Re: [R] Sweave - print \n ?
Thanks for your comments!
I think using just one backslash for \n is correct
because otherwise I get a \n literally printed out
in the generated .tex code. But what I'm trying to get
is just a line break, thus that the .tex code
continues on a new line from the point where I put the
\n.
All the best,
Werner
--- Abhijit Dasgupta [EMAIL PROTECTED]
schrieb:
you haven't escaped the \ for the \n, I think. Your
line should be
cat(\\hline \\n). You did escape the \ for hline,
though.
Abhijit Dasgupta, Ph.D
Assistant Professor | Division of Biostatistics
Dept of Pharmacology and Experimental Therapeutics |
Thomas Jefferson
University
1015 Chestnut St | Suite M100 | Philadelphia PA
19107
Ph: (215) 503-9201 | Fax: (215) 503-3804
adasgupt (at) mail (dot) jci (dot) tju (dot) edu
The documents accompanying this transmission may
contain confidential
health or business information. This information is
intended for the use
of the individual or entity named above. If you have
received this
information in error, please notify the sender
immediately and arrange
for the return or destruction of these documents.
Werner Wernersen wrote:
Hi,
this is probably quite stupid but I have no clue
what's wrong. Let's say I write the function
hline - function() {
cat(\\hline \n)
}
and call hline() from within a Sweave chunk. Why
is
there no carriage return after the \hline in the
resulting tex file?
if I call hline() hline() in the chunk, then I get
\hline \hline
in the tex code without a linebreak in between.
Thanks for any hints,
Werner
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Re: [R] installing a new package
Don MacQueen wrote: At the risk of oversimplifying, there are three steps to developing and using a package: 1) build 2) install 3) load Evidently your package does steps 1 and 2 but not 3. Furthermore, it tells you, not a valid package, and says something that is suggestive of a version problem: installed 2.0.0 I think you have to look very carefully at your package and look for what is invalid about it. There must be some requirement of package structure, or contents, or version of something, that your package doesn't meet or violates. Since your package can be installed, go into R, and try require(HighProbability) but set the verbose argument to something that gives more information than the default. Maybe that will give some helpful information, more than the check provides. Either that, or delve deeply into the CMD check script(s) and find out exactly what can trigger the error message. Anyway, that's the best I can come up with, without actually having the package files. And the having the latter, it would be much easier to help for all of us. Uwe Ligges -Don At 2:52 PM -0400 3/28/08, [EMAIL PROTECTED] wrote: Dear all, I have prepared a new package to install in R, I tried to check my package and I got the following message 232sub141:~ zahra$ R CMD check /Users/zahra/Desktop/HighProbability * checking for working latex ... OK * using log directory '/Users/zahra/HighProbability.Rcheck' * using R version 2.6.2 (2008-02-08) * checking for file 'HighProbability/DESCRIPTION' ... OK * this is package 'HighProbability' version '1.0-3' * checking package dependencies ... OK * checking if this is a source package ... OK * checking whether package 'HighProbability' can be installed ... OK * checking package directory ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... ERROR Error in library(HighProbability) : 'HighProbability' is not a valid package -- installed 2.0.0? Execution halted It looks like this package has a loading problem: see the messages for details. I don't know what the Error in library(package name) means and how can I solve it. I work with Mac. I'll appreciate it if you could help me. All the best, Zahra __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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: cannot allocate vector of size 3.0 Gb
Can you make the data.frame available somewhere. Actually, I am surprised it need that huge amount of memory to do the plot. Best, Uwe Ligges John wrote: Hello, I have read recent posts on this topic (Dr. Ronnen Levinson's Monday 02:39:55 pm), but before I install a 64 bit system, and purchase more RAM, I want to make sure I understand this interesting issue. I was attempting to plot a data frame containing Dow Jones stock information: length(Date) [1] 19957 length(Close) [1] 19957 head(DowJones) Date Open High LowClose Volume Adj.Close 1 03/26/08 12531.79 12531.79 12309.62 12422.86 405567 12422.86 2 03/25/08 12547.34 12639.82 12397.62 12532.60 414512 12532.60 3 03/24/08 12361.97 12687.61 12346.17 12548.64 449900 12548.64 4 03/20/08 12102.43 12434.34 12024.68 12361.32 207845 12361.32 5 03/19/08 12391.52 12525.19 12077.27 12099.66 120383 12099.66 6 03/18/08 11975.92 12411.63 11975.92 12392.66 126339 12392.66 tail(DowJones) Date Open HighLow Close Volume Adj.Close 19952 10/08/28 240.17 243.33 237.72 239.55 394239.55 19953 10/05/28 240.00 243.08 238.22 240.44 436240.44 19954 10/04/28 237.75 242.53 237.72 240.00 433240.00 19955 10/03/28 238.14 239.14 233.60 237.75 406237.75 19956 10/02/28 240.01 241.54 235.42 238.14 385238.14 19957 10/01/28 239.43 242.46 238.24 240.01 350240.01 plot(Date, Close) Error: cannot allocate vector of size 3.0 Gb I currently have installed R 2.60, from source, onto Linux SuSE 10.2. I believe it is a 32 bit install: dmesg | grep bit ... hpet0: 3 32-bit timers, 2500 Hz I have 1GB of RAM, with circa 883.61 not allocated to hardware after boot. I naively thought 19957 rows of data would be easily handled by a fairly new computer. R was able to cease execution, and place control back onto its interpreter, while a Chart attempt in OpenOffice locks up OpenOffice. So, will installation of a 64 bit Operating System, and at least an additional 1GB of RAM suffice to generate memory space for a 3.0 Gb vector, in R? Much appreciated, time to buy a new computer? 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. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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: cannot allocate vector of size 3.0 Gb
On Friday 28 March 2008 14:28, Daniel Nordlund wrote: -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of John Sent: Friday, March 28, 2008 12:04 PM To: r-help@r-project.org Subject: [R] Error: cannot allocate vector of size 3.0 Gb Hello, I have read recent posts on this topic (Dr. Ronnen Levinson's Monday 02:39:55 pm), but before I install a 64 bit system, and purchase more RAM, I want to make sure I understand this interesting issue. I was attempting to plot a data frame containing Dow Jones stock information: length(Date) [1] 19957 length(Close) [1] 19957 head(DowJones) Date Open High LowClose Volume Adj.Close 1 03/26/08 12531.79 12531.79 12309.62 12422.86 405567 12422.86 2 03/25/08 12547.34 12639.82 12397.62 12532.60 414512 12532.60 3 03/24/08 12361.97 12687.61 12346.17 12548.64 449900 12548.64 4 03/20/08 12102.43 12434.34 12024.68 12361.32 207845 12361.32 5 03/19/08 12391.52 12525.19 12077.27 12099.66 120383 12099.66 6 03/18/08 11975.92 12411.63 11975.92 12392.66 126339 12392.66 tail(DowJones) Date Open HighLow Close Volume Adj.Close 19952 10/08/28 240.17 243.33 237.72 239.55 394239.55 19953 10/05/28 240.00 243.08 238.22 240.44 436240.44 19954 10/04/28 237.75 242.53 237.72 240.00 433240.00 19955 10/03/28 238.14 239.14 233.60 237.75 406237.75 19956 10/02/28 240.01 241.54 235.42 238.14 385238.14 19957 10/01/28 239.43 242.46 238.24 240.01 350240.01 plot(Date, Close) Error: cannot allocate vector of size 3.0 Gb I currently have installed R 2.60, from source, onto Linux SuSE 10.2. I believe it is a 32 bit install: dmesg | grep bit ... hpet0: 3 32-bit timers, 2500 Hz I have 1GB of RAM, with circa 883.61 not allocated to hardware after boot. I naively thought 19957 rows of data would be easily handled by a fairly new computer. R was able to cease execution, and place control back onto its interpreter, while a Chart attempt in OpenOffice locks up OpenOffice. So, will installation of a 64 bit Operating System, and at least an additional 1GB of RAM suffice to generate memory space for a 3.0 Gb vector, in R? John, Am I missing something here? You have one 1 GB of RAM, you want to get a second 1 GB of RAM, and you want to know if you will be able to create a 3 GB vector? With or without a 64bit OS, I don't think you will be successful. In addition to total memory available, I believe you need to have sufficient contiguous memory to allocate an object. If memory is fragmented, you won't be able to create the vector, even if the total free space is sufficient. If I am incorrect, I'm sure someone will be along to correct me shortly. Hope this is helpful, Dan Daniel Nordlund Bothell, WA __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Hi Daniel, Thank you for the information. It has saved me from needlessly installing a 64-bit linux instance. In the short term, I'll try and generate multiple graphs, side by side. And purchase more RAM. A lot more. Enjoying the notion of multiple plots in R, 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.
[R] AD-model builder under R for mix logistics model, a problem.
the code is list below , i can run this code for laplace approximation but not importance sampling. the code work properly if use impSamp=0 , but error for any other number 0 . could you guys help me out. thanks so much ! source(http://www.mi.uib.no/~skaug/cash/lesaffre_dat.s;) library(glmmADMB) fit_glmmADMB_ip - glmm.admb(y~treat,random=~1,group=subject,impSamp =100,data=lesaffre,family=binomial,link=logit,save.dir= NULL) Initial statistics: 2 variables; iteration 0; function evaluation 0 Function value 1.5926934e+003; maximum gradient component mag 1.2500e+001 Var ValueGradient |Var ValueGradient |Var Value Gradient 1 0. 1.2500e+001 | 2 0. 6.2441e-001 | - final statistics: 2 variables; iteration 9; function evaluation 13 Function value 1.2593e+003; maximum gradient component mag -5.7984e-005 Exit code = 1; converg criter 1.e-004 Var ValueGradient |Var ValueGradient |Var Value Gradient 1-56.9607 -1.2327e-005 | 2 -3.7159 -5.7984e-005 | inner maxg = 9.681e-005 max separable g 9.681e-005 Newton raphson 1 f = 971.7651636 max g = 9.245773036e-010 max separable g 9.245775812e-010 Newton raphson 2 f = 971.7651636 max g = 2.220446049e-015 971.7651636 Error in glmm.admb(y ~ treat, random = ~1, group = subject, impSamp = 100, : The function maximizer failed In addition: Warning message: In shell(paste(.path.package(glmmADMB), /admb/, file_name, .exe, : 'cmd' execution failed with error code 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] Sweave - print \n ?
Try adding strip.white=false on the code chunks:
echo=false,results=tex, strip.white=false=
hline()
hline()
@
Read ?RweaveLatex for more settings.
or if you want this to happen in all code chunks add this early on in
the rnw file:
\SweaveOpts{strip.white=false}
Haris Skiadas
Department of Mathematics and Computer Science
Hanover College
On Mar 29, 2008, at 4:54 AM, Werner Wernersen wrote:
Thanks for your comments!
I think using just one backslash for \n is correct
because otherwise I get a \n literally printed out
in the generated .tex code. But what I'm trying to get
is just a line break, thus that the .tex code
continues on a new line from the point where I put the
\n.
All the best,
Werner
--- Abhijit Dasgupta [EMAIL PROTECTED]
schrieb:
you haven't escaped the \ for the \n, I think. Your
line should be
cat(\\hline \\n). You did escape the \ for hline,
though.
Abhijit Dasgupta, Ph.D
Assistant Professor | Division of Biostatistics
Dept of Pharmacology and Experimental Therapeutics |
Thomas Jefferson
University
1015 Chestnut St | Suite M100 | Philadelphia PA
19107
Ph: (215) 503-9201 | Fax: (215) 503-3804
adasgupt (at) mail (dot) jci (dot) tju (dot) edu
--
--
The documents accompanying this transmission may
contain confidential
health or business information. This information is
intended for the use
of the individual or entity named above. If you have
received this
information in error, please notify the sender
immediately and arrange
for the return or destruction of these documents.
--
--
Werner Wernersen wrote:
Hi,
this is probably quite stupid but I have no clue
what's wrong. Let's say I write the function
hline - function() {
cat(\\hline \n)
}
and call hline() from within a Sweave chunk. Why
is
there no carriage return after the \hline in the
resulting tex file?
if I call hline() hline() in the chunk, then I get
\hline \hline
in the tex code without a linebreak in between.
Thanks for any hints,
Werner
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/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] Defining reference category for a cph model summary inside of a for loop
Dr. Harrell,
Thanks for you help.
I tried:
print(summary(f,parse(text=paste(i,'=1st Quartile', sep=''
Same result. No error, the reference category simply doesn't change.
Brian
-Original Message-
From: Frank E Harrell Jr [mailto:[EMAIL PROTECTED]
Sent: Friday, March 28, 2008 8:34 PM
To: Wells, Brian
Cc: r-help@r-project.org
Subject: Re: [R] Defining reference category for a cph model summary
inside of a for loop
Wells, Brian wrote:
I have the following code.
f - cph(formula = Surv(TimeToDeath, Dead == Yes)
~1,data=single.dat, x=T, y=T, surv=T)
for(i in c('A', 'B', 'C', 'D', 'E', 'F')){
f -update(f,as.formula(paste('Surv(TimeToDeath, Dead ==
Yes)~',i,sep='')))
print(summary(f, paste(i,=1st Quartile, sep='')))
There is no error message generated in R, but R ignores the reference
category defined with paste in the summary function for the cph model.
The output uses the 1st Quartile as the reference category to
calculate hazards for some of the variables defined by i, but not all
of
them.
Your code is confusing. What is to the right of ~ in a formula is a
predictor variable name, not a value. If your variables are named A, B,
C, ... you are OK.
'1st Quartile' has no special meaning to R or Design, and you can't pass
a character string as a second argument to summary and expect it to
work.
You will need parse(text=paste(...)) to create an appropriate
expression.
But Design gives you inter-quartile range hazard ratios by default
anyway.
Beware of getting hazard ratios that are not adjusted for other
variables needed in the model.
Frank Harrell
Any help would be greatly appreciated.
thanks
Brian J. Wells, MD, MS
Research Associate
Quantitative Health Sciences
Cleveland Clinic
--
Frank E Harrell Jr Professor and Chair School of Medicine
Department of Biostatistics Vanderbilt
University
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[R] AD-MB problem in package:glmmADMB
Hi here, i recently notice the software built by otter company know as AD-MB tools . i explore a little bit this tools under the R Package for mixed logistics model. it is a very interesting tool. but i get several questions. first question: i tried the R code below, and have the error , i can run the code for switching the setting to impSamp=0 , it means i can only run the code under Laplace approximation but importance sampling. does anyone have same problem here ? second question: although i used save.dir=NULL option , but i can not see the folder which saves the intermedia output, i didn't find the nbmm.std file which save the BLUP. the strangest thing is i can see a temporary folder name as _glmm_ADMB_temp_dir_ when programing is running , but this fold mysteriously disappeared after the programing done . searched the whole computer desn't find any clue. I posted my output below. I really appreciate if you can help me with the questions. source(http://www.mi.uib.no/~skaug/cash/lesaffre_dat.s http://www.mi.uib.no/%7Eskaug/cash/lesaffre_dat.s) fit_glmmADMB_ip - glmm.admb(y~treat,random=~1,group=subject,impSamp =100,data=lesaffre,family=binomial,link=logit,save.dir= NULL) Initial statistics: 2 variables; iteration 0; function evaluation 0 Function value 1.5926934e+003; maximum gradient component mag 1.2500e+001 Var Value Gradient |Var Value Gradient |Var Value Gradient 1 0. 1.2500e+001 | 2 0. 6.2441e-001 | - final statistics: 2 variables; iteration 9; function evaluation 13 Function value 1.2593e+003; maximum gradient component mag -5.7984e-005 Exit code = 1; converg criter 1.e-004 Var Value Gradient |Var Value Gradient |Var Value Gradient 1-56.9607 -1.2327e-005 | 2 -3.7159 -5.7984e-005 | inner maxg = 9.681e-005 max separable g 9.681e-005 Newton raphson 1 f = 971.7651636 max g = 9.245773036e-010 max separable g 9.245775812e-010 Newton raphson 2 f = 971.7651636 max g = 2.220446049e-015 971.7651636 Error in glmm.admb(y ~ treat, random = ~1, group = subject, impSamp = 100, : The function maximizer failed In addition: Warning message: In shell(paste(.path.package(glmmADMB), /admb/, file_name, .exe, : 'cmd' execution failed with error code 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.
[R] S4 : the list of all the object
Hi the list, Is it possible to get the list of all the S4 user define classes? I would like to set up a package.skeleton.S4 but for that, I need the list of the classes... Thanks Christophe __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Singular Gradient in nls
sorry, the below should read: A QR decomposition is done on the weighted gradient matrix; if the estimate of the rank that results is less than min( the number of columns in the gradient (the number of nonlinear parameters), the number of rows (the number of observations) ) , nls stops. so you look at the number of observations, and the number of parameters, and take the smaller of the two. if the estimated rank of the weighted gradient is small than this number, you stop. On Fri, 28 Mar 2008, Katharine Mullen wrote: A QR decomposition is done on the weighted gradient matrix; if the estimate of the rank that results is less than the number of columns in the gradient (the number of nonlinear parameters), or less than the number of rows (the number of observations), nls stops. You can see the calls in the source code of nlsModel (https://svn.r-project.org/R/trunk/src/library/stats/R/nls.R). On Fri, 28 Mar 2008, glenn andrews wrote: //Referring to the response posted many years ago, copied below, what is the specific criterium used for singularity of the gradient matrix? Is a Singular Value Decomposition used to determine the singular values? Is it the gradient matrix condition number or some other criterion for determining singularity? // //Glenn // / / / What does the error 'singular gradient' mean during a nonlinear regression? / The gradient matrix to which the message refers is the derivative of the vector of predicted values with respect to the vector of parameters at the current parameter estimates. If you have 20 observations and three parameters, this will be a matrix with 20 rows and three columns. For the model to be estimable in a region of the current estimates, this matrix must have full column rank. When it fails to have full column rank the singular gradient message is given and the iterations stop. Generally this indicates that the model is overparameterized or that the starting estimates were poorly chosen. Try using trace = TRUE in the call to nls and watching the progress of the iterations. This will often show that the estimates are wandering into unreasonable regions of the parameter space. -- Douglas Bates[EMAIL PROTECTED] Statistics Department608/262-2598 University of Wisconsin - Madisonhttp://www.stat.wisc.edu/~bates/ http://www.stat.wisc.edu/%7Ebates/ -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hornik/R/R-FAQ.html http://www.ci.tuwien.ac.at/%7Ehornik/R/R-FAQ.html Send info, help, or [un]subscribe (in the body, not the subject !) To: [EMAIL PROTECTED] _._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._._ [[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-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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: cannot allocate vector of size 3.0 Gb
Dear John, note that you Date is a factor rather than some date object. If you convert it to some date object, just a few megabytes will suffice! Best wishes, Uwe John wrote: On Friday 28 March 2008 14:28, Daniel Nordlund wrote: -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of John Sent: Friday, March 28, 2008 12:04 PM To: r-help@r-project.org Subject: [R] Error: cannot allocate vector of size 3.0 Gb Hello, I have read recent posts on this topic (Dr. Ronnen Levinson's Monday 02:39:55 pm), but before I install a 64 bit system, and purchase more RAM, I want to make sure I understand this interesting issue. I was attempting to plot a data frame containing Dow Jones stock information: length(Date) [1] 19957 length(Close) [1] 19957 head(DowJones) Date Open High LowClose Volume Adj.Close 1 03/26/08 12531.79 12531.79 12309.62 12422.86 405567 12422.86 2 03/25/08 12547.34 12639.82 12397.62 12532.60 414512 12532.60 3 03/24/08 12361.97 12687.61 12346.17 12548.64 449900 12548.64 4 03/20/08 12102.43 12434.34 12024.68 12361.32 207845 12361.32 5 03/19/08 12391.52 12525.19 12077.27 12099.66 120383 12099.66 6 03/18/08 11975.92 12411.63 11975.92 12392.66 126339 12392.66 tail(DowJones) Date Open HighLow Close Volume Adj.Close 19952 10/08/28 240.17 243.33 237.72 239.55 394239.55 19953 10/05/28 240.00 243.08 238.22 240.44 436240.44 19954 10/04/28 237.75 242.53 237.72 240.00 433240.00 19955 10/03/28 238.14 239.14 233.60 237.75 406237.75 19956 10/02/28 240.01 241.54 235.42 238.14 385238.14 19957 10/01/28 239.43 242.46 238.24 240.01 350240.01 plot(Date, Close) Error: cannot allocate vector of size 3.0 Gb I currently have installed R 2.60, from source, onto Linux SuSE 10.2. I believe it is a 32 bit install: dmesg | grep bit ... hpet0: 3 32-bit timers, 2500 Hz I have 1GB of RAM, with circa 883.61 not allocated to hardware after boot. I naively thought 19957 rows of data would be easily handled by a fairly new computer. R was able to cease execution, and place control back onto its interpreter, while a Chart attempt in OpenOffice locks up OpenOffice. So, will installation of a 64 bit Operating System, and at least an additional 1GB of RAM suffice to generate memory space for a 3.0 Gb vector, in R? John, Am I missing something here? You have one 1 GB of RAM, you want to get a second 1 GB of RAM, and you want to know if you will be able to create a 3 GB vector? With or without a 64bit OS, I don't think you will be successful. In addition to total memory available, I believe you need to have sufficient contiguous memory to allocate an object. If memory is fragmented, you won't be able to create the vector, even if the total free space is sufficient. If I am incorrect, I'm sure someone will be along to correct me shortly. Hope this is helpful, Dan Daniel Nordlund Bothell, WA __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Hi Daniel, Thank you for the information. It has saved me from needlessly installing a 64-bit linux instance. In the short term, I'll try and generate multiple graphs, side by side. And purchase more RAM. A lot more. Enjoying the notion of multiple plots in R, 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. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Problem installing aroma.affymetrix on Solaris 9 with R-2.6.2
Hi List, I'm trying to install aroma.affymetrix, which depend on many packages, affyio is one of them. The task is done on 32-bit Linux without problem. The same task was done on Solaris 9 with R-2.5.1 without problem. Following is the error message when installation affyio. I did try to put a file stdint.h I got from the web in the path, but got more error messages. Jun [EMAIL PROTECTED] R# R CMD INSTALL affyio_1.6.1.tar.gz * Installing to library '/apps/R-2.6.2/lib/R/library' * Installing *source* package 'affyio' ... creating cache ./config.cache checking how to run the C preprocessor... grep: can't open conftest.out cc -E checking for main in -lz... no updating cache ./config.cache creating ./config.status creating src/Makevars ** libs gcc -std=gnu99 -I/apps/R-2.6.2/lib/R/include -I/apps/R-2.6.2/lib/R/include -I/apps/mpich-1.2.7p1/include-fPIC -g -O2 -c fread_functions.c -o fread_functions.o gcc -std=gnu99 -I/apps/R-2.6.2/lib/R/include -I/apps/R-2.6.2/lib/R/include -I/apps/mpich-1.2.7p1/include-fPIC -g -O2 -c read_abatch.c -o read_abatch.o gcc -std=gnu99 -I/apps/R-2.6.2/lib/R/include -I/apps/R-2.6.2/lib/R/include -I/apps/mpich-1.2.7p1/include-fPIC -g -O2 -c read_bpmap.c -o read_bpmap.o gcc -std=gnu99 -I/apps/R-2.6.2/lib/R/include -I/apps/R-2.6.2/lib/R/include -I/apps/mpich-1.2.7p1/include-fPIC -g -O2 -c read_cdf_xda.c -o read_cdf_xda.o read_cdf_xda.c: In function `isPM': read_cdf_xda.c:614: warning: implicit declaration of function `toupper' gcc -std=gnu99 -I/apps/R-2.6.2/lib/R/include -I/apps/R-2.6.2/lib/R/include -I/apps/mpich-1.2.7p1/include-fPIC -g -O2 -c read_cdffile2.c -o read_cdffile2.o gcc -std=gnu99 -I/apps/R-2.6.2/lib/R/include -I/apps/R-2.6.2/lib/R/include -I/apps/mpich-1.2.7p1/include-fPIC -g -O2 -c read_celfile_generic.c -o read_celfile_generic.o read_celfile_generic.c:31:20: stdint.h: No such file or directory *** Error code 1 make: Fatal error: Command failed for target `read_celfile_generic.o' chmod: WARNING: can't access /apps/R-2.6.2/lib/R/library/affyio/libs/* ERROR: compilation failed for package 'affyio' ** Removing '/apps/R-2.6.2/lib/R/library/affyio' - [[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] Generating maps in R
Greetings! I am trying plot some data on a map in R. Here's the scenario. I have a variable called probworkinghealthy which contains a predicted probability of employment for every individual in my sample (about 100,000 observations). I have another variable, called a001ter, which contains the subject of residency in the Russian Federation (akin to a US state) for every individual in the sample. I have a shape file with the boundaries of all the subjects, called russia.shp. I can plot boxplots of the probability by Federal Subject using plot(probworkinghealthy ~ a001ter). I can also plot the map using plot(russia.shp) Now, I would like to plot the mean probability of employment (i.e. mean(probworkinghealthy)) on a map of Russia using color coding all the Federal Subjects. Does anyone know how to do something like that? Much appreciated, Aleks Andreev Duke University __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] directory of R consultants for hire
Does anyone know of a directory that lists consultants with expertise in R, as well as other statistical and computing skills, ideally with geographic location and other pertinent information? If one does not exist, might this be a good resource to create? - You rock. That's why Blockbuster's offering you one month of Blockbuster Total Access, No Cost. [[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 installing aroma.affymetrix on Solaris 9 with R-2.6.2
This is the wrong list for questions about Bioconductor packages: please do study the posting guide (and no HTML mail, please). stdint.h is part of C99. My guess is that your unspecified compiler + obsolete OS is not C99 compliant. Since Solaris 8 has inttypes.h (which is supposed by POSIX to include stdint.h), it is a reasonable guess that you could might be able to replace stdint.h by inttypes.h (especially as R has been compiled on your OS and R uses inttypes.h as a fallback). When you find a solution, you should report it to the maintainer of the affyio package (see the posting guide). On Sat, 29 Mar 2008, Jun Zhang wrote: Hi List, I'm trying to install aroma.affymetrix, which depend on many packages, affyio is one of them. The task is done on 32-bit Linux without problem. The same task was done on Solaris 9 with R-2.5.1 without problem. Following is the error message when installation affyio. I did try to put a file stdint.h I got from the web in the path, but got more error messages. Jun [EMAIL PROTECTED] R# R CMD INSTALL affyio_1.6.1.tar.gz * Installing to library '/apps/R-2.6.2/lib/R/library' * Installing *source* package 'affyio' ... creating cache ./config.cache checking how to run the C preprocessor... grep: can't open conftest.out cc -E checking for main in -lz... no updating cache ./config.cache creating ./config.status creating src/Makevars ** libs gcc -std=gnu99 -I/apps/R-2.6.2/lib/R/include -I/apps/R-2.6.2/lib/R/include -I/apps/mpich-1.2.7p1/include-fPIC -g -O2 -c fread_functions.c -o fread_functions.o gcc -std=gnu99 -I/apps/R-2.6.2/lib/R/include -I/apps/R-2.6.2/lib/R/include -I/apps/mpich-1.2.7p1/include-fPIC -g -O2 -c read_abatch.c -o read_abatch.o gcc -std=gnu99 -I/apps/R-2.6.2/lib/R/include -I/apps/R-2.6.2/lib/R/include -I/apps/mpich-1.2.7p1/include-fPIC -g -O2 -c read_bpmap.c -o read_bpmap.o gcc -std=gnu99 -I/apps/R-2.6.2/lib/R/include -I/apps/R-2.6.2/lib/R/include -I/apps/mpich-1.2.7p1/include-fPIC -g -O2 -c read_cdf_xda.c -o read_cdf_xda.o read_cdf_xda.c: In function `isPM': read_cdf_xda.c:614: warning: implicit declaration of function `toupper' gcc -std=gnu99 -I/apps/R-2.6.2/lib/R/include -I/apps/R-2.6.2/lib/R/include -I/apps/mpich-1.2.7p1/include-fPIC -g -O2 -c read_cdffile2.c -o read_cdffile2.o gcc -std=gnu99 -I/apps/R-2.6.2/lib/R/include -I/apps/R-2.6.2/lib/R/include -I/apps/mpich-1.2.7p1/include-fPIC -g -O2 -c read_celfile_generic.c -o read_celfile_generic.o read_celfile_generic.c:31:20: stdint.h: No such file or directory *** Error code 1 make: Fatal error: Command failed for target `read_celfile_generic.o' chmod: WARNING: can't access /apps/R-2.6.2/lib/R/library/affyio/libs/* ERROR: compilation failed for package 'affyio' ** Removing '/apps/R-2.6.2/lib/R/library/affyio' - [[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. -- 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] DE optimization with equality constraint
On Sat, Mar 29, 2008 at 9:33 PM, Hans W. Borchers [EMAIL PROTECTED] wrote:
Reply to Optimization with constraint on March 14, 2008
One can get an accurate solutons applying the Differential Evolution
algorithm
as implemented in the DEoptim package:
f2 - function(x){
if (x[1] + x[2] 1 || x[1] + x[2] 1) {
r - Inf
} else {
r - x[1]^2 + x[2]^2
}
return(r)
}
lower - c(0, 0)
upper - c(1, 1)
DEoptim(f2, lower, upper, control=list(refresh=200))$bestmem
iteration: 200 best member: 0.5 0.5 best value: 0.5
This approach assumes nothing about the gradient, hessian or whatever. And
the
equality is split into two inequalities assuming no relaxation or penalty.
The problem with DEoptim approach is that is not guaranteed that it
converges to the solution. Moreover, from my experience, it seems to
be quite slow when the optimization problem is high-dimensional (i.e.,
with many variables).
Paul
Andreas Klein klein82517 at yahoo.de wrote:
Hello.
I have some problems, when I try to model an
optimization problem with some constraints.
The original problem cannot be solved analytically, so
I have to use routines like Simulated Annealing or
Sequential Quadric Programming.
But to see how all this works in R, I would like to
start with some simple problem to get to know the
basics:
The Problem:
min f(x1,x2)= (x1)^2 + (x2)^2
s.t. x1 + x2 = 1
The analytical solution:
x1 = 0.5
x2 = 0.5
Does someone have some suggestions how to model it in
R with the given functions optim or constrOptim with
respect to the routines SANN or SQP to obtain the
analytical solutions numerically?
Again, the simple example should only show me the
basic working of the complex functions in R.
Hope you can help me.
With regards
Andreas.
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[R] Alignment and Reshaping of the matrix
Dear R users, I have a matrix like 85 .90 86 .89 87 .98 86 .87 88 .98 90 .78 88 .76 89 .56 90 .67 95 .67 89 .89 90 .87 91 .56 96 .87 90 .76 92.98 each pair of columns present a variable name and next the value. I have matrix with more than 500 rows and column. Now I want to convert this matrix in to. 85 .90 00 .00 00 86 .00 .89 .00 .87 87 .00 00 .98 00 88 .98 00 .76 00 89 .00 00 .89 .56 90 .67 .78 .76 .87 91 .56 00 .00 00 92 .00 .00 .00 .98 93 .00 .0000 00 94 .00 .0000 00 95 .00 .6700 00 96 .00 .8700 00 Where first column represent the Variable name. And if the first matrix is transposed, then how to get the output in which First raw present the variable name. It will be great help for my research. Dinesh -- Dinesh Kumar Barupal Research Associate Metabolomics Fiehn Lab UCD Genome Center 451 East Health Science Drive GBSF Builidng University of California DAVIS 95616 http://fiehnlab.ucdavis.edu/staff/kumar [[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] Alignment and Reshaping of the matrix
Is this what you are after:
x - read.table(textConnection(85 .90 86 .89 87 .98 86 .87
+ 88 .98 90 .78 88 .76 89 .56
+ 90 .67 95 .67 89 .89 90 .87
+ 91 .56 96 .87 90 .76 92 .98))
closeAllConnections()
odd - seq(1, ncol(x), by=2)
x.r - range(x[,odd])
# create large array starting from 1
x.m - matrix(0, ncol=length(odd), nrow=max(x.r))
for (i in odd){
+ x.m[x[, i], (i + 1) / 2] -x[, i + 1] # save values
+ }
# add first column with index
x.m - cbind(seq(nrow(x.m)), x.m)
# only print out the rows of interest
x.m[x.r[1]:x.r[2],]
[,1] [,2] [,3] [,4] [,5]
[1,] 85 0.90 0.00 0.00 0.00
[2,] 86 0.00 0.89 0.00 0.87
[3,] 87 0.00 0.00 0.98 0.00
[4,] 88 0.98 0.00 0.76 0.00
[5,] 89 0.00 0.00 0.89 0.56
[6,] 90 0.67 0.78 0.76 0.87
[7,] 91 0.56 0.00 0.00 0.00
[8,] 92 0.00 0.00 0.00 0.98
[9,] 93 0.00 0.00 0.00 0.00
[10,] 94 0.00 0.00 0.00 0.00
[11,] 95 0.00 0.67 0.00 0.00
[12,] 96 0.00 0.87 0.00 0.00
On Sat, Mar 29, 2008 at 7:21 PM, dinesh kumar [EMAIL PROTECTED] wrote:
Dear R users,
I have a matrix like
85 .90 86 .89 87 .98 86 .87
88 .98 90 .78 88 .76 89 .56
90 .67 95 .67 89 .89 90 .87
91 .56 96 .87 90 .76 92.98
each pair of columns present a variable name and next the value. I have
matrix with more than 500 rows and column.
Now I want to convert this matrix in to.
85 .90 00 .00 00
86 .00 .89 .00 .87
87 .00 00 .98 00
88 .98 00 .76 00
89 .00 00 .89 .56
90 .67 .78 .76 .87
91 .56 00 .00 00
92 .00 .00 .00 .98
93 .00 .0000 00
94 .00 .0000 00
95 .00 .6700 00
96 .00 .8700 00
Where first column represent the Variable name.
And if the first matrix is transposed, then how to get the output in which
First raw present the variable name.
It will be great help for my research.
Dinesh
--
Dinesh Kumar Barupal
Research Associate
Metabolomics Fiehn Lab
UCD Genome Center
451 East Health Science Drive
GBSF Builidng
University of California
DAVIS
95616
http://fiehnlab.ucdavis.edu/staff/kumar
[[alternative HTML version deleted]]
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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.
--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
What is the problem you are trying to solve?
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and provide commented, minimal, self-contained, reproducible code.
[R] Second subsequent calls to function fails. Please help debug.
Dear R-helpers,
I'm running Sweave() on a file. First run:
Sweave('20080331.Rnw')
Writing to file 20080331.tex
Processing code chunks ...
1 : term hide (label=setup)
2 : echo term verbatim (label=oatvar)
3 : echo term verbatim (label=oatvar1)
4 : echo term verbatim (label=oat2wt)
5 : echo term verbatim (label=oat2wt)
6 : echo term verbatim (label=lm)
7 : echo term verbatim (label=diag)
8 : echo term verbatim (label=tukey)
9 : echo term verbatim (label=efficiency)
10 : echo term verbatim (label=wear)
11 : echo term verbatim (label=wearX)
12 : echo term verbatim (label=gyd)
Loading required package: crossdes
Loading required package: AlgDesign
Loading required package: gtools
Attaching package: 'gtools'
The following object(s) are masked from package:faraway :
logit
Loading required package: MASS
13 : echo term verbatim (label=2wt)
14 : echo term verbatim (label=ablm)
15 : echo term verbatim (label=abaov)
You can now run LaTeX on '20080331.tex'
There were 42 warnings (use warnings() to see them)
Second run:
Sweave('20080331.Rnw')
Writing to file 20080331.tex
Processing code chunks ...
1 : term hide (label=setup)
2 : echo term verbatim (label=oatvar)
3 : echo term verbatim (label=oatvar1)
4 : echo term verbatim (label=oat2wt)
5 : echo term verbatim (label=oat2wt)
6 : echo term verbatim (label=lm)
7 : echo term verbatim (label=diag)
8 : echo term verbatim (label=tukey)
Error: chunk 8 (label=tukey)
Error in parse(text = x) :
unexpected symbol in yield ~ variety + block + preds(yield+variety
+block+preds.sq)sq
It failed in:
tukey=
require(alr3)
tukey.nonadd.test(ov.lm)
@
At that point I ran debug() on the call:
debug(tukey.nonadd.test)
tukey.nonadd.test(ov.lm)
debugging in: tukey.nonadd.test(ov.lm1)
debug: {
envir - environment(formula(m))
dd - eval(m$call$data, envir)
subs - eval(m$call$subset, envir)
wgts - eval(m$call$weights, envir)
naa - m$call$na.action
dd - data.frame(dd, preds.sq = predict(m, dd)^2)
uf - update.formula(formula(m$terms), ~. + preds.sq)
environment(uf) - environment(NULL)
mup - if (is.null(naa))
lm(uf, data = dd, subset = subs, weights = wgts)
else lm(uf, data = dd, subset = subs, weights = wgts, na.action =
naa)
if (mup$rank m$rank) {
ans - summary(mup)$coef[, 3:4]
ans - ans[match(preds.sq, rownames(ans)), ]
ans[2] - pnorm(-abs(ans[1])) * 2
ans
}
else c(NA, NA)
}
Browse[1]
debug: envir - environment(formula(m))
Browse[1]
debug: dd - eval(m$call$data, envir)
Browse[1]
debug: subs - eval(m$call$subset, envir)
Browse[1]
debug: wgts - eval(m$call$weights, envir)
Browse[1]
debug: naa - m$call$na.action
Browse[1]
debug: dd - data.frame(dd, preds.sq = predict(m, dd)^2)
Browse[1]
debug: uf - update.formula(formula(m$terms), ~. + preds.sq)
Browse[1]
debug: environment(uf) - environment(NULL)
Browse[1]
debug: mup - if (is.null(naa)) lm(uf, data = dd, subset = subs,
weights = wgts) else lm(uf,
data = dd, subset = subs, weights = wgts, na.action = naa)
Browse[1]
Error in parse(text = x) :
unexpected symbol in yield ~ variety + preds(yield+variety
+preds.sq)sq
Advice?
_
Professor Michael Kubovy
University of Virginia
Department of Psychology
USPS: P.O.Box 400400Charlottesville, VA 22904-4400
Parcels:Room 102Gilmer Hall
McCormick RoadCharlottesville, VA 22903
Office:B011+1-434-982-4729
Lab:B019+1-434-982-4751
Fax:+1-434-982-4766
WWW:http://www.people.virginia.edu/~mk9y/
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Re: [R] Second subsequent calls to function fails. Please help debug.
On 29/03/2008 9:47 PM, Michael Kubovy wrote:
Dear R-helpers,
I'm running Sweave() on a file. First run:
Sweave('20080331.Rnw')
Writing to file 20080331.tex
Processing code chunks ...
1 : term hide (label=setup)
2 : echo term verbatim (label=oatvar)
3 : echo term verbatim (label=oatvar1)
4 : echo term verbatim (label=oat2wt)
5 : echo term verbatim (label=oat2wt)
6 : echo term verbatim (label=lm)
7 : echo term verbatim (label=diag)
8 : echo term verbatim (label=tukey)
9 : echo term verbatim (label=efficiency)
10 : echo term verbatim (label=wear)
11 : echo term verbatim (label=wearX)
12 : echo term verbatim (label=gyd)
Loading required package: crossdes
Loading required package: AlgDesign
Loading required package: gtools
Attaching package: 'gtools'
The following object(s) are masked from package:faraway :
logit
Loading required package: MASS
13 : echo term verbatim (label=2wt)
14 : echo term verbatim (label=ablm)
15 : echo term verbatim (label=abaov)
You can now run LaTeX on '20080331.tex'
There were 42 warnings (use warnings() to see them)
Second run:
Sweave('20080331.Rnw')
Writing to file 20080331.tex
Processing code chunks ...
1 : term hide (label=setup)
2 : echo term verbatim (label=oatvar)
3 : echo term verbatim (label=oatvar1)
4 : echo term verbatim (label=oat2wt)
5 : echo term verbatim (label=oat2wt)
6 : echo term verbatim (label=lm)
7 : echo term verbatim (label=diag)
8 : echo term verbatim (label=tukey)
Error: chunk 8 (label=tukey)
Error in parse(text = x) :
unexpected symbol in yield ~ variety + block + preds(yield+variety
+block+preds.sq)sq
It failed in:
tukey=
require(alr3)
tukey.nonadd.test(ov.lm)
@
At that point I ran debug() on the call:
debug(tukey.nonadd.test)
tukey.nonadd.test(ov.lm)
debugging in: tukey.nonadd.test(ov.lm1)
debug: {
envir - environment(formula(m))
dd - eval(m$call$data, envir)
subs - eval(m$call$subset, envir)
wgts - eval(m$call$weights, envir)
naa - m$call$na.action
dd - data.frame(dd, preds.sq = predict(m, dd)^2)
uf - update.formula(formula(m$terms), ~. + preds.sq)
environment(uf) - environment(NULL)
mup - if (is.null(naa))
lm(uf, data = dd, subset = subs, weights = wgts)
else lm(uf, data = dd, subset = subs, weights = wgts, na.action =
naa)
if (mup$rank m$rank) {
ans - summary(mup)$coef[, 3:4]
ans - ans[match(preds.sq, rownames(ans)), ]
ans[2] - pnorm(-abs(ans[1])) * 2
ans
}
else c(NA, NA)
}
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debug: envir - environment(formula(m))
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debug: dd - eval(m$call$data, envir)
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debug: subs - eval(m$call$subset, envir)
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debug: wgts - eval(m$call$weights, envir)
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debug: naa - m$call$na.action
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debug: dd - data.frame(dd, preds.sq = predict(m, dd)^2)
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debug: uf - update.formula(formula(m$terms), ~. + preds.sq)
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debug: environment(uf) - environment(NULL)
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debug: mup - if (is.null(naa)) lm(uf, data = dd, subset = subs,
weights = wgts) else lm(uf,
data = dd, subset = subs, weights = wgts, na.action = naa)
Browse[1]
Error in parse(text = x) :
unexpected symbol in yield ~ variety + preds(yield+variety
+preds.sq)sq
Advice?
I don't see anything obvious, so I guess it's the usual advice:
Use traceback() to see what function was trying to do the parsing.
Debug that function, and see why it was trying to parse that string.
If that doesn't make it obvious, put together a minimal reproducible
version that others can try, and see if anyone else can spot the problem.
Duncan Murdoch
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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.
