[R] pairs: altering pch options on upper and lower panel of pairwise scatter plots
Hello, I can't figure out how to use the upper.panel and lower.panel options in pairs to alter the label options for either panel independently of the other. I would like to be able to show the pairwise scatter plots for the data as they are (a vanilla pairs plot?) but separately to be able to label the points according to a factor level. It is easy enough to do this independently, but I can't figure out how to combine the two settings on the same plot. I have enclosed a toy example: Some made up data, e.g. ## make up some multivariate normal data using mvrnorm from MASS ## require(MASS) mu - c(0,0,0) digma - matrix(c(0.9,0.5,0.5, 0.5,0.9,0.5, 0.5,0.5,0.9) dummy.data - mvrnorm(100,mu,sigma) ## ## add a factor ## gender - as.factor(c(rep(Male,50),rep(Female,50))) I can create two separate pairs plots (upper and lower panel) as follows: ## pairs plot just showing the data pairs(dummy.data, lower.panel = NULL) ## pairs plot where the points are labelled according to a factor pairs(dummy.data, pch = levels(gender), upper.panel = NULL) But I would like to be able to combine the two panels on the same plot. I would be grateful for any advice. I've tried passing several combinations of functions to upper.panel and lower.panel but either they're the wrong function or I'm barking up the wrong tree entirely. Thanks Paul Hewson -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- Lecturer in Statistics University of Plymouth Drake Circus Plymouth PL4 8AA Tel ++ 44 1752 232778 Email [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] 3d bar plot
This graph - http://www.math.hope.edu/~tanis/dallas/images/disth36.gif
is an example I found at
http://www.math.hope.edu/~tanis/dallas/disth1.html
created by Maple.
Does anybody know how to create something similar in R?
I have a feeling it could be possible using scatterplot3d
(perhaps with type=h, the fourth example in help('scatterplot3d')?),
but I cannot figure it out.
Thanks in advance,
Jonne.
__
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] RWinEdt install problem
I am using WinEdt 5.4 (Build: 20040513 (v. 5.4), on XP service pack 2), and the following approach works for me: 1) Install RWinEdt_1.6-2.zip using RGui menus. 2) Include the following line in the Rprofile file. library(RWinEdt) This will launch WinEdt with R customizations whenever RGui is launched. hope this helps, Chuck Cleland Uwe Ligges wrote: Murray Eisenberg wrote: I cannot get the R button to appear in RWinEdt. I'm running R 2.0.1 under Windows XP. I did a clean install of the latest WinEdt. Previously (for an earlier installation of WinEdt) I had RWinEdt running OK. Now, even though I have the distributed RWinEdt_1.6-2.zip extracted to the right place in the R directory, and when I execute library(RWinEdt) in the R Console, when RWinEdt opens I do not have the R button on the toolbar. How do I fix this? In case it matters, note that I'm using a WinEdt User configuration (i.e., a directory that WinEdt refers to as %b) in addition to the main WinEdt directory (the one that WinEdt refers to as %B). If you don't have write access to the WinEdt directory, you have to copy the R.ini file to, e.g., your local directory (%b), use the *manual* installation procedure as described in the ReadMe, but replace the command line args -e=R.ini by the full path specification, e.g.: -E=/path/to/%b/R.ini In a second (apparently private mail), you told that WinEdt ... 5.4 builds ... including the most recent one of 14 January 2005... do not work with the recent version of R-WinEdt, because 1. The first time, immediately I get a message that WinEdt.ini is corrupted and that a default copy (from the RWinEdt distribution I presume) is being used. Is this version also configured to use a User configuration? I don't have a WinEdt 5.4 version installed (still working with 5.2), but I will certainly take a look during the next one or two weeks. Uwe Ligges __ 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 -- Chuck Cleland, Ph.D. NDRI, Inc. 71 West 23rd Street, 8th floor New York, NY 10010 tel: (212) 845-4495 (Tu, Th) tel: (732) 452-1424 (M, W, F) fax: (917) 438-0894 __ 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 wanted using R in a classroom
Hi everyone! I'm using R 2.0.1 for Mac OS X in a classroom with 40 eMacs running Mac OS X version 10.3.6. These Macs are network based, meaning that the students log in to an XServe G4 where their user accounts and home directories are stored. The problem that I'm having each time a group of students (usually 7 to 10) use R is that the whole system get incredibly slow. The response time for opening an application while the students are running R is around 5 minutes. If a student wants to log into the system while others are running R, it can take up to 10 minutes for the student to get logged in. Everything gets very slow that it's almost impossible to work. When I look at the server Graphs, the CPU usage of the first CPU is always 100% when these students are using R. The second CPU is left at 15%. When these students quit R, then everything's is back to normal again. The usage of both CPUs go back down to between 5-10%. Is there anyone out there using R in a university like this? Does anyone have an idea what this might depend one or maybe a solution? I can provide some more information if anyone wants, if you think you can help me. Thanks in advance /Sam [[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
RE: [R] 3d bar plot
You can check these packages,
?scatterplot3d
?scatter3d
Best Marwan
---
Marwan Khawaja http://staff.aub.edu.lb/~mk36/
---
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of R user
Sent: Monday, January 17, 2005 12:37 PM
To: r-help@stat.math.ethz.ch
Subject: [R] 3d bar plot
This graph -
http://www.math.hope.edu/~tanis/dallas/images/disth36.gif
is an example I found at
http://www.math.hope.edu/~tanis/dallas/disth1.html
created by Maple.
Does anybody know how to create something similar in R?
I have a feeling it could be possible using scatterplot3d
(perhaps with type=h, the fourth example in
help('scatterplot3d')?), but I cannot figure it out.
Thanks in advance,
Jonne.
__
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] bold face labelling/expression
Dear colleagues, I have a great problem in using expression for axes labels. I want the labels in bold face (i.e.: par(font.lab=2)). When typing boxplot(y ~ groups, names = , xlab = , ylab = , axes = F) axis(side=1, at=c(1,2), xlab=c(expression(H[2]*O),others)), I do not get a bold face labelling. Does anyone know, how I could proceed? Thank you very much. Best regards H. __ 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] Multiple plots in one screen
see ?par look for par(new=T) (if you want plot-overlay) or just ?lines (if you want several lines in one plot) __ 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] randomForest: too many element specified?
When I run randonForest with a 169453x5 matrix, I got the following message. Error in matrix(0, n, n) : matrix: too many elements specified Can you please advise me how to solve this problem? Thanks, Lu Uwe Ligges [EMAIL PROTECTED] wrote: Vera Hofer wrote: Dear colleagues, I have a great problem in using expression for axes labels. I want the labels in bold face (i.e.: par(font.lab=2)). When typing boxplot(y ~ groups, names = , xlab = , ylab = , axes = F) axis(side=1, at=c(1,2), xlab=c(expression(H[2]*O),others)), 1. If you don't mean labels instead of xlab in the axis() call, use xlab in the boxplot() call or in a call to title() (but then, you cannot use c(expression(), ...). 2. See ?plotmath and use, e.g., bold(H[2]*O) ... Uwe Ligges I do not get a bold face labelling. Does anyone know, how I could proceed? Thank you very much. Best regards V.H. __ 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 - [[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] Question about time series
I have data in the following format: DATE [1] 01/13/2004 In order to find the difference between two data points, I presently use brute force to calculate the day of the year: strptime(DATE, format=%m/%d/%Y)$yday [1] 12 Although this works, it may not be robust over different years. I assume that R is sufficiently clever that a much simpler approach exists, e.g., can I calculate the number of days since some fixed time? Unfortunately, the man pages and FAQ did not lead me to an obvious solution. Any help appreciated. Dennis Dennis Fisher MD P (The P Less Than Company) Phone: 1-866-PLessThan (1-866-753-7784) Fax: 1-415-564-2220 www.PLessThan.com __ 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] randomForest: too many element specified?
From: luk When I run randonForest with a 169453x5 matrix, I got the following message. Error in matrix(0, n, n) : matrix: too many elements specified Can you please advise me how to solve this problem? Thanks, Lu 1. When asking new questions, please don't reply to other posts. 2. When asking questions like these, please do show the commands you used. My guess is that you asked for the proximity matrix, or is running unsupervised randomForest (by not providing a response vector). This will requires a couple of n by n matrices to be created (on top of other things), n being 169453 in this case. To store a 169453 x 169453 matrix in double precision, you need 169453^2 * 8 bytes, or or nearly 214 GB of memory. Even if you have that kind of hardware, I doubt you'll be able to make much sense out of the result. Andy Uwe Ligges [EMAIL PROTECTED] wrote: Vera Hofer wrote: Dear colleagues, I have a great problem in using expression for axes labels. I want the labels in bold face (i.e.: par(font.lab=2)). When typing boxplot(y ~ groups, names = , xlab = , ylab = , axes = F) axis(side=1, at=c(1,2), xlab=c(expression(H[2]*O),others)), 1. If you don't mean labels instead of xlab in the axis() call, use xlab in the boxplot() call or in a call to title() (but then, you cannot use c(expression(), ...). 2. See ?plotmath and use, e.g., bold(H[2]*O) ... Uwe Ligges I do not get a bold face labelling. Does anyone know, how I could proceed? Thank you very much. Best regards V.H. __ 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 - [[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] 3d bar plot
Dear Marwan and Jonne,
I don't think that there's a scatter3d package, so perhaps Marwan is
referring to the scatter3d() function in the Rcmdr package. If so, that
function won't make the kind of 3D graph that Jonne wants -- though the rgl
package, on which scatter3d() is based, should be able to create the graph.
I don't believe that the scatterplot3d() function in the scatterplot3d
package can make the plot either, but I may be wrong.
I hope this helps.
John
John Fox
Department of Sociology
McMaster University
Hamilton, Ontario
Canada L8S 4M4
905-525-9140x23604
http://socserv.mcmaster.ca/jfox
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Marwan Khawaja
Sent: Sunday, January 16, 2005 7:04 PM
To: 'R user'; r-help@stat.math.ethz.ch
Subject: RE: [R] 3d bar plot
You can check these packages,
?scatterplot3d
?scatter3d
Best Marwan
---
Marwan Khawaja http://staff.aub.edu.lb/~mk36/
---
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of R user
Sent: Monday, January 17, 2005 12:37 PM
To: r-help@stat.math.ethz.ch
Subject: [R] 3d bar plot
This graph -
http://www.math.hope.edu/~tanis/dallas/images/disth36.gif
is an example I found at
http://www.math.hope.edu/~tanis/dallas/disth1.html
created by Maple.
Does anybody know how to create something similar in R?
I have a feeling it could be possible using scatterplot3d (perhaps
with type=h, the fourth example in help('scatterplot3d')?), but I
cannot figure it out.
Thanks in advance,
Jonne.
__
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-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] find source code
I am using R 2.0.2 on a WinXP I am trying to get the code of the Kruskal-Wallis test but kruskal.test function (x, ...) UseMethod(kruskal.test) environment: namespace:stats ls(3) [1] acf acf2AR add.scope .. [181] kruskal.test ks.test ksmooth ... [475] window- write.ftable xtabs class(kruskal.test) [1] function getS3method(kruskal.test,function) Error in getS3method(kruskal.test, function) : S3 method kruskal.test.function not found getS3method(stats::kruskal.test,function) Error in getS3method(stats::kruskal.test, function) : no function 'stats::kruskal.test' could be found I searched the archives and the answer was ' use getS3method ' . The help for getS3method is getS3method(f,class,optional=FALSE) so I am lost Can somebody tell me how to get the source listing of kruskal.test or of any other hidden function? Thanks Heberto Ghezzo Meakins-Christie Labs Canada __ 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 source code
stats:::kruskal.test.default On Mon, 17 Jan 2005 [EMAIL PROTECTED] wrote: I am using R 2.0.2 on a WinXP I am trying to get the code of the Kruskal-Wallis test but kruskal.test function (x, ...) UseMethod(kruskal.test) environment: namespace:stats ls(3) [1] acf acf2AR add.scope .. [181] kruskal.test ks.test ksmooth ... [475] window- write.ftable xtabs class(kruskal.test) [1] function getS3method(kruskal.test,function) Error in getS3method(kruskal.test, function) : S3 method kruskal.test.function not found getS3method(stats::kruskal.test,function) Error in getS3method(stats::kruskal.test, function) : no function 'stats::kruskal.test' could be found I searched the archives and the answer was ' use getS3method ' . The help for getS3method is getS3method(f,class,optional=FALSE) so I am lost Can somebody tell me how to get the source listing of kruskal.test or of any other hidden function? Thanks Heberto Ghezzo Meakins-Christie Labs Canada __ 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 source code
From: [EMAIL PROTECTED] I am using R 2.0.2 on a WinXP Does that version of R exist? I am trying to get the code of the Kruskal-Wallis test but kruskal.test function (x, ...) UseMethod(kruskal.test) environment: namespace:stats ls(3) [1] acf acf2AR add.scope .. [181] kruskal.test ks.test ksmooth ... [475] window- write.ftable xtabs class(kruskal.test) [1] function getS3method(kruskal.test,function) Error in getS3method(kruskal.test, function) : S3 method kruskal.test.function not found getS3method(stats::kruskal.test,function) Error in getS3method(stats::kruskal.test, function) : no function 'stats::kruskal.test' could be found I searched the archives and the answer was ' use getS3method ' . The help for getS3method is getS3method(f,class,optional=FALSE) so I am lost Can somebody tell me how to get the source listing of kruskal.test or of any other hidden function? Before you use getS3method(), you need to know which S3 method you want to get. To see what S3 methods are available, use: methods(kruskal.test) [1] kruskal.test.default* kruskal.test.formula* Non-visible functions are asterisked Andy Thanks Heberto Ghezzo Meakins-Christie Labs Canada __ 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] [basic ?] Merging result of by processing with a data frame
Dear All, I would like to merge a data frame such as: basetab subject dose cmax 1 1031 50 21.8 with the result of a by processing such as: tmax-by(pkga,subject,f.tmax) tmax subject: 1031 [1] 6 -- f.tmax being a function written by H. Nguyen (in applied statistics in the pharmaceutical industry). pkga is a data frame with subject conc time variates. The aim is to have a single data frame with subject dose cmax tmax etc (AUCs) ... so that I can do summary stats and plots by dose. I have tried unlist without success. Thanks for any help. Kind regards, Jean-Louis __ 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] Question about time series
Hi
TODAY - as.POSIXlt('2004-01-17')
LYTODAY - as.POSIXlt('2003-01-17')
DAYS - TODAY-LYTODAY
DAYS
Time difference of 365 days
DAYS[[1]]
[1] 365
perhaps it helps,
Christian
Dennis Fisher wrote:
I have data in the following format:
DATE
[1] 01/13/2004
In order to find the difference between two data points, I presently
use brute force to calculate the day of the year:
strptime(DATE, format=%m/%d/%Y)$yday
[1] 12
Although this works, it may not be robust over different years. I
assume that R is sufficiently clever that a much simpler approach
exists, e.g., can I calculate the number of days since some fixed
time? Unfortunately, the man pages and FAQ did not lead me to an
obvious solution.
Any help appreciated.
Dennis
Dennis Fisher MD
P (The P Less Than Company)
Phone: 1-866-PLessThan (1-866-753-7784)
Fax: 1-415-564-2220
www.PLessThan.com
__
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 source code
Simon Wood wrote: stats:::kruskal.test.default and how to get there: methods(kruskal.test) # note, you probably want the default method! getS3method(kruskal.test, default) Uwe On Mon, 17 Jan 2005 [EMAIL PROTECTED] wrote: I am using R 2.0.2 on a WinXP I am trying to get the code of the Kruskal-Wallis test but kruskal.test function (x, ...) UseMethod(kruskal.test) environment: namespace:stats ls(3) [1] acf acf2AR add.scope .. [181] kruskal.test ks.test ksmooth ... [475] window- write.ftable xtabs class(kruskal.test) [1] function getS3method(kruskal.test,function) Error in getS3method(kruskal.test, function) : S3 method kruskal.test.function not found getS3method(stats::kruskal.test,function) Error in getS3method(stats::kruskal.test, function) : no function 'stats::kruskal.test' could be found I searched the archives and the answer was ' use getS3method ' . The help for getS3method is getS3method(f,class,optional=FALSE) so I am lost Can somebody tell me how to get the source listing of kruskal.test or of any other hidden function? Thanks Heberto Ghezzo Meakins-Christie Labs Canada __ 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-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] 3d bar plot
John Fox wrote:
Dear Marwan and Jonne,
I don't think that there's a scatter3d package, so perhaps Marwan is
referring to the scatter3d() function in the Rcmdr package. If so, that
function won't make the kind of 3D graph that Jonne wants -- though the rgl
package, on which scatter3d() is based, should be able to create the graph.
I don't believe that the scatterplot3d() function in the scatterplot3d
package can make the plot either, but I may be wrong.
John, you are right. scatterplot3d is not designed to do stuff like
that. You can do some workarounds, but it will look rather ugly.
Uwe
I hope this helps.
John
John Fox
Department of Sociology
McMaster University
Hamilton, Ontario
Canada L8S 4M4
905-525-9140x23604
http://socserv.mcmaster.ca/jfox
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Marwan Khawaja
Sent: Sunday, January 16, 2005 7:04 PM
To: 'R user'; r-help@stat.math.ethz.ch
Subject: RE: [R] 3d bar plot
You can check these packages,
?scatterplot3d
?scatter3d
Best Marwan
---
Marwan Khawaja http://staff.aub.edu.lb/~mk36/
---
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of R user
Sent: Monday, January 17, 2005 12:37 PM
To: r-help@stat.math.ethz.ch
Subject: [R] 3d bar plot
This graph -
http://www.math.hope.edu/~tanis/dallas/images/disth36.gif
is an example I found at
http://www.math.hope.edu/~tanis/dallas/disth1.html
created by Maple.
Does anybody know how to create something similar in R?
I have a feeling it could be possible using scatterplot3d (perhaps
with type=h, the fourth example in help('scatterplot3d')?), but I
cannot figure it out.
Thanks in advance,
Jonne.
__
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-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] kmeans with weighted variables
Hello, I'm having troubles finding how to weight some variables for a k-means clustering. Can you please let me know what arguments I should had to: z - kmeans(A, 3, 10) if I want to put different weights for 3 of the 6 variables I'm using to classify these individuals. Many thanks Regards Matthieu HYRIEN GEOSYS S.A. Office: 0033 (0)5 62 47 80 92 Mob: 0044 (0)7791 789 467 www.geosys.com [[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
Re: [R] Setting the width and height of a Sweave figure
I haven't found any other solution than using fig=TRUE,height=7,width=14 theCode() @ (but of course that doesn't have any effect when theCode() is used interactively). -- Bjørn-Helge Mevik __ 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] Omitting constant in ols() from Design
Hi! I need to run ols regressions with Huber-White sandwich estimators and the correponding standard errors, without an intercept. What I'm trying to do is create an ols object and then use the robcov() function, on the order of: f - ols(depvar ~ ind1 + ind2, x=TRUE) robcov(f) However, when I go f - ols(depvar ~ ind1 + ind2 -1, x=TRUE) I get the following error: Error in ols(nareit ~ SnP500 + d3yrtr - 1) : length of dimnames [2] not equal to array extent same with +0 instead of -1. Is there a different way to create an ols object without a constant? I can't use lm(), because robcov() needs an object from the Design() series. Or is there a different way to go about this? Tobias Muhlhofer __ 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 source code
But how can I see the *documented* source code in Windows? I think i.e. in the /flexmix/library/man/all.rda file is the documented(?) code for all functions of Package flexmix, but the standard Windows XP cannot open .rda files correct. Is there a way to read the documented source code of a function under Windows and R2.0.1? Thanks in advance, Matthias Betreff: Re: [R] find source code stats:::kruskal.test.default On Mon, 17 Jan 2005 [EMAIL PROTECTED] wrote: I am using R 2.0.2 on a WinXP I am trying to get the code of the Kruskal-Wallis test but kruskal.test function (x, ...) UseMethod(kruskal.test) environment: namespace:stats ls(3) [1] acf acf2AR add.scope .. [181] kruskal.test ks.test ksmooth ... [475] window- write.ftable xtabs class(kruskal.test) [1] function getS3method(kruskal.test,function) Error in getS3method(kruskal.test, function) : S3 method kruskal.test.function not found getS3method(stats::kruskal.test,function) Error in getS3method(stats::kruskal.test, function) : no function 'stats::kruskal.test' could be found I searched the archives and the answer was ' use getS3method ' . The help for getS3method is getS3method(f,class,optional=FALSE) so I am lost Can somebody tell me how to get the source listing of kruskal.test or of any other hidden function? Thanks Heberto Ghezzo Meakins-Christie Labs Canada __ 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-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 source code
From: TEMPL Matthias But how can I see the *documented* source code in Windows? I think i.e. in the /flexmix/library/man/all.rda file is the documented(?) code for all functions of Package flexmix, but the standard Windows XP cannot open .rda files correct. Is there a way to read the documented source code of a function under Windows and R2.0.1? Do you mean `commented' rather than `documented' (i.e., having a help page)? If so, I believe the only guaranteed way of doing that is by getting the package _source_ (i.e., the .tar.gz file) from CRAN and read the file in the R/ subdirectory after unpacking. This has nothing to do with hardware/software platform. .rda files are really only readable by R, regardless of platform, and R on Windows doesn't behave differently than on other OS in this respect. Andy Thanks in advance, Matthias Betreff: Re: [R] find source code stats:::kruskal.test.default On Mon, 17 Jan 2005 [EMAIL PROTECTED] wrote: I am using R 2.0.2 on a WinXP I am trying to get the code of the Kruskal-Wallis test but kruskal.test function (x, ...) UseMethod(kruskal.test) environment: namespace:stats ls(3) [1] acf acf2AR add.scope .. [181] kruskal.test ks.test ksmooth ... [475] window- write.ftable xtabs class(kruskal.test) [1] function getS3method(kruskal.test,function) Error in getS3method(kruskal.test, function) : S3 method kruskal.test.function not found getS3method(stats::kruskal.test,function) Error in getS3method(stats::kruskal.test, function) : no function 'stats::kruskal.test' could be found I searched the archives and the answer was ' use getS3method ' . The help for getS3method is getS3method(f,class,optional=FALSE) so I am lost Can somebody tell me how to get the source listing of kruskal.test or of any other hidden function? Thanks Heberto Ghezzo Meakins-Christie Labs Canada __ 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-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 source code
TEMPL Matthias [EMAIL PROTECTED] writes: But how can I see the *documented* source code in Windows? I think i.e. in the /flexmix/library/man/all.rda file is the documented(?) code for all functions of Package flexmix, but the standard Windows XP cannot open .rda files correct. No that's not it. The .rda files are like R workspaces. Is there a way to read the documented source code of a function under Windows and R2.0.1? Yes. Fetch the source code for the package or R itself, and read the relevant source files. These are available from CRAN. -- O__ Peter Dalgaard Blegdamsvej 3 c/ /'_ --- Dept. of Biostatistics 2200 Cph. N (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ 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] How do I format something as 0.000?
Hi, I would like to use the format function to get numbers all with three digits to the right of the decimal point, even in cases where there is no significant digit left. For example, I would like to get c(0.3456789,0.053) as 0.346 0.000. It seems that it is not possible to force format to print a 0.000, i.e. without any significant decimal places. Is it possible to do this somehow in R? Thanks, Christian *** Christian Hennig Fachbereich Mathematik-SPST/ZMS, Universitaet Hamburg [EMAIL PROTECTED], http://www.math.uni-hamburg.de/home/hennig/ ### ich empfehle www.boag-online.de __ 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] Omitting constant in ols() from Design
On Mon, 17 Jan 2005 14:57:33 + Tobias Muhlhofer wrote: Hi! I need to run ols regressions with Huber-White sandwich estimators and the correponding standard errors, without an intercept. What I'm trying to do is create an ols object and then use the robcov() function, on the order of: f - ols(depvar ~ ind1 + ind2, x=TRUE) robcov(f) However, when I go f - ols(depvar ~ ind1 + ind2 -1, x=TRUE) I get the following error: Error in ols(nareit ~ SnP500 + d3yrtr - 1) : length of dimnames [2] not equal to array extent same with +0 instead of -1. Is there a different way to create an ols object without a constant? I can't use lm(), because robcov() needs an object from the Design() series. Or is there a different way to go about this? I am not sure if the problem can also be avoided or worked around in Design, but the functions hccm() from car or vcovHC() from sandwich can also compute the Huber-White (and other) HC covariance matrix estimates for fitted lm objects. For computing the corresponding t-tests or z-tests, you can use the function coeftest() in lmtest. See the corresponding man page for examples. Best, Z Tobias Muhlhofer __ 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] How do I format something as 0.000?
On Mon, 17 Jan 2005 16:49:35 +0100 (MET) Christian Hennig wrote: Hi, I would like to use the format function to get numbers all with three digits to the right of the decimal point, even in cases where there is no significant digit left. For example, I would like to get c(0.3456789,0.053) as 0.346 0.000. It seems that it is not possible to force format to print a 0.000, i.e. without any significant decimal places. Is it possible to do this somehow in R? You can round() before: R x - c(0.3456789,0.053) R round(x, digits = 3) [1] 0.346 0.000 R format(round(x, digits = 3)) [1] 0.346 0.000 hth, Z Thanks, Christian * ** Christian Hennig Fachbereich Mathematik-SPST/ZMS, Universitaet Hamburg [EMAIL PROTECTED], http://www.math.uni-hamburg.de/home/hennig/ # ### ich empfehle www.boag-online.de __ 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] Omitting constant in ols() from Design
Tobias Muhlhofer wrote: Hi! I need to run ols regressions with Huber-White sandwich estimators and the correponding standard errors, without an intercept. What I'm trying to do is create an ols object and then use the robcov() function, on the order of: f - ols(depvar ~ ind1 + ind2, x=TRUE) robcov(f) However, when I go f - ols(depvar ~ ind1 + ind2 -1, x=TRUE) I get the following error: Error in ols(nareit ~ SnP500 + d3yrtr - 1) : length of dimnames [2] not equal to array extent same with +0 instead of -1. Is there a different way to create an ols object without a constant? I can't use lm(), because robcov() needs an object from the Design() series. Or is there a different way to go about this? Tobias Muhlhofer ols does not support this. Sorry. -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University __ 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] merge data frames taking mean/mode of multiple macthes
Hello :) I have two data frames, one has properties taken on a piece by piece basis and the other has performance on a lot by lot basis. I wish to combine these two data frames but the problem is that each lot has multiple pieces and hence i need to take a mean of the properties of multiple pieces and match it to the row having data about the lot. I was wondering if there is a simple commmand, an extension of merge, or an option of merge i do not know which could easily do this work. Thank you :) = I believe in equality for everyone, except reporters and photographers. ~Mahatma Gandhi __ 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] RWinEdt install problem
The problem with RWinEdt can be resolved by NOT using User Profiles in WinEdt: I did a clean re-install of WinEdt 5.4, build 20050114. Then, executing library(RWinEdt) in the RGui did start up a properly configured R-WinEdt session of WinEdt. No error messages; the expected R buttons were now on the R-WinEdt menu bar. However, it would desirable if RWinEdt were revised so as to be compatible with WinEdt User Profiles. The reason is that WinEdt encourages use of User Profiles so that, when one upgrades WinEdt itself, the settings are not lost. (And, in general, the idea of separating a program such as WinEdt from user settings for it is a good one.) Uwe Ligges wrote: Murray Eisenberg wrote: I cannot get the R button to appear in RWinEdt. I'm running R 2.0.1 under Windows XP. I did a clean install of the latest WinEdt. Previously (for an earlier installation of WinEdt) I had RWinEdt running OK. Now, even though I have the distributed RWinEdt_1.6-2.zip extracted to the right place in the R directory, and when I execute library(RWinEdt) in the R Console, when RWinEdt opens I do not have the R button on the toolbar. How do I fix this? In case it matters, note that I'm using a WinEdt User configuration (i.e., a directory that WinEdt refers to as %b) in addition to the main WinEdt directory (the one that WinEdt refers to as %B). If you don't have write access to the WinEdt directory, you have to copy the R.ini file to, e.g., your local directory (%b), use the *manual* installation procedure as described in the ReadMe, but replace the command line args -e=R.ini by the full path specification, e.g.: -E=/path/to/%b/R.ini In a second (apparently private mail), you told that WinEdt ... 5.4 builds ... including the most recent one of 14 January 2005... do not work with the recent version of R-WinEdt, because 1. The first time, immediately I get a message that WinEdt.ini is corrupted and that a default copy (from the RWinEdt distribution I presume) is being used. Is this version also configured to use a User configuration? I don't have a WinEdt 5.4 version installed (still working with 5.2), but I will certainly take a look during the next one or two weeks. Uwe Ligges -- Murray Eisenberg [EMAIL PROTECTED] Mathematics Statistics Dept. Lederle Graduate Research Tower phone 413 549-1020 (H) University of Massachusetts413 545-2859 (W) 710 North Pleasant Streetfax 413 545-1801 Amherst, MA 01003-9305 __ 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 source code
-Ursprüngliche Nachricht- Von: Liaw, Andy [mailto:[EMAIL PROTECTED] Gesendet: Montag, 17. Jänner 2005 16:33 An: TEMPL Matthias; r-help@stat.math.ethz.ch Betreff: RE: [R] find source code From: TEMPL Matthias But how can I see the *documented* source code in Windows? I think i.e. in the /flexmix/library/man/all.rda file is the documented(?) code for all functions of Package flexmix, but the standard Windows XP cannot open .rda files correct. Is there a way to read the documented source code of a function under Windows and R2.0.1? Do you mean `commented' rather than `documented' (i.e., having a help page)? If so, I believe the only guaranteed way of doing that is by getting the package _source_ (i.e., the .tar.gz file) from CRAN and read the file in the R/ subdirectory after unpacking. This has nothing to do with hardware/software platform. Sorry for my poor english and thank you for your quick replies! I have meant the `commented' source code. Now I know that the commented source code is findable in the (unpacked) ..tar.gz file and not in the .zip file. Thank you very much, Matthias .rda files are really only readable by R, regardless of platform, and R on Windows doesn't behave differently than on other OS in this respect. Andy Thanks in advance, Matthias Betreff: Re: [R] find source code stats:::kruskal.test.default On Mon, 17 Jan 2005 [EMAIL PROTECTED] wrote: I am using R 2.0.2 on a WinXP I am trying to get the code of the Kruskal-Wallis test but kruskal.test function (x, ...) UseMethod(kruskal.test) environment: namespace:stats ls(3) [1] acf acf2AR add.scope .. [181] kruskal.test ks.test ksmooth ... [475] window- write.ftable xtabs class(kruskal.test) [1] function getS3method(kruskal.test,function) Error in getS3method(kruskal.test, function) : S3 method kruskal.test.function not found getS3method(stats::kruskal.test,function) Error in getS3method(stats::kruskal.test, function) : no function 'stats::kruskal.test' could be found I searched the archives and the answer was ' use getS3method ' . The help for getS3method is getS3method(f,class,optional=FALSE) so I am lost Can somebody tell me how to get the source listing of kruskal.test or of any other hidden function? Thanks Heberto Ghezzo Meakins-Christie Labs Canada __ 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-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 -- Notice: This e-mail message, together with any attachments, contains information of Merck Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates (which may be known outside the United States as Merck Frosst, Merck Sharp Dohme or MSD and in Japan, as Banyu) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system. -- __ 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] merge data frames taking mean/mode of multiple macthes
Dear Avneet the function aggregate (see also ?aggregate) could be useful for your problem. See the short example I've written below. dat1 - data.frame(lot = factor(1:10),y1 = rnorm(10)) str(dat1) dat2 - data.frame(nr = 1:100, lot = factor(rep(1:10, each = 10)),y2 = rnorm(100)) str(dat2) dat2.agr - aggregate(dat2$y, by = list(lot = dat2$lot), FUN = mean) names(dat2.agr)[2] - y2 dat.mer - merge(dat1, dat2.agr) str(dat.mer) Be careful about merging dataframes. There should always be a control that the right cases are merged together. Regards, Christoph Buser -- Christoph Buser [EMAIL PROTECTED] Seminar fuer Statistik, LEO C11 ETH (Federal Inst. Technology) 8092 Zurich SWITZERLAND phone: x-41-1-632-5414 fax: 632-1228 http://stat.ethz.ch/~buser/ avneet singh writes: Hello :) I have two data frames, one has properties taken on a piece by piece basis and the other has performance on a lot by lot basis. I wish to combine these two data frames but the problem is that each lot has multiple pieces and hence i need to take a mean of the properties of multiple pieces and match it to the row having data about the lot. I was wondering if there is a simple commmand, an extension of merge, or an option of merge i do not know which could easily do this work. Thank you :) = I believe in equality for everyone, except reporters and photographers. ~Mahatma Gandhi __ 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 -- Christoph Buser [EMAIL PROTECTED] Seminar fuer Statistik, LEO C11 ETH (Federal Inst. Technology) 8092 Zurich SWITZERLAND phone: x-41-1-632-5414 fax: 632-1228 http://stat.ethz.ch/~buser/ __ 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] 3d bar plot
On Mon, 17 Jan 2005 08:49:06 -0500, John Fox [EMAIL PROTECTED] wrote : Dear Marwan and Jonne, I don't think that there's a scatter3d package, so perhaps Marwan is referring to the scatter3d() function in the Rcmdr package. If so, that function won't make the kind of 3D graph that Jonne wants -- though the rgl package, on which scatter3d() is based, should be able to create the graph. I don't believe that the scatterplot3d() function in the scatterplot3d package can make the plot either, but I may be wrong. I had a function in my (Windows-only) djmrgl package to do plots like that; one of the things on my to-do list is to port it to rgl. This may happen in about a month. Duncan Murdoch __ 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] debian /etc/apt/sources.list for CRAN?
When I set up my debian linux (unstable) system, the only R debian packages were on CRAN, so I followed directions and added the last line to my /etc/apt/sources.list euclid: # m /etc/apt/sources.list deb http://debian.yorku.ca/debian/ unstable main non-free contrib deb http://debian.yorku.ca/debian/non-US unstable/non-US main contrib non-free deb http://hexamon.ccs.yorku.ca/ unixteam-debs/ deb http://cran.r-project.org/bin/linux/debian woody main But now, when I try to update the local package cache I get errors (below). Should I just delete the cran.r-project.org line above, or are there debian R packages elsewhere on CRAN that I should include instead? # apt-get update Hit http://debian.yorku.ca unstable/main Packages Hit http://debian.yorku.ca unstable/main Release Hit http://debian.yorku.ca unstable/non-free Packages Hit http://debian.yorku.ca unstable/non-free Release Hit http://debian.yorku.ca unstable/contrib Packages Hit http://debian.yorku.ca unstable/contrib Release Hit http://debian.yorku.ca unstable/non-US/main Packages Hit http://debian.yorku.ca unstable/non-US/main Release Hit http://debian.yorku.ca unstable/non-US/contrib Packages Hit http://debian.yorku.ca unstable/non-US/contrib Release Hit http://debian.yorku.ca unstable/non-US/non-free Packages Hit http://debian.yorku.ca unstable/non-US/non-free Release Hit http://hexamon.ccs.yorku.ca unixteam-debs/ Packages Ign http://hexamon.ccs.yorku.ca unixteam-debs/ Release Err http://cran.r-project.org woody/main Packages 404 Not Found Ign http://cran.r-project.org woody/main Release Failed to fetch http://cran.r-project.org/bin/linux/debian/dists/woody/main/binary-i386/Packages.gz 404 Not Found Reading Package Lists... Done E: Some index files failed to download, they have been ignored, or old ones used instead. -- Michael Friendly Email: [EMAIL PROTECTED] Professor, Psychology Dept. York University Voice: 416 736-5115 x66249 Fax: 416 736-5814 4700 Keele Streethttp://www.math.yorku.ca/SCS/friendly.html Toronto, ONT M3J 1P3 CANADA __ 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] Skewness test
Hi, is there a test for the H0 skewness=0 (or with skewness as test statistic and normality as H0) implemented in R? Thank you, Christian *** Christian Hennig Fachbereich Mathematik-SPST/ZMS, Universitaet Hamburg [EMAIL PROTECTED], http://www.math.uni-hamburg.de/home/hennig/ ### ich empfehle www.boag-online.de __ 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 source code
Thanks to all who answered my query, I forgot completely to call methods() first to check the true whole name of the function. Heberto Ghezzo Quoting Uwe Ligges [EMAIL PROTECTED]: Simon Wood wrote: stats:::kruskal.test.default and how to get there: methods(kruskal.test) # note, you probably want the default method! getS3method(kruskal.test, default) Uwe On Mon, 17 Jan 2005 [EMAIL PROTECTED] wrote: I am using R 2.0.2 on a WinXP I am trying to get the code of the Kruskal-Wallis test but kruskal.test function (x, ...) UseMethod(kruskal.test) environment: namespace:stats ls(3) [1] acf acf2AR add.scope .. [181] kruskal.test ks.test ksmooth ... [475] window- write.ftable xtabs class(kruskal.test) [1] function getS3method(kruskal.test,function) Error in getS3method(kruskal.test, function) : S3 method kruskal.test.function not found getS3method(stats::kruskal.test,function) Error in getS3method(stats::kruskal.test, function) : no function 'stats::kruskal.test' could be found I searched the archives and the answer was ' use getS3method ' . The help for getS3method is getS3method(f,class,optional=FALSE) so I am lost Can somebody tell me how to get the source listing of kruskal.test or of any other hidden function? Thanks Heberto Ghezzo Meakins-Christie Labs Canada __ 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-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] C-c C-c and tcltk cause R to get a segmentation fault
when tcltk is called and a C-c C-c is issued a message of Illegal instruction is issued and the R process is killed. To reproduce please do the following require(tcltk) C-c C-c It will say Illegal instruction I use a debian 2.4 kernel with R 2.0.1 tcltck version 2.0.1. I use tcltk to have gui for setwd, any other methods to graphically do this is also appreciated. Thanks so much for any solutions. Jean __ 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] debian /etc/apt/sources.list for CRAN?
On Mon, Jan 17, 2005 at 01:39:23PM -0500, Michael Friendly wrote: Should I just delete the cran.r-project.org line above, I think so. Plus, if you already point to Debian unstable, CRAN has nothing you wouldn't have otherwise. or are there debian R packages elsewhere on CRAN that I should include instead? Not that I know of. In the past, CRAN had current Debian packages of R itself for Debian flavours other than unstable which typically has the most current R version right at release time. However, migration to testing can take time so the we sometime kept the same . And for stable we used to have volunteer-donated rebuilds of the current R. This has gotten progressively more difficult as Debian stable got older and older, and process of creating the R packages started to take advantage of facilities to available to the versions of the tools in stable. We have talked at times about providing more CRAN packages as Debian packages, and possibly via CRAN itself rather than full Debian uploads. But I have not had time to work on that for a while, and that is unfortunately rather unlikely to change soon. Others have expressed an interest in helping as well but haven't gotten very far, unfortunately. Fellow Debian maintainer Matt Hope, has started a project on Debian's alioth host (that is open to non-Debianers who want to contribute) to coordinate debianisation of BioConductor. As this would use the same infrastructures, it could get used for CRAN too. But this project is also slow in progressing -- we're all overworked volunteers in this. Right now I'd say this is waiting for someone with a real itch to scratch. Regards, Dirk -- Better to have an approximate answer to the right question than a precise answer to the wrong question. -- John Tukey as quoted by John Chambers __ 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] Skewness test
On Mon, Jan 17, 2005 at 07:59:32PM +0100, Christian Hennig wrote: Hi, is there a test for the H0 skewness=0 (or with skewness as test statistic and normality as H0) implemented in R? Not that I know of, but tseries has the standard Jarque-Bera test that combines 3rd and 4th moment tests into a chisq(2) as on omnibus test for normality. Cutting and pasting from the code in tseries/R/test.R, one could probably take that apart and just use m1 - sum(x)/n m2 - sum((x-m1)^2)/n m3 - sum((x-m1)^3)/n m4 - sum((x-m1)^4)/n b1 - (m3/m2^(3/2))^2 STATISTICS - n * 1/6 * b1 as a chisq(1). But I have no idea what the power of that test would be. Hth, Dirk -- Better to have an approximate answer to the right question than a precise answer to the wrong question. -- John Tukey as quoted by John Chambers __ 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] bwplot: how not to draw outliers
RenE J.V. Bertin wrote:
Hello, and (somewhat belated) best wishes for 2005.
Can one order not to draw outliers in bwplot, or at least exclude them from the
vertical axis scaling? If so, how (or what doc do I need to consult)?
The options that have this effect in boxplot() do not appear to have any effect
with bwplot (although outline=FALSE in boxplot does *not* change the scaling).
Thanks,
RenE Bertin
RenE,
There may be other solutions but you can do this using the prepanel
option to set the ylim:
library(lattice)
set.seed(1)
z - data.frame(x = rt(100, 1), g = rep(letters[1:4], each = 25))
bwplot(x ~ g, z,
prepanel = function(x, y) {
bp - boxplot(split(y, x), plot = FALSE)
ylim - range(bp$stats)
list(ylim = ylim)
})
If you actually want to exclude the points (rather than just prevent
outliers from affecting the scale), you will have to modify the
panel.bwplot function in addition to using the above.
--sundar
__
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] subsetting like in SAS
I want to thank Petr Pikal, Robert Balshaw and Na Li for suggesting the use of unique or !duplicated on a subset of my data where unwanted variables have been removed. This worked perfectly. Denis Chabot On 13 Jan 2005 at 11:52, Denis Chabot wrote: Hi, Being in the process of translating some of my SAS programs to R, I encountered one difficulty. I have a solution, but it is not elegant (and not pleasant to implement). I have a large dataset with many variables needed to identify the origin of a sample, many to describe sample characteristics, others to describe site characteristics. I want only a (shorter) list of sites and their characteristics. If origin, ship_cat, ship_nb, trip and set are needed to identify a site, in SAS you'd sort on those variables, then read the data with: data sites; set alldata; by origin ship_cat ship_nb trip set; if first.set; keep list-of-variables-detailing-sites; run; In R I did this with the Lag function of Hmisc, and the original data set also needs to be sorted first: oL - Lag(origin) scL - Lag(ship_cat) snL - Lag(ship_nb) tL - Lag(trip) sL - Lag(set) same - origin==oL ship_cat==scL ship_nb==snL trip==tL set==sL sites - subset(alldata, !same, select=c(list-of-variables-detailing-sites) Could I do better than this? __ 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] problem installing RSPython
Hi,
I'm trying to install RSPython v0.5-4 on a debian machine (woody,
testing) but am having the following problem.
$R CMD INSTALL -c --library=/usr/lib/R/library RSPython_0.5-4.tar.gz 2err
But then...
$python
import RS
Error in .PythonInit() : Error in Python call: values
Error in library(RSPython) : .First.lib failed for 'RSPython'
Traceback (most recent call last):
File stdin, line 1, in ?
File /usr/lib/R/library/RSPython/Python/RS.py, line 69, in ?
library(RSPython)
File /usr/lib/R/library/RSPython/Python/RS.py, line 58, in library
return(call(library, name));
File /usr/lib/R/library/RSPython/Python/RS.py, line 21, in call
return RSInternal.call(name, args, other, convert, ref)
RuntimeError: error in calling R: Error in library(RSPython) : .First.lib
failed for 'RSPython'
Hmm... But the installation is ok, except for these warnings:
$more err
PythonCall.c: In function `RPy_get':
PythonCall.c:305: warning: passing arg 1 of `PyImport_ImportModule' discards
qualifiers from pointer target type
RCall.c: In function `RPy_callPython':
RCall.c:62: warning: passing arg 1 of `PyType_GenericNew' from incompatible
pointer type
I'm running R v2.0.1, Python v2.3.4 and have the r-base-dev and
python2.3-dev packages installed. Relevant environment variable settings:
PYTHONPATH=/usr/lib/python2.3:/usr/lib/python2.3/site-packages
R_HOME=/usr/lib/R
PYTHONPATH=${PYTHONPATH}:${R_HOME}/library/RSPython/Python
PYTHONPATH=${PYTHONPATH}:${R_HOME}/library/RSPython/libs
LD_LIBRARY_PATH=${R_HOME}/lib
Any suggestions? I'm probably overlooking something obvious. Thanks.
Robert
Robert Sams
SANCTUM FI LLP
Authorised and Regulated by the FSA.
Sending encrypted mail:
See http://pgp.mit.edu (search string 'sanctumfi') for updates.
-BEGIN PGP PUBLIC KEY BLOCK-
Version: GnuPG v1.0.6 (GNU/Linux)
Comment: For info see http://www.gnupg.org
mQGiBEHVOaIRBAC3kUplVB1o00GQXU9TkKmMWz/LiknbhLgDPBZ+1nw1ffb2FpXW
mYet2yja8YIG3H2LnVla1WGVyfAyZ+QRmnUgm2hOnP7LNZIoHctnGqLmtQvOXvHz
xoDonFAl/ztBFE9aNPbiL4nlgdz9GS6LN6hbw9GTdYGip71QhaeVIRR3HwCgySSl
rUtSV8C7nbHR9C+zwku3EpMD/0yoq1R4lQgJGNbyjzzCRWRblK5cKLh1XUYG3JSc
ltLhoCZMvR+359FUSz+jEbbJaLRpquX48Wjv+7WW5KNVm2nPHSZrZ6tr+nm/ov1Y
DQxbIvBHxLXxltDWJlL/gg3bPaSIRlj/KVw0fB0NU1b25eGFRTtlHEvkAROj92sv
MiaSA/9jjEi2H0+yWujcBxJ6syUjWLlgRxvm85sJBihyan4ufAMFRria+QKx7ZMf
A7MNJ+r7ULdqCPsPdZP3kC7GNfLXBzizy3d2HSB/0oB7AjIoXrYyQvXQjFNQQX+u
XjeRGhALxou3H1NEPiCiHJiiaPU6Uh+KYhBCDOYZpc82FgKwWLQzUm9iZXJ0IFNh
bXMgKFNhbmN0dW0gRkkgTExQKSA8cm9iZXJ0QHNhbmN0dW1maS5jb20+iF0EExEC
AB0FAkHVOaIFCQHhM4AFCwcKAwQDFQMCAxYCAQIXgAAKCRB4Q4+orHX8Yk0hAJ9+
odzCRiih6wZz4NOOSVboJP+lngCeNvFGVxVQW35/qpTaF6wsym9jehi5AQ0EQdU5
oxAEALZEnBUQqKiF/gUqK7zyLJarsVxGsmuj0pkV5gFwCbChA4RA7QgHjknJT3Qd
jLUJOa+rW49WtbDCOBv+VOVp//gLROByZpizW4BYaOw01kI9emMuoc6el6nYXarJ
6aZcA84IFBifdi2a8lB3ofhQuWc/YmxLjcOKbkaIC9lUYHrzAAMGA/0RRhkXCHCL
zRSQj+7nSBE4MTeMJycdytl1wnpWkRUa8MoUYBF6/3oiyCnO9bHbOAkQrULSWRLA
YsUJv0c1b6Dht5LVChGikJqKgCzWVEVUI7ob0F2LctvDxhZLlCctHapFGZn9+6pi
rZW+2XkBmbqhJ8ybKsRAIJNy7OV3sIHoVYhMBBgRAgAMBQJB1TmjBQkB4TOAAAoJ
EHhDj6isdfxizmIAn3I/mZyfAuBNZl0lG+9XpAhR80ThAKDAJEnXrH8dX30rRwDz
1mgpwRYCiw==
=59j7
-END PGP PUBLIC KEY BLOCK-
__
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] bwplot: how not to draw outliers
On Monday 17 January 2005 14:51, Sundar Dorai-Raj wrote:
RenE J.V. Bertin wrote:
Hello, and (somewhat belated) best wishes for 2005.
Can one order not to draw outliers in bwplot, or at least exclude
them from the vertical axis scaling? If so, how (or what doc do I
need to consult)? The options that have this effect in boxplot() do
not appear to have any effect with bwplot (although outline=FALSE
in boxplot does *not* change the scaling).
Thanks,
RenE Bertin
RenE,
There may be other solutions but you can do this using the prepanel
option to set the ylim:
library(lattice)
set.seed(1)
z - data.frame(x = rt(100, 1), g = rep(letters[1:4], each = 25))
bwplot(x ~ g, z,
prepanel = function(x, y) {
bp - boxplot(split(y, x), plot = FALSE)
ylim - range(bp$stats)
list(ylim = ylim)
})
If you actually want to exclude the points (rather than just prevent
outliers from affecting the scale), you will have to modify the
panel.bwplot function in addition to using the above.
Right. panel.bwplot calls
stats - boxplot.stats(y[x == xval], coef = coef)
I guess it should have a 'do.out' argument as well. A workaround
(without changing the panel function) might be to use something like
bwplot(voice.part ~ height, data = singer,
par.settings = list(plot.symbol = list(col = transparent)))
(neither of these would change the limits, of course)
-Deepayan
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] bwplot: how not to draw outliers
Sundar Dorai-Raj wrote:
RenE J.V. Bertin wrote:
Hello, and (somewhat belated) best wishes for 2005.
Can one order not to draw outliers in bwplot, or at least exclude them
from the vertical axis scaling? If so, how (or what doc do I need to
consult)?
The options that have this effect in boxplot() do not appear to have
any effect with bwplot (although outline=FALSE in boxplot does *not*
change the scaling).
Thanks,
RenE Bertin
RenE,
There may be other solutions but you can do this using the prepanel
option to set the ylim:
library(lattice)
set.seed(1)
z - data.frame(x = rt(100, 1), g = rep(letters[1:4], each = 25))
bwplot(x ~ g, z,
prepanel = function(x, y) {
bp - boxplot(split(y, x), plot = FALSE)
ylim - range(bp$stats)
list(ylim = ylim)
})
If you actually want to exclude the points (rather than just prevent
outliers from affecting the scale), you will have to modify the
panel.bwplot function in addition to using the above.
--sundar
You may also want to try
library(Hmisc)
library(lattice)
bwplot(..., panel=panel.bpplot)
?panel.bpplot
--
Frank E Harrell Jr Professor and Chair School of Medicine
Department of Biostatistics Vanderbilt University
__
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] How do I format something as 0.000?
On Mon, 2005-01-17 at 14:19 -0600, Dirk Eddelbuettel wrote: On Mon, Jan 17, 2005 at 04:49:35PM +0100, Christian Hennig wrote: Hi, I would like to use the format function to get numbers all with three digits to the right of the decimal point, even in cases where there is no significant digit left. For example, I would like to get c(0.3456789,0.053) as 0.346 0.000. It seems that it is not possible to force format to print a 0.000, i.e. without any significant decimal places. Is it possible to do this somehow in R? sprintf can do that sprintf(%3.3f %3.3f, 0.3456789, 0.0053) [1] 0.346 0.000 You'd have to loop over your vector to do it one by one, I think. To do this in vectorized fashion, you can use formatC(): x - c(0.3456789, 0.0053) formatC(x, format = f, digits = 3) [1] 0.346 0.000 See ?formatC for more help. HTH, Marc Schwartz __ 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 of mixed effect in R
Dear all, I have a question about mixed effect model in R. The data set has 5 variables, X(response),subject, times, repeat, indicator The model is X_hijk=a_h+Z_h*b_i+r(ij)+e_hijk , where h=0,1(indicator), i=1,...,n(subject), j=1,...,n_i(times within subject; nested effect),k=1,2,3(repeat). Z_h=1 if h=1 =0 if h=0 b_i~N(0,c^2) random effect of subject r(ij)~N(0,d^2) random effect of times within subject e_hijk~N(0,e^2) error term which is independent with the random effects. The purpose is to estimate the parameters a_h, c^2,d^2,e^2. My question is how to fit the model in R; more specifically, how to specify the formula of random effect in command lme in R. Thanks very much for your help. - Yahoo!©_¼¯¹q¤l«H½c [EMAIL PROTECTED]@«H°e·R¤ß¡AYahoo!©_¼¯¨àµ£§U¾Çpµe¡C°¨¤W°Ñ¥[ [[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
Re: [R] debian /etc/apt/sources.list for CRAN?
On Mon, Jan 17, 2005 at 02:14:04PM -0600, Dirk Eddelbuettel wrote: On Mon, Jan 17, 2005 at 01:39:23PM -0500, Michael Friendly wrote: Should I just delete the cran.r-project.org line above, I think so. Plus, if you already point to Debian unstable, CRAN has nothing you wouldn't have otherwise. or are there debian R packages elsewhere on CRAN that I should include instead? Not that I know of. In the past, CRAN had current Debian packages of R itself for Debian flavours other than unstable which typically has the most current R version right at release time. However, migration to testing can take time so the we sometime kept the same . And for stable we used to have volunteer-donated rebuilds of the current R. This has gotten progressively more difficult as Debian stable got older and older, and process of creating the R packages started to take advantage of facilities to available to the versions of the tools in stable. Not sure if this is still relevant, but the backport I made has been apt-getable from this address for a while: deb http://people.debian.org/~cts/debian stable/ I'd prefer if this where integrated in CRAN, but I don't think I can make that directory available via rsync (unless you are a debian developer). Probably the debian server can handle the extra load for a few people still running Debian/stable. I should be able to keep the packages current, but not necessarily within a day, like Dirk manages to do. Christian __ 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] rpart
Hi, there: I am working on a classification problem by using rpart. when my response variable y is binary, the trees grow very fast, but if I add one more case to y, that is making y has 3 cases, the tree growing cannot be finished. the command looks like: x-rpart(r0$V142~.,data=r0[,1:141], parms=list(split='gini'), cp=0.01) changing cp or removing parms does not help. summary($V142) gives like: summary(r0$V142) 0 1 2 370 14 16 I am not sure if rpart can do this or there is something wrong with my approach. Please be advised. Ed __ 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] debian /etc/apt/sources.list for CRAN?
I think the debian packages are now maintened in the official debian repository. http://packages.debian.org/cgi-bin/search_packages.pl?keywords=r-cransearchon=namessubword=1version=unstablerelease=all http://packages.debian.org/cgi-bin/search_packages.pl?keywords=r-basesearchon=namessubword=1version=unstablerelease=all So you don't need a specific entry in your source.list anymore. -- Julien Damon [EMAIL PROTECTED] http://julien.damon.free.fr __ 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] debian /etc/apt/sources.list for CRAN?
On Mon, Jan 17, 2005 at 09:00:53PM +0100, Julien Damon wrote: I think the debian packages are now maintened in the official debian repository. Yes, as they have been since December 1997. Dirk -- Better to have an approximate answer to the right question than a precise answer to the wrong question. -- John Tukey as quoted by John Chambers __ 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] Weighted least squares
Hi, I would like to run a weighted least squares with the the weighting matrix W. I ran the following two regressions, (W^-1)Y = Xb + e Y = WXb+ We In both cases, E[bhat] = b. I used the following commands in R lm1 - lm(Y/W ~ X) lm2 - lm(Y ~ W:X, weights = W) where Y - rnorm(10,1) X - Y + rnorm(10,1) W - 1:10 In lm2, I believe W is applied to the error term, resulting in WLS. However the estimated coefficients in lm1 and lm2 are really different. I tried glm as well, but the result was the same as lm. Any advice would be appreciated, Hsu Ming __ 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] lme confusion
Hi, this is my first time using the nlme package, and I ran into the following puzzling problem. I estimated a mixed effects model using lme, once using groupedData, once explicitly stating the equations. I had the following outputs. All the coefficients were similar, but they're always slightly different, making me think that it's not due to numerical error. Also, what is the Corr field in the Random Effects output? Is it the correlation between the various regressors? Here are the outputs. 1. Linear mixed-effects model fit by REML Data: groupedData(dPx ~ EMX + EMY | Session, data = X.cen) AIC BIClogLik 834.1692 862.532 -407.0846 Random effects: Formula: ~EMX + EMY | Session Structure: General positive-definite StdDevCorr (Intercept) 1.0205525 (Intr) EMX EMX 0.2708627 1 EMY 0.2795289 -1 -1 Residual5.5076376 Fixed effects: dPx ~ EMX + EMY Value Std.Error DF t-value p-value (Intercept) 1.3011219 0.6807083 121 1.911423 0.0583 EMX 0.7878296 0.2539316 121 3.102526 0.0024 EMY -0.1566070 0.1534066 121 -1.020862 0.3094 Correlation: (Intr) EMX EMX 0.151 EMY -0.573 -0.092 Standardized Within-Group Residuals: Min Q1 Med Q3 Max -3.00618687 -0.23680151 -0.03431868 0.15386198 6.27114243 Number of Observations: 129 Number of Groups: 6 === 2. Linear mixed-effects model fit by REML Data: X.cen AIC BIClogLik 834.457 862.8199 -407.2285 Random effects: Formula: ~EMX + EMY | Session Structure: General positive-definite, Log-Cholesky parametrization StdDevCorr (Intercept) 1.0101137 (Intr) EMX EMX 0.2108649 0.857 EMY 0.2995491 -0.944 -0.882 Residual5.5104113 Fixed effects: dPx ~ EMX + EMY Value Std.Error DF t-value p-value (Intercept) 1.3062194 0.6823464 121 1.914305 0.0579 EMX 0.7612238 0.2440504 121 3.119125 0.0023 EMY -0.1677985 0.1618076 121 -1.037025 0.3018 Correlation: (Intr) EMX EMX 0.059 EMY -0.552 -0.002 Standardized Within-Group Residuals: Min Q1 Med Q3 Max -3.00604994 -0.24210830 -0.01660797 0.14846499 6.27931955 Number of Observations: 129 Number of Groups: 6 __ 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] Why can't run Gamma Distribution by GLM?
y-cy-c(15,16,17,0,20,50,0,11,60,12) x-c(1,6,3,11,13,20,12,14,15,3) gamma-glm(y~x,family=Gamma()) Error in eval(expr, envir, enclos) : Non-positive values not allowed for the gamma family but if i change data of y is y1-c(15,16,17,12,20,50,51,11,60,12) ## doesn't have zero then I can run. Gamma Distribution can run for y = o ?? I would like to know, why? Thand and Best regards, Mathinee - Meet the all-new My Yahoo! Try it today! [[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] X11 installation problem Linux X86_64
Hello all, This is my first time posting, so forgive my ignorance. I've searched high and low but haven't come across the specific answer to my questions. configure runs fine, then make gives this error: ... gcc -shared -L/usr/local/lib -o R_X11.so dataentry.lo devX11.lo rotated.lo rbitmap.lo -L/usr/X11R6/lib -lX11 -ljpeg -lpng -lz -lreadline -ldl -lncurses -lm /usr/bin/ld: skipping incompatible /usr/X11R6/lib/libX11.so when searching for -lX11 /usr/bin/ld: skipping incompatible /usr/X11R6/lib/libX11.a when searching for -lX11 /usr/bin/ld: cannot find -lX11 collect2: ld returned 1 exit status make[4]: *** [R_X11.so] Error 1 make[4]: Leaving directory `/root/R-2.0.1/src/modules/X11' ... This is a 64-bit machine, so I'm wondering if the problem stems from make not looking in the /usr/X11R6/lib64 directory, as opposed to /usr/X11R6/lib64. Both dirs are in /etc/ld.so.conf. I also tried configure --x-libraries=/usr/X11R6/lib64, but that produced the same error. I believe that I have all the requisite packages installed. Could someone please point me in the right direction? Thanks in advance -Robert __ 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] 3d bar plot
This graph -
http://www.math.hope.edu/~tanis/dallas/images/disth36.gif
is an example I found at
http://www.math.hope.edu/~tanis/dallas/disth1.html
created by Maple.
Does anybody know how to create something similar in R?
I have a feeling it could be possible using scatterplot3d
(perhaps with type=h, the fourth example in help('scatterplot3d')?),
but I cannot figure it out.
Sorry to butt in with a more fundamental question. Is this really the kind
of graph we want to cultivate and support? In my oppinion, it is hardly ever
necessary to have a graph in 3D or even in higher dimensions (one certain
exception is if one tries to spin a higly dimensional dataset in search of
patterns as you can do in ggobi and there might certainly be others).
At least the graph presented in the example does - in my eyes - not warrant
a 3D plot. Why not just draw curves for each of the n's in a plot of 'A'
against 'row'? This would enable a reader to make straightforward
comparisons of the curves and allow to estimate the height of the 'columns'
along the 'A'-axis much more easily.
Only because we can easily create 3D graphs, I do not believe that we should
use them often. Only if a careful evaluation of alternatives was not
promising success I would resign myself to using 3D graphs.
Lorenz
-
Lorenz Gygax, Dr. sc. nat.
Centre for proper housing of ruminants and pigs
Swiss Federal Veterinary Office
agroscope FAT Tänikon, CH-8356 Ettenhausen / Switzerland
__
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] 3d bar plot
Dear John,
Yes, I meant the scatter3d function in the Rcmdr package -- I will 'behave' next
time :-)
Jonne asked for 'something similar in R' -- hence the suggestion to also use the
package scatterplot3d.
Best Marwan
---
Marwan Khawaja http://staff.aub.edu.lb/~mk36/
---
-Original Message-
From: John Fox [mailto:[EMAIL PROTECTED]
Sent: Monday, January 17, 2005 3:49 PM
To: 'Marwan Khawaja'; 'R user'
Cc: r-help@stat.math.ethz.ch
Subject: RE: [R] 3d bar plot
Dear Marwan and Jonne,
I don't think that there's a scatter3d package, so perhaps
Marwan is referring to the scatter3d() function in the Rcmdr
package. If so, that function won't make the kind of 3D graph
that Jonne wants -- though the rgl package, on which
scatter3d() is based, should be able to create the graph.
I don't believe that the scatterplot3d() function in the
scatterplot3d package can make the plot either, but I may be wrong.
I hope this helps.
John
John Fox
Department of Sociology
McMaster University
Hamilton, Ontario
Canada L8S 4M4
905-525-9140x23604
http://socserv.mcmaster.ca/jfox
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of
Marwan Khawaja
Sent: Sunday, January 16, 2005 7:04 PM
To: 'R user'; r-help@stat.math.ethz.ch
Subject: RE: [R] 3d bar plot
You can check these packages,
?scatterplot3d
?scatter3d
Best Marwan
---
Marwan Khawaja http://staff.aub.edu.lb/~mk36/
---
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of R user
Sent: Monday, January 17, 2005 12:37 PM
To: r-help@stat.math.ethz.ch
Subject: [R] 3d bar plot
This graph -
http://www.math.hope.edu/~tanis/dallas/images/disth36.gif
is an example I found at
http://www.math.hope.edu/~tanis/dallas/disth1.html
created by Maple.
Does anybody know how to create something similar in R?
I have a feeling it could be possible using scatterplot3d
(perhaps
with type=h, the fourth example in help('scatterplot3d')?), but I
cannot figure it out.
Thanks in advance,
Jonne.
__
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-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] rpart
On Mon, 17 Jan 2005, Weiwei Shi wrote: I am working on a classification problem by using rpart. when my response variable y is binary, the trees grow very fast, but if I add one more case to y, that is making y has 3 cases, Do you mean 3 classes?: you have many more than 3 cases below. the tree growing cannot be finished. Whatever does that mean? Please see the posting guide and supply the information it asks for, a reproducible example and what happens when you run it and why you think it is wrong. the command looks like: x-rpart(r0$V142~.,data=r0[,1:141], parms=list(split='gini'), cp=0.01) changing cp or removing parms does not help. summary($V142) gives like: summary(r0$V142) 0 1 2 370 14 16 I am not sure if rpart can do this or there is something wrong with my approach. What is `this' you want to do? Rpart works well with multiple classes: see for example MASS4. -- 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 __ 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] Weighted least squares
On Mon, 17 Jan 2005, Ming Hsu wrote: I would like to run a weighted least squares with the the weighting matrix W. This is generalized not weighted least squares if W really is a matrix and not a vector of case-by-case weights. I ran the following two regressions, (W^-1)Y = Xb + e Y = WXb+ We If W is a diagonal matrix, the weights for the second are W^(-2) and you used W below. In both cases, E[bhat] = b. I used the following commands in R lm1 - lm(Y/W ~ X) lm2 - lm(Y ~ W:X, weights = W) where Y - rnorm(10,1) X - Y + rnorm(10,1) W - 1:10 That W is not a matrix! In lm2, I believe W is applied to the error term, resulting in WLS. However the estimated coefficients in lm1 and lm2 are really different. I tried glm as well, but the result was the same as lm. Any advice would be appreciated, Please do check that you supply an example that agrees with your words. Use lm.gls in MASS or gls in nlme for generalized least squares, if that is what you meant. -- 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 __ 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
