[R] including Sweave tangled code in '.Rnw' document
Hello List,
I have been using Sweave for my homework this last quarter and have been
very impressed at how much time and effort it saves me. I, however, have
run up against a problem which I have not been able to solve using any of
the Sweave/LaTeX tricks I know. I work through my homework one problem at a
time, typesetting equations and writing R code, etc. and occasionally use
'Stangle()' from within R to extract the code if I need to pin down a
problem or experiment interactively. I would like to be able to include
this resultant code in a verbatim environment in my final TeX'ed up document
as an appendix so that the grader can look it over, etc. I could implement
this in any number of ways using linux tools, but would like to know if
there is a clean way to do so using LaTeX or Sweave so that the latest
version of the code is included in my homework each time I run 'R CMD Sweave
HW4.Rnw; pdflatex HW4.tex'.
e.g I envision something such as:
\begin{document}
fig3, echo=false, results=hide, fig=true, eps=F=
plot(runif(1000))
@
TA here is my code:
% some manner of Sweave/LaTeX macro to include the R code tangled out of
this '.Rnw' document
% in this case it would just be 'plot(runif(1000))', perhaps manually
enclosed in a verbatim environment
\end{document}
I am running R-2.6.2 on Ubuntu Hardy Heron.
Thanks for all your help with Sweave. I think it is a fantastic tool.
Kyle
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[R] function for simultaneous confidence interval of regression coefficients
List,
Would someone be so kind as to point me to a function that will calculate
simultaneous confidence intervals of regression coefficients based upon
their distribution as (under the assumption of normal errors, with
\mathbf{X} as the design matrix):
$\hat{\mathbf{\beta}} \sim N(\mathbf{\beta},
\sigma^2(\mathbf{X}^T\mathbf{X})^{-1})$.
'confint' calculates individual coefficients so far as I can tell, but I
need simultaneous CIs based on the confidence ellipse/ F distribution.
Inverting the ellipse gives this equation:
\mathbf{\hat{\beta}} \pm
\sqrt{\mathrm{diag}(s^2(\mathbf{X}^T\mathbf{X})^{-1}) \times p \times F_{p,
n-p, .95}}
Thanks, and sorry for such a dumb question. Either I am not searching for
the right thing or this hasn't already been addressed in the lists (perhaps
because it is so easy).
Kyle
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Re: [R] Drawing a tree in R
Severin Hacker wrote: Hi, I've been trying to make use of the dendrogram class to plot a tree. However, my attempts have failed so far because I'm not sure how to build up the nested list. (where do I have to store the nodes?). The tree I want to be drawn is like this: in the form (node, left child,right child) (root,(n1,1,(n2,2,3)),4) If it is not easily possible to draw a tree with the help of the dendrogram class I'm open to any other method to draw a tree in R!! Thanks! -Severin Severin, Check out the R package ape for plotting phylogenetic trees. require(ape) foo - read.tree(text = (root,(n1,1,(n2,2,3)),4);) plot(foo) HTH Peter -- View this message in context: http://www.nabble.com/Drawing-a-tree-in-R-tp20711698p20749736.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] about body-
In body(fun, envir = environment(fun)) - value, value can be an
expression or a list of R expressions.
But it seems that value must be length-1 list (if it is a list), is it right?
f2 - function(x) {}
body(f2) - list(quote(x- x^5),quote(return(y)))
Error in as.function.default(c(formals(fun), value), envir) :
invalid formal argument list for function
I want to construct a function by computing, what I do at this moment
is as follows:
f - function(x) {}
body(f)[[2]] - quote(x- x^5)
body(f)[[3]] - quote(return(y))
Is there a better way to do this?
Thanks
--
HUANG Ronggui, Wincent
Tel: (00852) 3442 3832
PhD Candidate, City University of Hong Kong
http://ronggui.huang.googlepages.com/
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] including Sweave tangled code in '.Rnw' document
G'day Kyle,
On Sat, 29 Nov 2008 11:11:37 -0800
Kyle Matoba [EMAIL PROTECTED] wrote:
I have been using Sweave for my homework this last quarter [...] but
would like to know if there is a clean way to do so using LaTeX or
Sweave so that the latest version of the code is included in my
homework each time I run 'R CMD Sweave HW4.Rnw; pdflatex HW4.tex'.
e.g I envision something such as:
A file HW4.Rnw such as the following seem to do what you want:
++ start HW4.Rnw ++
\documentclass[a4paper,11pt]{article}
\usepackage{listings}
\begin{document}
fig3, echo=FALSE, results=hide, fig=TRUE, eps=FALSE=
plot(runif(1000))
@
=
mean(runif(1000))
@
TA here is my code:
% some manner of Sweave/LaTeX macro to include the R code tangled out
% of this '.Rnw' document in this case it would just be
% 'plot(runif(1000))', perhaps manually enclosed in a verbatim
% environment
echo=FALSE, results=hide,split=TRUE=
Stangle(file=HW4.Rnw, output=XYZ.R, annotate=FALSE)
@
\lstinputlisting[emptylines=0]{XYZ.R}
\end{document}
++ end HW4.Rnw
If the last Stangle command should be included in the listing, remove
the split=TRUE option. And the file= argument to Stangle would
have to be correctly set for each .Rnw file; did not find a way to
automate this.
I am running R-2.6.2 on Ubuntu Hardy Heron.
R 2.6.2 is quite old by now, the current version is R 2.8.0. When you
upgrade, be aware of:
o The default for 'stylepath' in Sweave's (default) RweaveLatex
driver is now FALSE rather than TRUE if
SWEAVE_STYLEPATH_DEFAULT is unset : see ?RweaveLatex.
To support this, tools::texi2dvi adds the R 'texmf' directory
to the input search path.
which could mean that the way you process .Rnw file might no longer
work.
HTH.
Cheers,
Berwin
=== Full address =
Berwin A TurlachTel.: +65 6516 4416 (secr)
Dept of Statistics and Applied Probability+65 6516 6650 (self)
Faculty of Science FAX : +65 6872 3919
National University of Singapore
6 Science Drive 2, Blk S16, Level 7 e-mail: [EMAIL PROTECTED]
Singapore 117546http://www.stat.nus.edu.sg/~statba
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[R] simple question with table()
Dear List, my problem should be easy to fix, but I couldn't find a solution by myself... In my survey, there is a question with 14 possible answers. None of the respondents choose the 13th answer, so when I table() the results, R says: 1 2 3 4 5 6 7 8 9 10 11 12 14 31 52 7 21 40 7 8 2 28 2 2 1 17 13 is missing... anyone knows how to tell table() that there are 14 modalities in the answers? I tried with responseName =c(1,2,3,4,5,6,7,8,9,10,11,12,13,14) but all I have is: error in table all the arguments must have the same length thank you, Simone __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] simple question with table()
G'day Simone, On Sun, 30 Nov 2008 11:05:13 +0100 Simone Gabbriellini [EMAIL PROTECTED] wrote: my problem should be easy to fix, but I couldn't find a solution by myself... In my survey, there is a question with 14 possible answers. None of the respondents choose the 13th answer, so when I table() the results, R says: [...] 13 is missing... anyone knows how to tell table() that there are 14 modalities in the answers? The easiest way is probably to turn your data into a factor with the appropriate set of levels: R dat - sample(c(1:12,14), 100, replace=TRUE) R table(factor(dat, levels=min(dat):max(dat))) 1 2 3 4 5 6 7 8 9 10 11 12 13 14 9 5 4 7 7 11 8 10 9 8 6 11 0 5 that was once the solution of one of my colleagues and I find it somewhat nicer than the one I came up with: R rng - min(dat):max(dat) R res - colSums(outer(dat, min(dat):max(dat), ==)) R names(res) - rng R res 1 2 3 4 5 6 7 8 9 10 11 12 13 14 9 5 4 7 7 11 8 10 9 8 6 11 0 5 HTH. Best wishes, Berwin === Full address = Berwin A TurlachTel.: +65 6516 4416 (secr) Dept of Statistics and Applied Probability+65 6516 6650 (self) Faculty of Science FAX : +65 6872 3919 National University of Singapore 6 Science Drive 2, Blk S16, Level 7 e-mail: [EMAIL PROTECTED] Singapore 117546http://www.stat.nus.edu.sg/~statba __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] simple question with table()
On 11/30/2008 5:05 AM, Simone Gabbriellini wrote:
Dear List,
my problem should be easy to fix, but I couldn't find a solution by
myself...
In my survey, there is a question with 14 possible answers. None of the
respondents choose the 13th answer, so when I table() the results, R says:
12345678910111214
3152721407822822117
13 is missing... anyone knows how to tell table() that there are 14
modalities in the answers? I tried with
responseName=c(1,2,3,4,5,6,7,8,9,10,11,12,13,14)
but all I have is:
error in table
all the arguments must have the same length
Make the responses to the question a factor and set the levels of the
factor to include all 14 possible answers. For example:
table(factor(rep(c('1','2'), each=7), levels=c('1','2','3')))
1 2 3
7 7 0
?factor
thank you,
Simone
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--
Chuck Cleland, Ph.D.
NDRI, Inc. (www.ndri.org)
71 West 23rd Street, 8th floor
New York, NY 10010
tel: (212) 845-4495 (Tu, Th)
tel: (732) 512-0171 (M, W, F)
fax: (917) 438-0894
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Re: [R] simple question with table()
Dear Simone, Try this: x=c(1,1,2,3,4,3,2,2,2,1,2,3,4,4,3) table(factor(x,levels=1:5)) 1 2 3 4 5 3 5 4 3 0 HTH, Jorge On Sun, Nov 30, 2008 at 5:05 AM, Simone Gabbriellini [EMAIL PROTECTED] wrote: Dear List, my problem should be easy to fix, but I couldn't find a solution by myself... In my survey, there is a question with 14 possible answers. None of the respondents choose the 13th answer, so when I table() the results, R says: 1 2 3 4 5 6 7 8 9 10 11 12 14 31 52 7 21 40 7 8 2 28 2 2 1 17 13 is missing... anyone knows how to tell table() that there are 14 modalities in the answers? I tried with responseName=c(1,2,3,4,5,6,7,8,9,10,11,12,13,14) but all I have is: error in table all the arguments must have the same length thank you, Simone __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] simple question with table()
you have to use a factor, e.g., x - sample((1:14)[-13], 100, TRUE) f - factor(x, levels = 1:14) table(f) I hope it helps. Best, Dimitris Simone Gabbriellini wrote: Dear List, my problem should be easy to fix, but I couldn't find a solution by myself... In my survey, there is a question with 14 possible answers. None of the respondents choose the 13th answer, so when I table() the results, R says: 12345678910111214 3152721407822822117 13 is missing... anyone knows how to tell table() that there are 14 modalities in the answers? I tried with responseName=c(1,2,3,4,5,6,7,8,9,10,11,12,13,14) but all I have is: error in table all the arguments must have the same length thank you, Simone __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Dimitris Rizopoulos Assistant Professor Department of Biostatistics Erasmus Medical Center Address: PO Box 2040, 3000 CA Rotterdam, the Netherlands Tel: +31/(0)10/7043478 Fax: +31/(0)10/7043014 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] help: unbalanced repeated measures
Sumitrajit Dhar wrote: Hi folks, I am trying to figure out how run a repeated measures ANOVA on the following data set. subject trial frequency dplvl 1 FSI052A A 1NA 2 FSI052B B 1NA 3 FSI053A A 1NA .. Both frequency and trial are factorized. is.factor(trial) [1] TRUE is.factor(frequency) [1] TRUE levels(frequency) [1] 1 2 3 4 6 I know that I should be using 'lme' rather than aov, but summary(aov(dplvl~trial*frequency+Error(subject/ (trial*frequency)),data=tenB)) Error: subject Df Sum Sq Mean Sq F value Pr(F) trial1 7.157.15 0.2566 0.6203 frequency1 40.84 40.84 1.4657 0.2461 trial:frequency 1 0.030.03 0.0013 0.9723 Residuals 14 390.11 27.86 Error: subject:frequency Df Sum Sq Mean Sq F value Pr(F) frequency1 183.893 183.893 11.925 0.003271 ** trial:frequency 1 16.393 16.393 1.063 0.317866 Residuals 16 246.738 15.421 --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 Error: Within Df Sum Sq Mean Sq F value Pr(F) Residuals 35 269.137.69 What I do not understand is why I am getting df=1 for frequency when there are 5 levels of that factor. Is tenB$frequency also a factor? The prototypical error would be to have modified only a copy of it. By the way, with that amount of NA in the response, you are not going to undertand aov output in any case... (and what happened with the subject:trial stratum???) -- 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@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] barplot labels
Dear List, is it possible to plot vertical labels under vertical bars? for vertical labels I mean to rotate 90 degrees horizontal labels I suppose yes, because if excel can do this, R should do it twice better... thank you, Simone __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Fwd: simple question with table()
Dear ALL, thank you for this sunday morning help! It works great! all the best, Simone Il giorno 30/nov/08, alle ore 11:22, Jorge Ivan Velez ha scritto: Dear Simone, Try this: x=c(1,1,2,3,4,3,2,2,2,1,2,3,4,4,3) table(factor(x,levels=1:5)) 1 2 3 4 5 3 5 4 3 0 HTH, Jorge On Sun, Nov 30, 2008 at 5:05 AM, Simone Gabbriellini [EMAIL PROTECTED] wrote: Dear List, my problem should be easy to fix, but I couldn't find a solution by myself... In my survey, there is a question with 14 possible answers. None of the respondents choose the 13th answer, so when I table() the results, R says: 1 2 3 4 5 6 7 8 9 10 11 12 14 31 52 7 21 40 7 8 2 28 2 2 1 17 13 is missing... anyone knows how to tell table() that there are 14 modalities in the answers? I tried with responseName =c(1,2,3,4,5,6,7,8,9,10,11,12,13,14) but all I have is: error in table all the arguments must have the same length thank you, Simone __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. dott. Simone Gabbriellini - PhD Student Department of Social Sciences University of Pisa [EMAIL PROTECTED] [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] barplot labels
Hi Simone,
Yes. Take a look at the las argument in ?par. Here is an example with
barplot:
barplot(table(factor(x,levels=1:5)),names.arg=c('First','Second','Third','Forth','Fifth'),las=2)
HTH,
Jorge
On Sun, Nov 30, 2008 at 5:33 AM, Simone Gabbriellini
[EMAIL PROTECTED] wrote:
Dear List,
is it possible to plot vertical labels under vertical bars? for vertical
labels I mean to rotate 90 degrees horizontal labels
I suppose yes, because if excel can do this, R should do it twice better...
thank you,
Simone
__
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[[alternative HTML version deleted]]
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[R] about centralization
Hi all, Is there anyone who ever used igraph to calculate the index of centralization ? I tried my best but can't find it in igraph. The brief introduction to centralization can be found here , and I think it's an important index for measuring the centrality on the aggregated level.(http://faculty.ucr.edu/~hanneman/nettext/C10_Centrality.html) Thank you for any comments and suggestions. Best wishes! Weijia [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] about body-
Its also possible to build up a string:
f - function(x) {}
body(f) - parse(text = { x - x^5; return(x) })
f
function (x)
{
x - x^5
return(x)
}
On Sun, Nov 30, 2008 at 4:15 AM, ronggui [EMAIL PROTECTED] wrote:
In body(fun, envir = environment(fun)) - value, value can be an
expression or a list of R expressions.
But it seems that value must be length-1 list (if it is a list), is it right?
f2 - function(x) {}
body(f2) - list(quote(x- x^5),quote(return(y)))
Error in as.function.default(c(formals(fun), value), envir) :
invalid formal argument list for function
I want to construct a function by computing, what I do at this moment
is as follows:
f - function(x) {}
body(f)[[2]] - quote(x- x^5)
body(f)[[3]] - quote(return(y))
Is there a better way to do this?
Thanks
--
HUANG Ronggui, Wincent
Tel: (00852) 3442 3832
PhD Candidate, City University of Hong Kong
http://ronggui.huang.googlepages.com/
__
R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
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Re: [R] including Sweave tangled code in '.Rnw' document
You could achieve this from the LaTeX side of things using the
attachfile package:
http://www.ctan.org/tex-archive/macros/latex/contrib/attachfile/
I use this package to attach data files and R code to pdf's generated
with Sweave + pdflatex, so that the entire analysis can be reproduced
from a single document.
-Ista
-- Forwarded message --
From: Kyle Matoba [EMAIL PROTECTED]
To: r-help@r-project.org
Date: Sat, 29 Nov 2008 11:11:37 -0800
Subject: [R] including Sweave tangled code in '.Rnw' document
Hello List,
I have been using Sweave for my homework this last quarter and have been
very impressed at how much time and effort it saves me. I, however, have
run up against a problem which I have not been able to solve using any of
the Sweave/LaTeX tricks I know. I work through my homework one problem at a
time, typesetting equations and writing R code, etc. and occasionally use
'Stangle()' from within R to extract the code if I need to pin down a
problem or experiment interactively. I would like to be able to include
this resultant code in a verbatim environment in my final TeX'ed up document
as an appendix so that the grader can look it over, etc. I could implement
this in any number of ways using linux tools, but would like to know if
there is a clean way to do so using LaTeX or Sweave so that the latest
version of the code is included in my homework each time I run 'R CMD Sweave
HW4.Rnw; pdflatex HW4.tex'.
e.g I envision something such as:
\begin{document}
fig3, echo=false, results=hide, fig=true, eps=F=
plot(runif(1000))
@
TA here is my code:
% some manner of Sweave/LaTeX macro to include the R code tangled out of
this '.Rnw' document
% in this case it would just be 'plot(runif(1000))', perhaps manually
enclosed in a verbatim environment
\end{document}
I am running R-2.6.2 on Ubuntu Hardy Heron.
Thanks for all your help with Sweave. I think it is a fantastic tool.
Kyle
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Snow and multi-processing
I think I found a solution. I do not like to use global variable by fear of
unpredictable side-effects but, I think that in this case I don't have to much
chance.
Here is a mock function that pushes the content of a variable evaluated within
a function to the nodes on the cluster, do some computation on the nodes using
that variable and then return the result after cleaning up the newly created
global variable.
Let me know what you people think:
aTest - function(x,n.nodes=2){
library(snow)
#initialize a cluster
makeCluster(rep('locahost',n.nodes),type='SOCK')
#create a global variable
y - x
#export the variable to the cluster
clusterExport(cl,'y')
#do some computation on the cluster
c - clusterEvalQ(cl,y+2)
#remove the variable from the global environment
rm(y, envir=.GlobalEnv)
#stop the cluster
stopCluster(cl)
#exit and return the computation
return(c)
}
On 11/29/08 6:59 PM, Marco Blanchette [EMAIL PROTECTED] wrote:
Dear R gurus,
I have a very embarrassingly parallelizable job that I am trying to speed up
with snow on our local cluster. Basically, I am doing ~50,000 t.test for a
series of micro-array experiments, one gene at a time. Thus, I can easily
spread the load across multiple processors and nodes.
So, I have a master list object that tells me what rows to pick up for each
genes to do the t.test from series of microarray experiments containing
~500,000 rows and x columns per experiments.
While trying to optimize my function using parLapply(), I quickly realized that
I was not gaining any speed because every time a test was done on one of the
item in the list, the 500,000 line by x column matrix had to be shipped along
with the item in the list and the traffic time was actually longer than the
computing time.
However, if I export the 500,000 object first across the spawned processes as
in this mock script
cl - makeCluster(nnodes,method)
mArrayData - getData(experiments)
clusterExport(cl, 'mArrayData')
Results - parLapply(cl, theMapList, function(x) t.testFnc(x))
With a function that define the mArrayData argument as a default parameter as in
t.testFnc - function(probeList, array=mArrayData){
x - array[probeList$A,]
y - array[probeList$B,]
res - doSomeTest(x,y)
return(res)
}
Using this strategy, I was able to gain full advantage of my cluster and reduce
the analysis time by the number of nodes I have in our cluster. The large data
matrix was resident in each processes and didn't have to travel on the network
every time a item from the list was pass to the function t.testFnc()
However, I quickly realized that this works (the call to clusterExport() ) only
when I run the script one line at a time. When the process is enclosed in a
function, the object mArrayData is not exported, presumably because it's not a
global object from the Master process.
So, what is the alternative to push the content of an object to the slaves? The
documentation in the snow package is a bit light and I couldn't find good
example out there. I don't want to have the function getData() evaluated on
each nodes because the argument to that functions are humongous and that would
cause way too much traffic on the network. I want the result of the function
getData(), the object mArrayData, propagated to the cluster only once and be
available to downstream functions.
Hope this is clear and that a solution will be possible.
Many thanks
Marco
--
Marco Blanchette, Ph.D.
Assistant Investigator
Stowers Institute for Medical Research
1000 East 50th St.
Kansas City, MO 64110
Tel: 816-926-4071
Cell: 816-726-8419
Fax: 816-926-2018
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--
Marco Blanchette, Ph.D.
Assistant Investigator
Stowers Institute for Medical Research
1000 East 50th St.
Kansas City, MO 64110
Tel: 816-926-4071
Cell: 816-726-8419
Fax: 816-926-2018
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Re: [R] about centralization
Weijia, centralization was not included in igraph, because really, it takes only writing a one line function to do it. But it is on our TODO list and will be included soon. E.g. for degree see the thread that starts here: http://lists.gnu.org/archive/html/igraph-help/2008-11/msg00064.html You can do it similarly for other measures, but first you need to find out which structure is the most centralized for a given measure. E.g. for degree it is the star graph, but not for eigenvector centrality. Probably this is written in the classic Wasserman-Faust book. Best, Gabor On Sun, Nov 30, 2008 at 1:37 PM, Weijia You [EMAIL PROTECTED] wrote: Hi all, Is there anyone who ever used igraph to calculate the index of centralization ? I tried my best but can't find it in igraph. The brief introduction to centralization can be found here , and I think it's an important index for measuring the centrality on the aggregated level.(http://faculty.ucr.edu/~hanneman/nettext/C10_Centrality.html) Thank you for any comments and suggestions. Best wishes! Weijia [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Gabor Csardi [EMAIL PROTECTED] UNIL DGM __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] including Sweave tangled code in '.Rnw' document
Kyle,
In addition to listings already mentioned by Berwin, you may find
useful the answers package. This is what I use to create assignments/
exams/exercise sets with solutions all in one file.
HTH
Vincent
---
Vincent Goulet, Associate Professor
École d'actuariat
Université Laval, Québec
[EMAIL PROTECTED] http://vgoulet.act.ulaval.ca
Le sam. 29 nov. à 14:11, Kyle Matoba a écrit :
Hello List,
I have been using Sweave for my homework this last quarter and have
been
very impressed at how much time and effort it saves me. I, however,
have
run up against a problem which I have not been able to solve using
any of
the Sweave/LaTeX tricks I know. I work through my homework one
problem at a
time, typesetting equations and writing R code, etc. and
occasionally use
'Stangle()' from within R to extract the code if I need to pin down a
problem or experiment interactively. I would like to be able to
include
this resultant code in a verbatim environment in my final TeX'ed up
document
as an appendix so that the grader can look it over, etc. I could
implement
this in any number of ways using linux tools, but would like to know
if
there is a clean way to do so using LaTeX or Sweave so that the latest
version of the code is included in my homework each time I run 'R
CMD Sweave
HW4.Rnw; pdflatex HW4.tex'.
e.g I envision something such as:
\begin{document}
fig3, echo=false, results=hide, fig=true, eps=F=
plot(runif(1000))
@
TA here is my code:
% some manner of Sweave/LaTeX macro to include the R code tangled
out of
this '.Rnw' document
% in this case it would just be 'plot(runif(1000))', perhaps manually
enclosed in a verbatim environment
\end{document}
I am running R-2.6.2 on Ubuntu Hardy Heron.
Thanks for all your help with Sweave. I think it is a fantastic tool.
Kyle
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Re: [R] about centralization
Weijia, if you only need degree centralization, Gabor suggests me those lines of code and they work great: ## undirected graph centralization-(sum(max(degree(g))-degree(g)))/(vcount(g)-1)/ (vcount(g)-2 ## directed graph centralization-(sum(max(degree(g))-degree(g)))/(2*vcount(g)-1)/ (vcount(g)-2 hope it helps, Simone Il giorno 30/nov/08, alle ore 17:05, Gábor Csárdi ha scritto: Weijia, centralization was not included in igraph, because really, it takes only writing a one line function to do it. But it is on our TODO list and will be included soon. E.g. for degree see the thread that starts here: http://lists.gnu.org/archive/html/igraph-help/2008-11/msg00064.html You can do it similarly for other measures, but first you need to find out which structure is the most centralized for a given measure. E.g. for degree it is the star graph, but not for eigenvector centrality. Probably this is written in the classic Wasserman-Faust book. Best, Gabor On Sun, Nov 30, 2008 at 1:37 PM, Weijia You [EMAIL PROTECTED] wrote: Hi all, Is there anyone who ever used igraph to calculate the index of centralization ? I tried my best but can't find it in igraph. The brief introduction to centralization can be found here , and I think it's an important index for measuring the centrality on the aggregated level.(http://faculty.ucr.edu/~hanneman/nettext/C10_Centrality.html) Thank you for any comments and suggestions. Best wishes! Weijia [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Gabor Csardi [EMAIL PROTECTED] UNIL DGM __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] using wc-w (unix) in R on cluster
This command rows - as.numeric(system(paste(wc -l /path/myFile.txt,sep=), TRUE)) works when used directly in R and when I put it inside a shell script and submit it to the cluster. This command columns - as.numeric(system(paste(head -1 /path/myFile.txt | wc -w,sep=), TRUE)) works when used in R, however is not working when I submit it. I am using these commands to count the number of rows and columns on a large file. Any suggestions? Thanks, Juliet __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] how to input a string without quote
From: Yihui Xie xieyihui_at_gmail.com Date: Sun, 30 Nov 2008 15:32:35 +0800 Wow, you are so lazy... But sometimes R is just designed for lazy guys... Yeah, well, laziness is the mother of creativity :-) . But seriously: I know far too many engineers who plug madly away for hours/days on end, where I would just stop, take a breath, figure out a method or mini-algorithm, and get the job done quick and easy. That's what R is for. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] grouping similar column values into a single row
Hi, I have a following situation with data: col1 col2 mir-1 aaa mir-1 abc mir-1 aac mir-2 abb mir-2 aaa mir-3 cag mir-3 ccc mir-3 aaa I want to have output in this format: col1 col2 mir-1 aaa, abc, aac mir-2 abb, aaa mir-3 cag,ccc,aaa I have sorted column 1 so that the grouping could be possible. I could have done the same with mysql using a simple query, but I am not sure how I can do it in R. Please suggest me possible way. Thanks, Joshi __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] how to input a string without quote
On Sun, Nov 30, 2008 at 11:38 AM, Carl Witthoft [EMAIL PROTECTED] wrote: From: Yihui Xie xieyihui_at_gmail.com Date: Sun, 30 Nov 2008 15:32:35 +0800 Wow, you are so lazy... But sometimes R is just designed for lazy guys... Yeah, well, laziness is the mother of creativity :-) . But seriously: I know far too many engineers who plug madly away for hours/days on end, where I would just stop, take a breath, figure out a method or mini-algorithm, and get the job done quick and easy. That's what R is for. We will encourage you to develop the three great virtues of a programmer: laziness, impatience, and hubris. Larry Wall, Programming Perl Hadley -- http://had.co.nz/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] grouping similar column values into a single row
See ?tapply tapply(paste(DF$col2), DF$col1, c) $`mir-1` [1] aaa abc aac $`mir-2` [1] abb aaa $`mir-3` [1] cag ccc aaa # or t(t(tapply(paste(DF$col2), DF$col1, paste, collapse = ))) [,1] mir-1 aaa abc aac mir-2 abb aaa mir-3 cag ccc aaa # or t(do.call(cbind, tapply(paste(DF$col2), DF$col1, ts))) [,1] [,2] [,3] mir-1 aaa abc aac mir-2 abb aaa NA mir-3 cag ccc aaa On Sun, Nov 30, 2008 at 1:08 PM, T Joshi [EMAIL PROTECTED] wrote: Hi, I have a following situation with data: col1 col2 mir-1 aaa mir-1 abc mir-1 aac mir-2 abb mir-2 aaa mir-3 cag mir-3 ccc mir-3 aaa I want to have output in this format: col1 col2 mir-1 aaa, abc, aac mir-2 abb, aaa mir-3 cag,ccc,aaa I have sorted column 1 so that the grouping could be possible. I could have done the same with mysql using a simple query, but I am not sure how I can do it in R. Please suggest me possible way. Thanks, Joshi __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Regex: workaround for variable length negative lookbehind
Hi all
I have the following regular expression problem: I want to find
complete elements of a vector that end in a repeated character but
where the repetition doesn't make up the whole word. That is, for the
vector vec:
vec-c(, baaa, bbaa, bbba, baamm, aa)
I would like to get
baaa
bbaa
baamm
From tools where negative lookbehind can involve variable lengths, one
would think this would work:
grep((?!(?:\\1|^))(.)\\1{1,}$, vec, perl=T)
But then R doesn't like it that much ... I also know I can get it like this:
whole.word.rep - grep(^(.)\\1{1,}$, vec, perl=T) # 1 6
rep.at.end - grep((.)\\1{1,}$, vec, perl=T) # 1 2 3 5 6
setdiff(rep.at.end, whole.word.rep) # 2 3 5
But is there a one-line grep thingy to do this?
Thx for any pointers,
STG
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[R] Graphics for proportion within factor
BODY { font-family:Arial, Helvetica, sans-serif;font-size:12px; }I
am looking to draw what I hoped was a simple plot of proportion WITHIN
a strata, save % males by site. I seem to be able to get proportion of
males, by
site, where the proportion is across the whole dataset, but not the
proportion within each site.
thanks in advance,
Rob
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[R] using survey weights for correlations
Dear list, I have a data file which includes, alongside various variables representing questionnaire scores, a variable for survey weights computed as the number of observations in the sample drawn from that group divided by the number of observations in the population in the group. I need to calculate a covariance matrix of the questionnaire scores for use in sem. How do I apply the weights? Thanks in advance, Steve Powell www.promente.org proMENTE social research Krančevićeva 35 71000 Sarajevo skype stevepowell99 mob. +387 61 215 997 tel. +387 33 556 865 fax. +387 33 556 866 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Regex: workaround for variable length negative lookbehind
Hi Stefan! :-)
From tools where negative lookbehind can involve variable lengths,
one
would think this would work:
grep((?!(?:\\1|^))(.)\\1{1,}$, vec, perl=T)
But then R doesn't like it that much ...
It's really the PCRE library that doesn't like your regexp, not R.
The problem is that negative behind is only possible with a fixed-
length expression, and since \1 may hold an arbitrary string, the PCRE
library can't be sure it's just a single character. I'm also
surprised that you're allowed to use \1 before defining it.
But is there a one-line grep thingy to do this?
Can't think of a one-liner, but a three-line solution you can easily
enough wrap in a small function:
vec-c(, baaa, bbaa, bbba, baamm, aa)
idx.1 - grep((.)\\1$, vec)
idx.2 - grep(^(.)\\1*$, vec)
vec[setdiff(idx.1, idx.2)]
Cheers,
Stefan
--
The wonders of Googleology (episode 1)
from collectibles to cars
84,700,000 -- Google
9,443,672 -- Google N-grams (Web 1T5)
1 -- ukWaC
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Re: [R] function for simultaneous confidence interval of regression coefficients
see
?coef # extract the estimates
?vcov # extract their covariance matrix
?qf # get the F quantile of interest
Also, you may be interested in
?car::ellipse
?ellipse::ellipse.lm
?gmodels::glht.test
hth,
Kingsford Jones
On Sat, Nov 29, 2008 at 4:30 PM, Kyle Matoba [EMAIL PROTECTED] wrote:
List,
Would someone be so kind as to point me to a function that will calculate
simultaneous confidence intervals of regression coefficients based upon
their distribution as (under the assumption of normal errors, with
\mathbf{X} as the design matrix):
$\hat{\mathbf{\beta}} \sim N(\mathbf{\beta},
\sigma^2(\mathbf{X}^T\mathbf{X})^{-1})$.
'confint' calculates individual coefficients so far as I can tell, but I
need simultaneous CIs based on the confidence ellipse/ F distribution.
Inverting the ellipse gives this equation:
\mathbf{\hat{\beta}} \pm
\sqrt{\mathrm{diag}(s^2(\mathbf{X}^T\mathbf{X})^{-1}) \times p \times F_{p,
n-p, .95}}
Thanks, and sorry for such a dumb question. Either I am not searching for
the right thing or this hasn't already been addressed in the lists (perhaps
because it is so easy).
Kyle
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[R] Randomization of a two-way ANOVA?
Hello list, I wish to perform a randomization test on the F-statistics of a 2 way ANOVA but have not been able to find out how to do so - is there a package / function that can perform this that I am unaware of? FactorA has 6 levels (0,1,2,3,4,5) whereas FactorB has 3 (1,2,3). A sample: Resp. FactorA FactorB 2 0 2 3 1 2 1 2 2 0 3 2 0 4 2 0 5 2 4 0 1 6 1 1 1 2 1 0 3 1 1 4 1 0 5 1 2 0 2 3 1 2 1 2 2 2 3 2 1 4 2 0 5 2 3 0 1 3 1 1 1 2 1 0 3 1 0 4 1 7 1 3 2 2 3 0 3 3 1 4 3 0 5 3 1 0 3 Also, is the F-statistic an appropriate test-statistic for the randomization test when it is computed using non-normal data? Any insight into this issue would be much appreciated. Thanks. -- View this message in context: http://www.nabble.com/Randomization-of-a-two-way-ANOVA--tp20761769p20761769.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Regex: workaround for variable length negative lookbehind
Try this:
vec - c(, baaa, bbaa, bbba, baamm, aa)
grep(^(?!(.)\\1{1,}$).*(.)\\2{1,}$, vec, perl = TRUE)
[1] 2 3 5
The (?...) succeeds only if the string is not all the same
character and since that consumes no characters it
restarts at the beginning to match anything followed
by repeated characters to the end.
On Sun, Nov 30, 2008 at 2:33 PM, Stefan Th. Gries [EMAIL PROTECTED] wrote:
Hi all
I have the following regular expression problem: I want to find
complete elements of a vector that end in a repeated character but
where the repetition doesn't make up the whole word. That is, for the
vector vec:
vec-c(, baaa, bbaa, bbba, baamm, aa)
I would like to get
baaa
bbaa
baamm
From tools where negative lookbehind can involve variable lengths, one
would think this would work:
grep((?!(?:\\1|^))(.)\\1{1,}$, vec, perl=T)
But then R doesn't like it that much ... I also know I can get it like this:
whole.word.rep - grep(^(.)\\1{1,}$, vec, perl=T) # 1 6
rep.at.end - grep((.)\\1{1,}$, vec, perl=T) # 1 2 3 5 6
setdiff(rep.at.end, whole.word.rep) # 2 3 5
But is there a one-line grep thingy to do this?
Thx for any pointers,
STG
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[R] how to select cases based on value of one or more variables
dear list, I have read a spss file with read.spss() now I have a list with all my variable stored as vectors. is it possible to selec cases based on the value of one or more variables? thank you, Simone __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Regex: workaround for variable length negative lookbehind
Here is a very slight further simplification, i.e. we can drop the final {1,}
grep(^(?!(.)\\1{1,}$).*(.)\\2$, vec, perl = TRUE)
[1] 2 3 5
On Sun, Nov 30, 2008 at 3:26 PM, Gabor Grothendieck
[EMAIL PROTECTED] wrote:
Try this:
vec - c(, baaa, bbaa, bbba, baamm, aa)
grep(^(?!(.)\\1{1,}$).*(.)\\2{1,}$, vec, perl = TRUE)
[1] 2 3 5
The (?...) succeeds only if the string is not all the same
character and since that consumes no characters it
restarts at the beginning to match anything followed
by repeated characters to the end.
On Sun, Nov 30, 2008 at 2:33 PM, Stefan Th. Gries [EMAIL PROTECTED] wrote:
Hi all
I have the following regular expression problem: I want to find
complete elements of a vector that end in a repeated character but
where the repetition doesn't make up the whole word. That is, for the
vector vec:
vec-c(, baaa, bbaa, bbba, baamm, aa)
I would like to get
baaa
bbaa
baamm
From tools where negative lookbehind can involve variable lengths, one
would think this would work:
grep((?!(?:\\1|^))(.)\\1{1,}$, vec, perl=T)
But then R doesn't like it that much ... I also know I can get it like this:
whole.word.rep - grep(^(.)\\1{1,}$, vec, perl=T) # 1 6
rep.at.end - grep((.)\\1{1,}$, vec, perl=T) # 1 2 3 5 6
setdiff(rep.at.end, whole.word.rep) # 2 3 5
But is there a one-line grep thingy to do this?
Thx for any pointers,
STG
__
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Re: [R] how to select cases based on value of one or more variables
?subset On Nov 30, 2008, at 3:36 PM, Simone Gabbriellini wrote: dear list, I have read a spss file with read.spss() now I have a list with all my variable stored as vectors. is it possible to selec cases based on the value of one or more variables? thank you, Simone __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] how to select cases based on value of one or more variables
It is. For example, if you have a variable stored as a vector named x, and another variable stored as aa vector named y, you can select cases of y where x is greater than 3 by using y[x3] However, you're going to have to provide more information in order to get a better answer than that (see the posting guide, link included with every post to r-help). In particular, I'm guessing that the answer you really want looks somewhat different than my example -- but this depends on the exact structure of what read.spss() produces. I'd also suggest reading some of the documentation available from the R website (CRAN), notably, An Introduction to R. -Don At 9:36 PM +0100 11/30/08, Simone Gabbriellini wrote: dear list, I have read a spss file with read.spss() now I have a list with all my variable stored as vectors. is it possible to selec cases based on the value of one or more variables? thank you, Simone __ R-help@r-project.org mailing list https:// stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http:// www. R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- - Don MacQueen Lawrence Livermore National Laboratory Livermore, CA, USA 925-423-1062 [EMAIL PROTECTED] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Graphics for proportion within factor
You could see whether the stacked barchart in Sarkar's website meets
your needs:
http://lmdvr.r-forge.r-project.org/figures/figures.html
See figure 4.5
also look at:
?prop.table
Description
This is really sweep(x, margin, margin.table(x, margin), /) for
newbies
--
David Winsemius
On Nov 30, 2008, at 2:36 PM, Rob James wrote:
BODY { font-family:Arial, Helvetica, sans-serif;font-size:12px; }I
am looking to draw what I hoped was a simple plot of proportion WITHIN
a strata, save % males by site. I seem to be able to get proportion of
males, by
site, where the proportion is across the whole dataset, but not the
proportion within each site.
thanks in advance,
Rob
[[alternative HTML version deleted]]
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Re: [R] Regex: workaround for variable length negative lookbehind
But is there a one-line grep thingy to do this? Can't think of a one-liner, but a three-line solution you can easily enough wrap in a small function: vec-c(, baaa, bbaa, bbba, baamm, aa) idx.1 - grep((.)\\1$, vec) idx.2 - grep(^(.)\\1*$, vec) vec[setdiff(idx.1, idx.2)] Oops, my bad, that solution was in Stefan's original mail already. I got his example mixed up with some other text and thought he was talking about something different. Still, I think it's better to write a few lines of R code than to abuse regular expressions to do something they were never intended to do. How do other people on this list feel about that issue? Sorry again, and next time I'll trink a cup of coffee _before_ I post! Stefan __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] using survey weights for correlations
Dear Steve, You can use svyvar() in the svy package to compute a covariance matrix that properly reflects the weights (and other details of the sampling design), and from this, using cov2cor(), a correlation matrix (if you want that too). You should get consistent estimates from sem() in the sem package (assuming that's what you were planning to use), but standard errors and statistical tests won't be right. You should be able to get valid inferences by bootstrapping, making proper allowance for the weights in resampling. I hope this helps, John -- John Fox, Professor Department of Sociology McMaster University Hamilton, Ontario, Canada web: socserv.mcmaster.ca/jfox -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Steve Powell Sent: November-30-08 2:41 PM To: R-Help Subject: [R] using survey weights for correlations Dear list, I have a data file which includes, alongside various variables representing questionnaire scores, a variable for survey weights computed as the number of observations in the sample drawn from that group divided by the number of observations in the population in the group. I need to calculate a covariance matrix of the questionnaire scores for use in sem. How do I apply the weights? Thanks in advance, Steve Powell www.promente.org proMENTE social research Krančevićeva 35 71000 Sarajevo skype stevepowell99 mob. +387 61 215 997 tel. +387 33 556 865 fax. +387 33 556 866 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] selectively importing functions etc. from files
Hi Charles, Thanks for the reply. On Sun, 30 Nov 2008, Charles C. Berry wrote: On Sat, 29 Nov 2008, Faheem Mitha wrote: Hi, If I want to import the contents of a R file into another one, I can do source(foo.R) However, this imports everything from foo.R, including all functions and global variables. Is there a way of selectively importing individual functions etc., in a similar fashion to Python's from foo import bar There are probably a lot of ways to skin this cat. But you might want to explain why you want to do this in the first place. It may turn out that the problem you wish to solve is better addressed by placing your objects in a package that is attached far down the search list. Well, I just want to be able to selectively import specific functions from files, so I can control what has been imported. One minor advantage of this (there are many) is that it makes it difficult to accidentally overwrite objects of the same name with each other. This is quite standard practice across languages to avoid polluting the global namespace. And of course, I'd like to do this as simply as possible. A simple way to do what you say you want: Use source(foo.R, local=TRUE) from within a function. Then either assign( ..., envir=.GlobalEnv ) selected objects or attach( list( ) ) them. Not sure I follow this. I want to import into the global namespace. Why would I import from within a function? You mean first import locally into some function and then selectively export to the global namespace? Another way is to use parse, as.character.srcref, and friends to avoid evaluating each of the objects, then eval() selected expressions in the desired environment. And this one even less. Can you give a simple example? Regards, Faheem. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] how to select cases based on value of one or more variables
sorry for my bad presentation... read.spss gives me this: students $Auno [1] 6 1 2 2 1 3 4 2 4 2 4 4 1 1 NA 1 4 2 1 1 1 5 4 [24] 2 1 2 1 2 1 4 4 1 1 1 2 1 6 1 1 1 1 1 2 1 2 1 [47] 2 2 1 4 2 4 3 1 1 1 1 3 2 1 4 4 4 4 2 4 1 2 4 [70] 1 3 4 5 2 4 3 5 5 4 2 1 1 1 1 4 5 2 4 4 1 4 2 [93] 1 2 3 3 2 1 2 2 2 1 1 1 3 5 5 5 2 NA 2 1 NA 5 2 [116] 1 4 2 NA 1 4 5 2 3 1 1 1 1 4 2 1 1 3 2 4 2 4 2 [139] 1 4 1 2 4 1 2 3 2 1 1 2 4 4 3 4 1 1 3 2 1 1 2 [162] 1 2 5 5 5 1 4 3 2 3 3 2 1 1 5 1 2 1 1 2 1 2 1 [185] 1 2 1 1 1 1 3 4 2 1 4 2 4 1 4 2 1 1 1 2 1 4 1 [208] 5 1 1 4 4 2 1 1 5 4 1 1 5 5 4 1 4 $Sex [1] 2 1 2 1 2 2 2 2 1 2 1 1 2 1 0 2 2 2 2 2 2 2 2 1 2 2 1 2 2 1 2 2 2 1 [35] 2 2 2 1 1 2 2 2 2 2 2 2 2 2 1 1 1 1 2 2 2 2 2 2 2 1 1 2 2 2 2 2 1 2 [69] 2 1 2 1 2 1 2 2 2 2 2 2 1 2 2 2 1 2 2 2 1 1 1 2 1 2 1 2 2 2 2 2 2 2 [103] 2 2 2 2 1 2 2 2 2 2 2 2 2 2 1 2 0 2 2 2 1 2 2 1 2 1 2 2 1 1 2 1 2 1 [137] 2 1 2 1 1 1 1 1 1 2 1 1 2 2 2 2 1 1 2 2 2 2 2 2 2 2 2 2 2 2 1 1 2 2 [171] 2 2 2 2 2 1 1 1 1 2 2 2 2 2 2 2 2 1 2 2 1 1 1 1 1 2 0 2 2 1 2 1 2 2 [205] 1 2 2 2 2 2 2 2 2 2 1 2 2 1 1 2 2 2 2 2 I would like to filter - or subset - the dataset for $Sex = 1 (in this case means male...), for example... thanks anyway, Simone Il giorno 30/nov/08, alle ore 21:49, Don MacQueen ha scritto: It is. For example, if you have a variable stored as a vector named x, and another variable stored as aa vector named y, you can select cases of y where x is greater than 3 by using y[x3] However, you're going to have to provide more information in order to get a better answer than that (see the posting guide, link included with every post to r-help). In particular, I'm guessing that the answer you really want looks somewhat different than my example -- but this depends on the exact structure of what read.spss() produces. I'd also suggest reading some of the documentation available from the R website (CRAN), notably, An Introduction to R. -Don At 9:36 PM +0100 11/30/08, Simone Gabbriellini wrote: dear list, I have read a spss file with read.spss() now I have a list with all my variable stored as vectors. is it possible to selec cases based on the value of one or more variables? thank you, Simone __ R-help@r-project.org mailing list https:// stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http:// www. R-project.org/posting- guide.html and provide commented, minimal, self-contained, reproducible code. -- - Don MacQueen Lawrence Livermore National Laboratory Livermore, CA, USA 925-423-1062 [EMAIL PROTECTED] - __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] how to select cases based on value of one or more variables
It's generally easier to work with data frames, so read your data with students - read.spss(yourFile, to.data.frame=TRUE) Then subset will work as expected: subset(students, Sex == 1) If you would rather keep the data as a list you could do something like lapply(students, function(x) x[students$Sex == 1]) hth, Kingsford Jones On Sun, Nov 30, 2008 at 2:15 PM, Simone Gabbriellini [EMAIL PROTECTED] wrote: sorry for my bad presentation... read.spss gives me this: students $Auno [1] 6 1 2 2 1 3 4 2 4 2 4 4 1 1 NA 1 4 2 1 1 1 5 4 [24] 2 1 2 1 2 1 4 4 1 1 1 2 1 6 1 1 1 1 1 2 1 2 1 [47] 2 2 1 4 2 4 3 1 1 1 1 3 2 1 4 4 4 4 2 4 1 2 4 [70] 1 3 4 5 2 4 3 5 5 4 2 1 1 1 1 4 5 2 4 4 1 4 2 [93] 1 2 3 3 2 1 2 2 2 1 1 1 3 5 5 5 2 NA 2 1 NA 5 2 [116] 1 4 2 NA 1 4 5 2 3 1 1 1 1 4 2 1 1 3 2 4 2 4 2 [139] 1 4 1 2 4 1 2 3 2 1 1 2 4 4 3 4 1 1 3 2 1 1 2 [162] 1 2 5 5 5 1 4 3 2 3 3 2 1 1 5 1 2 1 1 2 1 2 1 [185] 1 2 1 1 1 1 3 4 2 1 4 2 4 1 4 2 1 1 1 2 1 4 1 [208] 5 1 1 4 4 2 1 1 5 4 1 1 5 5 4 1 4 $Sex [1] 2 1 2 1 2 2 2 2 1 2 1 1 2 1 0 2 2 2 2 2 2 2 2 1 2 2 1 2 2 1 2 2 2 1 [35] 2 2 2 1 1 2 2 2 2 2 2 2 2 2 1 1 1 1 2 2 2 2 2 2 2 1 1 2 2 2 2 2 1 2 [69] 2 1 2 1 2 1 2 2 2 2 2 2 1 2 2 2 1 2 2 2 1 1 1 2 1 2 1 2 2 2 2 2 2 2 [103] 2 2 2 2 1 2 2 2 2 2 2 2 2 2 1 2 0 2 2 2 1 2 2 1 2 1 2 2 1 1 2 1 2 1 [137] 2 1 2 1 1 1 1 1 1 2 1 1 2 2 2 2 1 1 2 2 2 2 2 2 2 2 2 2 2 2 1 1 2 2 [171] 2 2 2 2 2 1 1 1 1 2 2 2 2 2 2 2 2 1 2 2 1 1 1 1 1 2 0 2 2 1 2 1 2 2 [205] 1 2 2 2 2 2 2 2 2 2 1 2 2 1 1 2 2 2 2 2 I would like to filter - or subset - the dataset for $Sex = 1 (in this case means male...), for example... thanks anyway, Simone Il giorno 30/nov/08, alle ore 21:49, Don MacQueen ha scritto: It is. For example, if you have a variable stored as a vector named x, and another variable stored as aa vector named y, you can select cases of y where x is greater than 3 by using y[x3] However, you're going to have to provide more information in order to get a better answer than that (see the posting guide, link included with every post to r-help). In particular, I'm guessing that the answer you really want looks somewhat different than my example -- but this depends on the exact structure of what read.spss() produces. I'd also suggest reading some of the documentation available from the R website (CRAN), notably, An Introduction to R. -Don At 9:36 PM +0100 11/30/08, Simone Gabbriellini wrote: dear list, I have read a spss file with read.spss() now I have a list with all my variable stored as vectors. is it possible to selec cases based on the value of one or more variables? thank you, Simone __ R-help@r-project.org mailing list https:// stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http:// www. R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- - Don MacQueen Lawrence Livermore National Laboratory Livermore, CA, USA 925-423-1062 [EMAIL PROTECTED] - __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] how to select cases based on value of one or more variables
yes it's THE solution! thank you very much, Simone Il giorno 30/nov/08, alle ore 22:42, Kingsford Jones ha scritto: It's generally easier to work with data frames, so read your data with students - read.spss(yourFile, to.data.frame=TRUE) Then subset will work as expected: subset(students, Sex == 1) If you would rather keep the data as a list you could do something like lapply(students, function(x) x[students$Sex == 1]) hth, Kingsford Jones On Sun, Nov 30, 2008 at 2:15 PM, Simone Gabbriellini [EMAIL PROTECTED] wrote: sorry for my bad presentation... read.spss gives me this: students $Auno [1] 6 1 2 2 1 3 4 2 4 2 4 4 1 1 NA 1 4 2 1 1 1 5 4 [24] 2 1 2 1 2 1 4 4 1 1 1 2 1 6 1 1 1 1 1 2 1 2 1 [47] 2 2 1 4 2 4 3 1 1 1 1 3 2 1 4 4 4 4 2 4 1 2 4 [70] 1 3 4 5 2 4 3 5 5 4 2 1 1 1 1 4 5 2 4 4 1 4 2 [93] 1 2 3 3 2 1 2 2 2 1 1 1 3 5 5 5 2 NA 2 1 NA 5 2 [116] 1 4 2 NA 1 4 5 2 3 1 1 1 1 4 2 1 1 3 2 4 2 4 2 [139] 1 4 1 2 4 1 2 3 2 1 1 2 4 4 3 4 1 1 3 2 1 1 2 [162] 1 2 5 5 5 1 4 3 2 3 3 2 1 1 5 1 2 1 1 2 1 2 1 [185] 1 2 1 1 1 1 3 4 2 1 4 2 4 1 4 2 1 1 1 2 1 4 1 [208] 5 1 1 4 4 2 1 1 5 4 1 1 5 5 4 1 4 $Sex [1] 2 1 2 1 2 2 2 2 1 2 1 1 2 1 0 2 2 2 2 2 2 2 2 1 2 2 1 2 2 1 2 2 2 1 [35] 2 2 2 1 1 2 2 2 2 2 2 2 2 2 1 1 1 1 2 2 2 2 2 2 2 1 1 2 2 2 2 2 1 2 [69] 2 1 2 1 2 1 2 2 2 2 2 2 1 2 2 2 1 2 2 2 1 1 1 2 1 2 1 2 2 2 2 2 2 2 [103] 2 2 2 2 1 2 2 2 2 2 2 2 2 2 1 2 0 2 2 2 1 2 2 1 2 1 2 2 1 1 2 1 2 1 [137] 2 1 2 1 1 1 1 1 1 2 1 1 2 2 2 2 1 1 2 2 2 2 2 2 2 2 2 2 2 2 1 1 2 2 [171] 2 2 2 2 2 1 1 1 1 2 2 2 2 2 2 2 2 1 2 2 1 1 1 1 1 2 0 2 2 1 2 1 2 2 [205] 1 2 2 2 2 2 2 2 2 2 1 2 2 1 1 2 2 2 2 2 I would like to filter - or subset - the dataset for $Sex = 1 (in this case means male...), for example... thanks anyway, Simone Il giorno 30/nov/08, alle ore 21:49, Don MacQueen ha scritto: It is. For example, if you have a variable stored as a vector named x, and another variable stored as aa vector named y, you can select cases of y where x is greater than 3 by using y[x3] However, you're going to have to provide more information in order to get a better answer than that (see the posting guide, link included with every post to r-help). In particular, I'm guessing that the answer you really want looks somewhat different than my example -- but this depends on the exact structure of what read.spss() produces. I'd also suggest reading some of the documentation available from the R website (CRAN), notably, An Introduction to R. -Don At 9:36 PM +0100 11/30/08, Simone Gabbriellini wrote: dear list, I have read a spss file with read.spss() now I have a list with all my variable stored as vectors. is it possible to selec cases based on the value of one or more variables? thank you, Simone __ R-help@r-project.org mailing list https:// stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http:// www. R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- - Don MacQueen Lawrence Livermore National Laboratory Livermore, CA, USA 925-423-1062 [EMAIL PROTECTED] - __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] including Sweave tangled code in '.Rnw' document
Vincent, Ista, Berwin:
Thank you all for your help. It is great that a student like myself can
receive help from Professors and experts such as yourselves.
To the list, I found Berwin's solution to work excellently, though I chose
to change the font of the included text, e.g.
\texttt{ \lstinputlisting[emptylines=0]{XYZ.R} }
Ista's suggestion also seems excellent, though I am required to submit a
paper copy of the work and Ista's is a bit easier to manage with this goal
in mind.
Vincent's comment is also quite appropriate, unfortunately I have enough
trouble with LaTeX as it is and the problem has been solved to my
satisfaction I have chosen to put off exploration of this package for
another day.
Best,
Kyle
On Sun, Nov 30, 2008 at 8:42 AM, Vincent Goulet
[EMAIL PROTECTED] wrote:
Kyle,
In addition to listings already mentioned by Berwin, you may find useful
the answers package. This is what I use to create
assignments/exams/exercise sets with solutions all in one file.
HTH
Vincent
---
Vincent Goulet, Associate Professor
École d'actuariat
Université Laval, Québec
[EMAIL PROTECTED] http://vgoulet.act.ulaval.ca
Le sam. 29 nov. à 14:11, Kyle Matoba a écrit :
Hello List,
I have been using Sweave for my homework this last quarter and have been
very impressed at how much time and effort it saves me. I, however, have
run up against a problem which I have not been able to solve using any of
the Sweave/LaTeX tricks I know. I work through my homework one problem at
a
time, typesetting equations and writing R code, etc. and occasionally use
'Stangle()' from within R to extract the code if I need to pin down a
problem or experiment interactively. I would like to be able to include
this resultant code in a verbatim environment in my final TeX'ed up
document
as an appendix so that the grader can look it over, etc. I could
implement
this in any number of ways using linux tools, but would like to know if
there is a clean way to do so using LaTeX or Sweave so that the latest
version of the code is included in my homework each time I run 'R CMD
Sweave
HW4.Rnw; pdflatex HW4.tex'.
e.g I envision something such as:
\begin{document}
fig3, echo=false, results=hide, fig=true, eps=F=
plot(runif(1000))
@
TA here is my code:
% some manner of Sweave/LaTeX macro to include the R code tangled out of
this '.Rnw' document
% in this case it would just be 'plot(runif(1000))', perhaps manually
enclosed in a verbatim environment
\end{document}
I am running R-2.6.2 on Ubuntu Hardy Heron.
Thanks for all your help with Sweave. I think it is a fantastic tool.
Kyle
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[R] controlling the number of times a script is repeated in a loop
I am running a large for loop and at the end of each iteration a matrix is produced. The program changes the columns in the matrix, and each time a column is added the name of that column is y. All original columns have no column name. Due to the nature of the program, all original columns will eventually be replaced with new columns each with the column name y. It is at this point that I want the program to stop running the for loop (right now I just have it running for 20 iterations resulting in a matrix with a mix of old and new columns). I was thinking maybe I could do something with an if else statement and the command colnames. For example: If(colnames all are y) (stop) else (run the program again) Not entirely sure how to go about this though, or if I am even on the right track. Maybe I need to get rid of the master for loop as perhaps for loops are more constraining in the number of times the program is run? The number of runs to get all original columns replaced with new ones will never be the same (I plan on running this several times, with time steps ending when all original columns are replaced. Perhaps at the end of each time step I can set column names to have no column names (so from ys to nothing), allowing me to use this method for each time step)... I know it is always helpful to have some code to work with, but it seems impractical to send the whole program as one part if it I am still working on and would probably just create more confusion. Hopefully someone might be able to offer a few suggestions...I can try to come up with a toy program to send along but I am not good enough in R yet to do this quickly! Thank you for all the help and I am sorry if this question is perhaps a bit confusing! If I have not made my problem and what I hope to do clear, please let me know. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] selectively importing functions etc. from files
On Sun, 30 Nov 2008, Faheem Mitha wrote: Hi Charles, Thanks for the reply. On Sun, 30 Nov 2008, Charles C. Berry wrote: On Sat, 29 Nov 2008, Faheem Mitha wrote: Hi, If I want to import the contents of a R file into another one, I can do source(foo.R) However, this imports everything from foo.R, including all functions and global variables. Is there a way of selectively importing individual functions etc., in a similar fashion to Python's from foo import bar There are probably a lot of ways to skin this cat. But you might want to explain why you want to do this in the first place. It may turn out that the problem you wish to solve is better addressed by placing your objects in a package that is attached far down the search list. Well, I just want to be able to selectively import specific functions from files, so I can control what has been imported. One minor advantage of this (there are many) is that it makes it difficult to accidentally overwrite objects of the same name with each other. This is quite standard practice across languages to avoid polluting the global namespace. And of course, I'd like to do this as simply as possible. Right. And if you put all the objects in a package and do this: ## if you want to mask as little as possible, use library(mypkg, pos = package:base) you will achieve this. You can also set LazyLoad: yes in the DESCRIPTION file. Then if you want to 'promote' functions to the .GlobalEnv, you can do foo - mypkg:::foo Come to think of it, if the functions are all made local to the mypkg namespace, then they will only mask funcitons further down the search() list if they are called by other functions in mypkg. A simple way to do what you say you want: Use source(foo.R, local=TRUE) from within a function. Then either assign( ..., envir=.GlobalEnv ) selected objects or attach( list( ) ) them. Not sure I follow this. I want to import into the global namespace. Why would I import from within a function? You mean first import locally into some function and then selectively export to the global namespace? Exactly. The objects that are not assign()ed or attach()ed will 'disappear'. Another way is to use parse, as.character.srcref, and friends to avoid evaluating each of the objects, then eval() selected expressions in the desired environment. And this one even less. Can you give a simple example? OK. parse a file with two functions in it. Find one of the function expressions and evaluate it: cat(foo - function(x) x+1;bar - function(x) x*2,file=foobar.R) foobar.expr - parse(foobar.R) ls() [1] foobar.expr grep(foo -,sapply(attr(foobar.expr,'srcref'),function(x) as.character(x))) [1] 1 eval(foobar.expr[[ 1 ]]) ls() [1] foo foobar.expr foo function(x) x+1 --- Another way to achieve what you want is to put source of each function in its own file in a single directory. Then source(file.path(pkgpath,foo.R)) will load the single function in pkgpath/foo.R HTH, Chuck Regards, Faheem. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Charles C. Berry(858) 534-2098 Dept of Family/Preventive Medicine E mailto:[EMAIL PROTECTED] UC San Diego http://famprevmed.ucsd.edu/faculty/cberry/ La Jolla, San Diego 92093-0901 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] minor edit WAS: Re: selectively importing functions etc. from files
On Sun, 30 Nov 2008, Charles C. Berry wrote: On Sun, 30 Nov 2008, Faheem Mitha wrote: [much deleted] I missed a '\n ' in my previous post. It should have read: eval(foobar.expr[[ 1 ]]) ls() [1] foo foobar.expr foo function(x) x+1 Charles C. Berry(858) 534-2098 Dept of Family/Preventive Medicine E mailto:[EMAIL PROTECTED] UC San Diego http://famprevmed.ucsd.edu/faculty/cberry/ La Jolla, San Diego 92093-0901 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Rserve and creating a list of lists
Hello, I have some code which generates lattice objects. The function recieves serialized forms of the lattice objects which it then unserializes and then adds to an ArrayListREXP. REXPRaw rser = new REXPRaw( target ); //target contains the raw serialized forms of lattice objects rconn.assign(temp,rser); REXP ret = rconn.eval(invisible(unserialize(temp))); (1) rexpArr.add(ret); RList rlist = new RList(rexpArr); REXPList rl = new REXPList(rlist); The problem is when I do an assign rconn.assign(finalresult,rl); whence I get *** REXPFactory unable to interpret [EMAIL PROTECTED] * ** REXPFactory unable to interpret [EMAIL PROTECTED] *** REXPFactory unable to interpret [EMAIL PROTECTED] *** REXPFactory unable to interpret [EMAIL PROTECTED] *** REXPFactory unable to interpret [EMAIL PROTECTED] * ** REXPFactory unable to interpret [EMAIL PROTECTED] How can I in general,force the unserialize to return a list? Saptarshi Guha | [EMAIL PROTECTED] | http://www.stat.purdue.edu/~sguha Marijuana is nature's way of saying, Hi!. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] controlling the number of times a script is repeated in a loop
On Sun, Nov 30, 2008 at 12:21 PM, Salas, Andria Kay [EMAIL PROTECTED] wrote:
I am running a large for loop and at the end of each iteration a matrix is
produced. The program changes the columns in the matrix, and each time a
column is added the name of that column is y. All original columns have no
column name. Due to the nature of the program, all original columns will
eventually be replaced with new columns each with the column name y. It is
at this point that I want the program to stop running the for loop (right now
I just have it running for 20 iterations resulting in a matrix with a mix of
old and new columns). I was thinking maybe I could do something with an if
else statement and the command colnames. For example:
If(colnames all are y) (stop) else (run the program again)
Have a look at ?while :
while(!(colnames all are y)) { run the program again }
Hadley
--
http://had.co.nz/
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] Rserve and creating a list of lists
Hello, With reference to the problem below, I have narrowed it down to trellis objects containing language objects , e.g a trellis object has a list element called $prepanel.default which is a function. The same happens if assign the result of an 'dist' call since it contains as one of its attributes the calling function (as a language). The error returned by Rserve (latest version) is Error: unsupported type 0 So if the result of an eval is a language block, then it can't be assigned? Is there a work around this? Regards Saptarshi R.version = 2.8 On Nov 30, 2008, at 5:53 PM, Saptarshi Guha wrote: Hello, I have some code which generates lattice objects. The function recieves serialized forms of the lattice objects which it then unserializes and then adds to an ArrayListREXP. REXPRaw rser = new REXPRaw( target ); //target contains the raw serialized forms of lattice objects rconn.assign(temp,rser); REXP ret = rconn.eval(invisible(unserialize(temp))); (1) rexpArr.add(ret); RList rlist = new RList(rexpArr); REXPList rl = new REXPList(rlist); The problem is when I do an assign rconn.assign(finalresult,rl); whence I get *** REXPFactory unable to interpret [EMAIL PROTECTED] * ** REXPFactory unable to interpret [EMAIL PROTECTED] *** REXPFactory unable to interpret [EMAIL PROTECTED] *** REXPFactory unable to interpret [EMAIL PROTECTED] *** REXPFactory unable to interpret [EMAIL PROTECTED] * ** REXPFactory unable to interpret [EMAIL PROTECTED] How can I in general,force the unserialize to return a list? Saptarshi Guha | [EMAIL PROTECTED] | http://www.stat.purdue.edu/~sguha Marijuana is nature's way of saying, Hi!. Saptarshi Guha | [EMAIL PROTECTED] | http://www.stat.purdue.edu/~sguha An adequate bootstrap is a contradiction in terms. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] chron and R 2.8
Yes chron 2.3-25 zoo 1.5-4 R 2.8 Mac OS X 10.5.5 Gabor I don't know how to start up another verison of R on the mac. I will figure this out, and get back to you (I can then test both of them side by side). other fast installation (version numbers from description files in R 2.7.2 directory) chron 2.3-24 zoo 1.5-4 Mac OS X 10.5.5 thanks Stephen On Sat, Nov 29, 2008 at 10:19 AM, Gabor Grothendieck [EMAIL PROTECTED] wrote: Are you using the same version of chron both times? On Sat, Nov 29, 2008 at 10:05 AM, stephen sefick [EMAIL PROTECTED] wrote: has anyone had problems with the upgrade to R 2.8 and chron date classes. I have a large zoo object that has a chron index, and it is taking 5x or so longer to do the same calculation as with 2.7 if it doesn't fail. I will provide anything necessary I am not entirely sure what ya'll would need if anything to try and reproduce the behavior. I am using the package StreamMetabolism. thanks -- Stephen Sefick Let's not spend our time and resources thinking about things that are so little or so large that all they really do for us is puff us up and make us feel like gods. We are mammals, and have not exhausted the annoying little problems of being mammals. -K. Mullis __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Stephen Sefick Let's not spend our time and resources thinking about things that are so little or so large that all they really do for us is puff us up and make us feel like gods. We are mammals, and have not exhausted the annoying little problems of being mammals. -K. Mullis __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] chron and R 2.8
To run the old version of chron that you have under 2.7.2 into 2.8.0, on 2.7.2 issue the command (note initial dot): .libPaths() Suppose you find that the library that contains chron in 2.7.2 is /a/b. Then on 2.8.0 ensure that you don't have chron on the search path search() and if you do detach it: detach(package:chron) search() # should no longer be there Then run this where ... is the library that the old version of chron is in under 2.7.2. library(chron, lib = ...) To run the new version of chron detach the old version and just use: library(chron) On Sun, Nov 30, 2008 at 9:14 PM, stephen sefick [EMAIL PROTECTED] wrote: Yes chron 2.3-25 zoo 1.5-4 R 2.8 Mac OS X 10.5.5 Gabor I don't know how to start up another verison of R on the mac. I will figure this out, and get back to you (I can then test both of them side by side). other fast installation (version numbers from description files in R 2.7.2 directory) chron 2.3-24 zoo 1.5-4 Mac OS X 10.5.5 thanks Stephen On Sat, Nov 29, 2008 at 10:19 AM, Gabor Grothendieck [EMAIL PROTECTED] wrote: Are you using the same version of chron both times? On Sat, Nov 29, 2008 at 10:05 AM, stephen sefick [EMAIL PROTECTED] wrote: has anyone had problems with the upgrade to R 2.8 and chron date classes. I have a large zoo object that has a chron index, and it is taking 5x or so longer to do the same calculation as with 2.7 if it doesn't fail. I will provide anything necessary I am not entirely sure what ya'll would need if anything to try and reproduce the behavior. I am using the package StreamMetabolism. thanks -- Stephen Sefick Let's not spend our time and resources thinking about things that are so little or so large that all they really do for us is puff us up and make us feel like gods. We are mammals, and have not exhausted the annoying little problems of being mammals. -K. Mullis __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Stephen Sefick Let's not spend our time and resources thinking about things that are so little or so large that all they really do for us is puff us up and make us feel like gods. We are mammals, and have not exhausted the annoying little problems of being mammals. -K. Mullis __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Randomization of a two-way ANOVA?
The code below may not be the most optimized, but it should do the trick.
I've implemented the permutation test, which by some nomenclatures is
distinguished from the randomization test in that the latter is exhaustive
while the former is not.
I'm eager to hear the views of the list on whether the permutation test
fares when you use a parametric stat like the F as the focal statistic. I
know that David Howell introduction to the test employs the F (
http://www.uvm.edu/~dhowell/StatPages/Resampling/Resampling.html). I
personally think that in cases of known violation of normality and/or
homogeneity of variance, it seems odd to incorporate MSerror into the focal
statistic. I look forward to the list educating me if this view turns out to
be uninformed.
#make sure the factors are treated as such
FactorA = factor(FactorA)
FactorB = factor(FactorB)
#get the observed Fs
obs.aov = aov(Resp~FactorA*FactorB)
obs.mainA.F = summary(obs.aov)[[1]]$F[1]
obs.mainB.F = summary(obs.aov)[[1]]$F[2]
obs.AbyB.F = summary(obs.aov)[[1]]$F[3]
#prepare for the permutation loop
perms = 1e4
perm.mainA.F = rep(NA,perms)
perm.mainB.F = rep(NA,perms)
perm.AbyB.F = rep(NA,perms)
#run the permutation loop
for(i in 1:perms){
Randomized.Resp = Resp[order(runif(length(Resp)))]
perm.aov = aov(Randomized.Resp~FactorA*FactorB)
perm.mainA.F[i] = summary(perm.aov)[[1]]$F[1]
perm.mainB.F[i] = summary(perm.aov)[[1]]$F[2]
perm.AbyB.F[i] = summary(perm.aov)[[1]]$F[3]
}
#compute the p-values
p.mainA = mean(perm.mainA.Fobs.mainA.F)
p.mainB = mean(perm.mainB.Fobs.mainB.F)
p.AbyB = mean(perm.AbyB.Fobs.AbyB.F)
#print the p-values
print(p.mainA)
print(p.mainB)
print(p.AbyB)
--
Mike Lawrence
Graduate Student
Department of Psychology
Dalhousie University
www.thatmike.com
Looking to arrange a meeting? Do so at:
http://www.timetomeet.info/with/mike/
~ Certainty is folly... I think. ~
[[alternative HTML version deleted]]
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Examples of advanced data visualization
Hans W. Borchers wrote: Dear R-help, I am looking for ideas and presentations of new and advanced data visualization methods. As an example of what I am searching for, the 'Many Eyes' pages at http://manyeyes.alphaworks.ibm.com/manyeyes/ may provide a good paradigm. I would be interested even if it will not be easy to implement such examples in R, e.g. because of the interactive nature of these graphical displays. A few days before your mail, I started putting together some examples of using R and SVG/ECMAScript and R and Flash/Flex/MXML/ActionScript. There are some examples of R graphics that provide interactivity in various forms and ways at http://www.omegahat.org/SVGAnnoation/tests/examples.html (Most examples will work with Firefox, Opera is the most comprehensive browser however for these examples.) The Flex examples will take more time. D. Please answer to my e-mail address. In case enough interesting material comes up, I will enter a summary here. Hans Werner Borchers ABB Corporate Research __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] How to make a banner table.
I have a dataframe with the following variables: idnum areagender raceetc. I would like to make a table that looks like areagender race M FB W A 1 4 53 5 1 2 6 74 6 3 etc. Basically, I want to make a single broad table with a number of sub-set tables. I have tried: cbind(table(area, gender), table(area, race)) But, when I do this, I lose the labels gender / race. This makes it a lot harder to understand my factor labels. when I use cbind, I get this: M F B W A 1 4 5 3 5 1 2 6 7 4 6 3 Although, it is technically correct, I really want to keep my factor labels. I also tried this with xtabs and get the same results. Any ideas? I saw a relatively recent thread asking a similar question, but the proposed solution did not work for me, so I thought I would ask the questions again. If I am missing someting terribly obvious, I apologize. thanks. -- Insert something humorous here. :-) __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Examples of advanced data visualization
Sorry for the need for a second mail, but the URL missed a 't' http://www.omegahat.org/SVGAnnotation/tests/examples.html ^ Duncan Temple Lang wrote: Hans W. Borchers wrote: Dear R-help, I am looking for ideas and presentations of new and advanced data visualization methods. As an example of what I am searching for, the 'Many Eyes' pages at http://manyeyes.alphaworks.ibm.com/manyeyes/ may provide a good paradigm. I would be interested even if it will not be easy to implement such examples in R, e.g. because of the interactive nature of these graphical displays. A few days before your mail, I started putting together some examples of using R and SVG/ECMAScript and R and Flash/Flex/MXML/ActionScript. There are some examples of R graphics that provide interactivity in various forms and ways at http://www.omegahat.org/SVGAnnoation/tests/examples.html (Most examples will work with Firefox, Opera is the most comprehensive browser however for these examples.) The Flex examples will take more time. D. Please answer to my e-mail address. In case enough interesting material comes up, I will enter a summary here. Hans Werner Borchers ABB Corporate Research __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] explaining a model with rcs() terms
On Nov 30, 2008, at 10:23 PM, Dylan Beaudette wrote:
Hi, I am using the rcs() function in the Design library to model
non-linearity that is not well characterized by an otherwise
mechanistic function. I am able to make the model 'available' to
others through the excellent nomogram() function and the set of tables
that it can create. However, I would like to present the model in an
'expanded' format-- probably what rcspline.restate() or latex.Design()
produce on a model fit object.
Here is how the model was fit:
fit.ols - ols( log(k) ~ (rcs(activity) * (log(conc) + sar)) +
(rcs(sand) * (log(conc) + sar)), data=sm.clean, x=TRUE, y=TRUE)
Here is how I am accessing the 'expanded' format of the model
structure:
options(digits=3)
latex(fit.ols, file='fit_rcs.tex')
The output contains several notation elements that I am not familiar
with:
1. x_{+} -- it seems that this represent a term that should be set
to 0, when x is 0?
It is set to zero when the term inside the cubic is less than zero.
See pages 20-21 of Harrell's book where the basis functions are
described and illustrated.
i.e. the entire expression −453(activity −
0.842)_{+}^{3} = 0 when
'activity' = 0 ??
whenever (activity − 0.842) 0
2. the '!x' found in :
+log(conc) [ −0.0118sand + 9.58
! ×
!10−6 (sand − 11.6)
My guess is that this is 9.58 x 10^-6
− 0.000128(sand − 37.5)
+0.00045(sand − 47.2)
− 0.000350(sand − 51)
+ 1.86
! ×
!10−5 (sand − 69.8) ]
I don't see anything like that in Harrell's text and I am wondering if
a different character is getting rendering incorrectly. The only time
you see it is when the exponent is below -4.
what exactly does that mean?
An image version of the equation in question is attached.
Any input would be greatly appreciated!
Cheers,
Dylan
complex_equation.png__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] how to input a string without quote
Wow, you are so lazy... But sometimes R is just designed for lazy guys...
##
f = function(a) {
s = substitute(a)
as.character(s)
}
##
f(a = asdf)
[1] asdf
f(qwer)
[1] qwer
Regards,
Yihui
--
Yihui Xie [EMAIL PROTECTED]
Phone: +86-(0)10-82509086 Fax: +86-(0)10-82509086
Mobile: +86-15810805877
Homepage: http://www.yihui.name
School of Statistics, Room 1037, Mingde Main Building,
Renmin University of China, Beijing, 100872, China
Thanks!
However,
f(012345)
[1] 12345
f(0123-X)
[1] - 123 X
I hope to get:
012345
0-123-X
On Sat, Nov 29, 2008 at 10:59 PM, Gabor Grothendieck
[EMAIL PROTECTED] wrote:
This works if you type it in from the R console:
s - readline()
this is my string
s
[1] this is my string
Thanks! readline() works for my situation.
Regards,
Jinsong
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to make a banner table.
On Sun, 30 Nov 2008, Andrew Choens wrote: I have a dataframe with the following variables: idnum areagender raceetc. I would like to make a table that looks like areagender race M FB W A 1 4 53 5 1 2 6 74 6 3 etc. Basically, I want to make a single broad table with a number of sub-set tables. I have tried: Well you are asked to provide commented, minimal, self-contained, reproducible code, and I see nothing here I can reproduce. But here is a start: tab1 - xtabs(~agegp+tobgp,esoph) tab2 - xtabs(~agegp+alcgp,esoph) cat(paste(capture.output(tab1),capture.output(tab2),'\n')) tobgpalcgp agegp 0-9g/day 10-19 20-29 30+ agegp 0-39g/day 40-79 80-119 120+ 25-344 4 3 4 25-34 4 4 34 35-444 4 4 3 35-44 4 4 43 45-544 4 4 4 45-54 4 4 44 55-644 4 4 4 55-64 4 4 44 65-744 4 4 3 65-74 4 3 44 75+ 4 4 1 2 75+ 3 4 22 It is left as an exercise to figure out how to redo the first line to move 'alcgp' over ' 0-3' and how to delete the redundant 'agegp; column. See ?nchar ?substring and maybe ?sprintf for some pointers. HTH, Chuck cbind(table(area, gender), table(area, race)) But, when I do this, I lose the labels gender / race. This makes it a lot harder to understand my factor labels. when I use cbind, I get this: M F B W A 1 4 5 3 5 1 2 6 7 4 6 3 Although, it is technically correct, I really want to keep my factor labels. I also tried this with xtabs and get the same results. Any ideas? I saw a relatively recent thread asking a similar question, but the proposed solution did not work for me, so I thought I would ask the questions again. If I am missing someting terribly obvious, I apologize. thanks. -- Insert something humorous here. :-) __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Charles C. Berry(858) 534-2098 Dept of Family/Preventive Medicine E mailto:[EMAIL PROTECTED] UC San Diego http://famprevmed.ucsd.edu/faculty/cberry/ La Jolla, San Diego 92093-0901 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Attempting to get a STELLA model into R
To whomever may be of help, I am a student in a graduate modeling class at the University of North Carolina at Wilmington. I am trying to get a STELLA model converted into R. I am in the process of trying to 're-write' the script into R, but I seem to be missing pieces (i.e. parm values) that are keeping me from being able to replicate this model into R. Does anyone have an idea of a possible solution to my problem? Are there conversion programs or packages available that can convert STELLA models into R format? Thank you very much for you time, and I hope to hear back from you soon. -Tyler Gibson [EMAIL PROTECTED] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] factanal question
Dear R users: I'm wondering if it's possible to get the residual correlation matrix when using factanal. Since factanal assumes that the errors are normally distributed and independent (provided the factor model fits the data) this would be useful. Of course you would need to submit the data to the function to get the residuals (not just their correlation matrix), but it should be possible to get the residual correlation matrix if only the data correlation matrix is provided. Don McNeil __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] AIC function and Step function
Thanks for kind help from Steven and Christos last time. Now I got new
problem regarding the codes for calculating the weights (w) in AIC ()
function.
The original code is as below:
getAnywhere(logLik.lm)
function (object, REML = FALSE, ...)
{
res - object$residuals
p - object$rank
N - length(res)
if (is.null(w - object$weights)) {
w - rep.int(1, N)
}else {
excl - w == 0
if (any(excl)) {
res - res[!excl]
N - length(res)
w - w[!excl]
}
}
Now my question is, if I use lm() function to fit a multiple linear
regression model, such as mod.fit-lm(formula = Y~ X1 + X2 + X3, data =
set1), what code could I use to extract the weights (w) out? or how to
calculate the weights(w) shown in above codes? Thanks for your time and kind
help!
Dana
Steven McKinney wrote:
Hi Dana,
Many thanks to Christos Hatzis who sent
me an offline response, pointing out the
new functions that make this much
easier than my last suggestions:
methods() and getAnywhere()
methods(extractAIC)
[1] extractAIC.aov* extractAIC.coxph* extractAIC.glm*
extractAIC.lm* extractAIC.negbin*
[6] extractAIC.survreg*
Non-visible functions are asterisked
getAnywhere(extractAIC.coxph)
A single object matching extractAIC.coxph was found
It was found in the following places
registered S3 method for extractAIC from namespace stats
namespace:stats
with value
function (fit, scale, k = 2, ...)
{
edf - length(fit$coef)
loglik - fit$loglik[length(fit$loglik)]
c(edf, -2 * loglik + k * edf)
}
environment: namespace:stats
Thank you Christos.
That said, one of the advantages of getting
the source code is that it has comments that
are stripped out when the code is sourced into R
e.g. from the command line
getAnywhere(AIC.default)
A single object matching AIC.default was found
It was found in the following places
registered S3 method for AIC from namespace stats
namespace:stats
with value
function (object, ..., k = 2)
{
ll - if (stats4 %in% loadedNamespaces())
stats4:::logLik
else logLik
if (length(list(...))) {
object - list(object, ...)
val - lapply(object, ll)
val - as.data.frame(t(sapply(val, function(el) c(attr(el,
df), AIC(el, k = k)
names(val) - c(df, AIC)
Call - match.call()
Call$k - NULL
row.names(val) - as.character(Call[-1])
val
}
else AIC(ll(object), k = k)
}
environment: namespace:stats
From the source file
# File src/library/stats/R/AIC.R
# Part of the R package, http://www.R-project.org
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# A copy of the GNU General Public License is available at
# http://www.r-project.org/Licenses/
Return the object's value of the Akaike Information Criterion
(or An Inf.. Crit..)
AIC - function(object, ..., k = 2) UseMethod(AIC)
## AIC for logLik objects
AIC.logLik - function(object, ..., k = 2)
-2 * c(object) + k * attr(object, df)
AIC.default - function(object, ..., k = 2)
{
## AIC for various fitted objects --- any for which there's a logLik()
method:
ll - if(stats4 %in% loadedNamespaces()) stats4:::logLik else logLik
if(length(list(...))) {# several objects: produce data.frame
object - list(object, ...)
val - lapply(object, ll)
val - as.data.frame(t(sapply(val,
function(el)
c(attr(el, df), AIC(el, k = k)
names(val) - c(df, AIC)
Call - match.call()
Call$k - NULL
row.names(val) - as.character(Call[-1])
val
} else AIC(ll(object), k = k)
}
Steven McKinney
Statistician
Molecular Oncology and Breast Cancer Program
British Columbia Cancer Research Centre
email: smckinney +at+ bccrc +dot+ ca
tel: 604-675-8000 x7561
BCCRC
Molecular Oncology
675 West 10th Ave, Floor 4
Vancouver B.C.
V5Z 1L3
Canada
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--
View this message in context:
http://www.nabble.com/AIC-function-and-Step-function-tp20728043p20764062.html
Sent from the R help mailing
Re: [R] Regex: workaround for variable length negative lookbehind
Gabor Grothendieck wrote:
Try this:
vec - c(, baaa, bbaa, bbba, baamm, aa)
grep(^(?!(.)\\1{1,}$).*(.)\\2{1,}$, vec, perl = TRUE)
or even
grep(^(?!(.)\\1+$).*(.)\\2+$, vec, perl = TRUE)
vQ
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] AIC function and Step function
On Sun, Nov 30, 2008 at 5:05 PM, Dana77 [EMAIL PROTECTED] wrote:
Thanks for kind help from Steven and Christos last time. Now I got new
problem regarding the codes for calculating the weights (w) in AIC ()
function.
The original code is as below:
getAnywhere(logLik.lm)
function (object, REML = FALSE, ...)
{
res - object$residuals
p - object$rank
N - length(res)
if (is.null(w - object$weights)) {
w - rep.int(1, N)
}else {
excl - w == 0
if (any(excl)) {
res - res[!excl]
N - length(res)
w - w[!excl]
}
}
Now my question is, if I use lm() function to fit a multiple linear
regression model, such as mod.fit-lm(formula = Y~ X1 + X2 + X3, data =
set1), what code could I use to extract the weights (w) out? or how to
calculate the weights(w) shown in above codes?
mod.fit won't have weights because you didn't specify any through the
weights argument to lm. If you had, you could extract them using the
same technique used in the above code: w - mod.fit$weights
hth,
Kingsford Jones
Thanks for your time and kind
help!
Dana
Steven McKinney wrote:
Hi Dana,
Many thanks to Christos Hatzis who sent
me an offline response, pointing out the
new functions that make this much
easier than my last suggestions:
methods() and getAnywhere()
methods(extractAIC)
[1] extractAIC.aov* extractAIC.coxph* extractAIC.glm*
extractAIC.lm* extractAIC.negbin*
[6] extractAIC.survreg*
Non-visible functions are asterisked
getAnywhere(extractAIC.coxph)
A single object matching 'extractAIC.coxph' was found
It was found in the following places
registered S3 method for extractAIC from namespace stats
namespace:stats
with value
function (fit, scale, k = 2, ...)
{
edf - length(fit$coef)
loglik - fit$loglik[length(fit$loglik)]
c(edf, -2 * loglik + k * edf)
}
environment: namespace:stats
Thank you Christos.
That said, one of the advantages of getting
the source code is that it has comments that
are stripped out when the code is sourced into R
e.g. from the command line
getAnywhere(AIC.default)
A single object matching 'AIC.default' was found
It was found in the following places
registered S3 method for AIC from namespace stats
namespace:stats
with value
function (object, ..., k = 2)
{
ll - if (stats4 %in% loadedNamespaces())
stats4:::logLik
else logLik
if (length(list(...))) {
object - list(object, ...)
val - lapply(object, ll)
val - as.data.frame(t(sapply(val, function(el) c(attr(el,
df), AIC(el, k = k)
names(val) - c(df, AIC)
Call - match.call()
Call$k - NULL
row.names(val) - as.character(Call[-1])
val
}
else AIC(ll(object), k = k)
}
environment: namespace:stats
From the source file
# File src/library/stats/R/AIC.R
# Part of the R package, http://www.R-project.org
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# A copy of the GNU General Public License is available at
# http://www.r-project.org/Licenses/
Return the object's value of the Akaike Information Criterion
(or An Inf.. Crit..)
AIC - function(object, ..., k = 2) UseMethod(AIC)
## AIC for logLik objects
AIC.logLik - function(object, ..., k = 2)
-2 * c(object) + k * attr(object, df)
AIC.default - function(object, ..., k = 2)
{
## AIC for various fitted objects --- any for which there's a logLik()
method:
ll - if(stats4 %in% loadedNamespaces()) stats4:::logLik else logLik
if(length(list(...))) {# several objects: produce data.frame
object - list(object, ...)
val - lapply(object, ll)
val - as.data.frame(t(sapply(val,
function(el)
c(attr(el, df), AIC(el, k = k)
names(val) - c(df, AIC)
Call - match.call()
Call$k - NULL
row.names(val) - as.character(Call[-1])
val
} else AIC(ll(object), k = k)
}
Steven McKinney
Statistician
Molecular Oncology and Breast Cancer Program
British Columbia Cancer Research Centre
email: smckinney +at+ bccrc +dot+ ca
tel: 604-675-8000 x7561
BCCRC
Molecular Oncology
675 West 10th Ave, Floor 4
Vancouver B.C.
V5Z 1L3
Canada
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PLEASE do read the
Re: [R] Examples of advanced data visualization
Hans W. Borchers-4 wrote: Tom Backer Johnsen backer at psych.uib.no writes: I am also wondering if the R Wiki would be a better place to publish summaries on topics discussed here. On the mailing list, summaries are forgotten within one or two months time, only to be retrieved in specific searches. I have tried this once with a subject I found interesting and buried under too many quotes of previous mails: http://wiki.r-project.org/rwiki/doku.php?id=guides:lmer-tests Since the the reaction was mainly negative and legalese (you should ask permission to quote other people) that I will never try this again. Dieter -- View this message in context: http://www.nabble.com/Examples-of-advanced-data-visualization-tp20736795p20767389.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
