Call:
lm(formula = Y ~ X - 1)
Coefficients:
[,1] [,2]
X1 1.015 4.065
X2 2.483 5.366
X3 2.762 5.727
This gives an estimate for beta.
But I don't know of a ready-made R solution for estimating
the covariance of the elements of beta, or the sig matrix
for the covariance matrix of the observation errors.
Anyone?
On 30 Oct 2006, at 09:01, Andris Jankevics wrote:
Also you can take a look on Partial Least Squares (PLS) regression.
http://www.statsoft.com/textbook/stpls.html
R-package: http://mevik.net/work/software/pls.html
Andris Jankevics
On Sestdiena, 28. Oktobris 2006 06:04, Ritwik Sinha wrote:
You can use gee (
http://finzi.psych.upenn.edu/R/library/geepack/html/00Index.html)
or maybe
the function gls in nlme.
Ritwik.
On 10/27/06, Ravi Varadhan [EMAIL PROTECTED] wrote:
Hi,
Suppose I have a multivariate response Y (n x k) obtained at a
set of
predictors X (n x p). I would like to perform a linear
regression taking
into consideration the covariance structure of Y within each unit
- this
would be represented by a specified matrix V (k x k), assumed to
be the
same
across units. How do I use lm to do this?
One approach that I was thinking of is as follows:
Flatten Y to a vector, say, Yvec (n*k x 1). Create Xvec (n*k,
p*k) such
that it is made up of block matrices Bij (k x k), where Bij is a
diagonal
matrix with X_ij as the diagonal (i = 1,.n, and j = 1,.,p). Now
I can
use lm in a univariate mode to regress Yvec against Xvec, with
covariance matrix Vvec (n*k x n*k). Vvec is a block-diagonal
matrix with
blocks of V along the diagonal. This seems like a valid
approach, but I
still don't know how to specify the covariance structure to do
weighted
least squares.
Any help is appreciated.
Best,
Ravi.
-
--- ---
Ravi Varadhan, Ph.D.
Assistant Professor, The Center on Aging and Health
Division of Geriatric Medicine and Gerontology
Johns Hopkins University
Ph: (410) 502-2619
Fax: (410) 614-9625
Email: [EMAIL PROTECTED]
Webpage:
http://www.jhsph.edu/agingandhealth/People/Faculty/Varadhan.html
-
---
[[alternative HTML version deleted]]
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--
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Uncertainty Analyst
National Oceanography Centre, Southampton
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tel 023-8059-7743
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Re: [R] savePlot and dev.copy
Hi Mike Prager wrote: Dear R gurus, R 2.4.0 under Windows XP. We have developed several dozen R functions to make and save specialized plots. These use savePlot() to optionally save the plot to files (eps, jpg, png, ...). The thought has come up of putting the functions into an R package. Because savePlot is available only on Windows, we would instead detect the OS and use dev.copy in place of savePlot when not running under Windows. My question is, if this code is rewritten anyway, what are the pros and cons of using dev.copy under *all* operating systems vs. using savePlot on Windows and dev.copy on other platforms? The underlying mechanisms of dev.copy() and savePlot() are identical -- copy the display list from one device to another -- but savePlot() has some niceties wrapped around the outside. These boil down to making the copy the same size as the original. If you use dev.copy() naively, you can get a copy which is a very different size from the original. The function dev.print() does a bit better in terms of retaining the original size, but there is trouble when you copy from a device for which the size is specified in inches [like windows(), x11(), postscript() and pdf()] to a device for which the size is in pixels [png(), jpeg(), bitmap()]. savePlot() handles all of the sizing problems for you (but only works on Windows). dev.copy() works everywhere, but you would have to do a bit of mucking about yourself to get around the sizing problems -- see the source for dev.print() for a starting point. The authors of the Windows device might have more to say. Paul -- Dr Paul Murrell Department of Statistics The University of Auckland Private Bag 92019 Auckland New Zealand 64 9 3737599 x85392 [EMAIL PROTECTED] http://www.stat.auckland.ac.nz/~paul/ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] VGAM-vglm
Can somebody explain to me why I get different results using multinom(package nnet) and vglm(package VGAM)? The multinom function in the nnet package uses the first level of the factor as baseline, whereas the last level of the factor is used with multinomial(). Consequently the estimated regression coefficients differ. They can be reconciled very easily with some basic maths. cheers Thomas __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] [ggplot] controlling axis and major/minor tick marks
Hi Hadley! axis.colour should control the colour of the tickmarks, the axis labels, and the line which the ticks attach to. What is not working in your case? grid.colour only effects the grid lines inside the plot. Well, I used gopt to set the following global defaults for my plots: ggopt() List of 11 $ aspect.ratio : num 0.618 $ axis.colour : chr black $ background.colour: chr black $ background.fill : chr white $ grid.colour : chr white $ grid.fill: chr white $ legend.position : chr right $ save : logi FALSE $ strip.gp :List of 3 ..$ col : chr white ..$ fill: chr grey80 ..$ lwd : num 3 ..- attr(*, class)= chr gpar $ strip.text :function (variable, value) $ strip.text.gp: list() ..- attr(*, class)= chr gpar - attr(*, class)= chr options Then I plot my stuff with p2 - ggplot(knn, . ~ power , aes=list(y=log10(k2m/(degree*kSize)), x=log10(degree), shape=alpha)) p2 - ggpoint(p2) p2 and I do not see any axis at all. The tick marks are there, they are black as they should. By the way, I already wondered why I can not change the shapes of the symbols in use. I figured that they are set statically in map_shapes. How about introducing an option for this somewhere? Currently, ggplot has no notion of major and minor tick marks (mainly because I don't have a good algorithim to generate them), but it is on my to do list. I definetly need minor tick marks and will hack my way through ggplot to acheive this if it does not seem to difficult to me. May you give me a tip where to start / where should I have to modify things. Regards, Sebastian Regards, Hadley On 10/31/06, Sebastian Weber [EMAIL PROTECTED] wrote: Hello there! I'm starting with ggplot and was wondering how I could control the axis of a plot. I would like the axis of the plot to be drawn black which I thought to acheive with the option axis.colour=black. However, this had no real effect on the plot. Then I found grid.colour which I changed to black as well. Now I got my axis as I wanted them, but ggplot now draws the grid inside the plot with black lines as well, which definetly do not want to appear. So how can I get a black border around my plots? Furthermore, I would like to indicate positions of major and minor ticks in my plots. Where can I do this? Thanks in advance. Greetings, Sebastian Ah, I use R 2.3.1 and ggplot 0.4.0, if that is important ... __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] [R-pkgs] rcompletion: TAB completion for the R command line
Hi,
I've tried to compile rcompletion and perhaps have detected the reason for
failures, although I haven't succeeded yet.
Em Ter 31 Out 2006 02:10, Deepayan Sarkar escreveu:
However, there are known cases
of false negatives, i.e. installation failing when it shouldn't. If
this happens to you, any information you can provide to help resolve
the problem would be appreciated.
From config.lo generated by rcompletion configure
---8
/usr/local/lib/gcc/i686-pc-linux-gnu/4.0.3/../../../libreadline.so: undefined
reference to `tgetnum'
/usr/local/lib/gcc/i686-pc-linux-gnu/4.0.3/../../../libreadline.so: undefined
reference to `tgoto'
/usr/local/lib/gcc/i686-pc-linux-gnu/4.0.3/../../../libreadline.so: undefined
reference to `tgetflag'
/usr/local/lib/gcc/i686-pc-linux-gnu/4.0.3/../../../libreadline.so: undefined
reference to `BC'
/usr/local/lib/gcc/i686-pc-linux-gnu/4.0.3/../../../libreadline.so: undefined
reference to `tputs'
/usr/local/lib/gcc/i686-pc-linux-gnu/4.0.3/../../../libreadline.so: undefined
reference to `PC'
/usr/local/lib/gcc/i686-pc-linux-gnu/4.0.3/../../../libreadline.so: undefined
reference to `tgetent'
/usr/local/lib/gcc/i686-pc-linux-gnu/4.0.3/../../../libreadline.so: undefined
reference to `UP'
/usr/local/lib/gcc/i686-pc-linux-gnu/4.0.3/../../../libreadline.so: undefined
reference to `tgetstr'
---8
It seems configure can't figure where to find these functions.
From readline5.0 configure script
---8
checking for tgetent... no
checking for tgetent in -ltermcap... no
checking for tgetent in -ltinfo... no
checking for tgetent in -lcurses... yes
checking which library has the termcap functions... using libcurses
---8
The unresolved function calls (and perhaps symbols of other types) may be
located at libcurses. At least in my system they are.
From termcap.h
---8
#undef NCURSES_VERSION
#define NCURSES_VERSION 5.5
#include ncurses_dll.h
#ifdef __cplusplus
extern C
{
#endif /* __cplusplus */
#include sys/types.h
#undef NCURSES_CONST
#define NCURSES_CONST /*nothing*/
#undef NCURSES_OSPEED
#define NCURSES_OSPEED short
extern NCURSES_EXPORT_VAR(char) PC;
extern NCURSES_EXPORT_VAR(char *) UP;
extern NCURSES_EXPORT_VAR(char *) BC;
extern NCURSES_EXPORT_VAR(NCURSES_OSPEED) ospeed;
#if !defined(NCURSES_TERM_H_incl)
extern NCURSES_EXPORT(char *) tgetstr (NCURSES_CONST char *, char **);
extern NCURSES_EXPORT(char *) tgoto (const char *, int, int);
extern NCURSES_EXPORT(int) tgetent (char *, const char *);
extern NCURSES_EXPORT(int) tgetflag (NCURSES_CONST char *);
extern NCURSES_EXPORT(int) tgetnum (NCURSES_CONST char *);
extern NCURSES_EXPORT(int) tputs (const char *, int, int (*)(int));
#endif
---8
May be your configure needs some rewriting to include a check for the location
of unknown symbols like readline's configure does.
Best wishes,
--
Alexandre Aguiar
Independent consultant for medical research
SPS Consultoria
Voice: +55-11-9320-2046
Fax: +55-11-5549-8760
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Re: [R] one problem about how to hold graphic with R
I'm not familiar with Matlab, but from what I know, hold on is used to
overlay more stuff on the existing plot. In R such things are
accomplished a bit differently: One put up a plot, then use things like
lines(), points(), abline(), etc. to add to the existing plot. The
closest thing to hold on in Matlab, I think, is par(new=TRUE).
Andy
From: Gavin Simpson
On Tue, 2006-10-31 at 21:36 +0800, yang baohua wrote:
Sorry to disturb you, but can you help me to solve one
little problem?
I want to draw a graphic after another with R but I cannot find the
first one after that.
Do you know the command to hold the graphic with R?
I remember with Matlab you may use hold on.
Thanks.
You don't say which OS. On MS Windows one can turn on a
history of plots to the graphics device and replay your plots
- it is in the menu bar for example.
In all OSes, you can start up a new device to take the plot -
which is what Matlab does IIRC, so you have two or more plot
windows on screen at any one time. This is done like this:
plot(1:10)
x11()
plot(1:20)
x11()
plot(rnorm(100))
see ?Devices
You can set a device to be active, i.e. switch around between
plotting windows using dev.set(), e.g.:
dev.cur() # example from above leaves device 4 active
X11
4
dev.set(3) # switch to device
dev.cur() # check
X11
3
plot(sort(rnorm(100))) # plot something new on this device
Is this what you were looking for?
HTH
G
--
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Gavin Simpson [t] +44 (0)20 7679 0522
ECRC ENSIS, UCL Geography, [f] +44 (0)20 7679 0565
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Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/
UK. WC1E 6BT. [w] http://www.freshwaters.org.uk
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[R] plotting question
i have the axis line of code below in a plotting command and it works nicely but it puts tick values at every 5 of lt and i would like a tick value at every value of lt. i read about pretty() but that sounded tricky so instead , since i want a tick mark at every value of lt ( it's discrete and goes from o to some max value usually arounsd 35 or 40 ) i changed the line to at = seq(1,max(lt) ) but that gave me no tickmarks ? any help is appreciated. thanks. #--- axis(4, at = pretty(range(lt)),line=0.75,tick=TRUE) #--- -- This is not an offer (or solicitation of an offer) to buy/sell the securities/instruments mentioned or an official confirmation. Morgan Stanley may deal as principal in or own or act as market maker for securities/instruments mentioned or may advise the issuers. This is not research and is not from MS Research but it may refer to a research analyst/research report. Unless indicated, these views are the author's and may differ from those of Morgan Stanley research or others in the Firm. We do not represent this is accurate or complete and we may not update this. Past performance is not indicative of future returns. For additional information, research reports and important disclosures, contact me or see https://secure.ms.com/servlet/cls. You should not use e-mail to request, authorize or effect the purchase or sale of any security or instrument, to send transfer instructions, or to effect any other transactions. We cannot guarantee that any such requests received via ! e-mail will be processed in a timely manner. This communication is solely for the addressee(s) and may contain confidential information. We do not waive confidentiality by mistransmission. Contact me if you do not wish to receive these communications. In the UK, this communication is directed in the UK to those persons who are market counterparties or intermediate customers (as defined in the UK Financial Services Authority's rules). [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Odd behaviour of removing 'nothing' from an array or data frame
[EMAIL PROTECTED] writes: I've just found some behaviour which strikes me as odd, but I'm not sure whether it's a bug or a feature. If you don't mind, I'd like to explain via a couple of examples. Let x = 1:10. Then intuitively, to me at least, the command x[-integer(0)] should leave x untouched. However the actual output under R2.4.0 is integer(0). A slightly more involved example demonstrates why I think this behaviour is back to front. First we define a data frame, in this case some people, with their heights. peoples.heights = data.frame(names = c(Alice, Bob, Carol), heights = c(1.67, 1.85, 175)) To make sure the heights are sensible, we define a filter out impossibly tall people. dubious.records = which(peoples.heights$heights 2.5) #3 peoples.heights = peoples.heights[-dubious.records,] This all works fine since dubious.records is not empty. However, if all the records had been entered properly, then we would get #dubious.records = integer(0) Then the command peoples.heights = peoples.heights[-dubious.records,] strips all the rows to give #[1] names heights #0 rows (or 0-length row.names) i.e. instead of removing the bad records, I've lost everything. I know that it's possible to recode this so problems don't occur, but the point is that the answer is unexpected. Can anybody explain if this behaviour is intentional or useful in some way, or is it an oversight? Consistency! It's not particularly useful, but it follows from general principles, which it in the long run doesn't pay to depart from. The issue is that the result of using an indexing operator ([) should depend only on the _value_ of its argument, not the expression used to compute it. Just like you most likely expect log(2+2) not to be different from log(4). And since dubious.records - integer(0) identical(dubious.records, -dubious.records) [1] TRUE how can peoples.heights[-dubious.records,] be different from peoples.heights[dubious.records,]? R could actually look at the expression and act on the minus sign, but that way lies madness. Consider keep - -dubious.records drop - dubious.records peoples.heights[keep,] peoples.heights[-dubious.records,] peoples.heights[-keep,] etc... I think you'll get the picture. -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Put a normal curve on plot
Here is some sample code that shows 2 different approaches, which you
want to use depends on what exactly you want to do and which will be
easier for you, the one draws the normal around the 6,7 point, the other
around the 3,4 point, change those values to do your plot:
plot(1:10, 2:11)
xx - seq(-3,3,.1)
lines( 6+dnorm(xx,0,.75), 7+xx )
library(TeachingDemos)
subplot( plot(dnorm(xx),xx, type='l', axes=F,xlab='',ylab=''), 3,4,
hadj=0 )
Hope this helps,
--
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
[EMAIL PROTECTED]
(801) 408-8111
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Doran, Harold
Sent: Tuesday, October 31, 2006 6:26 AM
To: R-help@stat.math.ethz.ch
Subject: [R] Put a normal curve on plot
I would like to be able to place a normal distribution surrounding the
predicted values at various places on a plot. Below is some toy code
that creates a scatterplot and plots a regression line through the data.
library(MASS)
mu - c(0,1)
Sigma - matrix(c(1,.8,.8,1), ncol=2)
set.seed(123)
x - mvrnorm(50,mu,Sigma)
plot(x)
abline(lm(x[,2] ~ x[,1]))
Say I want to add a normal distribution surrounding the predicted values
at the x-values of -1, 0, and 1. That is, at the points
\hat{y} = \mu + \beta_1(-1)
\hat{y} = \mu + \beta_1(0)
\hat{y} = \mu + \beta_1(1)
How might I go about doing this?
Harold
version
_
platform i386-pc-mingw32
arch i386
os mingw32
system i386, mingw32
status
major 2
minor 4.0
year 2006
month 10
day03
svn rev39566
language R
version.string R version 2.4.0 (2006-10-03)
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] one problem about how to hold graphic with R
On Tue, 2006-10-31 at 22:12 +0800, yang baohua wrote: Thanks your reply is helpful but i want to draw two graphics on one window to compare them so i want to draw one then draw another with different color on the same window Can you tell me how to do so Waiting for your kind reply Please reply-all to ensure others on the list see the full thread. Again, it is not clear exactly (but that's me being dense probably) what you want. I see two options: 1) Side by side plots par(mfrow = c(1, 2)) plot(rnorm(100), rnorm(100)) plot(runif(100), rnorm(100), col = red) par(mfrow = c(1, 1)) or 2) overplotting one set of points on another plot(rnorm(100), rnorm(100)) points(runif(100), rnorm(100), col = red) If 1), see ?par (and ?layout and ?split.screen for alternative ways to splitting up a plotting device into n plotting regions), and if 2), see ?points and ?lines, and I strongly suggest you read the R manual An Introduction to R that came with R, especially section 12 on Graphics. HTH G 2006/10/31, Gavin Simpson [EMAIL PROTECTED]: On Tue, 2006-10-31 at 21:36 +0800, yang baohua wrote: Sorry to disturb you, but can you help me to solve one little problem? I want to draw a graphic after another with R but I cannot find the first one after that. Do you know the command to hold the graphic with R? I remember with Matlab you may use hold on. Thanks. You don't say which OS. On MS Windows one can turn on a history of plots to the graphics device and replay your plots - it is in the menu bar for example. In all OSes, you can start up a new device to take the plot - which is what Matlab does IIRC, so you have two or more plot windows on screen at any one time. This is done like this: plot(1:10) x11() plot(1:20) x11() plot(rnorm(100)) see ?Devices You can set a device to be active, i.e. switch around between plotting windows using dev.set(), e.g.: dev.cur() # example from above leaves device 4 active X11 4 dev.set(3) # switch to device dev.cur() # check X11 3 plot(sort(rnorm(100))) # plot something new on this device Is this what you were looking for? HTH G -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~ %~%~%~% Gavin Simpson [t] +44 (0)20 7679 0522 ECRC ENSIS, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/ UK. WC1E 6BT. [w] http://www.freshwaters.org.uk %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~ %~%~%~% -- Baohua Yang Department of Automation, Tsinghua University 228A, Zijing Bldg. No.2, Tsinghua Univ. Beijing, 100084, P.R.China Tel. 010-51532228 Email:[EMAIL PROTECTED] -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Gavin Simpson [t] +44 (0)20 7679 0522 ECRC ENSIS, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/ UK. WC1E 6BT. [w] http://www.freshwaters.org.uk %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] plotting question
On Tue, 2006-10-31 at 16:52 -0500, Leeds, Mark (IED) wrote: i have the axis line of code below in a plotting command and it works nicely but it puts tick values at every 5 of lt and i would like a tick value at every value of lt. i read about pretty() but that sounded tricky so instead , since i want a tick mark at every value of lt ( it's discrete and goes from o to some max value usually arounsd 35 or 40 ) i changed the line to at = seq(1,max(lt) ) but that gave me no tickmarks ? ?unique lt - sample(1:40, 50, replace = TRUE) # dummy data lt [1] 37 30 38 33 13 19 6 39 15 21 5 11 5 5 32 1 23 20 12 21 35 32 34 26 39 [26] 30 11 36 26 12 37 27 26 9 23 2 24 4 20 3 1 7 27 37 31 25 38 29 29 17 plot(lt, type = l) axis(4, at = unique(lt)) Looks a bit weird because of the number of unique values in lt, but will look OK with the data series you posted earlier. Also, plot(lt, type = l) axis(4, at = pretty(range(lt)),line=0.75,tick=TRUE) doesn't look right on my default device, do you really want to move the axis away from the plot margin? HTH G any help is appreciated. thanks. #--- axis(4, at = pretty(range(lt)),line=0.75,tick=TRUE) #--- -- This is not an offer (or solicitation of an offer) to buy/sell the securities/instruments mentioned or an official confirmation. Morgan Stanley may deal as principal in or own or act as market maker for securities/instruments mentioned or may advise the issuers. This is not research and is not from MS Research but it may refer to a research analyst/research report. Unless indicated, these views are the author's and may differ from those of Morgan Stanley research or others in the Firm. We do not represent this is accurate or complete and we may not update this. Past performance is not indicative of future returns. For additional information, research reports and important disclosures, contact me or see https://secure.ms.com/servlet/cls. You should not use e-mail to request, authorize or effect the purchase or sale of any security or instrument, to send transfer instructions, or to effect any other transactions. We cannot guarantee that any such requests received vi! a ! e-mail will be processed in a timely manner. This communication is solely for the addressee(s) and may contain confidential information. We do not waive confidentiality by mistransmission. Contact me if you do not wish to receive these communications. In the UK, this communication is directed in the UK to those persons who are market counterparties or intermediate customers (as defined in the UK Financial Services Authority's rules). [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Gavin Simpson [t] +44 (0)20 7679 0522 ECRC ENSIS, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/cv/ London, UK. WC1E 6BT. [w] http://www.ucl.ac.uk/~ucfagls/ %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] information about sna packages
Hello, I'm a student who want to use the R social network analysis package. I have a question: can this package analyse dynamical networks (network changing over time)? I didn't find this functionality in the package's user manual. Thank you Davide [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] (no subject)
Dear R users, Please excuse my inexperience. I am trying to contrain the coefficients of my linear regression to equal one when using the -lm(...) command. I've searched help(glm) help(model.offset) etc. but I am unable to figure out where to put this constraint. Your help would be greatly apprciated. Thanks. [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] did my searching but still couldn't find anything for bayesian dlm
I familarized myelf with kalmanlike and structts which are approaches for building and estimating ( and forecasting ) state space models ( or the equivalent arima models ). back in 2003, gavin simpson wrote an email describing the west and harrison apprach to estimate state space models and asked if anything was out there for using that approach. the goals of this approach are the same as kalman like and structts but priors are put on the variances and a bayesian approach is used to estimate the next state. in this manner, , all numerical optimization is avoided ( but obviously the results are different also so it's not necessarily a better approach. just different ). i'm dealing with minute by minute data so , for me, it's essential to avoid computing likelihoods over and over. is it possible, that , since gavin's email, the west and harrison approach has been built in one of the many packages out there. i looked really hard but i couldn't find it. my guess is that the answer is no. thanks for any input. mark This is not an offer (or solicitation of an offer) to buy/sell the securities/instruments mentioned or an official confirmation. Morgan Stanley may deal as principal in or own or act as market maker for securities/instruments mentioned or may advise the issuers. This is not research and is not from MS Research but it may refer to a research analyst/research report. Unless indicated, these views are the author's and may differ from those of Morgan Stanley research or others in the Firm. We do not represent this is accurate or complete and we may not update this. Past performance is not indicative of future returns. For additional information, research reports and important disclosures, contact me or see https://secure.ms.com/servlet/cls. You should not use e-mail to request, authorize or effect the purchase or sale of any security or instrument, to send transfer instructions, or to effect any other transactions. We cannot guarantee that any such requests received via ! e-mail will be processed in a timely manner. This communication is solely for the addressee(s) and may contain confidential information. We do not waive confidentiality by mistransmission. Contact me if you do not wish to receive these communications. In the UK, this communication is directed in the UK to those persons who are market counterparties or intermediate customers (as defined in the UK Financial Services Authority's rules). [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] coefficient constraints
Hi, Thank you for your help. I'm trying to constrain the coefficients on a linear regression model, -lm(...), to all equal one, except for the intercept. I've searched help(glm), help(model.fit), etc. but I can not find where to add the constraint. Your help would be greatly appreciated. Thanks. [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] coefficient constraints
Dear John, You can subtract the variables in question from the left-hand-side of the model [e.g., lm(y - x1 - x2 ~ 1)], or use the offset argument to lm [e.g., lm(y ~ 1, offset=x1 + x2)], or use offset() in the model formula [e.g., lm(y ~ offset(x1 + x2)]. All of these options are equivalent. I hope this helps, John John Fox Department of Sociology McMaster University Hamilton, Ontario Canada L8S 4M4 905-525-9140x23604 http://socserv.mcmaster.ca/jfox -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of John Gauss Sent: Tuesday, October 31, 2006 7:28 PM To: r-help@stat.math.ethz.ch Subject: [R] coefficient constraints Hi, Thank you for your help. I'm trying to constrain the coefficients on a linear regression model, -lm(...), to all equal one, except for the intercept. I've searched help(glm), help(model.fit), etc. but I can not find where to add the constraint. Your help would be greatly appreciated. Thanks. [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] graphics not find source
Hi, The plot function not produces graphics in linux. The msg: Error in X11(): it was not possible to find no source X11 Verifity if the way of sources is correct. Any ideas? Thanks, Ricardo __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] [R-pkgs] rcompletion: TAB completion for the R command line
On 10/31/06, Alexandre Aguiar [EMAIL PROTECTED] wrote:
Hi,
I've tried to compile rcompletion and perhaps have detected the reason for
failures, although I haven't succeeded yet.
Yes, this could very well be the reason. R's configure script has
checks for ncurses with the comment:
## only need ncurses if libreadline is not statically linked against it
I'll try to adapt that and put out a test version tomorrow.
-Deepayan
Em Ter 31 Out 2006 02:10, Deepayan Sarkar escreveu:
However, there are known cases
of false negatives, i.e. installation failing when it shouldn't. If
this happens to you, any information you can provide to help resolve
the problem would be appreciated.
From config.lo generated by rcompletion configure
---8
/usr/local/lib/gcc/i686-pc-linux-gnu/4.0.3/../../../libreadline.so: undefined
reference to `tgetnum'
/usr/local/lib/gcc/i686-pc-linux-gnu/4.0.3/../../../libreadline.so: undefined
reference to `tgoto'
/usr/local/lib/gcc/i686-pc-linux-gnu/4.0.3/../../../libreadline.so: undefined
reference to `tgetflag'
/usr/local/lib/gcc/i686-pc-linux-gnu/4.0.3/../../../libreadline.so: undefined
reference to `BC'
/usr/local/lib/gcc/i686-pc-linux-gnu/4.0.3/../../../libreadline.so: undefined
reference to `tputs'
/usr/local/lib/gcc/i686-pc-linux-gnu/4.0.3/../../../libreadline.so: undefined
reference to `PC'
/usr/local/lib/gcc/i686-pc-linux-gnu/4.0.3/../../../libreadline.so: undefined
reference to `tgetent'
/usr/local/lib/gcc/i686-pc-linux-gnu/4.0.3/../../../libreadline.so: undefined
reference to `UP'
/usr/local/lib/gcc/i686-pc-linux-gnu/4.0.3/../../../libreadline.so: undefined
reference to `tgetstr'
---8
It seems configure can't figure where to find these functions.
From readline5.0 configure script
---8
checking for tgetent... no
checking for tgetent in -ltermcap... no
checking for tgetent in -ltinfo... no
checking for tgetent in -lcurses... yes
checking which library has the termcap functions... using libcurses
---8
The unresolved function calls (and perhaps symbols of other types) may be
located at libcurses. At least in my system they are.
From termcap.h
---8
#undef NCURSES_VERSION
#define NCURSES_VERSION 5.5
#include ncurses_dll.h
#ifdef __cplusplus
extern C
{
#endif /* __cplusplus */
#include sys/types.h
#undef NCURSES_CONST
#define NCURSES_CONST /*nothing*/
#undef NCURSES_OSPEED
#define NCURSES_OSPEED short
extern NCURSES_EXPORT_VAR(char) PC;
extern NCURSES_EXPORT_VAR(char *) UP;
extern NCURSES_EXPORT_VAR(char *) BC;
extern NCURSES_EXPORT_VAR(NCURSES_OSPEED) ospeed;
#if !defined(NCURSES_TERM_H_incl)
extern NCURSES_EXPORT(char *) tgetstr (NCURSES_CONST char *, char **);
extern NCURSES_EXPORT(char *) tgoto (const char *, int, int);
extern NCURSES_EXPORT(int) tgetent (char *, const char *);
extern NCURSES_EXPORT(int) tgetflag (NCURSES_CONST char *);
extern NCURSES_EXPORT(int) tgetnum (NCURSES_CONST char *);
extern NCURSES_EXPORT(int) tputs (const char *, int, int (*)(int));
#endif
---8
May be your configure needs some rewriting to include a check for the location
of unknown symbols like readline's configure does.
Best wishes,
--
Alexandre Aguiar
Independent consultant for medical research
SPS Consultoria
Voice: +55-11-9320-2046
Fax: +55-11-5549-8760
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Re: [R] [R-pkgs] rcompletion: TAB completion for the R command line
Em Ter 31 Out 2006 19:43, Alexandre Aguiar escreveu: I've tried to compile rcompletion and perhaps have detected the reason for failures, although I haven't succeeded yet. The solution is actually trivial: Options: 1. set the environment variable LIBS to LIBS=-lcurses $ LIBS=-lcurses $ R install.packages(rcompletion) 2. change the line LIBS=-lreadline $LIBS in configure script to LIBS=-lreadline -lcurses $LIBS and then regenerate the tar.gz package. $ R install.packages(rcompletion, repos=NULL) During compilation the -lcurses option does not appear in the command lines, it seems necessary only during tests. Haven't tested thoroughly but rcompletion seems to work fine. Best wishes. -- Alexandre Aguiar Independent consultant for medical research SPS Consultoria Voice: +55-11-9320-2046 Fax: +55-11-5549-8760 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Problem with data type recognition and conversion
Hi, I have a CSV file with two columns; the first column is date, second column is numbers. I used read.csv() to load the file into the variable temp. Somehow, R could not recognize my numbers as double. Instead, it thinks these numbers are integer even though they all have decimal points (isn't that strange?). The problem I ran into is that if I tried to convert the numbers to double using as.double, R doesn't give me the original value; e.g. 9.92 becomes 805 (see below). temp[1,2] [1] 9.92 812 Levels: . 10.00 10.01 10.02 10.03 10.04 10.05 10.06 10.07 10.08 10.09 10.10 10.11 10.12 ... 9.99 typeof(temp[1,2]) [1] integer as.double(temp[1,2]) [1] 805 If I leave the numbers as integer, then I can't do arithmetic operations on them. Does anyone know what's going on? Thanks, Tom [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Hessian matrix
Dear all R users, Is there any way to calculate hessian matrix of a given function at any given point? Regards [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] avoiding 'for' loop
Hi R users
I have a 1000 * 11 matrix (or data.frame). The first 10 columns consist of 0
or 1 (i.e., binary data) and the last column consists of real values.
I would like to run a logistic regression with the first binary column as a
dependent variable, and the second binary column and the last real value
column as independent variables. After this, I save 'Z' value for the binary
independent variable. Then, with the first binary column as a dependent
variable, and the third binary column and the last real value column as
independent variables. After this, I saved 'Z' value for the binary
independent variable, keeping doing this ...
Here is my simple R codes
logistic.z.value -c()
for (i in 1:9)
{
for (j in (i+1):10)
{
model - glm(X[,i] ~ X[,11] + X[,j], family=binomial(logit))
logistic.z.value -
append(logistic.z.value,coef(summary(model))[3,3])
}
}
I would like to avoid using 'for' loop command. Is there any way for me to
use some fast codes instead of using 'for' loop?
Many thanks
Taka,
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Re: [R] Odd behaviour of removing 'nothing' from an array or data frame
Thanks to all for the swift replies. I'm willing to concede that changing
the behaviour of [-integer(0)] is probably going to end in tears, so I'll
stop arguing.
I've added a quick note on the traps page of the R wiki to explain things;
feel free to expand upon it.
http://wiki.r-project.org/rwiki/doku.php?id=tips:surprises:traps
Regards,
Richie.
Mathematical Sciences Unit
HSL
Buxton
SK17 9JN
01298 21(x8672)
ATTENTION:
This message contains privileged and confidential informatio...{{dropped}}
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[R] plot - X11()
Hi, The plot() function not produces graphics in linux. Msg: Error in X11(): it was not possible to find no source X11 Verify if the path of sources is correct. I hope it helps. Best, Ricardo ___ o discador agora! [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] How to find further informations on specific options?
Dear friends, When i read the R-help , i often find the following case: e.g.:surf.gls(np, covmod, x, y, z, nx = 1000, ...) #Package Spatial: Arguments: covmod: function to evaluate covariance or correlation function * ...: parameters for 'covmod'* How should i find the further information on *...: parameters for 'covmod'* ? I use the ?covmod, but can't find the information. Could anybody give me the general method to do so? -- With Kind Regards, oooO: (..): :\.(:::Oooo:: ::\_)::(..):: :::)./::: ::(_/ : [***] Zhi Jie,Zhang ,PHD Tel:86-21-54237149 [EMAIL PROTECTED] Dept. of Epidemiology,school of public health,Fudan University Address:No. 138 Yi Xue Yuan Road,Shanghai,China Postcode:200032 [***] oooO: (..): :\.(:::Oooo:: ::\_)::(..):: :::)./::: ::(_/ : [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to find further informations on specific options?
On Wed, 1 Nov 2006, zhijie zhang wrote: Dear friends, When i read the R-help , i often find the following case: e.g.:surf.gls(np, covmod, x, y, z, nx = 1000, ...) #Package Spatial: Arguments: covmod: function to evaluate covariance or correlation function * ...: parameters for 'covmod'* How should i find the further information on *...: parameters for 'covmod'* ? I use the ?covmod, but can't find the information. Could anybody give me the general method to do so? The spatial package is documented in full in Venables Ripley (2002) Modern Applied Statistics with S, Chapter 15, section 2, pp. 425-430 (in the References section of the help page). However, on ?surf.gls, the See Also section provides links to help pages describing expcov, gaucov, and sphercov, so looking at See Also seems to be the general method you need. -- Roger Bivand Economic Geography Section, Department of Economics, Norwegian School of Economics and Business Administration, Helleveien 30, N-5045 Bergen, Norway. voice: +47 55 95 93 55; fax +47 55 95 95 43 e-mail: [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
