Re: [R] rgl build warnings and loading error on Linux
On Wed, Apr 9, 2008 at 9:30 PM, Prof Brian Ripley [EMAIL PROTECTED] wrote: I've never seen that. Is there something unusual about the filesystem so it does not recognize rgl/configure is executable? (We've seen that on SMB filesystems with the wrong mount options.) In /etc/fstab, I have the following. tmpfs /tmptmpfs defaults,size=100M,mode=1777,noexec,nosuid 0 0 Mounting /tmp with noexec is a security measure, since /tmp may easily become a vulnerable spot on a Linux system. What I suggest you try is - unpack the rgl tarball. - cd rgl - R CMD ./configure - cd .. - R CMD INSTALL rgl Running R CMD INSTALL rgl from my reiserfs / partition was enough for the ./configure script to get executed and for rgl to build properly [1]. Now I can dyn.load() rgl with no error messages, although it is somewhat crashy. I will report here if I get any meaningful error messages. Thanks goes to all who contributed with their suggestions. Best regards, Liviu [1] http://www.geocities.com/landroni/rgl_build_02.txt __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Question: ACD?
Hello everyone, Is it possible to perform Autoregressive Conditional Duration (ACD) in R? I'm a graduate student at U of Oregon and want to use ACD in my research project. Please advise. Best, Yuki __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] rgl build warnings and loading error on Linux
From the 'R Installation and Administration Manual':
Note that @env{TMPDIR} will be used to execute @command{configure}
scripts when installing packages, so if @code{/tmp} has been mounted as
@samp{noexec}, @env{TMPDIR} needs to be set to a directory from which
execution is allowed.
'If all else fails, read the manual'.
On Thu, 10 Apr 2008, Liviu Andronic wrote:
On Wed, Apr 9, 2008 at 9:30 PM, Prof Brian Ripley [EMAIL PROTECTED] wrote:
I've never seen that. Is there something unusual about the filesystem so
it does not recognize rgl/configure is executable? (We've seen that on SMB
filesystems with the wrong mount options.)
In /etc/fstab, I have the following.
tmpfs /tmptmpfs
defaults,size=100M,mode=1777,noexec,nosuid 0 0
Mounting /tmp with noexec is a security measure, since /tmp may
easily become a vulnerable spot on a Linux system.
I suggest you talk to an expert about that.
What I suggest you try is
- unpack the rgl tarball.
- cd rgl
- R CMD ./configure
- cd ..
- R CMD INSTALL rgl
Running R CMD INSTALL rgl from my reiserfs / partition was enough
for the ./configure script to get executed and for rgl to build
properly [1]. Now I can dyn.load() rgl with no error messages,
although it is somewhat crashy. I will report here if I get any
meaningful error messages.
Thanks goes to all who contributed with their suggestions.
Best regards,
Liviu
[1] http://www.geocities.com/landroni/rgl_build_02.txt
--
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
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Re: [R] I have a 3 by 2 plots per page. How do I specify a title at the top centre of each page ?
Found the solution, p - par(mfrow = c(3, 2), oma = c(0, 0, 2.1, 0)) title(main = paste(Title is here), outer = TRUE, cex.main = 1.5, font.main = 4) On Thu, Apr 10, 2008 at 11:20 AM, Ng Stanley [EMAIL PROTECTED] wrote: Hi, I have a 3 by 2 plots per page. How do I specify a title at the top centre of each page ? [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] legend placement
Hi, I am plotting 5 charts using p - par(mfrow = c(3, 2), how can I place my legend in the last region ? I don't wan to put it into the margin. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Number of words in a string
On 10 Apr 2008, at 07:43, Shubha Vishwanath Karanth wrote: So powerful, the gsub... But I really don’t understand the how the regular expressions like *\\S+$, need to be used and how to make best use of it... Any article/material/links that I can go through? A good starting point is: type ?regex in your console. Furthermore search in the net for regular expression. http://en.wikipedia.org/wiki/Regular_expression http://en.wikipedia.org/wiki/Regular_expression_examples http://www.regular-expressions.info/ There are some variants of regexp engine on the market but the core syntax should be the same. Regards, --Hans __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Adding columns to a grouped data frame
Hello! I'm working with a big data set of patients. The data consists of different variables sorted rowwise for each patient. Now I want to add a new variable for each patient by adding two different variables of the data frame. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Stderr
Hi everyone, I need to get an error message as an object in the std output console. I can get it as a file with the following instructions: # Save error mesage: error1 - file(error1.txt, open=wt) sink(error1, type=message) experiment - function(data) With this, the error messages get saved in the file, but i need them as object in order to work with it in the console. Is it possible? Thanks -- Patricia García [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to create a legend without plot, and to use scientific notation for axes label ?
Ng Stanley wrote: Hi, I have a 3 by 2 plots per page, and would like to place a legend on the last region. How to do that ? Create an empty plot, e.g.: plot(1, type=n, axes=FALSE, xlab=, ylab=) legend(1, 1, legend = c(Hello, World), col=1:2, lwd=2, cex=3, xjust=0.5, yjust=0.5) Uwe Ligges Also, is there any way to specify scientific notation for axes label ? [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to create a legend without plot, and to use scientific notation for axes label ?
Uwe Ligges wrote: Ng Stanley wrote: Hi, I have a 3 by 2 plots per page, and would like to place a legend on the last region. How to do that ? Create an empty plot, e.g.: plot(1, type=n, axes=FALSE, xlab=, ylab=) legend(1, 1, legend = c(Hello, World), col=1:2, lwd=2, cex=3, xjust=0.5, yjust=0.5) Uwe Ligges Also, is there any way to specify scientific notation for axes label ? Oh, I was too quick and forgot the 2nd question: Use axis() with formatC(). Uwe Ligges [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] how to read data from table based a condition
Xin wrote: Dear All: I imported a table into R. But I want to read a variable (y) from this table conditional on another variable (x=1) in the table. y-data[,7] x-data[,3] I want to know the mean of y if corresponding x=1. I tried if (x==1) y3-y It does not work. Anyone can give a help? Is this homework? Please do read the posting guide and An Introduction to R! Uwe Ligges Thanks! Xin [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Beautifying axis tick labels
Hi, For example, the y axis shows 0 50 150. Is there any way to beautify the tick labels to get 0 5 10 15, and at the top of y-axis x10^5 (superscript 5) ? My plots all have different ylim, how to perform the beautification automatically ? Thanks Stanley [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Beautifying axis tick labels
For example, the y axis shows 0 50 150. Is there any way to
beautify the tick labels to get 0 5 10 15, and at the top of y-axis
x10^5
(superscript 5) ? My plots all have different ylim, how to perform the
beautification automatically ?
plot((0:15)*1e5, yaxt=n, ylab=)
axis(side=2, at=c(0,5,15)*1e5, labels=c(0,5,15))
mtext(x10^5, adj=-.1)
Regards,
Richie.
Mathematical Sciences Unit
HSL
ATTENTION:
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Re: [R] how to read data from table based a condition
Marc Moragues wrote: Xin jasonshi510 at hotmail.com writes: y-data[,7] x-data[,3] I want to know the mean of y if corresponding x=1. Try this: mean(data[data[,3]==1,data[,7]) Folks, please! 1. If you answer, please write at least syntactically valid code (look at your index brackets). Just mean(y[x==1]) should do the trick 2. It is a bad idea to do others' homeworks, they won't learn much this way. Best wishes, Uwe Ligges You can also look at ?subset. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Stderr
Hi, sorry for the last sentence, i was trying to make a generic statement by writing function So the code has to be: # Save error mesage: error1 - file(error1.txt, open=wt) sink(error1, type=message) experiment - somefunction(data) (I mean no matter what function is...) error1 is not a variable, y can't watch what contains, it is only the definition of a file What i wanted was in fact to create a variable with the error message, I can do it of course by reading the file, but my question is about doing it directly. Thanks 2008/4/10, Uwe Ligges [EMAIL PROTECTED]: Patricia García wrote: Hi everyone, I need to get an error message as an object in the std output console. I can get it as a file with the following instructions: # Save error mesage: error1 - file(error1.txt, open=wt) sink(error1, type=message) experiment - function(data) With this, the error messages get saved in the file, but i need them as object in order to work with it in the console. I'm not sure what you are going to do, note that the last line contains an incomplete statement... If you want an object: you already have got the object error1 ... If you want error handling facilities, see ?try and its See Also section. Uwe Ligges Is it possible? Thanks __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Patricia García [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Error: expected the collection operator c error pos 98 (error on line 1)
Quick inspection shows that we cannot do anything.
In BUGS, Y indicates a scalar and Y[] indicates a vector.
For scalar Y, you need Y=0.0E+00 in your data file, but for vector
Y[], you need Y=c(0.0E+00) in your data file.
This means you need to know what Y is in the model and I do not see any
API I can use to ask the BRugs.dll what Y actually is.
So question redirected to Andrew Thomas (in CC).
Best wishes,
Uwe
Uwe Ligges wrote:
Blanchard, Suzette wrote:
Greetings,
I implemented BRugs to run the EWOC model with a cohort size
N=1. I output the simulation data using bugsdata(data), where data
is the following list.
data
$Dose
[1] 140
$Y
[1] 0
bugsdata(data) puts out the file data.txt as follows.
list(Dose=1.4E+02, Y=0.0E+00)
after I type the following line
modelData(data.txt) # read data file
I get the ERROR:
expected the collection operator c error pos 98 (error on line 1)
If I rewrite the file
list(Dose=c(1.4E+02), c(Y=0.0E+00))
it runs fine. Can you suggest a way to get the output dataset to
automatically put the
c( ) on the data when the sample size is 1?
Hmmm, I will take a look how to implement it.
I guess you have modeled Y to be a vector by indexing with brackets in
your BUGS model? It works for me if I use Y without index brackets in a
BUGS model file.
Best wishes,
Uwe
Thank you,
Suzette
Suzette Blanchard, Ph.D.
Assistant Professor, Dept. of Biostatistics
City of Hope
1500 East Duarte Rd
Duarte, CA 91010-3000
ph: (626) 256-4673 ext:64446
[EMAIL PROTECTED]
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Re: [R] bucketing in histograms
Mark Farnell wrote: Hi I wish to draw a histogram for a numeric array and specify a bucket size (say 5 units per bar and the height of that bar equals to the average of that 5 units) how can I do that? Sometimes I wonder what is going on here. Folks, please read the posting guide and the help pages before posting! In this case ?hist clearly reveals how to set breaks. Uwe Ligges Thanks! Mark __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Error: expected the collection operator c error pos 98 (error on line 1)
Blanchard, Suzette wrote:
Greetings,
I implemented BRugs to run the EWOC model with a cohort size N=1. I
output the simulation data using bugsdata(data), where data is the following
list.
data
$Dose
[1] 140
$Y
[1] 0
bugsdata(data) puts out the file data.txt as follows.
list(Dose=1.4E+02, Y=0.0E+00)
after I type the following line
modelData(data.txt) # read data file
I get the ERROR:
expected the collection operator c error pos 98 (error on line 1)
If I rewrite the file
list(Dose=c(1.4E+02), c(Y=0.0E+00))
it runs fine. Can you suggest a way to get the output dataset to
automatically put the
c( ) on the data when the sample size is 1?
Hmmm, I will take a look how to implement it.
I guess you have modeled Y to be a vector by indexing with brackets in
your BUGS model? It works for me if I use Y without index brackets in a
BUGS model file.
Best wishes,
Uwe
Thank you,
Suzette
Suzette Blanchard, Ph.D.
Assistant Professor, Dept. of Biostatistics
City of Hope
1500 East Duarte Rd
Duarte, CA 91010-3000
ph: (626) 256-4673 ext:64446
[EMAIL PROTECTED]
-
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Re: [R] Stderr
Patricia García wrote: Hi, sorry for the last sentence, i was trying to make a generic statement by writing function So the code has to be: # Save error mesage: error1 - file(error1.txt, open=wt) sink(error1, type=message) experiment - somefunction(data) (I mean no matter what function is...) So you want to implement error handling for function somefunction()? error1 is not a variable, y can't watch what contains, it is only the definition of a file No, error1 is an *object* that contains information about the opened connection to the file. What i wanted was in fact to create a variable with the error message, I can do it of course by reading the file, but my question is about doing it directly. As I already said in my former mail, error handling is available, please read ?try. Uwe Ligges Thanks 2008/4/10, Uwe Ligges [EMAIL PROTECTED]: Patricia García wrote: Hi everyone, I need to get an error message as an object in the std output console. I can get it as a file with the following instructions: # Save error mesage: error1 - file(error1.txt, open=wt) sink(error1, type=message) experiment - function(data) With this, the error messages get saved in the file, but i need them as object in order to work with it in the console. I'm not sure what you are going to do, note that the last line contains an incomplete statement... If you want an object: you already have got the object error1 ... If you want error handling facilities, see ?try and its See Also section. Uwe Ligges Is it possible? Thanks __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to create a legend without plot, and to use scientific notation for axes label ?
Hi, How can I use formatC to convert 600 to 6e5 and not 6e+05 ? formatC(60) [1] 6e+05 formatC(60, format=e, digit=0) [1] 6e+05 -Original Message- From: Uwe Ligges [mailto:[EMAIL PROTECTED] Sent: Thursday, April 10, 2008 17:11 To: Ng Stanley Cc: r-help Subject: Re: [R] How to create a legend without plot, and to use scientific notation for axes label ? Uwe Ligges wrote: Ng Stanley wrote: Hi, I have a 3 by 2 plots per page, and would like to place a legend on the last region. How to do that ? Create an empty plot, e.g.: plot(1, type=n, axes=FALSE, xlab=, ylab=) legend(1, 1, legend = c(Hello, World), col=1:2, lwd=2, cex=3, xjust=0.5, yjust=0.5) Uwe Ligges Also, is there any way to specify scientific notation for axes label ? Oh, I was too quick and forgot the 2nd question: Use axis() with formatC(). Uwe Ligges [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] How to estimate a hazard ratio using an external hazard function
Hi, I would like to compare the hazard functions of two samples using the Cox proportional hazards model. For sample 1 I have individual time-to-event data. For sample 2 I don't have individual data, but grouped data that allows to obtain a hazard function. I am wondering if there is an R function that allows to obtain a hazard ratio of the two hazard funtions (under the proportionality assumption) taking into account the censoring of the data? I am aware of survexp and survdiff functions, but I am not sure if that is the best way to do what I need. Any help will be highly appreciated. Montse Rue Department of Basic Medical Sciences University of Lleida (Spain) P.S. I sent this message yesterday, but I think I did something wrong and it did not arrive to the list. I apologize if I sent it twice. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Skipping specified rows in scan or read.table
Hi Ravi, One thing I tend to do is, when using read.table, specify the option 'colClasses='character''. This forces everything to be read as a character. From there, as.numeric works fine, and you don't have to deal with factors and reconverting them. Hope this helps Abhijit Ravi Varadhan wrote: Hi, I have a data file, certain lines of which are character fields. I would like to skip these rows, and read the data file as a numeric data frame. I know that I can skip lines at the beginning with read.table and scan, but is there a way to skip a specified sequence of lines (e.g., 1, 2, 10, 11, 19, 20, 28, 29, etc.) ? If I read the entire data file, and then delete the character fields, the values are still kept as factors, with each value denoted by its level. Since, I have continuous variables, there are as many levels as there are values. I am unable to coerce this to numeric mode. Is there a way to do this so that I can then manipulate the numeric data frame? Thanks for any help. Best, Ravi. --- Ravi Varadhan, Ph.D. Assistant Professor, The Center on Aging and Health Division of Geriatric Medicine and Gerontology Johns Hopkins University Ph: (410) 502-2619 Fax: (410) 614-9625 Email: [EMAIL PROTECTED] Webpage: http://www.jhsph.edu/agingandhealth/People/Faculty/Varadhan.html [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] New user, requesting help with MAC installation of R
I guess that the default is to plot to a ps file rather than to a graphics window when using R from the terminal. hth, Ingmar On 10 Apr 2008, at 12:02, Sophia Yancopoulos wrote: Hi: Yesterday I downloaded R and got it up and running on my PC without a hitch, not so when I tried to do the same on my Mac powerbook, using Mac OSX: version 10.4.11.. I have virtually no experience, so I can't tell what exactly went wrong. At first it appeared that the software loaded correctly, it seemed like I was able to install R , and I even successfully unpacked the package 'scatterplot3d' and was able to run some rudimentary commands. However, I did not get a graphics window when I tried to follow the same sequence of commands (following a tutorial) that worked on my PC-- basically everything worked except for the actual plot command: plot(x,y) I did this in the command mode in a terminal window, but no graphics window came up. Can you please advise? THANKS IN ADVANCE! Sophia __ [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting- guide.html and provide commented, minimal, self-contained, reproducible code. Ingmar Visser Department of Psychology, University of Amsterdam Roetersstraat 15 1018 WB Amsterdam The Netherlands t: +31-20-5256723 [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Stderr
Patricia García wrote: Hi everyone, I need to get an error message as an object in the std output console. I can get it as a file with the following instructions: # Save error mesage: error1 - file(error1.txt, open=wt) sink(error1, type=message) experiment - function(data) With this, the error messages get saved in the file, but i need them as object in order to work with it in the console. I'm not sure what you are going to do, note that the last line contains an incomplete statement... If you want an object: you already have got the object error1 ... If you want error handling facilities, see ?try and its See Also section. Uwe Ligges Is it possible? Thanks __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] New user, requesting help with MAC installation of R
Hi: Yesterday I downloaded R and got it up and running on my PC without a hitch, not so when I tried to do the same on my Mac powerbook, using Mac OSX: version 10.4.11.. I have virtually no experience, so I can't tell what exactly went wrong. At first it appeared that the software loaded correctly, it seemed like I was able to install R , and I even successfully unpacked the package 'scatterplot3d' and was able to run some rudimentary commands. However, I did not get a graphics window when I tried to follow the same sequence of commands (following a tutorial) that worked on my PC-- basically everything worked except for the actual plot command: plot(x,y) I did this in the command mode in a terminal window, but no graphics window came up. Can you please advise? THANKS IN ADVANCE! Sophia __ [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] bucketing in histograms
Hi I wish to draw a histogram for a numeric array and specify a bucket size (say 5 units per bar and the height of that bar equals to the average of that 5 units) how can I do that? Thanks! Mark __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] how to read data from table based a condition
Dear All: I imported a table into R. But I want to read a variable (y) from this table conditional on another variable (x=1) in the table. y-data[,7] x-data[,3] I want to know the mean of y if corresponding x=1. I tried if (x==1) y3-y It does not work. Anyone can give a help? Thanks! Xin [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to create a legend without plot, and to use scientific notation for axes label ?
On 10 Apr 2008, at 12:33, Stanley Ng wrote: How can I use formatC to convert 600 to 6e5 and not 6e+05 ? formatC(60) [1] 6e+05 formatC(60, format=e, digit=0) [1] 6e+05 Try this: gsub(([eE])(\\+?)(\\-?)0+, \\1\\3, formatC(60, format=e, digit=0)) --Hans __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] legend placement
Ng Stanley wrote: Hi, I am plotting 5 charts using p - par(mfrow = c(3, 2), how can I place my legend in the last region ? I don't wan to put it into the margin. You should be able to do a blank plot, then plot the legend. For example, par(mfrow=c(3,2)) for (i in 1:5) plot(1) plot(1, axes=F, xlab=, ylab=, type=n) legend(center, pch=1, legend=points) Duncan Murdoch __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Orthogonal polynomial contrasts
How do you remove one of the terms from an ordered polynomial contrast in your linear model. For example, I have significant terms for linear and cubic but not quadratic, how would i remove the quadratic term from lm(response~treatment) Cheers, Chris -- View this message in context: http://www.nabble.com/Orthogonal-polynomial-contrasts-tp16608353p16608353.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] [R-pkgs] RcmdrPlugin.Export_0.2-0 released
Dear R users, I am pleased to announce the release of the Export plug-in for Rcmdr. At the moment, it is simply a graphical user interface to xtable(). Several developments are, however, planned. It is worth to note that the Manual offers several pointers on using Sweave together with LyX, and from this perspective the plugin is an attempt to simplify creating (LaTeX) reports by using graphical interfaces only. In the near future, only exporting to LaTeX and HTML will be supported. Exporting to other formats (say, RTF or ODF) could be integrated provided that someone is willing to contribute the code (say, personal scripts that were never published), or point to a sensible way of automating the process. Any such contributions are heartily welcome. Comments and suggestions are, of course, always welcome. Liviu ___ R-packages mailing list [EMAIL PROTECTED] https://stat.ethz.ch/mailman/listinfo/r-packages __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Orthogonal polynomial contrasts
Chris Bennett wrote: How do you remove one of the terms from an ordered polynomial contrast in your linear model. For example, I have significant terms for linear and cubic but not quadratic, how would i remove the quadratic term from lm(response~treatment) Cheers, Chris Are you _sure_ you want to do that? The interpretation can get tricky, but if you insist, just set the contrast matrix for the term accordingly, e.g., C(myterm, contr.poly(4)[,-2]) -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Beautifying axis tick labels
Ng Stanley wrote: Hi, For example, the y axis shows 0 50 150. Is there any way to beautify the tick labels to get 0 5 10 15, and at the top of y-axis x10^5 (superscript 5) ? My plots all have different ylim, how to perform the beautification automatically ? Hi Stanley, You may want axis.mult in the plotrix package Jim __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] two graphs in one figure?
Dear all, how can I plot a line graph and a bar graph in one single figure? I tried to combine barplot and plot. Even though they both have the same x-values (1 to 55), it just doesnt look as if they match in their scale (the barplot is much wider than the ploteven though I tried to put limits on the x-axis). Here is an example of what I did: barplot(y, xaxt=n,yaxt=n,ylim=c(-1,45), xlim=c(1,55)) ... par(new=TRUE) plot(x, ynew, lty=2, type=l, ylim=c(0,15), xlim=c(1,55)) Another question: how can I make sure that the 0-values from the barchart are displayed as well? Thank you so much! Anne-Katrin -- Psst! Geheimtipp: Online Games kostenlos spielen bei den GMX Free Games! http://games.entertainment.gmx.net/de/entertainment/games/free [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Orthogonal polynomial contrasts
Peter Dalgaard wrote:
Chris Bennett wrote:
How do you remove one of the terms from an ordered polynomial contrast in
your linear model. For example, I have significant terms for linear and
cubic but not quadratic, how would i remove the quadratic term from
lm(response~treatment)
Cheers,
Chris
Are you _sure_ you want to do that? The interpretation can get tricky,
but if you insist, just set the contrast matrix for the term
accordingly, e.g.,
C(myterm, contr.poly(4)[,-2])
Related to Peter's note of caution, using statistical significance as a
basis for this decision is asking for trouble. See
author = {Grambsch, P. M. and {O'Brien}, P. C.},
year = 1991,
title = {The effects of transformations and preliminary tests for
non-linearity in regression},
journal = Stat in Med,
volume = 10,
pages = {697-709}
Frank
--
Frank E Harrell Jr Professor and Chair School of Medicine
Department of Biostatistics Vanderbilt University
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[R] New Special Interest Groups?
Dear list, After some extensive searching, I have drawn a blank on this. So ... Who is the best contact for questions about starting a new special interest group mailing list? Cheers, Jeff *** Dr. Jeffrey W. Hollister US EPA Atlantic Ecology Division 27 Tarzwell Drive Narragansett, RI 02882 (401) 782-9655 *** __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] two graphs in one figure?
Dear Anne-Katrin, You could use ggplot to do this. The example below works, although it generates some warnings. library(ggplot2) dataset - data.frame(x = 0:55, y = rnorm(56, 10), z = runif(56, 9, 11)) ggplot(data = dataset) + geom_bar(aes(x = factor(x), y = y), position = dodge) + geom_line(aes(x = x, y = z)) HTH, Thierry ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest Cel biometrie, methodologie en kwaliteitszorg / Section biometrics, methodology and quality assurance Gaverstraat 4 9500 Geraardsbergen Belgium tel. + 32 54/436 185 [EMAIL PROTECTED] www.inbo.be To call in the statistician after the experiment is done may be no more than asking him to perform a post-mortem examination: he may be able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher The plural of anecdote is not data. ~ Roger Brinner The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data. ~ John Tukey -Oorspronkelijk bericht- Van: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Namens Anne-Katrin Link Verzonden: donderdag 10 april 2008 15:18 Aan: R Help Onderwerp: [R] two graphs in one figure? Dear all, how can I plot a line graph and a bar graph in one single figure? I tried to combine barplot and plot. Even though they both have the same x-values (1 to 55), it just doesnt look as if they match in their scale (the barplot is much wider than the ploteven though I tried to put limits on the x-axis). Here is an example of what I did: barplot(y, xaxt=n,yaxt=n,ylim=c(-1,45), xlim=c(1,55)) ... par(new=TRUE) plot(x, ynew, lty=2, type=l, ylim=c(0,15), xlim=c(1,55)) Another question: how can I make sure that the 0-values from the barchart are displayed as well? Thank you so much! Anne-Katrin -- Psst! Geheimtipp: Online Games kostenlos spielen bei den GMX Free Games! http://games.entertainment.gmx.net/de/entertainment/games/free [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] quantitative real time PCR
Hi, Please, I am looking for a way to analyze my qRT-PCR in my debian gnu linux and I found a package named qpcR on cran. Do you known another one that do this analysis (preferable a R addon)? If you already had do this one in a linux box, could you point me out how you did? Thank you very much Marcelo __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Structural Modelling in R-project
Hi all I was wondering if I could ask for some assistance on two little enquiries that I have got. In the R-project, when using the StructTS function on a times series Zt, the programs return this: Call: StructTS(x = Zt) Variances: level slope seasepsilon 0.168461 0.00 0.005113 10.743687 My frist question is the following: The variances obtained seem to be numerical values although in the literature (e.g., Kendall and Ord (1990)), they are detailed as matrices. I need to provide these matrices in my thesis but I am a bit lost as to how to write them down as. Secondly, how does the R-project decide on the dimensions of the matrices? Any help will be most appreciated Best Regards, Christian Ivaha PhD Student University of Glamorgan Faculty of Advanced Technology Treforest CF37 1DL [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Recovering SPlus GraphSheets
Hello, Is it possible with R to recover the contents of SPlus GraphSheets (*.sgr) without access to SPlus? Also, some of the .sgr files may have multiple pages. Thanx, DaveT. * Silviculture Data Analyst Ontario Forest Research Institute Ontario Ministry of Natural Resources [EMAIL PROTECTED] http://ofri.mnr.gov.on.ca __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] (no subject)
Subject: nls, step factor 0.000488281 reduced below 'minFactor' of 0.000976563 Hi there, I'm trying to conduct nls regression using roughly the below code: nls1 - nls(y ~ a*(1-exp(-b*x^c)), start=list(a=a1,b=b1,c=c1)) I checked my start values by plotting the relationship etc. but I kept getting an error message saying maximum iterations exceeded. I have tried changing these start values, and I heeded advice from other threads and ammended my code to include :, control = list(maxiter = 500), trace=TRUE)). Now I receive an error message saying step factor 0.000488281 reduced below 'minFactor' of 0.000976563. Any ideas? Many thanks in anticipation, LB ** Lindsay Banin School of Geography University of Leeds Leeds, LS2 9JT UK [EMAIL PROTECTED] ** __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] lme and confidence intervals
FWIW, the ci() function in the gmodels package supports generating confidence intervals for the fixed effects of lme objects. -G On Apr 8, 2008, at 1:34PM , Dieter Menne wrote: Cristian Carranza cristiancarranza_1 at hotmail.com writes: After fitting a mixed effects model to repeated measurements data set, and after several unsuccessful atempts to make a simple plot of the confidence interval for the fitted model, I gave up and now I am asking for help in this useful list. Could anyone be so kind to give me some code lines in order to make a plot of the fitted equation and the correspondent confidence interval? The fitted equation is simple: use predict in its variations. For the confidence interval, most people on the list will ask back what it means. But I know my colleagues, they or their reviewers insist on having error bar in the graphics, and don't care about the interpretation. Dimitri has given an approach that could be used to produce some reviewer-satisfaction plots limited borborygmy. http://finzi.psych.upenn.edu/R/Rhelp02a/archive/118174.html Note that his method is meant to estimate well-defined confidence intervals for the coefficients, but you can use the profiled fits and compute the confidence intervals at the data points. Alternatively, you could use mcmc to get a range of curves for averaging. Dieter __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting- guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] LSODA not accurate when RK4 is; what's going on?
John,
You should decrease atol and/or rtol to get accurate integration of your
function.
Try this:
fn - function(t,y,parms=0){return(list(t*y-1))}
t4 - seq(0, 5, by=.0001)
s4 - lsoda(y=sqrt(pi/2), times=t4, func=fn, parms=0, atol=1.e-10,
rtol=1.e-10)
plot(s4, type=l)
Hope this is helpful,
Ravi.
---
Ravi Varadhan, Ph.D.
Assistant Professor, The Center on Aging and Health
Division of Geriatric Medicine and Gerontology
Johns Hopkins University
Ph: (410) 502-2619
Fax: (410) 614-9625
Email: [EMAIL PROTECTED]
Webpage: http://www.jhsph.edu/agingandhealth/People/Faculty/Varadhan.html
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On
Behalf Of John Tillinghast
Sent: Wednesday, April 09, 2008 7:18 PM
To: r-help@r-project.org
Subject: [R] LSODA not accurate when RK4 is; what's going on?
I'm solving the differential equation dy/dx = xy-1 with y(0) = sqrt(pi/2).
This can be used in computing the tail of the normal distribution.
(The actual solution is y(x) = exp(x^2/2) * Integral_x_inf {exp(-t^2/2) dt}
= Integral_0_inf {exp (-xt - t^2/2) dt}. For large x, y ~ 1/x, starting
around x~2.)
I'm testing both lsoda and rk4 from the package odesolve.
rk4 is accurate using step length 10^-2 and probably would be with even
larger steps.
lsoda is pretty accurate out to about x=4, then starts acting strangely. For
step length 10^-3, y suddenly starts to increase after 4, when it should be
strictly decreasing. For step length 10^-4, y instead turns down and start
dropping precipitously.
Any ideas why lsoda would go off the rails when rk4 does so well? I will
soon be using R to solve more complicated systems of ODEs which I don't
understand as well, so I want to know when it can mislead me.
Code:
t4 - seq(0, 5, by=.0001)
fn
function(t,y,parms=0){return(list(t*y-1))}
s4 - lsoda(sqrt(pi/2), t4, fn, 0)
[[alternative HTML version deleted]]
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and provide commented, minimal, self-contained, reproducible code.
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Recovering SPlus GraphSheets
On 4/10/2008 9:56 AM, Thompson, David (MNR) wrote: Hello, Is it possible with R to recover the contents of SPlus GraphSheets (*.sgr) without access to SPlus? Also, some of the .sgr files may have multiple pages. Possible is probably not the right word here: I'm sure the answer to your question is yes, it's possible, someone just has to write the code to do it. But that really means no. As far as I've heard, nobody has done that. Duncan Murdoch __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] adonis (vegan package) and subsetted factors
Hi, I'm trying to use adonis on a subset of data from a dataframe. The actual data is in columns 5:118, and the first four columns are various factors. There are 3 levels of the factor Habitat, and I want to examine differences among only two of them. So I started with: CoastNear = subset(gel_data, Habitat != I) The resulting data.frame has three levels for Habitat, but only two of those levels have any records. Then I run: adonis(CoastNear[,5:118]~Habitat, data = CoastNear,permutations=1000, + method='jaccard') Call: adonis(formula = CoastNear[, 5:118] ~ Habitat, data = CoastNear, permutations = 1000, method = jaccard) Df SumsOfSqsMeanSqsF.Model R2 Pr(F) Habitat2.000 0.0092966 0.0046483 2.0549327 0.0707 0.005 Residuals 54.000 0.1221491 0.00226200.9293 Total 56.000 0.1314457 1. This appears to be wrong - with only two Habitat levels I should only have 1 Df, shouldn't I? I checked by forcibly excising the third factor level: CoastNear$Habitat - as.factor(as.character(CoastNear$Habitat)) adonis(CoastNear[,5:118]~Habitat, data = CoastNear,permutations=1000, + method='jaccard') Call: adonis(formula = CoastNear[, 5:118] ~ Habitat, data = CoastNear, permutations = 1000, method = jaccard) Df SumsOfSqsMeanSqsF.Model R2 Pr(F) Habitat1.000 0.0092966 0.0092966 4.1859740 0.0707 0.003 Residuals 55.000 0.1221491 0.00222090.9293 Total 56.000 0.1314457 1. This appears to be correct. Subsetting factors is something I always struggle with in R, but, based on previous experience with lda(), it seems that R generally does the right thing. Am I doing something wrong here, or is there a problem in adonis? Thanks, Tyler ps. Sorry for not supplying a reproducible bit of code. The data.frame is quite large. The general layout is: head(gel_data) # additional data columns trimmed for email Site Habitat Plot Concate A01 A02 A03 A04 A05 A06 A07 A08 A09 A10 1 PE C1PEC1 1 1 1 1 1 1 1 1 1 1 2 PE C3PEC3 1 1 1 1 0 1 1 1 1 1 3 PE C4PEC4 1 1 1 1 0 1 1 1 1 1 4 PE C6PEC6 1 1 1 1 0 1 1 1 1 1 5 PE C 12 PEC12 1 1 1 1 0 1 1 1 1 1 6 PE C 13 PEC13 1 1 1 1 0 1 1 1 1 1 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] LSODA not accurate when RK4 is; what's going on?
John,
I should also mention that by looking at the R source for lsoda() you can
see that the default values for atol and rtol are 1.e-06. This should
have been mentioned in the help file, but is not.
Another approach to solving your problem is to restrict hmax, the maximum
steplength.
s4 - lsoda(y=sqrt(pi/2), times=t4, func=fn, parms=0, hmax=0.001)
plot(s4, type=l)
Best,
Ravi.
---
Ravi Varadhan, Ph.D.
Assistant Professor, The Center on Aging and Health
Division of Geriatric Medicine and Gerontology
Johns Hopkins University
Ph: (410) 502-2619
Fax: (410) 614-9625
Email: [EMAIL PROTECTED]
Webpage: http://www.jhsph.edu/agingandhealth/People/Faculty/Varadhan.html
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On
Behalf Of John Tillinghast
Sent: Wednesday, April 09, 2008 7:18 PM
To: r-help@r-project.org
Subject: [R] LSODA not accurate when RK4 is; what's going on?
I'm solving the differential equation dy/dx = xy-1 with y(0) = sqrt(pi/2).
This can be used in computing the tail of the normal distribution.
(The actual solution is y(x) = exp(x^2/2) * Integral_x_inf {exp(-t^2/2) dt}
= Integral_0_inf {exp (-xt - t^2/2) dt}. For large x, y ~ 1/x, starting
around x~2.)
I'm testing both lsoda and rk4 from the package odesolve.
rk4 is accurate using step length 10^-2 and probably would be with even
larger steps.
lsoda is pretty accurate out to about x=4, then starts acting strangely. For
step length 10^-3, y suddenly starts to increase after 4, when it should be
strictly decreasing. For step length 10^-4, y instead turns down and start
dropping precipitously.
Any ideas why lsoda would go off the rails when rk4 does so well? I will
soon be using R to solve more complicated systems of ODEs which I don't
understand as well, so I want to know when it can mislead me.
Code:
t4 - seq(0, 5, by=.0001)
fn
function(t,y,parms=0){return(list(t*y-1))}
s4 - lsoda(sqrt(pi/2), t4, fn, 0)
[[alternative HTML version deleted]]
__
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https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] ggplot - plot with only legend?
Dear R'ers, I am trying to build a composite plot (with several plots in one figure). I have tried, but I cannot use facetting, as I need to customize each plot using grid. Since all the plots are the same (with different data, but same layout and categories), I would like to have only one legend, that I would place in its own viewport, below all the other plots. My questions are (a) is there is a way, in ggplot, to build a plot that is only the legend (no data), where the legend occupies the whole viewport; (b) How can I change the layout of the legend (e.g. have them written side-by side, instead of over each other). Thanks in advance, Pedro __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] LSODA not accurate when RK4 is; what's going on?
John,
In lsoda the increment for time-marching is adaptively chosen,
controlled by atol and rtol. The increment is restricted to lie in
(hmin, hmax). So you can ensure accuracy, perhaps, at the cost of
efficiency by specifying smaller than default values for atol, rtol, and
hmax, which are 1e-06, 1e-06, and Inf, respectively.
rk4, on the other hand is not so intelligent. It basically use fixed time
increment.
Ravi.
---
Ravi Varadhan, Ph.D.
Assistant Professor, The Center on Aging and Health
Division of Geriatric Medicine and Gerontology
Johns Hopkins University
Ph: (410) 502-2619
Fax: (410) 614-9625
Email: [EMAIL PROTECTED]
Webpage: http://www.jhsph.edu/agingandhealth/People/Faculty/Varadhan.html
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On
Behalf Of John Tillinghast
Sent: Wednesday, April 09, 2008 7:18 PM
To: r-help@r-project.org
Subject: [R] LSODA not accurate when RK4 is; what's going on?
I'm solving the differential equation dy/dx = xy-1 with y(0) = sqrt(pi/2).
This can be used in computing the tail of the normal distribution.
(The actual solution is y(x) = exp(x^2/2) * Integral_x_inf {exp(-t^2/2) dt}
= Integral_0_inf {exp (-xt - t^2/2) dt}. For large x, y ~ 1/x, starting
around x~2.)
I'm testing both lsoda and rk4 from the package odesolve.
rk4 is accurate using step length 10^-2 and probably would be with even
larger steps.
lsoda is pretty accurate out to about x=4, then starts acting strangely. For
step length 10^-3, y suddenly starts to increase after 4, when it should be
strictly decreasing. For step length 10^-4, y instead turns down and start
dropping precipitously.
Any ideas why lsoda would go off the rails when rk4 does so well? I will
soon be using R to solve more complicated systems of ODEs which I don't
understand as well, so I want to know when it can mislead me.
Code:
t4 - seq(0, 5, by=.0001)
fn
function(t,y,parms=0){return(list(t*y-1))}
s4 - lsoda(sqrt(pi/2), t4, fn, 0)
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Re: [R] Fit a nonlinear regression model with power exponentially distributed errors
You are making progress. Could you please provide a self-contained example of an attempt by you to make it work, as requested in the posting guide http://www.R-project.org/posting-guide.html? That should make it easier for someone else to provide an answer that will actually be useful. Hope this helps. Spencer Yan (Daniel) Zhao wrote: How to fit a nonlinear regression model with power exponentially distributed errors? I know gnlm has a function gnlr3 that could work, but I would be grateful if example R code is provided. Daniel [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Structural Modelling in R-project
From: Ivaha C (AT) [EMAIL PROTECTED] Date: 2008/04/10 Thu AM 08:51:14 CDT To: R Help r-help@r-project.org Subject: [R] Structural Modelling in R-project if you have a univariate time series and you want to break it into its various components, then you get the scalars based on a decomposition. if you have a kalman filter/ basic strucutural model type setup ( i.e see harvey 1990, can 't remember title ), then you'll get matrices but I don't think structTS is used for the latter ? Professor Ripley, correct me if i'm wrong on that because I don't use structTS. I can't say much else but you may want to look at the DLM package if you are trying to do what I think you might be trying to do ? Hi all I was wondering if I could ask for some assistance on two little enquiries that I have got. In the R-project, when using the StructTS function on a times series Zt, the programs return this: Call: StructTS(x = Zt) Variances: level slope seasepsilon 0.168461 0.00 0.005113 10.743687 My frist question is the following: The variances obtained seem to be numerical values although in the literature (e.g., Kendall and Ord (1990)), they are detailed as matrices. I need to provide these matrices in my thesis but I am a bit lost as to how to write them down as. Secondly, how does the R-project decide on the dimensions of the matrices? Any help will be most appreciated Best Regards, Christian Ivaha PhD Student University of Glamorgan Faculty of Advanced Technology Treforest CF37 1DL [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Structural Modelling in R-project
Thanks for this, it's a good start. I am using a univariate series indeed. Do you know where I could find the codes for StructTS please? I can't seem to find it. Thanks again Christian Ivaha PhD Student University of Glamorgan Faculty of Advanced Technology Treforest CF37 1DL -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Sent: 10 April 2008 15:41 To: Ivaha C (AT) Cc: r-help@r-project.org Subject: Re: [R] Structural Modelling in R-project From: Ivaha C (AT) [EMAIL PROTECTED] Date: 2008/04/10 Thu AM 08:51:14 CDT To: R Help r-help@r-project.org Subject: [R] Structural Modelling in R-project if you have a univariate time series and you want to break it into its various components, then you get the scalars based on a decomposition. if you have a kalman filter/ basic strucutural model type setup ( i.e see harvey 1990, can 't remember title ), then you'll get matrices but I don't think structTS is used for the latter ? Professor Ripley, correct me if i'm wrong on that because I don't use structTS. I can't say much else but you may want to look at the DLM package if you are trying to do what I think you might be trying to do ? Hi all I was wondering if I could ask for some assistance on two little enquiries that I have got. In the R-project, when using the StructTS function on a times series Zt, the programs return this: Call: StructTS(x = Zt) Variances: level slope seasepsilon 0.168461 0.00 0.005113 10.743687 My frist question is the following: The variances obtained seem to be numerical values although in the literature (e.g., Kendall and Ord (1990)), they are detailed as matrices. I need to provide these matrices in my thesis but I am a bit lost as to how to write them down as. Secondly, how does the R-project decide on the dimensions of the matrices? Any help will be most appreciated Best Regards, Christian Ivaha PhD Student University of Glamorgan Faculty of Advanced Technology Treforest CF37 1DL [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Adding average into a matplot?
Hi all, I have a matrix which is filled with simulation results for several years. Example of an output (7 years, 4 simulations): [,1] [,2] [,3] [,4] [1,] 500 500 500 500 [2,] 516 519 509 508 [3,] 559 573 556 566 [4,] 613 650 611 633 [5,] 676 714 667 716 [6,] 751 808 742 809 [7,] 816 890 823 879 My matplot gives me 4 lines, but I would like to add a line with the averages of each year for all simulations. Can anyone help me with this? Thanks in advance! -- View this message in context: http://www.nabble.com/Adding-average-into-a-matplot--tp16609064p16609064.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] two graphs in one figure?
On Thu, Apr 10, 2008 at 8:36 AM, ONKELINX, Thierry [EMAIL PROTECTED] wrote: Dear Anne-Katrin, You could use ggplot to do this. The example below works, although it generates some warnings. library(ggplot2) dataset - data.frame(x = 0:55, y = rnorm(56, 10), z = runif(56, 9, 11)) ggplot(data = dataset) + geom_bar(aes(x = factor(x), y = y), position = dodge) + geom_line(aes(x = x, y = z)) ggplot(data = dataset, aes(factor(x), y)) + geom_bar() + geom_line(aes(y=z, group=1)) does basically the same thing, but without warnings. Hadley -- http://had.co.nz/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] adonis (vegan package) and subsetted factors
On Thu, 2008-04-10 at 11:18 -0300, tyler wrote: Hi, I'm trying to use adonis on a subset of data from a dataframe. The actual data is in columns 5:118, and the first four columns are various factors. There are 3 levels of the factor Habitat, and I want to examine differences among only two of them. So I started with: Hi Tyler, This behaviour arises from the following, using the in-built dune data: example(dune) dune data(dune) dune data(dune.env) newdune.env - subset(dune.env, Management != NM) newdune.env$Management [1] BF SF SF SF HF SF HF HF BF BF HF SF SF HF Levels: BF HF NM SF Notice this hasn't dropped the empty level NM, and this is what is catching out adonis --- it is not checking for empty levels in the grouping factor, as this shows: newdune - dune[which(dune.env$Management != NM), ] adonis(newdune ~ Management*A1, data=newdune.env, permutations=100) Call: adonis(formula = newdune ~ Management * A1, data = newdune.env, permutations = 100) Df SumsOfSqs MeanSqs F.Model R2 Pr(F) Management 3.0 0.57288 0.19096 1.27735 0.2694 0.01 *** A1 1.0 0.29851 0.29851 1.99672 0.1404 0.33 Management:A1 3.0 0.35831 0.11944 0.79892 0.1685 0.87 Residuals 6.0 0.89699 0.14950 0.4218 Total 13.0 2.12669 1. --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 For now, forcibly remove empty factor levels as per your second example, but I'll take a look at fixing adonis() --- it looks easy but that could be deceptive! I've CC'd the maintainer (Jari Oksanen) here as well, as I don't think Jari follows R-help too closely at the moment. snip/ Thanks, Tyler ps. Sorry for not supplying a reproducible bit of code. The data.frame is quite large. The general layout is: It is often instructional to use one of the in-built data sets (as I have here), even if just to prove to yourself that it isn't a problem with your data. All the best, G -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/ UK. WC1E 6BT. [w] http://www.freshwaters.org.uk %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Tukey in R, extracting values
hey, how can i extract the values from the CI's when i use following code for a tukey test? the output shows three CI's and i know it should work with 'names but i don't really know how... thanks library(multcomp) data1$soort-as.factor(data1$soort) amod-aov(waarde~soort,data=data1) g-glht(amod, linfct=mcp(soort = Tukey)) confint(g) -- View this message in context: http://www.nabble.com/Tukey-in-R%2C-extracting-values-tp16609570p16609570.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] adonis (vegan package) and subsetted factors
On Thu, Apr 10, 2008 at 04:47:44PM +0100, Gavin Simpson wrote: This behaviour arises from the following, using the in-built dune data: newdune.env - subset(dune.env, Management != NM) newdune.env$Management [1] BF SF SF SF HF SF HF HF BF BF HF SF SF HF Levels: BF HF NM SF Notice this hasn't dropped the empty level NM, and this is what is catching out adonis --- it is not checking for empty levels in the grouping factor, as this shows: newdune - dune[which(dune.env$Management != NM), ] adonis(newdune ~ Management*A1, data=newdune.env, permutations=100) Call: adonis(formula = newdune ~ Management * A1, data = newdune.env, permutations = 100) Df SumsOfSqs MeanSqs F.Model R2 Pr(F) Management 3.0 0.57288 0.19096 1.27735 0.2694 0.01 *** For now, forcibly remove empty factor levels as per your second example, but I'll take a look at fixing adonis() Great, thanks! Tyler __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] 64-bit/32-bit
Our research group is thinking of buying a 64-bit windows workstation with an intel core2 duo processor, and I am going to use R on it. I have a couple of questions. Is it possible to run 32-bit build of R on a 64-bit computer without problems?(For windows) Would there be problems with contrib packages? From what I've read in the mailing lists, there is eventually going to be a 64-bit build for windows, but I can install linux on the machine and use 64-bit build for linux without problems, right? -- Sancar Adali Johns Hopkins University __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] New user, requesting help with MAC installation of R
Hi The graphics commands should work without problem. On Mac the default graphics window is a quarz device. Did you get the 'official' mac binary from CRAN with GUI? If the problem persits you can ask in the mailing list R-SIG-Mac (see instructions for posting: http://www.r-project.org/mail.html) -- Armin Goralczyk, M.D. -- Universitätsmedizin Göttingen Abteilung Allgemein- und Viszeralchirurgie Rudolf-Koch-Str. 40 39099 Göttingen -- Dept. of General Surgery University of Göttingen Göttingen, Germany -- http://www.gwdg.de/~agoralc __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] How to replace German umlauts in strings?
Dear R-users,
I have a file containing names of German students. These names
contain the characters ä, ö or ü (German umlauts). I use
read.table() to read the file and let's assume the table is then
stored in a variable called data. The names are then contained in
the first column, i.e. data[,1]. Now if I simply display the variable
data, I see, that ä is replaced by \x8a, ö is replaced by \x9a
and so forth. Now, I would like to have these characters replaced by
their LaTeX (or TeX) equivalents, meaning \x8a should be replaced by
\a, \x9a should be replaced by \o and so forth. I tried a lot,
especially with gsub(), however, the backslashes cause problems and I
do not know how to get this to work. The data.frame should then be
written to a file without destroying the replaced substrings (so that
indeed \a appears in the file for \x8a). Is this possible?
Here is a minimal example:
data=data.frame(names=c(Bj\x9arn,S\x9aren),points=c
(10,20),stringsAsFactors=F)
data[1,1]=gsub('\\x9a','\\o',data[1,1]) #does not work! (neither do
similar calls)
Thanks in advance
Marius
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[R] Problem installing and using package tseries
I have R 2.6.2, and have tried downloading and installing the package
tseries. I get the same error when I use two different mirror sites:
utils:::menuInstallPkgs()
trying URL
'http://cran.mirrors.hoobly.com/bin/windows/contrib/2.6/tseries_0.10-14.zip'
Content type 'application/zip' length 400799 bytes (391 Kb)
opened URL
downloaded 391 Kb
package 'tseries' successfully unpacked and MD5 sums checked
The downloaded packages are in
C:\Documents and Settings\User\Local
Settings\Temp\Rtmpk2jrvn\downloaded_packages
updating HTML package descriptions
library('tseries')
Error in dyn.load(file, ...) :
unable to load shared library
'C:/PROGRA~1/R/R-26~1.2/library/tseries/libs/tseries.dll':
LoadLibrary failure: The specified module could not be found.
Error: package/namespace load failed for 'tseries'
There doesn't seem to be anything unusual. The package is installed
like any other, and the required file is at C:\Program
Files\R\R-2.6.2\library\tseries\libs\tseries.dll. It is 36,864 bytes
and looks superficially okay.
Any ideas as to what's wrong here?
Thanks.
Robert A. LaBudde, PhD, PAS, Dpl. ACAFS e-mail: [EMAIL PROTECTED]
Least Cost Formulations, Ltd.URL: http://lcfltd.com/
824 Timberlake Drive Tel: 757-467-0954
Virginia Beach, VA 23464-3239Fax: 757-467-2947
Vere scire est per causas scire
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and provide commented, minimal, self-contained, reproducible code.
[R] QP.solve, QPmat, constraint matrix, and positive definite
hello all,
i'm trying to use QPmat, from the popbio package. it appears to be based
on solve.QP and is intended for making a population projection matrix.
QPmat asks for: nout, A time series of population vectors and C, C
constraint matrix, (with two more vectors, b and nonzero). i believe the
relevant code from QPmat is:
function (nout, C, b, nonzero)
{
if (!quadprog %in% (.packages())) {
library(quadprog)
}
n - dim(nout)
z - nout[, 2:n[2]]
z - matrix(z, n[1] * (n[2] - 1), 1)
M - c()
for (i in 1:(n[2] - 1)) {
N - kronecker(t(nout[, i]), diag(n[1]))
m - N[, nonzero]
M - rbind(M, m)
}
G - t(M) %*% M
f - t(M) %*% z
res - solve.QP(G, f, -t(C), -b)
i'm receiving the error
Error in solve.QP(G, f, -t(C), -b) :
matrix D in quadratic function is not positive definite!
solve.QP documentation says that Dmat goes into the place that is referred
to in the code as G. i've two matrices. nout is 31x3 and all elements are
0 or positive. my C matrix is 31 x 31 and has a -1 running diagonal from
the upper left to the lower right, with everything else 0. i'm somewhat
confused by what matrix or element is being multiplied as it leads up to G
and all i can guess is that i didn't construct the C matrix correctly. how
would i do that?
sorry if i have too much info or am missing something. thanks for your time.
john
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Re: [R] New Special Interest Groups?
Martin Maechler [EMAIL PROTECTED], who oversees the mailing lists, would be the best person to start with. On 4/10/08, [EMAIL PROTECTED] [EMAIL PROTECTED] wrote: Dear list, After some extensive searching, I have drawn a blank on this. So ... Who is the best contact for questions about starting a new special interest group mailing list? Cheers, Jeff *** Dr. Jeffrey W. Hollister US EPA Atlantic Ecology Division 27 Tarzwell Drive Narragansett, RI 02882 (401) 782-9655 *** __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to replace German umlauts in strings?
On 10.04.2008, at 18:03, Hofert Marius wrote:
I have a file containing names of German students. These names
contain the characters ä, ö or ü (German umlauts). I use
read.table() to read the file and let's assume the table is then
stored in a variable called data. The names are then contained in
the first column, i.e. data[,1]. Now if I simply display the variable
data, I see, that ä is replaced by \x8a, ö is replaced by \x9a
and so forth. Now, I would like to have these characters replaced by
their LaTeX (or TeX) equivalents, meaning \x8a should be replaced by
\a, \x9a should be replaced by \o and so forth. I tried a lot,
especially with gsub(), however, the backslashes cause problems and I
do not know how to get this to work. The data.frame should then be
written to a file without destroying the replaced substrings (so that
indeed \a appears in the file for \x8a). Is this possible?
Here is a minimal example:
data=data.frame(names=c(Bj\x9arn,S\x9aren),points=c
(10,20),stringsAsFactors=F)
data[1,1]=gsub('\\x9a','\\o',data[1,1]) #does not work! (neither do
similar calls)
Try this:
gsub('\\x9a','\\o',m, perl = TRUE, useBytes = TRUE)
Cheers,
--Hans
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] QP.solve, QPmat, constraint matrix, and positive definite
hello all,
i'm trying to use QPmat, from the popbio package. it appears to be based
on solve.QP and is intended for making a population projection matrix.
QPmat asks for: nout, A time series of population vectors and C, C
constraint matrix, (with two more vectors, b and nonzero). i believe the
relevant code from QPmat is:
function (nout, C, b, nonzero)
{
if (!quadprog %in% (.packages())) {
library(quadprog)
}
n - dim(nout)
z - nout[, 2:n[2]]
z - matrix(z, n[1] * (n[2] - 1), 1)
M - c()
for (i in 1:(n[2] - 1)) {
N - kronecker(t(nout[, i]), diag(n[1]))
m - N[, nonzero]
M - rbind(M, m)
}
G - t(M) %*% M
f - t(M) %*% z
res - solve.QP(G, f, -t(C), -b)
i'm receiving the error
Error in solve.QP(G, f, -t(C), -b) :
matrix D in quadratic function is not positive definite!
solve.QP documentation says that Dmat goes into the place that is referred
to in the code as G. i've two matrices. nout is 31x3 and all elements are
0 or positive. my C matrix is 31 x 31 and has a -1 running diagonal from
the upper left to the lower right, with everything else 0. i'm somewhat
confused by what matrix or element is being multiplied as it leads up to G
and all i can guess is that i didn't construct the C matrix correctly. how
would i do that?
sorry if i have too much info or am missing something. thanks for your time.
john
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/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] permutation test assumption?
Just an additional note: what I find interesting (that is an euphemism) is that a paper such as that got published on 2006 when a whole bunch of detailed papers on the same topic had been published in the past. For instance, the first I pick from the pile is by J. Romano, On the behavior of randomization tests without a group invariance assumption, JASA, 1990, 85 (411): 686-692. There are other related papers on that same issue of JASA. The relevance of same-variance assumption also shows up in permutation test textbooks (including, I think, Manly's, Good's, Noreen's, etc). Best, R. On Wed, Apr 9, 2008 at 9:11 PM, Greg Snow [EMAIL PROTECTED] wrote: A few comments, My first impression on reading that abstract was that it was complete nonsense. After thinking a bit about it and skimming the full article I decided that it was nonsense, but nonsense that is important to research and discuss (and therefore the paper is useful). Why is it nonsense? The permutation test is a test of the null hypothesis that the 2 (or k) groups are from the same distribution (or identically distributed, or exchangable). The abstract says that they looked at the type I error rate when the 2 groups had different variances or other differences. The type I error is defined when the null hypothesis is true, so computing a type I error rate when the null is by definition false does not make sense. However, statisticians often do analyses where all the assumptions are not necessarily true (is any population really distributed as a normal), but the tests are close enough. So with modern tools it is not suprising to see people doing permutation tests without understanding what they are really testing and the results may be close enough (or they might not be). The contribution of this paper is to test and see if the results are close enough or not when you use a permutation test to test the null that the means are equal when there are other differences in the groups. Their answer is that no, the results are not close enough and they suggest that if you want to test for equality of means, but not identical distributions, then don't use a permutation test. To expand on Thierry's original answer: If you are testing the correct hypotheses and doing a permutation test correctly, then You can do permutation tests on an unbalanced design and it will still be a correct test. Unbalance could affect the power, which you would want to take into account when designing a study, but does not affect the correctness of the test (when used properly). Hope this helps, -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare [EMAIL PROTECTED] (801) 408-8111 -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of João Fadista Sent: Tuesday, April 08, 2008 4:10 PM To: ONKELINX, Thierry; r-help@r-project.org Subject: Re: [R] permutation test assumption? Dear Thierry, Thanks for the reply. But as you may read in the paper http://bioinformatics.oxfordjournals.org/cgi/content/abstract/ 22/18/2244 when the sample sizes are not the same there may be an increase in the Type I error rate. Comments will be appreciated. Best regards, João Fadista De: ONKELINX, Thierry [mailto:[EMAIL PROTECTED] Enviada: ter 08-04-2008 15:27 Para: João Fadista; r-help@r-project.org Assunto: RE: [R] permutation test assumption? Dear João, You can do permutation tests on an unbalanced design. HTH, Thierry -- -- ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest Cel biometrie, methodologie en kwaliteitszorg / Section biometrics, methodology and quality assurance Gaverstraat 4 9500 Geraardsbergen Belgium tel. + 32 54/436 185 [EMAIL PROTECTED] www.inbo.be To call in the statistician after the experiment is done may be no more than asking him to perform a post-mortem examination: he may be able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher The plural of anecdote is not data. ~ Roger Brinner The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data. ~ John Tukey -Oorspronkelijk bericht- Van: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Namens João Fadista Verzonden: dinsdag 8 april 2008 15:18 Aan: r-help@r-project.org Onderwerp: [R] permutation test assumption? Dear all, Can I do a permutation test if the number of individuals in one group is much bigger than in the other group? I searched the literature but I didin´t find any assumption that refers to this subject
[R] Problem with loading package Matrix
Hello, I recently upgraded from R 2.6.1 to 2.6.2. I uninstalled 2.6.1, installed 2.6.2, and installed the packages I regularly use. Everyting seems to be running properly, including most of the packages, but when I try to call the Matrix package, I get the following error: require(Matrix) Loading required package: Matrix Error in dyn.load(file, ...) : unable to load shared library 'C:/PROGRA~1/R/R-26~1.2/library/Matrix/libs/Matrix.dll': LoadLibrary failure: The specified module could not be found. This is preceded by a pop-up window with: R Console: Rgui.exe - Unable To Locate DLL The dynamic link library Rblas could not be found in the specified path ... I've looked in the specified folder and the Matrix.dll file is there. I've also tried installing the Matrix package from another CRAN repository, but I'm still getting the error. Any suggestions? --- Peter Singleton USFS Pacific Northwest Research Station 1133 N. Western Ave. Wenatchee WA 98801 Phone: (509)664-1732 Fax: (509)665-8362 E-mail: [EMAIL PROTECTED] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] subtract the mean from each column
Hi, I am new to R an dI need some help I have a matrix of real values 100*300 and I would like to calculate the mean for each column , then for each entry in a column i need to subtract the mean so I will have a matrix where the columns have zero mean. any one know how to do that . Thanks -- View this message in context: http://www.nabble.com/subtract-the-mean-from-each-column-tp16610489p16610489.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] subtract the mean from each column
On 4/10/2008 1:03 PM, kayj wrote: Hi, I am new to R an dI need some help I have a matrix of real values 100*300 and I would like to calculate the mean for each column , then for each entry in a column i need to subtract the mean so I will have a matrix where the columns have zero mean. any one know how to do that . Thanks mymat - matrix(runif(10*4), ncol=4) colMeans(mymat) [1] 0.4711083 0.4825977 0.4757448 0.3037873 newmat - apply(mymat, 2, scale, scale=FALSE, center=TRUE) colMeans(newmat) [1] 1.110223e-17 -2.220446e-17 -1.110223e-17 1.110223e-17 ?scale -- Chuck Cleland, Ph.D. NDRI, Inc. (www.ndri.org) 71 West 23rd Street, 8th floor New York, NY 10010 tel: (212) 845-4495 (Tu, Th) tel: (732) 512-0171 (M, W, F) fax: (917) 438-0894 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Adding average into a matplot?
-Halcyon- [EMAIL PROTECTED] wrote: I have a matrix which is filled with simulation results for several years. Example of an output (7 years, 4 simulations): [...] My matplot gives me 4 lines, but I would like to add a line with the averages of each year for all simulations. Can anyone help me with this? Take a look at help pages of the following functions: mean, apply, abline. -- Mike Prager, NOAA, Beaufort, NC * Opinions expressed are personal and not represented otherwise. * Any use of tradenames does not constitute a NOAA endorsement. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] subtract the mean from each column
Or just: scale(mymat, scale = FALSE) On Thu, Apr 10, 2008 at 2:03 PM, kayj [EMAIL PROTECTED] wrote: Hi, I am new to R an dI need some help I have a matrix of real values 100*300 and I would like to calculate the mean for each column , then for each entry in a column i need to subtract the mean so I will have a matrix where the columns have zero mean. any one know how to do that . Thanks -- View this message in context: http://www.nabble.com/subtract-the-mean-from-each-column-tp16610489p16610489.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to replace German umlauts in strings?
Hans-Jörg Bibiko bibiko at eva.mpg.de writes:
On 10.04.2008, at 18:03, Hofert Marius wrote:
I have a file containing names of German students. These names
contain the characters ä, ö or ü (German umlauts). I use
read.table() to read the file and let's assume the table is then
stored in a variable called data. The names are then contained in
the first column, i.e. data[,1]. Now if I simply display the variable
data, I see, that ä is replaced by \x8a, ö is replaced by \x9a
and so forth.
This is strange. When I have a file umlaut.txt
Name
Äserich
Ömadel
Übermunsch
and read it in with
umlaut = read.table(umlaut.txt, header = TRUE)
umlautasis = read.table(umlaut.txt, header = TRUE,as.is = TRUE)
I get the following in both cases:
umlautasis
Name
1Äserich
2 Ömadel
3 Übermunsch
This is on Windows Vista. I use it every day without ever having seen nasty
codings, typically with the following in latex
\usepackage[T1]{fontenc}
\usepackage{textcomp}
\usepackage{babel}
\usepackage[latin1]{inputenc} % For ü,ä
Dieter
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] Tukey in R, extracting values
mad_bassie mad_bassie at hotmail.com writes: how can i extract the values from the CI's when i use following code for a tukey test? the output shows three CI's and i know it should work with 'names but i don't really know how... You forgot to post a self-running example. Chances are always better to get an answer if you include one more line that makes the examples reproducible on other computers. R is complex, so only very few people immediately see what was wrong without try it (and thus avoiding typos). Dieter library(multcomp) # Please include a line like the following next time data1 =data.frame(waarde = rnorm(100), soort=sample(1:3,100,replace=TRUE)) data1$soort-as.factor(data1$soort) amod-aov(waarde~soort,data=data1) g-glht(amod, linfct=mcp(soort = Tukey)) confint(g) coef(g) vcov(g) __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] polytomous or multinomial regression for matched data
Hi, I've been trying to find a program that will run a multinomial conditional regression on k:m matched data. Does anyone know of a package in R or another package that will allow this? It's not obvious that multinom within nnet or VGAM will allow matched sets. I've used a program (mcl) in STATA and SAS, but my parameter estimates from both packages do not match--can't figure out why, but I think it's because we have k:m matched sets. Any help is appreciated. Best, Sara __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to replace German umlauts in strings?
Dieter Menne wrote:
Hans-Jörg Bibiko bibiko at eva.mpg.de writes:
On 10.04.2008, at 18:03, Hofert Marius wrote:
I have a file containing names of German students. These names
contain the characters ä, ö or ü (German umlauts). I use
read.table() to read the file and let's assume the table is then
stored in a variable called data. The names are then contained in
the first column, i.e. data[,1]. Now if I simply display the variable
data, I see, that ä is replaced by \x8a, ö is replaced by \x9a
and so forth.
This is strange. When I have a file umlaut.txt
Name
Äserich
Ömadel
Übermunsch
and read it in with
umlaut = read.table(umlaut.txt, header = TRUE)
umlautasis = read.table(umlaut.txt, header = TRUE,as.is = TRUE)
I get the following in both cases:
umlautasis
Name
1Äserich
2 Ömadel
3 Übermunsch
This is on Windows Vista. I use it every day without ever having seen nasty
codings, typically with the following in latex
\usepackage[T1]{fontenc}
\usepackage{textcomp}
\usepackage{babel}
\usepackage[latin1]{inputenc} % For ü,ä
Dieter
Thing is that \x9a for o-umlaut is an unusual encoding:
names(which(sapply(iconvlist(),iconv, x=S\x9aren)==Sören))
[1] CP1282CSMACINTOSH MAC
[4] MAC-CENTRALEUROPE MACINTOSH MACIS
[7] MAC-ISMAC-SAMI
iconv(öäüÖÄÜ, to=MAC)
[1] \x9a\x8a\x9f\x85\x80\x86
and accordingly,
data$names - iconv(data$names,from=MAC)
data
names points
1 Björn 10
2 Sören 20
or, if you need to do it for many variables, this should work:
ix - sapply(data, is.character)
data[ix] - lapply(data[ix], iconv, from=MAC)
--
O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B
c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K
(*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918
~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] how to fit a model that is nonlinear with multiplicate errors
Hi fellow R-users, I am interested in fitting the following model yi=log(a+xi*b*e), e~N(0,sigma2) and where x is a known covariate and a and b are parameters to be estimated as is sigma2. I am not sure how to fit such a model using lm or nls. Is there another function I can use to fit this? Thanks for any help. Stacey - [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Problem with loading package Matrix
What OS is that? If it is Windows 2000, try copying Rblas.dll to Rblas in the bin folder. (We have no idea why that might be needed, but it has worked for some people -- others have no problem even with Windows 2000.) On Thu, 10 Apr 2008, Peter H Singleton wrote: Hello, I recently upgraded from R 2.6.1 to 2.6.2. I uninstalled 2.6.1, installed 2.6.2, and installed the packages I regularly use. Everyting seems to be running properly, including most of the packages, but when I try to call the Matrix package, I get the following error: require(Matrix) Loading required package: Matrix Error in dyn.load(file, ...) : unable to load shared library 'C:/PROGRA~1/R/R-26~1.2/library/Matrix/libs/Matrix.dll': LoadLibrary failure: The specified module could not be found. This is preceded by a pop-up window with: R Console: Rgui.exe - Unable To Locate DLL The dynamic link library Rblas could not be found in the specified path ... I've looked in the specified folder and the Matrix.dll file is there. I've also tried installing the Matrix package from another CRAN repository, but I'm still getting the error. Any suggestions? --- Peter Singleton USFS Pacific Northwest Research Station 1133 N. Western Ave. Wenatchee WA 98801 Phone: (509)664-1732 Fax: (509)665-8362 E-mail: [EMAIL PROTECTED] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Brian D. Ripley, [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@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to replace German umlauts in strings?
Or read the file with
read.table(file(umlaut.txt, encoding=MAC), ...)
On Thu, 10 Apr 2008, Peter Dalgaard wrote:
Dieter Menne wrote:
Hans-Jörg Bibiko bibiko at eva.mpg.de writes:
On 10.04.2008, at 18:03, Hofert Marius wrote:
I have a file containing names of German students. These names
contain the characters ä, ö or ü (German umlauts). I use
read.table() to read the file and let's assume the table is then
stored in a variable called data. The names are then contained in
the first column, i.e. data[,1]. Now if I simply display the variable
data, I see, that ä is replaced by \x8a, ö is replaced by \x9a
and so forth.
This is strange. When I have a file umlaut.txt
Name
Äserich
Ömadel
Übermunsch
and read it in with
umlaut = read.table(umlaut.txt, header = TRUE)
umlautasis = read.table(umlaut.txt, header = TRUE,as.is = TRUE)
I get the following in both cases:
umlautasis
Name
1Äserich
2 Ömadel
3 Übermunsch
This is on Windows Vista. I use it every day without ever having seen nasty
codings, typically with the following in latex
\usepackage[T1]{fontenc}
\usepackage{textcomp}
\usepackage{babel}
\usepackage[latin1]{inputenc} % For ü,ä
Dieter
Thing is that \x9a for o-umlaut is an unusual encoding:
names(which(sapply(iconvlist(),iconv, x=S\x9aren)==Sören))
[1] CP1282CSMACINTOSH MAC
[4] MAC-CENTRALEUROPE MACINTOSH MACIS
[7] MAC-ISMAC-SAMI
iconv(öäüÖÄÜ, to=MAC)
[1] \x9a\x8a\x9f\x85\x80\x86
and accordingly,
data$names - iconv(data$names,from=MAC)
data
names points
1 Björn 10
2 Sören 20
or, if you need to do it for many variables, this should work:
ix - sapply(data, is.character)
data[ix] - lapply(data[ix], iconv, from=MAC)
--
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__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Arbitrary Precision Numbers
Thanks Earl
Thats exactly what I was looking for - an extension that uses libgmp and
provides a bignum type that can be combined with standard operators and
numeric variables. Somehow my original search on CRAN missed this one.
Cheers
Rory
Earl F. Glynn wrote:
Rory Winston [EMAIL PROTECTED] wrote in message
news:[EMAIL PROTECTED]
(If you're wondering, this is a Project Euler question :))
If I wanted to calculate the sum of the digits in the decimal
representation
of 2^1000, what would be a good way to go about that?
Try this:
library(gmp)
for (N in c(10,16,32,100,1000))
+ {
+ s - as.character(pow.bigz(2,N))
+ t - as.numeric(unlist(strsplit(s,)))
+ cat(N, s, sum(t), \n)
+ }
10 1024 7
16 65536 25
32 4294967296 58
100 1267650600228229401496703205376 115
1000
10715086071862673209484250490600018105614048117055336074437503883703510511249361224931983788156958581275946729175531468251871452856923140435984577574698574803934567774824230985421074605062371141877954182153046474983581941267398767559165543946077062914571196477686542167660429831652624386837205668069376
1366
The first few can be verified manually.
--
efg
Earl F. Glynn
Bioinformatics
Stowers Institute for Medical Research
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Re: [R] two graphs in one figure?
Using par(new=TRUE) can be tricky. A better approach is to create one plot, then add the other information to it. You can add bars to an existing graph using barplot with add=TRUE, you can add lines to an existing plot using the lines function. If you give more detail of what you want (examples of x, y, and ynew) then we may be able to give more help. From: [EMAIL PROTECTED] on behalf of Anne-Katrin Link Sent: Thu 4/10/2008 7:18 AM To: R Help Subject: [R] two graphs in one figure? Dear all, how can I plot a line graph and a bar graph in one single figure? I tried to combine barplot and plot. Even though they both have the same x-values (1 to 55), it just doesnt look as if they match in their scale (the barplot is much wider than the ploteven though I tried to put limits on the x-axis). Here is an example of what I did: barplot(y, xaxt=n,yaxt=n,ylim=c(-1,45), xlim=c(1,55)) ... par(new=TRUE) plot(x, ynew, lty=2, type=l, ylim=c(0,15), xlim=c(1,55)) Another question: how can I make sure that the 0-values from the barchart are displayed as well? Thank you so much! Anne-Katrin -- Psst! Geheimtipp: Online Games kostenlos spielen bei den GMX Free Games! http://games.entertainment.gmx.net/de/entertainment/games/free [[alternative HTML version deleted]] [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Types in grouped multi-panel (lattice) xyplot
Apologetic prologue: I've looked through the mailing list for an answer to this (since I'm sure it's trivial) but I have not been able to find a fix. So the problem is that I want each group to have a different type of plot. Probes should be points and Segments should be lines (preferably using the segment plot command, but I've just been trying -- unsuccessfully -- to get lines to work). To be exact, the data looks like: loc val valtype mouse 1428 0.1812367 Probes 2 1439 -0.4534155 Probes 2 1499 -0.4957303 Probes 2 1559 0.2448838 Probes 2 1611 -0.2030937 Probes 2 1788 -0.2235331 Probes 2 1428 0.5Segment 2 1439 0.5Segment 2 1499 0.5Segment 2 1559 0.5Segment 2 1611 0.5Segment 2 1788 0.5Segment 2 1428 0.1812367 Probes 1 1439 -0.4534155 Probes 1 1499 -0.4957303 Probes 1 1559 0.2448838 Probes 1 1611 -0.2030937 Probes 1 1788 -0.2235331 Probes 1 1428 0.5Segment 1 1439 0.5Segment 1 1499 0.5Segment 1 1559 0.1Segment 1 1611 0.1Segment 1 1788 0.1Segment 1 * loc is the x-axis location * val is the y-axis value * valtype is equal to which had I been smart and used make.groups * mouse is the 'cond' variable The plot command I'm currently using is, xyplot(val ~ loc | mouse, data = df, groups=valtype aspect=0.5, layout=c(3,3), lty=0, lwd=3, type=p, col=c(black, blue), as.table = TRUE) which gives me black and blue points for the probes/segments (I've infered alphabetical order for the groups colors). When I change the type to c(p, l), I get xyplot(val ~ loc | mouse, data = df, groups=valtype aspect=0.5, layout=c(3,3), lty=0, lwd=3, type=c(p,l), col=c(black, blue), as.table = TRUE) I get the exact same plot. I've tried using a few of the panel functions I found on the list (I was particularly hopeful for http://tolstoy.newcastle.edu.au/R/help/06/07/30363.html) but I've either been misusing them, or they are not right for what I want to do. If anyone knows how to get points and lines in the same panel for the two different groups (probes/segments), I would love to hear about it. If you further know how to use the 'segment' plot in panels for the segments, I would really love to hear about it. Thanks in advance! Aaron __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Row mean scores differ association
Suppose that we have o 2-D contingency table where the row variable is nominal and the column one is ordinal. In SAS it is possible to compute the statistic named as row mean scores differ. How can we programmed it in R? (See also Aggresti (2002), Categorical Data Analysis, p. 302) With regards - [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Relational Databases or XML?
Dear R-Help, I am working on a paper in an R course for large file support in R using scan(), relational databases, and XML. I have never used SQL or heirarchical document formats such as XML (except where it occurs without user interaction), and knowledge in RDBs and XML is lacking in my program. I have tried finding a working example for the novices-novice on the topic, read many postings, the r-data I/O manual several times, and descriptions of packages RODBC, DBI, XML, among others. I understand that RDBs are (assumed at least) used widely among the R community. I have not been able to put all of the pieces together, but assuming that RDB use is actually quite widespread, it should be quite easy to fill me in and/or correct my understanding where necessary. For a cross-platform solution (PC/OSX at least, or in part) my questions/problems are about what preliminary steps are needed to get an SQL or XML query to work in R to begin with, what the appropriate data-file formats are, and how to convert to them if starting out with data in, say, a delimited ASCII text file. Very basic examples should suffice, say, a table with 20 random observations, a grouping variable with 2 levels, and a factor with 2 levels. ## untested code set.seed(1024) write.table(junk.txt, data.frame(Subj=c(rep(1,10),rep(2,10)),block=rep(c(rep(-1,5),rep(1,5)),2), obs=rnorm(20,0,1))) Specifically, 1- what are the minimum required non R components that are needed to support SQL or XML functionality, which may or may not need to be installed? 2- what R packages need to be installed, at a minimum (also as a cross-PC/Mac solution if possible or at least as much as possible) 3- I keep seeing reference to connections of a given name if previously setup. What kind of setup is needed outside of R, if any? 4- what steps are needed in R to then connect to a file and import a subset based on a query? 5- Do I then use standard R routines (e.g. write()) to export as a DB, or an RDB/XML specific function? Sincerely, KeithC. [U.S] 1/k^c __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Relational Databases or XML?
I'm not sure it is possible to parse an XML file in R directly. Well, I guess it's *possible*, but may not be the best way to do it. ElementTree in Python is an easy-to-use parser that you might use to first parse your XML file (or others hierarchically structured data), organize it anyway you want, and then bring those data into R for subsequent analysis. In fact, I have recently done just this. I have another statistical program that outputs data as an XML file. So, I wrote a python program that parses that XML file, pulls out the data of interest into a text file, and then I bring those data into R for analysis. -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Keith Alan Chamberlain Sent: Thursday, April 10, 2008 4:14 PM To: r-help@r-project.org Subject: [R] Relational Databases or XML? Dear R-Help, I am working on a paper in an R course for large file support in R using scan(), relational databases, and XML. I have never used SQL or heirarchical document formats such as XML (except where it occurs without user interaction), and knowledge in RDBs and XML is lacking in my program. I have tried finding a working example for the novices-novice on the topic, read many postings, the r-data I/O manual several times, and descriptions of packages RODBC, DBI, XML, among others. I understand that RDBs are (assumed at least) used widely among the R community. I have not been able to put all of the pieces together, but assuming that RDB use is actually quite widespread, it should be quite easy to fill me in and/or correct my understanding where necessary. For a cross-platform solution (PC/OSX at least, or in part) my questions/problems are about what preliminary steps are needed to get an SQL or XML query to work in R to begin with, what the appropriate data-file formats are, and how to convert to them if starting out with data in, say, a delimited ASCII text file. Very basic examples should suffice, say, a table with 20 random observations, a grouping variable with 2 levels, and a factor with 2 levels. ## untested code set.seed(1024) write.table(junk.txt, data.frame(Subj=c(rep(1,10),rep(2,10)),block=rep(c(rep(-1,5),r ep(1,5)),2), obs=rnorm(20,0,1))) Specifically, 1- what are the minimum required non R components that are needed to support SQL or XML functionality, which may or may not need to be installed? 2- what R packages need to be installed, at a minimum (also as a cross-PC/Mac solution if possible or at least as much as possible) 3- I keep seeing reference to connections of a given name if previously setup. What kind of setup is needed outside of R, if any? 4- what steps are needed in R to then connect to a file and import a subset based on a query? 5- Do I then use standard R routines (e.g. write()) to export as a DB, or an RDB/XML specific function? Sincerely, KeithC. [U.S] 1/k^c __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Relational Databases or XML?
Well, I guess it is possible with XML package on CRAN. But, it seems there is no windows binary (yet) -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Doran, Harold Sent: Thursday, April 10, 2008 4:29 PM To: Keith Alan Chamberlain; r-help@r-project.org Subject: Re: [R] Relational Databases or XML? I'm not sure it is possible to parse an XML file in R directly. Well, I guess it's *possible*, but may not be the best way to do it. ElementTree in Python is an easy-to-use parser that you might use to first parse your XML file (or others hierarchically structured data), organize it anyway you want, and then bring those data into R for subsequent analysis. In fact, I have recently done just this. I have another statistical program that outputs data as an XML file. So, I wrote a python program that parses that XML file, pulls out the data of interest into a text file, and then I bring those data into R for analysis. -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Keith Alan Chamberlain Sent: Thursday, April 10, 2008 4:14 PM To: r-help@r-project.org Subject: [R] Relational Databases or XML? Dear R-Help, I am working on a paper in an R course for large file support in R using scan(), relational databases, and XML. I have never used SQL or heirarchical document formats such as XML (except where it occurs without user interaction), and knowledge in RDBs and XML is lacking in my program. I have tried finding a working example for the novices-novice on the topic, read many postings, the r-data I/O manual several times, and descriptions of packages RODBC, DBI, XML, among others. I understand that RDBs are (assumed at least) used widely among the R community. I have not been able to put all of the pieces together, but assuming that RDB use is actually quite widespread, it should be quite easy to fill me in and/or correct my understanding where necessary. For a cross-platform solution (PC/OSX at least, or in part) my questions/problems are about what preliminary steps are needed to get an SQL or XML query to work in R to begin with, what the appropriate data-file formats are, and how to convert to them if starting out with data in, say, a delimited ASCII text file. Very basic examples should suffice, say, a table with 20 random observations, a grouping variable with 2 levels, and a factor with 2 levels. ## untested code set.seed(1024) write.table(junk.txt, data.frame(Subj=c(rep(1,10),rep(2,10)),block=rep(c(rep(-1,5),r ep(1,5)),2), obs=rnorm(20,0,1))) Specifically, 1- what are the minimum required non R components that are needed to support SQL or XML functionality, which may or may not need to be installed? 2- what R packages need to be installed, at a minimum (also as a cross-PC/Mac solution if possible or at least as much as possible) 3- I keep seeing reference to connections of a given name if previously setup. What kind of setup is needed outside of R, if any? 4- what steps are needed in R to then connect to a file and import a subset based on a query? 5- Do I then use standard R routines (e.g. write()) to export as a DB, or an RDB/XML specific function? Sincerely, KeithC. [U.S] 1/k^c __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Types in grouped multi-panel (lattice) xyplot
On 4/10/08, Aaron Arvey [EMAIL PROTECTED] wrote: Apologetic prologue: I've looked through the mailing list for an answer to this (since I'm sure it's trivial) but I have not been able to find a fix. So the problem is that I want each group to have a different type of plot. Probes should be points and Segments should be lines (preferably using the segment plot command, but I've just been trying -- unsuccessfully -- to get lines to work). To be exact, the data looks like: loc val valtype mouse 1428 0.1812367 Probes 2 1439 -0.4534155 Probes 2 1499 -0.4957303 Probes 2 1559 0.2448838 Probes 2 1611 -0.2030937 Probes 2 1788 -0.2235331 Probes 2 1428 0.5Segment 2 1439 0.5Segment 2 1499 0.5Segment 2 1559 0.5Segment 2 1611 0.5Segment 2 1788 0.5Segment 2 1428 0.1812367 Probes 1 1439 -0.4534155 Probes 1 1499 -0.4957303 Probes 1 1559 0.2448838 Probes 1 1611 -0.2030937 Probes 1 1788 -0.2235331 Probes 1 1428 0.5Segment 1 1439 0.5Segment 1 1499 0.5Segment 1 1559 0.1Segment 1 1611 0.1Segment 1 1788 0.1Segment 1 * loc is the x-axis location * val is the y-axis value * valtype is equal to which had I been smart and used make.groups * mouse is the 'cond' variable The plot command I'm currently using is, xyplot(val ~ loc | mouse, data = df, groups=valtype aspect=0.5, layout=c(3,3), lty=0, lwd=3, type=p, col=c(black, blue), as.table = TRUE) which gives me black and blue points for the probes/segments (I've infered alphabetical order for the groups colors). When I change the type to c(p, l), I get xyplot(val ~ loc | mouse, data = df, groups=valtype aspect=0.5, layout=c(3,3), lty=0, lwd=3, type=c(p,l), col=c(black, blue), as.table = TRUE) Try xyplot(val ~ loc | mouse, data = df, groups=valtype, type=c(p,l), ## distribute.type = TRUE, col=c(black, blue)) I get the exact same plot. I've tried using a few of the panel functions I found on the list (I was particularly hopeful for http://tolstoy.newcastle.edu.au/R/help/06/07/30363.html) but I've either been misusing them, or they are not right for what I want to do. If anyone knows how to get points and lines in the same panel for the two different groups (probes/segments), I would love to hear about it. If you further know how to use the 'segment' plot in panels for the segments, I would really love to hear about it. Well, panel.segments() draws segments, but you need your data in the form (x1, y1, x2, y2) for that. With your setup, it's probably easier to have lines with some NA-s inserted wherever you want line breaks. -Deepayan __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Types in grouped multi-panel (lattice) xyplot
On 4/10/08, Deepayan Sarkar [EMAIL PROTECTED] wrote: On 4/10/08, Aaron Arvey [EMAIL PROTECTED] wrote: Apologetic prologue: I've looked through the mailing list for an answer to this (since I'm sure it's trivial) but I have not been able to find a fix. So the problem is that I want each group to have a different type of plot. Probes should be points and Segments should be lines (preferably using the segment plot command, but I've just been trying -- unsuccessfully -- to get lines to work). To be exact, the data looks like: loc val valtype mouse 1428 0.1812367 Probes 2 1439 -0.4534155 Probes 2 1499 -0.4957303 Probes 2 1559 0.2448838 Probes 2 1611 -0.2030937 Probes 2 1788 -0.2235331 Probes 2 1428 0.5Segment 2 1439 0.5Segment 2 1499 0.5Segment 2 1559 0.5Segment 2 1611 0.5Segment 2 1788 0.5Segment 2 1428 0.1812367 Probes 1 1439 -0.4534155 Probes 1 1499 -0.4957303 Probes 1 1559 0.2448838 Probes 1 1611 -0.2030937 Probes 1 1788 -0.2235331 Probes 1 1428 0.5Segment 1 1439 0.5Segment 1 1499 0.5Segment 1 1559 0.1Segment 1 1611 0.1Segment 1 1788 0.1Segment 1 * loc is the x-axis location * val is the y-axis value * valtype is equal to which had I been smart and used make.groups * mouse is the 'cond' variable The plot command I'm currently using is, xyplot(val ~ loc | mouse, data = df, groups=valtype aspect=0.5, layout=c(3,3), lty=0, lwd=3, type=p, col=c(black, blue), as.table = TRUE) which gives me black and blue points for the probes/segments (I've infered alphabetical order for the groups colors). When I change the type to c(p, l), I get xyplot(val ~ loc | mouse, data = df, groups=valtype aspect=0.5, layout=c(3,3), lty=0, lwd=3, type=c(p,l), col=c(black, blue), as.table = TRUE) Try xyplot(val ~ loc | mouse, data = df, groups=valtype, type=c(p,l), ## distribute.type = TRUE, Sorry, that should be distribute.type = TRUE, col=c(black, blue)) I get the exact same plot. I've tried using a few of the panel functions I found on the list (I was particularly hopeful for http://tolstoy.newcastle.edu.au/R/help/06/07/30363.html) but I've either been misusing them, or they are not right for what I want to do. If anyone knows how to get points and lines in the same panel for the two different groups (probes/segments), I would love to hear about it. If you further know how to use the 'segment' plot in panels for the segments, I would really love to hear about it. Well, panel.segments() draws segments, but you need your data in the form (x1, y1, x2, y2) for that. With your setup, it's probably easier to have lines with some NA-s inserted wherever you want line breaks. -Deepayan __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Relational Databases or XML?
On Thu, 10 Apr 2008, Doran, Harold wrote: Well, I guess it is possible with XML package on CRAN. But, it seems there is no windows binary (yet) There certainly is -- did you try installing it from CRAN (extras)? -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Doran, Harold Sent: Thursday, April 10, 2008 4:29 PM To: Keith Alan Chamberlain; r-help@r-project.org Subject: Re: [R] Relational Databases or XML? I'm not sure it is possible to parse an XML file in R directly. Well, I guess it's *possible*, but may not be the best way to do it. ElementTree in Python is an easy-to-use parser that you might use to first parse your XML file (or others hierarchically structured data), organize it anyway you want, and then bring those data into R for subsequent analysis. In fact, I have recently done just this. I have another statistical program that outputs data as an XML file. So, I wrote a python program that parses that XML file, pulls out the data of interest into a text file, and then I bring those data into R for analysis. -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Keith Alan Chamberlain Sent: Thursday, April 10, 2008 4:14 PM To: r-help@r-project.org Subject: [R] Relational Databases or XML? Dear R-Help, I am working on a paper in an R course for large file support in R using scan(), relational databases, and XML. I have never used SQL or heirarchical document formats such as XML (except where it occurs without user interaction), and knowledge in RDBs and XML is lacking in my program. I have tried finding a working example for the novices-novice on the topic, read many postings, the r-data I/O manual several times, and descriptions of packages RODBC, DBI, XML, among others. I understand that RDBs are (assumed at least) used widely among the R community. I have not been able to put all of the pieces together, but assuming that RDB use is actually quite widespread, it should be quite easy to fill me in and/or correct my understanding where necessary. For a cross-platform solution (PC/OSX at least, or in part) my questions/problems are about what preliminary steps are needed to get an SQL or XML query to work in R to begin with, what the appropriate data-file formats are, and how to convert to them if starting out with data in, say, a delimited ASCII text file. Very basic examples should suffice, say, a table with 20 random observations, a grouping variable with 2 levels, and a factor with 2 levels. ## untested code set.seed(1024) write.table(junk.txt, data.frame(Subj=c(rep(1,10),rep(2,10)),block=rep(c(rep(-1,5),r ep(1,5)),2), obs=rnorm(20,0,1))) Specifically, 1- what are the minimum required non R components that are needed to support SQL or XML functionality, which may or may not need to be installed? 2- what R packages need to be installed, at a minimum (also as a cross-PC/Mac solution if possible or at least as much as possible) 3- I keep seeing reference to connections of a given name if previously setup. What kind of setup is needed outside of R, if any? 4- what steps are needed in R to then connect to a file and import a subset based on a query? 5- Do I then use standard R routines (e.g. write()) to export as a DB, or an RDB/XML specific function? Sincerely, KeithC. [U.S] 1/k^c __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- 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@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Problem installing and using package tseries
Can you please try to reinstall in roughly 12 hours from now from CRAN
master?
I have fixed the problem and recompiled tseries which will appear on
CRAN master within 12 hours.
Best wishes,
Uwe Ligges
Robert A. LaBudde wrote:
I have R 2.6.2, and have tried downloading and installing the package
tseries. I get the same error when I use two different mirror sites:
utils:::menuInstallPkgs()
trying URL
'http://cran.mirrors.hoobly.com/bin/windows/contrib/2.6/tseries_0.10-14.zip'
Content type 'application/zip' length 400799 bytes (391 Kb)
opened URL
downloaded 391 Kb
package 'tseries' successfully unpacked and MD5 sums checked
The downloaded packages are in
C:\Documents and Settings\User\Local
Settings\Temp\Rtmpk2jrvn\downloaded_packages
updating HTML package descriptions
library('tseries')
Error in dyn.load(file, ...) :
unable to load shared library
'C:/PROGRA~1/R/R-26~1.2/library/tseries/libs/tseries.dll':
LoadLibrary failure: The specified module could not be found.
Error: package/namespace load failed for 'tseries'
There doesn't seem to be anything unusual. The package is installed
like any other, and the required file is at C:\Program
Files\R\R-2.6.2\library\tseries\libs\tseries.dll. It is 36,864 bytes
and looks superficially okay.
Any ideas as to what's wrong here?
Thanks.
Robert A. LaBudde, PhD, PAS, Dpl. ACAFS e-mail: [EMAIL PROTECTED]
Least Cost Formulations, Ltd.URL: http://lcfltd.com/
824 Timberlake Drive Tel: 757-467-0954
Virginia Beach, VA 23464-3239Fax: 757-467-2947
Vere scire est per causas scire
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
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and provide commented, minimal, self-contained, reproducible code.
[R] function to calculate networkdays?
Hi, Does anyone know if R has a built-in function that is similar to Excel's NETWORKDAYS function? i.e., Returns the number of whole working days between two dates. Working days exclude weekends. Thanks, -- Tom [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] time series regression
Dear, I am doing a time series regression (one dependent time series variable, 7 independent time series variables and 32 annual observations). I have the problem of cointegration, autocorrelation and multicollinearity. I am considering an error correction model of the form: diff(lnY(t))=a+b1*lnY(t-1)+b2*lnX(t-1)+b3*diff(lnX(t))+error and not able to solve all problems. Any suggestion how to built a good model that solves these problems? I appreciate your help. Thanks, Bereket [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Relational Databases or XML?
You may wish to try out sqldf. It allows one to manipulate data frames using sql. The real work is done by sqlite and the RSQLite interface but it sets up the database for you and all the tables and then deletes them so its as easy a typing in one line of code. Check out the home page at http://sqldf.googlecode.com . On Windows sqlite is included in the RSQLite package so you have nothing to install but an ordinary R package. For XML there is the XML R package. The ctv and Ryacas packages are two packages that use XML (for the task view database and for parsing OpenMath respectively). At least on Windows you just install the XML package and it includes everything you need. On omegahat site there is more about the R XML package. There is also a package to handle pubmed in XML in bioconductor. On Thu, Apr 10, 2008 at 4:14 PM, Keith Alan Chamberlain [EMAIL PROTECTED] wrote: Dear R-Help, I am working on a paper in an R course for large file support in R using scan(), relational databases, and XML. I have never used SQL or heirarchical document formats such as XML (except where it occurs without user interaction), and knowledge in RDBs and XML is lacking in my program. I have tried finding a working example for the novices-novice on the topic, read many postings, the r-data I/O manual several times, and descriptions of packages RODBC, DBI, XML, among others. I understand that RDBs are (assumed at least) used widely among the R community. I have not been able to put all of the pieces together, but assuming that RDB use is actually quite widespread, it should be quite easy to fill me in and/or correct my understanding where necessary. For a cross-platform solution (PC/OSX at least, or in part) my questions/problems are about what preliminary steps are needed to get an SQL or XML query to work in R to begin with, what the appropriate data-file formats are, and how to convert to them if starting out with data in, say, a delimited ASCII text file. Very basic examples should suffice, say, a table with 20 random observations, a grouping variable with 2 levels, and a factor with 2 levels. ## untested code set.seed(1024) write.table(junk.txt, data.frame(Subj=c(rep(1,10),rep(2,10)),block=rep(c(rep(-1,5),rep(1,5)),2), obs=rnorm(20,0,1))) Specifically, 1- what are the minimum required non R components that are needed to support SQL or XML functionality, which may or may not need to be installed? 2- what R packages need to be installed, at a minimum (also as a cross-PC/Mac solution if possible or at least as much as possible) 3- I keep seeing reference to connections of a given name if previously setup. What kind of setup is needed outside of R, if any? 4- what steps are needed in R to then connect to a file and import a subset based on a query? 5- Do I then use standard R routines (e.g. write()) to export as a DB, or an RDB/XML specific function? Sincerely, KeithC. [U.S] 1/k^c __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Degrees of freedom in binomial glm
Hello, I am looking at the job satisfaction data below, from a problem in Agresti's book, and I am not sure where the degrees of freedom come from. The way I am fitting a binomial model, I have 168 observations, so in my understanding that should also be the number of fitted parameters in the saturated model. Since I have one intercept parameter, I was thinking to get 167 df for the Null model, but R tells me it's 165. Where does this number come from? Thanks in advance, Giovanni ### Agresti, Problem 5.23 race - c(White, Other) gender - c(M, F) age - c(35, 35-44, 44) loc - c(NE, MidAtl, S, MidW, NW, SW, Pac) sat - factor(c(Yes, No), levels = c(No, Yes)) Freq - c(288, 60, 224, 35, 337, 70, 38, 19, 32, 22, 21, 15, + 177, 57, 166, 19, 172, 30, 33, 35, 11, 20, 8, 10, +90, 19, 96, 12, 124, 17, 18, 13, 7, 0, 9, 1, +45, 12, 42, 5, 39, 2,6, 7, 2, 3, 2, 1, + 226, 88, 189, 44, 156, 70, 45, 47, 18, 13, 11, 9, + 128, 57, 117, 34, 73, 25, 31, 35, 3, 7, 2, 2, + 285, 110, 225, 53, 324, 60, 40, 66, 19, 25, 22, 11, + 179, 93, 141, 24, 140, 47, 25, 56, 11, 19, 2, 12, + 270, 176, 215, 80, 269, 110, 36, 25, 9, 11, 16, 4, + 180, 151, 108, 40, 136, 40, 20, 16, 7, 5, 3, 5, + 252, 97, 162, 47, 199, 62, 69, 45, 14, 8, 14, 2, + 126, 61, 72, 27, 93, 24, 27, 36, 7, 4, 5, 0, + 119, 62, 66, 20, 67, 25, 45, 22, 15, 10, 8, 6, +58, 33, 20, 10, 21, 10, 16, 15, 10, 8, 6, 2) satdata - data.frame(Freq, expand.grid(gender=gender, age=age, + race=race, sat=sat, loc=loc)) sat.glm0 - glm(sat ~ gender + age + race + loc, weights = Freq, + family = binomial, data = satdata) summary(sat.glm0) Call: glm(formula = sat ~ gender + age + race + loc, family = binomial, data = satdata, weights = Freq) Deviance Residuals: Min 1Q Median 3Q Max -19.456 -6.8390.0006.309 17.635 Coefficients: Estimate Std. Error z value Pr(|z|) (Intercept) 0.334265 0.056491 5.917 3.28e-09 *** genderF -0.180480 0.047575 -3.794 0.000149 *** age35-44 0.122422 0.051836 2.362 0.018191 * age44 0.361610 0.051576 7.011 2.36e-12 *** raceOther -0.005883 0.061605 -0.095 0.923919 locMidAtl0.437342 0.103821 4.212 2.53e-05 *** locS 0.178574 0.073033 2.445 0.014481 * locMidW 0.083189 0.066427 1.252 0.210449 locNW0.134337 0.067498 1.990 0.046563 * locSW0.295874 0.073488 4.026 5.67e-05 *** locPac 0.425480 0.096561 4.406 1.05e-05 *** --- Signif. codes: 0 â***â 0.001 â**â 0.01 â*â 0.05 â.â 0.1 â â 1 (Dispersion parameter for binomial family taken to be 1) Null deviance: 12987 on 165 degrees of freedom Residual deviance: 12880 on 155 degrees of freedom AIC: 12902 Number of Fisher Scoring iterations: 4 str(satdata) 'data.frame': 168 obs. of 6 variables: $ Freq : num 288 60 224 35 337 70 38 19 32 22 ... $ gender: Factor w/ 2 levels M,F: 1 2 1 2 1 2 1 2 1 2 ... $ age : Factor w/ 3 levels 35,35-44,..: 1 1 2 2 3 3 1 1 2 2 ... $ race : Factor w/ 2 levels White,Other: 1 1 1 1 1 1 2 2 2 2 ... $ sat : Factor w/ 2 levels No,Yes: 2 2 2 2 2 2 2 2 2 2 ... $ loc : Factor w/ 7 levels NE,MidAtl,..: 1 1 1 1 1 1 1 1 1 1 ... sessionInfo() R version 2.6.2 (2008-02-08) i686-pc-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] tools_2.6.2 -- Giovanni Petris [EMAIL PROTECTED] Associate Professor Department of Mathematical Sciences University of Arkansas - Fayetteville, AR 72701 Ph: (479) 575-6324, 575-8630 (fax) http://definetti.uark.edu/~gpetris/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Relational Databases or XML?
Its avaliable on CRAN extras: http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/ and can be downloaded even more easily through the Windows package menu in R. On Thu, Apr 10, 2008 at 4:45 PM, Doran, Harold [EMAIL PROTECTED] wrote: Well, I guess it is possible with XML package on CRAN. But, it seems there is no windows binary (yet) -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Doran, Harold Sent: Thursday, April 10, 2008 4:29 PM To: Keith Alan Chamberlain; r-help@r-project.org Subject: Re: [R] Relational Databases or XML? I'm not sure it is possible to parse an XML file in R directly. Well, I guess it's *possible*, but may not be the best way to do it. ElementTree in Python is an easy-to-use parser that you might use to first parse your XML file (or others hierarchically structured data), organize it anyway you want, and then bring those data into R for subsequent analysis. In fact, I have recently done just this. I have another statistical program that outputs data as an XML file. So, I wrote a python program that parses that XML file, pulls out the data of interest into a text file, and then I bring those data into R for analysis. -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Keith Alan Chamberlain Sent: Thursday, April 10, 2008 4:14 PM To: r-help@r-project.org Subject: [R] Relational Databases or XML? Dear R-Help, I am working on a paper in an R course for large file support in R using scan(), relational databases, and XML. I have never used SQL or heirarchical document formats such as XML (except where it occurs without user interaction), and knowledge in RDBs and XML is lacking in my program. I have tried finding a working example for the novices-novice on the topic, read many postings, the r-data I/O manual several times, and descriptions of packages RODBC, DBI, XML, among others. I understand that RDBs are (assumed at least) used widely among the R community. I have not been able to put all of the pieces together, but assuming that RDB use is actually quite widespread, it should be quite easy to fill me in and/or correct my understanding where necessary. For a cross-platform solution (PC/OSX at least, or in part) my questions/problems are about what preliminary steps are needed to get an SQL or XML query to work in R to begin with, what the appropriate data-file formats are, and how to convert to them if starting out with data in, say, a delimited ASCII text file. Very basic examples should suffice, say, a table with 20 random observations, a grouping variable with 2 levels, and a factor with 2 levels. ## untested code set.seed(1024) write.table(junk.txt, data.frame(Subj=c(rep(1,10),rep(2,10)),block=rep(c(rep(-1,5),r ep(1,5)),2), obs=rnorm(20,0,1))) Specifically, 1- what are the minimum required non R components that are needed to support SQL or XML functionality, which may or may not need to be installed? 2- what R packages need to be installed, at a minimum (also as a cross-PC/Mac solution if possible or at least as much as possible) 3- I keep seeing reference to connections of a given name if previously setup. What kind of setup is needed outside of R, if any? 4- what steps are needed in R to then connect to a file and import a subset based on a query? 5- Do I then use standard R routines (e.g. write()) to export as a DB, or an RDB/XML specific function? Sincerely, KeithC. [U.S] 1/k^c __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Row mean scores differ association
There is a R companion to Agresti's text at the following site, I believe the answer to your question is there: http://www.stat.ufl.edu/~aa/cda/cda.html --Matt Matt Austin Biostatistics Director Amgen, Inc -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of dt Excellent Sent: Thursday, April 10, 2008 1:18 PM To: R-Help Subject: [R] Row mean scores differ association Suppose that we have o 2-D contingency table where the row variable is nominal and the column one is ordinal. In SAS it is possible to compute the statistic named as row mean scores differ. How can we programmed it in R? (See also Aggresti (2002), Categorical Data Analysis, p. 302) With regards - [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] mixture distribution analisys
Hello, I'm analyzing some fish length-frequency data to access relative age and growth information and I would like to do something different from FiSAT / ELEFAN analysis. I found a package named MIX in http://www.math.mcmaster.ca/peter/mix/mix.html but it's compiled for R 2.0.0 So I have two questions: Is there any problem to run this package in R 2.7.0? - probably yes And, is there any other package in R that can be used to analyze and to separate mixture distributions? Thanks for any help. Best regards, Antonio Olinto Sao Paulo Fisheries Institute Brazil - WebMail Bignet - O seu provedor do litoral www.bignet.com.br __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Types in grouped multi-panel (lattice) xyplot
On Thu, 10 Apr 2008, Deepayan Sarkar wrote: On 4/10/08, Deepayan Sarkar [EMAIL PROTECTED] wrote: On 4/10/08, Aaron Arvey [EMAIL PROTECTED] wrote: Apologetic prologue: I've looked through the mailing list for an answer to this (since I'm sure it's trivial) but I have not been able to find a fix. So the problem is that I want each group to have a different type of plot. Probes should be points and Segments should be lines (preferably using the segment plot command, but I've just been trying -- unsuccessfully -- to get lines to work). To be exact, the data looks like: loc val valtype mouse 1428 0.1812367 Probes 2 1439 -0.4534155 Probes 2 1499 -0.4957303 Probes 2 1559 0.2448838 Probes 2 1611 -0.2030937 Probes 2 1788 -0.2235331 Probes 2 1428 0.5Segment 2 1439 0.5Segment 2 1499 0.5Segment 2 1559 0.5Segment 2 1611 0.5Segment 2 1788 0.5Segment 2 1428 0.1812367 Probes 1 1439 -0.4534155 Probes 1 1499 -0.4957303 Probes 1 1559 0.2448838 Probes 1 1611 -0.2030937 Probes 1 1788 -0.2235331 Probes 1 1428 0.5Segment 1 1439 0.5Segment 1 1499 0.5Segment 1 1559 0.1Segment 1 1611 0.1Segment 1 1788 0.1Segment 1 * loc is the x-axis location * val is the y-axis value * valtype is equal to which had I been smart and used make.groups * mouse is the 'cond' variable The plot command I'm currently using is, xyplot(val ~ loc | mouse, data = df, groups=valtype aspect=0.5, layout=c(3,3), lty=0, lwd=3, type=p, col=c(black, blue), as.table = TRUE) which gives me black and blue points for the probes/segments (I've infered alphabetical order for the groups colors). When I change the type to c(p, l), I get xyplot(val ~ loc | mouse, data = df, groups=valtype aspect=0.5, layout=c(3,3), lty=0, lwd=3, type=c(p,l), col=c(black, blue), as.table = TRUE) Try xyplot(val ~ loc | mouse, data = df, groups=valtype, type=c(p,l), ## distribute.type = TRUE, Sorry, that should be distribute.type = TRUE, col=c(black, blue)) That did exactly what I was looking for! I now have a very nice lattice plot with points and lines! I get the exact same plot. I've tried using a few of the panel functions I found on the list (I was particularly hopeful for http://tolstoy.newcastle.edu.au/R/help/06/07/30363.html) but I've either been misusing them, or they are not right for what I want to do. If anyone knows how to get points and lines in the same panel for the two different groups (probes/segments), I would love to hear about it. If you further know how to use the 'segment' plot in panels for the segments, I would really love to hear about it. Well, panel.segments() draws segments, but you need your data in the form (x1, y1, x2, y2) for that. With your setup, it's probably easier to have lines with some NA-s inserted wherever you want line breaks. That works perfectly! I was just planning on reformating the data, but this makes life even easier! Thanks! Aaron __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Fixing the physical size of Trellis graphs panels
Dear R-users,
Please consider the following script:
#
library(lattice)
ID - rep(1:8,each=2)
x - rep (c(1,2),8)
y - c(rep(c(0.5,2),4),rep(c(50,1000),4))
df-data.frame(ID,x,y)
g - rep(1:2,each=8)
df.split-split(df,g)
df.split
pdf(file=C:/Test.pdf)
for (i in 1:2) {
mydf-as.data.frame(df.split[i])
myplot-xyplot(mydf[,3]~mydf[,2]|mydf[,1],
data=mydf,
layout=c(2,2))
print(myplot)
}
dev.off()
You will find that the physical size of the panels are different on page
1 and 2 because the axis labels have different length. Is it possible to
fix the dimension of the panels regardless of the length of the axis labels?
Thank you for your input.
Sebastien
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Relational Databases or XML?
Harold -- you'll really want to check out the XML package. xmlTreeParse
+ xpathApply provides a very flexible solution. As a recent example,
parsing 189 XML files to extract 4 attributes from deeply nested
elements into a data frame:
fls - list.files('~/runBrowser', pattern=.*xml, full=TRUE)
f - function(fl) {
xq - function(xml, q)
unlist(xpathApply(xml, q, xmlValue, namespaces=xsi))
xml - xmlTreeParse(fl, useInternal=TRUE)
data.frame(idx=rep(as.numeric(xq(xml, //xsi:tile/@idx)), each=4),
lane=rep(as.numeric(xq(xml, //xsi:tile/@lane)), each=4),
base=xq(xml, '//xsi:image/@base'),
medSigInt=as.numeric(xq(xml, //xsi:sgnInt/@median)))
}
res - do.call('rbind', lapply(fls, f))
'res' has 54800 rows and 4 columns. The XML stays in C, so this is fast.
The data can be effectively (your mileage may vary) visualized with
lattice, e.g.,
xyplot(log(medSigInt)~idx|lane*base, res, strip=FALSE, pch=., cex=2)
Martin
Doran, Harold wrote:
I'm not sure it is possible to parse an XML file in R directly. Well, I
guess it's *possible*, but may not be the best way to do it. ElementTree
in Python is an easy-to-use parser that you might use to first parse
your XML file (or others hierarchically structured data), organize it
anyway you want, and then bring those data into R for subsequent
analysis.
In fact, I have recently done just this. I have another statistical
program that outputs data as an XML file. So, I wrote a python program
that parses that XML file, pulls out the data of interest into a text
file, and then I bring those data into R for analysis.
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Keith Alan
Chamberlain
Sent: Thursday, April 10, 2008 4:14 PM
To: r-help@r-project.org
Subject: [R] Relational Databases or XML?
Dear R-Help,
I am working on a paper in an R course for large file support
in R using scan(), relational databases, and XML. I have
never used SQL or heirarchical document formats such as XML
(except where it occurs without user interaction), and
knowledge in RDBs and XML is lacking in my program. I have
tried finding a working example for the novices-novice on the
topic, read many postings, the r-data I/O manual several
times, and descriptions of packages RODBC, DBI, XML, among
others. I understand that RDBs are (assumed at least) used
widely among the R community. I have not been able to put all
of the pieces together, but assuming that RDB use is actually
quite widespread, it should be quite easy to fill me in
and/or correct my understanding where necessary.
For a cross-platform solution (PC/OSX at least, or in part)
my questions/problems are about what preliminary steps are
needed to get an SQL or XML query to work in R to begin
with, what the appropriate data-file formats are, and how to
convert to them if starting out with data in, say, a
delimited ASCII text file. Very basic examples should
suffice, say, a table with 20 random observations, a grouping
variable with 2 levels, and a factor with 2 levels.
## untested code
set.seed(1024)
write.table(junk.txt,
data.frame(Subj=c(rep(1,10),rep(2,10)),block=rep(c(rep(-1,5),r
ep(1,5)),2), obs=rnorm(20,0,1)))
Specifically,
1- what are the minimum required non R components that are
needed to support SQL or XML functionality, which may or may
not need to be installed?
2- what R packages need to be installed, at a minimum (also
as a cross-PC/Mac solution if possible or at least as much as
possible)
3- I keep seeing reference to connections of a given name if
previously setup. What kind of setup is needed outside of R, if any?
4- what steps are needed in R to then connect to a file and
import a subset based on a query?
5- Do I then use standard R routines (e.g. write()) to export
as a DB, or an RDB/XML specific function?
Sincerely,
KeithC. [U.S]
1/k^c
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
Location: Arnold Building M2 B169
Phone: (206) 667-2793
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Fixing the physical size of Trellis graphs panels
On 4/10/08, Sébastien [EMAIL PROTECTED] wrote:
Dear R-users,
Please consider the following script:
#
library(lattice)
ID - rep(1:8,each=2)
x - rep (c(1,2),8)
y - c(rep(c(0.5,2),4),rep(c(50,1000),4))
df-data.frame(ID,x,y)
g - rep(1:2,each=8)
df.split-split(df,g)
df.split
pdf(file=C:/Test.pdf)
for (i in 1:2) {
mydf-as.data.frame(df.split[i])
myplot-xyplot(mydf[,3]~mydf[,2]|mydf[,1],
data=mydf,
layout=c(2,2))
print(myplot)
}
dev.off()
You will find that the physical size of the panels are different on page
1 and 2 because the axis labels have different length. Is it possible to
fix the dimension of the panels regardless of the length of the axis labels?
Yes, look at the entry for panel.width and panel.height in
?print.trellis. You could use it as
print(myplot, panel.width = list(x = 3, unit = inches))
etc. See ?unit in the grid package for details.
-Deepayan
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] mixture distribution analisys
The CRAN task view on cluster and mixture models likely has what you need. hth, Ingmar http://cran.r-project.org/web/views/Cluster.html On Apr 10, 2008, at 11:20 PM, Antonio Olinto wrote: Hello, I'm analyzing some fish length-frequency data to access relative age and growth information and I would like to do something different from FiSAT / ELEFAN analysis. I found a package named MIX in http://www.math.mcmaster.ca/peter/ mix/mix.html but it's compiled for R 2.0.0 So I have two questions: Is there any problem to run this package in R 2.7.0? - probably yes And, is there any other package in R that can be used to analyze and to separate mixture distributions? Thanks for any help. Best regards, Antonio Olinto Sao Paulo Fisheries Institute Brazil - WebMail Bignet - O seu provedor do litoral www.bignet.com.br __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting- guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
