[R] problem with working on R-Project from C#
Hi, i got a problem with initialising R-Project from C# in this i m sending what are all the code line I had been written and the error where i got sc1 = new STATCONNECTORSRVLib.StatConnector(); sc1.Init(R); and error at SCN_E_INVALIDINTERPRETERVERSION -2147221487 0x80040011 can any one suggest how can i resolve it thanks regards; kiran [[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] Sweave in LATEX
I have solved the problem. It seems that the \Sexpr{} sequence is processed
by R rather than latex. If you use:
Sweave(Sweave-test-1.Rnw, syntax=SweaveSyntaxNoweb)
When processing in R then this is handled in the appropriate way.
Duncan Murdoch-2 wrote:
On 1/6/2009 6:44 AM, Mr Derik wrote:
Hello
I have been setting up my computer to run Sweave. I have got the whole
thing
working on example files, except that my MikTex returns an Undefined
Control Sequence error for \Sexpr and my output file contains verbatim
code
sequences at the apropriate point in the text rather than the R output.
The
rest of the output file is fine with tables, R code sequences and figures
in
the right place and correctly formatted. I have searched everywhere for
advice on what to do about this, any ideas would be gratefully received.
You need to give more details. Which version of R are you running? How
are you running Sweave? Are you including \usepackage{Sweave} in your
Sweave document? (This is not always necessary, but is usually a good
idea).
Duncan Murdoch
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[R] request for StatConnecter oriented problem
hi, i got a problem with initialising R-Project from C# in this i m sending what are all the code line I had been written and the error where i got sc1 = new STATCONNECTORSRVLib.StatConnector(); sc1.Init(R); and error at SCN_E_INVALIDINTERPRETERVERSION -2147221487 0x80040011 can any one suggest how can i resolve it thanks regards; kiran [[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 Noobie questions
Allen,
I would suggest reading about the str() function. It's great for getting
inside model outputs and seeing how they are constructed so you can
extract all the specific calculations you want.
Its a bit fiddly to get used to but there are plenty of examples on this
forum.
Hope this helps.
Simon.
- Original Message -
From: AllenL allen.laroc...@gmail.com
To: r-help@r-project.org
Sent: Tuesday, January 06, 2009 7:47 PM
Subject: Re: [R] Two Noobie questions
Thanks for your help!
I combined the above two to get the following, which seems to work (if
somewhat inelegant):
int.List-unlist(lapply(lmList, function(x) {coef(x)[1]}),use.names=FALSE)
lmList is my list of lm objects.
-Allen
David Winsemius wrote:
On Jan 6, 2009, at 1:50 PM, AllenL wrote:
1. I have a list of lm (linear model) objects. Is it possible to
select,
through subscripts, a particular element (say, the intercept) from
all the
models? I've tried something like this:
?coef
if your list of models is ml, then perhaps something like this
partially tested idea:
lapply(ml, function(x) coef(x)[1] )
This is what I get using that formulation an available logistic model:
coef(lr.TC_HDL_BMI)[1]
Intercept
-6.132448
List[[1:length(list)]][1]
All members of the list are similar. My goal is to have a list of the
intercepts and lists of other estimated parameters. Is it better to
convert
to a matrix? How to do this?
2. Connected to this, how do I convert from a list back to a vector?
This
problem arose from using split to split a vector by a factor, then
selecting a subset of this (ie. length10), leaving me with subset
list of
my original. Unsplit(newList, factor) doesn't work, presumably due
to my
removal of some values. Thoughts?
?unlist
ll - list(1,2,3,4)
ll
[[1]]
[1] 1
[[2]]
[1] 2
[[3]]
[1] 3
[[4]]
[1] 4
unlist(ll)
[1] 1 2 3 4
str(unlist(ll))
num [1:4] 1 2 3 4
is.vector(unlist(ll))
[1] TRUE
--
David Winsemius
Thanks!
-Allen
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[R] Importing data from SPSS with Arabic encoding
Dear R-users, I'm facing a problem with the import of data in R. I have a sav file that, I presume, uses some Arabic encoding (but I don't know which one) and I would like to read it with R. When I use the function read.spss (I also tried spss.get(Hmisc)), I get the following message: read.spss(Hhld.sav) Erreur dans read.spss(Hhld.sav) : erreur à la lecture de l'entête du fichier système De plus : Warning message: In read.spss(Hhld.sav) : Hhld.sav : position 0 : le nom de la variable commence avec un caractère non autorisé The second and last lines can be translated into error reading system-file header and Hhld.sav: position 0: Variable name begins with invalid character. That's why I suppose it is a problem with the encoding. Does someone has an idea of the solution to my problem? Thanks Florent Bresson __ 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] Importing data from SPSS with Arabic encoding
On Wed, 7 Jan 2009, Florent Bresson wrote: Dear R-users, I'm facing a problem with the import of data in R. I have a sav file that, I presume, uses some Arabic encoding (but I don't know which one) and I would like to read it with R. When I use the function read.spss (I also tried spss.get(Hmisc)), I get the following message: read.spss(Hhld.sav) Erreur dans read.spss(Hhld.sav) : erreur à la lecture de l'entête du fichier système De plus : Warning message: In read.spss(Hhld.sav) : Hhld.sav : position 0 : le nom de la variable commence avec un caractère non autorisé The second and last lines can be translated into error reading system-file header and Hhld.sav: position 0: Variable name begins with invalid character. That's why I suppose it is a problem with the encoding. Does someone has an idea of the solution to my problem? 1) Please read the posting guide and supply the details you were asked to supply. E.g. what OS, what locale, what version of foreigh? 2) Read the help for read.spss, especially its 'reencode' argument. You will need to know what the encoding was, but most likely the output before the error which (you did not show us) told you (and would have told us). BTW, if you start R with LANGUAGE=en set, you will get English messages to quote here. PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595__ R-help@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] Large Dataset
There are several approaches to analyzing data sets much larger than memory, and the best approach does depend on the problem. It's certainly possible to process gigabytes of data on a 32-bit R system - the examples I've worked on are whole-genome association studies with 10^5-10^6 variables and 10^3-10^4 observations. Other people have worked with much larger data sets. Some approaches are: - incremental reading using a connection to the file, reading a few thousand lines at a time. The statistics Edwin wants can all be computed in a single pass through the data. This is what the biglm package does for linear models. - storing the data in a relational database and then either *) using SQL commands (the mean, min, max are all built in to SQL) to do most of the work and just reading results (or interim results) into R *) reading appropriate chunks of the data into R and doing the computations there - storing the data in netCDF or HDF5 formats and loading chunks into R. These are less flexible than relational databases but more efficient for certain sorts of subsets. - memory-mapping the data file (the ff package does this) to read sections of data. I haven't tried this, so I'm not sort where its advantages and disadvantages are. The bigmemory package does not address quite the same problem. It deals with objects that fit in memory, but are large enough that copying them is a bad idea, and it also deals with sharing between processors. -thomas On Tue, 6 Jan 2009, Simon Pickett wrote: Hi, I am not very knowledgeable about this kind of stuff but my guess is that if you have a fairly slow computer and massive data sets there isnt alot you can do except get a better computer, buy more RAM or use something like SAS instead? Hopefully someone else will chip in Edwin, best of luck. Simon. - Original Message - From: Edwin Sendjaja edw...@web.de To: Simon Pickett simon.pick...@bto.org Cc: r-help@r-project.org Sent: Tuesday, January 06, 2009 2:53 PM Subject: Re: [R] Large Dataset Hi Simon, My RAM is only 3.2 GB (actually it should be 4 GB, but my Motherboard doesnt support it. R use almost of all my RAM and half of my swap. I think memory.limit will not solve my problem. It seems that I need RAM. Unfortunately, I can't buy more RAM. Why R is slow reading big data set? Edwin Only a couple of weeks ago I had to deal with this. adjust the memory limit as follows, although you might not want 4000, that is quite high memory.limit(size = 4000) Simon. - Original Message - From: Edwin Sendjaja edw...@web.de To: Simon Pickett simon.pick...@bto.org Cc: r-help@r-project.org Sent: Tuesday, January 06, 2009 12:24 PM Subject: Re: [R] Large Dataset Hi Simon, Thank for your reply. I have read ?Memory but I dont understand how to use. I am not sure if that can solve my problem. Can you tell me more detail? Thanks, Edwin type ?memory into R and that will explain what to do... S - Original Message - From: Edwin Sendjaja edw...@web.de To: r-help@r-project.org Sent: Tuesday, January 06, 2009 11:41 AM Subject: [R] Large Dataset Hi alI, I have a 3.1 GB Dataset ( with 11 coloumns and lots data in int and string). If I use read.table; it takes very long. It seems that my RAM is not big enough (overload) I have 3.2 RAM and 7GB SWAP, 64 Bit Ubuntu. Is there a best sultion to read a large data R? I have seen, that people suggest to use bigmemory package, ff. But it seems very complicated. I dont know how to start with that packages. i have tried to use bigmemory. But I got some kind of errors. Then I gave up. can someone give me an simple example how ot use ff or bigmemory?or maybe re better sollution? Thank you in advance, Edwin __ 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. Thomas Lumley Assoc. Professor, Biostatistics tlum...@u.washington.eduUniversity of Washington, Seattle __ 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] Re : Importing data from SPSS with Arabic encoding
Thanks Brian for your help. I am sorry, I should have red the help page more carefully. I am working on Kubuntu 8.04 with R 2.8.0. The problem with the file is that I do not know what the encoding is. I do not understand what you mean with [...] but most likely the output before the error which (you did not show us) told you (and would have told us) since I just ran R, loaded the foreign package and then tried to get the data with the function read.spss(). I have just seen that I can get a list of the supported encodings using the function iconvlist(). Would it be possible to define some function to test which encodings fit my file? Thanks in advance - Message d'origine De : Prof Brian Ripley rip...@stats.ox.ac.uk À : Florent Bresson f_bres...@yahoo.fr Cc : r-h...@stat.math.ethz.ch Envoyé le : Mercredi, 7 Janvier 2009, 10h49mn 06s Objet : Re: [R] Importing data from SPSS with Arabic encoding On Wed, 7 Jan 2009, Florent Bresson wrote: Dear R-users, I'm facing a problem with the import of data in R. I have a sav file that, I presume, uses some Arabic encoding (but I don't know which one) and I would like to read it with R. When I use the function read.spss (I also tried spss.get(Hmisc)), I get the following message: read.spss(Hhld.sav) Erreur dans read.spss(Hhld.sav) : erreur à la lecture de l'entête du fichier système De plus : Warning message: In read.spss(Hhld.sav) : Hhld.sav : position 0 : le nom de la variable commence avec un caractère non autorisé The second and last lines can be translated into error reading system-file header and Hhld.sav: position 0: Variable name begins with invalid character. That's why I suppose it is a problem with the encoding. Does someone has an idea of the solution to my problem? 1) Please read the posting guide and supply the details you were asked to supply. E.g. what OS, what locale, what version of foreigh? 2) Read the help for read.spss, especially its 'reencode' argument. You will need to know what the encoding was, but most likely the output before the error which (you did not show us) told you (and would have told us). BTW, if you start R with LANGUAGE=en set, you will get English messages to quote here. PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@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] Subscript
A similar question: mtext(text=log2 intensity ) How can I change 2 to be subscript? (see picture below) http://www.nabble.com/file/p21326192/log2_intensity.jpg -- View this message in context: http://www.nabble.com/Subscript-tp12241351p21326192.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 with contrasts
Hello All R Gurus I'm a relatively new user to R and I'm having so problems fully grasping the contrasts notion. So any help will be appreciated. Lately I've been playing around with lme and I was looking at the help files of anova.lme where there is this example options(contrasts = c(contr.treatment, contr.poly)) fm1BW.lme - lme(weight ~ Time * Diet, BodyWeight, random = ~ Time) fm2BW.lme - update(fm1BW.lme, weights = varPower()) # Test a specific contrast anova(fm2BW.lme, L = c(Time:Diet2 = 1, Time:Diet3 = -1)) after running it I get the following result F-test for linear combination(s) Time:Diet2 Time:Diet3 1 -1 numDF denDF F-value p-value 1 1 157 2.862598 0.0926 My question is how can I test for the Time:Diet1 interaction term and compare all three diets. Best regards, Paschal -- View this message in context: http://www.nabble.com/Help-with-contrasts-tp21326943p21326943.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] A (Not So) Short Introduction to S4 (ex Contributed Documentation)
Here is the link : http://christophe.genolini.free.fr/webTutorial/index.php Any comments are welcome. Christophe On Tue, Jan 6, 2009 at 8:17 PM, Ben Bolker bol...@ufl.edu wrote: Christophe Genolini cgenolin at u-paris10.fr writes: Hi the list, I wrote a tutorial about S4. Is it possible to have a link to it in the page Contributed Documentation or R Documentation on the CRAN web site ? Who shall I contact ? Christophe Try c...@r-project.org . Posting to the development list (r-de...@r-project.org) might also be appropriate. I would be curious to see the tutorial myself. Ben Bolker _ I would too. On Tue, Jan 6, 2009 at 8:17 PM, Ben Bolker bol...@ufl.edu wrote: Christophe Genolini cgenolin at u-paris10.fr writes: Hi the list, I wrote a tutorial about S4. Is it possible to have a link to it in the page Contributed Documentation or R Documentation on the CRAN web site ? Who shall I contact ? Christophe Try c...@r-project.org . Posting to the development list (r-de...@r-project.org) might also be appropriate. I would be curious to see the tutorial myself. Ben Bolker _ __ 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] Subscript
Try this: mtext(text=bquote(log[2]~intensity)) On Wed, Jan 7, 2009 at 5:36 AM, Timthy Chang henchao.ch...@gmail.comwrote: A similar question: mtext(text=log2 intensity ) How can I change 2 to be subscript? (see picture below) http://www.nabble.com/file/p21326192/log2_intensity.jpg -- View this message in context: http://www.nabble.com/Subscript-tp12241351p21326192.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. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O [[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] for loop and if problem
Sake wrote: Hi, I'm heaving difficulties with a dataset containing gene names and positions of those genes. Not such a big problem, but each gene has multiple exons so it's hard to say where de gene starts and where it ends. I want the starting and ending position of each gene in my dataset. Attached is the dataset: http://www.nabble.com/file/p21312449/genlistchrompos.csv genlistchrompos.csv Column 'B' is the gene name, 'G' is the starting position and 'H' is the stop position. You can load the dataset by using: data-read.csv(genlistchrompos.csv, sep=;) I hope someone can help me, it's giving me headaches for a week now:-((. Thanks! Thanks for the tips, i'm going to test them today! The B,G,H columns I mentioned are the columns you see when you open the file in Excel, I should have said that. Sorry for the confusion about that:-) I thought I had to use the 'if' statement because I only want to search for the Min and Max if the Gene name is the same as the one directly under it. And the 'for loop' I wanted to use to apply the 'if' statement to the entire row of gene names. Edit: I have tested: aggregate(data[, c(Exon_Start.Chr.)], by = list(data$Gene), min) aggregate(data[, c(Exon_Stop.Chr.)], by = list(data$Gene), max) And it worked like a charm! thanx! -- View this message in context: http://www.nabble.com/for-loop-and-if-problem-tp21312449p21326557.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] can the pdf output page break be controlled manually?
I would like to control where to make a page break in my pdf file. The following code renders three pages of output. But I would like to be able to control the page breaks. pdf(file=test.pdf, paper=a4) par(mfrow=c(2,2)) hist(rnorm(100)) hist(rnorm(100)) hist(rnorm(100)) plot.new() par(mfrow=c(1,1)) hist(rnorm(100)) hist(rnorm(100)) dev.off() It would be much more convenient though, to enter a page break command within the code instead of plot.new(). Is there a way to do this? TIA, Mark __ 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] Subscript
try something like this: plot(0:1, 0:1, type = n) text(0.5, 0.5, expression(paste(plain(log)[2], intensity))) and check ?plotmath for more info. I hope it helps. Best, Dimitris Timthy Chang wrote: A similar question: mtext(text=log2 intensity ) How can I change 2 to be subscript? (see picture below) http://www.nabble.com/file/p21326192/log2_intensity.jpg -- Dimitris Rizopoulos Assistant Professor Department of Biostatistics Erasmus Medical Center Address: PO Box 2040, 3000 CA Rotterdam, the Netherlands Tel: +31/(0)10/7043478 Fax: +31/(0)10/7043014 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Re : Importing data from SPSS with Arabic encoding
Florent Bresson wrote: Thanks Brian for your help. I am sorry, I should have red the help page more carefully. I am working on Kubuntu 8.04 with R 2.8.0. The problem with the file is that I do not know what the encoding is. I do not understand what you mean with [...] but most likely the output before the error which (you did not show us) told you (and would have told us) since I just ran R, loaded the foreign package and then tried to get the data with the function read.spss(). And you did not show us all the R output. read.spss will produce notes or warnings if it finds one. And PLEASE, you still have not given us the information asked for in the posting guide, such as the output of sessionInfo(). Not doing so really does make the work of the helpers a lot harder. I have just seen that I can get a list of the supported encodings using the function iconvlist(). Would it be possible to define some function to test which encodings fit my file? No, you need to ask the person who gave you the file. Thanks in advance - Message d'origine De : Prof Brian Ripley rip...@stats.ox.ac.uk À : Florent Bresson f_bres...@yahoo.fr Cc : r-h...@stat.math.ethz.ch Envoyé le : Mercredi, 7 Janvier 2009, 10h49mn 06s Objet : Re: [R] Importing data from SPSS with Arabic encoding On Wed, 7 Jan 2009, Florent Bresson wrote: Dear R-users, I'm facing a problem with the import of data in R. I have a sav file that, I presume, uses some Arabic encoding (but I don't know which one) and I would like to read it with R. When I use the function read.spss (I also tried spss.get(Hmisc)), I get the following message: read.spss(Hhld.sav) Erreur dans read.spss(Hhld.sav) : erreur à la lecture de l'entête du fichier système De plus : Warning message: In read.spss(Hhld.sav) : Hhld.sav : position 0 : le nom de la variable commence avec un caractère non autorisé The second and last lines can be translated into error reading system-file header and Hhld.sav: position 0: Variable name begins with invalid character. That's why I suppose it is a problem with the encoding. Does someone has an idea of the solution to my problem? 1) Please read the posting guide and supply the details you were asked to supply. E.g. what OS, what locale, what version of foreigh? 2) Read the help for read.spss, especially its 'reencode' argument. You will need to know what the encoding was, but most likely the output before the error which (you did not show us) told you (and would have told us). BTW, if you start R with LANGUAGE=en set, you will get English messages to quote here. PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@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] NA and NaN question
Hi all, I ran into a problem in some of my code that could be traced back to 'mean' sometimes returning NA and sometimes NaN, depending on the value of na.rm: mean(c()) [1] NA mean(c(NA),na.rm=T) [1] NaN However, I don't understand the reasoning behind this and would appreciate and explanation. I understand that the mean of an empty vector is not definied, but I don't understand why it matters whether the vector was empty from the beginning or only after removing the NAs. Pascal Niklaus __ 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-help Digest, Vol 71, Issue 7
Thanks for your answer Here it is : http://christophe.genolini.free.fr/webTutorial/index.php Any comments are welcome... Christophe __ 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] for loop and if problem
On Wed, Jan 7, 2009 at 3:51 AM, Sake tlep.nav.e...@hccnet.nl wrote: aggregate(data[, c(Exon_Start.Chr.)], by = list(data$Gene), min) aggregate(data[, c(Exon_Stop.Chr.)], by = list(data$Gene), max) That could be written: aggregate(data[Excon_Start.Chr.], data[Gene], min) aggregate(data[Excon_Start.Chr.], data[Gene], max) __ 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] illustrating a report
Hi all I would like to know a bit more about illustrating an a4 page within R. Finally I would like to have a pdf with multiple pages containing some statistics. I'm already able to produce a pdf, containing a plot in the center of one a4 page. As a next step I would like to set a title on top of this a4 page (maybe with absolute positions, if not possible to set it relative?). The plots then should be centered horizontaly but not vertically... Can you give me some advice, how to realise this? Thank you already in advance. Stephan -- View this message in context: http://www.nabble.com/illustrating-a-report-tp21328500p21328500.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] NA and NaN question
Pascal A. Niklaus wrote: Hi all, I ran into a problem in some of my code that could be traced back to 'mean' sometimes returning NA and sometimes NaN, depending on the value of na.rm: mean(c()) [1] NA mean(c(NA),na.rm=T) [1] NaN However, I don't understand the reasoning behind this and would appreciate and explanation. I understand that the mean of an empty vector is not definied, Not so, it is well-defined as 0/0 = NaN. but I don't understand why it matters whether the vector was empty from the beginning You didn't try that case: mean(numeric(0)) is also NaN. The issue is that typeof(c()) [1] NULL is not numeric (not evan a vector), and so mean() of it is undefined. or only after removing the NAs. Speculation (and wrong). Pascal Niklaus __ 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. -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@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] NA and NaN question
Pascal A. Niklaus wrote:
Hi all,
I ran into a problem in some of my code that could be traced back to 'mean'
sometimes returning NA and sometimes NaN, depending on the value of na.rm:
mean(c())
[1] NA
mean(c(NA),na.rm=T)
[1] NaN
However, I don't understand the reasoning behind this and would appreciate
and
explanation.
note the types:
typeof(c())
typeof(c(NA))
typeof(c(NA)[-na.omit(c(NA))])
now,
mean(NULL)
mean(logical(0))
mean(c())
# NA, because you take the mean of a vector of non-{numeric,logical}
type (see the warning message)
mean(c(NA), na.rm=TRUE)
# NaN, because you take the mean of a zero-length logical vector
mean(c(NA), na.rm=FALSE)
# NA, because you take the mean of a logical vector containing an NA
you can argue that ?mean underspecifies this (it doesn't say anything
about the value for a zero-length logical, numeric, or complex vector,
though you can guess it will be the value of 0/0).
vQ
__
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] illustrating a report
I would like to know a bit more about illustrating an a4 page within R. Finally I would like to have a pdf with multiple pages containing some statistics. I'm already able to produce a pdf, containing a plot in the center of one a4 page. As a next step I would like to set a title on top of this a4 page (maybe with absolute positions, if not possible to set it relative?). The plots then should be centered horizontaly but not vertically... Can you give me some advice, how to realise this? You want Sweave() ;-) With Sweave you can mix R and LaTeX code to produce nicely formatted reports. cu Philipp -- Dr. Philipp Pagel Lehrstuhl f�r Genomorientierte Bioinformatik Technische Universit�t M�nchen Wissenschaftszentrum Weihenstephan 85350 Freising, Germany http://mips.gsf.de/staff/pagel __ 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] NA and NaN question
Wacek Kusnierczyk wrote: Pascal A. Niklaus wrote: Hi all, I ran into a problem in some of my code that could be traced back to 'mean' sometimes returning NA and sometimes NaN, depending on the value of na.rm: mean(c()) [1] NA mean(c(NA),na.rm=T) [1] NaN However, I don't understand the reasoning behind this and would appreciate and explanation. note the types: typeof(c()) typeof(c(NA)) typeof(c(NA)[-na.omit(c(NA))]) wrong, an artifact of some experimenting; should have been: typeof(na.omit(c(NA))) vQ __ 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] Duplicated messages
BertG == Bert Gunter gunter.ber...@gene.com on Tue, 6 Jan 2009 10:13:29 -0800 writes: BertG Folks: I am getting duplicate messages on BertG posts. Please correct my details if I'm wrong, but I BertG believe it's because folks are posting to **both** BertG the addresses, r-help@r-project.org and BertG r-h...@stat.math.eth.ch . I believe the first is just BertG an alias for the second, and that's why the suplicate BertG posts occur. BertG So please choose one or the other, not both. yes, indeed ! (thank you, Bert) __ 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 in the NY Times
This article is accompanied by nice pictures of Robert and Ross. Data Analysts Captivated by Power of R http://www.nytimes.com/2009/01/07/technology/business-computing/07program.html January 7, 2009 Data Analysts Captivated by R’s Power By ASHLEE VANCE To some people R is just the 18th letter of the alphabet. To others, it’s the rating on racy movies, a measure of an attic’s insulation or what pirates in movies say. R is also the name of a popular programming language used by a growing number of data analysts inside corporations and academia. It is becoming their lingua franca partly because data mining has entered a golden age, whether being used to set ad prices, find new drugs more quickly or fine-tune financial models. Companies as diverse as Google, Pfizer, Merck, Bank of America, the InterContinental Hotels Group and Shell use it. But R has also quickly found a following because statisticians, engineers and scientists without computer programming skills find it easy to use. “R is really important to the point that it’s hard to overvalue it,” said Daryl Pregibon, a research scientist at Google, which uses the software widely. “It allows statisticians to do very intricate and complicated analyses without knowing the blood and guts of computing systems.” It is also free. R is an open-source program, and its popularity reflects a shift in the type of software used inside corporations. Open-source software is free for anyone to use and modify. I.B.M., Hewlett-Packard and Dell make billions of dollars a year selling servers that run the open-source Linux operating system, which competes with Windows from Microsoft. Most Web sites are displayed using an open-source application called Apache, and companies increasingly rely on the open-source MySQL database to store their critical information. Many people view the end results of all this technology via the Firefox Web browser, also open-source software. R is similar to other programming languages, like C, Java and Perl, in that it helps people perform a wide variety of computing tasks by giving them access to various commands. For statisticians, however, R is particularly useful because it contains a number of built-in mechanisms for organizing data, running calculations on the information and creating graphical representations of data sets. Some people familiar with R describe it as a supercharged version of Microsoft’s Excel spreadsheet software that can help illuminate data trends more clearly than is possible by entering information into rows and columns. What makes R so useful — and helps explain its quick acceptance — is that statisticians, engineers and scientists can improve the software’s code or write variations for specific tasks. Packages written for R add advanced algorithms, colored and textured graphs and mining techniques to dig deeper into databases. Close to 1,600 different packages reside on just one of the many Web sites devoted to R, and the number of packages has grown exponentially. One package, called BiodiversityR, offers a graphical interface aimed at making calculations of environmental trends easier. Another package, called Emu, analyzes speech patterns, while GenABEL is used to study the human genome. The financial services community has demonstrated a particular affinity for R; dozens of packages exist for derivatives analysis alone. “The great beauty of R is that you can modify it to do all sorts of things,” said Hal Varian, chief economist at Google. “And you have a lot of prepackaged stuff that’s already available, so you’re standing on the shoulders of giants.” R first appeared in 1996, when the statistics professors Ross Ihaka and Robert Gentleman of the University of Auckland in New Zealand released the code as a free software package. According to them, the notion of devising something like R sprang up during a hallway conversation. They both wanted technology better suited for their statistics students, who needed to analyze data and produce graphical models of the information. Most comparable software had been designed by computer scientists and proved hard to use. Lacking deep computer science training, the professors considered their coding efforts more of an academic game than anything else. Nonetheless, starting in about 1991, they worked on R full time. “We were pretty much inseparable for five or six years,” Mr. Gentleman said. “One person would do the typing and one person would do the thinking.” Some statisticians who took an early look at the software considered it rough around the edges. But despite its shortcomings, R immediately gained a following with people who saw the possibilities in customizing the free software. John M. Chambers, a former Bell Labs researcher who is now a consulting professor of statistics at Stanford University, was an early champion. At Bell Labs, Mr. Chambers had helped develop S, another statistics software
Re: [R] R Threatens SAS According to The NYT
ao == ajay ohri ajayo...@yahoo.com on Wed, 7 Jan 2009 11:07:13 +0530 writes: ao On Wed, Jan 7, 2009 at 11:05 AM, ajay ohri ao ajayo...@yahoo.com wrote: FYI..not a R -Help Topic, buy I dont know which list to post discussions like this. Regards, Ajay R-help is fine. Thanks a lot, Ajay, for the pointer! At the bottom of the page it says __ A version of this article appeared in print on January 7, 2009, __ on page B6 of the New York edition. Now if any the NYT (print version) subscribers on R-help are willing to fulfill a New Year's wish for me, I'd be very grateful for a (digital scan) copy of that page. Martin Maechler, ETH Zurich [..] Thought you might be interested in reading this article, which appears in the 1/6/9 online edition of The New York Times: http://www.nytimes.com/2009/01/07/technology/business-computing/07program.html The headline is Data Analysts Captivated by R's Power, and towards the end of the story is the following paragraph: While it is difficult to calculate exactly how many people use R, those most familiar with the software estimate that close to 250,000 people work with it regularly. The popularity of R at universities could threaten SAS Institute, the privately held business software company that specializes in data analysis software. SAS, with more than $2 billion in annual revenue, has been the preferred tool of scholars and corporate managers. Andrew Karp Sierra Information Services www.SierraInfomation.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] R in the NY Times
Pardon my exuberance, but this is simply awesome. What a treat to find on the front web page of the NY Times this morning under Technology. I think the article is very well written by the author, and I think it captures top highlights of why the software and community are so special. Continued high gratitude to all of R-core and the R community for its unique accomplishments. Every bit of praise is well-earned and deserved. I have continuously claimed to colleagues (primarily pharma industry) for the past 8 years or so that R is the most exciting going on in the area of statistics. Thanks, Bill Bill Pikounis Statistician On Wed, Jan 7, 2009 at 08:10, Zaslavsky, Alan M. zasla...@hcp.med.harvard.edu wrote: This article is accompanied by nice pictures of Robert and Ross. Data Analysts Captivated by Power of R http://www.nytimes.com/2009/01/07/technology/business-computing/07program.html January 7, 2009 Data Analysts Captivated by R's Power By ASHLEE VANCE __ 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] can the pdf output page break be controlled manually?
Try just leaving off the 'plot.new()'; When you change mfrow it creates a new page. On Wed, Jan 7, 2009 at 5:01 AM, Mark Heckmann mark.heckm...@gmx.de wrote: I would like to control where to make a page break in my pdf file. The following code renders three pages of output. But I would like to be able to control the page breaks. pdf(file=test.pdf, paper=a4) par(mfrow=c(2,2)) hist(rnorm(100)) hist(rnorm(100)) hist(rnorm(100)) plot.new() par(mfrow=c(1,1)) hist(rnorm(100)) hist(rnorm(100)) dev.off() It would be much more convenient though, to enter a page break command within the code instead of plot.new(). Is there a way to do this? TIA, Mark __ 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. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem that you are trying to solve? __ 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 in the NY Times
This is great to see. It's interesting that SAS Institute feels that non-peer-reviewed software with hidden implementations of analytic methods that cannot be reproduced by others should be trusted when building aircraft engines. Frank Zaslavsky, Alan M. wrote: This article is accompanied by nice pictures of Robert and Ross. Data Analysts Captivated by Power of R http://www.nytimes.com/2009/01/07/technology/business-computing/07program.html January 7, 2009 Data Analysts Captivated by R’s Power By ASHLEE VANCE To some people R is just the 18th letter of the alphabet. To others, it’s the rating on racy movies, a measure of an attic’s insulation or what pirates in movies say. R is also the name of a popular programming language used by a growing number of data analysts inside corporations and academia. It is becoming their lingua franca partly because data mining has entered a golden age, whether being used to set ad prices, find new drugs more quickly or fine-tune financial models. Companies as diverse as Google, Pfizer, Merck, Bank of America, the InterContinental Hotels Group and Shell use it. But R has also quickly found a following because statisticians, engineers and scientists without computer programming skills find it easy to use. “R is really important to the point that it’s hard to overvalue it,” said Daryl Pregibon, a research scientist at Google, which uses the software widely. “It allows statisticians to do very intricate and complicated analyses without knowing the blood and guts of computing systems.” It is also free. R is an open-source program, and its popularity reflects a shift in the type of software used inside corporations. Open-source software is free for anyone to use and modify. I.B.M., Hewlett-Packard and Dell make billions of dollars a year selling servers that run the open-source Linux operating system, which competes with Windows from Microsoft. Most Web sites are displayed using an open-source application called Apache, and companies increasingly rely on the open-source MySQL database to store their critical information. Many people view the end results of all this technology via the Firefox Web browser, also open-source software. R is similar to other programming languages, like C, Java and Perl, in that it helps people perform a wide variety of computing tasks by giving them access to various commands. For statisticians, however, R is particularly useful because it contains a number of built-in mechanisms for organizing data, running calculations on the information and creating graphical representations of data sets. Some people familiar with R describe it as a supercharged version of Microsoft’s Excel spreadsheet software that can help illuminate data trends more clearly than is possible by entering information into rows and columns. What makes R so useful — and helps explain its quick acceptance — is that statisticians, engineers and scientists can improve the software’s code or write variations for specific tasks. Packages written for R add advanced algorithms, colored and textured graphs and mining techniques to dig deeper into databases. Close to 1,600 different packages reside on just one of the many Web sites devoted to R, and the number of packages has grown exponentially. One package, called BiodiversityR, offers a graphical interface aimed at making calculations of environmental trends easier. Another package, called Emu, analyzes speech patterns, while GenABEL is used to study the human genome. The financial services community has demonstrated a particular affinity for R; dozens of packages exist for derivatives analysis alone. “The great beauty of R is that you can modify it to do all sorts of things,” said Hal Varian, chief economist at Google. “And you have a lot of prepackaged stuff that’s already available, so you’re standing on the shoulders of giants.” R first appeared in 1996, when the statistics professors Ross Ihaka and Robert Gentleman of the University of Auckland in New Zealand released the code as a free software package. According to them, the notion of devising something like R sprang up during a hallway conversation. They both wanted technology better suited for their statistics students, who needed to analyze data and produce graphical models of the information. Most comparable software had been designed by computer scientists and proved hard to use. Lacking deep computer science training, the professors considered their coding efforts more of an academic game than anything else. Nonetheless, starting in about 1991, they worked on R full time. “We were pretty much inseparable for five or six years,” Mr. Gentleman said. “One person would do the typing and one person would do the thinking.” Some statisticians who took an early look at the software considered it rough around the edges. But despite its shortcomings, R immediately gained a following with people who saw the
Re: [R] can the pdf output page break be controlled manually?
On 1/7/2009 5:01 AM, Mark Heckmann wrote: I would like to control where to make a page break in my pdf file. The following code renders three pages of output. But I would like to be able to control the page breaks. pdf(file=test.pdf, paper=a4) par(mfrow=c(2,2)) hist(rnorm(100)) hist(rnorm(100)) hist(rnorm(100)) plot.new() par(mfrow=c(1,1)) hist(rnorm(100)) hist(rnorm(100)) dev.off() It would be much more convenient though, to enter a page break command within the code instead of plot.new(). The par(mfrow=c(1,1)) command will cause a page break, so just do nothing. I don't know if that's much more convenient than entering plot.new(), but it's a little better. Duncan Murdoch Is there a way to do this? TIA, Mark __ 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] R in the NY Times
Bill Pikounis wrote: Pardon my exuberance, but this is simply awesome. What a treat to find on the front web page of the NY Times this morning under Technology. I think the article is very well written by the author, and I think it captures top highlights of why the software and community are so special. Continued high gratitude to all of R-core and the R community for its unique accomplishments. Every bit of praise is well-earned and deserved. I have continuously claimed to colleagues (primarily pharma industry) for the past 8 years or so that R is the most exciting going on in the area of statistics. Thanks, Bill Amen to that, and in addition, R is now the top tool for everyday analysis, not just a research statistician's tool. Frank Bill Pikounis Statistician On Wed, Jan 7, 2009 at 08:10, Zaslavsky, Alan M. zasla...@hcp.med.harvard.edu wrote: This article is accompanied by nice pictures of Robert and Ross. Data Analysts Captivated by Power of R http://www.nytimes.com/2009/01/07/technology/business-computing/07program.html January 7, 2009 Data Analysts Captivated by R's Power By ASHLEE VANCE __ 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. -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University __ 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 in the NY Times
I would like to add that I would have spent many more years doing my PhD if it wasnt for R! all data management, statistics and graphics were conducted using it. This was the direction my university and many more research institutes appear to be heading. It probably doesnt get said enough and I am sure I speak for all young researchers I am very much in debt for all the kind souls who have helped me and other newbies on this forum over the years, Thanks very much R team. - Original Message - From: Frank E Harrell Jr f.harr...@vanderbilt.edu To: Bill Pikounis billpikou...@gmail.com Cc: r-help@r-project.org Sent: Wednesday, January 07, 2009 2:25 PM Subject: Re: [R] R in the NY Times Bill Pikounis wrote: Pardon my exuberance, but this is simply awesome. What a treat to find on the front web page of the NY Times this morning under Technology. I think the article is very well written by the author, and I think it captures top highlights of why the software and community are so special. Continued high gratitude to all of R-core and the R community for its unique accomplishments. Every bit of praise is well-earned and deserved. I have continuously claimed to colleagues (primarily pharma industry) for the past 8 years or so that R is the most exciting going on in the area of statistics. Thanks, Bill Amen to that, and in addition, R is now the top tool for everyday analysis, not just a research statistician's tool. Frank Bill Pikounis Statistician On Wed, Jan 7, 2009 at 08:10, Zaslavsky, Alan M. zasla...@hcp.med.harvard.edu wrote: This article is accompanied by nice pictures of Robert and Ross. Data Analysts Captivated by Power of R http://www.nytimes.com/2009/01/07/technology/business-computing/07program.html January 7, 2009 Data Analysts Captivated by R's Power By ASHLEE VANCE __ 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. -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University __ 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] R in the NY Times
Zaslavsky, Alan M. wrote: This article is accompanied by nice pictures of Robert and Ross. Data Analysts Captivated by Power of R http://www.nytimes.com/2009/01/07/technology/business-computing/07program.html January 7, 2009 Data Analysts Captivated by R’s Power By ASHLEE VANCE SAS says it has noticed R’s rising popularity at universities, despite educational discounts on its own software, but it dismisses the technology as being of interest to a limited set of people working on very hard tasks. “I think it addresses a niche market for high-end data analysts that want free, readily available code, said Anne H. Milley, director of technology product marketing at SAS. She adds, “We have customers who build engines for aircraft. I am happy they are not using freeware when I get on a jet.” Thanks for posting. Does anyone else find the statement by SAS to be humourous yet arrogant and short-sighted? Kevin -- Kevin E. Thorpe Biostatistician/Trialist, Knowledge Translation Program Assistant Professor, Dalla Lana School of Public Health University of Toronto email: kevin.tho...@utoronto.ca Tel: 416.864.5776 Fax: 416.864.6057 __ 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 in the NY Times-IAsians perspective
R and its GUI Rattle helped me establish a data mining consulting startup on my own, without taking bank credit . People I met on the forum and especially books like rforsasandspssusers.com/ http://rforsasandspssusers.com/ helped me ease the transition to the new Object Oriented method from the earlier - even a monkey can create shakespeare if he types enough kind of analytics software. .Since I am in India , the cost differences can cause almost a digital divide in who can and who cant use sophisticated software. Thanks to the Angels hereYes we Can R... Regards, Ajay www.decisionstats.com On Wed, Jan 7, 2009 at 8:03 PM, Simon Pickett simon.pick...@bto.org wrote: I would like to add that I would have spent many more years doing my PhD if it wasnt for R! all data management, statistics and graphics were conducted using it. This was the direction my university and many more research institutes appear to be heading. It probably doesnt get said enough and I am sure I speak for all young researchers I am very much in debt for all the kind souls who have helped me and other newbies on this forum over the years, Thanks very much R team. - Original Message - From: Frank E Harrell Jr f.harr...@vanderbilt.edu To: Bill Pikounis billpikou...@gmail.com Cc: r-help@r-project.org Sent: Wednesday, January 07, 2009 2:25 PM Subject: Re: [R] R in the NY Times Bill Pikounis wrote: Pardon my exuberance, but this is simply awesome. What a treat to find on the front web page of the NY Times this morning under Technology. I think the article is very well written by the author, and I think it captures top highlights of why the software and community are so special. Continued high gratitude to all of R-core and the R community for its unique accomplishments. Every bit of praise is well-earned and deserved. I have continuously claimed to colleagues (primarily pharma industry) for the past 8 years or so that R is the most exciting going on in the area of statistics. Thanks, Bill Amen to that, and in addition, R is now the top tool for everyday analysis, not just a research statistician's tool. Frank Bill Pikounis Statistician On Wed, Jan 7, 2009 at 08:10, Zaslavsky, Alan M. zasla...@hcp.med.harvard.edu wrote: This article is accompanied by nice pictures of Robert and Ross. Data Analysts Captivated by Power of R http://www.nytimes.com/2009/01/07/technology/business-computing/07program.html January 7, 2009 Data Analysts Captivated by R's Power By ASHLEE VANCE __ 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. -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University __ 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. [[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 in the NY Times
on 01/07/2009 08:44 AM Kevin E. Thorpe wrote: Zaslavsky, Alan M. wrote: This article is accompanied by nice pictures of Robert and Ross. Data Analysts Captivated by Power of R http://www.nytimes.com/2009/01/07/technology/business-computing/07program.html January 7, 2009 Data Analysts Captivated by R’s Power By ASHLEE VANCE SAS says it has noticed R’s rising popularity at universities, despite educational discounts on its own software, but it dismisses the technology as being of interest to a limited set of people working on very hard tasks. “I think it addresses a niche market for high-end data analysts that want free, readily available code, said Anne H. Milley, director of technology product marketing at SAS. She adds, “We have customers who build engines for aircraft. I am happy they are not using freeware when I get on a jet.” Thanks for posting. Does anyone else find the statement by SAS to be humourous yet arrogant and short-sighted? Kevin It is an ignorant comment by a marketing person who has been spoon fed her lines...it is also a comment being made from a very defensive and insecure posture. Congrats to R Core and the R Community. This is yet another sign of R's growth and maturity. Regards, Marc Schwartz __ 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] Frailty by strata interactions in coxph ( or coxme)
Hello,
I was hoping that someone could answer a few questions for me (the background
is given below):
1) Can the coxph accept an interaction between a covariate and a frailty term
2) If so, is it possible to
a) test the model in which the covariate and the frailty appear as main terms
using the penalized likelihood (for gaussian/t frailties)
b)augment model 1) by stratifying on the variable that appers in the frailty
term ?
Thanks in advance! I apologise for sending this as html earlier today.
Chris Argyropoulos
University of Pittsburgh Medical Center
Background
-
I am trying to fit a cox proportional hazards model tothe data from a two arm
(treatment indicator is 0/1)
multicenter trial, adjusting for the presence of covariates and testing for the
presence of a center
(and possibly a treatment X center interaction effect).
I would like to contrast the different approaches discussed in Glidden D.V. and
Eric Vittinghoff. Modelling clustered survival data from multicentre clinical
trials. Stat Med 2004, 23:369-388 (DOI: 10.1002/sim. 1599). in this paper the
authors present a decomposition of the hazard function for the ith individual,
receiving Z(k,i) treatment (0-1) in the kth center as:
lambda(k,i)=lambda(0,k)*exp(b*Z(k,i)+om(k)*Z(k,i))
where om(k) = center specific effect - mean treatment effect ~ distributed as a
(log-) gamma or normal frailty.
I coded this model in R as:
r1-coxph(Surv(d,e)~treat*frailty(center)+othercovars+strata(center))
coxph produces a table with the coefficients and standard errors for:
a) the treatment variable
b) the covariates as well as
c) the treatment x frailty interaction effect.
but the main effect of frailty is estimated to be zero (which I expected, since
it is absorbed into the baseline hazards for the strata).
Am I correct to assume that coxph can in fact fit the model from the Stat Med
paper?
If coxph cannot fit such models, could I simply fit:
coxph(Surv(d,e)~treat*frailty(center)+othercovars),
and interpret the coefficient for interaction between treatment and frailty {
treat:frailty(center) }as in the first model?
If so, could one view the coefficient of the main effect of the frailty
component, as a random intercept and the interaction term
as a random slope in a general mixed effects Cox model?
Can coxme be used to fit these models in a cleaner way?
_
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Re: [R] about randomForest
Apologies for catching this so late. Have been out for a few weeks and still
trying to recover from that...
From: Jim Porzak
Hi Wanghong,
Unless you have a huge linux box, you will need to sample
down your 300k
rows to a few thousand.
In marketing aps, I often have data sets of comparable size.
I would suggest you start with a just a few k rows to make
sure everything
else is working as you wish. Also, study carefully Andy's
randomForest docs
- including the R News article a couple years ago.
In particular,
1) the formula interface is a memory hog. Andy suggests just
using explicit
declaration. In you case, something like
randomForest(Memebers[42], Memebers[-42], ...
Actually that first argument probably should be Members[[42]]. I believe you
get a data frame with one variable if you do Members[42].
Best,
Andy
2) proximity matirx is also memory time intensive. Suggest
proximity =
FALSE until, other things sorted out.
HTH,
Jim Porzak
TGN.com
San Francisco, CA
http://www.linkedin.com/in/jimporzak
useR Group SF: http://ia.meetup.com/67/
2008/12/26 wanghong wangh...@neusoft.edu.cn
hello,
I want to use randomForest to classify a matrix which is
331030¡Á42,the last
column is class signal.I use £º
Memebers.rf-randomForest(class~.,data=Memebers,proximity=TRUE
,mtry=6,ntree=200)
which told me the error is matrix(0,n,n) set too elements
then I use:
Memebers.rf-randomForest(class~.,data=Memebers,importance=TRU
E,proximity=TRUE)
which told methe error is na.fail.default(list(class =
c(17L, 17L, 17L,
29L, 29L, 29L, :
missing values in object
what's wrong with it .Thanks a lot
wanghong
wangh...@neusoft.edu.cn
2008-12-26
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[R] Extracting degrees of freedom from a gnls object
Dear all, How can I extract the total and residual d.f. from a gnls object? I have tried str(summary(gnls.model)) and str(gnls.model) as well as gnls(), but couldn´t find the entry in the resulting lists. Many thanks! Best wishes Christoph -- Dr. rer.nat. Christoph Scherber University of Goettingen DNPW, Agroecology Waldweg 26 D-37073 Goettingen Germany phone +49 (0)551 39 8807 fax +49 (0)551 39 8806 Homepage http://www.gwdg.de/~cscherb1 __ 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] NA and NaN question
Thanks, now I understand what's happening. Maybe a line explaining this could be added to the help text for mean? Pascal Niklaus On Wed 07-Jan-2009 13:29:25 Prof Brian Ripley wrote: Pascal A. Niklaus wrote: Hi all, I ran into a problem in some of my code that could be traced back to 'mean' sometimes returning NA and sometimes NaN, depending on the value of na.rm: mean(c()) [1] NA mean(c(NA),na.rm=T) [1] NaN However, I don't understand the reasoning behind this and would appreciate and explanation. I understand that the mean of an empty vector is not definied, Not so, it is well-defined as 0/0 = NaN. but I don't understand why it matters whether the vector was empty from the beginning You didn't try that case: mean(numeric(0)) is also NaN. The issue is that typeof(c()) [1] NULL is not numeric (not evan a vector), and so mean() of it is undefined. or only after removing the NAs. Speculation (and wrong). Pascal Niklaus __ 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] R Stacked Histogram
That worked! Thank you very much for the help.
I think I have one last question about qplot in ggplot2, That is exporting the
plot to JPG while in a loop. I tried what was recommended in Re: [R] jpeg()
creating empty files with qplot() in a loop, however, I received some errors
(see below). I also tried using a PDF, but that did not work either, i.e. the
PDF produced was blank. Oddly enough the results produced using
dev.print(file=qplot_output.jpg, device=jpeg, width=600) in a loop are
blank, i.e. the JPG file is there, but it is blank. Unfortunately,
ggsave(file=ggsave_qplot_output.jpg) does not even produce a JPG file
output. Any help at this point is greatly appreciated. Is the problem related
to the fact that I need to use the plain hist and dev.print prior to using
ggplot's qplot?
Thanks again for all your help.
for(jj in 0:4)
+ {
+ rnorm_test_data-rnorm(1000,3,6)
+ hist(rnorm_test_data)
+ dev.print(file=test_data.jpg, device=jpeg, width=600)
+
+ plot.new()
+ qplot(rnorm_test_data, geom = histogram, binwidth = 1) +
+ scale_x_continuous(Test Data) + scale_y_continuous(Frequency) +
+ scale_fill_discrete(qplot histogram)
+
+ # Print the plot to a JPG or PDF
+ dev.print(file=qplot_output.jpg, device=jpeg, width=600)
+ ggsave(file=ggsave_qplot_output.jpg)
+ ggsave(file = ggsave_qplot_output.pdf)
+
+ }
Saving 6.9 x 6.89 image
Error in get(as.character(FUN), mode = function, envir = envir) :
variable jpg of mode function was not found
g 6.9 x 6.89 image
Error in get(as.character(FUN), mode = function, envir = envir) :
variable jpg of mode function was not found
P.S. Here is the
sessionInfo()
R version 2.8.0 (2008-10-20)
i386-pc-mingw32
locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
States.1252;LC_MONETARY=English_United
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
attached base packages:
[1] grid stats graphics grDevices utils datasets methods
base
other attached packages:
[1] ggplot2_0.8.1 reshape_0.8.2 RColorBrewer_1.0-2
proto_0.3-8 plyr_0.1.4 nortest_1.0 fBasics_280.74
timeSeries_290.79
[9] timeDate_290.81 vcd_1.2-1 MASS_7.2-44 colorspace_1.0-0
--- On Tue, 1/6/09, ONKELINX, Thierry thierry.onkel...@inbo.be wrote:
From: ONKELINX, Thierry thierry.onkel...@inbo.be
Subject: RE: [R] R Stacked Histogram
To: jasonkrup...@yahoo.com, r-help@r-project.org
Date: Tuesday, January 6, 2009, 9:54 AM
Dear Jason,
Have a look at scale_y_continuous() and scale_fill_discrete(). This might work
(untested as your example is not reproducible with a (dummy) dataset).
qplot(Age, data = recerts_combined_values, binwidth = 5, fill =
combined_values$Test.Type, main=Combined Age Histogram) +
scale_x_continuous(Age, months) +
scale_y_continuous(Counts) + scale_fill_discrete(Type of
Tests)
HTH,
Thierry
ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Research Institute for Nature and
Forest
Cel biometrie, methodologie en kwaliteitszorg / Section biometrics, methodology
and quality assurance
Gaverstraat 4
9500 Geraardsbergen
Belgium
tel. + 32 54/436 185
thierry.onkel...@inbo.be
www.inbo.be
To call in the statistician after the experiment is done may be no more than
asking him to perform a post-mortem examination: he may be able to say what the
experiment died of.
~ Sir Ronald Aylmer Fisher
The plural of anecdote is not data.
~ Roger Brinner
The combination of some data and an aching desire for an answer does not ensure
that a reasonable answer can be extracted from a given body of data.
~ John Tukey
-Oorspronkelijk bericht-
Van: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] Namens
Jason Rupert
Verzonden: dinsdag 6 januari 2009 16:00
Aan: r-help@r-project.org
Onderwerp: Re: [R] R Stacked Histogram
Great advice. I did a quick read and came up with the following:
qplot(Age, data = recerts_combined_values, binwidth = 5,
fill = combined_values$Test.Type,
ylab=Counts, xlab=Age, months,
main=Combined Age Histogram,
legend.name = Type of Tests)
Unfortunatley, here is a description of the results:
(1) the main title font size by default is too large and is clipped
by the image (guess I need to figure out how to fix this),
(2) ylab appears to fail - it does not replace the default count
label - what should I do to fix this?
(3) like (2), neither using legend.name nor
legend.title appears to replace/change the name of the legend
title/name.
By any chance can you provide some advice for tackeling these items? These
are probably due to me being a noobie on the ggplot2 package.
Thanks again.
--- On Mon, 1/5/09, hadley wickham h.wick...@gmail.com wrote:
From: hadley wickham h.wick...@gmail.com
Subject: Re: [R] R Stacked
Re: [R] R Stacked Histogram
On Wed, Jan 7, 2009 at 7:55 AM, Jason Rupert jasonkrup...@yahoo.com wrote: That worked! Thank you very much for the help. I think I have one last question about qplot in ggplot2, That is exporting the plot to JPG while in a loop. I tried what was recommended in Re: [R] jpeg() creating empty files with qplot() in a loop, however, I received some errors (see below). I also tried using a PDF, but that did not work either, i.e. the PDF produced was blank. Oddly enough the results produced using dev.print(file=qplot_output.jpg, device=jpeg, width=600) in a loop are blank, i.e. the JPG file is there, but it is blank. Unfortunately, ggsave(file=ggsave_qplot_output.jpg) does not even produce a JPG file output. Any help at this point is greatly appreciated. Is the problem related to the fact that I need to use the plain hist and dev.print prior to using ggplot's qplot? If you're using ggsave, you don't need to use the dev functions. The following should be sufficient: qplot(rnorm_test_data, geom = histogram, binwidth = 1) + scale_x_continuous(Test Data) + scale_y_continuous(Frequency) + scale_fill_discrete(qplot histogram) ggsave(file = ggsave_qplot_output.pdf) # Unfortunately due to a small bug in the current version of ggplot, you need to use # jpeg with an e to get jpegs ggsave(file = ggsave_qplot_output.jpeg) # But I'd recommend using png instead - much better quality ggsave(file = ggsave_qplot_output.png) # One final problem is that you're going to overwrite the plot # on each run of your loop. You probably want something like: ggsave(file = paste(ggsave_qplot_output_, i, .png, sep =)) Hadley -- http://had.co.nz/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R in the NY Times
Thank you for posting this, I found it a very enjoyable read! I am curious, is there an archive of 'R in the Media' or 'R in the Press' articles somewhere? It would be interesting to see how the perception of R has changed/evolved over time relative to other packages. Cheers, Tony Breyal On 7 Jan, 13:10, Zaslavsky, Alan M. zasla...@hcp.med.harvard.edu wrote: This article is accompanied by nice pictures of Robert and Ross. Data Analysts Captivated by Power of R http://www.nytimes.com/2009/01/07/technology/business-computing/07pro... January 7, 2009 Data Analysts Captivated by R’s Power By ASHLEE VANCE To some people R is just the 18th letter of the alphabet. To others, it’s the rating on racy movies, a measure of an attic’s insulation or what pirates in movies say. R is also the name of a popular programming language used by a growing number of data analysts inside corporations and academia. It is becoming their lingua franca partly because data mining has entered a golden age, whether being used to set ad prices, find new drugs more quickly or fine-tune financial models. Companies as diverse as Google, Pfizer, Merck, Bank of America, the InterContinental Hotels Group and Shell use it. But R has also quickly found a following because statisticians, engineers and scientists without computer programming skills find it easy to use. “R is really important to the point that it’s hard to overvalue it,” said Daryl Pregibon, a research scientist at Google, which uses the software widely. “It allows statisticians to do very intricate and complicated analyses without knowing the blood and guts of computing systems.” It is also free. R is an open-source program, and its popularity reflects a shift in the type of software used inside corporations. Open-source software is free for anyone to use and modify. I.B.M., Hewlett-Packard and Dell make billions of dollars a year selling servers that run the open-source Linux operating system, which competes with Windows from Microsoft. Most Web sites are displayed using an open-source application called Apache, and companies increasingly rely on the open-source MySQL database to store their critical information. Many people view the end results of all this technology via the Firefox Web browser, also open-source software. R is similar to other programming languages, like C, Java and Perl, in that it helps people perform a wide variety of computing tasks by giving them access to various commands. For statisticians, however, R is particularly useful because it contains a number of built-in mechanisms for organizing data, running calculations on the information and creating graphical representations of data sets. Some people familiar with R describe it as a supercharged version of Microsoft’s Excel spreadsheet software that can help illuminate data trends more clearly than is possible by entering information into rows and columns. What makes R so useful — and helps explain its quick acceptance — is that statisticians, engineers and scientists can improve the software’s code or write variations for specific tasks. Packages written for R add advanced algorithms, colored and textured graphs and mining techniques to dig deeper into databases. Close to 1,600 different packages reside on just one of the many Web sites devoted to R, and the number of packages has grown exponentially. One package, called BiodiversityR, offers a graphical interface aimed at making calculations of environmental trends easier. Another package, called Emu, analyzes speech patterns, while GenABEL is used to study the human genome. The financial services community has demonstrated a particular affinity for R; dozens of packages exist for derivatives analysis alone. “The great beauty of R is that you can modify it to do all sorts of things,” said Hal Varian, chief economist at Google. “And you have a lot of prepackaged stuff that’s already available, so you’re standing on the shoulders of giants.” R first appeared in 1996, when the statistics professors Ross Ihaka and Robert Gentleman of the University of Auckland in New Zealand released the code as a free software package. According to them, the notion of devising something like R sprang up during a hallway conversation. They both wanted technology better suited for their statistics students, who needed to analyze data and produce graphical models of the information. Most comparable software had been designed by computer scientists and proved hard to use. Lacking deep computer science training, the professors considered their coding efforts more of an academic game than anything else. Nonetheless, starting in about 1991, they worked on R full time. “We were pretty much inseparable for five or six years,” Mr. Gentleman said. “One person would do the typing and one person would do the thinking.” Some statisticians who took
[R] Question about the RWEKA package
Dear List, I´m trying to implement the functionalities from WEKA into my modeling project in R through the RWeka package. In this context I have a slightly special question about the filters implemented in WEKA. I want to convert nominal attributes with k values into k binary attributes through the NominalToBinary filter (weka.filters.supervised.attribute.NominalToBinary). But unfortunately I can`t apply the filter to my data. Here is my code: nombi - make_Weka_filter(weka/filters/supervised/attribute/NominalToBinary) x2bin - nombi(data=dat, control =Weka_control(N=TRUE, A=TRUE)) I didn't get an error message, but it still don't work. My nominal attribute is of class factor. Maybe the problem has to do with the argument list. Argument list: (formula, data, subset, na.action, control = NULL) What is meant with the argument formula? Any advice? I`d be glad for any hint! I`m using R 2.7.2 and RWEKA 0.3-14 TIM --- Dipl.-Geogr. Tim Häring Sachgebiet Standort und Bodenschutz (SG 2.1) Bayerische Landesanstalt für Wald und Forstwirtschaft Am Hochanger 11 D-85354 Freising E-Mail: tim.haer...@lwf.bayern.de http://www.lwf.bayern.de [[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] Extracting degrees of freedom from a gnls object
on 01/07/2009 09:01 AM Christoph Scherber wrote: Dear all, How can I extract the total and residual d.f. from a gnls object? I have tried str(summary(gnls.model)) and str(gnls.model) as well as gnls(), but couldn´t find the entry in the resulting lists. Many thanks! Best wishes Christoph Using the example from ?gnls: library(nlme) fm1 - gnls(weight ~ SSlogis(Time, Asym, xmid, scal), Soybean, weights = varPower()) fm1 Generalized nonlinear least squares fit Model: weight ~ SSlogis(Time, Asym, xmid, scal) Data: Soybean Log-likelihood: -486.8974 Coefficients: Asym xmid scal 17.356822 51.872316 7.620525 Variance function: Structure: Power of variance covariate Formula: ~fitted(.) Parameter estimates: power 0.8815436 Degrees of freedom: 412 total; 409 residual Residual standard error: 0.3662752 When reviewing the structure of the 'fm1' object in comparison to the output, you can see that the d.f. are stored in: fm1$dims $p [1] 3 $N [1] 412 $REML [1] FALSE So: fm1$dims$N [1] 412 and: fm1$dims$N - fm1$dims$p [1] 409 If you are unsure about where things are stored, one approach is to look at the code for the print method for the object class to see how the output is generated. In this case it is print.gls(), as a gnls object inherits from a gls object. Thus, reviewing the apropos snippet from nlme:::print.gls(): cat(Degrees of freedom:, dd[[N]], total;, dd[[N]] - dd[[p]], residual\n) where 'dd' is created earlier in the function as: dd - x$dims This is also covered in ?gnlsObject, which shows: dimsa list with basic dimensions used in the model fit, including the components N - the number of observations used in the fit and p - the number of coefficients in the nonlinear model. HTH, Marc Schwartz __ 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 in the NY Times
Zaslavsky, Alan M. wrote: This article is accompanied by nice pictures of Robert and Ross. Data Analysts Captivated by Power of R http://www.nytimes.com/2009/01/07/technology/business-computing/07program.html Thanks for the heads up. The R morale is going through the roof! I've given three courses on R since the second half of 2007 here in Chile (geostatistics, Fisheries Libraries for R, and generalized linear models) and all my three audiences (professionals working in academia, government, and private research institutions) were very much impressed by the power of R. I spent as much time on R itself as on the statistical topics, since students wanted to learn data management and graphics once they started to grasp the basic elements. R creators, Core Team, package creators and maintainers, and experts on the list, thanks so much for such a great work and such an open attitude. You lead by example. Rubén __ 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 in the NY Times
The article quotes John Chambers, but it doesn't mention that R started out as an implementation of the S language. I don't suppose Insightful is too happy about that. The SAS spokesman quoted in the article is clearly whistling past the graveyard. -- Jeff __ 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 in the NY Times
On Wed, Jan 07, 2009 at 08:00:28AM -0600, Frank E Harrell Jr wrote: This is great to see. It's interesting that SAS Institute feels that non-peer-reviewed software with hidden implementations of analytic methods that cannot be reproduced by others should be trusted when building aircraft engines. Frank Unfortunately, that type of FUD issued by the SAS marketing person still works. I see it at my employer (a large healthcare company.) It's a battle to change a culture, but ironically the recession helps. People are now taking notice of the obscene licensing fees for SAS. Darin __ 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 in the NY Times
On 1/7/2009 9:44 AM, Kevin E. Thorpe wrote: Zaslavsky, Alan M. wrote: This article is accompanied by nice pictures of Robert and Ross. Data Analysts Captivated by Power of R http://www.nytimes.com/2009/01/07/technology/business-computing/07program.html January 7, 2009 Data Analysts Captivated by R’s Power By ASHLEE VANCE SAS says it has noticed R’s rising popularity at universities, despite educational discounts on its own software, but it dismisses the technology as being of interest to a limited set of people working on very hard tasks. “I think it addresses a niche market for high-end data analysts that want free, readily available code, said Anne H. Milley, director of technology product marketing at SAS. She adds, “We have customers who build engines for aircraft. I am happy they are not using freeware when I get on a jet.” Thanks for posting. Does anyone else find the statement by SAS to be humourous yet arrogant and short-sighted? To me it just seemed like a blast from the past. Duncan Murdoch __ 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] rbind for matrices - rep argument
Dear R users,I'm facing a trivial problem, but I really can't solve it. I've tried a dozen of codes, but I can't get the result I want. The question is: I have a dataframe like this one [,1] [,2] [,3] [,4] [,5] [1,]12345 [2,]25549 [3,]16812 [4,]86415 made up of decimal numbers, of course. I want to append this dataframe to itself a number x of times, i.e. 3. That is I want a dataframe like this [,1] [,2] [,3] [,4] [,5] [1,]12345 [2,]25549 [3,]16812 [4,]86415 [5,]12345 [6,]25549 [7,]16812 [8,]86415 [9,]12345 [10,]25549 [11,]16812 [12,]86415 I'm searching for an authomatic way to do this (I've already used the rbind re-writing x times the name of the frame...), as it must enter a function where one argument is exactly the number x of times to repeat this frame. Any ideas?? Thanks in advance! Niccolò [[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 in the NY Times
Jeffrey J. Hallman wrote: The article quotes John Chambers, but it doesn't mention that R started out as an implementation of the S language. I don't suppose Insightful is too happy about that. You mean Tibco... The statement that S failed to generate broad interest is also a bit misleading. I believe S-PLUS had more than 10 users in its day, although it may be true that its success was mainly in the academic world. Obviously the pool of people who knew S from the preceding decade was very important for the early development of R. -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - (p.dalga...@biostat.ku.dk) FAX: (+45) 35327907 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R in the NY Times
You can look on the SAS message boards and see there is a proportional downturn in traffic. I think that I actually made this statement about both the SAS and Splus traffic... I wasn't really trying to be critical of SAS. I was trying to get across that SAS focused their resources on features that had nothing to do with *statistical analysis* (e.g. data warehousing etc.) -- Max __ 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] rbind for matrices - rep argument
you can use indexing, e.g., mat - matrix(rnorm(20), 4, 5) mat mat[rep(1:nrow(mat), 3), ] I hope it helps. Best, Dimitris Niccolò Bassani wrote: Dear R users,I'm facing a trivial problem, but I really can't solve it. I've tried a dozen of codes, but I can't get the result I want. The question is: I have a dataframe like this one [,1] [,2] [,3] [,4] [,5] [1,]12345 [2,]25549 [3,]16812 [4,]86415 made up of decimal numbers, of course. I want to append this dataframe to itself a number x of times, i.e. 3. That is I want a dataframe like this [,1] [,2] [,3] [,4] [,5] [1,]12345 [2,]25549 [3,]16812 [4,]86415 [5,]12345 [6,]25549 [7,]16812 [8,]86415 [9,]12345 [10,]25549 [11,]16812 [12,]86415 I'm searching for an authomatic way to do this (I've already used the rbind re-writing x times the name of the frame...), as it must enter a function where one argument is exactly the number x of times to repeat this frame. Any ideas?? Thanks in advance! Niccolò [[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. -- Dimitris Rizopoulos Assistant Professor Department of Biostatistics Erasmus Medical Center Address: PO Box 2040, 3000 CA Rotterdam, the Netherlands Tel: +31/(0)10/7043478 Fax: +31/(0)10/7043014 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Replace Function (How to replace numbers in a data frame with a specific number)
taxa - (structure(list(Date = structure(c(4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L), .Label = c(2006/04, 2006/05, 2006/07, 2006/10, 2006/12, 2007/02, 2007/04, 2007/06, 2007/08, 2007/10, 2007/12, 2008/01), class = factor), RiverMile = c(61L, 119L, 148L, 179L, 185L, 187L, 190L, 196L, 198L, 202L, 215L, 61L, 119L, 148L, 179L, 185L, 187L, 190L, 196L, 198L), Site = structure(c(9L, 1L, 2L, 3L, 4L, 10L, 5L, 11L, 6L, 7L, 8L, 9L, 1L, 2L, 3L, 4L, 10L, 5L, 11L, 6L ), .Label = c(119, 148, 179, 185, 190, 198, 202, 215, 61, BC, HC, SC), class = factor), location = structure(c(2L, 2L, 2L, 2L, 2L, 1L, 2L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 2L, 1L, 2L), .Label = c(creek, river), class = factor), Amphipoda = c(0, 0, 0, 1, 0, 1, 1, 0, 1, 1, 1, 0, 0, 0, 1, 0, 1, 1, 0, 1), Coleoptera = c(1, 1, 4, 1, 0, 1, 1, 2, 1, 2, 0, 0, 0, 1, 1, 0, 0, 0, 2, 1), Decapoda = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1), Diptera = c(6, 6, 14, 3, 16, 10, 12, 0, 3, 9, 6, 5, 3, 10, 0, 9, 3, 11, 2, 8), Ephemeroptera = c(5, 6, 4, 1, 3, 1, 3, 1, 0, 2, 0, 2, 2, 2, 0, 0, 0, 0, 1, 0)), .Names = c(Date, RiverMile, Site, location, Amphipoda, Coleoptera, Decapoda, Diptera, Ephemeroptera), row.names = c(61 2006/10, 119 2006/10, 148 2006/10, 179 2006/10, 185 2006/10, BC 2006/10, 190 2006/10, HC 2006/10, 198 2006/10, 202 2006/10, 215 2006/10, 61 2006/12, 119 2006/12, 148 2006/12, 179 2006/12, 185 2006/12, BC 2006/12, 190 2006/12, HC 2006/12, 198 2006/12), class = c(cast_df, data.frame))) replace(taxa, taxa0, 1) #Is preforms as I would like except that I only want to do this on columns 5:19 and I can't just use replace(taxa, taxa[,5:19]0, 1) #any suggestions Stephen Sefick -- Stephen Sefick Let's not spend our time and resources thinking about things that are so little or so large that all they really do for us is puff us up and make us feel like gods. We are mammals, and have not exhausted the annoying little problems of being mammals. -K. Mullis __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] rbind for matrices - rep argument
Try this: m[rep(seq_len(nrow(m)), 3),] On Wed, Jan 7, 2009 at 1:22 PM, Niccolò Bassani biostatist...@gmail.comwrote: Dear R users,I'm facing a trivial problem, but I really can't solve it. I've tried a dozen of codes, but I can't get the result I want. The question is: I have a dataframe like this one [,1] [,2] [,3] [,4] [,5] [1,]12345 [2,]25549 [3,]16812 [4,]86415 made up of decimal numbers, of course. I want to append this dataframe to itself a number x of times, i.e. 3. That is I want a dataframe like this [,1] [,2] [,3] [,4] [,5] [1,]12345 [2,]25549 [3,]16812 [4,]86415 [5,]12345 [6,]25549 [7,]16812 [8,]86415 [9,]12345 [10,]25549 [11,]16812 [12,]86415 I'm searching for an authomatic way to do this (I've already used the rbind re-writing x times the name of the frame...), as it must enter a function where one argument is exactly the number x of times to repeat this frame. Any ideas?? Thanks in advance! Niccolò [[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 [[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] rbind for matrices - rep argument
Dimitris Rizopoulos d.rizopoulos at erasmusmc.nl writes:
you can use indexing, e.g.,
mat - matrix(rnorm(20), 4, 5)
mat
mat[rep(1:nrow(mat), 3), ]
I hope it helps.
Best,
Dimitris
or matrix trickery:
z - as.data.frame(matrix(sample(1:9,20,replace=TRUE),nrow=4))
matrix(rep(as.matrix(z),3),ncol=ncol(z),byrow=TRUE)
I do sometimes wish there were a more generic Rep() defined as
Rep - function(x,n) {
result - list()
for (i in 1:n) {
result[[i]] - x
}
result
}
then one could say do.call(rbind,Rep(x,3))
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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] rbind for matrices - rep argument
On Wed, 2009-01-07 at 16:22 +0100, Niccolò Bassani wrote: Dear R users,I'm facing a trivial problem, but I really can't solve it. I've tried a dozen of codes, but I can't get the result I want. The question is: I have a dataframe like this one [,1] [,2] [,3] [,4] [,5] [1,]12345 [2,]25549 [3,]16812 [4,]86415 made up of decimal numbers, of course. I want to append this dataframe to itself a number x of times, i.e. 3. That is I want a dataframe like this [,1] [,2] [,3] [,4] [,5] [1,]12345 [2,]25549 [3,]16812 [4,]86415 [5,]12345 [6,]25549 [7,]16812 [8,]86415 [9,]12345 [10,]25549 [11,]16812 [12,]86415 I'm searching for an authomatic way to do this (I've already used the rbind re-writing x times the name of the frame...), as it must enter a function where one argument is exactly the number x of times to repeat this frame. Any ideas?? Thanks in advance! Hello, If your matrix is kk - matrix( 1:16, 4, 4) You can do kkk - lapply( 1:5, function(x) kk ) do.call(rbind, kkk) You can write your code in a single line, though. I used 5 here as a matter of example. You can build a function on these lines with an arbitrary argument if need be. Carlos J. Gil Bellosta http://www.datanalytics.com Niccol [[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.
[R] Cannot access packages
Although I have installed R many times on many machines without problems, I have recently encountered a problem with accessing packages. R has been installed successfully with the --internet2 option. The session info is below. sessionInfo() R version 2.8.1 (2008-12-22) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] tools_2.8.1 When I try to load a package (chron in this example) from the CMU mirror, I get the following error message: utils:::menuInstallPkgs() --- Please select a CRAN mirror for use in this session --- trying URL 'http://lib.stat.cmu.edu/R/CRAN/bin/windows/contrib/2.8/chron_2.3-28.zip' Error in download.file(url, destfile, method, mode = wb, ...) : cannot open URL 'http://lib.stat.cmu.edu/R/CRAN/bin/windows/contrib/2.8/chron_2.3-28.zip' In addition: Warning message: In download.file(url, destfile, method, mode = wb, ...) : cannot open: HTTP status was '403 Forbidden (Blocked by NG)' Warning in download.packages(p0, destdir = tmpd, available = available, : download of package 'chron' failed This error applies to ANY package. The option --internet2 must be used. If not, then I cannot even access the mirror. Can anyone help me out? Could this be a firewall problem? Joe [[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] Replace Function (How to replace numbers in a data frame with a specific number)
very good thanks On Wed, Jan 7, 2009 at 11:18 AM, Henrique Dallazuanna www...@gmail.com wrote: Try this: taxa[, 5:9][taxa[,5:9] 0] - 1 On Wed, Jan 7, 2009 at 1:36 PM, stephen sefick ssef...@gmail.com wrote: taxa - (structure(list(Date = structure(c(4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L), .Label = c(2006/04, 2006/05, 2006/07, 2006/10, 2006/12, 2007/02, 2007/04, 2007/06, 2007/08, 2007/10, 2007/12, 2008/01), class = factor), RiverMile = c(61L, 119L, 148L, 179L, 185L, 187L, 190L, 196L, 198L, 202L, 215L, 61L, 119L, 148L, 179L, 185L, 187L, 190L, 196L, 198L), Site = structure(c(9L, 1L, 2L, 3L, 4L, 10L, 5L, 11L, 6L, 7L, 8L, 9L, 1L, 2L, 3L, 4L, 10L, 5L, 11L, 6L ), .Label = c(119, 148, 179, 185, 190, 198, 202, 215, 61, BC, HC, SC), class = factor), location = structure(c(2L, 2L, 2L, 2L, 2L, 1L, 2L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 2L, 1L, 2L), .Label = c(creek, river), class = factor), Amphipoda = c(0, 0, 0, 1, 0, 1, 1, 0, 1, 1, 1, 0, 0, 0, 1, 0, 1, 1, 0, 1), Coleoptera = c(1, 1, 4, 1, 0, 1, 1, 2, 1, 2, 0, 0, 0, 1, 1, 0, 0, 0, 2, 1), Decapoda = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1), Diptera = c(6, 6, 14, 3, 16, 10, 12, 0, 3, 9, 6, 5, 3, 10, 0, 9, 3, 11, 2, 8), Ephemeroptera = c(5, 6, 4, 1, 3, 1, 3, 1, 0, 2, 0, 2, 2, 2, 0, 0, 0, 0, 1, 0)), .Names = c(Date, RiverMile, Site, location, Amphipoda, Coleoptera, Decapoda, Diptera, Ephemeroptera), row.names = c(61 2006/10, 119 2006/10, 148 2006/10, 179 2006/10, 185 2006/10, BC 2006/10, 190 2006/10, HC 2006/10, 198 2006/10, 202 2006/10, 215 2006/10, 61 2006/12, 119 2006/12, 148 2006/12, 179 2006/12, 185 2006/12, BC 2006/12, 190 2006/12, HC 2006/12, 198 2006/12), class = c(cast_df, data.frame))) replace(taxa, taxa0, 1) #Is preforms as I would like except that I only want to do this on columns 5:19 and I can't just use replace(taxa, taxa[,5:19]0, 1) #any suggestions Stephen Sefick -- Stephen Sefick Let's not spend our time and resources thinking about things that are so little or so large that all they really do for us is puff us up and make us feel like gods. We are mammals, and have not exhausted the annoying little problems of being mammals. -K. Mullis __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O -- Stephen Sefick Let's not spend our time and resources thinking about things that are so little or so large that all they really do for us is puff us up and make us feel like gods. We are mammals, and have not exhausted the annoying little problems of being mammals. -K. Mullis __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Replace Function (How to replace numbers in a data frame with a specific number)
Try this: taxa[, 5:9][taxa[,5:9] 0] - 1 On Wed, Jan 7, 2009 at 1:36 PM, stephen sefick ssef...@gmail.com wrote: taxa - (structure(list(Date = structure(c(4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L), .Label = c(2006/04, 2006/05, 2006/07, 2006/10, 2006/12, 2007/02, 2007/04, 2007/06, 2007/08, 2007/10, 2007/12, 2008/01), class = factor), RiverMile = c(61L, 119L, 148L, 179L, 185L, 187L, 190L, 196L, 198L, 202L, 215L, 61L, 119L, 148L, 179L, 185L, 187L, 190L, 196L, 198L), Site = structure(c(9L, 1L, 2L, 3L, 4L, 10L, 5L, 11L, 6L, 7L, 8L, 9L, 1L, 2L, 3L, 4L, 10L, 5L, 11L, 6L ), .Label = c(119, 148, 179, 185, 190, 198, 202, 215, 61, BC, HC, SC), class = factor), location = structure(c(2L, 2L, 2L, 2L, 2L, 1L, 2L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 2L, 1L, 2L), .Label = c(creek, river), class = factor), Amphipoda = c(0, 0, 0, 1, 0, 1, 1, 0, 1, 1, 1, 0, 0, 0, 1, 0, 1, 1, 0, 1), Coleoptera = c(1, 1, 4, 1, 0, 1, 1, 2, 1, 2, 0, 0, 0, 1, 1, 0, 0, 0, 2, 1), Decapoda = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1), Diptera = c(6, 6, 14, 3, 16, 10, 12, 0, 3, 9, 6, 5, 3, 10, 0, 9, 3, 11, 2, 8), Ephemeroptera = c(5, 6, 4, 1, 3, 1, 3, 1, 0, 2, 0, 2, 2, 2, 0, 0, 0, 0, 1, 0)), .Names = c(Date, RiverMile, Site, location, Amphipoda, Coleoptera, Decapoda, Diptera, Ephemeroptera), row.names = c(61 2006/10, 119 2006/10, 148 2006/10, 179 2006/10, 185 2006/10, BC 2006/10, 190 2006/10, HC 2006/10, 198 2006/10, 202 2006/10, 215 2006/10, 61 2006/12, 119 2006/12, 148 2006/12, 179 2006/12, 185 2006/12, BC 2006/12, 190 2006/12, HC 2006/12, 198 2006/12), class = c(cast_df, data.frame))) replace(taxa, taxa0, 1) #Is preforms as I would like except that I only want to do this on columns 5:19 and I can't just use replace(taxa, taxa[,5:19]0, 1) #any suggestions Stephen Sefick -- Stephen Sefick Let's not spend our time and resources thinking about things that are so little or so large that all they really do for us is puff us up and make us feel like gods. We are mammals, and have not exhausted the annoying little problems of being mammals. -K. Mullis __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O [[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 in the NY Times
On Wed, Jan 7, 2009 at 6:39 AM, Tony Breyal tony.bre...@googlemail.com wrote: Thank you for posting this, I found it a very enjoyable read! I am curious, is there an archive of 'R in the Media' or 'R in the Press' articles somewhere? It would be interesting to see how the perception of R has changed/evolved over time relative to other packages. That's a great idea, and I just created an Rmedia category on the REvolutions R blog to track exactly such articles. You can find it here: http://blog.revolution-computing.com/rmedia/ If anyone knows of any other mainstream articles about R available online please let me know, and I'll do a round-up post in that section to make sure they're captured. By the way, we're writing about R and issues related to R daily at: http://blog.revolution-computing.com # David Smith -- David M Smith da...@revolution-computing.com Director of Community, REvolution Computing www.revolution-computing.com Tel: +1 (206) 577-4778 x3203 (Seattle, USA) __ 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 in the NY Times
I believe the SAS person shot themselves in the foot more in more ways than one. In my mind, the reason you would pay, as Frank said, for non-peer-reviewed software with hidden implementations of analytic methods that cannot be reproduced by others Would be so that you can sue them later when a software problem in the designing of the engine makes your plane fall out of the sky! Bryan * Bryan Hanson Professor of Chemistry Biochemistry DePauw University, Greencastle IN USA ³I think it addresses a niche market for high-end data analysts that want free, readily available code, said Anne H. Milley, director of technology product marketing at SAS. She adds, ³We have customers who build engines for aircraft. I am happy they are not using freeware when I get on a jet.² Thanks for posting. Does anyone else find the statement by SAS to be humourous yet arrogant and short-sighted? Kevin __ 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 with ggplot2 - facet_wrap and boxplot
Hello R users and Hadley, Back again with a little problem in ggplot2 =o) (ggplot 0.8.1, R 2.8.0) Here the problem : library(ggplot2) df - data.frame(id = 1:100, x1 = c(rnorm(50), rnorm(50, 1)), x2 = c(rnorm(50), rnorm(50, 1.5)), x3 = c(rnorm(50, 0.5), rnorm(50, 2.5)), group = as.factor(rep(c(a, b), each = 50))) df.melt - melt(df, id = c(id, group)) head(df.melt) p - ggplot(df.melt, aes(variable, value)) p + geom_boxplot(aes(fill = group)) # This graph is great, but I would like to have two panels, one for group 'a', and one for group 'b' # With this code, I can't have one boxplot for each variable x1, x2 and x3 p + geom_boxplot(aes(fill = group)) + facet_wrap(~group) # but it's working with geom_point p + geom_point(aes(color = group)) + facet_wrap(~group) Best regards. david [[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] heatmap.2 and three colours for specific ran gesþ
a-matrix(rnorm(36,1,3),6,6) ifelse(a(-1),1,ifelse(a=1a=-1,2,3)) heatmap.2(a, col=rev(redgreen(3))) HTH -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Daren Tan Sent: January 6, 2009 11:53 PM To: r-help@r-project.org Subject: [R] heatmap.2 and three colours for specific rangesþ Hi, I hope to show a heatmap with thre colours, no gradation. How to specify heatmap.2 to map green for values less than -1, gray for values between -1 and 1, and red for values greater than 1 ? Thanks [[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] R in the NY Times
I would also point out that the use of the term freeware as opposed to FOSS by the SAS rep, comes off as being unprofessional and deliberately condescending... The author of the article, to his credit, was pretty consistent in using open source terminology. Regards, Marc on 01/07/2009 10:26 AM Bryan Hanson wrote: I believe the SAS person shot themselves in the foot more in more ways than one. In my mind, the reason you would pay, as Frank said, for non-peer-reviewed software with hidden implementations of analytic methods that cannot be reproduced by others Would be so that you can sue them later when a software problem in the designing of the engine makes your plane fall out of the sky! __ 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] smoothed contour lines
Here is one possible approach to get you started (this is not a final answer):
x - seq(-3,3)
y - seq(-3,3)
z - outer(x,y, function(x,y,...) x^2 + y^2 )
tmp - contourLines(x,y,z)
contour(x,y,z, lty=0)
lapply(tmp, function(l) {
x - l$x
y - l$y
if( length(x) 2 ){
if( isTRUE( all.equal( c(x[1],y[1]),
c(x[length(x)],y[length(y)] {
xspline(x[-1],y[-1], -1, FALSE)
} else {
xspline(x, y, -1, TRUE)
}
} else {
lines(x,y) # or whatever else should go here
}
} )
You can play with the settings to xspline to control the properties of the
curves, also it will look better if you thin some of the points from
contourLines (the points that are nearly identical cause the small loops).
Hope this helps,
--
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
greg.s...@imail.org
801.408.8111
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-
project.org] On Behalf Of Andrea Storto
Sent: Tuesday, January 06, 2009 9:52 AM
To: r-help@r-project.org
Subject: [R] smoothed contour lines
Hi all,
I'm trying to draw a contour plot
with rounded (smoothed) contour lines instead of sharp angles;
when the grid consists of only a few points
in x- and y- axis, the resulting contour
is in facts rather ugly since very sharp angles may appear.
I did not find any way to do it,
by using either contour or contourplot (from the lattice package),
I wonder if there exist a way for smoothing the angles,
apart from artificially increasing the grid resolution,
Thanks in advance
Andrea
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Re: [R] Question about the RWEKA package
On Wed, 7 Jan 2009, Häring, Tim (LWF) wrote: Dear List, I´m trying to implement the functionalities from WEKA into my modeling project in R through the RWeka package. In this context I have a slightly special question about the filters implemented in WEKA. I want to convert nominal attributes with k values into k binary attributes through the NominalToBinary filter (weka.filters.supervised.attribute.NominalToBinary). But unfortunately I can`t apply the filter to my data. Here is my code: nombi - make_Weka_filter(weka/filters/supervised/attribute/NominalToBinary) x2bin - nombi(data=dat, control =Weka_control(N=TRUE, A=TRUE)) I didn't get an error message, but it still don't work. My nominal attribute is of class factor. I do get a warning or an error, depending on what dat is exactly... Maybe the problem has to do with the argument list. Argument list: (formula, data, subset, na.action, control = NULL) What is meant with the argument formula? You need to supply formulas for filters, specifying which variables should be involved. For unsupervised filters, such as Normalize(), this is not very intuitive, but for supervised filters like Discretize() or your nombi() it seems quite natural. See help(Discretize, package = RWeka) for an example. hth, Z Any advice? I`d be glad for any hint! I`m using R 2.7.2 and RWEKA 0.3-14 TIM --- Dipl.-Geogr. Tim Häring Sachgebiet Standort und Bodenschutz (SG 2.1) Bayerische Landesanstalt für Wald und Forstwirtschaft Am Hochanger 11 D-85354 Freising E-Mail: tim.haer...@lwf.bayern.de http://www.lwf.bayern.de [[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 Threatens SAS According to The NYT
MM == Martin Maechler maech...@stat.math.ethz.ch on Wed, 7 Jan 2009 14:18:24 +0100 writes: [..] MM At the bottom of the page it says MM __ A version of this article appeared in print on MM January 7, 2009, __ on page B6 of the New York edition. MM Now if any the NYT (print version) subscribers on R-help MM are willing to fulfill a New Year's wish for me, I'd be MM very grateful for a (digital scan) copy of that page. MM Martin Maechler, ETH Zurich Just to let you know: As often, I'm overwhelmed by the helpfulness of several R-help readers in this issue, and I'm already expecting more than one copy. Thank you very much in advance! Martin MM [..] Thought you might be interested in reading this article, which appears in the 1/6/9 online edition of The New York Times: http://www.nytimes.com/2009/01/07/technology/business-computing/07program.html The headline is Data Analysts Captivated by R's Power, [] __ 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 with ggplot2 - facet_wrap and boxplot
Hi David, Here the problem : library(ggplot2) df - data.frame(id = 1:100, x1 = c(rnorm(50), rnorm(50, 1)), x2 = c(rnorm(50), rnorm(50, 1.5)), x3 = c(rnorm(50, 0.5), rnorm(50, 2.5)), group = as.factor(rep(c(a, b), each = 50))) df.melt - melt(df, id = c(id, group)) head(df.melt) p - ggplot(df.melt, aes(variable, value)) p + geom_boxplot(aes(fill = group)) # This graph is great, but I would like to have two panels, one for group 'a', and one for group 'b' # With this code, I can't have one boxplot for each variable x1, x2 and x3 p + geom_boxplot(aes(fill = group)) + facet_wrap(~group) # but it's working with geom_point p + geom_point(aes(color = group)) + facet_wrap(~group) This is an annoying bug I haven't figure out how to fix yet. The basic problem is that if you facet by a variable that has the same name as an aesthetic, it overrides that aesthetic (group in this case). Unfortunately, currently the only work around is call the variable something other than group. Regards, Hadley -- http://had.co.nz/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Multinomial Logit Model
I'm attempting to creat multinomial logistic regression model using the following code: mlogit- vglm(ME ~ HIST,family=multinomial(),na.action = na.pass) ME (dependent variable) has three levels (0,1,2) How do I declare a reference outcome (either 0,1,2)? __ 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 in the NY Times
Unfortunately, that type of FUD issued by the SAS marketing person still works. I see it at my employer (a large healthcare company.) It's a battle to change a culture, but ironically the recession helps. People are now taking notice of the obscene licensing fees for SAS. Darin I agree. I work for a consulting firm (human services) and my boss prefers us to use SPSS, rather than R. It's painful. I have version 11 installed on my Windows laptop. Next year, the license expires! For someone coming from a SPSS background, R is a little mind-blowing, simply because it is so much more powerful. But, perseverance pays off. Once I master Sweave and such, I'll be able to churn out reports much more quickly than I ever could with SPSS. I do wish the author of the article had included comments from SPSS, in addition to the humorous FUD from the SAS spokesperson. Newer versions of SPSS actually have the option of using R for data analysis, in addition to the SPSS engine. It would have been interesting to compare the corporate responses of the two companies. -- Insert something humorous here. :-) __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] rbind for matrices - rep argument
On 07-Jan-09 15:22:57, Niccolò Bassani wrote:
Dear R users,I'm facing a trivial problem, but I really can't solve it.
I've tried a dozen of codes, but I can't get the result I want.
The question is: I have a dataframe like this one
[,1] [,2] [,3] [,4] [,5]
[1,]12345
[2,]25549
[3,]16812
[4,]86415
made up of decimal numbers, of course.
I want to append this dataframe to itself a number x of times, i.e. 3.
That is I want a dataframe like this
[,1] [,2] [,3] [,4] [,5]
[1,]12345
[2,]25549
[3,]16812
[4,]86415
[5,]12345
[6,]25549
[7,]16812
[8,]86415
[9,]12345
[10,]25549
[11,]16812
[12,]86415
I'm searching for an authomatic way to do this (I've already used the
rbind re-writing x times the name of the frame...), as it must enter a
function where one argument is exactly the number x of times to repeat
this frame.
Any ideas??
Thanks in advance!
Niccolò
I don't know whether there is anywhere a ready-made function which
will implement a rep paramater for an rbind, but the following ad-hoc
function will do it for you efficiently (i.e. with the minimum number
of applications of the rbind() function).
To produce a result which consists of k replicates of x, row-bound:
Krbind - function(x,k){
y - x
if(k==1) return(x)
p - floor(log2(k))
for(i in (1:p)){
z - rbind(y,y)
y - z
}
k - (k - 2^p)
if(k==0) return(y) else return(rbind(y,Krbind(x,k)))
}
## Example:
Xdf - data.frame(X1=c(1.1,1.2),X2=c(2.1,2.2),
X3=c(3.1,3.2),X4=c(4.1,4.2))
Krbind(Xdf,6)
# X1 X2 X3 X4
# 1 1.1 2.1 3.1 4.1
# 2 1.2 2.2 3.2 4.2
# 3 1.1 2.1 3.1 4.1
# 4 1.2 2.2 3.2 4.2
# 5 1.1 2.1 3.1 4.1
# 6 1.2 2.2 3.2 4.2
# 7 1.1 2.1 3.1 4.1
# 8 1.2 2.2 3.2 4.2
# 9 1.1 2.1 3.1 4.1
# 10 1.2 2.2 3.2 4.2
# 11 1.1 2.1 3.1 4.1
# 12 1.2 2.2 3.2 4.2
Of course, if you're not worried by efficiency, then the simple loop
y - x
for(i in (1:(k-1))){y - rbind(y,x)}
will do it!
Hoping this helps,
Ted.
E-Mail: (Ted Harding) ted.hard...@manchester.ac.uk
Fax-to-email: +44 (0)870 094 0861
Date: 07-Jan-09 Time: 18:08:14
-- XFMail --
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] R Stacked Histogram
Sweet! The missing e. That was it! Yeah! Thanks again. I guess I will get some sleep tonight. Well, one last questions about stack plot (please forgive the lame example below). I thought the below allow me to resize the the title of the stacked histogram, but no luck. Any suggestions as to the modificaiton necessary to get it to work? Right now the title is obscured by the plot and my boss will be none too happy. Thanks again. I think this is my last stumper question for the day:). library(ggplot2) rnorm_test_data_1-rnorm(100,3,1) rnorm_test_data_2-rnorm(100,3,1) nor_1-cbind(Test=norm1, Data=rnorm_test_data_1) nor_2-cbind(Test=norm2, Data=rnorm_test_data_1) nor_data-rbind(nor_1, nor_2) nor_data_frame-data.frame(Test=nor_data[,1],Data=nor_data[,2]) qplot(nor_data_frame$Data, data = nor_data_frame, binwidth = 3.0, fill = nor_data_frame$Test, main = list(as.character(Test Histogram, cex=0.7, font=7))) sessionInfo() R version 2.8.0 (2008-10-20) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] grid stats graphics grDevices utils datasets methods base other attached packages: [1] ggplot2_0.8.1 reshape_0.8.2 RColorBrewer_1.0-2 proto_0.3-8 [5] plyr_0.1.4 nortest_1.0 fBasics_280.74 timeSeries_290.79 [9] timeDate_290.81 vcd_1.2-1 MASS_7.2-44 colorspace_1.0-0 --- On Wed, 1/7/09, hadley wickham h.wick...@gmail.com wrote: From: hadley wickham h.wick...@gmail.com Subject: Re: [R] R Stacked Histogram To: jasonkrup...@yahoo.com Cc: r-help@r-project.org Date: Wednesday, January 7, 2009, 9:20 AM On Wed, Jan 7, 2009 at 7:55 AM, Jason Rupert jasonkrup...@yahoo.com wrote: That worked! Thank you very much for the help. I think I have one last question about qplot in ggplot2, That is exporting the plot to JPG while in a loop. I tried what was recommended in Re: [R] jpeg() creating empty files with qplot() in a loop, however, I received some errors (see below). I also tried using a PDF, but that did not work either, i.e. the PDF produced was blank. Oddly enough the results produced using dev.print(file=qplot_output.jpg, device=jpeg, width=600) in a loop are blank, i.e. the JPG file is there, but it is blank. Unfortunately, ggsave(file=ggsave_qplot_output.jpg) does not even produce a JPG file output. Any help at this point is greatly appreciated. Is the problem related to the fact that I need to use the plain hist and dev.print prior to using ggplot's qplot? If you're using ggsave, you don't need to use the dev functions. The following should be sufficient: qplot(rnorm_test_data, geom = histogram, binwidth = 1) + scale_x_continuous(Test Data) + scale_y_continuous(Frequency) + scale_fill_discrete(qplot histogram) ggsave(file = ggsave_qplot_output.pdf) # Unfortunately due to a small bug in the current version of ggplot, you need to use # jpeg with an e to get jpegs ggsave(file = ggsave_qplot_output.jpeg) # But I'd recommend using png instead - much better quality ggsave(file = ggsave_qplot_output.png) # One final problem is that you're going to overwrite the plot # on each run of your loop. You probably want something like: ggsave(file = paste(ggsave_qplot_output_, i, .png, sep =)) Hadley -- http://had.co.nz/ [[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] proto question
Dear R Users,
I have a couple of proto objects like:
wedge - proto(expr={
start.year - 2008
end.year - 2050
})
star.rating - wedge$proto(
star = c(4, 5, 8, 10),
gain = c(0, .3, .5, .7),
cost = c(0, 2100, 4000, 7500),
star.rating - function(., year) 6.0,
setup = function(.){
.$cost.for.star - approxfun(.$star, .$cost)
.$gain.for.star - approxfun(.$star, .$gain)
},
test = function(., year) {
gs - .$with(gain.for.star)(.$star.rating(year))
}
)
And a function to create and modify 'instances':
create.star.rating - function(switch.years, star.ratings) {
res - star.rating$proto(switch.years = switch.years, star.ratings =
star.ratings)
res$setup()
res
}
When I use them as follows:
ee - create.star.rating(ratings, switch.years)
ee$test(2009)
The second line gives me the error message:
Error in .$with(gain.for.star)(.$star.rating(year)) :
object y not found
I understand why this happens (when objects are inserted into a proto
their environment is set to that of the proto)... but I can't figure out
how to get around it!
I have tried setting the environments of the functions created in setup
as follows:
setup = function(.){
t1 - approxfun(.$star, .$cost)
t2 - approxfun(.$star, .$gain)
.$cost.for.star - t1
.$gain.for.star - t2
environment(.$cost.for.star) - environment(t1)
environment(.$gain.for.star) - environment(t2)
}
But then I get the error:
Error in get(gain.for.star, env = `*tmp*`, inherits = TRUE) :
object *tmp* not found
Which I think occurs because the last two lines in 'setup' only create
references to their respective environments which disappear on exit of
'setup'.
Any ideas?
Regards,
Simon Knapp.
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[R] New York Times Article: Data Analysts Captivated by R's Power
Readers of this list might be interested in the following article in the New York Times and might find amusing the notion that Some people familiar with R describe it as a supercharged version of Microsoft's Excel spreadsheet software http://www.nytimes.com/2009/01/07/technology/business-computing/07progra m.html?_r=1ref=technology Art -- Art Burke Northwest Regional Educational Laboratory 101 SW Main St, Suite 500 Portland, OR 97204-3213 Phone: 503-275-9592 / 800-547-6339 Fax: 503-275-0450 bur...@nwrel.org [[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 estimate overdispersion in glmer models?
Dear all, I am using function glmer from package lme4 to fit a generalized linear mixed effect model. My model is as follows: model1 - glmer(fruitset ~ Dist*wire + (1|Site), data, binomial) summary(model1) Generalized linear mixed model fit by the Laplace approximation Formula: fruitset ~ Dist * wire + (1 | Site) Data: data AIC BIC logLik deviance 68.23 70.65 -29.1158.23 Random effects: Groups NameVariance Std.Dev. Lugar (Intercept) 3.5155e-14 1.8750e-07 Number of obs: 12, groups: Lugar, 2 Fixed effects: Estimate Std. Error z value Pr(|z|) (Intercept) -2.332132 0.856518 -2.723 0.006473 ** Dist 0.001137 0.001141 0.997 0.318902 WireControl 4.710750 1.196550 3.937 8.25e-05 *** Dist:WireControl -0.006180 0.001769 -3.494 0.000475 *** --- Signif. codes: 0 *** 0.001 ** 0.01 * 0.05 . 0.1 1 Correlation of Fixed Effects: (Intr) Dist WirCnt Dist-0.963 WireContrl -0.716 0.689 Dst:WirCntr 0.621 -0.645 -0.957 My question is, how can I check for overdispersion? In glm models you can check this by comparing the residual deviance with the residual degrees of freedom, but in glmer you don't get this information. Does anyone know how to get information about overdispersion in the model? Thanks in advance for your help, (Ubuntu Intrepid Ibex / R 2.7.1) Luis Cayuela Investigador Post-doctoral Grupo de Ecología Terrestre Departamento de Ecología Centro Andaluz de Medio Ambiente, Universidad de Granada - Junta de Andalucía Avda. del Mediterráneo S/N. 18006. Granada. España email: lcayu...@ugr.es Fax: +34 958137246 Tel: +34 958241000 (ext. 31202) __ 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] Fw: Re: R Stacked Histogram
Hi Jason, Well, one last questions about stack plot (please forgive the lame example below). I thought the below allow me to resize the the title of the stacked histogram, but no luck. Any suggestions as to the modificaiton necessary to get it to work? Right now the title is obscured by the plot and my boss will be none too happy. Thanks again. Yes, that's a really stupid bug that I accidentally introduced in the latest version. You can fix it with: qplot(mpg, wt, data = mtcars, main = My title) + opts(plot.title = theme_text(vjust = 0, size = 16)) or by adding a new line to the end of the title: qplot(mpg, wt, data = mtcars, main = My title\n) Regards, Hadley -- http://had.co.nz/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] rbind for matrices - rep argument
Ben Bolker wrote:
Dimitris Rizopoulos d.rizopoulos at erasmusmc.nl writes:
you can use indexing, e.g.,
mat - matrix(rnorm(20), 4, 5)
mat
mat[rep(1:nrow(mat), 3), ]
I hope it helps.
Best,
Dimitris
or matrix trickery:
z - as.data.frame(matrix(sample(1:9,20,replace=TRUE),nrow=4))
matrix(rep(as.matrix(z),3),ncol=ncol(z),byrow=TRUE)
I do sometimes wish there were a more generic Rep() defined as
Rep - function(x,n) {
result - list()
for (i in 1:n) {
result[[i]] - x
}
result
}
then one could say do.call(rbind,Rep(x,3))
You mean like:
do.call('rbind', rep(list(x), 3))
Patrick Burns
patr...@burns-stat.com
+44 (0)20 8525 0696
http://www.burns-stat.com
(home of S Poetry and A Guide for the Unwilling S User)
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Re: [R] R in the NY Times
you can use google alerts to track media coverage of R using some keywords regards, ajay On Wed, Jan 7, 2009 at 9:52 PM, David M Smith da...@revolution-computing.com wrote: On Wed, Jan 7, 2009 at 6:39 AM, Tony Breyal tony.bre...@googlemail.com wrote: Thank you for posting this, I found it a very enjoyable read! I am curious, is there an archive of 'R in the Media' or 'R in the Press' articles somewhere? It would be interesting to see how the perception of R has changed/evolved over time relative to other packages. That's a great idea, and I just created an Rmedia category on the REvolutions R blog to track exactly such articles. You can find it here: http://blog.revolution-computing.com/rmedia/ If anyone knows of any other mainstream articles about R available online please let me know, and I'll do a round-up post in that section to make sure they're captured. By the way, we're writing about R and issues related to R daily at: http://blog.revolution-computing.com # David Smith -- David M Smith da...@revolution-computing.com Director of Community, REvolution Computing www.revolution-computing.com Tel: +1 (206) 577-4778 x3203 (Seattle, USA) __ 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] R in the NY Times
On 07-Jan-09 18:03:19, Erik Iverson wrote: I pointed a friend of mine toward the article, to which he replied: I hope that they run SAS on Solaris too, god only knows how tainted the syscalls are in that linux freeware. Of course, now Solaris is 'freeware', too, so I suppose that according to SAS, running SAS on Windows is the best way to be sure you're getting the right answers. I'm not so sure about that. Since the article described R as a supercharged version of Microsoft's Excel, surely people should run R on Windows and be *ab*so*lute*ly* sure of getting the right answers (and supercharged to boot) Ted. On Wed, 07 Jan 2009 10:56:53 -0600, Marc Schwartz marc_schwa...@comcast.net wrote: I would also point out that the use of the term freeware as opposed to FOSS by the SAS rep, comes off as being unprofessional and deliberately condescending... The author of the article, to his credit, was pretty consistent in using open source terminology. Regards, Marc on 01/07/2009 10:26 AM Bryan Hanson wrote: I believe the SAS person shot themselves in the foot more in more ways than one. In my mind, the reason you would pay, as Frank said, for non-peer-reviewed software with hidden implementations of analytic methods that cannot be reproduced by others Would be so that you can sue them later when a software problem in the designing of the engine makes your plane fall out of the sky! __ 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. E-Mail: (Ted Harding) ted.hard...@manchester.ac.uk Fax-to-email: +44 (0)870 094 0861 Date: 07-Jan-09 Time: 18:30:39 -- XFMail -- __ 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 in the NY Times
2009/1/7 Darin A. England engl...@cs.umn.edu: Unfortunately, that type of FUD issued by the SAS marketing person still works. I see it at my employer (a large healthcare company.) I see it here, at a university. Quote: We couldn't possibly do our analysis using some software we've just downloaded from a web site *facepalm* It's a battle to change a culture, but ironically the recession helps. People are now taking notice of the obscene licensing fees for SAS. They'll just keep increasing their educational discount, or as we say, the first hit is free... BaRRy __ 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 with ggplot2 - facet_wrap and boxplot
o. Well, it's working (replace 'group' by 'trt') Thank you very much Hadley. david 2009/1/7 hadley wickham h.wick...@gmail.com Hi David, Here the problem : library(ggplot2) df - data.frame(id = 1:100, x1 = c(rnorm(50), rnorm(50, 1)), x2 = c(rnorm(50), rnorm(50, 1.5)), x3 = c(rnorm(50, 0.5), rnorm(50, 2.5)), group = as.factor(rep(c(a, b), each = 50))) df.melt - melt(df, id = c(id, group)) head(df.melt) p - ggplot(df.melt, aes(variable, value)) p + geom_boxplot(aes(fill = group)) # This graph is great, but I would like to have two panels, one for group 'a', and one for group 'b' # With this code, I can't have one boxplot for each variable x1, x2 and x3 p + geom_boxplot(aes(fill = group)) + facet_wrap(~group) # but it's working with geom_point p + geom_point(aes(color = group)) + facet_wrap(~group) This is an annoying bug I haven't figure out how to fix yet. The basic problem is that if you facet by a variable that has the same name as an aesthetic, it overrides that aesthetic (group in this case). Unfortunately, currently the only work around is call the variable something other than group. Regards, Hadley -- http://had.co.nz/ [[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] generating data
How do I simulate data with 100 points from a normal distribution with n=200, mean (5,0), and Σ=matrix(1,0,0,0.1). After how do I plot the dataset and include cluster centers found? -- View this message in context: http://www.nabble.com/generating-data-tp21337173p21337173.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] Cannot access packages
jlu...@ria.buffalo.edu wrote: Although I have installed R many times on many machines without problems, I have recently encountered a problem with accessing packages. R has been installed successfully with the --internet2 option. The session info is below. sessionInfo() R version 2.8.1 (2008-12-22) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] tools_2.8.1 When I try to load a package (chron in this example) from the CMU mirror, I get the following error message: utils:::menuInstallPkgs() --- Please select a CRAN mirror for use in this session --- trying URL 'http://lib.stat.cmu.edu/R/CRAN/bin/windows/contrib/2.8/chron_2.3-28.zip' Error in download.file(url, destfile, method, mode = wb, ...) : cannot open URL 'http://lib.stat.cmu.edu/R/CRAN/bin/windows/contrib/2.8/chron_2.3-28.zip' In addition: Warning message: In download.file(url, destfile, method, mode = wb, ...) : cannot open: HTTP status was '403 Forbidden (Blocked by NG)' Warning in download.packages(p0, destdir = tmpd, available = available, : download of package 'chron' failed This error applies to ANY package. The option --internet2 must be used. If not, then I cannot even access the mirror. Can anyone help me out? Could this be a firewall problem? Mirror problem, I guess. Just try another mirror. Uwe Ligges Joe [[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] smoothed contour lines
Greg Snow Greg.Snow at imail.org
Wed Jan 7 17:58:07 CET 2009
Here is one possible approach to get you started (this is not a final
answer):
x - seq(-3,3)
y - seq(-3,3)
z - outer(x,y, function(x,y,...) x^2 + y^2 )
tmp - contourLines(x,y,z)
contour(x,y,z, lty=0)
lapply(tmp, function(l) {
x - l$x
y - l$y
if( length(x) 2 ){
if( isTRUE( all.equal( c(x[1],y[1]),
c(x[length(x)],y[length(y)] {
xspline(x[-1],y[-1], -1, FALSE)
} else {
xspline(x, y, -1, TRUE)
}
} else {
lines(x,y) # or whatever else should go here
}
} )
You can play with the settings to xspline to control the properties
of the curves, also it will look better if you thin some of the points
from contourLines (the points that are nearly identical cause the
small loops).
Hope this helps,
--
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
greg.snow at imail.org
801.408.8111
It often works better to fit a smooth surface to the data, evaluate
that surface on a finer grid, and pass the result to contour. This
ensures that contour lines don't cross one another and tends to avoid
the spurious loops that you might get from smoothing the contour lines
themselves.
Thin plate splines (Tps from library(fields)) and loess (among others)
can fit the surface. E.g., with your data try
library(fields)
xy-as.matrix(expand.grid(x=x,y=y))
contour(predict.surface(Tps(as.matrix(expand.grid(x=x,y=y)),as.vector(z)
)))
These surface fitters have arguments to control the smoothness/flatness
of the
surface.
Bill Dunlap
TIBCO Software Inc - Spotfire Division
wdunlap tibco.com
-Original Message-
From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-
project.org] On Behalf Of Andrea Storto
Sent: Tuesday, January 06, 2009 9:52 AM
To: r-help at r-project.org
Subject: [R] smoothed contour lines
Hi all,
I'm trying to draw a contour plot
with rounded (smoothed) contour lines instead of sharp angles;
when the grid consists of only a few points
in x- and y- axis, the resulting contour
is in facts rather ugly since very sharp angles may appear.
I did not find any way to do it,
by using either contour or contourplot (from the lattice package),
I wonder if there exist a way for smoothing the angles,
apart from artificially increasing the grid resolution,
Thanks in advance
Andrea
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Re: [R] generating data
This sounds rather like homework. If so, then talk to your instructor for help. Otherwise: First you go to R Site Search at http://finzi.psych.upenn.edu/search.html or to google. Then you search for normal distribution. Then you search for plot. Then you search for cluster. If you have problems with that, then read the introduction to R documents, and the R-help posting guide, and if you still can't figure it out you can ask detailed and specific questions here. Sarah On Wed, Jan 7, 2009 at 1:16 PM, berzasca mioaratero...@yahoo.com wrote: How do I simulate data with 100 points from a normal distribution with n=200, mean (5,0), and Σ=matrix(1,0,0,0.1). After how do I plot the dataset and include cluster centers found? -- -- Sarah Goslee http://www.stringpage.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] troubles performing Moran.I test
dear R users,
I have troubles performing Moran.I test as suggested on
http://www.ats.ucla.edu/stat/r/faq/morans_i.htm
my spatial data are longitude and lattitide of communities. The
calculation of the inverse distance matrix according to the homepage
(using my data)
datAL - read.csv2(C:\\Konvergenz AL.csv, header=T)
ALdist - as.matrix(dist(cbind(datAL$Länge, datAL$Breite)))
ALdist.inv - 1/ALdist
for (i in 1:dim(ALdist)[1]){ALdist.inv[i,i]=0}
seems to work since the first 10 elements of my matrix look like this:
1 2 3 4 5
1 0. 0.06201737 0.06041221 0.03386427 0.05198752
2 0.06201737 0. 0.19611614 0.03562352 0.02964346
3 0.06041221 0.19611614 0. 0.03028913 0.03118914
4 0.03386427 0.03562352 0.03028913 0. 0.02138823
5 0.05198752 0.02964346 0.03118914 0.02138823 0.
the data which might be spatially autocorrelated is LN(Unem05/Unem98,
the LN of the development in unemployment rates in the communities
between 1998 and 2005. The first 5 elements of this vector are as
follows:
CommLN(Unem05/Unem98)
1 0.21
2 0.08
3 0.22
4 0.05
5 -0.22
I have 426 communities in total and I don's see what might be wrong
with the data...However, I have some NAs in there...
when I try to perform the test using:
Moran.I(datAL$LN.Rt05.Rt98., ALdist.inv, na.rm=TRUE)
I get the following error message:
Fehler in if (obs = ei) 2 * pv else 2 * (1 - pv) :
Fehlender Wert, wo TRUE/FALSE nötig ist
in english something like
error in if (obs = ei) 2 * pv else 2 * (1 - pv) :
missing value, where TRUE/FALSE is needed
can anyone give me a hint what is going wrong??
many thanks in advance!!
Barbara
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Re: [R] proto question
On Wed, Jan 7, 2009 at 10:22 AM, Simon Knapp
s.kn...@mmassociates.com.au wrote:
Dear R Users,
I have a couple of proto objects like:
wedge - proto(expr={
start.year - 2008
end.year - 2050
})
star.rating - wedge$proto(
star = c(4, 5, 8, 10),
gain = c(0, .3, .5, .7),
cost = c(0, 2100, 4000, 7500),
star.rating - function(., year) 6.0,
setup = function(.){
.$cost.for.star - approxfun(.$star, .$cost)
.$gain.for.star - approxfun(.$star, .$gain)
},
test = function(., year) {
gs - .$with(gain.for.star)(.$star.rating(year))
}
)
And a function to create and modify 'instances':
create.star.rating - function(switch.years, star.ratings) {
res - star.rating$proto(switch.years = switch.years, star.ratings =
star.ratings)
res$setup()
res
}
When I use them as follows:
ee - create.star.rating(ratings, switch.years)
Did you define switch.years somewhere? The order of
arguments in the call to create.star.rating seems
reversed from the definition. There may be other problems
too but suggest you start by fixing those.
ee$test(2009)
The second line gives me the error message:
Error in .$with(gain.for.star)(.$star.rating(year)) :
object y not found
I understand why this happens (when objects are inserted into a proto
their environment is set to that of the proto)... but I can't figure out
how to get around it!
I have tried setting the environments of the functions created in setup
as follows:
setup = function(.){
t1 - approxfun(.$star, .$cost)
t2 - approxfun(.$star, .$gain)
.$cost.for.star - t1
.$gain.for.star - t2
environment(.$cost.for.star) - environment(t1)
environment(.$gain.for.star) - environment(t2)
}
But then I get the error:
Error in get(gain.for.star, env = `*tmp*`, inherits = TRUE) :
object *tmp* not found
Which I think occurs because the last two lines in 'setup' only create
references to their respective environments which disappear on exit of
'setup'.
Any ideas?
Regards,
Simon Knapp.
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Re: [R] rbind for matrices - rep argument
For matrices you can use kronecker:
kronecker(rep(1, 6), data.matrix(Xdf))
[,1] [,2] [,3] [,4]
[1,] 1.1 2.1 3.1 4.1
[2,] 1.2 2.2 3.2 4.2
[3,] 1.1 2.1 3.1 4.1
[4,] 1.2 2.2 3.2 4.2
[5,] 1.1 2.1 3.1 4.1
[6,] 1.2 2.2 3.2 4.2
[7,] 1.1 2.1 3.1 4.1
[8,] 1.2 2.2 3.2 4.2
[9,] 1.1 2.1 3.1 4.1
[10,] 1.2 2.2 3.2 4.2
[11,] 1.1 2.1 3.1 4.1
[12,] 1.2 2.2 3.2 4.2
On Wed, Jan 7, 2009 at 1:08 PM, Ted Harding
ted.hard...@manchester.ac.uk wrote:
On 07-Jan-09 15:22:57, Niccolò Bassani wrote:
Dear R users,I'm facing a trivial problem, but I really can't solve it.
I've tried a dozen of codes, but I can't get the result I want.
The question is: I have a dataframe like this one
[,1] [,2] [,3] [,4] [,5]
[1,]12345
[2,]25549
[3,]16812
[4,]86415
made up of decimal numbers, of course.
I want to append this dataframe to itself a number x of times, i.e. 3.
That is I want a dataframe like this
[,1] [,2] [,3] [,4] [,5]
[1,]12345
[2,]25549
[3,]16812
[4,]86415
[5,]12345
[6,]25549
[7,]16812
[8,]86415
[9,]12345
[10,]25549
[11,]16812
[12,]86415
I'm searching for an authomatic way to do this (I've already used the
rbind re-writing x times the name of the frame...), as it must enter a
function where one argument is exactly the number x of times to repeat
this frame.
Any ideas??
Thanks in advance!
Niccolò
I don't know whether there is anywhere a ready-made function which
will implement a rep paramater for an rbind, but the following ad-hoc
function will do it for you efficiently (i.e. with the minimum number
of applications of the rbind() function).
To produce a result which consists of k replicates of x, row-bound:
Krbind - function(x,k){
y - x
if(k==1) return(x)
p - floor(log2(k))
for(i in (1:p)){
z - rbind(y,y)
y - z
}
k - (k - 2^p)
if(k==0) return(y) else return(rbind(y,Krbind(x,k)))
}
## Example:
Xdf - data.frame(X1=c(1.1,1.2),X2=c(2.1,2.2),
X3=c(3.1,3.2),X4=c(4.1,4.2))
Krbind(Xdf,6)
# X1 X2 X3 X4
# 1 1.1 2.1 3.1 4.1
# 2 1.2 2.2 3.2 4.2
# 3 1.1 2.1 3.1 4.1
# 4 1.2 2.2 3.2 4.2
# 5 1.1 2.1 3.1 4.1
# 6 1.2 2.2 3.2 4.2
# 7 1.1 2.1 3.1 4.1
# 8 1.2 2.2 3.2 4.2
# 9 1.1 2.1 3.1 4.1
# 10 1.2 2.2 3.2 4.2
# 11 1.1 2.1 3.1 4.1
# 12 1.2 2.2 3.2 4.2
Of course, if you're not worried by efficiency, then the simple loop
y - x
for(i in (1:(k-1))){y - rbind(y,x)}
will do it!
Hoping this helps,
Ted.
E-Mail: (Ted Harding) ted.hard...@manchester.ac.uk
Fax-to-email: +44 (0)870 094 0861
Date: 07-Jan-09 Time: 18:08:14
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Re: [R] Understanding dsyrk_ in C code
On Tue, Jan 6, 2009 at 8:54 PM, Nathan S. Watson-Haigh nathan.watson-ha...@csiro.au wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 I'm trying to understand some C code in an R package I'm using. I'm address this question here as it's matrix algebra...and I'm no pro at that! the C command reads: double alpha = 1.0, beta = 0.0; dsyrk_(L, N, nGenes, nGenes, alpha, mat1, nGenes, beta, mat2, nGenes); - From google, I've found out that dsyrk is for performing one of the symmetric rank k operations - whatever that means!? From here: http://linux.die.net/man/l/dsyrk I've found that the calculation being performed is: alpha*A*A' + beta*C However, since alpha is 1 and beta is 0, this reduces to: = 1*A*A' + 0*C = A*A' Which is simply the cross productam I correct? Not quite. The crossprod function in R computes A'A. This particular operation is what is computed by the tcrossprod function in R. Another difference is that this call modifies only the diagonal and lower triangle of mat2. The tcrossprod function calls the same underlying code then copies the lower triangle to the upper triangle so as to produce a symmetric matrix. When you are calling Lapack or BLAS routines from C it is helpful to look at the declarations in include/R_ext/BLAS.h and include/R_ext/Lapack.h /* DSYRK - perform one of the symmetric rank k operations */ /* C := alpha*A*A' + beta*C or C := alpha*A'*A + beta*C */ BLAS_extern void F77_NAME(dsyrk)(const char *uplo, const char *trans, const int *n, const int *k, const double *alpha, const double *a, const int *lda, const double *beta, double *c, const int *ldc); This helps to explain the mysterious L and N as the first two arguments in the call. By the way, the use of the literal name dsyrk_ in that code is risky. It is preferable to use the macro F77_SUB(dsyrk) which is defined in the include file include/R_ext/RS.h If you are wondering what the difference between F77_SUB and F77_NAME might be, there isn't a difference in R. Long, long ago there was a difference between the two macros in S and S-PLUS related to a peculiar Fortran compiler, if I recall correctly. Most of the time these macros simply append an underscore to the name but there may still be cases where something else occurs and it is best to allow for those cases. __ 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] smoothed contour lines
On Tue, Jan 6, 2009 at 8:52 AM, Andrea Storto andrea.sto...@met.no wrote: Hi all, I'm trying to draw a contour plot with rounded (smoothed) contour lines instead of sharp angles; when the grid consists of only a few points in x- and y- axis, the resulting contour is in facts rather ugly since very sharp angles may appear. I did not find any way to do it, by using either contour or contourplot (from the lattice package), I wonder if there exist a way for smoothing the angles, apart from artificially increasing the grid resolution, ?filled.contour is something to try out. -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] Another newbie question
Kia ora Allen I'm not sure what you have tried or what your level of understanding is. However, if your dataframe is: allen sp1 sp2 sp3 1 0 0 1 2 1 0 1 3 1 1 1 4 0 0 0 str(allen) 'data.frame': 4 obs. of 3 variables: $ sp1: int 0 1 1 0 $ sp2: int 0 0 1 0 $ sp3: int 1 1 1 0 Then looking at the output from: paste(names(allen)[as.logical(unlist(allen[2,]))], collapse='; ') may help you. Hei kona ra ... Peter Alspach -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of AllenL Sent: Thursday, 8 January 2009 7:28 a.m. To: r-help@r-project.org Subject: [R] Another newbie question Problem: I have a data frame with 1s and 0s denoting presence/absence of species (columns) for particular plot measurements (rows). What I want to do is make a new column whose entries for each row is a list of the column names in which a species is present (ie. for row one its entry might read: sp1,sp2, etc.). I've tried various functions etc. but can't seem to get the syntax right/ the correct combination of functions. Thanks in advance! -Allen -- View this message in context: http://www.nabble.com/Another-newbie-question-tp21337371p21337371.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. The contents of this e-mail are confidential and may be subject to legal privilege. If you are not the intended recipient you must not use, disseminate, distribute or reproduce all or any part of this e-mail or attachments. If you have received this e-mail in error, please notify the sender and delete all material pertaining to this e-mail. Any opinion or views expressed in this e-mail are those of the individual sender and may not represent those of The New Zealand Institute for Plant and Food Research Limited. __ 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] inter-timeseries correlation or corrections
Hello, I am currently working in the field of climate and environmental data analysis which is a lot founded on the analysis, preparation and combination of time series. About a bit more than one year ago I started to use python and the marvellous timeseries module [1]. Which offers a very convenient way to handle time series. This decision bases also on some experiences of other users [2]. Recently, I got drawn to R because the statistical functions in python are still in somewhat development. On my to do list is a result based comparison for some use cases. I am still new to R but hope to use it more often through the Rpy interface. For an actual project I would like to use a function to apply the distribution characteristics of a short-time series on a modelled long-term time series which encloses the shorter one. Which functions/libraries can you suggest? Is there already a use case for this? Thanks and kind regards, Timmie [1] http://pytseries.sourceforge.net/ [2] time series: Python vs. R - http://article.gmane.org/gmane.comp.python.scientific.user/14393 __ 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] xtable-longtable question
Hello: I am using Sweave to generate a PDF with figures and tables and was wondering if is possible to carry on table headers and some kind of caption like 'Continued' to the next PDF page when creating long tables. Felipe D. Carrillo Supervisory Fishery Biologist Department of the Interior US Fish Wildlife Service California, USA __ 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] Another newbie question
You did not provide any data, so I will take a guess at what it looks like: x - matrix(sample(0:1, 100, TRUE), 10) colnames(x) - LETTERS[1:10] x - as.data.frame(x) x A B C D E F G H I J 1 0 1 0 0 0 1 1 0 0 0 2 0 0 0 0 1 1 0 0 1 0 3 1 1 0 0 1 0 0 0 1 1 4 0 1 1 1 0 1 1 0 0 0 5 0 1 1 0 0 0 1 0 0 1 6 1 0 1 1 0 0 0 0 0 1 7 1 1 0 1 0 0 0 0 0 0 8 0 1 0 1 0 0 1 0 0 0 9 0 1 0 0 0 0 1 0 0 0 10 1 0 1 0 1 1 0 1 0 1 x$match - apply(x, 1, function(z) paste(colnames(x)[z == 1], collapse=,)) x A B C D E F G H I J match 1 0 1 0 0 0 1 1 0 0 0 B,F,G 2 0 0 0 0 1 1 0 0 1 0 E,F,I 3 1 1 0 0 1 0 0 0 1 1 A,B,E,I,J 4 0 1 1 1 0 1 1 0 0 0 B,C,D,F,G 5 0 1 1 0 0 0 1 0 0 1 B,C,G,J 6 1 0 1 1 0 0 0 0 0 1 A,C,D,J 7 1 1 0 1 0 0 0 0 0 0 A,B,D 8 0 1 0 1 0 0 1 0 0 0 B,D,G 9 0 1 0 0 0 0 1 0 0 0 B,G 10 1 0 1 0 1 1 0 1 0 1 A,C,E,F,H,J On Wed, Jan 7, 2009 at 1:28 PM, AllenL allen.laroc...@gmail.com wrote: Problem: I have a data frame with 1s and 0s denoting presence/absence of species (columns) for particular plot measurements (rows). What I want to do is make a new column whose entries for each row is a list of the column names in which a species is present (ie. for row one its entry might read: sp1,sp2, etc.). I've tried various functions etc. but can't seem to get the syntax right/ the correct combination of functions. Thanks in advance! -Allen -- View this message in context: http://www.nabble.com/Another-newbie-question-tp21337371p21337371.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. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem that you are trying to solve? __ 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 estimate overdispersion in glmer models?
lcayuela at ugr.es writes: [snip] model1 - glmer(fruitset ~ Dist*wire + (1|Site), data, binomial) summary(model1) Generalized linear mixed model fit by the Laplace approximation Formula: fruitset ~ Dist * wire + (1 | Site) Data: data AIC BIC logLik deviance 68.23 70.65 -29.1158.23 Random effects: Groups NameVariance Std.Dev. Lugar (Intercept) 3.5155e-14 1.8750e-07 Number of obs: 12, groups: Lugar, 2 [snip] My question is, how can I check for overdispersion? In glm models you can check this by comparing the residual deviance with the residual degrees of freedom, but in glmer you don't get this information. (Ubuntu Intrepid Ibex / R 2.7.1) a few thoughts -- (1) probably better to ask this question on the R-sig-mixed-models list, which specializes in these problems (2) try lme4:::sigma (3) do you really have just 12 observations in 2 groups? In that case I would strongly recommend just treating group as a fixed factor -- you have no power to estimate variance (note your random effect has a standard deviation of 2 x 10^-7), and you will avoid lots of heartache if you just fit glm(fruitset ~ Dist*wire + Site, data, binomial) [not everyone will agree with me about this ...] (4) I'm a little puzzled that your formula has Site as a random effect but your summary lists Lugar as a random effect. Did you edit the summary? __ 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] inter-timeseries correlation or corrections
look at zoo and ts, and it all depends on what you want to do. On Wed, Jan 7, 2009 at 2:27 PM, Tim Michelsen timmichel...@gmx-topmail.de wrote: Hello, I am currently working in the field of climate and environmental data analysis which is a lot founded on the analysis, preparation and combination of time series. About a bit more than one year ago I started to use python and the marvellous timeseries module [1]. Which offers a very convenient way to handle time series. This decision bases also on some experiences of other users [2]. Recently, I got drawn to R because the statistical functions in python are still in somewhat development. On my to do list is a result based comparison for some use cases. I am still new to R but hope to use it more often through the Rpy interface. For an actual project I would like to use a function to apply the distribution characteristics of a short-time series on a modelled long-term time series which encloses the shorter one. Which functions/libraries can you suggest? Is there already a use case for this? Thanks and kind regards, Timmie [1] http://pytseries.sourceforge.net/ [2] time series: Python vs. R - http://article.gmane.org/gmane.comp.python.scientific.user/14393 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Stephen Sefick Let's not spend our time and resources thinking about things that are so little or so large that all they really do for us is puff us up and make us feel like gods. We are mammals, and have not exhausted the annoying little problems of being mammals. -K. Mullis __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Another newbie question
try the following: dat - data.frame( sp1 = rbinom(10, 1, 0.5), sp2 = rbinom(10, 1, 0.5), sp3 = rbinom(10, 1, 0.5), sp4 = rbinom(10, 1, 0.5), sp5 = rbinom(10, 1, 0.5), sp6 = rbinom(10, 1, 0.5) ) ind - sapply(dat, as.logical) dat$Sp - apply(ind, 1, function (x, nams) paste(nams[x], collapse = ; ), nams = names(dat)) dat I hope it helps. Best, Dimitris AllenL wrote: Problem: I have a data frame with 1s and 0s denoting presence/absence of species (columns) for particular plot measurements (rows). What I want to do is make a new column whose entries for each row is a list of the column names in which a species is present (ie. for row one its entry might read: sp1,sp2, etc.). I've tried various functions etc. but can't seem to get the syntax right/ the correct combination of functions. Thanks in advance! -Allen -- Dimitris Rizopoulos Assistant Professor Department of Biostatistics Erasmus Medical Center Address: PO Box 2040, 3000 CA Rotterdam, the Netherlands Tel: +31/(0)10/7043478 Fax: +31/(0)10/7043014 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R in the NY Times
Google Alerts are great, but unfortuantly the brevity of R's name is the main problem i think. though, thinking about it, i suppose if one could work out the 'best' key words to use, it might be possible to not get too many miss- classified results, e.g., http://news.google.com/news?hl=enned=usnolr=1q=r+open+source+programming+languagebtnG=Search or something like that. Will be keeping an eye on David's page from time to time though, just in case he catches anything :-) lovely to see R getting the attention it so rightly deserves. On 7 Jan, 18:29, Ajay ohri ohri2...@gmail.com wrote: you can use google alerts to track media coverage of R using some keywords regards, ajay On Wed, Jan 7, 2009 at 9:52 PM, David M Smith da...@revolution-computing.com wrote: On Wed, Jan 7, 2009 at 6:39 AM, Tony Breyal tony.bre...@googlemail.com wrote: Thank you for posting this, I found it a very enjoyable read! I am curious, is there an archive of 'R in the Media' or 'R in the Press' articles somewhere? It would be interesting to see how the perception of R has changed/evolved over time relative to other packages. That's a great idea, and I just created an Rmedia category on the REvolutions R blog to track exactly such articles. You can find it here: http://blog.revolution-computing.com/rmedia/ If anyone knows of any other mainstream articles about R available online please let me know, and I'll do a round-up post in that section to make sure they're captured. By the way, we're writing about R and issues related to R daily at: http://blog.revolution-computing.com # David Smith -- David M Smith da...@revolution-computing.com Director of Community, REvolution Computingwww.revolution-computing.com Tel: +1 (206) 577-4778 x3203 (Seattle, USA) __ r-h...@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-h...@r-project.org mailing listhttps://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guidehttp://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] R in the NY Times
Kevin E. Thorpe wrote: Zaslavsky, Alan M. wrote: SAS says it has noticed R’s rising popularity at universities, despite educational discounts on its own software, but it dismisses the technology as being of interest to a limited set of people working on very hard tasks. “I think it addresses a niche market for high-end data analysts that want free, readily available code, said Anne H. Milley, director of technology product marketing at SAS. She adds, “We have customers who build engines for aircraft. I am happy they are not using freeware when I get on a jet.” Thanks for posting. Does anyone else find the statement by SAS to be humourous yet arrogant and short-sighted? there must be something wrong with me, but i can't find anything 'humorous yet arrogant and short-sighted' in the idea that engines for aircraft be built with software that does not advertise itself with 'ABSOLUTELY NO WARRANTY.' vQ __ 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.
