[R] Determining whether a function's return value is assigned
Dear all,
Does R offer a means by which a function can determine
whether its return value is assigned? I am using R
2.4.1 for Windows.
Suppose what I am looking for is called
return.value.assigned. Then one might use it like
this
myfunction - function () {
# Create bigobject here
if (return.value.assigned()) {
bigobject
} else {
summary(bigobject)
}
}
and
x - myfunction() # bigobject is assigned
myfunction() # summary of bigobject is printed
Octave and MATLAB have the nargout function that does
what I want, and Perl has the wantarray function
detecting the context in which a function is called.
Perhaps match.call() can be made to do what I want,
but, if so, I don't see it in reading the
documentation.
Sincerely,
Paul Laub
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[R] Importing Excel file with merged cells
Dear all, I have a problem with importing an excel file into R. I can open the file easily (either saving it as a CSV or using RODBC). But the original file is using merged cell in its first column, which gives the name of the observation. (I am dealing with repeated measurements for the same observation) So when I open the dataframe in R it looks like this Col1Col2 Col3 name1 val1 val2 val3 val4 name2 val5 val6 val7 val8 Everything is fine, except that the name of the observation is on the first line and the following are empty. Until a new observation starts, where a new name appears in the respective row and the following rows are empty and so on. The number of rows is fixed for each observation. How can I fill the column with the proper name (eg take the first string in this column until you hit a row with a new string, then take this string and go on until the next string). Or read the excel file in such a way, that when cells are merged that when importing it to R all cells created from this merged cell should have the same content. Unfortunately, I cannot change the lay-out of the original excel file as it comes from an commercial data-base and I will have to use it quite often. I have the gut feeling that there might be an easy solution out there as it does not seem to be an uncommon problem. So if you have hint or a solution I greatly appreciated it. Thanks and a nice weekend, Stefan __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Plots from categorial data
Software zur Erkennung von Spam auf dem Rechner hypatia.math.ethz.ch hat die eingegangene E-mail als mögliche Spam-Nachricht identifiziert. Die ursprüngliche Nachricht wurde an diesen Bericht angehängt, so dass Sie sie anschauen können (falls es doch eine legitime E-Mail ist) oder ähnliche unerwünschte Nachrichten in Zukunft markieren können. Bei Fragen zu diesem Vorgang wenden Sie sich bitte an the administrator of that system Vorschau: Hello everybody, I want to use R to generate plots from categorial data. The data contains results from OCR scans over images with are preprocessed by different image filtering techniques. A small sample data set looks as following: [...] Inhaltsanalyse im Detail: (5.5 Punkte, 5.0 benötigt) Pkte Regelname Beschreibung -- -- 0.0 DKIM_POLICY_SIGNSOME Domain Keys Identified Mail: policy says domain signs some mails 1.0 BAYES_60 BODY: Spamwahrscheinlichkeit nach Bayes-Test: 60-80% [score: 0.7481] 4.5 AWLAWL: From: address is in the auto white-list ---BeginMessage--- Hello everybody, I want to use R to generate plots from categorial data. The data contains results from OCR scans over images with are preprocessed by different image filtering techniques. A small sample data set looks as following: data - read.csv(d:/tmp_da/sql_data/filter_d_tool.csv, header=T) data ocrtool filter_setting avg.hit. 1 FineReader2x10.383 2 FineReader2x20.488 3 FineReader3x20.268 4 FineReader3x30.198 5 FineReader4x30.081 6 FineReader4x40.056 7gocr2x10.153 8gocr2x20.102 9gocr3x20.047 10 gocr3x30.052 11 gocr4x30.014 12 gocr4x40.002 13 ocrad2x10.085 14 ocrad2x20.094 15 ocrad3x20.045 16 ocrad3x30.050 17 ocrad4x30.025 18 ocrad4x40.009 I now want to draw a plot with the categories (filter_setting) as X axis, and the avg_hit as Y axis. There should be lines for each ocrtool. But when I draw a plot, the resulting plot always contains bars, even if I specify type=n. plot(data$filter_setting, data$avg.hit., type=n) When I only plot the categories, without data, there appear strange grey (but empty) boxes. plot(data$filter_setting, type=n) Warning messages: 1: Grafikparameter type ist veraltet in: plot.window(xlim, ylim, log, asp, ..) 2: Grafikparameter type ist veraltet in: axis(side, at, as.graphicsAnnot(labels), tick, line, pos, outer, 3: Grafikparameter type ist veraltet in: title(main, sub, xlab, ylab, line, outer, ...) 4: Grafikparameter type ist veraltet in: axis(side, at, as.graphicsAnnot(labels), tick, line, pos, outer, Who do I get a clean white box to draw the different lines in? Thanks and regards, Christoph ---End Message--- __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Importing Excel file that has merged cells
Dear all, I have a problem with importing an excel file into R. I can open the file easily (either saving it as a CSV or using RODBC). But the original file is using merged cell in its first column, which gives the name of the observation. (I am dealing with repeated measurements for the same observation) So when I open the dataframe in R it looks like this Col1Col2 Col3 name1 val1 val2 val3 val4 name2 val5 val6 val7 val8 Everything is fine, except that the name of the observation is on the first line and the following are empty. Until a new observation starts, where a new name appears in the respective row and the following rows are empty and so on. The number of rows is fixed for each observation. How can I fill the column with the proper name (eg take the first string in this column until you hit a row with a new string, then take this string and go on until the next string). Or read the excel file in such a way, that when cells are merged that when importing it to R all cells created from this merged cell should have the same content. Unfortunately, I cannot change the lay-out of the original excel file as it comes from an commercial data-base and I will have to use it quite often. I have the gut feeling that there might be an easy solution out there as it does not seem to be an uncommon problem. So if you have hint or a solution I greatly appreciated it. Thanks and a nice weekend, Stefan __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Problem installing RGTK2 on ubuntu 7.04
Thanks for the help. I installed libgtk2.0-dev and RGtk2 is being installed as I write. Andrew Muller McMaster University/Economics __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Importing an Excel file that has merged cells
Dear all,
I have a problem with importing an excel file into R. I can open the
file easily (either saving it as a CSV or using RODBC). But the
original file is using merged cell in its first column, which gives
the name of the observation. (I am dealing with repeated measurements
for the same observation)
So when I open the dataframe in R it looks like this
Col1Col2 Col3
name1 val1 val2
val3 val4
name2 val5 val6
val7 val8
Everything is fine, except that the name of the observation is on the
first line and the following rows are empty. Until a new observation
starts, where a new name appears in the respective row and the
following rows are empty and so on.
The number of rows is fixed for each observation. How can I fill the
column with the proper name (eg take the first string in this column
until you hit a row with a new string, then take this string and go on
until the next string).
Or read the excel file in such a way, that when cells are merged that
when importing it to R all cells created from this merged cell should
have the same content.
Unfortunately, I cannot change the lay-out of the original excel file
as it comes from an commercial data-base and I will have to use it
quite often.
I have the gut feeling that there might be an easy solution out there
as it does not seem to be an uncommon problem.
So if you have hint or a solution I greatly appreciated it.
Thanks and a nice weekend,
Stefan
--
This mail has been sent through the MPI for Demographic Rese...{{dropped}}
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Importing an Excel file that has merged cells
I think this does what you want using the 'na.locf' function is zoo:
x - read.csv('/tote.csv', header=FALSE, skip=4)
# fill blanks in name column with NAs
is.na(x$V2) - x$V2 ==
# load the 'zoo' library for the function na.locf
require(zoo)
x$V1 - na.locf(x$V1) # key
x$V2 - na.locf(x$V2) # name
head(x,30)
On 6/30/07, Lhachimi, Stefan [EMAIL PROTECTED] wrote:
Dear all,
I have a problem with importing an excel file into R. I can open the
file easily (either saving it as a CSV or using RODBC). But the
original file is using merged cell in its first column, which gives
the name of the observation. (I am dealing with repeated measurements
for the same observation)
So when I open the dataframe in R it looks like this
Col1Col2 Col3
name1 val1 val2
val3 val4
name2 val5 val6
val7 val8
Everything is fine, except that the name of the observation is on the
first line and the following rows are empty. Until a new observation
starts, where a new name appears in the respective row and the
following rows are empty and so on.
The number of rows is fixed for each observation. How can I fill the
column with the proper name (eg take the first string in this column
until you hit a row with a new string, then take this string and go on
until the next string).
Or read the excel file in such a way, that when cells are merged that
when importing it to R all cells created from this merged cell should
have the same content.
Unfortunately, I cannot change the lay-out of the original excel file
as it comes from an commercial data-base and I will have to use it
quite often.
I have the gut feeling that there might be an easy solution out there
as it does not seem to be an uncommon problem.
So if you have hint or a solution I greatly appreciated it.
Thanks and a nice weekend,
Stefan
--
This mail has been sent through the MPI for Demographic Rese...{{dropped}}
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
What is the problem you are trying to solve?
[[alternative HTML version deleted]]
__
R-help@stat.math.ethz.ch 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.
Re: [R] Determining whether a function's return value is assigned
Paul Laub wrote:
Dear all,
Does R offer a means by which a function can determine
whether its return value is assigned? I am using R
2.4.1 for Windows.
Short answer: No.
Long answer: You want to have a class for the object called bigobject
below and a print/show method that provides the summary for objects of
that class.
Uwe Ligges
Suppose what I am looking for is called
return.value.assigned. Then one might use it like
this
myfunction - function () {
# Create bigobject here
if (return.value.assigned()) {
bigobject
} else {
summary(bigobject)
}
}
and
x - myfunction() # bigobject is assigned
myfunction() # summary of bigobject is printed
Octave and MATLAB have the nargout function that does
what I want, and Perl has the wantarray function
detecting the context in which a function is called.
Perhaps match.call() can be made to do what I want,
but, if so, I don't see it in reading the
documentation.
Sincerely,
Paul Laub
__
R-help@stat.math.ethz.ch 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.
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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] import data
Hello! I wonder if you might help me with informations about how to import data with a 2.4.1 R version without the menu Import data. Best regards. Eric Duplex ZOUKEKANG Ingénieur Zootechnicien Montpellier SupAgro Master2 AAA-PARC tel : +33(0)661432340 [EMAIL PROTECTED] ___ [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Importing an Excel file that has merged cells
Hi Jim,
it looks perfect!
Thanx a lot!
Have a nice weekend,
Stefan
On 6/30/07, jim holtman [EMAIL PROTECTED] wrote:
I think this does what you want using the 'na.locf' function is zoo:
x - read.csv('/tote.csv', header=FALSE, skip=4)
# fill blanks in name column with NAs
is.na(x$V2) - x$V2 ==
# load the 'zoo' library for the function na.locf
require(zoo)
x$V1 - na.locf(x$V1) # key
x$V2 - na.locf(x$V2) # name
head(x,30)
On 6/30/07, Lhachimi, Stefan [EMAIL PROTECTED] wrote:
Dear all,
I have a problem with importing an excel file into R. I can open the
file easily (either saving it as a CSV or using RODBC). But the
original file is using merged cell in its first column, which gives
the name of the observation. (I am dealing with repeated measurements
for the same observation)
So when I open the dataframe in R it looks like this
Col1Col2 Col3
name1 val1 val2
val3 val4
name2 val5 val6
val7 val8
Everything is fine, except that the name of the observation is on the
first line and the following rows are empty. Until a new observation
starts, where a new name appears in the respective row and the
following rows are empty and so on.
The number of rows is fixed for each observation. How can I fill the
column with the proper name (eg take the first string in this column
until you hit a row with a new string, then take this string and go on
until the next string).
Or read the excel file in such a way, that when cells are merged that
when importing it to R all cells created from this merged cell should
have the same content.
Unfortunately, I cannot change the lay-out of the original excel file
as it comes from an commercial data-base and I will have to use it
quite often.
I have the gut feeling that there might be an easy solution out there
as it does not seem to be an uncommon problem.
So if you have hint or a solution I greatly appreciated it.
Thanks and a nice weekend,
Stefan
--
This mail has been sent through the MPI for Demographic Rese...{{dropped}}
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
What is the problem you are trying to solve?
[[alternative HTML version deleted]]
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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] Standard Probability Distributions.
Dear all, What are the standard probability distributions available in R? I need some as Normal-Truncated, Half-Normal, Gamma, Chi-squared, Wishard, etc. Thanks. Marcus Vinicius [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Dominant eigenvector displayed as third (Marco Visser)
Yes, Spencer, your observation is correct, because the characeristic equation det(A - \lambda*I) is a sixth degree polynomial: \lambda^6 - 5 = 0. So the eigenvalues are the complex numbers (generally) that are located at equal angles on the circle of radius 5^(1/6), at angles 2*pi*k/6, where k runs from 0 to 5. Thus, the roots are: z_k = 5^(1/6) * exp(i * 2*pi*k/6), k= 0, 1, ..., 5. where i = sqrt(-1). Ravi. - Original Message - From: Spencer Graves [EMAIL PROTECTED] Date: Friday, June 29, 2007 6:51 pm Subject: Re: [R] Dominant eigenvector displayed as third (Marco Visser) To: Marco Visser [EMAIL PROTECTED] Cc: r-help@stat.math.ethz.ch There is no dominant eigenvalue: The eigenvalues of that matrix are the 6 different roots of 5. All have modulus (or absolute value) = 1.307660. When I raised them all to the 6th power, all 6 were 5+0i. Someone else can tell us why this is, but this should suffice as an initial answer to your question. Hope this helps. Spencer Graves Marco Visser wrote: Dear R users Experts, This is just a curiousity, I was wondering why the dominant eigenvetor and eigenvalue of the following matrix is given as the third. I guess this could complicate automatic selection procedures. 000005 100000 010000 001000 000100 000010 Please copy paste the following into R; a=c(0,0,0,0,0,5,1,0,0,0,0,0,0,1,0,0,0,0,0,0,1,0,0,0,0,0,0,1,0,0,0,0,0,0,1,0) mat=matrix(a, ncol=6,byrow=T) eigen(mat) The matrix is a population matrix for a plant pathogen (Powell et al 2005). Basically I would really like to know why this happens so I will know if it can occur again. Thanks for any comments, Marco Visser Comment: In Matlab the the dominant eigenvetor and eigenvalue of the described matrix are given as the sixth. Again no idea why. reference J. A. Powell, I. Slapnicar and W. van der Werf. Epidemic spread of a lesion-forming plant pathogen - analysis of a mechanistic model with infinite age structure. (2005) Linear Algebra and its Applications 298. p 117-140. Ready for the edge of your seat? Check out tonight's top picks on Yahoo! TV. [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list PLEASE do read the posting guide and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list PLEASE do read the posting guide and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Standard Probability Distributions.
Have a look in the stats package for the distributions that come with base R. There is a package called SuppDists that has some others, and no doubt there are others. Try RSiteSearch to look for specific distributions. On 30/06/07, Marcus Vinicius [EMAIL PROTECTED] wrote: Dear all, What are the standard probability distributions available in R? I need some as Normal-Truncated, Half-Normal, Gamma, Chi-squared, Wishard, etc. Thanks. Marcus Vinicius [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- = David Barron Said Business School University of Oxford Park End Street Oxford OX1 1HP __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] import data
ha On 6/30/07, eric zoukekang [EMAIL PROTECTED] wrote: Hello! I wonder if you might help me with informations about how to import data with a 2.4.1 R version without the menu Import data. Best regards. Eric Duplex ZOUKEKANG Ingénieur Zootechnicien Montpellier SupAgro Master2 AAA-PARC tel : +33(0)661432340 [EMAIL PROTECTED] ___ [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Christophe Pallier (http://www.pallier.org) [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] import data
Oops, sorry for the previous empty reply. You do not tell us which Operating System you are using, so I assume it must be Windows... You should check the R import/export Data available from the Help/Manuals menu (in French: Aide/Manuels...) Christophe On 6/30/07, Christophe Pallier [EMAIL PROTECTED] wrote: ha On 6/30/07, eric zoukekang [EMAIL PROTECTED] wrote: Hello! I wonder if you might help me with informations about how to import data with a 2.4.1 R version without the menu Import data. Best regards. Eric Duplex ZOUKEKANG Ingénieur Zootechnicien Montpellier SupAgro Master2 AAA-PARC tel : +33(0)661432340 [EMAIL PROTECTED] ___ [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Christophe Pallier (http://www.pallier.org) -- Christophe Pallier (http://www.pallier.org) [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] import data
Hi Eric, eric zoukekang wrote: Hello! I wonder if you might help me with informations about how to import data with a 2.4.1 R version without the menu Import data. Best regards. the best information about importing data in R is contained in the manual R Data Import/Export which should be part of your distribution of R. I don't know if there were substantial changes between 2.4.1 and the current version of R (- 2.5.1), but the most up-to-date manual can be found here in html: http://cran.r-project.org/doc/manuals/R-data.html or here in pdf-format: http://cran.r-project.org/doc/manuals/R-data.pdf I hope this helps? Best, Roland __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] random numbers
Although this query was inspired by distributed random number generation, one of the questions (#2 below) is a single-machine issue. I call C++ code from R to generate simulated data. I'm doing this on a cluster, and use rmpi and rsprng. While rsprng randomizes R-level random numbers (e.g., from runif), it has no effect on the C code, which is completely SPRNG and MPI ignorant. Currently I generate a seed to pass into the C code, using as.integer(runif(1, max=.Machine$integer.max)-.Machine$integer.max/2) It seems to work. Any comments on this approach? Here are some issues I see: 1) The much simpler method of using the consecutive integers as seeds also seemed to work. This also has the advantage of repeatability. I avoided it because I was concerned it wouldn't be random enough. Would consecutive integers as in parLapply(cluster, seq(nSimulations), function(i) myfunction(seed=i)) be sufficient? I suppose I could also generate all the random seeds on the master. 2) This got me thinking about how to generate random integers that span the whole range of 32 bit signed integers. The method show above only spans half the range, since .Machine$integer.max = 2^31. It also makes some assumptions about the relation between the value in .Machine $integer.max and the seed for random numbers. Interestingly, integer.max was 2^31 despite running on a 64 bit powerpc, albeit under the mostly 32 bit OS-X (I think Leopard--not the current one; Darwin Kernel 7.9.0). My understanding is that random number generators internally produce 32 bit integers, which then get converted into the desired distribution. I'm a little surprised there doesn't seem to be a way to get at them. Or is one supposed to do runif()*2^32-2^31? 3) Vagaries of the underlying C++ random number generator could also complicate life. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Programming Contests for R?
Dear all, I just saw for the first time the 'Matlab Programming Contest' at http://www.mathworks.com/contest/overview.html Is there something comparable for R? Is someone interested in organizing such a thing? Of course, one can try to solve the Matlab Problems Sets in R, but I think it could be fun to have something like this also for R. Thanks and have a nice weekend everyone, Roland P.S. I have the impression that the R-Help ML is some kind of programming contest, when people try to contribute more efficient, elegant, smaller, faster, ... solutions to a question than someone before. :-D __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Programming Contests for R?
On 30 June 2007 at 15:31, Roland Rau wrote: | I just saw for the first time the 'Matlab Programming Contest' at | http://www.mathworks.com/contest/overview.html | | Is there something comparable for R? Is someone interested in organizing | such a thing? Well, AFAIK there will be some sort of 'R Programming Contest' at UseR in Ames in August -- see http://www.useR2007.org Dirk -- Hell, there are no rules here - we're trying to accomplish something. -- Thomas A. Edison __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] random numbers
On 30 June 2007 at 12:12, Ross Boylan wrote: | I call C++ code from R to generate simulated data. I'm doing this on a | cluster, and use rmpi and rsprng. While rsprng randomizes R-level | random numbers (e.g., from runif), it has no effect on the C code, which | is completely SPRNG and MPI ignorant. | | Currently I generate a seed to pass into the C code, using | as.integer(runif(1, max=.Machine$integer.max)-.Machine$integer.max/2) | It seems to work. | | Any comments on this approach? Here are some issues I see: I may be missing something but given that rsprng is running on your cluster, you are bound to also have sprng itself -- so why don't you use that from C or C++ for this purpose? Hth, Dirk -- Hell, there are no rules here - we're trying to accomplish something. -- Thomas A. Edison __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] random numbers
On Sat, 2007-06-30 at 14:50 -0500, Dirk Eddelbuettel wrote: On 30 June 2007 at 12:12, Ross Boylan wrote: | I call C++ code from R to generate simulated data. I'm doing this on a | cluster, and use rmpi and rsprng. While rsprng randomizes R-level | random numbers (e.g., from runif), it has no effect on the C code, which | is completely SPRNG and MPI ignorant. | | Currently I generate a seed to pass into the C code, using | as.integer(runif(1, max=.Machine$integer.max)-.Machine$integer.max/2) | It seems to work. | | Any comments on this approach? Here are some issues I see: I may be missing something but given that rsprng is running on your cluster, you are bound to also have sprng itself -- so why don't you use that from C or C++ for this purpose? Hth, Dirk Doing so would add considerable complexity, at least as far as I know. Sometimes I run within an MPI session and sometimes not. My understanding is that SPRNG will not work if MPI is absent. I think someone on the SPRNG list told me that there wasn't a good way to handle this at run-time. Unfortunately, a lot of SPRNG options seem to be compile-time settings. Using SPRNG would also complicate my build process, as I'd need autoconf magic to support it. Part of the issue is that I want something I can redistribute, not just something that will work for me on a one-off basis. One simple solution would be to build several versions of the library. A not so simple solution would be to build various random number generators as separate libraries, and dynamically load the appropriate one. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] R CMD INSTALL in R 2.5.1 (2007-06-27)
Hello, I'm moving from R 2.2.1 (Winows XP) to R 2.5.1 and have problems with installing myfuncs, which worked OK in 2.2.1 R CMD INSTALL myfuns # gives installing to '' -- Making package myfuncs adding build stamp to DESCRIPTION installing R files installing man source files installing indices installing help Building/Updating help pages for package 'myfuncs' Formats: text html latex example chm Bland.plottexthtmllatex example Cook.plot texthtmllatex example added.var.plottexthtmllatex example jit.plot texthtmllatex example waldtest texthtmllatex example preparing package myfuncs for lazy loading Warning in list.files(lib, pattern = paste(^, pkg_regexp, sep = ), full = TR UE) : list.files: '' is not a readable directory Error in findpack(package, lib.loc) : there is no package called 'myfuncs' Execution halted make: *** [lazyload] Error 1 *** Installation of myfuncs failed *** Removing '/myfuncs' # end installing to '' at the start appears to be the problem I have install Rtools 2.5.1 appropriately ( I hope) my PATH looks like this: PATH=C:\Program\Rtools\MinGW\bin;C:\Program\R\Rtools\bin;c:\program\imagemagick- 6.1.8-q16;C:\Program\TeXLive\bin\win32;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS \system32\WBEM;C:\Program\Aspell\bin;C:\Program\Perl\bin\;C:\Program\HTML Help W orkshop;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\Program\ATI T echnologies\ATI Control Panel;C:\Program\R\R-2.5.1\bin;C:\Program\sp2000\cmd;C:\ Program\XEmacs\XEmacs-21.4.13\i586-pc-win32;C:\Program\gnuplot\bin;C:\Program\Ma yura;C:\Program files\WinEdt Team\WinEdt;C:\Program\Internet Explorer;;C:\Progra m\WinBUGS;C:\Program\Adobe\Acrobat 7.0\Reader;C:\Program\QuickTime\QTSystem\ To me looks as if R don't know where to install - any help available? Sincerely Fredrik Lundgren __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R CMD INSTALL in R 2.5.1 (2007-06-27)
Fredrik Lundgren wrote: Hello, I'm moving from R 2.2.1 (Winows XP) to R 2.5.1 and have problems with installing myfuncs, which worked OK in 2.2.1 R CMD INSTALL myfuns # gives installing to '' Have you set an environment variable such as R_LIBS that is rather than a sensible directory? (my guess) Are all the tools up to date? Do you have another library (except the standard one) defined anywhere? Can you source() all the R files in your package separately in R-2.5.1? Uwe Ligges -- Making package myfuncs adding build stamp to DESCRIPTION installing R files installing man source files installing indices installing help Building/Updating help pages for package 'myfuncs' Formats: text html latex example chm Bland.plottexthtmllatex example Cook.plot texthtmllatex example added.var.plottexthtmllatex example jit.plot texthtmllatex example waldtest texthtmllatex example preparing package myfuncs for lazy loading Warning in list.files(lib, pattern = paste(^, pkg_regexp, sep = ), full = TR UE) : list.files: '' is not a readable directory Error in findpack(package, lib.loc) : there is no package called 'myfuncs' Execution halted make: *** [lazyload] Error 1 *** Installation of myfuncs failed *** Removing '/myfuncs' # end installing to '' at the start appears to be the problem I have install Rtools 2.5.1 appropriately ( I hope) my PATH looks like this: PATH=C:\Program\Rtools\MinGW\bin;C:\Program\R\Rtools\bin;c:\program\imagemagick- 6.1.8-q16;C:\Program\TeXLive\bin\win32;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS \system32\WBEM;C:\Program\Aspell\bin;C:\Program\Perl\bin\;C:\Program\HTML Help W orkshop;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\Program\ATI T echnologies\ATI Control Panel;C:\Program\R\R-2.5.1\bin;C:\Program\sp2000\cmd;C:\ Program\XEmacs\XEmacs-21.4.13\i586-pc-win32;C:\Program\gnuplot\bin;C:\Program\Ma yura;C:\Program files\WinEdt Team\WinEdt;C:\Program\Internet Explorer;;C:\Progra m\WinBUGS;C:\Program\Adobe\Acrobat 7.0\Reader;C:\Program\QuickTime\QTSystem\ To me looks as if R don't know where to install - any help available? Sincerely Fredrik Lundgren __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R CMD INSTALL in R 2.5.1 (2007-06-27)
Sorry, my fault! I had # install myfuncs library(myfuncs) in the RProfile.site before I had myfuncs installed # library(myfuncs) fixed everything. I could now R CMD INSTALL as before - no problems Thanks for your help Fredrik - Original Message - From: Uwe Ligges [EMAIL PROTECTED] To: Fredrik Lundgren [EMAIL PROTECTED] Cc: R-help r-help@stat.math.ethz.ch Sent: Saturday, June 30, 2007 11:03 PM Subject: Re: [R] R CMD INSTALL in R 2.5.1 (2007-06-27) Fredrik Lundgren wrote: Hello, I'm moving from R 2.2.1 (Winows XP) to R 2.5.1 and have problems with installing myfuncs, which worked OK in 2.2.1 R CMD INSTALL myfuns # gives installing to '' Have you set an environment variable such as R_LIBS that is rather than a sensible directory? (my guess) Are all the tools up to date? Do you have another library (except the standard one) defined anywhere? Can you source() all the R files in your package separately in R-2.5.1? Uwe Ligges -- Making package myfuncs adding build stamp to DESCRIPTION installing R files installing man source files installing indices installing help Building/Updating help pages for package 'myfuncs' Formats: text html latex example chm Bland.plottexthtmllatex example Cook.plot texthtmllatex example added.var.plottexthtmllatex example jit.plot texthtmllatex example waldtest texthtmllatex example preparing package myfuncs for lazy loading Warning in list.files(lib, pattern = paste(^, pkg_regexp, sep = ), full = TR UE) : list.files: '' is not a readable directory Error in findpack(package, lib.loc) : there is no package called 'myfuncs' Execution halted make: *** [lazyload] Error 1 *** Installation of myfuncs failed *** Removing '/myfuncs' # end installing to '' at the start appears to be the problem I have install Rtools 2.5.1 appropriately ( I hope) my PATH looks like this: PATH=C:\Program\Rtools\MinGW\bin;C:\Program\R\Rtools\bin;c:\program\imagemagick- 6.1.8-q16;C:\Program\TeXLive\bin\win32;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS \system32\WBEM;C:\Program\Aspell\bin;C:\Program\Perl\bin\;C:\Program\HTML Help W orkshop;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\Program\ATI T echnologies\ATI Control Panel;C:\Program\R\R-2.5.1\bin;C:\Program\sp2000\cmd;C:\ Program\XEmacs\XEmacs-21.4.13\i586-pc-win32;C:\Program\gnuplot\bin;C:\Program\Ma yura;C:\Program files\WinEdt Team\WinEdt;C:\Program\Internet Explorer;;C:\Progra m\WinBUGS;C:\Program\Adobe\Acrobat 7.0\Reader;C:\Program\QuickTime\QTSystem\ To me looks as if R don't know where to install - any help available? Sincerely Fredrik Lundgren __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] [R-SIG-Finance] Method dispatch in functions?
Look at the UseMethod function. The help for the print method, a heavily overloaded function, can also help. Regards, Carlos J. Gil Bellosta http://www.datanalytics.com On Thu, 2007-06-28 at 09:05 -0700, John McHenry wrote: Hi, Could someone point me in the right direction for documentation on the following question? Let's say I have two objects a and b of classes A and B, respectively. Now let's say I write a function foo that does something similar to objects of type A and B. Basically I want to overload the function in C++ talk, so if I give foo and object of type A something (and this is my question) dispatches the call to, say, foo.A, and if I give foo and object of type B something dispatches the call to, say, foo.B. I want to write foo.A and foo.B. How to I perform the method dispatch? From what I understand there are two ways in R: S3 and S4. What is the simple S3 way? Thanks! Jack. - [[alternative HTML version deleted]] ___ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-sig-finance -- Subscriber-posting only. -- If you want to post, subscribe first. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] speed and looping issues; calculations on big datasets
dear r users, i'm a little stuck with the following problem(s), hopefully somebody can offer some help: i have data organized in a binary matrix, which can become quite big like 60 rows x 10^5 columns (they represent SNP genotypes, for some background info). what i need to do is the following: let's suppose i have a matrix of size n x m. for each of the m columns, i want to know the counts of unique rows extended one by one from the core column, for both values at the core separately and in both directions. maybe better explained with a little example. data: 00 0 010 10 1 001 11 1 011 10 0 011 10 0 010 so the extended unique rows counts taking e.g. column 3 as core are: col 3 = 0: right: patterns / counts 00 / 3 001 / 3 0010, 0011 / 2,1 left: 00 / 3 000,001 / 1,2 and that for the other subset ( col3 = 1) as well, then doing the whole thing again for the next core column. the reason i need this counts is that i want to calculate frequencies of the different extended sequences to calculate the probability of drawing two identical sequences from the core up to an extended position from the whole set of sequences. my main problem is speed of the calculations. i tried different ways suggested here in the list of getting the counts of the unique rows, all of them using the table function. both a combination of table ( do.call( paste, c( as.data.frame( mymatrix) ) ) ) or table( apply ( mymatrix , 2 , paste , collapse = ) ) work fine, but are too slow for bigger matrices that i want to calculate (at least in my not very sophisticated function). then i found a great suggestion here to do a matrix multiplication with a vector of 2^(0:ncol-1) to convert each row into a decimal number, and do table on those. this speeds up things quite nicely, although the problem is that it of course does not work as soon as i extended for more than 60 columns, because the decimal numbers get to large to accurately distinguish between a 0 and 1 at the smallest digit: 2^60+2 == 2^60 [1] TRUE another thing is that so far i could not come up with an idea on how or if it is possible to do this without the loops i am using, one large loop for each column in turn as core, and then another loop within that extends the rows by growing column numbers. since i am not the best of programmers (and still quite new to R), i was hoping that somebody has some advice on doing this calculations in a more elegant and more importantly, fast way. just to get the idea, the approach with the matrix multiplication takes 20s for a 60 x 220 matrix on my macbook pro, which is obviously not perfect, considering i would like to use this function for matrices of size 10^2 x 10^5 or even more. so i would be very thankful for any ideas, suggestions etc to improve this cheers martin __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] MDS/NMDS: When and Why use or not use?
Dear all, I would like to know when I use NMDS stead PCA or CA analyses? Up to I know, I use PCA (or PCoA) for condense the great part of vaciance on the firsts axis, and CA (or DCA) when I would like to identify the structure/composition of data inside a matrix. But I have seem that nowadays many ecologists are using NMDS to dimension reduction on data matrices, and interpret the axis (1, 2 etc) like they do on CA or DCA. My question is if I can use the axis of NMDS output on regression like I can do when with PCA, PCoA, CA and/or DCA axis. What is the stress effect on the usage of NMDS axis on regression? Another question is if are there a good PDF text about MDS and NMDS available on the web. I know that on vegan library (Thanks Oksanen!!) there are same fuctions which deal with MDS, metaMDS. Are there other packages that also works with MDS/NMDS/isoMDS on R? What are the similarity/difference on them? All comments are very welcome! Kind regards, Miltinho Brazil http://yahoo.com.br/oqueeuganhocomisso [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] How to save results from chisq.test or mantelhaen.test to file
Hi, I am new to these functions. I'm wondering if there is anyway to save the entire results (all attributes of the result object) from the chisq.test or mantelhaen.test functions? For example, from chisq.test function, you will have statistic, parameter, p.value, expected, etc. in the result list. How can I save all of them in one shot to, says, a text file or csv file? Thank you. - adschai __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
