[R] Problems with dmvnorm and outer
Hello,
I try to create a persp-plot for the bivariate normal distribution.
There are a few solutions online ([1],[2]), but I did not want to
hard-code the formula like [2] did or use a kernel density estimate like
[1].
My plan was to use dmvnorm, and use outer to calculate the z-dimension
for each point. Here is what I tried:
library(mvtnorm)
x-seq(0,1,len=40)
y-x
g-function(a,b) {
dmvnorm(x=c(a,b))
}
z-outer(x,y,g)
Which results in the following error:
Error in dim(robj) - c(dX, dY) :
dims [product 1600] do not match the length of object [1]
What causes this error? If I set g to be a simple function like:
g-function(a,b){
a*b
}
Everything works fine. Why does it fail when I pass the parameters to
dmvnorm?
Thank you for your time,
Severin
[1]https://stat.ethz.ch/pipermail/r-help/2003-September/038314.html
[2]http://www.stat.ucl.ac.be/ISpersonnel/lecoutre/stats/fichiers/_gallery.pdf
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Re: [R] Poisson Lognormal
Chuck thank you very much for help. I will follow your advice and see what happen. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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 Cmdr memory
Is there a 64 bit R - and where can I get hold of it for Windows please? Your sizes function is useful thanks - but is there some R parameter to allow maximum usage of memory? -- View this message in context: http://n4.nabble.com/R-Cmdr-memory-tp1693483p1693978.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] any quick way to write this label
Hi r-users, Is there any quick way to write this label? c(0,50,100,150,200,250,300,350,400,450, 500,550,600,650,700,750,800,850,900) Thank you. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] any quick way to write this label
On Sun, Mar 28, 2010 at 8:56 AM, Roslina Zakaria zrosl...@yahoo.com wrote: Hi r-users, Is there any quick way to write this label? c(0,50,100,150,200,250,300,350,400,450, 500,550,600,650,700,750,800,850,900) Not sure what you mean by 'write this label'. But to generate that vector, yes there is a quick way... Hint: Use 'seq' to generate the numeric sequence and then use as.character to make it into character values. 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] any quick way to write this label
On 03/28/2010 07:56 PM, Roslina Zakaria wrote: Hi r-users, Is there any quick way to write this label? c(0,50,100,150,200,250,300,350,400,450, 500,550,600,650,700,750,800,850,900) Hi Rosalina, I'm going to take a leap in the dark and guess that you want to use these as axis labels and want them all to appear. Have a look at the staxlab function in the plotrix package. Jim __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Design of a survey using the survey package
I have looked through the new Complex Surveys book and the documentation for the survey package and it appears to me that there are no functions in survey that help one to design a sampling scheme. For example, in the book section 2.8 discusses the design of stratified samples, but there is no mention of any functions in the survey package that implement the discussed strategies. So, am I missing something obvious here or is the survey package meant only for analyzing survey data once you have it in hand? Tom -- View this message in context: http://n4.nabble.com/Design-of-a-survey-using-the-survey-package-tp1694075p1694075.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] Design of a survey using the survey package
Tom La Bone wrote: I have looked through the new Complex Surveys book and the documentation for the survey package and it appears to me that there are no functions in survey that help one to design a sampling scheme. For example, in the book section 2.8 discusses the design of stratified samples, but there is no mention of any functions in the survey package that implement the discussed strategies. So, am I missing something obvious here or is the survey package meant only for analyzing survey data once you have it in hand? Yes. packageDescription(survey) Package: survey Title: analysis of complex survey samples [...] For drawing samples, see e.g. the sampling package: http://cran.r-project.org/web/packages/sampling/index.html 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.
Re: [R] Assigning factors probabilistically based on the value of another variable.
It is really the same thing. One of many possibilities: theFrame - data.frame(theValues=runif(150,-10,10)) exact - diag(15)[1+ (rank(theFrame$theValues)-1)%/%10,] not.so.exact - diag(15)[1+ (rank(theFrame$theValues+runif(150,0,3))-1)%/%10,] If what you actually wanted was one factor with fifteen levels, just wrap the subscript in the last assignment in factor() instead. HTH, Chuck Thanks Chuck, this does what I asked for: theValues - runif(150,-10,10) exact - factor(1+(rank(theValues)-1)%/%100) Unfortunately, it looks like my example may have been too contrived for my actual program. In the solution that Chuck proposed he antisipated that I may not want the assignment of factor levels to be exact: notSoExact - factor(1+(rank(theValues+runif(150,0,3)-1)%/%100) This is close to what I need. However, in the real program what I need to be able to do is precisely vary the degree of exactness in the assignment. So I need to be able to have the assignment range from completely random assignment to the exact assignment that exact above provides. Anyone think of a simple way to do this? Thanks Agan, That Economics Guy __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Problems with dmvnorm and outer
On Mar 28, 2010, at 3:19 AM, Severin Kacianka wrote:
Hello,
I try to create a persp-plot for the bivariate normal distribution.
There are a few solutions online ([1],[2]), but I did not want to
hard-code the formula like [2] did or use a kernel density estimate
like [1].
My plan was to use dmvnorm, and use outer to calculate the z-
dimension for each point. Here is what I tried:
library(mvtnorm)
x-seq(0,1,len=40)
y-x
g-function(a,b) {
dmvnorm(x=c(a,b))
The construction c(a,b) would in the later function call turn those
two 40 element vectors into an 80 element vector. See if you get
better success with cbind.
}
z-outer(x,y,g)
Which results in the following error:
Error in dim(robj) - c(dX, dY) :
dims [product 1600] do not match the length of object [1]
What causes this error? If I set g to be a simple function like:
g-function(a,b){
a*b
}
Everything works fine. Why does it fail when I pass the parameters
to dmvnorm?
Thank you for your time,
Severin
[1]https://stat.ethz.ch/pipermail/r-help/2003-September/038314.html
[2]http://www.stat.ucl.ac.be/ISpersonnel/lecoutre/stats/fichiers/_gallery.pdf
David Winsemius, MD
West Hartford, CT
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] R Cmdr memory
On Mar 28, 2010, at 4:35 AM, ManInMoon wrote: Is there a 64 bit R - and where can I get hold of it for Windows please? For Windows XP?, Not that I know of. There are proprietary versions for Vista and I believe Professor Ripley is working on an experimental version for the 64 bit versions of Windows. Your sizes function is useful thanks - but is there some R parameter to allow maximum usage of memory? Read the Windows FAQ and seearch on memory. -- David Winsemius, MD 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] how to make stacked plot?
Dear friends: I'm interested to make a stacked plot of cumulative incidence. that's, the cuminc model is fitted [fit=cuminc(time, relapse)] and cumulative incidence is in place. I'd like to stack the cuminc plots(line 1: relapse of luekemia and line 2: treatment related mortality, for example) , then the constituent ratio of leukemia relapse and treatment related mortality is very clear. Can you give me some directions? Yours Ping Zhang [[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] survival data with competing risks and time-dependent covariates!
Dear friends: I’m very interested in the analysis of survival data of leukemic patients, which involves competing risks and time-dependent covariates (infections or relapse of leukemia after BMT). In my present work, I’d like to estimate the risk of chemotherapy, BMT or gvhd on the onset and prognosis of invasive fungal infections (IFI). In detail, the leukemic patients will receive several cycles of chemotherapy and some of them will receive BMT. The patients have three outcomes, that’s acquisition of IFI, death free from IFI or IFI free survival. My puzzle is: (1)Dose multi-state model fit this situation? (2)I tried to fit coxphf model: fit = coxphf(Surv(start,stop,ifi==1)~bmt, data=ifi). The system always goes wrong when variable “gvhd” was fitted. [coxphf(Surv(start,stop,ifi==1)~bmt+gvhd, data=ifi)]. Is there something wrong with my data format? Thank you! Ping Zhang Mar 26 2010 simulation dataset of six patients: (with ifi.csv in the attachment) id start stop ifi chemo bmt gvhd death 1 0 7 01 0 0 0 #chemo at d7 and died at d30 1 0 7 01 0 0 0 2 0 8 01 0 00#chemo1 at d7, ifi at d100, chemo2 at d120 ,bmt at d200 and death at d450 28 100 1 0 0 00 2100 120 0 1 0 0 0 2120 200 0 0 1 00 2200 450 00 0 01 30 6 0 1 0 00 #chemo1 at d6, ifi at d44, chemo2 at d60, censor at d300 3644 1 0 0 0 0 344 60 0 1 0 0 0 360 300 0 0 0 0 0 4 0 10 0 1 0 0 0 #chemo1 at d10, chemo2 at d60, 4 10 60 0 1 0 0 0 #bmt at d120, censor at d300 4 60 120 0 0 1 0 0 4 120 300 00 0 00 50 91 00 0 0 #ifi at d9, die at d30 59 30 0 0 0 0 0 6 300 301 0 0 1 0 0 #(left censored) bmt at d301, gvhd at d330, ifi at 340, death at 350 6 301 330 0 0 0 1 0 6 330 340 1 0 0 0 0 6 340 350 0 0 0 0 1 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R Cmdr memory
On 28/03/2010 9:03 AM, David Winsemius wrote: On Mar 28, 2010, at 4:35 AM, ManInMoon wrote: Is there a 64 bit R - and where can I get hold of it for Windows please? For Windows XP?, Not that I know of. There are proprietary versions for Vista and I believe Professor Ripley is working on an experimental version for the 64 bit versions of Windows. We're planning to release 64 bit builds with R 2.11.0. They are currently being built as part of the test process, though the builds are still a little irregular. You can download from CRAN mirror/bin/windows64/contrib for now, and soon from CRAN mirror/bin/windows64/base. The 64 bit versions of R will require a 64 bit version of Windows to run on. I think there may be 64 bit versions of XP, but they are uncommon and I don't know if they support our builds; we're testing in 64 bit Vista and Windows 7. Revolution Computing also sells a build produced with a different compiler. It has the advantage that the compiler is probably in better shape than the one we are using and they'll provide support with it; the disadvantage is that they'll charge for it, and they are probably not as up to date as us with respect to released version number. Duncan Murdoch Your sizes function is useful thanks - but is there some R parameter to allow maximum usage of memory? Read the Windows FAQ and seearch on memory. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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 make stacked plot?
Am 28.03.2010 15:06, schrieb sdzhangping: Dear friends: I'm interested to make a stacked plot of cumulative incidence. that's, the cuminc model is fitted [fit=cuminc(time, relapse)] and cumulative incidence is in place. I'd like to stack the cuminc plots(line 1: relapse of luekemia and line 2: treatment related mortality, for example) , then the constituent ratio of leukemia relapse and treatment related mortality is very clear. Can you give me some directions? Yours Ping Zhang Dear friend what makes you think that if you repost your question again and again with the same text you will somehow receive an answer? I believe the lack of an answer might be due to the lack of you showing some effort on explaining what you did, what you want and what went wrong. You already got an answer suggesting a package but you did not respond. There is a reason why every mail gets attached this text: PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. If you want help, make it people easy. Stefan. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Problems with dmvnorm and outer
Hello David and Dennis,
thank you two for your replies. You not only helped me solve my problem,
but also helper me to understand my problem better.
Here is my -now working- code:
x-y-seq(-4,4,len=40)
g-function(a,b) {
dmvnorm(x=cbind(a,b),sigma=matrix(c(4,2,2,3), ncol = 2))
}
z-outer(x,y,g)
persp(x,y,z)
Thank you a lot!
Severin
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] survival data with competing risks and time-dependent covariates!
Am 28.03.2010 15:08, schrieb sdzhangping: I??m very interested in the analysis of survival data of leukemic patients, which involves competing risks and time-dependent covariates (infections or relapse of leukemia after BMT). In my present work, I??d like to estimate the risk of chemotherapy, BMT or gvhd on the onset and prognosis of invasive fungal infections (IFI). In detail, the leukemic patients will receive several cycles of chemotherapy and some of them will receive BMT. The patients have three outcomes, that??s acquisition of IFI, death free from IFI or IFI free survival. My puzzle is: (1)Dose multi-state model fit this situation? (2)I tried to fit coxphf model: fit = coxphf(Surv(start,stop,ifi==1)~bmt, data=ifi). The system always goes wrong when variable ??gvhd?? was fitted. [coxphf(Surv(start,stop,ifi==1)~bmt+gvhd, data=ifi)]. Is there something wrong with my data format? ted, minimal, self-contained, reproducible code. You were posting exactly this question already on Friday twice and then today twice. You have been pointed out that you might be using the wrong function. So why should anyone answer you question when you do not show any effort? You did not even ask back. Stefan __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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 Cmdr memory
On 28.03.2010 15:20, Duncan Murdoch wrote: On 28/03/2010 9:03 AM, David Winsemius wrote: On Mar 28, 2010, at 4:35 AM, ManInMoon wrote: Is there a 64 bit R - and where can I get hold of it for Windows please? For Windows XP?, Not that I know of. There are proprietary versions for Vista and I believe Professor Ripley is working on an experimental version for the 64 bit versions of Windows. We're planning to release 64 bit builds with R 2.11.0. They are currently being built as part of the test process, though the builds are still a little irregular. You can download from CRAN mirror/bin/windows64/contrib for now, and soon from CRAN mirror/bin/windows64/base. The 64 bit versions of R will require a 64 bit version of Windows to run on. I think there may be 64 bit versions of XP, but they are uncommon and I don't know if they support our builds; we're testing in 64 bit Vista and Windows 7. Actually, the 64-bit version that you can currently download is a daily build on Windows Server 2008 (where all the package checks happen as well). Uwe Revolution Computing also sells a build produced with a different compiler. It has the advantage that the compiler is probably in better shape than the one we are using and they'll provide support with it; the disadvantage is that they'll charge for it, and they are probably not as up to date as us with respect to released version number. Duncan Murdoch Your sizes function is useful thanks - but is there some R parameter to allow maximum usage of memory? Read the Windows FAQ and seearch on memory. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] any quick way to write this label
On 28.03.2010 13:33 (UTC+1), Jim Lemon wrote: On 03/28/2010 07:56 PM, Roslina Zakaria wrote: Hi r-users, Is there any quick way to write this label? c(0,50,100,150,200,250,300,350,400,450, 500,550,600,650,700,750,800,850,900) If it is not for graphics, perhaps this helps? as.character(seq(0,900,50)) Rainer Hi Rosalina, I'm going to take a leap in the dark and guess that you want to use these as axis labels and want them all to appear. Have a look at the staxlab function in the plotrix package. Jim __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Matching pairs of values
Sorting is unnecesssary. If column order is unimportant, identical() is
unnecessary.
foo - function(x,lookfor)apply(x,1,function(x)all(lookfor %in% x
will do. If column order is important,
apply(x,1,identical,lookfor)
will do.
Bert Gunter
Genentech Nonclinical Statistics
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf Of David Scott
Sent: Saturday, March 27, 2010 8:36 PM
To: Peter Ehlers
Cc: r-help@r-project.org; Berend Hasselman
Subject: Re: [R] Matching pairs of values
Many thanks Peter and Berend.
I think I can make this work for my problem. Apologies for not giving an
example: I was a bit tired and frustrated when I posted to R-help and
only on later reflection realised that I didn't really follow the
posting guidelines.
David
Peter Ehlers wrote:
(Sorry, I think that I just hit a wrong button and managed
to send a non-reply.)
I think that David might have meant that the column order of the
numbers in lookfor is unimportant. In that case, a simple fix would
be either to check both lookfor and rev(lookfor) (since the
matrix is nX2) or to sort before testing:
vtest - function(x, lookfor){
any(apply(x, 1, function(v)
{identical(sort(v), sort(lookfor))}))}
-Peter Ehlers
On 2010-03-27 2:46, Berend Hasselman wrote:
David Scott-6 wrote:
I am sure someone can come up with a clever way of doing what I want---I
don't seem to be able to.
I want to check if a pair of numbers occurs as one of the rows of an n
by 2 matrix. If I was only checking whether a single number was in a
vector of numbers I would use %in% but I can't see how to generalize to
this case.
Would this help?
vtest- function(x, lookfor) any(apply(x,1, function(v)
identical(v,lookfor)))
ma- matrix(c(2,3,1,5,7,3),ncol=2)
ma
[,1] [,2]
[1,]25
[2,]37
[3,]13
vtest(ma,c(3,7))
[1] TRUE
vtest(ma,c(1,7))
[1] FALSE
Berend
--
_
David Scott Department of Statistics
The University of Auckland, PB 92019
Auckland 1142,NEW ZEALAND
Phone: +64 9 923 5055, or +64 9 373 7599 ext 85055
Email: d.sc...@auckland.ac.nz, Fax: +64 9 373 7018
Director of Consulting, Department of Statistics
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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Re: [R] Problems with dmvnorm and outer
On Mar 28, 2010, at 9:36 AM, Severin Kacianka wrote:
Hello David and Dennis,
thank you two for your replies. You not only helped me solve my
problem, but also helper me to understand my problem better.
Here is my -now working- code:
x-y-seq(-4,4,len=40)
g-function(a,b) {
dmvnorm(x=cbind(a,b),sigma=matrix(c(4,2,2,3), ncol = 2))
}
z-outer(x,y,g)
persp(x,y,z)
From that point, you will get a better idea of what you are looking
at with some additional views:
persp(x,y,z)
persp(x,y,z, theta=-45)
persp(x,y,z, theta=-60)
persp(x,y,z, theta=-90)
persp(x,y,z, theta=-135)
--
David Winsemius, MD
West Hartford, CT
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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Re: [R] insert/copy skipped lines to output
Hallo, have a look at the documentation of the different output functions (write(),cat(),write.table()). Most of them have an argument like append. If you set this to TRUE, your command adds the lines you are writing into the file to the lines already existent in that file. So if you run this write() command first with your additional data (header data) and then with the real data and append=TRUE, your information ends up in the same file. HTH Jannis Muhammad Rahiz schrieb: Hello all, I'd like some advise on this. When I read my files, I pass the argument, skip=6, to skip 6 lines of header information. After performing the desired calculations, I have the output. Now I want to copy the 6 lines of skipped information to the output. What I've been doing so far is to use a shell script (i.e. the cat function) to copy the header information to the output file. This means I need 2 additional files, namely a file containing the header information only, and the shell script to run the the function. Is there a direct way to perform this in R? The following forms the main component of my R script; x - as.matrix(read.table(file.txt,skip=6)) y - x*2 write.table(y,output.txt,row.names=FALSE,col.names=FALSE) Thanks Muhammad __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Calculate variance/covariance with complex numbers
Gang Chen gangchen6 at gmail.com writes: Thanks a lot for the help, Ben Bolker and Chuck! Chuck, it seems your version needs a little modification. Instead of this: xri - matrix(rnorm(1)+1i*rnorm(1),nc=2) crossprod(xri-colMeans(xri))/(nrow(xri)-1) it seems to me it should be this (maybe there is a more elegant modification than mine?): crossprod(t(apply(xri, 1, '-', colMeans(xri/(nrow(xri)-1) Not sure, but you could take a look at sweep() and scale( ,scale=FALSE) for slightly more specialized/efficient ways of doing the column centering, i.e. crossprod(scale(xri,scale=FALSE))/(nrow(xri)-1) (warning, almost completely untested) Ben __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] insert/copy skipped lines to output
Dear Jannis, Thanks for the tip. It works but I'd like to improve on the way I did it. x - array(1:50,dim=c(10,10)) # data h1 - c(ncols180) # header, line 1 h2 - c(nrows 290) # header, line 2 h3 - c(xllcorner -20) # header, line 3 h4 - c(yllcorner -20) # header, line 4 h5 - c(cellsize 5000) # header, line 5 h6 - c(NODATA_value NA) # header, line 6 h0 - rbind(h1,h2,h3,h4,h5,h6) write(ho,file.txt) write.table(x,file.txt,row.names=FALSE,col.names=FALSE,append=TRUE) The header should display as; ncols 180 nrows 290 xllcorner -20 yllcorner -20 cellsize 5000 NODATA_value NA Jannis wrote: Hallo, have a look at the documentation of the different output functions (write(),cat(),write.table()). Most of them have an argument like append. If you set this to TRUE, your command adds the lines you are writing into the file to the lines already existent in that file. So if you run this write() command first with your additional data (header data) and then with the real data and append=TRUE, your information ends up in the same file. HTH Jannis Muhammad Rahiz schrieb: Hello all, I'd like some advise on this. When I read my files, I pass the argument, skip=6, to skip 6 lines of header information. After performing the desired calculations, I have the output. Now I want to copy the 6 lines of skipped information to the output. What I've been doing so far is to use a shell script (i.e. the cat function) to copy the header information to the output file. This means I need 2 additional files, namely a file containing the header information only, and the shell script to run the the function. Is there a direct way to perform this in R? The following forms the main component of my R script; x - as.matrix(read.table(file.txt,skip=6)) y - x*2 write.table(y,output.txt,row.names=FALSE,col.names=FALSE) Thanks Muhammad __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] insert/copy skipped lines to output
On Mar 28, 2010, at 12:51 PM, Muhammad Rahiz wrote: Dear Jannis, Thanks for the tip. It works but I'd like to improve on the way I did it. x - array(1:50,dim=c(10,10)) # data h1 - c(ncols180) # header, line 1 h2 - c(nrows 290) # header, line 2 h3 - c(xllcorner -20) # header, line 3 h4 - c(yllcorner -20) # header, line 4 h5 - c(cellsize 5000) # header, line 5 h6 - c(NODATA_value NA) # header, line 6 h0 - rbind(h1,h2,h3,h4,h5,h6) write(ho,file.txt) write.table(x,file.txt,row.names=FALSE,col.names=FALSE,append=TRUE) The header should display as; ncols 180 nrows 290 xllcorner -20 yllcorner -20 cellsize 5000 NODATA_value NA Executing that code appears to deliver what you requested. So rather than asking us to read you mind, can you explain what is missing? ncols180 nrows 290 xllcorner -20 yllcorner -20 cellsize 5000 NODATA_value NA 1 11 21 31 41 1 11 21 31 41 2 12 22 32 42 2 12 22 32 42 3 13 23 33 43 3 13 23 33 43 4 14 24 34 44 4 14 24 34 44 5 15 25 35 45 5 15 25 35 45 6 16 26 36 46 6 16 26 36 46 7 17 27 37 47 7 17 27 37 47 8 18 28 38 48 8 18 28 38 48 9 19 29 39 49 9 19 29 39 49 10 20 30 40 50 10 20 30 40 50 -- David. Jannis wrote: Hallo, have a look at the documentation of the different output functions (write(),cat(),write.table()). Most of them have an argument like append. If you set this to TRUE, your command adds the lines you are writing into the file to the lines already existent in that file. So if you run this write() command first with your additional data (header data) and then with the real data and append=TRUE, your information ends up in the same file. HTH Jannis Muhammad Rahiz schrieb: Hello all, I'd like some advise on this. When I read my files, I pass the argument, skip=6, to skip 6 lines of header information. After performing the desired calculations, I have the output. Now I want to copy the 6 lines of skipped information to the output. What I've been doing so far is to use a shell script (i.e. the cat function) to copy the header information to the output file. This means I need 2 additional files, namely a file containing the header information only, and the shell script to run the the function. Is there a direct way to perform this in R? The following forms the main component of my R script; x - as.matrix(read.table(file.txt,skip=6)) y - x*2 write.table(y,output.txt,row.names=FALSE,col.names=FALSE) Thanks Muhammad __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. David Winsemius, MD 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] insert/copy skipped lines to output
Yes, it works. Just wondering if the technique can be optimized... David Winsemius wrote: On Mar 28, 2010, at 12:51 PM, Muhammad Rahiz wrote: Dear Jannis, Thanks for the tip. It works but I'd like to improve on the way I did it. x - array(1:50,dim=c(10,10)) # data h1 - c(ncols180) # header, line 1 h2 - c(nrows 290) # header, line 2 h3 - c(xllcorner -20) # header, line 3 h4 - c(yllcorner -20) # header, line 4 h5 - c(cellsize 5000) # header, line 5 h6 - c(NODATA_value NA) # header, line 6 h0 - rbind(h1,h2,h3,h4,h5,h6) write(ho,file.txt) write.table(x,file.txt,row.names=FALSE,col.names=FALSE,append=TRUE) The header should display as; ncols 180 nrows 290 xllcorner -20 yllcorner -20 cellsize 5000 NODATA_value NA Executing that code appears to deliver what you requested. So rather than asking us to read you mind, can you explain what is missing? ncols180 nrows 290 xllcorner -20 yllcorner -20 cellsize 5000 NODATA_value NA 1 11 21 31 41 1 11 21 31 41 2 12 22 32 42 2 12 22 32 42 3 13 23 33 43 3 13 23 33 43 4 14 24 34 44 4 14 24 34 44 5 15 25 35 45 5 15 25 35 45 6 16 26 36 46 6 16 26 36 46 7 17 27 37 47 7 17 27 37 47 8 18 28 38 48 8 18 28 38 48 9 19 29 39 49 9 19 29 39 49 10 20 30 40 50 10 20 30 40 50 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Coding of categorical variables for logistic regression?
Hello, I am trying to do a logistic regression and have one predictor variable (x) that is ratio and two predictor variables (y and z) that are categorical. These have three levels each which I have called High, Medium and Low. My question: do I need to use a numerical coding scheme for the categorical variables as required by some statistical software packages, with some sort of numeric dummy-variable coding? I am using: glm(binvar~x+y+z, family=binomial(link=logit)) Thanks, Ravi Kulkarni -- View this message in context: http://n4.nabble.com/Coding-of-categorical-variables-for-logistic-regression-tp1694250p1694250.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] Calculate variance/covariance with complex numbers
On Sun, 28 Mar 2010, Gang Chen wrote: Thanks a lot for the help, Ben Bolker and Chuck! Chuck, it seems your version needs a little modification. Instead of this: xri - matrix(rnorm(1)+1i*rnorm(1),nc=2) crossprod(xri-colMeans(xri))/(nrow(xri)-1) it seems to me it should be this (maybe there is a more elegant modification than mine?): crossprod(t(apply(xri, 1, '-', colMeans(xri/(nrow(xri)-1) Do you agree? Argh! Sorry for the 'thinko' (like a 'typo', but a misapplication of the brain rather than the fingers)! I'd use this: crossprod( sweep( xri, 2, colMeans(xri), - ))/(nrow(xri)-1) or crossprod(xri - rep(colMeans(xri),each=nrow(xri)))/(nrow(xri)-1) Chuck Gang On Sat, Mar 27, 2010 at 7:07 PM, Charles C. Berry cbe...@tajo.ucsd.edu wrote: On Sat, 27 Mar 2010, Gang Chen wrote: Anybody knows what functions can be used to calculate variance/covariance with complex numbers? var and cov don't seem to work: How about? xri - matrix(rnorm(1)+1i*rnorm(1),nc=2) crossprod(xri-colMeans(xri))/(nrow(xri)-1) HTH, Chuck a 1 V1 0.00810014+0.00169366i V2 0.00813054+0.00158251i V3 0.00805489+0.00163295i V4 0.00809141+0.00159533i V5 0.00813976+0.00161850i var(a) 1 1 1.141556e-09 Warning message: In var(a) : imaginary parts discarded in coercion cov(a) 1 1 1.141556e-09 Warning message: In cov(a) : imaginary parts discarded in coercion Thanks in advance, Gang __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Charles C. Berry (858) 534-2098 Dept of Family/Preventive Medicine E mailto:cbe...@tajo.ucsd.edu UC San Diego http://famprevmed.ucsd.edu/faculty/cberry/ La Jolla, San Diego 92093-0901 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Charles C. Berry(858) 534-2098 Dept of Family/Preventive Medicine E mailto:cbe...@tajo.ucsd.edu UC San Diego http://famprevmed.ucsd.edu/faculty/cberry/ La Jolla, San Diego 92093-0901 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Assigning factors probabilistically based on the value of another variable.
On Sun, 28 Mar 2010, Economics Guy wrote: It is really the same thing. One of many possibilities: theFrame - data.frame(theValues=runif(150,-10,10)) exact - diag(15)[1+ (rank(theFrame$theValues)-1)%/%10,] not.so.exact - diag(15)[1+ (rank(theFrame$theValues+runif(150,0,3))-1)%/%10,] If what you actually wanted was one factor with fifteen levels, just wrap the subscript in the last assignment in factor() instead. HTH, Chuck Thanks Chuck, this does what I asked for: theValues - runif(150,-10,10) exact - factor(1+(rank(theValues)-1)%/%100) Unfortunately, it looks like my example may have been too contrived for my actual program. In the solution that Chuck proposed he antisipated that I may not want the assignment of factor levels to be exact: notSoExact - factor(1+(rank(theValues+runif(150,0,3)-1)%/%100) This is close to what I need. However, in the real program what I need to be able to do is precisely vary the degree of exactness in the assignment. So I need to be able to have the assignment range from completely random assignment to the exact assignment that exact above provides. Anyone think of a simple way to do this? That's div 10, not div 100 (check your typing). The range of the runif() call determines the 'exactness'. Alternatively, apply weights of a and 1-a, for 0=a=1, to the components in rank(). Chuck Thanks Agan, That Economics Guy __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Charles C. Berry(858) 534-2098 Dept of Family/Preventive Medicine E mailto:cbe...@tajo.ucsd.edu UC San Diego http://famprevmed.ucsd.edu/faculty/cberry/ La Jolla, San Diego 92093-0901 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] insert/copy skipped lines to output
On Mar 28, 2010, at 1:11 PM, Muhammad Rahiz wrote: Yes, it works. Just wondering if the technique can be optimized... IN WHAT WAY -- David. David Winsemius wrote: On Mar 28, 2010, at 12:51 PM, Muhammad Rahiz wrote: Dear Jannis, Thanks for the tip. It works but I'd like to improve on the way I did it. x - array(1:50,dim=c(10,10)) # data h1 - c(ncols180) # header, line 1 h2 - c(nrows 290) # header, line 2 h3 - c(xllcorner -20) # header, line 3 h4 - c(yllcorner -20) # header, line 4 h5 - c(cellsize 5000) # header, line 5 h6 - c(NODATA_value NA) # header, line 6 h0 - rbind(h1,h2,h3,h4,h5,h6) write(ho,file.txt) write .table(x,file.txt,row.names=FALSE,col.names=FALSE,append=TRUE) The header should display as; ncols 180 nrows 290 xllcorner -20 yllcorner -20 cellsize 5000 NODATA_value NA Executing that code appears to deliver what you requested. So rather than asking us to read you mind, can you explain what is missing? ncols180 nrows 290 xllcorner -20 yllcorner -20 cellsize 5000 NODATA_value NA 1 11 21 31 41 1 11 21 31 41 2 12 22 32 42 2 12 22 32 42 3 13 23 33 43 3 13 23 33 43 4 14 24 34 44 4 14 24 34 44 5 15 25 35 45 5 15 25 35 45 6 16 26 36 46 6 16 26 36 46 7 17 27 37 47 7 17 27 37 47 8 18 28 38 48 8 18 28 38 48 9 19 29 39 49 9 19 29 39 49 10 20 30 40 50 10 20 30 40 50 David Winsemius, MD 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] Coding of categorical variables for logistic regression?
On Mar 28, 2010, at 1:15 PM, Ravi Kulkarni wrote: Hello, I am trying to do a logistic regression and have one predictor variable (x) that is ratio and two predictor variables (y and z) that are categorical. These have three levels each which I have called High, Medium and Low. My question: do I need to use a numerical coding scheme for the categorical variables as required by some statistical software packages, with some sort of numeric dummy-variable coding? No. If you have constructed those variables as factors, the regression functions in R will interpret them correctly, i.e. as though the dummies were in there. If you have not constructed them as factors, you should do so now. ?factor ?levels I am using: glm(binvar~x+y+z, family=binomial(link=logit)) Thanks, Ravi Kulkarni -- David Winsemius, MD 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] Preserving both yearmon and numeric data in an xls object
Hi R gourmets, I am trying to convert an HTML table into an xts object. The table has six columns, with the data of interest in a single row with each cell containing a long, \n-delimited character string. Initially, I work with these strings as elements in a list. This is necessary because the strings in each cell do not translate into a regular matrix with equal-length columns. Once I fix the entries, I'm ready to convert them into an xts object. The first two columns of the original table contain dates, and I want them to be of type yearmon in the xts object. The other four columns have numeric data. Here's my problem. If I convert the list into a data frame on the way to making it an xlt, the first two columns correctly keep the data as the yearmon class, but the remaining columns are converted to character class. Alternatively, if I convert the list into a matrix on the way to making the xlt, all six columns become numeric; the first two columns lose their yearmon class. How can I make an xlt from a list, such that the first two columns are yearmon and the last four are numeric? Thanks. Marsh Feldman P.S. Here is some sample code: #... input has been converted to a list of length 6; each element is a vector, but they themselves are of different length #... fix the 6 vectors to have equal length mylist[1:2] - lapply(mylist[1:2], as.yearmon)# Convert the first two elements into yearmon class #... Now try one of the following; tindex is the time index in yearmon format myxts - as.xts(as.data.frame(mylist), order.by=tindex)# this makes columns 3-6 of myxts all have class = character myxts - as.xts(matrix(unlist(mylist), ncol=6), order.by=tindex) # this makes myxts entirely numeric I even tried using the following statement afterwards but had no luck myxts[,1] - as.yearmon(myxts[,1]) [[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 Cmdr memory
On Sun, 28 Mar 2010, Duncan Murdoch wrote: On 28/03/2010 9:03 AM, David Winsemius wrote: On Mar 28, 2010, at 4:35 AM, ManInMoon wrote: Is there a 64 bit R - and where can I get hold of it for Windows please? For Windows XP?, Not that I know of. There are proprietary versions for Vista and I believe Professor Ripley is working on an experimental version for the 64 bit versions of Windows. We're planning to release 64 bit builds with R 2.11.0. They are currently being built as part of the test process, though the builds are still a little irregular. You can download from CRAN mirror/bin/windows64/contrib for now, and soon from CRAN mirror/bin/windows64/base. The 64 bit versions of R will require a 64 bit version of Windows to run on. I think there may be 64 bit versions of XP, but they are uncommon and I don't Rare indeed: they are really personal versions of Server 2003 (using that codebase, not XP's). But as it happens one of my IT staff uses x64 XP on his personal machine (he prefers XP to later versions of Windows) and has tested the R pre-2.11.0 installer there. know if they support our builds; we're testing in 64 bit Vista and Windows 7. And Server 2008 (win-builder). Revolution Computing also sells a build produced with a different compiler. It has the advantage that the compiler is probably in better shape than the one we are using Pros and cons. Yes, their compiler is more mature and better tested, but ours is a variant of gcc and a great deal of code (especially C++ in packages) is written for and tested on g++ and is more likely to give the intended answers on the R-core build. and they'll provide support with it; the disadvantage is that they'll charge for it, and they are probably not as up to date as us with respect to released version number. -- 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] Coding of categorical variables for logistic regression?
Ravi Kulkarni ravi.k...@gmail.com [Sun, Mar 28, 2010 at 07:15:52PM CEST]: [...] I am trying to do a logistic regression and have one predictor variable (x) that is ratio and two predictor variables (y and z) that are categorical. These have three levels each which I have called High, Medium and Low. You don't plan to use the information that y and z are apparently ordinal? -- Johannes Hüsing There is something fascinating about science. One gets such wholesale returns of conjecture mailto:johan...@huesing.name from such a trifling investment of fact. http://derwisch.wikidot.com (Mark Twain, Life on the Mississippi) __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] insert/copy skipped lines to output
something like this... x1 - as.matrix(read.table(input.txt))[1:6,] # reads only header x2 -array(1:6,dim=c(2,3)) write(x,output.txt) write.table(x3,output.txt,row.names=FALSE,col.names=FALSE,append=TRUE) But the results print; ncols nrows xllcorner yllcorner cellsize NODATA_value 180.00 290.00 -20.00 -20.00 5000.00 -.00 1 3 5 2 4 6 Muhammad Rahiz | Doctoral Student in Regional Climate Modeling Climate Research Laboratory, School of Geography the Environment Oxford University Centre for the Environment, University of Oxford South Parks Road, Oxford, OX1 3QY, United Kingdom Tel: +44 (0)1865-285194 Mobile: +44 (0)7854-625974 Email: muhammad.ra...@ouce.ox.ac.uk David Winsemius wrote: On Mar 28, 2010, at 1:11 PM, Muhammad Rahiz wrote: Yes, it works. Just wondering if the technique can be optimized... IN WHAT WAY -- David. David Winsemius wrote: On Mar 28, 2010, at 12:51 PM, Muhammad Rahiz wrote: Dear Jannis, Thanks for the tip. It works but I'd like to improve on the way I did it. x - array(1:50,dim=c(10,10)) # data h1 - c(ncols180) # header, line 1 h2 - c(nrows 290) # header, line 2 h3 - c(xllcorner -20) # header, line 3 h4 - c(yllcorner -20) # header, line 4 h5 - c(cellsize 5000) # header, line 5 h6 - c(NODATA_value NA) # header, line 6 h0 - rbind(h1,h2,h3,h4,h5,h6) write(ho,file.txt) write .table(x,file.txt,row.names=FALSE,col.names=FALSE,append=TRUE) The header should display as; ncols 180 nrows 290 xllcorner -20 yllcorner -20 cellsize 5000 NODATA_value NA Executing that code appears to deliver what you requested. So rather than asking us to read you mind, can you explain what is missing? ncols180 nrows 290 xllcorner -20 yllcorner -20 cellsize 5000 NODATA_value NA 1 11 21 31 41 1 11 21 31 41 2 12 22 32 42 2 12 22 32 42 3 13 23 33 43 3 13 23 33 43 4 14 24 34 44 4 14 24 34 44 5 15 25 35 45 5 15 25 35 45 6 16 26 36 46 6 16 26 36 46 7 17 27 37 47 7 17 27 37 47 8 18 28 38 48 8 18 28 38 48 9 19 29 39 49 9 19 29 39 49 10 20 30 40 50 10 20 30 40 50 David Winsemius, MD 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] insert/copy skipped lines to output
On Mar 28, 2010, at 2:41 PM, Muhammad Rahiz wrote: something like this... x1 - as.matrix(read.table(input.txt))[1:6,] # reads only header x2 -array(1:6,dim=c(2,3)) write(x,output.txt) write() will process the matrix elements in their natural vector order. write .table(x3,output.txt,row.names=FALSE,col.names=FALSE,append=TRUE) But the results print; ncols nrows xllcorner yllcorner cellsize NODATA_value 180.00 290.00 -20.00 -20.00 5000.00 -.00 1 3 5 2 4 6 ?write.table Add an appropriate , file= , to this and it should do what you expect write.table(x1, row.names=FALSE, col.names=FALSE, quote=FALSE) ncols 180 nrows 290 xllcorner -20 yllcorner -20 cellsize5000 NODATA_value NA Muhammad Rahiz | Doctoral Student in Regional Climate Modeling Climate Research Laboratory, School of Geography the Environment Oxford University Centre for the Environment, University of Oxford South Parks Road, Oxford, OX1 3QY, United Kingdom Tel: +44 (0)1865-285194 Mobile: +44 (0)7854-625974 Email: muhammad.ra...@ouce.ox.ac.uk David Winsemius wrote: On Mar 28, 2010, at 1:11 PM, Muhammad Rahiz wrote: Yes, it works. Just wondering if the technique can be optimized... IN WHAT WAY -- David. David Winsemius wrote: On Mar 28, 2010, at 12:51 PM, Muhammad Rahiz wrote: Dear Jannis, Thanks for the tip. It works but I'd like to improve on the way I did it. x - array(1:50,dim=c(10,10)) # data h1 - c(ncols180) # header, line 1 h2 - c(nrows 290) # header, line 2 h3 - c(xllcorner -20) # header, line 3 h4 - c(yllcorner -20) # header, line 4 h5 - c(cellsize 5000) # header, line 5 h6 - c(NODATA_value NA) # header, line 6 h0 - rbind(h1,h2,h3,h4,h5,h6) write(ho,file.txt) write .table(x,file.txt,row.names=FALSE,col.names=FALSE,append=TRUE) The header should display as; ncols 180 nrows 290 xllcorner -20 yllcorner -20 cellsize 5000 NODATA_value NA Executing that code appears to deliver what you requested. So rather than asking us to read you mind, can you explain what is missing? ncols180 nrows 290 xllcorner -20 yllcorner -20 cellsize 5000 NODATA_value NA 1 11 21 31 41 1 11 21 31 41 2 12 22 32 42 2 12 22 32 42 3 13 23 33 43 3 13 23 33 43 4 14 24 34 44 4 14 24 34 44 5 15 25 35 45 5 15 25 35 45 6 16 26 36 46 6 16 26 36 46 7 17 27 37 47 7 17 27 37 47 8 18 28 38 48 8 18 28 38 48 9 19 29 39 49 9 19 29 39 49 10 20 30 40 50 10 20 30 40 50 David Winsemius, MD West Hartford, CT David Winsemius, MD 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] Trouble loading package
I haven't seen an answer to this yet.
Your problem may stem from having defined a variable T.
I can replicate your error messages with:
T - hello
library(RMark)
So methinks that this probably indicates that there may be
a problem with using T for TRUE (when will Rusers finally
stop doing that???).
And sure enough, after loading RMark (with no T in my
workspace), I find that the authors of RMark have replaced
base R's .First.lib with their own version which contains
the line:
info - strsplit(library(help = pkgname, character.only = T)$info[[1]],
\\:[ ]+)
Note to RMark authors (and others): get used to using
TRUE and FALSE. The few characters saved by using T/F
are not worth it!
-Peter Ehlers
On 2010-03-26 15:40, Glenn E Stauffer wrote:
I am trying to load a package called Rmark, but when I run
library(Rmark)
I get the following:
library(RMark)
Error in !character.only : invalid argument type
Error in library(RMark) : .First.lib failed for 'RMark'
When I try to load Rmark from the packages menu, I get:
local({pkg- select.list(sort(.packages(all.available = TRUE)))
+ if(nchar(pkg)) library(pkg, character.only=TRUE)})
Error in !character.only : invalid argument type
Error in library(pkg, character.only = TRUE) :
.First.lib failed for 'RMark'
Any ideas what is causing this error?
My OS is Windows XP, and my R version is R.2.10.1
Thanks,
Glenn
*
Glenn E. Stauffer
Graduate Research Assistant
Department of Ecology
Montana State University
Bozeman, MT 59717
406-994-5677
gestauf...@gmail.com
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University of Calgary
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Re: [R] Calculate variance/covariance with complex numbers
Rolf Turner wrote:
On 28/03/2010, at 11:50 AM, Ben Bolker wrote:
Gang Chen gangchen6 at gmail.com writes:
Anybody knows what functions can be used to calculate
variance/covariance with complex numbers? var and cov don't seem to
work:
How about:
y - complex(real=5:1,imag=2:6)
z - complex(real=1:5,imag=6:10)
complex.var - function(x) {
mx - mean(x)
n - length(x)
mean((x-mx)^2)*n/(n-1)
}
SNIP
Don't you want variances to be positive (non-negative) reals?
IIRC the population variance of a complex random variable is
E(|X - mu|^2) not E((X - mu)^2)
So shouldn't your complex.var function have Mod(x-mx)^2 where
you currently have (x-mx)^2 ???
cheers,
Rolf
Probably. To be honest, I wasn't thinking about it that carefully.
It crossed my mind to wonder what the appropriate definition was of the
variance for complex numbers, but I didn't bother to go find out.
I guess it goes to show (yet again) that advice may be worth what you
pay for it ...
cheers
Ben
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[R] Fwd: col.axis
I need a help in the following code. I could not find any hint at the help files m - c( 58, 47, 51, 57, 48) plot(1:5, m, pch=19, col=1:5, axes=FALSE) axis(1, at=1:length(m), labels=LETTERS[1:5], col.axis=2) The labels A B C D E appear in this case with the red color. What I really want is that thay get the same color as the circles, but if I try the line axis(1, at=1:length(m), labels=LETTERS[1:5], col.axis=1:5) I get the message the graphic parameter col.axis has the wrong length. Is there any way to circumvent it? Thank you very much Enio Jelihovschi UESC, Brasil [[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] Renumbering
HI all, Is there a renumbering function in R? I would like to renumber the following id numbers *Input file * Id Father Mother 123 0 0 124 0 0 125 123 124 126 123 0 127 125 126 128 0 127 130 123 125 *Output* Id Father Mother 1 0 0 2 0 0 3 1 2 4 1 0 5 3 4 6 0 7 7 1 2 Any help is highly appreciated in Advance Val K [[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] Fwd: col.axis
Hi you can use mtext() m - c( 58, 47, 51, 57, 48) plot(1:5, m, pch=19, col=1:5, axes=FALSE) axis(1, at=1:length(m), labels=LETTERS[1:5], col.axis=FALSE) # color =FALSE to make them disappear at - axTicks(1) # get Ticks from Axis 1 mtext(side = 1, text = at, at = at, col = (1:5), line = 1) Lukas Schefczyk (btw my first message here) -- From: Enio Jelihovschi eniojelih...@gmail.com Sent: Sunday, March 28, 2010 10:07 PM To: r-help@r-project.org Subject: [R] Fwd: col.axis I need a help in the following code. I could not find any hint at the help files m - c( 58, 47, 51, 57, 48) plot(1:5, m, pch=19, col=1:5, axes=FALSE) axis(1, at=1:length(m), labels=LETTERS[1:5], col.axis=2) The labels A B C D E appear in this case with the red color. What I really want is that thay get the same color as the circles, but if I try the line axis(1, at=1:length(m), labels=LETTERS[1:5], col.axis=1:5) I get the message the graphic parameter col.axis has the wrong length. Is there any way to circumvent it? Thank you very much Enio Jelihovschi UESC, Brasil [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Renumbering
This is not really a renumbering and there is no builtin function. This is a case where you want to do some special remapping of numbers and you have to decide what it is in your case. Also use 'dput' to put data in email since what you sent was not parseable. Also I think the last two lines of your desired output is incorrect. Try this: x - read.table(textConnection( Id Father Mother + 123 0 0 + 124 0 0 + 125 123 124 + 126 123 0 + 127 125 126 + 128 0 127 + 130 123 125), header=TRUE) # convert to matrix x - as.matrix(x) closeAllConnections() # map numbers to a new sequence allNums - sort(unique(as.vector(x))) # new numbers newNums - seq(0, by=1, length=length(allNums)) # now remap the numbers x[] - newNums[match(x, allNums)] x Id Father Mother [1,] 1 0 0 [2,] 2 0 0 [3,] 3 1 2 [4,] 4 1 0 [5,] 5 3 4 [6,] 6 0 5 [7,] 7 1 3 On Sun, Mar 28, 2010 at 4:50 PM, Val valkr...@gmail.com wrote: HI all, Is there a renumbering function in R? I would like to renumber the following id numbers *Input file * Id Father Mother 123 0 0 124 0 0 125 123 124 126 123 0 127 125 126 128 0 127 130 123 125 *Output* Id Father Mother 1 0 0 2 0 0 3 1 2 4 1 0 5 3 4 6 0 7 7 1 2 Any help is highly appreciated in Advance Val K [[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. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem that you are trying to solve? [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] grid graphics - concatenating gLists - is there a function?
Hi Mark Heckmann wrote: I have to gList objects containing several grobs. Now, I want to combine them into a single gList object as e.g. gTree() does not take a nested gList as children argument. gl1 - gList(rectGrob(), rectGrob()) gl2 - gList(textGrob(Text 1)) Now I want to combine gl1 and gl2 into a single gList object, that is not nested. I think this should work ... gList(gl1, gl2) Paul Thanks, Mark ––– Mark Heckmann Blog: www.markheckmann.de R-Blog: http://ryouready.wordpress.com [[alternative HTML version deleted]] -- Dr Paul Murrell Department of Statistics The University of Auckland Private Bag 92019 Auckland New Zealand 64 9 3737599 x85392 p...@stat.auckland.ac.nz http://www.stat.auckland.ac.nz/~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] grid graphics - concatenating gLists - is there a function?
Hi Paul, unfortunately this did not work out. I use the following now: childgrobs - c(gl1, gl2) class(childgrobs) - gList This seems to work for me. Bests, Mark Am 28.03.2010 um 23:44 schrieb Paul Murrell: Hi Mark Heckmann wrote: I have to gList objects containing several grobs. Now, I want to combine them into a single gList object as e.g. gTree () does not take a nested gList as children argument. gl1 - gList(rectGrob(), rectGrob()) gl2 - gList(textGrob(Text 1)) Now I want to combine gl1 and gl2 into a single gList object, that is not nested. I think this should work ... gList(gl1, gl2) Paul Thanks, Mark Mark Heckmann Blog: www.markheckmann.de R-Blog: http://ryouready.wordpress.com [[alternative HTML version deleted]] -- Dr Paul Murrell Department of Statistics The University of Auckland Private Bag 92019 Auckland New Zealand 64 9 3737599 x85392 p...@stat.auckland.ac.nz http://www.stat.auckland.ac.nz/~paul/ Mark Heckmann Dipl. Wirt.-Ing. cand. Psych. Vorstraße 93 B01 28359 Bremen Blog: www.markheckmann.de R-Blog: http://ryouready.wordpress.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] Renumbering
Thank you for your quick response. You are right the ls two rows were not correct. Typ error. Is it possible to add the original ID number as a cross reference as well Like, Id Father Mother Original ID [1,] 1 0 0 123 [2,] 2 0 0 124 [3,] 3 1 2 125 [4,] 4 1 0 126 [5,] 5 3 4 127 [6,] 6 0 5 128 [7,] 7 1 3 130 Thanks again Val On Sun, Mar 28, 2010 at 5:09 PM, jim holtman jholt...@gmail.com wrote: This is not really a renumbering and there is no builtin function. This is a case where you want to do some special remapping of numbers and you have to decide what it is in your case. Also use 'dput' to put data in email since what you sent was not parseable. Also I think the last two lines of your desired output is incorrect. Try this: x - read.table(textConnection( Id Father Mother + 123 0 0 + 124 0 0 + 125 123 124 + 126 123 0 + 127 125 126 + 128 0 127 + 130 123 125), header=TRUE) # convert to matrix x - as.matrix(x) closeAllConnections() # map numbers to a new sequence allNums - sort(unique(as.vector(x))) # new numbers newNums - seq(0, by=1, length=length(allNums)) # now remap the numbers x[] - newNums[match(x, allNums)] x Id Father Mother [1,] 1 0 0 [2,] 2 0 0 [3,] 3 1 2 [4,] 4 1 0 [5,] 5 3 4 [6,] 6 0 5 [7,] 7 1 3 On Sun, Mar 28, 2010 at 4:50 PM, Val valkr...@gmail.com wrote: HI all, Is there a renumbering function in R? I would like to renumber the following id numbers *Input file * Id Father Mother 123 0 0 124 0 0 125 123 124 126 123 0 127 125 126 128 0 127 130 123 125 *Output* Id Father Mother 1 0 0 2 0 0 3 1 2 4 1 0 5 3 4 6 0 7 7 1 2 Any help is highly appreciated in Advance Val K [[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. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem that you are trying to solve? [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] grid graphics - concatenating gLists - is there a function?
On Mar 28, 2010, at 5:59 PM, Mark Heckmann wrote: Hi Paul, unfortunately this did not work out. I use the following now: childgrobs - c(gl1, gl2) class(childgrobs) - gList This seems to work for me. What about?: gl3 - gl1 gl3[length(g1)+1] - gl2 -- David Bests, Mark Am 28.03.2010 um 23:44 schrieb Paul Murrell: Hi Mark Heckmann wrote: I have to gList objects containing several grobs. Now, I want to combine them into a single gList object as e.g. gTree () does not take a nested gList as children argument. gl1 - gList(rectGrob(), rectGrob()) gl2 - gList(textGrob(Text 1)) Now I want to combine gl1 and gl2 into a single gList object, that is not nested. I think this should work ... gList(gl1, gl2) Paul Thanks, Mark Mark Heckmann Blog: www.markheckmann.de R-Blog: http://ryouready.wordpress.com [[alternative HTML version deleted]] -- Dr Paul Murrell Department of Statistics The University of Auckland Private Bag 92019 Auckland New Zealand 64 9 3737599 x85392 p...@stat.auckland.ac.nz http://www.stat.auckland.ac.nz/~paul/ Mark Heckmann Dipl. Wirt.-Ing. cand. Psych. Vorstraße 93 B01 28359 Bremen Blog: www.markheckmann.de R-Blog: http://ryouready.wordpress.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 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] Ellipse that Contains 95% of the Observed Data
I can take the results of a simulation with one random variable and generate an empirical interval that contains 95% of the observations, e.g., x - rnorm(1) quantile(x,probs=c(0.025,0.975)) Is there an R function that can take the results from two random variables and generate an empirical ellipse that contains 95% of the observations, e.g., x - rnorm(1) y - rnorm(1) ? I am specifically looking for an ellipse that does not assume normality. Tom -- View this message in context: http://n4.nabble.com/Ellipse-that-Contains-95-of-the-Observed-Data-tp1694538p1694538.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] CRAN (and crantastic) updates this week
CRAN (and crantastic) updates this week New packages Updated packages Amelia (1.2-16), AMORE (0.2-12), Bolstad (0.2-17), CADStat (2.2-4) This email provided as a service for the R community by http://crantastic.org. Like it? Hate it? Please let us know: crana...@gmail.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Renumbering
This should do it: x - read.table(textConnection( Id Father Mother + 123 0 0 + 124 0 0 + 125 123 124 + 126 123 0 + 127 125 126 + 128 0 127 + 130 123 125), header=TRUE) # convert to matrix x - as.matrix(x) closeAllConnections() # map numbers to a new sequence allNums - sort(unique(as.vector(x))) # new numbers newNums - seq(0, by=1, length=length(allNums)) # now remap the numbers x[] - newNums[match(x, allNums)] x - cbind(x, orig=allNums[x[, Id] + 1]) x Id Father Mother orig [1,] 1 0 0 123 [2,] 2 0 0 124 [3,] 3 1 2 125 [4,] 4 1 0 126 [5,] 5 3 4 127 [6,] 6 0 5 128 [7,] 7 1 3 130 On Sun, Mar 28, 2010 at 6:33 PM, Val valkr...@gmail.com wrote: Thank you for your quick response. You are right the ls two rows were not correct. Typ error. Is it possible to add the original ID number as a cross reference as well Like, Id Father Mother Original ID [1,] 1 0 0 123 [2,] 2 0 0 124 [3,] 3 1 2 125 [4,] 4 1 0 126 [5,] 5 3 4 127 [6,] 6 0 5 128 [7,] 7 1 3 130 Thanks again Val On Sun, Mar 28, 2010 at 5:09 PM, jim holtman jholt...@gmail.com wrote: This is not really a renumbering and there is no builtin function. This is a case where you want to do some special remapping of numbers and you have to decide what it is in your case. Also use 'dput' to put data in email since what you sent was not parseable. Also I think the last two lines of your desired output is incorrect. Try this: x - read.table(textConnection( Id Father Mother + 123 0 0 + 124 0 0 + 125 123 124 + 126 123 0 + 127 125 126 + 128 0 127 + 130 123 125), header=TRUE) # convert to matrix x - as.matrix(x) closeAllConnections() # map numbers to a new sequence allNums - sort(unique(as.vector(x))) # new numbers newNums - seq(0, by=1, length=length(allNums)) # now remap the numbers x[] - newNums[match(x, allNums)] x Id Father Mother [1,] 1 0 0 [2,] 2 0 0 [3,] 3 1 2 [4,] 4 1 0 [5,] 5 3 4 [6,] 6 0 5 [7,] 7 1 3 On Sun, Mar 28, 2010 at 4:50 PM, Val valkr...@gmail.com wrote: HI all, Is there a renumbering function in R? I would like to renumber the following id numbers *Input file * Id Father Mother 123 0 0 124 0 0 125 123 124 126 123 0 127 125 126 128 0 127 130 123 125 *Output* Id Father Mother 1 0 0 2 0 0 3 1 2 4 1 0 5 3 4 6 0 7 7 1 2 Any help is highly appreciated in Advance Val K [[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. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem that you are trying to solve? -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem that you are trying to solve? [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Calculate variance/covariance with complex numbers
On 03/29/2010 04:17 AM, Charles C. Berry wrote: ... Argh! Sorry for the 'thinko' (like a 'typo', but a misapplication of the brain rather than the fingers)! Well, a typo is the _result_ of a misapplication of the fingers to a keyboard, so I would expect that if the result of thinking can be called a meme, then the appropriate term for the mistake would be a memo. I have seen plenty of examples. Jim __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] tapply syntax
What is the function set()? Is that a typo? When I type ?set I get nothing, and when I try to evaluate that code R tells me it can't find the function. -- View this message in context: http://n4.nabble.com/tapply-syntax-tp1692503p1694586.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] tapply syntax
On 29/03/2010, at 1:27 PM, Jeff Brown wrote:
What is the function set()? Is that a typo? When I type ?set I get
nothing, and when I try to evaluate that code R tells me it can't find the
function.
Yeah, it's a typo. (S)he meant ``subset''.
cheers,
Rolf Turner
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Re: [R] tapply syntax
The message tells you everything - there is no function 'set' in the workspace you are using. Did you forget to load a library? What is the context in which you are trying to use it? On Sun, Mar 28, 2010 at 8:27 PM, Jeff Brown dopethatwantsc...@yahoo.comwrote: What is the function set()? Is that a typo? When I type ?set I get nothing, and when I try to evaluate that code R tells me it can't find the function. -- View this message in context: http://n4.nabble.com/tapply-syntax-tp1692503p1694586.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. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem that you are trying to solve? [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Heirarchical tree data structure
When I tried ??tree, I found something called dendrogram that looks like it might be what you want. -- View this message in context: http://n4.nabble.com/Heirarchical-tree-data-structure-tp1692838p1694575.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] Page width figures in Latex
bRotheRs sisteRs, I am once again attempting to learn enough Latex voodoo to get something done, and failing comically. The document RJAuthorguide.pdf mentions that one can get page width figures through the use of the figure* or table* environments, but despite considerable searching through the mail archives and reading Frank Harrell's discussion of Using Latex Figure Environments for Plots until my eyes went on strike, I am nowhere near a solution. Would anyone be kind enough to point me to the Idiot's Guide to Latex Figure Environments? Jim __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] tapply syntax
sorry - I use many abbreviations and I try to remove them before I post questions/answers - 'set' is my abb. for subset david On 3/28/2010 8:27 PM, Jeff Brown [via R] wrote: What is the function set()? Is that a typo? When I type ?set I get nothing, and when I try to evaluate that code R tells me it can't find the function. View message @ http://n4.nabble.com/tapply-syntax-tp1692503p1694586.html To unsubscribe from Re: tapply syntax, click here (link removed) =. -- View this message in context: http://n4.nabble.com/tapply-syntax-tp1692503p1694626.html Sent from the R help mailing list archive at Nabble.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.
[R] Question on entry exit tabulating in any R finance package
I asked the question in Rmetrics subforum, but for some reason, almost two weeks later, it keeps saying I haven't been approved to post yet there. I'll try again here on the open forum. I wanted to have a script that tabulates results by trade. I.e. instead of tabulating each day as a trade event, you enter on one date, exit another, and simply tabulate metrics based on one trade period. For example, you could have a moving average crossover system and the results would be tabulated based on each trade (including entry/exit date attributes). The package, Tradesys, is very close, but I can't seem to find any documentation beyond: http://r-forge.r-project.org/plugins/scmsvn/viewcvs.php/*checkout*/pkg/inst/doc/tradesys.pdf?rev=19root=tradesys And unfortunately, the definitions are a bit sparse and I had trouble reverse engineering them. For instance, in the table on page 3: Phase ETime XTime Time Numb EPrice XPrice PnL RoR 107 EL 2006-09-21 2007-09-12 356 244 1324.89 1471.10 146.21 0.264117052 Pnl Makes sense (1471.10-1324.89 )= 146.21, but, I would expect ROR to be ~1471.1/1324.89-1 ~ 11.03%, yet RoR col shows 26.411% I also looked at blotter, which shows an example that is long only and seems a bit cumbersome to run the simple metrics for trade entry/exit. Any ideas on packages that will do this, or why I'm misunderstanding the Tradesys results? thanks, rtist Pat W. -- View this message in context: http://n4.nabble.com/Question-on-entry-exit-tabulating-in-any-R-finance-package-tp1694607p1694607.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] Coding of categorical variables for logistic regression?
How do I use the extra information that two of my predictors are ordinal? (I did not know I could do that.) Thanks, Ravi -- View this message in context: http://n4.nabble.com/Coding-of-categorical-variables-for-logistic-regression-tp1694250p1694644.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] Ellipse that Contains 95% of the Observed Data
Tom La Bone booboo at gforcecable.com writes: I can take the results of a simulation with one random variable and generate an empirical interval that contains 95% of the observations, e.g., x - rnorm(1) quantile(x,probs=c(0.025,0.975)) Is there an R function that can take the results from two random variables and generate an empirical ellipse that contains 95% of the observations, e.g., x - rnorm(1) y - rnorm(1) ? I am specifically looking for an ellipse that does not assume normality. I'll be interested to hear what others come up with. I'm not sure the problem as you have stated it is well-posed, or necessarily possible. Suppose there is a true unknown bivariate probability distribution with a non-elliptical 95% quantile region. Will you be able to draw an ellipse that has the properties you want? Here's one possible alternative: library(coda) library(emdbook) plot(x,y) z = HPDregionplot(as.mcmc(cbind(x,y)),add=TRUE,col=2,lwd=2) is not an ellipse, but does contain (approximately) 95% of the points. Convex hulls are another plausible approach. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Coding of categorical variables for logistic regression?
?polr of the MASS package. On Mon, Mar 29, 2010 at 10:39 AM, Ravi Kulkarni ravi.k...@gmail.com wrote: How do I use the extra information that two of my predictors are ordinal? (I did not know I could do that.) Thanks, Ravi -- View this message in context: http://n4.nabble.com/Coding-of-categorical-variables-for-logistic-regression-tp1694250p1694644.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. -- CH Chan Research Assistant - KWH http://www.macgrass.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] Page width figures in Latex
Jim Lemon wrote:
bRotheRs sisteRs,
I am once again attempting to learn enough Latex voodoo to get something
done, and failing comically. The document RJAuthorguide.pdf
mentions that one can get page width figures through the use of the
figure* or table* environments, but despite considerable searching
through the mail archives and reading Frank Harrell's discussion of
Using Latex Figure Environments for Plots until my eyes went on
strike, I am nowhere near a solution. Would anyone be kind enough to
point me to the Idiot's Guide to Latex Figure Environments?
Jim
As far as I can recall, figure* and table* are used to create figures/tables
that span the entire page when the rest of the document is in twocolumn or
multicol mode. I.e. these environments allow you to break out of a
multi-column layout to place a figure that acts like it was in a normal
single-column layout.
There are a bunch of caveats such as the figure/table will only appear at
the top or bottom of a page and will not appear on the same page as the
point at which it was declared in the source. That is to say, when you
declare a figure* in a LaTeX document, one page break must pass before the
environment actually gets set in your document- no matter what !h or H vodoo
you pull.
If your document is not using multiple columns, then you may want to specify
the width of your figure when you place it using \includegraphics. In order
to scale the figure so that it spans the entire page, set the width argument
equal to \textwidth:
\begin{figure}
\centering
\caption{A graph of x verses y along with a linear regression fit.}
\label{fig:xVsY}
\includegraphics[width=\textwidth]{/path/to/your/figure}
\end{figure}
Some good resources are:
The LaTeX Wikibook:
http://en.wikibooks.org/wiki/LaTeX
Getting to Grips with LaTeX:
http://www.andy-roberts.net/misc/latex/
Hope this helps!
-Charlie
-
Charlie Sharpsteen
Undergraduate-- Environmental Resources Engineering
Humboldt State University
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Re: [R] Page width figures in Latex
On 29/03/2010, at 4:21 PM, Sharpie wrote:
SNIP
There are a bunch of caveats such as the figure/table will only appear at
the top or bottom of a page and will not appear on the same page as the
point at which it was declared in the source. That is to say, when you
declare a figure* in a LaTeX document, one page break must pass before the
environment actually gets set in your document- no matter what !h or H vodoo
you pull.
SNIP
I'm not convinced that this is correct; I'm sure I have had floats
(including figures) placed where I asked them to be placed. :-)
Be that as is it were; if you put:
\usepackage{float}
in your preamble and then do
\begin{figure}[H]
whatever
\end{figure}
the figure will appear ***exactly*** where you put it --- provided
of course that there is room for it there. Elsewise you'll get a
page break just before the figure.
cheers,
Rolf Turner
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Re: [R] Page width figures in Latex
On Mon, 29 Mar 2010 12:21:40 +1100, Jim Lemon j...@bitwrit.com.au
wrote:
bRotheRs sisteRs,
I am once again attempting to learn enough Latex voodoo to get something
done, and failing comically. The document RJAuthorguide.pdf
mentions that one can get page width figures through the use of the
figure* or table* environments, but despite considerable searching
through the mail archives and reading Frank Harrell's discussion of
Using Latex Figure Environments for Plots until my eyes went on
strike, I am nowhere near a solution. Would anyone be kind enough to
point me to the Idiot's Guide to Latex Figure Environments?
Jim
Jim,
You need a good book on Latex. I like this one:
http://www.amazon.com/Guide-LaTeX-4th-Helmut-Kopka/dp/0321173856/ref=sr_1_4?ie=UTF8s=booksqid=1269833347sr=8-4
The width of the figure is controlled by the \includegraphics
statement, not any particular part of the environment specification.
That assumes you have loaded the graphicx package. For example,
\begin{figure}[!th]
\begin{center}
\includegraphics[width=\textwidth]{myfig.eps}\\
\end{center}
\end{figure}%
HTH,
Mike
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Re: [R] Page width figures in Latex
Rolf Turner wrote:
On 29/03/2010, at 4:21 PM, Sharpie wrote:
SNIP
There are a bunch of caveats such as the figure/table will only appear at
the top or bottom of a page and will not appear on the same page as the
point at which it was declared in the source. That is to say, when you
declare a figure* in a LaTeX document, one page break must pass before
the
environment actually gets set in your document- no matter what !h or H
vodoo
you pull.
SNIP
I'm not convinced that this is correct; I'm sure I have had floats
(including figures) placed where I asked them to be placed. :-)
Be that as is it were; if you put:
\usepackage{float}
in your preamble and then do
\begin{figure}[H]
whatever
\end{figure}
the figure will appear ***exactly*** where you put it --- provided
of course that there is room for it there. Elsewise you'll get a
page break just before the figure.
cheers,
Rolf Turner
Aye, that is exactly true for the figure environment.
However, I was referring to the figure* environment (note the asterisk)
which is used when setting a figure that spans a full page in a document
with multiple columns. Under these conditions, I recall there being some
gotchas such as the figure having to appear at the top or bottom of the page
and one pagebreak having to pass before it appears.
-Charlie
-
Charlie Sharpsteen
Undergraduate-- Environmental Resources Engineering
Humboldt State University
--
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http://n4.nabble.com/Page-width-figures-in-Latex-tp1694612p1694686.html
Sent from the R help mailing list archive at Nabble.com.
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] large dataset
This was *very* useful for me when I dealt with a 1.5Gb text file http://www.csc.fi/sivut/atcsc/arkisto/atcsc3_2007/ohjelmistot_html/R_and_la rge_data/ Two hours is a *very* long time to transfer a csv file to a db. The author of the linked article has not documented how to use scan() arguments appropriately for the task. I take particular issue with the authors statement that R is said to be slow, memory hungry and only capable of handling small datasets, indicating he/she has crummy informants and not challenged the notion him/herself. n.vialma, 100,000 records is likely not a lot of data. If it is taking more than two or three minutes, something is wrong. Knowing the record limits in R is a good starting point, but will only get you part of the way. How many records does your file contain? Do you know how to find out? What are the data types of the records? What is the call you are using to import the records into R? What OS are you using? How much RAM does your system have? What is the size of the R-environment on your system? Do you have resource intensive applications running (such as MS-Office)? A lot of folks on this list have been through what you are now dealing with, so there is plenty of help. I find myself smiling inside wanting to say welcome! Sincerely, KeithC. -Original Message- From: Khanh Nguyen [mailto:nguyen.h.kh...@gmail.com] Sent: Saturday, March 27, 2010 8:59 AM To: n.via...@libero.it Cc: r-help Subject: Re: [R] large dataset This was *very* useful for me when I dealt with a 1.5Gb text file http://www.csc.fi/sivut/atcsc/arkisto/atcsc3_2007/ohjelmistot_html/R_and_lar ge_data/ On Sat, Mar 27, 2010 at 5:19 AM, n.via...@libero.it n.via...@libero.it wrote: Hi I have a question, as im not able to import a csv file which contains a big dataset(100.000 records) someone knows how many records R can handle without giving problems? What im facing when i try to import the file is that R generates more than 100.000 records and is very slow... thanks a lot!!! __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Page width figures in Latex
Hi
All you need to know to get started with figures (and even up to
intermediate level)-
Keith Reckdahl's Using Imported Graphics in LATEX and pdfLATEX
Regards
Duncan
Duncan Mackay
Department of Agronomy and Soil Science
University of New England
ARMIDALE NSW 2351
Email home: mac...@northnet.com.au
At 13:37 29/03/2010, you wrote:
On 29/03/2010, at 4:21 PM, Sharpie wrote:
SNIP
There are a bunch of caveats such as the figure/table will only appear at
the top or bottom of a page and will not appear on the same page as the
point at which it was declared in the source. That is to say, when you
declare a figure* in a LaTeX document, one page break must pass before the
environment actually gets set in your document- no matter what !h or H
vodoo
you pull.
SNIP
I'm not convinced that this is correct; I'm sure I have had floats
(including figures) placed where I asked them to be placed. :-)
Be that as is it were; if you put:
\usepackage{float}
in your preamble and then do
\begin{figure}[H]
whatever
\end{figure}
the figure will appear ***exactly*** where you put it --- provided
of course that there is room for it there. Elsewise you'll get a
page break just before the figure.
cheers,
Rolf Turner
##
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Re: [R] Page width figures in Latex
On 03/29/2010 02:34 PM, Mike Prager wrote:
...
\begin{figure}[!th]
\begin{center}
\includegraphics[width=\textwidth]{myfig.eps}\\
\end{center}
\end{figure}%
Hi Mike,
I wrote too soon, for there was one combination that I had not tried:
\begin{figure*}[!th]
\includegraphics[width=\textwidth]{hypertens.pdf}
\caption{\label{figure:hypertens}
Reported hypertension by age, sex and alcohol consumption}
\end{figure*}
did exactly what I wanted. Thanks.
Jim
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Re: [R] Coding of categorical variables for logistic regression?
Just because a covariate is ordered does not ensure that the relationship will be monotonic. -- David. On Mar 28, 2010, at 11:09 PM, C.H. wrote: ?polr of the MASS package. On Mon, Mar 29, 2010 at 10:39 AM, Ravi Kulkarni ravi.k...@gmail.com wrote: How do I use the extra information that two of my predictors are ordinal? (I did not know I could do that.) Thanks, Ravi -- View this message in context: http://n4.nabble.com/Coding-of-categorical-variables-for-logistic-regression-tp1694250p1694644.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. -- CH Chan Research Assistant - KWH http://www.macgrass.com __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. David Winsemius, MD West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Help with assigning a value based on existing numbers
Hi
Jessica Cathro jcat...@london.edu napsal dne 26.03.2010 15:33:19:
Hi
Can you explain what the purpose of the cut function is, and how I would
use it?
?cut
x-runif(100)*300
cut(x, breaks=seq(0,300,50), labels=letters[1:6])
Regards
Petr
Thanks
Jessica
_
Jessica Cathro | Business Analyst | Executive Education
London Business School | Regent's Park | London NW1 4SA | United Kingdom
Switchboard +44 (0)20 7000 7000| Direct line +44 (0)20 7000 7383 |
Email jcat...@london.edu
www.london.edu | London experience. World impact.
-Original Message-
From: Petr PIKAL [mailto:petr.pi...@precheza.cz]
Sent: 26 March 2010 14:00
To: Jessica Cathro
Cc: r-help@r-project.org
Subject: Odp: [R] Help with assigning a value based on existing numbers
Hi
again a work for cut.
See ?cut and notice a labels option.
Regards
Petr
r-help-boun...@r-project.org napsal dne 26.03.2010 11:37:20:
Hi All
I have a column/variable called time difference. It has a whole list
of
numbers from 0 through to the hundreds eg 236. I want to assign a
corresponding name to each variable from a predefined list: Month or
less, 1 -2 months, 2-3 months etc
So the result would look something like:
Time Difference Month
1 Month or less
365 1-2 years
52 2-3 months
Etc
I have tried using if elseif (as shown below), but it kept coming up
with the error:
Error:
In if (curvedata$Date.difference == NULL) { :
the condition has length 1 and only the first element will be used
2: In if (curvedata$Date.difference = 29) { :
the condition has length 1 and only the first element will be used
3: In if (curvedata$Date.difference = 59) { :
the condition has length 1 and only the first element will be used
If Else Statement:
month -if (curvedata$Date.difference ==NULL) {Month -0} ifelse
(curvedata$Date.difference =29) {Month -month or less} else if
(curvedata$Date.difference =59) {Month -1-2 months} else if
(curvedata$Date.difference =89) {Month -2-3 months} else if
(curvedata$Date.difference =119) {Month -3-4 months} else if
(curvedata$Date.difference =149) {Month -4-5 months} else if
(curvedata$Date.difference =179) {Month -5-6 months} else if
(curvedata$Date.difference =209) {Month -6-7 months} else if
(curvedata$Date.difference =239) {Month -7-8 months} else if
(curvedata$Date.difference =269) {Month -8-9 months} else if
(curvedata$Date.difference =299) {Month -9-10 months} else if
(curvedata$Date.difference =329) {Month -10-11 months} else if
(curvedata$Date.difference =359) {Month -11-12 months} else if
(curvedata$Date.difference =719) {Month -1-2 years} else
{Month -More than 2 years}
I'm pretty new to R, so any help would be appreciated.
Thanks
Jessica
_
Jessica Cathro | Business Analyst | Executive Education
London Business School | Regent's Park | London NW1 4SA | United
Kingdom
Switchboard +44 (0)20 7000 7000| Direct line +44 (0)20 7000 7383 |
Email jcat...@london.edu mailto:jcat...@london.edu
www.london.edu http://www.london.edu/ | London experience. World
impact.
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