Re: [R] question about non-linear least squares in R
Here is one way of getting a reasonable fit: 1. Scale your y's by dividing all values by 1e6. 2. Plot x vs. y. The plot looks like a quadratic function. 3. Fit a quadratic const. + B*x^2 - this a linear regression problem so use lm. 4. Plot the predictions. 5. Eyball the necessary shift - MA is around 0.01. Refit const. + B*(x-.01)^2. Should get const.=1.147 and B=139.144 6. Use start=list(const.= 1.147, A=0, B=1.147, MA=.01). nls should converge in 4 iterations. In general, good starting points may be crucial to nls convergence. Scaling the y's to reasonable values also helps. Hope this helps, Andy __ Andy Jaworski 518-1-01 Process Laboratory 3M Corporate Research Laboratory - E-mail: [EMAIL PROTECTED] Tel: (651) 733-6092 Fax: (651) 736-3122 Yu (Warren) Wang [EMAIL PROTECTED] To Sent by: r-help@stat.math.ethz.ch [EMAIL PROTECTED] r-help@stat.math.ethz.ch at.math.ethz.chcc Subject 09/05/2007 02:51 [R] question about non-linear least AMsquares in R Hi, everyone, My question is: It's not every time that you can get a converged result from the nls function. Is there any solution for me to get a reasonable result? For example: x - c(-0.06,-0.04,-0.025,-0.015,-0.005,0.005,0.015,0.025,0.04,0.06) y - c(1866760,1457870,1314960,1250560,1184850,1144920,1158850,1199910,1263850,1452520) fitOup- nls(y ~ constant + A*(x-MA)^4 + B*(x-MA)^2, start=list(constant=1000, A=1, B=-100, MA=0), control=nls.control(maxiter=100, minFactor=1/4096), trace=TRUE) For this one, I cannot get the converged result, how can I reach it? To use another funtion or to modify some settings for nls? Thank you very much! Yours, Warren __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] integrate
As Duncan Murdoch mentioned in his reply, the problem is with the fact that
your function is not really a properly defined function in the sense of
assigning a unique y to each x. The integrate function uses an adaptive
quadrature routine which probably makes multiple calls to the function
being integrated and expects to get the same y's for the same x's every
time.
If you want to get a number close to 20 (for your example) you need an
integration routine which will use single evaluation of your function at
each value of x. A simple method like rectangular approximation on a grid
or the so-called trapezoidal rule will do just that.
Here is a very crude prototype of such an integrator:
integrate1 - function(f, lower, upper){
f - match.fun(f)
xx - seq(lower, upper, length=100)
del - xx[2] - xx[1]
yy - f(xx[-100])
return(del*sum(yy))
Now when you run integrate1(my.fun, -10, 10) you will get a number close to
20 but, of course, every time you do it you will get a different value.
Hope this helps,
Andy
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Santanu
Pramanik
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[R] integrate
08/22/2007 02:56
PM
Hi,
I am trying to integrate a function which is approximately constant
over the range of the integration. The function is as follows:
my.fcn = function(mu){
+ m = 1000
+ z = 0
+ z.mse = 0
+ for(i in 1:m){
+ z[i] = rnorm(1, mu, 1)
+ z.mse = z.mse + (z[i] - mu)^2
+ }
+ return(z.mse/m)
+ }
my.fcn(-10)
[1] 1.021711
my.fcn(10)
[1] 0.9995235
my.fcn(-5)
[1] 1.012727
my.fcn(5)
[1] 1.033595
my.fcn(0)
[1] 1.106282
The function takes the value (approx) 1 over the range of mu. So the
integration result should be close to 20 if we integrate over (-10, 10).
But R gives:
integrate(my.fcn, -10, 10)
685.4941 with absolute error 7.6e-12
integrate(Vectorize(my.fcn), -10, 10) # this code never terminate
I have seen in the ?integrate page it is clearly written:
If the function is approximately constant (in particular, zero) over
nearly all its range it is possible that the result and error estimate
may be seriously wrong.
But this doesn't help in solving the problem.
Thanks,
Santanu
JPSM, 1218J Lefrak Hall
University of Maryland, College Park
Phone: 301-314-9916
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Re: [R] Moving data from one workspace to another
Walter, Here is what I do in similar situations. I am on WinXP but this should be similar on other systems (I hope). 1. I start R with the new .RData workspace (usually by double-clicking on it). 2. I go to File Change Dir menu item. 3. I change the directory to where the old .RData is. 4. I do attach(.RData) The old .RData is no in position 2 of the search path. You can see what is there by doing ls(2). Then you can copy anything, say a data frame named dd, by just doing dd - dd. Cheers, Andy __ Andy Jaworski 518-1-01 Process Laboratory 3M Corporate Research Laboratory - E-mail: [EMAIL PROTECTED] Tel: (651) 733-6092 Fax: (651) 736-3122 Walter R. Paczkowski [EMAIL PROTECTED] To rthlink.net r-help@stat.math.ethz.ch Sent by: cc [EMAIL PROTECTED] at.math.ethz.ch Subject [R] Moving data from one workspace to another 08/01/2007 04:27 PM Hi, Suppose I have a dataframe in one workspace (a .RData file) dedicated to one project. I then create a new workspace (a new .RData file) for another project but I want to move or copy the dataframe to the new workspace. How can I do this efficiently? Just do a dump and then a source? Is there another way? Thanks, Walt Paczkowski _ Walter R. Paczkowski, Ph.D. Data Analytics Corp. 44 Hamilton Lane Plainsboro, NJ 08536 (V) 609-936-8999 (F) 609-936-3733 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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] beta regressions in R
Walter, There is a betareg package in CRAN. Cheers, Andy __ Andy Jaworski 518-1-01 Process Laboratory 3M Corporate Research Laboratory - E-mail: [EMAIL PROTECTED] Tel: (651) 733-6092 Fax: (651) 736-3122 Walter R. Paczkowski [EMAIL PROTECTED] To rthlink.net r-help@stat.math.ethz.ch Sent by: cc [EMAIL PROTECTED] at.math.ethz.ch Subject [R] beta regressions in R 07/28/2007 11:09 AM Good morning, Does anyone know of a package or function to do a beta regression? Thanks, Walt Paczkowski _ Walter R. Paczkowski, Ph.D. Data Analytics Corp. 44 Hamilton Lane Plainsboro, NJ 08536 (V) 609-936-8999 (F) 609-936-3733 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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] Bad optimization solution
Paul,
I think the problem is the starting point. I do not remember the details
of the BFGS method, but I am almost sure the (.5, .5) starting point is
suspect, since the abs function is not differentiable at 0. If you perturb
the starting point even slightly you will have no problem.
Andy
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Subject
[R] Bad optimization solution
05/07/2007 04:30
PM
Dear All
I am trying to perform the below optimization problem, but getting
(0.5,0.5) as optimal solution, which is wrong; the correct solution
should be (1,0) or (0,1).
Am I doing something wrong? I am using R 2.5.0 on Fedora Core 6 (Linux).
Thanks in advance,
Paul
--
myfunc - function(x) {
x1 - x[1]
x2 - x[2]
abs(x1-x2)
}
optim(c(0.5,0.5),myfunc,lower=c(0,0),upper=c(1,1),method=L-BFGS-B,control=list(fnscale=-1))
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Re: [R] A problem with svIDE in Tinn-R?
Similar thing here. Happens in 2.5.0 patched and 2.6.0 (both April-25-2007) and svIDE 0.9-5 The only difference is that the warnings are: 1: '\A' is an unrecognized escape in a character string 2: unrecognized escape removed from ;for Options\AutoIndent: 0=Off, 1=follow language scoping and 2=copy from previous line\n Andy __ Andy Jaworski 518-1-01 Process Laboratory 3M Corporate Research Laboratory - E-mail: [EMAIL PROTECTED] Tel: (651) 733-6092 Fax: (651) 736-3122 Kenneth Cabrera [EMAIL PROTECTED] .co To Sent by: r-help@stat.math.ethz.ch [EMAIL PROTECTED] r-help@stat.math.ethz.ch at.math.ethz.chcc Subject 04/29/2007 09:38 [R] A problem with svIDE in Tinn-R? PM Hi R users: I want to know if any one of you had the problem with Tinn-R, when you call the library svIDE on the new R 2.5.0, (because in the old R 2.4.1 works with out any problem). I got this message: library(svIDE) Loading required package: tcltk Loading Tcl/Tk interface ... done Warning messages: 1: '\A' is an unrecognized escape in a character string 2: no se reconoce el valor 'save' Is it a critical warning? What would work and what not? What is it new in the new version that is not in the old version that makes this message appears? Thank you for your help. -- Kenneth Roy Cabrera Torres Cel 315 504 9339 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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] Computing the rank of a matrix.
How about qr(A)$rank or perhaps qr(A, LAPACK=TRUE)$rank Cheers, Andy __ Andy Jaworski 518-1-01 Process Laboratory 3M Corporate Research Laboratory - E-mail: [EMAIL PROTECTED] Tel: (651) 733-6092 Fax: (651) 736-3122 José Luis Aznarte M. [EMAIL PROTECTED] To .ugr.es r-help@stat.math.ethz.ch Sent by: cc [EMAIL PROTECTED] at.math.ethz.ch Subject [R] Computing the rank of a matrix. 04/06/2007 06:39 AM Hi! Maybe this is a silly question, but I need the column rank (http://en.wikipedia.org/wiki/Rank_matrix) of a matrix and R function 'rank()' only gives me the ordering of the elements of my matrix. How can I compute the column rank of a matrix? Is there not an R equivalent to Matlab's 'rank()'? I've been browsing for a time now and I can't find anything, so any help will be greatly appreciated. Best regards! -- -- Jose Luis Aznarte M. http://decsai.ugr.es/~jlaznarte Department of Computer Science and Artificial Intelligence Universidad de Granada Tel. +34 - 958 - 24 04 67 GRANADA (Spain) Fax: +34 - 958 - 24 00 79 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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] Integer Optimization
Dimitri, I am assuming you mean integer linear optimization problem. Try lpSolve. I think you will find it much easier to use. Cheers, Andy __ Andy Jaworski 518-1-01 Process Laboratory 3M Corporate Research Laboratory - E-mail: [EMAIL PROTECTED] Tel: (651) 733-6092 Fax: (651) 736-3122 Mahieux Dimitri dimitri.mahieux@ student.uclouvain To .be r-help@stat.math.ethz.ch Sent by: cc [EMAIL PROTECTED] at.math.ethz.ch Subject [R] Integer Optimization 03/21/2007 06:42 AM Hello everybody, I am looking for a function (or package) which can solve a integer optimization problem. I have found the glpk package but I don't known very well how to use it. Someone has another solution ? thx __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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] mixture of 2 normals - starting values
Hi, I have a problem of estimating a mixture of two normal distributions. I need to find the starting points automatically, since this is a part of a larger piece of image processing code. I found the mix2normal1 function in VGAM package that mentions a method of finding starting values for mu1 and mu2 but refers the reader to a book by Everitt and Hand. Unfortunately, I do not have an easy access to this book. Could anybody point me to a description of the method that I could use? Any help will be appreciated. Thanks in advance, Andy __ Andy Jaworski 518-1-01 Process Laboratory 3M Corporate Research Laboratory - E-mail: [EMAIL PROTECTED] Tel: (651) 733-6092 Fax: (651) 736-3122 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] matrix - change values
Rob, Try a[a5]-0 Yup. It works for matrices (and for arrays). It also works with the replacement value being a vector. For example, try b - array(1:24, dim=c(3, 4, 2)) b[(b8) (b17)] - 101:108 I think the reason it works like this is that internally array are stored as vectors. Cheers, Andy __ Andy Jaworski 518-1-01 Process Laboratory 3M Corporate Research Laboratory - E-mail: [EMAIL PROTECTED] Tel: (651) 733-6092 Fax: (651) 736-3122 [EMAIL PROTECTED] 2.pl Sent by: To [EMAIL PROTECTED] r-help@stat.math.ethz.ch at.math.ethz.chcc Subject 12/14/2006 08:01 [R] matrix - change values AM Dear R Users, I have a matrix A, and I want to change every value of this matrix if these values are greater than an assuming value. For a vector it is simple, e.g. a-c(1:10); a[a5]-0. Of course, I can change matrix to vector, assign a value then change vector to matrix. But does there exist simpler way? Any suggestion are appreciate. Rob __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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] Gantt chart problem after upgrade to R 2.4.0
This is interesting. I am on Win2000 running R version 2.4.0 Patched
(2006-11-15 r39915) and plotrix 2.1.5. I get the plot that scaled a little
differently that the 2.3.1 example but the dates look fine. I ran the
original code posted by John cane with no changes (copy and paste). I used
the windows device and did Save As... to save the PDF file.
Here is the code:
require(plotrix)
Ymd.format - %Y/%m/%d
Ymd - function(x){ as.POSIXct(strptime(x, format=Ymd.format))}
gantt.info - list(
labels=c(Dickens, Doyle,Kipling, Poe),
starts=Ymd(c(1824/01/01, 1850/01/01, 1865/01/01, 1815/11/01)),
ends=Ymd(c(1901/01/01, 1922/01/01, 1935/01/01, 1867/01/01)),
priorities =c(1,2,2,4))
gantt.chart(gantt.info,main=Writers,
xlim=as.POSIXct(c(1810/01/01,1940/01/01)))
Here is the result:
(See attached file: plot.pdf)
Cheers,
Andy
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No No
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Subject
Re: [R] Gantt chart problem after
11/17/2006 03:35 upgrade to R 2.4.0
PM
I am on ubuntu linux with R 2.4.0 compiled and I get the same picture
as with yours with R 2.4.0.
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plot.pdf
Description: Adobe PDF document
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Re: [R] Query about using table
Lalitha, Try something like with(data, table(cut(age, n), member_FLAG)) where data is a data frame with columns named age and member_FLAG and n is the number of age categories (bins) you want. This will give you the number of Ys and Ns in each bin, that you will need to convert to percentages. Also, you might want to check the help pages for table and cut. Cheers, Andy __ Andy Jaworski 518-1-01 Process Laboratory 3M Corporate Research Laboratory - E-mail: [EMAIL PROTECTED] Tel: (651) 733-6092 Fax: (651) 736-3122 lalitha viswanath lalithaviswanath @yahoo.comTo Sent by: r-help@stat.math.ethz.ch [EMAIL PROTECTED] cc at.math.ethz.ch Subject [R] Query about using table 10/26/2006 01:44 PM Hi I have data of the following form ID age member_FLAG 125 Y 236.75 N 375.5N . . I want to get a histogram of this data showing distribution of member_flag in each age-bin i.e. how many values in each age bin have a member_flag of 'Y' and how many have 'N'. I was able to do the same using barplot2. However I also need similar information in a tabular form using percentages. i.e in each age bin, what is the PERCENTAGE of IDs with a member_flag of 'Y' I am trying to work with table for the same, but would appreciate some guidance regarding the above. Thanks Lalitha __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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] compiling rgdal package on windows / macos
I just tried the PackagesInstall package(s).. menu item on my fresh R-2.4.0-patched and rgdal just shows up on the list of packages to install, so I am not sure what the problem is. Alternatively, you can download the Windows *.zip file from any CRAN repository and install it from your hard drive. Hope this helps, Andy __ Andy Jaworski 518-1-01 Process Laboratory 3M Corporate Research Laboratory - E-mail: [EMAIL PROTECTED] Tel: (651) 733-6092 Fax: (651) 736-3122 Dylan Beaudette dylan.beaudette@ gmail.com To Sent by: r-help@stat.math.ethz.ch [EMAIL PROTECTED] cc at.math.ethz.ch Subject [R] compiling rgdal package on 10/04/2006 05:46 windows / macos PM Please respond to [EMAIL PROTECTED] mail.com Greetings: As I am not a windows user, I cannot try this: is it possible to install rgdal on windows without having to compile it from source ? Compilation on MacOS is within my abilities, however each time i try and install the rgdal package it dies complaining that it cannot find gdal-config --- which was recently installed with GRASS. I have updated my PATH environment variable, logged out, but R still cannot find the gdal-config program. any tips on getting the rgdal package up and running on MacOS or Windows would be greatly appreciated. Cheers, -- Dylan Beaudette Soils and Biogeochemistry Graduate Group University of California at Davis 530.754.7341 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/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] Anybody ever notice...
I am guessing you are starting Rcmdr using library(Rcmdr). If this is the case, repeating the library command does nothing, since Rcmdr package is already attached. Try Commander() instead. Make sure you use capital C. Cheers, Andy __ Andy Jaworski 518-1-01 Process Laboratory 3M Corporate Research Laboratory - E-mail: [EMAIL PROTECTED] Tel: (651) 733-6092 Fax: (651) 736-3122 AKA [EMAIL PROTECTED] com To Sent by: r-help@stat.math.ethz.ch [EMAIL PROTECTED] cc at.math.ethz.ch Subject [R] Anybody ever notice... 06/12/2006 05:21 PM It could be a little bug or a fault in my setup but I notice that after I end an Rcmdr session I can't restart it without restarting Rgui (Windows) Do I need to add something to my environment variables? Is it an issue with Tcl/Tk or it's settings? Or what? It is not a big deal but if someone has a fix for this I would give it a shot I usually start Rcmd from the console library(Rcmdr) that have anything to do with it? __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] find position to last number in a vector
I am sure there are several ways of doing this but how about something like this: y - c(NA,NA,10,NA,2,NA,NA,1,NA,NA) x - c(10,20,30,40,50,60,70,80,85,100) tail(x[!is.na(y)], 1) or rev(x[!is.na(y)])[1] Rudimentary checks indicate that the second expression is much faster than the first. Also, if y is contains NAs only, the first expression returns numeric(0) and the second one NA. Hope this helps, Andy __ Andy Jaworski 518-1-01 Process Laboratory 3M Corporate Research Laboratory - E-mail: [EMAIL PROTECTED] Tel: (651) 733-6092 Fax: (651) 736-3122 Anders Bjørgesæter anders.bjorgesat To [EMAIL PROTECTED]r-help@stat.math.ethz.ch Sent by: cc [EMAIL PROTECTED] at.math.ethz.ch Subject [R] find position to last number in a vector 05/26/2006 01:30 PM Hello Is there a function to extract the position (i.e. row number or more desirable the value from another column with the same rownumber ) of last number in a vector? This is done in a loop with 1000s of columns. e.g. vector/column.n: na,na,10,na,2,na,na,1,na,na fixed column:10,20,30,40,50,60,70,80,85,100 result: 8 and/or 80 Thanks... Best Regards Anders __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R crashes during 'eigen'
It looks like there might be a bug in the symmetry detection routine of eigen. When I do eigen(M, symmetric=FALSE) it works fine. Eigenvalues (after omitting their imaginary parts, which are essentially zeros) are the same as the ones obtained with EISPACK to within a small multiple of machine epsilon. However, the eigenvector matrices seem different ! This happens on R-2.2.1-patched and R-2.3.0 (both compiled from daily snapshots). Andy PS. My system is Windows 2000 on a Xeon CPU. I use precompiled Pentium 4 Rblas DLL from CRAN, but the same thing happens with standard Rblas. __ Andy Jaworski 518-1-01 Process Laboratory 3M Corporate Research Laboratory - E-mail: [EMAIL PROTECTED] Tel: (651) 733-6092 Fax: (651) 736-3122 C.J.Albers [EMAIL PROTECTED] ac.uk To Sent by: r-help@stat.math.ethz.ch [EMAIL PROTECTED] cc at.math.ethz.ch Subject [R] R crashes during 'eigen' 03/28/2006 10:01 AM Hi all, Hi, When I want to compute the eigenvalues eigenvectors of a specific matrix, R crashes (i.e. it stops responding to any input). I've tried it with different versions of R (2.1.1, 2.2.0, 2.2.1) - all with crashing as result. What I did before the crash was: M - as.matrix(read.table(thematrix,header=T)) eigen(M) If, instead of eigen(M), I use eigen(M, EISPACK=T), R doesn't crash. So, I know a workaround my problem, but still don't understand why R crashes. Could anyone explain this? In case someone wants to download my matrix to see where it goes wrong, it can be downloaded from http://mcs.open.ac.uk/cja235/thematrix (warning: obviously, R might crash so save your unsaved work first). thanks, Casper Albers [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] bivariate normal distribution
Check out the mvtnorm package. Cheers, Andy __ Andy Jaworski 518-1-01 Process Laboratory 3M Corporate Research Laboratory - E-mail: [EMAIL PROTECTED] Tel: (651) 733-6092 Fax: (651) 736-3122 He, Yulei [EMAIL PROTECTED] rd.eduTo Sent by: r-help@stat.math.ethz.ch [EMAIL PROTECTED] cc at.math.ethz.ch Subject [R] bivariate normal distribution 02/13/2006 04:11 PM Hi, there. Does anyone know the R function for calculating the cdf of bivariate normal distribution function? Thanks. Yulei [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] nls() fit to Kahnemann/ Tversky function
Mark, The parameter of your model (gamma) should not be a part of the dataframe. In addition, the start argument should be a named list. Something like this works nls.dataframe - data.frame(p.kum,felt.prob.kum) nls.kurve - nls( formula = felt.prob.kum ~ p.kum^gamma/(p.kum^gamma+(1-p.kum)^gamma)^(1/gamma), data=nls.dataframe, start=list(gamma=.5), trace=TRUE) # trace shows convergence of the algorithm. but the fit is not very good as the fitted gamma is essentially 1. Hope this helps, Andy __ Andy Jaworski 518-1-01 Process Laboratory 3M Corporate Research Laboratory - E-mail: [EMAIL PROTECTED] Tel: (651) 733-6092 Fax: (651) 736-3122 Mark Hempelmann [EMAIL PROTECTED] e To Sent by: r-help@stat.math.ethz.ch [EMAIL PROTECTED] cc at.math.ethz.ch Subject [R] nls() fit to Kahnemann/ Tversky 10/31/2005 04:14 function PM Dear WizaRds, I would like to fit a curve to ten points with nls() for one unknown parameter gamma in the Kahnemann/ Tversky function, but somehow it won't work and I am unable to locate my mistake. p.kum - seq(0.1,1, by=0.1) felt.prob.kum - c(0.16, 0.23, 0.36, 0.49, 0.61, 0.71, 0.85, 0.89, 0.95, 1) ## how to find a function that fits these points nicely? plot(p.kum, felt.prob.kum) ## looks a little like an S gamma - rep(0.5, 10) nls.dataframe - data.frame(p.kum,felt.prob.kum, gamma) nls.kurve - nls( formula = felt.prob.kum ~ p.kum^gamma/(p.kum^gamma+(1-p.kum)^gamma)^(1/gamma), data=nls.dataframe, start=c(gamma=gamma), algorithm=plinear ) summary(nls.kurve) gives: Error in La.chol2inv(x, size) : 'size' cannot exceed nrow(x) = 10 If I go with the Gauss-Newton algorithm I get an singular gradient matrix error, so I tried the Golub-Pereyra algorithm for partially linear least-squares. It also seems the nls model tries to find ten different gammas, but I want only one single gamma parameter for the function. I appreciate your help and support. Thank you. sol lucet omnibus Mark Hempelmann __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] does column exist?
There may be a simpler way, but this is.na(match(X, names(df))) should return TRUE if the column name exists and FALSE otherwise. Cheers, Andy __ Andy Jaworski 518-1-01 Process Laboratory 3M Corporate Research Laboratory - E-mail: [EMAIL PROTECTED] Tel: (651) 733-6092 Fax: (651) 736-3122 Omar Lakkis [EMAIL PROTECTED] m To Sent by: r-help@stat.math.ethz.ch [EMAIL PROTECTED] cc at.math.ethz.ch Subject [R] does column exist? 05/19/2005 12:42 PM Please respond to Omar Lakkis [EMAIL PROTECTED] m How do I test if a data.frame has a column named X? exists(o) checks if the object exists or not, I want to test if a data.frame object (df) has a column names(X), something like: exists(df$X) __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] slowness of plot(x, type='l')
Thanks for the quick response and apologies for my sloppy post (nor mentioning the device) and sloppy example (the use of date()). Indeed, I was using the windows device. There is no timing problem with the postscript device. I just installed the R-devel May-9 and the problem went away. Here is an example: n - 15000 system.time(plot(rnorm(n), type='l')) [1] 0.07 0.41 0.48 NA NA An interesting footnote is the fact that the slowdown of the windows device did not happen for plot(*, type='c'). The 'c' option plots line segments without points, so it probably used the bunches of lines anyway. Andy __ Andy Jaworski 518-1-01 Process Laboratory 3M Corporate Research Laboratory - E-mail: [EMAIL PROTECTED] Tel: (651) 733-6092 Fax: (651) 736-3122 Prof Brian Ripley [EMAIL PROTECTED] ac.uk To Sent by: [EMAIL PROTECTED] [EMAIL PROTECTED] cc at.math.ethz.ch r-help@stat.math.ethz.ch Subject Re: [R] slowness of plot(x, 05/07/2005 12:36 type='l') AM Plotting times depend on the graphics device. That is nowhere mentioned here, which is unhelpful, and we have already seen a post saying it does not happen on another unmentioned device (presumably X11). Let us assume the unmentioned device was windows(), as that is the only one I see any slowdown for. (Others like win.metafile are windows() under the skin.) On Fri, 6 May 2005 [EMAIL PROTECTED] wrote: A couple of days ago a few messages indicated that something changed in the basic plot routine that made plot(*, type='l') slow for large data sets. Some people even reported crashes for very large data sets. As far as I remember, this was not reported as a formal bug. Well, _is_ there a bug in R (as distinct from in Windows graphics internals)? I am almost certain there is not in R and this is a bug in Windows. I am still not sure if this is a bug, so I report my findings here. First of all, I think I see a slowdown of the plot function, although I do not have older versions of R installed, so I cannot do side-by-side comparisons. Secondly, I noticed that the behavior of plot(*, type='l') differs. Before R-2.1, the plotted lines would appear on the plot gradually. Now, after the wait, the whole plot appears at once. Here are my timing results. I am on Windows2000, IBM Intellistation with Xenon 2.8MHz with 1Gb of memory. I checked May-06 versions of R-patched and R-devel built from sources. I ran the following simple test: x - rnorm(n) date(); plot(x, type='l'); date() Oh, PLEASE, use system.time() to time things. Had you done so you might have seen things like windows() n - 1 system.time(plot(rnorm(n), type=l)) [1] 0.03 13.11 13.21NANA postscript() system.time(plot(rnorm(n), type=l)) [1] 0.07 0.00 0.08 NA NA dev.off() system.time(plot(rnorm(n), type=p)) [1] 0.07 0.93 1.00 NA NA so the time is not being taken by R but by Windows. I can tell you the reason: it is the support for mitred etc line ends introduced in R 2.0.0 and only supported in windows() from 2.1.0. This has slowed solid lines down to the sort of times taken for dashed lines previously. Now, the best we can do to work around this is to follow what we did for dashed lines, and not attempt to be accurate for very large numbers of line segments. By plotting in bunches of 1000 lines I get system.time(plot(rnorm(n), type=l)) [1] 0.03 0.36 0.42 NA NA system.time(plot(rnorm(n), type=l, lty=3)) [1] 0.22 2.89 3.11 NA NA We have been here before, and as I recall this slowdown happens only in NT-based versions of Windows which seem _de facto_ restricted to about 1000 line elements in a path: what we were not aware of was that it happened for solid lines as well as dashed ones. I've put the bunching into R-patched. It is very regretable that this sort of thing was not tested for during beta-testing. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics,
[R] slowness of plot(x, type='l')
A couple of days ago a few messages indicated that something changed in the basic plot routine that made plot(*, type='l') slow for large data sets. Some people even reported crashes for very large data sets. As far as I remember, this was not reported as a formal bug. I am still not sure if this is a bug, so I report my findings here. First of all, I think I see a slowdown of the plot function, although I do not have older versions of R installed, so I cannot do side-by-side comparisons. Secondly, I noticed that the behavior of plot(*, type='l') differs. Before R-2.1, the plotted lines would appear on the plot gradually. Now, after the wait, the whole plot appears at once. Here are my timing results. I am on Windows2000, IBM Intellistation with Xenon 2.8MHz with 1Gb of memory. I checked May-06 versions of R-patched and R-devel built from sources. I ran the following simple test: x - rnorm(n) date(); plot(x, type='l'); date() Here are the timings: n seconds 5000 1 6000 2 7000 4 8000 6 9000 9 1 13 12000 22 14000 36 2 91 It looks like only type='l' and type='o' exhibit this behavior. All other types produce plots in approximately 1 second. Also, the (long) wait and plot at once behavior happens with the two types mentioned. All others (except 'n' of course) produce gradually appearing plots. Hope this helps, Andy __ Andy Jaworski 518-1-01 Process Laboratory 3M Corporate Research Laboratory - E-mail: [EMAIL PROTECTED] Tel: (651) 733-6092 Fax: (651) 736-3122 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Unbundling gregmisc (was: loading gap package)
I have one comment, although it is a little off topic. I have the gregmisc package installed (R-2.0.1 on Win2000). Whenever I use the help.search function it comes back with the following warning: Warning message: no Rd contents for package 'gregmisc' in 'C:/local/R/rw210/library' in: help.search(bundle) Apparently, the help.search function looks for the CONTENTS file in the .../library/gregmisc directory. I created an empty one and the warning went away. I know it is purely cosmetic, but if the gregmisc bundle is kept intact, and I think it should, I would suggest adding the empty CONTENTS file to its distribution. Perhaps there is a better way of handling this. For example, VR is a bundle but it does not create its VR directory in .../library. Andy __ Andy Jaworski 518-1-01 Process Laboratory 3M Corporate Research Laboratory - E-mail: [EMAIL PROTECTED] Tel: (651) 733-6092 Fax: (651) 736-3122 Warnes, Gregory R gregory.r.warnes To @pfizer.com 'Constantinos Antoniou' Sent by: [EMAIL PROTECTED], Prof Brian Ripley [EMAIL PROTECTED] [EMAIL PROTECTED] at.math.ethz.chcc R-help@stat.math.ethz.ch, Uwe Ligges 05/04/2005 09:56 [EMAIL PROTECTED] AMSubject [R] Unbundling gregmisc (was: loading gap package) Let me redirect the topic a bit. I've been considering unbundling gregmisc. The pro would be that people would find the component packages (i.e. gdata) more easily. The con is that the packages have a number of interdependencies, so you pretty much will need to get most of them anyway. As the latest gregmisc bundle contains a gregmisc package that is just a stub that depends on and loads the individual packages, there would still be a gregmisc object. Comments? -Greg -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Behalf Of Constantinos Antoniou Sent: Wednesday, May 04, 2005 6:36 AM To: Prof Brian Ripley Cc: R-help@stat.math.ethz.ch; Uwe Ligges Subject: Re: [R] loading gap package =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- =-=-=-=-= !!! IMPORTANT NOTICE !!! This email was addressed to you from the Internet using a legacy E-Mail Domain address. This email domain will no longer be in service on the Internet after 15 July 2005. If this is legitimate business email, please inform the sender to address all future correspondence to your @pfizer.com address. The original text of this email appears below this notice. =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- =-=-=-=-= On 4 2005, at 12:06 , Prof Brian Ripley wrote: On Wed, 4 May 2005, Constantinos Antoniou wrote: On 4 2005, at 11:35 , Uwe Ligges wrote: Eduwin Pakpahan wrote: Dear R users, I did install R. 2.0.1, and try to load gap package. However, below is the message shown when I did load it. Can anybody please let me know my mistakes? library() library(gap) Loading required package: MASS Loading required package: genetics Loading required package: combinat Loading required package: gdata Error: package 'gdata' could not be loaded In addition: Warning message: There is no package called 'gdata' in: library(pkg, character.only = TRUE, logical = TRUE, lib.loc = lib.loc) Let me read the error message for you: There is no package 'gdata' simply means the package is not there... So what about installing it? Hint: it is part of the package bundle gregmisc. I have a similar problem with R 2.1.0 on Mac OSX 10.3.9. library(gregmisc) Loading required package: gdata Error: package 'gdata' could not be loaded In addition: Warning message: there is no package called 'gdata' in: library(pkg, character.only = TRUE, logical = TRUE, lib.loc = lib.loc) At first I tried
Re: [R] multivariate Shapiro Wilks test
Anna, It looks like the mshapiro.test wants its data in the row format, that is, for a k-variate sample of size n you need the data in a k-by-n matrix. Try a - t(mvrnorm(1000, c(1,2,3,4,5), diag(5))) mshapiro.test(a) and it should work fine. Cheers, Andy __ Andy Jaworski 518-1-01 Process Laboratory 3M Corporate Research Laboratory - E-mail: [EMAIL PROTECTED] Tel: (651) 733-6092 Fax: (651) 736-3122 Anna Oganyan [EMAIL PROTECTED] g To Sent by: r-help@stat.math.ethz.ch [EMAIL PROTECTED] cc at.math.ethz.ch Subject [R] multivariate Shapiro Wilks test 05/03/2005 04:29 AM Hello, I have a question about multivariate Shapiro-Wilks test. I tried to analyze if the data I have are multivariate normal, or how far they are from being multivariate normal. However, any time I did mshapiro.test(mydata) I get the message: Error in solve.default(R %*% t(R), tol = 1e-18) : system is computationally singular: reciprocal condition number = 5.38814e-021 I tried also to generate some multivariate normal data and to see how the test would be working on it. So I did: a - mvrnorm(1000, c(1,2,3,4,5), diag(5)) mshapiro.test(a) But any time I get: Error in solve.default(R %*% t(R), tol = 1e-18) : system is computationally singular: reciprocal condition number = small number Could somebody help me what is wrong with this example? Thank you very much in advance! Anna __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] half-normal residual plots
There is a halfnorm function in the faraway package. Andy __ Andy Jaworski 518-1-01 Process Laboratory 3M Corporate Research Laboratory - E-mail: [EMAIL PROTECTED] Tel: (651) 733-6092 Fax: (651) 736-3122 MJ Price, Social Medicine [EMAIL PROTECTED] To istol.ac.uk r-help@stat.math.ethz.ch Sent by: cc [EMAIL PROTECTED] at.math.ethz.ch Subject [R] half-normal residual plots 04/07/2005 08:43 AM Hi all, I am trying to produce a half-normal plot of residuals from a GLM. I have found the qqnorm function for producing a normal plot but can't figure out how to produce a half-normal. Can anyone help with this? Thanks Malcolm -- MJ Price, Social Medicine [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] looking for a plot function
I am not sure about the scaling, but doing simply
matplot(xa, t(dfr), type=b)
does most of what you want.
Andy
__
Andy Jaworski
518-1-01
Process Laboratory
3M Corporate Research Laboratory
-
E-mail: [EMAIL PROTECTED]
Tel: (651) 733-6092
Fax: (651) 736-3122
Doran, Harold
[EMAIL PROTECTED]
Sent by: To
[EMAIL PROTECTED] bogdan romocea
at.math.ethz.ch [EMAIL PROTECTED],
r-help@stat.math.ethz.ch
cc
04/06/2005 03:24
PMSubject
RE: [R] looking for a plot function
If your data were in the long format you could use interaction.plot.
But, I think trellis plots in lattice are much better than this
approach.
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of bogdan romocea
Sent: Wednesday, April 06, 2005 4:19 PM
To: r-help@stat.math.ethz.ch
Subject: [R] looking for a plot function
Dear useRs,
I have a data frame and I want to plot all rows. Each row is represented
as a line that links the values in each column. The plot looks like
this:
dfr - data.frame(A=sample(1:50,10),B=sample(1:50,10),
C=sample(1:50,10),D=sample(1:50,10))
xa - 10*1:4
plot(c(10,40),c(0,50))
for (i in 1:nrow(dfr)) {
lines(xa,dfr[i,],pch=20,type=o)
}
Things get more complicated because I want the columns to be rescaled so
as to fit nicely on a graph (for example if A has values between 0 and
100 but B has values between 100 and 1000, then rescale A or B), labels
etc. Is there a function that can do plots like this?
Thank you,
b.
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Re: [R] plotmath question
Bert, This works fine and and seems a little simpler: x-seq(-3,to=3,by=.01) y-dnorm(x) plot(x,y,type='h',col='lightblue',axes=FALSE) lines(x,y,col='darkblue') axis(2) ll - expression(mu-3*sigma, mu-2*sigma, mu-sigma, mu, mu+sigma, mu+2*sigma, mu+3*sigma) axis(1, at=-3:3, lab=ll) box() Cheers, Andy __ Andy Jaworski 518-1-01 Process Laboratory 3M Corporate Research Laboratory - E-mail: [EMAIL PROTECTED] Tel: (651) 733-6092 Fax: (651) 736-3122 Berton Gunter [EMAIL PROTECTED] ne.comTo Sent by: 'R-help' [EMAIL PROTECTED] r-help@stat.math.ethz.ch at.math.ethz.chcc Subject 03/18/2005 03:41 [R] plotmath question PM R listers: I have been foiled by plotmath! (in R 2.01,Windows 2000) The task: Plot a normal density and label the ticks as mu - 3 sigma, mu - 2 sigma, , mu + 3 sigma, where the mu's and sigmas appear as Greek symbols, of course. The following code does this: x-seq(-3,to=3,by=.01) y-dnorm(x) plot(x,y,type='h',col='lightblue',axes=FALSE) lines(x,y,col='darkblue') axis(2) for(i in seq(-3,to=3)) axis(1,at=i, lab=switch(sign(i)+2, eval(substitute(expression(mu-j*sigma),list(j=-i))), expression(mu), eval(substitute(expression(mu+j*sigma),list(j=i) box() However, I think the code in the for loop is ugly and probably means that I'm doing it wrong. In particular: 1) Is there a neat way to use one axis() call and a vector (of expressions?) for the lab=argument? 2) The plotmath Help state that expressions can be used for axis labels, so I would have expected the above to work without the eval()call -- but it does not. Would someone kindly explain to me why not -- i.e., what I have misunderstood. That is, to be clear, why does the following not work: for(i in seq(-3,to=3)) axis(1,at=i, lab=switch(sign(i)+2, substitute(expression(mu-j*sigma),list(j=i)), expression(mu), substitute(expression(mu+j*sigma),list(j=i Any further ideas,insights, or pointers to reference materials would also be appreciated. Many thanks. -- Bert Gunter Genentech Non-Clinical Statistics South San Francisco, CA The business of the statistician is to catalyze the scientific learning process. - George E. P. Box __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] A question about r-help-bounce
Could somebody please tell me what does the r-help-bounce address do? When I try to respond to an r-help post, my mailer (Lotus Notes) generates the r-help bounce return address automatically in addition to the original sender address and the r-help address. I responded to an r-help message last night and I never saw my response posted. Could this be due to the r-help-bounce being there? Thanks in advance, Andy __ Andy Jaworski 518-1-01 Process Laboratory 3M Corporate Research Laboratory - E-mail: [EMAIL PROTECTED] Tel: (651) 733-6092 Fax: (651) 736-3122 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Graphical table in R
The outer two lines could also be done more easily (?) by: library(gplots) #part of gregmisc bundle textplot(txt) Check ?textplot for additional options. Andy __ Andy Jaworski 518-1-01 Process Laboratory 3M Corporate Research Laboratory - E-mail: [EMAIL PROTECTED] Tel: (651) 733-6092 Fax: (651) 736-3122 Thomas Lumley [EMAIL PROTECTED] gton.edu To Sent by: Peter Dalgaard [EMAIL PROTECTED] [EMAIL PROTECTED] at.math.ethz.chcc [EMAIL PROTECTED], R list r-help@stat.math.ethz.ch 01/10/2005 03:28 Subject PMRe: [R] Graphical table in R On Mon, 10 Jan 2005, Peter Dalgaard wrote: A screen shot of a ps file? That sounds ... weird. If you can view it, presumably you have Ghostscript and that can do png files. However, will textual output do? plot(0,type=n,axes=FALSE, xlab=, ylab=) con - textConnection(txt,w) sink(con); ftable(UCBAdmissions); sink() close(con) par(family=mono) text(1,0,paste(txt,collapse=\n)) and the middle three lines could also be done with txt-capture.output(ftable(UCBAdmissions)) -thomas __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Make a table
Muhammad, Try tapply(prevRND.dat$Z, list(X=prevRND.dat$X, Y=prevRND.dat$Y), mean) Cheers, Andy __ Andy Jaworski 518-1-01 Process Laboratory 3M Corporate Research Laboratory - E-mail: [EMAIL PROTECTED] Tel: (651) 733-6092 Fax: (651) 736-3122 Muhammad Subianto [EMAIL PROTECTED] l To Sent by: [EMAIL PROTECTED] [EMAIL PROTECTED] cc at.math.ethz.ch Subject [R] Make a table 12/22/2004 07:26 AM Dear useR, I have a dataset like this below, prevRND.dat - read.table(C:\\workdir\\prevRND.txt, + header=FALSE, # No header. + col.names = c(X,Y,Z), + sep = ,) prevRND.dat X YZ 1 A A 0.950933 2 A B 0.143600 3 A C 0.956133 4 B A 0.000533 5 B B 0.986467 6 B C 0.032066 7 C A 0.005333 8 C B 0.00 9 C C 0.009266 How can I make that data above as table, Y XA B C A 0.950933 0.143600 0.956133 B 0.000533 0.986467 0.032066 C 0.005333 0.00 0.009266 I cannot use table() or ftable() functions because the 3rd column (Z) is probability. Are there any function to make a table as I want? Kind regards, Muhammad Subianto __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] switching to Linux, suggestions?
The newest production release of Fedora is Core 3. I would use this one if I were you. Andy __ Andy Jaworski 518-1-01 Process Laboratory 3M Corporate Research Laboratory - E-mail: [EMAIL PROTECTED] Tel: (651) 733-6092 Fax: (651) 736-3122 Thomas Schönhoff [EMAIL PROTECTED] nfo.org To Sent by: R User-Liste [EMAIL PROTECTED] [EMAIL PROTECTED] at.math.ethz.chcc Subject 12/13/2004 10:22 Re: [R] switching to Linux, AMsuggestions? Hello, Thomas W Volscho schrieb: Dear List, I have acquired a new desktop and wanted to put a free OS on it. I am trying Fedora Core 1, but not sure what the best Linux OS is for using R 2.0.1? R is developed on Linux, so there shouldn't be too much restrictions on whatever distri you're going to use! If running a new shiny Desktop you might consider other aspects than using R, which should run with every Linux distribution. If you're looking for something comfortable to install and maintain you might give Quatian a try (http://dirk.eddelbuettel.com/quantian.html). This is a somewhat modified Knoppix trimmed to statistical analysis (not entirely, though) regards Thomas __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Non-Linear Regression on a Matrix
If your non-linear function (A, B) is parametric nls should do it for you. If you have R version 2 (perhaps even 1.9) do ?nls to see the help page. Older versions of R require library(nls) first. Hope this helps, Andy __ Andy Jaworski 518-1-01 Process Laboratory 3M Corporate Research Laboratory - E-mail: [EMAIL PROTECTED] Tel: (651) 733-6092 Fax: (651) 736-3122 Diana Abdueva [EMAIL PROTECTED] ail.com To Sent by: [EMAIL PROTECTED] [EMAIL PROTECTED] cc at.math.ethz.ch Subject [R] Non-Linear Regression on a 11/16/2004 08:33 Matrix PM Please respond to Diana Abdueva [EMAIL PROTECTED] ail.com Hi, I'm terribly sorry for submitting my primitive question, I'm a beginner in R and was hoping to get some help re: non-linear fit. I have a 2D data with the following structure: A BC 1 1 111 1 2 121 1 3 131 2 1 141 2 2 151 2 3 161 3 1 171 3 2 181 3 3 191 I'm trying to fit C = non-linear function (A,B). I was wondering if there's a package that would save my time of doing direct least square estimation. Thank you, Diana __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] xyplot and for loops
Dave,
I think inside the loop you have to explicitly print a trellis object,
i.e. say
print(yplot(tmp.df$y.tmp ~ tmp.df[,i]))
If you read the help page for xyplot, look under Value.
Hope this helps,
Andy
__
Andy Jaworski
518-1-01
Process Laboratory
3M Corporate Research Laboratory
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Tel: (651) 733-6092
Fax: (651) 736-3122
Dave Atkins
[EMAIL PROTECTED]
gton.edu To
Sent by: [EMAIL PROTECTED]
[EMAIL PROTECTED] cc
at.math.ethz.ch
Subject
[R] xyplot and for loops
05/04/2004 05:40
PM
I'm attempting to use xyplot() within a for() loop to plot the relationship
between a DV and a series of predictor variables, split by 2 conditioning
variables. However, xyplot() does not seem to be recognized within the
for()
loop; I don't receive any error message, but nothing is plotted and a
plotting
device is not opened. When I use the generic function plot(), everything
works
as expected. I'm using R v1.9.0 and lattice v0.9-11.
Here's a trivial example:
### create single outcome and two predictors
y.tmp - rnorm(20) ; x1.tmp - rnorm(20) ; x2.tmp - rnorm(20)
### combine into data.frame
tmp.df - data.frame(y.tmp, x1.tmp, x2.tmp)
tmp.df
y.tmp x1.tmp x2.tmp
1 1.5022759 -0.150326662 -1.36627981
[snip]
20 1.2667825 -0.070356651 -0.38433160
### simple loop calling the columns of tmp.df to specify x variables
for (i in 2:3){
+ plot(tmp.df$y.tmp ~ tmp.df[,i])
+ }
### works fine for plot()
### try the same with xyplot()
for (i in 2:3){
+ xyplot(tmp.df$y.tmp ~ tmp.df[,i])
+ }
### nothing happens; no error msg; no plotting device opened
xyplot(tmp.df$y.tmp ~ tmp.df[,2])
### without loop works fine and plots relationship of x1.tmp and y.tmp
Can someone see what I'm missing? Any directions/pointers appreciated.
cheers, Dave
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Re: [R] Matrix question
Gideon, Eigenvectors are normalized to unit length. The first eigenvector calculated by R is equal (ignoring the signs of course) to your stable distribution vector divided by its length. Andy __ Andy Jaworski 518-1-01 Process Laboratory 3M Corporate Research Laboratory - E-mail: [EMAIL PROTECTED] Tel: (651) 733-6092 Fax: (651) 736-3122 |-+ | | GIDEON WASSERBERG| | | [EMAIL PROTECTED]| | | Sent by: | | | [EMAIL PROTECTED]| | | ath.ethz.ch | | || | || | | 04/13/2004 18:28 | |-+ -| | | | To: [EMAIL PROTECTED] [EMAIL PROTECTED] | | cc: | | Subject: [R] Matrix question | -| Dear Friends I am doing a simple matrix analysis to calculate the eigenvalue, eigenvector using R for the below matrix, and comparing the result to those obtained from a projection (using excel) THE MATRIX: c [,1] [,2] [,3] [1,] 0.0 2.02 [2,] 0.8 0.00 [3,] 0.0 0.80 The dominant eigenvalue comes out comparable to that calculated numerically, but the eigenvectors do not( see below)! EIGENVALUES (calculated by R): eigen(c) $values [1] 1.5564082+0.00i -0.7782041+0.465623i -0.7782041-0.465623i EIGENVALUE numerically calculated: 1.556408145 EIGENVECTORS (calculated by R): $vectors [,1] [,2] [,3] [1,] -0.8658084+0i 0.6476861+0.000i 0.6476861+0.000i [2,] -0.4450290+0i -0.4902997-0.2933611i -0.4902997+0.2933611i [3,] -0.2287467+0i 0.2382837+0.4441499i 0.2382837-0.4441499i Stable age distribution (calculated numerically): 0.562365145 0.289057934 0.148576921 My questions are: 1. Both eigenvalue and eigenvectors are associated with some imaginary value (i). How should I relate to that information? 2. More importantly, a. I presume the 1st eigenvector collumn [,1] should correspond to the dominant eigenvalue. How come then that it comes out different from the one calculated numerically? Is there some conversion I should do? Many thanks Gideon Gideon Wasserberg (Ph.D.) Wildlife research unit, Department of wildlife ecology, University of Wisconsin 218 Russell labs, 1630 Linden dr., Madison, Wisconsin 53706, USA. Tel.:608 265 2130, Fax: 608 262 6099 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Xeon CPU and ATLAS
I am about to get a new machine at work - an IBM Intellistation with the Xeon 2.8 GB processor. It will run Windows 2000. I would like to install the proper ATLAS dll for this machine, but I am not sure if Xeon is P4? Does anybody have any experience with Xeon? Thanks in advance, Andy __ Andy Jaworski 518-1-01 Process Laboratory 3M Corporate Research Laboratory - E-mail: [EMAIL PROTECTED] Tel: (651) 733-6092 Fax: (651) 736-3122 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Xeon CPU and ATLAS
First of all thanks to Peter Dalgaard, Thomas Lumley and Prof Brian Ripley for quick responses. Indeed, I will be running Windows2000 on this machine (my company's standard). I will also install the full version of cygwin on it. When I asked my original question I thought about just copying the P4 dll from the ATLAS directory on CRAN. As I understand from the three answers I got, this should work, but perhaps not be the fastest BLAS possible. When I get the machine (beginning of April) I will try to configure and compile ATLAS and Goto and compare the results. Thanks again, Andy __ Andy Jaworski 518-1-01 Process Laboratory 3M Corporate Research Laboratory - E-mail: [EMAIL PROTECTED] Tel: (651) 733-6092 Fax: (651) 736-3122 |-+- | | Prof Brian Ripley | | | [EMAIL PROTECTED]| | | c.uk | | | | | | 03/12/2004 16:16 | | | | |-+- -| | | | To: Peter Dalgaard [EMAIL PROTECTED] | | cc: [EMAIL PROTECTED] | |[EMAIL PROTECTED] | | Subject: Re: [R] Xeon CPU and ATLAS | -| AFAIK all P4s are SSE2. He wants a Windows ATLAS build, and that is not hard, but you have to do that under Cygwin not MinGW. We have a Xeon, but have found Athlons and now Opterons better value. I don't have access to Windows Xeon machine: anyone who does could contribute a Xeon version of Rblas.dll (to Uwe Ligges, please). Note that for 1.9.0 you can use Goto's BLAS and he as a P4 version that is faster than ATLAS (under Windows). So I would start with that. Although Thomas Lumley is right about cache sizes, using a P4 512kb ATLAS or Goto BLAS is pretty good on a Xeon (only tested by me under Linux). Using a BLAS for too large a cache is disastrous, but underestimating by a factor of 2 is not bad at all. (I think most Xeons are 1Mb cache, with Xeon MP being 4Mb.) On 12 Mar 2004, Peter Dalgaard wrote: [EMAIL PROTECTED] writes: I am about to get a new machine at work - an IBM Intellistation with the Xeon 2.8 GB processor. It will run Windows 2000. I would like to install the proper ATLAS dll for this machine, but I am not sure if Xeon is P4? Does anybody have any experience with Xeon? Yes, we have a dual 2.8 Xeon running Linux. Very nice machine. We've had it for a bit more than a year and it's been of very good use. I can see that I did two ATLAS builds in feb 2003, one is called Linux_P4SSE2_2 and the other is Linux_Xeon_2. AFAIR (but it's been a while), the former is the preconfigured thing that came out of a quick-install and the other one is fully tuned version, and there was no difference worth speaking of between the two. I think the difference between P4 and Xeon is the SSE1 vs SSE2 thing, so you'd want the P4SSE2 DLL, but others may be able to speak more authoritatively. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] numerical equation
Check out the uniroot function. It will solve a single equation. There is also a packge RMinpack. It implements the original Fortran Minpack library and will solve systems of nonlinear equations. It is only available in source form (search Google for it). Andy __ Andy Jaworski 518-1-01 Process Laboratory 3M Corporate Research Laboratory - E-mail: [EMAIL PROTECTED] Tel: (651) 733-6092 Fax: (651) 736-3122 |-+ | | Abdou Ali| | | [EMAIL PROTECTED]| | | Sent by: | | | [EMAIL PROTECTED]| | | ath.ethz.ch | | || | || | | 03/10/2004 10:11 | | | Please respond to| | | Abdou.Ali| | || |-+ -| | | | To: [EMAIL PROTECTED] | | cc: | | Subject: [R] numerical equation | -| Hello, Is there R command to solve a nonlinear numerical equation. Thank you. __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] Statistical Quality Control
A new package named qcc just appeared on CRAN. It has standard QC charts, OC curves and process capability stuff. It even has a Minitab-like process capability sixpack. It looks like it is pretty nicely done. Andy __ Andy Jaworski 518-1-01 Process Laboratory 3M Corporate Research Laboratory - E-mail: [EMAIL PROTECTED] Tel: (651) 733-6092 Fax: (651) 736-3122 |-+ | | Nick Drew | | | [EMAIL PROTECTED] | | | Sent by: | | | [EMAIL PROTECTED]| | | ath.ethz.ch | | || | || | | 03/05/2004 19:00 | | | Please respond to| | | ndrew| | || |-+ -| | | | To: Holton, Blake [EMAIL PROTECTED] | |R-Help (E-mail) [EMAIL PROTECTED] | | cc: | | Subject: RE: [R] Statistical Quality Control | -| Just the other day I found this site, obtained the package, and tried some of the examples. http://www.cmis.csiro.au/S-PLUS/qtoolbox/index.html -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Behalf Of Holton, Blake Sent: Tuesday, February 24, 2004 11:23 AM To: R-Help (E-mail) Subject: [R] Statistical Quality Control Greetings, I've been familiarizing myself with the features of R over the past few days. I'm impressed with the quality and quantity of the features and packages. One feature that I would be interested in would be a package for statistical quality control. Does a package for statistical quality control exist that I've been unable to locate? If not, is anyone aware of efforts to develop a statistical quality control package? It has been awhile since I've coded in C, but I would be willing to contribute. Regards, Blake Blake Holton Technical Service Representative Dynea 475 28th Street Springfield, OR 97477-5100 Desk: 541.744.7238 Toll Free: 800.547.9525 FAX: 541.744.7249 Cell: 541.954.2696 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] test
I am trying to test whether I can post to the list. I responded to a couple of messages recently and I have not seen my response posted. __ Andy Jaworski 518-1-01 Process Laboratory 3M Corporate Research Laboratory - E-mail: [EMAIL PROTECTED] Tel: (651) 733-6092 Fax: (651) 736-3122 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Location of polr function
Peter, These things can be a little mysterious at the beginning. Lots of things in R are arranged in groups called packages (or libraries). Some basic ones come preinstalled with R, some you have to install yourself. If you type library() at your R prompt you should get a list of all packages installed on your system. In order to use the functionality of a package you have to load it by specifying its name as an argument to the library call. For example, library(nlme) will load the package named nlme (if it is installed on your system) and give you the functionality of the nlme package, i.e. access to its functions.. Typing search() will show you what packages are already loaded on your system. Search.help will allow you to find in which package your function resides in. Typing search.help(polr) on my system returns polr(MASS) Proportional Odds Logistic Regression meaning that the polr function belongs to the package MASS which is installed on your system. The only thing remaining to do is typing library(MASS) Of course, if MASS is not installed on your system you will get nothing in response (actually you will get a message saying that nothing appropriate was found). Then, you would need to go to a CRAN site and use their search engine to find things about polr function. Hope this helps, Andy __ Andy Jaworski 518-1-01 Process Laboratory 3M Corporate Research Laboratory - E-mail: [EMAIL PROTECTED] Tel: (651) 733-6092 Fax: (651) 736-3122 |-+--- | | Peter Flom [EMAIL PROTECTED]| | | Sent by:| | | [EMAIL PROTECTED]| | | ath.ethz.ch | | | | | | | | | 03/03/2004 14:42| | | | |-+--- -| | | | To: [EMAIL PROTECTED] | | cc: | | Subject: [R] Location of polr function | -| Hello I am running R 1.8.1 on a Windows platform I am attempting to fit an ordinal logistic regression model, using the polr function, as described in Venables and Ripley. But when I try model4 - polr(ypsxcat~committed + as.factor(sex) + as.factor(drugusey) + anycsw + as.factor(sex)*committed + as.factor(sex)*as.factor(drugusey)+as.factor(sex)*anycsw, data = duhray) I get a message that the polr function was not found. Any help appreciated thanks Peter Peter L. Flom, PhD Assistant Director, Statistics and Data Analysis Core Center for Drug Use and HIV Research National Development and Research Institutes 71 W. 23rd St www.peterflom.com New York, NY 10010 (212) 845-4485 (voice) (917) 438-0894 (fax) __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] bug in as.POSIXct ?
I think that there is a bug in the as.POSIXct function on Windows. Here is what I get on Win2000, Pentium III machine in R 1.8.1. dd1 - ISOdatetime(2003, 10, 26, 0, 59, 59) dd2 - ISOdatetime(2003, 10, 26, 1, 0, 0) dd2 - dd1 Time difference of 1.000278 hours Now, the 26th of October was the day that change to the standard time occurred, so I suspect that this has something to do with that. In fact dd1 [1] 2003-10-26 00:59:59 Central Daylight Time dd2 [1] 2003-10-26 01:00:00 Central Standard Time so it looks like the switch from CDT to CST happens at 1:00 (instead of 2:00 ?). Since the only thing the difftime function does is unclass the as.POSIXct values of its two arguments, the error seems to be in the as.POSIXct code. I looked at the C code of the as.POSIXct function but I do not know enough about R code and C handling of the time structures to find an error there. Perhaps, the error is actually in the C library handling of time structures on Windows machines. All this seems to work fine in version 1.8.1 patched 11-24 on a Linux machine, i.e. the above difference is 1second. However, the swicth between CDT and CSD also accurs at 1:00. Andy __ Andy Jaworski 518-1-01 Process Laboratory 3M Corporate Research Laboratory - E-mail: [EMAIL PROTECTED] Tel: (651) 733-6092 Fax: (651) 736-3122 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] Parameter estimation in nls
Your starting values for the parameters are no even in the general ballpark. Here is what I got for the final fit: Parameters: Estimate Std. Error t value Pr(|t|) a 3.806e+07 1.732e+06 21.971 2e-16 *** k -3.391e-02 6.903e-02 -0.4910.628 b 9.000e-01 1.240e-02 72.612 2e-16 *** As you can see only b has the same order of magnitude as your starting b and a is different by 7 orders! In general, an nls procedure needs starting values that are close. The same is true for any general nonlinear optimization algorithm. Only in special circumstances a nonlinear algorithm will converge from any starting point - one I know of is the convexity of the objective function. I do not think there is any nls program that will find starting values automatically for an arbitrary nonlinear model. It is possible for specific models, but is very much model dependent. Your model, for example, can be easily linearized by taking logs of both sides, i.e. mm - lm(log(y) ~ x + I(log(x))) Then doing aa - exp(coef(mm)[1]) bb - exp(coef(mm)[2]) kk - coef(mm)[3] mm1 - nls(y ~ a * x^k * b^x, start=list(a=aa,k=kk,b=bb)) results in convergence with no problems in 7 iterations. Hope this helps, Andy __ Andy Jaworski 518-1-01 Process Laboratory 3M Corporate Research Laboratory - E-mail: [EMAIL PROTECTED] Tel: (651) 733-6092 Fax: (651) 736-3122 |-+ | | Dr Andrew Wilson | | | [EMAIL PROTECTED]| | | .uk | | | Sent by: | | | [EMAIL PROTECTED]| | | ath.ethz.ch | | || | || | | 11/25/2003 03:09 | | || |-+ -| | | | To: [EMAIL PROTECTED] | | cc: | | Subject: [R] Parameter estimation in nls | -| I am trying to fit a rank-frequency distribution with 3 unknowns (a, b and k) to a set of data. This is my data set: y - c(37047647,27083970,23944887,22536157,20133224, 20088720,18774883,18415648,17103717,13580739,12350767, 8682289,7496355,7248810,7022120,6396495,6262477,6005496, 5065887,4594147,2853307,2745322,454572,448397,275136,268771) and this is the fit I'm trying to do: nlsfit - nls(y ~ a * x^k * b^x, start=list(a=5,k=1,b=3)) (It's a Yule distribution.) However, I keep getting: Error in nls(y ~ a * x^k * b^x, start = list(a = 5, k = 1, b = 3)) : singular gradient I guess this has something to do with the parameter start values. I was wondering, is there a fully automated way of estimating parameters which doesn't need start values close to the final estimates? I know other programs do it, so is it possible in R? Thanks, Andrew Wilson __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] USA map
I believe in R you need
library(maps)
before using usa(). Of course, the library has to be installed first.
Cheers,
Andy
__
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Engineering Systems Technology Center
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St. Paul, MN 55144-1000
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Tel: (651) 733-6092
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|-+
| | [EMAIL PROTECTED] |
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| | ath.ethz.ch |
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| | 11/03/2003 13:56 |
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| To: R-list [EMAIL PROTECTED]
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|Martin Wegmann [EMAIL PROTECTED]
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| cc: Owen, Jason [EMAIL PROTECTED]
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| Subject: Re: [R] USA map
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On 3 Nov 2003 at 16:33, Martin Wegmann wrote:
On Monday 03 November 2003 15:46, Owen, Jason wrote:
R users,
In S, there was a function called usa() that
would draw the map of the United States, plus
it had other options for graphics. I have looked
but I can't find the equivalent in R. Is there one?
Description
I don't know the usa() function in S but usa() in R gives a map of the US
Where did you find that function? In rw1080 on windows XP I get:
usa()
Error: couldn't find function usa
(and help.search(usa) does'nt give anything usefull)
Kjetil Halvorsen
that's the output of a usa search, perhaps that is what you are
looking
for:
cheers Martin
P.S.: www.freegis.org - GeoData is worth a look for more maps
usa() {map}
This database produces a map of the United States mainland generated
from US
Department of the Census data (see the reference).
Usage
data(usaMapEnv)
Format
The data file is merely an assignment to a character string which
specifies
the name of an environment variable which contains the base location of
the
binary files used by the map drawing functions. This environment variable
(R_MAP_DATA_DIR for the datasets in the maps package) is set at package
load
time if it does not already exist. Hence setting the environment variable
before loading the package can override the default location of the
binary
datasets.
References
Richard A. Becker, and Allan R. Wilks, Maps in S, ATT Bell
Laboratories
Statistics Research Report [93.2], 1993.
Richard A. Becker, and Allan R. Wilks, Constructing a Geographical
Database,
ATT Bell Laboratories Statistics Research Report [95.2], 1995.
US Department of Commerce, Census Bureau, County Boundary File, computer
tape,
available from Customer Services, Bureau of the Census, Washingdon DC
20233.
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Re: [R] Generating Data Sets -- Each with a Different Name
You need paste and assign functions. Paste will create a sequence of names
and assign will give values to the variables with these names.
This modification of your loop should work
for(i in 1:N)
{
assign(paste(Random.Data., i, sep=''), rnorm(10, 0, 1))
}
Cheers,
Andy
__
Andy Jaworski
Engineering Systems Technology Center
3M Center, 518-1-01
St. Paul, MN 55144-1000
-
E-mail: [EMAIL PROTECTED]
Tel: (651) 733-6092
Fax: (651) 736-3122
|-+
| | Ken Kelley |
| | [EMAIL PROTECTED] |
| | Sent by: |
| | [EMAIL PROTECTED]|
| | ath.ethz.ch |
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| | 10/23/2003 17:09 |
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| To: [EMAIL PROTECTED]
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| cc:
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| Subject: [R] Generating Data Sets -- Each with a Different Name
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-|
Hello all.
I was wondering if anyone had insight into how I might generate a large
number of data sets/vectors, where each of the data sets/vectors have a
different name?
For example, suppose I wanted to generate N data sets/vectors, each with a
different name such as:
Random.Data.1 - rnorm(10, 0, 1)
Random.Data.2 - rnorm(10, 0, 1)
Random.Data.3 - rnorm(10, 0, 1)
. .
. .
. .
Random.Data.N - rnorm(10, 0, 1)
Because I don't want to name each data set/vector myself, I want some sort
of looping/automatic procedure to do it for me. However, I'm not sure how
to do this.
What I want is something conceptually analogous to the following:
for(i in 1:N)
{
Random.Data.i - rnorm(10, 0, 1)
}
Note the i in the Random.Data.i vector. This is the value I want to
change for each iteration of the loop, so that I can have N data
sets/vectors automatically generated for me with different names.
Does anyone know of a method where I can accomplish such a procedure.
Thanks for your thoughts,
Ken
P.S. For those of you wondering why I would ever want to do such a thing,
it is because I need a large number of data sets to use in a Monte Carlo
study with specialized software. If I could do the simulation all is R,
then obviously I could loop the whole procedure. The program I am using has
a limited Monte Carlo facility where each of the (say 10,000) data sets
must be generated elsewhere.
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Re: [R] upgrading R
I am not sure if this is a proper way, but here is what I did recently installing consecutive alpha and beta releases of 1.8.0 on a Win2000 machine: (1) I uninstalled previous version using the uninstall provided with R. This leaves all the additional packages in the library folder (2) I reinstalled the new version into the same folder structure. The problem might be that some 1.7.1 packages might be different from 1.8.0, so it might be safer to reinstall them from CRAN. Andy __ Andy Jaworski Engineering Systems Technology Center 3M Center, 518-1-01 St. Paul, MN 55144-1000 - E-mail: [EMAIL PROTECTED] Tel: (651) 733-6092 Fax: (651) 736-3122 |-+ | | Weiming Zhang | | | [EMAIL PROTECTED]| | | edu | | | Sent by: | | | [EMAIL PROTECTED]| | | ath.ethz.ch | | || | || | | 10/09/2003 10:38 | | || |-+ -| | | | To: [EMAIL PROTECTED] | | cc: | | Subject: [R] upgrading R | -| Hi, I have installed a lot of extra packages for R 1.7.1. If I install R 1.8.0, will I have to reinstall all those packages? Is there a way that I can upgrading R without losing old packages? Thank you. wz __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
[R] bug in stack?
I am posting it here because I am not sure if the behavior described below
is actually a bug.
If I do something like this:
x1 - 1:3
x2 - 5:9
x3 - 21:27
ll - list(x1, x2, x3)
stack(x1,x2,x3)
I get the following error:
Error in rep.int(names(x), lapply(x, length)) :
invalid number of copies in rep
The problem seems to be that the generic list ll is lacking the names
attribute.
The stack.default function (in frametools.R) looks like this:
stack.default
function (x, ...)
{
x - as.list(x)
x - x[unlist(lapply(x, is.vector))]
data.frame(values = unlist(unname(x)), ind = factor(rep.int(names(x),
lapply(x, length
}
and the last statement generates an error if names(x) evaluates to NULL.
If we add the following line of code before the last statement
if(is.null(names(x))) names(x) - seq(along=x)
the stack function will work fine even for nameless lists.
Andy
__
Andy Jaworski
Engineering Systems Technology Center
3M Center, 518-1-01
St. Paul, MN 55144-1000
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Re: [R] all possible samples
I am not sure if this is the easiest way, but you can do something like this: library(gregmisc) combinations(N, n, x, repeats=TRUE) where x is an atomic vector of size N. The only restriction is that the x vector has to have N unique elements. The combinations function will return a matrix with n columns containing the combinations. The combinations function is defined recursively. Even for moderate values of N and n it will either take a long time or bomb out with the evaluation is nested too deeply error. For example, on my modest machine (PIII 1GHz with 1/5 Gbyte of memory) it takes almost a minute to evaluate combinations(30, 6, repeats=TRUE) (1623160 combinations) and combinations(44, 2, repeats=TRUE) (only 990 combinations) bombs out. If you need to work with larger numbers you will probably need a sequential code. Hope this helps, Andy __ Andy Jaworski Engineering Systems Technology Center 3M Center, 518-1-01 St. Paul, MN 55144-1000 - E-mail: [EMAIL PROTECTED] Tel: (651) 733-6092 Fax: (651) 736-3122 |-+ | | lamack lamack | | | [EMAIL PROTECTED]| | | Sent by: | | | [EMAIL PROTECTED]| | | ath.ethz.ch | | || | || | | 09/17/2003 09:52 | | || |-+ -| | | | To: [EMAIL PROTECTED] | | cc: | | Subject: [R] all possible samples | -| Dear all, there is an R function that return all possible samples of size n, with replacement, from a vector of length N ? Best regards __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] Transpose Data Frame Question
Here is a brute force way:
mm - NULL
for(i in unique(ID)){
zz - data.frame[ID==i, 3]
mm - rbind(mm, c(i, zz))
}
It will work as long as you have the same number of tests for each ID. If
not, you would need to pad shorter zz vectors with NAs.
Cheers,
Andy
__
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Engineering Systems Technology Center
3M Center, 518-1-01
St. Paul, MN 55144-1000
-
E-mail: [EMAIL PROTECTED]
Tel: (651) 733-6092
Fax: (651) 736-3122
|-+
| | Bruce Coate |
| | [EMAIL PROTECTED]|
| | m |
| | Sent by: |
| | [EMAIL PROTECTED]|
| | ath.ethz.ch |
| ||
| ||
| | 09/17/2003 12:30 |
| ||
|-+
-|
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| To: [EMAIL PROTECTED]
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| cc:
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| Subject: [R] Transpose Data Frame Question
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-|
Hi,
I have a data.frame that has 3 columns (ID, Test, Result) and looks like
this
1, Test1, 120
1, Test2, 34
2, Test1, 132
2, Test2, 28
etc
I would like to turn it around so that it looks like this
1, 120, 34
2, 132, 28
etc
I have played around some with t and reshape, but with no success.
Any suggestions or hints would be greatly appreciated.
Thanks,
Bruce
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Re: [R] Integer programming in R
Robin, This is not a direct answer to your question, but there exists a pretty good linear, mixted and integer programming package called lp_solve. I have used it successfully on a couple of projects. As far as I know it is in the public domain and there is source code available. There is also a precompiled version available for Windows Visual Basic environment containing a precompiled DLL and an interface module defining VB function calls to the DLL. I think, that having all that it should be possible to get something going in R, at least in the Windows environment. Hope this helps, Andy __ Andy Jaworski Engineering Systems Technology Center 3M Center, 518-1-01 St. Paul, MN 55144-1000 - E-mail: [EMAIL PROTECTED] Tel: (651) 733-6092 Fax: (651) 736-3122 |-+ | | Robin Naidoo | | | [EMAIL PROTECTED]| | | Sent by: | | | [EMAIL PROTECTED]| | | ath.ethz.ch | | || | || | | 07/24/2003 12:18 | | || |-+ -| | | | To: [EMAIL PROTECTED] | | cc: | | Subject: [R] Integer programming in R | -| Dear all, I am a relative newcomer to the R language, and am sussing out the possibilities of using R to do integer programming (which I am also new to). Is there something along the lines of the NUOPT S- PLUS package that is available, or on the way, for R? Are there other options for integer programming in R? Thanks very much in advance, Robin Naidoo University of Alberta Edmonton, AB, Canada __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] matrix manipulations
David, I am not sure if it can be done in a vectorized form, but this should work y - NULL for(i in 1:ncol(x)) y - c(y, cor(x[,i],apply(x[,-i],1,sum))) Cheers, Andy __ Andy Jaworski Engineering Systems Technology Center 3M Center, 518-1-01 St. Paul, MN 55144-1000 - E-mail: [EMAIL PROTECTED] Tel: (651) 733-6092 Fax: (651) 736-3122 |-+ | | David Andel| | | [EMAIL PROTECTED] | | | Sent by: | | | [EMAIL PROTECTED]| | | ath.ethz.ch | | || | || | | 07/15/2003 11:51 | | || |-+ -| | | | To: [EMAIL PROTECTED] | | cc: | | Subject: [R] matrix manipulations | -| Hi cor(x,apply(x,1,sum)) gives me the correlations of each column with the sums of each row (correct me if I'm wrong, please). What I need are the correlations of each column with the sums of each row except the entry in the given column. It seems that for any one column i I get it by doing: cor(x[,i],apply(x[,-i],1,sum)) But I struggle to get it for all the columns. I was trying things like: for(i in 1:ncol(x)) cor(x[,i],apply(x[,-i],1,sum)) which doesn't generate any output at all, and rbind(for(i in 1:ncol(x)) cor(x[,i],apply(x[,-i],1,sum))) [,1] [1,] 0.1880237 outputs just the result of the very last column. I know that it shouldn't be necessary to use for(), but I couldn't figure out a way how to do the task using e.g. apply(). How do you get the results of all columns? Thank you, David __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] lines and legend
Anna, I found this quite useful in positioning a legend: plot(1:10, 1:10) legend(locator(1), A legend) Now, go to the plot window and click your left mouse where you want the upper left corner of the legend to appear. Ithink, this should work no matter what your coordinate system is. Hope this helps, Andy __ Andy Jaworski Engineering Systems Technology Center 3M Center, 518-1-01 St. Paul, MN 55144-1000 - E-mail: [EMAIL PROTECTED] Tel: (651) 733-6092 Fax: (651) 736-3122 |-+ | | Anna H. Pryor | | | [EMAIL PROTECTED]| | | a.gov | | | Sent by: | | | [EMAIL PROTECTED]| | | ath.ethz.ch | | || | || | | 07/01/2003 12:45 | | || |-+ -| | | | To: R-help mailing list [EMAIL PROTECTED] | | cc: | | Subject: [R] lines and legend | -| When I am trying to put a legend on a plot where I am using lines, R just ignores it. I can do it with boxplot or plot, but just not with lines. Am I doing something wrong? Maybe I am just making a mistake? Anna __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
[R] Rcmdr active data set
Hi, This seems a very basic problem, but I cannot seem to find the solution to it. I am trying to use Rcmdr on a data frame I created in my current R session. More specifically, I did x - data.frame(matrix(0, ncol=3, nrow=5)) library(Rcmdr) Now I would like to be able to edit, view and perhaps analyze x, but I cannot seem to figure out how to make it active. Any hint will be welcome. Andy __ Andy Jaworski Engineering Systems Technology Center 3M Center, 518-1-01 St. Paul, MN 55144-1000 - E-mail: [EMAIL PROTECTED] Tel: (651) 733-6092 Fax: (651) 736-3122 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] Tukey's HSD
Simint is in the multcomp package. Cheers, Andy __ Andy Jaworski Engineering Systems Technology Center 3M Center, 518-1-01 St. Paul, MN 55144-1000 - E-mail: [EMAIL PROTECTED] Tel: (651) 733-6092 Fax: (651) 736-3122 |-+ | | Thomas W Blackwell | | | [EMAIL PROTECTED] | | | Sent by: | | | [EMAIL PROTECTED]| | | ath.ethz.ch | | || | || | | 03/19/2003 12:20 | | || |-+ -| | | | To: Peter B. Mandeville [EMAIL PROTECTED] | | cc: [EMAIL PROTECTED] | | Subject: Re: [R] Tukey's HSD | -| What function simint() ? At least using R 1.6.1 (Redhat linux), help.search(simint) returns No help files found Also, it's no surprise that na.omit() might omit rows with NA's but then NOT purge the levels attribute of each column that is a factor for factor levels that are no longer used. For a simple example of this, try table(def4$TP, def4$EL) (or some such object names - I no longer have the body of the original email). - tom blackwell - u michigan medical school - ann arbor - __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
[R] small error in regression tests
I just r-sync'ed the r-devel version of R-1.7.0 (2003-03-11), compiled it
under RH-8.0 and ran make check. The reg-tests-2 fails at the very end
with the message stating that object cement was not found. It looks like
this piece of the regression test is new to version 1.7. The the piece of
code generating the error is:
if(require(MASS)) {
teststep - function(formula, data)
{
d2 - data
fit - lm(formula, data=d2)
step(fit)
}
teststep(formula(y ~ .), cement)
detach(package:MASS)
}
It seems that it requires
data(cement)
statement before the call to teststep.
Andy
__
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Engineering Systems Technology Center
3M Center, 518-1-01
St. Paul, MN 55144-1000
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[R] lattice default theme
I have a feeling that this was already discussed here, but I cannot remember the outcome of the discussion. I would like to have the col.whitebg theme as a default and I cannot figure out how to do it. Functions like lset or trellis.par.set require that the device be active, so how does one set a different default for all invocations of trellis.device? Thanks in advance, Andy __ Andy Jaworski Engineering Systems Technology Center 3M Center, 518-1-01 St. Paul, MN 55144-1000 - E-mail: [EMAIL PROTECTED] Tel: (651) 733-6092 Fax: (651) 736-3122 __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] Probit Analysis
Jacqueline, This should be a simple application of GLM. Check the help pages for glm, family and dose.p in library MASS. Look at the example at the bottom of the dose.p help page - it does almost exactly what you need. Hope this helps, Andy __ Andy Jaworski Engineering Systems Technology Center 3M Center, 518-1-01 St. Paul, MN 55144-1000 - E-mail: [EMAIL PROTECTED] Tel: (651) 733-6092 Fax: (651) 736-3122 |-+-- | | Ngayee J Law | | | Ngayee.Law@celeradiagn| | | ostics.com| | | Sent by: | | | [EMAIL PROTECTED]| | | ethz.ch| | | | | | | | | 12/31/2002 16:17 | | | | |-+-- -| | | | To: [EMAIL PROTECTED] | | cc: | | Subject: [R] Probit Analysis | -| Hello all, I have a very simple set of data and I would like to analyze them with probit analysis. The data are: XEvent Trial 100 8 8 75 8 8 50 6 8 25 4 8 10 2 8 00 8 I want to estimate the value of X that will give a 95% hit rate (Event/Trial) and the corresponding 95% CI. Anyone can offer some help? Thanks!! - Jacqueline __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help
