Re: [R] r-package RDCOMClient
the windows version on both machines is the same, namely Microsoft Windows XP Professional Version 2002 Service Pack 2 the r-version is also the same: 2.5.1 RDCOMClient-version on both machines is 0.91-0 rcom-version on both machines is 1.5-2.2 what is different, for both machines is that they are installed in different networks. on the machine on which R crashes most of the software is installed by the adminstrator. when i install a software it is installed on L: but it is not possible to install it on the C: disk. it is also not possible to install packages via the Install packages menu on the machine where are crashes. there is an error, which says that R could not establish any connection, although i can open the homepages, where downloading packages manually is possible and i can download those packages without problems. another thing, which is suspicious to me: i tried to install many older versions of R on the machine where it crashes. i noticed two things. 1) when installing older versions, there is an option in the installation wizard Register R path for use by the (D)COM server (e.g. in rw2011.exe) which is not there anymore when installing newer versions of R (2.2.0 for instance). 2) just before the installation of older versions is finished i get error windows, which show the following messages: Error creating registry key: HKEY_LOCAL_MACHINE\Software\R-core HKEY_LOCAL_MACHINE\Software\R-core\R HKEY_CLASSES_ROOT\.Rdata HKEY_CLASSES_ROOT\RWorkspace HKEY_CLASSES_ROOT\RWorkspace\DefaultIcon HKEY_CLASSES_ROOT\RWorkspace\shell\open\command RegCreateKeyEx failed; code 5 Access denied the HKEY-part in every error window is different, the RegCreateKeyEx-part is always the same. i jump from one window to the other by clicking the IGNORE button. after clicking it for several times the installation is finished. this does not happen for instance with version 2.2.0 anymore. however, for this version require(RDCOMClient) doesn´t work. There is an error telling me error in load(dataFile, ns) : ReadItem: unknown Type 25 and a warning message, that RDCOMClient has been built under version 2.5.0 and that R could not load the code in package RDCOMClient. another thing is: two months ago or so, i had installed windows 2000 on the crash-machine. at that time all the RBloomberg-stuff worked perfectly without any problems. i´m not sure whether these information really helps, but that´s what i noticed so far. there are no differences between both machines beside those i described above. the question is still why on the crash machine .Call(R_create, name, PACKAGE = RDCOMClient) works and .Call(R_Invoke, obj, as.character(name), .args, ..) produces a crash of R. that have something to do with any adminstrator-access-permission-stuff? or windows xp itself? thx for your help Duncan Temple Lang wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Marcin Kopaczynski wrote: both versions work on my pc, but on the pc where i have bloomberg installed the things i described do not work. Can you give us some details about which versions of R you have, versions of RDCOMClient and rcom and also what versions of Windows you are running on each of the machines (indicating for which combination it works). Otherwise, it is very difficult to guess what might be the problem. the rcom peckage works, but comCreateObject creates an object which is somehow different from what COMCreate creates. especially the Slot ref: row is not present anymore and so RBloomberg package functions do not work. The two packages do similar things, but the representations and internal code are quite different. any idea? Gabor Grothendieck wrote: I have generally found that both RDCOMClient and rcom do work although around the time of new R versions one might be ready for it before the other so try both. On 10/3/07, Marcin Kopaczynski [EMAIL PROTECTED] wrote: hi, i was trying to perform a function from the RDCOMClient package. to make it short: i tried to run the example in ?.COM, namely e - COMCreate(Excel.Application) books - e[[Workbooks]] as soon as e[[Workbooks]] is called, the RGUI crashes. debugging the function .COM reveals that somehow the connection between R and the external funcions does not work, because the crash happens when .Call(R_Invoke, obj, as.character(name), .args, ..) is called. however, in the function COMCreate the .statement Call(R_create, name, PACKAGE = RDCOMClient) works. it doesnt work with the bloomberg connection, as well. maybe i have to install some additional things? thx in advance for your help, marcin __ 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] Windows OS, R and unicode
Richard, At present the \u notation only works on Windows in CJK locales, and only to represent characters defined in the locale in use. Now it seems that _does_ include the signs you mention in Japanese. So it is possible that if you start R with Rgui LC_CTYPE=ja then this will work: it does for me in 2.6.0 (and I see no reason why it would not in 2.5.1, but I updated my Windows box yesterday). I should perhaps add that only windows() devices will work and not say pdf(). Brian On Thu, 4 Oct 2007, Richard Rowe wrote: I'm trying to use the biological female and male signs in R2.5.1 under Windows XP. I can access and insert these symbols using word-processors. In general these should be available as \u2640 and \u2642 but I can't make them happen in R using (say) text(5,5, \u2640) message invalid \u sequence I've replaced Arial with Arial unicode MS in Rdevga and I've tried various setlocale options with no success (the Murrell/Ripley examples (Rnews 6/2) do work of course ... so I feel I should be able to do this myself, but after several hours it is time to ask for help). I understand from Google results that users on Mac OS and Linux aren't facing this problem ... Richard -- 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] tcltk question
Tae-Hoon Chung wrote: Is there any requirement for TclTk support for R? When I tried to call the tcltk library, it failed with the following message: library(tcltk) Error in firstlib(which.lib.loc, package) : Tcl/Tk support is not available on this system Error in library(tcltk) : .First.lib failed for 'tcltk' The system information is as follows: Linux osirus.tgen.org 2.6.9-42.0.10.ELsmp #1 SMP Fri Feb 16 17:13:42 EST 2007 x86_64 x86_64 x86_64 GNU/Linux (I take it that you meant to ask what the _prerequisites_ are. R does not _require_ tcltk; it will work without tcltk, except where it explicitly uses its features.) GNU/linux is not really information enough because this is distribution-dependent. The kernel name suggests that it could be Red Hat EL. In that case, you need tcl and tk libraries AND the tcl-devel and tk-devel RPMS at build time (it is picked up during the configure step). Tae-Hoon Chung Post-Doctoral Researcher Computational Biology Division, TGEN 445 N 5th St. Phoenix, AZ 85004 USA O: 1-602-343-8724 F: 1-602-343-8840 [[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. -- 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.
Re: [R] Making a table: collapsing across sub-strings
Hi, A sub string can occur anywhere in the main string. I think I could use TABLE and than add the numbers. But I don't know how to access the numbers in the result of table. Another problem is that there might be a hierarchy in the strings. This is, string a might be a subset of b while b might be a subset of c. So, when checking the strings, I would have to start with the longest string and find all subsets of that one. An than I should check the second longest string and so on... But I cannot find a way of ordering strings on their length. Regards, Dieter jim holtman wrote: How do you determine if one string is a subset of another? Does it only match at the beginning, or anywhere? How large is your set of strings? Can you use table as you describe and then determine what the groupings of subsets are and then just add the numbers together? You can use grep/regexpr to determine if one string is a subset of another. On 10/3/07, Dieter Vanderelst [EMAIL PROTECTED] wrote: Hi list, I'm currently processing textual data and I would really appreciate some help with one off my problems. I have a set of strings and I want to count how often each of this strings appears in this set. This is not very difficult and can be done as: TB-table(my_set) plot(TB) However, I also want to collapse across sub-strings. This is, I want a sub-string ss of string S to be counted as an occurrence of string S. So, 'abab' should be included in the count of 'ababaaa' and should not be listed as a separate entry in the frequency table. Does somebody has a pointer to a way to do this? I have been checking out the CRAN packages for handling DNA sequences, but this has not really brought me closer to a solution. Thanks, Dieter Vanderelst -- Dieter Vanderelst Eindhoven University of Technology Faculty of Industrial Design Designed Intelligence Group Den Dolech 2 5612 AZ Eindhoven The Netherlands Tel +31 40 247 91 11 __ 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] what does size of a plotting character mean?
Hi, plot(1,1, cex=2) means that the size of the plotting character (empty circle in this case) is double the default size. Now my question is: What characteristic of the symbol (circle) is double? Is it the area or the diameter? What if the symbol is not a circle, what is the generic meaning of size in that case? Thanks in advance, PK __ 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 from source file
Dear list
Maybe someone can help with the following problem:
I have a source file containing the following code for plotting:
pdf(file = 'data/mario/boxplot.pdf')
bwplot(sig100 ~ target | group, data = fish, main = 'Boxplot der
Signale in 100 Zellen nach Gruppe', xlab = '', ylab = 'Anzahl der
Signale')
dev.off()
pdf(file = 'data/mario/xyplot.pdf')
xyplot(sig100 ~ target | group, data = fish, main = 'Signale in 100
Zellen nach Gruppen', xlab = '', ylab = 'Anzahl der Signale',
panel = function(x,y, ...) {
panel.grid(h = -1, v = -1)
panel.xyplot(x,y, jitter.x=TRUE)
panel.lmline(x,y, lty = 2, col = 3)})
dev.off()
If I run the file from R with
source('lib/analysis_mario.R')
a two pdf-files will be created but they cannot be read.
When I use
source('lib/analysis_mario.R', echo=TRUE)
the files are created correctly.
Actually I don't want the echo, so what can I do to plot correctly and
omit the echo in one run.
I use
platform powerpc-apple-darwin8.9.1
arch powerpc
os darwin8.9.1
system powerpc, darwin8.9.1
status
major 2
minor 5.1
year 2007
month 06
day27
svn rev42083
language R
version.string R version 2.5.1 (2007-06-27)
--
Armin Goralczyk, M.D.
Dept. of General Surgery
University of Göttingen
Göttingen, Germany
http://www.chirurgie-goettingen.de
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] hessian matrix in arima
Hi, I am working or arima. I think arima uses non-linear optimisation for parameter optimisation. The standard error for parameters are computed from hessian matrix. When I use arima model, how can I see the finial hessian got from non-linear optimisation (BFGS for example). Any help is appreciated. Many thanks. Di [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] what does size of a plotting character mean?
On Thu, 4 Oct 2007, Prasenjit Kapat wrote: Hi, plot(1,1, cex=2) means that the size of the plotting character (empty circle in this case) is double the default size. Now my question is: What characteristic of the symbol (circle) is double? Is it the area or the diameter? Is it not obvious when you try it? Diameter. What if the symbol is not a circle, what is the generic meaning of size in that case? cex does linear scaling in each dimension. There is no generic definition of what cex=1 means: it depends on the device, the font (for pch =32 except .) or the symbols (pch=1...25). -- 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.
[R] SETAR and nonlinear model estimation
I am currently doing a research paper that requires the estimation of a thereshold model. I have gone through the reference manual for the pacjage tsdyn and i am failing to see how the the threshold models provided by R can estimate a model in which the other control variables exist or are included in the estiamtion of the model. Any help provided will be greatly appreciated Andrew Phiri Post-gratuate student at the North West University (NWU), South Africa - Luggage? GPS? Comic books? [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] how to specify bin width in hist()
Abu Naser wrote: Hi all user, I have been wondering how the bin width can be specified in hist(). Hi Abu, If you want constant bin widths (e.g. from 0 to 10), it's easy: my.bin.width-2 hist(...,breaks=seq(0,10,by=my.bin.width),...) and the by argument is your width. If you want completely customized bin widths (which may not be a great idea): my.bin.widths-c(2,3,4,1) hist(...,breaks=c(0,cumsum(my.bin.widths)),...) also look at the right= argument to decide whether to include the lower or higher break value in each bin. 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] hessian matrix in arima
On Thu, 4 Oct 2007, Di Wang wrote: Hi, I am working or arima. I think arima uses non-linear optimisation for parameter optimisation. The standard error for parameters are computed from hessian matrix. When I use arima model, how can I see the finial hessian got from non-linear optimisation (BFGS for example). By stepping through the code: it is not stored in the object returned. Any help is appreciated. Many thanks. Di [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Brian D. Ripley, [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] Data simulation with R
Hi Matiou: On Thursday 30 August 2007 13:25, Matiou wrote: Hi, I am currently on a placement here at GSK for my studies, and I'm working on Heckman Models. I have to make simulations, in order to see whether these models are efficient or not. I have to generate a dataset under the following constraints: - outcome is 0 or 1 - one control group, one treatment group, there must be no treatment effect - generate one continuous variable and one binary variable which are both perfectly correlated to treatment, but not correlated to outcome - generate one continuous variable and one binary variable which are both perfectly correlated to outcome, but not correlated to treatment - generate one continuous variable and one binary variable which are both perfectly correlated to both treatment and outcome Problem is, it's my first time generating data, so I'm having quite a hard time... I usually use SAS, but I didn't manage to generate data using it. Some people told me it's quite easy to do with R, but I'm not really used to this program. Is it really possible to simulate this kind of data with R ? If it is, can someone help me ? For an example, please take a look at the example section of function selection in the micEcon package. HTH, Arne Thanks in advance. -- Arne Henningsen Department of Agricultural Economics University of Kiel Olshausenstr. 40 D-24098 Kiel (Germany) Tel: +49-431-880 4445 Fax: +49-431-880 1397 [EMAIL PROTECTED] http://www.uni-kiel.de/agrarpol/ahenningsen/ pgpImYG9iC9hd.pgp Description: PGP signature __ 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] print Text on device
hi BioC, I need to plot a vector of characters on a pdf device, not as a legend, but as in image by itself. I tried text but it is only related to locate text in a plot. what do you suggest? sessionInfo() R version 2.6.0 (2007-10-03) x86_64-unknown-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] rcompgen_0.1-15 tools_2.6.0 [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] plot from source file
It's a FAQ #7.22
Wrap your plotting commands with print, that is,
print(bwplot( ))
and
print(xyplot( ))
Armin Goralczyk wrote:
Dear list
Maybe someone can help with the following problem:
I have a source file containing the following code for plotting:
pdf(file = 'data/mario/boxplot.pdf')
bwplot(sig100 ~ target | group, data = fish, main = 'Boxplot der
Signale in 100 Zellen nach Gruppe', xlab = '', ylab = 'Anzahl der
Signale')
dev.off()
pdf(file = 'data/mario/xyplot.pdf')
xyplot(sig100 ~ target | group, data = fish, main = 'Signale in 100
Zellen nach Gruppen', xlab = '', ylab = 'Anzahl der Signale',
panel = function(x,y, ...) {
panel.grid(h = -1, v = -1)
panel.xyplot(x,y, jitter.x=TRUE)
panel.lmline(x,y, lty = 2, col = 3)})
dev.off()
If I run the file from R with
source('lib/analysis_mario.R')
a two pdf-files will be created but they cannot be read.
When I use
source('lib/analysis_mario.R', echo=TRUE)
the files are created correctly.
Actually I don't want the echo, so what can I do to plot correctly and
omit the echo in one run.
I use
platform powerpc-apple-darwin8.9.1
arch powerpc
os darwin8.9.1
system powerpc, darwin8.9.1
status
major 2
minor 5.1
year 2007
month 06
day27
svn rev42083
language R
version.string R version 2.5.1 (2007-06-27)
--
Armin Goralczyk, M.D.
--
View this message in context:
http://www.nabble.com/plot-from-source-file-tf4566488.html#a13038038
Sent from the R help mailing list archive at Nabble.com.
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] Türk Patent Enstitüsü ve Moğolistan Fikri Mülkiyet Ofisi Dayanışması
Türk Patent Enstitüsü ve Moðolistan Fikri Mülkiyet Ofisi Dayanýþmasý Türk Patent Enstitüsü (TPE) ve Moðolistan Fikri Mülkiyet Ofisi (IPOM) arasýndaki teknik iþbirliði görüþmeleri 21-23 Aðustos 2007 tarihlerinde Moðolistan'ýn Ulan Batur þehrinde gerçekleþtirildi. IPOM personelinin coðrafi iþaretler ve enformasyon faaliyetleri eðitimi, TPE eþ-baþkanlýðýnda yürütülmekte olan Ýslam Konferansý Teþkilatý Projesi ve Ekonomik Ýþbirliði Örgütü altýnda düzenlenebilecek eðitimlere Moðolistan'ýn da katýlýmýný öngören bir faaliyet planý oluþturuldu.Kaynak: TPE Time'ýn Deðerlendirdiði 2006 Yýlýnýn En Ýyi Cihazlarý Time'ýn deðerlendirmelerine göre, 2006 yýlýnýn en iyi 8 cihazý; Logitech VX, Sanyo HDI Digital Media, Apple Macbook Pro, Nintendo DS Lite, Logitech Wireless DJ, Nike + ipod sport kid, Garmin Street Pilot c550 ve Palm Treo 700W yer almakta. Kaynak: time.com Ýstanbul Büyükþehir Belediyesi, Kentin Elektronik Haritasýný Çýkarttý! Ýstanbullularýn www.sehirrehberi.ibb.gov.tr internet adresinden ulaþabilecekleri rehberde turistik ve tarihi mekanlar, adres bilgileri, nöbetçi eczaneler, yol durumu gibi çok sayýda merak edilen konuya ulaþýlabiliyor. Ayrýca Ýstanbul'un uydu ve hava fotoðraflarýda bulunmakta. Ýstanbullular bu sanal rehberden trafik kazasý, yangýn, sel, kapalý yol ve yol daraltmasý gibi son geliþmeleride sýcaðý sýcaðýna takip edebilecekler. Bu buuml;ltenleri almak istemiyorsan1z [EMAIL PROTECTED] adresine bo_ bir mail gouml;ndermenizi rica ederiz. Bouml;yle bir talebiniz olmad1 1 suuml;rece duuml;zenli olarak buuml;ltenlerimizi alabilirsiniz. NETMARK PATENT T:0212 220 31 20 F:0212 220 74 21 [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] how to specify bin width in hist()
Thanks Jim for your response. I will use constant bin width. One more question: Is there anyway I can 2d or 3d histogram calculation/count? With regards, Abu __ 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] Türk Patent Enstitüsü ve Moğolistan Fikri Mülkiyet Ofisi Dayanışması
Türk Patent Enstitüsü ve Moðolistan Fikri Mülkiyet Ofisi Dayanýþmasý Türk Patent Enstitüsü (TPE) ve Moðolistan Fikri Mülkiyet Ofisi (IPOM) arasýndaki teknik iþbirliði görüþmeleri 21-23 Aðustos 2007 tarihlerinde Moðolistan'ýn Ulan Batur þehrinde gerçekleþtirildi. IPOM personelinin coðrafi iþaretler ve enformasyon faaliyetleri eðitimi, TPE eþ-baþkanlýðýnda yürütülmekte olan Ýslam Konferansý Teþkilatý Projesi ve Ekonomik Ýþbirliði Örgütü altýnda düzenlenebilecek eðitimlere Moðolistan'ýn da katýlýmýný öngören bir faaliyet planý oluþturuldu.Kaynak: TPE Time'ýn Deðerlendirdiði 2006 Yýlýnýn En Ýyi Cihazlarý Time'ýn deðerlendirmelerine göre, 2006 yýlýnýn en iyi 8 cihazý; Logitech VX, Sanyo HDI Digital Media, Apple Macbook Pro, Nintendo DS Lite, Logitech Wireless DJ, Nike + ipod sport kid, Garmin Street Pilot c550 ve Palm Treo 700W yer almakta. Kaynak: time.com Ýstanbul Büyükþehir Belediyesi, Kentin Elektronik Haritasýný Çýkarttý! Ýstanbullularýn www.sehirrehberi.ibb.gov.tr internet adresinden ulaþabilecekleri rehberde turistik ve tarihi mekanlar, adres bilgileri, nöbetçi eczaneler, yol durumu gibi çok sayýda merak edilen konuya ulaþýlabiliyor. Ayrýca Ýstanbul'un uydu ve hava fotoðraflarýda bulunmakta. Ýstanbullular bu sanal rehberden trafik kazasý, yangýn, sel, kapalý yol ve yol daraltmasý gibi son geliþmeleride sýcaðý sýcaðýna takip edebilecekler. Bu buuml;ltenleri almak istemiyorsan1z [EMAIL PROTECTED] adresine bo_ bir mail gouml;ndermenizi rica ederiz. Bouml;yle bir talebiniz olmad1 1 suuml;rece duuml;zenli olarak buuml;ltenlerimizi alabilirsiniz. NETMARK PATENT T:0212 220 31 20 F:0212 220 74 21 [[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] Bug or just a problem with the computer precision?
Hi I have the following problem: I have a lot of numbers that identify import goods according to the Harmonised System (8 numbers in two groups with a dot in between). I want to move to the 6 numbers (4 numbers, dot, two numbers). My trick to do this works for all the numbers in the Harmonised Sytem but not for this one: A-4709.9000 (A-floor(100 * A ) / 100) = 4709.89 But this has to be 4709.90 If I do this in Excel it works fine...Any idea how to make sure that I get 4709.90 and not 4709.89? Renger _ ECOPLAN Forschung und Beratung in Wirtschaft und Politik Economic Research and Policy Consultancy Thunstrasse 22 / CH-3005 Berne (Switzerland) Phone: +41 31 356 61 61 / Fax: +41 31 356 61 60 mailto:[EMAIL PROTECTED] / http://www.ecoplan.ch __ 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] Making a table: collapsing across sub-strings
How many strings are there? Now you could use 'outer' and 'regexpr' to determine which strings are subsets of another and then group them. So knowing the possible number of strings that you will be searching with and how you might want a hierarchy printed out would help in coming up with a solution. On 10/4/07, Dieter Vanderelst [EMAIL PROTECTED] wrote: Hi, A sub string can occur anywhere in the main string. I think I could use TABLE and than add the numbers. But I don't know how to access the numbers in the result of table. Another problem is that there might be a hierarchy in the strings. This is, string a might be a subset of b while b might be a subset of c. So, when checking the strings, I would have to start with the longest string and find all subsets of that one. An than I should check the second longest string and so on... But I cannot find a way of ordering strings on their length. Regards, Dieter jim holtman wrote: How do you determine if one string is a subset of another? Does it only match at the beginning, or anywhere? How large is your set of strings? Can you use table as you describe and then determine what the groupings of subsets are and then just add the numbers together? You can use grep/regexpr to determine if one string is a subset of another. On 10/3/07, Dieter Vanderelst [EMAIL PROTECTED] wrote: Hi list, I'm currently processing textual data and I would really appreciate some help with one off my problems. I have a set of strings and I want to count how often each of this strings appears in this set. This is not very difficult and can be done as: TB-table(my_set) plot(TB) However, I also want to collapse across sub-strings. This is, I want a sub-string ss of string S to be counted as an occurrence of string S. So, 'abab' should be included in the count of 'ababaaa' and should not be listed as a separate entry in the frequency table. Does somebody has a pointer to a way to do this? I have been checking out the CRAN packages for handling DNA sequences, but this has not really brought me closer to a solution. Thanks, Dieter Vanderelst -- Dieter Vanderelst Eindhoven University of Technology Faculty of Industrial Design Designed Intelligence Group Den Dolech 2 5612 AZ Eindhoven The Netherlands Tel +31 40 247 91 11 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem you are trying to solve? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Bug or just a problem with the computer precision?
You are getting round-off problems (I think it is FAQ 7.33). Use characters since thats what the numbers really are. Convert the characters and then use substring. Also sprintf works: sprintf(%.2f, A*100) [1] 470990.00 sprintf(%.2f, A) [1] 4709.90 On 10/4/07, Renger van Nieuwkoop [EMAIL PROTECTED] wrote: Hi I have the following problem: I have a lot of numbers that identify import goods according to the Harmonised System (8 numbers in two groups with a dot in between). I want to move to the 6 numbers (4 numbers, dot, two numbers). My trick to do this works for all the numbers in the Harmonised Sytem but not for this one: A-4709.9000 (A-floor(100 * A ) / 100) = 4709.89 But this has to be 4709.90 If I do this in Excel it works fine...Any idea how to make sure that I get 4709.90 and not 4709.89? Renger _ ECOPLAN Forschung und Beratung in Wirtschaft und Politik Economic Research and Policy Consultancy Thunstrasse 22 / CH-3005 Berne (Switzerland) Phone: +41 31 356 61 61 / Fax: +41 31 356 61 60 mailto:[EMAIL PROTECTED] / http://www.ecoplan.ch __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem you are trying to solve? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Contour plot (level curves)
On Thu, 4 Oct 2007, Caio Azevedo wrote: Hi all, I have a sample of n values from a bivariate distribution (from a MCMC procedure). How could I draw a contour plot of the joint density based on that sample ? You need to estimate the density, and contour that estimate. MASS has examples using its kde2d function. There are other methods available, e.g. in package sm. Sorry if I was not too clear. Thans in advance, Regards, Caio [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Brian D. Ripley, [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] Bug or just a problem with the computer precision?
jim holtman wrote: You are getting round-off problems (I think it is FAQ 7.33). Use characters since thats what the numbers really are. Convert the characters and then use substring. Also sprintf works: sprintf(%.2f, A*100) [1] 470990.00 sprintf(%.2f, A) [1] 4709.90 If sprintf works, so does round(A,2) and I suspect there was a reason not to use that (what is the result for 4709.8967 supposed to be?). It might be better to use a small amount of fuzz: floor(A *100+1e-10)/100 Or, as indicated: If these are really strings, treat them as such: A-4709.9000 substr(A,1,7) [1] 4709.90 On 10/4/07, Renger van Nieuwkoop [EMAIL PROTECTED] wrote: Hi I have the following problem: I have a lot of numbers that identify import goods according to the Harmonised System (8 numbers in two groups with a dot in between). I want to move to the 6 numbers (4 numbers, dot, two numbers). My trick to do this works for all the numbers in the Harmonised Sytem but not for this one: A-4709.9000 (A-floor(100 * A ) / 100) = 4709.89 But this has to be 4709.90 If I do this in Excel it works fine...Any idea how to make sure that I get 4709.90 and not 4709.89? Renger _ ECOPLAN Forschung und Beratung in Wirtschaft und Politik Economic Research and Policy Consultancy Thunstrasse 22 / CH-3005 Berne (Switzerland) Phone: +41 31 356 61 61 / Fax: +41 31 356 61 60 mailto:[EMAIL PROTECTED] / http://www.ecoplan.ch __ 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. -- 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.
Re: [R] Updating packages for R 2.6.0
You need to install the libc6-dev ubuntu package to be able to compile programs. sudo apt-get install libc6-dev Gabor On Thu, Oct 04, 2007 at 09:54:26AM -0400, Ricardo Pietrobon wrote: I must be making some really basic mistake, since I keep getting an error message when using update.packages(checkBuilt=TRUE, ask=FALSE) - an example for MASS is below. I am running ubuntu 7.04, with a clean install done today of version 2.6.0 straight from the R repository. here is the message: * Installing *source* package 'MASS' ... ** libs gcc -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include -fpic -g -O2 -c lqs.c -o lqs.o In file included from lqs.c:31: /usr/share/R/include/R.h:28:20: error: stdlib.h: No such file or directory /usr/share/R/include/R.h:29:19: 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/R.h:30, from lqs.c:31: /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 lqs.c:31: /usr/share/R/include/R.h:32:18: error: math.h: No such file or directory /usr/share/R/include/R.h:33:19: error: errno.h: No such file or directory In file included from /usr/share/R/include/R.h:50, from lqs.c:31: /usr/share/R/include/R_ext/RS.h:24:39: error: string.h: No such file or directory lqs.c: In function 'lqs_fitlots': lqs.c:222: warning: implicit declaration of function 'fabs' lqs.c:222: warning: incompatible implicit declaration of built-in function 'fabs' lqs.c:238: warning: implicit declaration of function 'sqrt' lqs.c:238: warning: incompatible implicit declaration of built-in function 'sqrt' lqs.c:239: warning: incompatible implicit declaration of built-in function 'fabs' lqs.c: In function 'do_one': lqs.c:319: warning: implicit declaration of function 'log' lqs.c:319: warning: incompatible implicit declaration of built-in function 'log' lqs.c:319: warning: incompatible implicit declaration of built-in function 'fabs' lqs.c: In function 'mve_fitlots': lqs.c:376: warning: incompatible implicit declaration of built-in function 'log' make: *** [lqs.o] Error 1 ERROR: compilation failed for package 'MASS' ** Removing '/usr/local/lib/R/site-library/MASS' ** Removing '/usr/local/lib/R/site-library/class' ** Removing '/usr/local/lib/R/site-library/nnet' ** Removing '/usr/local/lib/R/site-library/spatial' The downloaded packages are in /tmp/Rtmp7CXD5O/downloaded_packages Warning message: In install.packages() : installation of package 'VR' had non-zero exit status any thoughts appreciated On 10/4/07, Prof Brian Ripley [EMAIL PROTECTED] wrote: Since this has come up already: It is a good idea to re-install all packages for a minor-version increment of R, e.g. 2.5.1 - 2.6.0 (it is major.minor.patchlevel). This is most easily done by update.packages(checkBuilt=TRUE, ask=FALSE) However, if you don't want to do that yet, be aware that - Certain S4-using packages must be reinstalled, and using old versions can make R malfunction. I believe these are Brobdingnag, Matrix, NADA and kappalab. - Any S4 package that makes an existing function S4-generic will grab that function as it existed in the version of R under which they were installed. If it has changed, there is potential trouble. - Packages that create or change character strings at C level will have needed to be updated for R 2.6.0 (and some have not yet been). Using such a package can in principle result in other character data being changed (since most character strings now share storage). -- 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. __ 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. -- Csardi Gabor [EMAIL PROTECTED]MTA RMKI, ELTE TTK __ 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,
Re: [R] print Text on device
Can you provide an example of what your data looks like and how you might want it plotted. 'text' does 'put' data on your plot. What else do you want? On 10/4/07, John Lande [EMAIL PROTECTED] wrote: hi BioC, I need to plot a vector of characters on a pdf device, not as a legend, but as in image by itself. I tried text but it is only related to locate text in a plot. what do you suggest? sessionInfo() R version 2.6.0 (2007-10-03) x86_64-unknown-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] rcompgen_0.1-15 tools_2.6.0 [[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. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem you are trying to solve? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Bug or just a problem with the computer precision?
First, I think you are misusing numbers for what are probably character strings. But with numbers, A - 4709.9000 sprintf(%7.2f, A) [1] 4709.90 R will never print a single number as 4709.90: it will drop the trailing zero. With strings: A - 4709.9000 substr(A, 1, 7) [1] 4709.90 On Thu, 4 Oct 2007, Renger van Nieuwkoop wrote: Hi I have the following problem: I have a lot of numbers that identify import goods according to the Harmonised System (8 numbers in two groups with a dot in between). I want to move to the 6 numbers (4 numbers, dot, two numbers). My trick to do this works for all the numbers in the Harmonised Sytem but not for this one: A-4709.9000 (A-floor(100 * A ) / 100) = 4709.89 But this has to be 4709.90 No, as 4709.9000 is not the exact number represented in R. Consider A - 4709.9000 round(A, 2) [1] 4709.9 100*A - 470990 [1] -5.820766e-11 so A is represented a number slightly less than 4709.9000 If I do this in Excel it works fine...Any idea how to make sure that I get 4709.90 and not 4709.89? Then Excel would appear to have a different internal representation (or a bug). -- 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] Updating packages for R 2.6.0
I must be making some really basic mistake, since I keep getting an error message when using update.packages(checkBuilt=TRUE, ask=FALSE) - an example for MASS is below. I am running ubuntu 7.04, with a clean install done today of version 2.6.0 straight from the R repository. here is the message: * Installing *source* package 'MASS' ... ** libs gcc -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include -fpic -g -O2 -c lqs.c -o lqs.o In file included from lqs.c:31: /usr/share/R/include/R.h:28:20: error: stdlib.h: No such file or directory /usr/share/R/include/R.h:29:19: 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/R.h:30, from lqs.c:31: /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 lqs.c:31: /usr/share/R/include/R.h:32:18: error: math.h: No such file or directory /usr/share/R/include/R.h:33:19: error: errno.h: No such file or directory In file included from /usr/share/R/include/R.h:50, from lqs.c:31: /usr/share/R/include/R_ext/RS.h:24:39: error: string.h: No such file or directory lqs.c: In function 'lqs_fitlots': lqs.c:222: warning: implicit declaration of function 'fabs' lqs.c:222: warning: incompatible implicit declaration of built-in function 'fabs' lqs.c:238: warning: implicit declaration of function 'sqrt' lqs.c:238: warning: incompatible implicit declaration of built-in function 'sqrt' lqs.c:239: warning: incompatible implicit declaration of built-in function 'fabs' lqs.c: In function 'do_one': lqs.c:319: warning: implicit declaration of function 'log' lqs.c:319: warning: incompatible implicit declaration of built-in function 'log' lqs.c:319: warning: incompatible implicit declaration of built-in function 'fabs' lqs.c: In function 'mve_fitlots': lqs.c:376: warning: incompatible implicit declaration of built-in function 'log' make: *** [lqs.o] Error 1 ERROR: compilation failed for package 'MASS' ** Removing '/usr/local/lib/R/site-library/MASS' ** Removing '/usr/local/lib/R/site-library/class' ** Removing '/usr/local/lib/R/site-library/nnet' ** Removing '/usr/local/lib/R/site-library/spatial' The downloaded packages are in /tmp/Rtmp7CXD5O/downloaded_packages Warning message: In install.packages() : installation of package 'VR' had non-zero exit status any thoughts appreciated On 10/4/07, Prof Brian Ripley [EMAIL PROTECTED] wrote: Since this has come up already: It is a good idea to re-install all packages for a minor-version increment of R, e.g. 2.5.1 - 2.6.0 (it is major.minor.patchlevel). This is most easily done by update.packages(checkBuilt=TRUE, ask=FALSE) However, if you don't want to do that yet, be aware that - Certain S4-using packages must be reinstalled, and using old versions can make R malfunction. I believe these are Brobdingnag, Matrix, NADA and kappalab. - Any S4 package that makes an existing function S4-generic will grab that function as it existed in the version of R under which they were installed. If it has changed, there is potential trouble. - Packages that create or change character strings at C level will have needed to be updated for R 2.6.0 (and some have not yet been). Using such a package can in principle result in other character data being changed (since most character strings now share storage). -- 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. __ 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] Updating packages for R 2.6.0
On Thu, Oct 04, 2007 at 09:54:26AM -0400, Ricardo Pietrobon wrote: I must be making some really basic mistake, since I keep getting an error message when using update.packages(checkBuilt=TRUE, ask=FALSE) - an example for MASS is below. I am running ubuntu 7.04, with a clean install done today of version 2.6.0 straight from the R repository. From source? Or as a binary? Ubuntu backports of the R 2.6.0 package should be at CRAN within a few days. here is the message: You seem to be missing essential header files, so I'd start from $ sudo apt-get install r-base-dev and try again. I don't see you could compile R if you can't build MASS. Dirk * Installing *source* package 'MASS' ... ** libs gcc -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include -fpic -g -O2 -c lqs.c -o lqs.o In file included from lqs.c:31: /usr/share/R/include/R.h:28:20: error: stdlib.h: No such file or directory /usr/share/R/include/R.h:29:19: 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/R.h:30, from lqs.c:31: /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 lqs.c:31: /usr/share/R/include/R.h:32:18: error: math.h: No such file or directory /usr/share/R/include/R.h:33:19: error: errno.h: No such file or directory In file included from /usr/share/R/include/R.h:50, from lqs.c:31: /usr/share/R/include/R_ext/RS.h:24:39: error: string.h: No such file or directory lqs.c: In function 'lqs_fitlots': lqs.c:222: warning: implicit declaration of function 'fabs' lqs.c:222: warning: incompatible implicit declaration of built-in function 'fabs' lqs.c:238: warning: implicit declaration of function 'sqrt' lqs.c:238: warning: incompatible implicit declaration of built-in function 'sqrt' lqs.c:239: warning: incompatible implicit declaration of built-in function 'fabs' lqs.c: In function 'do_one': lqs.c:319: warning: implicit declaration of function 'log' lqs.c:319: warning: incompatible implicit declaration of built-in function 'log' lqs.c:319: warning: incompatible implicit declaration of built-in function 'fabs' lqs.c: In function 'mve_fitlots': lqs.c:376: warning: incompatible implicit declaration of built-in function 'log' make: *** [lqs.o] Error 1 ERROR: compilation failed for package 'MASS' ** Removing '/usr/local/lib/R/site-library/MASS' ** Removing '/usr/local/lib/R/site-library/class' ** Removing '/usr/local/lib/R/site-library/nnet' ** Removing '/usr/local/lib/R/site-library/spatial' The downloaded packages are in /tmp/Rtmp7CXD5O/downloaded_packages Warning message: In install.packages() : installation of package 'VR' had non-zero exit status any thoughts appreciated On 10/4/07, Prof Brian Ripley [EMAIL PROTECTED] wrote: Since this has come up already: It is a good idea to re-install all packages for a minor-version increment of R, e.g. 2.5.1 - 2.6.0 (it is major.minor.patchlevel). This is most easily done by update.packages(checkBuilt=TRUE, ask=FALSE) However, if you don't want to do that yet, be aware that - Certain S4-using packages must be reinstalled, and using old versions can make R malfunction. I believe these are Brobdingnag, Matrix, NADA and kappalab. - Any S4 package that makes an existing function S4-generic will grab that function as it existed in the version of R under which they were installed. If it has changed, there is potential trouble. - Packages that create or change character strings at C level will have needed to be updated for R 2.6.0 (and some have not yet been). Using such a package can in principle result in other character data being changed (since most character strings now share storage). -- 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. __ 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. -- Three out of two people have difficulties with fractions. __
[R] Invitation to my Viadeo network
Sophie Plantieux invites you to join the Viadeo network Hi, I'd like to invite you to be part of my Viadeo network. I use Viadeo to manage my professional contacts and get in touch with other people in my industry. Give it a look : it has paid off for me. Kind regards, Sophie Plantieux Registration only takes a few minutes !I want to join http://www.viadeo.com/action/index.jsp?actionId=002j6b8yyvh80caurlId=0021v1e4bjtkdcp0 Please join now by clicking on the above link.PS: By inviting your contacts to join your network on Viadeo you increase your networking opportunities exponentially. Some Internet Service Providers deactivate html links. If this is your case, to accept this invitation simply copy and paste this address in your Internet browser:http://www.viadeo.com/action/index.jsp?actionId=002j6b8yyvh80caurlId=0021v1e4bjtkdcp0 http://www.viadeo.com/action/index.jsp?actionId=002j6b8yyvh80caurlId=0021v1e4bjtkdcp0 [[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] RMySQL dbConnect
Hello, I have a problem.. I'm trying to make R communicate with MySQL, but I always receive an error.. My code is: library(DBI) library(RMySQL) drv - dbDriver(MySQL) conn-dbConnect(drv,username=,password=,dbname=prova,host=localhost) and I receive this message: Errore in function (classes, fdef, mtable) : unable to find an inherited method for function dbConnect, for signature MySQLDriver Can anyone help me? Thank you very much Giusy -- View this message in context: http://www.nabble.com/RMySQL-dbConnect-tf4569251.html#a13041284 Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] plot from source file
It's a FAQ (7.22)
-thomas
On Thu, 4 Oct 2007, Armin Goralczyk wrote:
Dear list
Maybe someone can help with the following problem:
I have a source file containing the following code for plotting:
pdf(file = 'data/mario/boxplot.pdf')
bwplot(sig100 ~ target | group, data = fish, main = 'Boxplot der
Signale in 100 Zellen nach Gruppe', xlab = '', ylab = 'Anzahl der
Signale')
dev.off()
pdf(file = 'data/mario/xyplot.pdf')
xyplot(sig100 ~ target | group, data = fish, main = 'Signale in 100
Zellen nach Gruppen', xlab = '', ylab = 'Anzahl der Signale',
panel = function(x,y, ...) {
panel.grid(h = -1, v = -1)
panel.xyplot(x,y, jitter.x=TRUE)
panel.lmline(x,y, lty = 2, col = 3)})
dev.off()
If I run the file from R with
source('lib/analysis_mario.R')
a two pdf-files will be created but they cannot be read.
When I use
source('lib/analysis_mario.R', echo=TRUE)
the files are created correctly.
Actually I don't want the echo, so what can I do to plot correctly and
omit the echo in one run.
I use
platform powerpc-apple-darwin8.9.1
arch powerpc
os darwin8.9.1
system powerpc, darwin8.9.1
status
major 2
minor 5.1
year 2007
month 06
day27
svn rev42083
language R
version.string R version 2.5.1 (2007-06-27)
--
Armin Goralczyk, M.D.
Dept. of General Surgery
University of G??ttingen
G??ttingen, Germany
http://www.chirurgie-goettingen.de
__
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.
Thomas Lumley Assoc. Professor, Biostatistics
[EMAIL PROTECTED] University of Washington, Seattle__
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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] what does size of a plotting character mean?
Hi, Thank you Prof Ripley for the response. On 10/4/07, Prof Brian Ripley [EMAIL PROTECTED] wrote: On Thu, 4 Oct 2007, Prasenjit Kapat wrote: Hi, plot(1,1, cex=2) means that the size of the plotting character (empty circle in this case) is double the default size. Now my question is: What characteristic of the symbol (circle) is double? Is it the area or the diameter? Is it not obvious when you try it? Diameter. What if the symbol is not a circle, what is the generic meaning of size in that case? cex does linear scaling in each dimension. I was hoping this would be true. There is no generic definition of what cex=1 means: it depends on the device, the font (for pch =32 except .) or the symbols (pch=1...25). Thanks PK __ 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 with .libPaths Rterm.exe (under Vista)
Dear list, I’m using R embedded in another program (coded in tcl/tk) under Windows Vista. In this context I don’t launch Rgui.exe but rather Rtem.exe. Now I have a problem finding libraries not specifically installed as administrator (and which are not in the path ‘program files’ but in Contacts\Documents of the current user). To be precise, the user launching my tcl/tk program can’t find the libraries he previously installed locally (as Vista does by default when not launched specifically with administrator rights). However, when (manually) launching Rterm.exe directly (or R.exe) the command .libPaths() returns correctly 2 locations (the personal local library and the ‘common’ one in ‘program files’) as it does with RGui.exe . Does anyone have an idea how or why I can’t see the location of the additional libraries ? Could it be a problem with the attributes of : Rterm.exe --vanilla -q myRcode.r (Note that I had no difficulties with these attributes calling R under Win XP or Linux, but never faced the problem of multiple locations for libraries.) please find below the code form *(a)* launching : Rterm.exe –vanilla –q myRcode.r (where ‘local’ libs are *NOT found*) :** .libPaths() C://PROGRA~1/R/R-26~1.0/library require(affy) Le chargement a nécessité le package : affy Warning messages: 1: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : aucun package nommé 'affy' n'est trouvé # this translates into no package called affy was found sessionInfo() R version 2.6.0 (2007-10-03) i386-pc-mingw32 locale: LC_COLLATE=French_France.1252;LC_CTYPE=French_France.1252;LC_MONETARY=French_France.1252;LC_NUMERattached base packages: [1] stats graphics grDevices utils datasets methods base and the code from (b) manually launching : Rterm.exe (where ‘local’ libs are found OK) : .libPaths() [1] C:\\Users\\wr\\Contacts\\Documents/R/win-library/2.6 [2] C:/PROGRA~1/R/R-26~1.0/library require(affy) # was NOT installed in : program files/... Le chargement a nécessité le package : affy Le chargement a nécessité le package : Biobase Le chargement a nécessité le package : tools Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()'. To cite Bioconductor, see 'citation(Biobase)' and for packages 'citation(pkgname)'. Le chargement a nécessité le package : affyio Le chargement a nécessité le package : preprocessCore sessionInfo() R version 2.6.0 (2007-10-03) i386-pc-mingw32 locale: LC_COLLATE=French_France.1252;LC_CTYPE=French_France.1252;LC_MONETARY=French_France.1252;LC_NUMERIC=C;LC_TIME=French_France.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base As you can see only a single path is found, which is the default collection of libraries in the path of the R installation itself. Does anyone have an idea how I could identify the libPath for a given user and by which argument added to R.exe I could allow accessing these libraries, too ? Thanks’ in advance, Wolfgang Raffelsberger . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Wolfgang Raffelsberger, PhD Laboratoire de BioInformatique et Génomique Intégratives IGBMC 1 rue Laurent Fries, 67404 Illkirch Strasbourg, France Tel (+33) 388 65 3300 Fax (+33) 388 65 3276 [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] A rebel boxplot question
I've altered the code slightly so one group has no data in one month. library(ggplot2) dataset - data.frame(Month = factor(rep(1:12, 20)), Value = c(rnorm(120) + 1:12, rnorm(120) + 12:1), Group = gl(2, 120, labels = LETTERS[1:2])) dataset - dataset[dataset$Month != 2 | dataset$Group != A, ] ggplot(dataset, aes(x = Month, y = Value, colour = Group)) + geom_boxplot() Cheers, Thierry ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest Cel biometrie, methodologie en kwaliteitszorg / Section biometrics, methodology and quality assurance Gaverstraat 4 9500 Geraardsbergen Belgium tel. + 32 54/436 185 [EMAIL PROTECTED] www.inbo.be Do not put your faith in what statistics say until you have carefully considered what they do not say. ~William W. Watt A statistical analysis, properly conducted, is a delicate dissection of uncertainties, a surgery of suppositions. ~M.J.Moroney -Oorspronkelijk bericht- Van: ONKELINX, Thierry Verzonden: donderdag 4 oktober 2007 17:55 Aan: '[EMAIL PROTECTED]'; r-help@r-project.org Onderwerp: RE: [R] A rebel boxplot question Merge both datasets into one with a grouping variable. Then have a look at the ggplot2 package. library(ggplot2) dataset - data.frame(Month = factor(rep(1:12, 20)), Value = c(rnorm(120) + 1:12, rnorm(120) + 12:1), Group = gl(2, 120, labels = LETTERS[1:2])) ggplot(dataset, aes(x = Month, y = Value, colour = Group)) + geom_boxplot() Cheers, Thierry -- -- ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest Cel biometrie, methodologie en kwaliteitszorg / Section biometrics, methodology and quality assurance Gaverstraat 4 9500 Geraardsbergen Belgium tel. + 32 54/436 185 [EMAIL PROTECTED] www.inbo.be Do not put your faith in what statistics say until you have carefully considered what they do not say. ~William W. Watt A statistical analysis, properly conducted, is a delicate dissection of uncertainties, a surgery of suppositions. ~M.J.Moroney -Oorspronkelijk bericht- Van: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Namens [EMAIL PROTECTED] Verzonden: donderdag 4 oktober 2007 17:40 Aan: r-help@r-project.org Onderwerp: [R] A rebel boxplot question Dear R list members I am trying to improve a boxplot with 2 data sets. I run somethinkg like boxplot(data1 ~ month, add=F, col = red, ...) boxplot(data2 ~ month, add=T, col = blue, ...) The problem is that the data from February are missing for data2, so R think that must take little more space between the data classes in data 2 and then both data gropus are not aligned. In the R documentation I do not find any posile solution for tell R that I want reserve a extra space for this month, So the boxplot is erroneous and the x axis have a strange numeration 1 2 3 4 54 65 76 ... etc I would be grateful if anyone could suggest how to tell R That the boxplots must be fitted to the same x class in both data groups. To make a false data group with a 0 valor for february is not aceptable in this case Sincerely Pablo Valdes __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Contour plot (level curves)
On 10/4/07, Prof Brian Ripley [EMAIL PROTECTED] wrote: On Thu, 4 Oct 2007, Caio Azevedo wrote: Hi all, I have a sample of n values from a bivariate distribution (from a MCMC procedure). How could I draw a contour plot of the joint density based on that sample ? You need to estimate the density, and contour that estimate. MASS has examples using its kde2d function. There are other methods available, e.g. in package sm. If you want something ready made, ggplot2 uses kde2d to draw contours from a kernel density estimate - http://had.co.nz/ggplot2/stat_density_2d.html Hadley -- http://had.co.nz/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Problem with .libPaths Rterm.exe (under Vista)
On Thu, 4 Oct 2007, Wolfgang Raffelsberger wrote: Dear list, I?m using R embedded in another program (coded in tcl/tk) under Windows Vista. In this context I don?t launch Rgui.exe but rather Rtem.exe. Now I have a problem finding libraries not specifically installed as administrator (and which are not in the path ?program files? but in Contacts\Documents of the current user). To be precise, the user launching my tcl/tk program can?t find the libraries he previously installed locally (as Vista does by default when not launched specifically with administrator rights). However, when (manually) launching Rterm.exe directly (or R.exe) the command .libPaths() returns correctly 2 locations (the personal local library and the ?common? one in ?program files?) as it does with RGui.exe . Does anyone have an idea how or why I can?t see the location of the additional libraries ? You mean the additional library what contains packages? It really does help to get your terminology straight here. What libraries are on .libPaths() is controlled by environment variables, so debugging those will be the key. This is all explained on the help page for .libPaths. Could it be a problem with the attributes of : Rterm.exe --vanilla -q myRcode.r Yes, it could. Look up what --vanilla does in ?Startup: it skips places where the environment variables are usually set. (Note that I had no difficulties with these attributes calling R under Win XP or Linux, but never faced the problem of multiple locations for libraries.) please find below the code form *(a)* launching : Rterm.exe ?vanilla ?q myRcode.r (where ?local? libs are *NOT found*) :** .libPaths() C://PROGRA~1/R/R-26~1.0/library require(affy) Le chargement a nécessité le package : affy Warning messages: 1: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : aucun package nommé 'affy' n'est trouvé # this translates into no package called affy was found sessionInfo() R version 2.6.0 (2007-10-03) i386-pc-mingw32 locale: LC_COLLATE=French_France.1252;LC_CTYPE=French_France.1252;LC_MONETARY=French_France.1252;LC_NUMERattached base packages: [1] stats graphics grDevices utils datasets methods base and the code from (b) manually launching : Rterm.exe (where ?local? libs are found OK) : .libPaths() [1] C:\\Users\\wr\\Contacts\\Documents/R/win-library/2.6 [2] C:/PROGRA~1/R/R-26~1.0/library require(affy) # was NOT installed in : program files/... Le chargement a nécessité le package : affy Le chargement a nécessité le package : Biobase Le chargement a nécessité le package : tools Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()'. To cite Bioconductor, see 'citation(Biobase)' and for packages 'citation(pkgname)'. Le chargement a nécessité le package : affyio Le chargement a nécessité le package : preprocessCore sessionInfo() R version 2.6.0 (2007-10-03) i386-pc-mingw32 locale: LC_COLLATE=French_France.1252;LC_CTYPE=French_France.1252;LC_MONETARY=French_France.1252;LC_NUMERIC=C;LC_TIME=French_France.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base As you can see only a single path is found, which is the default collection of libraries in the path of the R installation itself. Does anyone have an idea how I could identify the libPath for a given user and by which argument added to R.exe I could allow accessing these libraries, too ? Thanks? in advance, Wolfgang Raffelsberger . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Wolfgang Raffelsberger, PhD Laboratoire de BioInformatique et Génomique Intégratives IGBMC 1 rue Laurent Fries, 67404 Illkirch Strasbourg, France Tel (+33) 388 65 3300 Fax (+33) 388 65 3276 [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. -- 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] print Text on device
I would like to print on a pdf a table with element coming from a vector. such as example=c(a, b) pdf(table.pdf) print(example) dev.off() On 10/4/07, jim holtman [EMAIL PROTECTED] wrote: Can you provide an example of what your data looks like and how you might want it plotted. 'text' does 'put' data on your plot. What else do you want? On 10/4/07, John Lande [EMAIL PROTECTED] wrote: hi BioC, I need to plot a vector of characters on a pdf device, not as a legend, but as in image by itself. I tried text but it is only related to locate text in a plot. what do you suggest? sessionInfo() R version 2.6.0 (2007-10-03) x86_64-unknown-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] rcompgen_0.1-15 tools_2.6.0 [[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. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem you are trying to solve? [[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] grep in filename
Is there any version of grep that gets information from the filename? For example: x - myfile.txt y - grep.file(my text, x) should return in y the lines with my text. I know that x - myfile.txt y - grep(my text, readLines(x)) will probably work, but maybe there's a more direct (and less memory hungry) option. Alberto Monteiro __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] [R-pkgs] Amap new release
A new major version of Amap package is available on CRAN. For this major release, all clustering code has been rewritten in C++. Amap implements several tools in the field of clustering and robust statistics. New features are: * clustering possible in float precision (less memory needs) * new rank-based metric: Kendall distance, use for both matrix distance computation, K-means, and hierachical clustering. Best. Antoine. ___ R-packages mailing list [EMAIL PROTECTED] https://stat.ethz.ch/mailman/listinfo/r-packages __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] ggplot2: problem with geom_errorbar and geom_abline
Ben Bolker wrote: In http://www.nabble.com/plot-graph-with-error-bars-trouble-tf4535734.html Hadley Wickham says that this is a bug, fixed in the development version. However, I don't see that the update has propagated to my usual CRAN mirror yet ... The error-bar issue is mentioned in that thread, but the problem with geom_abline can be fixed (which in this example avoids the error-bar problem). Off list Hadley suggested the following alteration of the code: p + geom_point() + geom_errorbar(limits, width=0.2) + geom_abline(slope=0,intercept=3,linetype=2,aes(colour=NULL)) If you want to change the color of the abline, you may use the following: p + geom_point() + geom_errorbar(limits, width=0.2) + geom_abline(slope=0,intercept=3,linetype=2,aes(colour=NULL),colour=blue) -- View this message in context: http://www.nabble.com/ggplot2%3A-problem-with-geom_errorbar-and-geom_abline-tf4563163.html#a13044792 Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Updating packages for R 2.6.0
you got it. works perfectly now. thanks On 10/4/07, Gabor Csardi [EMAIL PROTECTED] wrote: You need to install the libc6-dev ubuntu package to be able to compile programs. sudo apt-get install libc6-dev Gabor On Thu, Oct 04, 2007 at 09:54:26AM -0400, Ricardo Pietrobon wrote: I must be making some really basic mistake, since I keep getting an error message when using update.packages(checkBuilt=TRUE, ask=FALSE) - an example for MASS is below. I am running ubuntu 7.04, with a clean install done today of version 2.6.0 straight from the R repository. here is the message: * Installing *source* package 'MASS' ... ** libs gcc -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include -fpic -g -O2 -c lqs.c -o lqs.o In file included from lqs.c:31: /usr/share/R/include/R.h:28:20: error: stdlib.h: No such file or directory /usr/share/R/include/R.h:29:19: 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/R.h:30, from lqs.c:31: /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 lqs.c:31: /usr/share/R/include/R.h:32:18: error: math.h: No such file or directory /usr/share/R/include/R.h:33:19: error: errno.h: No such file or directory In file included from /usr/share/R/include/R.h:50, from lqs.c:31: /usr/share/R/include/R_ext/RS.h:24:39: error: string.h: No such file or directory lqs.c: In function 'lqs_fitlots': lqs.c:222: warning: implicit declaration of function 'fabs' lqs.c:222: warning: incompatible implicit declaration of built-in function 'fabs' lqs.c:238: warning: implicit declaration of function 'sqrt' lqs.c:238: warning: incompatible implicit declaration of built-in function 'sqrt' lqs.c:239: warning: incompatible implicit declaration of built-in function 'fabs' lqs.c: In function 'do_one': lqs.c:319: warning: implicit declaration of function 'log' lqs.c:319: warning: incompatible implicit declaration of built-in function 'log' lqs.c:319: warning: incompatible implicit declaration of built-in function 'fabs' lqs.c: In function 'mve_fitlots': lqs.c:376: warning: incompatible implicit declaration of built-in function 'log' make: *** [lqs.o] Error 1 ERROR: compilation failed for package 'MASS' ** Removing '/usr/local/lib/R/site-library/MASS' ** Removing '/usr/local/lib/R/site-library/class' ** Removing '/usr/local/lib/R/site-library/nnet' ** Removing '/usr/local/lib/R/site-library/spatial' The downloaded packages are in /tmp/Rtmp7CXD5O/downloaded_packages Warning message: In install.packages() : installation of package 'VR' had non-zero exit status any thoughts appreciated On 10/4/07, Prof Brian Ripley [EMAIL PROTECTED] wrote: Since this has come up already: It is a good idea to re-install all packages for a minor-version increment of R, e.g. 2.5.1 - 2.6.0 (it is major.minor.patchlevel). This is most easily done by update.packages(checkBuilt=TRUE, ask=FALSE) However, if you don't want to do that yet, be aware that - Certain S4-using packages must be reinstalled, and using old versions can make R malfunction. I believe these are Brobdingnag, Matrix, NADA and kappalab. - Any S4 package that makes an existing function S4-generic will grab that function as it existed in the version of R under which they were installed. If it has changed, there is potential trouble. - Packages that create or change character strings at C level will have needed to be updated for R 2.6.0 (and some have not yet been). Using such a package can in principle result in other character data being changed (since most character strings now share storage). -- 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. __ 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. -- Csardi Gabor [EMAIL PROTECTED]MTA RMKI, ELTE TTK -- Ricardo Pietrobon, MD, PhD, MBA
[R] R2.6 + Error saving plots as PDF
Dear R users; After installing R 2.6.0 I got the following error when I try to save a plot as PDF or PS from the windows plot: Error: Invalid font type In addition: Warning messages: 1: font family not found in PostScript font database 2: font family not found in PostScript font database However in R 2.5.0 works just fine Any ideas how to make it work again (without having to install the previous version)? I'm running R under WinXP pro __ 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] grep in filename
On Thu, 4 Oct 2007, Alberto Monteiro wrote: Is there any version of grep that gets information from the filename? For example: x - myfile.txt y - grep.file(my text, x) should return in y the lines with my text. I know that x - myfile.txt y - grep(my text, readLines(x)) will probably work, but maybe there's a more direct (and less memory hungry) option. Let your system utilities handle the burden. For *NIXes, this approach: http://finzi.psych.upenn.edu/R/Rhelp02a/archive/101103.html and Windows XP http://finzi.psych.upenn.edu/R/Rhelp02a/archive/101220.html Chuck Alberto Monteiro __ 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. Charles C. Berry(858) 534-2098 Dept of Family/Preventive Medicine E mailto:[EMAIL PROTECTED] UC San Diego http://famprevmed.ucsd.edu/faculty/cberry/ La Jolla, San Diego 92093-0901 __ 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] combining vectors on unequal length
--- Nair, Murlidharan T [EMAIL PROTECTED] wrote:
If I have two vectors
X-1:10
Y-1:5
When I combine them using cbind, the shorter one is
repeated and both are made of the same length. Is
there a methods that does this without duplicating
the shorter one. I want to use this to store the
data back to a file.
Thanks ../Murli
It's not quite clear what you want to do. If you just
want to save an .Rdata file you could just put the
variables in a list.
X-1:10
Y-1:5
mylist -list(X,Y)
If you want to save to something like a data.frame to
a csv file then you probably need to add some padding
to the file. The function below adds NA's and turns
the matrix into a data.frame
padding - function(a,b) {
zz -rep(NA,length(X)-length(Y))
YY - c(Y,zz)
out - data.frame(cbind(a,YY))
}
dd - padding(X,Y)
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] combining vectors on unequal length
Something like this, perhaps: cbind( X, c(Y, rep(NA,length(X)-length(Y))) ) This just extends Y with NA instead of recycling Y. If you are going to cbind() the vectors must be the same length. You *must* have something there. -Don At 1:51 PM -0400 10/4/07, Nair, Murlidharan T wrote: If I have two vectors X-1:10 Y-1:5 When I combine them using cbind, the shorter one is repeated and both are made of the same length. Is there a methods that does this without duplicating the shorter one. I want to use this to store the data back to a file. Thanks ../Murli [[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. -- -- Don MacQueen Environmental Protection Department Lawrence Livermore National Laboratory Livermore, CA, USA 925-423-1062 __ 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] Windows OS, R and unicode
An alternative is to use the my.symbols function from the TeachingDemos package (improvements are welcome). -Original Message- From: Richard Rowe [EMAIL PROTECTED] To: R-help@r-project.org R-help@r-project.org Sent: 10/3/07 5:42 PM Subject: [R] Windows OS, R and unicode I'm trying to use the biological female and male signs in R2.5.1 under Windows XP. I can access and insert these symbols using word-processors. In general these should be available as \u2640 and \u2642 but I can't make them happen in R using (say) text(5,5, \u2640) message invalid \u sequence I've replaced Arial with Arial unicode MS in Rdevga and I've tried various setlocale options with no success (the Murrell/Ripley examples (Rnews 6/2) do work of course ... so I feel I should be able to do this myself, but after several hours it is time to ask for help). I understand from Google results that users on Mac OS and Linux aren't facing this problem ... Richard -- Dr Richard Rowe Zoology Tropical Ecology School of Marine Tropical Biology James Cook University Townsville 4811 AUSTRALIA ph +61 7 47 81 4851 fax +61 7 47 25 1570 JCU has CRICOS Provider Code 00117J __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] combining vectors on unequal length
Well, if you bind two vectors you form an array with dimensions 2 x length of the longest vector. So you need to decide how to fill up the 'empty' spacies corresponding to the shorter vector. Recycling the shorter vector is the default action. If you just want to save the data, you could create a list and save it as a R object. my.list=list(X,Y) save(my.list) Julian Nair, Murlidharan T wrote: If I have two vectors X-1:10 Y-1:5 When I combine them using cbind, the shorter one is repeated and both are made of the same length. Is there a methods that does this without duplicating the shorter one. I want to use this to store the data back to a file. Thanks ../Murli [[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] [R-pkgs] New version of GillespieSSA package uploaded to CRAN
Dear useRs, A new version of the package GillespieSSA (0.3-1) has been uploaded to CRAN. The GillespieSSA package (Gillespie's Stochastic Simulation Algorithm) provides a simple to use, versatile, and extensible interface to a number of Monte Carlo implementations of the stochastic simulation algorithm (SSA) and is intended for scientists, teachers, and students alike. The SSA is a numerical procedure for generating statistically correct trajectories of finite well-mixed populations in continuous time. The methods currently implemented are: the Direct method, Explicit tau-leaping, Binomial tau-leaping, and Optimized tau-leaping. The package also provides a library of molecular, ecological and epidemiological example models (as demos) that can easily be customized and extended. Currently the following models are included, Decaying-Dimerization Reaction Set, Linear Molecular Chain System, single-species logistic growth model, Lotka predator-prey model, Rosenzweig-MacArthur predator-prey model, and Kermack-McKendrick SIR model. The release consists of several bug fixes, improved documentation, and a revised more 'R-like' management of model parameters. A vignette providing a tutorial of basic SSA theory, usage of the package using additional example models is currently being finalized. Although it is not part of this release a preprint is available upon request. Comments are welcome, Mario Pineda-Krch --- Mario Pineda-Krch, Post Doctoral Fellow Center for Animal Disease Modeling and Surveillance (CADMS) University Of California, Davis, CA 95616, U.S.A. Phone: (530) 297-4621 Fax: (530) 297-4618 Email: [EMAIL PROTECTED] URL : http://pineda-krch.com ___ R-packages mailing list [EMAIL PROTECTED] https://stat.ethz.ch/mailman/listinfo/r-packages __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R2.6 + Error saving plots as PDF
On Thu, 4 Oct 2007, Prof Brian Ripley wrote: Pedro Mardones wrote: After installing R 2.6.0 I got the following error when I try to save a plot as PDF or PS from the windows plot: Error: Invalid font type In addition: Warning messages: 1: font family not found in PostScript font database 2: font family not found in PostScript font database However in R 2.5.0 works just fine Any ideas how to make it work again (without having to install the previous version)? It works if postscript() or pdf() has been used in the session, and also if initPSandPDFfonts() is called (so put that in your .Rprofile). To be specific, grDevices:::initPSandPDFfonts(). We'll arrange to do this automatically in R-patched. Done in patch r43083. -- 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.
[R] Convergence problem in gam(mgcv)
Dear all, I'm trying to fit a pure additive model of the following formula : fit - gam(y~x1+te(x2, x3, bs=cr)) ,with the smoothing parameter estimation method magic(default). Regarding this, I have two questions : Question 1 : In some cases the value of mgcv.conv$fully.converged becomes FALSE, which tells me that the method stopped with a steepest descent step failure. So I'd like to modify the arguments of magic() to make it easier to converge. But It doesn't seem like that I can do it by modifying the gam defaults through gam.control(). Is there any means to set magic() arguments from outside ? Question 2 : Sometimes the smoothing parameter for x2 is very large (in the order of 1E+8 or 1E+10), while that for x3 is modest(less than 1), and the opposite cases also happen. Does this indicate that something is wrong, or just that the data is actually linear with respect to x2 or x3 ? Thank you for your help in advance. __ 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] Matrix bar plot
On Thu, Oct 04, 2007 at 06:15:34PM -0500, hadley wickham wrote: Why would you want a plot that looks like that? Half the bars are hidden behind other bars! I would rotate it such that all bars are visible. -TAG __ 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] Matrix bar plot
On 10/4/07, Todd A. Gibson [EMAIL PROTECTED] wrote: On Thu, Oct 04, 2007 at 06:15:34PM -0500, hadley wickham wrote: Why would you want a plot that looks like that? Half the bars are hidden behind other bars! I would rotate it such that all bars are visible. If you are really, really, sure that you want to do this, take a look at ?panel.3dbars in the latticeExtra package. This will be fairly slow for large tables (and I have no plans to improve it). Another option is the rgl package, but you might need to do some work to get it to do what you want. -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] Matrix bar plot
On Thu, Oct 04, 2007 at 06:15:34PM -0500, hadley wickham wrote: Why would you want a plot that looks like that? Half the bars are hidden behind other bars! I would rotate it such that all bars are visible. -TAG -- thus distorting the perspective even more so that you can not make accurate (perhaps even relatively!) judgments of magnitude. I echo Hadley's sentiment: such 3-D bar plots are an abomination. Just because Excel can do them doesn't mean you should. (Dismount pulpit). -- Bert Gunter Genentech __ 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] plotting region
Hi, I have been playing with graphic parameters to meet my specific plot requirement. I would like to draw a plot in the top right region of the plot region, I can do that with a number of parameters such as plt, mar or oma. For example setting the parameters: par(plt=c(0.28,0.956,0.25,0.9)) or par(mar=c(10,8,4,1)) can do the job. But once I set those parameters, I could't add any text in the extra space left at the bottom left regions. Actually, S-plus allow me to add text in these white spaces, does anyone know how I can do that in R? thanks __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] plotting region
On 5/10/2007, at 12:07 PM, array chip wrote:
Hi, I have been playing with graphic parameters to
meet my specific plot requirement. I would like to
draw a plot in the top right region of the plot
region, I can do that with a number of parameters such
as plt, mar or oma. For example setting the
parameters:
par(plt=c(0.28,0.956,0.25,0.9))
or
par(mar=c(10,8,4,1))
can do the job. But once I set those parameters, I
could't add any text in the extra space left at the
bottom left regions. Actually, S-plus allow me to add
text in these white spaces, does anyone know how I can
do that in R?
(1) par(xpd=NA)
(2) ?layout
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and provide commented, minimal, self-contained, reproducible code.
[R] Sklyar's inline package: how to return a list?
Hi,
Below I have a mickey-mouse example using Oleg Sklyar's wonderful inline
package.
The question I have is, how do I return multiple values, say in a list?
Inside the C code, I've also calculated 'sum'. How do I return this along with
'res'?
Ultimately, I want to return multiple matrix results. Thanks in advance for
any code snipplets/advice!
Regards,
Ken
#
--
my.mat
[,1] [,2] [,3]
[1,] 1.5 4.5 7.5
[2,] 2.5 5.5 8.5
[3,] 3.5 6.5 9.5
funx( a=my.mat )
[,1] [,2] [,3]
[1,] -1.5 -4.5 -7.5
[2,] -2.5 -5.5 -8.5
[3,] -3.5 -6.5 -9.5
#
--
library( inline )
c.code -
SEXP res;
int nprotect = 0, nx, ny, x, y;
double *dptr, *resptr, sum;
PROTECT(res = Rf_duplicate(a)); nprotect++;
nx = INTEGER(GET_DIM(a))[0];
ny = INTEGER(GET_DIM(a))[1];
dptr = REAL(a);
resptr = REAL( res );
sum = 0.0;
for (x = 0; x nx; x++)
for (y = 0; y ny; y++)
{
resptr[ x + y*nx ] = -dptr[ x + y*nx ];
sum += -dptr[ x + y*nx ];
}
UNPROTECT(nprotect);
return res;
funx - cfunction(signature(a=array), c.code)
# test run
my.mat - matrix( 0.5 + 1:9, nrow=3, ncol=3 )
funx( a=my.mat)
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and provide commented, minimal, self-contained, reproducible code.
[R] Confused about Tukey mult. comp. after ANCOVA
Hi, I had a first occasion to try multiple comparisons (of intercepts, I suppose) following a significant result in an ANCOVA. As until now I was doing this with JMP, I compared my results and the post-hoc comparisons were different between R and JMP. I chose to use an example data set from JMP because it was small, so I can show it here. It is not the best example for an ANCOVA because the factor Drug does not have a significant effect, but it will do. drug$x [1] 11 8 5 14 19 6 10 6 11 3 6 6 7 8 18 8 19 8 5 15 16 13 11 9 21 16 12 [28] 12 7 12 drug$y [1] 6 0 2 8 11 4 13 1 8 0 0 2 3 1 18 4 14 9 1 9 13 10 18 5 23 12 5 [28] 16 1 20 drug$Drug [1] a a a a a a a a a a d d d d d d d d d d f f f f f f f f f f Levels: a d f I did not manage to get TukeyHSD to work if I fitted the ANCOVA with lm, so I used aov: my.anc - aov(y~x+Drug, data=drug) summary(my.anc) Df Sum Sq Mean Sq F valuePr(F) x1 802.94 802.94 50.0393 1.639e-07 *** Drug 2 68.55 34.28 2.13610.1384 Residuals 26 417.20 16.05 --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 I tried this to compare the Drugs, correcting for the effect of x. TukeyHSD(my.anc, Drug) Tukey multiple comparisons of means 95% family-wise confidence level Fit: aov(formula = y ~ x + Drug, data = drug) $Drug diff lwr upr p adj d-a 0.03131758 -4.420216 4.482851 0.9998315 f-a 3.04677613 -1.404758 7.498310 0.2239746 f-d 3.01545855 -1.436075 7.466992 0.2305187 Warning message: non-factors ignored: x in: replications(paste(~, xx), data = mf) I am not sure about the Warning, maybe it is the reason the differences shown here are different from those shown in JMP for the same analysis. Maybe TukeyHSD is not meant to be used with non- factors (i.e. not valid for ANCOVAs)? I just found the package multcomp and am not sure I understand it well yet, but its Tukey comparisons gave the same results as JMP. summary(glht(m3, linfct=mcp(Drug=Tukey))) Simultaneous Tests for General Linear Hypotheses Multiple Comparisons of Means: Tukey Contrasts Fit: aov(formula = y ~ x + Drug, data = drug) Linear Hypotheses: Estimate Std. Error t value p value d - a == 00.109 1.795 0.061 0.998 f - a == 03.446 1.887 1.826 0.181 f - d == 03.337 1.854 1.800 0.189 (Adjusted p values reported) I would very much like to understand why these two Tukey tests gave different results in R. Thanks in advance, Denis __ 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] Matrix bar plot
check out the 'rgl' package On 10/4/07, Todd A. Gibson [EMAIL PROTECTED] wrote: Hello, Does R have any facility to create a plot that looks similar to this: http://www.augustcouncil.com/~tgibson/barmatrix.jpg Thank you, -TAG Todd A. Gibson __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem you are trying to solve? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] plotting region
check out the 'grid' package On 10/4/07, array chip [EMAIL PROTECTED] wrote: Hi, I have been playing with graphic parameters to meet my specific plot requirement. I would like to draw a plot in the top right region of the plot region, I can do that with a number of parameters such as plt, mar or oma. For example setting the parameters: par(plt=c(0.28,0.956,0.25,0.9)) or par(mar=c(10,8,4,1)) can do the job. But once I set those parameters, I could't add any text in the extra space left at the bottom left regions. Actually, S-plus allow me to add text in these white spaces, does anyone know how I can do that in R? thanks __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem you are trying to solve? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] discrepancy in the result of R and SAS on same data in logistics regression
Dear Members, Greetings! I have come across a discrepancy shown by R and SAS results on same data for logistics regression.. When I processed the above csv file(1000.csv) for predicting the Action (i/c) by Age Group(1-7,Na) and Gender(M,F,Na) with GLM of R I get: R result Call: glm(formula = Action ~ Gender + AgeGroup, family = binomial, data = mydata1, na.action = na.pass) Deviance Residuals: Min 1Q Median 3Q Max -1.828 -0.973 -0.709 1.087 1.734 Coefficients: Estimate Std. Error z value Pr(|z|) (Intercept) 1.2939 0.3180 4.069 4.73e-05 *** GenderM -0.8794 0.1637 -5.371 7.85e-08 *** GenderNa -1.4407 0.2749 -5.240 1.60e-07 *** AgeGroup2-1.2053 0.3971 -3.035 0.00240 ** AgeGroup3-1.6670 0.3262 -5.110 3.21e-07 *** AgeGroup4-1.0786 0.3714 -2.904 0.00368 ** AgeGroup5-0.8232 0.3829 -2.150 0.03156 * AgeGroup6 0.1682 0.3501 0.481 0.63081 AgeGroup7-0.3361 0.3617 -0.929 0.35281 AgeGroupNa -1.7956 0.3433 -5.231 1.69e-07 *** --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 (Dispersion parameter for binomial family taken to be 1) Null deviance: 1342.7 on 999 degrees of freedom Residual deviance: 1213.2 on 990 degrees of freedom AIC: 1233.2 Number of Fisher Scoring iterations: 4 where as SAS gives on same data: Analysis of Maximum Likelihood Estimates Parameter Action DF Estimate Standard Error Wald Chi-Square Pr ChiSq Intercept c 1 0.3217 0.0953 11.4025 0.0007 AgeGroup 2 c 1 0.3631 0.2434 2.2260 0.1357 AgeGroup 3 c 1 0.8248 0.1411 34.1508 .0001 AgeGroup 4 c 1 0.2364 0.2146 1.2136 0.2706 AgeGroup 5 c 1 -0.0190 0.2299 0.0068 0.9343 AgeGroup 6 c 1 -1.0104 0.1822 30.7454 .0001 AgeGroup 7 c 1 -0.5061 0.1974 6.5711 0.0104 AgeGroup Na c 1 0.9534 0.1718 30.7884 .0001 Gender M c 1 0.1060 0.1103 0.9246 0.3363 Gender N c 1 0.6674 0.1686 15.6744 .0001 I compared the resultant probabilities of Action c on all three packages: R, SAS and StatGraphics and found that R and StatGraphics have same results but SAS has different results for some combinations of AgeGroup and Gender as in attached document for probability of Action. I will appreciate if you can help me sorting out the issue. Thanks and Best Regards Atul Malik StatGraphics results as follows: Estimated Regression Model (Maximum Likelihood) Standard Estimated Parameter Estimate Error Odds Ratio CONSTANT -1.94239 0.298622 AgeGroup=1 1.79555 0.343277 6.02282 AgeGroup=2 0.590229 0.316943 1.8044 AgeGroup=3 0.128605 0.216341 1.13724 AgeGroup=4 0.716996 0.288917 2.04827 AgeGroup=5 0.972326 0.30544 2.64409 AgeGroup=6 1.9638 0.262721 7.12638 AgeGroup=7 1.45945 0.275966 4.3036 Gender=F 1.44072 0.274922 4.22375 Gender=M 0.56134 0.256286 1.75302 Analysis of Deviance Source Deviance Df P-Value Model 129.506 9 0. Residual 1213.21 990 0. Total (corr.) 1342.71 999 __ 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.
