Re: [R] Matrix as input to xyplot {lattice} - proper extended formula syntax
For the example df below this also works: library(lattice); library(zoo) xyplot(zoo(df[1:4], df$x), type = p) On Sun, Sep 6, 2009 at 12:51 AM, David Winsemiusdwinsem...@comcast.net wrote: I'm not exactly sure what structure df has. Here's my effort to duplicate it: df - data.frame(y=matrix(rnorm(24), nrow=6), x=1:6) df y.1 y.2 y.3 y.4 x 1 0.1734636 0.2348417 -1.2375648 -1.3246439 1 2 1.9551669 -1.1027262 -0.7307332 0.3953752 2 3 -0.7645778 1.6297861 0.4743805 -0.4476145 3 4 -0.5308756 -0.5246534 -0.3854609 -1.609 4 5 0.7406525 -0.8691720 -0.8194084 1.6122059 5 6 -0.9625619 -1.0774165 1.0760829 0.3659436 6 And this seems to accomplish the desired task. Presumably you have assigned off-stage the value of title to a meaningful character string? p - xyplot(y.1+y.2+y.3+y.4 ~ x |1:4, data = df, main = title ,layout=c(1,4) ) p On Sep 5, 2009, at 11:52 PM, Bryan Hanson wrote: Hello R Folks... I have a list with the following structure: str(df) List of 3 $ y : num [1:4, 1:1242] -0.005379 0.029874 -0.023274 0.000655 -0.004537 .. $ x : num [1:1242] 501 503 505 507 509 ... $ names: Factor w/ 4 levels PC Loading 1,..: 1 2 3 4 I want to plot each row of df$y against df$x, and have each plot in it’s own panel according to the levels of df$names. The following works in the sense that the layout is right, but the y values have clearly been recycled or skipped in some fashion (and an error is thrown for each panel that the length of x and y aren’t the same): p - xyplot(y ~ x | names, data = df, main = title, layout = c(1, dim(y)[1]) In reviewing the extended formula interface in the Lattice Book, what I want to happen is y1 + y2 + y3 + y4 ~ x | names, outer = TRUE I see two options: figure out a way to create the extended formula on the fly (and the actual number of rows in y may vary), which seems potentially tricky, or create a data frame by stacking each row of y and repeating x and names to match. This seems like a waste of memory. I’ve looked through the archives and haven’t come across something quite like this, or at least I don’t recognize it if I have! Is there a more elegant way to tell xyplot I want to use each row of y repeatedly with the same x, in a loop-like fashion? TIA. Bryan * Bryan Hanson Professor of Chemistry Biochemistry DePauw University, Greencastle IN USA [[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. David Winsemius, MD Heritage Laboratories West Hartford, CT __ 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] Matrix as input to xyplot {lattice} - proper extended formula syntax
On Sat, Sep 5, 2009 at 10:43 PM, Bryan Hansonhan...@depauw.edu wrote: Thanks David, your way of constructing df is much more compact than what I was using, so I've incorporated it. I also had my rows and columns transposed relative to how xyplot wanted them (though I had tested for that, other problems interfered). In my case, I may have varying numbers of y columns, from y.1 to y.n let's say. Is there an easy way of creating the phrase y.1+y.2+...y.n to pass to xyplot, or even better, some sort of syntax that says take all y.n and plot them against x? lm() etc does have such syntax, but not lattice unfortunately. However, it's fairly easy (though inelegant) to create a formula from a character string; e.g. as.formula(sprintf(%s ~ x, paste(y., 1:5, sep = , collapse = +))) y.1 + y.2 + y.3 + y.4 + y.5 ~ x -Deepayan Thanks, Bryan On 9/6/09 12:51 AM, David Winsemius dwinsem...@comcast.net wrote: I'm not exactly sure what structure df has. Here's my effort to duplicate it: df - data.frame(y=matrix(rnorm(24), nrow=6), x=1:6) df y.1 y.2 y.3 y.4 x 1 0.1734636 0.2348417 -1.2375648 -1.3246439 1 2 1.9551669 -1.1027262 -0.7307332 0.3953752 2 3 -0.7645778 1.6297861 0.4743805 -0.4476145 3 4 -0.5308756 -0.5246534 -0.3854609 -1.609 4 5 0.7406525 -0.8691720 -0.8194084 1.6122059 5 6 -0.9625619 -1.0774165 1.0760829 0.3659436 6 And this seems to accomplish the desired task. Presumably you have assigned off-stage the value of title to a meaningful character string? p - xyplot(y.1+y.2+y.3+y.4 ~ x |1:4, data = df, main = title ,layout=c(1,4) ) p On Sep 5, 2009, at 11:52 PM, Bryan Hanson wrote: Hello R Folks... I have a list with the following structure: str(df) List of 3 $ y : num [1:4, 1:1242] -0.005379 0.029874 -0.023274 0.000655 -0.004537 .. $ x : num [1:1242] 501 503 505 507 509 ... $ names: Factor w/ 4 levels PC Loading 1,..: 1 2 3 4 I want to plot each row of df$y against df$x, and have each plot in it¹s own panel according to the levels of df$names. The following works in the sense that the layout is right, but the y values have clearly been recycled or skipped in some fashion (and an error is thrown for each panel that the length of x and y aren¹t the same): p - xyplot(y ~ x | names, data = df, main = title, layout = c(1, dim(y)[1]) In reviewing the extended formula interface in the Lattice Book, what I want to happen is y1 + y2 + y3 + y4 ~ x | names, outer = TRUE I see two options: figure out a way to create the extended formula on the fly (and the actual number of rows in y may vary), which seems potentially tricky, or create a data frame by stacking each row of y and repeating x and names to match. This seems like a waste of memory. I¹ve looked through the archives and haven¹t come across something quite like this, or at least I don¹t recognize it if I have! Is there a more elegant way to tell xyplot I want to use each row of y repeatedly with the same x, in a loop-like fashion? TIA. Bryan * Bryan Hanson Professor of Chemistry Biochemistry DePauw University, Greencastle IN USA [[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. David Winsemius, MD Heritage Laboratories West Hartford, CT __ 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] Video Analysis?
On Sun, Sep 6, 2009 at 1:07 AM, spencergspencer.gra...@prodsyse.com wrote: What software exists for digitizing video to quantify the motion of specific features in the image? I might be willing to use something that's NOT in R, though I'd prefer something in R (or at least with an R intereface). The 'Motion' project seems to do quite a bit: http://www.lavrsen.dk/foswiki/bin/view/Motion/WebHome Specifically it will capture frames from a video device, detect movement, and write jpeg or mpeg files when it detects movement. You can control it via http commands (which you can send from R) or it can start external commands on events (such as starting to detect motion) - these commands could trigger things in R. Motion is GPL licensed which means you can take the code and do stuff with it - it might be possible to link R directly to the underlying motion detection algorithms. So what's left for R to do? Or do you want to use it to develop new motion detection algorithms? Barry __ 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] Concentration ellipsoid
Hi all, Can anyone please guide me how to draw a Concentration ellipsoid for a bivariate system with a bivariate normal dist. having a VCV matrix : Sigma - matrix(c(1,2,2,5), 2, 2) I would like to draw in using GGPLOT. Your help will be highly appreciated. Thanks, -- View this message in context: http://www.nabble.com/Concentration-ellipsoid-tp25315705p25315705.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] struggling with split function
I am very sorry for such a simple question, but I am struggling with split. I have the following data frame: x-data.frame(A=c(NA,NA,NA,NA,split,NA,NA,NA,NA,split,NA,NA,NA,NA,split,NA,NA,NA,NA), B=c(Name1,text1,text2,text3,NA,Name2,text1,text2,text3,NA,Name3,text1,text2,text3,NA,Name4,text1,text2,text3), C=c(NA,1,NA,3,NA,NA,4,5,6,NA,NA,7,8,9,NA,NA,3,3,3),D=c(NA,1,1,2,NA,NA,5,6,NA,NA,NA,9,8,7,NA,NA,2,2,2), E=c(NA,3,2,1,NA,NA,6,5,4,NA,NA,7,7,8,NA,NA,1,NA,1)) print(x) All I want to do is to split x, i.e., to create a list of data frames that are currently separated by the word split in column A. In this example, it would be 4 data frames, the first of them being: A B C D E NA Name1 NA NA NA NA text1 1 1 3 NA text 2 NA 1 2 NA text3 3 2 1 etc. I tried: split(x, x$A) split(x,x$A == 'split') split(x,!is.na(x$A)) But nothing produces what I need. Tanks a lot for any hint! -- Dimitri Liakhovitski Ninah.com dimitri.liakhovit...@ninah.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] Video Analysis?
In my application you can transfer images or single frames from ImageJ to R very efficiently and easily. http://www.uni-bielefeld.de/biologie/Oekosystembiologie/bio7app/flashtut/processavis.htm http://www.uni-bielefeld.de/biologie/Oekosystembiologie/bio7app/flashtut/processavis.htm However, there are also several plugins for http://rsbweb.nih.gov/ij/ ImageJ available to detect and quantify motion in images. Another option would be to link and use the http://opencv.willowgarage.com/wiki/ OpenCV library with R which embedds algorithm to detect motion and more. With kind regards M. Austenfeld -- View this message in context: http://www.nabble.com/Video-Analysis--tp25313450p25315904.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] struggling with split function
one way is the following: ind - rle(is.na(x$A)) ind - rep(seq_along(ind$lengths), ind$lengths) na.ind - is.na(x$A) split(x[na.ind, -1], ind[na.ind]) I hope it helps. Best, Dimitris Dimitri Liakhovitski wrote: I am very sorry for such a simple question, but I am struggling with split. I have the following data frame: x-data.frame(A=c(NA,NA,NA,NA,split,NA,NA,NA,NA,split,NA,NA,NA,NA,split,NA,NA,NA,NA), B=c(Name1,text1,text2,text3,NA,Name2,text1,text2,text3,NA,Name3,text1,text2,text3,NA,Name4,text1,text2,text3), C=c(NA,1,NA,3,NA,NA,4,5,6,NA,NA,7,8,9,NA,NA,3,3,3),D=c(NA,1,1,2,NA,NA,5,6,NA,NA,NA,9,8,7,NA,NA,2,2,2), E=c(NA,3,2,1,NA,NA,6,5,4,NA,NA,7,7,8,NA,NA,1,NA,1)) print(x) All I want to do is to split x, i.e., to create a list of data frames that are currently separated by the word split in column A. In this example, it would be 4 data frames, the first of them being: A B C D E NA Name1 NA NA NA NA text1 1 1 3 NA text 2 NA 1 2 NA text3 3 2 1 etc. I tried: split(x, x$A) split(x,x$A == 'split') split(x,!is.na(x$A)) But nothing produces what I need. Tanks a lot for any hint! -- Dimitris Rizopoulos Assistant Professor Department of Biostatistics Erasmus University Medical Center Address: PO Box 2040, 3000 CA Rotterdam, the Netherlands Tel: +31/(0)10/7043478 Fax: +31/(0)10/7043014 __ 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] Concentration ellipsoid
In the mean time, i have found one package ellipse to do the same. The syntax is : plot(ellipse(Sigma), type='l') However I am still struggling on how to use qplot (in GGPLOT2) to draw above plot. I want to get some stylish view for my presentation preparation. Any help please? Thanks, RON70 wrote: Hi all, Can anyone please guide me how to draw a Concentration ellipsoid for a bivariate system with a bivariate normal dist. having a VCV matrix : Sigma - matrix(c(1,2,2,5), 2, 2) I would like to draw in using GGPLOT. Your help will be highly appreciated. Thanks, -- View this message in context: http://www.nabble.com/Concentration-ellipsoid-tp25315705p25316243.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 histogram to find cdf
Dear all, How can I use the histogram density estimate (hist) to find the value of the cdf at a certain point? Thanks Maram [[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] ggplot2::qplot() -- arbitary transformations of coordinate system?
Hi Stephen, Because coord_trans() does all the work of plotting the original values on the tranformed scale. See ?coord_trans. To quote: The difference between transforming the scales and transforming the coordinate system is that scale transformation occurs BEFORE statistics, and coordinate transformation afterwards. # After require(ggplot2) data(diamonds) # Three ways of doing transformating in ggplot: # * by transforming the data qplot(log10(carat), log10(price), data=diamonds) # * by transforming the scales qplot(carat, price, data=diamonds, log=xy) qplot(carat, price, data=diamonds) + scale_x_log10() + scale_y_log10() # * by transforming the coordinate system: qplot(carat, price, data=diamonds) + coord_trans(x = log10, y = log10) Michael On Sep 5, 2009, at 9:01 PM, stephen sefick wrote: why not transform the y-data? On Sat, Sep 5, 2009 at 8:03 PM, Michael Kubovykub...@virginia.edu wrote: Hi, Does anyone know how to do a coord_trans() in which the y-axis is tranformed into (for example) -1000/y? Stephen Sefick _ Professor Michael Kubovy University of Virginia Department of Psychology USPS: P.O.Box 400400Charlottesville, VA 22904-4400 Parcels:Room 102Gilmer Hall McCormick RoadCharlottesville, VA 22903 Office:B011+1-434-982-4729 Lab:B019+1-434-982-4751 Fax:+1-434-982-4766 WWW:http://www.people.virginia.edu/~mk9y/ __ 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] [Hmisc] Latex to pdf
I would like to print some tables and figures to a PDF device on a CentOS 5
vps. However, I cannot seem to get the latex function from Hmisc working. I
followed the example, and got an error: sh: xdvi: command not found. I tried
installing the 'tetex-xdvi' linux package, and now it returns: Error: Can't
open display. I guess the reason for this is that the machine is a VPS
terminal, so it has no display, however I dont understand why it does not
write to the PDF device. Some code:
pdf(test.pdf)
x - matrix(1:6, nrow=2, dimnames=list(c('a','b'),c('c','d','this that')))
latex(x) # creates x.tex in working directory
This is pdfeTeX, Version 3.141592-1.21a-2.2 (Web2C 7.5.4)
entering extended mode
(/tmp/Rtmp7bbXMN/file643c9869.tex
LaTeX2e 2003/12/01
Babel v3.8d and hyphenation patterns for american, french, german,
ngerman, b
ahasa, basque, bulgarian, catalan, croatian, czech, danish, dutch,
esperanto, e
stonian, finnish, greek, icelandic, irish, italian, latin, magyar, norsk,
polis
h, portuges, romanian, russian, serbian, slovak, slovene, spanish, swedish,
tur
kish, ukrainian, nohyphenation, loaded.
(/usr/share/texmf/tex/latex/base/report.cls
Document Class: report 2004/02/16 v1.4f Standard LaTeX document class
(/usr/share/texmf/tex/latex/base/size10.clo))
(/usr/share/texmf/tex/latex/geometry/geometry.sty
(/usr/share/texmf/tex/latex/graphics/keyval.sty)
(/usr/share/texmf/tex/latex/geometry/geometry.cfg))
No file file643c9869.aux.
[1] (./file643c9869.aux) )
Output written on file643c9869.dvi (1 page, 372 bytes).
Transcript written on file643c9869.log.
Error: Can't open display:
-
Jeroen Ooms * Dept. of Methodology and Statistics * Utrecht University
Visit http://www.jeroenooms.com www.jeroenooms.com to explore some of my
current projects.
--
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Re: [R] Video Analysis?
Thanks to Kevin Middleton, Barry Bowlingson, M. Austenfeld: The Hedrick reference is very interesting, digitizing a video of the flight of a moth. This shows the state of the art AND describes freely available MATLAB code. I've used Matlab before, but it would strain my budget right now to obtain it. I've translated Matlab into R before, and I could do that again if needed. First, however, I think I want to review the Motion and OpenCV projects -- and possibly ImageJ. I want to convert videos into functional time series, more complicated than the gait data set in the fda package but perhaps not as demanding as Hendrick's the flight of a moth. I want to measure dynamic bridge deflection midspan to see how that varies between spans and throughout a duty cycle. I will ultimately want to measure millimeters from high resolution video if possible. For a railroad bridge, a duty cycle will be the passing of a train, measuring both maximum deflection and oscillations. For highway bridges, I want to be able to measure the changes from the morning rush hour to midday to the late afternoon rush hour -- and preferably also the mostly unloaded period between 2 and 3 AM. I might be able to place corner reflectors on the bridge to mark the points I want to trace, though I'd prefer to be able to do it without that. In any event, I'd like to create a functional time series. I may also be able to get traffic counts, so I could model deflection as a function of traffic. Thanks again to Middleton, Bowlingson, and Austenfeld. Best Wishes, Spencer Barry Rowlingson wrote: On Sun, Sep 6, 2009 at 1:07 AM, spencergspencer.gra...@prodsyse.com wrote: What software exists for digitizing video to quantify the motion of specific features in the image? I might be willing to use something that's NOT in R, though I'd prefer something in R (or at least with an R intereface). The 'Motion' project seems to do quite a bit: http://www.lavrsen.dk/foswiki/bin/view/Motion/WebHome Specifically it will capture frames from a video device, detect movement, and write jpeg or mpeg files when it detects movement. You can control it via http commands (which you can send from R) or it can start external commands on events (such as starting to detect motion) - these commands could trigger things in R. Motion is GPL licensed which means you can take the code and do stuff with it - it might be possible to link R directly to the underlying motion detection algorithms. So what's left for R to do? Or do you want to use it to develop new motion detection algorithms? Barry -- Spencer Graves, PE, PhD President and Chief Operating Officer Structure Inspection and Monitoring, Inc. 751 Emerson Ct. San José, CA 95126 ph: 408-655-4567 __ 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] Video Analysis?
On 09/06/2009 01:51 PM, spencerg wrote: Thanks to Kevin Middleton, Barry Bowlingson, M. Austenfeld: The Hedrick reference is very interesting, digitizing a video of the flight of a moth. This shows the state of the art AND describes freely available MATLAB code. I've used Matlab before, but it would strain my budget right now to obtain it. I've translated Matlab into R before, and I could do that again if needed. First, however, I think I want to review the Motion and OpenCV projects -- and possibly ImageJ. The RImageJ R package provides some link between R and ImageJ, it is very simple (the package has 5 lines of R code), but might help you. See http://tr.im/qzSl for the annoucement on my blog. I want to convert videos into functional time series, more complicated than the gait data set in the fda package but perhaps not as demanding as Hendrick's the flight of a moth. I want to measure dynamic bridge deflection midspan to see how that varies between spans and throughout a duty cycle. I will ultimately want to measure millimeters from high resolution video if possible. For a railroad bridge, a duty cycle will be the passing of a train, measuring both maximum deflection and oscillations. For highway bridges, I want to be able to measure the changes from the morning rush hour to midday to the late afternoon rush hour -- and preferably also the mostly unloaded period between 2 and 3 AM. I might be able to place corner reflectors on the bridge to mark the points I want to trace, though I'd prefer to be able to do it without that. In any event, I'd like to create a functional time series. I may also be able to get traffic counts, so I could model deflection as a function of traffic. Thanks again to Middleton, Bowlingson, and Austenfeld. Best Wishes, Spencer Barry Rowlingson wrote: On Sun, Sep 6, 2009 at 1:07 AM, spencergspencer.gra...@prodsyse.com wrote: What software exists for digitizing video to quantify the motion of specific features in the image? I might be willing to use something that's NOT in R, though I'd prefer something in R (or at least with an R intereface). The 'Motion' project seems to do quite a bit: http://www.lavrsen.dk/foswiki/bin/view/Motion/WebHome Specifically it will capture frames from a video device, detect movement, and write jpeg or mpeg files when it detects movement. You can control it via http commands (which you can send from R) or it can start external commands on events (such as starting to detect motion) - these commands could trigger things in R. Motion is GPL licensed which means you can take the code and do stuff with it - it might be possible to link R directly to the underlying motion detection algorithms. So what's left for R to do? Or do you want to use it to develop new motion detection algorithms? Barry -- Romain Francois Professional R Enthusiast +33(0) 6 28 91 30 30 http://romainfrancois.blog.free.fr |- http://tr.im/xMdt : update on the ant package |- http://tr.im/xHLs : R capable version of ant `- http://tr.im/xHiZ : Tip: get java home from R with rJava __ 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] Anova over a list of models
Jeroen
This seems to work for (1):
anova(myModels[[1]], force(myModels[[2]]))
OR
anova(myModels[[1]], (myModels[[2]]))
I suspect this is about lazy-evaluation, looking at the source code
for anova for mer objects: selectMethod(anova,mer), something goes
wrong with the sapply to get the names, I think sapply(...,toString)
would work better for this particular case.
For (2), the best solution I could come up with is:
myParameters = lapply(1:length(myModels),function(x){ if(x==1)
paste(myModels[[,x,]],sep = ) else
paste(force(myModels[[,x,]]),sep = )})
myParStr = toString(paste( myParameters ))
eval(parse(text = paste(anova(,myParStr,
I would have expected do.call(anova, myModels) to work
Hope this helps
Schalk Heunis
On Sat, Sep 5, 2009 at 10:43 PM, Jeroen Oomsj.c.l.o...@uu.nl wrote:
2009/9/5 Henrique Dallazuanna www...@gmail.com
Try this:
anova(myModels[[1]],myModels[[2]])
do.call(anova, myModels)
Does this work for you? Both functions are failing here:
anova(myModels[[1]],myModels[[2]])
Error in names(mods) - sapply(as.list(mCall)[c(FALSE, TRUE, modp)],
as.character) :
'names' attribute [6] must be the same length as the vector [2]
do.call(anova, myModels)
Error in as.character.default(X[[1L]], ...) :
no method for coercing this S4 class to a vector
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[R] Simulation of population dynamics in R?
Hello, are there simulation packages to simulate population dynamics, for example for epidemiology? Or are there (open source) tools that can do that task and can be used from within R (or at least can read the resulting data files)? Oliver __ 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] struggling with split function
Thanks a lot, Dimitris. It totally works on my example data frame. I know, it's probably hard to address, but when I try to apply it to the real huge data frame I have, after the last line I get: Error in `[.default`(x$A, na.ind, -1) : incorrect number of dimensions. I know it's impossible to answer this question without seeing the data, but still: what do you think might be wrong? Do you think it could be because my first column contains something else but the split? No, I've just run the table on A and it is: split NA 204 6356 I also checked the first dimension of x and the length(na.ind) - the are the same length: 6560. No idea where the error might lye... Thanks a lot! Dimitri On Sun, Sep 6, 2009 at 5:43 AM, Dimitris Rizopoulosd.rizopou...@erasmusmc.nl wrote: one way is the following: ind - rle(is.na(x$A)) ind - rep(seq_along(ind$lengths), ind$lengths) na.ind - is.na(x$A) split(x[na.ind, -1], ind[na.ind]) I hope it helps. Best, Dimitris Dimitri Liakhovitski wrote: I am very sorry for such a simple question, but I am struggling with split. I have the following data frame: x-data.frame(A=c(NA,NA,NA,NA,split,NA,NA,NA,NA,split,NA,NA,NA,NA,split,NA,NA,NA,NA), B=c(Name1,text1,text2,text3,NA,Name2,text1,text2,text3,NA,Name3,text1,text2,text3,NA,Name4,text1,text2,text3), C=c(NA,1,NA,3,NA,NA,4,5,6,NA,NA,7,8,9,NA,NA,3,3,3),D=c(NA,1,1,2,NA,NA,5,6,NA,NA,NA,9,8,7,NA,NA,2,2,2), E=c(NA,3,2,1,NA,NA,6,5,4,NA,NA,7,7,8,NA,NA,1,NA,1)) print(x) All I want to do is to split x, i.e., to create a list of data frames that are currently separated by the word split in column A. In this example, it would be 4 data frames, the first of them being: A B C D E NA Name1 NA NA NA NA text1 1 1 3 NA text 2 NA 1 2 NA text3 3 2 1 etc. I tried: split(x, x$A) split(x,x$A == 'split') split(x,!is.na(x$A)) But nothing produces what I need. Tanks a lot for any hint! -- Dimitris Rizopoulos Assistant Professor Department of Biostatistics Erasmus University Medical Center Address: PO Box 2040, 3000 CA Rotterdam, the Netherlands Tel: +31/(0)10/7043478 Fax: +31/(0)10/7043014 -- Dimitri Liakhovitski Ninah.com dimitri.liakhovit...@ninah.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] DOE in R?
Hello, This is your starting point: http://cran.r-project.org/web/views/ExperimentalDesign.html Best regards, Carlos J. Gil Bellosta http://www.datanalytics.com On Thu, 2009-09-03 at 17:38 -0700, B_miner wrote: Hello! This is not a topic I am well versed in but required to become well versed in...I welcome any assistance! Using R, I want to create an optimal design for an experiment. I'll be analyzing the results with logistic regression or some generalized linear model. I am thinking that the algdesign package can help (but no idea where to start?). I'm presenting an example here that I have seen the answer to (in SAS) in order to make sure I would have gotten it *right*. There are 5 factors: 4 are quantitative with three levels each and 1 is qualitative with two levels. Factor and levels: Intro: 0, 1.99, 2.99 Duration: 6, 9 ,12 GOTO: 3.99, 4.99, 5.99 Fee: 0, 15, 45 Color: Red, White In order to screen these factors, I would want to get a design where I could evaluate all main effects, all first order interactions and the squared terms of Intro, Duration, GOTO and FEE (for example Intro*Intro). Looking for the D-optimal design. Is this something that R can provide? These are, according to the SAS paper I read the following: Obs intro duration goto fee color 1 0.00 6 3.99 0 WHITE 2 0.00 6 3.99 45 RED 3 0.00 6 5.99 0 RED 4 0.00 6 5.99 45 WHITE 5 0.00 9 3.99 45 RED 6 0.00 9 4.99 15 WHITE 7 0.00 9 5.99 0 RED 8 0.00 12 3.99 0 RED 9 0.00 12 3.99 45 WHITE 10 0.00 12 5.99 0 WHITE 11 0.00 12 5.99 45 RED 12 0.00 12 5.99 45 WHITE 13 1.99 6 3.99 15 RED 14 1.99 6 4.99 45 WHITE 15 1.99 6 5.99 0 WHITE 16 1.99 9 5.99 45 RED 17 1.99 12 3.99 0 WHITE 18 1.99 12 5.99 15 RED 19 2.99 6 3.99 0 WHITE 20 2.99 6 3.99 45 WHITE 21 2.99 6 4.99 0 RED 22 2.99 6 5.99 15 WHITE 23 2.99 6 5.99 45 RED 24 2.99 9 3.99 0 RED 25 2.99 12 3.99 15 WHITE 26 2.99 12 3.99 45 RED 27 2.99 12 4.99 0 WHITE 28 2.99 12 4.99 45 RED 29 2.99 12 5.99 0 RED 30 2.99 12 5.99 45 WHITE __ 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] About BIC
Hi Dan, On Sat, Sep 5, 2009 at 4:40 PM, dan.z...@uni-ulm.de wrote: Hello, I am working on getting optimal lags by using BIC, But I don't know how to calculate BIC. Is there any code or useful function for it? The second formula listed on the wikipedia page for BIC seems pretty straightforward to calculate: http://en.wikipedia.org/wiki/Bayesian_information_criterion BIC = n * ln(RSS/n) + k * ln(n) n = number of datapoints in your data RSS = residual sum of squares k = number of free params in your model Otherwise, there is a BIC function in the nlme package and maybe others since I just ran ??bic to find it. Hope that helps, -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact __ 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::qplot() -- arbitary transformations of coordinate system?
Hi Michael, You could use aes(y = 1000 * myyvar) and coord_trans(trans_y = inverse) Hadley On Sun, Sep 6, 2009 at 6:30 AM, Michael Kubovykub...@virginia.edu wrote: Hi Stephen, Because coord_trans() does all the work of plotting the original values on the tranformed scale. See ?coord_trans. To quote: The difference between transforming the scales and transforming the coordinate system is that scale transformation occurs BEFORE statistics, and coordinate transformation afterwards. # After require(ggplot2) data(diamonds) # Three ways of doing transformating in ggplot: # * by transforming the data qplot(log10(carat), log10(price), data=diamonds) # * by transforming the scales qplot(carat, price, data=diamonds, log=xy) qplot(carat, price, data=diamonds) + scale_x_log10() + scale_y_log10() # * by transforming the coordinate system: qplot(carat, price, data=diamonds) + coord_trans(x = log10, y = log10) Michael On Sep 5, 2009, at 9:01 PM, stephen sefick wrote: why not transform the y-data? On Sat, Sep 5, 2009 at 8:03 PM, Michael Kubovykub...@virginia.edu wrote: Hi, Does anyone know how to do a coord_trans() in which the y-axis is tranformed into (for example) -1000/y? Stephen Sefick _ Professor Michael Kubovy University of Virginia Department of Psychology USPS: P.O.Box 400400 Charlottesville, VA 22904-4400 Parcels: Room 102 Gilmer Hall McCormick Road Charlottesville, VA 22903 Office: B011 +1-434-982-4729 Lab: B019 +1-434-982-4751 Fax: +1-434-982-4766 WWW: http://www.people.virginia.edu/~mk9y/ __ 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. -- http://had.co.nz/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Concentration ellipsoid
On 06/09/2009 6:08 AM, RON70 wrote: In the mean time, i have found one package ellipse to do the same. The syntax is : plot(ellipse(Sigma), type='l') However I am still struggling on how to use qplot (in GGPLOT2) to draw above plot. I want to get some stylish view for my presentation preparation. Any help please? Unlike plot(), qplot() doesn't appear to use xy.coords to extract x and y from a single argument. So you need to do it: e - ellipse(Sigma) x - e[,x] y - e[,y] qplot(x,y,geom=path) Duncan Murdoch __ 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 histogram to find cdf
Hi, On Sun, Sep 6, 2009 at 7:03 AM, maram salemmarammagdysa...@yahoo.com wrote: Dear all, How can I use the histogram density estimate (hist) to find the value of the cdf at a certain point? Can you just use the ecdf function on your original data? -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact __ 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] Color index in image function
Hi, On Sat, Sep 5, 2009 at 7:06 AM, FMHkagba2...@yahoo.com wrote: Dear All, I was looking for the color index in image function, such as from topo.colors(n) and etc. but still never found it. For instance, from the help menu. The answer is in the code: ### # Volcano data visualized as matrix. Need to transpose and flip # matrix horizontally. image(t(volcano)[ncol(volcano):1,]) # A prettier display of the volcano x - 10*(1:nrow(volcano)) y - 10*(1:ncol(volcano)) image(x, y, volcano, col = terrain.colors(100), axes = FALSE) Right here: R terrrain.colors(100) [1] #00A600FF #03A700FF #07A800FF #0AAA00FF #0EAB00FF ... Is that what you mean? -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact __ 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] About BIC
The AIC function calculate the BIC. See ?AIC On Sat, Sep 5, 2009 at 5:40 PM, dan.z...@uni-ulm.de wrote: Hello, I am working on getting optimal lags by using BIC, But I don't know how to calculate BIC. Is there any code or useful function for it? Thanks and regards, Dan Zhao __ 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. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O [[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 do I draw this surface -- hand drawn in the attachemtn
Hi, On Sat, Sep 5, 2009 at 5:16 AM, gallon ligallon...@gmail.com wrote: Basially I have the observation for x, y, and z for each fixed z, the value of y moves from 0 to y0 as x moves from 0 to x0. I then move the curve for z from 0 to z0 and form a continuous surface. want to know if there is a way that R can replace my handdrawing. Do the examples in ?persp help? How about this example from the r graph gallery: http://addictedtor.free.fr/graphiques/graphcode.php?graph=42 I think lattice graphics also has functions to help plotting in 3d, but I've never used it. I've only seen it in actio in the lattics vs. ggplot series of posts on the learnr.wordpress.com blog (very helpful). -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact __ 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] saving large matrices with decimal numbers
Moreno Ignazio Coco wrote: Please tell us what you did exactly when you got the empty file: PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. well, that's exactly the point, I didn't do anything fancy or special, just save the matrix I gave you before (1024 X 768) either in format txt. That's strange, because image - matrix(0.1, 1024, 768) write.table(image, ~/data.txt, col.names=FALSE, row.names=FALSE) file.show(~/data.txt) works fine for me. Hence I suspect you did something very different, but since you have still not provided any piece of reproducible code, we cannot help. Uwe Ligges write.table(image, ~/mydata/blablabla/data.txt, col.names=F, row.names=F) or csv: write.csv (image, ~/mydata/blablabla/data.csv) both cases the output is an empty file. Do you know what can be the problem? Thanks a lot, Moreno write.csv (image, /afs/inf.ed.ac.uk/user/s07/s0788806/R/r_data/ProdEyeTrack/DataFrame/Clustered/Clut/Cluster1/Cl1Verb-tr.csv.1) Quoting Uwe Ligges lig...@statistik.tu-dortmund.de: Moreno Ignazio Coco wrote: Hi everybody, I am struggling to save txt. or csv. large sparse matrices (1024 X 768 image size), initialized at 0.1. image1[0:10,0:10] [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [1,] 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 [2,] 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 [3,] 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 [4,] 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 [5,] 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 [6,] 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 [7,] 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 [8,] 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 [9,] 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 [10,] 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.1 with small distributions located at different points of matrix. If I try the same matrix but initialized at 0, it can save it. It seems that R manages to save up around 800 X 600 decimal matrices but for bigger sizes the output is an empty file. Does anyone know whether there is a limit in saving such matrices and how can I work around this problem? Please tell us what you did exactly when you got the empty file: PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Best wishes, Uwe Ligges Thanks a lot, Regards, Moreno __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Matrix as input to xyplot {lattice} - proper extended formula syntax
On Sep 6, 2009, at 12:51 AM, David Winsemius wrote: I'm not exactly sure what structure df has. Here's my effort to duplicate it: df - data.frame(y=matrix(rnorm(24), nrow=6), x=1:6) df y.1y.2y.3y.4 x 1 0.1734636 0.2348417 -1.2375648 -1.3246439 1 2 1.9551669 -1.1027262 -0.7307332 0.3953752 2 3 -0.7645778 1.6297861 0.4743805 -0.4476145 3 4 -0.5308756 -0.5246534 -0.3854609 -1.609 4 5 0.7406525 -0.8691720 -0.8194084 1.6122059 5 6 -0.9625619 -1.0774165 1.0760829 0.3659436 6 And this seems to accomplish the desired task. Presumably you have assigned off-stage the value of title to a meaningful character string? p - xyplot(y.1+y.2+y.3+y.4 ~ x |1:4, data = df, main = title ,layout=c(1,4) ) p For the record, the xyplot call above does not give the desired output but Gabor's method does. I'm glad that construction of a sample df was useful, even is my efforts a driving xyplot with a surrogate grouping sequence was not. -- David. On Sep 5, 2009, at 11:52 PM, Bryan Hanson wrote: Hello R Folks... I have a list with the following structure: str(df) List of 3 $ y: num [1:4, 1:1242] -0.005379 0.029874 -0.023274 0.000655 -0.004537 .. $ x: num [1:1242] 501 503 505 507 509 ... $ names: Factor w/ 4 levels PC Loading 1,..: 1 2 3 4 I want to plot each row of df$y against df$x, and have each plot in it’s own panel according to the levels of df$names. The following works in the sense that the layout is right, but the y values have clearly been recycled or skipped in some fashion (and an error is thrown for each panel that the length of x and y aren’t the same): p - xyplot(y ~ x | names, data = df, main = title, layout = c(1, dim(y)[1]) In reviewing the extended formula interface in the Lattice Book, what I want to happen is y1 + y2 + y3 + y4 ~ x | names, outer = TRUE I see two options: figure out a way to create the extended formula on the fly (and the actual number of rows in y may vary), which seems potentially tricky, or create a data frame by stacking each row of y and repeating x and names to match. This seems like a waste of memory. I’ve looked through the archives and haven’t come across something quite like this, or at least I don’t recognize it if I have! Is there a more elegant way to tell xyplot I want to use each row of y repeatedly with the same x, in a loop-like fashion? TIA. Bryan * Bryan Hanson Professor of Chemistry Biochemistry DePauw University, Greencastle IN USA [[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. David Winsemius, MD Heritage Laboratories West Hartford, CT __ 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. David Winsemius, MD Heritage Laboratories West Hartford, CT __ 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::qplot() -- arbitary transformations of coordinate system?
Is there a place to find a list of the legal values for the coord_trans parameters. I spent a bunch of time searching the ggplot2 docs and r-help for same without success. I also made an attempt at looking at the code in R which also failed. -- David. On Sep 6, 2009, at 10:12 AM, hadley wickham wrote: Hi Michael, You could use aes(y = 1000 * myyvar) and coord_trans(trans_y = inverse) Hadley On Sun, Sep 6, 2009 at 6:30 AM, Michael Kubovykub...@virginia.edu wrote: Hi Stephen, Because coord_trans() does all the work of plotting the original values on the tranformed scale. See ?coord_trans. To quote: The difference between transforming the scales and transforming the coordinate system is that scale transformation occurs BEFORE statistics, and coordinate transformation afterwards. # After require(ggplot2) data(diamonds) # Three ways of doing transformating in ggplot: # * by transforming the data qplot(log10(carat), log10(price), data=diamonds) # * by transforming the scales qplot(carat, price, data=diamonds, log=xy) qplot(carat, price, data=diamonds) + scale_x_log10() + scale_y_log10() # * by transforming the coordinate system: qplot(carat, price, data=diamonds) + coord_trans(x = log10, y = log10) Michael On Sep 5, 2009, at 9:01 PM, stephen sefick wrote: why not transform the y-data? On Sat, Sep 5, 2009 at 8:03 PM, Michael Kubovykub...@virginia.edu wrote: Hi, Does anyone know how to do a coord_trans() in which the y-axis is tranformed into (for example) -1000/y? Stephen Sefick _ Professor Michael Kubovy University of Virginia Department of Psychology USPS: P.O.Box 400400Charlottesville, VA 22904-4400 Parcels:Room 102Gilmer Hall McCormick RoadCharlottesville, VA 22903 Office:B011+1-434-982-4729 Lab:B019+1-434-982-4751 Fax:+1-434-982-4766 WWW:http://www.people.virginia.edu/~mk9y/ __ 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. -- http://had.co.nz/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. David Winsemius, MD Heritage Laboratories West Hartford, CT __ 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] Color index in image function
Hi, Thank you for your response. I'm looking for the names of the colors denoted by these codes and what do these colors represent for. For instance, if we use topo.colors(5) in the image function, five different colors will be used in which its codes are denoted as: [1] #4C00 #004C #00E5 #00FF4DFF #00FF So, my first question is what type of color do these codes represent for? Are they white, red,...? My second question is, if we use this topo.colors(5) in image function to denote the temperature values for intance, what are these colors represent for? Does the first color, #4C00 represent the lower/medium/higher temperature? I do hope you could advice me on this matter? Thank you Fir - Original Message From: FMH kagba2...@yahoo.com To: Steve Lianoglou mailinglist.honey...@gmail.com Sent: Sunday, September 6, 2009 3:41:02 PM Subject: Re: [R] Color index in image function Hi, Thank you for your response. I'm looking for the name of the colors denoted by this code and what are these colors representing for. For instance, if we use topo.colors(5) in the image function, five different colors will be used in which its codes are denoted as: [1] #4C00 #004C #00E5 #00FF4DFF #00FF So, my first question is what type of color does these codes represent for? Are they white, red,...? My second question is, if we use this topo.colors(5) in image function to denote the temperature values for intance, what are these colors represent for? Does the first color, #4C00 represent the lower/medium/higher temperature? I do hope you could advice me on this matter? Thank you Fir - Original Message From: Steve Lianoglou mailinglist.honey...@gmail.com To: FMH kagba2...@yahoo.com Cc: r-help@r-project.org Sent: Sunday, September 6, 2009 3:20:25 PM Subject: Re: [R] Color index in image function Hi, On Sat, Sep 5, 2009 at 7:06 AM, FMHkagba2...@yahoo.com wrote: Dear All, I was looking for the color index in image function, such as from topo.colors(n) and etc. but still never found it. For instance, from the help menu. The answer is in the code: ### # Volcano data visualized as matrix. Need to transpose and flip # matrix horizontally. image(t(volcano)[ncol(volcano):1,]) # A prettier display of the volcano x - 10*(1:nrow(volcano)) y - 10*(1:ncol(volcano)) image(x, y, volcano, col = terrain.colors(100), axes = FALSE) Right here: R terrrain.colors(100) [1] #00A600FF #03A700FF #07A800FF #0AAA00FF #0EAB00FF ... Is that what you mean? -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact __ 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] selecting columns based on values of two variables
Dear R-list, I am having troubles selecting rows from a very large data-set containing distances between capitals. The structure of the data-set looks like this: numaida numbidb kmdist midist 12 USA 20 CAN 731 456 22 USA 31 BHM 16231012 32 USA 40 CUB 18131130 I want to select a subset of these dyads, and have tried the following code: subset(capdist,ida == c(DEN,SWD,FIN) idb == c(DEN,SWD,FIN)) This should ideally give me the dyads involving only Denmark, Sweden and Finland, however i get the error message: [1] numa idanumb idbkmdist midist 0 rows (or 0-length row.names) Warning messages: 1: In is.na(e1) | is.na(e2) : longer object length is not a multiple of shorter object length 2: In `==.default`(ida, c(DEN, SWD, FIN)) : longer object length is not a multiple of shorter object length 3: In is.na(e1) | is.na(e2) : longer object length is not a multiple of shorter object length 4: In `==.default`(idb, c(DEN, SWD, FIN)) : longer object length is not a multiple of shorter object length Any help would be greatly appreciated, Best, Thomas Jensen [[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] selecting columns based on values of two variables
probably you're looking for subset(capdist, ida %in% c(DEN,SWD,FIN) idb %in% c(DEN,SWD,FIN)) I hope it helps. Best, Dimitris Thomas Jensen wrote: Dear R-list, I am having troubles selecting rows from a very large data-set containing distances between capitals. The structure of the data-set looks like this: numaida numbidb kmdist midist 12 USA 20 CAN 731 456 22 USA 31 BHM 16231012 32 USA 40 CUB 18131130 I want to select a subset of these dyads, and have tried the following code: subset(capdist,ida == c(DEN,SWD,FIN) idb == c(DEN,SWD,FIN)) This should ideally give me the dyads involving only Denmark, Sweden and Finland, however i get the error message: [1] numa idanumb idbkmdist midist 0 rows (or 0-length row.names) Warning messages: 1: In is.na(e1) | is.na(e2) : longer object length is not a multiple of shorter object length 2: In `==.default`(ida, c(DEN, SWD, FIN)) : longer object length is not a multiple of shorter object length 3: In is.na(e1) | is.na(e2) : longer object length is not a multiple of shorter object length 4: In `==.default`(idb, c(DEN, SWD, FIN)) : longer object length is not a multiple of shorter object length Any help would be greatly appreciated, Best, Thomas Jensen [[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. -- Dimitris Rizopoulos Assistant Professor Department of Biostatistics Erasmus University Medical Center Address: PO Box 2040, 3000 CA Rotterdam, the Netherlands Tel: +31/(0)10/7043478 Fax: +31/(0)10/7043014 __ 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] Color index in image function
Try this to see which colors the codes are:
Color - function(color){
z - matrix(1:length(color), ncol = length(color))
image(y = seq(1, length(color)),
z, col = color, axes = FALSE)
text(0, y = z, labels = color, pos = 1, offset = 0, cex = 0.7)
}
Color(topo.colors(5))
Color(terrain.colors(10))
You can use levelplot from lattice package too.
On Sun, Sep 6, 2009 at 11:50 AM, FMH kagba2...@yahoo.com wrote:
Hi,
Thank you for your response. I'm looking for the names of the
colors denoted by these codes and what do these colors represent for.
For instance, if we use topo.colors(5) in the image function, five
different colors will be used in which its codes are denoted as:
[1] #4C00 #004C #00E5 #00FF4DFF #00FF
So, my first question is what type of color do these codes represent
for? Are they white, red,...?
My second question is, if we use this topo.colors(5) in image function to
denote the temperature values for intance, what are these colors represent
for? Does the first color, #4C00 represent the lower/medium/higher
temperature?
I do hope you could advice me on this matter?
Thank you
Fir
- Original Message
From: FMH kagba2...@yahoo.com
To: Steve Lianoglou mailinglist.honey...@gmail.com
Sent: Sunday, September 6, 2009 3:41:02 PM
Subject: Re: [R] Color index in image function
Hi,
Thank you for your response. I'm looking for the name of the colors denoted
by this code and what are these colors representing for.
For instance, if we use topo.colors(5) in the image function, five
different colors will be used in which its codes are denoted as:
[1] #4C00 #004C #00E5 #00FF4DFF #00FF
So, my first question is what type of color does these codes represent
for? Are they white, red,...?
My second question is, if we use this topo.colors(5) in image function to
denote the temperature values for intance, what are these colors represent
for? Does the first color, #4C00 represent the lower/medium/higher
temperature?
I do hope you could advice me on this matter?
Thank you
Fir
- Original Message
From: Steve Lianoglou mailinglist.honey...@gmail.com
To: FMH kagba2...@yahoo.com
Cc: r-help@r-project.org
Sent: Sunday, September 6, 2009 3:20:25 PM
Subject: Re: [R] Color index in image function
Hi,
On Sat, Sep 5, 2009 at 7:06 AM, FMHkagba2...@yahoo.com wrote:
Dear All,
I was looking for the color index in image function, such as from
topo.colors(n) and etc. but still never found it. For instance, from the
help menu.
The answer is in the code:
###
# Volcano data visualized as matrix. Need to transpose and flip
# matrix horizontally.
image(t(volcano)[ncol(volcano):1,])
# A prettier display of the volcano
x - 10*(1:nrow(volcano))
y - 10*(1:ncol(volcano))
image(x, y, volcano, col = terrain.colors(100), axes = FALSE)
Right here:
R terrrain.colors(100)
[1] #00A600FF #03A700FF #07A800FF #0AAA00FF #0EAB00FF ...
Is that what you mean?
-steve
--
Steve Lianoglou
Graduate Student: Computational Systems Biology
| Memorial Sloan-Kettering Cancer Center
| Weill Medical College of Cornell University
Contact Info:
http://cbio.mskcc.org/~lianos/contacthttp://cbio.mskcc.org/%7Elianos/contact
__
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https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Henrique Dallazuanna
Curitiba-Paraná-Brasil
25° 25' 40 S 49° 16' 22 O
[[alternative HTML version deleted]]
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] How can I appoint a small part of the whole data
Dear baptiste, many thanks for your suggestions ! best, yichih 2009/9/5, baptiste auguie baptiste.aug...@googlemail.com: Hi, you have two problems in your first scenario, 1- Wrong operator precedence. For example, 1 == 2 | 3 [1] TRUE where 1==2 is tested as FALSE, but 1 is not tested against 3 for equality as it would be using, 1 == 2 | 1 == 3 [1] FALSE or using %in% 2:3 Instead, R evaluates FALSE | 3, and 2- it so happens that non-zero integers are treated as TRUE, according to ?| as.logical(1) [1] TRUE as.logical(0) [1] FALSE HTH, baptiste 2009/9/5 Yichih Hsieh yichih.hs...@gmail.com Dear all, I got another problem: if education have five levels edu=1 edu=2 edu=3 edu=4 edu=5 If I want to appoint y=edu2~4 in 1990 which programs is correct? I tried this two programs, they both work, but two results is different. 1. fig2b-reldist(y=mu1990$wage[mu1990$edu==2|3|4],..) 2. fig2b-reldist(y=mu1990$wage[mu1990$edu%in%2:4],..) which one is correct? and why they have different results? All help high appreciated. best, Yichih 2009/9/5 Yichih Hsieh yichih.hs...@gmail.com Dear Petr, your suggestion is useful many thanks for your help ! best, Yichih 2009/9/3 Petr PIKAL petr.pi...@precheza.cz Hi use any of suitable selection ways that are in R. E.g. data[data$gender==1, ] selects only female values data$wage[(data$gender==1) (data$race=1)] selects black female wages. and see also ?subset Regards Petr r-help-boun...@r-project.org napsal dne 03.09.2009 10:51:59: Dear all, I have 1980~1990 eleven datas, every year have three variables, wage gender(1=female, 2=male) race(1=black, 2=white) My original commands is: fig2b-reldist(y=mu1990$wage,yo=mu1980$wage,...) I have three questions: 1. If I want to appoint y=women's wage in 1990 yo=women's wage in 1980 2. If I want to appoint y=women's wage in 1990 yo=men's wage in 1990 3. If I want to appoint y=black women's wage in 1990 yo=white women's wage in 1990 How can I modify the commands? All help highly appreciated. Best, Yichih -- Yichih Hsieh e-mail : yichih.hs...@gmail.com [[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.htmlhttp://www.r-project.org/posting-guide.html http://www.r-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Yichih Hsieh e-mail : yichih.hs...@gmail.com -- Yichih Hsieh e-mail : yichih.hs...@gmail.com [[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.htmlhttp://www.r-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- _ Baptiste Auguié School of Physics University of Exeter Stocker Road, Exeter, Devon, EX4 4QL, UK http://newton.ex.ac.uk/research/emag __ -- Yichih Hsieh e-mail : yichih.hs...@gmail.com [[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 can I appoint a small part of the whole data
Dear Mark, many thanks for your suggestions ! best, yichih -- Yichih Hsieh e-mail : yichih.hs...@gmail.com [[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] [Hmisc] Latex to pdf
Jeroen Ooms j.c.l.ooms at uu.nl writes: [...] Output written on file643c9869.dvi (1 page, 372 bytes). Transcript written on file643c9869.log. Error: Can't open display: The can't open display-error rather looks like an X11-problem. Are you reglar user on that system ? Try to look at the dvi with your dvi-viewer. xdvi, kdvi or something like that. Ciao, Oliver __ 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] Color index in image function
By default the z-values are split into equal ranges to match the number of colors. The first color is then for first interval from min(z) etc. Look at the code for image.default for clarity - there seems to be some influence from the oldstyle parameter. If you want to be 100% sure about which colors match which range, consider specifying the ranges in breaks. Schalk Heunis On Sun, Sep 6, 2009 at 4:50 PM, FMHkagba2...@yahoo.com wrote: Hi, Thank you for your response. I'm looking for the names of the colors denoted by these codes and what do these colors represent for. For instance, if we use topo.colors(5) in the image function, five different colors will be used in which its codes are denoted as: [1] #4C00 #004C #00E5 #00FF4DFF #00FF So, my first question is what type of color do these codes represent for? Are they white, red,...? My second question is, if we use this topo.colors(5) in image function to denote the temperature values for intance, what are these colors represent for? Does the first color, #4C00 represent the lower/medium/higher temperature? I do hope you could advice me on this matter? Thank you Fir - Original Message From: FMH kagba2...@yahoo.com To: Steve Lianoglou mailinglist.honey...@gmail.com Sent: Sunday, September 6, 2009 3:41:02 PM Subject: Re: [R] Color index in image function Hi, Thank you for your response. I'm looking for the name of the colors denoted by this code and what are these colors representing for. For instance, if we use topo.colors(5) in the image function, five different colors will be used in which its codes are denoted as: [1] #4C00 #004C #00E5 #00FF4DFF #00FF So, my first question is what type of color does these codes represent for? Are they white, red,...? My second question is, if we use this topo.colors(5) in image function to denote the temperature values for intance, what are these colors represent for? Does the first color, #4C00 represent the lower/medium/higher temperature? I do hope you could advice me on this matter? Thank you Fir - Original Message From: Steve Lianoglou mailinglist.honey...@gmail.com To: FMH kagba2...@yahoo.com Cc: r-help@r-project.org Sent: Sunday, September 6, 2009 3:20:25 PM Subject: Re: [R] Color index in image function Hi, On Sat, Sep 5, 2009 at 7:06 AM, FMHkagba2...@yahoo.com wrote: Dear All, I was looking for the color index in image function, such as from topo.colors(n) and etc. but still never found it. For instance, from the help menu. The answer is in the code: ### # Volcano data visualized as matrix. Need to transpose and flip # matrix horizontally. image(t(volcano)[ncol(volcano):1,]) # A prettier display of the volcano x - 10*(1:nrow(volcano)) y - 10*(1:ncol(volcano)) image(x, y, volcano, col = terrain.colors(100), axes = FALSE) Right here: R terrrain.colors(100) [1] #00A600FF #03A700FF #07A800FF #0AAA00FF #0EAB00FF ... Is that what you mean? -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact __ 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] linear mixed model question
Hello, I wanted to fit a linear mixed model to a data that is similar in terms of design to the 'Machines' data in 'nlme' package except that each worker (with triplicates) only operates one machine. I created a subset of observations from 'Machines' data such that it looks the same as the data I wanted to fit the model with (see code below). I fitted a model in which 'Machine' was a fixed effect and 'Worker' was random (intercept), which ran perfectly. Then I decided to complicate the model a little bit by fitting 'Worker' within 'Machine', which was saying variation among workers was nested within each machine. The model could be fitted by 'lme', but when I tried to get confidence intervals by 'intervals(fm2)' it gave me an error: Error in intervals.lme(fm2) : Cannot get confidence intervals on var-cov components: Non-positive definite approximate variance-covariance I am wondering if this is because it is impossible to fit a model like 'fm2' or there is some other reasons? Thanks a lot! Wen # library(nlme) data(Machines) new.data = Machines[c(1:6, 25:30, 49:54), ] fm1 = lme(score ~ Machine, random = ~1|Worker, data = new.data) fm1 fm2 = lme(score ~ Machine, random = ~Machine-1|Worker, data = new.data) fm2 intervals(fm2) __ 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 figure the type of a variable?
Hi, I want to know what is there returned values of 'lm'. 'class' and 'lm' does not show that the returned value has the variable coefficients, etc. I am wondering what is the command to show the detailed information. If possible, I aslo want the lower level information. For example, I want to show that 'coefficients' is a named list and it has 2 elements. Regards, Peng x=1:10 y=1:10 r=lm(x~y) class(r) [1] lm mode(r) [1] list r Call: lm(formula = x ~ y) Coefficients: (Intercept)y 1.123e-151.000e+00 r$coefficients[1] (Intercept) 1.123467e-15 r$coefficients[[1]] [1] 1.123467e-15 r$coefficients[2] y 1 r$coefficients[[2]] [1] 1 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to figure the type of a variable?
On 06/09/2009 12:33 PM, Peng Yu wrote: Hi, I want to know what is there returned values of 'lm'. 'class' and 'lm' does not show that the returned value has the variable coefficients, etc. I am wondering what is the command to show the detailed information. If possible, I aslo want the lower level information. For example, I want to show that 'coefficients' is a named list and it has 2 elements. Try the str() function, it shows a summary of the structure of an object. Duncan Murdoch Regards, Peng x=1:10 y=1:10 r=lm(x~y) class(r) [1] lm mode(r) [1] list r Call: lm(formula = x ~ y) Coefficients: (Intercept)y 1.123e-151.000e+00 r$coefficients[1] (Intercept) 1.123467e-15 r$coefficients[[1]] [1] 1.123467e-15 r$coefficients[2] y 1 r$coefficients[[2]] [1] 1 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to figure the type of a variable?
Dear Peng, Perhaps str(r) is what you are looking for. HTH, Jorge On Sun, Sep 6, 2009 at 12:33 PM, Peng Yu pengyu...@gmail.com wrote: Hi, I want to know what is there returned values of 'lm'. 'class' and 'lm' does not show that the returned value has the variable coefficients, etc. I am wondering what is the command to show the detailed information. If possible, I aslo want the lower level information. For example, I want to show that 'coefficients' is a named list and it has 2 elements. Regards, Peng x=1:10 y=1:10 r=lm(x~y) class(r) [1] lm mode(r) [1] list r Call: lm(formula = x ~ y) Coefficients: (Intercept)y 1.123e-151.000e+00 r$coefficients[1] (Intercept) 1.123467e-15 r$coefficients[[1]] [1] 1.123467e-15 r$coefficients[2] y 1 r$coefficients[[2]] [1] 1 __ 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 pop up the graphics window from Rscript?
I get the following error. $ Rscript plot.R x=1:10 y=1:10 windows() Error: could not find function windows Execution halted On Sun, Sep 6, 2009 at 11:59 AM, RIOS,ALFREDO ARTUROar...@ufl.edu wrote: maybe windows() On Sun Sep 06 12:53:14 EDT 2009, Peng Yu pengyu...@gmail.com wrote: Hi, I am wondering how to pop up the graphics window from Rscript. I run the following code, but I don't see the graphics window, even transiently. Regards, Peng $ Rscript plot.R x=1:10 y=1:10 plot(x,y) __ 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. -- RIOS,ALFREDO ARTURO __ 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 refer the element in a named list?
On 06/09/2009 1:04 PM, Peng Yu wrote: Hi, I thought that 'coefficients' is a named list, but I can not refer to its element by something like r$coefficients$y. I used str() to check r. It says the following. Can somebody let me know what it means? The line that matters is the one $ coefficients : Named num [1:2] 1.12e-15 1.00 It says that coefficients is a numeric (num) vector, not a list. So r$coefficients[y] will extract the y coefficient. Duncan Murdoch ..- attr(*, names)= chr [1:2] (Intercept) y $ Rscript lm.R x=1:10 y=1:10 r=lm(x~y) class(r) [1] lm mode(r) [1] list r Call: lm(formula = x ~ y) Coefficients: (Intercept)y 1.123e-151.000e+00 r$coefficients[1] (Intercept) 1.123467e-15 r$coefficients[[1]] [1] 1.123467e-15 r$coefficients[2] y 1 r$coefficients[[2]] [1] 1 str(r) List of 12 $ coefficients : Named num [1:2] 1.12e-15 1.00 ..- attr(*, names)= chr [1:2] (Intercept) y Regards, Peng __ 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 pop up the graphics window from Rscript?
Perhaps you should read the Posting Guide (again?) and then adopt a consistent practice of including system information in your questions to r-help. Not everyone keeps a mental list of what OS you are using. Graphics commands are highly OS specific. capabilities() # at an interactive R prompt anyway, will return a list of devices for your system. You may want X11() since you are on a Linux box, but my experience on Linux is virtually nil, so that's a guess based on reading prior postings. -- David. On Sep 6, 2009, at 1:07 PM, Peng Yu wrote: I get the following error. $ Rscript plot.R x=1:10 y=1:10 windows() Error: could not find function windows Execution halted On Sun, Sep 6, 2009 at 11:59 AM, RIOS,ALFREDO ARTUROar...@ufl.edu wrote: maybe windows() On Sun Sep 06 12:53:14 EDT 2009, Peng Yu pengyu...@gmail.com wrote: Hi, I am wondering how to pop up the graphics window from Rscript. I run the following code, but I don't see the graphics window, even transiently. Regards, Peng $ Rscript plot.R x=1:10 y=1:10 plot(x,y) __ David Winsemius, MD Heritage Laboratories West Hartford, CT __ 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 pop up the graphics window from Rscript?
Try this (contents of plot.R): png(mygraphic.png) plot(1:10) dev.off() browseURL(mygraphic.png) It will pop up the graphic in a browser window. On Sun, Sep 6, 2009 at 12:53 PM, Peng Yupengyu...@gmail.com wrote: Hi, I am wondering how to pop up the graphics window from Rscript. I run the following code, but I don't see the graphics window, even transiently. Regards, Peng $ Rscript plot.R x=1:10 y=1:10 plot(x,y) __ 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 refer the element in a named list?
On Sep 6, 2009, at 1:35 PM, Duncan Murdoch wrote: On 06/09/2009 1:04 PM, Peng Yu wrote: Hi, I thought that 'coefficients' is a named list, but I can not refer to its element by something like r$coefficients$y. I used str() to check r. It says the following. Can somebody let me know what it means? The line that matters is the one $ coefficients : Named num [1:2] 1.12e-15 1.00 It says that coefficients is a numeric (num) vector, not a list. So r$coefficients[y] will extract the y coefficient. And r$coefficients[`(Intercept)`] # note back-quote, should get you the intercept ?coef Generally coef(fit) will extract model coefficients across a wider range of R model objects. Duncan Murdoch ..- attr(*, names)= chr [1:2] (Intercept) y $ Rscript lm.R x=1:10 y=1:10 r=lm(x~y) class(r) [1] lm mode(r) [1] list r Call: lm(formula = x ~ y) Coefficients: (Intercept)y 1.123e-151.000e+00 r$coefficients[1] (Intercept) 1.123467e-15 r$coefficients[[1]] [1] 1.123467e-15 r$coefficients[2] y 1 r$coefficients[[2]] [1] 1 str(r) List of 12 $ coefficients : Named num [1:2] 1.12e-15 1.00 ..- attr(*, names)= chr [1:2] (Intercept) y Regards, Peng __ 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. David Winsemius, MD Heritage Laboratories West Hartford, CT __ 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] [Hmisc] Latex to pdf
On 9/6/09, Jeroen Ooms j.c.l.o...@uu.nl wrote: I would like to print some tables and figures to a PDF device on a CentOS 5 vps. However, I cannot seem to get the latex function from Hmisc working. I There is also xtable() for transferring tables to LaTeX. Liviu __ 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 wait for a user response in Rscript?
Hi Peng I think this is what you are looking for par(ask=T) Alfredo On Sun Sep 06 12:52:31 EDT 2009, Peng Yu pengyu...@gmail.com wrote: Hi, In 'example(barplot)' running in R, I see 'Hit Return to see next plot:', then R waits for my input. I am wondering how to wait for a user response in Rscript. Regards, Peng __ 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. -- RIOS,ALFREDO ARTURO __ 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 wait for a user response in Rscript?
Hi, In 'example(barplot)' running in R, I see 'Hit Return to see next plot:', then R waits for my input. I am wondering how to wait for a user response in Rscript. Regards, Peng __ 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 pop up the graphics window from Rscript?
maybe windows() On Sun Sep 06 12:53:14 EDT 2009, Peng Yu pengyu...@gmail.com wrote: Hi, I am wondering how to pop up the graphics window from Rscript. I run the following code, but I don't see the graphics window, even transiently. Regards, Peng $ Rscript plot.R x=1:10 y=1:10 plot(x,y) __ 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. -- RIOS,ALFREDO ARTURO __ 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 refer the element in a named list?
Hi, I thought that 'coefficients' is a named list, but I can not refer to its element by something like r$coefficients$y. I used str() to check r. It says the following. Can somebody let me know what it means? ..- attr(*, names)= chr [1:2] (Intercept) y $ Rscript lm.R x=1:10 y=1:10 r=lm(x~y) class(r) [1] lm mode(r) [1] list r Call: lm(formula = x ~ y) Coefficients: (Intercept)y 1.123e-151.000e+00 r$coefficients[1] (Intercept) 1.123467e-15 r$coefficients[[1]] [1] 1.123467e-15 r$coefficients[2] y 1 r$coefficients[[2]] [1] 1 str(r) List of 12 $ coefficients : Named num [1:2] 1.12e-15 1.00 ..- attr(*, names)= chr [1:2] (Intercept) y Regards, Peng __ 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 wait for a user response in Rscript?
On 06/09/2009 12:52 PM, Peng Yu wrote: Hi, In 'example(barplot)' running in R, I see 'Hit Return to see next plot:', then R waits for my input. I am wondering how to wait for a user response in Rscript. Rscript doesn't run R interactively, so I doubt if there's a way to do this. Rterm has the --ess option that asserts interactive use when reading piped input, so you might be able to do something like Rterm --ess script.R but that's not the intended use, so you may find other problems. If you want interactive use but don't want the full Rterm or Rgui, you really should be writing your own front-end. It's not trivial, but it's not impossible either, and there are samples included with the R sources. Duncan Murdoch __ 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 pop up the graphics window from Rscript?
Hi, I am wondering how to pop up the graphics window from Rscript. I run the following code, but I don't see the graphics window, even transiently. Regards, Peng $ Rscript plot.R x=1:10 y=1:10 plot(x,y) __ 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 pop up the graphics window from Rscript?
On Sep 6, 2009, at 1:42 PM, Gabor Grothendieck wrote: Try this (contents of plot.R): png(mygraphic.png) plot(1:10) dev.off() browseURL(mygraphic.png) It will pop up the graphic in a browser window. On a Mac that shows up in a Preview window. The X11() device does open a plot on a Mac when this file is submitted: x=1:10 y=1:10 X11() plot(x,y) dev.off() I was under the impression that no surrounding box was displayed since the points were visible for several seconds before the window disappeared. But testing from a GUI session, I see that the X11 device takes a long time to draw the axes, which has a side-effect in the Rscript session of displaying the points for several seconds and the axes for only milliseconds. -- David. Mac OS 10.5.7/R 2.9.1 Patched (2009-07-04 r48897) On Sun, Sep 6, 2009 at 12:53 PM, Peng Yupengyu...@gmail.com wrote: Hi, I am wondering how to pop up the graphics window from Rscript. I run the following code, but I don't see the graphics window, even transiently. Regards, Peng $ Rscript plot.R x=1:10 y=1:10 plot(x,y) David Winsemius, MD Heritage Laboratories West Hartford, CT __ 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] Creating mixed line and point graphs with xyplot
I think you have a couple of typos. Should it not be par(new=True) points(x,b) --- On Sat, 9/5/09, jim holtman jholt...@gmail.com wrote: From: jim holtman jholt...@gmail.com Subject: Re: [R] Creating mixed line and point graphs with xyplot To: Paul Sweeting m...@paulsweeting.co.uk Cc: r-help@r-project.org Received: Saturday, September 5, 2009, 6:37 PM I would use the base plot routine plot(x,c, type='l', ylim=range(a,c)) points(x,a) park(new=TRUE) plot(x,d,type='l', ylim=range(b,d), axes=FALSE,ylab='', xlab='') pints(x,b) axis(4) On Fri, Sep 4, 2009 at 11:28 AM, Paul Sweetingm...@paulsweeting.co.uk wrote: Hi Well, I think the title says it all! I've looked through the documentation but I can't find a way of doing this. The situation is that I have 4 series, say a, b, c and d. Series a and c are plotted on the lh y axis, series b and d are plotted on the rh (secondary) y axis. I've worked out how to do this. However, I need to plot series a and b a points (symbols only, no line), whislt c and d need plotting as lines (with no symbols). What is the easiest way to do this in xyplot? Or should I be using something else? Thanks! Paul __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem that you are trying to solve? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ Looking for the perfect gift? Give the gift of Flickr! http://www.flickr.com/gift/ __ 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] Creating mixed line and point graphs with xyplot
On Sep 6, 2009, at 3:03 PM, John Kane wrote: I think you have a couple of typos. Should it not be par(new=True) points(x,b) Probably not True --- On Sat, 9/5/09, jim holtman jholt...@gmail.com wrote: From: jim holtman jholt...@gmail.com Subject: Re: [R] Creating mixed line and point graphs with xyplot To: Paul Sweeting m...@paulsweeting.co.uk Cc: r-help@r-project.org Received: Saturday, September 5, 2009, 6:37 PM I would use the base plot routine plot(x,c, type='l', ylim=range(a,c)) points(x,a) park(new=TRUE) plot(x,d,type='l', ylim=range(b,d), axes=FALSE,ylab='', xlab='') pints(x,b) axis(4) On Fri, Sep 4, 2009 at 11:28 AM, Paul Sweetingm...@paulsweeting.co.uk wrote: Hi Well, I think the title says it all! I've looked through the documentation but I can't find a way of doing this. The situation is that I have 4 series, say a, b, c and d. Series a and c are plotted on the lh y axis, series b and d are plotted on the rh (secondary) y axis. I've worked out how to do this. However, I need to plot series a and b a points (symbols only, no line), whislt c and d need plotting as lines (with no symbols). What is the easiest way to do this in xyplot? Or should I be using something else? Thanks! Paul __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem that you are trying to solve? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ Looking for the perfect gift? Give the gift of Flickr! http://www.flickr.com/gift/ __ 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. David Winsemius, MD Heritage Laboratories West Hartford, CT __ 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] eps file with embedded font
I am going back to Simone's original query (though this will split the thread) because subsequent replies did not include his original. Some comments interspersed below; the main response at the end. I have had some private correspondence with Simone, who sent me two of his files that exhibit the problem, and this has enabled me to form an idea of where the trouble may lie. It would seem that either there is something seriously wrong with the function embedFonts(), or with ghostscript when executing the command generated by embedFonts(), or with both. I shal descibe the results of my esperminets, in the hope that some expert in embedFonts(), or in ghostscript, or in both, can make a useful suggestion. On 04-Sep-09 14:01:44, Simone Gabbriellini wrote: Dear list, I am trying to make eps file with embedded font. I use: postscript(ranking-exp-all.eps, horizontal=TRUE, onefile=FALSE, paper=special, height=8, width=12, family=Helvetica) # plot stuff dev.off() since R does not embed font, I then use: embedFonts(file=indegdistr.eps, outfile=indegdistrEMB.eps, fontpaths=System/Library/Fonts) I think Simone intended to use a different filename here, probably embedFonts(file=ranking-exp-all.eps, outfile=ranking-exp-all-EMB.eps, fontpaths=System/Library/Fonts) in line with his previous command above. This is not important here. the problem is that the second file, with font embedded, is cutted near the end, and the very last part of the plots and the border are off the page... In fact the bottom of the graphic is slightly clipped when viewed in ghostview, and the righthand side is severely clipped. I use R 2.8.1 on a Mac OSX any help more than welcome, regards, Simone Ths problem Simone encountered can be reproduced in a simple way as follows. postscript(file=test1.eps,family=Times,horizontal=FALSE, paper=special,width=10,height=5) plot(c(0,1,2),c(0,1,4),main=Test Plot,xlab=X,ylab=Y) dev.off() If I view this file test1.eps in ghostsript (using 'gv', on Linux), I see it fine. There is a nice clearance all round (about 24 points above the Test Plot title, about 6 points to the left of the Y y-axis label, about 30 points below the X x-axis label, and about 30 points to the right of the plot frame. The BoundingBox line in test1.eps is %%BoundingBox: 0 0 720 360 so it is indeed 10 inches wide and 5 inches high, as requested. So far, so good. Now I do the equivalent of Simone's embedFonts() command: embedFonts(file=test1.eps,format=pswrite, outfile=test1-EMB.eps) and view the result of this in 'gv'. The left, top and bottom of the plot just fit in (there is a miniscule space left around them), but the right-hand side of the plot is severely cropped. Instead of seeing the x-axis out to 2.0, with the right-hand side of the frame, and a little bit of space, it is truncated around x = 1.75 The BoundingBox in test1-EMB.eps is specified in the lines: %%BoundingBox: 4 18 595 336 %%HiResBoundingBox: 4.60 18.70 595.00 335.30 so the BBox 0 0 720 360 from test1.eps has been slightly trimmed on the left, substantially (18 points) from below and (14 points) from above, and hugely (125 points = 1.74 inches) from the right. The lesser trimmings on the left, bottom and top can be put down, perhaps, to ghostscript putting the BoundingBox just outside the marks on the page; but *not* the bad cropping of the right-hand side, since marks which ought to be included are way outside it. Next I tried editing a copy test1B-EMB.eps of test1-EMB.eps, to change the BoundingBox to what it ought to be (0 0 720,360). The ghostscript window now encloises the full BoundingBox, but the righthand part is blank (only what can be seen in test1-EMB.eps is shown, i.e. up to x = 1.75 approx, with what should be seen beyond this being totally blank). It follows that, despite the BoundingBox now being the correct one (and of course the BBox is a clipping-path for display in gv), there is additional clipping being done in the PostScript generate by ghostscript as a result of embedFonts(). Looking into the PostScript in test1-EMB.eps (or test1B-EMB.eps), there are several occurrenfces of clip therein. However, the additional PostScript generated by ghostscript is very obscure, and I cannot decipher what is going on. It next occurred to me that one may be able to add ghostsctript options to the call to embedFonts(), to try to ensure that it would respect the original BoundingBox. The command generated by embedFonts(file=test1.eps,format=pswrite, outfile=test1-EMB.eps) is: gs -dNOPAUSE -dBATCH -q -dAutoRotatePages=/None -sDEVICE=pswrite \ -sOutputFile=/tmp/RtmplPWs8l/Rembed24b931bd -sFONTPATH= test1.eps A quick study of the ghostscript documentation revealed the existence of some EPS Parameters, of which the only one that seemed relevant was: -dEPSCrop Crop an EPS file to the bounding box.
Re: [R] Combining expressions.
Many thanks to Gabor Grothendieck and William Dunlap who both
solved my problem for me, right rapidly!
cheers,
Rolf Turner
##
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[R] Two packages in one method
Hi!
I want to use one method combinations from gtools package but in my code
I must use also dprep method where is method combinations too. Mayby I
show you result my help function:
Help on topic 'combinations' was found in the following packages:
Package Library
dprep /usr/lib64/R/library
gtools/usr/lib64/R/library
Choose one
1: Constructing distinct permutations {dprep}
2: Enumerate the Combinations or Permutations of the Elements of a Vector
{gtools}
If I want to use combination method I use error:
combinations(3,2,letters[1:3])
Error in combinations(3, 2, letters[1:3]) :
unused argument(s) (2, letters[1:3])
Do you have any idea?
I try code similar to C++ gtools::combinations but in my opinion it's
wrong way.
If my explanation is't clear to you let me show my all attempts:
library(gtools)
combinations(3,2,letters[1:3])
[,1] [,2]
[1,] a b
[2,] a c
[3,] b c
library(dprep)
Loading required package: MASS
Loading required package: nnet
Loading required package: lattice
Loading required package: class
Attaching package: 'dprep'
The following object(s) are masked from package:gtools :
combinations
combinations(3,2,letters[1:3])
Error in combinations(3, 2, letters[1:3]) :
unused argument(s) (2, letters[1:3])
gtools::combinations
function (n, r, v = 1:n, set = TRUE, repeats.allowed = FALSE)
{
if (mode(n) != numeric || length(n) != 1 || n 1 || (n%%1) !=
0)
stop(bad value of n)
if (mode(r) != numeric || length(r) != 1 || r 1 || (r%%1) !=
0)
stop(bad value of r)
if (!is.atomic(v) || length(v) n)
stop(v is either non-atomic or too short)
if ((r n) repeats.allowed == FALSE)
stop(r n and repeats.allowed=FALSE)
if (set) {
v - unique(sort(v))
if (length(v) n)
stop(too few different elements)
}
v0 - vector(mode(v), 0)
if (repeats.allowed)
sub - function(n, r, v) {
if (r == 0)
v0
else if (r == 1)
matrix(v, n, 1)
else if (n == 1)
matrix(v, 1, r)
else rbind(cbind(v[1], Recall(n, r - 1, v)), Recall(n -
1, r, v[-1]))
}
else sub - function(n, r, v) {
if (r == 0)
v0
else if (r == 1)
matrix(v, n, 1)
else if (r == n)
matrix(v, 1, n)
else rbind(cbind(v[1], Recall(n - 1, r - 1, v[-1])),
Recall(n - 1, r, v[-1]))
}
sub(n, r, v[1:n])
}
environment: namespace:gtools
combinations(3,2,letters[1:3]) ### what I should do to
start working combinations?
Error in combinations(3, 2, letters[1:3]) :
unused argument(s) (2, letters[1:3])
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[R] avoid NA in list
Hi! I Have list, for example: ... [[22]] [1] 27 51 69 107 119 [[23]] [1] NA [[24]] [1] 54 57 62 And I would like to avoid NA value. Similar way like I may do it in vector using na.value() function. Do you have any idea? -- View this message in context: http://www.nabble.com/avoid-NA-in-list-tp25321020p25321020.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] Creating adjacency matrix from a data frame
Dear R-list, Sorry for spamming the list, but I am just learning how to manipulate data in R, so if this is a trivial question I am sorry. I have the following data which list the distance between capitals: ida idb kmdist 7108UK BEL 313 7110UK FRN 365 7116UK POR 1618 I would like to convert this into an a valued adjacency matrix that looks like this: BEL FRN POR UK 313 365 1618 The full data set has all possible pairings between countries, so the end goal should be a symmetric adjacency matrix. Thank you, Thomas Jensen __ 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] Creating adjacency matrix from a data frame
Try this: xtabs(kmdist ~ ida + idb, data = x) On Sun, Sep 6, 2009 at 5:12 PM, Thomas Jensen thomas.jen...@eup.gess.ethz.ch wrote: Dear R-list, Sorry for spamming the list, but I am just learning how to manipulate data in R, so if this is a trivial question I am sorry. I have the following data which list the distance between capitals: ida idb kmdist 7108UKBEL313 7110UKFRN365 7116UKPOR 1618 I would like to convert this into an a valued adjacency matrix that looks like this: BEL FRN POR UK 313 365 1618 The full data set has all possible pairings between countries, so the end goal should be a symmetric adjacency matrix. Thank you, Thomas Jensen __ 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. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O [[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] How many attributes are there of a variable?
Hi, According to the example below this email, attr(x,names) is the same as names(x). I am wondering how many attributes there are of a given variable. How to find out what they are? Can I always use some_attribute(x) instead of attr(x, some_attribute)? Regards, Peng x=c(1,2,3) attr(x,names)=c(a,b,c) x a b c 1 2 3 y=c(1,2,3) names(y)=c(a,b,c) y a b c 1 2 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.
Re: [R] How to refer the element in a named list?
On 06/09/2009 1:45 PM, David Winsemius wrote: On Sep 6, 2009, at 1:35 PM, Duncan Murdoch wrote: On 06/09/2009 1:04 PM, Peng Yu wrote: Hi, I thought that 'coefficients' is a named list, but I can not refer to its element by something like r$coefficients$y. I used str() to check r. It says the following. Can somebody let me know what it means? The line that matters is the one $ coefficients : Named num [1:2] 1.12e-15 1.00 It says that coefficients is a numeric (num) vector, not a list. So r$coefficients[y] will extract the y coefficient. And r$coefficients[`(Intercept)`] # note back-quote, should get you the intercept No, that says to get the element of the coefficients whose index is stored in a variable named `(Intercept)`. (Chances are that variable doesn't exist, unless you made an effort to create it. And if you perversely stored y in it you'd get the same coefficient as before!) You want regular (single or double, R doesn't care) quotes to say that you are giving the index directly: r$coefficients[(Intercept)] Duncan Murdoch ?coef Generally coef(fit) will extract model coefficients across a wider range of R model objects. Duncan Murdoch ..- attr(*, names)= chr [1:2] (Intercept) y $ Rscript lm.R x=1:10 y=1:10 r=lm(x~y) class(r) [1] lm mode(r) [1] list r Call: lm(formula = x ~ y) Coefficients: (Intercept)y 1.123e-151.000e+00 r$coefficients[1] (Intercept) 1.123467e-15 r$coefficients[[1]] [1] 1.123467e-15 r$coefficients[2] y 1 r$coefficients[[2]] [1] 1 str(r) List of 12 $ coefficients : Named num [1:2] 1.12e-15 1.00 ..- attr(*, names)= chr [1:2] (Intercept) y Regards, Peng __ 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. David Winsemius, MD Heritage Laboratories West Hartford, CT __ 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] Two packages ane one method
You have tried
gtools::combinations(3,2,letters[1:3])
?
On Sun, Sep 6, 2009 at 2:10 PM, Grzes gregori...@gmail.com wrote:
Hi!
I want to use one method combinations from gtools package but in my
code
I must use also dprep method where is method combinations too. Mayby I
show you result of help function:
Help on topic 'combinations' was found in the following packages:
Package Library
dprep /usr/lib64/R/library
gtools/usr/lib64/R/library
Choose one
1: Constructing distinct permutations {dprep}
2: Enumerate the Combinations or Permutations of the Elements of a Vector
{gtools}
If I want to use combination method I use error:
combinations(3,2,letters[1:3])
Error in combinations(3, 2, letters[1:3]) :
unused argument(s) (2, letters[1:3])
Do you have any idea?
I try code similar to C++ gtools::combinations but in my opinion it's
wrong way.
If my explanation is't clear to you let me show my all attempts:
library(gtools)
combinations(3,2,letters[1:3])
[,1] [,2]
[1,] a b
[2,] a c
[3,] b c
library(dprep)
Loading required package: MASS
Loading required package: nnet
Loading required package: lattice
Loading required package: class
Attaching package: 'dprep'
The following object(s) are masked from package:gtools :
combinations
combinations(3,2,letters[1:3])
Error in combinations(3, 2, letters[1:3]) :
unused argument(s) (2, letters[1:3])
gtools::combinations
function (n, r, v = 1:n, set = TRUE, repeats.allowed = FALSE)
{
if (mode(n) != numeric || length(n) != 1 || n 1 || (n%%1) !=
0)
stop(bad value of n)
if (mode(r) != numeric || length(r) != 1 || r 1 || (r%%1) !=
0)
stop(bad value of r)
if (!is.atomic(v) || length(v) n)
stop(v is either non-atomic or too short)
if ((r n) repeats.allowed == FALSE)
stop(r n and repeats.allowed=FALSE)
if (set) {
v - unique(sort(v))
if (length(v) n)
stop(too few different elements)
}
v0 - vector(mode(v), 0)
if (repeats.allowed)
sub - function(n, r, v) {
if (r == 0)
v0
else if (r == 1)
matrix(v, n, 1)
else if (n == 1)
matrix(v, 1, r)
else rbind(cbind(v[1], Recall(n, r - 1, v)), Recall(n -
1, r, v[-1]))
}
else sub - function(n, r, v) {
if (r == 0)
v0
else if (r == 1)
matrix(v, n, 1)
else if (r == n)
matrix(v, 1, n)
else rbind(cbind(v[1], Recall(n - 1, r - 1, v[-1])),
Recall(n - 1, r, v[-1]))
}
sub(n, r, v[1:n])
}
environment: namespace:gtools
combinations(3,2,letters[1:3]) ### what I should do to
start working combinations?
Error in combinations(3, 2, letters[1:3]) :
unused argument(s) (2, letters[1:3])
--
View this message in context:
http://www.nabble.com/Two-packages-ane-one-method-tp25319739p25319739.html
Sent from the R help mailing list archive at Nabble.com.
__
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PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Henrique Dallazuanna
Curitiba-Paraná-Brasil
25° 25' 40 S 49° 16' 22 O
[[alternative HTML version deleted]]
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] avoid NA in list
Try this: your_list[!is.na(your_list)] On Sun, Sep 6, 2009 at 4:32 PM, Grzes gregori...@gmail.com wrote: Hi! I Have list, for example: ... [[22]] [1] 27 51 69 107 119 [[23]] [1] NA [[24]] [1] 54 57 62 And I would like to avoid NA value. Similar way like I may do it in vector using na.value() function. Do you have any idea? -- View this message in context: http://www.nabble.com/avoid-NA-in-list-tp25321020p25321020.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. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O [[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 refer the element in a named list?
On Sun, Sep 6, 2009 at 12:45 PM, David Winsemiusdwinsem...@comcast.net wrote: On Sep 6, 2009, at 1:35 PM, Duncan Murdoch wrote: On 06/09/2009 1:04 PM, Peng Yu wrote: Hi, I thought that 'coefficients' is a named list, but I can not refer to its element by something like r$coefficients$y. I used str() to check r. It says the following. Can somebody let me know what it means? The line that matters is the one $ coefficients : Named num [1:2] 1.12e-15 1.00 It says that coefficients is a numeric (num) vector, not a list. So r$coefficients[y] will extract the y coefficient. And r$coefficients[`(Intercept)`] # note back-quote, should get you the intercept Back-quotes do not work. r$coefficients[`(Intercept)`] Error: object '(Intercept)' not found r$coefficients[(Intercept)] (Intercept) 1.123467e-15 ?coef Generally coef(fit) will extract model coefficients across a wider range of R model objects. Duncan Murdoch ..- attr(*, names)= chr [1:2] (Intercept) y $ Rscript lm.R x=1:10 y=1:10 r=lm(x~y) class(r) [1] lm mode(r) [1] list r Call: lm(formula = x ~ y) Coefficients: (Intercept) y 1.123e-15 1.000e+00 r$coefficients[1] (Intercept) 1.123467e-15 r$coefficients[[1]] [1] 1.123467e-15 r$coefficients[2] y 1 r$coefficients[[2]] [1] 1 str(r) List of 12 $ coefficients : Named num [1:2] 1.12e-15 1.00 ..- attr(*, names)= chr [1:2] (Intercept) y Regards, Peng __ 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. David Winsemius, MD Heritage Laboratories West Hartford, CT __ 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 many attributes are there of a variable?
Peng, You can create all the attributes you want, with one headache: R does not keep attributes across subsetting operations so you need to write classes and [.something methods when attributions need to be kept or adjusted upon subsetting rows. The Hmisc package uses attributes such as label, units, imputed. You might look at the code to see how it did that. For example, label(x) will use attr(x, 'label') to fetch the 'label' attribute. There are attribute-setting functions there too. Frank Peng Yu wrote: Hi, According to the example below this email, attr(x,names) is the same as names(x). I am wondering how many attributes there are of a given variable. How to find out what they are? Can I always use some_attribute(x) instead of attr(x, some_attribute)? Regards, Peng x=c(1,2,3) attr(x,names)=c(a,b,c) x a b c 1 2 3 y=c(1,2,3) names(y)=c(a,b,c) y a b c 1 2 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. -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University __ 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 wait for a user response in Rscript?
Hi, The following script will run without asking me anything. $ Rscript plot.R x=1:10 y=1:10 X11() plot(x,y) par(ask=T) Regards, Peng On Sun, Sep 6, 2009 at 11:55 AM, RIOS,ALFREDO ARTUROar...@ufl.edu wrote: Hi Peng I think this is what you are looking for par(ask=T) Alfredo On Sun Sep 06 12:52:31 EDT 2009, Peng Yu pengyu...@gmail.com wrote: Hi, In 'example(barplot)' running in R, I see 'Hit Return to see next plot:', then R waits for my input. I am wondering how to wait for a user response in Rscript. Regards, Peng __ 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. -- RIOS,ALFREDO ARTURO __ 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] avoid NA in list
Tena koe Alternatively, for instances where you have a list element which is a vector of all NA: grzes - list(a=1:4, b=NA, c=letters[1:5], d=c(1,NA,10), e=rep(NA,5)) grzes $a [1] 1 2 3 4 $b [1] NA $c [1] a b c d e $d [1] 1 NA 10 $e [1] NA NA NA NA NA grzes[sapply(grzes, function(x) !all(is.na(x)))] $a [1] 1 2 3 4 $c [1] a b c d e $d [1] 1 NA 10 grzes[!is.na(grzes)] $a [1] 1 2 3 4 $c [1] a b c d e $d [1] 1 NA 10 $e [1] NA NA NA NA NA HTH ... Peter Alspach -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Henrique Dallazuanna Sent: Monday, 7 September 2009 8:37 a.m. To: Grzes Cc: r-help@r-project.org Subject: Re: [R] avoid NA in list Try this: your_list[!is.na(your_list)] On Sun, Sep 6, 2009 at 4:32 PM, Grzes gregori...@gmail.com wrote: Hi! I Have list, for example: ... [[22]] [1] 27 51 69 107 119 [[23]] [1] NA [[24]] [1] 54 57 62 And I would like to avoid NA value. Similar way like I may do it in vector using na.value() function. Do you have any idea? -- View this message in context: http://www.nabble.com/avoid-NA-in-list-tp25321020p25321020.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. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O [[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 wait for a user response in Rscript?
Hello Peng Yu, Invert the order of plot and par. See below: x=1:10 y=1:10 X11() par(ask=T) plot(x,y) That should wait for some user input. I hope that helps, Joshua On Sun, Sep 6, 2009 at 2:23 PM, Peng Yu pengyu...@gmail.com wrote: Hi, The following script will run without asking me anything. $ Rscript plot.R x=1:10 y=1:10 X11() plot(x,y) par(ask=T) Regards, Peng On Sun, Sep 6, 2009 at 11:55 AM, RIOS,ALFREDO ARTUROar...@ufl.edu wrote: Hi Peng I think this is what you are looking for par(ask=T) Alfredo On Sun Sep 06 12:52:31 EDT 2009, Peng Yu pengyu...@gmail.com wrote: Hi, In 'example(barplot)' running in R, I see 'Hit Return to see next plot:', then R waits for my input. I am wondering how to wait for a user response in Rscript. Regards, Peng __ 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.htmlhttp://www.r-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- RIOS,ALFREDO ARTURO __ 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.htmlhttp://www.r-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Joshua Wiley Senior in Psychology University of California, Riverside http://www.joshuawiley.com/ [[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 wait for a user response in Rscript?
Sorry, did not realize that it was for Rscript -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Peng Yu Sent: Sunday, September 06, 2009 5:24 PM To: r-h...@stat.math.ethz.ch Subject: Re: [R] How to wait for a user response in Rscript? Hi, The following script will run without asking me anything. $ Rscript plot.R x=1:10 y=1:10 X11() plot(x,y) par(ask=T) Regards, Peng On Sun, Sep 6, 2009 at 11:55 AM, RIOS,ALFREDO ARTUROar...@ufl.edu wrote: Hi Peng I think this is what you are looking for par(ask=T) Alfredo On Sun Sep 06 12:52:31 EDT 2009, Peng Yu pengyu...@gmail.com wrote: Hi, In 'example(barplot)' running in R, I see 'Hit Return to see next plot:', then R waits for my input. I am wondering how to wait for a user response in Rscript. Regards, Peng __ 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. -- RIOS,ALFREDO ARTURO __ 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] Nested Fixed Effects - basic questions
You will have to talk to your local statistician/econometrician. Given that you say you will have three observations per student, your description of the data is incomplete. Therefore, it is impossible to tell what the right approach would be. Assumed that all observations are independent, you would fit fix3 as one dummy/factor variable (not fix1 or fix2), and then you would test linear hypotheses for sums of certain coefficients against sums of other coefficients in your case. Nested effects are what you can specify as random effects, afaik; you don't fit them in fixed-effects analyses (rather you would take the outlined linear-hypothesis approach). As far as I can tell from your post, your understanding of the subject matter is limited. As I said, you will have to get yourself an overview of the topic and search for materials that explain a.) nested effects and b.) the application of nested effects in R (e.g. with the nlme and lme4 libraries). So go ahead and put in the effort. Daniel ps: on a more general note, the R-help list is to help with the implementation in R rather than statistical/econometric questions, especially if these problems are extensive. - cuncta stricte discussurus - _ Von: Jojo Ziggy [mailto:jojo.zi...@yahoo.com] Gesendet: Saturday, September 05, 2009 2:14 PM An: Daniel Malter Betreff: Re: AW: [R] Nested Fixed Effects - basic questions Nesting would imply something like students nested in class nested in school, where each student is only member of one class and each class only member of one school. Yes, I think this is actually what I have going on - I guess I did not represent that correctly in the data table. So... I gather my data shown properly as nested effects should actually look more like: fix1fix2fix3response 00016.596 00016.564 00122.665 00122.801 01216.000 01215.930 01321.739 01321.628 12416.260 12416.128 12522.969 12523.245 13614.687 13614.635 13722.954 13723.345 In this case, how do I tell R that the effects are nested, as opposed to unnested? And how do I specify that they are fixed and not random effects? Will it somehow know automatically? I will in the end have 3 observations for each student - so 24 datapoints in this example. Certainly nothing close to 160, however. Thanks, jojo _ From: Daniel Malter dan...@umd.edu To: Jojo Ziggy jojo.zi...@yahoo.com; r-help@r-project.org Sent: Friday, September 4, 2009 4:37:14 PM Subject: AW: [R] Nested Fixed Effects - basic questions In R and experimental or mixed-model terminology, your lm model specifies fixed effects. As long as each data row represents a unique subject, you are fine with lm. If not, you have to account for the repeated measurement of subjects and will need other methods (potentially involving random effects). In your model, you perform a dummy variable OLS (ordinary least squares) regression. Mixed-effects models that allow for a combination of fixed and random effects or random-effects-only analyses are most prominently done with Doug Bates's nlme or lme4 libraries (though, there are more libraries that allow for mixed-effects modeling). Google for some manuals. Further, your effects are not nested. If each row stands for a different unit of observation (e.g., subject), and if subjects are randomized into treatments fix1, fix2, and fix3, then you have a completely randomized factorial design (CRF). Nesting would imply something like students nested in class nested in school, where each student is only member of one class and each class only member of one school. Then your fix columns should look like (with 8 students nested in 4 classes nested in 2 schools): fix1 fix2 fix3 111 211 321 421 532 632 742 842 Thus, your effects are really not nested (at least not for what you show us as the data). What you can do to figure out whether not only fix1 and fix2 have an independent effect, but also whether fix1 and fix2 interact in their effect on your response, you can include interaction effects. However, if the data you provided is your entire dataset, you will likely overfit the model and inflate the standard errors if you include all possible interactions (eats up 4 degrees of freedom) along with the direct effects and intercept (also 4 degrees of freedom), given that your provided data has only 16 observations. Example: #Simulate data fix1=rep(0:1,each=8) fix2=rep(c(0,0,1,1),4) fix3=rep(0:1,8) e=rnorm(16) #Dependent variable y=-1*fix1+2*fix2+1*fix3-0.75*fix1*fix2+0.9*fix1*fix3-2*fix2*fix3+1.5*fix1*fi x2*fix3+e #Run regression and show output reg0=lm(y~(fix1+fix2+fix3)^3) #all interactions up to three-way summary(reg0) #note that this is not very
[R] CRAN (and crantastic) updates this week
CRAN (and crantastic) updates this week New packages * AICcmodavg (1.01) Marc J. Mazerolle http://crantastic.org/packages/AICcmodavg This package includes functions to create model selection tables based on Akaike's information criterion (AIC) and the second-order AIC (AICc), as well as their quasi-likelihood counterparts (QAIC, QAICc). Tables are printed with delta AIC and Akaike weights. The package also includes functions to conduct model averaging (multimodel inference) for a given parameter of interest or predicted values. Other handy functions enable the computation of relative variable importance, evidence ratios, and confidence sets for the best model. The present version works with lm, glm, and lme object classes. * amer (0.5) Fabian Scheipl http://crantastic.org/packages/amer Fitting generalized additive mixed models based on the mixed model algorithm of lme4 * frbf (0.9) Fernando Martins http://crantastic.org/packages/frbf Flexible kernerl for radial basis function network implementation. * GGMselect (0.1-0) Annie Bouvier http://crantastic.org/packages/GGMselect GGMselect is a package dedicated to graph estimation in Gaussian Graphical Models. The main functions return the adjacency matrix of an undirected graph estimated from a data matrix. * lemma (1.2-1) Haim Bar http://crantastic.org/packages/lemma LEMMA is used to detect nonnull genes - genes for which the average response in treatment group 1 is significantly different from the average response in group 2, in normalized microarray data. LEMMA is an implementation of an approximate EM algorithm to estimate the parameters in the assumed linear model in Bar, Booth, Schifano, Wells (2009). Updated packages AICcmodavg (1.01), betareg (2.0-0), BioIDMapper (1.2), boolean (2.0-1), boolean (2.0-0), boot (1.2-39), cem (1.0.111), clue (0.3-30), DAKS (2.0-0), dcemri (0.10.5), dplR (1.1.9.1), drc (1.7-7), epicalc (2.9.2.0), etm (0.4-6), exams (1.0-2), feature (1.2.4), GenABEL (1.4-4), gnumeric (0.5-2), gputools (0.1-3), hash (0.40), Hmisc (3.7-0), Iso (0.0-7), ISOcodes (0.2-5), KernSmooth (2.23-3), longitudinalData (0.6), mapReduce (1.02), MCMCglmm (1.11), meta (1.0-6), mhsmm (0.3.0), multmod (0.5), nleqslv (1.5), nlme (3.1-94), OAIHarvester (0.0-5), orientlib (0.9.3), phmm (0.6), R.matlab (1.2.5), rainbow (1.4), Rcplex (0.2-3), relations (0.5-4), rgdal (0.6-17), Rmpfr (0.1-6), RWeka (0.3-21), sdef (1.2), SigWinR (1.0.1), simecol (0.6-9), simFrame (0.1.1), skmeans (0.1-1), Snowball (0.0-7), spgrass6 (0.6-8), spgrass6 (0.6-9), SubpathwayMiner (2.0), tau (0.0-3), tau (0.0-2), TeachingSampling (1.0.2), tsDyn (0.7-1), tseries (0.10-19), ttrTests (1.1), YourCast (1.1-2) New reviews --- * wavethresh, by cranktastic http://crantastic.org/reviews/27 This email provided as a service for the R community by http://crantastic.org. Like it? Hate it? Please let us know: crana...@gmail.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] Is there a package for generating standardized R script command line options?
Hi, In python, there is a package that helps generating command line options. I am wondering if there is such a package in R that helps generating the command options for a R script? http://docs.python.org/library/optparse.html Regards, Peng __ 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] Is there a package for generating standardized R script command line options?
Check out the getopt package on CRAN. On Sun, Sep 6, 2009 at 8:28 PM, Peng Yupengyu...@gmail.com wrote: Hi, In python, there is a package that helps generating command line options. I am wondering if there is such a package in R that helps generating the command options for a R script? http://docs.python.org/library/optparse.html Regards, Peng __ 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] Why tempdir() always give me the same results in the same session?
Hi, tempdir() always gives me the same result. Should it give a different result each time I call it? tempdir() [1] /tmp/RtmppB72wH tempdir() [1] /tmp/RtmppB72wH Regards, Peng __ 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] Why this statement does not print anything in an if-statement that includes 'q()'?
Hi,
I run the following script. I don't understand why the second
'length(args)' does not show anything but the first one shows '0'. Is
it because the command 'q()' affects anything in the if-statement.
However, if I change the second 'length(args)' to
'print(length(args))', the script will print the length of 'args'. Can
somebody let me know what is the difference between the 'print(x)'
statement and the 'x' statement where 'x' is a variable?
Regards,
Peng
$ Rscript not_print_in_if_block.R
args=commandArgs(T)
length(args)
[1] 0
if(length(args)!=3){
+ length(args)
+ q()
+ }
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Re: [R] Why tempdir() always give me the same results in the same session?
Peng Yu wrote: tempdir() always gives me the same result. Should it give a different result each time I call it? The help page for tempdir() contains the following explanation of the return value: ?tempdir ... For tempdir, the path of the per-session temporary directory. I would interpret that to mean that each time you start R a temporary directory is assigned which retains a static value until you close R and then open it again later. -Charlie - Charlie Sharpsteen Undergraduate Environmental Resources Engineering Humboldt State University -- View this message in context: http://www.nabble.com/Why-tempdir%28%29-always-give-me-the-same-results-in-the-same-session--tp25323681p25323805.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] Why this statement does not print anything in an if-statement that includes 'q()'?
You need to explicitly 'print' the second 'length' function call.
Only at the top level of the interactive session is the value of an
object printed out if you just reference the object.
On Sun, Sep 6, 2009 at 9:13 PM, Peng Yupengyu...@gmail.com wrote:
Hi,
I run the following script. I don't understand why the second
'length(args)' does not show anything but the first one shows '0'. Is
it because the command 'q()' affects anything in the if-statement.
However, if I change the second 'length(args)' to
'print(length(args))', the script will print the length of 'args'. Can
somebody let me know what is the difference between the 'print(x)'
statement and the 'x' statement where 'x' is a variable?
Regards,
Peng
$ Rscript not_print_in_if_block.R
args=commandArgs(T)
length(args)
[1] 0
if(length(args)!=3){
+ length(args)
+ q()
+ }
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
What is the problem that you are trying to solve?
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Re: [R] struggling with split function
Found a mistake - it was mine! Thanks a lot for your help! On Sun, Sep 6, 2009 at 8:43 AM, Dimitri Liakhovitskild7...@gmail.com wrote: Thanks a lot, Dimitris. It totally works on my example data frame. I know, it's probably hard to address, but when I try to apply it to the real huge data frame I have, after the last line I get: Error in `[.default`(x$A, na.ind, -1) : incorrect number of dimensions. I know it's impossible to answer this question without seeing the data, but still: what do you think might be wrong? Do you think it could be because my first column contains something else but the split? No, I've just run the table on A and it is: split NA 204 6356 I also checked the first dimension of x and the length(na.ind) - the are the same length: 6560. No idea where the error might lye... Thanks a lot! Dimitri On Sun, Sep 6, 2009 at 5:43 AM, Dimitris Rizopoulosd.rizopou...@erasmusmc.nl wrote: one way is the following: ind - rle(is.na(x$A)) ind - rep(seq_along(ind$lengths), ind$lengths) na.ind - is.na(x$A) split(x[na.ind, -1], ind[na.ind]) I hope it helps. Best, Dimitris Dimitri Liakhovitski wrote: I am very sorry for such a simple question, but I am struggling with split. I have the following data frame: x-data.frame(A=c(NA,NA,NA,NA,split,NA,NA,NA,NA,split,NA,NA,NA,NA,split,NA,NA,NA,NA), B=c(Name1,text1,text2,text3,NA,Name2,text1,text2,text3,NA,Name3,text1,text2,text3,NA,Name4,text1,text2,text3), C=c(NA,1,NA,3,NA,NA,4,5,6,NA,NA,7,8,9,NA,NA,3,3,3),D=c(NA,1,1,2,NA,NA,5,6,NA,NA,NA,9,8,7,NA,NA,2,2,2), E=c(NA,3,2,1,NA,NA,6,5,4,NA,NA,7,7,8,NA,NA,1,NA,1)) print(x) All I want to do is to split x, i.e., to create a list of data frames that are currently separated by the word split in column A. In this example, it would be 4 data frames, the first of them being: A B C D E NA Name1 NA NA NA NA text1 1 1 3 NA text 2 NA 1 2 NA text3 3 2 1 etc. I tried: split(x, x$A) split(x,x$A == 'split') split(x,!is.na(x$A)) But nothing produces what I need. Tanks a lot for any hint! -- Dimitris Rizopoulos Assistant Professor Department of Biostatistics Erasmus University Medical Center Address: PO Box 2040, 3000 CA Rotterdam, the Netherlands Tel: +31/(0)10/7043478 Fax: +31/(0)10/7043014 -- Dimitri Liakhovitski Ninah.com dimitri.liakhovit...@ninah.com -- Dimitri Liakhovitski Ninah.com dimitri.liakhovit...@ninah.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] Plot 2 ecdf in one graph
Hi r-users, I would like to compare the cdf between historical and predicted. My x.obs and x.pre are the frequency data in classes of 0-300. I tried: plot(ecdf(x.obs),ecdf(x.pre),type=l,col=red) and it gives me: Error in plot.stepfun(x, ..., ylab = ylab, verticals = verticals, pch = pch) : argument 4 matches multiple formal arguments Thank you so much for any help given. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Plot 2 ecdf in one graph
Two things:
(1) type=l won't work; plot.ecdf() calls plot.stepfun() and it
doesn't have a ``type'' argument.
(2) Giving plot two separate objects to plot makes no sense at all.
(3) If you've got ***frequency*** data then ecdf() is probably not
the right thing to do
in the first place.
(4) I can't count.
To get the ***plots** you want, do something like:
plot(ecdf(x.pre),do.points=FALSE,col=red,xlim=range(x.pre,x.obs))
plot(ecdf(x.obs),do.points=FALSE,col=blue,add=TRUE)
But as I said if x.obs and x.pre are counts, rather than the raw
data, this
does not appear to make any sense. You are getting the ecdf-s of the
counts
rather than of the raw data which is a toadally different story. And
toadally
misleading. Re-think.
cheers,
Rolf Turner
On 7/09/2009, at 1:52 PM, Roslina Zakaria wrote:
Hi r-users,
I would like to compare the cdf between historical and predicted.
My x.obs and x.pre are the frequency data in classes of 0-300.
I tried:
plot(ecdf(x.obs),ecdf(x.pre),type=l,col=red)
and it gives me:
Error in plot.stepfun(x, ..., ylab = ylab, verticals = verticals,
pch = pch) :
argument 4 matches multiple formal arguments
Thank you so much for any help given.
##
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Re: [R] DOE in R?
I attempted to use the package algdesign. I used the following code. However, the results were very much not matching the reference I noted (which is located at http://www2.sas.com/proceedings/sugi31/196-31.pdf). Instead of 30 design points, I received 25 and those that were returned, only half or so matched the reference. I am inexperienced with optimal designs so I dont know if I am doing something wrong, the package is not the correct one for the task or a combination. Here is the code in case anyone has any input: #CODE: runif(1) #for a bug in program (assumes random seed object exists) dat-gen.factorial(c(3,3,3,3,2),varNames=c(Intro,Duration,GOTO,Fee,Color)) dat #show design plan desD-optFederov(~Intro+Duration+GOTO+Fee+Color+quad(Intro)+quad(Duration)+quad(GOTO)+quad(Fee)+Intro*Duration+Intro*GOTO+Intro*Fee+Intro*Color+Duration*GOTO+Duration*Fee+Duration*Color+GOTO*Fee+GOTO*Color+Fee*Color,dat,crit=D,maxIteration=1000,eval=TRUE) #D desD$D #design desD$design design-desD$design Subject: Re: [R] DOE in R? From: c...@datanalytics.com To: b_mi...@live.com CC: r-help@r-project.org Date: Sun, 6 Sep 2009 14:57:36 +0200 Hello, This is your starting point: http://cran.r-project.org/web/views/ExperimentalDesign.html Best regards, Carlos J. Gil Bellosta http://www.datanalytics.com On Thu, 2009-09-03 at 17:38 -0700, B_miner wrote: Hello! This is not a topic I am well versed in but required to become well versed in...I welcome any assistance! Using R, I want to create an optimal design for an experiment. I'll be analyzing the results with logistic regression or some generalized linear model. I am thinking that the algdesign package can help (but no idea where to start?). I'm presenting an example here that I have seen the answer to (in SAS) in order to make sure I would have gotten it *right*. There are 5 factors: 4 are quantitative with three levels each and 1 is qualitative with two levels. Factor and levels: Intro: 0, 1.99, 2.99 Duration: 6, 9 ,12 GOTO: 3.99, 4.99, 5.99 Fee: 0, 15, 45 Color: Red, White In order to screen these factors, I would want to get a design where I could evaluate all main effects, all first order interactions and the squared terms of Intro, Duration, GOTO and FEE (for example Intro*Intro). Looking for the D-optimal design. Is this something that R can provide? These are, according to the SAS paper I read the following: Obs intro duration goto fee color 1 0.00 6 3.99 0 WHITE 2 0.00 6 3.99 45 RED 3 0.00 6 5.99 0 RED 4 0.00 6 5.99 45 WHITE 5 0.00 9 3.99 45 RED 6 0.00 9 4.99 15 WHITE 7 0.00 9 5.99 0 RED 8 0.00 12 3.99 0 RED 9 0.00 12 3.99 45 WHITE 10 0.00 12 5.99 0 WHITE 11 0.00 12 5.99 45 RED 12 0.00 12 5.99 45 WHITE 13 1.99 6 3.99 15 RED 14 1.99 6 4.99 45 WHITE 15 1.99 6 5.99 0 WHITE 16 1.99 9 5.99 45 RED 17 1.99 12 3.99 0 WHITE 18 1.99 12 5.99 15 RED 19 2.99 6 3.99 0 WHITE 20 2.99 6 3.99 45 WHITE 21 2.99 6 4.99 0 RED 22 2.99 6 5.99 15 WHITE 23 2.99 6 5.99 45 RED 24 2.99 9 3.99 0 RED 25 2.99 12 3.99 15 WHITE 26 2.99 12 3.99 45 RED 27 2.99 12 4.99 0 WHITE 28 2.99 12 4.99 45 RED 29 2.99 12 5.99 0 RED 30 2.99 12 5.99 45 WHITE _ Windows Live: Make it easier for your friends to see what youre up to on Facebook. http://windowslive.com/Campaign/SocialNetworking?ocid=PID23285::T:WLMTAGL:ON:WL:en-US:SI_SB_facebook:082009 [[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] get the command line
Hi, commandArgs gives me the arguments. I am wondering what command can give the whole command line. Regards, Peng __ 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] get the command line
Hi, On Sun, Sep 6, 2009 at 11:25 PM, Peng Yupengyu...@gmail.com wrote: Hi, commandArgs gives me the arguments. I am wondering what command can give the whole command line. What does the whole command line mean? Are you looking for the command args in one string? paste(commandArgs(), collapse= ) Can you give an example of what you're trying to get? -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact __ 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] get the command line
On Sun, Sep 6, 2009 at 10:50 PM, Steve Lianogloumailinglist.honey...@gmail.com wrote: Hi, On Sun, Sep 6, 2009 at 11:25 PM, Peng Yupengyu...@gmail.com wrote: Hi, commandArgs gives me the arguments. I am wondering what command can give the whole command line. What does the whole command line mean? Are you looking for the command args in one string? paste(commandArgs(), collapse= ) Can you give an example of what you're trying to get? For example, I run the following command in bash. Rscript some_script.R a b c I want to get the string Rscript some_script.R a b c in the script some_script.R. Regards, Peng __ 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] get the command line
On Mon, Sep 7, 2009 at 12:00 AM, Peng Yupengyu...@gmail.com wrote: On Sun, Sep 6, 2009 at 10:50 PM, Steve Lianogloumailinglist.honey...@gmail.com wrote: Hi, On Sun, Sep 6, 2009 at 11:25 PM, Peng Yupengyu...@gmail.com wrote: Hi, commandArgs gives me the arguments. I am wondering what command can give the whole command line. What does the whole command line mean? Are you looking for the command args in one string? paste(commandArgs(), collapse= ) Can you give an example of what you're trying to get? For example, I run the following command in bash. Rscript some_script.R a b c I want to get the string Rscript some_script.R a b c in the script some_script.R. If I print each arg in commandArgs() on its own line, when I call: Rscript test.R a b c I get: /Library/Frameworks/R.framework/Resources/bin/exec/i386/R --slave --no-restore --file=test.R --args a b c From that you can reconstruct the command line pretty easily, except for the missing Rscript part ... is that what's concerning you? I'm not sure how you would go about getting the Rscript, if that's what you're after ... -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact __ 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] (no subject)
Hi r-users, I would like to know how to put all the data that is greater than certain value in certain cell for my histogram. For example, since maximum value of p1 is 588 it doesn't fit in the breaks that we specified. Can we write breaks 300? max(p1[,2]) pre.hist - hist(p1[,2],breaks = c(0,50,100,150,200,250,300),right=FALSE) max(p1) [1] 587.2761 pre.hist - hist(p1[,2],breaks = c(0,50,100,150,200,250,300),right=FALSE) Error in hist.default(p1[, 2], breaks = c(0, 50, 100, 150, 200, 250, 300), : some 'x' not counted; maybe 'breaks' do not span range of 'x' max(p1[,2]) [1] 587.2761 Thank you. [[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] (no subject)
Hi Roslina, x-runif(1000,min=0, max=600) hist(x) x2-ifelse(x=300,x,300) summary(x2) hist(x2, ,breaks = c(0,50,100,150,200,250,300)) good luck milton On Mon, Sep 7, 2009 at 12:51 AM, Roslina Zakaria zrosl...@yahoo.com wrote: Hi r-users, I would like to know how to put all the data that is greater than certain value in certain cell for my histogram. For example, since maximum value of p1 is 588 it doesn't fit in the breaks that we specified. Can we write breaks 300? max(p1[,2]) pre.hist - hist(p1[,2],breaks = c(0,50,100,150,200,250,300),right=FALSE) max(p1) [1] 587.2761 pre.hist - hist(p1[,2],breaks = c(0,50,100,150,200,250,300),right=FALSE) Error in hist.default(p1[, 2], breaks = c(0, 50, 100, 150, 200, 250, 300), : some 'x' not counted; maybe 'breaks' do not span range of 'x' max(p1[,2]) [1] 587.2761 Thank you. [[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.htmlhttp://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] (no subject)
May be you also want: x-runif(1000,min=0, max=600) x3-x[x=300] summary(x3) hist(x3, ,breaks = c(0,50,100,150,200,250,300)) bests milton On Mon, Sep 7, 2009 at 1:01 AM, milton ruser milton.ru...@gmail.com wrote: Hi Roslina, x-runif(1000,min=0, max=600) hist(x) x2-ifelse(x=300,x,300) summary(x2) hist(x2, ,breaks = c(0,50,100,150,200,250,300)) good luck milton On Mon, Sep 7, 2009 at 12:51 AM, Roslina Zakaria zrosl...@yahoo.comwrote: Hi r-users, I would like to know how to put all the data that is greater than certain value in certain cell for my histogram. For example, since maximum value of p1 is 588 it doesn't fit in the breaks that we specified. Can we write breaks 300? max(p1[,2]) pre.hist - hist(p1[,2],breaks = c(0,50,100,150,200,250,300),right=FALSE) max(p1) [1] 587.2761 pre.hist - hist(p1[,2],breaks = c(0,50,100,150,200,250,300),right=FALSE) Error in hist.default(p1[, 2], breaks = c(0, 50, 100, 150, 200, 250, 300), : some 'x' not counted; maybe 'breaks' do not span range of 'x' max(p1[,2]) [1] 587.2761 Thank you. [[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.htmlhttp://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.
