Re: [R] Install local package
## Check the package R CMD check path.of.package ## Build the package R CMD build pathof.package ## INSTALL the package R CMD INSTALL path.of.package You can use _R --help _ (from within terminal) to get more information. Ronggui 2009/6/11 Jorge Cornejo cornejo...@gmail.com: Hi, I'm working on a package that I would someday put in CRAN. Now I want to test it on my computer. I already check and compile the files but I don't know how to install the package located on my hard drive. I'm running R under linux. Can anyone tell my how to do it? Thanks in advance. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- HUANG Ronggui, Wincent PhD Candidate Dept of Public and Social Administration City University of Hong Kong Home page: http://asrr.r-forge.r-project.org/rghuang.html __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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 order an data.table by values of an column?
See help(order) and help([.data.frame). df - data.frame(Categ=c(468,351,0,234,117),Perc=c(31.52,27.52,0.77,22.55,15.99)) df[order(df$Categ),] # Categ Perc # 3 0 0.77 # 5 117 15.99 # 4 234 22.55 # 2 351 27.52 # 1 468 31.52 Lesandro wrote: Hello! Can you help me? How to order an data.table by values of an column? Per example: Table no initial Categ Perc 468 31.52 351 27.52 0 0.77 234 22.55 117 15.99 table final Categ Perc 0 0.77 117 15.99 234 22.55 351 27.52 468 31.52 Lesandro Veja quais são os assuntos do momento no Yahoo! +Buscados [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] install local package
Hi, I'm working on a package that I would someday put in CRAN. Now I want to test it on my computer. I already check and compile the files but I don't know how to install the package located on my hard drive. I'm running R under linux. Can anyone tell my how to do it? Thanks in advance. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] [R-pkgs] package installation fails (RandomFields)
I have been unable to install the package RandomFields. I am using R 2.9.0-4 on Ubuntu 9.04. To install, I use the command: sudo R CMD INSTALL RandomFields_1.3.37.tar.gz The output follows below. Any help Would be appreciated. D. Hoysak Brandon University * Installing to library ‘/usr/local/lib/R/site-library’ * Installing *source* package ‘RandomFields’ ... ** libs g++ -I/usr/share/R/include -g -fpic -g -O2 -c D.H.cc -o D.H.o In file included from D.H.cc:27: RFsimu.h:38: warning: ‘typedef’ was ignored in this declaration RFsimu.h:261: warning: ‘typedef’ was ignored in this declaration RFsimu.h:309: warning: ‘typedef’ was ignored in this declaration g++ -I/usr/share/R/include -g -fpic -g -O2 -c Hyperfcts.cc -o Hyperfcts.o In file included from Hyperfcts.cc:27: RFsimu.h:38: warning: ‘typedef’ was ignored in this declaration RFsimu.h:261: warning: ‘typedef’ was ignored in this declaration RFsimu.h:309: warning: ‘typedef’ was ignored in this declaration Hyperfcts.cc: In function ‘int checkNinit_co(covinfo_type*, int*, int, SimulationType, bool)’: Hyperfcts.cc:145: warning: deprecated conversion from string constant to ‘char*’ Hyperfcts.cc:145: warning: deprecated conversion from string constant to ‘char*’ Hyperfcts.cc:145: warning: deprecated conversion from string constant to ‘char*’ Hyperfcts.cc:145: warning: deprecated conversion from string constant to ‘char*’ Hyperfcts.cc:145: warning: deprecated conversion from string constant to ‘char*’ Hyperfcts.cc: In function ‘int checkNinit_Stein(covinfo_type*, int*, int, SimulationType, bool)’: Hyperfcts.cc:261: warning: deprecated conversion from string constant to ‘char*’ Hyperfcts.cc:261: warning: deprecated conversion from string constant to ‘char*’ Hyperfcts.cc:261: warning: deprecated conversion from string constant to ‘char*’ Hyperfcts.cc:261: warning: deprecated conversion from string constant to ‘char*’ Hyperfcts.cc:261: warning: deprecated conversion from string constant to ‘char*’ Hyperfcts.cc:261: warning: deprecated conversion from string constant to ‘char*’ g++ -I/usr/share/R/include -g -fpic -g -O2 -c MPP.cc -o MPP.o In file included from MPP.cc:32: RFsimu.h:38: warning: ‘typedef’ was ignored in this declaration RFsimu.h:261: warning: ‘typedef’ was ignored in this declaration RFsimu.h:309: warning: ‘typedef’ was ignored in this declaration g++ -I/usr/share/R/include -g -fpic -g -O2 -c MPPFcts.cc -o MPPFcts.o In file included from MPPFcts.cc:48: RFsimu.h:38: warning: ‘typedef’ was ignored in this declaration RFsimu.h:261: warning: ‘typedef’ was ignored in this declaration RFsimu.h:309: warning: ‘typedef’ was ignored in this declaration g++ -I/usr/share/R/include -g -fpic -g -O2 -c RFCovFcts.cc -o RFCovFcts.o In file included from RFCovFcts.cc:47: RFsimu.h:38: warning: ‘typedef’ was ignored in this declaration RFsimu.h:261: warning: ‘typedef’ was ignored in this declaration RFsimu.h:309: warning: ‘typedef’ was ignored in this declaration g++ -I/usr/share/R/include -g -fpic -g -O2 -c RFcircembed.cc -o RFcircembed.o In file included from RFcircembed.cc:33: RFsimu.h:38: warning: ‘typedef’ was ignored in this declaration RFsimu.h:261: warning: ‘typedef’ was ignored in this declaration RFsimu.h:309: warning: ‘typedef’ was ignored in this declaration RFcircembed.cc: In function ‘void SetParamCircEmbed(int*, int*, double*, double*, int*, int*, double*, int*, int*, double*, int*)’: RFcircembed.cc:114: warning: deprecated conversion from string constant to ‘char*’ RFcircembed.cc: In function ‘void SetParamLocal(int*, int*, double*, double*, int*, double*, int*, double*, int*)’: RFcircembed.cc:124: warning: deprecated conversion from string constant to ‘char*’ g++ -I/usr/share/R/include -g -fpic -g -O2 -c RFdirect.cc -o RFdirect.o In file included from RFdirect.cc:28: RFsimu.h:38: warning: ‘typedef’ was ignored in this declaration RFsimu.h:261: warning: ‘typedef’ was ignored in this declaration RFsimu.h:309: warning: ‘typedef’ was ignored in this declaration g++ -I/usr/share/R/include -g -fpic -g -O2 -c RFempvario.cc -o RFempvario.o In file included from RFempvario.cc:28: RFsimu.h:38: warning: ‘typedef’ was ignored in this declaration RFsimu.h:261: warning: ‘typedef’ was ignored in this declaration RFsimu.h:309: warning: ‘typedef’ was ignored in this declaration g++ -I/usr/share/R/include -g -fpic -g -O2 -c RFgetNset.cc -o RFgetNset.o In file included from RFgetNset.cc:36: RFsimu.h:38: warning: ‘typedef’ was ignored in this declaration RFsimu.h:261: warning: ‘typedef’ was ignored in this declaration RFsimu.h:309: warning: ‘typedef’ was ignored in this declaration RFgetNset.cc: In function ‘SEXPREC* TooLarge(int*, int)’: RFgetNset.cc:1081: warning: deprecated conversion from string constant to ‘char*’ RFgetNset.cc:1081: warning: deprecated conversion from string constant to ‘char*’ RFgetNset.cc: In function ‘SEXPREC* GetModelInfo(covinfo_type*, int, int, long int)’: RFgetNset.cc:1106: warning: deprecated conversion from string
Re: [R] [R-pkgs] package installation fails (RandomFields)
[[ NOTE: This accidentally was approved to go to R-packages,
it should never have gone there, and I have deleted it
from the archives.
Please *only* reply to R-help (and the OP)!
]]
DH == Drew Hoysak hoy...@wcgwave.ca
on Wed, 10 Jun 2009 14:40:32 -0500 writes:
DH I have been unable to install the package RandomFields. I am using R
DH 2.9.0-4 on Ubuntu 9.04.
How exactly did you install R? Just as ubuntu package?
{probably, given the somewhat particular version number}
DH To install, I use the command:
DH sudo R CMD INSTALL RandomFields_1.3.37.tar.gz
DH The output follows below. Any help Would be appreciated.
DH D. Hoysak
DH Brandon University
DH * Installing to library ‘/usr/local/lib/R/site-library’
DH * Installing *source* package ‘RandomFields’ ...
DH ** libs
DH g++ -I/usr/share/R/include -g -fpic -g -O2 -c D.H.cc -o D.H.o
DH In file included from D.H.cc:27:
DH RFsimu.h:38: warning: ‘typedef’ was ignored in this declaration
DH RFsimu.h:261: warning: ‘typedef’ was ignored in this declaration
DH RFsimu.h:309: warning: ‘typedef’ was ignored in this declaration
[..]
[..]
DH RFsimu.h:309: warning: ‘typedef’ was ignored in this declaration
DH g++ -I/usr/share/R/include -g -fpic -g -O2 -c win_linux_aux.cc -o
DH win_linux_aux.o
DH g++ -shared -o RandomFields.so D.H.o Hyperfcts.o MPP.o MPPFcts.o
DH RFCovFcts.o RFcircembed.o RFdirect.o RFempvario.o RFgetNset.o
DH RFhyperplan.o RFinitNerror.o RFnugget.o RFother.o RFsimu.o RFspectral.o
DH RFtbm.o Xempvario.o addownfctns.o auxiliary.o avltr.o extremes.o
DH modelling.o win_linux_aux.o -llapack -L/usr/lib/R/lib -lR
DH /usr/bin/ld: cannot find -llapack
^
This looks like a setup problem of the R installation you have;
I'd guess that you would also see problems installing other R
packages that rely on LAPACK.
DH collect2: ld returned 1 exit status
DH make: *** [RandomFields.so] Error 1
DH ERROR: compilation failed for package ‘RandomFields’
DH * Removing ‘/usr/local/lib/R/site-library/RandomFields’
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[R] Variogram fitted by Cauchy
Hi I'm using R(2.9.0) and gstat package under Windows to plot sample variograms. When I want to fit them, I don't have the possibility to choose Cauchy functions. Under Mathematica for example, we have it and it seems to be the best one to fit the variograms I have I tested the others functions, they can fit but I would,if possible, use the Cauchy one. If anybody knows something about it, I would know, even with another package To show what I want to do, here is my code mydata=read.table(97MHz_15cm_V3.txt) colnames(mydata)=c(x,y,z,E,taille) g=gstat(id=zinc,formula=mydata[,4]~1,locations=~x+y+z,data=mydata) g.var=variogram(g,cutoff=2500,width=100) modele=vgm(model=Exp,range=2000) vario=fit.variogram(g.var,modele) Thanks! Cordialement Damien Landais __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Integrate function in R
?integrate, it is in the documentation Bhargab Chattopadhyay wrote: Hi! Can anyone please let me know what numerical integration procedure does the integrate function in package stats follow? Thank you in advance Shant [[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. -- Drs. Paul Hiemstra Department of Physical Geography Faculty of Geosciences University of Utrecht Heidelberglaan 2 P.O. Box 80.115 3508 TC Utrecht Phone: +3130 274 3113 Mon-Tue Phone: +3130 253 5773 Wed-Fri http://intamap.geo.uu.nl/~paul __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Splicing factors without losing levels
Titus von der Malsburg wrote:
On Tue, Jun 09, 2009 at 11:23:36AM +0200, ONKELINX, Thierry wrote:
For factors, you better convert them first back to character strings.
splice - function(x, y) {
x - levels(x)[x]
y - levels(y)[y]
factor(as.vector(rbind(x, y)))
}
Thank you very much, Thierry!
I failed to mention something important in my last mail: x and y have
the same levels. (I assume that the integer to level name mapping of
a factor defines its class and that it only makes sense to combine
factors of the same class.)
Say
x - factor(c(2,2,4,4), levels=1:4, labels=c(a,b,c,d))
then
x
[1] b b d d
Levels: a b c d
as.integer(x)
[1] 2 2 4 4
but
splice(x,x)
[1] b b b b d d d d
Levels: b d
as.integer(splice(x,x))
[1] 1 1 1 1 2 2 2 2
I'd like to have a splice function that retains the level to label
mapping. One candidate for a solution is:
splice - function(x,y) {
xy - as.vector(rbind(x, y))
if (is.factor(x) is.factor(y))
xy - factor(xy, levels=1:length(levels(x)), labels=levels(x))
xy
}
However, this relies on assumtions about the implementation of
factors that are neither mentioned nor guaranteed in the man page:
Levels are underlyingly integers starting from one and going to
length(levels). levels(x) gives me the labels of these integers in an
order corresponding to 1:length(levels(x)).
Without these assumptions I see no way to recover the integer to level
name mapping for levels that are defined in a factor but do not occur.
I'd be happy if somebody could clarify this issue!
Hm, well,... Some people have been quite insistent that factors should
be though of as isomorphic to vectors over small subsets of character
strings and not as isomorphic to small integers with labels. I tend to
disagree as it creates more complications than it solves.
Anyways, I would do it like this (generalizing 8 and the seq() bits is
left as an exercise)
x - factor(c(2,2,4,4), levels=1:4, labels=c(a,b,c,d))
xx - factor(rep(NA,8),levels=levels(x))
xx[seq(1,8,2)]-x
xx[seq(2,8,2)]-x
xx
[1] b b b b d d d d
Levels: a b c d
as.integer(xx)
[1] 2 2 2 2 4 4 4 4
Titus
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--
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
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[R] ctc package
Dear R-helpers, I would like to export hierarchical clusters e.g. fit - hclust(d, method=ward) in the newick format write(hc2Newick(fit),file='hclust.newick') Searching for a possibility I found this solution in the package ctc (http://www.bioconductor.org/packages/bioc/html/ctc.html). However, neither from this site nor via CRAN it is possible to install the package. Is there any other possibility? Is the package included in any other package? Thanks a lot in advance. With kind regards Johannes -- Project Coordinator BIOTA West Amphibians Museum of Natural History Dep. of Research (Herpetology) Invalidenstrasse 43 D-10115 Berlin Tel: +49 (0)30 2093 8708 Fax: +49 (0)30 2093 8565 http://www.biota-africa.org http://community-ecology.biozentrum.uni-wuerzburg.de __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Issues getting R to write image files
Hi All, Have spent the last couple of days learning R and shell scripting to do batch plotting jobs. I have had success getting R to complete a filled contour plot and output to a file (.jpg or .tiff etc). However, when I try to do the same thing with the simple plot command the script seems to execute correctly yet there is no output. Below is my R code: file - Sys.getenv(input_file) tiff(paste( file, tiff, sep=.)) z - read.table(file) plot(z, type=l, xlim=range(0.6,2), col = red, plot.title = title(main = file, xlab = Wavelength (um), ylab = Intensity (arb.)) q() The data file is simply 2 columns of real numbers. The system it is running on is a linux box from the command line, but does have the Xlibrarys and can clearly write tiff's as it managed it with the filled contours. Bear in mind I only started with both linux and R a couple of days ago, so be gentle if it is something silly! Cheers, Kenny -- View this message in context: http://www.nabble.com/Issues-getting-R-to-write-image-files-tp23977785p23977785.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] Issues getting R to write image files
Has tried to close the image file at the end? Do: dev.off() Hope it helps mario Kenny Larsen wrote: Hi All, Have spent the last couple of days learning R and shell scripting to do batch plotting jobs. I have had success getting R to complete a filled contour plot and output to a file (.jpg or .tiff etc). However, when I try to do the same thing with the simple plot command the script seems to execute correctly yet there is no output. Below is my R code: file - Sys.getenv(input_file) tiff(paste( file, tiff, sep=.)) z - read.table(file) plot(z, type=l, xlim=range(0.6,2), col = red, plot.title = title(main = file, xlab = Wavelength (um), ylab = Intensity (arb.)) q() The data file is simply 2 columns of real numbers. The system it is running on is a linux box from the command line, but does have the Xlibrarys and can clearly write tiff's as it managed it with the filled contours. Bear in mind I only started with both linux and R a couple of days ago, so be gentle if it is something silly! Cheers, Kenny -- Ing. Mario Valle Data Analysis and Visualization Group| http://www.cscs.ch/~mvalle Swiss National Supercomputing Centre (CSCS) | Tel: +41 (91) 610.82.60 v. Cantonale Galleria 2, 6928 Manno, Switzerland | Fax: +41 (91) 610.82.82 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Predict GARCH
So christofer proved (carry on the same procedure infinite times) that the forecast of the variance converge to the long run variance when a+b1 E(Sigma[t+2]^2) = w/(1-a-b) + [(a+b)^t]* Sigma[t+1]^2 Therefore when you predict n.ahead = 20 it must to converge to the long run variance. It can be fast depending on the data. Regards, Marlene. 2009/6/10 bogaso.christofer bogaso.christo...@gmail.com Suppose the GARCH(1,1) equation is : Sigma[t]^2 = w + a* Sigma[t-1]^2 + b*r[t-1]^2 One step ahead forecast : Sigma[t+1]^2 = w + a* Sigma[t]^2 + b*r[t]^2 All informations are available here Two step ahead forecast : Sigma[t+2]^2 = w + a* Sigma[t+1]^2 + b*r[t+1]^2 Here r[t+1] is not known at time t therefore is a r.v. Replacing this with it's expected value as r[t+1]^2 = E[r[t+1]^2] = sigma[t+1]^2, assuming E[r[t+1]] = 0 Therefore Sigma[t+2]^2 = w + a* Sigma[t+1]^2 + b*r[t+1]^2 = w + a* Sigma[t+1]^2 + b* Sigma[t+1]^2 = w + (a+b)* Sigma[t+1]^2 Carry on same procedure for next period forecast. Hope this helps. -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Daniel Mail Sent: 10 June 2009 18:55 To: r-help@r-project.org Subject: [R] Predict GARCH hello, i was trying to predict values for a garch, so i did: predict(fitgarch,n.ahead = 20) but this doesn't work. Someone can tell me how to get the 20 values ahead of a garch model. thanks in advance _ O Windows Live ajuda-o a manter-se em contacto com todos os seus amigos, num ss local. http://www.microsoft.com/portugal/windows/windowslive/products/social-networ k-connector.aspxhttp://www.microsoft.com/portugal/windows/windowslive/products/social-networ%0Ak-connector.aspx [[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] Issues getting R to write image files
Hi Kenny, Have spent the last couple of days learning R and shell scripting to do batch plotting jobs. I have had success getting R to complete a filled contour plot and output to a file (.jpg or .tiff etc). However, when I try to do the same thing with the simple plot command the script seems to execute correctly yet there is no output. Below is my R code: file - Sys.getenv(input_file) tiff(paste( file, tiff, sep=.)) z - read.table(file) plot(z, type=l, xlim=range(0.6,2), col = red, plot.title = title(main = file, xlab = Wavelength (um), ylab = Intensity (arb.)) dev.off() q() You need to close the tiff graphics device you opened using dev.off() before quitting. HTH, Tobias __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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 on drawing stars and radars in R (update)
Hi I don't know if you can help. I am a 2nd year Bsc Cosmetic Science student and in R I need some help in drawing stars. The problem that I have is I want to recreate a radar diagram similar to the one in excel. I have put in these commands in a script window: stars(shampoo1[, 1:6], locations = c(0,0), radius = TRUE, key.loc=c(0,0), main = Ranked Results for the Sensory Evaluation of the Shampoo , frame.plot = TRUE, key.labels = c(Foam Texture, Skin Feel, Rinsability, Wet Combability, Wet Feel, Odour), lty = 2, ) This gives me a black and white radar which is fine. Now according to the reference manual to colour the stars i need to add: col.stars = rainbow (30) Which colours in each star segment. The problem I have with this is that the segments are filled with colour and the segments overlap each other and each segment is not visible. So I desperately need the command that only colours the outline of the segments or stars instead of filling it. This is the example given in the reference manual: stars(mtcars[, 1:7], locations = c(0,0), radius = FALSE, key.loc=c(0,0), main=Motor Trend Cars, lty = 2) Can u help? Thank You Caroline __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Issues getting R to write image files
Thanks all, I added the dev.off() and although it didn't solve it it no doubt tidies things up on closing. I have got it working now, it is something in the plot() line, as removing all teh options solves it. I will work through adding them in one by one! Kenny Mario Valle wrote: Has tried to close the image file at the end? Do: dev.off() Hope it helps mario Kenny Larsen wrote: Hi All, Have spent the last couple of days learning R and shell scripting to do batch plotting jobs. I have had success getting R to complete a filled contour plot and output to a file (.jpg or .tiff etc). However, when I try to do the same thing with the simple plot command the script seems to execute correctly yet there is no output. Below is my R code: file - Sys.getenv(input_file) tiff(paste( file, tiff, sep=.)) z - read.table(file) plot(z, type=l, xlim=range(0.6,2), col = red, plot.title = title(main = file, xlab = Wavelength (um), ylab = Intensity (arb.)) q() The data file is simply 2 columns of real numbers. The system it is running on is a linux box from the command line, but does have the Xlibrarys and can clearly write tiff's as it managed it with the filled contours. Bear in mind I only started with both linux and R a couple of days ago, so be gentle if it is something silly! Cheers, Kenny -- Ing. Mario Valle Data Analysis and Visualization Group| http://www.cscs.ch/~mvalle Swiss National Supercomputing Centre (CSCS) | Tel: +41 (91) 610.82.60 v. Cantonale Galleria 2, 6928 Manno, Switzerland | Fax: +41 (91) 610.82.82 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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://www.nabble.com/Issues-getting-R-to-write-image-files-tp23977785p23978106.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] ctc package
The web page recommends installing using biocLite() so that is probably what you should do, but see also help(setRepositories) which seems to allow you to pick up (a version of) the package using the normal install.packages() method if you are somehow adverse to follow the recommended practise. Allan. Penner, Johannes wrote: [...] Searching for a possibility I found this solution in the package ctc (http://www.bioconductor.org/packages/bioc/html/ctc.html). However, neither from this site nor via CRAN it is possible to install the package. Is there any other possibility? Is the package included in any other package? [...] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Issues getting R to write image files
On 11-Jun-09 09:24:42, Tobias Verbeke wrote: Hi Kenny, Have spent the last couple of days learning R and shell scripting to do batch plotting jobs. I have had success getting R to complete a filled contour plot and output to a file (.jpg or .tiff etc). However, when I try to do the same thing with the simple plot command the script seems to execute correctly yet there is no output. Below is my R code: file - Sys.getenv(input_file) tiff(paste( file, tiff, sep=.)) z - read.table(file) plot(z, type=l, xlim=range(0.6,2), col = red, plot.title = title(main = file, xlab = Wavelength (um), ylab = Intensity (arb.)) dev.off() q() You need to close the tiff graphics device you opened using dev.off() before quitting. HTH, Tobias I thought of that too -- since the graphics device needs to be closed before writing out to the file is completed and the file is closed. However, it occurred to me that possibly q() would also have that effect, since it closes down R which should have the effect of closing devices, flushing buffers, and closing files (though I do not see this documented under ?q). So I experimented. 1. New R session. 2. Assign values to some variables. 3. Open a tiff() device, plot them, and quit R (no dev.off): tiff(file=temp.tif) plot (X,P, type=l) lines(X,I.b, col=blue ) lines(X,I.m, col=green) lines(X,I.bm^2, col=red) q() 4. End of R session, and temp.tif (which did not exist at the start) contains a good TIFF file with exactly what I expected to see. This confirmed my suspicions. So it sould seem that dev.off() is not the answer. Probably something is wrong along the line of reading in the data, or in specifying what to plot. But I can't see anything obvious in the code, so it may depend on what sort of structure z is, for instance. Ted. E-Mail: (Ted Harding) ted.hard...@manchester.ac.uk Fax-to-email: +44 (0)870 094 0861 Date: 11-Jun-09 Time: 10:43:51 -- 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] Help on drawing stars and radars in R (update)
On Thu, Jun 11, 2009 at 10:01 AM, Caroline Gideon-Adeniyic.gideon-adeni...@fashion.arts.ac.uk wrote: Hi I don't know if you can help. I am a 2nd year Bsc Cosmetic Science student and in R I need some help in drawing stars. The problem that I have is I want to recreate a radar diagram similar to the one in excel. I have put in these commands in a script window: stars(shampoo1[, 1:6], locations = c(0,0), radius = TRUE, key.loc=c(0,0), main = Ranked Results for the Sensory Evaluation of the Shampoo , frame.plot = TRUE, key.labels = c(Foam Texture, Skin Feel, Rinsability, Wet Combability, Wet Feel, Odour), lty = 2, ) This gives me a black and white radar which is fine. Now according to the reference manual to colour the stars i need to add: col.stars = rainbow (30) Which colours in each star segment. The problem I have with this is that the segments are filled with colour and the segments overlap each other and each segment is not visible. So I desperately need the command that only colours the outline of the segments or stars instead of filling it. This is the example given in the reference manual: stars(mtcars[, 1:7], locations = c(0,0), radius = FALSE, key.loc=c(0,0), main=Motor Trend Cars, lty = 2) Can u help? The stars are drawn using R's polygon function, and that has two colours - the fill colour and the border colour. It seems that the stars function only lets you set the fill colour and not the border colour which is what you want. It is possible to modify the stars function to also set the border colour, but that can be a bit beyond beginners skills. I reckon someone on this list will come up with a modified stars() function before the end of the day that does it. It might be me, if it wasn't for the fact I have other things I should be doing! All that needs doing is to add a col.border argument to stars, and then make sure border= is used when stars calls polygon. I've half done it already. Is this the first use of R in cosmetic science? Maybe next time I see a shampoo advert on TV and they do the 'here comes the science' bit, we'll see a plot made in R... 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.
Re: [R] Issues getting R to write image files
Hi all, Silly missing ) at the end of the plot command! is working now, just need to remove the V1 and V2 that appear under my axis labels! Cheers for all your help guys, much appreciated. Kenny Ted.Harding-2 wrote: On 11-Jun-09 09:24:42, Tobias Verbeke wrote: Hi Kenny, Have spent the last couple of days learning R and shell scripting to do batch plotting jobs. I have had success getting R to complete a filled contour plot and output to a file (.jpg or .tiff etc). However, when I try to do the same thing with the simple plot command the script seems to execute correctly yet there is no output. Below is my R code: file - Sys.getenv(input_file) tiff(paste( file, tiff, sep=.)) z - read.table(file) plot(z, type=l, xlim=range(0.6,2), col = red, plot.title = title(main = file, xlab = Wavelength (um), ylab = Intensity (arb.)) dev.off() q() You need to close the tiff graphics device you opened using dev.off() before quitting. HTH, Tobias I thought of that too -- since the graphics device needs to be closed before writing out to the file is completed and the file is closed. However, it occurred to me that possibly q() would also have that effect, since it closes down R which should have the effect of closing devices, flushing buffers, and closing files (though I do not see this documented under ?q). So I experimented. 1. New R session. 2. Assign values to some variables. 3. Open a tiff() device, plot them, and quit R (no dev.off): tiff(file=temp.tif) plot (X,P, type=l) lines(X,I.b, col=blue ) lines(X,I.m, col=green) lines(X,I.bm^2, col=red) q() 4. End of R session, and temp.tif (which did not exist at the start) contains a good TIFF file with exactly what I expected to see. This confirmed my suspicions. So it sould seem that dev.off() is not the answer. Probably something is wrong along the line of reading in the data, or in specifying what to plot. But I can't see anything obvious in the code, so it may depend on what sort of structure z is, for instance. Ted. E-Mail: (Ted Harding) ted.hard...@manchester.ac.uk Fax-to-email: +44 (0)870 094 0861 Date: 11-Jun-09 Time: 10:43:51 -- 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. -- View this message in context: http://www.nabble.com/Issues-getting-R-to-write-image-files-tp23977785p23978518.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 Courses in Toronto
Dear R users, Does anybody know if there any good R courses within the Toronto area? 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] [R-pkgs] package installation fails (RandomFields)
Drew, Wrong list -- please use r-help. Re-directing from r-packages. On 10 June 2009 at 14:40, Drew Hoysak wrote: | I have been unable to install the package RandomFields. I am using R | 2.9.0-4 on Ubuntu 9.04. | | To install, I use the command: | sudo R CMD INSTALL RandomFields_1.3.37.tar.gz | | | The output follows below. Any help Would be appreciated. | | D. Hoysak | Brandon University | | | * Installing to library ‘/usr/local/lib/R/site-library’ | * Installing *source* package ‘RandomFields’ ... | ** libs | g++ -I/usr/share/R/include -g -fpic -g -O2 -c D.H.cc -o D.H.o [...] | g++ -shared -o RandomFields.so D.H.o Hyperfcts.o MPP.o MPPFcts.o | RFCovFcts.o RFcircembed.o RFdirect.o RFempvario.o RFgetNset.o | RFhyperplan.o RFinitNerror.o RFnugget.o RFother.o RFsimu.o RFspectral.o | RFtbm.o Xempvario.o addownfctns.o auxiliary.o avltr.o extremes.o | modelling.o win_linux_aux.o -llapack -L/usr/lib/R/lib -lR | /usr/bin/ld: cannot find -llapack ^ Did you install r-base-dev, which then pulls in libblas-dev and liblapack-dev (or their libatlas-* equivalents) as well as a bunch of other -dev packages? If no do 'sudo apt-get install r-base-dev' and try again. Dirk | collect2: ld returned 1 exit status | make: *** [RandomFields.so] Error 1 | ERROR: compilation failed for package ‘RandomFields’ | * Removing ‘/usr/local/lib/R/site-library/RandomFields’ | | ___ | R-packages mailing list | r-packa...@r-project.org | https://stat.ethz.ch/mailman/listinfo/r-packages | | __ | R-help@r-project.org mailing list | https://stat.ethz.ch/mailman/listinfo/r-help | PLEASE do read the posting guide http://www.R-project.org/posting-guide.html | and provide commented, minimal, self-contained, reproducible code. -- Three out of two people have difficulties with fractions. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Issues getting R to write image files
q() does call the internal version of graphics.off() which closes all open graphics devices. On Thu, 11 Jun 2009, Mario Valle wrote: Has tried to close the image file at the end? Do: dev.off() Hope it helps mario Kenny Larsen wrote: Hi All, Have spent the last couple of days learning R and shell scripting to do batch plotting jobs. I have had success getting R to complete a filled contour plot and output to a file (.jpg or .tiff etc). However, when I try to do the same thing with the simple plot command the script seems to execute correctly yet there is no output. Below is my R code: file - Sys.getenv(input_file) tiff(paste( file, tiff, sep=.)) z - read.table(file) plot(z, type=l, xlim=range(0.6,2), col = red, plot.title = title(main = file, xlab = Wavelength (um), ylab = Intensity (arb.)) q() The data file is simply 2 columns of real numbers. The system it is running on is a linux box from the command line, but does have the Xlibrarys and can clearly write tiff's as it managed it with the filled contours. Bear in mind I only started with both linux and R a couple of days ago, so be gentle if it is something silly! Cheers, Kenny -- Ing. Mario Valle Data Analysis and Visualization Group| http://www.cscs.ch/~mvalle Swiss National Supercomputing Centre (CSCS) | Tel: +41 (91) 610.82.60 v. Cantonale Galleria 2, 6928 Manno, Switzerland | Fax: +41 (91) 610.82.82 -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R Courses in Toronto
Dear Leo, The York University Statistical Consulting Service often teaches R-related courses. For past examples, see http://www.yorku.ca/isr/scs/links.html and http://www.yorku.ca/isr/spida2009/index.html. I hope this helps, John On Thu, 11 Jun 2009 06:15:44 -0400 Leo Guelman leo.guel...@gmail.com wrote: Dear R users, Does anybody know if there any good R courses within the Toronto area? 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. John Fox, Professor Department of Sociology McMaster University Hamilton, Ontario, Canada http://socserv.mcmaster.ca/jfox/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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 1:p : NA/NaN argument when running model comparisons
Hi there,
I am trying to compare nonlinear least squares regression with AIC and anova.
The simplest model is one nonlinear curve, and in the more complex model I have
a categorical variable (producing parameter estimates for four curves).
Both models run fine, but when I try to produce an AIC value for the second
model I get the error:
AIC(pow.nls1)
[1] 114408.3
AIC(pow.nls2)
Error in 1:p : NA/NaN argument
And similarly, when I try to compare the models with ANOVA, I get:
anova(pow.nls1, pow.nls2)
Error in if (df[i] 0) { : missing value where TRUE/FALSE needed
It seemed as if this could be a problem with the dataset, but I have checked
thoroughly and there are no missing values etc.
What do these error messages actually indicate?
Many thanks in advance!
Lindsay
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[R] triangular plot
Sorry for probably again an easy question but I can not find the solution... Using the ade4 package I am drawing a triangular graph: triangle.plot(data2, label = row.names(data2), clab=0.6, show.position=FALSE, box=FALSE) Which is what I want. Unfortunately the labels have a frame and a white background. I would like to have them without frame and colour, similar to what you get with type=text. I tried various things (box, boxes, label.color and settings of par via fg or bg=transparent) without luck. Any help is highly appreciated. Thanks a lot in advance With kind regards Johannes -- Project Coordinator BIOTA West Amphibians Museum of Natural History Dep. of Research (Herpetology) Invalidenstrasse 43 D-10115 Berlin Tel: +49 (0)30 2093 8708 Fax: +49 (0)30 2093 8565 http://www.biota-africa.org http://community-ecology.biozentrum.uni-wuerzburg.de __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] ctc package
Dear Allan, Thank you very much! Sometimes the forest is difficult to see when you are looking at the trees only... as we would say... With kind regards Johannes __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] ctc package
Hi Johannes -- Penner, Johannes wrote: Dear R-helpers, I would like to export hierarchical clusters e.g. fit - hclust(d, method=ward) in the newick format write(hc2Newick(fit),file='hclust.newick') Searching for a possibility I found this solution in the package ctc (http://www.bioconductor.org/packages/bioc/html/ctc.html). However, neither from this site nor via CRAN it is possible to install the package. Not sure what you mean -- did you try source(http://bioconductor.org/biocLite.R;) biocLite(ctc) as suggested on the page you mention? If this does not work, then please provide a transcript showing the error condition; it also helps to provide the output of the command sessionInfo() Martin Is there any other possibility? Is the package included in any other package? Thanks a lot in advance. With kind regards Johannes -- Project Coordinator BIOTA West Amphibians Museum of Natural History Dep. of Research (Herpetology) Invalidenstrasse 43 D-10115 Berlin Tel: +49 (0)30 2093 8708 Fax: +49 (0)30 2093 8565 http://www.biota-africa.org http://community-ecology.biozentrum.uni-wuerzburg.de __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] triangular plot
On Jun 11, 2009, at 8:56 AM, Penner, Johannes wrote:
Sorry for probably again an easy question but I can not find the
solution...
Using the ade4 package I am drawing a triangular graph:
triangle.plot(data2, label = row.names(data2), clab=0.6,
show.position=FALSE, box=FALSE)
Which is what I want. Unfortunately the labels have a frame and a
white
background. I would like to have them without frame and colour,
similar
to what you get with type=text.
I tried various things (box, boxes, label.color and settings of par
via
fg or bg=transparent) without luck. Any help is highly appreciated.
Thanks a lot in advance
triangle.plot does not have optional parameters to be passed to
accessory functions. Furthermore, it calls scatterutil.eti for the
plotting of boxes which has hard-coded white background in the boxes.
As far as I can tell triangle.plot does not pass a color argument for
the borders of the boxes.
scatterutil.eti
function (x, y, label, clabel, boxes = TRUE, coul = rep(1, length(x)),
horizontal = TRUE)
snipped code
if (boxes) {
rect(x1 - xh/2, y1 - yh/2, x1 + xh/2, y1 + yh/2,
col = white, border = coul[i])
snipped code
scatterutil.eti2
function (x, y, label, clabel, boxes = TRUE, coul = rep(1, length(x)),
horizontal = TRUE)
snipped code
if (boxes) {
rect(x1 - xh/2, y1 - yh/2, x1 + xh/2, y1 + yh/2,
col = transparent, border = coul[i])
snipped code
I made up a triangle.plot2 and a scatterutil.eti2 with
col=transparent and provision for passing color parameters to the
borders of the boxes and a got part of the way toward what you are
asking requesting. There is a remaining glitch when I use the first
example in the triangle.plot help page. A minority of items still get
boxes even though they are transparent. Probably has to do with the
default assignment of coul[i] to border. That could certainly be
altered as well.
I could not tell exactly what you mean by have them without frame and
colour either because of your use of the indefinite English pronoun
or the use of Aristotelean logic. They (the boxes anyway) currently
have no color. Did you want color added to something? At any rate
you can do the same sort of function hacking as I did. There are no
methods or other complicating issues in your way. All the source is
at the surface.
--
David Winsemius, MD
Heritage Laboratories
West Hartford, CT
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[R] problem with the legend when having two plots
I am trying to plot survival curves and here is the code plot(survfit(Surv(days,status)~group, data=g3), lty=1:2, mark.time=F, ylab=Probability, xlab=Suvival Time in Month) legend(10, 0.2,legend=c(Control,RIT), lty=c(2,1), title=Hormonal Therapy, bty=n) I will get two survival plots with the Control on the top of the RIT but if I switch to legend=c(“RIT”,”Control”), I will have the same plots but now the top on is named as RIT and the bottom as Control! It does not seem that R can tell which graph corresponds to what, am I missing something. Thanks for the help -- View this message in context: http://www.nabble.com/problem-with-the-legend-when-having-two-plots-tp23981238p23981238.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] GRASS raster data processing
Hi, I just imported two raster maps into R using the SPGRASS6 package, one containing elevation data and the other containing an erosion index: Kar_inc -readRAST6(Incis_Kar, plugin=FALSE) Kar_dem - readRAST6(DEM_Kar, plugin=FALSE) I just wanted to make a xy plot of erosion parameter vs elevation. How does this work? I don't get how to handle SpatialGridDataFrames... Thanks a lot Maarten -- View this message in context: http://www.nabble.com/GRASS-raster-data-processing-tp23981740p23981740.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] S4 Package with definition of method 'names'
Dear List,
Is it possible to build a package with 'names' method for a S4-Class?
The following works if directly pasted into R:
(a simple test class with 1 attribute that is returned by invoking 'names')
#class definition
setClass(test, representation = representation(name = character),
prototype = prototype(name = thisIsMyName))
#definition of names for class test
setMethod(names, test, function(x)
{
x...@name
}
)
#definition of names- for class test
setReplaceMethod(names, test, function(x, value)
{
x...@name - value
x
}
)
test = new(test)
names(test) #returns thisIsMyName
However 'R CMD check ' for building a package fails with
Error in setMethod(f, signature, NULL, where = where) :
the method for function names and signature = is sealed and cannot
be re-defined
Calls: Anonymous ... sys.source - eval - eval - removeMethod -
setMethod
Execution halted
make[2]: *** [lazyload] Error 1
make[1]: *** [all] Error 2
make: *** [pkg-DAP] Error 2
This is somewhat confusing since it works nicely if pasted into R.
Any Ideas
Thank you for your time
Thomas Roth
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Re: [R] [R-pkgs] package installation fails (RandomFields)
The offending lines don't look right to me:
38 typedef struct key_type;
261 typedef struct mpp_storage;
309 typedef struct cov_fct;
Shouldn't they be 'typedef struct struct_name typedefed_name'?
Later in the file there are proper typedef's for these things.
Bill Dunlap
TIBCO Software Inc - Spotfire Division
wdunlap tibco.com
-Original Message-
From: r-help-boun...@r-project.org
[mailto:r-help-boun...@r-project.org] On Behalf Of Martin Maechler
Sent: Thursday, June 11, 2009 12:42 AM
To: Drew Hoysak
Cc: r-help@r-project.org
Subject: Re: [R] [R-pkgs] package installation fails (RandomFields)
[[ NOTE: This accidentally was approved to go to R-packages,
it should never have gone there, and I have deleted it
from the archives.
Please *only* reply to R-help (and the OP)!
]]
DH == Drew Hoysak hoy...@wcgwave.ca
on Wed, 10 Jun 2009 14:40:32 -0500 writes:
DH I have been unable to install the package
RandomFields. I am using R
DH 2.9.0-4 on Ubuntu 9.04.
How exactly did you install R? Just as ubuntu package?
{probably, given the somewhat particular version number}
DH To install, I use the command:
DH sudo R CMD INSTALL RandomFields_1.3.37.tar.gz
DH The output follows below. Any help Would be appreciated.
DH D. Hoysak
DH Brandon University
DH * Installing to library '/usr/local/lib/R/site-library'
DH * Installing *source* package 'RandomFields' ...
DH ** libs
DH g++ -I/usr/share/R/include -g -fpic -g -O2 -c D.H.cc -o D.H.o
DH In file included from D.H.cc:27:
DH RFsimu.h:38: warning: 'typedef' was ignored in this
declaration
DH RFsimu.h:261: warning: 'typedef' was ignored in this
declaration
DH RFsimu.h:309: warning: 'typedef' was ignored in this
declaration
[..]
[..]
DH RFsimu.h:309: warning: 'typedef' was ignored in this
declaration
DH g++ -I/usr/share/R/include -g -fpic -g -O2 -c
win_linux_aux.cc -o
DH win_linux_aux.o
DH g++ -shared -o RandomFields.so D.H.o Hyperfcts.o
MPP.o MPPFcts.o
DH RFCovFcts.o RFcircembed.o RFdirect.o RFempvario.o RFgetNset.o
DH RFhyperplan.o RFinitNerror.o RFnugget.o RFother.o
RFsimu.o RFspectral.o
DH RFtbm.o Xempvario.o addownfctns.o auxiliary.o avltr.o
extremes.o
DH modelling.o win_linux_aux.o -llapack -L/usr/lib/R/lib -lR
DH /usr/bin/ld: cannot find -llapack
^
This looks like a setup problem of the R installation you have;
I'd guess that you would also see problems installing other R
packages that rely on LAPACK.
DH collect2: ld returned 1 exit status
DH make: *** [RandomFields.so] Error 1
DH ERROR: compilation failed for package 'RandomFields'
DH * Removing '/usr/local/lib/R/site-library/RandomFields'
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Re: [R] problem with the legend when having two plots
On Jun 11, 2009, at 9:23 AM, kayj wrote: I am trying to plot survival curves and here is the code plot(survfit(Surv(days,status)~group, data=g3), lty=1:2, mark.time=F, ylab=Probability, xlab=Suvival Time in Month) legend(10, 0.2,legend=c(Control,RIT), lty=c(2,1), title=Hormonal Therapy, bty=n) I will get two survival plots with the Control on the top of the RIT but if I switch to legend=c(“RIT”,”Control”), I will have the same plots but now the top on is named as RIT and the bottom as Control! It does not seem that R can tell which graph corresponds to what, am I missing something. I think it more that R and the legend function does not do semantic checking of plotting activities that preceded it and cannot read minds. You seem to be attributing cognitive capacity to R. Tempting for the magical thinking inclined (as we all are to various degrees), but not helpful in understanding what a computer does at this stage in silicon evolution. The survfit.object had names for the strata already and you simply overwrote that name in the legend. It does not have the facility to check to see if the names you supplied reversed any of the internal names. You are supposed to know in what order your curves are labeled, and if you do not, it is a simple matter to use str() on the survfit object. Your approach (reversing both label and line-type should have changed only the order that the legend entries appeared ... which would seem to be useful ability available to you, the wetware operator. Thanks for the help -- 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] Cluster analysis, defining center seeds or number of clusters
I use kmeans to classify spectral events in high and low 1/3 octave bands: #Do cluster analysis CyclA-data.frame(LlowA,LhghA) CntrA-matrix(c(0.9,0.8,0.8,0.75,0.65,0.65), nrow = 3, ncol=2, byrow=TRUE) ClstA-kmeans(CyclA,centers=CntrA,nstart=50,algorithm=MacQueen) This works well when the actual data shows 1,2 or 3 groups that are not too close in a cross plot. The MacQueen algorithm will give one or more empty groups which is what I want. However, there are cases when the groups are closer together, less compact or diffuse which leads to the situation where visually only 2 groups are apparent but the algorithm returns 3 splitting one group in two. I looked at the package 'cluster' specifically at clara (cannot use pam as I have 1 observations). But clara always returns as many groups as you aks for. Is there a way to help find a seed for the intial cluster centers? Equivalently, is there a way to find a priori the number of groups? I know this is not an easy problem. I have looked at principal components (princomp, prcomp) because there is a connection with cluster analysis. It is not obvious to me how to program that connection though. http://en.wikipedia.org/wiki/Principal_Component_Analysis http://ranger.uta.edu/~chqding/papers/Zha-Kmeans.pdf http://ranger.uta.edu/~chqding/papers/KmeansPCA1.pdf Thanks in advance, Alex van der Spek __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] GRASS raster data processing
Maayt: I just imported two raster maps into R using the SPGRASS6 package, one containing elevation data and the other containing an erosion index: Kar_inc -readRAST6(Incis_Kar, plugin=FALSE) Kar_dem - readRAST6(DEM_Kar, plugin=FALSE) I just wanted to make a xy plot of erosion parameter vs elevation. How does this work? I don't get how to handle SpatialGridDataFrames... Maarten, you can check some web-pages with respect to GRASS R [1][2]. This is a question for grass-stats actually [3]. A quick answer: check the structure of the newly created object and you will find that the numbers are to be found in (e.g. for Incis_Kar ) kar_...@data$incis_kar. So use @data and the $ to access a slot. Kind regards, Nikos --- [1] http://grass.osgeo.org/wiki/R [2] http://grass.ibiblio.org/statsgrass/index.php#grassR [3] http://grass.osgeo.org/statsgrass/index.php __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Install local package
Ronggui Huang wrote: ## Check the package R CMD check path.of.package ## Build the package R CMD build pathof.package ## INSTALL the package R CMD INSTALL path.of.package It is recommended to build the tar.gz first and then isntall and check from the tarball rather than from the source directory. Uwe Ligges You can use _R --help _ (from within terminal) to get more information. Ronggui 2009/6/11 Jorge Cornejo cornejo...@gmail.com: Hi, I'm working on a package that I would someday put in CRAN. Now I want to test it on my computer. I already check and compile the files but I don't know how to install the package located on my hard drive. I'm running R under linux. Can anyone tell my how to do it? Thanks in advance. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] [R-pkgs] package installation fails (RandomFields)
William Dunlap wrote:
The offending lines don't look right to me:
38 typedef struct key_type;
261 typedef struct mpp_storage;
309 typedef struct cov_fct;
Shouldn't they be 'typedef struct struct_name typedefed_name'?
Later in the file there are proper typedef's for these things.
In that case, can you please report it to the RandomFields maintainer?
Thank you very much,
Uwe Ligges
Bill Dunlap
TIBCO Software Inc - Spotfire Division
wdunlap tibco.com
-Original Message-
From: r-help-boun...@r-project.org
[mailto:r-help-boun...@r-project.org] On Behalf Of Martin Maechler
Sent: Thursday, June 11, 2009 12:42 AM
To: Drew Hoysak
Cc: r-help@r-project.org
Subject: Re: [R] [R-pkgs] package installation fails (RandomFields)
[[ NOTE: This accidentally was approved to go to R-packages,
it should never have gone there, and I have deleted it
from the archives.
Please *only* reply to R-help (and the OP)!
]]
DH == Drew Hoysak hoy...@wcgwave.ca
on Wed, 10 Jun 2009 14:40:32 -0500 writes:
DH I have been unable to install the package
RandomFields. I am using R
DH 2.9.0-4 on Ubuntu 9.04.
How exactly did you install R? Just as ubuntu package?
{probably, given the somewhat particular version number}
DH To install, I use the command:
DH sudo R CMD INSTALL RandomFields_1.3.37.tar.gz
DH The output follows below. Any help Would be appreciated.
DH D. Hoysak
DH Brandon University
DH * Installing to library '/usr/local/lib/R/site-library'
DH * Installing *source* package 'RandomFields' ...
DH ** libs
DH g++ -I/usr/share/R/include -g -fpic -g -O2 -c D.H.cc -o D.H.o
DH In file included from D.H.cc:27:
DH RFsimu.h:38: warning: 'typedef' was ignored in this
declaration
DH RFsimu.h:261: warning: 'typedef' was ignored in this
declaration
DH RFsimu.h:309: warning: 'typedef' was ignored in this
declaration
[..]
[..]
DH RFsimu.h:309: warning: 'typedef' was ignored in this
declaration
DH g++ -I/usr/share/R/include -g -fpic -g -O2 -c
win_linux_aux.cc -o
DH win_linux_aux.o
DH g++ -shared -o RandomFields.so D.H.o Hyperfcts.o
MPP.o MPPFcts.o
DH RFCovFcts.o RFcircembed.o RFdirect.o RFempvario.o RFgetNset.o
DH RFhyperplan.o RFinitNerror.o RFnugget.o RFother.o
RFsimu.o RFspectral.o
DH RFtbm.o Xempvario.o addownfctns.o auxiliary.o avltr.o
extremes.o
DH modelling.o win_linux_aux.o -llapack -L/usr/lib/R/lib -lR
DH /usr/bin/ld: cannot find -llapack
^
This looks like a setup problem of the R installation you have;
I'd guess that you would also see problems installing other R
packages that rely on LAPACK.
DH collect2: ld returned 1 exit status
DH make: *** [RandomFields.so] Error 1
DH ERROR: compilation failed for package 'RandomFields'
DH * Removing '/usr/local/lib/R/site-library/RandomFields'
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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Re: [R] Error in 1:p : NA/NaN argument when running model comparisons
Lindsay Banin wrote:
Hi there,
I am trying to compare nonlinear least squares regression with AIC and anova.
The simplest model is one nonlinear curve, and in the more complex model I have
a categorical variable (producing parameter estimates for four curves).
Both models run fine, but when I try to produce an AIC value for the second
model I get the error:
AIC(pow.nls1)
[1] 114408.3
AIC(pow.nls2)
Error in 1:p : NA/NaN argument
Well, without model specification and data it is impossible for us to
know why exactly the AIC cannot be calculated.
Uwe Ligges
And similarly, when I try to compare the models with ANOVA, I get:
anova(pow.nls1, pow.nls2)
Error in if (df[i] 0) { : missing value where TRUE/FALSE needed
It seemed as if this could be a problem with the dataset, but I have checked
thoroughly and there are no missing values etc.
What do these error messages actually indicate?
Many thanks in advance!
Lindsay
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Re: [R] Help on drawing stars and radars in R (update)
Barry Rowlingson wrote: On Thu, Jun 11, 2009 at 10:01 AM, Caroline Gideon-Adeniyic.gideon-adeni...@fashion.arts.ac.uk wrote: Hi I don't know if you can help. I am a 2nd year Bsc Cosmetic Science student and in R I need some help in drawing stars. The problem that I have is I want to recreate a radar diagram similar to the one in excel. I have put in these commands in a script window: stars(shampoo1[, 1:6], locations = c(0,0), radius = TRUE, key.loc=c(0,0), main = Ranked Results for the Sensory Evaluation of the Shampoo , frame.plot = TRUE, key.labels = c(Foam Texture, Skin Feel, Rinsability, Wet Combability, Wet Feel, Odour), lty = 2, ) This gives me a black and white radar which is fine. Now according to the reference manual to colour the stars i need to add: col.stars = rainbow (30) Which colours in each star segment. The problem I have with this is that the segments are filled with colour and the segments overlap each other and each segment is not visible. So I desperately need the command that only colours the outline of the segments or stars instead of filling it. This is the example given in the reference manual: stars(mtcars[, 1:7], locations = c(0,0), radius = FALSE, key.loc=c(0,0), main=Motor Trend Cars, lty = 2) Can u help? The stars are drawn using R's polygon function, and that has two colours - the fill colour and the border colour. It seems that the stars function only lets you set the fill colour and not the border colour which is what you want. It is possible to modify the stars function to also set the border colour, but that can be a bit beyond beginners skills. I reckon someone on this list will come up with a modified stars() function before the end of the day that does it. It might be me, if it wasn't for the fact I have other things I should be doing! OK, if Caroline requests more help here, we are probably both willing to add change the two lines of code. All that needs doing is to add a col.border argument to stars, and then make sure border= is used when stars calls polygon. I've half done it already. Is this the first use of R in cosmetic science? At least I heard of studies like clinical trials by cosmetic companies to proof that some lotions/shampoos really increase some features of your skin/hair, Barry. Well, perhaps I am buying the wrong shampoo and should look at the statistics here since the amount of my hair has been reduced significantly over the last couple of years. This does not mean I want to encourage people to send shampoo commercials to R-help or my mail address. Best, Uwe Maybe next time I see a shampoo advert on TV and they do the 'here comes the science' bit, we'll see a plot made in R... 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] [Ann] RMate, a bundle for TextMate and E-Texteditor
I have uploaded RMate to Github. From the readme: RMate is a [TextMate](http://macromates.com/) bundle for [R](http://www.r-project.org/about.html). It is based on the [R/R Console/Rdaemon](http://svn.textmate.org/trunk/Bundles) bundles and is focused on: - easy to use, clear interface/menu - support for Windows ([E-Texteditor](http://www.e-texteditor.com/)) - editing code, R/Rd snippets and getting help/info - connect to the standard R frontends (R.app and RGui) Install via git:pre INSTDIR=~/Library/Application Support/TextMate/Bundles cd $INSTDIR git clone git://github.com/swissr/rmate.tmbundle.git rmate.tmbundle osascript -e 'tell app TextMate to reload bundles' /pre or by hand:pre - download - the [master](http://github.com/swissr/rmate.tmbundle/zipball/master) (i.e. most recent) version or - choose the (latest) tagged version [here](http://github.com/swissr/rmate.tmbundle/downloads) - unzip and rename to 'rmate.tmbundle' (i.e. remove swissr- and -hash) - double click to import into TextMate' /pre Cheers, Hans-Peter __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Syntax question: assigning sparse matrix elements
Hopefully this is straightfoward. I have an matrix which is mostly zeroes. I want to assign it some non-zero elements whose rows, columns, and values I know. As a simple example, say I create a 3x2 matrix of zeros: m - matrix(rep(0,6),nrow=3) Now say I want to make the [1,1] and [3,2] elements of this matrix be non-zer, so I create two vectors, one for rows and one for cols: rows - c(1,3) cols - c(1,2) And I have two values to be put in these locations: vals - c(-1,1) What I'd like to do is something like: m[rows,cols] - vals But what I get instead is: m [,1] [,2] [1,] -1 -1 [2,]00 [3,]11 What I hoped to see is: m [,1] [,2] [1,] -10 [2,]00 [3,]01 If anyone can offer some advice I'd be most thankful. Regards Dan __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Cluster analysis, defining center seeds or number of clusters
Dear Alex, actually fixing the number of clusters in kmeans end then ending up with a smaller number because of empty clusters is not a standard method of estimating the number of clusters. I may happen (as apparently in some of your examples), but it is generally rather unusual. In most cases, kmeans, as well as clara, pam and other clustering methods, only give you the number of clusters you ask for. Even with some reasonable separation between clusters kmeans cannot generally be expected to come up with empty clusters if the number is initially chosen too high or too many initially centers are specified. The help page for pam.object in library cluster shows you a method to estimate the optimal number of clusters based on pam. However, this problem strongly depends on what cluster concept you have in mind and what you want to use your clusters for. There are alternative indexes that could be optimised to find the best number of clusters. Some of them are implemented in the function cluster.stats in package fpc. I strongly advise reading some literature about this to understand the problem better; the help page of cluster.stats gives a few references. The BIC gives you an estimate of the number of cluster together with Gaussian mixtures, see package mclust. If you can specify things like maximum within-cluster distances, you may get something from using cutree together with a hierarchical clustering method in hclust, for example complete linkage. dbscan and fixmahal in package fpc are further alternatives, requiring one or two tuning constants to come up with an automatical number of clusters. Best regards, Christian On Thu, 11 Jun 2009, am...@xs4all.nl wrote: I use kmeans to classify spectral events in high and low 1/3 octave bands: #Do cluster analysis CyclA-data.frame(LlowA,LhghA) CntrA-matrix(c(0.9,0.8,0.8,0.75,0.65,0.65), nrow = 3, ncol=2, byrow=TRUE) ClstA-kmeans(CyclA,centers=CntrA,nstart=50,algorithm=MacQueen) This works well when the actual data shows 1,2 or 3 groups that are not too close in a cross plot. The MacQueen algorithm will give one or more empty groups which is what I want. However, there are cases when the groups are closer together, less compact or diffuse which leads to the situation where visually only 2 groups are apparent but the algorithm returns 3 splitting one group in two. I looked at the package 'cluster' specifically at clara (cannot use pam as I have 1 observations). But clara always returns as many groups as you aks for. Is there a way to help find a seed for the intial cluster centers? Equivalently, is there a way to find a priori the number of groups? I know this is not an easy problem. I have looked at principal components (princomp, prcomp) because there is a connection with cluster analysis. It is not obvious to me how to program that connection though. http://en.wikipedia.org/wiki/Principal_Component_Analysis http://ranger.uta.edu/~chqding/papers/Zha-Kmeans.pdf http://ranger.uta.edu/~chqding/papers/KmeansPCA1.pdf Thanks in advance, Alex van der Spek __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. *** --- *** Christian Hennig University College London, Department of Statistical Science Gower St., London WC1E 6BT, phone +44 207 679 1698 chr...@stats.ucl.ac.uk, www.homepages.ucl.ac.uk/~ucakche __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] need help with strsplit function
Hi, if I have this string: a.b.c.d and I use this function: unlist(strsplit(a.b.c.d, \\.)), I get this as my output: a, b, c, and d. Is there a way to just split on the first period so I obtain only two pieces like: a and b.c.d? Anyways, thanks in advance! -- View this message in context: http://www.nabble.com/need-help-with-strsplit-function-tp23983888p23983888.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] deSolve question
Dear All,
I like to simulate a physiologically based pharmacokinetics model using R
but am having a problem with the daspk routine.
The same problem has been implemented in Berkeley madonna and Winbugs so
that I know that it is working. However, with daspk it is not, and the
numbers are everywhere!
Please see the following and let me know if I am missing something...
Thanks a lot in advance,
In-Sun
#---
library(deSolve)
y - c(Agi = 0,Alu = 0, Abr = 0, Ah = 0, Ali = 0, Ak = 0, Am = 0, Ask =
0, Aad = 0, Apa = 0, Asp = 0, Aar = 0, Ave = 0)
times = seq(0, 100, length=100)
pars - c(
dose = 80 * 0.26,
doseduration = 10,
Vmax = 1.44,
Km = 0.96,
s = 1.33,
fp = 0.236,
Kpfgi=0.324,
Kpflu = 1.092,
Kpfbr= 0.155 ,
Kpfh=0.767,
Kpfli = 0.551,
Kpfk=0.537,
Kpfm=0.339,
Kpfsk=0.784,
Kpfad=0.465,
Kpfpa=0.595,
Kpfsp=0.410,
Qar = 51.9,
Qve = 51.9,
Qgi = 12.3,
Qlu = 51.9,
Qbr = 3.2,
Qh = 6.4,
Qli = 16.5,
Qk = 12.8,
Qm = 7.6,
Qsk = 5.0,
Qad = 0.4,
Qpa = 1.0,
Qsp = 1.0,
Var = 7.0,
Vve = 14.1,
Vgi = 12.4,
Vlu = 1.3,
Vbr = 1.3,
Vh = 1.2,
Vli = 12.4,
Vk = 2.2,
Vm = 140.0,
Vsk = 49.0,
Vad = 11.2,
Vpa = 1.0,
Vsp = 1.0
)
Fun_ODE - function(t,y, pars){
with (as.list(c(y, pars)), {
It - dose/doseduration
Car - Aar/Var
Cve - Ave/Vve
Clu - Alu/Vlu
Cli - Ali/Vli
Cbr - Abr/Vbr
Ch - Ah/Vh
Cpa - Apa/Vpa
Csp - Asp/Vsp
Cgi - Agi/Vgi
Ck - Ak/Vk
Cm - Am/Vm
Cad - Aad/Vad
Csk - Ask/Vsk
Kpbbr - s*fp*Kpfbr
Kpbli - s*fp*Kpfli
Kpbh - s*fp*Kpfh
Kpbpa - s*fp*Kpfpa
Kpbsp - s*fp*Kpfsp
Kpbgi - s*fp*Kpfgi
Kpbk - s*fp*Kpfk
Kpbm - s*fp*Kpfm
Kpbad - s*fp*Kpfad
Kpbsk - s*fp*Kpfsk
Kpblu - s*fp*Kpflu
dAar - (Clu/Kpblu - Car)*Qar
dAve - if (t 10) It + Cbr*Qbr/Kpbbr + Ch *Qh/Kpbh + Cli*Qli/Kpbli +
Ck*Qk/Kpbk + Cm*Qm/Kpbm + Csk * Qsk /Kpbsk + Cad*Qad/Kpbad - Cve*Qve
else Cbr*Qbr/Kpbbr + Ch *Qh/Kpbh + Cli*Qli/Kpbli + Ck*Qk/Kpbk +
Cm*Qm/Kpbm + Csk * Qsk /Kpbsk + Cad*Qad/Kpbad - Cve*Qve
dAlu - (Cve-Clu/Kpblu)*Qlu
dAli - ((Qli - Qgi- Qpa-Qsp)*Car + Cgi*Qgi/Kpbgi + Csp*Qsp/Kpbsp +
Cpa*Qpa/Kpbpa - Cli*Qli/Kpbli) - Vmax*Cli/Kpfli/(Km + Cli/Kpfli)
dAbr - (Car - Cbr/Kpbbr)*Qbr
dAh - (Car - Ch/Kpbh)*Qh
dApa - (Car - Cpa/Kpbpa)*Qpa
dAsp - (Car - Csp/Kpbsp)*Qsp
dAgi - (Car - Cgi/Kpbgi)*Qgi
dAk - (Car - Ck/Kpbk)*Qk
dAm - (Car - Cm/Kpbm)*Qm
dAad - (Car - Cad/Kpbad)*Qad
dAsk - (Car - Csk/Kpbsk)*Qsk
return(list(dy = c(dAar, dAve, dAlu, dAli, dAbr, dAh, dApa, dAsp, dAgi, dAk,
dAm, dAad, dAsk),
Car = Car, Cve=Cve, Clu=Clu, Cli=Cli, Cbr=Cbr, Ch=Ch, Cpa=Cpa,
Csp=Csp, Cgi=Cgi, Ck=Ck, Cm=Cm, Cad=Cad, Csk=Csk))
})
}
ODE - as.data.frame(daspk(y = y, times = times, func = Fun_ODE,
parms = pars, atol = 1e-10, rtol = 1e-10))
--
Dr In-Sun Nam Knutsson
Research Associate
The Centre for Applied Pharmacokinetic Research (CAPKR)
School of Pharmacy and Pharmaceutical Sciences
University of Manchester
Stopford Building
Oxford Road
Manchester
U.K.
Phone: +44 161 275 2355
Email: in-sunnam.knuts...@manchester.ac.uk
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Re: [R] [R-pkgs] package installation fails (RandomFields) - SOLVED
Thanks to all who replied so quickly. Installing liblapack-dev solved the problem and I can now install RandomFields. Drew Hoysak Brandon 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.
[R] How to force R to print 2 decimal places in column of a data.frame?
How to force R to print 2 decimal places in column of a data.frame? I tried to do so: x = inp(format(rounf(inp$Tamanho, 2), nsmall = 2),) where INP is data.frame and Size is the name of column. But has error: Error in eval.with.vis(expr, envir, enclos) : could not find function inp Lesandro Veja quais são os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.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] need help with strsplit function
Using strapply in gsubfn we can match by contents rather than delimiter. Parentheses in the regular expression surround captured portions. The first such captured portion is any string not containing a dot. We then follow that by matching a dot and a second captured expression which is anything. c just concatenates the captured strings into a vector of strings. x - a.b.c.d library(gsubfn) Loading required package: proto strapply(x, ([^.]*)[.](.*), c) [[1]] [1] a b.c.d On Thu, Jun 11, 2009 at 11:44 AM, njhuang86njhuan...@yahoo.com wrote: Hi, if I have this string: a.b.c.d and I use this function: unlist(strsplit(a.b.c.d, \\.)), I get this as my output: a, b, c, and d. Is there a way to just split on the first period so I obtain only two pieces like: a and b.c.d? Anyways, thanks in advance! -- View this message in context: http://www.nabble.com/need-help-with-strsplit-function-tp23983888p23983888.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] need help with strsplit function
On Jun 11, 2009, at 10:44 AM, njhuang86 wrote: Hi, if I have this string: a.b.c.d and I use this function: unlist(strsplit(a.b.c.d, \\.)), I get this as my output: a, b, c, and d. Is there a way to just split on the first period so I obtain only two pieces like: a and b.c.d? Anyways, thanks in advance! Try this: strsplit(sub(\\., *, a.b.c.d), \\*) [[1]] [1] a b.c.d The inner sub() replaces the first '.' with a '*' allowing you to split on the unique character. You can modify the replacement character as your data may actually require. HTH, Marc Schwartz __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Expand a contingency table based on the value in one column
Hi R-helpers, I have the following (dummy) dataframe: test DATE LOCATION KIND CLASS COUNT 111 CAR A 2 211 TRUCK D 3 311 BUS E 4 412 CAR E 2 512 TRUCK A 7 612 BUS F 1 That I would like to turn into this: test2 DATE LOCATION KIND CLASS 1 11 CAR A 2 11 CAR A 3 11 TRUCK D 4 11 TRUCK D 5 11 TRUCK D 6 11 BUS E 7 11 BUS E 8 11 BUS E 9 11 BUS E 1012 CAR E 1112 CAR E 1212 TRUCK A 1312 TRUCK A 1412 TRUCK A 1512 TRUCK A 1612 TRUCK A 1712 TRUCK A 1812 TRUCK A 1912 BUS F So, basically it's a case of expanding (adding rows to) the first dataframe by the value in the COUNT column. I have solved this problem with the following code: test2-with(test, data.frame(DATE=rep(DATE,COUNT), LOCATION=rep(LOCATION,COUNT), KIND=rep(KIND,COUNT), CLASS=rep(CLASS,COUNT))) but I'm unsatisfied with that solution because it's verbose and I think there must a more elegant way. If I had more variables than 4 (which I do in my real data) it would be a nuisance to repeat each column within the rep function. I would prefer to do this with Base R or package(reshape) than relying on another package. Any ideas? Thanks! Mark Na [[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] saving loess fit
Hi, pv.lo - loess(Affy ~ DABG, DA, span=0.2, degree=2, family=symmetric) I would like to know how to save the output from the loess fit so that I can read it again into another session of R. Can someone help me figure this out? Lana Schaffer Biostatistics/Informatics The Scripps Research Institute DNA Array Core Facility La Jolla, CA 92037 (858) 784-2263 (858) 784-2994 schaf...@scripps.edu __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] difficulty in Installing
Hello, I have openSUSE 11.1 Trying to install randomForest as SU after invoking R install.packages(randomForest) and I get this * Installing *source* package randomForest ... ** libs gcc -std=gnu99 -I/usr/lib/R/include -I/usr/local/include-fpic -O2 -c classTree.c -o classTree.o gcc -std=gnu99 -I/usr/lib/R/include -I/usr/local/include-fpic -O2 -c regTree.c -o regTree.o gcc -std=gnu99 -I/usr/lib/R/include -I/usr/local/include-fpic -O2 -c regrf.c -o regrf.o gcc -std=gnu99 -I/usr/lib/R/include -I/usr/local/include-fpic -O2 -c rf.c -o rf.o gfortran -fpic -O2 -c rfsub.f -o rfsub.o make: gfortran: Command not found make: *** [rfsub.o] Error 127 ERROR: compilation failed for package randomForest * Removing /usr/lib/R/library/randomForest The downloaded packages are in /tmp/RtmpLEyfgR/downloaded_packages Updating HTML index of packages in '.Library' Warning message: In install.packages(randomForest) : installation of package 'randomForest' had non-zero exit status I checked that I have th fortran library S | Name | Summary | Type --+---+--+ i | libgfortran41 | The GNU Fortran Compiler Runtime Library | package i | libgfortran43 | The GNU Fortran Compiler Runtime Library | package Any ideas how to solve this impass? Alon Ben-Ari, MD Dept Of Anesthesiology. University of Pittsburgh [[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] Expand a contingency table based on the value in one column
On Jun 11, 2009, at 1:13 PM, Mark Na wrote: Hi R-helpers, I have the following (dummy) dataframe: test DATE LOCATION KIND CLASS COUNT 111 CAR A 2 211 TRUCK D 3 311 BUS E 4 412 CAR E 2 512 TRUCK A 7 612 BUS F 1 That I would like to turn into this: test2 DATE LOCATION KIND CLASS 1 11 CAR A 2 11 CAR A 3 11 TRUCK D 4 11 TRUCK D 5 11 TRUCK D 6 11 BUS E 7 11 BUS E 8 11 BUS E 9 11 BUS E 1012 CAR E 1112 CAR E 1212 TRUCK A 1312 TRUCK A 1412 TRUCK A 1512 TRUCK A 1612 TRUCK A 1712 TRUCK A 1812 TRUCK A 1912 BUS F test2 - test[rep(1:nrow(test), test$COUNT),] rownames(test2) - 1:nrow(test2) test2 So, basically it's a case of expanding (adding rows to) the first dataframe by the value in the COUNT column. I have solved this problem with the following code: test2-with(test, data.frame(DATE=rep(DATE,COUNT), LOCATION=rep(LOCATION,COUNT), KIND=rep(KIND,COUNT), CLASS=rep(CLASS,COUNT))) but I'm unsatisfied with that solution because it's verbose and I think there must a more elegant way. If I had more variables than 4 (which I do in my real data) it would be a nuisance to repeat each column within the rep function. I would prefer to do this with Base R or package(reshape) than relying on another package. Any ideas? Thanks! Mark Na [[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] Syntax question: assigning sparse matrix elements
On 6/11/2009 12:34 PM, Dan Ruderman wrote: Hopefully this is straightfoward. I have an matrix which is mostly zeroes. I want to assign it some non-zero elements whose rows, columns, and values I know. As a simple example, say I create a 3x2 matrix of zeros: m - matrix(rep(0,6),nrow=3) Now say I want to make the [1,1] and [3,2] elements of this matrix be non-zer, so I create two vectors, one for rows and one for cols: rows - c(1,3) cols - c(1,2) And I have two values to be put in these locations: vals - c(-1,1) What I'd like to do is something like: m[rows,cols] - vals But what I get instead is: m [,1] [,2] [1,] -1 -1 [2,]00 [3,]11 What I hoped to see is: m [,1] [,2] [1,] -10 [2,]00 [3,]01 If anyone can offer some advice I'd be most thankful. If the index to a matrix is a two column matrix, then the first column is taken to be a row number, the second a column number. So you get what you want with m[cbind(rows,cols)] - vals This is discussed (and other indexing methods too) in the R Language Definition manual in the section on indexing matrices and arrays. Duncan Murdoch __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Restrict AIC comparison to succesful models?
Hello list, I'm doing a bootstrap analysis where some models occasionally fail to converge. I'd like to automate the process of restricting AIC to the models that do converge. A contrived example of what I'd like to do is below: resp - c(1,1,2) pred - c(1,2,3) m1 - lm(resp~pred) m2 - lm(resp~poly(pred,2)) m3 - lm(resp~poly(pred,3)) # Fails, obviously ## Some test to see which models were successful models - test(m1,m2,m3) ## AIC on these models only AIC(models) -- http://mutualism.williams.edu __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] gfortran command not found?
Hello, I have openSUSE 11.1 Trying to install randomForest as SU after invoking R install.packages(randomForest) and I get this * Installing *source* package randomForest ... ** libs gcc -std=gnu99 -I/usr/lib/R/include -I/usr/local/include-fpic -O2 -c classTree.c -o classTree.o gcc -std=gnu99 -I/usr/lib/R/include -I/usr/local/include-fpic -O2 -c regTree.c -o regTree.o gcc -std=gnu99 -I/usr/lib/R/include -I/usr/local/include-fpic -O2 -c regrf.c -o regrf.o gcc -std=gnu99 -I/usr/lib/R/include -I/usr/local/include-fpic -O2 -c rf.c -o rf.o gfortran -fpic -O2 -c rfsub.f -o rfsub.o make: gfortran: Command not found make: *** [rfsub.o] Error 127 ERROR: compilation failed for package randomForest * Removing /usr/lib/R/library/randomForest The downloaded packages are in /tmp/RtmpLEyfgR/downloaded_packages Updating HTML index of packages in '.Library' Warning message: In install.packages(randomForest) : installation of package 'randomForest' had non-zero exit status I checked that I have th fortran library S | Name | Summary | Type --+---+--+ i | libgfortran41 | The GNU Fortran Compiler Runtime Library | package i | libgfortran43 | The GNU Fortran Compiler Runtime Library | package Any ideas how to solve this impass? Alon Ben-Ari, MD Dept Of Anesthesiology. University of Pittsburgh [[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] Expand a contingency table based on the value in one column
On Jun 11, 2009, at 12:13 PM, Mark Na wrote: Hi R-helpers, I have the following (dummy) dataframe: test DATE LOCATION KIND CLASS COUNT 111 CAR A 2 211 TRUCK D 3 311 BUS E 4 412 CAR E 2 512 TRUCK A 7 612 BUS F 1 That I would like to turn into this: test2 DATE LOCATION KIND CLASS 1 11 CAR A 2 11 CAR A 3 11 TRUCK D 4 11 TRUCK D 5 11 TRUCK D 6 11 BUS E 7 11 BUS E 8 11 BUS E 9 11 BUS E 1012 CAR E 1112 CAR E 1212 TRUCK A 1312 TRUCK A 1412 TRUCK A 1512 TRUCK A 1612 TRUCK A 1712 TRUCK A 1812 TRUCK A 1912 BUS F So, basically it's a case of expanding (adding rows to) the first dataframe by the value in the COUNT column. I have solved this problem with the following code: test2-with(test, data.frame(DATE=rep(DATE,COUNT), LOCATION=rep(LOCATION,COUNT), KIND=rep(KIND,COUNT), CLASS=rep(CLASS,COUNT))) but I'm unsatisfied with that solution because it's verbose and I think there must a more elegant way. If I had more variables than 4 (which I do in my real data) it would be a nuisance to repeat each column within the rep function. I would prefer to do this with Base R or package(reshape) than relying on another package. Any ideas? Thanks! Mark Na Mark, A quick and dirty solution: test[rep(1:nrow(test), test$COUNT), -ncol(test)] DATE LOCATION KIND CLASS 1 11 CAR A 1.111 CAR A 2 11 TRUCK D 2.111 TRUCK D 2.211 TRUCK D 3 11 BUS E 3.111 BUS E 3.211 BUS E 3.311 BUS E 4 12 CAR E 4.112 CAR E 5 12 TRUCK A 5.112 TRUCK A 5.212 TRUCK A 5.312 TRUCK A 5.412 TRUCK A 5.512 TRUCK A 5.612 TRUCK A 6 12 BUS F For a more general solution to taking a tabulated data frame and converting it back to the raw data see my expand.dft() function: https://stat.ethz.ch/pipermail/r-help/2009-January/185561.html For example: expand.dft(test, freq = COUNT) DATE LOCATION KIND CLASS 1 11 CAR A 2 11 CAR A 3 11 TRUCK D 4 11 TRUCK D 5 11 TRUCK D 6 11 BUS E 7 11 BUS E 8 11 BUS E 9 11 BUS E 1012 CAR E 1112 CAR E 1212 TRUCK A 1312 TRUCK A 1412 TRUCK A 1512 TRUCK A 1612 TRUCK A 1712 TRUCK A 1812 TRUCK A 1912 BUS F HTH, Marc Schwartz __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Installing the Rstem package
Hi,
I can't find the package for LSA. When I try
http://www.statistik.uni-dortmund.de/~ligges/Rstem_0.3-1.zip
http://www.statistik.uni-dortmund.de/%7Eligges/Rstem_0.3-1.zip
It says file not found.
Is there an updated link?
Ravi
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Re: [R] saving loess fit
See save() and load(), but the following might be easier because it does not mess with your existing object names: library(R.utils) saveObject(pv.lo, myLoessFit.Rbin) pv.lo - loadObject(myLoessFit.Rbin) foo - loadObject(myLoessFit.Rbin) print(identical(pv.lo, foo)) # = TRUE /Henrik On Thu, Jun 11, 2009 at 10:22 AM, Lana Schafferschaf...@scripps.edu wrote: Hi, pv.lo - loess(Affy ~ DABG, DA, span=0.2, degree=2, family=symmetric) I would like to know how to save the output from the loess fit so that I can read it again into another session of R. Can someone help me figure this out? Lana Schaffer Biostatistics/Informatics The Scripps Research Institute DNA Array Core Facility La Jolla, CA 92037 (858) 784-2263 (858) 784-2994 schaf...@scripps.edu __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Installing the Rstem package
Google Rstem package - first hit. It is hosted by the Omegahat project. /H
On Thu, Jun 11, 2009 at 10:29 AM, Rajan, Ravira...@rand.org wrote:
Hi,
I can't find the package for LSA. When I try
http://www.statistik.uni-dortmund.de/~ligges/Rstem_0.3-1.zip
http://www.statistik.uni-dortmund.de/%7Eligges/Rstem_0.3-1.zip
It says file not found.
Is there an updated link?
Ravi
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and provide commented, minimal, self-contained, reproducible code.
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Re: [R] Installing the Rstem package
Yep...except it looks like the package has not been submitted to CRAN for some time, which would facilitate the building of a Windows binary. From a check of the list archives, it looks like Uwe's link was a temporary solution. Prof Ripley appears to be building a binary of the package and the 2.9.0 version is available from: http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/2.9/ HTH, Marc Schwartz On Jun 11, 2009, at 12:57 PM, Henrik Bengtsson wrote: Google Rstem package - first hit. It is hosted by the Omegahat project. /H On Thu, Jun 11, 2009 at 10:29 AM, Rajan, Ravira...@rand.org wrote: Hi, I can't find the package for LSA. When I try http://www.statistik.uni-dortmund.de/~ligges/Rstem_0.3-1.zip http://www.statistik.uni-dortmund.de/%7Eligges/Rstem_0.3-1.zip It says file not found. Is there an updated link? Ravi __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] gfortran command not found?
On Jun 11, 2009, at 12:34 PM, Alon Ben-Ari wrote: Hello, I have openSUSE 11.1 Trying to install randomForest as SU after invoking R install.packages(randomForest) and I get this * Installing *source* package randomForest ... ** libs gcc -std=gnu99 -I/usr/lib/R/include -I/usr/local/include-fpic - O2 -c classTree.c -o classTree.o gcc -std=gnu99 -I/usr/lib/R/include -I/usr/local/include-fpic - O2 -c regTree.c -o regTree.o gcc -std=gnu99 -I/usr/lib/R/include -I/usr/local/include-fpic - O2 -c regrf.c -o regrf.o gcc -std=gnu99 -I/usr/lib/R/include -I/usr/local/include-fpic - O2 -c rf.c -o rf.o gfortran -fpic -O2 -c rfsub.f -o rfsub.o make: gfortran: Command not found make: *** [rfsub.o] Error 127 ERROR: compilation failed for package randomForest * Removing /usr/lib/R/library/randomForest The downloaded packages are in /tmp/RtmpLEyfgR/downloaded_packages Updating HTML index of packages in '.Library' Warning message: In install.packages(randomForest) : installation of package 'randomForest' had non-zero exit status I checked that I have th fortran library S | Name | Summary | Type --+---+--+ i | libgfortran41 | The GNU Fortran Compiler Runtime Library | package i | libgfortran43 | The GNU Fortran Compiler Runtime Library | package Any ideas how to solve this impass? I have not worked on SUSE, but check to see where gfortran is located: $ which gfortran and be sure that it returns the path to the executable and that the path to it is in your $PATH. You might also want to review: http://cran.r-project.org/doc/manuals/R-admin.html#Using-FORTRAN HTH, Marc Schwartz __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to force R to print 2 decimal places in column of a data.frame?
On Jun 11, 2009, at 11:48 AM, Lesandro wrote: How to force R to print 2 decimal places in column of a data.frame? I tried to do so: x = inp(format(rounf(inp$Tamanho, 2), nsmall = 2),) where INP is data.frame and Size is the name of column. But has error: Error in eval.with.vis(expr, envir, enclos) : could not find function inp Lesandro Your code and description above appear to have some typos in it and the use of the round() and format() functions are not what you want here. You code has inp(...), where R is presuming that you are referring to a function called 'inp', hence the error message, since the function does not exist. Better to use sprintf() with an appropriate format specifier: set.seed(1) vec - rnorm(10) vec [1] -0.6264538 0.1836433 -0.8356286 1.5952808 0.3295078 -0.8204684 [7] 0.4874291 0.7383247 0.5757814 -0.3053884 sprintf(%.2f, vec) [1] -0.63 0.18 -0.84 1.60 0.33 -0.82 0.49 0.74 [9] 0.58 -0.31 See ?sprintf for more information. Note that the presumption here is that you want to output the numeric values to a formatted character vector for display purposes, perhaps in a table, etc. So if your actual data frame is called 'INP' and the column is called 'Size', you would use: sprintf(%.2f, INP$Size) HTH, Marc Schwartz __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Matrix manipulation
Hello everyone, I have a couple of fairly simple questions (I hope) the answers to which I cannot find through the documentation at the moment. 1. I would like to delete the a row from a matrix if a certain elimination criterion is met. I am familiar with x - x[-7,] (to remove row 7, for example). Are there any other means of removing an entire row? 2. Is there a single command that will rename the index of each row to match the row number once a row has been deleted. For example, when row 7 is deleted above, the old row 8 is now row 7, but the row name is still 8. I have figured out how to assign a sequence vector to the row names, but I am wondering if there is a built-in command that does the same thing. (I.e., change the name of row 7 to 7 from 8.) Thank you very much. Payam -- Payam Minoofar, Ph.D. Scientist Meissner Filtration Products 4181 Calle Tesoro Camarillo, CA 93012 USA +1 805 388 9911 +1 805 388 5948 fax payam.minoo...@meissner.com [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Installing the Rstem package
On Thu, 11 Jun 2009, Marc Schwartz wrote: Yep...except it looks like the package has not been submitted to CRAN for some time, which would facilitate the building of a Windows binary. From a check of the list archives, it looks like Uwe's link was a temporary solution. It is perhaps worth noting that until ca a year ago Omegahat did distribute Windows binaries, but no longer (as far as I recall they existed for R 2.7.x but not 2.8.x, and I know for sure not for R 2.9.x). Prof Ripley appears to be building a binary of the package and the 2.9.0 version is available from: http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/2.9/ And in the corresponding directory for 2.8.x (an older version of Rstem), which means that Rstem should just install from the Rgui menus for users of recent versions of R. (Assumming this is for Windows -- we were not actually told). For the record, Windows builds of the Omegahat packages RCurl, XML (also on CRAN) Rcompression, SSOAP, Rstem, XMLSchema are on CRANextras. Builds of (in some cases older versions) of RCurl, Rlibstree, SSOAP, XML and XMLSchema are available from 'BioC extras' (which you can select as a repository from the menu). HTH, Marc Schwartz On Jun 11, 2009, at 12:57 PM, Henrik Bengtsson wrote: Google Rstem package - first hit. It is hosted by the Omegahat project. /H On Thu, Jun 11, 2009 at 10:29 AM, Rajan, Ravira...@rand.org wrote: Hi, I can't find the package for LSA. When I try http://www.statistik.uni-dortmund.de/~ligges/Rstem_0.3-1.zip http://www.statistik.uni-dortmund.de/%7Eligges/Rstem_0.3-1.zip It says file not found. Is there an updated link? Ravi __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Re strict AIC comparison to succesful models?
Manuel Morales wrote: Hello list, I'm doing a bootstrap analysis where some models occasionally fail to converge. I'd like to automate the process of restricting AIC to the models that do converge. A contrived example of what I'd like to do is below: resp - c(1,1,2) pred - c(1,2,3) m1 - lm(resp~pred) m2 - lm(resp~poly(pred,2)) m3 - lm(resp~poly(pred,3)) # Fails, obviously ## Some test to see which models were successful models - test(m1,m2,m3) How about models - list(m1,m2,m3) is.OK - sapply(models,test) do.call(AIC,models[is.OK]) ? -- View this message in context: http://www.nabble.com/Restrict-AIC-comparison-to-succesful-models--tp23985797p23987185.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] Count observation
Hi listers, I have the following code... data-as.matrix(c(1,2,3,4,5,6,7,8,9,10),nrow=10,ncol=1,byrow=TRUE) n-nrow(data) m-n-1 boot-data[sample(m,replace=T),] So, I need to count the number of times each observation was selected at the sample with replacement... Suppose I sampled... 4 5 1 3 7 5 1 4 7 So, I would count... x count 1 2 2 0 3 1 4 2 5 2 6 0 7 2 8 0 9 0 10 0 Thanks in advance, Marcio -- View this message in context: http://www.nabble.com/Count-observation-tp23987251p23987251.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] standard error beta glm
Dear All, The std. error of the estimated coefficients obtained by the summary.lm function can be calculated as: y=rnorm(20) x=y+rnorm(20) fit - lm(y ~ x) summary(fit) sqrt( sum(fit$resid**2)/fit$df.resid * solve(t(model.matrix(fit))%*%model.matrix(fit)) ) Is posible calculate Std. Error for glm as lm, using cov(hat beta) = phi * solve(t(X) %*% hat W %*% X)^-1 on R? Who is hat W and phi output glm? y=rpois(20,4) fit.glm - glm(y ~ x, family=poisson summary(fit.glm) Fitted to a model glm using constrast contr.sum and need compute the error standard for last level of the factor. best wishes for all, Ricardo. Veja quais são os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.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] Count observation
Hi Marcio, data.frame(table(boot)) ? milton brazil=toronto On Thu, Jun 11, 2009 at 3:13 PM, MarcioRibeiro mes...@pop.com.br wrote: Hi listers, I have the following code... data-as.matrix(c(1,2,3,4,5,6,7,8,9,10),nrow=10,ncol=1,byrow=TRUE) n-nrow(data) m-n-1 boot-data[sample(m,replace=T),] So, I need to count the number of times each observation was selected at the sample with replacement... Suppose I sampled... 4 5 1 3 7 5 1 4 7 So, I would count... x count 1 2 2 0 3 1 4 2 5 2 6 0 7 2 8 0 9 0 10 0 Thanks in advance, Marcio -- View this message in context: http://www.nabble.com/Count-observation-tp23987251p23987251.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.htmlhttp://www.r-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] formula for degrees of freedom for nonlinear mixed model in nlme
Dear forum members, What is the formula to calculate denominator degrees of freedom (den df) for nonlinear mixed-effect models with covariates? My model is similar to a CO2 uptake example from Pinheiro and Bates (2000, page 376). In this CO2 dataset, there are two treatments and two types (84 observations in total), but den df for each parameter of the model is 64. Isnt it too high? Your help is greatly appreciated, Julia Summary of the CO2 example: summary(fm4CO2.nlme) Nonlinear mixed-effects model fit by maximum likelihood Model: uptake ~ SSasympOff(conc, Asym, lrc, c0) Data: CO2 AIC BIClogLik 388.4185 420.0191 -181.2092 Random effects: Formula: list(Asym ~ 1, lrc ~ 1) Level: Plant Structure: General positive-definite, Log-Cholesky parametrization StdDev Corr Asym.(Intercept) 2.349640 As.(I) lrc.(Intercept) 0.079597 -0.92 Residual 1.791962 Fixed effects: list(Asym + lrc ~ Type * Treatment, c0 ~ 1) Value Std.Error DF t-value p-value Asym.(Intercept) 41.81756 1.562426 64 26.76451 0. Asym.TypeMississippi -10.53045 2.208318 64 -4.76854 0. Asym.Treatmentchilled -2.96943 2.213172 64 -1.34171 0.1844 Asym.TypeMississippi:Treatmentchilled -10.90037 3.112220 64 -3.50244 0.0008 lrc.(Intercept)-4.55724 0.096291 64 -47.32785 0. lrc.TypeMississippi-0.10412 0.121683 64 -0.85570 0.3954 lrc.Treatmentchilled -0.17124 0.111959 64 -1.52953 0.1311 lrc.TypeMississippi:Treatmentchilled0.74188 0.221742 64 3.34570 0.0014 c0 50.51075 4.364727 64 11.57249 0. Correlation: As.(I) Asy.TM Asym.T A.TM:T lr.(I) lrc.TM Asym.TypeMississippi -0.703 Asym.Treatmentchilled -0.701 0.496 Asym.TypeMississippi:Treatmentchilled 0.497 -0.709 -0.711 lrc.(Intercept) -0.627 0.415 0.407 -0.278 lrc.TypeMississippi0.458 -0.680 -0.322 0.482 -0.535 lrc.Treatmentchilled 0.500 -0.351 -0.717 0.509 -0.594 0.445 lrc.TypeMississippi:Treatmentchilled -0.262 0.375 0.362 -0.547 0.365 -0.553 c0-0.086 0.014 0.001 0.019 0.590 -0.033 lrc.Tr l.TM:T Asym.TypeMississippi Asym.Treatmentchilled Asym.TypeMississippi:Treatmentchilled lrc.(Intercept) lrc.TypeMississippi lrc.Treatmentchilled lrc.TypeMississippi:Treatmentchilled -0.511 c0-0.057 0.140 Standardized Within-Group Residuals: Min Q1 Med Q3 Max -2.86206487 -0.49445730 -0.04217037 0.56599012 3.04061332 Number of Observations: 84 Number of Groups: 12 Link to the book: http://books.google.com/books?id=N3WeyHFbHLQCpg=PA139lpg=PA139dq=mixed-effect+model+building+first+stepsource=blots=pR7PWIuKu8sig=TLhq-k5O4ZNwkBWcyQI8VZk9Umkhl=enei=1HguSrKaPJi0Nb3DnfUJsa=Xoi=book_resultct=resultresnum=1#PPA376,M1 _ [[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] Count observation
Dear Marcio, Here is one way. Please notice that even thought I changed the name of your data as well as its structure, you can easily modify it to your needs. # Data somedata - 1:10 n-length(somedata) m-n-1 # 1 sample boot - somedata[ sample(m,replace=T) ] table(factor( boot, levels=1:10 ) ) # 100 samples boots - replicate(100, somedata[ sample(m,replace=T)] ) # The counts apply(boots, 2, function(x) table(factor(x,levels=1:10)) ) see ?replicate, and ?apply for more information. HTH, Jorge On Thu, Jun 11, 2009 at 3:13 PM, MarcioRibeiro mes...@pop.com.br wrote: Hi listers, I have the following code... data-as.matrix(c(1,2,3,4,5,6,7,8,9,10),nrow=10,ncol=1,byrow=TRUE) n-nrow(data) m-n-1 boot-data[sample(m,replace=T),] So, I need to count the number of times each observation was selected at the sample with replacement... Suppose I sampled... 4 5 1 3 7 5 1 4 7 So, I would count... x count 1 2 2 0 3 1 4 2 5 2 6 0 7 2 8 0 9 0 10 0 Thanks in advance, Marcio -- View this message in context: http://www.nabble.com/Count-observation-tp23987251p23987251.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Re strict AIC comparison to succesful models?
On Thu, 2009-06-11 at 12:08 -0700, Ben Bolker wrote: Manuel Morales wrote: Hello list, I'm doing a bootstrap analysis where some models occasionally fail to converge. I'd like to automate the process of restricting AIC to the models that do converge. A contrived example of what I'd like to do is below: resp - c(1,1,2) pred - c(1,2,3) m1 - lm(resp~pred) m2 - lm(resp~poly(pred,2)) m3 - lm(resp~poly(pred,3)) # Fails, obviously ## Some test to see which models were successful models - test(m1,m2,m3) How about models - list(m1,m2,m3) is.OK - sapply(models,test) do.call(AIC,models[is.OK]) ? Good idea but unfortunately I get an error message with: models - list(m1,m2,m3) test - function(x) length(x)1 is.OK - sapply(models,test) do.call(AIC,models[is.OK]) I think the issue is that AIC is expecting a ... of model objects (not a list or a vector) and I'm not sure how to construct that. Manuel __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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 force R to print 2 decimal places in column of a data.frame?
Hi Marc Schwartz, Your suggestion solved my problem. Thanks you. --- Em qui, 11/6/09, Marc Schwartz marc_schwa...@me.com escreveu: De: Marc Schwartz marc_schwa...@me.com Assunto: Re: [R] How to force R to print 2 decimal places in column of a data.frame? Para: Lesandro lesand...@yahoo.com.br Cc: r-help@r-project.org Data: Quinta-feira, 11 de Junho de 2009, 15:45 On Jun 11, 2009, at 11:48 AM, Lesandro wrote: How to force R to print 2 decimal places in column of a data.frame? I tried to do so: x = inp(format(rounf(inp$Tamanho, 2), nsmall = 2),) where INP is data.frame and Size is the name of column. But has error: Error in eval.with.vis(expr, envir, enclos) : could not find function inp Lesandro Your code and description above appear to have some typos in it and the use of the round() and format() functions are not what you want here. You code has inp(...), where R is presuming that you are referring to a function called 'inp', hence the error message, since the function does not exist. Better to use sprintf() with an appropriate format specifier: set.seed(1) vec - rnorm(10) vec [1] -0.6264538 0.1836433 -0.8356286 1.5952808 0.3295078 -0.8204684 [7] 0.4874291 0.7383247 0.5757814 -0.3053884 sprintf(%.2f, vec) [1] -0.63 0.18 -0.84 1.60 0.33 -0.82 0.49 0.74 [9] 0.58 -0.31 See ?sprintf for more information. Note that the presumption here is that you want to output the numeric values to a formatted character vector for display purposes, perhaps in a table, etc. So if your actual data frame is called 'INP' and the column is called 'Size', you would use: sprintf(%.2f, INP$Size) HTH, Marc Schwartz Veja quais são os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.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] Re strict AIC comparison to succesful models?
Manuel Morales wrote: On Thu, 2009-06-11 at 12:08 -0700, Ben Bolker wrote: Manuel Morales wrote: Hello list, I'm doing a bootstrap analysis where some models occasionally fail to converge. I'd like to automate the process of restricting AIC to the models that do converge. A contrived example of what I'd like to do is below: resp - c(1,1,2) pred - c(1,2,3) m1 - lm(resp~pred) m2 - lm(resp~poly(pred,2)) m3 - lm(resp~poly(pred,3)) # Fails, obviously ## Some test to see which models were successful models - test(m1,m2,m3) How about models - list(m1,m2,m3) is.OK - sapply(models,test) do.call(AIC,models[is.OK]) ? Good idea but unfortunately I get an error message with: models - list(m1,m2,m3) test - function(x) length(x)1 is.OK - sapply(models,test) do.call(AIC,models[is.OK]) I think the issue is that AIC is expecting a ... of model objects (not a list or a vector) and I'm not sure how to construct that. Manuel The problem is that when your fitting function fails, NOTHING gets created. Try this: # resp - c(1,1,2) pred - c(1,2,3) m1 - try(lm(resp~pred)) m2 - try(lm(resp~poly(pred,2))) m3 - try(lm(resp~poly(pred,3))) # Fails, obviously models - list(m1,m2,m3) test - function(x) !inherits(x,try-error) is.OK - sapply(models,test) AIC(m1,m2) ## works ## all these work but lead to objects with ugly row names do.call(AIC,models[is.OK]) do.call(AIC,models[is.OK]) do.call(stats:::AIC.default,models[is.OK]) dd - do.call(AIC,list(m1,m2)) rownames(dd) - NULL dd -- Ben Bolker Associate professor, Biology Dep't, Univ. of Florida bol...@ufl.edu / www.zoology.ufl.edu/bolker GPG key: www.zoology.ufl.edu/bolker/benbolker-publickey.asc signature.asc Description: OpenPGP digital signature __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] formula for degrees of freedom for nonlinear mixed model in nlme
The FAQ 7.35 links to this posting: https://stat.ethz.ch/pipermail/r-help/2006-May/094765.html On Jun 11, 2009, at 3:57 PM, J S wrote: Dear forum members, What is the formula to calculate denominator degrees of freedom (den df) for nonlinear mixed-effect models with covariates? My model is similar to a CO2 uptake example from Pinheiro and Bates (2000, page 376). In this CO2 dataset, there are two treatments and two types (84 observations in total), but den df for each parameter of the model is 64. Isnt it too high? Your help is greatly appreciated, Julia Summary of the CO2 example: summary(fm4CO2.nlme) Nonlinear mixed-effects model fit by maximum likelihood Model: uptake ~ SSasympOff(conc, Asym, lrc, c0) Data: CO2 AIC BIClogLik 388.4185 420.0191 -181.2092 Random effects: Formula: list(Asym ~ 1, lrc ~ 1) Level: Plant Structure: General positive-definite, Log-Cholesky parametrization StdDev Corr Asym.(Intercept) 2.349640 As.(I) lrc.(Intercept) 0.079597 -0.92 Residual 1.791962 Fixed effects: list(Asym + lrc ~ Type * Treatment, c0 ~ 1) Value Std.Error DF t- value p-value Asym.(Intercept) 41.81756 1.562426 64 26.76451 0. Asym.TypeMississippi -10.53045 2.208318 64 -4.76854 0. Asym.Treatmentchilled -2.96943 2.213172 64 -1.34171 0.1844 Asym.TypeMississippi:Treatmentchilled -10.90037 3.112220 64 -3.50244 0.0008 lrc.(Intercept)-4.55724 0.096291 64 -47.32785 0. lrc.TypeMississippi-0.10412 0.121683 64 -0.85570 0.3954 lrc.Treatmentchilled -0.17124 0.111959 64 -1.52953 0.1311 lrc.TypeMississippi:Treatmentchilled0.74188 0.221742 64 3.34570 0.0014 c0 50.51075 4.364727 64 11.57249 0. Correlation: As.(I) Asy.TM Asym.T A.TM:T lr. (I) lrc.TM Asym.TypeMississippi -0.703 Asym.Treatmentchilled -0.701 0.496 Asym.TypeMississippi:Treatmentchilled 0.497 -0.709 -0.711 lrc.(Intercept) -0.627 0.415 0.407 -0.278 lrc.TypeMississippi0.458 -0.680 -0.322 0.482 -0.535 lrc.Treatmentchilled 0.500 -0.351 -0.717 0.509 -0.594 0.445 lrc.TypeMississippi:Treatmentchilled -0.262 0.375 0.362 -0.547 0.365 -0.553 c0-0.086 0.014 0.001 0.019 0.590 -0.033 lrc.Tr l.TM:T Asym.TypeMississippi Asym.Treatmentchilled Asym.TypeMississippi:Treatmentchilled lrc.(Intercept) lrc.TypeMississippi lrc.Treatmentchilled lrc.TypeMississippi:Treatmentchilled -0.511 c0-0.057 0.140 Standardized Within-Group Residuals: Min Q1 Med Q3 Max -2.86206487 -0.49445730 -0.04217037 0.56599012 3.04061332 Number of Observations: 84 Number of Groups: 12 Link to the book: http://books.google.com/books?id=N3WeyHFbHLQCpg=PA139lpg=PA139dq=mixed-effect+model+building+first+stepsource=blots=pR7PWIuKu8sig=TLhq-k5O4ZNwkBWcyQI8VZk9Umkhl=enei=1HguSrKaPJi0Nb3DnfUJsa=Xoi=book_resultct=resultresnum=1#PPA376,M1 _ [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. David Winsemius, MD Heritage Laboratories West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] color in grouped lattice xyplot plot
Hi,
I've got a data.frame object which I would like to plot in a lattice
xyplot grouped by a variable and using a value for the color of each
point which is stored in a variable in the same data.frame.
I tried the following code:
my.panel.xy - function(x, y, ...){
panel.xyplot(x, y, ...)
panel.lmline(x, y, lwd = 2)
panel.abline(0, 1, col=red, lty=2)
panel.grid(h = -1, v = -1, lty=1)
}
xyplot(log(AGB) ~ log(BM_roots) | as.character(taxa),
data=sub_agb_data,main=list(AGB in dependence of BM_root [per
taxa!],cex=0.7),
ylab=list(log(AGB),cex=0.7),xlab=list(log(BM_root),cex=0.7),col=sub_agb_data$color,
panel = my.panel.xy)
xyplot(log(AGB) ~ log(BM_roots) | as.character(species),
data=sub_agb_data,main=list(AGB in dependence of BM_root [per
species!],cex=0.7),
ylab=list(log(AGB),cex=0.7),xlab=list(log(BM_root),cex=0.7),col=sub_agb_data$color,
panel = my.panel.xy)
Somehow the colors are not displayed correctly (it works if I use plot
in a for loop for each value for the variables for which I group my
lattice plots. The color variable is of type character so this
shouldn't be the reason)
The object sub_agb_object can be downloaded here:
http://www.wzw.tum.de/oekophys/fileadmin/sub_agb_data.rData
Maybe somebody has any idea how to make this work or what the problem might be?
Thanks,
Katharina
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[R] Automatically placing legend in location of most whitespace.
Just read the following: https://stat.ethz.ch/pipermail/r-help/2003-October/039940.html Is the labcurve function, really the putKey function, in the Hmisc package the best way the to go about automatically placing legend in location of most whitespace? Thanks for any insights. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Matrix manipulation
Try this: For the first and the second question: transform(subset(d, row.names(d) != 2), row.names=NULL) On Thu, Jun 11, 2009 at 3:53 PM, Payam Minoofar payam.minoo...@meissner.com wrote: Hello everyone, I have a couple of fairly simple questions (I hope) the answers to which I cannot find through the documentation at the moment. 1. I would like to delete the a row from a matrix if a certain elimination criterion is met. I am familiar with x - x[-7,] (to remove row 7, for example). Are there any other means of removing an entire row? 2. Is there a single command that will rename the index of each row to match the row number once a row has been deleted. For example, when row 7 is deleted above, the old row 8 is now row 7, but the row name is still 8. I have figured out how to assign a sequence vector to the row names, but I am wondering if there is a built-in command that does the same thing. (I.e., change the name of row 7 to 7 from 8.) Thank you very much. Payam -- Payam Minoofar, Ph.D. Scientist Meissner Filtration Products 4181 Calle Tesoro Camarillo, CA 93012 USA +1 805 388 9911 +1 805 388 5948 fax payam.minoo...@meissner.com [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Matrix manipulation
On Jun 11, 2009, at 2:53 PM, Payam Minoofar wrote: Hello everyone, I have a couple of fairly simple questions (I hope) the answers to which I cannot find through the documentation at the moment. 1. I would like to delete the a row from a matrix if a certain elimination criterion is met. I am familiar with x - x[-7,] (to remove row 7, for example). Are there any other means of removing an entire row? ?which # useful for converting logical vectors into argument for functions that require numerics M10 - matrix(1:100, nrow = 10) # find row with 63 which( sapply( 1:10, function(x) 63 %in% M10[x, ]) ) [1] 3 M10[-which( sapply( 1:10, function(x) 63 %in% M10[x, ]) ), ] # remove row with 63 [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [1,]1 11 21 31 41 51 61 71 8191 [2,]2 12 22 32 42 52 62 72 8292 [3,]4 14 24 34 44 54 64 74 8494 [4,]5 15 25 35 45 55 65 75 8595 [5,]6 16 26 36 46 56 66 76 8696 [6,]7 17 27 37 47 57 67 77 8797 [7,]8 18 28 38 48 58 68 78 8898 [8,]9 19 29 39 49 59 69 79 8999 [9,] 10 20 30 40 50 60 70 80 90 100 2. Is there a single command that will rename the index of each row to match the row number once a row has been deleted. For example, when row 7 is deleted above, the old row 8 is now row 7, but the row name is still 8. I have figured out how to assign a sequence vector to the row names, but I am wondering if there is a built-in command that does the same thing. (I.e., change the name of row 7 to 7 from 8.) Thank you very much. Payam -- Payam Minoofar, Ph.D. Scientist Meissner Filtration Products 4181 Calle Tesoro Camarillo, CA 93012 USA +1 805 388 9911 +1 805 388 5948 fax payam.minoo...@meissner.com [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. 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] Re strict AIC comparison to succesful models?
On Thu, 2009-06-11 at 16:10 -0400, Ben Bolker wrote: Manuel Morales wrote: On Thu, 2009-06-11 at 12:08 -0700, Ben Bolker wrote: Manuel Morales wrote: Hello list, I'm doing a bootstrap analysis where some models occasionally fail to converge. I'd like to automate the process of restricting AIC to the models that do converge. A contrived example of what I'd like to do is below: resp - c(1,1,2) pred - c(1,2,3) m1 - lm(resp~pred) m2 - lm(resp~poly(pred,2)) m3 - lm(resp~poly(pred,3)) # Fails, obviously ## Some test to see which models were successful models - test(m1,m2,m3) How about models - list(m1,m2,m3) is.OK - sapply(models,test) do.call(AIC,models[is.OK]) ? Good idea but unfortunately I get an error message with: models - list(m1,m2,m3) test - function(x) length(x)1 is.OK - sapply(models,test) do.call(AIC,models[is.OK]) I think the issue is that AIC is expecting a ... of model objects (not a list or a vector) and I'm not sure how to construct that. Manuel The problem is that when your fitting function fails, NOTHING gets created. Try this: # resp - c(1,1,2) pred - c(1,2,3) m1 - try(lm(resp~pred)) m2 - try(lm(resp~poly(pred,2))) m3 - try(lm(resp~poly(pred,3))) # Fails, obviously models - list(m1,m2,m3) test - function(x) !inherits(x,try-error) is.OK - sapply(models,test) AIC(m1,m2) ## works ## all these work but lead to objects with ugly row names do.call(AIC,models[is.OK]) do.call(AIC,models[is.OK]) do.call(stats:::AIC.default,models[is.OK]) dd - do.call(AIC,list(m1,m2)) rownames(dd) - NULL dd I see, it wasn't an error message just a very ugly output. Reassigning the row names works great! Thanks, Manuel -- http://mutualism.williams.edu __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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 extract from a matrix based on indices in a vector?
Thanks, guys. I'll take at a look at these solutions. BTW, my apologies, by
A,B,C,D,... I meant just some real number, not characters A,B,..., but
I wasn't clear about that. If that effects the solution approach please let
me know, but I don't think it does. Thanks again, Doug
Marc Schwartz-3 wrote:
On Jun 10, 2009, at 7:05 PM, William Dunlap wrote:
Subscripting by a 2-column matrix
M[cbind(v, seq_len(ncol(M)))]
uses much less space (hence time) than making
the ncol(M) by ncol(M) intermediate matrix just
to extract its diagonal. E.g.
test - function(n, seed) {
if (!missing(seed))
set.seed(seed)
M - matrix(sample(LETTERS, 2*n, replace = TRUE), 2)
v - sample(2, n, replace=T)
t1-system.time(r1-M[cbind(v,seq_len(ncol(M)))])
t2-system.time(r2-diag(M[v, 1:ncol(M)]))
list(identical=identical(r1,r2), time(matrix subscript)=t1,
time(diag(big matrix))=t2)
}
test(100)
$identical
[1] TRUE
$`time(matrix subscript)`
user system elapsed
0.000 0.000 0.001
$`time(diag(big matrix))`
user system elapsed
0.001 0.000 0.001
test(1000)
$identical
[1] TRUE
$`time(matrix subscript)`
user system elapsed
0.000 0.000 0.001
$`time(diag(big matrix))`
user system elapsed
0.082 0.021 0.103
test(5000)
$identical
[1] TRUE
$`time(matrix subscript)`
user system elapsed
0.001 0.000 0.001
$`time(diag(big matrix))`
user system elapsed
3.379 0.552 3.932
Nicely done comparison Bill.
Thanks,
Marc
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[R] Optimization Question
Hi All Apologies if this is not the correct list for this question. The Rglpk package offers the following example in its documentation library(Rglpk) ## Simple mixed integer linear program. ## maximize: 3 x_1 + 1 x_2 + 3 x_3 ## subject to: -1 x_1 + 2 x_2 + x_3 = 4 ## 4 x_2 - 3 x_3 = 2 ## x_1 - 3 x_2 + 2 x_3 = 3 ## x_1, x_3 are non-negative integers ## x_2 is a non-negative real number obj - c(3, 1, 3) mat - matrix(c(-1, 0, 1, 2, 4, -3, 1, -3, 2), nrow = 3) dir - c(=, =, =) rhs - c(4, 2, 3) types - c(I, C, I) max - TRUE Rglpk_solve_LP(obj, mat, dir, rhs, types, max) ## Same as before but with bounds replaced by ## -Inf x_1 = 4 ## 0 = x_2 = 100 ## 2 = x_3 Inf bounds - list(lower = list(ind = c(1L, 3L), val = c(-Inf, 2)), upper = list(ind = c(1L, 2L), val = c(4, 100))) Rglpk_solve_LP(obj, mat, dir, rhs, types, max, bounds) I have 2 questions 1. What is the purpose of the L in the bounds statement (e.g. 1L, 3L etc)? 2. Is it possible to further constrain a variable such that in the optimal solution to the objective function it will be a specific integer or an integer multiple of that integer. For example, x_3 must be 2 or 4,6,8,10 etc Thanks Pete This e-mail may contain confidential or proprietary information belonging to the BP group and is intended only for the use of the recipients named above. If you are not the intended recipient, please immediately notify the sender and either delete this email or return to the sender immediately. You may not review, copy or distribute this email. Within the bounds of law, this part of BP retains all emails and IMs and may monitor them to ensure compliance with BP's internal policies and for other legitimate business purposes. [[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] TCLTK Times out Leopard.
I'm trying to get the Tcltk package loaded on R 2.9 (I think, it's just recently updated). At first it was looking for X11 files in the wrong library so created an alias to point it in the right direction. Now when I load it nothing happens, the program stops responding. Any ideas? I should point out I'm just starting to use this program. Kailer -- View this message in context: http://www.nabble.com/TCLTK-Times-out-Leopard.-tp23988562p23988562.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] Matrix manipulation
-Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of David Winsemius Sent: Thursday, June 11, 2009 1:49 PM To: Payam Minoofar Cc: r-help@r-project.org Subject: Re: [R] Matrix manipulation On Jun 11, 2009, at 2:53 PM, Payam Minoofar wrote: Hello everyone, I have a couple of fairly simple questions (I hope) the answers to which I cannot find through the documentation at the moment. 1. I would like to delete the a row from a matrix if a certain elimination criterion is met. I am familiar with x - x[-7,] (to remove row 7, for example). Are there any other means of removing an entire row? ?which # useful for converting logical vectors into argument for functions that require numerics M10 - matrix(1:100, nrow = 10) # find row with 63 which( sapply( 1:10, function(x) 63 %in% M10[x, ]) ) [1] 3 M10[-which( sapply( 1:10, function(x) 63 %in% M10[x, ]) ), ] # remove row with 63 [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [1,]1 11 21 31 41 51 61 71 8191 [2,]2 12 22 32 42 52 62 72 8292 [3,]4 14 24 34 44 54 64 74 8494 [4,]5 15 25 35 45 55 65 75 8595 [5,]6 16 26 36 46 56 66 76 8696 [6,]7 17 27 37 47 57 67 77 8797 [7,]8 18 28 38 48 58 68 78 8898 [8,]9 19 29 39 49 59 69 79 8999 [9,] 10 20 30 40 50 60 70 80 90 100 which() is dangerous here. E.g., if you wanted to use that idiom to delete any row containing 666 you would get a 0-row by 10-column matrix, not the expected copy of the input matrix M10[-which( sapply( 1:10, function(x) 666 %in% M10[x, ]) ), ] [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] (This happens because -integer(0) is no different than integer(0): both are 0-long vectors.) I think you should use logical subscripts unless you are really pressed for space. M10[ !sapply(1:10, function(x)666 %in% M10[x,]), ] When you read '[', say 'such that'. Bill Dunlap TIBCO Software Inc - Spotfire Division wdunlap tibco.com 2. Is there a single command that will rename the index of each row to match the row number once a row has been deleted. For example, when row 7 is deleted above, the old row 8 is now row 7, but the row name is still 8. I have figured out how to assign a sequence vector to the row names, but I am wondering if there is a built-in command that does the same thing. (I.e., change the name of row 7 to 7 from 8.) Thank you very much. Payam -- Payam Minoofar, Ph.D. Scientist Meissner Filtration Products 4181 Calle Tesoro Camarillo, CA 93012 USA +1 805 388 9911 +1 805 388 5948 fax payam.minoo...@meissner.com [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. David Winsemius, MD Heritage Laboratories West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Inf in nnet final value for validation data
Andrea, You can calculate predictions for your validation data based on nnet objects using the predict function (the predict function can also be used for regressions, quantile regressions, etc.) If you create a neural net with the following code: library(nnet) # 3 hidden neurons, for classification (linout = F), and not a skip layer network (skip = F, or T if you want) mynet.nn - nnet(dependent_variable ~ ., data = train, size = 3, decay = 1e-3, linout = F, skip = F, maxit = 1000, Hess = T) # calculate predictions for your training data and append to data frame called train train$predictions - predict(mynet.nn) # calculate predictions for your validation data and append to data frame called valid valid$predictions - predict(mynet.nn, valid) # you need to pass your neural net object and your validation dataset to the predict function To just get the predictions for your validation dataset this is all you need. I do not know why you need to calculate the log likelihood. Hope this helps. Jude Andrea wrote: Hi, I use nnet for my classification problem and have a problem concerning the calculation of the final value for my validation data.(nnet only calculates the final value for the training data). I made my own final value formula (for the training data I get the same value as nnet): # prob-matrix pmatrix - cat*fittedValues tmp - rowSums(pmatrix) # -log likelihood finalValue - sum(-log(tmp)) # add penalty term finalValue + sum(decay * weights^2) where cat is a matrix with cols for each possible category and a row for each data record. The values are 1 for the target categories of a data record and 0 otherwise. My problem is, that I get Inf-values for some validation data records, because the rowsum of cat*fittedValues gets 0 and the log gets Inf. Has anyone an idea how to deal with that problem properly? How does nnet? I´m thinking of a penalty value for those values. That means if cat*fittedValues == 0 not to calculate the log but add e.g. 100 instead of -log(tmp) to the finalValue-sum?? But how to determine the penalty value??? I´m looking forwar for all suggestions, Andrea. ___ Jude Ryan Director, Client Analytical Services Strategy Business Development UBS Financial Services Inc. 1200 Harbor Boulevard, 4th Floor Weehawken, NJ 07086-6791 Tel. 201-352-1935 Fax 201-272-2914 Email: jude.r...@ubs.com Please do not transmit orders or instructions regarding a UBS account electronically, including but not limited to e-mail, fax, text or instant messaging. The information provided in this e-mail or any attachments is not an official transaction confirmation or account statement. For your protection, do not include account numbers, Social Security numbers, credit card numbers, passwords or other non-public information in your e-mail. Because the information contained in this message may be privileged, confidential, proprietary or otherwise protected from disclosure, please notify us immediately by replying to this message and deleting it from your computer if you have received this communication in error. Thank you. UBS Financial Services Inc. UBS International Inc. UBS Financial Services Incorporated of Puerto Rico UBS AG UBS reserves the right to retain all messages. Messages are protected and accessed only in legally justified cases.__ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Tables without names
A table without names displays like a vector: unname(table(2:3)) [1] 1 1 1 and preserves the table class (as with unname in general): dput(unname(table(2:3))) structure(c(1L, 1L), .Dim = 2L, class = table) Does that make sense? R is not consistent in its treatment of such unname'd tables: In plot, they are considered erroneous input: plot(unname(table(2:3))) Error in xy.coords(x, y, xlabel, ylabel, log) : 'x' and 'y' lengths differ but in melt, they act as though they have names 1:n: melt(unname(table(2:3))) indicies value 11 1 22 1 (By the way, is the spelling error built into too much code to be corrected?) -s PS What is the standard way of extracting just the underlying vector? c(unname(...)) works -- is that what is recommended? [[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 installing Rmpi
Hello R users and developers, I would like to install Rmpi so that I may take advantage of all of the CPUs in my computer, but I cannot get it to install and I am not very good with linux so it is adding to the headache. I have looked through the help archive, but I have not been successful at getting Rmpi to work. I am not sure if I am even installing openMPI correctly in linux. I would really like to get Rmpi to work so that I can take advantage of libraries that use Rmpi and more importantly reduce my computation time from several days to maybe a day. I am using fedora 11 (64-bit) on a AMD phenom III (AM3) system and I am not an expert at linux so I run into trouble compiling and installing software out of inexperience. I would truly appreciated it if someone could please provide me with some instructions on how to get openMPI installed correctly on Fedora11 and Rmpi to work? I have included the processes I attempted below. Thank you, Alan Smith # what I have attempted so far #I have tried two different ways to install openMPI in fedora in the linux shell #in the linux shell cd Download wget http://www.open-mpi.org/software/ompi/v1.3/downloads/openmpi-1.3.2.tar.gz tar -xzf openmpi* cd openmpi* ./configure make make install #AND #in the linux shell cd Download wget ftp://rpmfind.net/linux/fedora/releases/11/Everything/x86_64/os/Packages/openmpi-1.3.1-1.fc11.x86_64.rpm sudo yum install openmpi-devel # I find the program in this path /usr/lib64/openmpi/1.3.1-gcc/openmpi #I then try to install Rmpi using two methods neither of which work #Using the linux shell I have tried wget http://cran.r-project.org/src/contrib/Rmpi_0.5-7.tar.gz R CMD INSTALL Rmpi_0.5-7.tar.gz #and R CMD INSTALL Rmpi_0.5-7.tar.gz --configure-args=--with-mpi=/usr/lib64/openmpi/1.3.1-gcc R CMD INSTALL Rmpi_0.5-7.tar.gz --configure-args=--with-mpi=/usr/lib64/openmpi/ #All of these attempt lead to error cannot find mpi head file and tell me to use with-mpi=path/to/mpi or specify the MPI_ROOT which I clearly cant find #I have also tried this in R using R install.packages(Rmpi) #but it gives the same error. sessionInfo() R version 2.9.0 (2009-04-17) x86_64-unknown-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base -- Alan Smith __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Matrix manipulation
Or perhaps: M10[rowSums(M10 == 63) == 0, ] On Thu, Jun 11, 2009 at 4:49 PM, David Winsemiusdwinsem...@comcast.net wrote: On Jun 11, 2009, at 2:53 PM, Payam Minoofar wrote: Hello everyone, I have a couple of fairly simple questions (I hope) the answers to which I cannot find through the documentation at the moment. 1. I would like to delete the a row from a matrix if a certain elimination criterion is met. I am familiar with x - x[-7,] (to remove row 7, for example). Are there any other means of removing an entire row? ?which # useful for converting logical vectors into argument for functions that require numerics M10 - matrix(1:100, nrow = 10) # find row with 63 which( sapply( 1:10, function(x) 63 %in% M10[x, ]) ) [1] 3 M10[-which( sapply( 1:10, function(x) 63 %in% M10[x, ]) ), ] # remove row with 63 [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [1,] 1 11 21 31 41 51 61 71 81 91 [2,] 2 12 22 32 42 52 62 72 82 92 [3,] 4 14 24 34 44 54 64 74 84 94 [4,] 5 15 25 35 45 55 65 75 85 95 [5,] 6 16 26 36 46 56 66 76 86 96 [6,] 7 17 27 37 47 57 67 77 87 97 [7,] 8 18 28 38 48 58 68 78 88 98 [8,] 9 19 29 39 49 59 69 79 89 99 [9,] 10 20 30 40 50 60 70 80 90 100 2. Is there a single command that will rename the index of each row to match the row number once a row has been deleted. For example, when row 7 is deleted above, the old row 8 is now row 7, but the row name is still 8. I have figured out how to assign a sequence vector to the row names, but I am wondering if there is a built-in command that does the same thing. (I.e., change the name of row 7 to 7 from 8.) Thank you very much. Payam -- Payam Minoofar, Ph.D. Scientist Meissner Filtration Products 4181 Calle Tesoro Camarillo, CA 93012 USA +1 805 388 9911 +1 805 388 5948 fax payam.minoo...@meissner.com [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. David Winsemius, MD Heritage Laboratories West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Postcript font size
Hello I'm doing a number of plots and in all of them I'm specifying the same font size. However, comparing one plot to the other, they have fonts of different sizes, so it appears some scaling is being done. I tried using both postcript(pointsize = ...) and par(ps = ...), but the results were the same. Is there a way to specify a font size that is consistent among calls to plot()? Thanks, Andre __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Postcript font size
On Thu, 2009-06-11 at 19:09 -0300, Andre Nathan wrote: Is there a way to specify a font size that is consistent among calls to plot()? To put it correctly: is there a way to specify a font size that is consistent among calls to postcript()? All the fonts in the same file have the same size, but comparing files, even when par(ps = ...) or postcript(pointsize = ...) are specified the same way, the fonts have different sizes. Best regards, Andre __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Postcript font size
On 11-Jun-09 22:16:22, Andre Nathan wrote: On Thu, 2009-06-11 at 19:09 -0300, Andre Nathan wrote: Is there a way to specify a font size that is consistent among calls to plot()? To put it correctly: is there a way to specify a font size that is consistent among calls to postcript()? All the fonts in the same file have the same size, but comparing files, even when par(ps = ...) or postcript(pointsize = ...) are specified the same way, the fonts have different sizes. Best regards, Andre How are you comparing? A: Looking into the PostScript code in the files, and identifying the font-sizes where they are set in the code? B: Comparing apparent font sizes when looking at two plots on screen? C: Comparing apparent font sizes when looking at plots as printed on paper (and, in this case, have the plots been included in an enacapsulated document as EPS graphics)? Ted. E-Mail: (Ted Harding) ted.hard...@manchester.ac.uk Fax-to-email: +44 (0)870 094 0861 Date: 11-Jun-09 Time: 23:47:59 -- 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] Count observation
Hey... Milton... Is that a equation... Brazil=Toronto If so, mine is... Brazil=Montreal You got it... I am not having a good time with R... There is no help for data manipulation at all... Thanks for the help... Marcio milton ruser wrote: Hi Marcio, data.frame(table(boot)) ? milton brazil=toronto On Thu, Jun 11, 2009 at 3:13 PM, MarcioRibeiro mes...@pop.com.br wrote: Hi listers, I have the following code... data-as.matrix(c(1,2,3,4,5,6,7,8,9,10),nrow=10,ncol=1,byrow=TRUE) n-nrow(data) m-n-1 boot-data[sample(m,replace=T),] So, I need to count the number of times each observation was selected at the sample with replacement... Suppose I sampled... 4 5 1 3 7 5 1 4 7 So, I would count... x count 1 2 2 0 3 1 4 2 5 2 6 0 7 2 8 0 9 0 10 0 Thanks in advance, Marcio -- View this message in context: http://www.nabble.com/Count-observation-tp23987251p23987251.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.htmlhttp://www.r-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- View this message in context: http://www.nabble.com/Count-observation-tp23987251p23988982.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] Count observation
Try this also: cbind(data, tabulate(boot, nbins=nrow(data))) On Thu, Jun 11, 2009 at 4:13 PM, MarcioRibeiro mes...@pop.com.br wrote: Hi listers, I have the following code... data-as.matrix(c(1,2,3,4,5,6,7,8,9,10),nrow=10,ncol=1,byrow=TRUE) n-nrow(data) m-n-1 boot-data[sample(m,replace=T),] So, I need to count the number of times each observation was selected at the sample with replacement... Suppose I sampled... 4 5 1 3 7 5 1 4 7 So, I would count... x count 1 2 2 0 3 1 4 2 5 2 6 0 7 2 8 0 9 0 10 0 Thanks in advance, Marcio -- View this message in context: http://www.nabble.com/Count-observation-tp23987251p23987251.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Postcript font size
On Thu, 2009-06-11 at 23:48 +0100, ted.hard...@manchester.ac.uk wrote: How are you comparing? A: Looking into the PostScript code in the files, and identifying the font-sizes where they are set in the code? This. To get the size I wanted in both files, I had to use par(ps = 15) in one of them, and par(ps = 18) in the other. Strangely, the generated files had the following PS code: /ps 12 def /Font1 findfont 12 s I don't know PostScript, but I assume this means pointsize = 12. Best, Andre __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] More basic question
I have encountered a more fundamental problem in my data set. I'm using read.csv, and all the data are imported as character. How do I do a string comparison in a line like this: M10[ !sapply(1:10, function(x)666 %in% M10[x,]), ] Alternately, how do I change the class type on a column in a data frame from character to numeric? Thank you very much. Payam [[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] More basic question
Never mind the query regarding setting attributes. I just found the relevant section in the manual. The only remaining question is regarding doing string comparisons in sapply argument below. Thank you. Payam I have encountered a more fundamental problem in my data set. I'm using read.csv, and all the data are imported as character. How do I do a string comparison in a line like this: M10[ !sapply(1:10, function(x)666 %in% M10[x,]), ] Alternately, how do I change the class type on a column in a data frame from character to numeric? Thank you very much. Payam [[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] More basic question
Hi there, It may works: df$myvar-as.numeric(as.character(df$myvar)) bests milton brazil=toronto On Thu, Jun 11, 2009 at 7:37 PM, Payam Minoofar payam.minoo...@meissner.com wrote: I have encountered a more fundamental problem in my data set. I'm using read.csv, and all the data are imported as character. How do I do a string comparison in a line like this: M10[ !sapply(1:10, function(x)666 %in% M10[x,]), ] Alternately, how do I change the class type on a column in a data frame from character to numeric? Thank you very much. Payam [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.htmlhttp://www.r-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] formula for degrees of freedom for nonlinear mixed model in nlme
David Winsemius wrote: The FAQ 7.35 links to this posting: https://stat.ethz.ch/pipermail/r-help/2006-May/094765.html Actually, this is a different question from the usual why don't I get denominator df? question -- it is how are these calculated (since the poster is using nlme, not (n)lmer). The answer in this case is check Pinheiro and Bates 2000 -- I don't remember the page number exactly, looks like it's page 91 -- see Google books: http://tinyurl.com/ntygq3 If the denominator df don't agree with your intuition, you can always recompute p-values with the appropriate den df: (two-tailed) 2*pt(abs(t.score),df=dendf,lower.tail=FALSE) -- View this message in context: http://www.nabble.com/formula-for-degrees-of-freedom-for-nonlinear-mixed-model-in-nlme-tp23987913p23991255.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] deSolve question
Dear In-Sun:
I have not seen a reply, so I will offer some suggestions, hoping
I can help without understanding all the details.
1. Have you run that code with options(warn=2)? It
produced over 50 warnings for me, and options(warn=2) will convert the
warnings to errors, making it easier for you to find the exact problem
lines of code. With this, have you used the debug function to trace
through your code line by line to provide more detail about what the
code is doing? I use that routinely.
2. Have you considered the PKfit package? I don't know if
it includes your model, but it includes code for many pharmacokinetic
models. If your interest in deSolve is as a means to solve this
problem, you might consider PKfit.
3. Have you tried writing directly to the authors? Names
and email addresses are available in help(pac=deSolve).
Hope this helps.
Spencer Graves
insun nam wrote:
Dear All,
I like to simulate a physiologically based pharmacokinetics model using R
but am having a problem with the daspk routine.
The same problem has been implemented in Berkeley madonna and Winbugs so
that I know that it is working. However, with daspk it is not, and the
numbers are everywhere!
Please see the following and let me know if I am missing something...
Thanks a lot in advance,
In-Sun
#---
library(deSolve)
y - c(Agi = 0,Alu = 0, Abr = 0, Ah = 0, Ali = 0, Ak = 0, Am = 0, Ask =
0, Aad = 0, Apa = 0, Asp = 0, Aar = 0, Ave = 0)
times = seq(0, 100, length=100)
pars - c(
dose = 80 * 0.26,
doseduration = 10,
Vmax = 1.44,
Km = 0.96,
s = 1.33,
fp = 0.236,
Kpfgi=0.324,
Kpflu = 1.092,
Kpfbr= 0.155 ,
Kpfh=0.767,
Kpfli = 0.551,
Kpfk=0.537,
Kpfm=0.339,
Kpfsk=0.784,
Kpfad=0.465,
Kpfpa=0.595,
Kpfsp=0.410,
Qar = 51.9,
Qve = 51.9,
Qgi = 12.3,
Qlu = 51.9,
Qbr = 3.2,
Qh = 6.4,
Qli = 16.5,
Qk = 12.8,
Qm = 7.6,
Qsk = 5.0,
Qad = 0.4,
Qpa = 1.0,
Qsp = 1.0,
Var = 7.0,
Vve = 14.1,
Vgi = 12.4,
Vlu = 1.3,
Vbr = 1.3,
Vh = 1.2,
Vli = 12.4,
Vk = 2.2,
Vm = 140.0,
Vsk = 49.0,
Vad = 11.2,
Vpa = 1.0,
Vsp = 1.0
)
Fun_ODE - function(t,y, pars){
with (as.list(c(y, pars)), {
It - dose/doseduration
Car - Aar/Var
Cve - Ave/Vve
Clu - Alu/Vlu
Cli - Ali/Vli
Cbr - Abr/Vbr
Ch - Ah/Vh
Cpa - Apa/Vpa
Csp - Asp/Vsp
Cgi - Agi/Vgi
Ck - Ak/Vk
Cm - Am/Vm
Cad - Aad/Vad
Csk - Ask/Vsk
Kpbbr - s*fp*Kpfbr
Kpbli - s*fp*Kpfli
Kpbh - s*fp*Kpfh
Kpbpa - s*fp*Kpfpa
Kpbsp - s*fp*Kpfsp
Kpbgi - s*fp*Kpfgi
Kpbk - s*fp*Kpfk
Kpbm - s*fp*Kpfm
Kpbad - s*fp*Kpfad
Kpbsk - s*fp*Kpfsk
Kpblu - s*fp*Kpflu
dAar - (Clu/Kpblu - Car)*Qar
dAve - if (t 10) It + Cbr*Qbr/Kpbbr + Ch *Qh/Kpbh + Cli*Qli/Kpbli +
Ck*Qk/Kpbk + Cm*Qm/Kpbm + Csk * Qsk /Kpbsk + Cad*Qad/Kpbad - Cve*Qve
else Cbr*Qbr/Kpbbr + Ch *Qh/Kpbh + Cli*Qli/Kpbli + Ck*Qk/Kpbk +
Cm*Qm/Kpbm + Csk * Qsk /Kpbsk + Cad*Qad/Kpbad - Cve*Qve
dAlu - (Cve-Clu/Kpblu)*Qlu
dAli - ((Qli - Qgi- Qpa-Qsp)*Car + Cgi*Qgi/Kpbgi + Csp*Qsp/Kpbsp +
Cpa*Qpa/Kpbpa - Cli*Qli/Kpbli) - Vmax*Cli/Kpfli/(Km + Cli/Kpfli)
dAbr - (Car - Cbr/Kpbbr)*Qbr
dAh - (Car - Ch/Kpbh)*Qh
dApa - (Car - Cpa/Kpbpa)*Qpa
dAsp - (Car - Csp/Kpbsp)*Qsp
dAgi - (Car - Cgi/Kpbgi)*Qgi
dAk - (Car - Ck/Kpbk)*Qk
dAm - (Car - Cm/Kpbm)*Qm
dAad - (Car - Cad/Kpbad)*Qad
dAsk - (Car - Csk/Kpbsk)*Qsk
return(list(dy = c(dAar, dAve, dAlu, dAli, dAbr, dAh, dApa, dAsp, dAgi, dAk,
dAm, dAad, dAsk),
Car = Car, Cve=Cve, Clu=Clu, Cli=Cli, Cbr=Cbr, Ch=Ch, Cpa=Cpa,
Csp=Csp, Cgi=Cgi, Ck=Ck, Cm=Cm, Cad=Cad, Csk=Csk))
})
}
ODE - as.data.frame(daspk(y = y, times = times, func = Fun_ODE,
parms = pars, atol = 1e-10, rtol = 1e-10))
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Re: [R] Tables without names
On Jun 11, 2009, at 5:35 PM, Stavros Macrakis wrote: A table without names displays like a vector: unname(table(2:3)) [1] 1 1 1 and preserves the table class (as with unname in general): dput(unname(table(2:3))) structure(c(1L, 1L), .Dim = 2L, class = table) Does that make sense? R is not consistent in its treatment of such unname'd tables: In plot, they are considered erroneous input: plot(unname(table(2:3))) Error in xy.coords(x, y, xlabel, ylabel, log) : 'x' and 'y' lengths differ but in melt, they act as though they have names 1:n: melt(unname(table(2:3))) indicies value 11 1 22 1 (By the way, is the spelling error built into too much code to be corrected?) -s PS What is the standard way of extracting just the underlying vector? c(unname(...)) works -- is that what is recommended? I think of R (contingency) tables as just integer arrays with attitude ... er, attributes. tt - table(c(1,1,1,3,3,3,5,5)) is.array(tt) [1] TRUE is.matrix( with(warpbreaks, table(wool, tension)) ) [1] TRUE So what would you do with a matrix that had row or column names? -- 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] formula for degrees of freedom for nonlinear mixed model in nlme
On Jun 11, 2009, at 8:47 PM, Ben Bolker wrote: David Winsemius wrote: The FAQ 7.35 links to this posting: https://stat.ethz.ch/pipermail/r-help/2006-May/094765.html Actually, this is a different question from the usual why don't I get denominator df? question -- it is how are these calculated (since the poster is using nlme, not (n)lmer). The answer in this case is check Pinheiro and Bates 2000 -- I don't remember the page number exactly, looks like it's page 91 -- see Google books: http://tinyurl.com/ntygq3 If the denominator df don't agree with your intuition, you can always recompute p-values with the appropriate den df: (two-tailed) 2*pt(abs(t.score),df=dendf,lower.tail=FALSE) Point well taken. So neither my citation nor page 91 (which also deals with LME models) are on point to the OP's question. P B say that inference regarding covariates in nlme models (which i believe was the question posed) are generally Wald statistics, and so don't really have denominator degrees of freedom, only numerators DFs. The numerator is then the observation count minus the model degrees of freedom. See 365-368 which deals with the sort of nlme model about which the OP is asking. A method for generating an anova analysis is also demonstrated on page 374. 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.
