[R] How to display an image on RGL plot?
Hi all. It's been a long time since I wrote to this list. Glad to see the R project well and working. I am working with a 3D plot similar to this: http://old.nabble.com/file/p26525258/rgl-device.png rgl-device.png The underlying picture is a JPEG image, loaded with the rimage package and coerced to the matrix. Spheres denote control points, collected from this picture and must be situated over the certain points of the image. I display the image with rgl.points. In case of the standard video camera image (704x576) it has to display over 40 points which is rather slow and memory consuming. How can I put an original JPEG on this plot? Another problem is that the picture is color initially, but was converted to the grayscale. I'd like to preserve colors. Any hints would be appreciated. -- View this message in context: http://old.nabble.com/How-to-display-an-image-on-RGL-plot--tp26525258p26525258.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] How to display an image on RGL plot?
Hi all. It's been a long time since I wrote to this list. Glad to see the R project well and working. I am working with a 3D plot similar to this: http://old.nabble.com/file/p26525259/rgl-device.png rgl-device.png The underlying picture is a JPEG image, loaded with the rimage package and coerced to the matrix. Spheres denote control points, collected from this picture and must be situated over the certain points of the image. I display the image with rgl.points. In case of the standard video camera image (704x576) it has to display over 40 points which is rather slow and memory consuming. How can I put an original JPEG on this plot? Another problem is that the picture is color initially, but was converted to the grayscale. I'd like to preserve colors. Any hints would be appreciated. -- View this message in context: http://old.nabble.com/How-to-display-an-image-on-RGL-plot--tp26525259p26525259.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] How to display an image on RGL plot?
Hi all. It's been a long time since I wrote to this list. Glad to see the R project well and working. I am working with a 3D plot similar to this: http://old.nabble.com/file/p26525263/rgl-device.png rgl-device.png The underlying picture is a JPEG image, loaded with the rimage package and coerced to the matrix. Spheres denote control points, collected from this picture and must be situated over the certain points of the image. I display the image with rgl.points. In case of the standard video camera image (704x576) it has to display over 40 points which is rather slow and memory consuming. How can I put an original JPEG on this plot? Another problem is that the picture is color initially, but was converted to the grayscale. I'd like to preserve colors. Any hints would be appreciated. -- View this message in context: http://old.nabble.com/How-to-display-an-image-on-RGL-plot--tp26525263p26525263.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] How to display an image on RGL plot?
Hi all. It's been a long time since I wrote to this list. Glad to see the R project well and working. I am working with a 3D plot similar to this: http://old.nabble.com/file/p26525269/rgl-device.png rgl-device.png The underlying picture is a JPEG image, loaded with the rimage package and coerced to the matrix. Spheres denote control points, collected from this picture and must be situated over the certain points of the image. I display the image with rgl.points. In case of the standard video camera image (704x576) it has to display over 40 points which is rather slow and memory consuming. How can I put an original JPEG on this plot? Another problem is that the picture is color initially, but was converted to the grayscale. I'd like to preserve colors. Any hints would be appreciated. -- View this message in context: http://old.nabble.com/How-to-display-an-image-on-RGL-plot--tp26525269p26525269.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] How to display an image on RGL plot?
Hi all. It's been a long time since I wrote to this list. Glad to see the R project well and working. I am working with a 3D plot similar to this: http://old.nabble.com/file/p26525261/rgl-device.png rgl-device.png The underlying picture is a JPEG image, loaded with the rimage package and coerced to the matrix. Spheres denote control points, collected from this picture and must be situated over the certain points of the image. I display the image with rgl.points. In case of the standard video camera image (704x576) it has to display over 40 points which is rather slow and memory consuming. How can I put an original JPEG on this plot? Another problem is that the picture is color initially, but was converted to the grayscale. I'd like to preserve colors. Any hints would be appreciated. -- View this message in context: http://old.nabble.com/How-to-display-an-image-on-RGL-plot--tp26525261p26525261.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] How to display an image on RGL plot?
Hi all. It's been a long time since I wrote to this list. Glad to see the R project well and working. I am working with a 3D plot similar to this: http://old.nabble.com/file/p26525260/rgl-device.png rgl-device.png The underlying picture is a JPEG image, loaded with the rimage package and coerced to the matrix. Spheres denote control points, collected from this picture and must be situated over the certain points of the image. I display the image with rgl.points. In case of the standard video camera image (704x576) it has to display over 40 points which is rather slow and memory consuming. How can I put an original JPEG on this plot? Another problem is that the picture is color initially, but was converted to the grayscale. I'd like to preserve colors. Any hints would be appreciated. -- View this message in context: http://old.nabble.com/How-to-display-an-image-on-RGL-plot--tp26525260p26525260.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] How to display an image on RGL plot?
Hi all. It's been a long time since I wrote to this list. Glad to see the R project well and working. I am working with a 3D plot similar to this: http://old.nabble.com/file/p26525268/rgl-device.png rgl-device.png The underlying picture is a JPEG image, loaded with the rimage package and coerced to the matrix. Spheres denote control points, collected from this picture and must be situated over the certain points of the image. I display the image with rgl.points. In case of the standard video camera image (704x576) it has to display over 40 points which is rather slow and memory consuming. How can I put an original JPEG on this plot? Another problem is that the picture is color initially, but was converted to the grayscale. I'd like to preserve colors. Any hints would be appreciated. -- View this message in context: http://old.nabble.com/How-to-display-an-image-on-RGL-plot--tp26525268p26525268.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to display an image on RGL plot?
Vladimir Eremeev wrote: Hi all. It's been a long time since I wrote to this list. Glad to see the R project well and working. The r-project would prefer to see one and only one copy of your post, though. I count five copies till now!!! -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - (p.dalga...@biostat.ku.dk) FAX: (+45) 35327907 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] How to display an image on RGL plot?
Hi all. It's been a long time since I wrote to this list. Glad to see the R project well and working. I am working with a 3D plot similar to this: http://old.nabble.com/file/p26525264/rgl-device.png rgl-device.png The underlying picture is a JPEG image, loaded with the rimage package and coerced to the matrix. Spheres denote control points, collected from this picture and must be situated over the certain points of the image. I display the image with rgl.points. In case of the standard video camera image (704x576) it has to display over 40 points which is rather slow and memory consuming. How can I put an original JPEG on this plot? Another problem is that the picture is color initially, but was converted to the grayscale. I'd like to preserve colors. Any hints would be appreciated. -- View this message in context: http://old.nabble.com/How-to-display-an-image-on-RGL-plot--tp26525264p26525264.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] Arrhenius Plot 2 with lattice
Hello,
sorry for incomplete code...
with this I read the file and calculate my stuff. I have a plenty of
them 80-300K every 5 Kelvin. I start with 79K, 80K...300K
test-read.table(T300_both.txt,header=FALSE,sep=)
RH2-c(RH2,2.5e7*.32e-4/100e-6/5100*(test$V3[c(2)]-test$V3[c(1)]+test
$V3[c(4)]-test$V3[c(3)]))
n2-c(n2,-1/(RH2[c(46)]*1.60217e-19))
PA2-c(1.1331/100e-6*.32e-4*(test$V1[c(2)]+test$V1[c(4)]-test
$V1[c(1)]-test$V1[c(3)]))
PB2-c(1.1331/100e-6*.32e-4*(test$V1[c(6)]+test$V1[c(8)]-test
$V1[c(5)]-test$V1[c(7)]))
P2-c(P2,(PA2+PB2)/2)
bew2-c(bew2,-RH2[c(46)]/P2[c(46)])
QA2-c(QA2,(test$V1[c(2)]-test$V1[c(1)])/(test$V1[c(4)]-test$V1[c(3)]))
QB2-c(QB2,(test$V1[c(6)]-test$V1[c(5)])/(test$V1[c(8)]-test$V1[c(7)]))
#...
Temp-c(79,80,85,90,95,100,106,110,115,120,125,132,135,140,145,151,156,160,165,170,175,180,185,190,195,200,206,210,216,220,225,230,235,240,247,250,255,261,265,270,275,280,285,290,295,300)
#Here I transform my data to make this Arrhenius Plot:
Temp2-c(1000/Temp)
n2log-c(log10(n2))
#This function should be plottet as log10(n)~1000/T into the data:
kurve2-function(T)2^-.5*sqrt(1e17*2*6*I(T^1.5)*(2*pi*0.689*9.109e-31*1.38e-23/43.9e-68)^1.5)*exp(-.047*1.6e-19/(2*1.38e-23*T))
#Here is the plot-function, but I don't know the argument for
#panel.curve()
trellis.device(jpeg,file=Tabh1.jpg,color=FALSE)
n2plot-xyplot(n2log~Temp2,xlab=list(label=1000/T
(1/K),fontsize=20),ylab=list(label=log(n/cm^3),fontsize=20),scales=list(cex=1.5),panel=function(){panel.xyplot(Temp2,n2log);panel.curve(kurve2)})
print(n2plot)
dev.off()
thanks
Markus
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[R] How to display an image on RGL plot?
Hi all. It's been a long time since I wrote to this list. Glad to see the R project well and working. I am working with a 3D plot similar to this: http://old.nabble.com/file/p26525266/rgl-device.png rgl-device.png The underlying picture is a JPEG image, loaded with the rimage package and coerced to the matrix. Spheres denote control points, collected from this picture and must be situated over the certain points of the image. I display the image with rgl.points. In case of the standard video camera image (704x576) it has to display over 40 points which is rather slow and memory consuming. How can I put an original JPEG on this plot? Another problem is that the picture is color initially, but was converted to the grayscale. I'd like to preserve colors. Any hints would be appreciated. -- View this message in context: http://old.nabble.com/How-to-display-an-image-on-RGL-plot--tp26525266p26525266.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to display an image on RGL plot?
On Thu, Nov 26, 2009 at 7:14 AM, Vladimir Eremeev wl2...@gmail.com wrote: The underlying picture is a JPEG image, loaded with the rimage package and coerced to the matrix. Spheres denote control points, collected from this picture and must be situated over the certain points of the image. I display the image with rgl.points. In case of the standard video camera image (704x576) it has to display over 40 points which is rather slow and memory consuming. How can I put an original JPEG on this plot? Another problem is that the picture is color initially, but was converted to the grayscale. I'd like to preserve colors. Try using surface3d with a flat surface (z=0) and a matrix of colours in the col= argument. See help(surface3d) for an example. Also STOP POSTING!!! There seems to be about 8 copies of your message in my inbox!!! 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] How to display an image on RGL plot?
Hi all. It's been a long time since I wrote to this list. Glad to see the R project well and working. I am working with a 3D plot similar to this: http://old.nabble.com/file/p26525271/rgl-device.png rgl-device.png The underlying picture is a JPEG image, loaded with the rimage package and coerced to the matrix. Spheres denote control points, collected from this picture and must be situated over the certain points of the image. I display the image with rgl.points. In case of the standard video camera image (704x576) it has to display over 40 points which is rather slow and memory consuming. How can I put an original JPEG on this plot? Another problem is that the picture is color initially, but was converted to the grayscale. I'd like to preserve colors. Any hints would be appreciated. -- View this message in context: http://old.nabble.com/How-to-display-an-image-on-RGL-plot--tp26525271p26525271.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] arg min ???
Petr that is what i was looking for.
Thanks
p.s. ak si nahodou z Prahy mas u mna Pivo
Petr Pikal wrote:
Hi
r-help-boun...@r-project.org napsal dne 25.11.2009 16:50:49:
This is nice, but i have to define vector of possible theta, this is not
what
i want to do.
I have vector of unknow parameters theta. I have som estimate of theta,
but
i want to do better estimate of them, using some criterion function.
I mean it is clasical argmin f(x_1,x_2,...x_n) to fit vector
(x_1,x_2...,x_n)`
I am not sure what you mean by argmin, but maybe you could look at ?optim
Regards
Petr
David Winsemius wrote:
On Nov 25, 2009, at 9:15 AM, Peterko wrote:
Is there function what aproximate vector of parameters some function
to
minimum ?
tet={tet1,tet2} i have they starting value
and i want to find the tet what minimalizing some function of tet ?
?which.min
Perhaps:
which.min( fn(tet) )
thanks
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David Winsemius, MD
Heritage Laboratories
West Hartford, CT
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[R] How to display an image on RGL plot?
Hi all. It's been a long time since I wrote to this list. Glad to see the R project well and working. I am working with a 3D plot similar to this: http://old.nabble.com/file/p26525270/rgl-device.png rgl-device.png The underlying picture is a JPEG image, loaded with the rimage package and coerced to the matrix. Spheres denote control points, collected from this picture and must be situated over the certain points of the image. I display the image with rgl.points. In case of the standard video camera image (704x576) it has to display over 40 points which is rather slow and memory consuming. How can I put an original JPEG on this plot? Another problem is that the picture is color initially, but was converted to the grayscale. I'd like to preserve colors. Any hints would be appreciated. -- View this message in context: http://old.nabble.com/How-to-display-an-image-on-RGL-plot--tp26525270p26525270.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] Concave hull
Dear David and other concave-hull-ists, yes, I meant concave hulls indeed. I know about the algorithm mentioed (www.concavehull.com) but it is not open source, so you cannot integrate it in R, and it is apparently patented, so even if you find the description you cannot apply it to implement a solution (even if patenting algorithms is at least questionable and has a rather patchy validity). Some questions / comments which applies to David's approach but in general even to convex hulls (question 2): 1) How do you extend it to n dimensions (in R)? 2) How do you do set calculus (horrible expression to mean: union, intersection, difference, and particularly membership, and so on ) on these hulls (in R)? Finally, I am at the moment using a gis to do it, but I did not find any command for concave hulls in grass. There is a rather long a convoluted way of doing them, but nearly impossible to automatise (see http://grass.osgeo.org/wiki/Create_concave_hull). Looking for the capability of extending it to the n-dimensional case does not sound right, because gis is thought for working in 2d/3d. Best, On Nov 26 2009, David Winsemius wrote: On Nov 25, 2009, at 7:51 PM, David Winsemius wrote: Drats; Forgot the plot: xx - runif(100, -1, 1) yy - abs(xx)+rnorm(100,0,.2); plot(xx,yy, xlim=c( min(xx)-sd(xx), max(xx)+sd(xx)), ylim =c( min(yy)-sd(yy), max(yy)+sd(yy))) dens2 - kde2d(xx, yy, lims=c(min(xx)-sd(xx), max(xx)+sd(xx), min(yy)-sd(yy), max(yy)+sd(yy) ) ) contour(dens2, add=TRUE) # You can pick a single contour if you like: contour(dens2, level=0.05, col=red, add=TRUE) contour(dens2, level=0.10, col=blue, add=TRUE) And as a further note you can drop the bandwidth and lower the density level to get a tighter fit: xx - runif(1, -1, 1) yy - abs(xx)+rnorm(1 ,0,.2); plot(xx,yy, xlim=c( min(xx)- sd(xx), max(xx)+sd(xx)), ylim =c( min(yy)-sd(yy), max(yy)+sd(yy)), cex=.2) dens2 - kde2d(xx, yy, lims=c(min(xx)-sd(xx), max(xx)+sd(xx), min(yy)- sd(yy), max(yy)+sd(yy) ) , h=c(bandwidth.nrd(xx)/4, bandwidth.nrd(xx)/ 4) ) contour(dens2, add=TRUE) # You can pick a single contour if you like: contour(dens2, level=0.05, col=red, add=TRUE) contour(dens2, level=0.10, col=blue, add=TRUE) contour(dens2, level=0.005, col=red, add=TRUE) (More bat-like.) -- Corrado Topi Global Climate Change Biodiversity Indicators Area 18,Department of Biology University of York, York, YO10 5YW, UK Phone: + 44 (0) 1904 328645, E-mail: ct...@york.ac.uk __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Sorry for repeated posts.
I was sending my messages through Nabble, while it has went down for maintenance. -- View this message in context: http://old.nabble.com/Sorry-for-repeated-posts.-tp26525299p26525299.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] order of panels in xyplots
Peter, thanks for your response! The problem is not how indexing works, but rather the question what is being indexed here. If I understand the description correctly then it is wrong. In the special and common case where all possible levels do actually occur in the data frame it coincidentally happens to work the way it is described but not when the data frame contains only data points for some of the levels. Then it appears that the indexing vector has to be bound to 1:length(unique(f)) which is unequal 1:nlevels(f). (f is a factor here.) Titus On Wed, Nov 25, 2009 at 10:32 PM, Peter Ehlers ehl...@ucalgary.ca wrote: Titus Malsburg wrote: The documentation of xyplot could be improved here. It says: If 'index.cond' is a list, it has to be as long as the number of conditioning variables, and the 'i'-th component has to be a valid indexing vector for the integer vector '1:nlevels(g_i)' (which can, among other things, repeat some of the levels or drop some altogether). It should make explicit that nlevels is the number of levels actually used in the data and not length(levels(f)). It does say ... _valid_ indexing vector ... (my emphasis). If nlevels(g) = 5, but you're only plotting 3 panels, it seems to me that c(3,1,5) might be a valid indexing vector. -Peter Ehlers Cheers, Titus __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] difference of two rows
Yes, thanks, that works perfectly! great command b. jholtman wrote: Try this: x - read.table(textConnection(ID YEAR + 13 2007 + 15 2003 + 15 2006 + 15 2008 + 21 2006 + 21 2007), header=TRUE) x$diff - ave(x$YEAR, x$ID, FUN=function(a) c(diff(a), NA)) x ID YEAR diff 1 13 2007 NA 2 15 20033 3 15 20062 4 15 2008 NA 5 21 20061 6 21 2007 NA On Wed, Nov 25, 2009 at 10:55 AM, clion birt...@hotmail.com wrote: Dear R user, I'd like to calculate the difference of two rows, where ID is the same. eg.: I've got the following dataframe: ID YEAR 13 2007 15 2003 15 2006 15 2008 21 2006 21 2007 and I'd like to get the difference, like this: ID YEAR diff 13 2007 NA 15 2003 3 15 2006 2 15 2008 NA 21 2006 1 21 2007 NA that should be fairly easy...I hope Thanks for any helpful comments B. -- View this message in context: http://old.nabble.com/difference-of-two-rows-tp26515212p26515212.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. -- 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. -- View this message in context: http://old.nabble.com/difference-of-two-rows-tp26515212p26525340.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] Arrhenius Plot 2 with lattice
Please provide minimal and self-contained code. Without being able to
read in the dataset, it's impossible to check the code.
Cheers
Joris
On Thu, Nov 26, 2009 at 9:13 AM, Markus Häge markus_ha...@gmx.de wrote:
Hello,
sorry for incomplete code...
with this I read the file and calculate my stuff. I have a plenty of
them 80-300K every 5 Kelvin. I start with 79K, 80K...300K
test-read.table(T300_both.txt,header=FALSE,sep=)
RH2-c(RH2,2.5e7*.32e-4/100e-6/5100*(test$V3[c(2)]-test$V3[c(1)]+test
$V3[c(4)]-test$V3[c(3)]))
n2-c(n2,-1/(RH2[c(46)]*1.60217e-19))
PA2-c(1.1331/100e-6*.32e-4*(test$V1[c(2)]+test$V1[c(4)]-test
$V1[c(1)]-test$V1[c(3)]))
PB2-c(1.1331/100e-6*.32e-4*(test$V1[c(6)]+test$V1[c(8)]-test
$V1[c(5)]-test$V1[c(7)]))
P2-c(P2,(PA2+PB2)/2)
bew2-c(bew2,-RH2[c(46)]/P2[c(46)])
QA2-c(QA2,(test$V1[c(2)]-test$V1[c(1)])/(test$V1[c(4)]-test$V1[c(3)]))
QB2-c(QB2,(test$V1[c(6)]-test$V1[c(5)])/(test$V1[c(8)]-test$V1[c(7)]))
#...
Temp-c(79,80,85,90,95,100,106,110,115,120,125,132,135,140,145,151,156,160,165,170,175,180,185,190,195,200,206,210,216,220,225,230,235,240,247,250,255,261,265,270,275,280,285,290,295,300)
#Here I transform my data to make this Arrhenius Plot:
Temp2-c(1000/Temp)
n2log-c(log10(n2))
#This function should be plottet as log10(n)~1000/T into the data:
kurve2-function(T)2^-.5*sqrt(1e17*2*6*I(T^1.5)*(2*pi*0.689*9.109e-31*1.38e-23/43.9e-68)^1.5)*exp(-.047*1.6e-19/(2*1.38e-23*T))
#Here is the plot-function, but I don't know the argument for
#panel.curve()
trellis.device(jpeg,file=Tabh1.jpg,color=FALSE)
n2plot-xyplot(n2log~Temp2,xlab=list(label=1000/T
(1/K),fontsize=20),ylab=list(label=log(n/cm^3),fontsize=20),scales=list(cex=1.5),panel=function(){panel.xyplot(Temp2,n2log);panel.curve(kurve2)})
print(n2plot)
dev.off()
thanks
Markus
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Re: [R] R help with princomp and pam clustering
On Thu, Nov 26, 2009 at 1:04 AM, Tyler82 procaccianti.clau...@gmail.com wrote: Hi all! I am working with R package cluster and I have a little problem: let's say I have two datasets...first one (A) is divided into 4 clusters by means of Pam algorythm. Let's say I want to project the second database (B) onto the Comp.1 X Comp.2 graph, and see where its elements are placed. The two datasets are made of different dim (54x19 and 28x19). I tried to extract the $loadings of the A clustering but I can't seem to figure out how to use them with B :( Prin - princomp(A) predict(Prin,B) in the assumption that the variable names in both dataframes are equal. Using princomp I menaged to extract the $scores and plot the graph. Wouldn't using princomp on the B dataset generate different PC? Indeed, it would. Thank you all! Bye!! Claudio -- View this message in context: http://old.nabble.com/R-help-with-princomp-and-pam-clustering-tp26522485p26522485.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] analyse tab delimited textfile microarray data(help)
Hello I have microarray data in tab delimited text file.The main headers and some fields are as: following are the header: FEATURES FeatureNum Row Col SubTypeMask ControlType ProbeName SystematicName PositionX PositionY LogRatio LogRatioError PValueLogRatio gProcessedSignal rProcessedSignal gProcessedSigError rProcessedSigError gMedianSignal rMedianSignal gBGMedianSignal rBGMedianSignal gBGPixSDev rBGPixSDev gIsSaturated rIsSaturated gIsFeatNonUnifOL rIsFeatNonUnifOL gIsBGNonUnifOL rIsBGNonUnifOL gIsFeatPopnOL rIsFeatPopnOL gIsBGPopnOL rIsBGPopnOL IsManualFlag gBGSubSignal rBGSubSignal gIsPosAndSignif rIsPosAndSignif gIsWellAboveBG rIsWellAboveBG SpotExtentX gBGMeanSignal rBGMeanSignal following is the data corresponding to the above header : DATA 1 1 1 66 1 DarkCorner DarkCorner 379.607 199.729 -5.98E-01 1.10E+00 5.86E-01 2.46E+00 6.21E-01 3.02E+00 1.51E+00 0 0 241 273 1.35E+02 1.48E+02 0 0 0 0 0 0 0 0 0 0 0 16.0892 -4.46689 1 0 0 0 65 135.479 148.517 DATA 2 1 2 66 1 DarkCorner DarkCorner 405 199.545 -4.71E-01 1.27E+00 7.11E-01 1.83E+00 6.20E-01 2.88E+00 1.55E+00 135 145.5 238 266 1.31E+02 1.48E+02 0 0 0 0 0 0 0 0 0 0 0 12.0031 2.05821 1 0 0 0 65 131.295 147.49 DATA 3 1 3 66 1 DarkCorner DarkCorner 430.5 199.5 -2.62E-01 1.55E+00 8.66E-01 1.13E+00 6.18E-01 2.66E+00 1.45E+00 128 142.5 237.5 270.5 1.30E+02 1.47E+02 0 0 0 0 0 0 0 0 0 0 0 7.41805 -0.318846 1 0 0 0 64.8204 130.996 148.231 DATA 4 1 4 0 0 GT_MTB_142632 chr1:2567359-2567418 455.648 199.519 1.89E-03 6.14E-02 9.75E-01 1.18E+03 1.18E+03 1.18E+02 1.18E+02 7776 15813 231.5 266 1.29E+02 1.48E+02 0 0 0 0 0 0 0 0 0 0 0 7741.9 15324.2 1 1 1 1 57.5363 129.226 148.004 Please tell me how can we analyse this tab delimited text file of microarray data. Please tell me the procedure of analysis. thanks [[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] multi variate plot with string data
is there something wrong with the way i asked the question frenchcr wrote: Ive got two columns in data_set that are strings the first column is called character and has levels: good, bad, ugly the second column is called abusive and has levels: aggressive, moderately aggressive, mildly aggressive I want to do a stacked boxplot that has this sort of structure: %aggressive %aggressive %aggressive %moderately aggressive %moderately aggressive %moderately aggressive %mildly aggressive %mildly aggressive %mildly aggressive %not agressive %not agressive %not agressive bad good ugly ...with legend at the size showing which colour each of the abusive levels takes. How is it done? -- View this message in context: http://old.nabble.com/multi-variate-plot-with-string-data-tp26517211p26525342.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] JMP - R ?
A wild thought ... ... anyone out there know if it's possible to call R code from JMP ? Bob Kinley - Eli Lilly co, UK [[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] Error in do.call(expand.grid, dimnames(x)) :
Hi Friends,
I am getting this error when I am running my R scripts. Can u please
tell me how this error will happened. My script is given below.
Errot: Error in do.call(expand.grid, dimnames(x)) :
Script:
#!/usr/bin/R
s-c(GG,GA,GV,GL,GI,GM,GF,GW,GP,GS,GT,GC,GY,GN,GQ,GD,GE,GK,GR,GH,AG,s[l],AV,AL,AI,AM,AF,AW,AP,AS,AT,AC,AY,AN,AQ,AD,AE,AK,AR,AH,VG,VA,VV,VL,VI,VM,VF,VW,VP,VS,VT,VC,VY,VN,VQ,VD,VE,VK,VR,VH,LG,LA,LV,LL,LI,LM,LF,LW,LP,LS,LT,LC,LY,LN,LQ,LD,LE,LK,LR,LH,IG,IA,IV,IL,II,IM,IF,IW,IP,IS,IT,IC,IY,IN,IQ,ID,IE,IK,IR,IH,MG,MA,MV,ML,MI,MM,MF,MW,MP,MS,MT,MC,MY,MN,MQ,MD,ME,MK,MR,MH,FG,FA,FV,FL,FI,FM,FF,FW,FP,FS,FT,FC,FY,FN,FQ,FD,FE,FK,FR,FH,WG,WA,WV,WL,WI,WM,WF,WW,WP,WS,WT,WC,WY,WN,WQ,WD,WE,WK,WR,WH,PG,PA,PV,PL,PI,PM,PF,PW,PP,PS,PT,PC,PY,PN,PQ,PD,PE,PK,PR,PH,SG,SA,SV,SL,SI,SM,SF,SW,SP,SS,ST,SC,SY,SN,SQ,SD,S!
E,SK,SR,SH,TG,TA,TV,TL,TI,TM,TF,TW,TP,TS,TT,TC,TY,TN,TQ,TD,TE,TK,TR,TH,CG,CA,CV,CL,CI,CM,CF,CW,CP,CS,CT,CC,CY,CN,CQ,CD,CE,CK,CR,CH,YG,YA,YV,YL,YI,YM,YF,YW,YP,YS,YT,YC,YY,YN,YQ,YD,YE,YK,YR,YH,NG,NA,NV,NL,NI,NM,NF,NW,NP,NS,NT,NC,NY,NN,NQ,ND,NE,NK,NR,NH,QG,QA,QV,QL,QI,QM,QF,QW,QP,QS,QT,QC,QY,QN,QQ,QD,QE,QK,QR,QH,DG,DA,DV,DL,DI,DM,DF,DW,DP,DS,DT,DC,DY,DN,DQ,DD,DE,DK,DR,DH,EG,EA,EV,EL,EI,EM,EF,EW,EP,ES,ET,EC,EY,EN,EQ,ED,EE,EK,ER,EH,KG,KA,KV,KL,KI,KM,KF,KW,KP,KS,KT,KC,KY,KN,KQ,KD,KE,KK,KR,KH,RG,RA,RV,RL,RI,RM,RF,RW,RP,RS,RT,RC,RY,RN,RQ,RD,RE,RK,RR,RH,HG,HA,HV,HL,HI,HM,HF,HW,HP,HS,HT,HC,HY,HN,!
HQ,HD,HE,HK,HR,HH)
for(l in 1:length(s))
{
for(j in 1:50)
{
if(file.info(paste(/media/_1/BootStrap/All_alpha_proteins/,s[l],/alp,s[l],mean,j,.bootstrap,sep=))$size1)
{
a-read.table(paste(/media/_1/BootStrap/All_alpha_proteins/,s[l],/alp,s[l],mean,j,.bootstrap,sep=))
A-a[,1]
Amax-max(A)
Amin-min(A)
Salpha-summary(A)
df-data.frame(P=Salpha)
color-aquamarine1
flg-All Alpha
}
if(file.info(paste(/media/_1/BootStrap/All_beta_proteins/,s[l],/bet,s[l],mean,j,.bootstrap,sep=))$size1)
{
b-read.table(paste(/media/_1/BootStrap/All_beta_proteins/,s[l],/bet,s[l],mean,j,.bootstrap,sep=))
B-b[,1]
Bmax-max(B)
Bmin-min(B)
Sbeta-summary(B)
df-data.frame(df,Q=Sbeta)
color-c(color,brown1)
flg-c(flg,All Beta)
}
if(file.info(paste(/media/_1/BootStrap/Alpha_and_beta_proteins_aorb/,s[l],/aob,s[l],mean,j,.bootstrap,sep=))$size1)
{
c-read.table(paste(/media/_1/BootStrap/Alpha_and_beta_proteins_aorb/,s[l],/aob,s[l],mean,j,.bootstrap,sep=))
C-c[,1]
Cmax-max(C)
Cmin-min(C)
Saob-summary(C)
df-data.frame(df,R=Saob)
color-c(color,cadetblue1)
flg-c(flg,Alpha or Beta)
}
if(file.info(paste(/media/_1/BootStrap/Alpha_and_beta_proteins_a+b/,s[l],/apb,s[l],mean,j,.bootstrap,sep=))$size1)
{
d-read.table(paste(/media/_1/BootStrap/Alpha_and_beta_proteins_a+b/,s[l],/apb,s[l],mean,j,.bootstrap,sep=))
D-d[,1]
Dmax-max(D)
Dmin-min(D)
Sapb-summary(D)
df-data.frame(df,S=Sapb)
color-c(color,darkorchid1)
flg-c(flg,Alpha plus Beta)
}
Tmax-c(Amax,Bmax,Cmax,Dmax)
Tmin-c(Amin,Bmin,Cmin,Dmin)
pdf (paste(s[l],mean,j,_bootstrap.pdf,sep=))
boxplot(df,names=flg,ylim=c(min(Tmin),max(Tmax)),col=color,style = tukey)
title(paste(Residue Pair Distance Statistics,\n,s[l],
Paired
Distance of ,j,sep=),ylab=Distance in Angstrom,xlab=Protein
Classes)
dev.off()
}
}
*
--
**
Deepak.M.R
Research Scholar
Biocomputing Group,
Department of Computer Science,
University of Bologna (Italy).
http://deepak.web.cs.unibo.it/.
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Re: [R] Concave hull
On 26/11/2009 4:02 AM, Corrado Topi wrote: Dear David and other concave-hull-ists, yes, I meant concave hulls indeed. I know about the algorithm mentioed (www.concavehull.com) but it is not open source, so you cannot integrate it in R, and it is apparently patented, so even if you find the description you cannot apply it to implement a solution (even if patenting algorithms is at least questionable and has a rather patchy validity). Some questions / comments which applies to David's approach but in general even to convex hulls (question 2): 1) How do you extend it to n dimensions (in R)? 2) How do you do set calculus (horrible expression to mean: union, intersection, difference, and particularly membership, and so on ) on these hulls (in R)? Finally, I am at the moment using a gis to do it, but I did not find any command for concave hulls in grass. There is a rather long a convoluted way of doing them, but nearly impossible to automatise (see http://grass.osgeo.org/wiki/Create_concave_hull). Looking for the capability of extending it to the n-dimensional case does not sound right, because gis is thought for working in 2d/3d. I don't see a clear definition of what a concave hull should be, but the following version of the algorithm above looks automatisable, if slow on big sets: Generate all pairwise distances, and generate the undirected graph formed of edges below a certain length threshold. Take each connected component of that graph, and discard any internal points and edges. (An internal edge is one whose midpoint is in the interior of a polygon formed by other edges in the graph. I'd build it up by starting with an arbitrary pair of points and growing from there.) Duncan Murdoch Best, On Nov 26 2009, David Winsemius wrote: On Nov 25, 2009, at 7:51 PM, David Winsemius wrote: Drats; Forgot the plot: xx - runif(100, -1, 1) yy - abs(xx)+rnorm(100,0,.2); plot(xx,yy, xlim=c( min(xx)-sd(xx), max(xx)+sd(xx)), ylim =c( min(yy)-sd(yy), max(yy)+sd(yy))) dens2 - kde2d(xx, yy, lims=c(min(xx)-sd(xx), max(xx)+sd(xx), min(yy)-sd(yy), max(yy)+sd(yy) ) ) contour(dens2, add=TRUE) # You can pick a single contour if you like: contour(dens2, level=0.05, col=red, add=TRUE) contour(dens2, level=0.10, col=blue, add=TRUE) And as a further note you can drop the bandwidth and lower the density level to get a tighter fit: xx - runif(1, -1, 1) yy - abs(xx)+rnorm(1 ,0,.2); plot(xx,yy, xlim=c( min(xx)- sd(xx), max(xx)+sd(xx)), ylim =c( min(yy)-sd(yy), max(yy)+sd(yy)), cex=.2) dens2 - kde2d(xx, yy, lims=c(min(xx)-sd(xx), max(xx)+sd(xx), min(yy)- sd(yy), max(yy)+sd(yy) ) , h=c(bandwidth.nrd(xx)/4, bandwidth.nrd(xx)/ 4) ) contour(dens2, add=TRUE) # You can pick a single contour if you like: contour(dens2, level=0.05, col=red, add=TRUE) contour(dens2, level=0.10, col=blue, add=TRUE) contour(dens2, level=0.005, col=red, add=TRUE) (More bat-like.) __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] homals (level numerical, scoremat and catscores...)
Just run this code: library(homals) data(sleeping) sleeping res - homals(sleeping[,2:4], level = c(rep(numerical,2),nominal), ndim=1) plot(sleeping[,2],res$scoremat[,,1][,1],axes=F) axis(1,sleeping[,2]) abline(h=res$scoremat[,,1][,1]) box() It looks strange, innit? There is something which does not come out right among catscores and scoremat... which are the right transformed values? :working: -- View this message in context: http://old.nabble.com/homals-%28level-numerical%2C-scoremat-and-catscores...%29-tp26526489p26526489.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] R: RE: R: Re: R: Re: chol( neg.def.matrix ) WAS: Re: Choleski and Choleski with pivoting of matrix fails
Thanks for your message! Actually it works quite well for me too. If I then take the trace of the final result below, I end up with a number made up of both a real and an imaginary part. This does not probably mean much if the trace of the matrix below givens me info about the degrees of freedom of a model... Simona Messaggio originale Da: rvarad...@jhmi.edu Data: 25-nov-2009 18.55 A: simona.racio...@libero.it, p.dalga...@biostat.ku.dk Cc: r-help@r-project.org Ogg: RE: [R] R: Re: R: Re: chol( neg.def.matrix ) WAS: Re: Choleski and Choleski with pivoting of matrix fails I do not understand what the problem is, as it works just fine for me: A - matrix(c(0.5401984,-0.3998675,-1.3785897,-0.3998675,1.0561872, 0.8158639,-1.3785897, 0.8158639, 1.6073119), 3, 3, byrow=TRUE) eA - eigen(A) chA - eA$vec %*% diag(sqrt(eA$val+0i)) %*% t(eA$vec) all.equal(A, Re(chA %*% t(chA))) Y - diag(c(1,2,3)) solve(chA %*% Y) Ravi. --- Ravi Varadhan, Ph.D. Assistant Professor, The Center on Aging and Health Division of Geriatric Medicine and Gerontology Johns Hopkins University Ph: (410) 502-2619 Fax: (410) 614-9625 Email: rvarad...@jhmi.edu Webpage: http://www.jhsph. edu/agingandhealth/People/Faculty_personal_pages/Varadhan.html -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of simona.racio...@libero.it Sent: Wednesday, November 25, 2009 9:59 AM To: p.dalga...@biostat.ku.dk Cc: r-help@r-project.org Subject: [R] R: Re: R: Re: chol( neg.def.matrix ) WAS: Re: Choleski and Choleski with pivoting of matrix fails Dear Peter, thank you very much for your answer. My problem is that I need to calculate the following quantity: solve(chol(A)%*%Y) Y is a 3*3 diagonal matrix and A is a 3*3 matrix. Unfortunately one eigenvalue of A is negative. I can anyway take the square root of A but when I multiply it by Y, the imaginary part of the square root of A is dropped, and I do not get the right answer. I tried to exploit the diagonal structure of Y by using 2*2 matrices for A and Y. In this way the problem mentioned above disappears (since all eigenvalues of A are positive) and when I perform the calculation above I get approximately the right answer. The approximation is quite good. However it is an approximation. Any suggestion? Thank you very much! Simon Messaggio originale Da: p.dalga...@biostat.ku.dk Data: 23-nov-2009 14.09 A: simona.racio...@libero.itsimona.racio...@libero.it Cc: Charles C. Berrycbe...@tajo.ucsd.edu, r-help@r-project.org Ogg: Re: R: Re: [R] chol( neg.def.matrix ) WAS: Re: Choleski and Choleski with pivoting of matrix fails simona.racio...@libero.it wrote: It works! But Once I have the square root of this matrix, how do I convert it to a real (not imaginary) matrix which has the same property? Is that possible? No. That is theoretically impossible. If A = B'B, then x'Ax = ||Bx||^2 = 0 for any x, which implies in particular that all eigenvalues of A should be nonnegative. Best, Simon Messaggio originale Da: p.dalga...@biostat.ku.dk Data: 21-nov-2009 18.56 A: Charles C. Berrycbe...@tajo.ucsd.edu Cc: simona.racio...@libero.itsimona.racio...@libero.it, r-h...@r- project.org Ogg: Re: [R] chol( neg.def.matrix ) WAS: Re: Choleski and Choleski with pivoting of matrix fails Charles C. Berry wrote: On Sat, 21 Nov 2009, simona.racio...@libero.it wrote: Hi Everyone, I need to take the square root of the following matrix: [,1] [,2][,3] [1,] 0.5401984 -0.3998675 -1.3785897 [2,] -0.3998675 1.0561872 0.8158639 [3,] -1.3785897 0.8158639 1.6073119 I tried Choleski which fails. I then tried Choleski with pivoting, but unfortunately the square root I get is not valid. I also tried eigen decomposition but i did no get far. Any clue on how to do it?! If you want to take the square root of a negative definite matrix, you could use sqrtm( neg.def.mat ) from the expm package on rforge: http://r-forge.r-project.org/projects/expm/ But that matrix is not negative definite! It has 2 positive and one negative eigenvalue. It is non-positive definite. It is fairly easy in any case to get a matrix square root from the eigen decomposition: v%*%diag(sqrt(d+0i))%*%t(v) [,1] [,2] [,3] [1,] 0.5164499+0.4152591i -0.1247682-0.0562317i -0.7257079+0.3051868i [2,] -0.1247682-0.0562317i 0.9618445+0.0076145i 0.3469916-0.0413264i [3,] -0.7257079+0.3051868i 0.3469916-0.0413264i 1.0513849+0.2242912i ch - v%*%diag(sqrt(d+0i))%*%t(v) t(ch)%*% ch [,1] [,2] [,3] [1,] 0.5401984+0i -0.3998675-0i -1.3785897-0i [2,] -0.3998675-0i 1.0561872+0i
Re: [R] How to display an image on RGL plot?
On 26/11/2009 2:14 AM, Vladimir Eremeev wrote: Hi all. It's been a long time since I wrote to this list. Glad to see the R project well and working. I am working with a 3D plot similar to this: http://old.nabble.com/file/p26525177/rgl-device.png rgl-device.png The underlying picture is a JPEG image, loaded with the rimage package and coerced to the matrix. Spheres denote control points, collected from this picture and must be situated over the certain points of the image. I display the image with rgl.points. In case of the standard video camera image (704x576) it has to display over 40 points which is rather slow and memory consuming. How can I put an original JPEG on this plot? Another problem is that the picture is color initially, but was converted to the grayscale. I'd like to preserve colors. I can't see that image; the link doesn't work. But the best way to display an image in rgl is to use texture mapping. There are examples in ?persp3d (where the texture is a world map, displayed on a globe) and demo(flag). See ?rgl.surface for a description of how texture coordinates are specified. 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] How to display an image on RGL plot?
Barry Rowlingson b.rowling...@lancaster.ac.uk on Thu, 26 Nov 2009 08:18:51 + writes: On Thu, Nov 26, 2009 at 7:14 AM, Vladimir Eremeev wl2...@gmail.com wrote: The underlying picture is a JPEG image, loaded with the rimage package and coerced to the matrix. Spheres denote control points, collected from this picture and must be situated over the certain points of the image. I display the image with rgl.points. In case of the standard video camera image (704x576) it has to display over 40 points which is rather slow and memory consuming. How can I put an original JPEG on this plot? Another problem is that the picture is color initially, but was converted to the grayscale. I'd like to preserve colors. Try using surface3d with a flat surface (z=0) and a matrix of colours in the col= argument. See help(surface3d) for an example. Also STOP POSTING!!! There seems to be about 8 copies of your message in my inbox!!! I hope it has ended now, with 12 copies. We've seen this once in the past, and also there, it was the Nabble interface (!) Personally I'd really prefer people would use regular subscriptions and regular e-mail for posting to the R mailing lists. Martin Maechler, ETH Zurich, provider of the major R mailing lists 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-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Testing for strength of fit using R
Dear all, I am trying to validate a model by comparing simulated output values against observed values. I have produced a simple X-y scatter plot with a 1:1 line, so that the closer the points fall to this line, the better the 'fit' between the modelled data and the observation data. I am now attempting to quantify the strength of this fit by using a statistical test in R. I am no statistics guru, but from my limited understanding, I suspect that I need to use the Chi Squared test (I am more than happy to be corrected on this though!). However, this results in the following: chisq.test(data$Simulation,data$Observation) Pearson's Chi-squared test data: data$Simulation and data$Observation X-squared = 567, df = 550, p-value = 0.2989 Warning message: In chisq.test(data$Simulation, data$Observation) : Chi-squared approximation may be incorrect The ?chisq.test document suggests that the objects should be of vector or matrix format, so I tried the following, but still receive a warning message (and different results): chisq.test(as.matrix(data[,4:5])) Pearson's Chi-squared test data: as.matrix(data[, 4:5]) X-squared = 130.8284, df = 26, p-value = 6.095e-16 Warning message: In chisq.test(as.matrix(data[, 4:5])) : Chi-squared approximation may be incorrect What am I doing wrong and how can I successfully measure how well the simulated values fit the observed values? If it's of any help, here are how my data are structured - note that I am only using columns 4 and 5 (Observation and Simulation). str(data) 'data.frame': 27 obs. of 5 variables: $ Location : Factor w/ 27 levels Australia,Brazil,..: 8 2 13 19 22 14 16 23 6 7 ... $ Vegetation : Factor w/ 21 levels Beech,Broadleaf evergreen laurel,..: 17 21 2 16 15 16 9 16 3 4 ... $ Vegetation.Class: Factor w/ 4 levels Boreal and Temperate Evergreen,..: 3 3 4 1 1 1 4 1 4 1 ... $ Observation : num 24 8.9 14.7 26.7 42.4 31.7 30.8 7.5 14 22 ... $ Simulation : num 33.9 7.8 9.74 7.6 11.8 10.7 12 28.1 1.7 1.7 ... I hope someone is able to point me in the right direction. Many thanks, Steve _ Have more than one Hotmail account? Link them together to easily access both http://clk.atdmt.com/UKM/go/186394591/direct/01/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Vista truncated Sys.getenv(PATH) when and only when running as administrator
This is rather strange and I suspect is a Windows issue rather than an R issue, but it does not seem to be mentioned on the lists so I am logging it in case it gives anyone else problems. Running Vista Business Version 6.0.6002 Service Pack 2 Build 6002, with the latest R 2.10.0 patched. A normal 'R' gui process: p - Sys.getenv(PATH) nchar(p) PATH 1199 sessionInfo() R version 2.10.0 Patched (2009-11-23 r50548) i386-pc-mingw32 locale: [1] LC_COLLATE=English_United Kingdom.1252 [2] LC_CTYPE=English_United Kingdom.1252 [3] LC_MONETARY=English_United Kingdom.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United Kingdom.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base Running R gui as administrator, however, the same path variable is truncated: p - Sys.getenv(PATH) nchar(p) PATH 1024 sessionInfo() R version 2.10.0 Patched (2009-11-23 r50548) i386-pc-mingw32 locale: [1] LC_COLLATE=English_United Kingdom.1252 [2] LC_CTYPE=English_United Kingdom.1252 [3] LC_MONETARY=English_United Kingdom.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United Kingdom.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base This may be related to http://tolstoy.newcastle.edu.au/R/e6/devel/09/01/0259.html Keith Ponting Aurix Ltd, Malvern WR14 3SZ UK [[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] Kerning issues with CairoPDF
Karl Ove Hufthammer wrote: I'm using CairoPDF to generate PDF (because of its font embedding and support for transparent colours). However, at least on my (Windows) system, the text it outputs seems to have completely wrong kerning. Here's an example: CairoPDF(test.pdf) plot(rnorm(100),xlab=Ovreset) dev.off() The v is (slightly) too far away from the O, it's much too close to the r, partially overlapping it, and the e is too far away from the s. For the record, there are no problems with R 2.9.2 on my Mandriva Linux 2010 system. But it’s a different font which gets embedded (Liberation Sans on Linux vs. Arial on Windows). -- Karl Ove Hufthammer E-mail: k...@huftis.org Jabber: huf...@jabber.no __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] order of panels in xyplots
You're right, Titus. I misunderstood. It looks like index.cond has to be in 1:(number of panels being plotted for factor f). While this can arguably be covered by the phrase valid indexing vector, I agree that this could be made more explicit. -Peter Ehlers Titus Malsburg wrote: Peter, thanks for your response! The problem is not how indexing works, but rather the question what is being indexed here. If I understand the description correctly then it is wrong. In the special and common case where all possible levels do actually occur in the data frame it coincidentally happens to work the way it is described but not when the data frame contains only data points for some of the levels. Then it appears that the indexing vector has to be bound to 1:length(unique(f)) which is unequal 1:nlevels(f). (f is a factor here.) Titus On Wed, Nov 25, 2009 at 10:32 PM, Peter Ehlers ehl...@ucalgary.ca wrote: Titus Malsburg wrote: The documentation of xyplot could be improved here. It says: If 'index.cond' is a list, it has to be as long as the number of conditioning variables, and the 'i'-th component has to be a valid indexing vector for the integer vector '1:nlevels(g_i)' (which can, among other things, repeat some of the levels or drop some altogether). It should make explicit that nlevels is the number of levels actually used in the data and not length(levels(f)). It does say ... _valid_ indexing vector ... (my emphasis). If nlevels(g) = 5, but you're only plotting 3 panels, it seems to me that c(3,1,5) might be a valid indexing vector. -Peter Ehlers Cheers, Titus __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] ow to have R automatically print traceback upon errors
Hi Jim, Thanks for your suggestion. It is working now. The earlier message recover called non-interactively; frames dumped, use debugger() to view happened within a R-IDE but doesn't occur in a R console. Jeff -Original Message- From: jim holtman [mailto:jholt...@gmail.com] Sent: Monday, November 23, 2009 11:00 PM To: Hao Cen Cc: r-help@r-project.org Subject: Re: [R] ow to have R automatically print traceback upon errors I use this: options(error=utils::recover) and anytime an error occurs in the interactive mode, it will print out the traceback and then allow you to explore the variables at each level of the stack; just like putting 'browser()' in the code at the error point. Here is what I get in running under Windows: x - function() xyz() # non-existent function x() # caa the function Error in x() : could not find function xyz == error message Enter a frame number, or 0 to exit 1: x() == traceback Selection: 0 On Mon, Nov 23, 2009 at 7:52 PM, Hao Cen h...@andrew.cmu.edu wrote: Hi, I wonder how to have R automatically print stack trace produced by traceback upon errors during interactive uses. I tried the suggestions on http://old.nabble.com/Automatically-execute-traceback-when-execution-of-scri pt-causes-error--td22368483.html#a22368775 and used options(error = recover) options(showErrorCalls = T) It just produces an extra message like recover called non-interactively; frames dumped, use debugger() to view Thanks Jeff __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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.
Re: [R] makefile for sweave
Dear all,
I can't get texi2dvi working right. Basically I'd like to convert a .lex
to .pdf without having to fiddle with the issue Sweave.sty not being in
my current directory (as this was sugested in other posts on this list).
When I'm in the R-Gui I can get the help via
?texi2dvi
(So I conclude its installed.)
However, when I try to use it to concert a .tex to .pdf I get trouble ...
For example :
A)
The file test02.r contains :
Sweave(Sweave_test01.rnw)
library(tools)
texi2dvi(Sweave_test01.tex, pdf =T)
Now, when I run on the linux command line :
R --vanilla -q test02.r
I get :
Sweave(Sweave_test01.rnw)
Writing to file Sweave_test01.tex
Processing code chunks ...
1 : term hide (label=chunk_ini)
2 : term verbatim eps pdf (label=Fig01)
3 : term tex (label=packageVersionInfo)
Loading required package: xtable
You can now run LaTeX on 'Sweave_test01.tex'
library(tools)
texi2dvi(Sweave_test01.tex, pdf =T)
Error in texi2dvi(Sweave_test01.tex, pdf = T) :
Running 'texi2dvi' on 'Sweave_test01.tex' failed.
Messages:
sh: texi2dvi: command not found
Execution halted
B)
In a previous message on this list I found the following command line(s)
suggested, but I my case it won't work
star5_R_test_ R CMD texi2dvi --help
/usr/local/lib64/R/bin/Rcmd: line 62: exec: texi2dvi: not found
similarly, when execute (as sugested) I get the same error message
star5_R_test_ R CMD texi2dvi -p Sweave_test01.tex
/usr/local/lib64/R/bin/Rcmd: line 62: exec: texi2dvi: not found
I don't understand how can a command can be present (= installed) and
still not being found as the error messages suggest ?
For completeness :
sessionInfo()
R version 2.10.0 (2009-10-26)
x86_64-unknown-linux-gnu
locale:
[1] C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] xtable_1.5-6 mouse4302probe_2.5.0 AnnotationDbi_1.8.1
[4] mouse4302cdf_2.5.0 MASS_7.3-3 fdrtool_1.2.5
[7] limma_3.2.1 affyPLM_1.22.0 preprocessCore_1.8.0
[10] gcrma_2.18.0 affy_1.24.2 Biobase_2.6.0
loaded via a namespace (and not attached):
[1] Biostrings_2.14.3 DBI_0.2-4 IRanges_1.4.4 RSQLite_0.7-3
[5] affyio_1.14.0 splines_2.10.0tools_2.10.0
Thank's in advance,
Wolfgang
Charles C. Berry a écrit :
On Tue, 8 Sep 2009, Welma Pereira wrote:
Hello, I have the following makefile. The problem is that the
bibliography
doesn t work. Any help would be appreciated! I really don t don t
what to
do..:-(
# The sources of the report (tex, Rnw and other files (e.g. bib, idx))
TEX_CMPS = Report problem
RNW_CMPS = prop1 prop2 ExeExps
OTHER = Report.bib
# The name of the report to produce
all: Report.pdf
code: $(RNW_CMPS:=.R)
clean:
rm -f *.log *.dvi *~
# On what does the report depends?
Report.pdf: $(TEX_CMPS:=.tex) $(RNW_CMPS:=.tex) ${OTHER} makefile
TEXINPUTS=${TPUTS} pdflatex $
TEXINPUTS=${TPUTS} pdflatex $
IIRC
R CMD texi2dvi -p target.tex
takes care of finding sweave.sty and running latex thru all the
iterations needed to build cross-references and a usable pdf.
Try
R CMD texi2dvi --help
at the shell prompt.
HTH,
Chuck
rm *.log
#mv *.aux $(dir $)
# How to build the tex files from the Rnw (Sweave) files
%.tex: %.Rnw
echo library(utils); options(width=60); Sweave('$') | ${R_PRG}
--no-save --vanilla
mv $(notdir $*.tex) $(dir $)
# How to build the R code files from the Rnw (Sweave) files
%.R: %.Rnw
echo library(utils); Stangle('$') | ${R_PRG} --no-save --vanilla
%.bib:
TEXINPUTS=${TPUTS} pdflatex $
bibtex $
%.aux:
TEXINPUTS=${TPUTS} pdflatex $
bibtex $
%.idx:
TEXINPUTS=${TPUTS} pdflatex $
makeindex $
cheers!
[[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.
Charles C. Berry(858) 534-2098
Dept of Family/Preventive
Medicine
E mailto:cbe...@tajo.ucsd.eduUC San Diego
http://famprevmed.ucsd.edu/faculty/cberry/ La Jolla, San Diego
92093-0901
__
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Wolfgang Raffelsberger, PhD
Laboratoire de BioInformatique et Génomique Intégratives
IGBMC,
1 rue Laurent Fries, 67404 Illkirch Strasbourg, France
Tel (+33) 388 65 3300 Fax (+33) 388 65 3276
wolfgang.raffelsberger (at) igbmc.fr
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/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] makefile for sweave
Is texi2dvi in your PATH? What happens if you open a CMD window and
type texi2dvi at the prompt?
--sundar
On Thu, Nov 26, 2009 at 6:14 AM, Wolfgang Raffelsberger wr...@igbmc.fr wrote:
Dear all,
I can't get texi2dvi working right. Basically I'd like to convert a .lex to
.pdf without having to fiddle with the issue Sweave.sty not being in my
current directory (as this was sugested in other posts on this list).
When I'm in the R-Gui I can get the help via
?texi2dvi
(So I conclude its installed.)
However, when I try to use it to concert a .tex to .pdf I get trouble ...
For example :
A)
The file test02.r contains :
Sweave(Sweave_test01.rnw)
library(tools)
texi2dvi(Sweave_test01.tex, pdf =T)
Now, when I run on the linux command line :
R --vanilla -q test02.r
I get :
Sweave(Sweave_test01.rnw)
Writing to file Sweave_test01.tex
Processing code chunks ...
1 : term hide (label=chunk_ini)
2 : term verbatim eps pdf (label=Fig01)
3 : term tex (label=packageVersionInfo)
Loading required package: xtable
You can now run LaTeX on 'Sweave_test01.tex'
library(tools)
texi2dvi(Sweave_test01.tex, pdf =T)
Error in texi2dvi(Sweave_test01.tex, pdf = T) :
Running 'texi2dvi' on 'Sweave_test01.tex' failed.
Messages:
sh: texi2dvi: command not found
Execution halted
B)
In a previous message on this list I found the following command line(s)
suggested, but I my case it won't work
star5_R_test_ R CMD texi2dvi --help
/usr/local/lib64/R/bin/Rcmd: line 62: exec: texi2dvi: not found
similarly, when execute (as sugested) I get the same error message
star5_R_test_ R CMD texi2dvi -p Sweave_test01.tex
/usr/local/lib64/R/bin/Rcmd: line 62: exec: texi2dvi: not found
I don't understand how can a command can be present (= installed) and still
not being found as the error messages suggest ?
For completeness :
sessionInfo()
R version 2.10.0 (2009-10-26)
x86_64-unknown-linux-gnu
locale:
[1] C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] xtable_1.5-6 mouse4302probe_2.5.0 AnnotationDbi_1.8.1
[4] mouse4302cdf_2.5.0 MASS_7.3-3 fdrtool_1.2.5 [7]
limma_3.2.1 affyPLM_1.22.0 preprocessCore_1.8.0
[10] gcrma_2.18.0 affy_1.24.2 Biobase_2.6.0
loaded via a namespace (and not attached):
[1] Biostrings_2.14.3 DBI_0.2-4 IRanges_1.4.4 RSQLite_0.7-3
[5] affyio_1.14.0 splines_2.10.0 tools_2.10.0
Thank's in advance,
Wolfgang
Charles C. Berry a écrit :
On Tue, 8 Sep 2009, Welma Pereira wrote:
Hello, I have the following makefile. The problem is that the
bibliography
doesn t work. Any help would be appreciated! I really don t don t what to
do..:-(
# The sources of the report (tex, Rnw and other files (e.g. bib, idx))
TEX_CMPS = Report problem
RNW_CMPS = prop1 prop2 ExeExps
OTHER = Report.bib
# The name of the report to produce
all: Report.pdf
code: $(RNW_CMPS:=.R)
clean:
rm -f *.log *.dvi *~
# On what does the report depends?
Report.pdf: $(TEX_CMPS:=.tex) $(RNW_CMPS:=.tex) ${OTHER} makefile
TEXINPUTS=${TPUTS} pdflatex $
TEXINPUTS=${TPUTS} pdflatex $
IIRC
R CMD texi2dvi -p target.tex
takes care of finding sweave.sty and running latex thru all the iterations
needed to build cross-references and a usable pdf.
Try
R CMD texi2dvi --help
at the shell prompt.
HTH,
Chuck
rm *.log
# mv *.aux $(dir $)
# How to build the tex files from the Rnw (Sweave) files
%.tex: %.Rnw
echo library(utils); options(width=60); Sweave('$') | ${R_PRG}
--no-save --vanilla
mv $(notdir $*.tex) $(dir $)
# How to build the R code files from the Rnw (Sweave) files
%.R: %.Rnw
echo library(utils); Stangle('$') | ${R_PRG} --no-save --vanilla
%.bib:
TEXINPUTS=${TPUTS} pdflatex $
bibtex $
%.aux:
TEXINPUTS=${TPUTS} pdflatex $
bibtex $
%.idx:
TEXINPUTS=${TPUTS} pdflatex $
makeindex $
cheers!
[[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.
Charles C. Berry (858) 534-2098
Dept of Family/Preventive
Medicine
E mailto:cbe...@tajo.ucsd.edu UC San Diego
http://famprevmed.ucsd.edu/faculty/cberry/ La Jolla, San Diego 92093-0901
__
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Wolfgang Raffelsberger, PhD
Laboratoire de BioInformatique et Génomique Intégratives
IGBMC, 1 rue Laurent Fries, 67404 Illkirch Strasbourg, France
Tel (+33) 388 65 3300 Fax (+33) 388 65 3276
wolfgang.raffelsberger (at) igbmc.fr
Re: [R] questions on the ff package
Hi Jens, Thanks for your prompt and informative answers. ff is a fabulous package and your suggestions helped me solve my problems at hands. As I need to incrementally increase each of several large matrices (about 1000 rows *1 columns, 1000 matrices) by a row every day. I wonder how efficiently it is to do the following command on a frequent basis. nrow(matFF) - nrow(matFF)+1 as far as I know for mmap, a fixed size of file is preallocated. I don't know the ff implementation and how it handle file size changes. Does the command in the line above preallocate, say 10% more space of the current size so that no large file copying is needed each time the nrow is changed? Another problem I am facing is that I have over 2000 large matrices that need the help of ff. Suppose I have a list of 2000 ff objects. My computing environment is 64bit linux, 64Gb mem. I remember there is some limitations on the maximum of files that can be opened in linux. If I need to access each matrix, would you think I can open each matrix and leave them open or I need to close it after it is opened and used? Thanks a lot Jeff -Original Message- From: Jens Oehlschlägel [mailto:oehl_l...@gmx.de] Sent: Wednesday, November 25, 2009 8:04 AM To: h...@andrew.cmu.edu Cc: r-h...@lists.r-project.org Subject: [R] questions on the ff package Jeff, I need to save a matrix as a memory-mapped file and load it back later. To save the matrix, I use mat = matrix(1:20, 4, 5) matFF = ff(mat, dim=dim(mat), filename=~/a.mat , overwrite=TRUE, dimnames = dimnames(mat)) # This stores the data in an ff file, # but not the metadata in R's ff object. # To do the latter you need to do save(matFF, file=~/matFF.RData) # Assuming that your ff file remains in the same location, # in a new R session you simply load(file=~/matFF.RData) # and the ff file is available automagically However, I don't always know the dimension when loading the matrix back. If I miss the dim attributes, ff will return it as vector. Is there a way to load the matrix without specifying the dimension? # You can create an ff object using your existing ff file by matFF - ff(filename=~/a.mat, vmode=double, dim=c(4,5)) # You can do the same at unknown file size with matFF - ff(filename=~/a.mat, vmode=double) # which gives you the length of the ff object length(matFF) # if you know the number of columns you can calculate the number of rows and give your ff object the interpretation of a matrix dim(matFF) - c(length(matFF)/5, 5) the matrix may grow in terms of the number of rows. Is there an efficient way to do this? # there are two ways to grow a matrix by rows # 1) you create the matrix in major row order matFF - ff(1:20, dim=c(4,5), dimorder=c(2:1)) # then you require a higher number of rows nrow(matFF) - 6 # as you can see there are new empty rows in the file matFF # 2) Instead of a matrix you create a ffdf data.frame #which you can also give more rows using nrow- #An example of this is in read.table.ffdf #which reads a csv file in chunks and extends the #number of rows in the ffdf Jens Oehlschlägel -- Preisknaller: GMX DSL Flatrate für nur 16,99 Euro/mtl.! http://portal.gmx.net/de/go/dsl02 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Moving quantile()?
Is there a faster way to get moving quantiles from a time series than to run quantile() at each step in the series? Thanks, Rob __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Best way to preallocate numeric NA array?
These are the ways that occur to me. ## This produces a logical vector, which will get converted to a numeric ## vector the first time a number is assigned to it. That seems ## wasteful. x - rep(NA, n) ## This does the conversion ahead of time but it's still creating a ## logical vector first, which seems wasteful. x - as.numeric(rep(NA, n)) ## This avoids type conversion but still involves two assignments for ## each element in the vector. x - numeric(n) x[] - NA ## This seems reasonable. x - rep(as.numeric(NA), n) Comments? Thanks, Rob __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] analyse tab delimited textfile microarray data(help)
Kumar -- ask on the Bioconductor mailing list http://bioconductor.org/docs/mailList.html see basic workflows at http://bioconductor.org/docs/workflows/oligoarrays/ You cannot analyze the data without understanding its source or questions you are asking, so determine where this data is coming from and what you are expected to do with it before posting. Martin kumar kk wrote: Hello I have microarray data in tab delimited text file.The main headers and some fields are as: following are the header: FEATURES FeatureNum Row Col SubTypeMask ControlType ProbeName SystematicName PositionX PositionY LogRatio LogRatioError PValueLogRatio gProcessedSignal rProcessedSignal gProcessedSigError rProcessedSigError gMedianSignal rMedianSignal gBGMedianSignal rBGMedianSignal gBGPixSDev rBGPixSDev gIsSaturated rIsSaturated gIsFeatNonUnifOL rIsFeatNonUnifOL gIsBGNonUnifOL rIsBGNonUnifOL gIsFeatPopnOL rIsFeatPopnOL gIsBGPopnOL rIsBGPopnOL IsManualFlag gBGSubSignal rBGSubSignal gIsPosAndSignif rIsPosAndSignif gIsWellAboveBG rIsWellAboveBG SpotExtentX gBGMeanSignal rBGMeanSignal following is the data corresponding to the above header : DATA 1 1 1 66 1 DarkCorner DarkCorner 379.607 199.729 -5.98E-01 1.10E+00 5.86E-01 2.46E+00 6.21E-01 3.02E+00 1.51E+00 0 0 241 273 1.35E+02 1.48E+02 0 0 0 0 0 0 0 0 0 0 0 16.0892 -4.46689 1 0 0 0 65 135.479 148.517 DATA 2 1 2 66 1 DarkCorner DarkCorner 405 199.545 -4.71E-01 1.27E+00 7.11E-01 1.83E+00 6.20E-01 2.88E+00 1.55E+00 135 145.5 238 266 1.31E+02 1.48E+02 0 0 0 0 0 0 0 0 0 0 0 12.0031 2.05821 1 0 0 0 65 131.295 147.49 DATA 3 1 3 66 1 DarkCorner DarkCorner 430.5 199.5 -2.62E-01 1.55E+00 8.66E-01 1.13E+00 6.18E-01 2.66E+00 1.45E+00 128 142.5 237.5 270.5 1.30E+02 1.47E+02 0 0 0 0 0 0 0 0 0 0 0 7.41805 -0.318846 1 0 0 0 64.8204 130.996 148.231 DATA 4 1 4 0 0 GT_MTB_142632 chr1:2567359-2567418 455.648 199.519 1.89E-03 6.14E-02 9.75E-01 1.18E+03 1.18E+03 1.18E+02 1.18E+02 7776 15813 231.5 266 1.29E+02 1.48E+02 0 0 0 0 0 0 0 0 0 0 0 7741.9 15324.2 1 1 1 1 57.5363 129.226 148.004 Please tell me how can we analyse this tab delimited text file of microarray data. Please tell me the procedure of analysis. thanks [[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. -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Best way to preallocate numeric NA array?
On Thu, Nov 26, 2009 at 10:03 AM, Rob Steele freenx.10.robste...@xoxy.net wrote: These are the ways that occur to me. ## This produces a logical vector, which will get converted to a numeric ## vector the first time a number is assigned to it. That seems ## wasteful. x - rep(NA, n) ## This does the conversion ahead of time but it's still creating a ## logical vector first, which seems wasteful. x - as.numeric(rep(NA, n)) ## This avoids type conversion but still involves two assignments for ## each element in the vector. x - numeric(n) x[] - NA ## This seems reasonable. x - rep(as.numeric(NA), n) Comments? My intuition would be to go with the third method (allocate a numeric vector then assign NA to its contents) but I haven't tested the different. In fact, it would be difficult to see differences in, for example, execution time unless n was very large. This brings up a different question which is, why do you want to consider this? Are you striving for readability, for speed, for low memory footprint, for efficiency in some other way? When we were programming in S on machines with 1 mips processors and a couple of megabytes of memory, such considerations were important. I'm not sure they are quite as important now. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Missing and number of days
Hi all, Assume that I have a data set (xcv) with several variables and some of the variables have a missing observation represented by -9 as shown below. I want to exclude these observations from the analysis ( as a NA). Is there a command that I can do it for the entire data set rather than one by one for each variable ( tmp - xcv[xcv$v1 != -9, ]) V1 v2 v3 v4 1123 14 -9 12-9 21 3 -9 30 41 25 15 07 -9 10 and I want the results as follows V1v2 v3 v4 11 2314 NA 12 NA21 3 NA 3041 25 15 07 NA10 The second question is I want to calculate the number of days between two dates Start end number of days 2002062620020805 40 2003010120030421 110 How do I do it in R? Thanks in advance [[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] Best way to preallocate numeric NA array?
You can try this also: rep(NA_integer_, 10) On Thu, Nov 26, 2009 at 2:03 PM, Rob Steele freenx.10.robste...@xoxy.net wrote: These are the ways that occur to me. ## This produces a logical vector, which will get converted to a numeric ## vector the first time a number is assigned to it. That seems ## wasteful. x - rep(NA, n) ## This does the conversion ahead of time but it's still creating a ## logical vector first, which seems wasteful. x - as.numeric(rep(NA, n)) ## This avoids type conversion but still involves two assignments for ## each element in the vector. x - numeric(n) x[] - NA ## This seems reasonable. x - rep(as.numeric(NA), n) Comments? Thanks, Rob __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Testing for strength of fit using R
On Nov 26, 2009, at 9:48 AM, Steve Murray wrote: Dear all, I am trying to validate a model by comparing simulated output values against observed values. I have produced a simple X-y scatter plot with a 1:1 line, so that the closer the points fall to this line, the better the 'fit' between the modelled data and the observation data. I am now attempting to quantify the strength of this fit by using a statistical test in R. I am no statistics guru, but from my limited understanding, I suspect that I need to use the Chi Squared test (I am more than happy to be corrected on this though!). However, this results in the following: chisq.test(data$Simulation,data$Observation) Pearson's Chi-squared test data: data$Simulation and data$Observation X-squared = 567, df = 550, p-value = 0.2989 Warning message: In chisq.test(data$Simulation, data$Observation) : Chi-squared approximation may be incorrect The ?chisq.test document suggests that the objects should be of vector or matrix format, so I tried the following, but still receive a warning message (and different results): chisq.test(as.matrix(data[,4:5])) Pearson's Chi-squared test data: as.matrix(data[, 4:5]) X-squared = 130.8284, df = 26, p-value = 6.095e-16 When you look at your data you see only 27 cases, so it would be implausible that your first invocation with a degree of freedom = 550 would be giving you something meaningful. The second one might have been more meaningful goodness of fit. I cannot explain why code # 1 did not give the same results since I would have thought that the positional matching of R would have resulted in the same results for both calls. What happens if you try: chisq.test(data$Simulation, y=data$Observation) # ? All of that being said, chisq.test is primarily intended for contingency tables. Testing association between two paired continuous variables is usually approached with regression and correlation tests. E.g.: ?cor ?lm Also may want to look at the Q-Q plot. ?qqplot -- David Winsemius Warning message: In chisq.test(as.matrix(data[, 4:5])) : Chi-squared approximation may be incorrect What am I doing wrong and how can I successfully measure how well the simulated values fit the observed values? If it's of any help, here are how my data are structured - note that I am only using columns 4 and 5 (Observation and Simulation). str(data) 'data.frame':27 obs. of 5 variables: $ Location: Factor w/ 27 levels Australia,Brazil,..: 8 2 13 19 22 14 16 23 6 7 ... $ Vegetation : Factor w/ 21 levels Beech,Broadleaf evergreen laurel,..: 17 21 2 16 15 16 9 16 3 4 ... $ Vegetation.Class: Factor w/ 4 levels Boreal and Temperate Evergreen,..: 3 3 4 1 1 1 4 1 4 1 ... $ Observation : num 24 8.9 14.7 26.7 42.4 31.7 30.8 7.5 14 22 ... $ Simulation : num 33.9 7.8 9.74 7.6 11.8 10.7 12 28.1 1.7 1.7 ... I hope someone is able to point me in the right direction. Many thanks, 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] Best way to preallocate numeric NA array?
Or best: rep(NA_real_, 10) On Thu, Nov 26, 2009 at 2:31 PM, Henrique Dallazuanna www...@gmail.com wrote: You can try this also: rep(NA_integer_, 10) On Thu, Nov 26, 2009 at 2:03 PM, Rob Steele freenx.10.robste...@xoxy.net wrote: These are the ways that occur to me. ## This produces a logical vector, which will get converted to a numeric ## vector the first time a number is assigned to it. That seems ## wasteful. x - rep(NA, n) ## This does the conversion ahead of time but it's still creating a ## logical vector first, which seems wasteful. x - as.numeric(rep(NA, n)) ## This avoids type conversion but still involves two assignments for ## each element in the vector. x - numeric(n) x[] - NA ## This seems reasonable. x - rep(as.numeric(NA), n) Comments? Thanks, Rob __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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 -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] mcp.area vs. kernel.area Output... ?
I am trying to estimate home range size using 2 different methods in the adehabitat package, but I am slightly confounded by the results. ## Attached is an R object file containing animal relocations with a field for id, and x y coordinates ## (in metres) load(temp) require(adehabitat) ## This produces the 95% Minimum Convex Polygon area for animal 2002007 mcp.area(xy=temp[,2:3], id=temp$id, percent=95, unin=m, unout=km2, plotit=FALSE)[1] ## This produces an estimation of area under the 95% Fixed Kernel Density kernel.area(temp[,2:3], temp$id, h=href, levels=95, unin=m, unout=km2)[1] Now my question: Why are the two responses not more similar? Since the kernel estimation is more conservative, why is the area obtained by this method more than two times bigger than what is obtained using the Minimum Convex Polygon method? Tyler http://old.nabble.com/file/p26531917/temp temp -- View this message in context: http://old.nabble.com/mcp.area-vs.-kernel.area-Output...---tp26531917p26531917.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] Missing and number of days
For your first question, I believe that
dat[dat==-9]=NA
should do the trick
For your second, are you dates in the Date() format? If not, try ?Date
Once you get them in Date format, then you can simply subtract them
d1 = as.Date('20090604',format=%Y%m%d)
d2 = as.Date('20080604',format=%Y%m%d)
d1-d2
Time difference of 365 days
On Thu, Nov 26, 2009 at 12:30 PM, Val valkr...@gmail.com wrote:
Hi all,
Assume that I have a data set (“xcv”) with several variables and some of
the variables have a missing observation represented by -9 as shown below.
I want to exclude these observations from the analysis ( as a NA). Is
there a command that I can do it for the entire data set rather than one by
one for each variable ( tmp - xcv[xcv$v1 != -9, ])
V1 v2 v3 v4
11 23 14 -9
12 -9 21 3
-9 30 41 25
15 07 -9 10
and I want the results as follows
V1 v2 v3 v4
11 23 14 NA
12 NA 21 3
NA 30 41 25
15 07 NA 10
The second question is I want to calculate the number of days between two
dates
Start end number of days
20020626 20020805 40
20030101 20030421 110
How do I do it in R?
Thanks in advance
[[alternative HTML version deleted]]
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[R] different fits for geese and geeglm in geepack?
Dear all, I am trying to fit a GEE model on eagle productivity (number of hatched offspring per nest) using the geeglm function in the library geepack and I found an odd result. My understanding is that the function geese and geeglm should give the same fits, as actually geeglm uses geese to fit the model, providing a glm style output. However, if I fit the same model with geeglm and geese I get slightly different estimates of the parameters. Most striking is the difference between the estimates of the correlation parameter where the differences are huge: (geese: alpha= -0.0727, se= 0.0608; geeglm: -0.219, se= 0.091). Anybody knows why this is like that and which of the two I should rather trust? (I attach the outputs of the two models at the end of this mail) thanks a lot for your hints! Achaz von Hardenberg PS: One more question actually: anybody has got some code to calculate the QICu values to compare GEE models with and without specific fixed factors using geepack? ## GEESE OUTPUT: Call: geese(formula = PROD ~ as.factor(clas3) + Twinter + Tprecova, id = Nterr, waves = anno, data = aquile.dat2, family = poisson, corstr = ar1) Mean Model: Mean Link: log Variance to Mean Relation: poisson Coefficients: estimate san.se waldp (Intercept)-1.7850 0.3661 23.77 1.08e-06 as.factor(clas3)2 0.7165 0.2475 8.38 3.79e-03 as.factor(clas3)3 0.5052 0.3368 2.25 1.34e-01 Twinter-0.1066 0.0464 5.28 2.16e-02 Tprecova -0.0549 0.0368 2.22 1.36e-01 Scale Model: Scale Link:identity Estimated Scale Parameters: estimate san.se waldp (Intercept)0.764 0.123 38.6 5.17e-10 Correlation Model: Correlation Structure: ar1 Correlation Link: identity Estimated Correlation Parameters: estimate san.se wald p alpha -0.0727 0.0608 1.43 0.232 Returned Error Value:0 Number of clusters: 21 Maximum cluster size: 20 ### GEEGLM OUTPUT: Call: geeglm(formula = PROD ~ as.factor(clas3) + Twinter + Tprecova, family = poisson, data = aquile.dat2, id = Nterr, waves = anno, corstr = ar1) Coefficients: Estimate Std.err Wald Pr(|W|) (Intercept)-1.7992 0.3751 23.01 1.6e-06 *** as.factor(clas3)2 0.7412 0.2623 7.99 0.0047 ** as.factor(clas3)3 0.5253 0.3335 2.48 0.1152 Twinter-0.1083 0.0473 5.24 0.0220 * Tprecova -0.0483 0.0354 1.86 0.1721 --- Signif. codes: 0 *** 0.001 ** 0.01 * 0.05 . 0.1 1 Estimated Scale Parameters: Estimate Std.err (Intercept)0.773 0.117 Correlation: Structure = ar1 Link = identity Estimated Correlation Parameters: Estimate Std.err alpha -0.219 0.091 Number of clusters: 21 Maximum cluster size: 20 Dr. Achaz von Hardenberg Centro Studi Fauna Alpina - Alpine Wildlife Research Centre Servizio Sanitario e della Ricerca Scientifica Parco Nazionale Gran Paradiso, Degioz, 11, 11010-Valsavarenche (Ao), Italy Present address: National Centre for Statistical Ecology School of Mathematics, Statistics and Actuarial Science, University of Kent, Canterbury, UK E-mail: achaz.hardenb...@pngp.it fa...@pngp.it Skype: achazhardenberg Mobile: +44.(0)783.266.5995 Dr. Achaz von Hardenberg Centro Studi Fauna Alpina - Alpine Wildlife Research Centre Servizio Sanitario e della Ricerca Scientifica Parco Nazionale Gran Paradiso, Degioz, 11, 11010-Valsavarenche (Ao), Italy Present address: National Centre for Statistical Ecology School of Mathematics, Statistics and Actuarial Science, University of Kent, Canterbury, UK E-mail: achaz.hardenb...@pngp.it fa...@pngp.it Skype: achazhardenberg Mobile: +44.(0)783.266.5995 [[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] Best way to preallocate numeric NA array?
Douglas Bates wrote: On Thu, Nov 26, 2009 at 10:03 AM, Rob Steele freenx.10.robste...@xoxy.net wrote: These are the ways that occur to me. ## This produces a logical vector, which will get converted to a numeric ## vector the first time a number is assigned to it. That seems ## wasteful. x - rep(NA, n) ## This does the conversion ahead of time but it's still creating a ## logical vector first, which seems wasteful. x - as.numeric(rep(NA, n)) ## This avoids type conversion but still involves two assignments for ## each element in the vector. x - numeric(n) x[] - NA ## This seems reasonable. x - rep(as.numeric(NA), n) Comments? My intuition would be to go with the third method (allocate a numeric vector then assign NA to its contents) but I haven't tested the different. In fact, it would be difficult to see differences in, for example, execution time unless n was very large. This brings up a different question which is, why do you want to consider this? Are you striving for readability, for speed, for low memory footprint, for efficiency in some other way? When we were programming in S on machines with 1 mips processors and a couple of megabytes of memory, such considerations were important. I'm not sure they are quite as important now. Thanks--good questions. For any code, I'd order the requirements like this: 1) Correct 2) Readable 3) Space efficient 4) Time efficient Compromises are sometimes necessary. R is such an odd language that it really helps readability to settle on easily recognizable idioms. That's true in any language where there's more than one way to do things but I find it especially true in R. I agree that the efficiency of this operation only matters with very large vectors or very many repetitions. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Does nargin and nargout work with R functions?
I am porting some MATLAB functions over to R and hopefully into a package, so I
am curious if nargin and nargout work with R functions.
Here is kind of an example of where I need to head in order to port
control-1.0.11 from Octave over to R. The Octave control-1.0.11 package
has the capability to produce bode plots of transfer functions. I hope to post
this package once the port over to R is complete.
Thanks again for all the feedback and insights.
bode-function(sys, w, outputs, inputs, plot_style)
{
# ...
if (nargin 1 || nargin 5)
{
print(This works)
}
if (nargout 1)
{
print(This also works)
}
return(list(mag_r, phase_r, w_r))
}
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Re: [R] Best way to preallocate numeric NA array?
Douglas Bates wrote: On Thu, Nov 26, 2009 at 10:03 AM, Rob Steele freenx.10.robste...@xoxy.net wrote: These are the ways that occur to me. ## This produces a logical vector, which will get converted to a numeric ## vector the first time a number is assigned to it. That seems ## wasteful. x - rep(NA, n) ## This does the conversion ahead of time but it's still creating a ## logical vector first, which seems wasteful. x - as.numeric(rep(NA, n)) ## This avoids type conversion but still involves two assignments for ## each element in the vector. x - numeric(n) x[] - NA ## This seems reasonable. x - rep(as.numeric(NA), n) Comments? My intuition would be to go with the third method (allocate a numeric vector then assign NA to its contents) but I haven't tested the different. In fact, it would be difficult to see differences in, for example, execution time unless n was very large. This brings up a different question which is, why do you want to consider this? Are you striving for readability, for speed, for low memory footprint, for efficiency in some other way? When we were programming in S on machines with 1 mips processors and a couple of megabytes of memory, such considerations were important. I'm not sure they are quite as important now. Thanks--good questions. For any code, I'd order the requirements like this: 1) Correct 2) Readable 3) Space efficient 4) Time efficient Compromises are sometimes necessary. R is such an odd language that it really helps readability to settle on easily recognizable idioms. That's true in any language where there's more than one way to do things but I find it especially true in R. I agree that the efficiency of this operation only matters with very large vectors or very many repetitions. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Testing for strength of fit using R
Steve Murray wrote: Dear all, I am trying to validate a model by comparing simulated output values against observed values. I have produced a simple X-y scatter plot with a 1:1 line, so that the closer the points fall to this line, the better the 'fit' between the modelled data and the observation data. I am now attempting to quantify the strength of this fit by using a statistical test in R. I am no statistics guru, but from my limited understanding, I suspect that I need to use the Chi Squared test (I am more than happy to be corrected on this though!). However, this results in the following: chisq.test(data$Simulation,data$Observation) Pearson's Chi-squared test data: data$Simulation and data$Observation X-squared = 567, df = 550, p-value = 0.2989 Warning message: In chisq.test(data$Simulation, data$Observation) : Chi-squared approximation may be incorrect The ?chisq.test document suggests that the objects should be of vector or matrix format, so I tried the following, but still receive a warning message (and different results): chisq.test(as.matrix(data[,4:5])) Pearson's Chi-squared test data: as.matrix(data[, 4:5]) X-squared = 130.8284, df = 26, p-value = 6.095e-16 Warning message: In chisq.test(as.matrix(data[, 4:5])) : Chi-squared approximation may be incorrect What am I doing wrong and how can I successfully measure how well the simulated values fit the observed values? If it's of any help, here are how my data are structured - note that I am only using columns 4 and 5 (Observation and Simulation). str(data) 'data.frame':27 obs. of 5 variables: $ Location: Factor w/ 27 levels Australia,Brazil,..: 8 2 13 19 22 14 16 23 6 7 ... $ Vegetation : Factor w/ 21 levels Beech,Broadleaf evergreen laurel,..: 17 21 2 16 15 16 9 16 3 4 ... $ Vegetation.Class: Factor w/ 4 levels Boreal and Temperate Evergreen,..: 3 3 4 1 1 1 4 1 4 1 ... $ Observation : num 24 8.9 14.7 26.7 42.4 31.7 30.8 7.5 14 22 ... $ Simulation : num 33.9 7.8 9.74 7.6 11.8 10.7 12 28.1 1.7 1.7 ... The chisquare test is not the right thing here. You may have been fooled by the goodness-of-fit phrase associated with the test. I would do a cor.test(). But if the above is the real data, then there probably isn't much to test; you have very little agreement for the first 10 pairs. -Peter Ehlers I hope someone is able to point me in the right direction. Many thanks, Steve _ Have more than one Hotmail account? Link them together to easily access both http://clk.atdmt.com/UKM/go/186394591/direct/01/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Save workspace with ff objects
Hi All, My script generates a mixture of normal and ff objects. I need to run the script for different parameter settings. Very often I would like to save the workspace for each parameter setting, so that I can get back to it later on. Is there an easy way to do this, instead of needing to save individual ff objects separately? I've tried the naive way of just saving the workspace, only to find that ff objects are empty. Thanks for help. Yue Sheng [[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] Does nargin and nargout work with R functions?
Hi,
I think you can use match.call() to retrieve the number of arguments
passed to a function (see below), but I don't think nargout makes
sense in R like it does in Matlab.
foo - function(...){
print(match.call())
nargin - length(as.list(match.call())) -1
print(nargin)
}
foo(a=1, b=2)
foo()
foo(1:3, a=2, c=3)
HTH,
baptiste
2009/11/26 Jason Rupert jasonkrup...@yahoo.com:
I am porting some MATLAB functions over to R and hopefully into a package, so
I am curious if nargin and nargout work with R functions.
Here is kind of an example of where I need to head in order to port
control-1.0.11 from Octave over to R. The Octave control-1.0.11 package
has the capability to produce bode plots of transfer functions. I hope to
post this package once the port over to R is complete.
Thanks again for all the feedback and insights.
bode-function(sys, w, outputs, inputs, plot_style)
{
# ...
if (nargin 1 || nargin 5)
{
print(This works)
}
if (nargout 1)
{
print(This also works)
}
return(list(mag_r, phase_r, w_r))
}
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[R] How shall one present LRT test statistic in a scientific journal ?
Hello !! I'm recently having a debate with my PhD supervisor regarding how to write the result of a likelihood ratio test in an article I'm about to submit. I analysed my data using lme mixed modelling. To get some p-values for my fixed effect I used model simplification and the typical output R gives looks like this: model2 = update ( model1,~.-factor A) anova (model1, model2) Model df AIC BIC logLik Test L.Ratio p-value model 1 1 26 -78.73898 15.29707 65.36949 model 2 2 20 -73.70539 -1.36997 56.85270 1 vs 217.03359 0.0092 I thought about presenting it very simply copying/pasting R table and writing it like: factor A had a significant effect on the response variable (Likelihood ratio test, L-ratio = 17.033, p = 0.0092) But my boss argued that it's too unusual (at least in our field of evolutionary biology) and that I should present instead the LR statistic together with the corresponding Chi^2 statistic since the likelihood ratio is almost distributed like a Chi2 (df1-df2), and then write down the p-value corresponding to this value of Chi. I looked up in the current litterature but cannot really find a proper answer to that dilmena. So, dear evolutionary biologists R users, how would you present it ? Thank you very much, Julien. -- View this message in context: http://old.nabble.com/How-shall-one-present-LRT-test-statistic-in-a-scientific-journal---tp26532480p26532480.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] Grouped Boxplot
Thanks Petr!
On Thu, Nov 26, 2009 at 12:31 AM, Petr PIKAL petr.pi...@precheza.cz wrote:
Hi
r-help-boun...@r-project.org napsal dne 24.11.2009 18:44:43:
Back in March Soren Vogel asked exactly the same thing:
Here is the solution that was offered then. (He offered a dataset as
requested in the Posting Guide.) ... with only a minor adjustment:
g - rep.int(c(A, B, C, D), 125)
t - rnorm(5000)
a - sample(t, 500, replace=TRUE)
b - sample(t, 500, replace=TRUE)
dta - data.frame(val = sample(t,1000), g = gl(4, 250, labels=c(A,
B, C, D)) , G2 = gl(2,1, labels=c(XX, YY)))
boxplot( val ~ g + G2, data=dta, at = 0.8*c(1,2,3,4,6,7,8,9),
boxwex=0.8)
This should have shown up with this:
RSiteSearch(grouped boxplot)
or ggplot2 variant
p - ggplot(dta, aes(factor(G2), val))
p + geom_boxplot(aes(fill = factor(g)))
Regards
Petr
--
David
On Nov 24, 2009, at 10:35 AM, Gary wrote:
Thanks Uwe and Petr for your suggestion. Please see Fig. 3 on the
attached
file. Thanks!
On Tue, Nov 24, 2009 at 6:44 AM, Petr PIKAL petr.pi...@precheza.cz
wrote:
Hi
try ggplot2. It has some functionality to make groups of boxplots.
Regards
Petr
Your attachment did not pass the list's filters. Anyway, see ?boxplot.
Uwe Ligges
r-help-boun...@r-project.org napsal dne 24.11.2009 03:33:49:
Hi R Users,
I'm interested in plotting a grouped boxplot (please see attached
file
for
sample). Can anyone suggest a function{package} which can help me
achieve
this.
Thanks,
Gary
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GroupedBoxplot.pdf__
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David Winsemius, MD
Heritage Laboratories
West Hartford, CT
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Re: [R] How shall one present LRT test statistic in a scientific journal ?
On Nov 26, 2009, at 12:14 PM, JVezilier wrote: Hello !! I'm recently having a debate with my PhD supervisor regarding how to write the result of a likelihood ratio test in an article I'm about to submit. I analysed my data using lme mixed modelling. To get some p-values for my fixed effect I used model simplification and the typical output R gives looks like this: model2 = update ( model1,~.-factor A) anova (model1, model2) Model df AIC BIC logLik Test L.Ratio p-value model 1 1 26 -78.73898 15.29707 65.36949 model 2 2 20 -73.70539 -1.36997 56.85270 1 vs 2 17.03359 0.0092 I thought about presenting it very simply copying/pasting R table and writing it like: factor A had a significant effect on the response variable (Likelihood ratio test, L-ratio = 17.033, p = 0.0092) But my boss argued that it's too unusual (at least in our field of evolutionary biology) and that I should present instead the LR statistic together with the corresponding Chi^2 statistic since the likelihood ratio is almost distributed like a Chi2 (df1-df2), and then write down the p-value corresponding to this value of Chi. I looked up in the current litterature but cannot really find a proper answer to that dilmena. So, dear evolutionary biologists R users, how would you present it ? I am not an evolutionary biologist, but presumably your supervisor is one. Why are you picking a fight not only with him but with your prospective audience when there is no meaningful difference? Here is the p-value you would get with his method: 1-pchisq( 2*(65.36949 - 56.85270), df=6) [1] 0.009160622 -- David Winsemius, just a guy who formerly argued about such matters. Thank you very much, Julien. -- View this message in context: http://old.nabble.com/How-shall-one-present-LRT-test-statistic-in-a-scientific-journal---tp26532480p26532480.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. 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] Help: Beanplots calculating wrong average
Hi Tom, Thank you for the friendly and informative answer. It does explain a lot of things, actually. As with any good answer, it inevitably leads to other questions. In the first place, I need the arithmetic mean. It's what we base our calculations on... My code is currently this: Metall-c(Cu,Cu,Cu,Cu,Cu,Cu,Cu,Cu,Cu,Cr,Cr,Cr,Cr, Cr,Cr,Cr,Cr,Cr,As,As,As,As,As,As,As,As,As,Pb,P b,Pb,Pb,Pb,Pb,Pb,Pb,Pb,Zn,Zn,Zn,Zn,Zn,Zn,Zn,Zn ,Zn) Halt-c(85,13,13,340,18,13,88,24,12,216,33,21,454,20,18,88,30,21,1254,22,4.2 ,1081,35,6,1772,192,7.6,43,20,12,3107,21,12,30,24,19,1109,57,46,269,68,50,58 5,131,52) beanplot(Halt~Metall, log = y, yaxt = n, ylab=Halt (mg/kg),cex.lab=1.2) axis(2,c(1,10,100,1000,1)) polygon(c(0.2966510,0.2966510,1.4832033,1.4832033,3.6160162,3.6160162,4.4921 444,4.4921444,5.6968371,5.6968371),c(2.763021e-01,10,10,80,80,40,40,250,250, 2.763021e-01),col=#66FF0090, border=#66FF0090) text(5.58,10,KM, cex=1.2, font=2) polygon(c(0.2966510,0.29665101,1.4832033,1.4832033),c(10,25,25,10),col=#FFF F0090,border=#0090) polygon(c(1.4832033,1.4832033,2.5027348,2.5027348,3.6160162,3.6160162,4.4921 444,4.4921444,5.6968371,5.6968371,4.4921444,4.4921444,3.6160162,3.6160162,1. 4832033),c(80,150,150,200,200,400,400,500,500,250,250,40,40,80,80),col=#FFF F0090,border=#0090) text(5.54,350,MKM, cex=1.2, font=2) polygon(c(0.2966510,0.2966510,5.6968371,5.6968371,4.4921444,4.4921444,3.6160 162,3.6160162,2.5027348,2.5027348,1.4832033,1.4832033),c(25,30085.997183,300 85.997183,500,500,400,400,200,200,150,150,25),col=#FF90,border=#FF000 090) text(5.54,2500,MKM, cex=1.2, font=2) The polygons convey information on whether each sample is higher than the soil guideline value. If I take away, the log scale, the vast difference in values obscures the polygons... Ideally I'd like the average beanline to be the arithmetic mean or to be gone altogether. Can't seem to make beanplot do this... Sincerely, Michael Hopgood -Ursprungligt meddelande- Från: Tom Wainwright [mailto:thomas.wainwri...@noaa.gov] Skickat: den 24 november 2009 18:43 Till: Michael Hopgood Kopia: r-help@r-project.org Ämne: Re: [R] Help: Beanplots calculating wrong average Hi Michael, Looking at the help for beanplot(), note that the 'log' option defaults to 'auto' which means the function will automatically log-transform data like yours. This also implies that the mean it shows is the geometric mean, not the arithmetic mean. As you note, the transformation doesn't affect the median. If you don't want this behavior, I think setting log= will do the trick. Hope this helps. Tom Wainwright On 11/24/2009 03:52 AM, Michael Hopgood wrote: Hi there, I have a set of data that looks like this: As1988-c(1254.0, 22.0, 4.2, 1081.0, 35.0, 6.0, 1772.0, 192.0, 7.6) The mean of this (as calculated by R) is: 485.9778 The median of this (as calculated by R) is: 35 If I then make a beanplot(As1988), I find that the beanline (average) is now 77.68561 while the beanline (median) is 35.39739 (using the locator function to check the graph and log axis). While I can understand the small discrepancy of the median(mouse hovering over the line), I am at a loss to explain the huge difference between the means. Is this a flaw in the package or is there something I am missing? My gut feeling is that the log scales are affecting the calculations somehow. Sincerely, Michael Hopgood [[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. -- Tom Wainwright NOAA Northwest Fisheries Science Center Newport, Oregon ~~~ The contents of this message are mine personally and do not necessarily reflect any position of the Government or the National Oceanic and Atmospheric Administration. ~~~ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Export kde object as shapefile
I am trying to estimate home range size using the plug-in method with kernel density estimation in the kernel smoothing (ks) package. Unless there is another way I am not familiar with, in order to calculate spatial area under the space I need to convert my kde () object into a spatial object somehow in order to calculate its spatial area. Could someone demonstrate how this might be done? -- View this message in context: http://old.nabble.com/Export-kde-object-as-shapefile-tp26532782p26532782.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How shall one present LRT test statistic in a scientific journal ?
David Winsemius wrote: On Nov 26, 2009, at 12:14 PM, JVezilier wrote: Hello !! I'm recently having a debate with my PhD supervisor regarding how to write the result of a likelihood ratio test in an article I'm about to submit. I analysed my data using lme mixed modelling. To get some p-values for my fixed effect I used model simplification and the typical output R gives looks like this: model2 = update ( model1,~.-factor A) anova (model1, model2) Model df AIC BIC logLik Test L.Ratio p-value model 1 1 26 -78.73898 15.29707 65.36949 model 2 2 20 -73.70539 -1.36997 56.85270 1 vs 217.03359 0.0092 I thought about presenting it very simply copying/pasting R table and writing it like: factor A had a significant effect on the response variable (Likelihood ratio test, L-ratio = 17.033, p = 0.0092) But my boss argued that it's too unusual (at least in our field of evolutionary biology) and that I should present instead the LR statistic together with the corresponding Chi^2 statistic since the likelihood ratio is almost distributed like a Chi2 (df1-df2), and then write down the p-value corresponding to this value of Chi. I looked up in the current litterature but cannot really find a proper answer to that dilmena. So, dear evolutionary biologists R users, how would you present it ? I am not an evolutionary biologist, but presumably your supervisor is one. Why are you picking a fight not only with him but with your prospective audience when there is no meaningful difference? Here is the p-value you would get with his method: 1-pchisq( 2*(65.36949 - 56.85270), df=6) [1] 0.009160622 As I understood the question, it *is* purely formalistic. I.e., what to write, not what to do. I'd say L-ratio is plain wrong, since this is not a ratio, but the log of a ratio. -2lnQ or -2logQ is what my old teachers would write, but pragmatically, I'd expect the best chances with editors and reviewers to be LRT: chi-square=17.03, df=6, p=0.092, possibly with LRT spelled out. (Some journals like to have the df because it allows reviewers to catch glaring mistakes like categorical variables treated as numeric.) -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - (p.dalga...@biostat.ku.dk) FAX: (+45) 35327907 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] makefile for sweave
On 26/11/2009 9:14 AM, Wolfgang Raffelsberger wrote:
Dear all,
I can't get texi2dvi working right. Basically I'd like to convert a .lex
to .pdf without having to fiddle with the issue Sweave.sty not being in
my current directory (as this was sugested in other posts on this list).
When I'm in the R-Gui I can get the help via
?texi2dvi
(So I conclude its installed.)
Bad conclusion. That tells you that the R function texi2dvi() is
installed. That function tries to run the system level command
texi2dvi; that's the part that is failing. As Sundar said, this may
just be because you don't have your PATH set to include the directory
it's in.
Duncan Murdoch
However, when I try to use it to concert a .tex to .pdf I get trouble ...
For example :
A)
The file test02.r contains :
Sweave(Sweave_test01.rnw)
library(tools)
texi2dvi(Sweave_test01.tex, pdf =T)
Now, when I run on the linux command line :
R --vanilla -q test02.r
I get :
Sweave(Sweave_test01.rnw)
Writing to file Sweave_test01.tex
Processing code chunks ...
1 : term hide (label=chunk_ini)
2 : term verbatim eps pdf (label=Fig01)
3 : term tex (label=packageVersionInfo)
Loading required package: xtable
You can now run LaTeX on 'Sweave_test01.tex'
library(tools)
texi2dvi(Sweave_test01.tex, pdf =T)
Error in texi2dvi(Sweave_test01.tex, pdf = T) :
Running 'texi2dvi' on 'Sweave_test01.tex' failed.
Messages:
sh: texi2dvi: command not found
Execution halted
B)
In a previous message on this list I found the following command line(s)
suggested, but I my case it won't work
star5_R_test_ R CMD texi2dvi --help
/usr/local/lib64/R/bin/Rcmd: line 62: exec: texi2dvi: not found
similarly, when execute (as sugested) I get the same error message
star5_R_test_ R CMD texi2dvi -p Sweave_test01.tex
/usr/local/lib64/R/bin/Rcmd: line 62: exec: texi2dvi: not found
I don't understand how can a command can be present (= installed) and
still not being found as the error messages suggest ?
For completeness :
sessionInfo()
R version 2.10.0 (2009-10-26)
x86_64-unknown-linux-gnu
locale:
[1] C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] xtable_1.5-6 mouse4302probe_2.5.0 AnnotationDbi_1.8.1
[4] mouse4302cdf_2.5.0 MASS_7.3-3 fdrtool_1.2.5
[7] limma_3.2.1 affyPLM_1.22.0 preprocessCore_1.8.0
[10] gcrma_2.18.0 affy_1.24.2 Biobase_2.6.0
loaded via a namespace (and not attached):
[1] Biostrings_2.14.3 DBI_0.2-4 IRanges_1.4.4 RSQLite_0.7-3
[5] affyio_1.14.0 splines_2.10.0tools_2.10.0
Thank's in advance,
Wolfgang
Charles C. Berry a écrit :
On Tue, 8 Sep 2009, Welma Pereira wrote:
Hello, I have the following makefile. The problem is that the
bibliography
doesn t work. Any help would be appreciated! I really don t don t
what to
do..:-(
# The sources of the report (tex, Rnw and other files (e.g. bib, idx))
TEX_CMPS = Report problem
RNW_CMPS = prop1 prop2 ExeExps
OTHER = Report.bib
# The name of the report to produce
all: Report.pdf
code: $(RNW_CMPS:=.R)
clean:
rm -f *.log *.dvi *~
# On what does the report depends?
Report.pdf: $(TEX_CMPS:=.tex) $(RNW_CMPS:=.tex) ${OTHER} makefile
TEXINPUTS=${TPUTS} pdflatex $
TEXINPUTS=${TPUTS} pdflatex $
IIRC
R CMD texi2dvi -p target.tex
takes care of finding sweave.sty and running latex thru all the
iterations needed to build cross-references and a usable pdf.
Try
R CMD texi2dvi --help
at the shell prompt.
HTH,
Chuck
rm *.log
#mv *.aux $(dir $)
# How to build the tex files from the Rnw (Sweave) files
%.tex: %.Rnw
echo library(utils); options(width=60); Sweave('$') | ${R_PRG}
--no-save --vanilla
mv $(notdir $*.tex) $(dir $)
# How to build the R code files from the Rnw (Sweave) files
%.R: %.Rnw
echo library(utils); Stangle('$') | ${R_PRG} --no-save --vanilla
%.bib:
TEXINPUTS=${TPUTS} pdflatex $
bibtex $
%.aux:
TEXINPUTS=${TPUTS} pdflatex $
bibtex $
%.idx:
TEXINPUTS=${TPUTS} pdflatex $
makeindex $
cheers!
[[alternative HTML version deleted]]
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PLEASE do read the posting guide
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and provide commented, minimal, self-contained, reproducible code.
Charles C. Berry(858) 534-2098
Dept of Family/Preventive
Medicine
E mailto:cbe...@tajo.ucsd.eduUC San Diego
http://famprevmed.ucsd.edu/faculty/cberry/ La Jolla, San Diego
92093-0901
__
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Wolfgang Raffelsberger, PhD
Laboratoire de BioInformatique et Génomique Intégratives
IGBMC,
1
Re: [R] How shall one present LRT test statistic in a scientific journal ?
On Nov 26, 2009, at 12:46 PM, Peter Dalgaard wrote: David Winsemius wrote: On Nov 26, 2009, at 12:14 PM, JVezilier wrote: Hello !! I'm recently having a debate with my PhD supervisor regarding how to write the result of a likelihood ratio test in an article I'm about to submit. I analysed my data using lme mixed modelling. To get some p-values for my fixed effect I used model simplification and the typical output R gives looks like this: model2 = update ( model1,~.-factor A) anova (model1, model2) Model df AIC BIC logLik Test L.Ratio p-value model 1 1 26 -78.73898 15.29707 65.36949 model 2 2 20 -73.70539 -1.36997 56.85270 1 vs 2 17.03359 0.0092 I thought about presenting it very simply copying/pasting R table and writing it like: factor A had a significant effect on the response variable (Likelihood ratio test, L-ratio = 17.033, p = 0.0092) But my boss argued that it's too unusual (at least in our field of evolutionary biology) and that I should present instead the LR statistic together with the corresponding Chi^2 statistic since the likelihood ratio is almost distributed like a Chi2 (df1-df2), and then write down the p-value corresponding to this value of Chi. I looked up in the current litterature but cannot really find a proper answer to that dilmena. So, dear evolutionary biologists R users, how would you present it ? I am not an evolutionary biologist, but presumably your supervisor is one. Why are you picking a fight not only with him but with your prospective audience when there is no meaningful difference? Here is the p-value you would get with his method: 1-pchisq( 2*(65.36949 - 56.85270), df=6) [1] 0.009160622 As I understood the question, it *is* purely formalistic. I.e., what to write, not what to do. I'd say L-ratio is plain wrong, since this is not a ratio, but the log of a ratio. -2lnQ or -2logQ is what my old teachers would write, but pragmatically, I'd expect the best chances with editors and reviewers to be LRT: chi-square=17.03, df=6, p=0.092, possibly with LRT spelled out. (Some journals like to have the df because it allows reviewers to catch glaring mistakes like categorical variables treated as numeric.) I wonder about the phrase used model simplification. Wouldn't that raise a question about the proper degrees of freedom to use? If terms were dropped from the model based simply on the basis of non- significance shouldn't there be some appropriate penalization of subsequent tests of significance? -- David. -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - (p.dalga...@biostat.ku.dk) FAX: (+45) 35327907 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] barchart() {Lattice} help.
Hi R Users, I'm trying to plot a stacked barplot. Here is data: Sample Col1 Col2 Col3 Row1 -2 4 -1 Row2 3 -2 4 Row3 3 5 -2 Row4 4 1 -1 I'm using following R code: library(lattice) dta-read.table(data.txt, header=TRUE, row.names=Sample) barchart(data.matrix(dta), horizontal=FALSE, stack=TRUE, col=2:4, auto.key=list(space=right, title=names(dimnames(dta))[2]) ) Above code is working fine, but I need help with: 1) Legend boxes have default colors, whereas I'm looking them to match with barplot colors (col=2:4). 2) Can I increase scale for y axis, like currently it plotting -2,0,2,4,... I would like it as -2,-1,0,1,... Any help would be greatly appreciated, Thanks, Peng [[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] Export kde object as shapefile
On Nov 26, 2009, at 12:40 PM, T.D.Rudolph wrote: I am trying to estimate home range size using the plug-in method with kernel density estimation in the kernel smoothing (ks) package. Unless there is another way I am not familiar with, in order to calculate spatial area under the space I need to convert my kde () object into a spatial object somehow in order to calculate its spatial area. Could someone demonstrate how this might be done? Can you explain what you mean by spatial area under the space or what it is for which you think there is a well defined area in a ks:::kde object? (Some example data would, as always, be welcome.) -- View this message in context: http://old.nabble.com/Export-kde-object-as-shapefile-tp26532782p26532782.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. 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] Export kde object as shapefile
Can you explain what you mean by spatial area under the space or what it is for which you think there is a well defined area in a ks:::kde object? My knowledge is not extensive in this area but I am aware that kernel methods can be used to estimate home range size. The function kernel.area in the adehabitat package, for example, produces a spatial area I interpret as being equivalent to estimated home range size using one of two possible smoothing parameters. I would like to use the plug-in method because I am convinced it will serve me best, but the ks package doesn't have a simple option like kde.area that produces what I'm looking for. Some example data would, as always, be welcome. Attached is an example subset of my data. I've only gotten so far as to produce the kde object and explore potential solutions. tmp.Hpi-Hpi(x=temp[,2:3]) tmp.kde-kde(x=temp[,2:3], H=tmp.Hpi) Tyler http://old.nabble.com/file/p26533942/temp temp David Winsemius wrote: On Nov 26, 2009, at 12:40 PM, T.D.Rudolph wrote: I am trying to estimate home range size using the plug-in method with kernel density estimation in the kernel smoothing (ks) package. Unless there is another way I am not familiar with, in order to calculate spatial area under the space I need to convert my kde () object into a spatial object somehow in order to calculate its spatial area. Could someone demonstrate how this might be done? Can you explain what you mean by spatial area under the space or what it is for which you think there is a well defined area in a ks:::kde object? (Some example data would, as always, be welcome.) -- View this message in context: http://old.nabble.com/Export-kde-object-as-shapefile-tp26532782p26532782.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. 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. -- View this message in context: http://old.nabble.com/Export-kde-object-as-shapefile-tp26532782p26533942.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] Insert elements into a vector in a defined positions
That's good . Your solution works for me.
Than you Rolf.
Rolf Turner-3 wrote:
On 26/11/2009, at 10:46 AM, Manuel Ramon wrote:
Dear R users,
I have a vector of length n and I want to insert some elements (in
my case
the NA string) into a defined positions. For example, my vector is
z1 and I
want to add NA's in positions 4, 6 y 7 so after that, my new
vector, z2,
should have a length of 10+3.
z1 - 1:10
id - c(4,6,7)
# And z2 should be:
z2 - c(1,2,3,NA,4,5,NA,NA,6,7,8,9,10)
Anyone knows how can I do that?
At first I thought append() might work ... but the after
argument to append seems to have to be of length 1.
How about:
z2 - numeric(length(z1)+length(id))
z2[id] - NA
z2[!is.na(z2)] - z1
A bit kludgy, but it appears to work.
cheers,
Rolf Turner
##
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Re: [R] Feature request for as.Date() function
On Thu, Nov 26, 2009 at 12:08 AM, jim holtman - jholt...@gmail.com +nabble+miller_2555+9dc9649aca.jholtman#gmail@spamgourmet.com wrote: An easy way is just to write your own function that will accept NA, convert it to NA and then call as.Date. I have written such a function, which has provided the temporary workaround mentioned. ( I am not that lazy yet :-) ) R is a functional language, so write some functions. Don't try to overload existing functions with new options that may break a lot of existing code. If you have special requirements, then adapt your code to them. You would probably have to wait around for a long time before an new option got in, so it is easier to create your own. I do not mind waiting for the additional functionality (and it is no longer an immediate need given the workaround). I was attempting to contribute to the continued enhancement of an open source project. Since the as.Date() function already defines standard unambiguous formats, and since NA (and NaN, Inf, etc) are not ambiguous within the transform to their numeric counterparts, it stands to reason that this is logical behaviour of this function. I also doubt this enhancement would break moderate-to-well-designed code since: (1) Existing code would enact a stop() condition based on the current implementation, forcing error-handling, if any. (2) Converting NA (and NaN, inf, etc) is not ambiguous. Coders feeding such strings should expect their numeric counterparts. In all likelihood, coders would convert these strings manually in error-handling code anyway. I have my solution, but wanted to better the project for use by other community members. The R Core Development Team is welcome to accept or ignore the suggestion. I do appreciate the time to discuss this topic, but will consider the matter closed for my part. Thanks. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] rattle(): unable to load shared library
Sometimes I've seen this under MS/Windows and the solution has been to reinstall the gtk libraries independent of R and to make sure this is the one installed: http://downloads.sourceforge.net/gladewin32/gtk-2.12.9-win32-2.exe. It looks like glade was not in the gtk libraries you installed? Hope that helps. Regards, Graham 2009/11/26 Matthieu Stigler matthieu.stig...@gmail.com Hi I'm trying to install the rattle GUI on winwos 2000, with last version R 2.10. I had a first problem using the rattle package, as it was asking pkg XMl, which is no more in the CRAN repo. I instead simply install in R/libraries the XML pkg from: http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/2.10/ Maybe I mised something here... So now I was able to run the library(rattle) then, using: rattle() I have following error message, it wants to install GTK+, what I do, restart R but then it does not work and I have following error message: Error in inDL(x, as.logical(local), as.logical(now), ...) : unable to load shared library 'C:/Programme/R/R-2.10.0/library/RGtk2/libs/RGtk2.dll': LoadLibrary failure: Die angegebene Prozedur wurde nicht gefunden. Failed to load RGtk2 dynamic library, attempting to install it. Learn more about GTK+ at http://www.gtk.org If the package still does not load, please ensure that GTK+ is installed and that it is on your PATH environment variable IN ANY CASE, RESTART R BEFORE TRYING TO LOAD THE PACKAGE AGAIN Error in .Call(name, ..., PACKAGE = PACKAGE) : C symbol name S_glade_xml_new not in DLL for package RGtk2 Rattle timestamp (for the error above): 2009-11-25 17:47:50 Checked for the install of GTK+, it's on the disk, and even on the PATH... don't know what I should do... any idea? Thanks!! Matthieu Stigler [[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] lattice --- different properties of lines corresponding to type=c(l, a) respectively
I think the subject says it all. I want to make a simple lattice plot,
using xyplot with the
argument type=c(l,a).
The problem then is that in the resulting plot it is
difficult/impossible to see which plot corresponds to the average
and which to the individual profiles. I triedthings like extra
arguments lwd=c(1,3) or col=c(blue,red)
hoping this would be interpreteded parallely to the type= argument,
but no. Like:
xyplot(response ~ time|group, repa0, groups=~Participant, type=c(b,
a), lwd=c(1, 3),
ylim=c(0, 10))
and many other variants ...
Then I vent for writing my own panel functions:
mypanel - function(x, y, ..., type){
panel.average(x, y, ..., horizontal=FALSE)
panel.xyplot(x, y, ..., type=type)
}
xyplot(response ~ time|group, repa0, groups=~Participant, type=l,
ylim=c(0, 10),
panel=panel.superpose, panel.groups=mypanel)
(which doesn't work)
???
Kjetil Halvorsen
To recreate the data:
repa0 -
structure(list(group = structure(c(1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L), .Label = c(1, 2), class = factor),
Participant = c(1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L,
11L, 12L, 13L, 14L, 1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L,
11L, 12L, 13L, 14L, 1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L,
11L, 12L, 13L, 14L, 1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L,
11L, 12L, 13L, 14L, 1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L,
11L, 12L, 13L, 14L, 1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L,
11L, 12L, 13L, 14L, 1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L,
11L, 12L, 13L, 14L, 1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L,
11L, 12L, 13L, 14L, 1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L,
11L, 12L, 13L, 14L, 1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 10L,
11L, 12L, 13L, 14L), time = c(1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L,
3L, 3L, 3L, 3L, 3L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L,
4L, 4L, 4L, 4L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L,
5L, 5L, 5L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L,
4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 5L,
5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L), response = c(2L,
10L, 8L, 4L, 0L, 4L, 10L, 2L, 3L, 4L, 1L, 2L, 3L, 3L, 5L,
2L, 10L, 3L, 0L, 3L, 10L, 1L, 7L, 3L, 2L, 10L, 8L, 5L, 8L,
0L, 10L, 2L, 0L, 2L, 10L, 10L, 3L, 2L, 10L, 4L, 6L, 0L, 5L,
0L, 6L, 2L, 0L, 2L, 10L, 5L, 3L, 2L, 6L, 4L, 5L, 0L, 5L,
0L, 5L, 0L, 0L, 0L, 10L, 0L, 0L, 2L, 5L, 0L, 5L, 0L, 3L,
8L, 6L, 1L, 3L, 0L, 5L, 4L, 10L, 0L, 3L, 3L, 6L, 5L, 2L,
0L, 2L, 0L, 4L, 0L, 5L, 4L, 5L, 1L, 0L, 2L, 0L, 5L, 3L, 1L,
8L, 2L, 4L, 0L, 0L, 0L, 10L, 4L, 3L, 0L, 0L, 10L, 3L, 3L,
6L, 1L, 4L, 0L, 0L, 0L, 10L, 3L, 3L, 2L, 2L, 10L, 2L, 3L,
5L, 0L, 1L, 0L, 0L, 0L, 10L, 2L, 3L, 2L, 0L, 6L)), .Names = c(group,
Participant, time, response), row.names = c(1.1, 2.1,
3.1, 4.1, 5.1, 6.1, 7.1, 8.1, 9.1, 10.1, 11.1,
12.1, 13.1, 14.1, 1.2, 2.2, 3.2, 4.2, 5.2, 6.2,
7.2, 8.2, 9.2, 10.2, 11.2, 12.2, 13.2, 14.2,
1.3, 2.3, 3.3, 4.3, 5.3, 6.3, 7.3, 8.3, 9.3,
10.3, 11.3, 12.3, 13.3, 14.3, 1.4, 2.4, 3.4,
4.4, 5.4, 6.4, 7.4, 8.4, 9.4, 10.4, 11.4, 12.4,
13.4, 14.4, 1.5, 2.5, 3.5, 4.5, 5.5, 6.5, 7.5,
8.5, 9.5, 10.5, 11.5, 12.5, 13.5, 14.5, 1.11,
2.11, 3.11, 4.11, 5.11, 6.11, 7.11, 8.11, 9.11,
10.11, 11.11, 12.11, 13.11, 14.11, 1.21, 2.21,
3.21, 4.21, 5.21, 6.21, 7.21, 8.21, 9.21, 10.21,
11.21, 12.21, 13.21, 14.21, 1.31, 2.31, 3.31, 4.31,
5.31, 6.31, 7.31, 8.31, 9.31, 10.31, 11.31, 12.31,
13.31, 14.31, 1.41, 2.41, 3.41, 4.41, 5.41, 6.41,
7.41, 8.41, 9.41, 10.41, 11.41, 12.41, 13.41, 14.41,
1.51, 2.51, 3.51, 4.51, 5.51, 6.51, 7.51, 8.51,
9.51, 10.51, 11.51, 12.51, 13.51, 14.51), class = data.frame)
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Re: [R] Has anyone had success with RGTK2/rattle and windows 7 64-bit?
I don't have a Windows 7 to test this on yet - works on Vista and XP. Did you install the GTK libraries (separately to R)? Regards, Graham 2009/11/21 Tetrick, Scott scott.tetr...@intel.com I have been unable to get rattle to run in my new Windows7-64 bit configuration. For wither Rgtk2 or rattle, I get an error: Entry point not found The procedure entry point g_assetion_message_expr could not be located in the dynamic link library libglib-2.0-0.dll. Any help is really appreciated. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] different fits for geese and geeglm in geepack?
It looks strange. If you send me data for a small reproducible example then I'll look into the issue. Regards Søren Fra: r-help-boun...@r-project.org [r-help-boun...@r-project.org] P#229; vegne af Achaz von Hardenberg [achaz.hardenb...@gmail.com] Sendt: 26. november 2009 17:17 Til: r-help@r-project.org Emne: [R] different fits for geese and geeglm in geepack? Dear all, I am trying to fit a GEE model on eagle productivity (number of hatched offspring per nest) using the geeglm function in the library geepack and I found an odd result. My understanding is that the function geese and geeglm should give the same fits, as actually geeglm uses geese to fit the model, providing a glm style output. However, if I fit the same model with geeglm and geese I get slightly different estimates of the parameters. Most striking is the difference between the estimates of the correlation parameter where the differences are huge: (geese: alpha= -0.0727, se= 0.0608; geeglm: -0.219, se= 0.091). Anybody knows why this is like that and which of the two I should rather trust? (I attach the outputs of the two models at the end of this mail) thanks a lot for your hints! Achaz von Hardenberg PS: One more question actually: anybody has got some code to calculate the QICu values to compare GEE models with and without specific fixed factors using geepack? ## GEESE OUTPUT: Call: geese(formula = PROD ~ as.factor(clas3) + Twinter + Tprecova, id = Nterr, waves = anno, data = aquile.dat2, family = poisson, corstr = ar1) Mean Model: Mean Link: log Variance to Mean Relation: poisson Coefficients: estimate san.se waldp (Intercept)-1.7850 0.3661 23.77 1.08e-06 as.factor(clas3)2 0.7165 0.2475 8.38 3.79e-03 as.factor(clas3)3 0.5052 0.3368 2.25 1.34e-01 Twinter-0.1066 0.0464 5.28 2.16e-02 Tprecova -0.0549 0.0368 2.22 1.36e-01 Scale Model: Scale Link:identity Estimated Scale Parameters: estimate san.se waldp (Intercept)0.764 0.123 38.6 5.17e-10 Correlation Model: Correlation Structure: ar1 Correlation Link: identity Estimated Correlation Parameters: estimate san.se wald p alpha -0.0727 0.0608 1.43 0.232 Returned Error Value:0 Number of clusters: 21 Maximum cluster size: 20 ### GEEGLM OUTPUT: Call: geeglm(formula = PROD ~ as.factor(clas3) + Twinter + Tprecova, family = poisson, data = aquile.dat2, id = Nterr, waves = anno, corstr = ar1) Coefficients: Estimate Std.err Wald Pr(|W|) (Intercept)-1.7992 0.3751 23.01 1.6e-06 *** as.factor(clas3)2 0.7412 0.2623 7.99 0.0047 ** as.factor(clas3)3 0.5253 0.3335 2.48 0.1152 Twinter-0.1083 0.0473 5.24 0.0220 * Tprecova -0.0483 0.0354 1.86 0.1721 --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 Estimated Scale Parameters: Estimate Std.err (Intercept)0.773 0.117 Correlation: Structure = ar1 Link = identity Estimated Correlation Parameters: Estimate Std.err alpha -0.219 0.091 Number of clusters: 21 Maximum cluster size: 20 Dr. Achaz von Hardenberg Centro Studi Fauna Alpina - Alpine Wildlife Research Centre Servizio Sanitario e della Ricerca Scientifica Parco Nazionale Gran Paradiso, Degioz, 11, 11010-Valsavarenche (Ao), Italy Present address: National Centre for Statistical Ecology School of Mathematics, Statistics and Actuarial Science, University of Kent, Canterbury, UK E-mail: achaz.hardenb...@pngp.it fa...@pngp.it Skype: achazhardenberg Mobile: +44.(0)783.266.5995 Dr. Achaz von Hardenberg Centro Studi Fauna Alpina - Alpine Wildlife Research Centre Servizio Sanitario e della Ricerca Scientifica Parco Nazionale Gran Paradiso, Degioz, 11, 11010-Valsavarenche (Ao), Italy Present address: National Centre for Statistical Ecology School of Mathematics, Statistics and Actuarial Science, University of Kent, Canterbury, UK E-mail: achaz.hardenb...@pngp.it fa...@pngp.it Skype: achazhardenberg Mobile: +44.(0)783.266.5995 [[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] barchart() {Lattice} help.
Peng Cai wrote: Hi R Users, I'm trying to plot a stacked barplot. Here is data: Sample Col1 Col2 Col3 Row1 -2 4 -1 Row2 3 -2 4 Row3 3 5 -2 Row4 4 1 -1 I'm using following R code: library(lattice) dta-read.table(data.txt, header=TRUE, row.names=Sample) barchart(data.matrix(dta), horizontal=FALSE, stack=TRUE, col=2:4, auto.key=list(space=right, title=names(dimnames(dta))[2]) ) Above code is working fine, but I need help with: 1) Legend boxes have default colors, whereas I'm looking them to match with barplot colors (col=2:4). replace the line col = 2:4, with par.settings = simpleTheme(col = 2:4), 2) Can I increase scale for y axis, like currently it plotting -2,0,2,4,... I would like it as -2,-1,0,1,... add the line scales = list(y = list(at = -2:8)), or whatever tick locations you prefer. -Peter Ehlers Any help would be greatly appreciated, Thanks, Peng [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Moving quantile()?
On Thu, 26 Nov 2009, Rob Steele wrote: Is there a faster way to get moving quantiles from a time series than to run quantile() at each step in the series? Yes. Run help.request() Since you have already done the first 4 items below (right?) you will answer 'y', but when you get to the fifth one (which you evidently have not done), you will have to answer 'n'. Checklist: Have you read the posting guide? (y/n) y Have you checked the FAQ? (y/n) y Have you checked An Introduction to R? (y/n) y Have you checked the NEWS of the latest development release? (y/n) y Have you looked on RSiteSearch? (y/n) n This will start a browser with the RSiteSearch URL loaded. Now comes the tricky part --- you have to type something into the 'Query' box and then click on 'Search'. Perhaps moving quantiles will work?? It did for me, and the function I found by that strategy seems to be faster than apply(embed(x[1:1],100),1,quantile,.75) by about 3 orders of magnitude. HTH, Chuck Thanks, Rob __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Charles C. Berry(858) 534-2098 Dept of Family/Preventive Medicine E mailto:cbe...@tajo.ucsd.edu UC San Diego http://famprevmed.ucsd.edu/faculty/cberry/ La Jolla, San Diego 92093-0901 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] r code to combine random forest and glm
Hi, is it possible to have r code which runs random forests and takes the top 7 variables based on variable importance and builds a model of trying interactions terms for each variable. Then builds 7 models and keeps the one with the lowest aic. this would be like a new form of step wise regression using random forests with interaction terms. any code help would be much appreciated. thanks Dhruv [[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] Concave hull
Raising a rather general question here. This is a tantalising discussion, but the notion of concave hull strikes me as extremely ill-defined! I'd like to see statement of what it is (generically) supposed to be. The examples discussed so far seem to rely on a person's inner feelings of what it is supposed to be. Consider the following simple example (where I have drawn a concave hull by hand, using sentimental criteria). set.seed(54321) X - c(-1+rnorm(10),1+rnorm(10)) Y - rnorm(20) plot(X,Y,pch=+,col=blue,xlim=c(-4,4),ylim=c(-3,3)) for(i in (1:20)) text(X[i]+0.150,Y[i],i,cex=0.25) ## Find their convex hull: ix0 - chull(X,Y) ; n - length(CH.ix0) ix1 - c(ix0,ix0[1]) # close it lines(X[ix1],Y[ix1],col=green) ## Draw a concave hull: concix - c(19,18,8,16,11,1,3,2,4,7,15,5,10,9,14,13,20,12,17,19) lines(X[concix],Y[concix],col=red) I have deliberately left the single point 6 dangling, since I am agonising over the choice between: [A] Leaving it as it is, as in interior point, on the grounds that the resulting concave hull boundary is fairly smooth; [B] Inserting it between c( ... ,2,4,7,6,15, ... ), which is the least uncomfortable of the two obvious possibilities; [C] Inserting it between c( ... ,2,4,6,7,15, ... ), which is the more uncomfortsable of the two onvious possibilities. Can someone provide counselling for me? I am hearing too many voices about this! Should I have tried to be less inclusive? Ted. E-Mail: (Ted Harding) ted.hard...@manchester.ac.uk Fax-to-email: +44 (0)870 094 0861 Date: 26-Nov-09 Time: 20:52:03 -- XFMail -- __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] {ggplot2} Adding Mean to (grouped) Boxplot.
Hi R Users, I am using following R code to plot a grouped boxplot. I'm hoping if I can add MEAN to these boxplots. Data is copied below and attached as text file. install.packages(ggplot2) library(ggplot2) dta-read.table(Sample.txt,header=T) attach(dta) p - ggplot(dta, aes(factor(month), nail)) p + geom_boxplot(aes(fill = factor(trt))) Data: month nail trt 6 7.2 1 12 9.3 1 0 5.8 1 1 6 1 2 6.5 1 3 7 1 6 9.1 1 12 7.9 1 0 3.3 1 1 4.9 1 2 1.4 2 3 2.7 2 6 3.7 2 12 9.4 2 0 3.1 2 1 2.7 2 2 5.4 2 3 8.3 2 6 12.3 2 12 17.7 2 Any help would be greatly appreciated, Thanks, Peng month nail trt 6 7.2 1 12 9.3 1 0 5.8 1 1 6 1 2 6.5 1 3 7 1 6 9.1 1 12 7.9 1 0 3.3 1 1 4.9 1 2 1.4 2 3 2.7 2 6 3.7 2 12 9.4 2 0 3.1 2 1 2.7 2 2 5.4 2 3 8.3 2 6 12.3 2 12 17.7 2 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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 shall one present LRT test statistic in a scientific journal ?
David Winsemius wrote: On Nov 26, 2009, at 12:46 PM, Peter Dalgaard wrote: David Winsemius wrote: On Nov 26, 2009, at 12:14 PM, JVezilier wrote: Hello !! I'm recently having a debate with my PhD supervisor regarding how to write the result of a likelihood ratio test in an article I'm about to submit. I analysed my data using lme mixed modelling. To get some p-values for my fixed effect I used model simplification and the typical output R gives looks like this: model2 = update ( model1,~.-factor A) anova (model1, model2) Model df AIC BIC logLik Test L.Ratio p-value model 1 1 26 -78.73898 15.29707 65.36949 model 2 2 20 -73.70539 -1.36997 56.85270 1 vs 2 17.03359 0.0092 I thought about presenting it very simply copying/pasting R table and writing it like: factor A had a significant effect on the response variable (Likelihood ratio test, L-ratio = 17.033, p = 0.0092) But my boss argued that it's too unusual (at least in our field of evolutionary biology) and that I should present instead the LR statistic together with the corresponding Chi^2 statistic since the likelihood ratio is almost distributed like a Chi2 (df1-df2), and then write down the p-value corresponding to this value of Chi. I looked up in the current litterature but cannot really find a proper answer to that dilmena. So, dear evolutionary biologists R users, how would you present it ? I am not an evolutionary biologist, but presumably your supervisor is one. Why are you picking a fight not only with him but with your prospective audience when there is no meaningful difference? Here is the p-value you would get with his method: 1-pchisq( 2*(65.36949 - 56.85270), df=6) [1] 0.009160622 As I understood the question, it *is* purely formalistic. I.e., what to write, not what to do. I'd say L-ratio is plain wrong, since this is not a ratio, but the log of a ratio. -2lnQ or -2logQ is what my old teachers would write, but pragmatically, I'd expect the best chances with editors and reviewers to be LRT: chi-square=17.03, df=6, p=0.092, possibly with LRT spelled out. (Some journals like to have the df because it allows reviewers to catch glaring mistakes like categorical variables treated as numeric.) I wonder about the phrase used model simplification. Wouldn't that raise a question about the proper degrees of freedom to use? If terms were dropped from the model based simply on the basis of non-significance shouldn't there be some appropriate penalization of subsequent tests of significance? Absolutely. At the least, the unbiased estimate of sigma^2 from the fullest model fit should be inserted into sigma^2 for the model used. More severe corrections are probably warranted though. Frank -- 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] Concave hull
2009/11/26 Ted Harding ted.hard...@manchester.ac.uk: Raising a rather general question here. This is a tantalising discussion, but the notion of concave hull strikes me as extremely ill-defined! I'd like to see statement of what it is (generically) supposed to be. I'm curious too, but I can imagine the following definition, Consider a sphere (n-dimensional maybe) that we let come in contact with the scatter of points from outside. The set of points that the sphere can attain may define unambiguously (I think) a concave hull, for a specified sphere radius. The convex hull is obtained in the limit of infinite radius (plane). It's probably not exactly this, but I guess that's the rough idea. Just a thought, baptiste __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Barplot with confidence intervals
I have a file in the following format: Scenario1 Scenario1CIL Scenario1CIU Scenario2 Scenario2CIL Scenario2CIU 60 57 62 45 48 50 110 101 111 51 50 52 120 117 122 64 62 66 192 190 194 79 75 79 where: First column = Scenario1 mean value Second column = Scenario1 Low Confidence Interval Third column = Scenario1 Upper Confidence Interval Fourth column = Scenario2 mean value Fifth column = Scenario2 Low Confidence Interval Sixth column = Scenario2 Upper Confidence Interval Then, I tried this: library(gplots) data - read.table(data.file, header=T, sep= ) legend - c(line1,line2,line3,line4) ci.l - as.matrix(c(c(data$Scenario1CIL), c(data$Scenario2CIL))) ci.u - as.matrix(c(c(data$Scenario1CIU), c(data$Scenario2CIU))) barplot2(as.matrix(c(c(data$Scenario1), c(data$Scenario2))), beside=TRUE, legend=legend, ylim=c(0, 200), main=Experiment X, ylab=Total size, font.main=4, cex.axis=1.2, cex.lab=1.5, cex.names=1.5, plot.ci=TRUE, ci.l=ci.l, ci.u=ci.u, plot.grid=TRUE) But this code doesn't group the values in Scenario1 and Scenario2, as expected. All plotted bars are joined side by side. Considering the letter 'H' a bar, the expected result was: ' ' but the result of the above code was: '' (no space between the Scenario1's values and Scenario2'values) and no legends (Scenario1 and Scenario2). How I must to do? Thanks in advance! -- Jonhnny Weslley Sousa Silva MSc. Candidate in Computer Science Distributed Systems Laboratory Federal University of Campina Grande -- OurFS http://www.lsd.ufcg.edu.br/ourfs -- http://www.jonhnnyweslley.net [[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} Adding Mean to (grouped) Boxplot.
Hi Dennis, Thanks for your reply. Answers are below: On Thu, Nov 26, 2009 at 4:14 PM, Dennis Murphy djmu...@gmail.com wrote: Two questions: (1) Do you want monthly means (averaged over groups), group means (averaged over months), overall average, other??? I need mean (of nail) for each treatment (trt) at each value of Month (so its a two-way mean). (2) Why do you have month 0 and month 12? That would suggest a 13 month year (at minimum). Actually Month column denotes: Visit at 0th Month, Visit after 1st Month,...,Visit after 12th Month -- so you can safely treat them as factor with 6 levels. Please let me know if you have any further question, Thanks, Peng DM On Thu, Nov 26, 2009 at 1:00 PM, Peng Cai pengcaimaill...@gmail.comwrote: Hi R Users, I am using following R code to plot a grouped boxplot. I'm hoping if I can add MEAN to these boxplots. Data is copied below and attached as text file. install.packages(ggplot2) library(ggplot2) dta-read.table(Sample.txt,header=T) attach(dta) p - ggplot(dta, aes(factor(month), nail)) p + geom_boxplot(aes(fill = factor(trt))) Data: month nail trt 6 7.2 1 12 9.3 1 0 5.8 1 1 6 1 2 6.5 1 3 7 1 6 9.1 1 12 7.9 1 0 3.3 1 1 4.9 1 2 1.4 2 3 2.7 2 6 3.7 2 12 9.4 2 0 3.1 2 1 2.7 2 2 5.4 2 3 8.3 2 6 12.3 2 12 17.7 2 Any help would be greatly appreciated, Thanks, 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. [[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] Concave hull
On 26-Nov-09 21:11:02, baptiste auguie wrote: 2009/11/26 Ted Harding ted.hard...@manchester.ac.uk: Raising a rather general question here. This is a tantalising discussion, but the notion of concave hull strikes me as extremely ill-defined! I'd like to see statement of what it is (generically) supposed to be. I'm curious too, but I can imagine the following definition, Consider a sphere (n-dimensional maybe) that we let come in contact with the scatter of points from outside. The set of points that the sphere can attain may define unambiguously (I think) a concave hull, for a specified sphere radius. The convex hull is obtained in the limit of infinite radius (plane). It's probably not exactly this, but I guess that's the rough idea. Just a thought, baptiste Yes, it's the sort of idea I have had too! I imagined the true convex hull as made of a stretchable material (like a soap bubble). With that in place, now gently raise the air pressure outside the bubble. This pushes the envelope inwards. When the envelope, moving inwards, meets a point, it sticks to it and does not move further at that point. The parameter under your control is the pressure. You can stop when you feel like it. Once you have stopped, the set of points in contact with the envelope can then be joined by lines (or, in higher dimensions, faces/simplexes). This even has the merit that the surface has a definite equation (with boundary conditions), so could be programmed! However, the main thing left hanging in the air by this idea is that you may want to arrange things so that the envelope gets pushed further in from some directions than from others -- i.e. on the soap-bubble analogy, you want to apply different levels of extra pressure to different parts of the envelope. For instance, in the example I included in my previous post, you might want the envelope between points 19 3 to be under greater pressure than the envelope between points 13 17. So it is still an undefined solution. As is yours -- since you might want to use different radii of spheres from different directions. Ted. E-Mail: (Ted Harding) ted.hard...@manchester.ac.uk Fax-to-email: +44 (0)870 094 0861 Date: 26-Nov-09 Time: 21:45:47 -- XFMail -- __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Concave hull
On Thu, Nov 26, 2009 at 9:45 PM, Ted Harding ted.hard...@manchester.ac.uk wrote: So it is still an undefined solution. As is yours -- since you might want to use different radii of spheres from different directions. I think the formal and rigorous definition is a nice polygon that goes round my points. 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] How to suppress errors generated by readHTMLTable?
library(XML)
download.file('http://polya.umdnj.edu/polya_db2/gene.php?llid=109079unigene=submit=Submit','index.html')
tables=readHTMLTable(index.html,error=function(...){})
tables
readHTMLTable gives me the following errors. Could somebody let me
know how to suppress them?
Opening and ending tag mismatch: center and table
htmlParseEntityRef: expecting ';'
htmlParseEntityRef: expecting ';'
htmlParseEntityRef: expecting ';'
htmlParseEntityRef: expecting ';'
htmlParseEntityRef: expecting ';'
htmlParseEntityRef: expecting ';'
htmlParseEntityRef: expecting ';'
htmlParseEntityRef: expecting ';'
htmlParseEntityRef: expecting ';'
htmlParseEntityRef: expecting ';'
htmlParseEntityRef: expecting ';'
htmlParseEntityRef: expecting ';'
htmlParseEntityRef: expecting ';'
htmlParseEntityRef: expecting ';'
Opening and ending tag mismatch: td and tr
htmlParseEntityRef: expecting ';'
htmlParseEntityRef: expecting ';'
htmlParseEntityRef: expecting ';'
htmlParseEntityRef: expecting ';'
htmlParseEntityRef: expecting ';'
htmlParseEntityRef: expecting ';'
htmlParseEntityRef: expecting ';'
htmlParseEntityRef: expecting ';'
htmlParseEntityRef: expecting ';'
htmlParseEntityRef: expecting ';'
htmlParseEntityRef: expecting ';'
htmlParseEntityRef: expecting ';'
Unexpected end tag : form
Opening and ending tag mismatch: body and center
Opening and ending tag mismatch: body and center
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Re: [R] barchart() {Lattice} help.
Thanks Peter and Dennis for your help!
On Thu, Nov 26, 2009 at 3:50 PM, Dennis Murphy djmu...@gmail.com wrote:
Hi:
In addition to Peter's suggestions, I would suggest that you get rid of the
row names as the
first column of your data frame, as it confuses barchart (and the
interpretation of the plot).
I used x for your data frame, and this is the bar chart I ended up with:
x
Sample Col1 Col2 Col3
1 Row1 -24 -1
2 Row23 -24
3 Row335 -2
4 Row441 -1
The bar chart using your code, and the data set in this form (Sample is
column1), is given below:
dta - x# change names to conform to
your code
barchart(data.matrix(dta),
horizontal=FALSE,
stack=TRUE,
par.settings = simpleTheme(col = 2:4),
auto.key=list(space=right, title=names(dimnames(dta))[2]),
scales = list(y = list(at = -2:8)) )
Notice that barchart tries to incorporate the row names as legitimate
categories; I can't make
heads or tails out of this...
As it turns out, dta is a data frame with dim(dta) = c(4, 4). You want rows
1:4 to be row labels,
not data, so...
x - x[, 2:4]
x
Col1 Col2 Col3
1 -24 -1
23 -24
335 -2
441 -1
rownames(x) - paste('Row', 1:4, sep = '')
x
Col1 Col2 Col3
Row1 -24 -1
Row23 -24
Row335 -2
Row441 -1
x now has dimension c(4, 3). Let's try barchart again...
barchart(data.matrix(x), horizontal = FALSE, stack = TRUE,
par.settings = simpleTheme(col = 2:4),
auto.key = list(space = 'right', title = names(colnames(x))),
scales = list(y = list(at = -2:8)) )
Not your conventional stacked bar chart, but at least it seems more
interepretable.
HTH,
Dennis
On Thu, Nov 26, 2009 at 10:53 AM, Peng Cai pengcaimaill...@gmail.comwrote:
Hi R Users,
I'm trying to plot a stacked barplot. Here is data:
Sample Col1 Col2 Col3
Row1 -2 4 -1
Row2 3 -2 4
Row3 3 5 -2
Row4 4 1 -1
I'm using following R code:
library(lattice)
dta-read.table(data.txt, header=TRUE, row.names=Sample)
barchart(data.matrix(dta),
horizontal=FALSE,
stack=TRUE,
col=2:4,
auto.key=list(space=right,
title=names(dimnames(dta))[2])
)
Above code is working fine, but I need help with:
1) Legend boxes have default colors, whereas I'm looking them to match
with
barplot colors (col=2:4).
2) Can I increase scale for y axis, like currently it plotting
-2,0,2,4,...
I would like it as -2,-1,0,1,...
Any help would be greatly appreciated,
Thanks,
Peng
[[alternative HTML version deleted]]
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[[alternative HTML version deleted]]
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] barchart() {Lattice} help.
Hi Peter, I'm not sure but it seems scales command works only with integer values. If the y-axis values are very small (such as -0.03, -0.02, -0.01, 0, 0.01,..., 0.08). My current plot has values 0, 0.05, and 0.10 only. But I need it to extend it to negative numbers and reduce the scale width (like -0.04, -0.02, 0, 0.02,...). Can I change these too? Thanks! Peng On Thu, Nov 26, 2009 at 3:18 PM, Peter Ehlers ehl...@ucalgary.ca wrote: Peng Cai wrote: Hi R Users, I'm trying to plot a stacked barplot. Here is data: Sample Col1 Col2 Col3 Row1 -2 4 -1 Row2 3 -2 4 Row3 3 5 -2 Row4 4 1 -1 I'm using following R code: library(lattice) dta-read.table(data.txt, header=TRUE, row.names=Sample) barchart(data.matrix(dta), horizontal=FALSE, stack=TRUE, col=2:4, auto.key=list(space=right, title=names(dimnames(dta))[2]) ) Above code is working fine, but I need help with: 1) Legend boxes have default colors, whereas I'm looking them to match with barplot colors (col=2:4). replace the line col = 2:4, with par.settings = simpleTheme(col = 2:4), 2) Can I increase scale for y axis, like currently it plotting -2,0,2,4,... I would like it as -2,-1,0,1,... add the line scales = list(y = list(at = -2:8)), or whatever tick locations you prefer. -Peter Ehlers Any help would be greatly appreciated, Thanks, Peng [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] barchart() {Lattice} help.
Peng Cai wrote: Hi Peter, I'm not sure but it seems scales command works only with integer values. If the y-axis values are very small (such as -0.03, -0.02, -0.01, 0, 0.01,..., 0.08). My current plot has values 0, 0.05, and 0.10 only. But I need it to extend it to negative numbers and reduce the scale width (like -0.04, -0.02, 0, 0.02,...). Can I change these too? Thanks! Use, e.g. myYscale - seq(-0.04, 0.08, 0.02) barchart(..., ..., scales = list(y = list(at = myYscale)), ... ) -Peter Ehlers Peng On Thu, Nov 26, 2009 at 3:18 PM, Peter Ehlers ehl...@ucalgary.ca wrote: Peng Cai wrote: Hi R Users, I'm trying to plot a stacked barplot. Here is data: Sample Col1 Col2 Col3 Row1 -2 4 -1 Row2 3 -2 4 Row3 3 5 -2 Row4 4 1 -1 I'm using following R code: library(lattice) dta-read.table(data.txt, header=TRUE, row.names=Sample) barchart(data.matrix(dta), horizontal=FALSE, stack=TRUE, col=2:4, auto.key=list(space=right, title=names(dimnames(dta))[2]) ) Above code is working fine, but I need help with: 1) Legend boxes have default colors, whereas I'm looking them to match with barplot colors (col=2:4). replace the line col = 2:4, with par.settings = simpleTheme(col = 2:4), 2) Can I increase scale for y axis, like currently it plotting -2,0,2,4,... I would like it as -2,-1,0,1,... add the line scales = list(y = list(at = -2:8)), or whatever tick locations you prefer. -Peter Ehlers Any help would be greatly appreciated, Thanks, Peng [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Concave hull
There is a package on CRAN implementing such an idea: alphahull, phull is other package, kjetil On Thu, Nov 26, 2009 at 6:11 PM, baptiste auguie baptiste.aug...@googlemail.com wrote: 2009/11/26 Ted Harding ted.hard...@manchester.ac.uk: Raising a rather general question here. This is a tantalising discussion, but the notion of concave hull strikes me as extremely ill-defined! I'd like to see statement of what it is (generically) supposed to be. I'm curious too, but I can imagine the following definition, Consider a sphere (n-dimensional maybe) that we let come in contact with the scatter of points from outside. The set of points that the sphere can attain may define unambiguously (I think) a concave hull, for a specified sphere radius. The convex hull is obtained in the limit of infinite radius (plane). It's probably not exactly this, but I guess that's the rough idea. Just a thought, baptiste __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] barchart() {Lattice} help.
Thanks a lot Peter! One more help, is there a similar function abline() for barchart(). I'm trying to add a (light gray colored) horizontal lines, one for each y-value. Peng On Thu, Nov 26, 2009 at 5:59 PM, Peter Ehlers ehl...@ucalgary.ca wrote: Peng Cai wrote: Hi Peter, I'm not sure but it seems scales command works only with integer values. If the y-axis values are very small (such as -0.03, -0.02, -0.01, 0, 0.01,..., 0.08). My current plot has values 0, 0.05, and 0.10 only. But I need it to extend it to negative numbers and reduce the scale width (like -0.04, -0.02, 0, 0.02,...). Can I change these too? Thanks! Use, e.g. myYscale - seq(-0.04, 0.08, 0.02) barchart(..., ..., scales = list(y = list(at = myYscale)), ... ) -Peter Ehlers Peng On Thu, Nov 26, 2009 at 3:18 PM, Peter Ehlers ehl...@ucalgary.ca wrote: Peng Cai wrote: Hi R Users, I'm trying to plot a stacked barplot. Here is data: Sample Col1 Col2 Col3 Row1 -2 4 -1 Row2 3 -2 4 Row3 3 5 -2 Row4 4 1 -1 I'm using following R code: library(lattice) dta-read.table(data.txt, header=TRUE, row.names=Sample) barchart(data.matrix(dta), horizontal=FALSE, stack=TRUE, col=2:4, auto.key=list(space=right, title=names(dimnames(dta))[2]) ) Above code is working fine, but I need help with: 1) Legend boxes have default colors, whereas I'm looking them to match with barplot colors (col=2:4). replace the line col = 2:4, with par.settings = simpleTheme(col = 2:4), 2) Can I increase scale for y axis, like currently it plotting -2,0,2,4,... I would like it as -2,-1,0,1,... add the line scales = list(y = list(at = -2:8)), or whatever tick locations you prefer. -Peter Ehlers Any help would be greatly appreciated, Thanks, Peng [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[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 suppress errors generated by readHTMLTable?
Just this morning, I made suppressing these parser messages
the default behavior for htmlParse() and that will apply
to readHTMLTable() also.
Until I release that (along with another potentially
non-backward compatible change regarding character encoding),
you can use
readHTMLTable(htmlParse(index.html, error = function(...){}))
i.e. parse the document yourself and hand it to readHTMLTable().
D.
Peng Yu wrote:
library(XML)
download.file('http://polya.umdnj.edu/polya_db2/gene.php?llid=109079unigene=submit=Submit','index.html')
tables=readHTMLTable(index.html,error=function(...){})
tables
readHTMLTable gives me the following errors. Could somebody let me
know how to suppress them?
Opening and ending tag mismatch: center and table
htmlParseEntityRef: expecting ';'
htmlParseEntityRef: expecting ';'
htmlParseEntityRef: expecting ';'
htmlParseEntityRef: expecting ';'
htmlParseEntityRef: expecting ';'
htmlParseEntityRef: expecting ';'
htmlParseEntityRef: expecting ';'
htmlParseEntityRef: expecting ';'
htmlParseEntityRef: expecting ';'
htmlParseEntityRef: expecting ';'
htmlParseEntityRef: expecting ';'
htmlParseEntityRef: expecting ';'
htmlParseEntityRef: expecting ';'
htmlParseEntityRef: expecting ';'
Opening and ending tag mismatch: td and tr
htmlParseEntityRef: expecting ';'
htmlParseEntityRef: expecting ';'
htmlParseEntityRef: expecting ';'
htmlParseEntityRef: expecting ';'
htmlParseEntityRef: expecting ';'
htmlParseEntityRef: expecting ';'
htmlParseEntityRef: expecting ';'
htmlParseEntityRef: expecting ';'
htmlParseEntityRef: expecting ';'
htmlParseEntityRef: expecting ';'
htmlParseEntityRef: expecting ';'
htmlParseEntityRef: expecting ';'
Unexpected end tag : form
Opening and ending tag mismatch: body and center
Opening and ending tag mismatch: body and center
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Re: [R] barchart() {Lattice} help.
On Nov 26, 2009, at 6:12 PM, Peng Cai wrote: Thanks a lot Peter! One more help, is there a similar function abline() for barchart(). ?panel.abline I'm trying to add a (light gray colored) horizontal lines, one for each y-value. Peng On Thu, Nov 26, 2009 at 5:59 PM, Peter Ehlers ehl...@ucalgary.ca wrote: Peng Cai wrote: Hi Peter, I'm not sure but it seems scales command works only with integer values. If the y-axis values are very small (such as -0.03, -0.02, -0.01, 0, 0.01,..., 0.08). My current plot has values 0, 0.05, and 0.10 only. But I need it to extend it to negative numbers and reduce the scale width (like -0.04, -0.02, 0, 0.02,...). Can I change these too? Thanks! Use, e.g. myYscale - seq(-0.04, 0.08, 0.02) barchart(..., ..., scales = list(y = list(at = myYscale)), ... ) -Peter Ehlers Peng On Thu, Nov 26, 2009 at 3:18 PM, Peter Ehlers ehl...@ucalgary.ca wrote: Peng Cai wrote: Hi R Users, I'm trying to plot a stacked barplot. Here is data: Sample Col1 Col2 Col3 Row1 -2 4 -1 Row2 3 -2 4 Row3 3 5 -2 Row4 4 1 -1 I'm using following R code: library(lattice) dta-read.table(data.txt, header=TRUE, row.names=Sample) barchart(data.matrix(dta), horizontal=FALSE, stack=TRUE, col=2:4, auto.key=list(space=right, title=names(dimnames(dta))[2]) ) Above code is working fine, but I need help with: 1) Legend boxes have default colors, whereas I'm looking them to match with barplot colors (col=2:4). replace the line col = 2:4, with par.settings = simpleTheme(col = 2:4), 2) Can I increase scale for y axis, like currently it plotting -2,0,2,4,... I would like it as -2,-1,0,1,... add the line scales = list(y = list(at = -2:8)), or whatever tick locations you prefer. -Peter Ehlers Any help would be greatly appreciated, Thanks, Peng [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[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.
Re: [R] Help on Html format R 2.10
Hello: I´m trying to change the plain text help to html help but I don´t know if this is possible with R 2.10.0 (Windows XP). The installation process always set to plain text. I found this: http://old.nabble.com/change-in-default-behavior-of--functionname-in-R-2.10--td26115436.html Thanks in advance, Ruben Cabrera __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] barchart() {Lattice} help.
Thanks David, I tried panel.abline(h=somevalue) -- both inside and outside of barchart() function but its not working. Any suggestions? Peng On Thu, Nov 26, 2009 at 6:42 PM, David Winsemius dwinsem...@comcast.netwrote: On Nov 26, 2009, at 6:12 PM, Peng Cai wrote: Thanks a lot Peter! One more help, is there a similar function abline() for barchart(). ?panel.abline I'm trying to add a (light gray colored) horizontal lines, one for each y-value. Peng On Thu, Nov 26, 2009 at 5:59 PM, Peter Ehlers ehl...@ucalgary.ca wrote: Peng Cai wrote: Hi Peter, I'm not sure but it seems scales command works only with integer values. If the y-axis values are very small (such as -0.03, -0.02, -0.01, 0, 0.01,..., 0.08). My current plot has values 0, 0.05, and 0.10 only. But I need it to extend it to negative numbers and reduce the scale width (like -0.04, -0.02, 0, 0.02,...). Can I change these too? Thanks! Use, e.g. myYscale - seq(-0.04, 0.08, 0.02) barchart(..., ..., scales = list(y = list(at = myYscale)), ... ) -Peter Ehlers Peng On Thu, Nov 26, 2009 at 3:18 PM, Peter Ehlers ehl...@ucalgary.ca wrote: Peng Cai wrote: Hi R Users, I'm trying to plot a stacked barplot. Here is data: Sample Col1 Col2 Col3 Row1 -2 4 -1 Row2 3 -2 4 Row3 3 5 -2 Row4 4 1 -1 I'm using following R code: library(lattice) dta-read.table(data.txt, header=TRUE, row.names=Sample) barchart(data.matrix(dta), horizontal=FALSE, stack=TRUE, col=2:4, auto.key=list(space=right, title=names(dimnames(dta))[2]) ) Above code is working fine, but I need help with: 1) Legend boxes have default colors, whereas I'm looking them to match with barplot colors (col=2:4). replace the line col = 2:4, with par.settings = simpleTheme(col = 2:4), 2) Can I increase scale for y axis, like currently it plotting -2,0,2,4,... I would like it as -2,-1,0,1,... add the line scales = list(y = list(at = -2:8)), or whatever tick locations you prefer. -Peter Ehlers Any help would be greatly appreciated, Thanks, Peng [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[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 [[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] Export kde object as shapefile
On Nov 26, 2009, at 2:25 PM, T.D.Rudolph wrote: Can you explain what you mean by spatial area under the space or what it is for which you think there is a well defined area in a ks:::kde object? My knowledge is not extensive in this area but I am aware that kernel methods can be used to estimate home range size. The function kernel.area in the adehabitat package, for example, produces a spatial area I interpret as being equivalent to estimated home range size using one of two possible smoothing parameters. I would like to use the plug-in method because I am convinced it will serve me best, but the ks package doesn't have a simple option like kde.area that produces what I'm looking for. Some example data would, as always, be welcome. Attached is an example subset of my data. I've only gotten so far as to produce the kde object and explore potential solutions. tmp.Hpi-Hpi(x=temp[,2:3]) tmp.kde-kde(x=temp[,2:3], H=tmp.Hpi) The situation that I see (after looking at the documentation for adehabit) is that for some as yet unarticulated reason, you have decided that the methods used in prior publications in your domain are not the best and you are going to invent new ones, but you are as yet unable to provided a detailed specification or offer an implementation of the methods. Furthermore, you are unable even to manipulate the objects you have thus far created in service toward this effort. I am being somewhat harsh in my assessment because it seems that you really need is a statistical collaborator with whom you can bang ideas together and arrive, first at a more detailed rationale and plan, and then a forward effort using your data and his programming expertise to demonstrate the superiority of your method. That would seem to be most reasonably a joint effort with joint authorship as an outcome. -- David. Tyler http://old.nabble.com/file/p26533942/temp temp David Winsemius wrote: On Nov 26, 2009, at 12:40 PM, T.D.Rudolph wrote: I am trying to estimate home range size using the plug-in method with kernel density estimation in the kernel smoothing (ks) package. Unless there is another way I am not familiar with, in order to calculate spatial area under the space I need to convert my kde () object into a spatial object somehow in order to calculate its spatial area. Could someone demonstrate how this might be done? Can you explain what you mean by spatial area under the space or what it is for which you think there is a well defined area in a ks:::kde object? (Some example data would, as always, be welcome.) -- View this message in context: http://old.nabble.com/Export-kde-object-as-shapefile-tp26532782p26532782.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. 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. -- View this message in context: http://old.nabble.com/Export-kde-object-as-shapefile-tp26532782p26533942.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. 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] Help on Html format R 2.10
Hello Again: Let me answer myself because I already solved my problem: I found the file ...R\R-2.10.0\Rprofile.site and used options(help_type=html). Thanks. Ruben Cabrera On Thu, Nov 26, 2009 at 7:41 PM, Ruben Cabrera ruben...@gmail.com wrote: Hello: I´m trying to change the plain text help to html help but I don´t know if this is possible with R 2.10.0 (Windows XP). The installation process always set to plain text. I found this http://old.nabble.com/change-in-default-behavior-of--functionname-in-R-2.10--td26115436.html Thanks in advance, Ruben Cabrera __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] barchart() {Lattice} help.
Peng Cai wrote:
Thanks David, I tried panel.abline(h=somevalue) -- both inside and outside
of barchart() function but its not working. Any suggestions?
Peng
Here's some code related to the data you posted earlier.
barchart(data.matrix(dta), horizontal = FALSE, stack = TRUE,
par.settings = simpleTheme(col = 2:4),
panel=function(x,y,...){
panel.abline(h=c(-2,0,3,4), col.line=gray)
panel.barchart(x,y,...)
},
scales = list(y = list(at = -2:8)),
auto.key = list(space = 'right', rectangles=TRUE,
points=FALSE)
)
If you want the gray lines in front of the bars, switch the
order of the panel functions. With lattice, it's all about
what goes into each panel (you have only one panel here).
If you want more than one thing in a panel, you have to set
up a function to do those things.
I had to add the rectangles= and points= arguments to
auto.key to get the same key as you had earlier.
-Peter Ehlers
On Thu, Nov 26, 2009 at 6:42 PM, David Winsemius dwinsem...@comcast.netwrote:
On Nov 26, 2009, at 6:12 PM, Peng Cai wrote:
Thanks a lot Peter! One more help, is there a similar function abline()
for
barchart().
?panel.abline
I'm trying to add a (light gray colored) horizontal lines, one for each
y-value.
Peng
On Thu, Nov 26, 2009 at 5:59 PM, Peter Ehlers ehl...@ucalgary.ca wrote:
Peng Cai wrote:
Hi Peter,
I'm not sure but it seems scales command works only with integer
values.
If the y-axis values are very small (such as -0.03, -0.02, -0.01, 0,
0.01,..., 0.08). My current plot has values 0, 0.05, and 0.10 only. But
I
need it to extend it to negative numbers and reduce the scale width
(like
-0.04, -0.02, 0, 0.02,...).
Can I change these too? Thanks!
Use, e.g.
myYscale - seq(-0.04, 0.08, 0.02)
barchart(...,
...,
scales = list(y = list(at = myYscale)),
...
)
-Peter Ehlers
Peng
On Thu, Nov 26, 2009 at 3:18 PM, Peter Ehlers ehl...@ucalgary.ca
wrote:
Peng Cai wrote:
Hi R Users,
I'm trying to plot a stacked barplot. Here is data:
Sample Col1 Col2 Col3
Row1 -2 4 -1
Row2 3 -2 4
Row3 3 5 -2
Row4 4 1 -1
I'm using following R code:
library(lattice)
dta-read.table(data.txt, header=TRUE, row.names=Sample)
barchart(data.matrix(dta),
horizontal=FALSE,
stack=TRUE,
col=2:4,
auto.key=list(space=right,
title=names(dimnames(dta))[2])
)
Above code is working fine, but I need help with:
1) Legend boxes have default colors, whereas I'm looking them to match
with
barplot colors (col=2:4).
replace the line
col = 2:4,
with
par.settings = simpleTheme(col = 2:4),
2) Can I increase scale for y axis, like currently it plotting
-2,0,2,4,...
I would like it as -2,-1,0,1,...
add the line
scales = list(y = list(at = -2:8)),
or whatever tick locations you prefer.
-Peter Ehlers
Any help would be greatly appreciated,
Thanks,
Peng
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
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PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/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.
David Winsemius, MD
Heritage Laboratories
West Hartford, CT
__
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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] barchart() {Lattice} help.
Cannot reproduce. Seems to work as documented. Maybe your code (whatever it might be) is not correct? -- David. On Nov 26, 2009, at 6:53 PM, Peng Cai wrote: Thanks David, I tried panel.abline(h=somevalue) -- both inside and outside of barchart() function but its not working. Any suggestions? Peng On Thu, Nov 26, 2009 at 6:42 PM, David Winsemius dwinsem...@comcast.net wrote: On Nov 26, 2009, at 6:12 PM, Peng Cai wrote: Thanks a lot Peter! One more help, is there a similar function abline() for barchart(). ?panel.abline I'm trying to add a (light gray colored) horizontal lines, one for each y-value. Peng On Thu, Nov 26, 2009 at 5:59 PM, Peter Ehlers ehl...@ucalgary.ca wrote: Peng Cai wrote: Hi Peter, I'm not sure but it seems scales command works only with integer values. If the y-axis values are very small (such as -0.03, -0.02, -0.01, 0, 0.01,..., 0.08). My current plot has values 0, 0.05, and 0.10 only. But I need it to extend it to negative numbers and reduce the scale width (like -0.04, -0.02, 0, 0.02,...). Can I change these too? Thanks! Use, e.g. myYscale - seq(-0.04, 0.08, 0.02) barchart(..., ..., scales = list(y = list(at = myYscale)), ... ) -Peter Ehlers Peng On Thu, Nov 26, 2009 at 3:18 PM, Peter Ehlers ehl...@ucalgary.ca wrote: Peng Cai wrote: Hi R Users, I'm trying to plot a stacked barplot. Here is data: Sample Col1 Col2 Col3 Row1 -2 4 -1 Row2 3 -2 4 Row3 3 5 -2 Row4 4 1 -1 I'm using following R code: library(lattice) dta-read.table(data.txt, header=TRUE, row.names=Sample) barchart(data.matrix(dta), horizontal=FALSE, stack=TRUE, col=2:4, auto.key=list(space=right, title=names(dimnames(dta))[2]) ) Above code is working fine, but I need help with: 1) Legend boxes have default colors, whereas I'm looking them to match with barplot colors (col=2:4). replace the line col = 2:4, with par.settings = simpleTheme(col = 2:4), 2) Can I increase scale for y axis, like currently it plotting -2,0,2,4,... I would like it as -2,-1,0,1,... add the line scales = list(y = list(at = -2:8)), or whatever tick locations you prefer. -Peter Ehlers Any help would be greatly appreciated, Thanks, Peng [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[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 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] Moving quantile()?
Charles C. Berry wrote: On Thu, 26 Nov 2009, Rob Steele wrote: Is there a faster way to get moving quantiles from a time series than to run quantile() at each step in the series? Yes. Run help.request() Since you have already done the first 4 items below (right?) you will answer 'y', but when you get to the fifth one (which you evidently have not done), you will have to answer 'n'. Checklist: Have you read the posting guide? (y/n) y Have you checked the FAQ? (y/n) y Have you checked An Introduction to R? (y/n) y Have you checked the NEWS of the latest development release? (y/n) y Have you looked on RSiteSearch? (y/n) n This will start a browser with the RSiteSearch URL loaded. Now comes the tricky part --- you have to type something into the 'Query' box and then click on 'Search'. Perhaps moving quantiles will work?? It did for me, and the function I found by that strategy seems to be faster than apply(embed(x[1:1],100),1,quantile,.75) by about 3 orders of magnitude. HTH, Chuck runquantile() in library caTools. Beautiful. Thanks! Btw, love your music. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] multi variate plot with string data
Thanks!! this works perfectly dat = data.frame(Aggressive = data_set$var1 , Behaviour=data_set$var2) plot(table(dat)) ...its better than a stacked boxplot as it gives also different width of columns on the diagram...an extra layer of information. frenchcr wrote: Ive got two columns in data_set that are strings the first column is called character and has levels: good, bad, ugly the second column is called abusive and has levels: aggressive, moderately aggressive, mildly aggressive I want to do a stacked boxplot that has this sort of structure: %aggressive %aggressive %aggressive %moderately aggressive %moderately aggressive %moderately aggressive %mildly aggressive %mildly aggressive %mildly aggressive %not agressive %not agressive %not agressive bad good ugly ...with legend at the size showing which colour each of the abusive levels takes. How is it done? -- View this message in context: http://old.nabble.com/multi-variate-plot-with-string-data-tp26517211p26534782.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] Moving quantile()?
Charles C. Berry wrote: On Thu, 26 Nov 2009, Rob Steele wrote: Is there a faster way to get moving quantiles from a time series than to run quantile() at each step in the series? Yes. Run help.request() Since you have already done the first 4 items below (right?) you will answer 'y', but when you get to the fifth one (which you evidently have not done), you will have to answer 'n'. Checklist: Have you read the posting guide? (y/n) y Have you checked the FAQ? (y/n) y Have you checked An Introduction to R? (y/n) y Have you checked the NEWS of the latest development release? (y/n) y Have you looked on RSiteSearch? (y/n) n This will start a browser with the RSiteSearch URL loaded. Now comes the tricky part --- you have to type something into the 'Query' box and then click on 'Search'. Perhaps moving quantiles will work?? It did for me, and the function I found by that strategy seems to be faster than apply(embed(x[1:1],100),1,quantile,.75) by about 3 orders of magnitude. HTH, Chuck runquantile() in library caTools. Beautiful. Thanks! Btw, love your music. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
