[R] R-2.6.0 and RWinEdt
Dear Listers, I have just installed R-2.6.0 and the RWinEdt package 1.7-6 under Windows XP. The R-WinEdt menu well appears at launching (the command library(RWinEdt) is in .Rprofile), but WinEdt is NOT started automatically (this was not the case in the earlier versions of R). When WinEdt is started by hand (eg double-click on a RWinEdt alias after R launching), syntax highlighting and connexion to R works well. Any idea about how to fix this and get WinEdt automatically started when library(RWinEdt) is called? Patrick __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Tart charts
roger koenker wrote: It being friday, I would like to call your attention to an innovative data analysis by Leslie Lamport available from: http://research.microsoft.com/users/lamport/pubs/hair.pdf I particularly liked the graphics. Stone the flamin' crows, why didn't I think of that? Jim __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] installing Rmpi
On Fri, 5 Oct 2007, Erin Hodgess wrote: Hi R people: I installed R-2.6.0 on a Red Hat Linux system and am now trying to install the Rmpi package. The installation cannot seem to find the mpi.h file, even though it exists. Is there a variable that I should be exporting into the process, please? It's tricky, and we may need to know a bit more about your OS. I presume you have the latest Rmpi 0.5-4: if not get it from the CRAN master (it may still be propagating). On the RH systems I have seen the mpi.h file is in /usr/include/lam. So you need to ensure you have that installed, and it is in the lam-devel RPM (which has other dependencies, including lam and lam-libs). If that is installed and this is still failing you need to look at the config.log to see why -- that's not R-help territory and I think you need to find some local expertise to help you: if that is not possible, use R-devel. The problems I usually find are with the next step, finding the libraries. I've seen systems where /usr/lib64/lam was not in the ld.so cache, and others where you needed to link against -lutil as well as -lmpi -llam. Only someone with essentially the same OS on the same cputype will be able to help you find things like this. (For some reaons Rmpi tests for static libraries on 32-bit systems and dynamic ones on 64-bit systems.) Incidentally, the lam RPMs have things in quite different places from a vanilla source install of lam, so you do need to tell us exactly when your MPI libraries came from. -- 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@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Mac GUI and .Renviron
Jacob, As Steven mentioned, [EMAIL PROTECTED] is a list specific for OSX only questions. I think you can achieve something similar by going into the preference settings of R.app, select the Startup section and select 'Source input file', de-select 'Always apply' and make the R history file something like 'Rhistory', no fixed path. You can up the number of history entries, although with R.app's multiline history and with 'Cleanup history entries' and ' Remove duplicate entries in history' selected, 250 in a GUI is in many cases a lot. In Finder, double-click an .R file you want to work on (or drag its icon onto the R icon in the Dock), R will open in the dir of the file and read the correct history file. It will open the double-clicked or dragged file in either the internal or external editor, whichever one is selected. I do not think you can, without some further steps, run multiple R.apps at the same time. Let me know if that is critical for you. Hope this helps, regards, Rob On Oct 5, 2007, at 2:17 PM, jwegelin wrote: The .Renviron and .First functions do not seem to work the same way on a Mac OS 10.4 as on a Windows XP machine. From working in Windows I am used to creating a new directory for each data analysis project. In the new directory I place First, an .Renviron file consisting of the following text: R_HISTFILE=history.txt R_HISTSIZE=100 Second, an .RData file containing a .First function designed for the particular project. Then each project has, in its own directory, its own history.txt file of practically unlimited size recording each command I type; I can open a separate instance of R for each project by doubleclicking .RData in the appropriate directory; and the .First function for a particular project is run automatically each time I doubleclick .RData in the directory for that project. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Rounding of lme coefficients: Mac vs Windows
All, I have an lme model estimated in R 2.5.1 on my Mac; when I estimate the same model on Windows, the parameter coefficients are rounded to integers. Below is a similar example for the Orthodont data. Is there some option I need to set in the Windows version to prevent rounding? Didn't see this in the archives. Thanks, David Afshartous sessionInfo() R version 2.5.1 (2007-06-27) i386-apple-darwin8.9.1 locale: en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: nlme 3.1-84 fm1 - lme(distance ~ age, data = Orthodont) # random is ~ age fm1 Linear mixed-effects model fit by REML Data: Orthodont Log-restricted-likelihood: -221.3183 Fixed: distance ~ age (Intercept) age 16.761 0.6601852 Random effects: Formula: ~age | Subject Structure: General positive-definite StdDevCorr (Intercept) 2.3270338 (Intr) age 0.2264276 -0.609 Residual1.3100399 Number of Observations: 108 Number of Groups: 27 sessionInfo() R version 2.6.0 (2007-10-03) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] nlme_3.1-85 foreign_0.8-23arm_1.0-33R2WinBUGS_2.1-6 [5] coda_0.12-1 lme4_0.99875-8Matrix_0.999375-2 lattice_0.16-5 [9] MASS_7.2-36 loaded via a namespace (and not attached): [1] grid_2.6.0 tools_2.6.0 fm1 - lme(distance ~ age, data = Orthodont) # random is ~ age fm1 Linear mixed-effects model fit by REML Data: Orthodont Log-restricted-likelihood: -221 Fixed: distance ~ age (Intercept) age 16.760.66 Random effects: Formula: ~age | Subject Structure: General positive-definite StdDev Corr (Intercept) 2.33 (Intr) age 0.23 -0.61 Residual1.31 Number of Observations: 108 Number of Groups: 27 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Linux editor for R+LaTeX, but not Emacs
On 6 October 2007 at 11:01, Scionforbai wrote: | What features are you missing in emacs that you wish were there? Are | these ESS features or LaTeX related features? | | is it only me or has anyone else the problem that running an R process | within emacs is way much slower than in a regular terminal/console? | (linux here) It's just you, and if you think some more about it, you'll see why we are all grinning. [ Hint: it can't be slower, outside of ridiculous corner sitations where there isn't enough ram for Emacs and R at the same time. Or foobared setups. In all normal situations, it'll be the same. ] But the proof of the pudding is in the eating. So here from the console: system.time(replicate(100, svd(matrix(rnorm(100*100), ncol=100 user system elapsed 2.792 0.048 2.842 and cutpasted from ESS system.time(replicate(100, svd(matrix(rnorm(100*100), ncol=100 user system elapsed 2.736 0.048 2.787 (Heaven's, ESS is even faster :) Output to the console, ie the Emacs buffer, may appear slower, or be slower. I don't care. I try not to print that many line. But then you get goodies like C-c C-o to 'eat up' output you didn't mean to flood the console with. Seriously, outside of spreading R on sliced bread, there is no better way to use it than with ESS. Dirk -- Three out of two people have difficulties with fractions. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Tart charts
Try this alternative: # from http://research.microsoft.com/users/lamport/pubs/hair.pdf hairsex - matrix( c(46, 45, 13, 12, 1, 101, 0, 20), 2, 4, byrow=TRUE) dimnames(hairsex) - list(Gender=c(Female, Male), Hair color=c(Blond, Brown, Red, Other) ) library(vcd) mosaic(hairsex, shade=TRUE) There are uses for pie charts, but this isn't one of the better ones. -Michael roger koenker wrote: It being friday, I would like to call your attention to an innovative data analysis by Leslie Lamport available from: http://research.microsoft.com/users/lamport/pubs/hair.pdf I particularly liked the graphics. url:www.econ.uiuc.edu/~rogerRoger Koenker email[EMAIL PROTECTED]Department of Economics vox: 217-333-4558University of Illinois fax: 217-244-6678Champaign, IL 61820 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. York University Voice: 416 736-5115 x66249 Fax: 416 736-5814 4700 Keele Streethttp://www.math.yorku.ca/SCS/friendly.html Toronto, ONT M3J 1P3 CANADA __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Bug or not
I have this sample from help. I try use command erase.screen() but in split mode sreen dont erase. Why? split.screen(c(2,1)) # split display into two screens split.screen(c(1,2),2) # split bottom half in two plot(1:10) # screen 3 is active, draw plot erase.screen() # forgot label, erase and redraw IN THIS PLACE SCREEN DONT ERASE plot(1:10, ylab= ylab 3) IN THIS PLACE COMMAND PLOT ON TOP screen(1) # prepare screen 1 for output __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] help_R2.5 updating
Hi, I run windows vista ultimate in my laptop and run R 2.5 I am trying to update the packages but it comes up with an error message Warning in install.packages(update[instlib == l, Package], l, contriburl = contriburl, : 'lib' is not writable Error in install.packages(update[instlib == l, Package], l, contriburl = contriburl, : unable to install packages I am the adminsitrator on this computer and logged in as administrator. can anyone advise. I treid to switch off most security - windows firewall is off and so is macfee. many thanks for your advise bragadeesh _ Climb to the top of the charts! Play Star Shuffle: the word scramble challenge with star power. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Simulate data based on correlation coefficient
Hello all, I have a vector with 1000 values and I would like to generate other correlated vector, but with different correlation coefficient (for example, r = 0.7). Any ideas how can I do this? Regards, Gustavo. ___ Experimente já e veja as novidades. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Question about Distinguishable Permutation
Hi, How can I list all possilities of Distinguishable Permutation by R? For example, N=6, n1=n2=n3=2, the total possible answers are 6!/(2!2!2!)=90. Please help me. Thank you So much. ¡A [EMAIL PROTECTED]://tw.mobile.yahoo.com/texts/mail.php [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] list matching
Dear list, Given a list of elements like: aa - list(one=c(o, n, e), tea=c(t, e, a), thre=c(t, h, r, e)) Is there a function that returns the intersection between all? Both match() and intersect() only deal with two arguments, but sometimes I have more. Here, it should return e (or NA if none of the letters are common). I have a solution to apply %in% multiple times (here two times, first between the first two and then between the result and the third) but... perhaps there is a better and quicker way. Thanks in advance, Adrian -- Adrian Dusa Romanian Social Data Archive 1, Schitu Magureanu Bd 050025 Bucharest sector 5 Romania Tel./Fax: +40 21 3126618 \ +40 21 3120210 / int.101 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] problem installing fields package 3.5 on R 1.8.1 on linux
I am returning to using R after a little time away. Saw some great new functions in the fields package and decided to upgrade. Everything seems to go fine until I tried to actually load the package, when I get an error: library(fields) Error in parse(file, n, text, prompt) : syntax error on line 227 And (of course) I am unable to access any of the functions in the fields package. Below is the full install session. thanks for any help! Jim -- [EMAIL PROTECTED] R R : Copyright 2003, The R Foundation for Statistical Computing Version 1.8.1 (2003-11-21), ISBN 3-900051-00-3 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for a HTML browser interface to help. Type 'q()' to quit R. [Previously saved workspace restored] update.packages(ask=TRUE) trying URL `http://cran.r-project.org/src/contrib/PACKAGES' Content type `text/plain' length 144627 bytes opened URL .. .. .. .. .. .. .. .. .. .. .. .. .. .. . downloaded 141Kb fields : Version 1.4.2 in /usr/lib/R/library Version 3.5 on CRAN Update (y/N)? y xgobi : Version 1.2-12 in /usr/lib/R/library Version 1.2-13 on CRAN Update (y/N)? N trying URL `http://cran.r-project.org/src/contrib/fields_3.5.tar.gz' Content type `application/x-gzip' length 447560 bytes opened URL .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. .. ... downloaded 437Kb * Installing *source* package 'fields' ... ** libs g77 -mieee-fp -fPIC -O2 -g -pipe -march=i386 -mcpu=i686 -c css.f -o css.o g77 -mieee-fp -fPIC -O2 -g -pipe -march=i386 -mcpu=i686 -c csstr.f -o csstr.o g77 -mieee-fp -fPIC -O2 -g -pipe -march=i386 -mcpu=i686 -c cvrf.f -o cvrf.o g77 -mieee-fp -fPIC -O2 -g -pipe -march=i386 -mcpu=i686 -c dchold.f -o dchold.o g77 -mieee-fp -fPIC -O2 -g -pipe -march=i386 -mcpu=i686 -c dcopy.f -o dcopy.o g77 -mieee-fp -fPIC -O2 -g -pipe -march=i386 -mcpu=i686 -c ddot.f -o ddot.o g77 -mieee-fp -fPIC -O2 -g -pipe -march=i386 -mcpu=i686 -c dlv.f -o dlv.o g77 -mieee-fp -fPIC -O2 -g -pipe -march=i386 -mcpu=i686 -c dmaket.f -o dmaket.o g77 -mieee-fp -fPIC -O2 -g -pipe -march=i386 -mcpu=i686 -c drdfun.f -o drdfun.o g77 -mieee-fp -fPIC -O2 -g -pipe -march=i386 -mcpu=i686 -c dsetup.f -o dsetup.o g77 -mieee-fp -fPIC -O2 -g -pipe -march=i386 -mcpu=i686 -c expbs.f -o expbs.o g77 -mieee-fp -fPIC -O2 -g -pipe -march=i386 -mcpu=i686 -c expfn.f -o expfn.o g77 -mieee-fp -fPIC -O2 -g -pipe -march=i386 -mcpu=i686 -c gaspbs.f -o gaspbs.o g77 -mieee-fp -fPIC -O2 -g -pipe -march=i386 -mcpu=i686 -c gaspfn.f -o gaspfn.o g77 -mieee-fp -fPIC -O2 -g -pipe -march=i386 -mcpu=i686 -c gcvcss.f -o gcvcss.o g77 -mieee-fp -fPIC -O2 -g -pipe -march=i386 -mcpu=i686 -c gcvfc.f -o gcvfc.o g77 -mieee-fp -fPIC -O2 -g -pipe -march=i386 -mcpu=i686 -c hsort.f -o hsort.o g77 -mieee-fp -fPIC -O2 -g -pipe -march=i386 -mcpu=i686 -c ifind.f -o ifind.o g77 -mieee-fp -fPIC -O2 -g -pipe -march=i386 -mcpu=i686 -c inpoly.f -o inpoly.o g77 -mieee-fp -fPIC -O2 -g -pipe -march=i386 -mcpu=i686 -c lscv.f -o lscv.o g77 -mieee-fp -fPIC -O2 -g -pipe -march=i386 -mcpu=i686 -c m2deb.f -o m2deb.o g77 -mieee-fp -fPIC -O2 -g -pipe -march=i386 -mcpu=i686 -c mkpoly.f -o mkpoly.o g77 -mieee-fp -fPIC -O2 -g -pipe -march=i386 -mcpu=i686 -c mltdrb.f -o mltdrb.o g77 -mieee-fp -fPIC -O2 -g -pipe -march=i386 -mcpu=i686 -c mltdtd.f -o mltdtd.o g77 -mieee-fp -fPIC -O2 -g -pipe -march=i386 -mcpu=i686 -c msort.f -o msort.o g77 -mieee-fp -fPIC -O2 -g -pipe -march=i386 -mcpu=i686 -c multeb.f -o multeb.o g77 -mieee-fp -fPIC -O2 -g -pipe -march=i386 -mcpu=i686 -c multgb.f -o multgb.o g77 -mieee-fp -fPIC -O2 -g -pipe -march=i386 -mcpu=i686 -c multrb.f -o multrb.o g77 -mieee-fp -fPIC -O2 -g -pipe -march=i386 -mcpu=i686 -c radbas.f -o radbas.o g77 -mieee-fp -fPIC -O2 -g -pipe -march=i386 -mcpu=i686 -c radfun.f -o radfun.o g77 -mieee-fp -fPIC -O2 -g -pipe -march=i386 -mcpu=i686 -c rcss.f -o rcss.o g77 -mieee-fp -fPIC -O2 -g -pipe -march=i386 -mcpu=i686 -c rcssr.f -o rcssr.o g77 -mieee-fp -fPIC -O2 -g -pipe -march=i386 -mcpu=i686 -c rcsswt.f -o rcsswt.o g77 -mieee-fp -fPIC -O2 -g -pipe -march=i386
Re: [R] list matching
On Sat, 2007-10-06 at 19:49 +, Adrian Dusa wrote:
Dear list,
Given a list of elements like:
aa - list(one=c(o, n, e),
tea=c(t, e, a),
thre=c(t, h, r, e))
Is there a function that returns the intersection between all?
Both match() and intersect() only deal with two arguments, but sometimes I
have more.
Here, it should return e (or NA if none of the letters are common).
I have a solution to apply %in% multiple times (here two times, first between
the first two and then between the result and the third) but... perhaps there
is a better and quicker way.
Thanks in advance,
Adrian
intersectList - function(x)
{
res - table(unlist(sapply(x, unique)))
names(res[res == length(x)])
}
In the first line, I use unique() to ensure that if the same letter
appears more than once in the same list element, it is not included in
the result set in error, such as in 'L' here:
L - list(a = c(a, b, b), b = c(d, b, a), c = c(d, a))
L
$a
[1] a b b
$b
[1] d b a
$c
[1] d a
So:
intersectList(aa)
[1] e
intersectList(L)
[1] a
HTH,
Marc Schwartz
__
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https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] problem installing fields package 3.5 on R 1.8.1 on linux
On Sat, 2007-10-06 at 14:05 -0600, jpgirard wrote: I am returning to using R after a little time away. Saw some great new functions in the fields package and decided to upgrade. Everything seems to go fine until I tried to actually load the package, when I get an error: library(fields) Error in parse(file, n, text, prompt) : syntax error on line 227 And (of course) I am unable to access any of the functions in the fields package. Below is the full install session. thanks for any help! Jim -- [EMAIL PROTECTED] R R : Copyright 2003, The R Foundation for Statistical Computing Version 1.8.1 (2003-11-21), ISBN 3-900051-00-3 You are almost four years out of date here. R version 2.6.0 was released this past week. I would strongly urge you to remove your old R installation completely and install R from scratch, along with new versions of all the packages you require. Once you have done that, re-install the fields package. There is almost certainly a conflict between the latest version of fields and your old version of R. If there is a still a problem, post back and/or contact the package maintainer. HTH, Marc Schwartz __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Linux editor for R+LaTeX, but not Emacs
On 10/6/07, Dirk Eddelbuettel [EMAIL PROTECTED] wrote: On 6 October 2007 at 11:01, Scionforbai wrote: | What features are you missing in emacs that you wish were there? Are | these ESS features or LaTeX related features? | | is it only me or has anyone else the problem that running an R process | within emacs is way much slower than in a regular terminal/console? | (linux here) It's just you, and if you think some more about it, you'll see why we are all grinning. [ Hint: it can't be slower, outside of ridiculous corner sitations where there isn't enough ram for Emacs and R at the same time. Or foobared setups. In all normal situations, it'll be the same. ] Actually, copying multi-line R code (e.g. C-c C-r) is way slower with ESS if you use Emacs22 (and its derivatives such as AquaMacs). Things are perfect with Emacs21 though (and I'm sticking with it). Maybe that explains the discrepancy. -Deepayan __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] list matching
On Saturday 06 October 2007, Marc Schwartz wrote:
[...]
intersectList - function(x)
{
res - table(unlist(sapply(x, unique)))
names(res[res == length(x)])
}
In the first line, I use unique() to ensure that if the same letter
appears more than once in the same list element, it is not included in
the result set in error, such as in 'L' here:
L - list(a = c(a, b, b), b = c(d, b, a), c = c(d, a))
L
$a
[1] a b b
$b
[1] d b a
$c
[1] d a
So:
intersectList(aa)
[1] e
intersectList(L)
[1] a
Neat :o)
Of course, this was the right way to follow... in my particular case the
elements are always unique but generally this is the best approach indeed.
Thanks Marc,
Adrian
--
Adrian Dusa
Romanian Social Data Archive
1, Schitu Magureanu Bd
050025 Bucharest sector 5
Romania
Tel./Fax: +40 21 3126618 \
+40 21 3120210 / int.101
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Linux editor for R+LaTeX, but not Emacs
On Sat, 2007-10-06 at 13:42 -0500, Dirk Eddelbuettel wrote: On 6 October 2007 at 11:01, Scionforbai wrote: | What features are you missing in emacs that you wish were there? Are | these ESS features or LaTeX related features? | | is it only me or has anyone else the problem that running an R process | within emacs is way much slower than in a regular terminal/console? | (linux here) It's just you, and if you think some more about it, you'll see why we are all grinning. [ Hint: it can't be slower, outside of ridiculous corner sitations where there isn't enough ram for Emacs and R at the same time. Or foobared setups. In all normal situations, it'll be the same. ] But the proof of the pudding is in the eating. So here from the console: system.time(replicate(100, svd(matrix(rnorm(100*100), ncol=100 user system elapsed 2.792 0.048 2.842 and cutpasted from ESS system.time(replicate(100, svd(matrix(rnorm(100*100), ncol=100 user system elapsed 2.736 0.048 2.787 (Heaven's, ESS is even faster :) Output to the console, ie the Emacs buffer, may appear slower, or be slower. I don't care. I try not to print that many line. But then you get goodies like C-c C-o to 'eat up' output you didn't mean to flood the console with. Seriously, outside of spreading R on sliced bread, there is no better way to use it than with ESS. I nominate that last line for a fortune candidate... :-) Regards, Marc __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] plot the chi-square distribution for n=1 through 10, on one plot
Dear help list. I would like to plot the chi-square distribution for n=1 through 10, on one plot. How do I go about doing that? I know how to plot one chi-square (using curve() for example), but plotting 10 on one plot, that is too difficult for me. I greatly appreciate your help. -- fb [EMAIL PROTECTED] -- __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] plot the chi-square distribution for n=1 through 10, on one plot
fb wrote: Dear help list. I would like to plot the chi-square distribution for n=1 through 10, on one plot. How do I go about doing that? I know how to plot one chi-square (using curve() for example), but plotting 10 on one plot, that is too difficult for me. I greatly appreciate your help. Here is one way: curve(dchisq(x,1), from=0, to=15) for(i in 2:9) curve(dchisq(x,i), add=T, from=0, to=15) -- 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@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Tricky vectorization problem
Hi all,
I'm using the code below within a loop that I run thousands of times
and even with the super-computing resources at my disposal this is
just too slow. The snippet below takes about 10s on my machines,
which is an order of magnitude or two slower than would be
preferable; in the end I'd like to set the number of monte carlo
experiments to 1e4 or even 1e5 to ensure stable results. I've tried
my hand at vectorizing it myself but I'm finding it tricky. Any help
would be greatly appreciated!
This code attempts to find the distribution of observed correlation
values between A B when each are measured imperfectly:
start = proc.time()[1] #start a timer
rho = .5 #set the true correllation
Ns = 100 #set the number of Subjects
a.No = 1:100 #for each subject, set a number of observations in A
(1:100 chosen arbitrarily for demonstration)
b.No = 1:100 #for each subject, set a number of observations in B
v.a = 1 #set the between Ss variance in condition A
v.b = 2 #set the between Ss variance in condition B
s.a.w = 1:100 #for each subject, set a standard deviation in A (1:100
chosen arbitrarily for demonstration)
s.b.w = 1:100 #for each subject, set a standard deviation in B
mce = 1e3 #set the number of monte carlo experiments
sim.r = vector(length=mce) #set up a collector for the simulated
correlations
Sigma=matrix(c(v.a,sqrt(v.a*v.b)*rho,sqrt(v.a*v.b)*rho,v.b),2,2)
#define a covariance matrix for use in generating the correlated data
a = vector(length=Ns) #set up a collector for subject means in A
b = vector(length=Ns) #set up a collector for subject means in B
for(i in 1:mce){ #start a monte carlo experiment
sub.means=mvrnorm(Ns,rep(0,2),Sigma) #generate correlated ideal
means for for each subject in each condition
for(s in 1:Ns){ #for each subject
a[s] = mean(rnorm(a.No[s],sub.means[s,1],s.a.w[s])) #generate
some
data for A and grab the mean
b[s] = mean(rnorm(b.No[s],sub.means[s,2],s.b.w[s])) #generate
some
data for B and grab the mean
}
sim.r[i] = cor(a,b) #store the observed correlation between A and B
}
print(proc.time()[1]-start) #show the total time this took
--
Mike Lawrence
Graduate Student, Department of Psychology, Dalhousie University
Website: http://memetic.ca
Public calendar: http://icalx.com/public/informavore/Public
The road to wisdom? Well, it's plain and simple to express:
Err and err and err again, but less and less and less.
- Piet Hein
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Re: [R] list matching
zoo's merge can do a multiway intersection. We turn each component of aa into the times of a dataless zoo object (assuming the elements of each component are unique) and merge them together using all = FALSE which will only leave those points at times in all components. Extracting the time and stripping off the names gives the result. library(zoo) as.vector(time(do.call(merge, c(lapply(aa, function(x) zoo(,x)), all = FALSE On 10/6/07, Adrian Dusa [EMAIL PROTECTED] wrote: Dear list, Given a list of elements like: aa - list(one=c(o, n, e), tea=c(t, e, a), thre=c(t, h, r, e)) Is there a function that returns the intersection between all? Both match() and intersect() only deal with two arguments, but sometimes I have more. Here, it should return e (or NA if none of the letters are common). I have a solution to apply %in% multiple times (here two times, first between the first two and then between the result and the third) but... perhaps there is a better and quicker way. Thanks in advance, Adrian -- Adrian Dusa Romanian Social Data Archive 1, Schitu Magureanu Bd 050025 Bucharest sector 5 Romania Tel./Fax: +40 21 3126618 \ +40 21 3120210 / int.101 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] a function to compute the cumulative distribution function (cdf) of the gamma
Dear Forum, I would need to write a function to calculate the cumulative distribution function (cdf) of the gamma random variable. I am allowed to use the following precoded functions: rgamma, pgamma, and dgamma. I am a little overwhelmed by this project, I am wondering how I should start. Should I sum dgamma (or pgamma) from 0 to x, in order to obtain the cdf at x? Thanks in advance for your input. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] constructing a self-starting non-linear model
Dear all, I am trying to define a selfStart function for a non-linear model, which is a log-transformed SSmicmen model with multiplicative errors and so it is required to make them additive: log(y)=log(a)+log(x)-log(1+x/b) Any ideas about how to use the peeling method to derive the initial argument and get the initial values? Thank you for being always there!:) Irene __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Tricky vectorization problem
Seems there were some line break issues when pasting the code, trying
again with a different commenting style:
#start a timer
start = proc.time()[1]
#set the true correllation
rho = .5
#set the number of Subjects
Ns = 100
#for each subject, set a number of observations in A
a.No = 1:100
#for each subject, set a number of observations in B
b.No = 1:100
#set the between Ss variance in condition A
v.a = 1
#set the between Ss variance in condition B
v.b = 2
#for each subject, set a standard deviation in A
s.a.w = 1:100
#for each subject, set a standard deviation in B
s.b.w = 1:100
#set the number of monte carlo experiments
mce = 1e3
#set up a collector for the simulated correlations
sim.r = vector(length=mce)
#define a covariance matrix for use in generating the correlated data
Sigma=matrix(c(v.a,sqrt(v.a*v.b)*rho,sqrt(v.a*v.b)*rho,v.b),2,2)
#set up a collector for subject means in A
a = vector(length=Ns)
#set up a collector for subject means in B
b = vector(length=Ns)
#start a monte carlo experiment
for(i in 1:mce){
#generate correlated ideal means for for each subject in each condition
sub.means=mvrnorm(Ns,rep(0,2),Sigma)
#for each subject
for(s in 1:Ns){
#generate some data for A and grab the mean
a[s] = mean(rnorm(a.No[s],sub.means[s,1],s.a.w[s]))
#generate some data for B and grab the mean
b[s] = mean(rnorm(b.No[s],sub.means[s,2],s.b.w[s]))
}
#store the observed correlation between A and B
sim.r[i] = cor(a,b)
}
#show the total time this took
print(proc.time()[1]-start)
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Re: [R] help_R2.5 updating
I found that installing R into %userprofile%\Documents\R and placing the source packages I was developing there too solved my permissions problems. R automatically created a %userprofile%\Documents\R\win-library\2.6 folder for my library and put packages that I was installing from CRAN in it. In R I can now do this: setwd(~/R) to get to that directory On 10/6/07, Thanjavur Bragadeesh [EMAIL PROTECTED] wrote: Hi, I run windows vista ultimate in my laptop and run R 2.5 I am trying to update the packages but it comes up with an error message Warning in install.packages(update[instlib == l, Package], l, contriburl = contriburl, : 'lib' is not writable Error in install.packages(update[instlib == l, Package], l, contriburl = contriburl, : unable to install packages I am the adminsitrator on this computer and logged in as administrator. can anyone advise. I treid to switch off most security - windows firewall is off and so is macfee. many thanks for your advise bragadeesh _ Climb to the top of the charts! Play Star Shuffle: the word scramble challenge with star power. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Re-ordering factors
A small example before I begin my query: educ - read.table(efile, header=TRUE) educ Education Age_Group Count 1 IncompleteHS 25-34 5416 2 IncompleteHS 35-44 5030 3 IncompleteHS 45-54 5777 4 IncompleteHS 55-64 7606 5 IncompleteHS 64 13746 6 CompletedHS 25-34 16431 7 CompletedHS 35-44 1855 8 CompletedHS 45-54 9435 9 CompletedHS 55-64 8795 10 CompletedHS 64 7558 11 Uni1-3 25-34 8555 12 Uni1-3 35-44 5576 13 Uni1-3 45-54 3124 14 Uni1-3 55-64 2524 15 Uni1-3 64 2503 16Uni4+ 25-34 9771 17Uni4+ 35-44 7596 18Uni4+ 45-54 3904 19Uni4+ 55-64 3109 20Uni4+ 64 2483 xtabs(Count ~ Education + Age_Group, data=educ) Age_Group Education64 25-34 35-44 45-54 55-64 CompletedHS 7558 16431 1855 9435 8795 IncompleteHS 13746 5416 5030 5777 7606 Uni1-32503 8555 5576 3124 2524 Uni4+ 2483 9771 7596 3904 3109 Naturally I would prefer the factor levels in their natural ordering in the table. I would like to re-order the levels of the factors to achieve this. I have tried reorder() in the gdata package: ed - reorder(Education,neworder= c(IncompleteHS,CompletedHS, + Uni1-3,Uni4+)) agrp - reorder(Age_Group,neworder= + c(25-34,35-44,45-54,55-64,64)) xtabs(Count ~ ed + agrp) agrp ed 25-34 35-44 45-54 55-64 64 CompletedHS 16431 1855 9435 8795 7558 IncompleteHS 5416 5030 5777 7606 13746 Uni1-38555 5576 3124 2524 2503 Uni4+ 9771 7596 3904 3109 2483 which works on one factor but not the other. I have fooled a bit with reorder.factor() but I can't seem to figure out how to drive it! Cheers, Murray Jorgensen -- Dr Murray Jorgensen http://www.stats.waikato.ac.nz/Staff/maj.html Department of Statistics, University of Waikato, Hamilton, New Zealand Email: [EMAIL PROTECTED]Fax 7 838 4155 Phone +64 7 838 4773 wkHome +64 7 825 0441Mobile 021 1395 862 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Re-ordering factors
Using reorder.factor from the stats package seems to work: educ$ed - reorder(educ$Education, sort(rep(1:4,5))) levels(educ$Education) [1] CompletedHS IncompleteHS Uni1-3 Uni4+ levels(educ$ed) [1] IncompleteHS CompletedHS Uni1-3 Uni4+ xtabs(Count ~ ed + Age_Group, data=educ) Age_Group ed 25-34 35-44 45-54 55-64 64 IncompleteHS 5416 5030 5777 7606 13746 CompletedHS 16431 1855 9435 8795 7558 Uni1-38555 5576 3124 2524 2503 Uni4+ 9771 7596 3904 3109 2483 James On 7/10/07 4:52 PM, [EMAIL PROTECTED] wrote: A small example before I begin my query: educ - read.table(efile, header=TRUE) educ Education Age_Group Count 1 IncompleteHS 25-34 5416 2 IncompleteHS 35-44 5030 3 IncompleteHS 45-54 5777 4 IncompleteHS 55-64 7606 5 IncompleteHS 64 13746 6 CompletedHS 25-34 16431 7 CompletedHS 35-44 1855 8 CompletedHS 45-54 9435 9 CompletedHS 55-64 8795 10 CompletedHS 64 7558 11 Uni1-3 25-34 8555 12 Uni1-3 35-44 5576 13 Uni1-3 45-54 3124 14 Uni1-3 55-64 2524 15 Uni1-3 64 2503 16Uni4+ 25-34 9771 17Uni4+ 35-44 7596 18Uni4+ 45-54 3904 19Uni4+ 55-64 3109 20Uni4+ 64 2483 xtabs(Count ~ Education + Age_Group, data=educ) Age_Group Education64 25-34 35-44 45-54 55-64 CompletedHS 7558 16431 1855 9435 8795 IncompleteHS 13746 5416 5030 5777 7606 Uni1-32503 8555 5576 3124 2524 Uni4+ 2483 9771 7596 3904 3109 Naturally I would prefer the factor levels in their natural ordering in the table. I would like to re-order the levels of the factors to achieve this. I have tried reorder() in the gdata package: ed - reorder(Education,neworder= c(IncompleteHS,CompletedHS, + Uni1-3,Uni4+)) agrp - reorder(Age_Group,neworder= + c(25-34,35-44,45-54,55-64,64)) xtabs(Count ~ ed + agrp) agrp ed 25-34 35-44 45-54 55-64 64 CompletedHS 16431 1855 9435 8795 7558 IncompleteHS 5416 5030 5777 7606 13746 Uni1-38555 5576 3124 2524 2503 Uni4+ 9771 7596 3904 3109 2483 which works on one factor but not the other. I have fooled a bit with reorder.factor() but I can't seem to figure out how to drive it! Cheers, Murray Jorgensen -- James Reilly Department of Statistics, University of Auckland Private Bag 92019, Auckland, New Zealand __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] help_R2.5 updating
There is no 'R 2.5'! Advice as requested: 1) Study the R posting guide and give the details it asks you for, accurately. 2) Read the rw-FAQ. Very relevant for Windows Vista users. 3) Don't use obsolete versions of R. R 2.6.0 is current, and we do make R better at each release. If you have R 2.5.0, it is possible that the intended behaviour (it should create a personal library directory for you) may not work on Vista: this *is* covered in the rw-FAQ for 2.5.0. Comments from the rw-FAQ: For an installation to be used by a single user, the simplest way is to make use of the `personal library' introduced in R 2.5.0: ... You can also have you a personal library, which defaults to the directory `R\win-library\X.Y' of your home directory for versions X.Y.Z of R. This location can be changed by setting the environment variable `R_LIBS_USER', and can be found from inside R by running `Sys.getenv(R_LIBS_USER)'. This will only be used if it exists so you may need to create it: you can use dir.create(Sys.getenv(R_LIBS_USER), recursive = TRUE) to do so. If you use `install.packages' and do not have permission to write to the main or site library, it should offer to create a personal library for you and install the packages there. This will also happen if `update.packages' offers to update packages for you in a library where you do not have write permission. There can be additional security issues under Windows Vista: *Note Does R run under Windows Vista?::. In particular, the detection that a standard user has suitable permissions appears to be unreliable under Vista, so we recommend that you do create a personal directory yourself. The last point works better under R = 2.5.1 than in 2.5.0. It now errs on the side of caution, and occasionally says you do not have permission when you do. On Sat, 6 Oct 2007, Thanjavur Bragadeesh wrote: Hi, I run windows vista ultimate in my laptop and run R 2.5 I am trying to update the packages but it comes up with an error message Warning in install.packages(update[instlib == l, Package], l, contriburl = contriburl, : 'lib' is not writable Error in install.packages(update[instlib == l, Package], l, contriburl = contriburl, : unable to install packages I am the adminsitrator on this computer and logged in as administrator. can anyone advise. I treid to switch off most security - windows firewall is off and so is macfee. many thanks for your advise bragadeesh _ Climb to the top of the charts! Play Star Shuffle: the word scramble challenge with star power. [[alternative HTML version deleted]] -- 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@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
