[R] bayesm, rmnlIndepMetrop
Hi,
I tried to use rmnlIndepMetrop (bayesm package) for my MNL model with 4
choice alternatives, 5 independent variables, 69 observations,
dim(X) [1] 276 5, nu=6. So I run such code:
if(nchar(Sys.getenv(LONG_TEST)) != 0) {R=2000} else {R=10}
set.seed(66)
df=read.table(X_metrop.dat,header=TRUE)
inp=as.matrix(df)
y=as.numeric(inp[,1])
n=length(y)
p=4
nvar=ncol(X)
X=cbind(1,inp[,2:5])
XTXI=chol2inv(chol(crossprod(X)))
bhat=XTXI%*%t(X)%*%y
#create X matrix with dim nobs*p x nvar
index=1:n
index2=rep(index,p)
index3=sort(index2)
X=X[index3,]
beta=array(bhat,dim=c(nvar))
A=diag(c(rep(.01,length(beta;
betabar=rep(0,length(beta))
Data=list(y=y,X=X,p=p);
Mcmc=list(R=R,keep=1) ;
Prior=list(A=A,betabar=betabar)
out=rmnlIndepMetrop(Data=Data,Prior=Prior,Mcmc=Mcmc)
Ouput:
Starting Independence Metropolis Sampler for Multinomial Logit Model
with 4 alternatives
Prior Parms:
betabar
[1] 0 0 0 0 0
A
[,1] [,2] [,3] [,4] [,5]
[1,] 0.01 0.00 0.00 0.00 0.00
[2,] 0.00 0.01 0.00 0.00 0.00
[3,] 0.00 0.00 0.01 0.00 0.00
[4,] 0.00 0.00 0.00 0.01 0.00
[5,] 0.00 0.00 0.00 0.00 0.01
MCMC parms:
R= 10 keep= 1 nu (df for st candidates) = 6
Mistake in chol(mhess) : the leading Minor of the order 1 is not positive
defined
By debugging: debug(rmnlIndepMetrop)
rmnlIndepMetrop(Data=Data,Prior=Prior,Mcmc=Mcmc)
beta
[1] 1.46867390 -0.52889086 0.23710427 0.00188178 0.06021696
mhess=mnlHess(y,X,beta)
mhess
X0 X0.1 X0.2 X0.3
0 0000
X0 0 0000
X0.1 0 0000
X0.2 0 0000
X0.3 0 0000
chol(mhess)
Mistake in chol(mhess) : the leading Minor of the order 1 is not positive
defined
Is something wrong with my data? But I tried another dataset and got the
same mistake.
Whether everybody knows how I could manage it?
I have no ideas anymore(.
Thank you in advance,
Tatjana
---
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Department of Electronic Commerce
Johann Wolfgang Goethe-University
Mertonstrasse 17
D-60054, Frankfurt/Main
Germany
phone: +49 069 798 22380
http://www.ecommerce.wiwi.uni-frankfurt.de
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Re: [R] difference between rnorm(1000, 0, 1) and running rnorm(500, 0, 1) twice
Le 08.02.2006 04:21, Taka Matzmoto a écrit : Hi R users This looks a simple question Is there any difference between between rnorm(1000,0,1) and running rnorm(500,0,1) twice in terms of outcome ? TM Not here : R set.seed(1) R x - rnorm(1000, 0, 1) R set.seed(1) R y - rnorm(500, 0, 1) R z - rnorm(500, 0, 1) R all(x == c(y,z)) [1] TRUE Romain -- visit the R Graph Gallery : http://addictedtor.free.fr/graphiques mixmod 1.7 is released : http://www-math.univ-fcomte.fr/mixmod/index.php +---+ | Romain FRANCOIS - http://francoisromain.free.fr | | Doctorant INRIA Futurs / EDF | +---+ __ 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] ARULES -- Filtering Rules by RHS
Dear Colleagues,
I would like to only inspect rules that contain a certain label substring on
the rhs. In this special case the item labels are built like this:
itemtype_itemvalue e.g. Artikelgruppe_E0815 what I want to do is only
show rules where Artikelgruppe is contained in the rhs - has anybody an idea
how this could work?
Sincerely
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Re: [R] difference between rnorm(1000, 0, 1) and running rnorm(500, 0, 1) twice
Romain Francois wrote: Le 08.02.2006 04:21, Taka Matzmoto a écrit : Hi R users This looks a simple question Is there any difference between between rnorm(1000,0,1) and running rnorm(500,0,1) twice in terms of outcome ? TM Not here : R set.seed(1) R x - rnorm(1000, 0, 1) R set.seed(1) R y - rnorm(500, 0, 1) R z - rnorm(500, 0, 1) R all(x == c(y,z)) [1] TRUE Romain Indeed! The pseudo-random number generator is initialized at the same state, and thus, returns the same 1000 pseudo-random numbers in both cases. So, no differences. Best, Philippe Grosjean __ 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] Graphics Package -- stars()
Dear Collegues,
does anybody know how I can place a legend at a sensible position in a star
diagram automatically? The legend should tell the name of the variable (from
colnames) for every color used.
Sincerely, Markus
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Consultant
Client Vela GmbH
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81369 München
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[R] How to install the server version of rpad
Hi, How can I install the server version of rpad on a website. I have read the instructions in http://www.rpad.org/Rpad/ServerNotes.html, but could not figure out how. Do I have to have something like Apache on the website? Is there any instructions in addition to those on http://www.rpad.org/Rpad/. Thanks, - Reza __ 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] lme help
Hi list, I am fitting microarray data (intensity) model using the lme package in R environment. I have 5 fixed variables in the model. One of the fixed variables is genes. I am trying to get p-values for different genes. But I am getting only one p-value for all genes together. I can get a list of p-value when I run lm. Why can't this work in lme? My aim is to do multiple comaprison of all the genes that I have and I can only do this if I have a list of their p-vales I was wondering if you can help me solve this problem. That is getting a list of p-value for each gene in the model using the lme. Thanks in advance for your help Regards Mahdi -- --- Mahdi Osman (PhD) 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
Re: [R] difference between rnorm(1000, 0, 1) and running rnorm(500, 0, 1) twice
Why don't you test it yourself? E.g., set.seed(42) bob1 - rnorm(1000,0,1) set.seed(42) bob2 - rnorm(500,0,1) bob3 - rnorm(500,0,1) identical(bob1, c(bob2, bob3)) I won't tell you the answer. :-) -- Bjørn-Helge Mevik __ 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] problem with maptree
Hello, I'm trying to draw a simplified tree of a cluster object with maptree, but I get an error message: class(vars.agn) [1] agnes twins draw.clust (clip.clust (vars.agn, k=5)) Error in names-.default(`*tmp*`, value = c(merge, height, order,'names' attribute [8] must be the same length as the vector [7] Trying converting first to object of class hclust: draw.clust (clip.clust (as.hclust(vars.agn), k=5)) Error in split(x, f) : first argument must be a vector But conversion seems to work fine: vars.hclust=as.hclust(vars.agn) vars.hclust Call: agnes(x = daisy(vars.cluster), diss = TRUE, method = ward) Cluster method : ward Number of objects: 295 draw.clust (clip.clust (vars.hclust, k=5)) Error in split(x, f) : first argument must be a vector A previous version of maptree successfully clipped the three from the same data. Any orientation will be greatly appreciated. Thank you in advance. -- Héctor Villalobos [EMAIL PROTECTED] IPN-CICIMAR. A.P. 592. Col. Centro La Paz, Baja California Sur, MÉXICO. 23000 __ 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] Bloomberg Data Import to R
Hi R-Experts,
Can anyone tell me how Bloomberg data can be directly downloaded to R?
Is there any package?
Sumanta Basak.
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[R] rotating axis / mtext labels
Hello list. Is it possible to use par(srt=45) to rotate text by 45 degrees along the x-axis of a plot. Using: code x_names-c(C57 Nv, C57 Vacc, 129 Nv, 129 Vacc, IFNgR Nv, IFNgR Vacc) par(srt=45) mtext(font=2, x_names, side=1, line=1, at=l, cex=1.2) par(srt=0) /code doesn't seem to work in R 2.2.0 on SUSE linux. Suggestions would be appreciated thanks. Iain __ 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] Reference for R
Hello! Could anyone please tell me how should I include R in a text section for References? Regards, Sara Mouro [[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
Re: [R] Reference for R
citation() 2006/2/8, Sara Mouro [EMAIL PROTECTED]: Hello! Could anyone please tell me how should I include R in a text section for References? Regards, Sara Mouro [[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 -- Johan Sandblom N8, MRC, Karolinska sjh t +46851776108 17176 Stockholm m +46735521477 Sweden What is wanted is not the will to believe, but the will to find out, which is the exact opposite - Bertrand Russell __ 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] Reference for R
Hi Sara.
From the R faq here:
http://cran.r-project.org/doc/FAQ/R-FAQ.html#Citing-R
2.8 Citing R
To cite R in publications, use
@Manual{,
title= {R: A Language and Environment
for Statistical
Computing},
author = {{R Development Core Team}},
organization = {R Foundation for Statistical
Computing},
address = {Vienna, Austria},
year = 2005,
note = {{ISBN} 3-900051-07-0},
url = {http://www.R-project.org}
}
Citation strings (or BibTeX entries) for R and R
packages can also be obtained by citation().
Cheers
Iain
--- Sara Mouro [EMAIL PROTECTED] wrote:
Hello!
Could anyone please tell me how should I include R
in a text section for
References?
Regards,
Sara Mouro
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[R] large lines of data
Dear All, I have to enter many lines of data in the same object. I usually use copy-paste to transfer data from an Word file to R. But, for large lines of data, R gets confused and gives an error message, i.e. it breaks one line somewhere, and lines get no meaning at all. Some times I solve that problem adding enters and making each line shorter, before I do copy-paste. Some times I add spaces in the word document, until R breaks each line (automatically adds a +) in any point where it still correct.. But it stills too subjective for me! :o\ What is the best way to do that? Regards, Sara Mouro [[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
Re: [R] large lines of data
Sara Mouro wrote: Dear All, I have to enter many lines of data in the same object. I usually use copy-paste to transfer data from an Word file to R. What is the best way to do that? Use 'Save As' to save your Word file - or rather just the data section - as a plain text or Ascii file. Then read into R with scan() or read.table() as appropriate. Barry __ 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] large lines of data
On 2/8/06 6:55 AM, Sara Mouro [EMAIL PROTECTED] wrote: Dear All, I have to enter many lines of data in the same object. I usually use copy-paste to transfer data from an Word file to R. But, for large lines of data, R gets confused and gives an error message, i.e. it breaks one line somewhere, and lines get no meaning at all. Some times I solve that problem adding enters and making each line shorter, before I do copy-paste. Some times I add spaces in the word document, until R breaks each line (automatically adds a +) in any point where it still correct.. But it stills too subjective for me! :o\ What is the best way to do that? I assume you mean that you are editing code and then pasting into R. If so, you might look into using one of several editors that work with R. Look in the mail archives for some of these. Sean __ 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] (second round) creating a certain type of matrix
I cleaned up your function a bit but please double check
generate.matrix - function(nr, runs=5){
h - nr/2## half of nr
nc - nr/10 + 1
mat - matrix(0, nr, nc) ## initialize
mat[ ,1] - c( rep(1, h), rnorm(h) ) ## 1st column
mat[ (h+1):(h+5), 2] - rnorm(5) ## 2nd column
if( nc 3 ){
for (i in 3:nc){ ## column 3 - end
start - h + 5*(i-2) + 1
end - start + runs - 1
mat[ start:end, i] - rnorm( runs )
}
}
return(mat)
}
However you can simplify this greatly. If you ignore the first column
(which looks like some initialisation column in simulation process),
then you have a matrix with nr/2 rows and nr/10 columns with diagonal
blocks 5 runs filled with rnorm values. Here is what I propose :
gen.mat - function(x, runs=5){
if( (x %% 2*runs)!=0 ) stop(x, is not a multiple of , 2*runs)
nr - x/2
nc - x/(2*runs)
mat - matrix(0, nr, nc)
for (i in 1:nc) mat[ ((i-1)*runs + 1) : (i*runs), i ] - rnorm(runs)
down - cbind( rnorm(nr), mat )
top - cbind( 1, matrix( 0, nr=nr, nc=nc ) )
out - rbind( top, down )
return(out)
}
# Examples
gen.mat(50)
gen.mat(55) ## should generate an error
gen.mat(24, runs=6)
Does this function do what you want to ?
Regards, Adai
On Tue, 2006-02-07 at 11:03 -0600, Taka Matzmoto wrote:
Hi R users
Here is what I got with help from Petr Pikal (Thanks Petr Pikal). I modified
Petr Pikal's code to a little
to meet my purpose.
I created a function to generate a matrix
generate.matrix-function(n.variable)
{
mat-matrix(0,n.variable,(n.variable/2)/5+1) #matrix of zeroes
dd-dim(mat) # actual dimensions
mat[1:(dd[1]/2),1]-1 #put 1 in first half of first column
mat[((dd[1]/2)+1):dd[1],1]-rnorm(dd[1]/2,0,1) #put random numbers in
following part of the matrix column 1
mat[((dd[1]/2)+1):((dd[1]/2)+5),2]-rnorm(5,0,1) #put random numbers in
column2
for (i in 3:(dd[2]))
{
length.of.rand.numbers - 5
my.rand.num- rnorm(length.of.rand.numbers, 0,1)
start - dd[1]/2+5*(i-2)+1
end - start + length.of.rand.numbers-1
mat[((start):end), i]- my.rand.num
}
mat
}
Do you (any R users) have any suggestion to this function to make this
function work better or efficiently?
Taka
It works but I
From: Petr Pikal [EMAIL PROTECTED]
To: Taka Matzmoto [EMAIL PROTECTED],r-help@stat.math.ethz.ch
Subject: Re: [R] creating a certain type of matrix
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Hi
as only you know perfectly which halves and other portions of your
matrices contain zeroes and which contain random numbers you has to
finalize the function yourself.
Here are few ideas.
n-20
mat-matrix(0,n,(n/2)/5+1) #matrix of zeroes
dd-dim(mat) # actual dimensions
mat[1:(dd[1]/2),1]-1 #put 1 in first half of first column
mat[((dd[1]/2)+1):dd[1],1]-rnorm(dd[1]/2,0,1) #put random numbers in
following part of the matrix column 1
mat[((dd[1]/2)+1):(dd[1]/2)+dd[1]/4,2]-rnorm(dd[1]/4,0,1) #put
random numbers in column2
than according to n and dd values you can put any numbers anywhere in
your matrix e.g. in for loop (not.tested :-)
for (i in 3:dd[2]) {
arrange everything into following desired columns
e.g.
length.of.rand.numbers - (i-2)*5
my.rand.num-
Re: [R] large lines of data
How does the data look and how are you storing in R (e.g. matrix, list)? I think this an issue related to Word where it is using either unequal spaces or different carriage returns. I would not recommend storing data, especially numerical ones in the form of a matrix, in Word files. I would recommend that you try to copy-and-paste into Excel first and clean it up there. Next save the file as tab delimited and use read.delim() in R. My experience is that that Excel seems understands the oddities of Word better than R does. Regards, Adai On Wed, 2006-02-08 at 11:55 +, Sara Mouro wrote: Dear All, I have to enter many lines of data in the same object. I usually use copy-paste to transfer data from an Word file to R. But, for large lines of data, R gets confused and gives an error message, i.e. it breaks one line somewhere, and lines get no meaning at all. Some times I solve that problem adding enters and making each line shorter, before I do copy-paste. Some times I add spaces in the word document, until R breaks each line (automatically adds a +) in any point where it still correct.. But it stills too subjective for me! :o\ What is the best way to do that? Regards, Sara Mouro [[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] rotating axis / mtext labels
Iain Gallagher wrote: Hello list. Is it possible to use par(srt=45) to rotate text by 45 degrees along the x-axis of a plot. Using: code x_names-c(C57 Nv, C57 Vacc, 129 Nv, 129 Vacc, IFNgR Nv, IFNgR Vacc) par(srt=45) mtext(font=2, x_names, side=1, line=1, at=l, cex=1.2) par(srt=0) /code doesn't seem to work in R 2.2.0 on SUSE linux. Suggestions would be appreciated thanks. mtext does not support string rotation. You can rather use text() with par(xpd=TRUE) if you need it. Uwe Ligges Iain __ 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] lme help
Please read the posting 1) I think BioConductor mailing list might be better as some of these could be implemented via LIMMA (I believe) 2) Provide sufficient information and perhaps a simple example. Regards, Adai On Wed, 2006-02-08 at 10:42 +0100, Mahdi Osman wrote: Hi list, I am fitting microarray data (intensity) model using the lme package in R environment. I have 5 fixed variables in the model. One of the fixed variables is genes. I am trying to get p-values for different genes. But I am getting only one p-value for all genes together. I can get a list of p-value when I run lm. Why can't this work in lme? My aim is to do multiple comaprison of all the genes that I have and I can only do this if I have a list of their p-vales I was wondering if you can help me solve this problem. That is getting a list of p-value for each gene in the model using the lme. Thanks in advance for your help Regards Mahdi __ 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] Mixture normal distribution
Dear R helper, I hope that u can help me to sort out my problem because I sent an E-mail last night to R-list but I have not receive any help and at the same time I think this problem is not so hard. I have used the following functions before K-10 prime-c(2,3,5,7,11,13,17) UN-seq(1:K)%*%t(sqrt(prime)) U1-UN-as.integer(UN) U-matrix(qnorm(U1),K,7) U [,1][,2][,3][,4] [,5] [,6] [1,] -0.2167193 0.61902728 -0.71900806 0.37387492 -0.47715805 0.2677426 [2,] 0.9479680 -0.09010569 -0.06990169 -0.54900030 0.34047235 -0.8026015 [3,] -0.6978334 -0.85544499 0.54814530 1.53212280 1.64363675 0.9026864 [4,] 0.4038929 1.46253909 1.59168198 0.20958766 -0.62343558 -0.1962555 [5,] -1.4678844 0.41315654 -0.91407055 -0.74294809 0.20989183 -1.9148412 [6,] -0.0369025 -0.27331681 -0.21109168 1.14796196 1.28012119 0.3406266 [7,] 1.2786790 -1.15348516 0.39201340 0.05080407 -0.78449952 -0.7099779 [8,] -0.4853656 1.06431267 1.21882042 -0.97005119 0.08280907 1.0127500 [9,] 0.6065405 0.22357828 -1.15223725 0.88440727 1.03481830 -0.1257587 [10,] -1.0707736 -0.46627852 -0.35664238 -0.10670096 -0.96909898 -1.5936006 [,7] [1,] -1.15960110 [2,] -0.68646092 [3,] -0.33366316 [4,] -0.01899511 [5,] 0.29375681 [6,] 0.63913903 [7,] 1.08816734 [8,] 2.16601566 [9,] -1.23750068 [10,] -0.73537275 Now I want instead of using (qnorm) the inverse of slandered normal distribution, I want to use the mixture of normal distribution, and also, I want to know how to read the data to txt file. Many thanks for your help in advance. Al-Eid ___ Win a BlackBerry device from O2 with Yahoo!. Enter now. http://www.yahoo.co.uk/blackberry __ 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] Application of R
No Excel attachment came through. Just taking a guess here but there seems to be very little variation the columns V10 till column V23. BTW, can you not issue the following call : mydata[ , 1:7] ~ mydata[ , 8] + mydata[ ,9] instead of creating y1, y2, ... separately then cbind-ing them ? Regards, Adai On Tue, 2006-02-07 at 21:52 +0800, Andy Wong wrote: I have applied the R and MNP to carry out the data analysis. However, there is an error called SWP : singular matrix. Can someone tell me what is the problem of my formula or the file mydata. I have attached the data file mydata in Excel format and the result printed in pdf format for your information. Thanks for your advice. __ 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] difference between rnorm(1000, 0, 1) and running rnorm(500, 0, 1) twice
On 2/8/2006 4:53 AM, Bjørn-Helge Mevik wrote: Why don't you test it yourself? E.g., set.seed(42) bob1 - rnorm(1000,0,1) set.seed(42) bob2 - rnorm(500,0,1) bob3 - rnorm(500,0,1) identical(bob1, c(bob2, bob3)) I won't tell you the answer. :-) This isn't really something that can be proved by a test. Perhaps the current implementation makes those equal only because 500 is even, or divisible by 5, or whatever... I think the intention is that those should be equal, but in a quick search I've been unable to find a documented guarantee of that. So I would take a defensive stance and assume that there may be conditions where c(rnorm(m), rnorm(n)) is not equal to rnorm(m+n). If someone can point out the document I missed, I'd appreciate it. Duncan Murdoch __ 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 install the server version of rpad
Reza, Yes, you will need Apache and Perl already installed, then follow the install notes you linked to above. I tried for a long time to get it to work with Microsoft IIS and could not for the life of me, but when I tried it with Apache 2.0 it worked pretty easily. I have never set up a web server before either, so I was pretty confused. Just install Apache and Perl and following the instructions, then set permissions on all the Rpad and perl files so they can be ran by everyone. If it doesn't work, just keep playing with the configuation file until it does. Thanks, Roger On 2/8/06, Seyed Reza Jafarzadeh [EMAIL PROTECTED] wrote: Hi, How can I install the server version of rpad on a website. I have read the instructions in http://www.rpad.org/Rpad/ServerNotes.html, but could not figure out how. Do I have to have something like Apache on the website? Is there any instructions in addition to those on http://www.rpad.org/Rpad/. Thanks, - Reza __ 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 [[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
Re: [R] lme syntax for PB examples
Paul: It is a little difficult to understand what you are trying to translate since you do not show what the model would look like using lme. If you show lme, then it is easy to translate into lmer syntax. A few thoughts, first, use lmer in the Matrix package and not in lme4. Second, see the Bates article in R news at the link below for dealing with nesting structures. Last, a colleague and I have a paper in press showing how to fit models using lme which we submitted a year or so ago. Since lme has evolved to lmer, we created an appendix that translates all of our lme models to the lmer syntax so readers can see equivalences. I am happy to send this to you (or others) upon request. http://cran.r-project.org/doc/Rnews/Rnews_2005-1.pdf Harold -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Paul Cossens Sent: Wednesday, February 08, 2006 12:08 AM To: r-help@stat.math.ethz.ch Subject: [R] lme syntax for PB examples Hi helpeRs, I've been working through some examples in Pinhiero Bates( 2000) trying to understand how to translate to the new Lme4 syntax but without much luck. Below is what I think I should do, but either the answers don't come out the same or I get errors. In the Oxide problems I'm particularly interested in obtaining the levels coeficients but this options no longer seems to be available in lme4. How can levels infor be obtained in lme4? If someone can recreate the examples below in lme4 syntax so I can follow what is happening in the text I'd be grateful. Cheers Paul Cossens #Pixel # PB(2000) p40-45 Pixel-read.csv(Pixel.csv,header=TRUE); Pixel$Side-as.factor(Pixel$Side) Pixel$Dog-as.factor(Pixel$Dog) (fm1Pixel - lmer(pixel ~ day + I(day^2) +(day|Dog)+(1|Side), data = Pixel)) (fm2Pixel - lmer(pixel ~ day + I(day^2) +(day|Dog), data = Pixel)) (fm3Pixel - lmer(pixel ~ day + I(day^2) +(1|Dog:Side), data = Pixel)) or should I do it this way? Pixel$DS-with(Pixel,Dog:Side)[drop=TRUE] (fm3Pixel - lmer(pixel ~ day + I(day^2) +(1|DS), data = Pixel)) (fm4Pixel - lmer(pixel ~ day + I(day^2) +Side , data = Pixel)) #Oxide # PB(2000) p167-170 Oxide-read.csv(Oxide.csv,header=TRUE); Oxide$Source-as.factor(Oxide$Source) Oxide$Lot-as.factor(Oxide$Lot) Oxide$Wafer-as.factor(Oxide$Wafer) Oxide$Site-as.factor(Oxide$Site) fm1Oxide-lmer(Thickness~ (1|Lot)+(1|Lot:Wafer),data=Oxide) ) (fm2Oxide-lmer(Thickness~ (1|Lot),data=Oxide) ) coef(fm1Oxide) [[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] Bloomberg Data Import to R
Hello Sumanto,
your question might be more appropriately been posted to the R-sig-finance
list:
[EMAIL PROTECTED] (I have cc'ed this mail to this list).
To my knowledge neither a function nor a CRAN-package does exist. However,
on the last useR! conference Dirk Edelbuettel presented a proprietary
package that utilised the C API of Bloomberg (type WAPI GO on a Bloomberg
terminal). I am not sure whether Dirk is nowadays inclined or allowed by his
employee to share this package.
As an alternative, you could download data from Bloomberg into Excel, first
(assuming that you are working in a Windows environment) and then load it
into R via RODBC, for example.
Cheers,
Bernhard
Hi R-Experts,
Can anyone tell me how Bloomberg data can be directly downloaded to R?
Is there any package?
Sumanta Basak.
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[R] nested random effects in glmm.admb
Hello all, In a previous posting regarding glmm.admb it is stated that glmm.admb can handle 2 nested random effects. I can only fit a single random term at the moment, and wondered if anyone could provide me with some information on how to specify a model with 2 (nested or cross-classified) random terms? Thanks, Jarrod. __ 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] rotating axis / mtext labels
On Wed, 2006-02-08 at 10:33 +, Iain Gallagher wrote: Hello list. Is it possible to use par(srt=45) to rotate text by 45 degrees along the x-axis of a plot. Using: code x_names-c(C57 Nv, C57 Vacc, 129 Nv, 129 Vacc, IFNgR Nv, IFNgR Vacc) par(srt=45) mtext(font=2, x_names, side=1, line=1, at=l, cex=1.2) par(srt=0) /code doesn't seem to work in R 2.2.0 on SUSE linux. Suggestions would be appreciated thanks. Iain See R FAQ 7.27 How can I create rotated axis labels: http://cran.r-project.org/doc/FAQ/R-FAQ.html#How-can-I-create-rotated-axis-labels_003f HTH, Marc Schwartz __ 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 rnorm(1000, 0, 1) and running rnorm(5
On 08-Feb-06 Duncan Murdoch wrote: On 2/8/2006 4:53 AM, Bjørn-Helge Mevik wrote: Why don't you test it yourself? E.g., set.seed(42) bob1 - rnorm(1000,0,1) set.seed(42) bob2 - rnorm(500,0,1) bob3 - rnorm(500,0,1) identical(bob1, c(bob2, bob3)) I won't tell you the answer. :-) This isn't really something that can be proved by a test. Perhaps the current implementation makes those equal only because 500 is even, or divisible by 5, or whatever... I think the intention is that those should be equal, but in a quick search I've been unable to find a documented guarantee of that. So I would take a defensive stance and assume that there may be conditions where c(rnorm(m), rnorm(n)) is not equal to rnorm(m+n). If someone can point out the document I missed, I'd appreciate it. Duncan Murdoch On my understanding, once the seed is set the sequence generated by the underlying RNG is determined, whether it is the result of a single call to produce a long sequence or multiple calls to generate many shorter sequences. Example: set.seed(42) multi-numeric(20) set.seed(42) single-rnorm(20) set.seed(42) for(i in (1:20)) multi[i]-rnorm(1) print(max(multi-single),digits=22) [1] 0 print(min(multi-single),digits=22) [1] 0 In other words: identical! Whether there are possible exceptions, in some implementations of rdist where dist is other than norm, has to be answered by people who are familiar with the internals of these functions. Best wishes to all, Ted. E-Mail: (Ted Harding) [EMAIL PROTECTED] Fax-to-email: +44 (0)870 094 0861 Date: 08-Feb-06 Time: 13:26:10 -- XFMail -- __ 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] Mixture normal distribution
We did get your previous message. See the posting guide about what to do if you do not get an answer. See MASS4, chapter 16 (and see the FAQ for what MASS4 is) for fitting mixtures of normals and testing their fit. I want to know how to read the data to txt file. What does that mean? (You 'read from' or 'write to'.) On Wed, 8 Feb 2006 [EMAIL PROTECTED] wrote: Dear R helper, I hope that u can help me to sort out my problem because I sent an E-mail last night to R-list but I have not receive any help and at the same time I think this problem is not so hard. I have used the following functions before K-10 prime-c(2,3,5,7,11,13,17) UN-seq(1:K)%*%t(sqrt(prime)) U1-UN-as.integer(UN) U-matrix(qnorm(U1),K,7) U [,1][,2][,3][,4] [,5] [,6] [1,] -0.2167193 0.61902728 -0.71900806 0.37387492 -0.47715805 0.2677426 [2,] 0.9479680 -0.09010569 -0.06990169 -0.54900030 0.34047235 -0.8026015 [3,] -0.6978334 -0.85544499 0.54814530 1.53212280 1.64363675 0.9026864 [4,] 0.4038929 1.46253909 1.59168198 0.20958766 -0.62343558 -0.1962555 [5,] -1.4678844 0.41315654 -0.91407055 -0.74294809 0.20989183 -1.9148412 [6,] -0.0369025 -0.27331681 -0.21109168 1.14796196 1.28012119 0.3406266 [7,] 1.2786790 -1.15348516 0.39201340 0.05080407 -0.78449952 -0.7099779 [8,] -0.4853656 1.06431267 1.21882042 -0.97005119 0.08280907 1.0127500 [9,] 0.6065405 0.22357828 -1.15223725 0.88440727 1.03481830 -0.1257587 [10,] -1.0707736 -0.46627852 -0.35664238 -0.10670096 -0.96909898 -1.5936006 [,7] [1,] -1.15960110 [2,] -0.68646092 [3,] -0.33366316 [4,] -0.01899511 [5,] 0.29375681 [6,] 0.63913903 [7,] 1.08816734 [8,] 2.16601566 [9,] -1.23750068 [10,] -0.73537275 Now I want instead of using (qnorm) the inverse of slandered normal distribution, I want to use the mixture of normal distribution, and also, I want to know how to read the data to txt file. Many thanks for your help in advance. Al-Eid -- 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] difference between rnorm(1000, 0, 1) and running rnorm(500, 0, 1) twice
On Wed, 8 Feb 2006, Duncan Murdoch wrote: On 2/8/2006 4:53 AM, Bj?rn-Helge Mevik wrote: Why don't you test it yourself? E.g., set.seed(42) bob1 - rnorm(1000,0,1) set.seed(42) bob2 - rnorm(500,0,1) bob3 - rnorm(500,0,1) identical(bob1, c(bob2, bob3)) I won't tell you the answer. :-) This isn't really something that can be proved by a test. Perhaps the current implementation makes those equal only because 500 is even, or divisible by 5, or whatever... I think the intention is that those should be equal, but in a quick search I've been unable to find a documented guarantee of that. So I would take a defensive stance and assume that there may be conditions where c(rnorm(m), rnorm(n)) is not equal to rnorm(m+n). If someone can point out the document I missed, I'd appreciate it. It's various source files in R_HOME/src/main. Barring bugs, they will be the same. As you know R is free software and comes with ABSOLUTELY NO WARRANTY. -- 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] lme question
Mahdi Osman m_osm at gmx.net writes: Hi list, I am fitting microarray data (intensity) model using the lme package in R environment. I have 5 fixed variables in the model. One of the fixed variables is genes. I am trying to get p-values for different genes. But I am getting only one p-value for all genes together. I can get a list of p-value when I run lm. Why can't this work in lme? I was wondering if some one can help me solve this problem. That is getting a list of p-value for each gene in the model using the lme. The bioconductor list might be a better place for this question, and an example would haven been welcome. So my only guess is: could it be that you forgot to make genes a factor variable? When genes is a number, you get a linear regression which is probably not what you want. Dieter __ 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 formula on plot
I estimate some parameters and I want to print them (pretty) on my plot: # somehow estimated parameters z-c(1.543523e+00, 1.23453e+00, 3.454000e+00) x-seq(-1,1,length=100) plot(x,z[3]*x^2+z[2]*x+z[3],type=l, main=My nice plot of the estimated function) zs-format(z,digits=4,scientific=FALSE,trim=TRUE) text(-0.9,7,expression(1.54*x^2)) # is what I want, but DYNAMIC text(-0.9,6,expression(paste(zf[1],x^3))) # not really text(-0.9,5,expression(paste(toSting(zf[1]),x^3))) # not really #using z (double) instead of zf (string) does not help. So my question is: How do I evaluate zf[1] from the variable to it's (String) value? Here it is used within an expression: this makes all the trouble. Thanks for help, I tried 2 hrs now... 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] print formula on plot
I found it immediately after posting :( substitute is my friend: text(0.5,5,substitute(f[Sv] ==k*x^2, list(k=zf[1]))) __ 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 rnorm(1000, 0, 1) and running rnorm(500, 0, 1) twice
On 2/8/2006 8:30 AM, Brian D Ripley wrote: On Wed, 8 Feb 2006, Duncan Murdoch wrote: On 2/8/2006 4:53 AM, Bj�rn-Helge Mevik wrote: Why don't you test it yourself? E.g., set.seed(42) bob1 - rnorm(1000,0,1) set.seed(42) bob2 - rnorm(500,0,1) bob3 - rnorm(500,0,1) identical(bob1, c(bob2, bob3)) I won't tell you the answer. :-) This isn't really something that can be proved by a test. Perhaps the current implementation makes those equal only because 500 is even, or divisible by 5, or whatever... I think the intention is that those should be equal, but in a quick search I've been unable to find a documented guarantee of that. So I would take a defensive stance and assume that there may be conditions where c(rnorm(m), rnorm(n)) is not equal to rnorm(m+n). If someone can point out the document I missed, I'd appreciate it. It's various source files in R_HOME/src/main. Barring bugs, they will be the same. As you know R is free software and comes with ABSOLUTELY NO WARRANTY. I didn't mean guarantee in the sense of warranty, just guarantee in the sense that if someone found a situation where they weren't equal, we would consider it a bug and fix it or document it as an exception. Should we add a statement to the RNG man page or manuals somewhere that says this is the intention? For others who aren't as familiar with the issues as Brian: this isn't necessarily a good idea. We have a lot of RNGs, and it's fairly easy to write one so that this isn't true. For example, the Box-Muller method naturally generates pairs of normals; a naive implementation would just throw one away at the end if asked for an odd number. (Ours doesn't do that.) Duncan Murdoch __ 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] font size/disappearing labels
I am using vioplot to make nice boxplots, which I am outputting to postscript. I am using the paper=special and width and height to get the graphs to look nice. I do however have a problem with the size of the labels and titles. When I set fontsize as an option to the postscript call too high, one of the labels disappear, although there is enough space for it (imo, that is). This I have understood is an effect of the system trying to avoid overlapping numbers. Is there a way I can override this function though? Can I force it to show all of the labels, although they might be too close? Karin -- Karin Lagesen, PhD student [EMAIL PROTECTED] http://www.cmbn.no/rognes/ __ 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] Using R to process spectroscopic data
Dirk De Becker wrote: * Determine the range of the spectrum to be used - For this, I should be able to calculate the regression coefficients You can get the regression coefficients from a PLSR/PCR with the coef() function. See ?coef.mvr However, using the regression coefficients alone for selecting variables/regions, can be 'dangerous' because the variables are highly correlated. One alternative is 'variable importance' measures, e.g. VIP (variable importance in projections) as described in Chong, Il-Gyo Jun, Chi-Hyuck, 2005, Performance of some variable selection methods when multicollinearity is present, Chemometrics and Intelligent Laboratory Systems 78, 103--112. A crude implementation of VIP can be found in http://mevik.net/work/software/pls.html Another alternative is to use jackknife-estimated uncertainties of the regression coefficients in significance tests. (I don't have any reference or implementation, sorry. :-) The correlation loadings can also give valuable information about which variables that might be important for the regression. See ?corrplot in the pls package. -- Bjørn-Helge Mevik __ 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] dataframe subset
I have a dataframe with a column, say x consisting of values, each value appearing different times, e.g. x: 1,1,1,1,2,2,4,4,4,9,10,10,10,10,10 ... and a vector, including e.g.: y: 2,9,10,... I need a subset of the dataframe: all rows where x is equal to one of the values in y. Currently I use a loop for this, but because x and y are large this is very slow. Is there any idea how to solve this problem faster? Thank you, Bernhard __ 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 formula on plot
Only put the expression inside the expression? plot(x,z[3]*x^2+z[2]*x+z[3],type=l, main=My nice plot) text(-0.9,5,paste(zs[1],' ',expression(x^3))) # should work Robert W. Baer, Ph.D. Associate Professor Department of Physiology A. T. Still University of Health Science 800 W. Jefferson St. Kirksville, MO 63501-1497 USA - Original Message - From: Thomas Steiner [EMAIL PROTECTED] To: r-help@stat.math.ethz.ch Sent: Wednesday, February 08, 2006 7:47 AM Subject: [R] print formula on plot I estimate some parameters and I want to print them (pretty) on my plot: # somehow estimated parameters z-c(1.543523e+00, 1.23453e+00, 3.454000e+00) x-seq(-1,1,length=100) plot(x,z[3]*x^2+z[2]*x+z[3],type=l, main=My nice plot of the estimated function) zs-format(z,digits=4,scientific=FALSE,trim=TRUE) text(-0.9,7,expression(1.54*x^2)) # is what I want, but DYNAMIC text(-0.9,6,expression(paste(zf[1],x^3))) # not really text(-0.9,5,expression(paste(toSting(zf[1]),x^3))) # not really #using z (double) instead of zf (string) does not help. So my question is: How do I evaluate zf[1] from the variable to it's (String) value? Here it is used within an expression: this makes all the trouble. Thanks for help, I tried 2 hrs now... 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-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 formula on plot
Also see ?bquote On 2/8/06, Thomas Steiner [EMAIL PROTECTED] wrote: I found it immediately after posting :( substitute is my friend: text(0.5,5,substitute(f[Sv] ==k*x^2, list(k=zf[1]))) __ 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] print formula on plot
text(-0.9,5,paste(zs[1],' ',expression(x^3))) # should work this produces a 2x^3 and not 2xsuperscript(3) - just execute it and you see what I mean. anyway, substitute helps and bquote could shorten it a bit. Anywa 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] dataframe subset
On 2/8/2006 9:21 AM, Bernhard Baumgartner wrote: I have a dataframe with a column, say x consisting of values, each value appearing different times, e.g. x: 1,1,1,1,2,2,4,4,4,9,10,10,10,10,10 ... and a vector, including e.g.: y: 2,9,10,... I need a subset of the dataframe: all rows where x is equal to one of the values in y. Currently I use a loop for this, but because x and y are large this is very slow. Is there any idea how to solve this problem faster? It's actually very easy. Assume your dataframe is df, then subset(df, x %in% y) will give you what you want (assuming there is no column y in the dataframe). Duncan Murdoch Thank you, Bernhard __ 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] dataframe subset
Bernhard Baumgartner wrote: I have a dataframe with a column, say x consisting of values, each value appearing different times, e.g. x: 1,1,1,1,2,2,4,4,4,9,10,10,10,10,10 ... and a vector, including e.g.: y: 2,9,10,... I need a subset of the dataframe: all rows where x is equal to one of the values in y. Currently I use a loop for this, but because x and y are large this is very slow. Is there any idea how to solve this problem faster? mydata - data.frame(X = sample(1:10, 1, replace=TRUE), Y = sample(c(2,9,10), 1, replace=TRUE)) newdata - mydata[mydata$X %in% unique(mydata$Y),] ?%in% -- Chuck Cleland, Ph.D. NDRI, Inc. 71 West 23rd Street, 8th floor New York, NY 10010 tel: (212) 845-4495 (Tu, Th) tel: (732) 452-1424 (M, W, F) fax: (917) 438-0894 __ 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] R: dataframe subset
Dear Bernhard, if I understand correctly your question may be you want something like df-data.frame(x=sample(1:10, 100, repl=T), y=sample(1:5, 100, repl=T)) subset(df, x%in%y) Regards, Stefano -Messaggio originale- Da: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] conto di Bernhard Baumgartner Inviato: 08 February 2006 15:22 A: r-help@stat.math.ethz.ch Oggetto: [R] dataframe subset I have a dataframe with a column, say x consisting of values, each value appearing different times, e.g. x: 1,1,1,1,2,2,4,4,4,9,10,10,10,10,10 ... and a vector, including e.g.: y: 2,9,10,... I need a subset of the dataframe: all rows where x is equal to one of the values in y. Currently I use a loop for this, but because x and y are large this is very slow. Is there any idea how to solve this problem faster? Thank you, Bernhard __ 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] dataframe subset
Sounds like you may need no use match(). On Wed, 2006-02-08 at 15:21 +0100, Bernhard Baumgartner wrote: I have a dataframe with a column, say x consisting of values, each value appearing different times, e.g. x: 1,1,1,1,2,2,4,4,4,9,10,10,10,10,10 ... and a vector, including e.g.: y: 2,9,10,... I need a subset of the dataframe: all rows where x is equal to one of the values in y. Currently I use a loop for this, but because x and y are large this is very slow. Is there any idea how to solve this problem faster? Thank you, Bernhard __ 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] dataframe subset
Hi something like xx-data.frame(x=sample(1:10,100,replace=T)) y-c(2,5,8) xx[xx$x%in%y,] HTH Petr On 8 Feb 2006 at 15:21, Bernhard Baumgartner wrote: From: Bernhard Baumgartner [EMAIL PROTECTED] Organization: Universitaet Regensburg To: r-help@stat.math.ethz.ch Date sent: Wed, 08 Feb 2006 15:21:46 +0100 Priority: normal Subject:[R] dataframe subset I have a dataframe with a column, say x consisting of values, each value appearing different times, e.g. x: 1,1,1,1,2,2,4,4,4,9,10,10,10,10,10 ... and a vector, including e.g.: y: 2,9,10,... I need a subset of the dataframe: all rows where x is equal to one of the values in y. Currently I use a loop for this, but because x and y are large this is very slow. Is there any idea how to solve this problem faster? Thank you, Bernhard __ 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 Petr Pikal [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] Compiling errors for Matrix_0.995-5.tar.gz under XP
I installed the MinGW-5.0.0 compilers today (gcc-3.4.2 is now contained in the 'Current' distribution. When the current compilers failed to compile the referenced Matrix update and not knowing how to check the exact version numbers for individual files, I applied the Id.exe and f771.exe fixes from the 'Building R for Windows' page (http://www.murdoch-sutherland.com/Rtools/#ldbug). More compiler errors were obtained. I then checked my Pearl version (5.8.7) and updated my R tools since I couldn't tell how old they were. At that point, I obtained the following output: C:\Documents and Settings\Whitece.AMED\My Documents\1 Pocket Office\R Repository \lme4rcmd install matrix_0.995-5.tar.gz latex: not found latex: not found latex: not found -- Making package matrix latex: not found adding build stamp to DESCRIPTION latex: not found installing NAMESPACE file and metadata latex: not found running src/Makefile.win ... latex: not found make[3]: `Matrix.dll' is up to date. ... done installing DLL latex: not found installing R files latex: not found installing inst files FIND: Parameter format not correct make[2]: *** [C:/PROGRA~1/R/R-22~1.1/library/matrix/inst] Error 2 make[1]: *** [all] Error 2 make: *** [pkg-matrix] Error 2 *** Installation of matrix failed *** Removing 'C:/PROGRA~1/R/R-22~1.1/library/matrix' Restoring previous 'C:/PROGRA~1/R/R-22~1.1/library/matrix' If I need to read one of R's many friendly manuals, I'd appreciate a reference to which one and approximately which section. Thanks. Chuck Charles E. White, Senior Biostatistician, MS Walter Reed Army Institute of Research 503 Robert Grant Ave., Room 1w102 Silver Spring, MD 20910-1557 301 319-9781 Personal/Professional Site: http://users.starpower.net/cwhite571/professional/ __ 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] dataframe subset
Thanks to all, the %in% function solved my problem! Bernhard __ 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] dataframe subset
Here's one way, x - data.frame(V=c(1,1,1,1,2,2,4,4,4,9,10,10,10,10,10)) y - data.frame(V=c(2,9,10)) xy - merge(x,y,all=FALSE) Pay close attention to what happens if you have duplicate values in y, say y - data.frame(V=c(2,9,10,10)) -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Bernhard Baumgartner Sent: Wednesday, February 08, 2006 9:22 AM To: r-help@stat.math.ethz.ch Subject: [R] dataframe subset I have a dataframe with a column, say x consisting of values, each value appearing different times, e.g. x: 1,1,1,1,2,2,4,4,4,9,10,10,10,10,10 ... and a vector, including e.g.: y: 2,9,10,... I need a subset of the dataframe: all rows where x is equal to one of the values in y. Currently I use a loop for this, but because x and y are large this is very slow. Is there any idea how to solve this problem faster? Thank you, Bernhard __ 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] difference between rnorm(1000, 0, 1) and running rnorm(500, 0, 1) twice
Duncan Murdoch [EMAIL PROTECTED] writes: This isn't really something that can be proved by a test. Perhaps the current implementation makes those equal only because 500 is even, or divisible by 5, or whatever... I think the intention is that those should be equal, but in a quick search I've been unable to find a documented guarantee of that. So I would take a defensive stance and assume that there may be conditions where c(rnorm(m), rnorm(n)) is not equal to rnorm(m+n). If someone can point out the document I missed, I'd appreciate it. I think it's a fair assumption that *uniform* random numbers have the property, since these are engines that produce a continuous stream of values, of which we select the next n and m values. As long as the normal.kind (see ?RNGkind) is Inversion, we can be sure that the property carries to rnorm, but it might not be the case for other methods. In particular the ones that generate normal variates in batches are suspect. However, empirically, I can't seem to provoke the effect with any of R's built-in generators. One *could* of course check the source code and see whether there is state information being kept between invokations... -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ R-help@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] ARULES -- Filtering Rules by RHS
On 8 Feb 2006, [EMAIL PROTECTED] wrote: I would like to only inspect rules that contain a certain label substring on the rhs. In this special case the item labels are built like this: itemtype_itemvalue e.g. Artikelgruppe_E0815 what I want to do is only show rules where Artikelgruppe is contained in the rhs - has anybody an idea how this could work? I think there is a rhs() method you can use to get an itemMatrix instance containing just the RHS. Then one options might be something like (untested): isets - LIST(items(rhs(foo))) lapply(isets, function(x) grep(Artikelgruppe, isets)) oop, I just realized: do you mean RHS of the association rule or RHS of the foo_bar? hth, + seth __ 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] logLik == -Inf in gls
I am trying to fit a generalised least squares model using gls in the nlme package. The model seems to fit very well when I plot the fitted values against the original values, and the model parameters have quite narrow confidence intervals (all are significant at p5%). The problem is that the log likelihood is always given as -Inf. This doesn't seem to make sense because the model seems to fit my data so well. I have checked that the residuals are stationary using an adf test. I can't work out whether - the model really doesn't fit at all - there is something in my data that stops the implementation of logLik working correctly (the -Inf value says the calculation hasn't worked) Possible causes are: - There are lots of NAs in my data (model and response variables) - There is some autocorrelation in the data that is not accounted for by the model (most is accounted for). But, I've tried recreating the problem using a simpler data set, and have never found the same problem. The command I use to fit the model is... result2 - gls(lci4150 ~ propCapInStomachs + temperature + as.factor(monthNumber) + lagLci1 + lagcap1 + lagcap2, data = monthly, subset = subset1985, na.action = na.approx, weights = varFixed( ~ 1/numob4150) ) The output I get is... Generalized least squares fit by REML Model: lci4150 ~ propCapInStomachs + temperature + as.factor(monthNumber) + lagLci1 + lagcap1 + lagcap2 Data: monthly Subset: subset1985 AIC BIC logLik Inf Inf -Inf Variance function: Structure: fixed weights Formula: ~1/numob4150 Coefficients: Value Std.Error t-value p-value (Intercept) -0.3282412 0.5795665 -0.566356 0.5717 propCapInStomachs 0.0093283 0.0039863 2.340107 0.0202 temperature 0.4342514 0.1526104 2.845490 0.0048 as.factor(monthNumber)2 0.3990717 0.3869991 1.031195 0.3036 as.factor(monthNumber)3 1.3788334 0.3675690 3.751223 0.0002 as.factor(monthNumber)4 1.4037195 0.3857764 3.638686 0.0003 as.factor(monthNumber)5 0.9903316 0.3436177 2.882074 0.0043 as.factor(monthNumber)6 0.3453741 0.3043698 1.134719 0.2577 as.factor(monthNumber)7 0.3948442 0.3035142 1.300909 0.1946 as.factor(monthNumber)8 0.5021812 0.3532413 1.421638 0.1565 as.factor(monthNumber)9 -0.0794319 0.3598981 -0.220707 0.8255 as.factor(monthNumber)10 0.3536805 0.3790538 0.933061 0.3518 as.factor(monthNumber)11 0.7874834 0.3557116 2.213826 0.0278 as.factor(monthNumber)12 0.1854279 0.3178320 0.583415 0.5602 lagLci1 0.5488437 0.0576144 9.526151 0. lagcap1 0.0110994 0.0043669 2.541714 0.0117 lagcap2 -0.0088080 0.0041099 -2.143127 0.0332 Does anyone have any suggestions of how I can get a meaningful value for logLik? Or some other way that I can compare models. Thankyou for your help, Lillian. -- Lillian Sandeman PhD Student School of Biological Sciences University of Aberdeen AB24 2TZ Tel.: 01224 272648 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] Logistic regression - confidence intervals
Please forgive a rather naïve question... Could someone please give a quick explanation for the differences in conf intervals achieved via confint.glm (based on profile liklihoods) and the intervals achieved using the Design library. For example, the intervals in the following two outputs are different. library(Design) x = rnorm(100) y = gl(2,50) d = data.frame(x = x, y = y) dd = datadist(d); options(datadist = 'dd') m1 = lrm(y~x, data = d) summary(m1) m2 = glm(y~x, family = binomial, data = d) confint(m2) I have spent time trying to figure this out via archives, but have not had much luck. Regards Stephen __ 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] Changing labels on the scale of image.plot(fields)
Dear R-Users,
I am searching a way of changing the labels of the scale of a image.plot
function in library(fields). Taking the following example I would like
to add my own labels on the right side of the scale and it would be nice
to decide also where to have the ticks.
In this particular template I am sending you, I would like to have on
the scale my.labels instead of 0,5,10...30.
Thanks in advance,
Carlo Giovanni Camarda
A - matrix(1:20, ncol=4)
my.breaks - c(0,6,8,10,12,14,30)
my.colors - c(black, green, blue, red, yellow, pink)
my.labels - c( , LETTERS[1:5], )
library(fields)
image.plot(A, breaks=my.breaks, col=my.colors, zlim=range(my.breaks))
+
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Re: [R] difference between rnorm(1000, 0, 1) and running rnorm(500, 0, 1) twice
On Wed, 8 Feb 2006, Duncan Murdoch wrote: On 2/8/2006 8:30 AM, Brian D Ripley wrote: On Wed, 8 Feb 2006, Duncan Murdoch wrote: On 2/8/2006 4:53 AM, Bjÿÿrn-Helge Mevik wrote: Why don't you test it yourself? E.g., set.seed(42) bob1 - rnorm(1000,0,1) set.seed(42) bob2 - rnorm(500,0,1) bob3 - rnorm(500,0,1) identical(bob1, c(bob2, bob3)) I won't tell you the answer. :-) This isn't really something that can be proved by a test. Perhaps the current implementation makes those equal only because 500 is even, or divisible by 5, or whatever... I think the intention is that those should be equal, but in a quick search I've been unable to find a documented guarantee of that. So I would take a defensive stance and assume that there may be conditions where c(rnorm(m), rnorm(n)) is not equal to rnorm(m+n). If someone can point out the document I missed, I'd appreciate it. It's various source files in R_HOME/src/main. Barring bugs, they will be the same. As you know R is free software and comes with ABSOLUTELY NO WARRANTY. I didn't mean guarantee in the sense of warranty, just guarantee in the sense that if someone found a situation where they weren't equal, we would consider it a bug and fix it or document it as an exception. Should we add a statement to the RNG man page or manuals somewhere that says this is the intention? I think that is part of the sense of `no warranty': we allow ourselves to change anything which is not documented, and so things are as a result deliberately not documented. For others who aren't as familiar with the issues as Brian: this isn't necessarily a good idea. We have a lot of RNGs, and it's fairly easy to write one so that this isn't true. For example, the Box-Muller method naturally generates pairs of normals; a naive implementation would just throw one away at the end if asked for an odd number. (Ours doesn't do that.) I think we should allow future methods to do things like that, and preferably document that they do them. -- 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] Logistic regression model selection with overdispersed/autocorrelated data
Thanks for pointing out the aod package and the beta-binomial logistic models Renaud. While I see how betabinom could be applied to some of our other analyses , I don't see how it can be used in our habitat selection analysis where individual locations are coded as 0 or 1 rather than proportions. Gee models (geeglm from geepack) could be used for our analyses. Even though these models are fit using maximum likelihood estimation, they do not solve our model selection problem. Beta-coefficients from gee, glm, glmm's, and lrm are nearly identical. The only thing that varies is the variance-covariance matrix and the resulting standard errors. Consequently, the deviances should be similar because predicted values (p) are calculated from the beta-coefficients. For an individual data point, the loglikelihood = y * log(p) + (1 - y) * log(1-p) and the deviance = -2 * sum(loglikelihoods). Consequently, the difference in deviance between two models is amplified by autocorrelated data and causes models to be overparamaterized when using AIC or likelihood ratio tests. I am curious how others select models with autocorrelated data. Thanks for your help, Jesse Renaud Lancelot renaud.lancelot@To: [EMAIL PROTECTED] [EMAIL PROTECTED] gmail.com cc: r-help@stat.math.ethz.ch Subject: Re: [R] Logistic regression model selection with overdispersed/autocorrelated 31/01/2006 01:02 data If you're not interested in fitting caribou-specific responses, you can use beta-binomial logistic models. There are several package available for this purpose on CRAN, among which aod. Because these models are fitted using maximum-likelihood methods, you can use AIC (or other information criteria) to compare different models. Best, Renaud 2006/1/30, [EMAIL PROTECTED] [EMAIL PROTECTED]: I am creating habitat selection models for caribou and other species with data collected from GPS collars. In my current situation the radio-collars recorded the locations of 30 caribou every 6 hours. I am then comparing resources used at caribou locations to random locations using logistic regression (standard habitat analysis). The data is therefore highly autocorrelated and this causes Type I error two ways – small standard errors around beta-coefficients and over-paramaterization during model selection. Robust standard errors are easily calculated by block-bootstrapping the data using animal as a cluster with the Design library, however I haven't found a satisfactory solution for model selection. A couple options are: 1. Using QAIC where the deviance is divided by a variance inflation factor (Burnham Anderson). However, this VIF can vary greatly depending on the data set and the set of covariates used in the global model. 2. Manual forward stepwise regression using both changes in deviance and robust p-values for the beta-coefficients. I have been looking for a solution to this problem for a couple years and would appreciate any advice. Jesse __ 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 -- Renaud LANCELOT Département Elevage et Médecine Vétérinaire (EMVT) du CIRAD Directeur adjoint chargé des affaires scientifiques CIRAD, Animal Production and Veterinary Medicine Department Deputy director for scientific affairs Campus international de Baillarguet TA 30 / B (Bât. B, Bur. 214) 34398 Montpellier Cedex 5 - France Tél +33 (0)4 67 59 37 17 Secr. +33 (0)4 67 59 39 04 Fax +33 (0)4 67 59 37 95 __ 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] Bloomberg Data Import to R
Hi Sumanta, 1. This messages is much more appropriate for the sig-finance DL instead. Consider signing up (I read up on Amba, so I am sure you have good contributions to make in that forum). 2. To my knowledge, there isn't a direct package. However, if you use Bloomberg's excel plugin, just get the data into excel, save and then bring it in as usual. I suspect that that's what you are doing already. 3. You may have better luck with the S-Plus plugins. I am just getting started (an don't have any support/maintenace contract), so I don't know what all Insightful has up its sleeve, but I talked to Carol Wedekind about this just thing yesterday. Dr. Yollin, who also listens in on the sig-finance list, may be able to advise you better about what exists. With warm regards, Vivek Message: 70 Date: Wed, 8 Feb 2006 15:51:13 +0530 From: Sumanta Basak [EMAIL PROTECTED] Subject: [R] Bloomberg Data Import to R To: r-help@stat.math.ethz.ch Message-ID: [EMAIL PROTECTED] Content-Type: text/plain Hi R-Experts, Can anyone tell me how Bloomberg data can be directly downloaded to R? Is there any package? Sumanta Basak. __ 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] nested random effects in glmm.admb
Hi Jarrod , I think you are right that neither nested or cross-classified models can be specified in glmm.admb() as it stands (except in ad-hoc ways). This is not a restriction of the underlying software AD Model Builder, but it is a feature of how I wrote the R-interface. I will try to figure out how to do 2-level nesting, and include that in future releases. hans -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Jarrod Hadfield Sent: Wednesday, February 08, 2006 2:26 PM To: r-help@stat.math.ethz.ch Subject: [R] nested random effects in glmm.admb Hello all, In a previous posting regarding glmm.admb it is stated that glmm.admb can handle 2 nested random effects. I can only fit a single random term at the moment, and wondered if anyone could provide me with some information on how to specify a model with 2 (nested or cross-classified) random terms? Thanks, Jarrod. __ 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
[R] rob var/cov + LAD regression
Hi, after looking around I was not able to get info about these two questions: 1. Is there a function to have a jackknifed corrected var/cov estimate (as described in MacKinnon and White 1985) in a standard OLS regression? 2. Does R possess a LAD (Least Absolute Deviation) regression function? Any help? Thanks -- Angelo Secchi PGP Key ID:EA280337 __ 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] envi clone in R
Hello all, Research Systems (www.rsinc.com) have developed and distributes the language IDL, and the GIS ENVI, written in IDL. To my oppinion, R language is superior, compared to IDL, in all aspects. However, ENVI is the rather convenient and feature rich tool. Is anyone aware about any work, dedicated to the creation of something, similar to the ENVI, but in R? Also, recently, the R bindings to the GTK library have appeared... --- Best regards, Wladimirmailto:[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] insert value according to indice
R-Helpers,
I am trying to insert a value into a dataframe. This value is a proportion
calculated by counting the number of those individuals with that value and then
inserting the proportion at the end of the dataframe to only those individuals
with the given value. The problem I am running into is that the proportions are
not being attached to only those individuals with the specified value for that
proportion.
Below is an example of the code that I am using. I have also attached the
data file that I am using to create this dataframe.
#Read in Data
age.int - read.csv('C:/intage.csv',header = TRUE)
asubs112 - subset(age.int, rs1042364 != (2,2))
ages112 - sort(unique(na.omit(asubs112$first_drink)))
for ( i in ages112) {
indce - which(na.omit(asubs112$first_drink == i))
prop - length(indce)/nrow(asubs112)
asubs112[indce,5] - prop
asubs112[indce,]
}
Below is the output that I get from the script above. Notice the proportion
for the first NA but not any of the others. Not sure what I am doing wrong, any
suggestions are a big help.
TIA,
Adrian
asubs112[1:50,]
IND_ID rs1042364 first_drink age_int V5
4 10008007 (1,2) NA 16 0.003891051
6 10013012 (1,2) 13 14 0.116731518
7 10015006 (1,2) 12 17 0.105058366
8 10015007 (1,1) 12 16 0.105058366
10 10021009 (1,2) NA 15 NA
14 10039036 (1,2) NA 15 NA
15 10039037 (1,2) NA 13 NA
17 10045005 (1,2) 13 17 0.116731518
18 10045014 (1,2) 13 14 0.116731518
21 10055022 (1,2) NA 15 NA
22 10059006 (1,2) 12 NA 0.105058366
23 10060021 (1,2) NA 15 NA
24 10060022 (1,2) NA 13 NA
27 10069028 (1,2) 16 17 0.066147860
29 10071022 (1,1) 14 16 0.116731518
30 10071026 (1,2) NA 13 NA
31 10071028 (1,2) NA 13 NA
32 10071032 (1,2) 16 16 0.066147860
34 10072004 (1,2) 16 17 0.066147860
37 10073021 (1,2) 12 NA 0.105058366
39 10077013 (1,2) NA 14 NA
40 10077076 (1,2) 15 15 0.062256809
41 10084005 (1,2) 14 15 0.116731518
44 10088017 (1,2) 15 15 0.062256809
50 10093005 (1,2) NA NA NA
51 10096003 (1,2) 17 NA 0.023346304
56 10108005 (1,2) 14 NA 0.116731518
57 10112001 (1,2) 6 16 0.003891051
58 10114003 (1,1) 13 17 0.116731518
59 10114004 (1,1) 11 NA 0.027237354
60 10114005 (1,2) 12 14 0.105058366
61 10114006 (1,1) 13 17 0.116731518
62 10114007 (1,2) 15 15 0.062256809
63 10115006 (1,2) 13 14 0.116731518
69 10118011 (1,2) 14 14 0.116731518
70 10118012 (1,2) 16 17 0.066147860
73 10123024 (1,2) 13 15 0.116731518
76 10130019 (1,2) NA 13 NA
77 10130020 (1,2) 12 15 0.105058366
78 10130021 (1,2) NA 14 NA
87 10144039 (1,2) 12 13 0.105058366
91 10155016 (1,2) NA 13 NA
92 10156004 (1,2) 14 15 0.116731518
99 10170009 (1,2) 16 17 0.066147860
100 10171016 (1,2) NA 15 NA
104 10171027 (1,2) 13 14 0.116731518
107 10175013 (1,2) 9 16 0.011673152
108 10181013 (1,2) 11 13 0.027237354
110 10181017 (1,1) 14 16 0.116731518
111 10181024 (1,1) 16 17 0.066147860
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Re: [R] Compiling errors for Matrix_0.995-5.tar.gz under XP
Please read the R-admin manual and as it suggests use the candidate compilers, now gcc 3.4.5. You also need the Rtools at the front of your path, so you find find.exe not FIND.exe. Finally, it seems to be requiring latex, so you may need to install that (I am really not sure why though). On Wed, 8 Feb 2006, White, Charles E WRAIR-Wash DC wrote: I installed the MinGW-5.0.0 compilers today (gcc-3.4.2 is now contained in the 'Current' distribution. When the current compilers failed to compile the referenced Matrix update and not knowing how to check the exact version numbers for individual files, I applied the Id.exe and f771.exe fixes from the 'Building R for Windows' page (http://www.murdoch-sutherland.com/Rtools/#ldbug). More compiler errors were obtained. I then checked my Pearl version (5.8.7) and updated my R tools since I couldn't tell how old they were. At that point, I obtained the following output: C:\Documents and Settings\Whitece.AMED\My Documents\1 Pocket Office\R Repository \lme4rcmd install matrix_0.995-5.tar.gz latex: not found latex: not found latex: not found -- Making package matrix latex: not found adding build stamp to DESCRIPTION latex: not found installing NAMESPACE file and metadata latex: not found running src/Makefile.win ... latex: not found make[3]: `Matrix.dll' is up to date. ... done installing DLL latex: not found installing R files latex: not found installing inst files FIND: Parameter format not correct make[2]: *** [C:/PROGRA~1/R/R-22~1.1/library/matrix/inst] Error 2 make[1]: *** [all] Error 2 make: *** [pkg-matrix] Error 2 *** Installation of matrix failed *** Removing 'C:/PROGRA~1/R/R-22~1.1/library/matrix' Restoring previous 'C:/PROGRA~1/R/R-22~1.1/library/matrix' If I need to read one of R's many friendly manuals, I'd appreciate a reference to which one and approximately which section. Thanks. Chuck Charles E. White, Senior Biostatistician, MS Walter Reed Army Institute of Research 503 Robert Grant Ave., Room 1w102 Silver Spring, MD 20910-1557 301 319-9781 Personal/Professional Site: http://users.starpower.net/cwhite571/professional/ __ 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 -- 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] GEE Modelle in Stata und R
Hall Christian Ich habe Dir hier den Output desselben Models mir den selben Daten mit R und mit Stata gerechnet angehängt. Wie Du siehst sind die Unterschiede nicht unbeträchtlich. Da Du bestimmt schon ähnliche Erfahrungen gemacht hast, wollte ich Dich fragen, ob diese Unterschiede im Rahmen dessen sind, wie man sie zwischen zwei verschiedenen packages erwarten kann, oder nicht. Für eine kurze Antwort wäre ich Dir sehr dankbar. Liebe Grüsse Christian R output: GEE: GENERALIZED LINEAR MODELS FOR DEPENDENT DATA gee S-function, version 4.13 modified 98/01/27 (1998) Model: Link: Logit Variance to Mean Relation: Binomial Correlation Structure: Exchangeable Call: gee(formula = y ~ Var1 * Var2 + Var3, id = Var4, data = mydata, family = binomial, corstr = exchangeable, scale.fix = TRUE) Summary of Residuals: Min 1Q Median 3Q Max -0.16457139 -0.10916961 -0.05774320 -0.01334249 0.98519918 Coefficients: Estimate Naive S.E. Naive z Robust S.E. Robust z (Intercept) -2.02946378 0.6152142 -3.29879234 0.6276423 -3.23347186 Var1med -0.06978758 0.8108207 -0.08607031 0.8280726 -0.08427713 Var1hi 0.08988940 0.9738316 0.09230487 0.9851523 0.09124417 Var2yes -2.16869738 1.2386945 -1.75079278 1.4269696 -1.51979227 Var3yes -0.10520805 0.5724176 -0.18379597 0.6881670 -0.15288157 Var1med:Var2yes 1.58088457 1.3503015 1.17076411 1.3682419 1.15541309 Var1hi:Var2yes 2.48367129 1.4694804 1.69016976 1.4707481 1.68871291 Estimated Scale Parameter: 1 Stata Output: xi: xtgee y i.Var1*i.Var2 Var3, family(binomial) link(logit) i(Var4) GEE population-averaged model Number of obs = 309 Group variable: Var4 Number of groups = 215 Link:logit Obs per group: min = 1 Family: binomial avg = 1.4 Correlation: exchangeable max = 8 Wald chi2(6) = 7.68 Scale parameter: 1 Prob chi2 =0.2628 -- y | Coef. Std. Err. zP|z| [95% Conf. Interval] -+ _cons | -1.938584 .8662878-2.24 0.025-3.636477 -.2406913 _IVar1_2 | -.0610133 .8087995-0.08 0.940 -1.6462311.524205 _IVar1_3 | .0944082 .9720986 0.10 0.923 -1.810871.999686 _IVar2_2 | -2.178428 1.240422-1.76 0.079 -4.60961.2527538 Var3 | -.0977918 .5719084-0.17 0.864 -1.2187121.023128 _IVarXVa~2_2 | 1.575095 1.351553 1.17 0.244 -1.073901 4.22409 _IVarXVa~3_2 | 2.483814 1.470152 1.69 0.091 -.3976316 5.36526 -- Christian -- Christian Bieli, project assistant Institute of Social and Preventive Medicine University of Basel, Switzerland Steinengraben 49 CH-4051 Basel Tel.: +41 61 270 22 12 Fax: +41 61 270 22 25 [EMAIL PROTECTED] www.unibas.ch/ispmbs __ 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] Logistic regression - confidence intervals
On Wed, 8 Feb 2006, Cox, Stephen wrote: Please forgive a rather naïve question... Could someone please give a quick explanation for the differences in conf intervals achieved via confint.glm (based on profile liklihoods) and the intervals achieved using the Design library. Well, the Design library is not giving you confidence intervals for parameters, is it? (Since there is no summary method for lrm it is a long haul to find out what it is giving you, which I leave to you.) For example, the intervals in the following two outputs are different. library(Design) x = rnorm(100) y = gl(2,50) d = data.frame(x = x, y = y) dd = datadist(d); options(datadist = 'dd') m1 = lrm(y~x, data = d) summary(m1) m2 = glm(y~x, family = binomial, data = d) confint(m2) I have spent time trying to figure this out via archives, but have not had much luck. Regards Stephen -- 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] Logistic regression - confidence intervals
Cox, Stephen wrote: Please forgive a rather naïve question... Could someone please give a quick explanation for the differences in conf intervals achieved via confint.glm (based on profile liklihoods) and the intervals achieved using the Design library. For example, the intervals in the following two outputs are different. library(Design) x = rnorm(100) y = gl(2,50) d = data.frame(x = x, y = y) dd = datadist(d); options(datadist = 'dd') m1 = lrm(y~x, data = d) summary(m1) m2 = glm(y~x, family = binomial, data = d) confint(m2) I have spent time trying to figure this out via archives, but have not had much luck. Regards Stephen Design uses Wald(large sample normality of parameter estimates) -based confidence intervals. These are good for most situations but profile confidence intervals are preferred. Someday I'll make Design do those. One advantage to Wald statistics is that they extend readily to cluster sampling (e.g., using cluster sandwich covariance estimators) and other complications (e.g., adjustment of variances for multiple imputation), whereas likelihood ratio statistics do not (unless e.g. you have an explicit model for the correlation structure or other facits of the model). Also note that confint is probably giving a confidence interval for a one-unit change in x whereas summary.Design is computing an interquartile-range effect (difference in x-values is shown in the summary output). When posting a nice simulated example it's best to do set.seed(something) so everyone will get the same data. Frank -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University __ 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] (no subject)
* Gary A. Nelson, Ph.D Massachusetts Division of Marine Fisheries 30 Emerson Avenue Gloucester, MA 01930 Phone: (978) 282-0308 x114 Fax: (617) 727-3337 Email: [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] Help with the ts function
I have a time series of temperature data recorded every 2 hours and I would like to generate a spectrogram using the spectrum function that examines cycles per day. My statement for coding the series using the ts function is bevtemp-ts(bevtemp,deltat=0.084) where 0.084 is 2 hours/24 hours. I am wondering if this is the correct way to code the data? Thanks for your help. Gary Nelson. * Gary A. Nelson Massachusetts Division of Marine Fisheries 30 Emerson Avenue Gloucester, MA 01930 Phone: (978) 282-0308 x114 Fax: (617) 727-3337 Email: [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] what are the limits on R array sizes?
I have some computers with a massive amount of memory, and I have some jobs that could use very large matrix sizes. Can R handle matrices of larger than 2GB? If I were to create a matrix of 1,000,000 x 1,000, it would use about 8GB. Can R work with an array of that size if I have compiled R on an IA64 Linux system with 15GB of RAM? Mike __ 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 variable into dataframe by indice
R-Helpers,
I am trying to insert a value into a dataframe. This value is a proportion
calculated by counting the number of those individuals with that value and then
inserting the proportion at the end of the dataframe to only those individuals
with the given value. The problem I am running into is that the proportions are
not being attached to only those individuals with the specified value for that
proportion.
Below is an example of the code that I am using. The data is made up for the
dataframe. Should give you an idea, but the original has 'NA' in many rows. The
original data is what is reported in the output below.
#Read in Data
age.int - data.frame(IND_ID = seq(1, 140, 10), rs1042364 = sample(
c((1,1),(1,2),(2,2)),14,replace = T),
first_drink = sample(5:17,14,replace = T))
asubs112 - subset(age.int, rs1042364 != (2,2))
ages112 - sort(unique(na.omit(asubs112$first_drink)))
for ( i in ages112) {
indce - which(na.omit(asubs112$first_drink == i))
prop - length(indce)/nrow(asubs112)
asubs112[indce,4] - prop
asubs112[indce,]
}
Below is the output that I get from the script above. Notice the proportion
for the first NA but not any of the others. Not sure what I am doing wrong, any
suggestions are a big help.
TIA,
Adrian
asubs112[1:50,]
IND_ID rs1042364 first_drink age_int V5
4 10008007 (1,2) NA 16 0.003891051
6 10013012 (1,2) 13 14 0.116731518
7 10015006 (1,2) 12 17 0.105058366
8 10015007 (1,1) 12 16 0.105058366
10 10021009 (1,2) NA 15 NA
14 10039036 (1,2) NA 15 NA
15 10039037 (1,2) NA 13 NA
17 10045005 (1,2) 13 17 0.116731518
18 10045014 (1,2) 13 14 0.116731518
21 10055022 (1,2) NA 15 NA
[[alternative HTML version deleted]]
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[R] Lexis maps in R
Dear R-users,
Sorry for bothering you twice in a day, but I was wondering whether
there is any R-function which can easily plot the single elements of a
Lexis diagram. I though that Lexis.diagram(Epi) could be the case, but
it just plot life times in a frame.
In particular I have been searching for something similar to the
function image which can plot either the single triangles of a Lexis
diagram or the parallelograms (e.g. probability of dying if the event is
the death).
I wrote down a simple example in which I played around with the function
polygon, but in this case the procedure would be too long (normally data
are set in matrix) and also the colors are messed up.
Thanks,
Carlo Giovanni Camarda
## a wrong example for giving an idea of what I'd like to plot
x - 0:4
A - matrix(1:16,ncol=4)
image(x,x,A, col=white)
colo - rainbow(12)
for(i in 1:4){
x1 - c(0,1,2,1)
y1 - c(0,0,1,1) + i -1
x2 - x1+1
y2 - y1
x3 - x2+1
y3 - y2
polygon(x1,y1,col=colo[i + i - 1])
polygon(x2,y2,col=colo[i+i])
polygon(x3,y3,col=colo[i+i+1])
}
+
This mail has been sent through the MPI for Demographic Rese...{{dropped}}
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Re: [R] Compiling errors for Matrix_0.995-5.tar.gz under XP
White, Charles E WRAIR-Wash DC [EMAIL PROTECTED] writes: I installed the MinGW-5.0.0 compilers today (gcc-3.4.2 is now contained in the 'Current' distribution. When the current compilers failed to compile the referenced Matrix update and not knowing how to check the exact version numbers for individual files, I applied the Id.exe and f771.exe fixes from the 'Building R for Windows' page (http://www.murdoch-sutherland.com/Rtools/#ldbug). More compiler errors were obtained. I then checked my Pearl version (5.8.7) and updated my R tools since I couldn't tell how old they were. At that point, I obtained the following output: C:\Documents and Settings\Whitece.AMED\My Documents\1 Pocket Office\R Repository \lme4rcmd install matrix_0.995-5.tar.gz latex: not found latex: not found latex: not found -- Making package matrix latex: not found adding build stamp to DESCRIPTION latex: not found installing NAMESPACE file and metadata latex: not found running src/Makefile.win ... latex: not found make[3]: `Matrix.dll' is up to date. ... done installing DLL latex: not found installing R files latex: not found installing inst files FIND: Parameter format not correct This looks like an issue with your PATH setting. You're picking up the wrong find command. make[2]: *** [C:/PROGRA~1/R/R-22~1.1/library/matrix/inst] Error 2 make[1]: *** [all] Error 2 make: *** [pkg-matrix] Error 2 *** Installation of matrix failed *** Removing 'C:/PROGRA~1/R/R-22~1.1/library/matrix' Restoring previous 'C:/PROGRA~1/R/R-22~1.1/library/matrix' If I need to read one of R's many friendly manuals, I'd appreciate a reference to which one and approximately which section. According to README.packages, Instructions for installing the toolset and building packages using the standard methods are in the `R Installation and Administration' manual (which is available in various formats as R-admin.* in the doc/manual directory). As fara as I can see Appendix F is the most relevant part, but also look in Ch 3 and 6. Thanks. Chuck Charles E. White, Senior Biostatistician, MS Walter Reed Army Institute of Research 503 Robert Grant Ave., Room 1w102 Silver Spring, MD 20910-1557 301 319-9781 Personal/Professional Site: http://users.starpower.net/cwhite571/professional/ __ 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 -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ R-help@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] Bloomberg Data Import to R
Check this out:
https://stat.ethz.ch/pipermail/r-sig-finance/2004q3/51.html
You should consider adapting it with rcom instead of RDCOMClient
Neuro
From: Sumanta Basak [EMAIL PROTECTED]
To: r-help@stat.math.ethz.ch
Subject: [R] Bloomberg Data Import to R
Date: Wed, 8 Feb 2006 15:51:13 +0530
Hi R-Experts,
Can anyone tell me how Bloomberg data can be directly downloaded to R?
Is there any package?
Sumanta Basak.
---
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[R] slightly off-topic re prcomp()
Hi, I was wondering if anyone could tell me why prcomp() will Invent modes of variation in a PCA on identical replicates of data? I would have expected 50 (or whatever number) of identical replicates to return a null score in such an analysis (or at the least, all variables would share the same PC score). This is not the case and I was wondering could someone point me in the direction of some literature to explain the reason behind this? Laura Quinn Institute of Atmospheric Science School of Earth and Environment University of Leeds Leeds LS2 9JT tel: +44 113 343 1596 fax: +44 113 343 6716 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] tutorials on statistical aspects of R
[EMAIL PROTECTED] wrote: There are lots of tutorials at http://cran.r-project.org/other-docs.html. I have those of course. I was looking for further tutorials. What do you mean the statistical aspect of R? I mean using and building statistical models for data analysis specifying the possibilities of variations appearing in R. An example would be specifying Split-plot ANOVA with both random and fixed factors. A lot of the tutorials in above url try to explain R as a programming language and therefore cannot allow too many explanation. That is the case of Jack of all trades... etc. R is useful for quite a lot of things, however I'm looking for something like a statistics course in R. Just to prevent misunderstanding, I do own, and am familiar with, exhaustive statistical texts. So I don't exactly need a course in statistics. Thanks in advance, Gil (I'm redirecting this to the general R list, since it's not particularly Mac specific any more.) Despite your claim, there are statistics-oriented tutorials available in the other docs section (esp. Faraway and Fox). However, if I recall correctly and if you need split-plot ANOVA etc., these may not be quite advanced enough (statistically) for you (Faraway has about 5 pages on block designs). You may need to buy or borrow a book: I would recommend Crawley's books (Statistics: an Introduction using R has only 4 or so pages, Statistical Computing has a whole 16-page chapter); Venables and Ripley (the bible) has a chapter on random and mixed effects, and Pinheiro and Bates is an entire book on mixed models ... all of these except Statistical Computing are listed on the R books page. Faraway also has Linear models with R, which has a chapter on block designs. That should give you some starting points ... Ben Bolker __ 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] rob var/cov + LAD regression
RSiteSearch() is your friend.
For 1) Try RSiteSearch('Jackknife',restrict='functions')
For 2) see package quantreg
-- Bert Gunter
Genentech Non-Clinical Statistics
South San Francisco, CA
The business of the statistician is to catalyze the scientific learning
process. - George E. P. Box
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Angelo Secchi
Sent: Wednesday, February 08, 2006 8:23 AM
To: r-help@stat.math.ethz.ch
Subject: [R] rob var/cov + LAD regression
Hi,
after looking around I was not able to get info about these
two questions:
1. Is there a function to have a jackknifed corrected
var/cov estimate (as described in MacKinnon and White 1985)
in a standard OLS regression?
2. Does R possess a LAD (Least Absolute Deviation) regression
function?
Any help?
Thanks
--
Angelo Secchi PGP Key ID:EA280337
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[R] expand.grid without expanding
Dear list,
I've recently came across a problem that I think I've solved and that I wanted
to share with you for two reasons:
- Maybe others come across the same problem.
- Maybe someone has a much simpler solution that wants to share with me ;-)
The problem is as follows: expand.grid() allows you to generate a data.frame
with all combinations of a set of values, e.g.:
expand.grid(par1=-1:1,par2=c('a','b'))
par1 par2
1 -1a
20a
31a
4 -1b
50b
61b
There is nothing wrong with this nice function except when you have too many
combinations to fit in your computer memory, and that was my problem: I
wanted to do something for each combination of a set of variants, but this
set was to large for storing in memory in a data.frame generated by
expand.grid. A possible solution would be to have a set of nested for()
cycles but I preferred a solution that involved a single for() cycle going
from 1 to the number of combinations and then at each iteration having some
form of generating the combination i. And this was the real problem: how
to generate a function that picks the same style of arguments as
expand.grid() and provides me with the values corresponding to line i of
the data frame that would have been created bu expand.grid(). For instance,
if I wanted the line 4 of the above call to expand.grid() I should get the
same as doing:
expand.grid(par1=-1:1,par2=c('a','b'))[4,]
par1 par2
4 -1b
but obviously without having to use expand.grid() as that involves generating
a data frame that in my case wouldn't fit in the memory of my computer.
Now, the function I've created was the following:
getVariant - function(id,vars) {
if (!is.list(vars)) stop('vars needs to be a list!')
nv - length(vars)
lims - sapply(vars,length)
if (id prod(lims)) stop('id above the number of combinations!')
res - vector(list,nv)
for(i in nv:2) {
f - prod(lims[1:(i-1)])
res[[i]] - vars[[i]][ceiling(id / f)]
id - id - (ceiling(id/f)-1)*f
}
res[[1]] - vars[[1]][id]
names(res) - names(vars)
res
}
--
expand.grid(par1=-1:1,par2=c('a','b'))[4,]
par1 par2
4 -1b
getVariant(4,list(par1=-1:1,par2=c('a','b')))
$par1
[1] -1
$par2
[1] b
I would be glad to know if somebody came across the same problem and has a
better suggestion on how to solve this.
Thanks,
Luis
--
Luis Torgo
FEP/LIACC, University of Porto Phone : (+351) 22 339 20 93
Machine Learning Group Fax : (+351) 22 339 20 99
R. de Ceuta, 118, 6o email : [EMAIL PROTECTED]
4050-190 PORTO - PORTUGALWWW : http://www.liacc.up.pt/~ltorgo
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Re: [R] rob var/cov + LAD regression
Angelo Secchi wrote: Hi, after looking around I was not able to get info about these two questions: 1. Is there a function to have a jackknifed corrected var/cov estimate (as described in MacKinnon and White 1985) in a standard OLS regression? Not sure, but look at package sandwich (on CRAN). 2. Does R possess a LAD (Least Absolute Deviation) regression function? This can be done with package quantreg (on CRAN). Kjetil Any help? Thanks __ 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] problem to install R on linux
Dear members, this can sound trivial for some people but I don't have experience on compilation. I'm trying to install R-2.2.1 on a laptop running Mandriva 2006. I already installed many of the recommended packages/libraries but it seems that something is still missing. The problem is that I cannot identify... Could somebody give me some advise? I put the output of the command ./configure bellow. When I tryed to install the R-2.0.0-1mdk.i586.rpm I got: [EMAIL PROTECTED] Download]# rpm -i R-2.0.0-1mdk.i586.rpm warning: R-2.0.0-1mdk.i586.rpm: Header V3 DSA signature: NOKEY, key ID 6c60ceea error: Failed dependencies: info is needed by R-2.0.0-1mdk.i586 [EMAIL PROTECTED] Download]# Thanks in advance, AB [EMAIL PROTECTED] R-2.2.1]# ./configure checking build system type... i686-pc-linux-gnu checking host system type... i686-pc-linux-gnu loading site script './config.site' loading build specific script './config.site' checking for pwd... /bin/pwd checking whether builddir is srcdir... yes checking for working aclocal... found checking for working autoconf... found checking for working automake... found checking for working autoheader... found checking for working makeinfo... found checking for gawk... gawk checking for egrep... grep -E checking whether ln -s works... yes checking for ranlib... ranlib checking for bison... no checking for byacc... no checking for ar... ar checking for a BSD-compatible install... /usr/bin/install -c checking for sed... /bin/sed checking for less... /usr/bin/less checking for perl... /usr/bin/perl checking whether perl version is at least 5.004... yes checking for dvips... /usr/bin/dvips checking for tex... /usr/bin/tex checking for latex... /usr/bin/latex checking for makeindex... /usr/bin/makeindex checking for pdftex... /usr/bin/pdftex checking for pdflatex... /usr/bin/pdflatex checking for makeinfo... /usr/bin/makeinfo checking for unzip... /usr/bin/unzip checking for zip... /usr/bin/zip checking for gzip... /bin/gzip checking for firefox... no checking for mozilla... no checking for netscape... no checking for galeon... no checking for kfmclient... no checking for opera... no checking for gnome-moz-remote... /usr/bin/gnome-moz-remote using default browser ... /usr/bin/gnome-moz-remote checking for acroread... /usr/bin/acroread checking for gcc... gcc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ANSI C... none needed checking how to run the C preprocessor... gcc -E checking whether gcc needs -traditional... no checking how to run the C preprocessor... gcc -E checking for gfortran... gfortran checking whether we are using the GNU Fortran 77 compiler... no checking whether gfortran accepts -g... no checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking how to run the C++ preprocessor... g++ -E checking for a sed that does not truncate output... /bin/sed checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for /usr/bin/ld option to reload object files... -r checking for BSD-compatible nm... /usr/bin/nm -B checking how to recognise dependent libraries... pass_all checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking dlfcn.h usability... yes checking dlfcn.h presence... yes checking for dlfcn.h... yes checking the maximum length of command line arguments... 32768 checking command to parse /usr/bin/nm -B output from gcc object... ok checking for objdir... .libs checking for ranlib... (cached) ranlib checking for strip... strip checking if gcc static flag works... yes checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC checking if gcc PIC flag -fPIC works... yes checking if gcc supports -c -o file.o... yes checking whether the gcc linker (/usr/bin/ld) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... no configure: creating libtool appending configuration tag CXX to libtool checking for ld used by g++... /usr/bin/ld checking if the linker (/usr/bin/ld)
Re: [R] [R-sig-Geo] envi clone in R
Wladimir Eremeev wrote: Hello all, Research Systems (www.rsinc.com) have developed and distributes the language IDL, and the GIS ENVI, written in IDL. I find it hard to believe they wrote it all in IDL! I'm guessing its probably scriptable in IDL, but underneath its written in something else... I could be wrong though! To my oppinion, R language is superior, compared to IDL, in all aspects. However, ENVI is the rather convenient and feature rich tool. I clicked on 'Product Documentation' on the ENVI site and it wanted me to log in or create a new user. To see the documentation? To find out what the program is about? Oh, what I really wanted was the Feature Tour.. Is anyone aware about any work, dedicated to the creation of something, similar to the ENVI, but in R? Last year I looked at GIS-R linkages, with the added criteria of being open source and cross-platform. There are now a few free GIS packages that can do this kind of thing, with a little added glue. I settled on OpenEV - it has vector and raster support, its extensible in Python and uses Gtk for dialogs which you can customise. All I needed was to get Python talking to R, so I wrote some Python bindings to Rserve. Now I've got a GIS with a menu that drops down, you choose the point layers you want to work on, click 'Go', and R does some analysis that ends up as a raster layer back in the GIS. The user doesnt care that R did it. Other GIS solutions are available! Barry __ 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] logical condition in vector operation
HI All,
I have a data frame such as:
test
x y p d
[1,] 1 0 10 21 0
[2,] 2 3 11 12 0
[3,] 3 4 12 23 0
[4,] 3 5 13 24 0
and I want to perfor some operations on the first two coulums,
conditional on the uneqaulity values on the 3rd and 4th columns.
For instance:
j = 3
test[test[,1] == j, 5] = test[test[,1] == j,2] + test[test[,2] == j,1]
gives me the result:
test:
x y p d
[1,] 1 0 10 21 0
[2,] 2 3 11 12 0
[3,] 3 4 12 23 6
[4,] 3 5 13 24 7
My probblem is the following: I want to perform the operation
test[test[,1] == j,2] + test[test[,2] == j,1] only if the value of
column p and column d are different at the positions where x or y = j.
In practice, I don't want to perform the first operation because
test[2,4 is 12 and test[1,3] is 12 as well.
I tried an if statement with little success:
if(test[test[,1] == j,3] != test[test[,2] == j,4]){
test[test[,1] == j, 5] = test[test[,1] == j,2] + test[test[,2] == j,1]
}
Warning message:
the condition has length 1 and only the first element will be used in:
if (test[test[, 1] == j, 3] != test[test[, 2] == j, 4]) {
Could anyone lend some advice?
Cheers,
Federico
--
Federico C. F. Calboli
Department of Epidemiology and Public Health
Imperial College, St Mary's Campus
Norfolk Place, London W2 1PG
Tel +44 (0)20 7594 1602 Fax (+44) 020 7594 3193
f.calboli [.a.t] imperial.ac.uk
f.calboli [.a.t] gmail.com
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[R] last command history???
Hi, I am using R 2.2.0 on Mac OS X 10.3.9. But I test the issue also with R 2.2.1 on OS X 10.4 (Tiger) I have a question regarding the functioning of the history from the command line. When I press the 'up-arrow' I call back the last command (everything ok), let's say that I go back until the level n-5, but when I get down to return to the empty line, I cannot reach the empty line... The empty line 'level' show me the content of the line n-4. example, let's say I did this sequence of command: x - c(1:10) mean(x) [1] 5.5 sd(x) [1] 3.027650 x [1] 1 2 3 4 5 6 7 8 9 10 # If I return to the command 'x - c(1:10)' and then get down the bottom line is : mean(x) Well it doesn't work like that under Windows and I guess under Linux. What is the setting that I should change? Or where is the error I made... David __ 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] rob var/cov + LAD regression
On Feb 8, 2006, at 10:22 AM, Angelo Secchi wrote: 1. Is there a function to have a jackknifed corrected var/cov estimate (as described in MacKinnon and White 1985) in a standard OLS regression? package: sandwich 2. Does R possess a LAD (Least Absolute Deviation) regression function? package: quantreg url:www.econ.uiuc.edu/~rogerRoger Koenker email[EMAIL PROTECTED]Department of Economics vox: 217-333-4558University of Illinois fax: 217-244-6678Champaign, IL 61820 __ 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] slightly off-topic re prcomp()
If you don't get a response: reproducible example, please. I suspect that you're looking at numerical analysis artifacts, assuming I have correctly interpreted you. -- Bert Gunter Genentech Non-Clinical Statistics South San Francisco, CA The business of the statistician is to catalyze the scientific learning process. - George E. P. Box -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Laura Quinn Sent: Wednesday, February 08, 2006 9:50 AM To: r-help@stat.math.ethz.ch Subject: [R] slightly off-topic re prcomp() Hi, I was wondering if anyone could tell me why prcomp() will Invent modes of variation in a PCA on identical replicates of data? I would have expected 50 (or whatever number) of identical replicates to return a null score in such an analysis (or at the least, all variables would share the same PC score). This is not the case and I was wondering could someone point me in the direction of some literature to explain the reason behind this? Laura Quinn Institute of Atmospheric Science School of Earth and Environment University of Leeds Leeds LS2 9JT tel: +44 113 343 1596 fax: +44 113 343 6716 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-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] slightly off-topic re prcomp()
On 2/8/2006 12:50 PM, Laura Quinn wrote: Hi, I was wondering if anyone could tell me why prcomp() will Invent modes of variation in a PCA on identical replicates of data? I would have expected 50 (or whatever number) of identical replicates to return a null score in such an analysis (or at the least, all variables would share the same PC score). This is not the case and I was wondering could someone point me in the direction of some literature to explain the reason behind this? I think you'll need to show us an example. I just tried what I think you described, and got all the components with 0 standard deviation, as I would have expected. Duncan Murdoch Laura Quinn Institute of Atmospheric Science School of Earth and Environment University of Leeds Leeds LS2 9JT tel: +44 113 343 1596 fax: +44 113 343 6716 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-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] what are the limits on R array sizes?
On Wed, 8 Feb 2006, Mike Miller wrote: I have some computers with a massive amount of memory, and I have some jobs that could use very large matrix sizes. Can R handle matrices of larger than 2GB? If I were to create a matrix of 1,000,000 x 1,000, it would use about 8GB. Can R work with an array of that size if I have compiled R on an IA64 Linux system with 15GB of RAM? Yes. See ?Memory-limits. help.search(limits) gets you there. -- 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] problem to install R on linux
Hi I had similar issue which was resolved by ensuring that I have the lib/include folder for readline in my LD_LIBRARY_PATH and PATH respectively. Thanks Gautam Bhola -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of André Beló Sent: Wednesday, February 08, 2006 1:09 PM To: r-help@stat.math.ethz.ch Subject: [R] problem to install R on linux Dear members, this can sound trivial for some people but I don't have experience on compilation. I'm trying to install R-2.2.1 on a laptop running Mandriva 2006. I already installed many of the recommended packages/libraries but it seems that something is still missing. The problem is that I cannot identify... Could somebody give me some advise? I put the output of the command ./configure bellow. When I tryed to install the R-2.0.0-1mdk.i586.rpm I got: [EMAIL PROTECTED] Download]# rpm -i R-2.0.0-1mdk.i586.rpm warning: R-2.0.0-1mdk.i586.rpm: Header V3 DSA signature: NOKEY, key ID 6c60ceea error: Failed dependencies: info is needed by R-2.0.0-1mdk.i586 [EMAIL PROTECTED] Download]# Thanks in advance, AB [EMAIL PROTECTED] R-2.2.1]# ./configure checking build system type... i686-pc-linux-gnu checking host system type... i686-pc-linux-gnu loading site script './config.site' loading build specific script './config.site' checking for pwd... /bin/pwd checking whether builddir is srcdir... yes checking for working aclocal... found checking for working autoconf... found checking for working automake... found checking for working autoheader... found checking for working makeinfo... found checking for gawk... gawk checking for egrep... grep -E checking whether ln -s works... yes checking for ranlib... ranlib checking for bison... no checking for byacc... no checking for ar... ar checking for a BSD-compatible install... /usr/bin/install -c checking for sed... /bin/sed checking for less... /usr/bin/less checking for perl... /usr/bin/perl checking whether perl version is at least 5.004... yes checking for dvips... /usr/bin/dvips checking for tex... /usr/bin/tex checking for latex... /usr/bin/latex checking for makeindex... /usr/bin/makeindex checking for pdftex... /usr/bin/pdftex checking for pdflatex... /usr/bin/pdflatex checking for makeinfo... /usr/bin/makeinfo checking for unzip... /usr/bin/unzip checking for zip... /usr/bin/zip checking for gzip... /bin/gzip checking for firefox... no checking for mozilla... no checking for netscape... no checking for galeon... no checking for kfmclient... no checking for opera... no checking for gnome-moz-remote... /usr/bin/gnome-moz-remote using default browser ... /usr/bin/gnome-moz-remote checking for acroread... /usr/bin/acroread checking for gcc... gcc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ANSI C... none needed checking how to run the C preprocessor... gcc -E checking whether gcc needs -traditional... no checking how to run the C preprocessor... gcc -E checking for gfortran... gfortran checking whether we are using the GNU Fortran 77 compiler... no checking whether gfortran accepts -g... no checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking how to run the C++ preprocessor... g++ -E checking for a sed that does not truncate output... /bin/sed checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for /usr/bin/ld option to reload object files... -r checking for BSD-compatible nm... /usr/bin/nm -B checking how to recognise dependent libraries... pass_all checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking dlfcn.h usability... yes checking dlfcn.h presence... yes checking for dlfcn.h... yes checking the maximum length of command line arguments... 32768 checking command to parse /usr/bin/nm -B output from gcc object... ok checking for objdir... .libs checking for ranlib... (cached) ranlib checking for strip... strip checking if gcc static flag works... yes checking if gcc supports -fno-rtti -fno-exceptions... no checking for gcc option to produce PIC... -fPIC checking if gcc PIC flag -fPIC works... yes checking if gcc supports -c -o file.o... yes checking whether the gcc linker (/usr/bin/ld) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... GNU/Linux ld.so checking how to hardcode library
[R] ERROR: no applicable method for TukeyHSD
Why do I see this error? library(stats) require(stats) [1] TRUE tHSD - TukeyHSD(aov) Error in TukeyHSD(aov) : no applicable method for TukeyHSD In case it helps: aov Call: aov(formula = roi ~ (Cue * Hemisphere) + Error(Subject/(Cue * Hemisphere)), data = roiDataframe) Grand Mean: 8.195069 Stratum 1: Subject Terms: Residuals Sum of Squares 645.7444 Deg. of Freedom 7 Residual standard error: 9.604645 Stratum 2: Subject:Cue Terms: Cue Residuals Sum of Squares 0.386987 4.015740 Deg. of Freedom1 7 Residual standard error: 0.7574148 1 out of 2 effects not estimable Estimated effects are balanced Stratum 3: Subject:Hemisphere Terms: Hemisphere Residuals Sum of Squares153.4860 827.6699 Deg. of Freedom 1 7 Residual standard error: 10.87376 1 out of 2 effects not estimable Estimated effects are balanced Stratum 4: Subject:Cue:Hemisphere Terms: Cue:Hemisphere Residuals Sum of Squares5.085930 4.279707 Deg. of Freedom 1 7 Residual standard error: 0.7819122 Estimated effects are balanced [[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] jpeg or tiff file formats
I have been creating some graphic postscript files using xyplot but now I find that I need then in either the jpeg or tiff format. I have tried re-running just the lattice plot so that it is on the screen and then using the jpeg(filename=myplot. from the bmp, jpec and png graphics devices documentation. It seems to create an empty file. Is it that this function can not work with lattice plots? Can R directly write a jpeg or pgn file? -- Dean Sonneborn, MS Programmer Analyst Department of Public Health Sciences University of California, Davis (530) 754-9516 __ 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-sig-Geo] envi clone in R
Barry, I hope you will share your code! We've been using QGIS and I have in mind just such an interface to R. We have ENVI in the lab and it is very powerful for image processing. It would take many many person years to reproduce all of the advanced algorithms in that package. (It does a lot of simple operations as well and those could easily be recoded in R.) THK On Wed, 2006-02-08 at 18:09 +, Barry Rowlingson wrote: Wladimir Eremeev wrote: Hello all, Research Systems (www.rsinc.com) have developed and distributes the language IDL, and the GIS ENVI, written in IDL. I find it hard to believe they wrote it all in IDL! I'm guessing its probably scriptable in IDL, but underneath its written in something else... I could be wrong though! To my oppinion, R language is superior, compared to IDL, in all aspects. However, ENVI is the rather convenient and feature rich tool. I clicked on 'Product Documentation' on the ENVI site and it wanted me to log in or create a new user. To see the documentation? To find out what the program is about? Oh, what I really wanted was the Feature Tour.. Is anyone aware about any work, dedicated to the creation of something, similar to the ENVI, but in R? Last year I looked at GIS-R linkages, with the added criteria of being open source and cross-platform. There are now a few free GIS packages that can do this kind of thing, with a little added glue. I settled on OpenEV - it has vector and raster support, its extensible in Python and uses Gtk for dialogs which you can customise. All I needed was to get Python talking to R, so I wrote some Python bindings to Rserve. Now I've got a GIS with a menu that drops down, you choose the point layers you want to work on, click 'Go', and R does some analysis that ends up as a raster layer back in the GIS. The user doesnt care that R did it. Other GIS solutions are available! Barry ___ R-sig-Geo mailing list R-sig-Geo@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-geo -- Timothy H. Keitt Assistant Professor http://www.keittlab.org/ http://www.utexas.edu/directory/index.php?q=Keitt __ 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] bwplot: how to display response variables separately in same panel?
Hi - I have two response variables 'y1' and 'y2' and a factor 'x'. I would like to create paired box-whiskers plots for y1~x and y2~x and labeled for the same x. the b-w plots would be side-by-side in the same panel - almost like a barchart with two parallel columns for the same x. the code 'bwplot(y1+y2~x, outer=T)' gives me two side-by-side panels. this is ok, but not exactly what i am looking for. any ideas? thanks, chris Christopher Behr Principal Analyst eDesign Dynamics www.edesigndynamics.com 4024 Calvert St. NW Washington DC 20007 (202) 298-6437 (t/f) (551) 998-4823 (c) __ 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] jpeg or tiff file formats
On Wed, 8 Feb 2006, Dean Sonneborn wrote: I have been creating some graphic postscript files using xyplot but now I find that I need then in either the jpeg or tiff format. I have tried re-running just the lattice plot so that it is on the screen and then using the jpeg(filename=myplot. from the bmp, jpec and png graphics devices documentation. It seems to create an empty file. Is it that this function can not work with lattice plots? Can R directly write a jpeg or pgn file? Either FAQ 7.22 or dev.off()? -- Roger Bivand Economic Geography Section, Department of Economics, Norwegian School of Economics and Business Administration, Helleveien 30, N-5045 Bergen, Norway. voice: +47 55 95 93 55; fax +47 55 95 95 43 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
Re: [R] expand.grid without expanding
From: =?iso-8859-1?q?Lu=EDs_Torgo?= [EMAIL PROTECTED]
Date: Wed, 8 Feb 2006 18:08:40 +
Dear list,
I've recently came across a problem that I think I've solved and that I
wanted
to share with you for two reasons:
- Maybe others come across the same problem.
- Maybe someone has a much simpler solution that wants to share with me ;-)
The problem is as follows: expand.grid() allows you to generate a data.frame
with all combinations of a set of values, e.g.:
expand.grid(par1=-1:1,par2=c('a','b'))
par1 par2
1 -1a
20a
31a
4 -1b
50b
61b
There is nothing wrong with this nice function except when you have too many
combinations to fit in your computer memory, and that was my problem: I
wanted to do something for each combination of a set of variants, but this
set was to large for storing in memory in a data.frame generated by
expand.grid. A possible solution would be to have a set of nested for()
cycles but I preferred a solution that involved a single for() cycle going
from 1 to the number of combinations and then at each iteration having some
form of generating the combination i. And this was the real problem: how
to generate a function that picks the same style of arguments as
expand.grid() and provides me with the values corresponding to line i of
the data frame that would have been created bu expand.grid(). For instance,
if I wanted the line 4 of the above call to expand.grid() I should get the
same as doing:
expand.grid(par1=-1:1,par2=c('a','b'))[4,]
par1 par2
4 -1b
but obviously without having to use expand.grid() as that involves generating
a data frame that in my case wouldn't fit in the memory of my computer.
Now, the function I've created was the following:
getVariant - function(id,vars) {
if (!is.list(vars)) stop('vars needs to be a list!')
nv - length(vars)
lims - sapply(vars,length)
if (id prod(lims)) stop('id above the number of combinations!')
res - vector(list,nv)
for(i in nv:2) {
f - prod(lims[1:(i-1)])
res[[i]] - vars[[i]][ceiling(id / f)]
id - id - (ceiling(id/f)-1)*f
}
res[[1]] - vars[[1]][id]
names(res) - names(vars)
res
}
--
expand.grid(par1=-1:1,par2=c('a','b'))[4,]
par1 par2
4 -1b
getVariant(4,list(par1=-1:1,par2=c('a','b')))
$par1
[1] -1
$par2
[1] b
I would be glad to know if somebody came across the same problem and has a
better suggestion on how to solve this.
A few minor improvements:
1) let id be a vector of indices
2) use %% and %/% instead of ceiling (perhaps debateable)
3) return a data frame as does expand.grid
So your function now looks like:
getVariant - function(id, vars) {
if (!is.list(vars)) stop('vars needs to be a list!')
nv - length(vars)
lims - sapply(vars, length)
if (any(id prod(lims))) stop('id above the number of combinations!')
res - vector(list, nv)
for(i in nv:2) {
f - prod(lims[1:(i-1)])
res[[i]] - vars[[i]][(id - 1)%/%f + 1]
id - (id - 1)%%f + 1
}
res[[1]] - vars[[1]][id]
names(res) - names(vars)
return(as.data.frame(res))
}
Now, for example, you get:
expand.grid(par1=-1:1,par2=c('a','b'),par3=c('w','x','y','z'))[12:15,]
par1 par2 par3
121bx
13 -1ay
140ay
151ay
getVariant(12:15,list(par1=-1:1,par2=c('a','b'), par3=c('w','x','y','z')))
par1 par2 par3
11bx
2 -1ay
30ay
41ay
Note that you will run into trouble when the product of the lengths is
greater than the largest representable integer on your system.
Hope this helps,
Ray Brownrigg
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[R] Simple optim - question
Hello,
I want to find the parameters mu and sigma that minimize the following
function.
It's important, that mu and sigma are strictly positive.
-
optimiere = function(fmean,smean,d,x,mu,sigma)
{
merk = c()
for (i in 1:length(d))
merk=c(merk,1/(d[i]^2)*(d[i]-1/(fmean*(1-plnorm(x[i],mu,sigma^2)
return(sum(merk))
}
-
To do that I'm using the nlm function, but I only get results for ONE of the
two parameters.
I cannot cope with optimizing the two parameter problem simultaneously.
I've started with:
nlm(optimiere,p=5,fmean=10,smean=1,d=c(40,10),x=c(50,5),sigma=3.
5)
Then I tried to combine mu and sigma in one Vector. I get back two
parameters but the results are unreasonable since mu and sigma are
-0.3247726 and 4.7905308 but have to be strictly positive.
I've given up after hours and hope to get your help..
I'm sure the problem should be easily solved by one of the experts.
Thanks a lot.
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[R] Plotting a count process
hello everybody, i want to plot a count process in the following way, but i don't know how i can do that. i have data for example x-(0,2,6,2,8,4,.) and dates y which is a vector of weekly dates for example (01/01/06, 08/01/06, 15/01/06, 22/01/06, ), now i want to plot the y's an the horizontal axis. On each date the count process jumps upwards 1 unit, so the vertical axis is 0, 1, 2, 3, .. the distance between the dates is shown in vector x, so for example the distance between 08/01/06 and 15/01/06 should be 2. maybe i can use some times series functions for doing this? i would be very thankful for any advice. best regards Andreas __ 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] ROracle installation problem with R2.2
Hi, I just installed R version 2.2.1, I installed DBI package and worked fine and then I installed ROracle but I got this error: [EMAIL PROTECTED] bin]$ R CMD INSTALL --configure-args='--enable-extralibs' ../../ROracle_0.5-5.tar.gz * Installing *source* package 'ROracle' ... creating cache ./config.cache checking how to run the C preprocessor... cc -E updating cache ./config.cache creating ./config.status creating src/Makevars sed: file conftest.s1 line 29: Unterminated `s' command creating src/Makefile sed: file conftest.s1 line 29: Unterminated `s' command ** libs make: *** No targets. Stop. ERROR: compilation failed for package 'ROracle' ** Removing '/home/drapeau/download/R-2.2.1/library/ROracle' Any idea what could cause this problem? I used to install the same ROracle version with R version 1.9 and it worked. Thanks, Mathieu __ 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] bwplot: how to display response variables separately in same panel?
On 2/8/06, Chris Behr [EMAIL PROTECTED] wrote: Hi - I have two response variables 'y1' and 'y2' and a factor 'x'. I would like to create paired box-whiskers plots for y1~x and y2~x and labeled for the same x. the b-w plots would be side-by-side in the same panel - almost like a barchart with two parallel columns for the same x. the code 'bwplot(y1+y2~x, outer=T)' gives me two side-by-side panels. this is ok, but not exactly what i am looking for. any ideas? Unless you want to write your own panel function, you need to start by coercing the data into the `long' format, e.g. df - data.frame(y = c(y1, y2), x = rep(x, 2), which = gl(2, length(x))) Then you can probably do [untested] bwplot(y ~ which | x, df, layout = c(nlevels(x), 1)) or bwplot(y ~ x:which, df) Deepayan __ 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] Newton-Raphson algorithm
Hi, I want to maximize a liklihood function with multiple parameters. There is no closed-form analytical solution to the estimates of the parameters, and I would like to implement a Newton-Raphson iterrative approach. Is there a maximization procedure, such as the Newton-Raphson algorithm, available in R? If not, does anybody have an idea how to best go about solving simultenous equations numerically in R? Thanks for your help. Frank. -- love email again __ 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] List Conversion
Hello, I have a list (mode and class are list) in R that is many elements long and of the form: length(list) [1] 5778 list[1:4] $ID1 [1] num1 $ID2 [1] num2 num3 $ID3 [1] num4 $ID4 [1] NA I'd like to convert the $ID2 value to be in one element rather than in two. It shows up as c(\num2\, \num3\) if I try to use paste(list[2], collapse=). I need to do this over the length of the entire list, however list2 - apply(list, 1, paste, collapse=) tells me 'Error in apply : dim(X) must have a positive length'. dim(list) does not have a positive length, which I think is due to the fact that it's a list and not a matrix or data frame. What I want to get is: list[1:4] $ID1 [1] num1 $ID2 [1] num2 num3 $ID3 [1] num4 $ID4 [1] NA Thanks. Liz -- ___ Play 100s of games for FREE! http://games.mail.com/ __ 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] List Conversion
LD == Liz Dem [EMAIL PROTECTED] writes: LD I have a list (mode and class are list) in R that is many elements long and of the form: length(list) LD [1] 5778 list[1:4] LD $ID1 LD [1] num1 LD $ID2 LD [1] num2 num3 LD $ID3 LD [1] num4 LD $ID4 LD [1] NA LD I'd like to convert the $ID2 value to be in one element rather LD than in two. It shows up as c(\num2\, \num3\) if I try to LD use paste(list[2], collapse=). You want list[[2]], not list[2]: tt - list(ID1=num1, ID2=c(num2, num3), ID3 = num4, ID4 =NA) tt $ID1 [1] num1 $ID2 [1] num2 num3 $ID3 [1] num4 $ID4 [1] NA paste(tt[2], collapse=) [1] c(\num2\, \num3\) paste(tt[[2]], collapse=) [1] num2num3 paste(tt[[2]], collapse= ) [1] num2 num3 LD I need to do this over the length of the entire list, however LD list2 - apply(list, 1, paste, collapse=) tells me 'Error in LD apply : dim(X) must have a positive length'. You want to use `lapply' not `apply': tt1 - lapply(tt, paste, collapse= ) tt1 $ID1 [1] num1 $ID2 [1] num2 num3 $ID3 [1] num4 $ID4 [1] NA LD What I want to get is: list[1:4] LD $ID1 LD [1] num1 LD $ID2 LD [1] num2 num3 LD $ID3 LD [1] num4 LD $ID4 LD [1] NA In that case, if you don't want NA's to turn into strings: tt2 - lapply(tt, function(x) if(is.na(x[1])) NA else paste(x, collapse= )) tt2 $ID1 [1] num1 $ID2 [1] num2 num3 $ID3 [1] num4 $ID4 [1] NA HTH. Cheers, Berwin == Full address Berwin A Turlach Tel.: +61 (8) 6488 3338 (secr) School of Mathematics and Statistics+61 (8) 6488 3383 (self) The University of Western Australia FAX : +61 (8) 6488 1028 35 Stirling Highway Crawley WA 6009e-mail: [EMAIL PROTECTED] Australiahttp://www.maths.uwa.edu.au/~berwin __ 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
