Re: [R] R on Linux - a primer
Thanks for sharing the interesting information about cran2deb. I was unaware of that project (but I did know that Dirk E. had been doing Octave and R binaries for Debian for years). Dirk Eddelbuettel (you spelled his name correctly) and Charles Blundell gave a talk at UseR! 2009... http://dirk.eddelbuettel.com/papers/useR2009cran2deb.pdf ...where they seem to claim that they chose to develop for Debian partly because of its similarity to Ubuntu: Common platform -- as Debian forms the base for Ubuntu and several other derivative or single-focus distributions Audience -- given the reach of Debian and Ubuntu, large number of users can be reached with little effort But that was in July. This what he was saying in November: http://www.mail-archive.com/r-sig-deb...@r-project.org/msg00892.html And this is what he was saying a month ago: https://stat.ethz.ch/pipermail/r-sig-debian/2010-February/001042.html I guess we just don't know if cran2deb works on Unbuntu and we don't know if Charles and Dirk will be providing binaries for Ubuntu. Apparently, they want to reach the Ubuntu user base, but it is a lot of work for them and they aren't getting the resources they need to pull it off. Mike On Tue, 16 Mar 2010, Emmanuel Charpentier wrote: Le dimanche 14 mars 2010 à 18:04 -0400, Axel Urbiz a écrit : Hi, I'm looking to move from Windows into a 64-bit Linux environment. Which is the best Linux Flavor to use within R? To install R on this environment, do I need to do any compiling? I'd like to add two cents of folly to the (wise) advice you've received already. Indeed , Ubuntu is one very good distribution whose management system has made the care and feeding of a Linux system a *lot* easier for the not-so-system-oriented people like yours truly. Whereas my first contacts with a Unix-like system were about 30 years ago (Oh my, how time flies, and how far away are Xenix and our 68000 systems ...), I'm *still* not fond of system maintenance for it's own sake. Ubuntu added an (almost) fool-proof maintenance system to an excellent distribution called Debian, thus lowering the Linux entry bar to as low as it can be humanely made. Some pretended that Ubuntu was a code word for I'm too stupid to configure Debian ; quite untrue ! It only means I'm too busy|lazy to configure Debian, which is a Good Thing (TM). But Debian has its strong points, and one of them is *extremely* strong for an R user : Dirk Eddelbuettel (whose name I'm almost surely misspelling (sorry, Dirk !)) has created a marvelous system called cran2deb which routinely creates binary Debian packages from (almost) the 2000+ R packages available nowadays. That might look small change : the basic tools used for developing/compiling most R packages are small beer (at least by today's standards).But some of them might depend on fiendishly difficult-to-maintain foreign libraries. Dirk's cran2deb takes care of that and creates any information that Debian's dpkg maintenance system needs to automate *your* R maintenance chores by integrating them in Debian's maintenance scheme, which is as automatic as you can get without becoming an incomprehensible beast. In fact, cran2deb is so good that Im seriously tempted to go back to Debian (after almost 8 years of Debian use, Ubuntu's ease-of-use, easy access to no-so-exotic hardware drivers (and the then-incessant politically correct yack-yacking on some Debian mailing lists...) made me switch to an early Ubuntu distribution). I did not yet switch back (mostly for not-so-superficial hardware support reasons), but I maintain a backup Debian installation for the hell of it and to test waters. So far, they have been a lot less rough than they used to be, but there are still occasional rows (e. g. a recent gotcha with openoffice.org, which would have render myself unable to work with those d*mn Word files for about a month, or forced me to do a maual repair (which I hate...)). So consider Debian as a (desirable) alternative to Ubuntu. HTH, Emmanuel Charpentier, DDS, MSc affiliation withdrawn, notwithstanding Frank Harrell's whims...__ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Adding text outside (lattice barchart) plotting region.
On Thu, Mar 18, 2010 at 5:26 AM, Peng Cai pengcaimaill...@gmail.com wrote: Thanks Richard and Jim for your reply! @All: Is there a way to do this without altering default x-labels (because in my case there could be up to 30-40 x-labels and I may have to repeat the script multiple times with different x-lables). OR, not sure but can it be done by extending plotting region parameters for lattice plots (though I'm aware of how to change these). The most general solution I can think of is to use the legend functionality (whereby new grid objects can be used as legends). A simple example is dotplot(yield ~ year, data = barley, legend = list(bottom = list(fun = textGrob, args = list(x = c(0.5, 1, 2), y = 0.5, label = c(Month:, March, April), just = center, default.units = native, vp = viewport(xscale = c(0.4, 2.6), yscale = c(0, 1)) More complex layouts will typically need frameGrob (see lattice::draw.colorkey for an example). Note that the legend doesn't know what the panel limits are, so you will need to tell it explicitly. -Deepayan Thanks, Peng Cai On Wed, Mar 17, 2010 at 7:27 PM, Jim Lemon j...@bitwrit.com.au wrote: On 03/18/2010 09:50 AM, Peng Cai wrote: Hi All, I need some help with adding text at the bottom of the graph (outside of default outline of graph). Say, I need to write Month: 01 04 below each of the two years in the following R code, something like this: ___ | | | Plot | |___ __| 1931 1932 Month: 01 04 # R code require(lattice) barchart(yield ~ year, data = barley, stack=TRUE, col=black, ylim=c(0,85) ) Hi Peng, Try using mtext: mtext(Month: 01 04,side=1,line=2,at=0,adj=0) You may have to adjust the last three arguments to get it in the correct position. Jim [[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] Date conversion issue
Thanks - that works -- View this message in context: http://n4.nabble.com/Date-conversion-issue-tp1596548p1597627.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] Using indexing to manipulate data
On 03/18/2010 04:05 PM, duncandonutz wrote:
I know one of R's advantages is it's ability to index, eliminating the need
for control loops to select relevant data, so I thought this problem would
be easy. I can't crack it. I have looked through past postings, but
nothing seems to match this problem
I have a data set with one column of actors and one column of acts. I need
a list that will give me a pair of actors in each row, provided they both
participated in the act.
Example:
The Data looks like this:
Jim A
BobA
BobC
Larry D
Alice C
Tom F
Tom D
Tom A
Alice B
NancyB
I would like this:
Jim Bob
Jim Tom
Bob Alice
Larry Tom
AliceNancy
The order doesn't matter (Jim-Bob vs. Bob-Jim), but each pairing should be
counted only once.
Hi duncandonutz,
Try this:
actnames-read.table(junkfunc/names.dat,stringsAsFactors=FALSE)
actorpairs-NULL
for(act in unique(actnames$V2)) {
actors-actnames$V1[actnames$V2 == act]
nactors-length(actors)
if(nactors 1) {
indices-combn(nactors,2)
for(i in 1:dim(indices)[2])
actorpairs-
rbind(actorpairs,c(actors[indices[1,i]],actors[indices[2,i]]))
}
}
actorpairs
Jim
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Re: [R] Using indexing to manipulate data
One approach is the following:
Dat - read.table(textConnection(
Jim A
BobA
BobC
Larry D
Alice C
Tom F
Tom D
Tom A
Alice B
NancyB))
closeAllConnections()
names(Dat) - c(name, act)
out - tapply(as.character(Dat$name), Dat$act, function (x) {
if (length(x) 2) c(x, ) else t(combn(x, 2))
})
unique(do.call(rbind, out))
I hope it helps.
Best,
Dimitris
On 3/18/2010 6:05 AM, duncandonutz wrote:
I know one of R's advantages is it's ability to index, eliminating the need
for control loops to select relevant data, so I thought this problem would
be easy. I can't crack it. I have looked through past postings, but
nothing seems to match this problem
I have a data set with one column of actors and one column of acts. I need
a list that will give me a pair of actors in each row, provided they both
participated in the act.
Example:
The Data looks like this:
Jim A
BobA
BobC
Larry D
Alice C
Tom F
Tom D
Tom A
Alice B
NancyB
I would like this:
Jim Bob
Jim Tom
Bob Alice
Larry Tom
AliceNancy
The order doesn't matter (Jim-Bob vs. Bob-Jim), but each pairing should be
counted only once.
Thanks!
--
Dimitris Rizopoulos
Assistant Professor
Department of Biostatistics
Erasmus University Medical Center
Address: PO Box 2040, 3000 CA Rotterdam, the Netherlands
Tel: +31/(0)10/7043478
Fax: +31/(0)10/7043014
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Re: [R] Using indexing to manipulate data
Here are two solutions. The first uses merge and the second uses sqldf. They both do a self join picking off the unique pairs. The sqldf solution also sorts the result: # input DF - structure(list(Actor = c(Jim, Bob, Bob, Larry, Alice, Tom, Tom, Tom, Alice, Nancy), Act = c(A, A, C, D, C, F, D, A, B, B)), .Names = c(Actor, Act ), class = data.frame, row.names = c(NA, -10L)) subset(unique(merge(DF, DF, by = 2)), Actor.x Actor.y) library(sqldf) # see http://sqldf.googlecode.com sqldf(select A.Actor, A.Act, B.Act from DF A join DF B where A.Act = B.Act and A.Actor B.Actor order by A.Act, A.Actor) On Thu, Mar 18, 2010 at 1:05 AM, duncandonutz dwads...@unm.edu wrote: I know one of R's advantages is it's ability to index, eliminating the need for control loops to select relevant data, so I thought this problem would be easy. I can't crack it. I have looked through past postings, but nothing seems to match this problem I have a data set with one column of actors and one column of acts. I need a list that will give me a pair of actors in each row, provided they both participated in the act. Example: The Data looks like this: Jim A Bob A Bob C Larry D Alice C Tom F Tom D Tom A Alice B Nancy B I would like this: Jim Bob Jim Tom Bob Alice Larry Tom Alice Nancy The order doesn't matter (Jim-Bob vs. Bob-Jim), but each pairing should be counted only once. Thanks! -- View this message in context: http://n4.nabble.com/Using-indexing-to-manipulate-data-tp1597547p1597547.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Care to share an R presentation?
Have a look at this presentation of Matthew Keller: http://www.matthewckeller.com/Lecture1.ppt Best regards, Thierry ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek team Biometrie Kwaliteitszorg Gaverstraat 4 9500 Geraardsbergen Belgium Research Institute for Nature and Forest team Biometrics 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 Paul Johnson Verzonden: donderdag 18 maart 2010 5:54 Aan: R-help Onderwerp: [R] Care to share an R presentation? The R movement is picking up steam in the center of America. People that ignored my R-enthusiasm 10 years ago are now calling me up asking for presentations. I need to make a 2 hour presentation to a collection of faculty and grad students who might like to use R. I don't want to make it seem too complicated (as I often do), but I don't want to mislead them to think it will be easy. I expect other r-help readers have been in this same situation. I have a recollection (5, 6 years ago) that one of the R leaders had a slideshow for this exact purpose. But I can't find it now. There is a R-help similar request and both John Fox and Deepayan Sarkar offered links to their materials. However, the links aren't valid anymore. If I don't find a pre-existing example to work from, I'll slap together a Beamer/Sweave presentation and post it where future speech givers can get it. -- Paul E. Johnson Professor, Political Science 1541 Lilac Lane, Room 504 University of Kansas __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Druk dit bericht a.u.b. niet onnodig af. Please do not print this message unnecessarily. Dit bericht en eventuele bijlagen geven enkel de visie van de schrijver weer en binden het INBO onder geen enkel beding, zolang dit bericht niet bevestigd is door een geldig ondertekend document. The views expressed in this message and any annex are purely those of the writer and may not be regarded as stating an official position of INBO, as long as the message is not confirmed by a duly signed document. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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 remove levels?
new_ns$chr - factor(new_ns$chr, levels=paste(1:22))
Soyeon Kim yunni0...@gmail.com 18/03/2010 00:57
Dear All,
My data looks like this
new_ns
chr nc_two nc_not_two
11488 58
22325114
33233 79
44200153
55239 53
66196313
77229 45
88231137
99164111
10 10156 45
11 11181 92
12 12179 52
13 13 72 30
14 14 73 62
15 15185 25
16 16 93 42
17 17 84 50
18 18 33 17
19 19 31 40
20 20 49 8
21 21 12 16
22 22 26 37
new_ns$chr
[1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22
Levels: 1 10 11 12 13 14 15 16 17 18 19 2 20 21 22 3 4 5 6 7 8 9
but when I run this : plot(new_ns$chr,new_ns$nc_two)
the order of new_ns$chr is 1 10 11 12 13 14 15 16 17 18 19 2 20 21 22
3 4 5 6 7 8 9
how can fix this order to 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
16 17 18 19 20 21 22 in the plot ?
I attached the plot.
Thank you ahead.
***
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Re: [R] Locating an error
Worik R wrote: Related: I found the problem eventually. It was a parameter that was too large and the function called stop. Looking at the documentation I see I can supply my own error handler. Cool. Are there already written error handlers that dump a stack trace? See http://www.stats.uwo.ca/faculty/murdoch/software/debuggingR/, particularly the section on post-mortem debugging. One of the choices described there is to set options(error=recover). Duncan Murdoch cheers Worik On Thu, Mar 18, 2010 at 2:58 PM, Worik R wor...@gmail.com wrote: I have a large programme that after running half an hour or so fails with an error Error in x[value] - NA : only 0's may be mixed with negative subscripts How can I find out where that error occurs? If I have to do a binary search using error messages it will take a long time! Is there some way I can generate a stack trace? cheers Worik [[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] question about multinom function (nnet)
Hello Again, Doesn't anyone know where the problem might be? I could not get any more information from the help page. Many thanks Best Sergii [R] question about multinom function (nnet) * This message: [ Message body http://tolstoy.newcastle.edu.au/R/e9/help/10/03/9009.html#start ] [ More options http://tolstoy.newcastle.edu.au/R/e9/help/10/03/9009.html#options2 ] * Related messages: [ Next message http://tolstoy.newcastle.edu.au/R/e9/help/10/03/9010.html ] [ Previous message http://tolstoy.newcastle.edu.au/R/e9/help/10/03/9008.html ] From: Sergii Ivakhno Sergii.Ivakhno_at_cancer.org.uk mailto:Sergii.Ivakhno_at_cancer.org.uk?Subject=Re:%20[R]%20question%20a bout%20multinom%20function%20%28nnet%29 Date: Wed, 17 Mar 2010 14:59:10 + Hello Again, Dear All. I have the following table that I want to analyze using multinom function freq segments sample 4271 Seg1 tumour 4311 Seg2 tumour 3515 Seg1 normal 3561 Seg2 normal I want to compare model with both factors to the one where only sample is present. model1=multinom(freq~segments+sample,data=table) model2=multinom(freq~ sample,data=table) anova(model2,model1) Likelihood ratio tests of Multinomial Models Response: freq Model Resid. df Resid. Dev Test Df LR stat. Pr(Chi) 1 sample 6 5.5452609828 2 segments + sample 3 0.0001600513 1 vs 2 3 5.545101 0.1359658 What I do not understand is where df of 6 and 3 come from? Shouldn't they be 2 and 1? Many thanks for your help in advance Sincerely Sergii Sergii Ivakhno PhD student Computational Biology Group Cancer Research UK Cambridge Research Institute Li Ka Shing Centre Robinson Way Cambridge CB2 0RE England +44 (0)1223 404293 (O) +44 (0)1223 404128 (F) http://www.compbio.group.cam.ac.uk http://www.compbio.group.cam.ac.uk/ http://www.compbio.group.cam.ac.uk/ http://www.compbio.group.cam.ac.uk/ / This communication is from Cancer Research UK. Our website is at www.cancerresearchuk.org. We are a charity registered under number 1089464 and a company limited by guarantee registered in England Wales under number 4325234. Our registered address is 61 Lincoln's Inn Fields, London WC2A 3PX. Our central telephone number is 020 7242 0200. This communication and any attachments contain information which is confidential and may also be privileged. It is for the exclusive use of the intended recipient(s). If you are not the intended recipient(s) please note that any form of disclosure, distribution, copying or use of this communication or the information in it or in any attachments is strictly prohibited and may be unlawful. If you have received this communication in error, please notify the sender and delete the email and destroy any copies of it. E-mail communications cannot be guaranteed to be secure or error free, as information could be intercepted, corrupted, amended, lost, destroyed, arrive late or incomplete, or contain viruses. We do not accept liability for any such matters or their consequences. Anyone who communicates with us by e-mail is taken to accept the risks in doing so. [[alternative HTML version deleted]] -- Sergii Ivakhno PhD student Computational Biology Group Cancer Research UK Cambridge Research Institute Li Ka Shing Centre Robinson Way Cambridge CB2 0RE England +44 (0)1223 404293 (O) +44 (0)1223 404128 (F) http://www.compbio.group.cam.ac.uk http://www.compbio.group.cam.ac.uk/ / This communication is from Cancer Research UK. Our website is at www.cancerresearchuk.org. We are a charity registered under number 1089464 and a company limited by guarantee registered in England Wales under number 4325234. Our registered address is 61 Lincoln's Inn Fields, London WC2A 3PX. Our central telephone number is 020 7242 0200. This communication and any attachments contain information which is confidential and may also be privileged. It is for the exclusive use of the intended recipient(s). If you are not the intended recipient(s) please note that any form of disclosure, distribution, copying or use of this communication or the information in it or in any attachments is strictly prohibited and may be unlawful. If you have received this communication in error, please notify the sender and delete the email and destroy any copies of it. E-mail communications cannot be guaranteed to be secure or error free, as information could be intercepted, corrupted, amended, lost, destroyed, arrive late or incomplete, or contain viruses. We do not accept liability for any such matters or their consequences. Anyone who communicates with us by e-mail is taken to accept the risks in doing so. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting
Re: [R] replace NA value with 0
Hi r-help-boun...@r-project.org napsal dne 17.03.2010 18:01:50: Building on the question how to replace NA with 0. My data set below has date, station 1, flags for station 1, station 2, flags for station 2, etc... I would like to make the values in the station columns equal to 1 and the NA in the station columns equal to 0 and then sum each row for the number of 1 present in the row. head(data.matrix, n=10) date 05AE005 flg_05AE005 05AF010 flg_05AF010 05BM014 flg_05BM014 1 1900-01-01 NANA NANA NA NA 2 1900-01-02 NANA NANA .23 NA 3 1900-01-03 NANA NANA .45 NA 4 1900-01-04 NANA NANA NA NA 5 1900-01-05 NANA NANA NA NA 6 1900-01-06 NANA NANA NA NA 7 1900-01-07 0.75 NA .09NA NA NA 8 1900-01-08 0.87 NA .23NA NA NA 9 1900-01-09 0.26 NA .78NA NA NA 10 1900-01-10 0.23 NA NANA NA NA # figure out which columns the data are in colpos - seq(2, by = 2, length.out = n) What relation is colpos to data.matrix? # make value 1 and NA 0 colpos[!is.na(colpos)] - 1.0 colpos[is.na(colpos)] - 0.0 # sum number of values on a given day rowsum(colpos, ) Do you want by chance to get how many nonnumeric values are in each row of your data frame in station columns? If yes, try colpos - seq(2, 7, by = 2) rowSums(!is.na(data.matrix)[,colpos]) Regards Petr The above script is what i have tried - and does not work. The values are not being replaced with 1s and the NAs with 0s and the rows are not being summed. any help would be greatly appreciated. E -- View this message in context: http://n4.nabble.com/replace-NA-value-with-0- tp834446p1596779.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] recommendations on use of - operator
I have never used - but I noticed at http://github.com/jiho/r-utils/blob/master/beamer_colors.R that some people do. In fact, the above-named code has a sort of elegance about it (except for the use of = for assignment...). To my eye, - calls to mind a type of assignment that is meant to stand out. For example, perhaps it would make sense to use - to assign to things that are not expected to vary through the rest of the code block. Q1: is there a convention, informal or otherwise, on when to use the - operator? Q2: if there is no convention, but if people think a convention might help, what would that convention be? Dan Kelley, PhD Professor and Graduate Coordinator Dept. Oceanography, Dalhousie University, Halifax NS B3H 4J1 kelley@gmail.com (1-minute path on US server) or dan.kel...@dal.ca (2-hour path on Cdn server) Phone 902 494 1694; Fax 902 494 3877 [[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] language!!!
Hi, there´s something that really bothers me about R and after hours and hours of internet research, I´m still stuck with the same problem: I installed R and it is in Spanish, as the system on my work. I would really like it in English and there seems to be no way to change that!?! I´m doing an abroad internship, so my Spanish is far from perfect and my tutorial is in English. Is there any way that I´m not aware of to change the language environment of R? Thanks a lot! Katharina _ [[elided Hotmail spam]] [[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] Converting factors to numeric in a dataframe
Hi petr, Thanks for the reply. My original data is in comma separated variable (csv) format with variable names in column 1 and numeric data in the remaining columns. The read.csv command reads this data set into object name pcrdata as a dataframe where the variable names and numeric data are conserved (as required). However, when I transpose the table it becomes a matrix and all the data become character. Using the as.data.frame command coerces the matrix to a dataframe but, at the same time, changes all the data to factor. As far as I can see, for my analysis I need to coerce the data in the matrix, formed by transposition of the raw data, to factor in row 1 and numeric for the remaining rows before then converting the matrix to a dataframe, using the as.data.frame command. Is this the information you required and, if so, is what I am asking at all possible? Best wishes, Mike On 17 March 2010 15:13, Petr PIKAL petr.pi...@precheza.cz wrote: Hi r-help-boun...@r-project.org napsal dne 17.03.2010 15:23:34: I am currently trying to write a program that minimises the amount of work required for auditable qPCR data. At the moment I am using an Excel (.csv) spreadsheet as source data that has been transposed to the column format required for R to read. Unfortunately, this means I have* *to manually confirm the whole data set prior to doing any analysis, which is taking a considerable amount of time! My idea now is to read the raw data in directly and get R to do the transformation prior to analysis. The problem I now have is that, upon transposition, the data are converted to character in a matrix, rather than factor and numeric in a dataframe. I have succeeded in changing the matrix to a dataframe (via as.data.frame(object)), but this then converts all the data to factor which I cant use for my analysis since, other than the column headings, I need the data to be numeric. I have tried coercing the data to numeric using the as() and as.numeric() commands, but this has no effect on the data format. I have no experience in programming and so am at a loss as to what to do: am I making a basic error in my programming or missing something essential (or both!)? I am using R version 2.9.0 at the moment, but this will change as soon as I have sorted this issue out. Below is the code I have put together, as you can see it is VERY brief but essential to allow my analysis to proceed: pcrdata-read.csv(File_path,header=FALSE) This is supposed to be data frame already. As you did not show us any of possible clues of data type like str(pcrdata) it is difficult to say. However from your description your original data are in columns which have numeric and character data together which is not possible. I believe that there are options for reading such data. pcrdata-as.data.frame(t(pcrdata)) OK. Here you say you get data in columns but they are all character. pcrdata[2:51]-as.numeric(as.character(pcrdata)) Here it depends whether they are all numeric or if some of them shall be character (factor). Functions like those above can not be used directly on data frames. You need to use apply. apply(pcrdata, 1, as.character) Exact sequence of required functions is impossible to guess without knowing structure of your objects. You shall also consult R intro and R data manuals. Regards Petr Any help would be gratefully appreciated, Mike Glanville [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.htmlhttp://www.r-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Converting factors to numeric in a dataframe
Hi Michael r-help-boun...@r-project.org napsal dne 18.03.2010 12:02:19: Hi petr, Thanks for the reply. My original data is in comma separated variable (csv) format with variable names in column 1 and numeric data in the remaining columns. The read.csv command reads this data set into object name pcrdata as a dataframe where the variable names and numeric data are conserved (as required). However, So why not transpose only numeric part, then set it to data frame and add column names from first column. Something like (untested) pcrdata-read.csv(File_path,header=FALSE) numdata-t(pcrdata[,-1]) numdata-data.frame(numdata) names(numdata) - pcrdata[,1] Regards Petr when I transpose the table it becomes a matrix and all the data become character. Using the as.data.frame command coerces the matrix to a dataframe but, at the same time, changes all the data to factor. As far as I can see, for my analysis I need to coerce the data in the matrix, formed by transposition of the raw data, to factor in row 1 and numeric for the remaining rows before then converting the matrix to a dataframe, using the as.data.frame command. Is this the information you required and, if so, is what I am asking at all possible? Best wishes, Mike On 17 March 2010 15:13, Petr PIKAL petr.pi...@precheza.cz wrote: Hi r-help-boun...@r-project.org napsal dne 17.03.2010 15:23:34: I am currently trying to write a program that minimises the amount of work required for “auditable” qPCR data. At the moment I am using an Excel (.csv) spreadsheet as source data that has been transposed to the column format required for R to read. Unfortunately, this means I have* *to manually confirm the whole data set prior to doing any analysis, which is taking a considerable amount of time! My idea now is to read the raw data in directly and get R to do the transformation prior to analysis. The problem I now have is that, upon transposition, the data are converted to “character” in a matrix, rather than “factor” and “numeric” in a dataframe. I have succeeded in changing the matrix to a dataframe (via as.data.frame(object)), but this then converts all the data to “factor” which I can’t use for my analysis since, other than the column headings, I need the data to be numeric. I have tried coercing the data to numeric using the as() and as.numeric() commands, but this has no effect on the data format. I have no experience in programming and so am at a loss as to what to do: am I making a basic error in my programming or missing something essential (or both!)? I am using R version 2.9.0 at the moment, but this will change as soon as I have sorted this issue out. Below is the code I have put together, as you can see it is VERY brief but essential to allow my analysis to proceed: pcrdata-read.csv(File_path,header=FALSE) This is supposed to be data frame already. As you did not show us any of possible clues of data type like str(pcrdata) it is difficult to say. However from your description your original data are in columns which have numeric and character data together which is not possible. I believe that there are options for reading such data. pcrdata-as.data.frame(t(pcrdata)) OK. Here you say you get data in columns but they are all character. pcrdata[2:51]-as.numeric(as.character(pcrdata)) Here it depends whether they are all numeric or if some of them shall be character (factor). Functions like those above can not be used directly on data frames. You need to use apply. apply(pcrdata, 1, as.character) Exact sequence of required functions is impossible to guess without knowing structure of your objects. You shall also consult R intro and R data manuals. Regards Petr Any help would be gratefully appreciated, Mike Glanville [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.htmlhttp://www.r-project.org/ posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Using nlme and coxme (both!): Looking for workaround
I am trying to use nlme and coxme in one Sweave document. I have read the
thread in r-devel on the subject,
http://markmail.org/thread/snchg6ynofrzbf2v
and nlme::fixef works, but I did not understand what workaround to use when
I am calling a function in a package that I do not want to change.
Dieter
library(nlme)
library(coxme) # hides fixef, among others
deplynestedforeingpackagefunction = function(x){
# I do not want to change this function in another package
fixef(x)
}
fit - coxme(Surv(time, status) ~ age + (1|ph.ecog), lung)
fixef(fit)
fm1 - lme(distance ~ age, data = Orthodont)
nlme::fixef(fm1) # can use nlme::
#
deplynestedforeingpackagefunction(fm1) #error
R version 2.10.1 (2009-12-14)
i386-pc-mingw32
locale:
[1] LC_COLLATE=German_Germany.1252 LC_CTYPE=German_Germany.1252
[3] LC_MONETARY=German_Germany.1252 LC_NUMERIC=C
[5] LC_TIME=German_Germany.1252
attached base packages:
[1] splines stats graphics grDevices datasets utils methods
base
other attached packages:
[1] coxme_2.0 bdsmatrix_1.0 survival_2.35-8 nlme_3.1-96
loaded via a namespace (and not attached):
[1] grid_2.10.1lattice_0.18-3 tools_2.10.1
__
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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.
[R] Odp: language!!!
Hi r-help-boun...@r-project.org napsal dne 18.03.2010 11:16:26: Hi, there´s something that really bothers me about R and after hours and hours of internet research, I´m still stuck with the same problem: I installed R and it is in Spanish, as the system on my work. I would really like it in English and there seems to be no way to change that!?! I´m doing an abroad internship, so my Spanish is far from perfect and my tutorial is in English. Is there any way that I´m not aware of to change the language environment of R? Maybe ?Sys.getlocale Sys.setlocale(LC_ALL, Czech) # for Czech locale Regards Petr Thanks a lot! Katharina _ [[elided Hotmail spam]] [[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] language!!!
G'day Katharina, On Thu, 18 Mar 2010 11:16:26 +0100 Katharina Gerstendorf katharin...@hotmail.com wrote: there_s something that really bothers me about R and after hours and hours of internet research, I_m still stuck with the same problem: And during these hours of research you did not come across the R Windows FAQ available on CRAN and all mirrors? E.g.: http://cran.ms.unimelb.edu.au/bin/windows/base/rw-FAQ.html particularly question 3.2 of that FAQ: http://cran.ms.unimelb.edu.au/bin/windows/base/rw-FAQ.html#I-want-R-in-English_0021 Thanks a lot! You are welcome. Cheers, Berwin == Full address Berwin A Turlach Tel.: +61 (8) 6488 3338 (secr) School of Maths and Stats (M019)+61 (8) 6488 3383 (self) The University of Western Australia FAX : +61 (8) 6488 1028 35 Stirling Highway Crawley WA 6009e-mail: ber...@maths.uwa.edu.au Australiahttp://www.maths.uwa.edu.au/~berwin __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] language!!!
You haven't told us your OS, so it is probably Windows ... This is an FAQ, specifically http://cran.r-project.org/bin/windows/base/rw-FAQ.html#I-want-R-in-English_0021 Since you seem to be unfamiliar with FAQs, there is a lot more useful information there, and the posting guide asked you to search them before posting. (And certainly before 'hours and hours of internet research'.) If you are not on Windows, see the 'R Installation and Administration Manual' section 7.2, or if you use the R.app GUI on Mac OS X see the relevant FAQ section 9. But in general R will use the same language as your OS, and if you don't want Spanish, simply change the language of the OS. On Thu, 18 Mar 2010, Katharina Gerstendorf wrote: Hi, there?s something that really bothers me about R and after hours and hours of internet research, I?m still stuck with the same problem: I installed R and it is in Spanish, as the system on my work. I would really like it in English and there seems to be no way to change that!?! I?m doing an abroad internship, so my Spanish is far from perfect and my tutorial is in English. Is there any way that I?m not aware of to change the language environment of R? Thanks a lot! Katharina -- 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] language!!!
On 18/03/2010 6:16 AM, Katharina Gerstendorf wrote: Hi, there´s something that really bothers me about R and after hours and hours of internet research, I´m still stuck with the same problem: I installed R and it is in Spanish, as the system on my work. I would really like it in English and there seems to be no way to change that!?! I´m doing an abroad internship, so my Spanish is far from perfect and my tutorial is in English. Is there any way that I´m not aware of to change the language environment of R? Yes, set the environment variable LANGUAGE to what you want. This is described in detail in the R Installation and Administration manual. You can do this on the R command line, e.g. I normally get R in English, but can switch to Spanish by starting it as Rgui LANGUAGE=es The two letter language abbreviations are listed in http://en.wikipedia.org/wiki/ISO_639-1 and a document it links to. Duncan Murdoch Thanks a lot! Katharina _ [[elided Hotmail spam]] [[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] recommendations on use of - operator
On 18/03/2010 7:08 AM, Dan Kelley wrote: I have never used - but I noticed at http://github.com/jiho/r-utils/blob/master/beamer_colors.R that some people do. In fact, the above-named code has a sort of elegance about it (except for the use of = for assignment...). To my eye, - calls to mind a type of assignment that is meant to stand out. For example, perhaps it would make sense to use - to assign to things that are not expected to vary through the rest of the code block. Q1: is there a convention, informal or otherwise, on when to use the - operator? My recommendation would be never. It's rarely used and unnecessary, so you'll just confuse people. It also looks identical to the - operator in C for pointing to a member of a structure, another cause for confusion for some people. Duncan Murdoch Q2: if there is no convention, but if people think a convention might help, what would that convention be? Dan Kelley, PhD Professor and Graduate Coordinator Dept. Oceanography, Dalhousie University, Halifax NS B3H 4J1 kelley@gmail.com (1-minute path on US server) or dan.kel...@dal.ca (2-hour path on Cdn server) Phone 902 494 1694; Fax 902 494 3877 [[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] Care to share an R presentation?
Dear Paul, There are links to materials from two R courses that I taught fairly recent on my home page at http://socserv.mcmaster.ca/jfox/, and I always keep links to course materials there. Regards, John John Fox Senator William McMaster Professor of Social Statistics Department of Sociology McMaster University Hamilton, Ontario, Canada web: socserv.mcmaster.ca/jfox -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Paul Johnson Sent: March-18-10 12:54 AM To: R-help Subject: [R] Care to share an R presentation? The R movement is picking up steam in the center of America. People that ignored my R-enthusiasm 10 years ago are now calling me up asking for presentations. I need to make a 2 hour presentation to a collection of faculty and grad students who might like to use R. I don't want to make it seem too complicated (as I often do), but I don't want to mislead them to think it will be easy. I expect other r-help readers have been in this same situation. I have a recollection (5, 6 years ago) that one of the R leaders had a slideshow for this exact purpose. But I can't find it now. There is a R-help similar request and both John Fox and Deepayan Sarkar offered links to their materials. However, the links aren't valid anymore. If I don't find a pre-existing example to work from, I'll slap together a Beamer/Sweave presentation and post it where future speech givers can get it. -- Paul E. Johnson Professor, Political Science 1541 Lilac Lane, Room 504 University of Kansas __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] recommendations on use of - operator
- is usually only used when you suddenly remember you wanted to keep result of a computation, especially in the days before command-line editors were universal. fn(a,b) ... oh I'd better keep that ... - z On Thu, 18 Mar 2010, Dan Kelley wrote: I have never used - but I noticed at http://github.com/jiho/r-utils/blob/master/beamer_colors.R that some people do. In fact, the above-named code has a sort of elegance about it (except for the use of = for assignment...). To my eye, - calls to mind a type of assignment that is meant to stand out. For example, perhaps it would make sense to use - to assign to things that are not expected to vary through the rest of the code block. Q1: is there a convention, informal or otherwise, on when to use the - operator? Q2: if there is no convention, but if people think a convention might help, what would that convention be? Dan Kelley, PhD Professor and Graduate Coordinator Dept. Oceanography, Dalhousie University, Halifax NS B3H 4J1 kelley@gmail.com (1-minute path on US server) or dan.kel...@dal.ca (2-hour path on Cdn server) Phone 902 494 1694; Fax 902 494 3877 [[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. -- 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] Converting factors to numeric in a dataframe
Hi as you did not provide data it is hard to say what is wrong. You can see that it is working on dates similar what you described. test - data.frame(x=letters[1:10], y=rnorm(10), z=runif(10)) test x y z 1 a 0.09980806 0.32211567 2 b 0.70559139 0.32204076 3 c -1.50514354 0.28267338 testnum-data.frame(t(test[,-1])) names(testnum)-test[,1] testnum a b c d e f g y 0.09980806 0.7055914 -1.5051435 0.4421971 0.1041789 -1.54683799 0.3405809 z 0.32211567 0.3220408 0.2826734 0.8819248 0.5189688 0.05171076 0.4583101 h i j y 2.3137394 -0.4953507 0.7668954 z 0.7515886 0.5876854 0.4192073 Regards Petr Michael Glanville michael.glanvill...@googlemail.com napsal dne 18.03.2010 12:37:21: Thanks Petr, your suggestion has worked to a certain extent. The only issue is that the sample names don't appear in the final dataframe. However, I will persevere and see what I can do. Many thanks for you invaluable help, Mike On 18 March 2010 11:23, Petr PIKAL petr.pi...@precheza.cz wrote: Hi Michael r-help-boun...@r-project.org napsal dne 18.03.2010 12:02:19: Hi petr, Thanks for the reply. My original data is in comma separated variable (csv) format with variable names in column 1 and numeric data in the remaining columns. The read.csv command reads this data set into object name pcrdata as a dataframe where the variable names and numeric data are conserved (as required). However, So why not transpose only numeric part, then set it to data frame and add column names from first column. Something like (untested) pcrdata-read.csv(File_path,header=FALSE) numdata-t(pcrdata[,-1]) numdata-data.frame(numdata) names(numdata) - pcrdata[,1] Regards Petr __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Reg GARCH+ARIMA
ya it looks like you can't use predict to take in data. In general you could do the following: fit a model to n-(prediction sample set length). Then use the predict function to do a 1 step forward forecast. Test to see how close it is to the actual 1 value ahead. Then train your model on n-(prediction sample set length-1). predict 1 step ahead and compare to the next value. rinse and repeat. -Rob On Thu, Mar 18, 2010 at 2:59 AM, RAGHAVENDRA PRASAD raghav.npra...@gmail.com wrote: Hi, Thanks a lot.It was very useful to me.If i m correct we cant do real time Stock forecasting using R with ARIMA+GARCH model using garchFit or any other available packages which are avaibale in R as Predict function wont take any test data. Eg: predict(garch11sp500t, 10) We just need to give how for how many periods we need the forecast results.Is there any work around any packages avaiable where we can use test data for prediction like we have in Neural Nets package. Regards, Raghav On Wed, Mar 17, 2010 at 8:40 PM, Rob Forler rfor...@uchicago.edu wrote: Hi, I can help, but what you are saying doesn't make sense. firstly what is fitted.ga? You can use predict from the garchFit that will give the predictions for fitted.gar for example. For example, library(fGarch) library(tseries) library(moments) data = get.hist.quote(instrument=^GSPC, 1990-01-01, 2010-02-01, quote = c(AdjClose),provider=c(yahoo)) ret = diff(log(data)) garch11sp500t = garchFit(~arma(1,1) +garch(1,1), data=ret, cond.dist=std) predtsp500 = predict(garch11sp500t, 10) predtsp500 meanForecast meanError standardDeviation 1 0.0013071158 0.010497830.01049783 2 0.0011799772 0.010515550.01050872 3 0.0010749574 0.010531070.01051959 4 0.0009882084 0.010545090.01053042 5 0.0009165514 0.010558070.01054123 6 0.0008573608 0.010570340.01055201 7 0.0008084679 0.010582110.01056276 8 0.0007680811 0.010593540.01057349 9 0.0007347205 0.010604720.01058418 10 0.0007071638 0.010615720.01059485 you will see that both the mean and the standard deviation is forecasted. This gives you both the stock forecast and the stocks' volatility forecast. now comparing the models you have a lot of different options. And it cares what you are looking to use the predictions for. In the above example imagine you were using the model to trade. You would want to pick the model that gives you the best pnl. Secondly you want to look at the acf and the pacf of the standarized residuals to makes sure that there are not any significant lags. Also you may want to look at the distribution of the residuals! are they really t-distributed? you can use a qq type test to determine this. if not you may have a model misspecification. you may need to use a skewed distribution or you may need to use something like aparch (in garchFit) which fits an asymmetric model/ you also want to look at summary(garch11sp500t) look at : Error Analysis: Estimate Std. Error t value Pr(|t|) mu 1.003e-04 3.718e-052.697 0.00701 ** ar1 8.260e-01 5.913e-02 13.971 2e-16 *** ma1-8.621e-01 5.267e-02 -16.368 2e-16 *** omega 4.090e-07 1.365e-072.998 0.00272 ** alpha1 5.743e-02 6.607e-038.693 2e-16 *** beta1 9.409e-01 6.484e-03 145.123 2e-16 *** shape 6.990e+00 6.820e-01 10.249 2e-16 *** --- you can see here that all the coefficients are very significant. also, AIC BIC SIC HQIC -6.539617 -6.530588 -6.539621 -6.536455 are computed from the summary. Google these. Picking a model with a lower aic or bic can be another way to choose the model. If you need more help let me nkow, Rob On Wed, Mar 17, 2010 at 1:11 AM, RAGHAVENDRA PRASAD raghav.npra...@gmail.com wrote: Hi, Although my doubt is pretty,as i m not from stats background i am not sure how to proceed on this. Currently i am doing a forecasting.I used ARIMA to forecast and time series was volatile i used garchFit for residuals. How to use the output of Garch to correct the forecasted values from ARIMA. Here is my code: ###delta is the data fit-arima(delta,order=c(2,,0,1)) fit.res - resid(fit) ##Check for Residuals acf((fit.res-mean(fit.res))/sd(fit.res)) acf(((fit.res-mean(fit.res))/sd(fit.res))^2) fit.fore = predict(fit, n.ahead=test) ##Use ARIMA GARCH To fit residuals from ARIMA Model 1. fitted.gar-garchFit(formula =~arma(2,1)+garch(1,1),data=*fit.res*,cond.dist = std,trace=FALSE) sresi=fitted@residuals/fitted@sigma.t ###Standardised Residuals acf(sresi) acf(sresi^2) fore.res-predict(fitted.ga, n.ahead=test) OR 2. fitted.gar-garchFit(formula =~arma(2,1)+garch(1,1),data=*delta*,cond.dist = std,trace=FALSE) sresi=fitted@residuals/fitted@sigma.t ###Standardised Residuals acf(sresi) acf(sresi^2) fore.res-predict(fitted.ga, n.ahead=test)
[R] unbind matrix?
I have a function that take a variable number of arguments, each of which
must be a vector.
Is there a way to unbind a matrix that would pass the columns as vectors?
Myfunc-function(...) {
[My code]
}
Myfunc(z[,1],z[,2]) works
but Myfunc(z[,1:2]) is passing a submatrix
Is there something like Myfunc(unbind(z[,1:2])) ??
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[R] package debug not available in Ubuntu
Hi, i have 8.10 Ubuntu, R version 2.7.1 on 64 bit pc. I install packages fine, but when i try to do install.packages(debug) i get error message package 'debug' is not available Does this package exist for Ubuntu? -- View this message in context: http://n4.nabble.com/package-debug-not-available-in-Ubuntu-tp1597844p1597844.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] how to take multiple subsets from a matrix
Thank! This worked great! -- View this message in context: http://n4.nabble.com/how-to-take-multiple-subsets-from-a-matrix-tp1597411p1597899.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] Regress a matrix on another matrix column by column
Hi everyone, I have a response matrix (y) and two predictor matrices (x.a, x.b), how should i proceed if i want to regress y on x.a and x.b column by column? To be specific, what i want to do is: y[,1]~x.a[,1]+x.b[,1] y[,2]~x.a[,2]+x.b[,2] . . . I have tried lm(y~x1+x2) but it does not work as R treat that as: y[,1]~x.a[,1]+x.a[,2]+...+x.b[,1]+x.b[,2]+... . . . Thanks. Regards, Fred [[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] IRT simulation repeated
Hello R: i work on an IRT simulation research. I've written a code to generate a single dataset.As i will repeat simulating the data 100 times under every condition, how can i write the R code to make it run the single simulation code 100 times and save the generate results each time? Thanks so much~ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] package debug not available in Ubuntu
zerdna azege at yahoo.com writes: Hi, i have 8.10 Ubuntu, R version 2.7.1 on 64 bit pc. I install packages fine, but when i try to do install.packages(debug) i get error message package 'debug' is not available Does this package exist for Ubuntu? Your problem is probably R 2.7.1 (several years old) rather than Ubuntu. I have no problem installing it (Ubuntu 8.10, R 2.10.1). 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] unbind matrix?
?c
On Mar 18, 2010, at 8:39 AM, ManInMoon wrote:
I have a function that take a variable number of arguments, each of
which
must be a vector.
Is there a way to unbind a matrix that would pass the columns as
vectors?
Myfunc-function(...) {
[My code]
}
Myfunc(z[,1],z[,2]) works
but Myfunc(z[,1:2]) is passing a submatrix
Is there something like Myfunc(unbind(z[,1:2])) ??
--
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Re: [R] Regress a matrix on another matrix column by column
try this:
y - matrix(rnorm(100*100), 100, 100)
x.a - matrix(rnorm(100*100), 100, 100)
x.b - matrix(rnorm(100*100), 100, 100)
M - ncol(y)
models - vector(list, M)
for (m in 1:M) {
Dat - data.frame(y = y[, m], x.a = x.a[, m], x.b = x.b[, m])
models[[m]] - lm(y ~ ., data = Dat)
}
Moreover and depending on what exactly you want to extract from these
models, it may be even faster if you use lm.fit() instead of lm().
I hope it helps.
Best,
Dimitris
On 3/18/2010 12:35 PM, Frederick Ho wrote:
Hi everyone,
I have a response matrix (y) and two predictor matrices (x.a, x.b), how
should i proceed if i want to regress y on x.a and x.b column by column?
To be specific, what i want to do is:
y[,1]~x.a[,1]+x.b[,1]
y[,2]~x.a[,2]+x.b[,2]
.
.
.
I have tried lm(y~x1+x2) but it does not work as R treat that as:
y[,1]~x.a[,1]+x.a[,2]+...+x.b[,1]+x.b[,2]+...
.
.
.
Thanks.
Regards,
Fred
[[alternative HTML version deleted]]
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--
Dimitris Rizopoulos
Assistant Professor
Department of Biostatistics
Erasmus University Medical Center
Address: PO Box 2040, 3000 CA Rotterdam, the Netherlands
Tel: +31/(0)10/7043478
Fax: +31/(0)10/7043014
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Re: [R] Help with calculating entropy of data
Thanks Marsh, I'll look in to those references. MS -- View this message in context: http://n4.nabble.com/Help-with-calculating-entropy-of-data-tp1593954p1597963.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] PCA - blank loadings
On 17.03.2010 00:16, Xanthe Walker wrote: Hi, I have successfully completed a PCA and printed the loadings, however, numerous values are blank. I know that this means the values are just very small but not equal to zero. Is there a way to print out the loadings, including the very small values, I need them for graphing purposes. See ?loadings and find that print(loadings(pca_object), cutoff=0) shoudl print everything. Although, if you want to use the loadings for generating graphics, you should work with the output directly, since thge information in the loadings object is much more precise than its pinted representation. Too see a bit more, type, e.g.: l - loadings(pca_object) l[] Uwe Ligges Thanks, Xan [[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] Regress a matrix on another matrix column by column
Try this: mapply(function(y, x, z)lm(y ~ x + z), as.data.frame(y), as.data.frame(x.a), as.data.frame(x.b), SIMPLIFY = FALSE) On Thu, Mar 18, 2010 at 8:35 AM, Frederick Ho cres...@gmail.com wrote: Hi everyone, I have a response matrix (y) and two predictor matrices (x.a, x.b), how should i proceed if i want to regress y on x.a and x.b column by column? To be specific, what i want to do is: y[,1]~x.a[,1]+x.b[,1] y[,2]~x.a[,2]+x.b[,2] . . . I have tried lm(y~x1+x2) but it does not work as R treat that as: y[,1]~x.a[,1]+x.a[,2]+...+x.b[,1]+x.b[,2]+... . . . Thanks. Regards, Fred [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] unbind matrix?
I am trying to un-c... -- View this message in context: http://n4.nabble.com/unbind-matrix-tp1597887p1597987.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] cumsum for matrix
IIs there an equivalent of cumsum for a matrix? i.e cumsum is applied to each column ? -- View this message in context: http://n4.nabble.com/cumsum-for-matrix-tp1597985p1597985.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] unbind matrix?
Did you try it? On Mar 18, 2010, at 10:03 AM, ManInMoon wrote: I am trying to un-c... -- View this message in context: http://n4.nabble.com/unbind-matrix-tp1597887p1597987.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. David Winsemius, MD West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Using nlme and coxme (both!): Looking for workaround
On Thu, Mar 18, 2010 at 6:26 AM, Dieter Menne
dieter.me...@menne-biomed.de wrote:
I am trying to use nlme and coxme in one Sweave document. I have read the
thread in r-devel on the subject,
http://markmail.org/thread/snchg6ynofrzbf2v
and nlme::fixef works, but I did not understand what workaround to use when
I am calling a function in a package that I do not want to change.
We discussed a fix for that which is to add a line to the NAMESPACE
file for any packages that want to define methods for the fixef or
ranef generic. The line is simply
importFrom(nlme, fixef, ranef)
I thought Terry was going to add that in the coxme sources.
library(nlme)
library(coxme) # hides fixef, among others
deplynestedforeingpackagefunction = function(x){
# I do not want to change this function in another package
fixef(x)
}
fit - coxme(Surv(time, status) ~ age + (1|ph.ecog), lung)
fixef(fit)
fm1 - lme(distance ~ age, data = Orthodont)
nlme::fixef(fm1) # can use nlme::
#
deplynestedforeingpackagefunction(fm1) #error
R version 2.10.1 (2009-12-14)
i386-pc-mingw32
locale:
[1] LC_COLLATE=German_Germany.1252 LC_CTYPE=German_Germany.1252
[3] LC_MONETARY=German_Germany.1252 LC_NUMERIC=C
[5] LC_TIME=German_Germany.1252
attached base packages:
[1] splines stats graphics grDevices datasets utils methods
base
other attached packages:
[1] coxme_2.0 bdsmatrix_1.0 survival_2.35-8 nlme_3.1-96
loaded via a namespace (and not attached):
[1] grid_2.10.1 lattice_0.18-3 tools_2.10.1
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Re: [R] cumsum for matrix
Hi ManInMoon, Perhaps the following apply(yourmatrix, 2, cumsum, na.rm = TRUE) ? See ?cumsum and ?apply for more information. HTH, Jorge On Thu, Mar 18, 2010 at 10:01 AM, ManInMoon wrote: IIs there an equivalent of cumsum for a matrix? i.e cumsum is applied to each column ? -- View this message in context: http://n4.nabble.com/cumsum-for-matrix-tp1597985p1597985.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. [[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] How good is R at making publication quality tables?
Hello Everyone, At last count, I had 14 responses to my question. Thanks very much to everyone who replied, for helping me to understand that R is in fact capable of making publication quality tables and is very flexible in rendering these outputs. I'm still working my way through some of the basics of the program, but when it comes time to learn how to make tables I'll certainly know where to look for the necessary resources and information. Thanks again, Paul __ Make your browsing faster, safer, and easier with the new Internet Explorer[[elided Yahoo spam]] com/ca/internetexplorer/ [[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] unbind matrix?
I think I may have figured out what you _might_ have meant. An example would have speeded this process up considerably. Try: apply(mtx, 2, function) # perhaps within the MyFunc ... that you also did not provide. -- David. On Mar 18, 2010, at 10:03 AM, ManInMoon wrote: I am trying to un-c... -- David Winsemius, MD West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] two scales for one plot
Dear all, i am looking for a possibility to use two lines in the same plot with different scales. i.e the standard y-axis should represent the line created by vector x and the vertical line vice versa should be used as a second y-axis for the plot of vector y. I´ve seen that often, particularly in the visualization of timelines (because the x-axis remains the same) and wonder if there´s a possibility to do so in R, too. If I am on the wrong list, please let me know. Thx in advance for any help. best regards bunny __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Pedigree / Identifying Immediate Family of Index Animal
I have a data frame containing the Id, Mother, Father and Sex from about
10,000 animals in our colony. I am interested in graphing simple family
trees for a given subject or small number of subjects. The basic idea is:
start with data frame from entire colony and list of index animals. I need
to identify all immediate relatives of these index animals and plot the
pedigree for them. We're not trying to do any sort of real analysis, just
present a visualization of the family structure. I have used the kinship
and pedigree packages to plot the pedigree. My question relates to
efficiently identifying the animals to include in the pedigree:
Starting with the data frame of ~10,000 records, I want to use a set of
index animals to extract the immediate relatives and plot only a small
number in the pedigree. 'Immediate relatives' is somewhat of an ambiguous
term - I am currently defining it as 3 generations forward and 3 backward.
Currently, I have a somewhat ugly approach where I recursively calculate
each generation forward or backward and build a new dataframe. Is there a
better approach or package that does this? I realize my code should be
written better to get rid of the loops, so if anyone has suggestions there I
would appreciate this as well. Thanks in advance.
Code to calculate generations forward and backward:
#queryIds holds the unique Ids for parents of the index animals
queryIds = unique(c(ped$Sire, ped$Dam));
for(i in 1:gens){
if (length(queryIds) == 0){break};
#allPed is the dataframe with Id,Dam,Sire and Sex for animals in our
colony
newRows - subset(allPed, Id %in% queryIds);
queryIds = c(newRows$Sire, newRows$Dam);
ped - unique(rbind(newRows,ped));
}
#build forwards
#when calculating children, queryIds holds the Ids of the previous
generation
queryIds = unique(ped$Id);
for(i in 1:gens){
if (length(queryIds)==0){break};
#allPed is the dataframe with Id,Dam,Sire and Sex for animals in our
colony
newRows - subset(allPed, Sire %in% queryIds | Dam %in% queryIds);
queryIds = newRows$Id;
ped - unique(rbind(newRows,ped));
}
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Re: [R] two scales for one plot
In some sense you _are_ in the wrong list because there is a strong opposition to that presentation strategy, but there are plenty of worked examples in the archives and I believe that some plotting functions in plotrix will also do this, twoord.plot perhaps? On Mar 18, 2010, at 10:40 AM, Bunny, lautloscrew.com wrote: Dear all, i am looking for a possibility to use two lines in the same plot with different scales. i.e the standard y-axis should represent the line created by vector x and the vertical line vice versa should be used as a second y-axis for the plot of vector y. I´ve seen that often, particularly in the visualization of timelines (because the x- axis remains the same) and wonder if there´s a possibility to do so in R, too. If I am on the wrong list, please let me know. Thx in advance for any help. best regards bunny -- David Winsemius, MD West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] offlist Re: Dataframe manipulation
David,
A quick correction. I have been posting for less than one month (my first
posting was Mar 5, verify if so inclined). Thank you for making me aware of
dput and dump capabilities, I will use them in future posts. Secondly, I would
assume that all of us are either directly or indirectly seeking assistance with
'work' related R issues, either for a government agency, in school as
preparation for future paid work, or in academics where one receives a salary
for doing research, among other things. So, I don't see the relevance of your
second point. I doubt anyone here is learning R for the fun of it. I would
rather be fishing, lol. I think my attached dataframe clearly shows what I want
to do, and all I really want is some specific guidance (i.e. given relevant
functions, etc.). I would LOVE to code this on my own. Thank you for your help
thus far.
Mike
-Original Message-
From: David Winsemius [mailto:dwinsem...@comcast.net]
Sent: Thursday, March 18, 2010 10:31 AM
To: Hosack, Michael
Subject: offlist Re: [R] Dataframe manipulation
Here's why I am not taking this one one. You've been posting similar
problems for the last 6 months and you still have not learned how to
use dput or dump to create cut and pastable R object descriptions...
plus this looks like its a job and you are asking us to do your
work... but that's only of secondary importance. It's the first
concern that is primary. You are asking us to figure out what your
data really looks like and repeat lots of steps that are already done.
--
David.
On Mar 18, 2010, at 9:48 AM, Hosack, Michael wrote:
Hello R users,
I spent most of my workday yesterday trying unsuccessfully to
write code that will perform a series of calculations on my
dataframe (partial copy is attached). What I need to do is
multiply the 24 hr time in the 'DEPART' column by the time
(in the 'TRAVEL' column (travel time in minutes), and store this
result in the 'ARRIVE' column for the following 'SITE1' number.
Then I need to add the 'WAIT' time (minutes) for that site's row
to its 'ARRIVE' time to calculate the next 'DEPART' time and
then proceed down the dataframe independently for each unique 'MM'
by 'DD' combination. What I want to do I hope will be obvious after
you
view the dataframe. Basically, for each unique 'MM' (month) by
'DD'(day) grouping
I have four sites that are surveyed sequentially, and the starting
site for a survey day was chosen randomly. The route is circular,
proceeding from site 101 to 104. I really hope someone can help
me with this, because I am so close to finishing it.
BTW, the code that adds minutes to 24 hr time to create 24 hr time
is as follows:
addTime2-function(timeTxt,mins){
orig.date-as.POSIXct(paste(2001-01-01,timeTxt))
new.Date-orig.date+mins*60
new.Date-strsplit(as.character(new.Date), )
new.Time-(sapply(new.Date,[,2))
return(new.Time)
}
SCHEDULE2$DEPART-addTime2(SCHEDULE2$ARRIVE,SCHEDULE2$WAIT)
(code courtesy of Gustaf)
Thank you,
Mike
Dataframe.pdf__
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Re: [R] Dimnames of array inside loop
I read the post http://n4.nabble.com/Error-setting-rowname-if-rowname-currently-NULL-td794579.html#a794579 where it says that the problem is that dimnames(acuracia) is Null -equivalent to rownames(fred) is NULL (in the post) Then I tried to define all the dimnames first as random names to be then replaced in the loop but it did not work either? Does anyone have a clue? Thanks a lot -- View this message in context: http://n4.nabble.com/Dimnames-of-array-inside-loop-tp1594215p1598069.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] two scales for one plot
Maybe this is what you are searching for: 2-Y-axes on same plot https://stat.ethz.ch/pipermail/r-help/2008-December/182374.html Best regards, Christian Bunny, lautloscrew.com wrotes: Dear all, i am looking for a possibility to use two lines in the same plot with different scales. i.e the standard y-axis should represent the line created by vector x and the vertical line vice versa should be used as a second y-axis for the plot of vector y. I´ve seen that often, particularly in the visualization of timelines (because the x-axis remains the same) and wonder if there´s a possibility to do so in R, too. If I am on the wrong list, please let me know. Thx in advance for any help. best regards bunny __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] R takes long time to open
Hello. Until today I've been using R2.9 and since today R2.10 (on a PC). In both of them it takes about 20 sec for the prompt to appear IN R console after I start R. And every time it says: Previous saved work space restored - even if I have not saved any workspace or, in case of R2.10 - even though I have not used it once. In the older versions - R would start within 2-3 sec. Is there any way to change some setting to make R open faster? Thank you! -- Dimitri Liakhovitski Ninah.com dimitri.liakhovit...@ninah.com __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] two scales for one plot
thx everybody. The twoord.plot from the plotrix packages just helped ! Sometimes you just don´t find what you´re looking for - even if it is that simple... On 18.03.2010, at 15:59, Christian Ruckert wrote: Maybe this is what you are searching for: 2-Y-axes on same plot https://stat.ethz.ch/pipermail/r-help/2008-December/182374.html Best regards, Christian Bunny, lautloscrew.com wrotes: Dear all, i am looking for a possibility to use two lines in the same plot with different scales. i.e the standard y-axis should represent the line created by vector x and the vertical line vice versa should be used as a second y-axis for the plot of vector y. I´ve seen that often, particularly in the visualization of timelines (because the x-axis remains the same) and wonder if there´s a possibility to do so in R, too. If I am on the wrong list, please let me know. Thx in advance for any help. best regards bunny __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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 takes long time to open
Someone gave me a tip - it turns out I accidentally saved a workspace in the directory R opens in and forgot about it. I deleted it and my problem was solved. Dimitri On Thu, Mar 18, 2010 at 11:08 AM, Dimitri Liakhovitski ld7...@gmail.com wrote: Hello. Until today I've been using R2.9 and since today R2.10 (on a PC). In both of them it takes about 20 sec for the prompt to appear IN R console after I start R. And every time it says: Previous saved work space restored - even if I have not saved any workspace or, in case of R2.10 - even though I have not used it once. In the older versions - R would start within 2-3 sec. Is there any way to change some setting to make R open faster? Thank you! -- Dimitri Liakhovitski Ninah.com dimitri.liakhovit...@ninah.com -- Dimitri Liakhovitski Ninah.com dimitri.liakhovit...@ninah.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] Reshape dataframe according to ordered variables
Dear all, I am still a R apprentice... Apologies for the basic question. I am trying to reshape a dataframe based on the order of two variables (a character variable and a numerical variable). To simplify it, consider the following dataframe df-data.frame(id=c(b,b,a,a,a),ord=c(2,1,1,3,2)) id ord 1 b 2 2 b 1 3 a 1 4 a 3 5 a 2 I want to reshape it such that it results in this dataframe (id alphabetically ordered and ranked according to the ord order) df1-data.frame(id=c(a,a,a,b,b),ord=c(1,2,3,1,2)) id ord 1 a 1 2 a 2 3 a 3 4 b 1 5 b 2 Thanks in advance, Duarte Viana __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Unable to install Cairo package
Dear R users, I'm running R version 2.10.1. I tried installing the Cairo package and I got the following message: * installing *source* package Cairo ... checking for gcc... gcc -std=gnu99 checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc -std=gnu99 accepts -g... yes checking for gcc -std=gnu99 option to accept ISO C89... none needed checking how to run the C preprocessor... gcc -std=gnu99 -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/wait.h that is POSIX.1 compatible... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for string.h... (cached) yes checking sys/time.h usability... yes checking sys/time.h presence... yes checking for sys/time.h... yes checking for unistd.h... (cached) yes checking for an ANSI C-conforming const... yes checking for pkg-config... /usr/bin/pkg-config checking whether pkg-config knows about cairo... no configure: CAIRO_LIBS is unset, attempting to guess it. configure: CAIRO_CFLAGS= checking if R was compiled with the RConn patch... no checking cairo.h usability... no checking cairo.h presence... no checking for cairo.h... no configure: error: Cannot find cairo.h! Please install cairo (http://www.cairogra phics.org/) and/or set CAIRO_CFLAGS/LIBS correspondingly. ERROR: configuration failed for package Cairo Any help would be greatly appreciated. Alla __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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 takes long time to open
I have--no-save --no-restoreon my startup of R since I only save/load explicitly what I want. On Thu, Mar 18, 2010 at 11:24 AM, Dimitri Liakhovitski ld7...@gmail.comwrote: Someone gave me a tip - it turns out I accidentally saved a workspace in the directory R opens in and forgot about it. I deleted it and my problem was solved. Dimitri On Thu, Mar 18, 2010 at 11:08 AM, Dimitri Liakhovitski ld7...@gmail.com wrote: Hello. Until today I've been using R2.9 and since today R2.10 (on a PC). In both of them it takes about 20 sec for the prompt to appear IN R console after I start R. And every time it says: Previous saved work space restored - even if I have not saved any workspace or, in case of R2.10 - even though I have not used it once. In the older versions - R would start within 2-3 sec. Is there any way to change some setting to make R open faster? Thank you! -- Dimitri Liakhovitski Ninah.com dimitri.liakhovit...@ninah.com -- Dimitri Liakhovitski Ninah.com dimitri.liakhovit...@ninah.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.htmlhttp://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? [[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 return date part of POSIXct
How do I get a number representing a date from a POSIXct i.e. removing the time elements? -- View this message in context: http://n4.nabble.com/how-to-return-date-part-of-POSIXct-tp1598109p1598109.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] Reshape dataframe according to ordered variables
try this: df id ord 1 b 2 2 b 1 3 a 1 4 a 3 5 a 2 df[order(df$id, df$ord),] id ord 3 a 1 5 a 2 4 a 3 2 b 1 1 b 2 On Thu, Mar 18, 2010 at 11:27 AM, Duarte Viana viana.s...@gmail.com wrote: Dear all, I am still a R apprentice... Apologies for the basic question. I am trying to reshape a dataframe based on the order of two variables (a character variable and a numerical variable). To simplify it, consider the following dataframe df-data.frame(id=c(b,b,a,a,a),ord=c(2,1,1,3,2)) id ord 1 b 2 2 b 1 3 a 1 4 a 3 5 a 2 I want to reshape it such that it results in this dataframe (id alphabetically ordered and ranked according to the ord order) df1-data.frame(id=c(a,a,a,b,b),ord=c(1,2,3,1,2)) id ord 1 a 1 2 a 2 3 a 3 4 b 1 5 b 2 Thanks in advance, Duarte Viana __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.htmlhttp://www.r-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem that you are trying to solve? [[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] unbind matrix?
Sorry David,
Here's cut down version of my function - real version does some fancy plot
formatting.
I have found a way round my problem because cbind will bind vectors and
matrices into a single matrix, which I can work with. It is not the answer I
was looking for - but it does the job.
Many thanks...
Myfunc-function(...) {
parms-cbind(...)
for (i in 1:ncol(parms)) {
plot(parms[,i])
}
}
--
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Re: [R] how to return date part of POSIXct
Does one of these work for you:
x - as.POSIXct('2010-03-18 12:15')
x
[1] 2010-03-18 12:15:00 EDT
unclass(x)
[1] 1268928900
attr(,tzone)
[1]
as.vector(x)
[1] 1268928900
On Thu, Mar 18, 2010 at 11:18 AM, ManInMoon xmoon2...@googlemail.comwrote:
How do I get a number representing a date from a POSIXct i.e. removing the
time elements?
--
View this message in context:
http://n4.nabble.com/how-to-return-date-part-of-POSIXct-tp1598109p1598109.html
Sent from the R help mailing list archive at Nabble.com.
__
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PLEASE do read the posting guide
http://www.R-project.org/posting-guide.htmlhttp://www.r-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
What is the problem that you are trying to solve?
[[alternative HTML version deleted]]
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Re: [R] Reshape dataframe according to ordered variables
Hello Duarte, It seems that order is what you are looking for : df - df[order(df$id, df$ord), ] Regards, François -Message d'origine- De : r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] De la part de Duarte Viana Envoyé : jeudi 18 mars 2010 16:27 À : r-help Objet : [R] Reshape dataframe according to ordered variables Dear all, I am still a R apprentice... Apologies for the basic question. I am trying to reshape a dataframe based on the order of two variables (a character variable and a numerical variable). To simplify it, consider the following dataframe df-data.frame(id=c(b,b,a,a,a),ord=c(2,1,1,3,2)) id ord 1 b 2 2 b 1 3 a 1 4 a 3 5 a 2 I want to reshape it such that it results in this dataframe (id alphabetically ordered and ranked according to the ord order) df1-data.frame(id=c(a,a,a,b,b),ord=c(1,2,3,1,2)) id ord 1 a 1 2 a 2 3 a 3 4 b 1 5 b 2 Thanks in advance, Duarte Viana __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] how to return date part of POSIXct
On Mar 18, 2010, at 11:37 AM, jim holtman wrote:
Does one of these work for you:
x - as.POSIXct('2010-03-18 12:15')
x
[1] 2010-03-18 12:15:00 EDT
unclass(x)
[1] 1268928900
attr(,tzone)
[1]
as.vector(x)
[1] 1268928900
I was guessing he wanted:
x - as.POSIXct('2010-03-18 12:15')
as.Date(x)
[1] 2010-03-18
Or perhaps:
unclass(as.Date(x))
[1] 14686
Hard to know since he persists in not following the Posting Guide's
request to provide examples and specifics for the desired result.
--
David.
On Thu, Mar 18, 2010 at 11:18 AM, ManInMoon
xmoon2...@googlemail.comwrote:
How do I get a number representing a date from a POSIXct i.e.
removing the
time elements?
--
View this message in context:
http://n4.nabble.com/how-to-return-date-part-of-POSIXct-tp1598109p1598109.html
Sent from the R help mailing list archive at Nabble.com.
__
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https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.htmlhttp://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?
[[alternative HTML version deleted]]
__
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and provide commented, minimal, self-contained, reproducible code.
David Winsemius, MD
West Hartford, CT
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Re: [R] unbind matrix?
Convert your matrix to a data frame and use do.call().
?do.call
do.call(Myfunc, data.frame(yourMatrix))
You need to do the data frame conversion because do.call wants the arguments
as a list and a data frame **is** a list (the columns are the list members)
with a dim attribute (+ others).
Bert Gunter
Genentech Nonclinical Biostatistics
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf Of ManInMoon
Sent: Thursday, March 18, 2010 5:39 AM
To: r-help@r-project.org
Subject: [R] unbind matrix?
I have a function that take a variable number of arguments, each of which
must be a vector.
Is there a way to unbind a matrix that would pass the columns as vectors?
Myfunc-function(...) {
[My code]
}
Myfunc(z[,1],z[,2]) works
but Myfunc(z[,1:2]) is passing a submatrix
Is there something like Myfunc(unbind(z[,1:2])) ??
--
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Re: [R] IRT simulation repeated
result - lapply(1:100, yourFunction) On Thu, Mar 18, 2010 at 9:05 AM, Helena helenaguchen...@hotmail.com wrote: Hello R: i work on an IRT simulation research. I've written a code to generate a single dataset.As i will repeat simulating the data 100 times under every condition, how can i write the R code to make it run the single simulation code 100 times and save the generate results each time? Thanks so much~ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.htmlhttp://www.r-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem that you are trying to solve? [[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] [R-pkgs] package JM -- version 0.6-0
Dear R-users, I'd like to announce the release of the new version of package JM (soon available from CRAN) for the joint modelling of longitudinal and time-to-event data using shared parameter models. These models are applicable in mainly two settings. First, when focus is in the time-to-event outcome and we wish to account for the effect of a time-dependent covariate measured with error. Second, when focus is in the longitudinal outcome and we wish to correct for nonrandom dropout. New features include: * function survfitJM() has been added that calculates predictions of subject-specific survival probabilities given a history of longitudinal responses. * function dynC() has been added that calculates a dynamic concordance index for joint models. The function also returns time-dependent areas under the ROC curve. * method = ch-GH has been replaced by method = spline-PH-GH that fits a relative risk model with a B-spline-approximated baseline risk function. Similarly to method = ch-GH, the plan is that the same relative risk model with a B-spline-approximated baseline risk will also replace method = ch-Laplace. * method = spline-PH-GH allows for stratification, i.e., different spline coefficients are estimated for the different levels of a stratification factor. By default the knots positions are the same across strata -- this can be changed by either directly specifying the knots or by setting the control argument 'equal.strata.knots' to FALSE. * the new function wald.strata() can be used to test for equality of the spline coefficients among strata. * jointModel() has now the extra argument 'lag' that allows for lagged effects in the time-dependent covariate represented by the linear mixed model. * method = ph-GH that fits a relative risk with an unspecified baseline risk function has been renamed to method = Cox-PH-GH. * a bug was corrected in joint models with piecewise constant baseline risk function. In particular, the 'xi' parameters were reported as double their actual value. As always, any kind of feedback (e.g., questions, suggestions, bug-reports, etc.) is more than welcome. Best, Dimitris -- Dimitris Rizopoulos Assistant Professor Department of Biostatistics Erasmus University Medical Center Address: PO Box 2040, 3000 CA Rotterdam, the Netherlands Tel: +31/(0)10/7043478 Fax: +31/(0)10/7043014 ___ R-packages mailing list r-packa...@r-project.org https://stat.ethz.ch/mailman/listinfo/r-packages __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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 output to Rich Text Format
Hi, Does anyone know of an existing package that will output to rtf?
Something along the lines of pdf(ds,'file.pdf') or write.csv(ds,'file.csv').
Thanks,
//
// Alex Bryant
// Software Developer
// Integrated Clinical Systems, Inc.
// 908-996-7208
Confidentiality Note: This e-mail, and any attachment to...{{dropped:13}}
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[R] Regression of a time series on its Quarters
# Dear List, # I want to characterize a time series according to its Quarter components. # My data (a.ts: http://docs.google.com/View?id=dfvvwzr2_478cr9k4cdb) look like: # Qtr1 Qtr2 Qtr3 Qtr4 # 1948 -0.0714961837 0.0101747827 0.0654816569 -0.0227830729 # 1949 -0.1175517556 0.1151378692 0.1015777858 -0.1971535900 # 1950 0.0716002123 0.2551020416 0.0977574743 -0.0739337411 # ... # The time series is 216 long # The easiest way I could figure out, is to create # Quarter dummies: Q1 - rep(c(1,0,0,0),54) Q2 - rep(c(0,1,0,0),54) Q3 - rep(c(0,0,1,0),54) Q4 - rep(c(0,0,0,1),54) qtr - cbind(Q1,Q2,Q3,Q4) # and then regress my data on the dummies. summary(lm(a.ts ~ qtr - 1)) # The regression on 'Quarters' works fine. # It does exactly what I want it to do. # But! Surely there must be a more elegant way # to accomplish the same thing ?! # I have looked at the following packages (amongst others): # tseries, timeSeries, TSA, AER, fSeries, vars, FinTS, xts, fArma, # fRegression, tsfa, uroot, urca, ... # without finding anything more convenient (simpler, nicer!). # Any suggestion? # Thank you. # Len Vir __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] multiple print commands in win.metafile()
Hi All, I need a file which I can import to MS Word, I'm trying win.metafile(), but it does not seem to support multiple print commands at once (please see below). Is there an alternative to get plots file which can be used in powerpoint/word? # R code: # this does not work; but same thing works with pdf() library(lattice) win.metafile(test.wmf) p1 - xyplot(decrease ~ treatment, OrchardSprays, groups = rowpos, type = a, auto.key = list(space = right, points = FALSE, lines = TRUE)) p2 - xyplot(sunspot.year ~ 1700:1988, xlab = , type = l, scales = list(x = list(alternating = 2)), main = Yearly Sunspots) print(p1, split=c(1,1,2,1), more=TRUE) print(p2, split=c(2,1,2,1)) dev.off() Can anyone help please, thanks, Kim [[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 match two matrices with different dates
Dear R users, I am experiencing a problem, I am trying to merge two matrices composed like this: Matrix1 : Col1 datetime // Col2 Data1 Matrix2: Col1 datetime // Col2 Data2 The datetime are matching most of the time, but on both matrices, there are some values missing, and this generates a gap, so the two matrices don't match. Do you know which function I could use/create in order to make one matrix out of this, like: Matrix: Col1 = datetime // Col2 = Data1 // Col3 = Data2 Thank you very much for your help, Loïc. [[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] multiple print commands in win.metafile()
?win.metafile For win.metafile only one plot is allowed per file, and Windows seems to disallow reusing the file. So the *only* way to allow multiple plots is to use a parametrized filename as in the example. win.metafile(Rplot%02d.wmf, pointsize = 10) Notice the %02d in the file name. On Thu, Mar 18, 2010 at 12:36 PM, Kim Jung Hwa kimhwamaill...@gmail.comwrote: Hi All, I need a file which I can import to MS Word, I'm trying win.metafile(), but it does not seem to support multiple print commands at once (please see below). Is there an alternative to get plots file which can be used in powerpoint/word? # R code: # this does not work; but same thing works with pdf() library(lattice) win.metafile(test.wmf) p1 - xyplot(decrease ~ treatment, OrchardSprays, groups = rowpos, type = a, auto.key = list(space = right, points = FALSE, lines = TRUE)) p2 - xyplot(sunspot.year ~ 1700:1988, xlab = , type = l, scales = list(x = list(alternating = 2)), main = Yearly Sunspots) print(p1, split=c(1,1,2,1), more=TRUE) print(p2, split=c(2,1,2,1)) dev.off() Can anyone help please, thanks, Kim [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.htmlhttp://www.r-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem that you are trying to solve? [[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] Unable to install Cairo package
Alla Bulashevska wrote:
Dear R users,
I'm running R version 2.10.1.
I tried installing the Cairo package and I got the
following message:
* installing *source* package Cairo ...
{snip}
checking cairo.h usability... no
checking cairo.h presence... no
checking for cairo.h... no
configure: error: Cannot find cairo.h! Please install cairo
(http://www.cairogra
phics.org/) and/or set
CAIRO_CFLAGS/LIBS correspondingly.
ERROR: configuration failed for package Cairo
Any help would be greatly appreciated.
Alla
The Cairo package for R provides an interface to the Cairo graphics library-
therefore that library must be installed for the package to work. Configure
scripts are notorious for having cryptic error messages, but this one is
actually very explicit about stating what the problem is.
You need to:
1. Install Cairo and try installing the package again.
Or, if you have Cairo installed in a non-standard location that the
configure script can't find:
2. Set -L/path/to/libcairo in the CAIRO_CFLAGS option and try installing
again.
In cases when package installation is failing, it is also very important to
tell us what operating system you are using as these issues are often
platform-dependent.
Hope this helps!
-Charlie
-
Charlie Sharpsteen
Undergraduate-- Environmental Resources Engineering
Humboldt State University
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Re: [R] How to match two matrices with different dates
PLEASE do read the posting guide http://www.R-project.org/posting-guide.htmlhttp://www.r-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. example data would be useful. Try 'merge' and the post processing of the data, but with no data, no idea of what that might entail. On Thu, Mar 18, 2010 at 12:40 PM, Loïc Marechal lym.marec...@gmail.comwrote: Dear R users, I am experiencing a problem, I am trying to merge two matrices composed like this: Matrix1 : Col1 datetime // Col2 Data1 Matrix2: Col1 datetime // Col2 Data2 The datetime are matching most of the time, but on both matrices, there are some values missing, and this generates a gap, so the two matrices don't match. Do you know which function I could use/create in order to make one matrix out of this, like: Matrix: Col1 = datetime // Col2 = Data1 // Col3 = Data2 Thank you very much for your help, LoÄc. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.htmlhttp://www.r-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem that you are trying to solve? [[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] Constrained non linear regression using ML
Dear Gabor, Arne, Ravi, R users, I am firstly trying the maximum likelihood approach, then will try the Bayesian approach. The likelihood function, and the log likelihood function, will depend on the pdf of the error e in the formula: y=f(theta*x)+e Now let's say that e is Gaussian distributed, then I can use LS which is the same as ML in this case, and the residuals would be distributed Gaussian. Is that right? If e is distributed differently (for example: beta, in the continuous case, or binomial, in the discrete case), then I am better off by using Maximum Likelihood. How would the residual be distributed? Should they not be distributed the same as e? Best, Gabor Grothendieck wrote: For specific questions on the betareg package contact the maintainer. If the likelihood based approaches are giving too much difficulty try moving to a Bayesian framework (WinBUGS/R2WinBUGS, JAGS/r2jags, etc.) On Wed, Mar 17, 2010 at 10:03 AM, Corrado ct...@york.ac.uk wrote: Dear Arne, Gabor, I solved the problem with betareg (downloaded the package). I run it on my data, and unfortunately the constraint is definitively active, if I remove the active variables, I then remove the most significant variables! Of course the error is important, not the distribution of the variable. In this case, one of the assumptions is that the error may be distributed ~ beta. I think that betareg makes this assumption, am I right? I am finding it difficult to solve two problems: 1) write the maximum likelihood function (what do you suggest?) 2) deal with the fact that a few factors actually have values of y (the response) at the extremes: that is 0 and 1. But that mean that the link function returns Infinite values in that case 3) the error is dependent on E(y). PS: Additional silly question: what is the discrete equivalent of beta? binomial? Arne Henningsen wrote: On 17 March 2010 14:22, Gabor Grothendieck ggrothendi...@gmail.com wrote: Contact the maintainer regarding problems with the package. Not sure if this is acceptable but if you get it to run you could consider just dropping the variables from your model that correspond to active constraints. Also try the maxLik package. You will have to define the likelihood yourself but it does support constraints. Yes. And specifying the likelihood function is probably (depending on your distributional assumptions) not too complicated. BTW: Even if your y follows a beta distribution, it does not mean that your error term also follows a beta distribution. And it the distribution of the error term which is crucial for specifying the likelihood function. /Arne -- Corrado Topi PhD Researcher Global Climate Change and Biodiversity Area 18,Department of Biology University of York, York, YO10 5YW, UK Phone: + 44 (0) 1904 328645, E-mail: ct...@york.ac.uk -- Corrado Topi PhD Researcher Global Climate Change and Biodiversity Area 18,Department of Biology University of York, York, YO10 5YW, UK Phone: + 44 (0) 1904 328645, E-mail: ct...@york.ac.uk __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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 multiple output
I am trying pairwise t-test with thousands of genes in different sample group
so I am trying some code like:
for (i in 1:length(GENE)){
array[i]-pairwise.t.test(AGE6TTEST[[GENE[i]]],Lable,p.adj=fdr)
}
I want to put the output in an array list, then I can check them, but seems
I have the problem since there are multiple lines in the output of
pairwise.t.test. I usually only got the first line in the array[i] and also
warning messages.
I tried
a1-pairwise.t.test(AGE6TTEST[[GENe[1]]],Lable,p.adj=fdr)
It worked
My questions, when I do these huge pairwise comparison, how can I output the
results ?
Thanks,
Meng
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Re: [R] how to return date part of POSIXct
You are right David - I found the as.Date by myself eventually(must be getting better at this!) But unclass is new to me - thanks very much -- View this message in context: http://n4.nabble.com/how-to-return-date-part-of-POSIXct-tp1598109p1598250.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] [R-pkgs] spikeslab 1.0.0 now available on CRAN
Please find release 1.0.0 of the new CRAN package spikeslab now available for download. Thank you. - RELEASE 1.0.0 is the first and initial release of this package. Fits a rescaled spike and slab model using a continuous bimodal prior. Can be used for prediction and variable selection in low and high-dimensional linear regression models. Key features include: o Option for ultra-fast handling of high-dimensional data. o Variable selection using the generalized elastic net (gnet). o Grouping of variables with unique regularization (no limit on the number). o Predict wrapper for predicting on test data. o Sparse PC approach for multiclass analysis of gene expression data. o Depends on the randomForest and lars R-packages. - kogalursh...@gmail.com Udaya B. Kogalur, Ph.D. Adjunct Staff, Dept of Quantitative Health Sciences, Cleveland Clinic Foundation President, Kogalur Shear Corporation 5425 Nestleway Drive, Suite L1 Clemmons, NC 27012 ___ R-packages mailing list r-packa...@r-project.org https://stat.ethz.ch/mailman/listinfo/r-packages __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Using indexing to manipulate data
-Original Message-
From: r-help-boun...@r-project.org
[mailto:r-help-boun...@r-project.org] On Behalf Of Jim Lemon
Sent: Thursday, March 18, 2010 1:33 AM
To: duncandonutz
Cc: r-help@r-project.org
Subject: Re: [R] Using indexing to manipulate data
On 03/18/2010 04:05 PM, duncandonutz wrote:
I know one of R's advantages is it's ability to index,
eliminating the need
for control loops to select relevant data, so I thought
this problem would
be easy. I can't crack it. I have looked through past
postings, but
nothing seems to match this problem
I have a data set with one column of actors and one column
of acts. I need
a list that will give me a pair of actors in each row,
provided they both
participated in the act.
Example:
The Data looks like this:
Jim A
BobA
BobC
Larry D
Alice C
Tom F
Tom D
Tom A
Alice B
NancyB
I would like this:
Jim Bob
Jim Tom
Bob Alice
Larry Tom
AliceNancy
The order doesn't matter (Jim-Bob vs. Bob-Jim), but each
pairing should be
counted only once.
You can use merge() to get all possible within-
group pairings and then eliminate the self-pairings
and the same-but-for-order pairings with the following
code:
data - read.table(header=FALSE, textConnection(
+ Jim A
+ BobA
+ BobC
+ Larry D
+ Alice C
+ Tom F
+ Tom D
+ Tom A
+ Alice B
+ NancyB
+ )) # column names are now V1 and V2
# add seqence numbers for elimination step
data$seq - seq_len(nrow(data))
tmp - merge(data,data,by=V2)
result - tmp[tmp$seq.x tmp$seq.y,] # omit unwanted pairings
result
V2 V1.x seq.x V1.y seq.y
2 A Jim 1 Bob 2
3 A Jim 1 Tom 8
6 A Bob 2 Tom 8
11 B Alice 9 Nancy10
15 C Bob 3 Alice 5
20 D Larry 4 Tom 7
Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com
Hi duncandonutz,
Try this:
actnames-read.table(junkfunc/names.dat,stringsAsFactors=FALSE)
actorpairs-NULL
for(act in unique(actnames$V2)) {
actors-actnames$V1[actnames$V2 == act]
nactors-length(actors)
if(nactors 1) {
indices-combn(nactors,2)
for(i in 1:dim(indices)[2])
actorpairs-
rbind(actorpairs,c(actors[indices[1,i]],actors[indices[2,i]]))
}
}
actorpairs
Jim
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Re: [R] How to match two matrices with different dates
Hello jim, thank you for your quick answer! Here is an example: *TIME1**DATA1* *TIME2 DATA2* 2 14:38:00 1.07212 14:38:00 1.51339 3 *14:40:00 1.07195 14:39:00 1.51330* 4 14:41:00 1.07218 14:40:00 1.51335 5 14:42:00 1.07246 14:41:00 1.51326 6 14:43:00 1.07229 14:42:00 1.51310 7 14:45:00 1.07226 14:45:00 1.51310 8 *14:46:00 1.07205 14:48:00 1.51357* 9 14:47:00 1.07078 14:49:00 1.51375 10 14:48:00 1.07155 14:50:00 1.51359 11 14:49:00 1.07184 14:51:00 1.51406 12 14:50:00 1.07114 14:52:00 1.51458 And I would like to get from this only one matrix, with the matching time and the corresponding data. Of course, some rows from one or another matrix will have to be removed. Thank you very much again for your help! Loïc. 2010/3/18 jim holtman jholt...@gmail.com PLEASE do read the posting guide http://www.R-project.org/posting-guide.htmlhttp://www.r-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. example data would be useful. Try 'merge' and the post processing of the data, but with no data, no idea of what that might entail. On Thu, Mar 18, 2010 at 12:40 PM, Loïc Marechal lym.marec...@gmail.comwrote: Dear R users, I am experiencing a problem, I am trying to merge two matrices composed like this: Matrix1 : Col1 datetime // Col2 Data1 Matrix2: Col1 datetime // Col2 Data2 The datetime are matching most of the time, but on both matrices, there are some values missing, and this generates a gap, so the two matrices don't match. Do you know which function I could use/create in order to make one matrix out of this, like: Matrix: Col1 = datetime // Col2 = Data1 // Col3 = Data2 Thank you very much for your help, LoÄc. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.htmlhttp://www.r-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem that you are trying to solve? [[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] Regression of a time series on its Quarters
Try this: lm(a.ts ~ factor(cycle(a.ts)) - 1) On Thu, Mar 18, 2010 at 12:30 PM, Len Vir len...@gmail.com wrote: # Dear List, # I want to characterize a time series according to its Quarter components. # My data (a.ts: http://docs.google.com/View?id=dfvvwzr2_478cr9k4cdb) look like: # Qtr1 Qtr2 Qtr3 Qtr4 # 1948 -0.0714961837 0.0101747827 0.0654816569 -0.0227830729 # 1949 -0.1175517556 0.1151378692 0.1015777858 -0.1971535900 # 1950 0.0716002123 0.2551020416 0.0977574743 -0.0739337411 # ... # The time series is 216 long # The easiest way I could figure out, is to create # Quarter dummies: Q1 - rep(c(1,0,0,0),54) Q2 - rep(c(0,1,0,0),54) Q3 - rep(c(0,0,1,0),54) Q4 - rep(c(0,0,0,1),54) qtr - cbind(Q1,Q2,Q3,Q4) # and then regress my data on the dummies. summary(lm(a.ts ~ qtr - 1)) # The regression on 'Quarters' works fine. # It does exactly what I want it to do. # But! Surely there must be a more elegant way # to accomplish the same thing ?! # I have looked at the following packages (amongst others): # tseries, timeSeries, TSA, AER, fSeries, vars, FinTS, xts, fArma, # fRegression, tsfa, uroot, urca, ... # without finding anything more convenient (simpler, nicer!). # Any suggestion? # Thank you. # Len Vir __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Regression of a time series on its Quarters
On Thu, 18 Mar 2010, Gabor Grothendieck wrote: Try this: lm(a.ts ~ factor(cycle(a.ts)) - 1) An equivalent but somewhat more convenient interface is available in dynlm where you can say dynlm(a.ts ~ season(a.ts)) or dynlm(a.ts ~ season(a.ts) - 1): R dynlm(a.ts ~ season(a.ts)) Time series regression with ts data: Start = 1947(2), End = 2000(4) Call: dynlm(formula = a.ts ~ season(a.ts)) Coefficients: (Intercept) season(a.ts)Q2 season(a.ts)Q3 season(a.ts)Q4 0.03069 0.01310-0.19455 0.09481 Best, Z On Thu, Mar 18, 2010 at 12:30 PM, Len Vir len...@gmail.com wrote: # Dear List, # I want to characterize a time series according to its Quarter components. # My data (a.ts: http://docs.google.com/View?id=dfvvwzr2_478cr9k4cdb) look like: # Qtr1 Qtr2 Qtr3 Qtr4 # 1948 -0.0714961837 0.0101747827 0.0654816569 -0.0227830729 # 1949 -0.1175517556 0.1151378692 0.1015777858 -0.1971535900 # 1950 0.0716002123 0.2551020416 0.0977574743 -0.0739337411 # ... # The time series is 216 long # The easiest way I could figure out, is to create # Quarter dummies: Q1 - rep(c(1,0,0,0),54) Q2 - rep(c(0,1,0,0),54) Q3 - rep(c(0,0,1,0),54) Q4 - rep(c(0,0,0,1),54) qtr - cbind(Q1,Q2,Q3,Q4) # and then regress my data on the dummies. summary(lm(a.ts ~ qtr - 1)) # The regression on 'Quarters' works fine. # It does exactly what I want it to do. # But! Surely there must be a more elegant way # to accomplish the same thing ?! # I have looked at the following packages (amongst others): # tseries, timeSeries, TSA, AER, fSeries, vars, FinTS, xts, fArma, # fRegression, tsfa, uroot, urca, ... # without finding anything more convenient (simpler, nicer!). # Any suggestion? # Thank you. # Len Vir __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] list names
So I have a list variable, and each item has a name. Is it possible to return just the names in the list and not the contents of each one? Example: Currently, if I have a list variable matrices, and it contains 3 matrices, M1, M2, and M3, if I type: matrices, R returns $M1 - listing of numbers in matrix; $M2 - listing of numbers in matrix, and $M3 - listing of numbers in the matrix. Is there a way to have it return only the names $M1, $M2, $M3? I know this seems trivial and I'm sure it has been asked before, but I can't find it. Thanks in advance. -Robert Robert M. Flight, Ph.D. Bioinformatics and Biomedical Computing Laboratory University of Louisville Louisville, KY PH 502-852-0467 EM robert.fli...@louisville.edu EM rfligh...@gmail.com Williams and Holland's Law: If enough data is collected, anything may be proven by statistical methods. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] list names
Robert M. Flight wrote: So I have a list variable, and each item has a name. Is it possible to return just the names in the list and not the contents of each one? Example: Currently, if I have a list variable matrices, and it contains 3 matrices, M1, M2, and M3, if I type: matrices, R returns $M1 - listing of numbers in matrix; $M2 - listing of numbers in matrix, and $M3 - listing of numbers in the matrix. Is there a way to have it return only the names $M1, $M2, $M3? I know this seems trivial and I'm sure it has been asked before, but I can't find it. Thanks in advance. -Robert ?names The help.search() function can be useful for finding functions when you know what you want to get done, but not which function does it. For example: help.search( names ) Would list several functions and their descriptions would help you find the one you wanted. -Charlie - Charlie Sharpsteen Undergraduate-- Environmental Resources Engineering Humboldt State University -- View this message in context: http://n4.nabble.com/list-names-tp1598316p1598330.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] list names
On Mar 18, 2010, at 1:12 PM, Robert M. Flight wrote: So I have a list variable, and each item has a name. Is it possible to return just the names in the list and not the contents of each one? ?names Example: Currently, if I have a list variable matrices, and it contains 3 matrices, M1, M2, and M3, if I type: matrices, R returns $M1 - listing of numbers in matrix; $M2 - listing of numbers in matrix, and $M3 - listing of numbers in the matrix. Is there a way to have it return only the names $M1, $M2, $M3? I know this seems trivial and I'm sure it has been asked before, but I can't find it. Thanks in advance. -Robert Robert M. Flight, Ph.D. Bioinformatics and Biomedical Computing Laboratory University of Louisville Louisville, KY PH 502-852-0467 EM robert.fli...@louisville.edu EM rfligh...@gmail.com Williams and Holland's Law: If enough data is collected, anything may be proven by statistical methods. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. David Winsemius, MD West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Pedigree / Identifying Immediate Family of Index Animal
On Thu, 18 Mar 2010, Ben Bimber wrote:
I have a data frame containing the Id, Mother, Father and Sex from about
10,000 animals in our colony. I am interested in graphing simple family
trees for a given subject or small number of subjects. The basic idea is:
start with data frame from entire colony and list of index animals. I need
to identify all immediate relatives of these index animals and plot the
pedigree for them. We're not trying to do any sort of real analysis, just
present a visualization of the family structure. I have used the kinship
and pedigree packages to plot the pedigree. My question relates to
efficiently identifying the animals to include in the pedigree:
Starting with the data frame of ~10,000 records, I want to use a set of
index animals to extract the immediate relatives and plot only a small
number in the pedigree. 'Immediate relatives' is somewhat of an ambiguous
term - I am currently defining it as 3 generations forward and 3 backward.
Currently, I have a somewhat ugly approach where I recursively calculate
each generation forward or backward and build a new dataframe. Is there a
better approach or package that does this? I realize my code should be
written better to get rid of the loops, so if anyone has suggestions there I
would appreciate this as well. Thanks in advance.
Using an indicator matrix for parent/child relations, you can identify
future/past generations using matrix multiplication(s).
Since you have 1 animals, the matrix indicating parents/children will
be 1 x 1, but will have 2 non-zero elements.
To me, this sounds like a good candidate for a sparse matrix
representation. Packages 'Matrix' and 'SparseM' provide these.
HTH,
Chuck
Code to calculate generations forward and backward:
#queryIds holds the unique Ids for parents of the index animals
queryIds = unique(c(ped$Sire, ped$Dam));
for(i in 1:gens){
if (length(queryIds) == 0){break};
#allPed is the dataframe with Id,Dam,Sire and Sex for animals in our
colony
newRows - subset(allPed, Id %in% queryIds);
queryIds = c(newRows$Sire, newRows$Dam);
ped - unique(rbind(newRows,ped));
}
#build forwards
#when calculating children, queryIds holds the Ids of the previous
generation
queryIds = unique(ped$Id);
for(i in 1:gens){
if (length(queryIds)==0){break};
#allPed is the dataframe with Id,Dam,Sire and Sex for animals in our
colony
newRows - subset(allPed, Sire %in% queryIds | Dam %in% queryIds);
queryIds = newRows$Id;
ped - unique(rbind(newRows,ped));
}
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Charles C. Berry(858) 534-2098
Dept of Family/Preventive Medicine
E mailto:cbe...@tajo.ucsd.edu UC San Diego
http://famprevmed.ucsd.edu/faculty/cberry/ La Jolla, San Diego 92093-0901
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[R] Using a function to consolidate variables
Dear List,
I'm getting the error: object of type 'closure' is not subsettable
And am not sure how to get around the problem. I've included two
short code sets below. One that shows what I want to do and works,
but without using the function much, and another that tries to use the
function but causes the error.
# THIS WORKS AND SHOWS WHAT I'D LIKE TO DO
a - c(1,2,3)
b - c(5,6,0)
c - data.frame(a,b)
# TAKES THE MAX OF TWO VARS AND SAVES IT TO A NEW VARIABLE AND DELETES OLD
VARIABLES
consolidate.fun - function( data, var1, var2, saved.max ) {
max - apply( data[,c(var1, var2)], 1, max)
# THIS WORKS BUT I HAVE TO CALL THE DATA FRAME BY NAME RATHER THEN USING THE
FUNCTION DATA NAME
c[,var.max] - max
c$a - NULL
c$b - NULL
}
consolidate.fun( data=c , var1=a, var2=b, saved.max=var.max )
c
# THIS SHOWS THE MORE COMPLETE USE OF THE FUNCTION'S INTENT, BUT
# CAUSES THE ERROR IN R.
a - c(1,2,3)
b - c(5,6,0)
c - data.frame(a,b)
# TAKES THE MAX OF TWO VARS AND SAVES IT TO A NEW VARIABLE AND DELETES OLD
VARIABLES
consolidate.fun - function( data, var1, var2, saved.max ) {
max - apply( data[,c(var1, var2)], 1, max)
# SOURCE OF ERROR. I'VE TRIED CALLING THE DATA FRAME IN DIFFERENT
# WAYS, BUT NONE SEEM TO WORK FOR ME.
data[, saved.max ] - max
data[, var1 ] - NULL
data[, var2 ] - NULL
}
consolidate.fun( data=c , var1=a, var2=b, saved.max=var.max )
c
Any helpful comments would be appreciated.
mailto:dyo...@telefonica.net
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Re: [R] multiple print commands in win.metafile()
Hi Jim, thank you for your reply. Apart from win.metafile(), is there some other function available which can handle multiple prints or par(mfrow=c(2,2)) command and eventually can be used in powerpoint/word. thanks, Kim On Thu, Mar 18, 2010 at 12:42 PM, jim holtman jholt...@gmail.com wrote: ?win.metafile For win.metafile only one plot is allowed per file, and Windows seems to disallow reusing the file. So the *only* way to allow multiple plots is to use a parametrized filename as in the example. win.metafile(Rplot%02d.wmf, pointsize = 10) Notice the %02d in the file name. On Thu, Mar 18, 2010 at 12:36 PM, Kim Jung Hwa kimhwamaill...@gmail.com wrote: Hi All, I need a file which I can import to MS Word, I'm trying win.metafile(), but it does not seem to support multiple print commands at once (please see below). Is there an alternative to get plots file which can be used in powerpoint/word? # R code: # this does not work; but same thing works with pdf() library(lattice) win.metafile(test.wmf) p1 - xyplot(decrease ~ treatment, OrchardSprays, groups = rowpos, type = a, auto.key = list(space = right, points = FALSE, lines = TRUE)) p2 - xyplot(sunspot.year ~ 1700:1988, xlab = , type = l, scales = list(x = list(alternating = 2)), main = Yearly Sunspots) print(p1, split=c(1,1,2,1), more=TRUE) print(p2, split=c(2,1,2,1)) dev.off() Can anyone help please, thanks, Kim [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.htmlhttp://www.r-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem that you are trying to solve? [[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 output to Rich Text Format
Hi, Does anyone know of an existing package that will output to rtf? Something along the lines of pdf(ds,'file.pdf') or write.csv(ds,'file.csv'). You could use odfWeave and then use OpenOffice to generate an RTF file. Regards, Tom __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R and getting a file through https
Thank you! I did not know about this resource. Caveman On Thu, Mar 18, 2010 at 6:26 AM, David Winsemius dwinsem...@comcast.net wrote: On Mar 18, 2010, at 12:03 AM, Orvalho Augusto wrote: Dears! I have a system that generates links on a https webserver. I have to be logged on with a username and password; Then follow at least fife links to get into the link where I can download the file. The question is: How can I accomplish that with R? RSiteSearch(password https rcurl) Leading to: http://finzi.psych.upenn.edu/Rhelp10/2009-August/208582.html Caveman __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] merge.zoo produces non unique chron time series
Dear all, merge.zoo produces duplicated time indexes in the example stated below. Can anybody explain, what I am doing wrong? Many thanks! Jan (R 2.10.0, WindowsXP) require(chron) require(zoo) # create time series (zoo.ts) with no data from 31Aug2009 14:50 to 3Sep2009 7:25 t.st - chron(31/08/2009,09:20:00,format=c(d/m/Y,h:m:s)) t.nd - chron(31/08/2009,14:50:00,format=c(d/m/Y,h:m:s)) t.indexA-seq(t.st,t.nd,by=1/(24*12)) t.st - chron(03/09/2009,07:25:00,format=c(d/m/Y,h:m:s)) t.nd - chron(03/09/2009,23:55:00,format=c(d/m/Y,h:m:s)) t.indexB-seq(t.st,t.nd,by=1/(24*12)) t.index-c(t.indexA,t.indexB) zoo.ts - zoo(0,t.index) # create reference time series (zoo.ts.pot) without missing time steps t.st - head(time(zoo.ts),1) t.nd - tail(time(zoo.ts),1) t.index-seq(t.st,t.nd,by=1/(24*12)) zoo.ts.pot - zoo(NA,t.index) # merge erroneous time series with reference time series zoo.ts.cor - merge.zoo(zoo.ts.pot,zoo.ts) Do not run: Results: zoo.ts.pot zoo.ts (31/08/09 09:20:00) NA 0 (31/08/09 09:25:00) NA 0 (31/08/09 09:30:00) NA 0 ... (31/08/09 14:50:00) NA 0 (31/08/09 14:55:00) NA NA (31/08/09 15:00:00) NA NA (31/08/09 15:05:00) NA NA ... (03/09/09 07:15:00) NA NA (03/09/09 07:20:00) NA NA (03/09/09 07:25:00) NA 0 (03/09/09 07:30:00) NA 0 (03/09/09 07:35:00) NA 0 (03/09/09 07:40:00) NA 0 (03/09/09 07:45:00) NA 0 (03/09/09 07:50:00) NA 0 (03/09/09 07:55:00) NA 0 (03/09/09 08:00:00) NA 0 # everything o.k. up to here (03/09/09 08:00:00) NA NA # from here: every tenth time stamp is duplicated. Why? ... (03/09/09 08:45:00) NA 0 (03/09/09 08:45:00) NA NA .. (03/09/09 09:30:00) NA 0 (03/09/09 09:30:00) NA NA ... __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] greek symbols on ylab=
Hi All, I'm trying to get following but not successfully: # this works okay ylab=expression(PM2.5 Concentration (*mu*g/m^3*)) # But I need 2.5 as a subscript to PM and below this an additional line saying some text, like. ylab=expression(PM[2.5] Concentration (*mu*g/m^3*)\n(random text in brackets)) Square brackets doesn't seem to work because I'm using them in and \n operator is not working too. Any help would be highly appreciated, thanks, Peng Cai [[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] strptime(): on Linux system it seems to call system time?
Dear List, For what I understand, strptime() simply converts from one class representation to another; i.e., from character to POSIXct/POSIXlt. One strange feature of this command running on Linux is that there are repeated calls to system time (as was revealed in a trace of system calls), which considerably affect performance. These system calls end up taking almost 75% of the execution time, and are completely unnecessary. Code: ptm - proc.time() for (i in 1:10) strptime(2010-03-10 17:00:00, %F %H:%M:%S) (proc.time() -ptm) Output on Windows Box (32-bit R 2.9.1 running on Intel X5472 @ 3.0 GHz): user system elapsed 1.310.021.30 Output on Linux Box (64-bit R 2.10.1 running on Intel Xeon E5520 @ 2.27GHz): user system elapsed 3.338.94112.273 Any help would be appreciated. Also, if I should turn to a different mailing list for this, please let me know. Regards, Alex [[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] greek symbols on ylab=
Try this: par(mar = c(5.1, 6, 4, 2)) plot(1, ylab = '') mtext(expression(PM[2.5] ~ Concentration ~(mu*g/m^3)), side = 2, line = 4) mtext((random text in brackets), side = 2, line = 3, cex = 0.8) On Thu, Mar 18, 2010 at 3:02 PM, Peng Cai pengcaimaill...@gmail.com wrote: Hi All, I'm trying to get following but not successfully: # this works okay ylab=expression(PM2.5 Concentration (*mu*g/m^3*)) # But I need 2.5 as a subscript to PM and below this an additional line saying some text, like. ylab=expression(PM[2.5] Concentration (*mu*g/m^3*)\n(random text in brackets)) Square brackets doesn't seem to work because I'm using them in and \n operator is not working too. Any help would be highly appreciated, thanks, Peng Cai [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] multiple print commands in win.metafile()
It depends on what you want them for. With win.metafile, what is the problem with multiple files? You can still include them in powerpoint/word. If you want it in one file, then use PDF and you can cut/paste the graph from the pages that you want. I typically create a PDF file if I have a number of graphs and then use the 'snapshot' under Adobe Reader to capture the output for my document. It usually has enough resolution. On Thu, Mar 18, 2010 at 1:41 PM, Kim Jung Hwa kimhwamaill...@gmail.comwrote: Hi Jim, thank you for your reply. Apart from win.metafile(), is there some other function available which can handle multiple prints or par(mfrow=c(2,2)) command and eventually can be used in powerpoint/word. thanks, Kim On Thu, Mar 18, 2010 at 12:42 PM, jim holtman jholt...@gmail.comwrote: ?win.metafile For win.metafile only one plot is allowed per file, and Windows seems to disallow reusing the file. So the *only* way to allow multiple plots is to use a parametrized filename as in the example. win.metafile(Rplot%02d.wmf, pointsize = 10) Notice the %02d in the file name. On Thu, Mar 18, 2010 at 12:36 PM, Kim Jung Hwa kimhwamaill...@gmail.com wrote: Hi All, I need a file which I can import to MS Word, I'm trying win.metafile(), but it does not seem to support multiple print commands at once (please see below). Is there an alternative to get plots file which can be used in powerpoint/word? # R code: # this does not work; but same thing works with pdf() library(lattice) win.metafile(test.wmf) p1 - xyplot(decrease ~ treatment, OrchardSprays, groups = rowpos, type = a, auto.key = list(space = right, points = FALSE, lines = TRUE)) p2 - xyplot(sunspot.year ~ 1700:1988, xlab = , type = l, scales = list(x = list(alternating = 2)), main = Yearly Sunspots) print(p1, split=c(1,1,2,1), more=TRUE) print(p2, split=c(2,1,2,1)) dev.off() Can anyone help please, thanks, Kim [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.htmlhttp://www.r-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem that you are trying to solve? -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem that you are trying to solve? [[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] probable timezone confusion with as.yearmon
It looks like a timezone issue, and it's causing confusion to me at least. My original data: gmt - c(19880101 , 19880101 0100, 19880101 0300, 19880101 0400, 19880101 0500, 19880101 0600) These were converted to local dates/times with akst-strptime(gmt,format=%Y%m%d %H%M)-(3600*9) # because I want local standard, not daylight savings time. dput(akst) structure(c(567993600, 567997200, 568004400, 568008000, 568011600, 568015200), class = c(POSIXt, POSIXct), tzone = ) Which looks like this on my system: akst [1] 1987-12-31 15:00:00 AKST 1987-12-31 16:00:00 AKST 1987-12-31 18:00:00 AKST [4] 1987-12-31 19:00:00 AKST 1987-12-31 20:00:00 AKST 1987-12-31 21:00:00 AKST but why does this happen? z-as.yearmon(akst); z [1] Jan 1988 Jan 1988 Jan 1988 Jan 1988 Jan 1988 Jan 1988 I would expect this: [1] Dec 1987 Dec 1987 Dec 1987 Dec 1987 Dec 1987 Dec 1987 which I can get to by doing this: z-as.yearmon(akst-(3600*9)); z [1] Dec 1987 Dec 1987 Dec 1987 Dec 1987 Dec 1987 Dec 1987 But I don't understand why the first one doesn't give the answer I expect (and would like). Thanks for any help- Peter sessionInfo() R version 2.10.1 Patched (2010-03-16 r51294) i386-pc-mingw32 locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] zoo_1.6-2 loaded via a namespace (and not attached): [1] grid_2.10.1lattice_0.18-3 tools_2.10.1 Sys.timezone() [1] AKDT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] greek symbols on ylab=
xyplot(1:10 ~ 1:10, ylab=list(expression(atop(PM[2.5] ~ Concentration ~ frac(mu*g,m^3),(random text in brackets, crt=90) See ?plotmath for atop and many more functions [[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] Please help with loop, thanks
indiv - LETTERS[1:4]
for(i in seq_along(indiv)) assign(indiv[i], rnorm(10))
A
[1] -0.4140121 -0.8506043 -1.6704603 -0.3153009 1.9337826 -0.7736769
[7] -0.7906979 0.6925713 2.4678820 0.3889229
B
[1] -0.03521033 -0.01071611 -0.74209425 1.36974281 -1.22775441 0.29621976
[7] 0.28208192 -2.11044822 0.06657930 -0.18036208
C
[1] 0.8473888 0.5028627 2.4445523 0.6908494 2.2145275 -0.1589881
[7] -0.4135572 0.1313484 -0.8689705 -0.9267220
D
[1] -1.95177791 0.12495833 0.06847564 1.18425425 -1.16638075 -0.30278432
[7] -0.30268288 0.79178229 0.53021849 -0.32030840
HTH,
Dennis
On Thu, Mar 18, 2010 at 11:44 AM, Mark Na mtb...@gmail.com wrote:
Dear R helpers,
I would like to write a loop that makes 4 objects (called A, B, C, and D)
each of which contains ten random numbers.
This attempt:
individuals-c(A,B,C,D)
for(i in 1:length(individuals)) {
individuals[i]-rnorm(10)
}
does not work because individuals[i] is not the proper way to extract
each
letter from the object called individuals (rather, it tries to assign the
random numbers to various positions within individual)
So, my question is, what should be to the left of the gets operator in the
third line?
Many thanks,
Mark Na
[[alternative HTML version deleted]]
__
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PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[[alternative HTML version deleted]]
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] Please help with loop, thanks
Dear R helpers,
I would like to write a loop that makes 4 objects (called A, B, C, and D)
each of which contains ten random numbers.
This attempt:
individuals-c(A,B,C,D)
for(i in 1:length(individuals)) {
individuals[i]-rnorm(10)
}
does not work because individuals[i] is not the proper way to extract each
letter from the object called individuals (rather, it tries to assign the
random numbers to various positions within individual)
So, my question is, what should be to the left of the gets operator in the
third line?
Many thanks,
Mark Na
[[alternative HTML version deleted]]
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] merge.zoo produces non unique chron time series
It occurs because the two series have times that are slightly
different. For example, it may appear that the times at positions 909
and 910 are the same but in fact they are different:
tt - time(zoo.ts.cor)[909:910]; tt
[1] (03/09/09 12:30:00) (03/09/09 12:30:00)
diff(as.numeric(tt))
[1] 1.818989e-12
Here are two ways to deal with this:
# 1. Use a different date/time class.
# 2. Round off inputs to merge:
rnd - function(x) round(24 * 3600 * x + 0.5) / (24 * 3600)
Rnd - function(x) {
time(x) - chron(rnd(as.numeric(time(x
x
}
zoo.ts.cor.rnd - merge.zoo(Rnd(zoo.ts.pot), Rnd(zoo.ts))
# 3. zoo provides a facility for the user to change how matching is done.
#Define a MATCH method for the class of interest. In this case
its done like this:
# rnd function is from above
MATCH.chron - function(x, table, nomatch = NA, ...) {
match(rnd(as.numeric(x)), rnd(as.numeric(table)), nomatch = nomatch,
...)
}
zoo.ts.cor.ok - merge.zoo(zoo.ts.pot, zoo.ts)
On Thu, Mar 18, 2010 at 2:00 PM, Jan Schwanbeck jschw...@gmail.com wrote:
Dear all,
merge.zoo produces duplicated time indexes in the example stated below. Can
anybody explain, what I am doing wrong?
Many thanks!
Jan
(R 2.10.0, WindowsXP)
require(chron)
require(zoo)
# create time series (zoo.ts) with no data from 31Aug2009 14:50 to 3Sep2009
7:25
t.st - chron(31/08/2009,09:20:00,format=c(d/m/Y,h:m:s))
t.nd - chron(31/08/2009,14:50:00,format=c(d/m/Y,h:m:s))
t.indexA-seq(t.st,t.nd,by=1/(24*12))
t.st - chron(03/09/2009,07:25:00,format=c(d/m/Y,h:m:s))
t.nd - chron(03/09/2009,23:55:00,format=c(d/m/Y,h:m:s))
t.indexB-seq(t.st,t.nd,by=1/(24*12))
t.index-c(t.indexA,t.indexB)
zoo.ts - zoo(0,t.index)
# create reference time series (zoo.ts.pot) without missing time steps
t.st - head(time(zoo.ts),1)
t.nd - tail(time(zoo.ts),1)
t.index-seq(t.st,t.nd,by=1/(24*12))
zoo.ts.pot - zoo(NA,t.index)
# merge erroneous time series with reference time series
zoo.ts.cor - merge.zoo(zoo.ts.pot,zoo.ts)
Do not run: Results:
zoo.ts.pot zoo.ts
(31/08/09 09:20:00) NA 0
(31/08/09 09:25:00) NA 0
(31/08/09 09:30:00) NA 0
...
(31/08/09 14:50:00) NA 0
(31/08/09 14:55:00) NA NA
(31/08/09 15:00:00) NA NA
(31/08/09 15:05:00) NA NA
...
(03/09/09 07:15:00) NA NA
(03/09/09 07:20:00) NA NA
(03/09/09 07:25:00) NA 0
(03/09/09 07:30:00) NA 0
(03/09/09 07:35:00) NA 0
(03/09/09 07:40:00) NA 0
(03/09/09 07:45:00) NA 0
(03/09/09 07:50:00) NA 0
(03/09/09 07:55:00) NA 0
(03/09/09 08:00:00) NA 0
# everything o.k. up to here
(03/09/09 08:00:00) NA NA
# from here: every tenth time stamp is duplicated. Why?
...
(03/09/09 08:45:00) NA 0
(03/09/09 08:45:00) NA NA
..
(03/09/09 09:30:00) NA 0
(03/09/09 09:30:00) NA NA
...
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Using a function to consolidate variables
David -
I think what you're looking for is something like this:
mydat = data.frame(a=c(1,2,3),b=c(5,1,4))
consolidate.fun = function(data,var1,var2,saved.max){
+data$saved.max = apply(data[,c(var1,var2)],1,max)
+data[,var1] = NULL
+data[,var2] = NULL
+data
+ }
mydat = consolidate.fun(mydat,'a','b','var.max')
mydat
saved.max
1 5
2 6
3 3
(I changed the name of the data frame, because c is a function
name, and using it as a data frame name causes confusiion.)
The - operator only operates on complete objects, not
columns within a data frame.
- Phil Spector
Statistical Computing Facility
Department of Statistics
UC Berkeley
spec...@stat.berkeley.edu
On Thu, 18 Mar 2010, David Young wrote:
Dear List,
I'm getting the error: object of type 'closure' is not subsettable
And am not sure how to get around the problem. I've included two
short code sets below. One that shows what I want to do and works,
but without using the function much, and another that tries to use the
function but causes the error.
# THIS WORKS AND SHOWS WHAT I'D LIKE TO DO
a - c(1,2,3)
b - c(5,6,0)
c - data.frame(a,b)
# TAKES THE MAX OF TWO VARS AND SAVES IT TO A NEW VARIABLE AND DELETES OLD
VARIABLES
consolidate.fun - function( data, var1, var2, saved.max ) {
max - apply( data[,c(var1, var2)], 1, max)
# THIS WORKS BUT I HAVE TO CALL THE DATA FRAME BY NAME RATHER THEN USING THE
FUNCTION DATA NAME
c[,var.max] - max
c$a - NULL
c$b - NULL
}
consolidate.fun( data=c , var1=a, var2=b, saved.max=var.max )
c
# THIS SHOWS THE MORE COMPLETE USE OF THE FUNCTION'S INTENT, BUT
# CAUSES THE ERROR IN R.
a - c(1,2,3)
b - c(5,6,0)
c - data.frame(a,b)
# TAKES THE MAX OF TWO VARS AND SAVES IT TO A NEW VARIABLE AND DELETES OLD
VARIABLES
consolidate.fun - function( data, var1, var2, saved.max ) {
max - apply( data[,c(var1, var2)], 1, max)
# SOURCE OF ERROR. I'VE TRIED CALLING THE DATA FRAME IN DIFFERENT
# WAYS, BUT NONE SEEM TO WORK FOR ME.
data[, saved.max ] - max
data[, var1 ] - NULL
data[, var2 ] - NULL
}
consolidate.fun( data=c , var1=a, var2=b, saved.max=var.max )
c
Any helpful comments would be appreciated.
mailto:dyo...@telefonica.net
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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__
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Re: [R] Please help with loop, thanks
better yet consider using a list:
result - list()
individuals-c(A,B,C,D)
for (i in individuals) result[[i]] - runif(10)
result
$A
[1] 0.61464497 0.55715954 0.32877732 0.45313145 0.50044097 0.18086636
0.52963060 0.07527575 0.27775593 0.21269952
$B
[1] 0.28479048 0.89509410 0.44623532 0.77998489 0.88061903 0.41312421
0.06380848 0.33548749 0.72372595 0.33761533
$C
[1] 0.6304141 0.8406146 0.8561317 0.3913593 0.3804939 0.8954454 0.6443158
0.7410786 0.6053034 0.9030816
$D
[1] 0.2937302 0.1912601 0.8864509 0.5033395 0.8770575 0.1891936 0.7581031
0.7244989 0.9437248 0.5476466
On Thu, Mar 18, 2010 at 2:44 PM, Mark Na mtb...@gmail.com wrote:
Dear R helpers,
I would like to write a loop that makes 4 objects (called A, B, C, and D)
each of which contains ten random numbers.
This attempt:
individuals-c(A,B,C,D)
for(i in 1:length(individuals)) {
individuals[i]-rnorm(10)
}
does not work because individuals[i] is not the proper way to extract
each
letter from the object called individuals (rather, it tries to assign the
random numbers to various positions within individual)
So, my question is, what should be to the left of the gets operator in the
third line?
Many thanks,
Mark Na
[[alternative HTML version deleted]]
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PLEASE do read the posting guide
http://www.R-project.org/posting-guide.htmlhttp://www.r-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
What is the problem that you are trying to solve?
[[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] Please help with loop, thanks
Many thanks to everyone who helped me solve this problem.
I think I must have described my problem poorly, but Phil, Patrick and Jim
were able to see through the haze and suggest that I use a list to contain
the output from my loop. This solution works very well.
Thanks again for your help, Mark
On Thu, Mar 18, 2010 at 12:44 PM, Mark Na mtb...@gmail.com wrote:
Dear R helpers,
I would like to write a loop that makes 4 objects (called A, B, C, and D)
each of which contains ten random numbers.
This attempt:
individuals-c(A,B,C,D)
for(i in 1:length(individuals)) {
individuals[i]-rnorm(10)
}
does not work because individuals[i] is not the proper way to extract
each letter from the object called individuals (rather, it tries to assign
the random numbers to various positions within individual)
So, my question is, what should be to the left of the gets operator in the
third line?
Many thanks,
Mark Na
--
Mark Na
University of Saskatchewan
Saskatoon, Canada
[[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.
