Re: [R] (no subject)
Hi Jeff
If you tried to search e.g. in Google
detrended canonical correspondence R
would give you some hints
e.g.
decorana {vegan}
R Documentation
Detrended Correspondence Analysis and
Basic Reciprocal Averaging
Cheers
Petr
On 4 Jan 2005 at 12:13, [EMAIL PROTECTED] wrote:
Hi
I'd like to know if the R can do the DCCA? Because I can't find the
package about the DCCA in R. If it can not, please introduce a free
software to me, which you think can easily do the work , thanks!
jeff
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Petr Pikal
[EMAIL PROTECTED]
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Re: [R] ISNAN() broken? in ver 2.x on MacOS X
This is a good example of why it is necessary to include all the pertinent details (and I know that demands knowing the answer, but using standalone Rmath.h is *not* `an extension'). That you were using C++ was also pertinent. I don't think you should be using R.h if you are building against standalone libRmath. On Tue, 4 Jan 2005, Bill Northcott wrote: I see you are quite correct that IEEE_754 is defined in Rconfig.h on MacOS X. However, I was building against a standalone libRmath v1.9.1. So I was including Rmath.h only and IEEE_754 was not defined. The result was that I got R_IsNaNorNA in the preprocessed source. I finally found it. The culprit is #include iostream which is used in our real code If I preprocess the following code then the substitution is ISNAN() -- (isnan(x)!=0) #include iostream #include R.h #include Rmath.h ISNAN(x); Removing the #include iostream the substitution becomes ISNAN(x) -- (( ( sizeof ( x ) == sizeof(double) ) ? __isnand ( x ) : ( sizeof ( x ) == sizeof( float) ) ? __isnanf ( x ) : __isnan ( x ) )!=0) which is correct. This behaviour is the same with both gcc 3.3 and pre-release gcc 4.0 on MacOS X 10.3.7. Is this a bug we should report to someone such the gcc maintainers? You might want to swap the order of inclusion of headers. Using C headers in a C++ program is always slightly dodgy. Bill Northcott On 04/01/2005, at 1:48 PM, Thomas Lumley wrote: In R 1.9.1 Arith.h and Rmath.h contained code like #ifdef IEEE_754 # define ISNAN(x) (isnan(x)!=0) #else # define ISNAN(x) R_IsNaNorNA(x) #endif #define R_FINITE(x)R_finite(x) int R_IsNaNorNA(double); Although you have clearly gone to some effort to diagnose this, I think your diagnosis is incorrect. 1) In R 1.9.1 IEEE_754 was #defined on OS X, so we would already have had #define ISNAN(x) (isnan(x)!=0) 2) The gcc C preprocessor documentation says When the preprocessor expands a macro name, the macro's expansion replaces the macro invocation, then the expansion is examined for more macros to expand. For example, #define TABLESIZE BUFSIZE #define BUFSIZE 1024 TABLESIZE == BUFSIZE == 1024 TABLESIZE is expanded first to produce BUFSIZE, then that macro is expanded to produce the final result, 1024. and while I haven't been able to find anything definitive about the ANSI standard, the gcc documentation usually flags extensions fairly well and in any case you are presumably using gcc (though you don't say explicitly). A work-around would be to use isnan() rather than ISNAN(). -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] about kriging
Dear R-project users I want to use kriging method to interpolate irregularly distributed temperature data (station data) with latitude, longtitude and altitude in order to produce a gridded dataset altidude corrected. Do you have any idea which package to use? I look forward for your hints. With best regards Prodromos Zanis -- Dr. Prodromos Zanis Centre for Atmospheric Physics and Climatology Academy of Athens 3rd September, Athens 15784, Greece Tel. +30 210 8832048 Fax: +30 210 8832048 e-mail: [EMAIL PROTECTED] Web address: http://users.auth.gr/~zanis/ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] about kriging
Hi, Take a look at http://agec144.agecon.uiuc.edu/csiss/Rgeo/ Regards EJ On Tue, 2005-01-04 at 09:09, Prodromos Zanis wrote: Dear R-project users I want to use kriging method to interpolate irregularly distributed temperature data (station data) with latitude, longtitude and altitude in order to produce a gridded dataset altidude corrected. Do you have any idea which package to use? I look forward for your hints. With best regards Prodromos Zanis __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Question about creating error bars
On Tue, 28 Dec 2004, Dan Bolser wrote:
On Thu, 23 Dec 2004, Dan Bolser wrote:
I have data that looks (very roughly) like this...
Declarative:
Several 'groups', each group with a very variable number of
data points associated.
Procedural:
v.1 - c(rep(50,1), rep(5,5), rep(2,10)) # Set up
v.2 - c('a','b','c','d','e','f','g','h', # the
'i','j','k','l','m','n','o','p') # groups
v.3 - rep(v.2,v.1) # here.
v.4 - rnorm(length(v.3)) # Simulate data.
v.5 - tapply(v.4,v.3,mean) # My analysis.
plot(v.5)
As the number of data points in a group gets smaller, so the variance of
the mean value for that group goes up. I would like to bootstrap some
error bars to show roughly how variable the value for each group is. Here
we have a normal distribution, but mostly my data is binary (i.e. each
group has a different number of (nearly) binary observations). The groups
are ordered, and I want to see any trend in my data accross the groups.
Dan.
Nothing I can do to help pal, sorry.
No, me either. Reading the ?boot documentation (in the library(boot)) is
less than useful too. The docs appear to be written for an expert in the
field (and R) rather than someone who would like to pick up the function
and run with it.
Its funny because on contrast to the complexity of the (tecnical)
spefication of the required functions is the conceptual simplicity of what
I want to do ...
Sample from some bins and create an error bar (of some kind) from the
samples.
It seems that without knowing how to do this (or exactly where to
look) their is nothing you can do.
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[R] Difference between R CMD build --binary and R CMD INSTALL --build
As the title suggests, when building R packages on Windows, what is the difference between: R CMD build --binary mypack And R CMD INSTALL --build mypack ?? The former is suggested by my previous notes and seems to work, and the latter is suggested by http://www.biostat.jhsph.edu/~kbroman/Rintro/Rwinpack.html, and also seems to work. Thanks in advance Mick __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Where to put example files?
I'm writing an R package which includes some text file parsing functions, and I want to include with my package some example files to be used with those functions. My question is which directory should I put these example files in for the user to access? I have tried demo, example, doc and sample but none seem to work or fit. Thanks in advance Mick __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] ISNAN() broken? in ver 2.x on MacOS X
I was attempting builds using both the standalone library including only Rmath.h and the using the installed R using R.h as well. Basically I have the following in relevant programs: #ifndef MATHLIB_STANDALONE #include R.h #endif /* MATHLIB_STANDALONE */ As far as I can see, the only difference is the version of R. ISNAN() will always fail on MacOS X with R 2.0.x whereas it might work with a standalone v1.9.x libRmath. I tried reordering the headers but without any success. The minimal test case to illustrate the problem is: #include iostream #include math.h isnan(x) Preprocess this on MacOS X and the isnan(x) will be unchanged which is wrong as isnan(x) is a macro in math.h. Remove the iostream include and it will work properly. In short there is a problem with the IEEE macros and C++ on MacOS X. Bill Northcott On 04/01/2005, at 7:09 PM, Prof Brian Ripley wrote: This is a good example of why it is necessary to include all the pertinent details (and I know that demands knowing the answer, but using standalone Rmath.h is *not* `an extension'). That you were using C++ was also pertinent. I don't think you should be using R.h if you are building against standalone libRmath. I finally found it. The culprit is #include iostream which is used in our real code If I preprocess the following code then the substitution is ISNAN() -- (isnan(x)!=0) #include iostream #include R.h #include Rmath.h ISNAN(x); Removing the #include iostream the substitution becomes ISNAN(x) -- (( ( sizeof ( x ) == sizeof(double) ) ? __isnand ( x ) : ( sizeof ( x ) == sizeof( float) ) ? __isnanf ( x ) : __isnan ( x ) )!=0) which is correct. This behaviour is the same with both gcc 3.3 and pre-release gcc 4.0 on MacOS X 10.3.7. Is this a bug we should report to someone such the gcc maintainers? You might want to swap the order of inclusion of headers. Using C headers in a C++ program is always slightly dodgy. Bill Northcott On 04/01/2005, at 1:48 PM, Thomas Lumley wrote: In R 1.9.1 Arith.h and Rmath.h contained code like #ifdef IEEE_754 # define ISNAN(x) (isnan(x)!=0) #else # define ISNAN(x) R_IsNaNorNA(x) #endif #define R_FINITE(x)R_finite(x) int R_IsNaNorNA(double); Although you have clearly gone to some effort to diagnose this, I think your diagnosis is incorrect. 1) In R 1.9.1 IEEE_754 was #defined on OS X, so we would already have had #define ISNAN(x) (isnan(x)!=0) 2) The gcc C preprocessor documentation says When the preprocessor expands a macro name, the macro's expansion replaces the macro invocation, then the expansion is examined for more macros to expand. For example, #define TABLESIZE BUFSIZE #define BUFSIZE 1024 TABLESIZE == BUFSIZE == 1024 TABLESIZE is expanded first to produce BUFSIZE, then that macro is expanded to produce the final result, 1024. and while I haven't been able to find anything definitive about the ANSI standard, the gcc documentation usually flags extensions fairly well and in any case you are presumably using gcc (though you don't say explicitly). A work-around would be to use isnan() rather than ISNAN(). -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] ISNAN() broken? in ver 2.x on MacOS X
This sort of confirms that it is a bug. From: Andrew Pinski [EMAIL PROTECTED] Date: 4 January 2005 7:39:38 PM To: Bill Northcott [EMAIL PROTECTED] Cc: gcc@gcc.gnu.org Subject: Re: C++ header file problem - is this a bug? On Jan 4, 2005, at 2:13 AM, Bill Northcott wrote: Is this a bug or is it expected behaviour and if so why? Yes this is a bug but it is already filed see PR 14608. Thanks, Andrew Pinski __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Difference between R CMD build --binary and R CMD INSTALL --build
On Tue, 4 Jan 2005 11:31:27 -, michael watson \(IAH-C\) [EMAIL PROTECTED] wrote: As the title suggests, when building R packages on Windows, what is the difference between: R CMD build --binary mypack And R CMD INSTALL --build mypack ?? The former is suggested by my previous notes and seems to work, and the latter is suggested by http://www.biostat.jhsph.edu/~kbroman/Rintro/Rwinpack.html, and also seems to work. The former builds the package in a temporary directory. The latter installs the package in the standard library location, then builds from the installed copy. This does a better job because it allows help links to other packages. Duncan __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Where to put example files?
On Tue, 4 Jan 2005, michael watson (IAH-C) wrote: I'm writing an R package which includes some text file parsing functions, and I want to include with my package some example files to be used with those functions. My question is which directory should I put these example files in for the user to access? I have tried demo, example, doc and sample but none seem to work or fit. Try using a subdirectory to inst/ in the package source. For example, inst/shapes/sids.shp in package maptools can be accessed by: system.file(shapes/sids.shp, package=maptools)[1] See examples in the pixmap package. Roger Thanks in advance Mick __ 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 -- Roger Bivand Economic Geography Section, Department of Economics, Norwegian School of Economics and Business Administration, Breiviksveien 40, N-5045 Bergen, Norway. voice: +47 55 95 93 55; fax +47 55 95 93 93 e-mail: [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Adding values to the end of a vector?
I want to add values onto the end of a vector, for example...
x - vector
for (i in 1:5){
add_to_end_of_vector(i,x)
}
I just cant find the answer to this question!
Sorry for such a basic question, I tried...
x - c()
for (i in 1:5) x[length(x)] - i
but it didn't work.
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RE: [R] Adding values to the end of a vector?
Is this what you're looking for?
x - numeric(0)
for (i in 1:5) x - append(x, i)
x
[1] 1 2 3 4 5
Andy
From: Dan Bolser
I want to add values onto the end of a vector, for example...
x - vector
for (i in 1:5){
add_to_end_of_vector(i,x)
}
I just cant find the answer to this question!
Sorry for such a basic question, I tried...
x - c()
for (i in 1:5) x[length(x)] - i
but it didn't work.
__
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Re: [R] Adding values to the end of a vector?
The following works, but there may be more efficient ways to do this ...
x=numeric(0)
for(i in 1:5) {
+ x[length(x)+1]=i
+ }
x
[1] 1 2 3 4 5
Best, ingmar
On 1/4/05 2:41 PM, Dan Bolser [EMAIL PROTECTED] wrote:
I want to add values onto the end of a vector, for example...
x - vector
for (i in 1:5){
add_to_end_of_vector(i,x)
}
I just cant find the answer to this question!
Sorry for such a basic question, I tried...
x - c()
for (i in 1:5) x[length(x)] - i
but it didn't work.
__
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
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Re: [R] Adding values to the end of a vector?
On Tue, 4 Jan 2005, Dan Bolser wrote:
I want to add values onto the end of a vector, for example...
x - vector
for (i in 1:5){
add_to_end_of_vector(i,x)
}
?append
I just cant find the answer to this question!
Sorry for such a basic question, I tried...
x - c()
for (i in 1:5) x[length(x)] - i
but it didn't work.
__
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--
Roger Bivand
Economic Geography Section, Department of Economics, Norwegian School of
Economics and Business Administration, Breiviksveien 40, N-5045 Bergen,
Norway. voice: +47 55 95 93 55; fax +47 55 95 93 93
e-mail: [EMAIL PROTECTED]
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RE: [R] Adding values to the end of a vector?
Dear Dan,
The following also works:
x - numeric(0)
for (i in 1:5) x[i] - i
x
[1] 1 2 3 4 5
It's worth noting, however, that extending a vector in this manner can be
very inefficient for large vectors, since the vector is recopied each time.
If you can anticipate the number of elements (or place an upper bound on
it), then it's better to do something like
x - numeric(5)
for (i in 1:5) x[i] - i
I hope this helps,
John
John Fox
Department of Sociology
McMaster University
Hamilton, Ontario
Canada L8S 4M4
905-525-9140x23604
http://socserv.mcmaster.ca/jfox
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Liaw, Andy
Sent: Tuesday, January 04, 2005 8:51 AM
To: 'Dan Bolser'; R mailing list
Subject: RE: [R] Adding values to the end of a vector?
Is this what you're looking for?
x - numeric(0)
for (i in 1:5) x - append(x, i)
x
[1] 1 2 3 4 5
Andy
From: Dan Bolser
I want to add values onto the end of a vector, for example...
x - vector
for (i in 1:5){
add_to_end_of_vector(i,x)
}
I just cant find the answer to this question!
Sorry for such a basic question, I tried...
x - c()
for (i in 1:5) x[length(x)] - i
but it didn't work.
__
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
__
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Re: [R] Adding values to the end of a vector?
why not :
x-vector()
for (i in 1:5) { x -c(x,i) }
x
[1] 1 2 3 4 5
for (i in 1:5) { x -c(x,i) }
x
[1] 1 2 3 4 5 1 2 3 4 5
On Tuesday 04 January 2005 14:57, Ingmar Visser wrote:
x=numeric(0)
for(i in 1:5) {
+ x[length(x)+1]=i
+ }
x
--
Tristan LEFEBURE
Laboratoire d'écologie des hydrosystèmes fluviaux (UMR 5023)
Université Lyon I - Campus de la Doua
Bat. Darwin C 69622 Villeurbanne - France
Phone: (33) (0)4 26 23 44 02
Fax: (33) (0)4 72 43 15 23
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Re: [R] Adding values to the end of a vector?
Liaw, Andy [EMAIL PROTECTED] writes: Is this what you're looking for? x - numeric(0) for (i in 1:5) x - append(x, i) x [1] 1 2 3 4 5 Andy Also notice that in R many things are vectorized, so you may prefer append(x,1:5) [1] 1 2 3 4 5 Extending a vector is done by allocating a longer vector and copying the original. You really don't want to do that for every element if you at all can avoid it. So vectorize, or at least preallocate the extra storage, if you can. -- O__ Peter Dalgaard Blegdamsvej 3 c/ /'_ --- Dept. of Biostatistics 2200 Cph. N (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] Adding values to the end of a vector?
I am curious. How are these suggestions different (better, worse?) from
x - NULL
for (i in 1:5) x - c(x, i)
Thanks,
Danny
On Tue, 4 Jan 2005, John Fox wrote:
Dear Dan,
The following also works:
x - numeric(0)
for (i in 1:5) x[i] - i
x
[1] 1 2 3 4 5
It's worth noting, however, that extending a vector in this manner can be
very inefficient for large vectors, since the vector is recopied each time.
If you can anticipate the number of elements (or place an upper bound on
it), then it's better to do something like
x - numeric(5)
for (i in 1:5) x[i] - i
I hope this helps,
John
John Fox
Department of Sociology
McMaster University
Hamilton, Ontario
Canada L8S 4M4
905-525-9140x23604
http://socserv.mcmaster.ca/jfox
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Liaw, Andy
Sent: Tuesday, January 04, 2005 8:51 AM
To: 'Dan Bolser'; R mailing list
Subject: RE: [R] Adding values to the end of a vector?
Is this what you're looking for?
x - numeric(0)
for (i in 1:5) x - append(x, i)
x
[1] 1 2 3 4 5
Andy
From: Dan Bolser
I want to add values onto the end of a vector, for example...
x - vector
for (i in 1:5){
add_to_end_of_vector(i,x)
}
I just cant find the answer to this question!
Sorry for such a basic question, I tried...
x - c()
for (i in 1:5) x[length(x)] - i
but it didn't work.
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide!
http://www.R-project.org/posting-guide.html
__
R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide!
http://www.R-project.org/posting-guide.html
__
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[R] How to verify using more than 2GB of memory
My machine has 4Gb of memory under WinXP Pro. Re-reading R for Windows FAQ 2.7 I discovered that I can use editbin to add the /LARGEADDRESSAWARE tag in the header without re-compiling, so that is what I did. I also check that it worked using dumpbin. I then edited my Boot.ini file to add the /3GB switch. Then I went to my R.0.0.1 patched that I modified as above and checked memory limit: memory.limit(NA) [1] 1073741824 This is usual default. memory.limit(3*1024) NULL memory.limit(4*1024) Error in memory.size(size) : cannot decrease memory limit It seems to work, since I am able to allocate 3Gb of memory, but not 4Gb (though the error message I get isn't very helpful since I am clearly not trying to decrease the memory limit). However, this does not seem a good way to check that my LARGEADDRESSAWARE version of R is working properly, because when I do the same memory.limit operations on 2.0.1.0 dev that I downloaded this morning I get the same results, without having made the program LARGEADDRESSAWARE Also, although trying to allocate 4Gb of memory does produce an error, I can allocate 3.9Gb, which seems hard to beleive because the OS is supposed to reserve 1Gb. memory.limit(3.9*1024) NULL memory.limit(NA) [1] 4187593113 So, finally, here are my questions, in order of interest: 1) Once I have made my version of R LARGEADDRESSAWARE, how do I best verify that all is well? 2) Why was I able to increase the memory.limit to 3.9Gb on the new version of R.0.1.0 that I did not make LARGEADDRESSAWARE? 3) Is there any side-effect to making a program LARGEADDRESSAWARE? I don't want to sound lazy, but for the benefit of those who don't have Visual Studio, why not make the distributed binary LARGEADDRESSAWARE? Thanks in advance for any insight. Roger J. Bos __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] boot and variances of the bootstrap replicates of the variable of interest?
I want to use boot.ci to generate confidence intervals over the bootstrapped mean(s) of a group of observations (i.e. I have 10 observations and I want to know how confident I can be on the value for the mean). I don't know (or want to know) the details of bootstrapping - I just have the simplistic idea of taking samples, measuring a statistic on the sample, and getting some confidence in the result based on the variance of the sample statistics. I am not sure which type of interval [is] required, so I wanted to try studentized intervals, because some of my groups have a small number of samples (like one or two). However, variance estimates are required for studentized intervals. I can generate the variance for the statistic like this.. # Shame the 'mean' function dosn't work with boot mean.x - function(xx,ii) mean(xx[ii]) # Don't know how (or why) to pick a value for this. nboot - 1000 # The 10 or so observations (in this case) boot.sub - boot(data=shabby.sub$a, statistic=mean.x, R=nboot) # Variance of the statistic over the 1000 replicates my.var.t - var(boot.sub$t) # t: A matrix with 'R' rows each of which is a bootstrap replicate #of 'statistic'. However, I need the variance for each R statistic... I think... It is a shame that boot and boot.ci cant work more together better, without me (a patent idiot) having to pass values (correctly) from the results of boot into boot.ci. Any help with the above would be appreciated, as I am about to weep horrible tears (once more) at the alter of R. (not really :) Dan. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] How to verify using more than 2GB of memory
roger bos wrote: My machine has 4Gb of memory under WinXP Pro. Re-reading R for Windows FAQ 2.7 I discovered that I can use editbin to add the /LARGEADDRESSAWARE tag in the header without re-compiling, so that is what I did. I also check that it worked using dumpbin. I then edited my Boot.ini file to add the /3GB switch. Then I went to my R.0.0.1 patched that I modified as above and checked memory limit: memory.limit(NA) [1] 1073741824 This is usual default. memory.limit(3*1024) NULL memory.limit(4*1024) memory.limit(4*1024-1) should work (you get an overflow with 4*1024). Error in memory.size(size) : cannot decrease memory limit It seems to work, since I am able to allocate 3Gb of memory, but not 4Gb (though the error message I get isn't very helpful since I am clearly not trying to decrease the memory limit). However, this does not seem a good way to check that my LARGEADDRESSAWARE version of R is working properly, because when I do the same memory.limit operations on 2.0.1.0 dev that I downloaded this morning I get the same results, without having made the program LARGEADDRESSAWARE Also, although trying to allocate 4Gb of memory does produce an error, I can allocate 3.9Gb, which seems hard to beleive because the OS is supposed to reserve 1Gb. Yes, but R does have the permission now to request 3.9 Gb, even if it does not get it from the OS. memory.limit(3.9*1024) NULL memory.limit(NA) [1] 4187593113 So, finally, here are my questions, in order of interest: 1) Once I have made my version of R LARGEADDRESSAWARE, how do I best verify that all is well? If you don't trust the FAQ, you can try it out by assigning some big objects and look what happens. if it crashes, you will see... 2) Why was I able to increase the memory.limit to 3.9Gb on the new version of R.0.1.0 that I did not make LARGEADDRESSAWARE? I think you won't get that many memory from the OS, but R is now allowed to ask the OS in order to get it. 3) Is there any side-effect to making a program LARGEADDRESSAWARE? I don't want to sound lazy, but for the benefit of those who don't have Visual Studio, why not make the distributed binary LARGEADDRESSAWARE? I guess because of license issues. Is it permitted to distribute such a software (modified by Visual Studio) given both the Visual Studio license and the GPL from R??? Uwe Ligges Thanks in advance for any insight. Roger J. Bos __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] Adding values to the end of a vector?
On Tue, 4 Jan 2005, Daniel Almirall wrote:
I am curious. How are these suggestions different (better, worse?) from
x - NULL
for (i in 1:5) x - c(x, i)
One imporant difference is between solutions that preallocate storage and
those that don't.
x-numeric(5)
for(i in 1:5) x[i]-i
allocates one vector of length 5 and then modifies it, but
x-NULL
for(i in 1:5) x-c(x,i)
allocates vectors of length 1, 2, 3, 4, 5 in turn.
You can't tell this from anything in the language definition, since
conceptually x[i]-i also copies: it does
x - [-(x,i,i)
and for more complicated replacement functions it will really copy. Even
if the first version really copied there would be some potential for
having more efficient memory allocation with all the objects being of size
5 (at least, for very large values of 5).
If you don't know how long the vector needs to be then you can't
preallocate, but a common programming strategy in other languages is to
allocate powers of 2 (eg start out with x-numeric(4) and if that isn't
big enough do something like x-c(x,numeric(4)) to double the size). I
don't know if anyone has looked at whether this is ever useful in R.
-thomas
Thanks,
Danny
On Tue, 4 Jan 2005, John Fox wrote:
Dear Dan,
The following also works:
x - numeric(0)
for (i in 1:5) x[i] - i
x
[1] 1 2 3 4 5
It's worth noting, however, that extending a vector in this manner can be
very inefficient for large vectors, since the vector is recopied each time.
If you can anticipate the number of elements (or place an upper bound on
it), then it's better to do something like
x - numeric(5)
for (i in 1:5) x[i] - i
I hope this helps,
John
John Fox
Department of Sociology
McMaster University
Hamilton, Ontario
Canada L8S 4M4
905-525-9140x23604
http://socserv.mcmaster.ca/jfox
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Liaw, Andy
Sent: Tuesday, January 04, 2005 8:51 AM
To: 'Dan Bolser'; R mailing list
Subject: RE: [R] Adding values to the end of a vector?
Is this what you're looking for?
x - numeric(0)
for (i in 1:5) x - append(x, i)
x
[1] 1 2 3 4 5
Andy
From: Dan Bolser
I want to add values onto the end of a vector, for example...
x - vector
for (i in 1:5){
add_to_end_of_vector(i,x)
}
I just cant find the answer to this question!
Sorry for such a basic question, I tried...
x - c()
for (i in 1:5) x[length(x)] - i
but it didn't work.
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Thomas Lumley Assoc. Professor, Biostatistics
[EMAIL PROTECTED] University of Washington, Seattle
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[R] R help search and Java(tm)?
I found this great search source(http://www.statslab.cam.ac.uk/~djw1005/Stats/Interests/search.R;) helpHTML() Has (or will) this become the standard search method? Is R 'Free Software'? The dependence on Java seems a bit of a pain for 'freeness'. Did the above make it into CRAN? Cheers, Dan. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Statistical Learning and Data Mining Course
Short course: Statistical Learning and Data Mining Trevor Hastie and Robert Tibshirani, Stanford University Sheraton Hotel, Palo Alto, California February 24 25, 2005 This two-day course gives a detailed overview of statistical models for data mining, inference and prediction. With the rapid developments in internet technology, genomics and other high-tech industries, we rely increasingly more on data analysis and statistical models to exploit the vast amounts of data at our fingertips. This sequel to our popular Modern Regression and Classification course covers many new areas of unsupervised learning and data mining, and gives an in-depth treatment of some of the hottest tools in supervised learning. The first course is not a prerequisite for this new course. Most of the techniques discussed in the course are implemented by the authors and others in the S language (S-plus or R), and all of the examples were developed in S. Day one focuses on state-of-art methods for supervised learning, including PRIM, boosting, support vector machines, and very recent work on least angle regression and the lasso. Day two covers unsupervised learning, including clustering, principal components, principal curves and self-organizing maps. Many applications will be discussed, including the analysis of DNA expression arrays - one of the hottest new areas in biology! ### Much of the material is based on the book: Elements of Statistical Learning: data mining, inference and prediction Hastie, Tibshirani Friedman, Springer-Verlag, 2001 http://www-stat.stanford.edu/ElemStatLearn/ A copy of this book will be given to all attendees. ### For more information, and to register, visit the course homepage: http://www-stat.stanford.edu/~hastie/mrc.html --- Trevor Hastie [EMAIL PROTECTED] Professor, Department of Statistics, Stanford University Phone: (650) 725-2231 (Statistics) Fax: (650) 725-8977 (650) 498-5233 (Biostatistics) Fax: (650) 725-6951 URL: http://www-stat.stanford.edu/~hastie address: room 104, Department of Statistics, Sequoia Hall 390 Serra Mall, Stanford University, CA 94305-4065 [[alternative text/enriched version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] rownames and plot lablels
I have a question about changing rownames. In the following function I am plotting the regression coeficients with their corresponding mean. Right now, the labels on the plot and the rownames in the dataframe are x1,x2,x3...etc. Is there a way to make the row names the same as the variable name entered into the formula? I.E. if x1 was a vector called opinions, it would be labeled opinions on the plot instead of x1. I have tried using variations of rownames(x)- namevector but have not been successful. I keep getting a null. Any suggestions would be appreciated Quadplot-function(y, x1, x2, x3 = NULL, x4 = NULL,x5=NULL,x6=NULL,x7=NULL,x8=NULL,x9=NULL,x10=NULL, x11=NULL, x12=NULL, x13=NULL, x14=NULL) #section of code ommitted my.formula - as.formula(y ~ x1 + x2 + x3+ x4+ x5+ x6+ x7+ x8+ x9+x10+x11+x12+x13+x14) outlm - lm(my.formula) #section of code ommitted meanvec-c(mean(x1,na.rm=TRUE),mean(x2,na.rm=TRUE),mean(x3,na.rm=TRUE),mean(x4,na.rm=TRUE),mean(x5,na.rm=TRUE),mean(x6,na.rm=TRUE),mean(x7,na.rm=TRUE),mean(x8,na.rm=TRUE),mean(x9,na.rm=TRUE),mean(x10,na.rm=TRUE),mean(x11,na.rm=TRUE) ,mean(x12,na.rm=TRUE) ,mean(x13,na.rm=TRUE) ,mean(x14,na.rm=TRUE)) } meanper-meanvec/6 meanper1-meanper*100 #This is the data frame created mf - data.frame(Impact = abs(outlm$coef[-1]), Performance = meanper1) meanx-mean(abs(outlm$coef[-1])) meany-mean(meanper1) n-length(meanvec) color-rep(blue,n) color[(mf$Impactmeanx mf$Performancemeany)]-green color[(mf$Impactmeanx mf$Performancemeany)]-red color[(mf$Impactmeanx mf$Performancemeany)]-gray plot((mf),col=color,main=Perfomance vs. Impact,xlab=Impact,ylab=Performance, type = n) points(mf, pch=21, bg=color, cex=4) text(x = mf$Impact, y = mf$Performance, labels = rownames(mf)) abline(h=mean(mf$Performance)) abline(v=mean(mf$Impact)) print(mf) } Thanks Derek __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R help search and Java(tm)?
Dan Bolser [EMAIL PROTECTED] writes: I found this great search source(http://www.statslab.cam.ac.uk/~djw1005/Stats/Interests/search.R;) helpHTML() Has (or will) this become the standard search method? I think it got superseded by Jon Baron's RSiteSearch() function which is finding its way into r-devel. Is R 'Free Software'? The dependence on Java seems a bit of a pain for 'freeness'. A pain yes, but free software can rely on non-free compilers and OS's if need be. It's just more convenient to build on tools that everyone can get hold of. Did the above make it into CRAN? Well, you could check... It doesn't look like there is enough of the ancillary matter (help pages etc.) for a CRAN package. -- O__ Peter Dalgaard Blegdamsvej 3 c/ /'_ --- Dept. of Biostatistics 2200 Cph. N (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] How to verify using more than 2GB of memory
You forgot that 32-bit machines do integer operation mod 2^32. So you actually asked for a memory limit of 0, which was a decrease. We do recommend that you use the command-line flag, e.g. in the rw-FAQ. % rterm --max-mem-size=4096M WARNING: --max-mem-size=4096`M': too large and ignored would have told you the error. You don't seem to appreciate the difference between `limit' and `allocate': please read the help page for memory.limit with a modicum of care. Once you appreciate that you have seriously misread the page, things will become a lot clearer. On Tue, 4 Jan 2005, roger bos wrote: My machine has 4Gb of memory under WinXP Pro. Re-reading R for Windows FAQ 2.7 I discovered that I can use editbin to add the /LARGEADDRESSAWARE tag in the header without re-compiling, so that is what I did. I also check that it worked using dumpbin. I then edited my Boot.ini file to add the /3GB switch. Then I went to my R.0.0.1 patched that I modified as above and checked memory limit: memory.limit(NA) [1] 1073741824 This is usual default. memory.limit(3*1024) NULL memory.limit(4*1024) Error in memory.size(size) : cannot decrease memory limit It seems to work, since I am able to allocate 3Gb of memory, but not 4Gb (though the error message I get isn't very helpful since I am clearly not trying to decrease the memory limit). However, this does not seem a good way to check that my LARGEADDRESSAWARE version of R is working properly, because when I do the same memory.limit operations on 2.0.1.0 dev that I downloaded this morning I get the same results, without having made the program LARGEADDRESSAWARE Also, although trying to allocate 4Gb of memory does produce an error, I can allocate 3.9Gb, which seems hard to beleive because the OS is supposed to reserve 1Gb. memory.limit(3.9*1024) NULL memory.limit(NA) [1] 4187593113 So, finally, here are my questions, in order of interest: 1) Once I have made my version of R LARGEADDRESSAWARE, how do I best verify that all is well? 2) Why was I able to increase the memory.limit to 3.9Gb on the new version of R.0.1.0 that I did not make LARGEADDRESSAWARE? 3) Is there any side-effect to making a program LARGEADDRESSAWARE? I don't want to sound lazy, but for the benefit of those who don't have Visual Studio, why not make the distributed binary LARGEADDRESSAWARE? The maintainer does not have it. Simple! -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] x11 is not available
Dear list, I have problems installing R-2.0.1 on SUSE Linux 9.2. I used the following commands in order install R in /usr/local ./configure --with x11 --with-readline make make install When starting R and trying to display a plot on the X-window system output is written to a postscript file. When I try to run x11 with x11() Error in X11(): X11 is not available. I do have a running x11 window system with KDE Any help is appreciated. Many thanks Peter Schlattmann __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Non linear Square fit Function
Hi all, I'm trying to use the nls function to do a nls curve fit. I have a histogram for my data. I need to get athe best curve fit for this. i am plotting experimental vs the theoretical values. my experimental values are got from my dnorm function, mean=mean of my mid values(hist) and sd=sd of my mid values. For the theoretical i'm using mean and sd of all 2 raw values as the start values. I'm getting no sd in my new curve. Can someone gimme some pointers to get started here. I need my nls to spit out sd and mean of the new fit which it does'nt. is there a better function or can i somehow get around this. Thanks in advance. Choudary Jagarlamudi Instructor Southwestern Oklahoma State University STF 254 100 campus Drive Weatherford OK 73096 Tel 580-774-7136 [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] scree plot
Hi! Is there an easy way to add to the scree-plot labels to each value pertaining to the cumulative proportion of explained variance? Thanks and a happy new year Anne Anne Piotet Tel: +41 79 359 83 32 (mobile) Email: [EMAIL PROTECTED] --- M-TD Modelling and Technology Development PSE-C CH-1015 Lausanne Switzerland Tel: +41 21 693 83 98 Fax: +41 21 646 41 33 -- [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] bootstrap proportions?
Hello, I have several ordered groups (20), each with several observations. Each group has fewer observations roughly linearly from 30 to 0. Each observation is a proportion. As I know the max and min values for a proporion are 1 and 0, I am adding these values to each group to allow bootstrap for groups with = 1 observations. Sometimes the bootstrap confidence interval is 1, which makes me think that I am doing something deeply wrong. How can I do bootstrap properly with observations which are proportions? What special precautions should I be taking for very low sample sizes with bootstrap? Is this a bad question for R-help? Thanks, Dan. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] x11 is not available
If I remember correctly, the correct command line switch is: -with-x11 Note the dash. Sean On Jan 4, 2005, at 4:41 PM, [EMAIL PROTECTED] wrote: Dear list, I have problems installing R-2.0.1 on SUSE Linux 9.2. I used the following commands in order install R in /usr/local ./configure --with x11 --with-readline make make install When starting R and trying to display a plot on the X-window system output is written to a postscript file. When I try to run x11 with x11() Error in X11(): X11 is not available. I do have a running x11 window system with KDE Any help is appreciated. Many thanks Peter Schlattmann __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] x11 is not available
My guess is that you have a 'Desktop' version of SUSE installed which does not include the needed X11 development environment; from the R Installation and Administration manual: Unless you do not want to view graphs on-screen you need X11 installed, including its headers and client libraries. (On Fedora Core 2 Linux this means the xorg-x11-devel and xorg-x11-libs RPMs, for example. Older Linuxen used XFree86-.) Good luck, Gardar On Tue, 2005-01-04 at 13:41, [EMAIL PROTECTED] wrote: Dear list, I have problems installing R-2.0.1 on SUSE Linux 9.2. I used the following commands in order install R in /usr/local ./configure --with x11 --with-readline make make install When starting R and trying to display a plot on the X-window system output is written to a postscript file. When I try to run x11 with x11() Error in X11(): X11 is not available. I do have a running x11 window system with KDE Any help is appreciated. Many thanks Peter Schlattmann __ 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 Gardar Johannesson [EMAIL PROTECTED] Applied Statistics Economics Group Tel: 925 422-3901 Systems Decision Sciences SectionFax: 925 422-4141 Lawrence Livermore National Laboratory Loc: B141/R1128 7000 East Ave., L-229 Livermore, CA 94550-9234 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] print(cat(bleh)) shows up strange NULL
I am trying the following code...
for(i in 1:bins){
print(cat(c(i, length(var1[var1==i]
}
Where var1 is a vector with zero or more values = {1, 2, ..., bins} (or
something like that).
The result I get is...
1 33NULL
2 28NULL
3 39NULL
4 27NULL
5 32NULL
6 30NULL
7 23NULL
8 16NULL
9 10NULL
10 15NULL
11 13NULL
12 7NULL
13 3NULL
14 7NULL
15 2NULL
16 0NULL
17 2NULL
18 0NULL
19 0NULL
20 3NULL
I don't know what I am doing to get those stray NULL characters printed.
I also tried...
for(i in 1:bins){
print(cat(i, length(var1[var1==i])))
}
Which is essentially the same.
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[R] warnings and errors with R CMD INSTALL
Hello, unfortunately I had to compile latest version of R-2.0.1 by myself. I'd rather would prefer vendors binaries but since the current version of Ubuntu defaults to 1.9.x I had to compile R on my own in order to be up to date! So far, everything went fine and R runs smoothly. Unfortunately I am not able to use R CMD INSTALL command to install add-on packages. I followed RNews 3/3 and used: 1. R CMD INSTALL package_version.tar.gz and 2.options(CRAN=http://umfragen.sowi.uni-mainz.de/CRAN/;) install.packages(pkg1. pkg2) Both approaches end up i.e.: WARNING: invalid package 'pkg1.tar.gz' ERROR: no packages specified Well, R administration manual and RNews give some examples which I took as basis to install further packages. I, as suggested in RNews and administration manual alike, omitted the -l option, since I want to stay with default library location! Obviously I am stuck in a situation not covered by the docs! Well, most likely I misunderstand something, can anyone help out with this? greetings Thomas system: platform i686-pc-linux-gnu arch i686 os linux-gnu system i686, linux-gnu status major2 minor0.1 year 2004 month11 day 15 language R __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Re : Frequency count
Dear list,
I have a dataset as follow and I would like to count the frequencies for
the combination of the two variables (f1 and f2) for each id. I know it is
should be straight forward, but I just don't know how to do it in R. Here
is the SAS code I will use to get the output I want :
proc means nway;
class id f1 f2;
var flag
output out=temp;
Dataset:
idf1f2flag
798 1 2 1
777 0 2 1
798 2 2 1
777 0 2 1
777 1 1 1
Output:
Id=798
1-2 1
2-2 1
Id=777
0-2 2
1-1 1
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Re: [R] print(cat(bleh)) shows up strange NULL
Dan Bolser [EMAIL PROTECTED] writes:
I am trying the following code...
for(i in 1:bins){
print(cat(c(i, length(var1[var1==i]
}
Where var1 is a vector with zero or more values = {1, 2, ..., bins} (or
something like that).
The result I get is...
1 33NULL
2 28NULL
19 0NULL
20 3NULL
I don't know what I am doing to get those stray NULL characters printed.
You're printing them, will you believe it...?
Consider this:
x - cat(abc)
abc print(x)
NULL
x
NULL
print(cat(abc))
abcNULL
I.e. cat() always returns NULL, invisibly unless you force it to be
printed.
--
O__ Peter Dalgaard Blegdamsvej 3
c/ /'_ --- Dept. of Biostatistics 2200 Cph. N
(*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918
~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907
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Re: [R] print(cat(bleh)) shows up strange NULL
On 4 Jan 2005, Peter Dalgaard wrote:
Dan Bolser [EMAIL PROTECTED] writes:
I am trying the following code...
for(i in 1:bins){
print(cat(c(i, length(var1[var1==i]
}
Where var1 is a vector with zero or more values = {1, 2, ..., bins} (or
something like that).
The result I get is...
1 33NULL
2 28NULL
19 0NULL
20 3NULL
I don't know what I am doing to get those stray NULL characters printed.
You're printing them, will you believe it...?
Consider this:
x - cat(abc)
abc print(x)
NULL
x
NULL
print(cat(abc))
abcNULL
I.e. cat() always returns NULL, invisibly unless you force it to be
printed.
never trust a cat!
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[R] quantiles for geometric distribution
Dear list, I have got an array with observational values t and I would like to fit a geometric distribution to it. As I understand the geometric distribution, there is only one parameter, the probability p. I estimated it by 1/mean(t). Now I plotted the estimated density function by plot(ecdf(t),do.points=FALSE,col.h=blue); and I would like to add the geometric distribution. This should be possibly with the function pgeom(). Unfortunately I do not understand what is meant by the argument q, vector of quantiles representing the number of failures in a sequence of Bernoulli trials before success occurs according to R help. I am familiar with quantiles, but why do I need them here? Does anybody know what this means? What am I supposed to do? Thanks again for all the help. Cheers, Dax [[alternative text/enriched version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] print(cat(bleh)) shows up strange NULL
Consider the following:
for(i in 1:2)cat(i, )
1 2
for(i in 1:2)print(i)
[1] 1
[1] 2
for(i in 1:2)print(cat(i))
1NULL
2NULL
hope this helps. spencer graves
Dan Bolser wrote:
I am trying the following code...
for(i in 1:bins){
print(cat(c(i, length(var1[var1==i]
}
Where var1 is a vector with zero or more values = {1, 2, ..., bins} (or
something like that).
The result I get is...
1 33NULL
2 28NULL
3 39NULL
4 27NULL
5 32NULL
6 30NULL
7 23NULL
8 16NULL
9 10NULL
10 15NULL
11 13NULL
12 7NULL
13 3NULL
14 7NULL
15 2NULL
16 0NULL
17 2NULL
18 0NULL
19 0NULL
20 3NULL
I don't know what I am doing to get those stray NULL characters printed.
I also tried...
for(i in 1:bins){
print(cat(i, length(var1[var1==i])))
}
Which is essentially the same.
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Re: [R] print(cat(bleh)) shows up strange NULL
On Tue, 4 Jan 2005, Dan Bolser wrote:
On 4 Jan 2005, Peter Dalgaard wrote:
Dan Bolser [EMAIL PROTECTED] writes:
I am trying the following code...
for(i in 1:bins){
print(cat(c(i, length(var1[var1==i]
}
Where var1 is a vector with zero or more values = {1, 2, ..., bins} (or
something like that).
The result I get is...
1 33NULL
2 28NULL
19 0NULL
20 3NULL
I don't know what I am doing to get those stray NULL characters printed.
You're printing them, will you believe it...?
Consider this:
x - cat(abc)
abc print(x)
NULL
x
NULL
print(cat(abc))
abcNULL
I.e. cat() always returns NULL, invisibly unless you force it to be
printed.
never trust a cat!
I meant to add that this was causing me problems when trying to create a
file name for use with the png command.
png tries to create a 'NULL' file name, and returns a rather cryptic
message...
Error in X11(paste(png::, filename, sep = ), width, height, pointsize,:
unable to start device PNG
In addition: Warning message:
could not open PNG file `'
However, the warning provides the answer to the problem... use paste
instead of cat.
Cheers,
Dan.
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Re: [R] Re : Frequency count
Try table(), aggregate(), or tapply(), using length() in the last two
functions.
I hope that this helps,
Andrew
On Wed, Jan 05, 2005 at 11:36:07AM +1300, [EMAIL PROTECTED] wrote:
Dear list,
I have a dataset as follow and I would like to count the frequencies for
the combination of the two variables (f1 and f2) for each id. I know it is
should be straight forward, but I just don't know how to do it in R. Here
is the SAS code I will use to get the output I want :
proc means nway;
class id f1 f2;
var flag
output out=temp;
Dataset:
idf1f2flag
798 1 2 1
777 0 2 1
798 2 2 1
777 0 2 1
777 1 1 1
Output:
Id=798
1-2 1
2-2 1
Id=777
0-2 2
1-1 1
___
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--
Andrew Robinson Ph: 208 885 7115
Department of Forest Resources Fa: 208 885 6226
University of Idaho E : [EMAIL PROTECTED]
PO Box 441133W : http://www.uidaho.edu/~andrewr
Moscow ID 83843 Or: http://www.biometrics.uidaho.edu
No statement above necessarily represents my employer's opinion.
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RE: [R] Re : Frequency count
This might help...
Here KI is a matrix such as your dataset (without the flag)
dups - function (intab=KI) {
# CREATE A MATRIX WITH ONLY THE UNIQUE ROWS OF intab
intabunique - unique(intab)
# COLLAPSE THE FULL TABLE
a2 - apply(intab, 1, paste, collapse=:)
# COLLAPSE THE UNIQUE TABLE
b2 - apply(intabunique, 1, paste, collapse=:)
# COUNT UNIQUE ROW OCCURRENCES AND WRITE TO .COUNT
assign(.COUNT,c(table(c(a2,unique(b2)))[b2] - 1) ,pos=1)
# WRITE THE UNIQUE TABLE TO .KIUNIQUE
assign(.KIUNIQUE, intabunique, pos=1)
}
KI
col1 col2 col3
[1,]111
[2,]211
[3,]121
[4,]111
[5,]121
[6,]111
[7,]222
dups(KI)
.KIUNIQUE
col1 col2 col3
[1,]111
[2,]211
[3,]121
[4,]222
.COUNT
1:1:1 2:1:1 1:2:1 2:2:2
3 1 2 1
__
Tarmo Remmel B.E.S., M.Sc.F., Ph.D. Candidate
GUESS Lab, Department of Geography
University of Toronto, Toronto, ON, Canada
http://eratos.erin.utoronto.ca/remmelt
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] Behalf Of [EMAIL PROTECTED]
Sent: Tuesday, January 04, 2005 5:36 PM
To: r-help@stat.math.ethz.ch
Subject: [R] Re : Frequency count
Dear list,
I have a dataset as follow and I would like to count the frequencies for
the combination of the two variables (f1 and f2) for each id. I
know it is
should be straight forward, but I just don't know how to do it in R. Here
is the SAS code I will use to get the output I want :
proc means nway;
class id f1 f2;
var flag
output out=temp;
Dataset:
idf1f2flag
798 1 2 1
777 0 2 1
798 2 2 1
777 0 2 1
777 1 1 1
Output:
Id=798
1-2 1
2-2 1
Id=777
0-2 2
1-1 1
__
_
This message, including attachments, is confidential. If you...{{dropped}}
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Re: [R] Re : Frequency count
[EMAIL PROTECTED] writes: Dear list, I have a dataset as follow and I would like to count the frequencies for the combination of the two variables (f1 and f2) for each id. I know it is should be straight forward, but I just don't know how to do it in R. Here is the SAS code I will use to get the output I want : proc means nway; class id f1 f2; var flag output out=temp; Dataset: idf1f2flag 798 1 2 1 777 0 2 1 798 2 2 1 777 0 2 1 777 1 1 1 Output: Id=798 1-2 1 2-2 1 Id=777 0-2 2 1-1 1 Here's one way: dd - read.table(stdin(),header=TRUE) 0: idf1f2flag 1: 798 1 2 1 2: 777 0 2 1 3: 798 2 2 1 4: 777 0 2 1 5: 777 1 1 1 6: by(dd, dd$id, function(x)table(paste(x$f1,x$f2,sep=-))) dd$id: 777 0-2 1-1 2 1 dd$id: 798 1-2 2-2 1 1 -- O__ Peter Dalgaard Blegdamsvej 3 c/ /'_ --- Dept. of Biostatistics 2200 Cph. N (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Re : Frequency count
On Wed, 5 Jan 2005 [EMAIL PROTECTED] wrote: Dear list, I have a dataset as follow and I would like to count the frequencies for the combination of the two variables (f1 and f2) for each id. I know it is should be straight forward, but I just don't know how to do it in R. Here is the SAS code I will use to get the output I want : table() will count frequencies, and interaction() will create a variable with all combinations of a set of variables, so something like table(interaction(f1,f2)) -thomas __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Histogram
I have data on a single variable LOGT. It has about 300,000 observations. I am trying to make a Histogram out of this data set. Following is my effort. Could anyone help me to solve this error. hist(x) Error in hist.default(x) : `x' must be numeric class(x) [1] data.frame is.object(x) [1] TRUE is.vector(x) [1] FALSE is.numeric(x) [1] FALSE is.factor(x) [1] FALSE note:plot(x) works okay durai __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] warnings and errors with R CMD INSTALL
Hello, Am Dienstag, den 04.01.2005, 23:25 + schrieb Prof Brian Ripley: On Tue, 4 Jan 2005, thomas wrote: I followed RNews 3/3 and used: 1. R CMD INSTALL package_version.tar.gz and 2.options(CRAN=http://umfragen.sowi.uni-mainz.de/CRAN/;) install.packages(pkg1. pkg2) Both approaches end up i.e.: WARNING: invalid package 'pkg1.tar.gz' ERROR: no packages specified But there is no package `pkg1' on CRAN. Try a real name like install.packages(tree) Well, of cause I didn't want install pkg1 or pkg2, the precise commandline was: 1. R CMD INSTALL epitools_0.3-3.tar.gz and 2. install.packages(accuracy, zoo, abind) Sorry for being so unclear in my first message! I did take the package names from R-CRAN website, copied and pasted to commandline Thanks Thomas __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Histogram
x is not a numeric vector, so R doesn't know how to take a histogram. Here are your clues: class(x) [1] data.frame is.numeric(x) [1] FALSE so, try names(x) I speculate that LOGT is contained in the dataframe x. If so, try hist(x$LOGT) I hope that this helps. Andrew On Tue, Jan 04, 2005 at 03:37:16PM -0800, duraikannan sundaramoorthi wrote: I have data on a single variable LOGT. It has about 300,000 observations. I am trying to make a Histogram out of this data set. Following is my effort. Could anyone help me to solve this error. hist(x) Error in hist.default(x) : `x' must be numeric class(x) [1] data.frame is.object(x) [1] TRUE is.vector(x) [1] FALSE is.numeric(x) [1] FALSE is.factor(x) [1] FALSE note:plot(x) works okay durai __ 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 -- Andrew Robinson Ph: 208 885 7115 Department of Forest Resources Fa: 208 885 6226 University of Idaho E : [EMAIL PROTECTED] PO Box 441133W : http://www.uidaho.edu/~andrewr Moscow ID 83843 Or: http://www.biometrics.uidaho.edu No statement above necessarily represents my employer's opinion. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] subsetting within a function using lme
Thankyou for your help with subsetting within a function. I have now tried
to apply the same theory in the framework of an lme as follows:
fit1.lme - eval(substitute(lme(fixed=fixed, data=dataframe,
random=random, correlation=corCAR1(form= corr), na.action=na.omit,
subset=subset),list(subset=subs)))
but I get the following error:
Error in switch(mode(object), name = , numeric = , call = object,
character = as.name(object), :
[[ cannot be of mode logical
I'm not sure why. Can anyone help me with this?
kind regards
Pam
On Thu, 30 Dec 2004, Thomas Lumley wrote:
On Thu, 30 Dec 2004, Pamela McCaskie wrote:
And so my attempt to wrap a simple function around this looks like:
test.fun - function(formula, mydata, sub=NULL){
subs - with(mydata, eval(sub))
fit.glm - glm(formula=formula, data=mydata, family=binomial, subset=subs)
return(fit.glm)
}
But when I tested it out with
test - test.fun(y~x1+x2, mydata=testdata, sub=expression(SEX==0))
I get:
Error in [.data.frame(structure(list(N_ASTHMA = as.integer(c(0, 0, 0, :
invalid subscript type
I get a different error: it may be that you have an object called `subs`
in the global environment
I'm guessing that it's looking in the global environment for
subs,
More precisely, it is looking in environment where `formula` was created,
which happens to be the global environment.
This is the sort of thing that happens with the fitting functions because
they go to such lengths to break the basic scoping of R.
You probably have to substitute() the evaluated subset into the glm call.
fit.glm - eval(substitute(glm(formula=formula, data=mydata,
family=binomial, subset=subset),list(subset=subs)))
-thomas
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RE: [R] Non linear Square fit Function
Have you tried fitdistr in the MASS package (should be installed with R by default)? Andy From: Jagarlamudi, Choudary Hi all, I'm trying to use the nls function to do a nls curve fit. I have a histogram for my data. I need to get athe best curve fit for this. i am plotting experimental vs the theoretical values. my experimental values are got from my dnorm function, mean=mean of my mid values(hist) and sd=sd of my mid values. For the theoretical i'm using mean and sd of all 2 raw values as the start values. I'm getting no sd in my new curve. Can someone gimme some pointers to get started here. I need my nls to spit out sd and mean of the new fit which it does'nt. is there a better function or can i somehow get around this. Thanks in advance. Choudary Jagarlamudi Instructor Southwestern Oklahoma State University STF 254 100 campus Drive Weatherford OK 73096 Tel 580-774-7136 [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] subsetting within a function using lme
Hi Pam,
can you provide just enough code for us to reproduce the error on one
of the sample datasets included with lme? No more and no less than
the minimum necessary, please.
I find it easier to debug when things are concrete :)
Thanks,
Andrew
On Wed, Jan 05, 2005 at 08:48:45AM +0800, Pamela McCaskie wrote:
Thankyou for your help with subsetting within a function. I have now tried
to apply the same theory in the framework of an lme as follows:
fit1.lme - eval(substitute(lme(fixed=fixed, data=dataframe,
random=random, correlation=corCAR1(form= corr), na.action=na.omit,
subset=subset),list(subset=subs)))
but I get the following error:
Error in switch(mode(object), name = , numeric = , call = object,
character = as.name(object), :
[[ cannot be of mode logical
I'm not sure why. Can anyone help me with this?
kind regards
Pam
On Thu, 30 Dec 2004, Thomas Lumley wrote:
On Thu, 30 Dec 2004, Pamela McCaskie wrote:
And so my attempt to wrap a simple function around this looks like:
test.fun - function(formula, mydata, sub=NULL){
subs - with(mydata, eval(sub))
fit.glm - glm(formula=formula, data=mydata, family=binomial,
subset=subs)
return(fit.glm)
}
But when I tested it out with
test - test.fun(y~x1+x2, mydata=testdata, sub=expression(SEX==0))
I get:
Error in [.data.frame(structure(list(N_ASTHMA = as.integer(c(0, 0, 0, :
invalid subscript type
I get a different error: it may be that you have an object called `subs`
in the global environment
I'm guessing that it's looking in the global environment for
subs,
More precisely, it is looking in environment where `formula` was created,
which happens to be the global environment.
This is the sort of thing that happens with the fitting functions because
they go to such lengths to break the basic scoping of R.
You probably have to substitute() the evaluated subset into the glm call.
fit.glm - eval(substitute(glm(formula=formula, data=mydata,
family=binomial, subset=subset),list(subset=subs)))
-thomas
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--
Andrew Robinson Ph: 208 885 7115
Department of Forest Resources Fa: 208 885 6226
University of Idaho E : [EMAIL PROTECTED]
PO Box 441133W : http://www.uidaho.edu/~andrewr
Moscow ID 83843 Or: http://www.biometrics.uidaho.edu
No statement above necessarily represents my employer's opinion.
__
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Re: [R] subsetting within a function using lme
Here you go
A simplified version of the function looks like this:
test.fun - function(fixed, random, mydata, sub=NULL){
library(nlme)
subs - with(mydata, eval(sub))
fit.lme - eval(substitute(lme(fixed=fixed, data=mydata, random=random,
na.action=na.omit, subset=subset),list(subset=subs)))
return(fit.lme)
}
So using the Orthodont dataset I tried:
test - snp.long(fixed=distance~age, random=~1|Subject, mydata=Orthodont,
sub=expression(Sex==Male))
and get that error.
Error in switch(mode(object), name = , numeric = , call = object,
character = as.name(object), :
[[ cannot be of mode logical
Thanks for your help
Hi Pam,
can you provide just enough code for us to reproduce the error on one
of the sample datasets included with lme? No more and no less than
the minimum necessary, please.
I find it easier to debug when things are concrete :)
Thanks,
Andrew
On Wed, Jan 05, 2005 at 08:48:45AM +0800, Pamela McCaskie wrote:
Thankyou for your help with subsetting within a function. I have now tried
to apply the same theory in the framework of an lme as follows:
fit1.lme - eval(substitute(lme(fixed=fixed, data=dataframe,
random=random, correlation=corCAR1(form= corr), na.action=na.omit,
subset=subset),list(subset=subs)))
but I get the following error:
Error in switch(mode(object), name = , numeric = , call = object,
character = as.name(object), :
[[ cannot be of mode logical
I'm not sure why. Can anyone help me with this?
kind regards
Pam
On Thu, 30 Dec 2004, Thomas Lumley wrote:
On Thu, 30 Dec 2004, Pamela McCaskie wrote:
And so my attempt to wrap a simple function around this looks like:
test.fun - function(formula, mydata, sub=NULL){
subs - with(mydata, eval(sub))
fit.glm - glm(formula=formula, data=mydata, family=binomial,
subset=subs)
return(fit.glm)
}
But when I tested it out with
test - test.fun(y~x1+x2, mydata=testdata, sub=expression(SEX==0))
I get:
Error in [.data.frame(structure(list(N_ASTHMA = as.integer(c(0, 0, 0,
:
invalid subscript type
I get a different error: it may be that you have an object called `subs`
in the global environment
I'm guessing that it's looking in the global environment for
subs,
More precisely, it is looking in environment where `formula` was created,
which happens to be the global environment.
This is the sort of thing that happens with the fitting functions because
they go to such lengths to break the basic scoping of R.
You probably have to substitute() the evaluated subset into the glm call.
fit.glm - eval(substitute(glm(formula=formula, data=mydata,
family=binomial, subset=subset),list(subset=subs)))
-thomas
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--
Andrew Robinson Ph: 208 885 7115
Department of Forest Resources Fa: 208 885 6226
University of Idaho E : [EMAIL PROTECTED]
PO Box 441133W : http://www.uidaho.edu/~andrewr
Moscow ID 83843 Or: http://www.biometrics.uidaho.edu
No statement above necessarily represents my employer's opinion.
__
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RE: [R] scree plot
I thought this would be simple enough and in some ways it is, but I don't have
an answer I would call easy
The manual process would be to use barplot instead of screeplot, so that you
could return the x values. The other choice would be to hack the screeplot
function to return the values. (see the end)
Then you need to get the y values. If you follow the example in screeplot
## The variances of the variables in the
## USArrests data vary by orders of magnitude, so scaling is appropriate
(pc.cr - princomp(USArrests, cor = TRUE)) # inappropriate
screeplot(pc.cr)
then you might use
pc.cr$sdev^2 * 0.9
My difficulty came when I looked at pc.cr$loadings. This uses the
print.loadings method to calulate the cumulative values
a very quick kludge gives me
cumvar - function (x, digits = 3, cutoff = 0.1, sort = FALSE, ...)
{
Lambda - unclass(x)
p - nrow(Lambda)
factors - ncol(Lambda)
if (sort) {
mx - max.col(abs(Lambda))
ind - cbind(1:p, mx)
mx[abs(Lambda[ind]) 0.5] - factors + 1
Lambda - Lambda[order(mx, 1:p), ]
}
cat(\nLoadings:\n)
fx - format(round(Lambda, digits))
names(fx) - NULL
nc - nchar(fx[1])
fx[abs(Lambda) cutoff] - paste(rep( , nc), collapse = )
vx - colSums(x^2)
varex - rbind(SS loadings = vx)
if (is.null(attr(x, covariance))) {
varex - rbind(varex, Proportion Var = vx/p)
if (factors 1)
varex - rbind(varex, Cumulative Var = cumsum(vx/p))
}
invisible(return(cumsum(vx/p)))
}
screeplot - function (x, npcs = min(10, length(x$sdev)), type = c(barplot,
lines), main = deparse(substitute(x)), ...)
{
main
type - match.arg(type)
pcs - x$sdev^2
xp - seq(length = npcs)
if (type == barplot)
tt - barplot(pcs[xp], names = names(pcs[xp]), main = main,
ylab = Variances, ...)
else {
plot(xp, pcs[xp], type = b, axes = FALSE, main = main,
xlab = , ylab = Variances, ...)
axis(2)
axis(1, at = xp, labels = names(pcs[xp]))
}
invisible(return(tt))
}
here - screeplot(pc.cr)
text(here,pc.cr$sdev^2 + 0.1,paste(cumvar(pc.cr$loadings)*100,%,sep =
),xpd=T)
-Original Message-
From: Anne [mailto:[EMAIL PROTECTED]
Sent: Wednesday, 5 January 2005 5:45 AM
To: R list
Subject: [R] scree plot
Hi!
Is there an easy way to add to the scree-plot labels to each
value pertaining to the cumulative proportion of explained variance?
Thanks and a happy new year
Anne
Anne Piotet
Tel: +41 79 359 83 32 (mobile)
Email: [EMAIL PROTECTED]
---
M-TD Modelling and Technology Development
PSE-C
CH-1015 Lausanne
Switzerland
Tel: +41 21 693 83 98
Fax: +41 21 646 41 33
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Re: [R] quantiles for geometric distribution
dax42 Dax42 at web.de writes: : : Dear list, : : I have got an array with observational values t and I would like to fit : a geometric distribution to it. : As I understand the geometric distribution, there is only one : parameter, the probability p. I estimated it by 1/mean(t). p=1/EX if the geometric distribution starts at 1 but in R the geometric distribution starts at 0. That is, in R the geometric distribution is the number of failures before a success, not the number of trials including the success. If X is a geometric random variable then EX = 0p + (EX+1)(1-p) and solving for EX gives 1/p-1. : : Now I plotted the estimated density function by : plot(ecdf(t),do.points=FALSE,col.h=blue); : : and I would like to add the geometric distribution. This should be : possibly with the function pgeom(). : : Unfortunately I do not understand what is meant by the argument q, : vector of quantiles representing the number of failures in a sequence : of Bernoulli trials before success occurs according to R help. : : I am familiar with quantiles, but why do I need them here? : Does anybody know what this means? What am I supposed to do? The quantiles are just the values of the geometric random variable. That is if you have a data vector x in which the ith element of x is the ith observation (where each observation is the number of failures before a success, viz. a non-negative integer) then dgeom(x, .2) would give a vector of density values assuming the probability of a success is .2 . __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] warnings and errors with R CMD INSTALL
On Wed, 5 Jan 2005, thomas wrote: Hello, Am Dienstag, den 04.01.2005, 23:25 + schrieb Prof Brian Ripley: On Tue, 4 Jan 2005, thomas wrote: I followed RNews 3/3 and used: 1. R CMD INSTALL package_version.tar.gz and 2.options(CRAN=http://umfragen.sowi.uni-mainz.de/CRAN/;) install.packages(pkg1. pkg2) Both approaches end up i.e.: WARNING: invalid package 'pkg1.tar.gz' ERROR: no packages specified But there is no package `pkg1' on CRAN. Try a real name like install.packages(tree) Well, of cause I didn't want install pkg1 or pkg2, the precise commandline was: 1. R CMD INSTALL epitools_0.3-3.tar.gz Have you downloaded the file first to the current directory? and 2. install.packages(accuracy, zoo, abind) The syntax is install.packages(c(accuracy, zoo, abind)) [I did suggest an example you could have tried, deliberately with one package. I don't get the error message you said you got from your line.] -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
