[R] R validation

2007-11-03 Thread delphine . fontaine
Dear R-Users,

A message to continue the discussions we had in March and June. I have
read the documents written since then
(http://www.r-project.org/doc/R-FDA.pdf ;
http://user2007.org/program/presentations/harrell.pdf ;
http://user2007.org/program/presentations/rossini.pdf ;
http://user2007.org/program/presentations/soukup.pdf) which are very
interesting and useful.

I work in a CRO and we strongly believe that R could be our standard
statistical tool for all our analyses. I agree that it is more relevant
(and easier) to validate an analysis than the whole software but anyway,
if we want to systematically use R, we must convince our top management
first and then our clients that R is reliable. Most of them do not know
the R environment and it is more that likely that we will be asked for any
validation documentation.

I am sure that the Core team has thoroughly tested “Base R” functions and
the recommended packages. Is it possible to have access to the scripts or
any documents that would attest that R gives reliable/validated results ?
All the discussions, documents mentioned above are a big step for the use
of R in the pharma/biotech environment but I also think that validation
documents or scripts are indispensable to convince our top management, our
clients and regulatory bodies.

If validation documentation or scripts do not exist or are not available,
could anyone tell me in concrete terms which are the minimum requirements
to validate R functions or packages ?

Thanks !

Delphine Fontaine

Delphine Fontaine
Statistician
Data  Statistics Department - Genexion SA

29, Quai du Mont-Blanc
Geneva, CH-1201
Switzerland

Office: +41 22 704 32 44
Fax:+41 22 704 32 42
Email: [EMAIL PROTECTED]

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Re: [R] how to split data.frame by row?

2007-11-03 Thread XU Denver
maybe you need this
q-matrix(1:60,20,3)
matrix(q,10,6)
matrix(q,5,12)





2007/10/29, Weiwei Shi [EMAIL PROTECTED]:
 hi,

 if I have 20 x 3 data.frame, how to split it into
 10 x 6 (moving the lower part of 10x3 to column)

 or

 5 x 12

 thanks

 --
 Weiwei Shi, Ph.D
 Research Scientist
 GeneGO, Inc.

 Did you always know?
 No, I did not. But I believed...
 ---Matrix III

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[R] cumsum

2007-11-03 Thread threshold

Hi, my problem belongs to the basic ones. I want to get cumulated sum over
the matrix columns by one command (if such exists). Ordinary R's cumsum(x)
when x is:
 [,1] [,2]
[1,]15
[2,]26
[3,]37
[4,]48

yields:  1  3  6 10 15 21 28 36
I want:
 [,1] [,2]
[1,]15
[2,]3   11
[3,]6   18
[4,]   10   26
Is there any command to do so??

best, robert



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Re: [R] cumsum

2007-11-03 Thread Sundar Dorai-Raj


threshold said the following on 11/3/2007 4:41 AM:
 Hi, my problem belongs to the basic ones. I want to get cumulated sum over
 the matrix columns by one command (if such exists). Ordinary R's cumsum(x)
 when x is:
  [,1] [,2]
 [1,]15
 [2,]26
 [3,]37
 [4,]48
 
 yields:  1  3  6 10 15 21 28 36
 I want:
  [,1] [,2]
 [1,]15
 [2,]3   11
 [3,]6   18
 [4,]   10   26
 Is there any command to do so??
 
 best, robert
 
 
 

Try

apply(x, 2, cumsum)

HTH,

--sundar

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[R] R validation. If you know what you want, it's simple. If you don't know what you need to do, there are problems...(with any validation)

2007-11-03 Thread A.J. Rossini
 From: [EMAIL PROTECTED]
 To: [EMAIL PROTECTED]
 Date: Sat, 3 Nov 2007 09:03:39 +0100 (CET)
 Subject: [R] R validation
 Dear R-Users,

 A message to continue the discussions we had in March and June. I have
 read the documents written since then
 (http://www.r-project.org/doc/R-FDA.pdf ;
 http://user2007.org/program/presentations/harrell.pdf ;
 http://user2007.org/program/presentations/rossini.pdf ;
 http://user2007.org/program/presentations/soukup.pdf) which are very
 interesting and useful.

 I work in a CRO and we strongly believe that R could be our standard
 statistical tool for all our analyses. I agree that it is more relevant
 (and easier) to validate an analysis than the whole software but anyway,
 if we want to systematically use R, we must convince our top management
 first and then our clients that R is reliable. Most of them do not know
 the R environment and it is more that likely that we will be asked for any
 validation documentation.

 I am sure that the Core team has thoroughly tested Base R functions and
 the recommended packages. Is it possible to have access to the scripts or
 any documents that would attest that R gives reliable/validated results ?
 All the discussions, documents mentioned above are a big step for the use
 of R in the pharma/biotech environment but I also think that validation
 documents or scripts are indispensable to convince our top management, our
 clients and regulatory bodies.

 If validation documentation or scripts do not exist or are not available,
 could anyone tell me in concrete terms which are the minimum requirements
 to validate R functions or packages ?

Please read again, you are missing something.

R comes with IQ if you build your own.

All other validation and qualification scripts will need to be
specified by the relevant concerned parties in your company.

i.e. to answer the questions, what do we require, what
specifications must be met, etc, for a relevant subset of things that
must be required and specs that must be met for this to meet your
needs.

Good practice is to establish your needs, and then verify that you've
met them.

Of course, you can outsource the whole thing, there are some very good
companies that can help with this, who can tell you what
specifications you want to meet, and what you will require.  In my
opinion, they might even be able to do it without going too wrong.

(disclaimer: I work for one of the largest pharmas as a pointy-headed
boss, and my group (not clin statistics, but in clinical development
and on the regulated side) will be using R and Linux for clinical work
as soon as we (well, I) finish some paperwork.   Of course, read
Dilbert if you think I'm making any sense...).

best,
-tony

[EMAIL PROTECTED]
Muttenz, Switzerland.
Commit early,commit often, and commit in a repository from which we
can easily roll-back your mistakes (AJR, 4Jan05).

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[R] Pearson residuals

2007-11-03 Thread Jorge Manuel de Almeida Magalhães
Dear Sirs

What is the best aproximation to the standardized normal distribution:

  necessidade = c(sem necessidade,com necessidade)
  tipo =c(CE-1, CE-2, CE-3)
  dados=c(20,34,44,69,9,3)
Tabela =cbind(expand.grid(list(Necessidade=necessidade, Tipo=tipo)), 
count=dados)
Tabela.array=tapply(Tabela$count, Tabela[,1:2], sum)
  ni = rowSums(Tabela.array)
  nj = colSums(Tabela.array)
n = sum(Tabela.array)
fit.glm=glm(count~Necessidade+Tipo, data=Tabela, family=poisson)


#
chisq.test(Tabela.array)

resid.pear=residuals(fit.glm, type=pearson) %%% This one? (no 
residuals are outside the range -1,96 to 1,96
###
resid.pear.mat=matrix(resid.pear, nc=3, byrow=F,dimnames=list(c(sem 
necessidade,com necessidade),c(CE-1, CE-2,CE-3)))
n*resid.pear.mat/sqrt(outer(n-ni,n-nj,*)) %%%  Or this one? 
(residuals are outside the range -1,96, 1,96)

Thanks

Jorge

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[R] Categorical data

2007-11-03 Thread batela
Dear Sirs

What is the best aproximation to the standardized normal distribution:

  necessidade = c(sem necessidade,com necessidade)
  tipo =c(CE-1, CE-2, CE-3)
  dados=c(20,34,44,69,9,3)
Tabela =cbind(expand.grid(list(Necessidade=necessidade, Tipo=tipo)), 
count=dados)
Tabela.array=tapply(Tabela$count, Tabela[,1:2], sum)
  ni = rowSums(Tabela.array)
  nj = colSums(Tabela.array)
n = sum(Tabela.array)
fit.glm=glm(count~Necessidade+Tipo, data=Tabela, family=poisson)


#
chisq.test(Tabela.array)

resid.pear=residuals(fit.glm, type=pearson) %%% This one? (no 
residuals are outside the range -1,96 to 1,96
###
resid.pear.mat=matrix(resid.pear, nc=3, byrow=F,dimnames=list(c(sem 
necessidade,com necessidade),c(CE-1, CE-2,CE-3)))
n*resid.pear.mat/sqrt(outer(n-ni,n-nj,*)) %%%  Or this one? 
(residuals are outside the range -1,96, 1,96)

Thanks

Jorge

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Re: [R] Pearson residuals

2007-11-03 Thread Ben Bolker



Jorge Manuel de Almeida Magalhães wrote:
 
 Dear Sirs
 
 What is the best aproximation to the standardized normal distribution:
 
 

 How about 

http://www.statsci.org/s/qres.html

(which gives S-PLUS code: haven't checked to see if it works in R
or not, but it looks like it probably will)

   My other question is how much you should expect to derive
strong conclusions from the residuals from this small a data set ...

   Ben Bolker
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[R] Job opening at Merck, NJ

2007-11-03 Thread Liaw, Andy
Apologies for the cross-posting...

Computational statisticians

The Biometrics Research Department at Merck Research Laboratories, Merck
 Co., Inc. in Rahway, NJ is seeking highly motivated statisticians/data
analysts (2 positions) to work in its basic research and drug discovery
area.  The applicant should have broad expertise in statistics and
computer science, with substantial experience in either medical imaging
analysis (1 position) or bio-signal analysis (1 position). For the
position in imaging analysis this includes image registration and
segmentation, fMRI, and advanced pattern recognition.  For the position
in bio-signal analysis this includes signal processing, time-series
analysis, and advanced pattern recognition. These positions will provide
statistical, mathematical, and software development support to Merck
scientists. Merck has its own facilities for CT, PET, MRI, and
ultrasound imaging as well EEG labs and numerous telemetry modalities.
We are looking for a Ph.D. in Statistics, Electrical/Computer or
Biomedical Engineering, Computer Science, Applied Mathematics, or
Physics.  Advanced computer programming skills (including, but not
limited to Matlab, C/C++, Visual Basic),  and good communication skills
are essential, as is familiarity with statistical software like R.
These positions may also involve general statistical consulting and
training.  An ability to lead statistical analysis efforts within a
multidisciplinary team is required. 

Our dedication to delivering quality medicines in innovative ways and
our commitment to bringing out the best in our people are just some of
the reasons why we're ranked among Fortune magazine's 100 Best
Companies to Work for in America.  We offer a competitive salary, an
oustanding benefits package, and a professional work environment with a
company known for scientific excellence.  To apply, please forward your
CV or resume and cover letter to

ATTENTION: Open Positions
Vladimir Svetnik, Ph.D.
Biometrics Research Dept.
Merck Research Laboratories, RY33-300 
126 E. Lincoln Avenue
Rahway, NJ 07065-0900
[EMAIL PROTECTED] 





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Re: [R] Pearson residuals

2007-11-03 Thread Jorge Manuel de Almeida Magalhães




 Jorge Manuel de Almeida Magalhães wrote:

 Dear Sirs

 What is the best aproximation to the standardized normal distribution:



  How about

 http://www.statsci.org/s/qres.html

 (which gives S-PLUS code: haven't checked to see if it works in R
 or not, but it looks like it probably will)

My other question is how much you should expect to derive
 strong conclusions from the residuals from this small a data set ...

You are reason. Such date is a example. The p-value ( 0.043518) it is 
inconsistency with the Pearson Residuals:
   CE-1  CE-2   CE-3
sem necessidade -0.4309469 0.3576286 -0.3069599
com necessidade  0.2547359 1.8561316 -1.5403424

We can compare them against standard normal critical values such as 
1.96. All residuals are in range -1,96, +1.96.

But, if I do

n*resid.pear.mat/sqrt(outer(n-ni,n-nj,*))

   CE-1   CE-2  CE-3
sem necessidade -0.6701451 -0.6569159  2.497185
com necessidade  0.6701451  0.6569159 -2.497185

I found that the group CE-3 is responsible by the lack of the 
independence model. This is consistency with the p-value.

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[R] mantel tests

2007-11-03 Thread Pickett, Simon
This is a general statistics question so I'm sorry if its outside the field of 
r help.
 
Anyway, I have a suite of female and male traits and I have made a matrix of 
correlation coefficients using rcorr(). This results in a 6 by 6 matrix like 
this..
 
[1] 0.11287990 0.20441361 0.23837442 0.04713234 0.04331637 0.01461611
 [7] 0.22627981 0.11720108 0.14252307 0.19531625 0.29989953 0.09989502
[13] 0.03888750 0.11157971 0.02693303 0.01373447 0.08913154 0.06770636
[19] 0.01984838 0.10047978 0.05200218 0.16317234 0.2663 0.10412373
[25] 0.06269722 0.14366454 0.13123054 0.27550149 0.43863848 0.28909831
[31] 0.01454485 0.02551081 0.05645427 0.15819397 0.16508231 0.12399349

I want to test 2 hypotheses
 
1) is there a pattern to the matrix, does it differ from random?
2) do the top left and bottom right quadrants differ from the other 2 quadrants 
and if so, which one has the highest values of r2.
 
I have read alot about permutation tests, bootstrapping and mantel tests but 
cant decide which is best in this situation? 
 
Could anyone please provide a starting point?
 
Thankyou in advance, Simon

[[alternative HTML version deleted]]

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[R] rank-deficient model matrix

2007-11-03 Thread colorful1017
Dear:
  I want to construct a gee model in R. When I ran the program, there was a 
warning in the output.
The warning is Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27
   gee(cbind(hyper, nohyper) ~ I(Ethnic) + I(Gender) + 
I(drink) +  : 
   rank-deficient model matrix
What is the rank-deficient model matrix? What should I do to solve the problem?
Thanks all.
  Lian


  
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[R] are there any R-help list in spanish.

2007-11-03 Thread Horacio Castellini
Hi all, I have a question, are there any R-help list in spanish or
forus, and which is its subscribe adress ...?

Thanks Horacio.

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Re: [R] Pearson residuals

2007-11-03 Thread Henric Nilsson (Public)
Jorge Manuel de Almeida Magalhães wrote:


 Jorge Manuel de Almeida Magalhães wrote:
 Dear Sirs

 What is the best aproximation to the standardized normal distribution:


  How about

 http://www.statsci.org/s/qres.html

 (which gives S-PLUS code: haven't checked to see if it works in R
 or not, but it looks like it probably will)

Code for randomized quantile residuals do exist for R as part of Gordon 
Smyth's `statmod' package. See `?qresiduals'.


HTH,
Henric




My other question is how much you should expect to derive
 strong conclusions from the residuals from this small a data set ...
 
 You are reason. Such date is a example. The p-value ( 0.043518) it is 
 inconsistency with the Pearson Residuals:
CE-1  CE-2   CE-3
 sem necessidade -0.4309469 0.3576286 -0.3069599
 com necessidade  0.2547359 1.8561316 -1.5403424
 
 We can compare them against standard normal critical values such as 
 1.96. All residuals are in range -1,96, +1.96.
 
 But, if I do
 
 n*resid.pear.mat/sqrt(outer(n-ni,n-nj,*))
 
CE-1   CE-2  CE-3
 sem necessidade -0.6701451 -0.6569159  2.497185
 com necessidade  0.6701451  0.6569159 -2.497185
 
 I found that the group CE-3 is responsible by the lack of the 
 independence model. This is consistency with the p-value.
 
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[R] installing packages on OS X -- lgfortran problem

2007-11-03 Thread Stefanie Hartmann


I am trying to install two packages that are not available at CRAN  
(rmutil, dna). When trying the R CMD INSTALL with either file, I get  
an error message that ends with

/usr/libexec/gcc/i686-apple-darwin8/4.0.1/libtool: can't locate file  
for: -lgfortran
/usr/libexec/gcc/i686-apple-darwin8/4.0.1/libtool: file: -lgfortran  
is not an object file (not allowed in a library)

Can anyone please help?
I have R 2.6 on a Macbook running 10.4.10. I have installed XCode 2.5.

A complete error message is given below.

Thank you!

Stefanie



* Installing to library '/Library/Frameworks/R.framework/Resources/ 
library'
* Installing *source* package 'rmutil' ...
** libs
** arch - i386
gcc-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk - 
std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/ 
include -I/Library/Frameworks/R.framework/Resources/include/i386  - 
msse3-fPIC  -g -O2 -march=nocona -c cutil.c -o cutil.o
gcc-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk - 
std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/ 
include -I/Library/Frameworks/R.framework/Resources/include/i386  - 
msse3-fPIC  -g -O2 -march=nocona -c dist.c -o dist.o
gfortran-4.0 -arch i386  -isysroot /Developer/SDKs/MacOSX10.4u.sdk   - 
fPIC  -g -O2 -march=nocona -c gettvc.f -o gettvc.o
gcc-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk - 
std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/ 
include -I/Library/Frameworks/R.framework/Resources/include/i386  - 
msse3-fPIC  -g -O2 -march=nocona -c romberg.c -o romberg.o
gcc-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk - 
std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/ 
include -I/Library/Frameworks/R.framework/Resources/include/i386  - 
msse3-fPIC  -g -O2 -march=nocona -c toms614.c -o toms614.o
gcc-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk - 
std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -Wl,- 
macosx_version_min -Wl,10.3 -undefined dynamic_lookup -single_module - 
multiply_defined suppress -o rmutil.so cutil.o dist.o gettvc.o  
romberg.o toms614.o -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.1 - 
lgfortran -lgcc_s.10.4
/usr/libexec/gcc/i686-apple-darwin8/4.0.1/libtool: can't locate file  
for: -lgfortran
/usr/libexec/gcc/i686-apple-darwin8/4.0.1/libtool: file: -lgfortran  
is not an object file (not allowed in a library)
make: *** [rmutil.so] Error 1
ERROR: compilation failed for package 'rmutil'
** Removing '/Library/Frameworks/R.framework/Versions/2.6/Resources/ 
library/rmutil'

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[R] R CMD SHLIB gives error: bad value (generic) for -mtune= switch

2007-11-03 Thread McKay Curtis
Hello,

I am trying to compile C code using the R CMD SHLIB command.  I get this error:

 R CMD SHLIB gibbs.c
making gibbs.d from gibbs.c
gibbs.c:0: error: bad value (generic) for -mtune= switch
make: [gibbs.d] Error 1 (ignored)
cat: gibbs.d: No such file or directory
make: [makeMakedeps] Error 1 (ignored)
gcc-sjlj  -std=gnu99  -IC:/PROGRA~1/R/R-26~1.0/include-Wall -O3
-c gibbs.c -o gibbs.o
gibbs.c:1: error: bad value (generic) for -mtune= switch
make: *** [gibbs.o] Error 1


where gibbs.c contains

#include R.h
#include Rmath.h
#include gibbsiso.h

void gibbsiso(int *nmc){
  Rprintf(Hello!);
  }

and gibbsiso.h contains

void gibbsiso(int *);


I have installed or am using the following

* Rtools.exe 2.6.0
* R version 2.6.0 (2007-10-03)
* Windows Vista
* Toshiba Laptop, Intel Centrino Duo, T2250 @1.73 GHz w/ 1GB of RAM

My path variable is
c:\Rtools\bin;c:\Rtools\perl\bin;c:\Rtools\MinGW\bin;c:\Rtools\MinGW\libexec\gcc\mingw32\3.4.5;C:\Program
Files\MiKTeX 
2.5\miktex\bin;C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Program
Files\Common Files\Ulead Systems\MPEG;C:\Program
Files\R\R-26~1.0;C:\Program Files\R\R-26~1.0\bin;C:\Program
Files\gs\gs8.54\bin;

I would appreciate any insight into this error.

Thanks for your time!
McKay Curtis
(Stats grad student at NCSU)

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and provide commented, minimal, self-contained, reproducible code.


Re: [R] unable to install package ff

2007-11-03 Thread Adrian Dragulescu
Matthew,

Did you take a look at the R.huge package?  It works well with numerical
data.

If you describe the problem you're trying to solve in more detail, it may
help us give you a better solution.

Btw, we use the filehash package with great success in accessing very large
amounts of data.

Best,
Adrian Dragulescu


On 11/1/07, Matthew Keller [EMAIL PROTECTED] wrote:

 Hi all,

 I've had one of my most miserable R weeks in memory. I'm trying to
 deal with huge datasets (1GB each) but am running up against those
 pesky memory limits. The libraries filehash and g.data are not very
 suitable for what I need. I haven't gotten into the sql thing yet.
 Most recently I've been trying to install the new package ff (not yet
 on the CRAN repository). I can't find emails of the folks developing
 ff, so I was hoping someone here might have an idea how to deal with
 this.

 From http://wsopuppenkiste.wiso.uni-goettingen.de/ff/ I've downloaded
 the ff_1.0.tar.gz.

  install.packages
 (pkgs=ff_1.0.tar.gz,repos=NULL,destdir=/temp,type=source)
 much output omitted
 g++-4.0: installation problem, cannot exec
 'i686-apple-darwin8-g++-4.0.0': No such file or directory
 make: *** [Error.o] Error 255
 chmod:
 /Library/Frameworks/R.framework/Versions/2.5/Resources/library/ff/libs/i386/*:
 No such file or directory
 ERROR: compilation failed for package 'ff'

 So it cannot find i686-apple-darwin8-g++-4.0.0. What the hell is that?
 A compiler I suppose. I HAVE installed the Mac OS developer tools. I
 have an MacBook Pro with 4GB RAM and am using the 32bit R:

 sessionInfo()
 R version 2.5.1 (2007-06-27)
 i386-apple-darwin8.9.1

 locale:
 en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

 attached base packages:
 [1] stats graphics  grDevices utils datasets
 methods   base


 Any ideas how to get ff to install properly on my system? Most
 appreciative of any advice!

 Matt


 --
 Matthew C Keller
 Asst. Professor of Psychology
 University of Colorado at Boulder
 www.matthewckeller.com

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[R] install problem 2.6 mac os x 10.5

2007-11-03 Thread Emilio Gagliardi
Hi everyone,

I am trying to install R-2.6 over my 2.5.1 installation on Mac OS X  
10.5.

R version 2.5.1 (2007-06-27)

I double-click the installer package,
1) Click Continue
2) Click Continue
3) Click Continue + Click Agree

On the Installation Type dialog screen, all four options are grayed  
out, with skip beside them.  The Install button is also grayed out.   
If I click the Standard Install button, it allows me to change the  
directory to install onto, but then brings me back to the same screen.

So I can't install.  If I click any one the four options [R Framework,  
R GUI, etc] the message says There is a more recent version of this  
software installed on your system.  There is no need to install this  
older version.

What am I missing here?

Thanks for your help.

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[R] structure vs. matrix

2007-11-03 Thread Edna Bell
Hi R Gurus!

When creating a matrix, is it better to use the structure function or
the matrix function, please?

Thanks,
Edna Bell

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