Re: [R] licensing of R packages
G'day Duncan, On Fri, 14 Nov 2008 15:24:03 -0500 Duncan Murdoch [EMAIL PROTECTED] wrote: Moreover, if you write a C/C++ program that makes use of GNU extensions, you'd be in violation of the GPL if you were to distribute it without GPLing it. Even the FSF doesn't believe that: http://www.fsf.org/licensing/licenses/gpl-faq.html#CanIUseGPLToolsForNF Could you please explain how you come to this opinion? I believe your argument was that if my program can't be used without a library that is currently only available under the GPL, then my program must be considered as a derivative work, so I must license it under the GPL as well. It depends now what you mean with my program. I was making my comments specifically within the context of the original posters questions about Numerit's behaviour and Barry's assertion that he could write a C program that relies on a GPL'd library, distribute the compiled binary of that C program without the GPL'd library and just ask the user to get the GPL'd library from somewhere else so that he or she could then run the program. You seem to extend the scope to a more general definition of what a program constitutes, including the distribution of source code for an interpreter. As I tried to point out, if you distribute source code to be interpreted by an interpreter that is GPL'd, you bring up all kind of issues. Well, if my program uses GNU extensions, it can only be used when compiled by gcc, which I believe is GPL'd. So your argument would imply that it is a derivative work. Not at all. Please read what I said. Is the program compiled from C code that uses GNU extensions all of a sudden linked to a GPL'd /usr/lib/libgnuextension library, with that library being the only source of the needed functionality? The C code is input (data) to the GNU compiler. The license of the GNU compiler does not specify that the output (i.e. the binary) has to be GPL'd. Nor does the FSF claim copyright to that output. (IIRC, when reading the EULA of some commercial compilers in the 80's, some software houses seriously claimed the copyright of any program compiled with their compilers. I think this clause disappeared rather soon when users realised its implication.) None of us (you, me or the FSF) think the latter argument is valid. Agreed, and in my case, and presumably also the FSF's case, it is because such an argument was never made and never claimed. To be, hopefully, completely precise: if you distribute a binary program which can only be run if linked against a GPL'd library, i.e. no alternative implementation of the library providing the functionality your binary needed exists, then that binary is a derivative work of the GPL'd library. Hence, in order to distribute it, you would have to adhere to the rules under which use of the GPL'd library was granted to you. Distributing your binary, and asking your users to get the GPL'd library separately from somewhere else, does not absolve you from your responsibilities under the GPL. I don't see a material difference from the former argument, so I conclude the former argument is invalid as well. My scenario: a binary program is distributed which can only be run if it is linked by the user to a GPL'd library. The source code of that binary program is not distributed and there is no offer of providing it. There is no way of using that program except with the GPL'd library, i.e. you need to have the GPL'd library libXXX, there is no other (whether commercial or not) provider of libXXX that implements the same featuers. Thus, it is clear that when you produced the binary, you had the GPL'd library on your system, you linked the binary against that library and at that moment you created a derivative work of the GPL'd library. Your scenario (as I understand it): You use a GPL'd compiler to compile your program which is then only linked to system libraries available on any similar OS. The compiler offers extension to the language that other compilers don't offer, but produces binaries that are only linked to said standard libraries. The GPL'd compiler makes no claims on the binary that it produces. Sorry, but if you do not see a material difference here, then I guess it is best that we just agree to disagree. :) The argument in the latter FAQ does seem to imply that R scripts must be GPL'd, and again: that's nonsense. Not at all, read the complete FAQ, especially the part I mention above about interpreted languages. I think the complete FAQ is inconsistent. I guess that comes from the fact that you do not see a material difference where other do. :) Some of it is accurate (e.g. the bits that say you can use GPL'd software without GPL'ing your own work) and some of it is not (the parts that imply dynamic linking makes something a derivative work.) As far as I understand, there have been people who shared that thought, namely that dynamic linking does not imply
Re: [R] GAM and Poisson distribution
sallyr wrote: Hi -I'm running a GAM with 7 explanatory variables with a Poisson error structure. All of the variables are continuous so I'm getting error messages in R. cod.fall.full.gam.model-gam(Kept.CPUE~s(HOUR)+s(LAT_dec)+s(LONG_dec)+s(meantemp_C)+s(meandepth_fa)+s(change_depth)+s(seds), data=cod.fall.version2,family=poisson) In dpois(y, mu, log = TRUE) ... : non-integer x = 5.325517 Thanks Sally If your response variable is an intensity (catch per unit effort) you probably need to include an offset for the total effort, e.g. something like offset=log(effort) -- View this message in context: http://www.nabble.com/GAM-and-Poisson-distribution-tp20508604p20513810.html 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] configuring graphics device in Linux
Erik Iverson wrote: You should begin by telling us what you did to produce the result. That way we can tell if it's something in your R commands or not. If you give us step by step instructions to reproduce the problem (with simulated data, or a dataset distributed with R), it becomes much easier to debug. Good advice in general, but in this case I think John is right in assuming that the issue is mainly with his graphics hardware setup, and he did tell us about that. The R version would have been nice though; we have fixed various issues in this area over time. i'm trying plot() from Owen's _The R Guide_ and having trouble with being able to view the result. the Graphics Device 2 draws an image i can only see the top part of and when i try to manipulate the window to see the image, the window then says: ...ure margins too lar... in large letters. i guess it says something about picture margins too large. i'm not sure how to determine all my video settings in Ubuntu (8.04), what i do know is this: 1280X800 60Hz Intel 945GM graphics and according to /var/log/Xorg.0.log: DPI set to (96,96) i found x11(), but i'm not sure what to change there, if i should even change it. can someone advise how to adjust settings, please? These are generic symptoms of using a too large font for your display, but that can happen for a number of reasons. According to your setup, the system should believe that you have an ~8 inch screen (800/96) and the default X11 window is 7x7 inches so there _should_ be plenty of room, but some systems try to outsmart the user and use the actual physical dimensions, which could be smaller (higher DPI). You might want to check with xdpyinfo (from the shell). In any case, you can try reducing width, height, and (especially) pointsize in the call to x11() (which you'd issue _before_ the plot()). Or set them with X11.options(). -- 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] ggplot2 - two or more axis
Thank you very much for the answer. I have seen very often the number of subject at risk on survival graph (see my pdf file). It is very easy to plot the curve with geom_step(), but is there a better way to show the number of subjects at risk at each time ? Thank you for your advice. 2008/11/14 hadley wickham [EMAIL PROTECTED] Hi David, I'm trying to learn how to make a plot with the amazing package ggplot2. I was wondering if it was possible to draw 2 (or more) x (or y) axis in the same graph. For example : - I want to show two informations at each x coordinate : a survival curve, I want to show the time (0, 12 and 24 months) and the number of subject at risk at each time. - I want to draw two curves that don't have the same unit Unfortunately, the capability is currently unavailable in ggplot2 and is unlikely to ever be available because I believe it is a fundamentally inaccurate means of presenting data. However, in the next version it will be much easier to created faceted displays with varying scales, which should be a better solution for many of these types of problems. Regards, Hadley -- http://had.co.nz/ surv.pdf Description: Adobe PDF document __ 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] configuring graphics device in Linux
megha patnaik wrote: Hi John, an R problem, but an X11 bug in Ubuntu. This is evident from plot(rnorm(10)) failing to perform. If you are seeing this, then it is because X11 does not automatically detect Intel graphic cards. The solution is to edit your xorg.conf file, changing it to something like (this is from my xorg.conf): Section Device IdentifierIntel Corporation Mobile 945GM/GMS, 943/940GML Express Integrated Graphics Controller (rev 03) Driverintel EndSection Megha, thanks for your help. i tried plot(rnorm(10)) and still was not able to see a plot. i checked /etc/X11/xorg.conf and it looks like this, without me editing it: Section Device Identifier Intel Corporation Mobile 945GM/GMS, 943/940GML Express Integrated Graphics Controller Driver intel BusID PCI:0:2:0 EndSection Section Monitor Identifier Generic Monitor Option DPMS EndSection Section Screen Identifier Default Screen Device Intel Corporation Mobile 945GM/GMS, 943/940GML Express Integrated Graphics Controller Monitor Generic Monitor DefaultDepth24 SubSection Display Modes 1280x800 EndSubSection EndSection The steps I carried out to detect where the problem was were as follows: 1. Checked whether basic plots in R worked 2. Created a new UID ( which did not have my saved settings in R) and tried basic plots. If 2. told me that margins were too large, then this was not a problem due to my past commands in R. i have tried your suggested plot and the one from the tutorial. neither worked. i'm using R 2.6.2 straight from the install through Unbuntu's package manager, so i don't think there are any scripts or whathaveyou on start. xorg.conf is a dangerous file to meddle with. The other symptoms I was seeing of poor graphics was an XL font size on my login screen and broken images in google earth. Are you seeing anything of the sort? yes, actually i do get the large fonts at start up like you do. i tried trolling around the Ubuntu forums for stuff about video settings, but only briefly. I am relatively new to the mailing list. Do tell me if this is better taken offline. i'm kind of new too. maybe someone else will tell me(us) to take this somewhere else. Peter Dalgaard wrote: Good advice in general, but in this case I think John is right in assuming that the issue is mainly with his graphics hardware setup, and he did tell us about that. The R version would have been nice though; we have fixed various issues in this area over time. thank you Peter. i appreciate you assistance. it's version 2.6.2 According to your setup, the system should believe that you have an ~8 inch screen (800/96) and the default X11 window is 7x7 inches so there _should_ be plenty of room, but some systems try to outsmart the user and use the actual physical dimensions, which could be smaller (higher DPI). You might want to check with xdpyinfo (from the shell). from xdpyinfo: screen #0: dimensions:1280x800 pixels (289x21 millimeters) resolution:112x968 dots per inch In any case, you can try reducing width, height, and (especially) pointsize in the call to x11() (which you'd issue _before_ the plot()). Or set them with X11.options(). i tried playing with plot(),halving (and again) the w,h, and pointsize, to no avail. and help.search(X11.options) reveals nothing. __ 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] configuring graphics device in Linux
My xorg.conf has Configured Monitor as opposed to Generic Monitor. Here is the relevant portion of my xorg.conf: Section Device IdentifierIntel Corporation Mobile 945GM/GMS, 943/940GML Express Integrated Graphics Controller (rev 03) Driverintel EndSection Section Monitor IdentifierConfigured Monitor EndSection Section Screen IdentifierDefault Screen MonitorConfigured Monitor Device00:02.0 VGA compatible controller: Intel Corporation Mo bile 945GM/GMS, 943/940GML Express Integrated Graphics Controller (rev 03) EndSection Section ServerLayout IdentifierDefault Layout ScreenDefault Screen InputDeviceSynaptics Touchpad EndSection If this doesn't work and you want to dig deeper: https://bugs.launchpad.net/ubuntu/+source/xserver-xorg-video-intel/+bug/221179 2008/11/15 john polo [EMAIL PROTECTED] megha patnaik wrote: Hi John, an R problem, but an X11 bug in Ubuntu. This is evident from plot(rnorm(10)) failing to perform. If you are seeing this, then it is because X11 does not automatically detect Intel graphic cards. The solution is to edit your xorg.conf file, changing it to something like (this is from my xorg.conf): Section Device IdentifierIntel Corporation Mobile 945GM/GMS, 943/940GML Express Integrated Graphics Controller (rev 03) Driverintel EndSection Megha, thanks for your help. i tried plot(rnorm(10)) and still was not able to see a plot. i checked /etc/X11/xorg.conf and it looks like this, without me editing it: Section Device Identifier Intel Corporation Mobile 945GM/GMS, 943/940GML Express Integrated Graphics Controller Driver intel BusID PCI:0:2:0 EndSection Section Monitor Identifier Generic Monitor Option DPMS EndSection Section Screen Identifier Default Screen Device Intel Corporation Mobile 945GM/GMS, 943/940GML Express Integrated Graphics Controller Monitor Generic Monitor DefaultDepth24 SubSection Display Modes 1280x800 EndSubSection EndSection The steps I carried out to detect where the problem was were as follows: 1. Checked whether basic plots in R worked 2. Created a new UID ( which did not have my saved settings in R) and tried basic plots. If 2. told me that margins were too large, then this was not a problem due to my past commands in R. i have tried your suggested plot and the one from the tutorial. neither worked. i'm using R 2.6.2 straight from the install through Unbuntu's package manager, so i don't think there are any scripts or whathaveyou on start. xorg.conf is a dangerous file to meddle with. The other symptoms I was seeing of poor graphics was an XL font size on my login screen and broken images in google earth. Are you seeing anything of the sort? yes, actually i do get the large fonts at start up like you do. i tried trolling around the Ubuntu forums for stuff about video settings, but only briefly. I am relatively new to the mailing list. Do tell me if this is better taken offline. i'm kind of new too. maybe someone else will tell me(us) to take this somewhere else. Peter Dalgaard wrote: Good advice in general, but in this case I think John is right in assuming that the issue is mainly with his graphics hardware setup, and he did tell us about that. The R version would have been nice though; we have fixed various issues in this area over time. thank you Peter. i appreciate you assistance. it's version 2.6.2 According to your setup, the system should believe that you have an ~8 inch screen (800/96) and the default X11 window is 7x7 inches so there _should_ be plenty of room, but some systems try to outsmart the user and use the actual physical dimensions, which could be smaller (higher DPI). You might want to check with xdpyinfo (from the shell). from xdpyinfo: screen #0: dimensions:1280x800 pixels (289x21 millimeters) resolution:112x968 dots per inch In any case, you can try reducing width, height, and (especially) pointsize in the call to x11() (which you'd issue _before_ the plot()). Or set them with X11.options(). i tried playing with plot(),halving (and again) the w,h, and pointsize, to no avail. and help.search(X11.options) reveals nothing. [[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] Which data structure in R can mimic hash in PERL best?
Dear all, Which data structure in R can mimic hash in PERL? I'd like to set up a lookup table, which could be accomplished by HASH if using PERL. Which of the data structures in R is the most efficient for lookup table? Thanks for your help. Best regards, Leon __ 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] PostScript File Dimensions
Hi List, here I go again.
Well I need to save plotted objects as .eps using the postscript() function,
well I can do that but all resulting object are perfect squared dimensions
(x = y). I need a rectangular output something like x = 2y dimension. Is it
possible? The Im new to R and postscript image format!
Im doing this
postscript('ClusterWardBC.eps',setEPS(),bg='white')
plot(WardBC,which.plots=2,main='Living Fauna')
dev.off()
and I got the square image
I tried this to solve
postscript('ClusterWardBC.eps',setEPS(width=600,height=300),bg='white')
plot(WardBC,which.plots=2,main='Living Fauna')
dev.off()
and I got and output but any software or printer can handle it. So its
useless.
Any ideas?!
Ps.: The plotted object is a cluster tree, but it also occurs with other
plots Ive done.
Thank you for the attention.
___
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Centro de Estudos do Mar/UFPR
Laboratório de Micropaleontologia
Avenida Beira Mar s/n - CEP 83255-000
Pontal do Paraná - PR - BRASIL
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[R] r2html output gives NULL
Win xp sp2, R v2.7.1, R2HTML v1.59 Hi. I have tried searching this extensively but to no avail. While using the R2HTML package, everytime I use HTMLStart() followed by HTML.title or HTML functions, I get a NULL in the output. For instance, HTMLStart(outdir='dir name',filename=file,extension=html,echo=FALSE) HTML.title(hello,HR=3); summary(regression_model); HTML(world); HTMLStop(); gives the following output: hello NULL summary values world NULL I tried but couldn't figure out why this happens. Any help please? -- View this message in context: http://www.nabble.com/r2html-output-gives-%22NULL%22-tp20515832p20515832.html 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.
[R] Lattice: groups and no groups with panel.superpose
Dear R listers,
I am trying to create a lattice plot with independent regression lines per group
for each panel, plus one overall regression line per panel. I succeed in having
the separate regression lines for each group per panel, but I can't figure out
how to add the overall regression line over all groups. I have learnt a lot from
the list, but I can't find an example for what I want to do...
with the following example data (from another post):
years-2000:2006
weeks-1:20
yr-rep(years,rep(length(weeks)*6,length(years)))
wk-rep(weeks,rep(6,length(weeks)))
temp-rep(4:9,length(years)*length(weeks))
yvar-round(rnorm(length(years)*length(weeks)*6,mean=30,sd=4),0)
xvar-(rnorm(length(years)*length(weeks)*6)+5)/10
df-data.frame(year=yr,week=wk,temp=temp, yvar=yvar,
xvar=xvar)
I get the regression lines per group for each panel using:
xyplot(yvar~year|week,data=df,layout = c(4, 5),
type='p',
groups = temp ,
panel = panel.superpose,
panel.groups = function(x, y, ..., lty) {
panel.xyplot(x, y, ..., lty = lty)
panel.abline(lm(y~x), lty=3, ...)
})
And obviously the overall regression lines with:
xyplot(yvar~year|week,data=df,layout = c(4, 5),
type='p',
panel = function(x, y, ...) {
panel.xyplot(x, y, ...)
panel.abline(lm(y~x))
})
Any advice on how to merge the output from the two above graphs would be
greatly appreciated!
Kind regards,
Robert Buitenwerf
Ecologist
SAEON
South Africa
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Re: [R] configuring graphics device in Linux
john polo wrote: According to your setup, the system should believe that you have an ~8 inch screen (800/96) and the default X11 window is 7x7 inches so there _should_ be plenty of room, but some systems try to outsmart the user and use the actual physical dimensions, which could be smaller (higher DPI). You might want to check with xdpyinfo (from the shell). from xdpyinfo: screen #0: dimensions:1280x800 pixels (289x21 millimeters) resolution:112x968 dots per inch Ick! Yes that will do that to you. You might want to try putting DisplaySize 339 212 in the Monitor section of xorg.conf -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Problems with rbind
Dear R Users, A recent update on base packages on my R installation has introduced a problem to my code which did not exist before the update. The offending function is rbind, which fails where it was working just fine before the update. I have two zoo objects, foo and bar, indexed by class Date. foo starts from 2007-10-09 and bar from 2007-10-10. I attempt to pad bar with a zero on Date 2007-10-09. foo-zoo(1,order.by=as.Date(2007-10-09)) bar-zoo(2,order.by=as.Date(2007-10-10)) bar - rbind(zoo(0, order.by = index(foo)[1]), bar) Error in rep.int(, nrow(r)) : incorrect type for second argument Weird. I am certain the problem is due to a recent update to this package as I have an R installation on two pcs, the same line of code works well on one and not on the other. Any help/pointers appreciated ? Is this perhaps a bug in rbind ? I am on R version 2.7.2, Windows XP SP2. Thanks in advance, Tolga Tolga Uzuner Cross-Markets Chief Investments Office JP Morgan 6th Floor, 100 Wood Street London EC2V 7RF United Kingdom Asst. Lee Hesketh Tel: +44-20-3303 Fax: +44-20-77422840 Generally, this communication is for informational purposes only and it is not intended as an offer or solicitation for the purchase or sale of any financial instrument or as an official confirmation of any transaction. In the event you are receiving the offering materials attached below related to your interest in hedge funds or private equity, this communication may be intended as an offer or solicitation for the purchase or sale of such fund(s). All market prices, data and other information are not warranted as to completeness or accuracy and are subject to change without notice. Any comments or statements made herein do not necessarily reflect those of JPMorgan Chase Co., its subsidiaries and affiliates. This transmission may contain information that is privileged, confidential, legally privileged, and/or exempt from disclosure under applicable law. If you are not the intended recipient, you are hereby notified that any disclosure, copying, distribution, or use of the information contained herein (including any reliance thereon) is STRICTLY PROHIBITED. Although this transmission and any attachments are believed to be free of any virus or other defect that might affect any computer system into which it is received and opened, it is the responsibility of the recipient to ensure that it is virus free and no responsibility is accepted by JPMorgan Chase Co., its subsidiaries and affiliates, as applicable, for any loss or damage arising in any way from its use. If you received this transmission in error, please immediately contact the sender and destroy the material in its entirety, whether in electronic or hard copy format. Thank you. Please refer to http://www.jpmorgan.com/pages/disclosures for disclosures relating to UK legal entities. [[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] creating matrices from vectors
If I have 4 vectors (a, b, c, and d) each of length 1000, how do I then create 1000 two by two matrices from these vectors, such that: myMatrix[i] = matrix(c(a[i],b[i],c[i],d[i]),2) Then I'd like to create a single vector containing the largest eigenvalues of each matrix? (Sorry I am quite new to R) Many thanks, James _ [[elided Hotmail spam]] __ 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] warning : increasing the PDF version to 1.3
What does the warning mean? In dev.off() : increasing the PDF version to 1.3 __ 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] How to calculate?
hi, How can i calculate means with catergory of variable... like x yz 2 3y 3 4n 1 2y 6 3n 9 1y 2 2n 8 3y i want to get mean of x and y with respective to its category(y,n) thanks... regards, Muhammad Faisal -- View this message in context: http://www.nabble.com/How-to-calculate--tp20516515p20516515.html 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] How to calculate?
see ?tapply, for example: tapply(df$x, df$z, mean) Might also look at ?ave and ?aggregate depending on what form you want the result to have... or the plyr package on CRAN. Lots of options! stat4u wrote: hi, How can i calculate means with catergory of variable... like x yz 2 3y 3 4n 1 2y 6 3n 9 1y 2 2n 8 3y i want to get mean of x and y with respective to its category(y,n) thanks... regards, Muhammad Faisal __ 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] how to join these two models?
Dear R users, I have this 2 models that fit to my data: M3varI - update (M3, weights=varIdent(form= ~ 1|SITE)) M3AR1-update(M3,correlation=corAR1()) The first one, updates my M3 so that I can account for the variance structure of random erros. The second one, updates my M3 so that I can account for the correlation structure of random errors. How can I put them toghether in one final model? I have tryed it using gls but I could not do it. Could you please help me o this? Bets regards, Sara Maltez Mouro Centro de Ecologia Funcional Departamento de Botânica Universidade de Coimbra [EMAIL PROTECTED] www.uc.pt/ecology/saramaltezmouro [[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 join these two models?
Sara Mouro wrote: I have this 2 models that fit to my data: M3varI - update (M3, weights=varIdent(form= ~ 1|SITE)) M3AR1-update(M3,correlation=corAR1()) How can I put them toghether in one final model? This looks like lme in package nlme, but it is pure guesswork, since your example is incomplete. Probably you should not use update, but something like lme(x~, random =., weights=varIdent..., correlation=corAR1()) but I am not sure if this somewhat overloaded fit will converge. Dieter -- View this message in context: http://www.nabble.com/how-to-join-these-two-models--tp20516771p20516980.html 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] Which data structure in R can mimic hash in PERL best?
You could use new.env(hash = TRUE, emptyenv()) and you can even specify an initial size. Seth Falcon has a package named dict that allows for different choices of hash function. D. Leon Yee wrote: Dear all, Which data structure in R can mimic hash in PERL? I'd like to set up a lookup table, which could be accomplished by HASH if using PERL. Which of the data structures in R is the most efficient for lookup table? Thanks for your help. Best regards, Leon __ 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] Which data structure in R can mimic hash in PERL best?
Dear all,
Which data structure in R can mimic hash in PERL? I'd like to set
up a lookup table, which could be accomplished by HASH if using PERL.
Which of the data structures in R is the most efficient for lookup
table?
Thanks for your help.
Best regards,
Leon
The regular answer to this is named arrays/vectors or environments
and has been given several times here on R-help. Unfortunately,
everybody is applying a different terminology such as 'maps', 'hashes',
'tables' or 'dictionaries', etc., so it's difficult to search for those
entries.
Below I enclose a solution that I have written some month ago. It is
given in pythonic language, but you can easily translate it into the
corresponding Perl terms. One drawback is that one cannot use numbers
as keys, only keys following the naming conventions for variable names
are allowed.
Hans Werner Borchers
ABB Corporate Research
#-- Define functions on Hash Tuples (Python alike) -
def.h - function() new.env(hash=TRUE)
len.h - function(dict) length(ls(envir=dict))
set.h - function(key, val, dict) assign(key, val, envir=dict)
get.h - function(key, dict, default=NULL) {
if (exists(key, envir=dict)) { get(key, dict)
} else { default }
}
has_key - function(key, dict) exists(key, envir=dict)
keys.h - function(dict) ls(envir=dict)
items.h - function(dict) as.list(dict)
values.h - function(dict, mode='character') {
l - as.list(dict)
n - length(l)
if (n==0) invisible(NULL)
v - vector('character', n)
for (i in 1:n) v[i] - l[[i]]
if (mode=='numeric') v - as.numeric(v)
return(v)
}
del.h - function(key, dict) {
if (exists(key, envir=dict)) {
val - get.h(key, dict)
rm(list=c(key), envir=dict)
} else {
val - NULL
}
invisible(val)
}
clear.h - function(dict) {
rm(list=keys.h(dict), envir=dict)
}
#---
--
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Re: [R] Which data structure in R can mimic hash in PERL best?
Hans W. Borchers wrote:
Dear all,
Which data structure in R can mimic hash in PERL? I'd like to set
up a lookup table, which could be accomplished by HASH if using PERL.
Which of the data structures in R is the most efficient for lookup
table?
Thanks for your help.
Best regards,
Leon
The regular answer to this is named arrays/vectors or environments
and has been given several times here on R-help. Unfortunately,
everybody is applying a different terminology such as 'maps', 'hashes',
'tables' or 'dictionaries', etc., so it's difficult to search for those
entries.
Below I enclose a solution that I have written some month ago. It is
given in pythonic language, but you can easily translate it into the
corresponding Perl terms. One drawback is that one cannot use numbers
as keys, only keys following the naming conventions for variable names
are allowed.
I imagine that you want to add inherits = FALSE
to calls to exists() and get() in your code or
else you risk quite unusual semantics of a hash table.
D.
Hans Werner Borchers
ABB Corporate Research
#-- Define functions on Hash Tuples (Python alike) -
def.h - function() new.env(hash=TRUE)
len.h - function(dict) length(ls(envir=dict))
set.h - function(key, val, dict) assign(key, val, envir=dict)
get.h - function(key, dict, default=NULL) {
if (exists(key, envir=dict)) { get(key, dict)
} else { default }
}
has_key - function(key, dict) exists(key, envir=dict)
keys.h - function(dict) ls(envir=dict)
items.h - function(dict) as.list(dict)
values.h - function(dict, mode='character') {
l - as.list(dict)
n - length(l)
if (n==0) invisible(NULL)
v - vector('character', n)
for (i in 1:n) v[i] - l[[i]]
if (mode=='numeric') v - as.numeric(v)
return(v)
}
del.h - function(key, dict) {
if (exists(key, envir=dict)) {
val - get.h(key, dict)
rm(list=c(key), envir=dict)
} else {
val - NULL
}
invisible(val)
}
clear.h - function(dict) {
rm(list=keys.h(dict), envir=dict)
}
#---
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Re: [R] Lattice: groups and no groups with panel.superpose
Hi,
I think the following code should do what you want,
xyplot(yvar~year|week,data=df,layout = c(4, 5),
type='p',
groups = temp ,
panel = function(x, y, ...) {
panel.superpose(x, y, ...)
panel.abline(lm(y~x))
},
panel.groups = function(x, y, ..., lty) {
panel.xyplot(x, y, ..., lty = lty)
panel.abline(lm(y~x), lty=3, ...)
})
Hope this helps,
baptiste
On 15 Nov 2008, at 14:25, Robert Buitenwerf wrote:
Dear R listers,
I am trying to create a lattice plot with independent regression
lines per group
for each panel, plus one overall regression line per panel. I
succeed in having
the separate regression lines for each group per panel, but I can't
figure out
how to add the overall regression line over all groups. I have
learnt a lot from
the list, but I can't find an example for what I want to do...
with the following example data (from another post):
years-2000:2006
weeks-1:20
yr-rep(years,rep(length(weeks)*6,length(years)))
wk-rep(weeks,rep(6,length(weeks)))
temp-rep(4:9,length(years)*length(weeks))
yvar-round(rnorm(length(years)*length(weeks)*6,mean=30,sd=4),0)
xvar-(rnorm(length(years)*length(weeks)*6)+5)/10
df-data.frame(year=yr,week=wk,temp=temp, yvar=yvar,
xvar=xvar)
I get the regression lines per group for each panel using:
xyplot(yvar~year|week,data=df,layout = c(4, 5),
type='p',
groups = temp ,
panel = panel.superpose,
panel.groups = function(x, y, ..., lty) {
panel.xyplot(x, y, ..., lty = lty)
panel.abline(lm(y~x), lty=3, ...)
})
And obviously the overall regression lines with:
xyplot(yvar~year|week,data=df,layout = c(4, 5),
type='p',
panel = function(x, y, ...) {
panel.xyplot(x, y, ...)
panel.abline(lm(y~x))
})
Any advice on how to merge the output from the two above graphs
would be
greatly appreciated!
Kind regards,
Robert Buitenwerf
Ecologist
SAEON
South Africa
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_
Baptiste Auguié
School of Physics
University of Exeter
Stocker Road,
Exeter, Devon,
EX4 4QL, UK
Phone: +44 1392 264187
http://newton.ex.ac.uk/research/emag
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[R] Statistics forums
Hi, Given that the R forum is mostly a site to discuss issues related to the language, are there any forums that discuss statistical issues? I am specifically interested in the statistical issues in experimental design. TIA, Anjan -- = anjan purkayastha, phd bioinformatics analyst whitehead institute for biomedical research nine cambridge center cambridge, ma 02142 purkayas [at] wi [dot] mit [dot] edu 703.740.6939 [[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] Problems with rbind
TU wrote: A recent update on base packages on my R installation has introduced a problem to my code which did not exist before the update. The offending function is rbind, which fails where it was working just fine before the update. I have two zoo objects, foo and bar, indexed by class Date. foo starts from 2007-10-09 and bar from 2007-10-10. I attempt to pad bar with a zero on Date 2007-10-09. Your example works for me: library(zoo) Attaching package: 'zoo' The following object(s) are masked from package:base : as.Date.numeric foo-zoo(1,order.by=as.Date(2007-10-09)) bar-zoo(2,order.by=as.Date(2007-10-10)) bar - rbind(zoo(0, order.by = index(foo)[1]), bar) bar 2007-10-09 2007-10-10 0 2 sessionInfo() R version 2.8.0 (2008-10-20) i386-pc-mingw32 locale: LC_COLLATE=German_Germany.1252;LC_CTYPE=German_Germany.1252;LC_MONETARY=German_Germany.1252;LC_NUMERIC=C;LC_TIME=German_Germany.1252 attached base packages: [1] stats graphics grDevices datasets utils methods base other attached packages: [1] zoo_1.5-4 loaded via a namespace (and not attached): [1] grid_2.8.0 lattice_0.17-15 tools_2.8.0 -- View this message in context: http://www.nabble.com/Problems-with-rbind-tp20516377p20517592.html 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.
[R] GAMs and GAMMS with correlated acoustic data
Greetings This is a long email. I'm struggling with a data set comprising 2,278 hydroacoustic estimates of fish biomass density made along line transects in two lakes (lakes Michigan and Huron, three years in each lake). The data represent lakewide surveys in each year and each data point represents the estimate for a horizontal interval 1 km in length. I'm interested in comparing biomass density and bathymetric distribution (bottom depth) in the two lakes and there is graphical evidence of a non-linear relationship between biomass density and bottom depth. Hence my interest in GAMs. Predictors of primary interest are lake (factor) and bottom depth (continuous). The fish data are autocorrelated at varying ranges, depending on species and year. I've tested this using correlog (package ncf) The bottom depth data are also highly autocorrelated. Because of the autocorrelations in data, autocorrelations in GAM residuals (up to 20 lags in some cases), patterns in residual plots from GAM models, and very narrow confidence intervals for the predictions, I feel that GAM results are biased and have attempted to use GAMM. Data and procedure examples: # fish[1:10, ] Transect yaoalebiom yaosmeltbiom yaobloaterbiom year depth lake x y interval 1 nn_1 12.019655 34.910370110 2.647370 2005 97.075252 526601.8 48502061 2 nn_1 12.164686 35.331548810 3.982028 2005 98.370242 526742.2 48493392 3 nn_1 11.176009 32.460052230 1.646604 2005 99.982182 526886.9 48483483 4 nn_1 0.00 0.036457091 5.306225 2005 81.446162 526993.4 48508494 5 nn_1 40.808118 10.988825410 3.222485 2005 101.457072 526997.5 48473595 6 nn_1 6.273421 18.176753520 18.832348 2005 98.691972 527084.1 48463666 7 nn_1 6.225799 16.050983390 66.941892 2005 94.142832 527214.7 48453727 8 nn_1 7.322910 19.001196850 47.273341 2005 91.217712 527331.6 48446368 9 nn_1 0.00 0.067646462 20.912908 2005 87.761232 527495.9 48433909 10 nn_1 0.00 0.006012106 26.611785 2005 87.597672 527606.6 4842426 10 #GAM example bloat.gam8 - gam(log10(yaobloaterbiom+0.00325) ~ lakef +s(depth, by=lakef), data=fish3) #GAMM example: bloat.gamm1 - gamm(log10(yaobloaterbiom+0.00325) ~ lakef + s(depth, by=lakef), correlation=corAR1(form = ~ interval|tranf), data=fish3) However, GAMM results from models including a wide variety of correlation structures (corExp, CorSpher, CorLin, AR1, ARMA) produce autocorrelated residuals (similar lag range as GAM), patterns in residuals plots, and confidence intervals for predictions that are only slightly large than for GAMs. This suggests to me that GAMM is not performing much better than GAM (or I've not specified models correctly). Is my assessment of the GAMM performance reasonable? None of the models (GAM or GAMM) explain much of the deviance (~20%). I'm interested in an information-theoretic approach to selecting the best model from a set of possible models (AICc, dAICc, AICc weights), but cannot run some of the GAM models with GAM because they lack a random term. I'm not sure how to use the GAMM output to compare the models I can run with this procedure. Finally, as a last resort, I've subsampled the original data set so that I have 1 record per transect per lake per year for a total N=99. I get different best models from GAM (original data) GAMM (original data but including correlation structure), and GAM (subsetted data). Selection of different models leads to fairly different conclusions about the similarities and differences between the lakes. I'm not sure where to go with this as a result. Any thoughts/comments would be appreciated. Dave David Warner Research Fishery Biologist USGS Great Lakes Science Center 1451 Green Road Ann Arbor MI 48105 734.214.9392 [[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] Superimposing y-variables in Lattice formulas
On Fri, Nov 14, 2008 at 6:55 PM, Deepayan Sarkar [EMAIL PROTECTED] wrote: ...But how do I specify that I want to display all the Subjects on a... single graph, superimposing them all? Have you tried xyplot ( conc ~ time , Indometh, groups = Subject ) ? Thanks very much for your help! That works beautifully. Any particular reason this can't be specified in the formula? For a small number of levels, you can write xyplot( ifelse(Subject==1,conc,NA) + ifelse(Subject==2,conc,NA) ~ time, ...) but obviously that doesn't generalize. I'd have thought that something like conc*Subject or (conc | Subject) should mean the same thing, but these aren't allowed for some reason. But I don't know what the semantics of the formula operators are. Neither the 'formula' nor the 'logic' man page even defines `|`, and the 'xyplot' man page only gives examples, not a definition of the general case: the formula is generally of the form... can also be supplied as ... a special case is Thanks, -s __ 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] PostScript File Dimensions
You may be new to R but that does not mean you should stay new to
the help pages. It looks as though postscript() is ignoring your
setEPS efforts,,, with perfectly legitimate reason since that is not a
defined parameter for that function. It is a separate function. What
happens when you use the height= and width= parameters that the
postscript help page defines for you? That worked for me (on a Mac
OS X 10.5.5/ R2.8.0-64bit GUI device). Or you could try executing
setEPS before your postscript call.
Further questions, as is always the case with output sorts of
questions, should include your systemInfo. This is an example in the
help page with an added plot. to make the otherwise blank 4 x 3 eps
file look more interesting:
postscript(cm_test.eps, width = 4.0, height = 3.0,
+horizontal = FALSE, onefile = FALSE, paper = special,
+family = ComputerModern, encoding = TeXtext.enc)
plot(1:10,10:1)
dev.off()
--
David Winsemius
Heritage Labs
On Nov 15, 2008, at 9:00 AM, Rodrigo Aluizio wrote:
Hi List, here I go again.
Well I need to save plotted objects as .eps using the postscript()
function,
well I can do that but all resulting object are perfect squared
dimensions
(x = y). I need a rectangular output something like x = 2y
dimension. Is it
possible? The I’m new to R and postscript image format!
I’m doing this…
postscript('ClusterWardBC.eps',setEPS(),bg='white')
plot(WardBC,which.plots=2,main='Living Fauna')
dev.off()
and I got the square image
I tried this to solve
postscript
('ClusterWardBC.eps',setEPS(width=600,height=300),bg='white')
plot(WardBC,which.plots=2,main='Living Fauna')
dev.off()
and I got and output but any software or printer can handle it. So
it’s
useless.
Any ideas?!
Ps.: The plotted object is a cluster tree, but it also occurs with
other
plots I’ve done.
Thank you for the attention.
___
MSc. mailto:[EMAIL PROTECTED] Rodrigo Aluizio
Centro de Estudos do Mar/UFPR
Laboratório de Micropaleontologia
Avenida Beira Mar s/n - CEP 83255-000
Pontal do Paraná - PR - BRASIL
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Re: [R] make a triple summation more efficient
On Sat, 15 Nov 2008, kathie wrote:
Dear R users...
I made the R-code for this triple summation computation
http://www.nabble.com/file/p20517134/a.jpg
-
Here is my code..
x=seq(.1,1,.1); l=10
y=seq(1,10); m=10
z=seq(.1,1,.1); n=10
sum(sapply(1:l, function(i) {sum(sapply(1:m, function(j) {sum(sapply(1:n,
function(k){exp(x[i]*y[j]*z[k] )/gamma(y[j]+1)}))^(1.5) }))}))
-
In fact, this is a part of optimization and in my real data the number of x
is about 5000. So, I guess if it is vectorized, then the running time could
be shortened.
How could I vectorize this? or any suggestion will be greatly appreciated.
gamma and exp ARE vectorized. Do all the computations in the inner most
loop in a single call, then sum those, then raise to 1.5, then sum the
result
something like
foo - function(x,y,z) {exp( x * y * z )/gamma( y+1 )}
dat - expand.grid( x=x, y=y, z=z )
res - do.call( foo, dat )
sum( rowSums( matrix( res, nc= n) )^1.5 )
[1] 1090.613
HTH,
Chuck
Kathryn Lord
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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
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Re: [R] Problems with rbind
It also works for me using zoo 1.5-4 and R 2.7.2. Try it running at the beginning of a vanilla session. If still a problem reinstall zoo: install.packages(zoo, dep = TRUE) If still a problem reinstall R and then reinstall zoo, preferable going to R 2.8.0. On Sat, Nov 15, 2008 at 12:19 PM, Dieter Menne [EMAIL PROTECTED] wrote: TU wrote: A recent update on base packages on my R installation has introduced a problem to my code which did not exist before the update. The offending function is rbind, which fails where it was working just fine before the update. I have two zoo objects, foo and bar, indexed by class Date. foo starts from 2007-10-09 and bar from 2007-10-10. I attempt to pad bar with a zero on Date 2007-10-09. Your example works for me: library(zoo) Attaching package: 'zoo' The following object(s) are masked from package:base : as.Date.numeric foo-zoo(1,order.by=as.Date(2007-10-09)) bar-zoo(2,order.by=as.Date(2007-10-10)) bar - rbind(zoo(0, order.by = index(foo)[1]), bar) bar 2007-10-09 2007-10-10 0 2 sessionInfo() R version 2.8.0 (2008-10-20) i386-pc-mingw32 locale: LC_COLLATE=German_Germany.1252;LC_CTYPE=German_Germany.1252;LC_MONETARY=German_Germany.1252;LC_NUMERIC=C;LC_TIME=German_Germany.1252 attached base packages: [1] stats graphics grDevices datasets utils methods base other attached packages: [1] zoo_1.5-4 loaded via a namespace (and not attached): [1] grid_2.8.0 lattice_0.17-15 tools_2.8.0 -- View this message in context: http://www.nabble.com/Problems-with-rbind-tp20516377p20517592.html 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. __ 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] configuring graphics device in Linux
Peter Dalgaard wrote: from xdpyinfo: screen #0: dimensions:1280x800 pixels (289x21 millimeters) resolution:112x968 dots per inch Ick! Yes that will do that to you. You might want to try putting DisplaySize 339 212 in the Monitor section of xorg.conf it game me some kind of warning about low resolution on restart, but it looks like it worked. thank you very much john __ 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] configuring graphics device in Linux
Great! You can navigate to choosing the resolution from the warning window. 2008/11/16 john polo [EMAIL PROTECTED] Peter Dalgaard wrote: from xdpyinfo: screen #0: dimensions:1280x800 pixels (289x21 millimeters) resolution:112x968 dots per inch Ick! Yes that will do that to you. You might want to try putting DisplaySize 339 212 in the Monitor section of xorg.conf it game me some kind of warning about low resolution on restart, but it looks like it worked. thank you very much john [[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] Which data structure in R can mimic hash in PERL best?
Duncan Temple Lang wrote:
Hans W. Borchers wrote:
Below I enclose a solution that I have written some month ago. It is
given in pythonic language, but you can easily translate it into the
corresponding Perl terms. One drawback is that one cannot use numbers
as keys, only keys following the naming conventions for variable names
are allowed.
I imagine that you want to add inherits = FALSE
to calls to exists() and get() in your code or
else you risk quite unusual semantics of a hash table.
as far as i can see, an alternative is to use empty parent environments:
def.h - function() new.env(hash=TRUE, parent=emptyenv())
vQ
D.
Hans Werner Borchers
ABB Corporate Research
#-- Define functions on Hash Tuples (Python alike) -
def.h - function() new.env(hash=TRUE)
len.h - function(dict) length(ls(envir=dict))
set.h - function(key, val, dict) assign(key, val, envir=dict)
get.h - function(key, dict, default=NULL) {
if (exists(key, envir=dict)) { get(key, dict)
} else { default } }
has_key - function(key, dict) exists(key, envir=dict)
keys.h - function(dict) ls(envir=dict)
items.h - function(dict) as.list(dict)
values.h - function(dict, mode='character') {
l - as.list(dict)
n - length(l)
if (n==0) invisible(NULL)
v - vector('character', n)
for (i in 1:n) v[i] - l[[i]]
if (mode=='numeric') v - as.numeric(v)
return(v)
}
del.h - function(key, dict) {
if (exists(key, envir=dict)) {
val - get.h(key, dict)
rm(list=c(key), envir=dict)
} else {
val - NULL
}
invisible(val)
}
clear.h - function(dict) {
rm(list=keys.h(dict), envir=dict)
}
#---
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--
---
Wacek Kusnierczyk, MD PhD
Email: [EMAIL PROTECTED]
Phone: +47 73591875, +47 72574609
Department of Computer and Information Science (IDI)
Faculty of Information Technology, Mathematics and Electrical Engineering (IME)
Norwegian University of Science and Technology (NTNU)
Sem Saelands vei 7, 7491 Trondheim, Norway
Room itv303
Bioinformatics Gene Regulation Group
Department of Cancer Research and Molecular Medicine (IKM)
Faculty of Medicine (DMF)
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Re: [R] warning : increasing the PDF version to 1.3
On Sun, 16 Nov 2008, June Kim wrote: What does the warning mean? In dev.off() : increasing the PDF version to 1.3 It means you have an obsolete version of R, and failed to follow the posting guide in telling us what it is. ?pdf should explain the message to you in your version of R. E.g. 2.6.0 has version: a string describing the PDF version that will be required to view the output. This is a minimum, and will be increased (with a warning) if necessary. The 'version' argument declares the version of PDF that gets produced. The version must be at least 1.4 for semi-transparent output to be understood, and at least 1.3 if CID fonts are to be used: if these features are used the version number will be increased (with a warning). Specifying a low version number (as the default) is useful if you want to produce PDF output that can be viewed on older or non-Adobe PDF viewers. (PDF 1.4 requires Acrobat 5 or later.) The default value is 1.4 these days. -- 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] Superimposing y-variables in Lattice formulas
On 11/15/08, Stavros Macrakis [EMAIL PROTECTED] wrote: On Fri, Nov 14, 2008 at 6:55 PM, Deepayan Sarkar [EMAIL PROTECTED] wrote: ...But how do I specify that I want to display all the Subjects on a... single graph, superimposing them all? Have you tried xyplot ( conc ~ time , Indometh, groups = Subject ) ? Thanks very much for your help! That works beautifully. Any particular reason this can't be specified in the formula? For a Mostly historical, but the 'groups' approach makes the design cleaner and more generalizable, although that fact is difficult to appreciate without some experience. small number of levels, you can write xyplot( ifelse(Subject==1,conc,NA) + ifelse(Subject==2,conc,NA) ~ time, ...) but obviously that doesn't generalize. I'd have thought that something like conc*Subject or (conc | Subject) should mean the same thing, but these aren't allowed for some reason. But I don't know what the semantics of the formula operators are. Neither the 'formula' nor the 'logic' man page even defines `|`, and the 'xyplot' man page only gives examples, not a definition of the general case: the formula is generally of the form... can also be supplied as ... a special case is There is no general interpretation for a formula, it is always function-specific. I consider the part of the help page you quoted (without the omissions) a completely general description of the formula as applicable to xyplot(): The formula is generally of the form 'y ~ x | g1 * g2 * ...' (along with a later paragraph documenting the special interpretation of '+' ). Note that a help page is intended to describe the capabilities of the function/object it is documenting, not the capabilities that are missing, even though those who have preconceived ideas of how certain things should behave often think that it is somehow the responsibility of the help page to anticipate all such misunderstandings. If you want a holistic introduction to a suite of tools like lattice, function documentation (which is by definition function-centric) is not the best place to look. -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.
[R] R: How to enable R on-line search in HTML help
-Messaggio originale- Da: Prof Brian Ripley [mailto:[EMAIL PROTECTED] Inviato: ven 14/11/2008 18.27 A: [EMAIL PROTECTED] Cc: r-help@r-project.org Oggetto: Re: [R] How to enable R on-line search in HTML help First, there is a R-sig-mac list for Mac OS questions. I will try the channel you suggest if I cannot get this problem fixed soon. On Fri, 14 Nov 2008, [EMAIL PROTECTED] wrote: I use FireFox as my favourite web browser on my Mac OS/X 10.5 Which version of Firefox? There is a known issue with all released versions = 3, discussed in the R-admin manual (and R has had a workarounf in place for a while now). In fact I am running version 3.0.4 I saw the suggestion: This is a bug in the way Firefox is interpreting relative URLs, and can be circumvented by opening the HTML search page (.../doc/html/SearchEngine.html) directly rather than from .../doc/html/index.html as shown by help.start(). But I have no control on where OS generates the link to R help-search started from the top bar menu. I double-checked that Java and Java scripts are enabled for FireFox. Nevertheless, I cannot use R on-line search help. How are you trying to use it? And what exactly happens? I click on the Help item in the top menu bar which appears as R GUI is loaded. As a result a new window pops up which contains three sections named Manuals, Reference, Miscellaneous Material. I click on the link Search Engine Keyword in the Reference section. Another page pops up with a number of links to R main topics. None of such links works for me no matter how many time I click on any of them. The only lik that works is R Installation and Administration even if I double-checked that mybrowser (FireFox) has all Java boxes checked (flags enabled). In fact I do not see any Applet SearchEngine started anywhere on the browser window. The help.search utility works fine when started on R command line. There is no difference if I replace FireFox with Safari as the main web browser. You might be using help.start (in which case check its help page for the workaround). Or are you referring to help in the R.app GUI (in which case this is the wrong list)? Actually this problam arises when I click on the Help item of the top menu bar which is loaded with R GUI I called Apple Tech Assistance but they do not support FireFox. We tried to set Saphari as the favourite browser but evidently R does not support it. In what sense? I've used search in help.start() with Safari in the past: I even tested it on Windows. With reference to the Hep item in the top menu bar, the behaviour is the same regardless of choosing either FireFox or Safari Does any one knw of a workaround this annoying problem ? We need to understand the problem first: see the footer to this and every R-help message. There may be a mailing list where these GUI-related issues are discussed. I would be happy to redirect my question to the pertinent channel. Best regrds, Maura E. Thanks a lot, Maura Alice Messenger ;-) chatti anche con gli amici di Windows Live Messenger e tutti i telefonini TIM! Vai su http://maileservizi.alice.it/alice_messenger/index.html?pmk=footer [[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 Alice Messenger ;-) chatti anche con gli amici di Windows Live Messenger e tutti i telefonini TIM! Vai su http://maileservizi.alice.it/alice_messenger/index.html?pmk=footer [[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] 3D trajectory plot?
Are you talking about a 'streamline' like might be made with 'vtk'? or in a number of fluid dynamics, groundwater packages, particle physics codes, etc.? There was an exploratory hook up of R and vtk by M. Kondrin a year or two back (linux only). Search the archives. Parsing a vtk dataset in R should relatively straight-forward. HTH Michael Grant --- On Tue, 11/11/08, Chris Jarman [EMAIL PROTECTED] wrote: From: Chris Jarman [EMAIL PROTECTED] Subject: [R] 3D trajectory plot? To: r-help@r-project.org Date: Tuesday, November 11, 2008, 9:55 PM Hello, I'm attempting to create a smooth, 3D plot of a trajectory (rather than the cloud or wireframe functions). I would rather the individual data points not be visible. I've had no luck finding this on the graphics or help pages. Thank you in advance. Chris Some example data, just in case: 2532 40 1225 32 2 12 25 2 2 12 202 2 1 20 2 6 1 20 5 6 1 5 5 6 __ 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] configuring graphics device in Linux
Megha Patnaik wrote: Great! You can navigate to choosing the resolution from the warning window. will do. thanks for your help. __ 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] HOW to provide a CITATION file?
Greetings, R-ians: I am sure I am missing something obvious. How do I provide a CITATION file for my home-brew package, so that it will be packaged using R CMD build --binary myPackage? I have placed a CITATION file in the myPackage directory along with the DESCRIPTION file, but it is ignored. Thanks for your guidance. Charles Annis, P.E. [EMAIL PROTECTED] phone: 561-352-9699 eFax: 614-455-3265 http://www.StatisticalEngineering.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.
[R] rgamma with rate as vector
Hi - I have a question about the following code from Bayesian
Computation with R (Jim Albert).
par(mfrow=c(2,2))
m = 500
alphas = c(5, 20, 80, 400)
for (j in 1:4) {
mu = rgamma(m, shape=10, rate=10)
lambda1 = rgamma(m, shape=alphas[j], rate=alphas[j]/mu)
lambda2 = rgamma(m, shape=alphas[j], rate=alphas[j]/mu)
plot(lambda1, lambda2)
title(main=paste('alpha=', alphas[j]))
}
How does the function rgamma work in the instance with the rate
specified as a vector of values? My understanding is that rgamma
returns m random values from the gamma distribution for a given shape,
rate. But I don't understand what the resulting lambda1's mean with
many rate values.
Thanks!
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[R] RES: PostScript File Dimensions
Thanks David, you are absolutely right, the solution was more simple than I
was wondering, sorry for the mistake.
I always read the help files and search the older topic of the list before
posting, but this time I wasn't able found out a solution for such a simple
thing. I got very closer to your suggestion with other tries I've not
included in my first mail. But I got an error saying The image is to large
and gave up. It was only a question of changing the width and height
values...
Once again thank you, I'll try harder a next time.
Rodrigo.
-Mensagem original-
De: David Winsemius [mailto:[EMAIL PROTECTED]
Enviada em: sábado, 15 de novembro de 2008 15:57
Para: Rodrigo Aluizio
Cc: R Help
Assunto: Re: [R] PostScript File Dimensions
You may be new to R but that does not mean you should stay new to
the help pages. It looks as though postscript() is ignoring your
setEPS efforts,,, with perfectly legitimate reason since that is not a
defined parameter for that function. It is a separate function. What
happens when you use the height= and width= parameters that the
postscript help page defines for you? That worked for me (on a Mac
OS X 10.5.5/ R2.8.0-64bit GUI device). Or you could try executing
setEPS before your postscript call.
Further questions, as is always the case with output sorts of
questions, should include your systemInfo. This is an example in the
help page with an added plot. to make the otherwise blank 4 x 3 eps
file look more interesting:
postscript(cm_test.eps, width = 4.0, height = 3.0,
+horizontal = FALSE, onefile = FALSE, paper = special,
+family = ComputerModern, encoding = TeXtext.enc)
plot(1:10,10:1)
dev.off()
--
David Winsemius
Heritage Labs
On Nov 15, 2008, at 9:00 AM, Rodrigo Aluizio wrote:
Hi List, here I go again.
Well I need to save plotted objects as .eps using the postscript()
function,
well I can do that but all resulting object are perfect squared
dimensions
(x = y). I need a rectangular output something like x = 2y
dimension. Is it
possible? The Im new to R and postscript image format!
Im doing this
postscript('ClusterWardBC.eps',setEPS(),bg='white')
plot(WardBC,which.plots=2,main='Living Fauna')
dev.off()
and I got the square image
I tried this to solve
postscript
('ClusterWardBC.eps',setEPS(width=600,height=300),bg='white')
plot(WardBC,which.plots=2,main='Living Fauna')
dev.off()
and I got and output but any software or printer can handle it. So
its
useless.
Any ideas?!
Ps.: The plotted object is a cluster tree, but it also occurs with
other
plots Ive done.
Thank you for the attention.
___
MSc. mailto:[EMAIL PROTECTED] Rodrigo Aluizio
Centro de Estudos do Mar/UFPR
Laboratório de Micropaleontologia
Avenida Beira Mar s/n - CEP 83255-000
Pontal do Paraná - PR - BRASIL
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Re: [R] Statistics forums
On Sat, Nov 15, 2008 at 12:19 PM, ANJAN PURKAYASTHA [EMAIL PROTECTED] wrote: Hi, Given that the R forum is mostly a site to discuss issues related to the language, are there any forums that discuss statistical issues? I am specifically interested in the statistical issues in experimental design. TIA, Anjan -- = anjan purkayastha, phd bioinformatics analyst whitehead institute for biomedical research nine cambridge center cambridge, ma 02142 purkayas [at] wi [dot] mit [dot] edu 703.740.6939 [[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. [[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 provide a CITATION file?
See 'Writing R Extensions' via help.start() and then search for CITATION. My $.02 /Henrik On Sat, Nov 15, 2008 at 2:35 PM, Charles Annis, P.E. [EMAIL PROTECTED] wrote: Greetings, R-ians: I am sure I am missing something obvious. How do I provide a CITATION file for my home-brew package, so that it will be packaged using R CMD build --binary myPackage? I have placed a CITATION file in the myPackage directory along with the DESCRIPTION file, but it is ignored. Thanks for your guidance. Charles Annis, P.E. [EMAIL PROTECTED] phone: 561-352-9699 eFax: 614-455-3265 http://www.StatisticalEngineering.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. __ 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] Statistics forums
I am also curious if someone can direct us to a good statistical group mailing list. I have been using R since few days and I find this groups amazing (with so many discussions pouring in!! I just love it.) But, I also seem to hit a roadblock for deciding which test to use, sometimes. It will helpful, if someone would provide some advice about other mailing lists. Sagar Doctoral Candidate in Bioengineering, University of Pittsburgh On Sat, Nov 15, 2008 at 8:26 PM, s j [EMAIL PROTECTED] wrote: On Sat, Nov 15, 2008 at 12:19 PM, ANJAN PURKAYASTHA [EMAIL PROTECTED] wrote: Hi, Given that the R forum is mostly a site to discuss issues related to the language, are there any forums that discuss statistical issues? I am specifically interested in the statistical issues in experimental design. TIA, Anjan -- = anjan purkayastha, phd bioinformatics analyst whitehead institute for biomedical research nine cambridge center cambridge, ma 02142 purkayas [at] wi [dot] mit [dot] edu 703.740.6939 [[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. [[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] I want my row name to be a variable
Hi R users Imagine this data.frame: X Var1Var2 A 22 13 B5 2 C12 8 D199 A,B,C,D are the rows names (or index) Is there a way to create a new variable in this data frame which name is Var3 and which contains the rows names: Var1Var2Var3 A 22 13A B5 2 B C12 8 C D199D I tried as.data.frame(array(x, dim(x), dimnames(x))) but it doesn'work Sincerely yours -- View this message in context: http://www.nabble.com/I-want-my-row-name-to-be-a-variable-tp20520180p20520180.html 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] readPDF() -- unsure how to install xpdf to make this work?
Hello, I was just wondering if you had found a solution? I am having the same difficulty of converting pdf's into plain text documents in R. I originally thought I could use the readLines() function, but as you can see below that did not work. R my.destfile - C:\\Documents and Settings\\clair\\Desktop\\test\\r- intro.pdf R my.url - http://cran.r-project.org/doc/manuals/R-intro.pdf; R download.file(url = my.url, destfile=my.destfile, mode='wb') R txt - readLines(my.destfile) R txt [1] %PDF-1.4 [2] %ÐÔÅØ [3] 1 0 obj [4] /Length 587 [5] /Filter / FlateDecode [6] [7] stream [8] [EMAIL PROTECTED]ÎÁ±?\024tBL\020$ñ°ãd4›½*´.‰\002\001øï·_•èÌf \017’W¯_wÕ«îrðãc;Šòê`GæUŠOÛV׳£øç¾ö\006ƒ¤Ê®\027[vïÖæ6ïWÛ7ñÑTÙÖvb \030¯“uYt/N¼.³ó5·½êÿ¢¥=\025åS‚b¸³¿G›� Warm Regards, Clair On 13 Nov, 15:10, Tony Breyal [EMAIL PROTECTED] wrote: Dear R-Help, I need to convert a set of '.pdf' files into an equivalent set of '.txt' files. This is so that i can do some text mining on the content. In the latest R-News letter (http://cran.r-project.org/doc/Rnews/ Rnews_2008-2.pdf), the package 'tm' for text mining is mentioned. In that lovely package, there is a function called 'readPDF()'. In order to use this, ?readPDF says Note that this PDF reader needs both the tools pdftotext and pdfinfo installed and accessable on your system. These tools are available fromhttp://www.foolabs.com/xpdf/download.html I am able to download this and use it easily from a dos window to convert a pdf file into a txt file. Question: how do i make these tools available to R, so that i can use the readPDF() function? Thank you in advance for any help, and I hope the above made sense. Tony Breyal ###OS = Windows Vista Ultimate sessionInfo() R version 2.8.0 (2008-10-20) i386-pc-mingw32 locale: LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United Kingdom. 1252;LC_MONETARY=English_United Kingdom. 1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252 attached base packages: [1] grid stats graphics grDevices utils datasets methods base other attached packages: [1] tm_0.3-1 XML_1.98-1 Snowball_0.0-3 RWeka_0.3-14 rJava_0.6-0 Matrix_0.999375-16 lattice_0.17-15 filehash_2.0 loaded via a namespace (and not attached): [1] proxy_0.4-1 __ [EMAIL PROTECTED] mailing listhttps://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guidehttp://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] I need to compare ranking (1-15) across 10 replicates to see if the ranking changes significantly- how???
Hi there all suggestions much appreciated! so our investigation is looking into the time pairs of guppies spend interacting... we have raw data in minutes, but have ranked each possible association between pairs (out of 15 possible) in order of frequency of occurence during a 20 min recording period. then rinse and repeat 10 times... :-D so this is what we have: (rows are replicates, columns different interactions) L/L L/S L/B L/D L/LTS/S S/B S/D S/LT B/B B/D B/LTD/D D/LTLT/LT 1 12 10 3 1 8 11 6 5 15 14 7 4 8 2 12 2 4 2 1 3 5 15 13 6 12 11 14 6 8 10 9 3 12 14 8 6 2 15 12 4 5 7 10 1 11 8 3 4 7 11 1 10 4 6 5 8 12 14 13 2 9 14 3 5 4 10 2 10 12 8 7 3 6 12 14 1 14 9 5 6 2 8 9 5 13 11 12 7 6 1 15 4 13 3 10 7 3 4 6 13 11 8 2 14 12 1 14 9 10 5 7 8 2 9 3 5 1 5 4 10 15 11 13 12 7 7 14 9 5 6 1 9 11 13 4 10 3 8 13 2 15 7 12 10 3 11 9 15 7 10 6 4 8 1 13 2 12 4 14 Score 54 85 43 77 74 102 71 71 94 80 126 43 107 69 89 Ranking 3 10 1 8 7 13 5 5 12 9 15 1 14 4 11 is it possible to run an ANOVA on this, to assess the stability of interactions? With the idea that if the ranking changes a significant amount between replicates, associations are not being maintained...?? all help and advice gratefully received! Thanks -- View this message in context: http://www.nabble.com/I-need-to-compare-ranking-%281-15%29-across-10-replicates-to-see-if-the-ranking-changes-significantly--howtp20515523p20515523.html 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.
[R] Using n+1 instances of R to utilise n processors on one machine - something like R with tabbed browsing?
Dear R-help, Please forgive me if any of the following sounds naieve/confused, i've just got back from a mini-pub-crawl, slightly tipsy, and am feeling brave to ask a possibly silly question... also, not to shiny on the technical side of things. Problem - I need to text mine a collection of 10,000 plain text documents, all of which are sitting in a single folder. i don't have any money to buy a database package, and even if i did i have no idea how that would speed things up if i want to do all the processing in R Assumption - It is my understanding that R can only use one processor on a machine when handeling calculations. If you wanted to use 4 processors, than you would have to open up 4 seperate instances of R and share the work between them eg. give each instance of R 25% of the documents you want processed Question - It is possible to have one instance of R to divide the workload, and then that instance opens up 4 other instances of R to do the processing? Or, is sometihng akin to tabbed browsing, where you have one main window and several tabs, each corresponding to a different instance of R? appologies if none of hte above made sense :o) Clair xx O/S: Windows Vista R 2.8.0 __ 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] unable to view vignette in R
Hello All R-Gurus: ISSUE: Cannot view R vignettes due in Ubuntu Linux (a debian variant). note: this issue has been posted to this list before with no responses given see https://stat.ethz.ch/pipermail/r-help/2007-September/141178.html DETAILS: I am trying to view an R vignette. Here is the situation: I issue the openvignette(), then select the vignette I wish to view...and the system returns: Could not get a file descriptor referring to the console. This action should spawn a ps viewer displaying the contents of the vignette for my enjoyment. I suspect it may have something to do with the call to the postscript viewer application. Is there a simple way to change this behavior within R? Any Thoughts? Here is the copy paste of my session Code: openVignette() Please select a vignette: 1: annotate - Annotation Overview 2: annotate - Basic GO Usage 3: annotate - HowTo: Get HTML Output 4: annotate - HowTo: use chromosomal information 5: annotate - HOWTO: Use the online query tools 6: annotate - Using Affymetrix Probe Level Data 7: annotate - Using Data Packages 8: annotate - Using the homology package 9: AnnotationDbi - AnnotationDbi 10: AnnotationDbi - SQLForge 11: Biobase - An introduction to Biobase and ExpressionSets 12: Biobase - Bioconductor Overview 13: Biobase - esApply Introduction 14: Biobase - Notes for eSet developers 15: Biobase - Notes for writing introductory 'how to' documents 16: Biobase - quick views of eSet instances 17: geneplotter - How to assemble a chromLocation object 18: geneplotter - Visualization of Microarray Data 19: xtable - xtable Gallery Selection: 17) Opening /home/lbthrice/R/i486-pc-linux-gnu-library/2.8/geneplotter/doc/byChroms.pdf Couldnt get a file descriptor referring to the console Could not get a file descriptor referring to the console __ 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] Classes
Code: # svm is an S3 class, so: setOldClass(svm) # Create the super class model: setClass(model) # For svm from e1071 this works (well gives no error): setIs(svm, model) # For rvm from kernlab this gives and error: setIs(rvm, model) # the superclass list for class rvm includes an undefined class vm Is there any way round this? I am trying to write a super class so that I can use the same interface for both of these classes. 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] I want my row name to be a variable
X$Var3 - row.names(X) CE.KA wrote: Hi R users Imagine this data.frame: X Var1Var2 A 22 13 B5 2 C12 8 D199 A,B,C,D are the rows names (or index) Is there a way to create a new variable in this data frame which name is Var3 and which contains the rows names: Var1Var2Var3 A 22 13A B5 2 B C12 8 C D199D I tried as.data.frame(array(x, dim(x), dimnames(x))) but it doesn'work Sincerely yours __ 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] unable to view vignette in R
I never could figure this out, I had the exact same issue though. My solution was to simply set options(pdfviewer = evince) in my .Rprofile. Presumably, you could set it to whatever PDF viewer is your favorite. I never looked further into why the default was doing what it was doing. Lionel Brooks wrote: Hello All R-Gurus: ISSUE: Cannot view R vignettes due in Ubuntu Linux (a debian variant). note: this issue has been posted to this list before with no responses given see https://stat.ethz.ch/pipermail/r-help/2007-September/141178.html DETAILS: I am trying to view an R vignette. Here is the situation: I issue the openvignette(), then select the vignette I wish to view...and the system returns: Could not get a file descriptor referring to the console. This action should spawn a ps viewer displaying the contents of the vignette for my enjoyment. I suspect it may have something to do with the call to the postscript viewer application. Is there a simple way to change this behavior within R? Any Thoughts? Here is the copy paste of my session Code: openVignette() Please select a vignette: 1: annotate - Annotation Overview 2: annotate - Basic GO Usage 3: annotate - HowTo: Get HTML Output 4: annotate - HowTo: use chromosomal information 5: annotate - HOWTO: Use the online query tools 6: annotate - Using Affymetrix Probe Level Data 7: annotate - Using Data Packages 8: annotate - Using the homology package 9: AnnotationDbi - AnnotationDbi 10: AnnotationDbi - SQLForge 11: Biobase - An introduction to Biobase and ExpressionSets 12: Biobase - Bioconductor Overview 13: Biobase - esApply Introduction 14: Biobase - Notes for eSet developers 15: Biobase - Notes for writing introductory 'how to' documents 16: Biobase - quick views of eSet instances 17: geneplotter - How to assemble a chromLocation object 18: geneplotter - Visualization of Microarray Data 19: xtable - xtable Gallery Selection: 17) Opening /home/lbthrice/R/i486-pc-linux-gnu-library/2.8/geneplotter/doc/byChroms.pdf Couldnt get a file descriptor referring to the console Could not get a file descriptor referring to the console __ 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] HOW to provide a CITATION file?
Are you referring to the update that you now reach 'R: Search Engine'(*) when you call help.start() whereas before you got to the 'Statistical Data Analysis' main menu from where 'Writing R Extensions' is available (in HTML format)? You can reach the latter from the former by clicking on the up-arrow icon. [Suggestion to R-core: Maybe clicking on the R-logo could also bring you to the main menu.]. /Henrik (*) At least with R v2.8.0 and Firefox 3.0 On Sat, Nov 15, 2008 at 5:51 PM, Spencer Graves [EMAIL PROTECTED] wrote: Writing R Extensions is no longer available via help.start(), at least not in the standard Windows install since R 2.7.2. If there is a way to get it to work again like it used to, I'd like to know. The only way I know to get it is to go to www.r-project.org - Manuals - Writing R Extensions. From there, if I want to make a local copy, I must avoid the obvious File - Save Page As, because that gives me HTML. Instead, there is a Save a copy button in the upper left of the subwindow containing R-exts.pdf, which I must press to get that particular document. Best Wishes, Spencer Henrik Bengtsson wrote: See 'Writing R Extensions' via help.start() and then search for CITATION. My $.02 /Henrik On Sat, Nov 15, 2008 at 2:35 PM, Charles Annis, P.E. [EMAIL PROTECTED] wrote: Greetings, R-ians: I am sure I am missing something obvious. How do I provide a CITATION file for my home-brew package, so that it will be packaged using R CMD build --binary myPackage? I have placed a CITATION file in the myPackage directory along with the DESCRIPTION file, but it is ignored. Thanks for your guidance. Charles Annis, P.E. [EMAIL PROTECTED] phone: 561-352-9699 eFax: 614-455-3265 http://www.StatisticalEngineering.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. __ 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-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] Spatial ANCOVA in R
Hi: Does anyone know if it is possible to run an ANCOVA in R while accounting or controlling for spatial autocorrelation? I have found usefull information into how to account for spatial autocorrelaion in regression models but not much into how to deal with the problem in an ANCOVA. Thanks, Camilo Camilo Mora, Ph.D. SCRIPPS Institute of Oceanography University of California San Diego San Diego, USA Phone: (858) 822 1642 http://cmbc.ucsd.edu/People/Faculty_and_Researchers/mora/ And Department of Biology Dalhouisie University Halifax, Canada Phone: (902) 494 3910 http://as01.ucis.dal.ca/fmap/people.php?pid=53 __ 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] I want my row name to be a variable
Dear CE.KA, Try this: X=read.table(textConnection( Var1Var2 A 22 13 B5 2 C12 8 D199),header=TRUE) closeAllConnections() X$Var3-rownames(X) X HTH, Jorge On Sat, Nov 15, 2008 at 5:34 PM, CE.KA [EMAIL PROTECTED] wrote: Hi R users Imagine this data.frame: X Var1Var2 A 22 13 B5 2 C12 8 D199 A,B,C,D are the rows names (or index) Is there a way to create a new variable in this data frame which name is Var3 and which contains the rows names: Var1Var2Var3 A 22 13A B5 2 B C12 8 C D199D I tried as.data.frame(array(x, dim(x), dimnames(x))) but it doesn'work Sincerely yours -- View this message in context: http://www.nabble.com/I-want-my-row-name-to-be-a-variable-tp20520180p20520180.html 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. [[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] birthday problem (factorial limit)---fortune candidate
The function ... works for different values of two Thomas Lumley __ 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] Statistics forums
There are three sci.stat.* newsgroups on the original USENET hierarchy and at least one GoogleGroups location with activity. The Medstats group has reputable people contributing. If you post a difficult problem in integration or numerical analysis to sci.math or sci.math.num-analysis you may get very credible responses. One doc's opinion: The sci.stat.math groups has people of variable quality (as with any open Internet forum). Some such as Marc Schwartz and Frank Harrell who also post here, are extremely good, but some of the other regular contributors may not be as sophisticated. Caveat emptor. You can see all of these groups through a variety of news clients. USENET groups are canonically read with newsreaders but are also accessible through Google's interface. The Medstats group can only be seen with Google's interface. -- David Winsemius, MD (not speaking in any way for my employer.) On Nov 15, 2008, at 12:19 PM, ANJAN PURKAYASTHA wrote: Hi, Given that the R forum is mostly a site to discuss issues related to the language, are there any forums that discuss statistical issues? I am specifically interested in the statistical issues in experimental design. TIA, Anjan -- = anjan purkayastha, phd bioinformatics analyst whitehead institute for biomedical research nine cambridge center cambridge, ma 02142 __ 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 provide a CITATION file?
On Sat, 15 Nov 2008, Spencer Graves wrote: Writing R Extensions is no longer available via help.start(), at least not in the standard Windows install since R 2.7.2. If there is a way to get it to work again like it used to, I'd like to know. The only way I Are you getting the search page? Hit the 'Up' arrow icon. Or use help.search(searchEngine=TRUE) . Why have you (not anyone else) reported this over two releases? know to get it is to go to www.r-project.org - Manuals - Writing R Extensions. From there, if I want to make a local copy, I must avoid the obvious File - Save Page As, because that gives me HTML. Instead, there is a Save a copy button in the upper left of the subwindow containing R-exts.pdf, which I must press to get that particular document. Best Wishes, Spencer Henrik Bengtsson wrote: See 'Writing R Extensions' via help.start() and then search for CITATION. My $.02 /Henrik On Sat, Nov 15, 2008 at 2:35 PM, Charles Annis, P.E. [EMAIL PROTECTED] wrote: Greetings, R-ians: I am sure I am missing something obvious. How do I provide a CITATION file for my home-brew package, so that it will be packaged using R CMD build --binary myPackage? I have placed a CITATION file in the myPackage directory along with the DESCRIPTION file, but it is ignored. Thanks for your guidance. Charles Annis, P.E. [EMAIL PROTECTED] phone: 561-352-9699 eFax: 614-455-3265 http://www.StatisticalEngineering.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. __ 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. -- 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] unable to view vignette in R
Why not ask on r-sig-debian?: presumably it is a setting in the binary install of R you are using that is inappropriate on your systems. On Sat, 15 Nov 2008, Erik Iverson wrote: I never could figure this out, I had the exact same issue though. My solution was to simply set options(pdfviewer = evince) in my .Rprofile. Presumably, you could set it to whatever PDF viewer is your favorite. I never looked further into why the default was doing what it was doing. You could also set the environment variable R_PDFVIEWER . Lionel Brooks wrote: Hello All R-Gurus: ISSUE: Cannot view R vignettes due in Ubuntu Linux (a debian variant). note: this issue has been posted to this list before with no responses given see https://stat.ethz.ch/pipermail/r-help/2007-September/141178.html DETAILS: I am trying to view an R vignette. Here is the situation: I issue the openvignette(), then select the vignette I wish to view...and the system returns: Could not get a file descriptor referring to the console. This action should spawn a ps viewer displaying the contents of the vignette for my enjoyment. I suspect it may have something to do with the call to the postscript viewer application. Is there a simple way to change this behavior within R? Any Thoughts? Here is the copy paste of my session Code: openVignette() Please select a vignette: 1: annotate - Annotation Overview 2: annotate - Basic GO Usage 3: annotate - HowTo: Get HTML Output 4: annotate - HowTo: use chromosomal information 5: annotate - HOWTO: Use the online query tools 6: annotate - Using Affymetrix Probe Level Data 7: annotate - Using Data Packages 8: annotate - Using the homology package 9: AnnotationDbi - AnnotationDbi 10: AnnotationDbi - SQLForge 11: Biobase - An introduction to Biobase and ExpressionSets 12: Biobase - Bioconductor Overview 13: Biobase - esApply Introduction 14: Biobase - Notes for eSet developers 15: Biobase - Notes for writing introductory 'how to' documents 16: Biobase - quick views of eSet instances 17: geneplotter - How to assemble a chromLocation object 18: geneplotter - Visualization of Microarray Data 19: xtable - xtable Gallery Selection: 17) Opening /home/lbthrice/R/i486-pc-linux-gnu-library/2.8/geneplotter/doc/byChroms.pdf Couldnt get a file descriptor referring to the console Could not get a file descriptor referring to the console __ 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. -- 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] Spatial ANCOVA in R
Hi Camilo, try gls() in the nlme package. Andrew On Sat, Nov 15, 2008 at 11:34:57PM -0400, Camilo Mora wrote: Hi: Does anyone know if it is possible to run an ANCOVA in R while accounting or controlling for spatial autocorrelation? I have found usefull information into how to account for spatial autocorrelaion in regression models but not much into how to deal with the problem in an ANCOVA. Thanks, Camilo Camilo Mora, Ph.D. SCRIPPS Institute of Oceanography University of California San Diego San Diego, USA Phone: (858) 822 1642 http://cmbc.ucsd.edu/People/Faculty_and_Researchers/mora/ And Department of Biology Dalhouisie University Halifax, Canada Phone: (902) 494 3910 http://as01.ucis.dal.ca/fmap/people.php?pid=53 __ 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. -- Andrew Robinson Department of Mathematics and StatisticsTel: +61-3-8344-6410 University of Melbourne, VIC 3010 Australia Fax: +61-3-8344-4599 http://www.ms.unimelb.edu.au/~andrewpr http://blogs.mbs.edu/fishing-in-the-bay/ __ 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] Using n+1 instances of R to utilise n processors on one machine - something like R with tabbed browsing?
This is what e.g. package snow does: it will also collect the results for you. See also package pvapply. On Sat, 15 Nov 2008, [EMAIL PROTECTED] wrote: Dear R-help, Please forgive me if any of the following sounds naieve/confused, i've just got back from a mini-pub-crawl, slightly tipsy, and am feeling brave to ask a possibly silly question... also, not to shiny on the technical side of things. Problem - I need to text mine a collection of 10,000 plain text documents, all of which are sitting in a single folder. i don't have any money to buy a database package, and even if i did i have no idea how that would speed things up if i want to do all the processing in R Assumption - It is my understanding that R can only use one processor on a machine when handeling calculations. If you wanted to use 4 processors, than you would have to open up 4 seperate instances of R and share the work between them eg. give each instance of R 25% of the documents you want processed Question - It is possible to have one instance of R to divide the workload, and then that instance opens up 4 other instances of R to do the processing? Or, is sometihng akin to tabbed browsing, where you have one main window and several tabs, each corresponding to a different instance of R? appologies if none of hte above made sense :o) Clair xx O/S: Windows Vista R 2.8.0 __ 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] Using n+1 instances of R to utilise n processors on one machine - something like R with tabbed browsing?
On Sun, 16 Nov 2008, Prof Brian Ripley wrote: This is what e.g. package snow does: it will also collect the results for you. See also package pvapply. Typo: 'papply' On Sat, 15 Nov 2008, [EMAIL PROTECTED] wrote: Dear R-help, Please forgive me if any of the following sounds naieve/confused, i've just got back from a mini-pub-crawl, slightly tipsy, and am feeling brave to ask a possibly silly question... also, not to shiny on the technical side of things. Problem - I need to text mine a collection of 10,000 plain text documents, all of which are sitting in a single folder. i don't have any money to buy a database package, and even if i did i have no idea how that would speed things up if i want to do all the processing in R Assumption - It is my understanding that R can only use one processor on a machine when handeling calculations. If you wanted to use 4 processors, than you would have to open up 4 seperate instances of R and share the work between them eg. give each instance of R 25% of the documents you want processed Question - It is possible to have one instance of R to divide the workload, and then that instance opens up 4 other instances of R to do the processing? Or, is sometihng akin to tabbed browsing, where you have one main window and several tabs, each corresponding to a different instance of R? appologies if none of hte above made sense :o) Clair xx O/S: Windows Vista R 2.8.0 __ 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. -- 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.
