[R] pMCMC versus Pr(|t)
These are generally very similar, for obvious reasons. But in the analysis I have just done: pvals.fnc(Vcso.lmerC2trimmed, nsim=1)$fixed Estimate MCMCmean HPD95lower HPD95upper pMCMC Pr(|t|) (Intercept) 6.5878 6.5870 6.5126 6.6591 0.0001 0. cTrial -0.0002 -0.0002-0.0006 0.0002 0.4088 0.3996 lexword-0.0977 -0.0968-0.1228-0.0698 0.0001 0. conditionpure 0.0892 0.0896 0.0022 0.1781 0.0482 0.1744 lexword:conditionpure -0.0563 -0.0569-0.0853-0.0287 0.0002 0.0001 there's a large discrepancy for the conditionpure row. I have not been able to find examples of, or discussions of, how to respond to such discrepancies; so any help would be much appreciated. Max Coltheart _ Professor Max Coltheart AM DSc FASSA FAA FBA Emeritus Professor of Cognitive Science, Macquarie University Honorary Professor of Psychology, University of Queensland [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Reading multiple csv files
Dear R helpers
Some particular analysis leads me to various number of output csv files
depending on some conditions. Say e.g. I have output files variable1.csv,
variable2.csv, .. Problem is I don't know how many csv files been
generated. They could be 4, 5 or even 10. Each file will have a column called
amount.
My problem is to find filewise mean(amount) and sd(amount). I need to write a
loop where all these individual csv files will be read and after reading each
file, mean and sd will be calculated.
I have tried to write some R code which is very absurd.
for (i in 1 : n) # n is no of input files
{
data[i] = read.csv(file = paste(variable, i, .csv, sep = ))$amount
mean(data[i])
sd(data[i])
}
I get following error.
Error in file(file, rt) : cannot open the connection
In addition: Warning message:
In file(file, rt) :
cannot open file 'paste(output, i, .csv, sep = )': Invalid argument
Please guide
Regards
Madhavi
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Re: [R] error in lmLists in lme4 package (bug?)
Elizabeth Purdom-2 wrote: I am trying to use lmLists in the lme4 package and copying over very standard code from the nlme package given in 'Mixed-Effects Models in S and S-Plus'. It appears to not accept an 'I(age-11)' in the formula, though it will accept the formula with out the subtraction of 11 from age. Looks like a bug to me (checked on Windows with lme4a, the development version). It is specific to lmList, I(age-11) works for lmer. The special mailing list for lme4-problems is r-sig-mixed-mod...@r-project.org I have forwarded the link to your message to Douglas Bates. Dieter -- View this message in context: http://n4.nabble.com/error-in-lmLists-in-lme4-package-bug-tp1569432p1570296.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] R: MANOVA help
Hello everyone! I did a search, didn't quite find what I was looking for. I should warn you I'm not very good at programming. I am trying to do a simulation. I have generated data in two separate files. I want to do a MANOVA, using the files as my categorical variable. Each files has 4 variables that I generated with the rmnorm() method, the only difference between them is that I used different means. Any ideas? Thank you for your time :-D -- View this message in context: http://n4.nabble.com/R-MANOVA-help-tp1570300p1570300.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] Adjust lattice graph axis label on final page
On Thu, Feb 25, 2010 at 3:45 AM, Sebastien Bihorel sebastien.biho...@cognigencorp.com wrote: Dear R-users, I was wondering if there was a way to adjust the placement of the axis titles for the last page of a multi-page lattice plot (see example below). Depending on the total number of panels, the placement of these titles might look strange on the last page, if the layout is not adjusted (e.g. in some template code). It's not possible to adjust the labels on a per-page basis. It _is_ possible to have the two plots fill up the last page, but that may not be what you want. xyplot(y~x|id,as.table=T,data=mydata,layout=c(2,3))[1:6] xyplot(y~x|id,as.table=T,data=mydata,layout=c(2,1))[7:8] -Deepayan __ 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] Plotting a Trivial Matrix
Dear All, Consider a matrix (N x N) where each entry is either zero or one (can hardly get any simpler). Now, I would like to plot it as a 'chessboard' where every matrix entry is a black (1) or white (0) square. Whatever tool I use to plot it, it should not try to interpolate the data at all. I found some online references http://www.phaget4.org/R/image_matrix.html but probably I can resort to something much simpler. Can anyone provide me with a simple example I can modify later on? Many thanks Lorenzo __ 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] Reading multiple csv files
On Fri, 26-Feb-2010 at 12:15AM -0800, Madhavi Bhave wrote:
| Dear R helpers
| ?
| Some particular analysis leads me to various number of output csv
| files depending on some conditions. Say e.g. I have output files
| variable1.csv, variable2.csv, .. Problem is I don't
| know how many csv files been generated. They could be 4, 5 or even
| 10. Each file will have a column called amount. ?
| My problem is to find filewise mean(amount) and sd(amount). I need
| to write a loop where all these individual csv files will be read
| and after reading each file, mean and sd will be calculated. ?
| I have tried to write some R code which is very absurd.
| ?
| for (i in 1 : n)? # n is no of input files
There's a bit of a problem with your character encoding. On my
system, I get that question mark which doesn't make syntactic sense.
Just what you have there, I can't guess, so it's a bit hard to work
out what could be the problem (apart from not knowing what size n
should be).
| ?
| {
| data[i] = read.csv(file = paste(variable, i, .csv, sep = ))$amount
| mean(data[i])
| sd(data[i])
You'll need to tell us what your object 'data' is. You probably need a
list, in which case data[[i]] might work.
| }
| ?
| I get following error.
| ?
| Error in file(file, rt) : cannot open the connection
| In addition: Warning message:
| In file(file, rt) :
| ? cannot open file 'paste(output, i, .csv, sep = )': Invalid argument
|
| ?
| Please guide
The posting guide might have given you a few ideas. We don't know
what you did that used output in it to have any idea what could be
behind the Invalid argument message.
| PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
HTH
--
~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.
___Patrick Connolly
{~._.~} Great minds discuss ideas
_( Y )_ Average minds discuss events
(:_~*~_:) Small minds discuss people
(_)-(_) . Eleanor Roosevelt
~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.
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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] bwplot() {lattice}
On Fri, Feb 26, 2010 at 8:30 AM, Peng Cai pengcaimaill...@gmail.com wrote: Hi All, I'm trying to plot boxplot graph. I tried barchart with groups= option and it worked fine. But when I try to generate same kind of graph using bwplot(), groups= option doesn't seem to work. Though this works, yield ~ variety | site * year I'm thinking why groups= doesn't work in this case, can anyone help please... Let's see...you have exactly one observation per site/variety/year combination (otherwise the barchart wouldn't have made sense). So in the boxplot you want (which is supposed to summarize a distribution, not a single point), you only have that single point to plot. For that, you can use dotplot(yield ~ variety | site, data = barley, auto.key = TRUE, groups = year, layout = c(6,1), scales=(x=list(rot=45))) If you try to come up with a more sensible example, you would realize that boxplots are already grouped (the grouping variable is the categorical variable in the formula y ~ x, not the 'groups' argument). Compare ## Is this really what you want? bwplot(yield ~ variety, data = barley, col = 1, pch = 16, panel = panel.superpose, panel.groups = panel.bwplot, groups = year, scales=(x=list(rot=45))) bwplot(yield ~ year | variety, data = barley, scales=(x=list(rot=45)), layout = c(10, 1)) -Deepayan #Code: library(lattice) barchart(yield ~ variety | site, data = barley, groups = year, layout = c(1,6), auto.key = list(points = FALSE, rectangles = TRUE, space = right)) bwplot(yield ~ variety | site, data = barley, groups = year, layout = c(6,1), scales=(x=list(rot=45)), auto.key = list(points = FALSE, rectangles = TRUE, space = right)) __ 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] two questions for R beginners
Since you want input from beginners, here are some thoughts I had and still have two big problems with R: - this vectorization thing. I've read many manuals (including R inferno), but I'm still not completely clear about it. In simple examples, it's fine. But when it gets a bit more complex, then... Related to it, the *apply functions are still a bit difficult to understand. When I have to use them, I just try one and see what happens. I don't understand them well enough to know which one I need. - the second problem is where to find the functions/packages I need. There are many options, and that's actually the problem. R Wiki, Rseek, RSiteSearch, Crantastic, etc... When you start with R, you discover that the capabilities of R are almost unlimited and you don't really know where to start, where to find what you need. As noted in earlier posts, the mailing list is really great, but some people are really hard with beginners. It was noted in a discussion a few days ago, but it looks like some don't realize how difficult it is at the beginning to formulate a good question, clear, with self-contained example and so on. Moreover, not everybody speaks English natively. I don't mean that you must help, even when the question is really vague and not clear and whatever. I'm just saying that if you don't want to help (whatever the reason), you don't have to say it badly. But in any cases, the mailing list is still really helpful. As someone noted (sorry I erased the email so I don't remember who), it might be a good idea to split it. Hope that's what you wanted Ivan Le 2/26/2010 08:39, Dieter Menne a écrit : Patrick Burns wrote: * What were your biggest misconceptions or stumbling blocks to getting up and running with R? (This derives partly from teaching) The fact that this xapply-stuff was not idempotent (worse: not always) and that you need a monster like do.call() to straighten this out. Nowadays, plyr comes close. The concept of environment. With S it was worse, though. That you cannot change values passed by reference. I noted that the latter is no problem for students who have not worked with c(++/#) before. That there is only one return-result in functions. [ and the likes as an operator. 10 years ago, when I started, the message was: S4 is the future, S3 is legacy. So I learned S4. Only to never use is in self-written code later. Might be different for BioConductor people. That sometimes you can use vectors not in data= (lattice), and sometimes not (ggplot2). Still a VERY confusing inconsistency. The why-does-this-not-print FAQ. Why does par(oma..) not work with lattice? Dieter __ 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] Plotting a Trivial Matrix
Hi,
A minimalist example using Grid graphics,
library(RGraphics)
bwImage - function(m, cols=c(white, black),
draw=TRUE, gp=gpar()){
g - imageGrob(nrow(m), ncol(m),
cols=cols[m+1], gp=gp)
if(draw)
grid.draw(g)
return(g)
}
m - matrix(rnorm(200) 0, ncol=20)
bwImage(m)
HTH,
baptiste
On 26 February 2010 09:29, Lorenzo Isella lorenzo.ise...@gmail.com wrote:
Dear All,
Consider a matrix (N x N) where each entry is either zero or one (can
hardly get any simpler).
Now, I would like to plot it as a 'chessboard' where every matrix entry
is a black (1) or white (0) square.
Whatever tool I use to plot it, it should not try to interpolate the
data at all.
I found some online references
http://www.phaget4.org/R/image_matrix.html
but probably I can resort to something much simpler.
Can anyone provide me with a simple example I can modify later on?
Many thanks
Lorenzo
__
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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.
--
Baptiste Auguié
Departamento de Química Física,
Universidade de Vigo,
Campus Universitario, 36310, Vigo, Spain
tel: +34 9868 18617
http://webs.uvigo.es/coloides
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[R] One ploblem
I use the function 'read.table' to read a data file. it has cases.but R only read 75. why ? I need your help.thx. -- View this message in context: http://n4.nabble.com/One-ploblem-tp1570329p1570329.html Sent from the R help mailing list archive at Nabble.com. [[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] R and Wordpress
Hi CH, My solution for this is to work only on the code editor, and never to move to the visual editor (once I put an R code inside it). Let me know if it works for you (and what is the link to your blog :) ) Cheers, Tal Contact Details:--- Contact me: tal.gal...@gmail.com | 972-52-7275845 Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) | www.r-statistics.com (English) -- On Thu, Feb 25, 2010 at 6:40 AM, C.H. chainsawti...@gmail.com wrote: Dear R helpers, I have a question regarding wordpress and R. I have asked this question in Wordpress support ( http://wordpress.org/support/topic/368312 ) but there is no answer so far, maybe the R community can have a better answer. I followed the excellent tutorial on r-statistics-blog ( http://www.r-statistics.com/2010/02/r-syntax-highlight-on-your-blog-a-wordpress-plugin/ ) to enable syntax hightlighting but Wordpress keeps breaking - into - and I have to use = instead. (I think = is confusing.) And I think it is not related to the theme as well. Is there any clue to solve this? I am using Wordpress 2.9.2. Regards, CH -- CH Chan Research Assistant - KWH http://www.macgrass.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. [[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] two questions for R beginners
My difficulties: 1) Statistics :-) well, I'm learning. 2) Understand what is available *per subject area*. Something like the task view for packages, should be compiled for basic commands/functions. Like: all things related to string manipulation, all things related to number formatting, all *apply things, and so on. Something similar is available for C runtime library functions (like in http://msdn.microsoft.com/en-us/library/2aza74he(VS.71).aspx ) and is really useful, also to expand the number of functions known. 3) The Diktakt-like: avoid for loops! without clear examples of alternatives. I have found them later in the maillist, but at the beginning it is not simple, especially coming from C/C++. 4) for statement behavior different from C/C++: for(i in 1:0) counts backward instead of stopping. 5) missing small things like ++var On the positive side: - it is not too difficult to setup something simple to create a decent chart. - it is possible to use for loops without feeling guilty. :-) - documentation is very well done. Maybe some page are still clear only to who already know the argument. - there are zillions of courses/papers/tutorials to read - after studying R by myself, now I'm becoming the local R expert, that from a workplace point of view is not bad... Hope it helps. Ciao! mario Ivan Calandra wrote: Since you want input from beginners, here are some thoughts I had and still have two big problems with R: - this vectorization thing. I've read many manuals (including R inferno), but I'm still not completely clear about it. In simple examples, it's fine. But when it gets a bit more complex, then... Related to it, the *apply functions are still a bit difficult to understand. When I have to use them, I just try one and see what happens. I don't understand them well enough to know which one I need. - the second problem is where to find the functions/packages I need. There are many options, and that's actually the problem. R Wiki, Rseek, RSiteSearch, Crantastic, etc... When you start with R, you discover that the capabilities of R are almost unlimited and you don't really know where to start, where to find what you need. As noted in earlier posts, the mailing list is really great, but some people are really hard with beginners. It was noted in a discussion a few days ago, but it looks like some don't realize how difficult it is at the beginning to formulate a good question, clear, with self-contained example and so on. Moreover, not everybody speaks English natively. I don't mean that you must help, even when the question is really vague and not clear and whatever. I'm just saying that if you don't want to help (whatever the reason), you don't have to say it badly. But in any cases, the mailing list is still really helpful. As someone noted (sorry I erased the email so I don't remember who), it might be a good idea to split it. Hope that's what you wanted Ivan Le 2/26/2010 08:39, Dieter Menne a écrit : Patrick Burns wrote: * What were your biggest misconceptions or stumbling blocks to getting up and running with R? (This derives partly from teaching) The fact that this xapply-stuff was not idempotent (worse: not always) and that you need a monster like do.call() to straighten this out. Nowadays, plyr comes close. The concept of environment. With S it was worse, though. That you cannot change values passed by reference. I noted that the latter is no problem for students who have not worked with c(++/#) before. That there is only one return-result in functions. [ and the likes as an operator. 10 years ago, when I started, the message was: S4 is the future, S3 is legacy. So I learned S4. Only to never use is in self-written code later. Might be different for BioConductor people. That sometimes you can use vectors not in data= (lattice), and sometimes not (ggplot2). Still a VERY confusing inconsistency. The why-does-this-not-print FAQ. Why does par(oma..) not work with lattice? Dieter __ 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. -- Ing. Mario Valle Data Analysis and Visualization Group| http://www.cscs.ch/~mvalle Swiss National Supercomputing Centre (CSCS) | Tel: +41 (91) 610.82.60 v. Cantonale Galleria 2, 6928 Manno, Switzerland | Fax: +41 (91) 610.82.82 __ 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] Plotting a Trivial Matrix
On 02/26/2010 07:29 PM, Lorenzo Isella wrote: Dear All, Consider a matrix (N x N) where each entry is either zero or one (can hardly get any simpler). Now, I would like to plot it as a 'chessboard' where every matrix entry is a black (1) or white (0) square. Whatever tool I use to plot it, it should not try to interpolate the data at all. I found some online references http://www.phaget4.org/R/image_matrix.html but probably I can resort to something much simpler. Can anyone provide me with a simple example I can modify later on? Hi Lorenzo, trivial_matrix-matrix(sample(0:1,100,TRUE),nrow=10) require(plotrix) color2D.matplot(trivial_matrix,main=A trivial Plot) Jim __ 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] two questions for R beginners
Saeed, If the R-help list were split, what do you see as the pieces? Pat On 26/02/2010 01:53, Saeed Abu Nimeh wrote: On Thu, Feb 25, 2010 at 9:31 AM, Patrick Burnspbu...@pburns.seanet.com wrote: * What were your biggest misconceptions or stumbling blocks to getting up and running with R? 1- Compared to other programming languages it is hard to learn R by example, because it is hard to find code on the web that will do the exact thing you are looking for, sometimes you might get lucky though. By contrast, take Perl for example, it is an easy language to learn by example. 2- The R mailing list. Beginners get frustrated after they struggle for a long time to solve a problem and the easiest thing then is to send an email to the R mailing list. I did this in the past. The best thing that happened was that my request was neglected and I had to spend more time on the problem and find a solution by myself eventually. Do not get me wrong, I am not saying that the mailing list is bad, but it should be more organized. Maybe broken down into couple of other mailing lists. This might bring up a good discussion thread. * What documents helped you the most in this initial phase? An Introduction to R by Venables simpleR – Using R for Introductory Statistics by Verzani -- Patrick Burns pbu...@pburns.seanet.com http://www.burns-stat.com (home of 'The R Inferno' and 'A Guide for the Unwilling S User') __ 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] One ploblem
On 02/26/2010 07:50 PM, Lesong Tsai wrote:
I use the function 'read.table' to read a data file.
it has cases.but R only read 75.
why ? I need your help.thx.
Hi Lesong,
There were one or two similar posts recently. Are there any single
quotes (') in your data file?
Jim
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Re: [R] R and Wordpress
Hi, The visual editor should take HTML code, shouldn't it? - would then be written lt;- Haven't tried it though. Cheers, Tsjerk On Fri, Feb 26, 2010 at 10:19 AM, Tal Galili tal.gal...@gmail.com wrote: Hi CH, My solution for this is to work only on the code editor, and never to move to the visual editor (once I put an R code inside it). Let me know if it works for you (and what is the link to your blog :) ) Cheers, Tal Contact Details:--- Contact me: tal.gal...@gmail.com | 972-52-7275845 Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) | www.r-statistics.com (English) -- On Thu, Feb 25, 2010 at 6:40 AM, C.H. chainsawti...@gmail.com wrote: Dear R helpers, I have a question regarding wordpress and R. I have asked this question in Wordpress support ( http://wordpress.org/support/topic/368312 ) but there is no answer so far, maybe the R community can have a better answer. I followed the excellent tutorial on r-statistics-blog ( http://www.r-statistics.com/2010/02/r-syntax-highlight-on-your-blog-a-wordpress-plugin/ ) to enable syntax hightlighting but Wordpress keeps breaking - into - and I have to use = instead. (I think = is confusing.) And I think it is not related to the theme as well. Is there any clue to solve this? I am using Wordpress 2.9.2. Regards, CH -- CH Chan Research Assistant - KWH http://www.macgrass.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. [[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. -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist __ 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] Plotting a Trivial Matrix
baptiste auguie wrote:
Hi,
A minimalist example using Grid graphics,
library(RGraphics)
bwImage - function(m, cols=c(white, black),
draw=TRUE, gp=gpar()){
g - imageGrob(nrow(m), ncol(m),
cols=cols[m+1], gp=gp)
if(draw)
grid.draw(g)
return(g)
}
m - matrix(rnorm(200) 0, ncol=20)
bwImage(m)
HTH,
baptiste
On 26 February 2010 09:29, Lorenzo Isella lorenzo.ise...@gmail.com wrote:
Dear All,
Consider a matrix (N x N) where each entry is either zero or one (can
hardly get any simpler).
Now, I would like to plot it as a 'chessboard' where every matrix entry
is a black (1) or white (0) square.
Whatever tool I use to plot it, it should not try to interpolate the
data at all.
I found some online references
http://www.phaget4.org/R/image_matrix.html
but probably I can resort to something much simpler.
Can anyone provide me with a simple example I can modify later on?
Many thanks
Lorenzo
__
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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.
Thanks Augustine and Jim for the prompt reply.
You both answered my question. To avoid another post, I would simply
like to know if something along these lines is doable also with ggplot2.
Many thanks
Lorenzo
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Re: [R] Plotting a Trivial Matrix
What about http://www.phaget4.org/R/image_matrix.html try function f.matrix.plot Tobias Mathow Forest Research Institute Baden-Wuerttemberg (FVA) Wonnhaldestr. 4, D- 79100 Freiburg Phone: ++49-761-4018-365 www.fva-bw.de -Ursprüngliche Nachricht- Von: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] Im Auftrag von Lorenzo Isella Gesendet: Freitag, 26. Februar 2010 09:30 An: r-help Betreff: [R] Plotting a Trivial Matrix Dear All, Consider a matrix (N x N) where each entry is either zero or one (can hardly get any simpler). Now, I would like to plot it as a 'chessboard' where every matrix entry is a black (1) or white (0) square. Whatever tool I use to plot it, it should not try to interpolate the data at all. I found some online references http://www.phaget4.org/R/image_matrix.html but probably I can resort to something much simpler. Can anyone provide me with a simple example I can modify later on? Many thanks Lorenzo __ 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] R: error using pvcm() on unbalanced panel data
Dear Liviu, in general, pvcm is capable of fitting variable coefficients models on unbalanced data sets: e.g., data(Grunfeld) grun-Grunfeld[-1,] ## 'unbalance' it pvcm(inv~value+capital, data=grun) Model Formula: inv ~ value + capital Coefficients: (Intercept) value capital 1 -193.77819 0.1272949 0.3765985 2-49.19832 0.1748560 0.3896419 3 -9.95631 0.0265512 0.1516939 4 -6.18996 0.0779478 0.3157182 5 22.70712 0.1623777 0.0031017 6 -8.68554 0.1314548 0.0853743 7 -4.49953 0.0875272 0.1237814 8 -0.50939 0.0528941 0.0924065 9 -7.72284 0.0753879 0.0821036 10 0.16152 0.0045734 0.4373692 pvcm(inv~value+capital, data=grun, model=random) Model Formula: inv ~ value + capital Coefficients: (Intercept) value capital -11.7417540.0850460.199632 so the problem must be within the dataset and the minimum-T requirements for fitting vc models. The error message may not be the friendliest, but it actually tells you where the problem is. Let us look at the Hedonic data you used as an example: this is not a panel dataset but you can treat it as one, as you did, by grouping obs. for the same town. So your N is length(unique(Hedonic$townid)) [1] 92 and your T (although here it is not time) is: summary(tapply(Hedonic$townid,Hedonic$townid,length)) Min. 1st Qu. MedianMean 3rd Qu.Max. 1.0 2.0 4.0 5.5 7.030.0 as you can see, there are many single observation towns which(tapply(Hedonic$townid,Hedonic$townid,length)==1) 1 10 11 12 13 15 34 45 50 51 52 53 65 66 69 70 73 1 10 11 12 13 15 34 45 50 51 52 53 65 66 69 70 73 So the within model cannot work, as it needs T(K+1) for estimating the separate regressions for each town. Why the random vcm doesn't is less straightforward. Let us try a reduced pvcm with K=9 on a subset of data with T10: hedo-Hedonic[(Hedonic$townid %in% which(tapply(Hedonic$townid,Hedonic$townid,length)10)),] dim(hedo) [1] 208 15 Hed - pvcm(mv ~ crim + zn + indus + chas + nox + rm + age + dis +rad + , data=hedo, model = within,index = townid) This works, but gives bad coefficients, because as it turns out there are also many time-invariant variables in the dataset, and of course these are discarded in doing timewise regressions! A closer look at the data reveals that 'chas' is a factor, 'zn' is either 0 or 20, 'age' is truncated at 100 and so on. Let's see what's in the town with the most obs.: tapply(hedo$townid,hedo$townid,length) 5 25 28 29 39 41 46 60 80 81 83 84 85 22 11 15 30 11 18 12 12 11 13 19 23 11 summary(hedo[hedo$townid==29,]) mv crim zninduschas Min. : 9.376 Min. :1.127 Min. :0 Min. :19.58 no :23 1st Qu.: 9.655 1st Qu.:1.472 1st Qu.:0 1st Qu.:19.58 yes: 7 Median : 9.878 Median :2.152 Median :0 Median :19.58 Mean : 9.973 Mean :2.111 Mean :0 Mean :19.58 3rd Qu.:10.093 3rd Qu.:2.430 3rd Qu.:0 3rd Qu.:19.58 Max. :10.820 Max. :4.097 Max. :0 Max. :19.58 nox rm age dis Min. :36.60 Min. :24.04 Min. : 79.20 Min. :0.2788 1st Qu.:36.60 1st Qu.:30.26 1st Qu.: 93.82 1st Qu.:0.4349 Median :75.86 Median :35.69 Median : 96.05 Median :0.5615 Mean :57.54 Mean :37.83 Mean : 95.16 Mean :0.5876 3rd Qu.:75.86 3rd Qu.:39.71 3rd Qu.: 98.42 3rd Qu.:0.7354 Max. :75.86 Max. :70.14 Max. :100.00 Max. :0.8862 rad tax ptratio blacks Min. :1.609 Min. :403 Min. :14.7 Min. :0.08801 1st Qu.:1.609 1st Qu.:403 1st Qu.:14.7 1st Qu.:0.29349 Median :1.609 Median :403 Median :14.7 Median :0.35000 Mean :1.609 Mean :403 Mean :14.7 Mean :0.31745 3rd Qu.:1.609 3rd Qu.:403 3rd Qu.:14.7 3rd Qu.:0.37402 Max. :1.609 Max. :403 Max. :14.7 Max. :0.39690 lstattownid Min. :-4.058 Min. :29 1st Qu.:-2.534 1st Qu.:29 Median :-2.064 Median :29 Mean :-2.186 Mean :29 3rd Qu.:-1.801 3rd Qu.:29 Max. :-1.220 Max. :29 whence we see that 'zn', 'indus', 'rad', 'tax', 'ptratio' and, of course, 'townid' are T-invariant, 'chas' is a factor but at least it varies between yes and no. 'nox' is also problematic in that it varies only from time to time... A feasible formula, whatever this model means, is: fm - mv ~ crim + rm + age + dis + blacks + lstat newmodr - pvcm(fm, data=hedo, model=random, index=townid) newmodw - pvcm(fm, data=hedo, model=within, index=townid) ## all is well now I hope hereby to have given you some methodological hint for a critical overview of your data. PS the pooltest() problem is much the same, as pooltest() needs to fit separate regressions. Best, Giovanni -Messaggio originale- Da: Liviu Andronic
[R] Boot R
Hello, This is my first post, and my english is not very good, but I will try... I have a problem with boot the R. After that I install ubuntu 9.10 the R don't run. When I open the terminal and digit R, appear the message: */usr/lib/R/bin/exec/R: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory* What's happening? Can anyone help me? Thank you -- Cassiano Sousa Rosa Universidade Federal de Viçosa -UFV Dept. Biologia Animal Pós-graduação em Entomologia Lab. Termitologia Viçosa-MG, Brazil CEP 36570-000 Tel: (31) 38994017 (31) 97972730 [[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] Plotting a Trivial Matrix
On 26 February 2010 11:12, Lorenzo Isella lorenzo.ise...@gmail.com wrote: Thanks Augustine and Jim for the prompt reply. You both answered my question. To avoid another post, I would simply like to know if something along these lines is doable also with ggplot2. Many thanks Lorenzo Augustine??? Anyhow, with ggplot2, m - matrix(rnorm(200) 0, ncol=20) require(ggplot2) d - melt(m) qplot(X1, X2, data=d, fill=value, geom=tile) + scale_fill_manual(values=c(white, black)) HTH, baptiste __ 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] Odp: two questions for R beginners
Hi It was class, mode or type.of imported data which I usually believed they are something but actually they were something else until I learned that when something does not look as I would expect I shall blame myself for wrong expectation. For the time being I would say that reshape and factor ordering especially with groupedData objects from nlme are still giving me a headache and many trials and errors to get desired result. And of course regular expressions but they are not related with R but with my laziness to learn it due to fact that on this list there are many clever experts which can solve the problem for a fraction of time I could do it myself. For documents in the beginning I would vote for Paul Johnsons Rtips. About 10 yars ago it was nice collection of several useful Howto's. Regards Petr r-help-boun...@r-project.org napsal dne 25.02.2010 18:31:19: * What were your biggest misconceptions or stumbling blocks to getting up and running with R? * What documents helped you the most in this initial phase? I especially want to hear from people who are lazy and impatient. Feel free to write to me off-list. Definitely write off-list if you are just confirming what has been said on-list. -- Patrick Burns pbu...@pburns.seanet.com http://www.burns-stat.com (home of 'The R Inferno' and 'A Guide for the Unwilling S User') __ 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] Boot R
Try to use: sudo R best regards. 2010/2/26 Cassiano cassian...@gmail.com: Hello, This is my first post, and my english is not very good, but I will try... I have a problem with boot the R. After that I install ubuntu 9.10 the R don't run. When I open the terminal and digit R, appear the message: */usr/lib/R/bin/exec/R: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory* What's happening? Can anyone help me? Thank you -- Cassiano Sousa Rosa Universidade Federal de Viçosa -UFV Dept. Biologia Animal Pós-graduação em Entomologia Lab. Termitologia Viçosa-MG, Brazil CEP 36570-000 Tel: (31) 38994017 (31) 97972730 [[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. -- - Dr. Alberto Goldoni Bologna, Italy __ 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] Boot R
same error... -- View this message in context: http://n4.nabble.com/Boot-R-tp1570427p1570441.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] block matrices
Thank you Duncan, Kjetil and William. Kjetil, with rep(0,2), I get a vector. So I have to transpose it. cbind(A,B, t( rep(0,2) ) ) if C is of length 2. Is that right ? I like very much Duncan's general solution. Thanks a lot, Gustave 2010/2/24 Kjetil Halvorsen kjetilbrinchmannhalvor...@gmail.com see below. On Wed, Feb 24, 2010 at 12:56 PM, Gustave Lefou gustave5...@gmail.com wrote: Dear all, I do not know how to deal with block matrices in R. For example I have 3 matrices A, B and C. And I want to produce a new matrix of this form ( A B 0 ) ( 0 0 C ) where A, B and C are one-row matrices. cbind(A,B,0) or maybe cbind(a,B,rep(0, 12)) cbind(rep(0,2), C) Apart from A, B and C, all the coefficients are 0. Is there an easy solution in R for every block matrices ? Combine rbind and cbind: ?rbind Kjetil Thanks for your help, Gustave P.S. : I have had a look at a function called zoo which looked quite complicated to me. [[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.htmlhttp://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.
[R] Hartley's table
Hi, Does anyone know how to generate Hartley's table in R? -- Silvano Cesar da Costa Departamento de Estatística Universidade Estadual de Londrina Fone: 3371-4346 __ 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] Hartley's table
Hi Silvano, Is it library(SuppDists) ?maxFratio you are looking for ? Best, Tobias Silvano wrote: Hi, Does anyone know how to generate Hartley's table in R? -- Silvano Cesar da Costa Departamento de Estatística Universidade Estadual de Londrina Fone: 3371-4346 __ 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] Boot R
Really, I had ubuntu 9.04 with R normal, so I did upgrade to ubuntu 9.10 then R not run. After this I remove and reinstall the R by way of synaptic, but the error continue. -- View this message in context: http://n4.nabble.com/Boot-R-tp1570427p1570550.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] Boot R
Cassiano wrote: Hello, This is my first post, and my english is not very good, but I will try... I have a problem with boot the R. After that I install ubuntu 9.10 the R don't run. When I open the terminal and digit R, appear the message: */usr/lib/R/bin/exec/R: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory* Hi, R tries to find libgfortran.so.3, which it cannot find. Either it's not on your computer, or it's the wrong version. Check if it is installed: dpkg -l | grep libgfortran If this last command does not return anything, you need to install using: sudo apt-get update sudo apt-get install libgfortran3 probably it is not installed by default and this will solve the problem. cheers, Paul What's happening? Can anyone help me? Thank you __ 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. -- Drs. Paul Hiemstra Department of Physical Geography Faculty of Geosciences University of Utrecht Heidelberglaan 2 P.O. Box 80.115 3508 TC Utrecht Phone: +3130 274 3113 Mon-Tue Phone: +3130 253 5773 Wed-Fri http://intamap.geo.uu.nl/~paul __ 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] Unique Values of a Matrix
I have a 280,000 x 11 matrix with various values and many NA values. What I would like to do is get a vector of every unique value in the matrix. For example: X = [ 12NA 43 1 7 NA 2 ] Returns: Unique_X = [ 1, 2, 3, 4, 7] Thanks, Todd [[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] Boot R
I think I have 'libgfortran'. After that I digit 'dpkg -l | grep libgfortran' in terminal, I got this message: ii libgfortran2 4.2.4-5ubuntu1 Runtime library for GNU Fortran applications ii libgfortran2-dbg 4.2.4-5ubuntu1 Runtime library for GNU Fortran applications ii libgfortran3 4.4.1-4ubuntu9 Runtime library for GNU Fortran applications ii libgfortran3-dbg 4.4.1-4ubuntu9 Runtime library for GNU Fortran applications And the error continue: /usr/lib/R/bin/exec/R: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory -- View this message in context: http://n4.nabble.com/Boot-R-tp1570427p1570558.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] Unique Values of a Matrix
Try this: unique(c(X)) On Fri, Feb 26, 2010 at 10:06 AM, Todd DeWees t.dew...@cpse.dundee.ac.uk wrote: I have a 280,000 x 11 matrix with various values and many NA values. What I would like to do is get a vector of every unique value in the matrix. For example: X = [ 1 2 NA 4 3 1 7 NA 2 ] Returns: Unique_X = [ 1, 2, 3, 4, 7] Thanks, Todd [[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. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O __ 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 with simple bootstrap test
Thanks that's exactly what I wanted - and yes resampling of the rows with replacement was what I should have said. Now i'm stuck on how to do a bootstrap of the data in each column of the table separately, but all done in the same go. -- View this message in context: http://n4.nabble.com/Help-with-simple-bootstrap-test-tp1569459p1570575.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] Error in Aggregate function
Hi, When I run the Aggregate function in repeat loop, I got the following error: Error in sort.list(unique.default(x), na.last = TRUE) : 'x' must be atomic for 'sort.list' Have you called 'sort' on a list? How to solve this error. Anyone can help me. Urgent. Thanks. Meenakshi. -- View this message in context: http://n4.nabble.com/Error-in-Aggregate-function-tp1570370p1570370.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] two questions for R beginners
On 25/02/2010 20:42, Greg Snow wrote: Patrick, I would add one more question: * where did you look for help expecting answers, but did not find them? Yes, an excellent additional question. Pat If you add hubris to laziness and impatience, you have Larry Wall's 3 virtues of a programmer. [...] -- Patrick Burns pbu...@pburns.seanet.com http://www.burns-stat.com (home of 'The R Inferno' and 'A Guide for the Unwilling S User') __ 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] Loop overwrite and data output problems
Hello R users,
I have been using R for a while now for basic stats but I'm now trying to
get my head around looping scripts and in some places I am failing!
I have a data set with c. 1200 data points on 98 individual animals with
data on each row representing a daily measure and I am asking the question
what variables affect the animal's behaviour?
the dataset includes these variables for analyses:
presence of behaviour, absence of behaviour, site, year, rain, air temp, ID,
Day
Listed below as they appear in the data set:
BEH_T, BEH_F, SITE, YEAR, PRECIP_MM_DAY, PUP_AGE_EST, MO_AIR_TEMP, ID2,
DAY
with BEH_T BEH_F = the response variable for a binomial GLM
here is the head of the dataset
(NB there are only two years and two sites)
BEH_T BEH_F SITE YEAR PRECIP_MM_DAY PUP_AGE_EST MO_AIR_TEMP ID2 DAY
[1,]14101 2007 0 1210.98750 1 1
[2,]37231 2007 0 1311.47333 1 2
[3,]56221 2007 0 1412.16667 1 3
[4,]43231 2007 0 1610.91515 1 5
[5,]62161 2007 0 1712.81026 1 6
[6,]30201 2007 0 19 8.67037 1 8
(Sorry the headings are skewed)
Because I don't want to do too complex a model to start with (just wanting
to learn first with a 'simple' model) I have issues with independence of the
data as there are repeats of individuals - i.e. data taken on the same IDs
on different days. So in order to account for that I have decided to random
sample one data point for each ID then run the GLM on that data for x number
of simulations to see if the explanatory variables are the same/similar
across all models. (This will reduce my data set to 98 data points, but it
is the best way I can see of doing this without doing mixed-effects models,
since not all IDs are seen at both sites in both years).
I am also using the MuMIn package for running all subsets of your model
the code I'm using is:
for (S in 1:2){
Sample.dat-ALL.R[1,]
for (I in 1:98) {
tmp-ALL.R[ALL.R$ID2==I,]
max-dim(tmp)[1]
if (I==1) Sample.dat-tmp[sample(1:max,1),] else {
Sample.dat-rbind(Sample.dat,tmp[sample(1:max,1),])
m1.R-glm(cbind(Sample.dat$BEH_T, Sample.dat$BEH_F) ~
Sample.dat$SITE +
Sample.dat$YEAR + Sample.dat$PRECIP_MM_DAY + Sample.dat$PUP_AGE_EST +
Sample.dat$MO_AIR_TEMP, family=binomial)
mod-dredge(m1.R)}}}
At this point I have two issues if I do it manually then it seems to work
i.e. gives me one output (e.g shown at bottom of post) where I then want to
take the first line, the model with the best AIC using mod[1,] - no problem!
However, letting the code run and for example using print ((mod[1,])) at the
end it prints out the first line of 98 outputs - so I'm not too sure what
I've done wrong here, but it appears to be running a model for each ID -
something basic no doubt!
Ideally, what I want to do is take a random sample of the data then run the
model get one output for that take the top line (i.e. the best AIC) and save
this, then run this routine say 100 times, saving that top line every time,
then having a look at the results and take a model average. Anytime I've got
close to this I have issues with overwriting the previous first line of the
model selection and I can't seem to identify how to set this loop up
properly.
Any advice or guidance would be most appreciated, I have tried to explain my
issues clearly but if more info is required please just ask,
Many thanks in advance to those of you that took the time to read this!
Ross
Ross Culloch
Ph.D. Student
Durham University
UK
Here is an example of the model selection table from usingMuMIn:
Model selection table
(Intr) S.$MO_ S.$PRE S.$PUP S.$SIT S.$YEA k Dev. AIC AICc
delta weight
30 645.8000 0.03841-0.02148 0.2882 -0.3212 5 304.0 687.1 687.7
0.000 0.707
32 648.8000 0.03811 0.0009399 -0.02172 0.2857 -0.3227 6 304.0 689.0 690.0
2.249 0.230
26 785.1000-0.02543 0.4678 -0.3905 4 312.8 693.9 694.3
6.630 0.026
31 794.2000 0.0037260 -0.02627 0.4519 -0.3950 5 312.5 695.5 696.2
8.493 0.010
22 582.7000 0.04703 0.2641 -0.2899 4 314.7 695.8 696.2
8.529 0.010
21 582.8000 0.06893-0.01967-0.2899 4 314.9 696.0 696.4
8.717 0.009
29 573.1000 0.04787 -0.0039980 0.2762 -0.2851 5 314.3 697.4 698.0
10.330 0.004
28 600.1000 0.06612 0.0046710 -0.02092-0.2985 5 314.4 697.4 698.1
10.370 0.004
20 0.7526 0.05509-0.01808 0.2450 4 321.0 702.0 702.5
14.770 0.000
10 530.4000 0.07447-0.2639 3 324.0 703.1 703.3
15.640 0.000
27 0.7493 0.05556 -0.0022820 -0.01753 0.2519 5 320.8 703.9 704.6
16.850 0.000
19 530. 0.07455 -0.0001489 -0.2637 4
Re: [R] Unique Values of a Matrix
Thank you. That worked. I had tried it before and failed, but after checking with you I realized that the problem was that my data was in a frame instead of a matrix. Thanks again, Todd Todd DeWees, PhD Statistician University of Dundee Mackenzie Building Kirsty Semple Way Dundee DD2 4BF Scotland UK PH: 01382-420119 -Original Message- From: Henrique Dallazuanna [mailto:www...@gmail.com] Sent: 26 February 2010 1:17 PM To: Todd DeWees Cc: r-help@r-project.org Subject: Re: [R] Unique Values of a Matrix Try this: unique(c(X)) On Fri, Feb 26, 2010 at 10:06 AM, Todd DeWees t.dew...@cpse.dundee.ac.uk wrote: I have a 280,000 x 11 matrix with various values and many NA values. What I would like to do is get a vector of every unique value in the matrix. For example: X = [ 1 2 NA 4 3 1 7 NA 2 ] Returns: Unique_X = [ 1, 2, 3, 4, 7] Thanks, Todd [[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. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O __ 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] Unique Values of a Matrix
On Feb 26, 2010, at 8:17 AM, Henrique Dallazuanna wrote: Try this: unique(c(X)) I did but it returned NA as did:unique(as.vector(X)). To get rid of the NA's I needed to do: X[!duplicated(as.vector(X)) !is.na(X)] (Logical indexing and does need as.vector() , or c() , to straighten out the index expression.) Not sure why applying the straightening to the second logical term is not equivalent: X[!duplicated(X) !is.na(as.vector(X))] [1] 1 2 4 3 1 7 2 This also: unique(c(X))[!is.na(unique(c(X)))] [1] 1 2 4 3 7 On Fri, Feb 26, 2010 at 10:06 AM, Todd DeWees t.dew...@cpse.dundee.ac.uk wrote: I have a 280,000 x 11 matrix with various values and many NA values. What I would like to do is get a vector of every unique value in the matrix. For example: X = [ 12NA 43 1 7 NA 2 ] Returns: Unique_X = [ 1, 2, 3, 4, 7] Thanks, Todd [[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. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O __ 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. David Winsemius, MD Heritage Laboratories West Hartford, CT __ 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] Unique Values of a Matrix
I found that using Sort(unique(c(X)) also works to remove NA if you don't mind the unique values being sorted Todd DeWees, PhD Statistician University of Dundee Mackenzie Building Kirsty Semple Way Dundee DD2 4BF Scotland UK PH: 01382-420119 -Original Message- From: David Winsemius [mailto:dwinsem...@comcast.net] Sent: 26 February 2010 1:49 PM To: Henrique Dallazuanna Cc: Todd DeWees; r-help@r-project.org Subject: Re: [R] Unique Values of a Matrix On Feb 26, 2010, at 8:17 AM, Henrique Dallazuanna wrote: Try this: unique(c(X)) I did but it returned NA as did:unique(as.vector(X)). To get rid of the NA's I needed to do: X[!duplicated(as.vector(X)) !is.na(X)] (Logical indexing and does need as.vector() , or c() , to straighten out the index expression.) Not sure why applying the straightening to the second logical term is not equivalent: X[!duplicated(X) !is.na(as.vector(X))] [1] 1 2 4 3 1 7 2 This also: unique(c(X))[!is.na(unique(c(X)))] [1] 1 2 4 3 7 On Fri, Feb 26, 2010 at 10:06 AM, Todd DeWees t.dew...@cpse.dundee.ac.uk wrote: I have a 280,000 x 11 matrix with various values and many NA values. What I would like to do is get a vector of every unique value in the matrix. For example: X = [ 12NA 43 1 7 NA 2 ] Returns: Unique_X = [ 1, 2, 3, 4, 7] Thanks, Todd [[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. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O __ 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. David Winsemius, MD Heritage Laboratories West Hartford, CT __ 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] Error in mvpart example
Dear all, I'm getting an error in one of the stock examples in the 'mvpart' package. I tried: require(mvpart) data(spider) fit3 - rpart(gdist(spider[,1:12],meth=bray,full=TRUE,sq=TRUE)~water+twigs+reft+herbs+moss+sand,spider,method=dist) #directly from ?rpart summary(fit3) ...which returned the following: Error in apply(formatg(yval, digits - 3), 1, paste, collapse = ,, sep = ) : dim(X) must have a positive length This seems to be a problem with the cross-validation, since the xerror and xstd columns are missing from the summary table as well. Using the mpart() wrapper results in the same error: fit4-mvpart(gdist(spider[,1:12],meth=bray,full=TRUE,sq=TRUE)~water+twigs+reft+herbs+moss+sand,spider,method=dist) summary(fit4) Note, changing the 'method' argument to =mrt seems, superficially, to solve the problem. However, when the dependent variable is a dissimilarity matrix, shouldn't method=dist be used (as per the examples)? Thanks, in advance, for any help on this error. Oliver __ 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] Unique Values of a Matrix
Or: na.exclude(unique(c(X))) On Fri, Feb 26, 2010 at 10:50 AM, Todd DeWees t.dew...@cpse.dundee.ac.uk wrote: I found that using Sort(unique(c(X)) also works to remove NA if you don't mind the unique values being sorted Todd DeWees, PhD Statistician University of Dundee Mackenzie Building Kirsty Semple Way Dundee DD2 4BF Scotland UK PH: 01382-420119 -Original Message- From: David Winsemius [mailto:dwinsem...@comcast.net] Sent: 26 February 2010 1:49 PM To: Henrique Dallazuanna Cc: Todd DeWees; r-help@r-project.org Subject: Re: [R] Unique Values of a Matrix On Feb 26, 2010, at 8:17 AM, Henrique Dallazuanna wrote: Try this: unique(c(X)) I did but it returned NA as did: unique(as.vector(X)). To get rid of the NA's I needed to do: X[!duplicated(as.vector(X)) !is.na(X)] (Logical indexing and does need as.vector() , or c() , to straighten out the index expression.) Not sure why applying the straightening to the second logical term is not equivalent: X[!duplicated(X) !is.na(as.vector(X))] [1] 1 2 4 3 1 7 2 This also: unique(c(X))[!is.na(unique(c(X)))] [1] 1 2 4 3 7 On Fri, Feb 26, 2010 at 10:06 AM, Todd DeWees t.dew...@cpse.dundee.ac.uk wrote: I have a 280,000 x 11 matrix with various values and many NA values. What I would like to do is get a vector of every unique value in the matrix. For example: X = [ 1 2 NA 4 3 1 7 NA 2 ] Returns: Unique_X = [ 1, 2, 3, 4, 7] Thanks, Todd [[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. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O __ 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. David Winsemius, MD Heritage Laboratories West Hartford, CT -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O __ 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] ggplot2 : bug in coord_equal() ?
Hello, I think there is a bug in coord_equal when x s a factor : ggplot(diamonds, aes(clarity, fill=cut)) + geom_bar() ggplot(diamonds, aes(clarity, fill=cut)) + geom_bar() + coord_equal(1/2) David __ 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] Odp: Error in Aggregate function
Hi r-help-boun...@r-project.org napsal dne 26.02.2010 10:32:34: Hi, When I run the Aggregate function in repeat loop, I got the following error: Why and how exactly you use aggregate in loop? Error in sort.list(unique.default(x), na.last = TRUE) : 'x' must be atomic for 'sort.list' Have you called 'sort' on a list? How to solve this error. Anyone can help me. Urgent. Using this weird construction on my data I do not get any error. for (i in 2:5) print(aggregate(zeta[,i], list(zeta[,dus]), mean)) Group.1x 1 ano 6.865000 2 ne 6.592727 Group.1x 1 ano 6.785000 2 ne 6.635455 Group.1 x 1 ano 0.9426667 2 ne 0.5016364 Group.1x 1 ano 1.345167 2 ne 1.183727 Please provide at least a code, better with some simple fake data. Regards Petr Thanks. Meenakshi. -- View this message in context: http://n4.nabble.com/Error-in-Aggregate- function-tp1570370p1570370.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-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] two questions for R beginners
Ivan Calandra wrote: Since you want input from beginners, here are some thoughts I had and still have two big problems with R: - this vectorization thing. I've read many manuals (including R inferno), but I'm still not completely clear about it. In simple examples, it's fine. But when it gets a bit more complex, then... Related to it, the *apply functions are still a bit difficult to understand. When I have to use them, I just try one and see what happens. I don't understand them well enough to know which one I need. - the second problem is where to find the functions/packages I need. There are many options, and that's actually the problem. R Wiki, Rseek, RSiteSearch, Crantastic, etc... When you start with R, you discover that the capabilities of R are almost unlimited and you don't really know where to start, where to find what you need. As noted in earlier posts, the mailing list is really great, but some people are really hard with beginners. It was noted in a discussion a few days ago, but it looks like some don't realize how difficult it is at the beginning to formulate a good question, clear, with self-contained example and so on. Moreover, not everybody speaks English natively. I don't mean that you must help, even when the question is really vague and not clear and whatever. I'm just saying that if you don't want to help (whatever the reason), you don't have to say it badly. But in any cases, the mailing list is still really helpful. As someone noted (sorry I erased the email so I don't remember who), it might be a good idea to split it. Hi everyone, My 2ct about the mailing list :). I understand that beginners have a hard time formulating a good question. But the problem is that we can't answer the question when it is unclear. So either I: - Don't bother answering - Try do discuss with the author of the question, taking lots of time to find out what exactly is the question. - Send a read the posting guide answer I mostly do the first, as I have to get things done during my PhD :). So this leaves us with kind of a problem, the person mailing the list doesn't have the knowledge to ask the right question, the list can't answer properly and consequently, the person mailing the list still doesn't get the information he/she needs. We could start an R-beginner mailing list, but this would also suffer from this problem. What do you guys think? Maybe the mailing list is not the right medium for really basic stuff. For that I would recommend a good R-book or (better) a course in R or (even better) some colleagues who work with R that you can ask questions to. cheers, Paul Hope that's what you wanted Ivan Le 2/26/2010 08:39, Dieter Menne a écrit : Patrick Burns wrote: * What were your biggest misconceptions or stumbling blocks to getting up and running with R? (This derives partly from teaching) The fact that this xapply-stuff was not idempotent (worse: not always) and that you need a monster like do.call() to straighten this out. Nowadays, plyr comes close. The concept of environment. With S it was worse, though. That you cannot change values passed by reference. I noted that the latter is no problem for students who have not worked with c(++/#) before. That there is only one return-result in functions. [ and the likes as an operator. 10 years ago, when I started, the message was: S4 is the future, S3 is legacy. So I learned S4. Only to never use is in self-written code later. Might be different for BioConductor people. That sometimes you can use vectors not in data= (lattice), and sometimes not (ggplot2). Still a VERY confusing inconsistency. The why-does-this-not-print FAQ. Why does par(oma..) not work with lattice? Dieter __ 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. -- Drs. Paul Hiemstra Department of Physical Geography Faculty of Geosciences University of Utrecht Heidelberglaan 2 P.O. Box 80.115 3508 TC Utrecht Phone: +3130 274 3113 Mon-Tue Phone: +3130 253 5773 Wed-Fri http://intamap.geo.uu.nl/~paul __ 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] Adjust lattice graph axis label on final page
Thanks Deepayan, This confirms what I thought I should do... One follow-up question about your suggested code: is it possible to create a lattice graph object myplot and modify the layout just for panel 7 and 8, rather than creating two graphs with different layouts? Sebastien Deepayan Sarkar wrote: On Thu, Feb 25, 2010 at 3:45 AM, Sebastien Bihorel sebastien.biho...@cognigencorp.com wrote: Dear R-users, I was wondering if there was a way to adjust the placement of the axis titles for the last page of a multi-page lattice plot (see example below). Depending on the total number of panels, the placement of these titles might look strange on the last page, if the layout is not adjusted (e.g. in some template code). It's not possible to adjust the labels on a per-page basis. It _is_ possible to have the two plots fill up the last page, but that may not be what you want. xyplot(y~x|id,as.table=T,data=mydata,layout=c(2,3))[1:6] xyplot(y~x|id,as.table=T,data=mydata,layout=c(2,1))[7:8] -Deepayan __ 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] R and Wordpress
I use Wordpress.com (free public version) and add my R scripts by using simple html pre ... / wrap around my script. Here's an example post with R Script. http://chartsgraphs.wordpress.com/2009/02/05/r-script-to-automatically-chart-web-based-global-temperature-data/ link D Kelly O'Day http://chartsgraphs.wordpress.com -- View this message in context: http://n4.nabble.com/R-and-Wordpress-tp1568499p1570653.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] t-distribution values
Dear all, how to calculate values of t-distribution for given values of d.f. using R functions? Anton __ 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 install rattle for data mining
Besides the suggestions made by others, you may want to look at the R-wiki, where there is a section on installing rattle and its dependencies, but mostly for Linux distros. Rattle involves lots of other tools, which makes it challenging to install. You could do the community a service by adding a section on Windows installs. And someone with Mac experience might do likewise. The wiki offers a chance -- but not a guarantee -- that information that appears over several posts here can be consolidated. JN Message: 1 Date: Thu, 25 Feb 2010 03:06:40 -0800 (PST) From: chinna durgache...@gmail.com To: r-help@r-project.org Subject: [R] how to install rattle for data mining Message-ID: 1267096000783-1568841.p...@n4.nabble.com Content-Type: text/plain; charset=us-ascii library(rattle) Loading required package: pmml Loading required package: XML Error: package 'XML' could not be loaded In addition: Warning message: In library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc) : there is no package called 'XML' i have installed glade package install.packages(RGtk2) install.packages(rattle) __ 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] t-distribution values
Hi ! I would try pt for the probability distribution function. ?pt pt(q=-2, df=5) 2010/2/26 áÎÔÏÎ íÏÒËÏ×ÉÎ a-morko...@yandex.ru Dear all, how to calculate values of t-distribution for given values of d.f. using R functions? Anton __ 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.htmlhttp://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] two questions for R beginners
You are definitely right... What to do with bad beginner's questions is not a simple issue. If a beginner's mailing list is created, who will answer to such questions? And moreover, the beginners won't take advantage of the other questions (I've personally learned a lot trying to understand the questions and answers to other's problems). And also, as you said, the problems might persist. The beginner's mailing list might be good in one aspect though: the experts who subscribe to it would be willing to help the beginners to get started with R, knowing that the questions might not be clearly stated. As you pointed out, the mailing list is not the best for basic stuff (the question is of course what is basic?). Not everybody knows some colleagues who work with R (I'm personally the 1st one to use R in my lab). I think, somehow and I have no idea how, documentation and guidance to search for help should be more accessible as soon as you start with R. Maybe a _*clear*_ section on the R homepage or in the introduction to R manual like where to find help, including all of the most common and useful resources available (from ? and RSiteSearch() to R Wiki and Crantastic). I hope that this whole discussion might help to make the R world better. Thank you Patrick for initiating it! Regards, Ivan Le 2/26/2010 15:09, Paul Hiemstra a écrit : Ivan Calandra wrote: Since you want input from beginners, here are some thoughts I had and still have two big problems with R: - this vectorization thing. I've read many manuals (including R inferno), but I'm still not completely clear about it. In simple examples, it's fine. But when it gets a bit more complex, then... Related to it, the *apply functions are still a bit difficult to understand. When I have to use them, I just try one and see what happens. I don't understand them well enough to know which one I need. - the second problem is where to find the functions/packages I need. There are many options, and that's actually the problem. R Wiki, Rseek, RSiteSearch, Crantastic, etc... When you start with R, you discover that the capabilities of R are almost unlimited and you don't really know where to start, where to find what you need. As noted in earlier posts, the mailing list is really great, but some people are really hard with beginners. It was noted in a discussion a few days ago, but it looks like some don't realize how difficult it is at the beginning to formulate a good question, clear, with self-contained example and so on. Moreover, not everybody speaks English natively. I don't mean that you must help, even when the question is really vague and not clear and whatever. I'm just saying that if you don't want to help (whatever the reason), you don't have to say it badly. But in any cases, the mailing list is still really helpful. As someone noted (sorry I erased the email so I don't remember who), it might be a good idea to split it. Hi everyone, My 2ct about the mailing list :). I understand that beginners have a hard time formulating a good question. But the problem is that we can't answer the question when it is unclear. So either I: - Don't bother answering - Try do discuss with the author of the question, taking lots of time to find out what exactly is the question. - Send a read the posting guide answer I mostly do the first, as I have to get things done during my PhD :). So this leaves us with kind of a problem, the person mailing the list doesn't have the knowledge to ask the right question, the list can't answer properly and consequently, the person mailing the list still doesn't get the information he/she needs. We could start an R-beginner mailing list, but this would also suffer from this problem. What do you guys think? Maybe the mailing list is not the right medium for really basic stuff. For that I would recommend a good R-book or (better) a course in R or (even better) some colleagues who work with R that you can ask questions to. cheers, Paul Hope that's what you wanted Ivan Le 2/26/2010 08:39, Dieter Menne a écrit : Patrick Burns wrote: * What were your biggest misconceptions or stumbling blocks to getting up and running with R? (This derives partly from teaching) The fact that this xapply-stuff was not idempotent (worse: not always) and that you need a monster like do.call() to straighten this out. Nowadays, plyr comes close. The concept of environment. With S it was worse, though. That you cannot change values passed by reference. I noted that the latter is no problem for students who have not worked with c(++/#) before. That there is only one return-result in functions. [ and the likes as an operator. 10 years ago, when I started, the message was: S4 is the future, S3 is legacy. So I learned S4. Only to never use is in self-written code later. Might be different for BioConductor people. That sometimes you can
Re: [R] Loop overwrite and data output problems
Hi,
Since I'm not an expert, I still have problems understanding when it's
not my own work, but I have something that might help you.
if (I==1) Sample.dat-tmp[sample(1:max,1),] else {
Sample.dat-rbind(Sample.dat,tmp[sample(1:max,1),])
This part might not be the best.
I would do something like:
Sample.dat[[I]] - tmp[sample(1:max, 1),]
That way, you will store your line in the Ith element of the list
Sample.dat. 5you might have to define it first like: Sample.dat -
list() )
You can then convert it to a matrix using: do.call(rbind, Sample.dat)
It might get you started
HTH,
Ivan
Le 2/26/2010 14:31, RCulloch a écrit :
Hello R users,
I have been using R for a while now for basic stats but I'm now trying to
get my head around looping scripts and in some places I am failing!
I have a data set with c. 1200 data points on 98 individual animals with
data on each row representing a daily measure and I am asking the question
what variables affect the animal's behaviour?
the dataset includes these variables for analyses:
presence of behaviour, absence of behaviour, site, year, rain, air temp, ID,
Day
Listed below as they appear in the data set:
BEH_T, BEH_F, SITE, YEAR, PRECIP_MM_DAY, PUP_AGE_EST, MO_AIR_TEMP, ID2,
DAY
with BEH_T BEH_F = the response variable for a binomial GLM
here is the head of the dataset
(NB there are only two years and two sites)
BEH_T BEH_F SITE YEAR PRECIP_MM_DAY PUP_AGE_EST MO_AIR_TEMP ID2 DAY
[1,]14101 2007 0 1210.98750 1 1
[2,]37231 2007 0 1311.47333 1 2
[3,]56221 2007 0 1412.16667 1 3
[4,]43231 2007 0 1610.91515 1 5
[5,]62161 2007 0 1712.81026 1 6
[6,]30201 2007 0 19 8.67037 1 8
(Sorry the headings are skewed)
Because I don't want to do too complex a model to start with (just wanting
to learn first with a 'simple' model) I have issues with independence of the
data as there are repeats of individuals - i.e. data taken on the same IDs
on different days. So in order to account for that I have decided to random
sample one data point for each ID then run the GLM on that data for x number
of simulations to see if the explanatory variables are the same/similar
across all models. (This will reduce my data set to 98 data points, but it
is the best way I can see of doing this without doing mixed-effects models,
since not all IDs are seen at both sites in both years).
I am also using the MuMIn package for running all subsets of your model
the code I'm using is:
for (S in 1:2){
Sample.dat-ALL.R[1,]
for (I in 1:98) {
tmp-ALL.R[ALL.R$ID2==I,]
max-dim(tmp)[1]
if (I==1) Sample.dat-tmp[sample(1:max,1),] else {
Sample.dat-rbind(Sample.dat,tmp[sample(1:max,1),])
m1.R-glm(cbind(Sample.dat$BEH_T, Sample.dat$BEH_F) ~
Sample.dat$SITE +
Sample.dat$YEAR + Sample.dat$PRECIP_MM_DAY + Sample.dat$PUP_AGE_EST +
Sample.dat$MO_AIR_TEMP, family=binomial)
mod-dredge(m1.R)}}}
At this point I have two issues if I do it manually then it seems to work
i.e. gives me one output (e.g shown at bottom of post) where I then want to
take the first line, the model with the best AIC using mod[1,] - no problem!
However, letting the code run and for example using print ((mod[1,])) at the
end it prints out the first line of 98 outputs - so I'm not too sure what
I've done wrong here, but it appears to be running a model for each ID -
something basic no doubt!
Ideally, what I want to do is take a random sample of the data then run the
model get one output for that take the top line (i.e. the best AIC) and save
this, then run this routine say 100 times, saving that top line every time,
then having a look at the results and take a model average. Anytime I've got
close to this I have issues with overwriting the previous first line of the
model selection and I can't seem to identify how to set this loop up
properly.
Any advice or guidance would be most appreciated, I have tried to explain my
issues clearly but if more info is required please just ask,
Many thanks in advance to those of you that took the time to read this!
Ross
Ross Culloch
Ph.D. Student
Durham University
UK
Here is an example of the model selection table from usingMuMIn:
Model selection table
(Intr) S.$MO_ S.$PRE S.$PUP S.$SIT S.$YEA k Dev. AIC AICc
delta weight
30 645.8000 0.03841-0.02148 0.2882 -0.3212 5 304.0 687.1 687.7
0.000 0.707
32 648.8000 0.03811 0.0009399 -0.02172 0.2857 -0.3227 6 304.0 689.0 690.0
2.249 0.230
26 785.1000-0.02543 0.4678 -0.3905 4 312.8 693.9 694.3
6.630 0.026
31 794.2000 0.0037260 -0.02627 0.4519 -0.3950 5 312.5 695.5 696.2
8.493 0.010
22 582.7000 0.04703 0.2641 -0.2899 4 314.7
[R] counting the number of ones in a vector
Dear R users, I want to count the number of ones in a vector x. That's what I did : length( x[x==1] ) Is that a good solution ? Thank you very much, Randall [[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] Odp: two questions for R beginners
Petr Pikal wrote: For the time being I would say that reshape and factor ordering especially with groupedData objects from nlme are still giving me a headache and many trials and errors to get desired result. For documents in the beginning I would vote for Paul Johnsons Rtips. About 10 yars ago it was nice collection of several useful Howto's. Add me for reshape (the base one); the only printed documentation on my desk. Hadley's Reshape package has tried hard, but was not successful as plyr. Factor ordering: yes, definitively, and the risks involved in reordering. Not, however, groupedData: I was lucky enough to find out rather early that this was the most confusing feature in nlme, and not required. So my student script for nlme starts: whenever you read about groupedData, try to forget it and look for a different example. There is no groupedData in lme4. And a ++ for Rtips. I never understand, however, why this was possible, because I know of similar attempts that were blocked because people complained that permission was required for quotes. The early days... Dieter -- View this message in context: http://n4.nabble.com/two-questions-for-R-beginners-tp1569384p1570701.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] Odp: Loop overwrite and data output problems
Hi
I am bit confused what you want to achieve. As I can not reproduce code
without your data I just guess.
If I understand you want to select from all your data randomly 98 values
for 98 animals (one for each animal). I presume your id2 is sorted.
One option
# make sorted ids
id2-sample(1:5, 100, replace=T)
id2-sort(id2)
# how many unique ids
len-rle(id2)$lengths
# how many values are from beginning
shift.len-c(0,cumsum(len))[-(length(len)+1)]
# get one value from each id
samp-sapply(sapply(split(id2, id2), function(x) 1:length(x)), sample, 1)
# just test
id2[samp+shift.len]
[1] 1 2 3 4 5
The other option is randomise vector of indices
ss-sample(1:100)
sort data.frame according those randomised indices and select let say
first one
sapply(split(daf[ss,], daf[ss,1]), function(x) x[1,])
But i believe that there are even better options.
Regards
Petr
r-help-boun...@r-project.org napsal dne 26.02.2010 14:31:06:
Hello R users,
I have been using R for a while now for basic stats but I'm now trying
to
get my head around looping scripts and in some places I am failing!
I have a data set with c. 1200 data points on 98 individual animals with
data on each row representing a daily measure and I am asking the
question
what variables affect the animal's behaviour?
the dataset includes these variables for analyses:
presence of behaviour, absence of behaviour, site, year, rain, air temp,
ID,
Day
Listed below as they appear in the data set:
BEH_T, BEH_F, SITE, YEAR, PRECIP_MM_DAY, PUP_AGE_EST, MO_AIR_TEMP, ID2,
DAY
with BEH_T BEH_F = the response variable for a binomial GLM
here is the head of the dataset
(NB there are only two years and two sites)
BEH_T BEH_F SITE YEAR PRECIP_MM_DAY PUP_AGE_EST MO_AIR_TEMP ID2 DAY
[1,]14101 2007 0 1210.98750 1 1
[2,]37231 2007 0 1311.47333 1 2
[3,]56221 2007 0 1412.16667 1 3
[4,]43231 2007 0 1610.91515 1 5
[5,]62161 2007 0 1712.81026 1 6
[6,]30201 2007 0 19 8.67037 1 8
(Sorry the headings are skewed)
Because I don't want to do too complex a model to start with (just
wanting
to learn first with a 'simple' model) I have issues with independence of
the
data as there are repeats of individuals - i.e. data taken on the same
IDs
on different days. So in order to account for that I have decided to
random
sample one data point for each ID then run the GLM on that data for x
number
of simulations to see if the explanatory variables are the same/similar
across all models. (This will reduce my data set to 98 data points, but
it
is the best way I can see of doing this without doing mixed-effects
models,
since not all IDs are seen at both sites in both years).
I am also using the MuMIn package for running all subsets of your model
the code I'm using is:
for (S in 1:2){
Sample.dat-ALL.R[1,]
for (I in 1:98) {
tmp-ALL.R[ALL.R$ID2==I,]
max-dim(tmp)[1]
if (I==1) Sample.dat-tmp[sample(1:max,1),] else {
Sample.dat-rbind(Sample.dat,tmp[sample(1:max,1),])
m1.R-glm(cbind(Sample.dat$BEH_T, Sample.dat$BEH_F) ~
Sample.dat$SITE +
Sample.dat$YEAR + Sample.dat$PRECIP_MM_DAY + Sample.dat$PUP_AGE_EST +
Sample.dat$MO_AIR_TEMP, family=binomial)
mod-dredge(m1.R)}}}
At this point I have two issues if I do it manually then it seems to
work
i.e. gives me one output (e.g shown at bottom of post) where I then want
to
take the first line, the model with the best AIC using mod[1,] - no
problem!
However, letting the code run and for example using print ((mod[1,])) at
the
end it prints out the first line of 98 outputs - so I'm not too sure
what
I've done wrong here, but it appears to be running a model for each ID -
something basic no doubt!
Ideally, what I want to do is take a random sample of the data then run
the
model get one output for that take the top line (i.e. the best AIC) and
save
this, then run this routine say 100 times, saving that top line every
time,
then having a look at the results and take a model average. Anytime I've
got
close to this I have issues with overwriting the previous first line of
the
model selection and I can't seem to identify how to set this loop up
properly.
Any advice or guidance would be most appreciated, I have tried to
explain my
issues clearly but if more info is required please just ask,
Many thanks in advance to those of you that took the time to read this!
Ross
Ross Culloch
Ph.D. Student
Durham University
UK
Here is an example of the model selection table from usingMuMIn:
Model selection table
(Intr) S.$MO_ S.$PRE S.$PUP S.$SIT S.$YEA k Dev. AIC
AICc
delta weight
30 645.8000 0.03841-0.02148
Re: [R] two questions for R beginners
Ivan Calandra ivan.calan...@uni-hamburg.de writes: Related to it, the *apply functions are still a bit difficult to understand. When I have to use them, I just try one and see what happens. I don't understand them well enough to know which one I need. Ditto. I have ended up with a small collection of black magic invocations copied from other folks' code, designed to do things like I wrote a function to read a file and generate a data frame. Now I want to iterate (vectorize) this over many files, and get a much larger data frame. This may be one specific case of the larger challenge of transforming R data structures. A somewhat pedantic set of recipes might usefully be evolved on e.g. the wiki. - Allen S. Rout __ 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] counting the number of ones in a vector
What you did works well. You could also try the following.
table(x)[1]
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org]
On Behalf Of Randall Wrong
Sent: Friday, February 26, 2010 9:41 AM
To: r-help@r-project.org
Subject: [R] counting the number of ones in a vector
Dear R users,
I want to count the number of ones in a vector x.
That's what I did : length( x[x==1] )
Is that a good solution ?
Thank you very much,
Randall
[[alternative HTML version deleted]]
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Visit us online at http://www.clevelandclinic.org for
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[R] counting the number of ones in a vector
Dear R users, I want to count the number of ones in a vector x. That's what I did : length( x[x==1] ) Is that a good solution ? Thank you very much, Randall [[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] counting the number of ones in a vector
Try: sum(x == 1) On Fri, Feb 26, 2010 at 11:40 AM, Randall Wrong randall.wr...@gmail.com wrote: Dear R users, I want to count the number of ones in a vector x. That's what I did : length( x[x==1] ) Is that a good solution ? Thank you very much, Randall [[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. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O __ 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] counting the number of ones in a vector
Nutter, Benjamin wrote:
What you did works well. You could also try the following.
table(x)[1]
or
sum(x==1)
HTH,
Tobias
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org]
On Behalf Of Randall Wrong
Sent: Friday, February 26, 2010 9:41 AM
To: r-help@r-project.org
Subject: [R] counting the number of ones in a vector
Dear R users,
I want to count the number of ones in a vector x.
That's what I did : length( x[x==1] )
Is that a good solution ?
Thank you very much,
Randall
[[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.
===
P Please consider the environment before printing this e-mail
Cleveland Clinic is ranked one of the top hospitals
in America by U.S.News World Report (2009).
Visit us online at http://www.clevelandclinic.org for
a complete listing of our services, staff and
locations.
Confidentiality Note: This message is intended for use\...{{dropped:13}}
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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] locfit: max number of predictors = 6? How interpolate in 5-10D?
Thanks for that suggestion
I've investigated a little more using...
y - rowSums(x) + runif(n)
... just so I had some correlation to play with.
The error I get when it fails is Invalid what in exvval, which I don't
understand either!
With n=5e3 it worked with 6 variables but not with 7.
I wasn't sure the error was caused by number of variables rather than
something else, so I tried with...
n - 100
I also tried locfit rather than locfit.raw using...
xd - lapply(1:10, function(x) runif(n))
xd - as.data.frame(xd)
names(xd) - paste(x, 1:10, sep=)
y=rowSums(xd)
xd$y - y
aF - formula(paste(y ~ lp(,paste(names(xd)[1:6], collapse=,), )))
locfit(aF, xd)
Both of these gave the same results, success with 6 variables but not with
7.
IT APPEARS, the maximum number of predictors is 6, but I don't know locfit
well, and it may be that other settings would allow more variables.
CAN anyone give a more DEFINITIVE ANSWER?
My current data sets currently reach 5 predictors, and I expect this it
increase.
In S-Plus (v6.2.1) I used loess in which Locally quadratic models may have
at most 4 predictor variables; locally linear models may have at most 15.
In R stats::loess allows only one to four numeric predictors.
I'd assumed (foolishly) that because locfit didn't mention limits, the only
limits were practical (memory, time,...) - it seems not :-(
I guess I could write something myself, I only need rough interpolation,
even straight line interpolation between nearest neighbours would be OK.
But at first glance it seems non-trivial with a substantial non-fixed number
of dimensions (nnclust::nnfind to identify neighbours??), and I don't want
to re-invent wheels.
Can anyone suggest an ALTERNATIVE route for INTERPOLATION in 5-10
DIMENSIONS?
Best...
(apologies for capitals, not shouting, just highlighting key points for
those skimming quickly)
Keith Jewell
Liaw, Andy andy_l...@merck.com wrote in message
news:b10baa7d28d88b45af82813c4a6ffa934ce...@usctmx1157.merck.com...
Well, I should think there's an obvious (if not elegant) way to test it:
n - 5e3
m - 20
x - matrix(runif(n * m), nrow=n)
y - rnorm(n)
require(locfit)
fit - locfit.raw(x[, 1:10], y)
The code above took a while on my laptop, and ended up giving some error
I don't understand. Not sure if the error was caused by insufficient
sample size, or some inherent limitation. At least it didn't choke on
five variables. However, if all 20 columns of x is used, locfit.raw()
will choke because it can't compute the dimension of some variable that
it needs to allocate memory for.
I had vague recollection of reading that 5 is the limit somewhere.
Unfortunately my copy of Local Regression and Likelihood has been MIA
for a few years, so I can't check there. In any case it doesn't seem
like the number of data points and/or computing power are bigger issue.
Andy
-Original Message-
From: r-help-boun...@r-project.org
[mailto:r-help-boun...@r-project.org] On Behalf Of Keith Jewell
Sent: Thursday, February 25, 2010 4:11 AM
To: r-h...@stat.math.ethz.ch
Subject: [R] locfit: max number of predictors?
Hi All,
In another thread Andy Liaw, who CRAN lists as locfit
maintainer; said:
quote
From: Liaw, Andy andy_l...@merck.com
To: Guy Green guygr...@netvigator.com; r-help@r-project.org
Subject: Re: Alternatives to linear regression with multiple variables
Date: 22 February 2010 17:50
You can try the locfit package, which I believe can handle up to 5
variables. E.g.,
/quote
Looking in the locfit documentation (e.g.
http://www.stats.bris.ac.uk/R/web/packages/locfit/locfit.pdf)
I can't see an
upper limit on the number of predictors; if it is 5 I'm
getting close in one
of my applications.
Can anyone confirm or deny the existence of a 'crisp' upper
limit on the
number of predictors in locfit?
If it is 5, or thereabouts, can anyone suggest an alternative
which can
handle a few more? (I'm using it for multidimensional interpolation).
Best regards,
Keith Jewell
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Re: [R] counting the number of ones in a vector
Hi Randall, Try also sum( x==1 ) HTH, Jorge On Fri, Feb 26, 2010 at 9:40 AM, Randall Wrong wrote: Dear R users, I want to count the number of ones in a vector x. That's what I did : length( x[x==1] ) Is that a good solution ? Thank you very much, Randall [[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. [[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] counting the number of ones in a vector
Hi Randall, Try also sum( x==1 ) HTH, Jorge On Fri, Feb 26, 2010 at 9:40 AM, Randall Wrong wrote: Dear R users, I want to count the number of ones in a vector x. That's what I did : length( x[x==1] ) Is that a good solution ? Thank you very much, Randall [[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. [[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] two questions for R beginners
Honestly what I remember as the most difficult thing when I 'first' started using R was figuring out how to read in my own datasets. I eventually discovered the R import/export manual, but somehow this alluded me initially. All the R tutorials I was working from simply generated data or used the built in datasets, and I was ready to work on my own datasets. The things that led from frustration to independence was understanding the difference between data types like matrix and dataframe and learning there were commands to tell what you were working with at any given time. Did the data read in as character, numeric, or factor, etc. Commands like: str, class, mode, ls, search, help, help.search, etc can help you figure out what you are doing. Rob -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Patrick Burns Sent: Thursday, February 25, 2010 11:31 AM To: r-help@r-project.org Subject: [R] two questions for R beginners * What were your biggest misconceptions or stumbling blocks to getting up and running with R? * What documents helped you the most in this initial phase? I especially want to hear from people who are lazy and impatient. Feel free to write to me off-list. Definitely write off-list if you are just confirming what has been said on-list. -- Patrick Burns pbu...@pburns.seanet.com http://www.burns-stat.com (home of 'The R Inferno' and 'A Guide for the Unwilling S User') __ 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] clogit comparison between Stata and R
Hi Thomas Sorry to bug you again after 6 months! I just wondered if there is a simple way to find the N after dropping groups with invariant outcomes - I am reading coxph.object and the structure of the returned object, but nothing jumps out at me. With best wishes, David Hugh-Jones On 9 July 2009 14:37, Thomas Lumley tlum...@u.washington.edu wrote: On Wed, 8 Jul 2009, David Hugh-Jones wrote: Hello all I'm moving back and forth between stata and R at the moment - of course, using R whenever possible :-) I'm running conditional logits on some panel data and I get slightly different results and different N in the two programs. That's probably because you are using method=approximate in R. I understand why Stata is dropping the groups with all outcomes the same... this is inevitable in a conditional logit, right? Yes. Is R doing the same? Yes. -thomas __ 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] two questions for R beginners
I don't want to sound bad but the first thing beginners should do is to look at the manual An Introduction to R because most of the simple questions have their answers into it. In the same idea, before posting to this mailing list, people should (must?) follow the posting guide. Indeed it is written there to use some functions like help.search(), RSiteSearch() or to read An Introduction to R before posting. Too often I think how much I would like people to do their homeworks before posting. I would like to add that I don't feel an R expert but I don't like to waste my time answering questions which have an answer you can find easily if you respect the posting guide. Regards, Alain On 26-Feb-10 15:30, Ivan Calandra wrote: You are definitely right... What to do with bad beginner's questions is not a simple issue. If a beginner's mailing list is created, who will answer to such questions? And moreover, the beginners won't take advantage of the other questions (I've personally learned a lot trying to understand the questions and answers to other's problems). And also, as you said, the problems might persist. The beginner's mailing list might be good in one aspect though: the experts who subscribe to it would be willing to help the beginners to get started with R, knowing that the questions might not be clearly stated. As you pointed out, the mailing list is not the best for basic stuff (the question is of course what is basic?). Not everybody knows some colleagues who work with R (I'm personally the 1st one to use R in my lab). I think, somehow and I have no idea how, documentation and guidance to search for help should be more accessible as soon as you start with R. Maybe a _*clear*_ section on the R homepage or in the introduction to R manual like where to find help, including all of the most common and useful resources available (from ? and RSiteSearch() to R Wiki and Crantastic). I hope that this whole discussion might help to make the R world better. Thank you Patrick for initiating it! Regards, Ivan Le 2/26/2010 15:09, Paul Hiemstra a écrit : Ivan Calandra wrote: Since you want input from beginners, here are some thoughts I had and still have two big problems with R: - this vectorization thing. I've read many manuals (including R inferno), but I'm still not completely clear about it. In simple examples, it's fine. But when it gets a bit more complex, then... Related to it, the *apply functions are still a bit difficult to understand. When I have to use them, I just try one and see what happens. I don't understand them well enough to know which one I need. - the second problem is where to find the functions/packages I need. There are many options, and that's actually the problem. R Wiki, Rseek, RSiteSearch, Crantastic, etc... When you start with R, you discover that the capabilities of R are almost unlimited and you don't really know where to start, where to find what you need. As noted in earlier posts, the mailing list is really great, but some people are really hard with beginners. It was noted in a discussion a few days ago, but it looks like some don't realize how difficult it is at the beginning to formulate a good question, clear, with self-contained example and so on. Moreover, not everybody speaks English natively. I don't mean that you must help, even when the question is really vague and not clear and whatever. I'm just saying that if you don't want to help (whatever the reason), you don't have to say it badly. But in any cases, the mailing list is still really helpful. As someone noted (sorry I erased the email so I don't remember who), it might be a good idea to split it. Hi everyone, My 2ct about the mailing list :). I understand that beginners have a hard time formulating a good question. But the problem is that we can't answer the question when it is unclear. So either I: - Don't bother answering - Try do discuss with the author of the question, taking lots of time to find out what exactly is the question. - Send a read the posting guide answer I mostly do the first, as I have to get things done during my PhD :). So this leaves us with kind of a problem, the person mailing the list doesn't have the knowledge to ask the right question, the list can't answer properly and consequently, the person mailing the list still doesn't get the information he/she needs. We could start an R-beginner mailing list, but this would also suffer from this problem. What do you guys think? Maybe the mailing list is not the right medium for really basic stuff. For that I would recommend a good R-book or (better) a course in R or (even better) some colleagues who work with R that you can ask questions to. cheers, Paul Hope that's what you wanted Ivan Le 2/26/2010 08:39, Dieter Menne a écrit : Patrick Burns wrote: * What were your biggest misconceptions or stumbling blocks to getting up and running with R? (This derives
Re: [R] two questions for R beginners
Ivan Calandra wrote: You are definitely right... What to do with bad beginner's questions is not a simple issue. If a beginner's mailing list is created, who will answer to such questions? And moreover, the beginners won't take advantage of the other questions (I've personally learned a lot trying to understand the questions and answers to other's problems). And also, as you said, the problems might persist. The beginner's mailing list might be good in one aspect though: the experts who subscribe to it would be willing to help the beginners to get started with R, knowing that the questions might not be clearly stated. As you pointed out, the mailing list is not the best for basic stuff (the question is of course what is basic?). Not everybody knows some colleagues who work with R (I'm personally the 1st one to use R in my lab). I think, somehow and I have no idea how, documentation and guidance to search for help should be more accessible as soon as you start with R. Maybe a _*clear*_ section on the R homepage or in the introduction to R manual like where to find help, including all of the most common and useful resources available (from ? and RSiteSearch() to R Wiki and Crantastic). Hi Ivan (and list), I think the main problem is not as much that there isn't structure in the way R provides documentation / tutorials, but that people have a hard time finding the structure. There are task views for certain specific fields, but I think a lot of beginners do not know that they exist. There are separate mailing lists for specific fields, but I often see geographical (my field of expertise) oriented questions on R-help that would fit much better on R-sig-geo. So I think a O my God, I've downloaded R and what now tutorial might be a good idea to put very close to the download button of R on CRAN. This tutorial would focus not on how to do things in R, but would provide guidance to the most obvious sources of information such as Task views, specific mailing lists, ways to search list archives, information for beginners how to write a good e-mail etc. I think for a lot of beginners it is not as much the answer to a specific question that they need, but more guidance how to look for answers themselves. But at the end of the day, R is still not very easy to learn when coming from GUI oriented stats programs. In addition, to become reasonably fluent in R, you need spend at least a few hours a week on it. SO I think we can ease the pain for beginners, but not take away that it takes quite some time to become fluent in R. cheers, Paul I hope that this whole discussion might help to make the R world better. Thank you Patrick for initiating it! Regards, Ivan Le 2/26/2010 15:09, Paul Hiemstra a écrit : Ivan Calandra wrote: Since you want input from beginners, here are some thoughts I had and still have two big problems with R: - this vectorization thing. I've read many manuals (including R inferno), but I'm still not completely clear about it. In simple examples, it's fine. But when it gets a bit more complex, then... Related to it, the *apply functions are still a bit difficult to understand. When I have to use them, I just try one and see what happens. I don't understand them well enough to know which one I need. - the second problem is where to find the functions/packages I need. There are many options, and that's actually the problem. R Wiki, Rseek, RSiteSearch, Crantastic, etc... When you start with R, you discover that the capabilities of R are almost unlimited and you don't really know where to start, where to find what you need. As noted in earlier posts, the mailing list is really great, but some people are really hard with beginners. It was noted in a discussion a few days ago, but it looks like some don't realize how difficult it is at the beginning to formulate a good question, clear, with self-contained example and so on. Moreover, not everybody speaks English natively. I don't mean that you must help, even when the question is really vague and not clear and whatever. I'm just saying that if you don't want to help (whatever the reason), you don't have to say it badly. But in any cases, the mailing list is still really helpful. As someone noted (sorry I erased the email so I don't remember who), it might be a good idea to split it. Hi everyone, My 2ct about the mailing list :). I understand that beginners have a hard time formulating a good question. But the problem is that we can't answer the question when it is unclear. So either I: - Don't bother answering - Try do discuss with the author of the question, taking lots of time to find out what exactly is the question. - Send a read the posting guide answer I mostly do the first, as I have to get things done during my PhD :). So this leaves us with kind of a problem, the person mailing the list doesn't have the knowledge to ask the right question, the list can't
[R] question to make a vector without loop
Hello all, I want to define a vector like w[k+1]=w[k]*a/(b+k) for k=1,...,N-1 without use loop. Is it posible to do in R? Regards khazaei __ 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: Compare Two dendrograms (Hierarchical Clusterings) ?
Hi, To compare two dendrogamas, you can use a measure of correlation between the cophenetic matrices. Example: mdist - dist(iris[,-5], method=euclidean) # dendrogram from cluster 1 (single-linkage) hc1 - hclust(mdist, method=single) plot(hc1) # dendrogram from cluster 2 (complete-linkage) hc2 - hclust(mdist, method=complete) plot(hc2) # correlation cor(cophenetic(hc1),cophenetic(hc2)) For a confidence level, use the Mantel Test from package vegan. mantel(cophenetic(hc1), cophenetic(hc2)) Good Look. __ 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] Normal distribution (Lillie.test())
Hi Greg, I'm making NoiseGenerators with different noise sources and components, the meaning of my tests with R is to know which NoiseGenerator approached most the Normal distribution function... Thanks, for all the reactions. Bosken Greg Snow-2 wrote: Do your NoiseGenerotors need to generate exactly normal data (they don't, see SnowsPenultimateNormalityTest), or is there a level of close enough? If I remember correctly, you were testing 2000 values, with that sample size most normality tests will find very small differences to be significantly different, even if those small differences are practically meaningless. -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111 -- View this message in context: http://n4.nabble.com/Normal-distribution-Lillie-test-tp1565083p1570710.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] treemap grouping
Hi, Is there a way to create a treemap with more than 1 grouping. I've seen a lot of examples like this: http://flowingdata.com/2010/02/11/an-easy-way-to-make-a-treemap/ but what if some of my categories have sub-categories. Is there an existing function that can handle this thanks -- View this message in context: http://n4.nabble.com/treemap-grouping-tp1570721p1570721.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] How to calculate the Transitivity (Clustering coefficient) of a Directed graph?
Hi all How can you use iGraph Transitivity function to get the Clustering coefficient of a Directed graph? Or how can you use iGraph to get the Clustering coefficient of a Directed graph? Thanks, Sara [[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.
[R] pallet with open intervals
Hi, I have a question concerning color pallets. I am currently plotting geophysical fields with spplot (sp package) and I would like to create a pallet with open boundaries. For instance, I have a field whose values vary between -7 et 1, but a few values are much higher, for instance 28 or 32. As a result, I would like to create a palette with, for instance, 8 intervals within the range [-7,1] and two more colors for values lower than -7 or higher than 1. Here is an example of such a pallet: http://n4.nabble.com/file/n1570791/pallet.jpg Do you have any idea of how to create such a pallet? Thanks, Julien -- View this message in context: http://n4.nabble.com/pallet-with-open-intervals-tp1570791p1570791.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] question to make a vector without loop
Dear Khazaei, What about this? w - 1:10 N - length(w) a - 1 b - 1 w[2:(N-1)] - w[2:(N-1)]*(a/(b+(2:(N-1 w [1] 1.000 0.667 0.750 0.800 0.833 0.8571429 [7] 0.875 0.889 0.900 10.000 Note that here I assumed a and b were constants 1 and 1, respectively. It is no problem to substitute vectors in for them. As long as a and b are the same length or a multiple of k...N-1, you can substitute them directly in the formula above and R will just keep using them until it is done. Hope that helps, Josh On Fri, Feb 26, 2010 at 7:23 AM, khaz...@ceremade.dauphine.fr wrote: Hello all, I want to define a vector like w[k+1]=w[k]*a/(b+k) for k=1,...,N-1 without use loop. Is it posible to do in R? Regards khazaei __ 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.htmlhttp://www.r-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Joshua Wiley Senior in Psychology University of California, Riverside http://www.joshuawiley.com/ [[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.
[R] How to calculate the Transitivity (Clustering coefficient) of a Directed graph?
Hi all How can you use iGraph Transitivity function to get the Clustering coefficient of a Directed graph? Or how can you use iGraph to get the Clustering coefficient of a Directed graph? Thanks, Sara [[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] question to make a vector without loop
On 26.02.2010 16:23, khaz...@ceremade.dauphine.fr wrote:
Hello all,
I want to define a vector like w[k+1]=w[k]*a/(b+k) for k=1,...,N-1 without
use loop. Is it posible to do in R?
Sure:
wMake - function(w, a, b, n){
w * (a^(0:(n-1))) / cumprod(c(1, (b+1):(b+n-1)))
}
wMake(w=1, a=2, b=3, n=10)
Uwe Ligges
Regards
khazaei
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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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and provide commented, minimal, self-contained, reproducible code.
Re: [R] two questions for R beginners
Hi again Paul, Hi Ivan (and list), I think the main problem is not as much that there isn't structure in the way R provides documentation / tutorials, but that people have a hard time finding the structure. There are task views for certain specific fields, but I think a lot of beginners do not know that they exist. You're definitely right... what is it?! where to find them? So I think a O my God, I've downloaded R and what now tutorial might be a good idea to put very close to the download button of R on CRAN. This tutorial would focus not on how to do things in R, but would provide guidance to the most obvious sources of information such as Task views, specific mailing lists, ways to search list archives, information for beginners how to write a good e-mail etc. I think for a lot of beginners it is not as much the answer to a specific question that they need, but more guidance how to look for answers themselves. I think that would indeed help a lot. I can only agree with your last sentence. Is someone already working on this kind of manual? Is it planed? etc? cheers, Paul Regards, Ivan __ 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] update.packages with UNC library path
Hi all, I hit a small snag. Here is my workaround (copied verbatim from my aide memoire) in case it helps others. (or anyone knows a better way... ;-) Best regards, Keith Jewell. The site library file is defined (in Renviron.site R_LIBS_SITE=//Server02/stats/R/library/%v) via a UNC name something like //Server02/stats/R/library/2.10. As of now [Feb 2010, R version 2.10.1 (2009-12-14)] the menu Packages|Update Packages... [=update.packages(ask='graphics')] fails at the last step when it can't copy files to a directory named like that. It works if the site library is defined via a mapped drive like L:\\R\\library\\2.10, but we don't want to require all users to have this drive mapped. The workaround is thus: In order to update packages: a) have an appropriate mapped drive (e.g. Stats on 'server02') b) start R-Gui from that mapped drive. This will give the site library via the UNC and the base library via the mapped drive thus: .libPaths() [1] //Server02/stats/R/library/2.10 L:/R/R-Current/library c) use .LibPaths(new= ) to add the drive mapped path to the beginning of the list .libPaths(new=choose.dir()) # navigate to folder on mapped drive .libPaths() [1] L:\\R\\library\\2.10//Server02/stats/R/library/2.10 L:/R/R-Current/library update.packages(ask='graphics') will now work __ 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] two questions for R beginners
Paul, I think your point you need [to] spend at least a few hours a week on it is key. Since I am not doing statistics daily, more in fits starts as my latest project -may- require, my approach has been more task oriented. A less-than-ideal approach. So, I think your suggestion is on-the-mark. Tom Paul Hiemstra wrote: Ivan Calandra wrote: You are definitely right... What to do with bad beginner's questions is not a simple issue. If a beginner's mailing list is created, who will answer to such questions? And moreover, the beginners won't take advantage of the other questions (I've personally learned a lot trying to understand the questions and answers to other's problems). And also, as you said, the problems might persist. The beginner's mailing list might be good in one aspect though: the experts who subscribe to it would be willing to help the beginners to get started with R, knowing that the questions might not be clearly stated. As you pointed out, the mailing list is not the best for basic stuff (the question is of course what is basic?). Not everybody knows some colleagues who work with R (I'm personally the 1st one to use R in my lab). I think, somehow and I have no idea how, documentation and guidance to search for help should be more accessible as soon as you start with R. Maybe a _*clear*_ section on the R homepage or in the introduction to R manual like where to find help, including all of the most common and useful resources available (from ? and RSiteSearch() to R Wiki and Crantastic). Hi Ivan (and list), I think the main problem is not as much that there isn't structure in the way R provides documentation / tutorials, but that people have a hard time finding the structure. There are task views for certain specific fields, but I think a lot of beginners do not know that they exist. There are separate mailing lists for specific fields, but I often see geographical (my field of expertise) oriented questions on R-help that would fit much better on R-sig-geo. So I think a O my God, I've downloaded R and what now tutorial might be a good idea to put very close to the download button of R on CRAN. This tutorial would focus not on how to do things in R, but would provide guidance to the most obvious sources of information such as Task views, specific mailing lists, ways to search list archives, information for beginners how to write a good e-mail etc. I think for a lot of beginners it is not as much the answer to a specific question that they need, but more guidance how to look for answers themselves. But at the end of the day, R is still not very easy to learn when coming from GUI oriented stats programs. In addition, to become reasonably fluent in R, you need spend at least a few hours a week on it. SO I think we can ease the pain for beginners, but not take away that it takes quite some time to become fluent in R. cheers, Paul I hope that this whole discussion might help to make the R world better. Thank you Patrick for initiating it! Regards, Ivan Le 2/26/2010 15:09, Paul Hiemstra a écrit : Ivan Calandra wrote: Since you want input from beginners, here are some thoughts I had and still have two big problems with R: - this vectorization thing. I've read many manuals (including R inferno), but I'm still not completely clear about it. In simple examples, it's fine. But when it gets a bit more complex, then... Related to it, the *apply functions are still a bit difficult to understand. When I have to use them, I just try one and see what happens. I don't understand them well enough to know which one I need. - the second problem is where to find the functions/packages I need. There are many options, and that's actually the problem. R Wiki, Rseek, RSiteSearch, Crantastic, etc... When you start with R, you discover that the capabilities of R are almost unlimited and you don't really know where to start, where to find what you need. As noted in earlier posts, the mailing list is really great, but some people are really hard with beginners. It was noted in a discussion a few days ago, but it looks like some don't realize how difficult it is at the beginning to formulate a good question, clear, with self-contained example and so on. Moreover, not everybody speaks English natively. I don't mean that you must help, even when the question is really vague and not clear and whatever. I'm just saying that if you don't want to help (whatever the reason), you don't have to say it badly. But in any cases, the mailing list is still really helpful. As someone noted (sorry I erased the email so I don't remember who), it might be a good idea to split it. Hi everyone, My 2ct about the mailing list :). I understand that beginners have a hard time formulating a good question. But the problem is that we can't answer the question when it is unclear. So either I: - Don't bother answering - Try do discuss with the author of
Re: [R] Defective help pages
On 24.02.2010 21:34, Peter Danenberg wrote: I'm trying to diagnose a bizarre problem in which the help files invoked from R are partially defective. help(), for instance, is missing the Description, Arguments and See Also sections; as are help files for other commands (see below). Peter, I just tried ?help with R-2.10.1 on 2 Windows and 2 Linux flavours. All of them had correct help pages. Looks like something is broken on your OS (unreported). This seems to be plain text help, right? Does the html version give the same result? Best wishes, Uwe I've built 2.8.1, 2.10.1 and HEAD with the same results; do I need to set an environment or configuration variable? help package:utils R Documentation Documentation Description: Usage: help(topic, package = NULL, lib.loc = NULL, verbose = getOption(verbose), try.all.packages = getOption(help.try.all.packages), help_type = getOption(help_type)) Arguments: Details: The following types of help are available: * Plain text help Offline help: Note: References: Becker, R. A., Chambers, J. M. and Wilks, A. R. (1988) _The New S Language_. Wadsworth Brooks/Cole. See Also: Examples: help() help(help) # the same help(lapply) help(for) # or ?for, but quotes/backticks are needed help(package=splines) # get help even when package is not loaded topi- women help(topi) try(help(bs, try.all.packages=FALSE)) # reports not found (an error) help(bs, try.all.packages=TRUE) # reports can be found # in package 'splines' __ 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] question to make a vector without loop
For general purpose of recursion formula, you could do it like this: make.vector - function(w, n, a, b) c(w, sapply(1:(n-1), function(x) w - w * a / (b + x))) make.vector(w = 1, n = 4, a = 24, b = 1) [1] 1 12 96 576 On Fri, Feb 26, 2010 at 11:23 PM, khaz...@ceremade.dauphine.fr wrote: Hello all, I want to define a vector like w[k+1]=w[k]*a/(b+k) for k=1,...,N-1 without use loop. Is it posible to do in R? Regards khazaei __ 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] text editors
Dear all, Do you use a text editor ? What would you recommend for Windows users ? What about Tinn-R ? Thank you very much, Dwayne [[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.
[R] Problem accessing sub-methods of functions stored in a vector
Hi folks,
I am having trouble accessing sub-functions when the main function is
stored in an array. For example, the following test code works fine:
fcns = c(abs, sqrt)
fcns[[1]](-2)
fcns[[2]](2)
However, when I try to access sub-functions declared within list() in a
function, this only works directly. When I try to access these within an
array only the first declared sub-function is run. For example I have
the function:
agent - function(id) {
# MANY VARIABLES DECLARED
list(
set_id = function(newid) {
id - newid
},
get_id = function(newid) {
return(id)
},
# LOTS MORE SUB FUNCTIONS
)
}
If I create a variable to hold this function, I can then access all the
subfunctions without problem Example:
myAgent = agent(1)
myAgent$get_id() # Works fine
However, once this function is stored in a vector, I can no longer
access the subfunctions.
agents = c(agent(1), agent(2))
agents[[1]] # This shows the set_id function only, unnamed
agents[[1]]$get_id() # Leads to error below:
Error in agents[[1]]$get_id : object of type 'closure' is not subsettable
How can I access these sub methods within the vector?
I am using R version 2.8.1
TIA for the help!
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[R] biclust package
Dear all, I am using biclust package for biclustering. I wanted to know how can I extract my clusters from the object? library(biclust) test - matrix(rnorm(5000), 100, 50) test[11:20,11:20] - rnorm(100, 3, 0.1) loma - binarize(test,2) res - biclust(x=loma, method=BCBimax(), minr=4, minc=4, number=10) res Thanks for your help -- Linda Garcia [[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] ggplot2 : bug in coord_equal() ?
Hi David, That's the behaviour I'd expect - the plot is 5 x 13000. What were you expecting? Hadley On Fri, Feb 26, 2010 at 8:06 AM, David Hajage dhajag...@gmail.com wrote: Hello, I think there is a bug in coord_equal when x s a factor : ggplot(diamonds, aes(clarity, fill=cut)) + geom_bar() ggplot(diamonds, aes(clarity, fill=cut)) + geom_bar() + coord_equal(1/2) David __ 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. -- Assistant Professor / Dobelman Family Junior Chair Department of Statistics / Rice University 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] question to make a vector without loop
-Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of khaz...@ceremade.dauphine.fr Sent: Friday, February 26, 2010 7:23 AM To: r-help@r-project.org Subject: [R] question to make a vector without loop Hello all, I want to define a vector like w[k+1]=w[k]*a/(b+k) for k=1,...,N-1 without use loop. Is it posible to do in R? It would be nice to see your loopy solution. However, you could use cumprod (cumulative products): c(w[1], w[1] * cumprod(a/(b+seq_len(N-1))) E.g., w-7 a-2 b-1 for(k in 1:9) w[k+1] - w[k] * a / (b+k) w [1] 7.00 7.00 4.67 2.33 0.93 [6] 0.31 0.09 0.02 0.0049382716 0.0009876543 c(w[1], w[1]*cumprod(a/(b+seq_len(9 [1] 7.00 7.00 4.67 2.33 0.93 [6] 0.31 0.09 0.02 0.0049382716 0.0009876543 Bill Dunlap Spotfire, TIBCO Software wdunlap tibco.com Regards khazaei __ 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] counting the number of ones in a vector
But if x has any missing values:
x - c(1, 1, 1, NA, NA, 2, 1, NA)
sum( x == 1)
[1] NA
sum(x==1, na.rm=TRUE)
[1] 4
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf Of Henrique Dallazuanna
Sent: Friday, February 26, 2010 9:47 AM
To: Randall Wrong
Cc: r-help@r-project.org
Subject: Re: [R] counting the number of ones in a vector
Try:
sum(x == 1)
On Fri, Feb 26, 2010 at 11:40 AM, Randall Wrong randall.wr...@gmail.com wrote:
Dear R users,
I want to count the number of ones in a vector x.
That's what I did : length( x[x==1] )
Is that a good solution ?
Thank you very much,
Randall
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Re: [R] Legend's attribute
On 26.02.2010 05:22, Yi Du wrote: Hi there, I use plot(type=o) to draw the line. And I need put some legend to this line. But how can I let the legend to display the line type in the graph generated from type=o? I can only find the lty in the legend. But I tried several times and still failed. Use both pch=1, lty=1 as arguments. Also, if I use abline(h=0.08) to draw a horizontal line and I also want to show 0.08 in the y-axis, how can I do it? See ?mtext Uwe Ligges Many thanks, Yi __ 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] text editors
Dwayne Blind wrote: Dear all, Do you use a text editor ? What would you recommend for Windows users ? What about Tinn-R ? Dwayne, Perhaps you have seen http://www.sciviews.org/_rgui/ , it has information on several possibilities. It would be hard to pull me away from using Emacs with ESS (http://ess.r-project.org/), both on Windows and Linux. I use Emacs for a lot of things now, but ESS was the gateway that helped me learn it. The fact that there is always a version of Emacs on all the platforms I might be faced with helps a lot too. I know nothing about Tinn-R, but my recollection is that people who use it seem to like it just fine. Erik __ 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] Problem accessing sub-methods of functions stored in a vector
On 26.02.2010 16:33, Matt Asher wrote:
Hi folks,
I am having trouble accessing sub-functions when the main function is
stored in an array. For example, the following test code works fine:
fcns = c(abs, sqrt)
fcns[[1]](-2)
fcns[[2]](2)
However, when I try to access sub-functions declared within list() in a
function, this only works directly. When I try to access these within an
array only the first declared sub-function is run. For example I have
the function:
agent - function(id) {
# MANY VARIABLES DECLARED
list( set_id = function(newid) {
id - newid
},
get_id = function(newid) {
return(id)
},
# LOTS MORE SUB FUNCTIONS
)
}
If I create a variable to hold this function, I can then access all the
subfunctions without problem Example:
myAgent = agent(1)
myAgent$get_id() # Works fine
However, once this function is stored in a vector, I can no longer
access the subfunctions.
agents = c(agent(1), agent(2))
agents is still a list (or in other words a vector of mode list), but
since you c()'ed, it has one hierarchy level less than you expect.
In order to make your code below work, you rather need:
agents - list(agent(1), agent(2))
Anyway, I hope you know that lexical scoping will yield in the
environments attached to all those functions they have been generated in
and you know about possible consequences. If not, you really should not
be doing this ... (nor using - ) ...
agents[[1]] # This shows the set_id function only, unnamed
agents[[1]]$get_id() # Leads to error below:
Error in agents[[1]]$get_id : object of type 'closure' is not subsettable
How can I access these sub methods within the vector?
I am using R version 2.8.1
... and upgrade to some recent version of R.
Uwe Ligges
TIA for the help!
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Re: [R] Restructure some data
Thank you both for your replies; both are very useful. The larger issue at hand
is that the data will actually be huge, thus the end result will be a very
large, sparse data frame.
So, I decided to put all three possible solutions to a timing test and see what
they yield. I simulated 15000 possible students and created an item pool of 300
total items that could be selected. I fixed the number of total items each
students sees to 3, although this will truly be on the order of 50 in the real
world problem.
So, first the new data for testing all three solutions.
item.pool - paste(item, 1:300, sep = )
N - 15000
set.seed(54321)
dat - data.frame(id = c(1:N), first.item = sample(item.pool, N, replace=TRUE),
second.item = sample(item.pool, N,replace=TRUE), third.item =
sample(item.pool, N,replace=TRUE),
score1 = sample(c(0,1), N,replace=TRUE), score2 = sample(c(0,1),
N,replace=TRUE), score3 = sample(c(0,1), N,replace=TRUE))
Now, my original loop is in the function 'harold', I created a new function
bill and phil. I modified Bill's code only to reflect my original naming
conventions. Timing results for each solution are below.
system.time(result - harold(dat))
user system elapsed
1347.85 441.92 1799.75
system.time(result - bill(dat))
user system elapsed
0.040.040.09
system.time(result - phil(dat))
user system elapsed
4.420.004.42
The loop timing is laughable; so it is out. Clearly, Phil wins from the golf
viewpoint, but Bill's solution is quite fast. Phil, it is actually quite
irrelevant that the original ordering of the columns is not preserved since
that can be easily remedied in a post-hoc reordering of columns.
Again, thank you both.
Harold
harold - function(dat){
Nstu - nrow(dat)
df - matrix(NA, ncol = length(item.pool), nrow = Nstu)
colnames(df) - item.pool
for(i in 1:Nstu){
for(j in 2:4){
rr - which(dat[i,j] == colnames(df))
df[i,rr] - dat[i, (j+3)]
}
}
df
}
system.time(result - harold(dat))
bill - function(dat) {
L - length(item.pool)
items - as.matrix(dat[2:4])
scores - as.matrix(dat[, 5:7])
retval - matrix(NA_real_, nrow = nrow(dat), ncol = L,
dimnames = list(character(), item.pool))
retval[cbind(dat$id, match(items, item.pool))] - scores
retval
}
system.time(result - bill(dat))
phil - function(dat){
df - tapply(as.vector(as.matrix(dat[5:7])),
list(rep(dat$id,3),as.vector(as.matrix(dat[2:4]))),I)
df
}
system.time(result - phil(dat))
-Original Message-
From: Phil Spector [mailto:spec...@stat.berkeley.edu]
Sent: Thursday, February 25, 2010 5:38 PM
To: Doran, Harold
Cc: r-help@r-project.org
Subject: Re: [R] Restructure some data
Harold -
Here's what I came up with:
tapply(as.vector(as.matrix(dat[5:7])),
+ list(rep(dat$id,3),as.vector(as.matrix(dat[2:4]))),I)
item1 item10 item2 item3 item4 item5 item7 item9
1NA NA 1NANA 1NA 0
2 0 NANANANA 1 1NA
3 1 NA 0 1NANANANA
4NA NANA 1 0NA 0NA
5NA 1NA 0 1NANANA
I thought there would be a way to use xtabs, but I had
trouble preserving the NAs.
The columns aren't in the right order, and the item6 column is
missing, but it's pretty close.
Thanks for the easily reproducible example, and the interesting
puzzle.
- Phil Spector
Statistical Computing Facility
Department of Statistics
UC Berkeley
spec...@stat.berkeley.edu
On Thu, 25 Feb 2010, Doran, Harold wrote:
Suppose I have a data frame like dat below. For some context, this is the
format that represents student's taking a computer adaptive test. first.item
is the first item that student was administered and then score.1 is the
student's response to that item and so forth.
item.pool - paste(item, 1:10, sep = )
set.seed(54321)
dat - data.frame(id = c(1,2,3,4,5), first.item = sample(item.pool, 5,
replace=TRUE),
second.item = sample(item.pool, 5,replace=TRUE), third.item =
sample(item.pool, 5,replace=TRUE),
score1 = sample(c(0,1), 5,replace=TRUE), score2 =
sample(c(0,1), 5,replace=TRUE), score3 = sample(c(0,1), 5,replace=TRUE))
I need to restructure this into a new format. The new matrix df (after the
loop) is exactly what I want in the end. But, I'm annoyed at myself for not
thinking of a more efficient way to restructure this without using a loop.
df - matrix(NA, ncol = length(item.pool), nrow = nrow(dat))
colnames(df) - unique(item.pool)
for(i in 1:5){
for(j in 2:4){
Re: [R] Adjust lattice graph axis label on final page
On Fri, Feb 26, 2010 at 6:14 AM, Sebastien Bihorel sebastien.biho...@cognigencorp.com wrote: Thanks Deepayan, This confirms what I thought I should do... One follow-up question about your suggested code: is it possible to create a lattice graph object myplot and modify the layout just for panel 7 and 8, rather than creating two graphs with different layouts? Sure: p - xyplot(y~x|id,as.table=T,data=mydata) update(p[1:6], layout = c(2, 3)) update(p[7:8], layout = c(2, 1)) -Deepayan Sebastien Deepayan Sarkar wrote: On Thu, Feb 25, 2010 at 3:45 AM, Sebastien Bihorel sebastien.biho...@cognigencorp.com wrote: Dear R-users, I was wondering if there was a way to adjust the placement of the axis titles for the last page of a multi-page lattice plot (see example below). Depending on the total number of panels, the placement of these titles might look strange on the last page, if the layout is not adjusted (e.g. in some template code). It's not possible to adjust the labels on a per-page basis. It _is_ possible to have the two plots fill up the last page, but that may not be what you want. xyplot(y~x|id,as.table=T,data=mydata,layout=c(2,3))[1:6] xyplot(y~x|id,as.table=T,data=mydata,layout=c(2,1))[7:8] -Deepayan __ 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] possible arrangements of across sample ties for runs test
I'm trying to implement the two-sample Wald-Wolfowitz runs test. Daniel (1990) suggests a method to deal with ties across samples. His suggestion is to prepare ordered arrangements, one resulting in the fewest number of runs, and one resulting in the largest number of runs. Then take the mean of these. The code below counts 9 runs for my example data where '60' is tied across samples. X - c(58, 62, 55, 60, 60, 67) n1 - length(X) Y - c(60, 59, 72, 73, 56, 53, 50, 50) n2 - length(Y) data - c(X, Y) names(data) - c(rep(X, n1), rep(Y, n2)) data - sort(data) runs - rle(names(data)) r - length(runs$lengths) r Y Y Y X Y X Y X X Y X X Y Y 50 50 53 55 56 58 59 60 60 60 62 67 72 73 -- r = 9 runs The other possible orderings are: Y Y Y X Y X Y X Y X X X Y Y -- 9 runs 50 50 53 55 56 58 59 60 60 60 62 67 72 73 Y Y Y X Y X Y Y X X X X Y Y -- 7 runs 50 50 53 55 56 58 59 60 60 60 62 67 72 73 How to I generate the other possible orderings? Thus, far, I've found a day to identify cross sample duplicates... # find the ties across samples dd - data[duplicated(data)] #find all duplicates idd - dd %in% X dd %in% Y #determine found in both X and Y duplicates - dd[idd] Thanks! --Dale [[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] question to make a vector without loop
A general facility for this is Reduce: f - function(w, k, a = 2, b = 1) w*a / (b+k) c(7, Reduce(f, 2:9, 7, accumulate = TRUE)) the result of which is: c(7, Reduce(f, 2:9, 7, accumulate = TRUE)) [1] 7.00 7.00 4.67 2.33 0.93 0.31 0.09 0.02 0.0049382716 0.0009876543 On Fri, Feb 26, 2010 at 10:23 AM, khaz...@ceremade.dauphine.fr wrote: Hello all, I want to define a vector like w[k+1]=w[k]*a/(b+k) for k=1,...,N-1 without use loop. Is it posible to do in R? Regards khazaei __ 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] text editors
There is a list here: http://www.sciviews.org/_rgui/projects/Editors.html On Fri, Feb 26, 2010 at 11:10 AM, Dwayne Blind dwaynebl...@gmail.com wrote: Dear all, Do you use a text editor ? What would you recommend for Windows users ? What about Tinn-R ? Thank you very much, Dwayne [[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. __ 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] two questions for R beginners
Thomas Adams wrote: Paul, I think your point you need [to] spend at least a few hours a week on it is key. Since I am not doing statistics daily, more in fits starts as my latest project -may- require, my approach has been more task oriented. A less-than-ideal approach. So, I think your suggestion is on-the-mark. Tom I also see co-workers who would like to work with R, see the benefit of R etc, but don't have the time to learn and maintain R. But I'm not really sure how to fix this, it seems impossible to have both easy, intuitive to use and power and flexibility. cheers, Paul Paul Hiemstra wrote: Ivan Calandra wrote: You are definitely right... What to do with bad beginner's questions is not a simple issue. If a beginner's mailing list is created, who will answer to such questions? And moreover, the beginners won't take advantage of the other questions (I've personally learned a lot trying to understand the questions and answers to other's problems). And also, as you said, the problems might persist. The beginner's mailing list might be good in one aspect though: the experts who subscribe to it would be willing to help the beginners to get started with R, knowing that the questions might not be clearly stated. As you pointed out, the mailing list is not the best for basic stuff (the question is of course what is basic?). Not everybody knows some colleagues who work with R (I'm personally the 1st one to use R in my lab). I think, somehow and I have no idea how, documentation and guidance to search for help should be more accessible as soon as you start with R. Maybe a _*clear*_ section on the R homepage or in the introduction to R manual like where to find help, including all of the most common and useful resources available (from ? and RSiteSearch() to R Wiki and Crantastic). Hi Ivan (and list), I think the main problem is not as much that there isn't structure in the way R provides documentation / tutorials, but that people have a hard time finding the structure. There are task views for certain specific fields, but I think a lot of beginners do not know that they exist. There are separate mailing lists for specific fields, but I often see geographical (my field of expertise) oriented questions on R-help that would fit much better on R-sig-geo. So I think a O my God, I've downloaded R and what now tutorial might be a good idea to put very close to the download button of R on CRAN. This tutorial would focus not on how to do things in R, but would provide guidance to the most obvious sources of information such as Task views, specific mailing lists, ways to search list archives, information for beginners how to write a good e-mail etc. I think for a lot of beginners it is not as much the answer to a specific question that they need, but more guidance how to look for answers themselves. But at the end of the day, R is still not very easy to learn when coming from GUI oriented stats programs. In addition, to become reasonably fluent in R, you need spend at least a few hours a week on it. SO I think we can ease the pain for beginners, but not take away that it takes quite some time to become fluent in R. cheers, Paul I hope that this whole discussion might help to make the R world better. Thank you Patrick for initiating it! Regards, Ivan Le 2/26/2010 15:09, Paul Hiemstra a écrit : Ivan Calandra wrote: Since you want input from beginners, here are some thoughts I had and still have two big problems with R: - this vectorization thing. I've read many manuals (including R inferno), but I'm still not completely clear about it. In simple examples, it's fine. But when it gets a bit more complex, then... Related to it, the *apply functions are still a bit difficult to understand. When I have to use them, I just try one and see what happens. I don't understand them well enough to know which one I need. - the second problem is where to find the functions/packages I need. There are many options, and that's actually the problem. R Wiki, Rseek, RSiteSearch, Crantastic, etc... When you start with R, you discover that the capabilities of R are almost unlimited and you don't really know where to start, where to find what you need. As noted in earlier posts, the mailing list is really great, but some people are really hard with beginners. It was noted in a discussion a few days ago, but it looks like some don't realize how difficult it is at the beginning to formulate a good question, clear, with self-contained example and so on. Moreover, not everybody speaks English natively. I don't mean that you must help, even when the question is really vague and not clear and whatever. I'm just saying that if you don't want to help (whatever the reason), you don't have to say it badly. But in any cases, the mailing list is still really helpful. As someone noted (sorry I erased the email so I don't remember who), it might be a good
Re: [R] biclust package
On 26.02.2010 17:04, linda garcia wrote: Dear all, I am using biclust package for biclustering. I wanted to know how can I extract my clusters from the object? library(biclust) test- matrix(rnorm(5000), 100, 50) test[11:20,11:20]- rnorm(100, 3, 0.1) loma- binarize(test,2) res- biclust(x=loma, method=BCBimax(), minr=4, minc=4, number=10) res Thanks for your help According to ?biclust which links to the Biclust class, there are slots that indicate cluster assigmnets in: r...@rowxnumber r...@numberxcol Uwe Ligges __ 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] Boot R
Cassiano wrote: I think I have 'libgfortran'. After that I digit 'dpkg -l | grep libgfortran' in terminal, I got this message: ii libgfortran2 4.2.4-5ubuntu1 Runtime library for GNU Fortran applications ii libgfortran2-dbg 4.2.4-5ubuntu1 Runtime library for GNU Fortran applications ii libgfortran3 4.4.1-4ubuntu9 Runtime library for GNU Fortran applications ii libgfortran3-dbg 4.4.1-4ubuntu9 Runtime library for GNU Fortran applications And the error continue: /usr/lib/R/bin/exec/R: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory if you do: sudo updatedb locate libgfortran | grep so does it find the file? And in which path? cheers, Paul -- Drs. Paul Hiemstra Department of Physical Geography Faculty of Geosciences University of Utrecht Heidelberglaan 2 P.O. Box 80.115 3508 TC Utrecht Phone: +3130 274 3113 Mon-Tue Phone: +3130 253 5773 Wed-Fri http://intamap.geo.uu.nl/~paul __ 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] Boot R
Cassiano wrote: I think I have 'libgfortran'. After that I digit 'dpkg -l | grep libgfortran' in terminal, I got this message: ii libgfortran2 4.2.4-5ubuntu1 Runtime library for GNU Fortran applications ii libgfortran2-dbg 4.2.4-5ubuntu1 Runtime library for GNU Fortran applications ii libgfortran3 4.4.1-4ubuntu9 Runtime library for GNU Fortran applications ii libgfortran3-dbg 4.4.1-4ubuntu9 Runtime library for GNU Fortran applications And the error continue: /usr/lib/R/bin/exec/R: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory Cassiano wrote: After sudo updatedb - nothing after locate libgfortran | grep so //usr/lib/libgfortran.so.2 /usr/lib/libgfortran.so.2.0.0 /usr/lib/libgfortran.so.3.0.0 /usr/lib/debug/usr/lib/libgfortran.so.2.0.0 /usr/lib/debug/usr/lib/libgfortran.so.3.0.0 /usr/lib/gcc/i486-linux-gnu/4.4/libgfortran.so / My reply: The point is that R is expecting /usr/lib/libgfortran.so.3 but your computer has /usr/lib/libgfortran.so.3.0.0. A trick is to make a symbolic link from /usr/lib/libgfortran.so.3 to /usr/lib/libgfortran.so.3.0.0. /usr/lib/libgfortran.so only points to /usr/lib/libgfortran.so.3.0.0 in that case: sudo ln -s /usr/lib/libgfortran.so.3.0.0 /usr/lib/libgfortran.so.3 This should fix the problem. cheers, Paul -- Drs. Paul Hiemstra Department of Physical Geography Faculty of Geosciences University of Utrecht Heidelberglaan 2 P.O. Box 80.115 3508 TC Utrecht Phone: +3130 274 3113 Mon-Tue Phone: +3130 253 5773 Wed-Fri http://intamap.geo.uu.nl/~paul __ 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] question to make a vector without loop
My apologies, I misread your formula. Here is a clearer example anyways: w - 1:10 N - length(w) a - 1 b - 1 k - 1:(N-1) w[k+1] - w[k]*(a/(b+k)) w [1] 1.000 0.500 0.667 0.750 0.800 0.833 0.8571429 [8] 0.875 0.889 0.900 Best, Josh On Fri, Feb 26, 2010 at 7:23 AM, khaz...@ceremade.dauphine.fr wrote: Hello all, I want to define a vector like w[k+1]=w[k]*a/(b+k) for k=1,...,N-1 without use loop. Is it posible to do in R? Regards khazaei __ 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.htmlhttp://www.r-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Joshua Wiley Senior in Psychology University of California, Riverside http://www.joshuawiley.com/ [[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.
