Re: [R] appending to a vector
Neither is the fastest method. The best way would be to vectorize func so
that it accepts and returns a vector. Many builtin R functions do this and
say so in their documentation.
The slower way would be to use one of the apply functions, such as:
?lapply
x2 - lapply(x, func)
If you must use a for loop, your second example is faster since it does
not rewrite x2 each iteration.
An excellent reference on this subject and many other R pitfalls is 'The R
Inferno'
http://lib.stat.cmu.edu/s/Spoetry/Tutor/R_inferno.pdf
--
Jonathan P. Daily
Technician - USGS Leetown Science Center
11649 Leetown Road
Kearneysville WV, 25430
(304) 724-4480
Is the room still a room when its empty? Does the room,
the thing itself have purpose? Or do we, what's the word... imbue it.
- Jubal Early, Firefly
r-help-boun...@r-project.org wrote on 04/14/2011 04:59:04 AM:
[image removed]
[R] appending to a vector
dirknbr
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Which one is more efficient?
x2=c()
for (i in 1:length(x)) {
x2=c(x2,func(x[i]))
}
or
x2=x
for (i in 1:length(x)) {
x2=func(x[i])
}
where func is any function?
Dirk
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Re: [R] Using help in Windows version of R with disabled browser
try: options(help_type = 'text') ?options If this works, you can create a site profile (A default is created automatically in windows, if I remember correctly) where you can set this to run in each session. -- Jonathan P. Daily Technician - USGS Leetown Science Center 11649 Leetown Road Kearneysville WV, 25430 (304) 724-4480 Is the room still a room when its empty? Does the room, the thing itself have purpose? Or do we, what's the word... imbue it. - Jubal Early, Firefly From: Ranjan Maitra mai...@iastate.edu To: R-help r-h...@stat.math.ethz.ch Date: 04/12/2011 01:56 PM Subject: [R] Using help in Windows version of R with disabled browser Sent by: r-help-boun...@r-project.org Dear colleagues, I am trying to get someone to use R on MS Windows with the browser disabled. My question is how does he/she get to use R-help which goes off the browser (and correspondingly complains about the inability to start firefox, etc). In linux, which is what I use, this is not a problem: what needs to be set in Windows to replicate this behavior? Sorry if I am not clear: please feel free to ask me for clarifications. Thanks again for the helpful advice! Best wishes, Ranjan __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] RExcel
It is asking the obvious, but did you run the commands from the rcom package after installation (see inline ***s)? -- Jonathan P. Daily Technician - USGS Leetown Science Center 11649 Leetown Road Kearneysville WV, 25430 (304) 724-4480 Is the room still a room when its empty? Does the room, the thing itself have purpose? Or do we, what's the word... imbue it. - Jubal Early, Firefly r-help-boun...@r-project.org wrote on 04/11/2011 02:08:02 PM: [image removed] [R] RExcel array chip to: r-help 04/11/2011 02:12 PM Sent by: r-help-boun...@r-project.org Hi, I am installing Excel using package RExcelInstaller. When I tried to run installRExcel() I got this error message: You don not have the R package rcom installed. The (D)COM server installed which will aloow you to use the background server in RExcel. Since rcom is not installed, foreground mode will be unavailable. You may continue with the installation, but in most circumstances you probably should cancel current installation, install the package rcom properly (do not forget to run the commands library(rcom) comRegisterRegistry() immediately after installation) and after that run this installer once again But rcom package was installed without any problem, somehow the installer keeps saying that rcom is not installed. Any suggestions? Thanks John sessionInfo() R version 2.12.2 (2011-02-25) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] 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] RExcelInstaller_3.1-13 rcom_2.2-3.1 rscproxy_1.3-1 loaded via a namespace (and not attached): [1] tools_2.12.2 [[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] Estimates at each iteration
I'm assuming that English is not your first language. In light of that, I would suggest that you post your question in a language that we both speak: R. Please include: 1) E-step and M-step functions. 2) The proposed optim/maxLik call. Mostly because (at least optim) does not have a parameter called limiter. HtoH, Jon -- Jonathan P. Daily Technician - USGS Leetown Science Center 11649 Leetown Road Kearneysville WV, 25430 (304) 724-4480 Is the room still a room when its empty? Does the room, the thing itself have purpose? Or do we, what's the word... imbue it. - Jubal Early, Firefly r-help-boun...@r-project.org wrote on 04/08/2011 08:16:36 AM: [image removed] [R] Estimates at each iteration hello bye to: r-help 04/08/2011 11:45 AM Sent by: r-help-boun...@r-project.org Dear Sir\ Madam I am trying to maximise a complicated loglikelihood function via EM algorithm which consists of two step E-step and M-stepand in this case I need to maximize the expected of like lihood function which I get from E- step and take those estimates of parameter to update the E-step and repate these till convargence has been met. So I need to know if I control the number of iterlim in maxLik or optim Package by puting this number equals to one to maximize M-step and getting just the estimates of parameter for one iteration and hence use them to update the E-step and again maximaize M-step by using maxLik or optim by contoling the number of limiter and putting the number equals to 1 is it true and acceptance? I mean if I do this my results can be reasonable?. please I am waiting your response. Regards Fauzia Taweab phd.student. [[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] How to *completely* stop a script after stop()?
Would options(error = recover) be of some help? -- Jonathan P. Daily Technician - USGS Leetown Science Center 11649 Leetown Road Kearneysville WV, 25430 (304) 724-4480 Is the room still a room when its empty? Does the room, the thing itself have purpose? Or do we, what's the word... imbue it. - Jubal Early, Firefly r-help-boun...@r-project.org wrote on 04/08/2011 12:38:37 PM: [image removed] Re: [R] How to *completely* stop a script after stop()? Duncan Murdoch to: algorimancer 04/08/2011 12:40 PM Sent by: r-help-boun...@r-project.org Cc: r-help On 08/04/2011 11:47 AM, algorimancer wrote: I too am encountering this problem. When I have a large script, if I select all in the editor and then ctrl-r to run, if it encounters a stop() function it simply prints an error message and continues to execute the remainder of the script, as opposed to terminating execution at that line. The quit() function exits R altogether, which I don't want. Yes, I could manually select only the portion of script which I want to run, but for lengthy scripts which I run repeatedly (generally changing only the name of the file I want analyzed), this can be quite tedious. It appears that the only solution is to put most of the code in a separate file and call it using source(); this has the downside of reducing the clarity of the code -- it's a sort-of structural spaghetti code approach. It sounds as though you are talking about the Windows GUI. That's important, because other GUIs probably have different behaviour. To run a script up to the first error, do this: Highlight the part you want to run (or Ctrl-a for everything). Copy the code using Ctrl-c. In the console, run source(clipboard) (perhaps with echo=TRUE if you want to see it as it goes). This is a lot of typing the first time you do it, but after that, the up arrow can bring back the command. It would probably make sense for Ctrl-R to do something functionally equivalent to Ctrl-C, source(clipboard, echo=TRUE) rather than the current behaviour. Not going to happen in 2.13.x, but maybe in 2.14.x in the fall. Duncan Murdoch -- View this message in context: http://r.789695.n4.nabble.com/How- to-completely-stop-a-script-after-stop-tp3218808p3436704.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-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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 graphics straight from R into published articles
I think you should google search Sweave, as well as check out the ?Sweave page. Not to mention the graphics devices that embed quite nicely into documents, like ?postscript. HTH, Jon -- Jonathan P. Daily Technician - USGS Leetown Science Center 11649 Leetown Road Kearneysville WV, 25430 (304) 724-4480 Is the room still a room when its empty? Does the room, the thing itself have purpose? Or do we, what's the word... imbue it. - Jubal Early, Firefly r-help-boun...@r-project.org wrote on 03/29/2011 12:31:18 PM: [image removed] [R] Using graphics straight from R into published articles blanco to: r-help 03/29/2011 12:44 PM Sent by: r-help-boun...@r-project.org Hi, I have been working with R for the past couple of years; analyzing data and producing some graphics. I was just wondering if people use graphics from R straight into articles or are they always edited in some way; fonts, headers, axis, color etc? Using photoshop or some other programs? I would like to think it is possible, better and more profession to do it all in R. I tried google and the search option but found nothing on the topic. What are the experiences for all the professionals out there that use R? Are there any articles on this specific subject? thanks, blanco -- View this message in context: http://r.789695.n4.nabble.com/Using- graphics-straight-from-R-into-published-articles-tp3415401p3415401.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] passing arguments via ...
It is not clear to me exactly what you are looking to do, but if you are
trying to check whether an argument has been passed via ..., I have used
this convention before.
fun - function(arg, ...) {
opts - list(...)
if('opt' %in% names(opts)) # Do something...
}
Does that help?
--
Jonathan P. Daily
Technician - USGS Leetown Science Center
11649 Leetown Road
Kearneysville WV, 25430
(304) 724-4480
Is the room still a room when its empty? Does the room,
the thing itself have purpose? Or do we, what's the word... imbue it.
- Jubal Early, Firefly
r-help-boun...@r-project.org wrote on 03/29/2011 01:47:41 PM:
[image removed]
[R] passing arguments via ...
Cable, Samuel B Civ USAF AFMC AFRL/RVBXI
to:
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03/29/2011 01:51 PM
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I would like to do something like the following:
Fancyhist-function(x,...) {
# first, process x into xprocess somehow, then ...
if (is.null(breaks)) { # yes, I know this is wrong
# define the histogram breaks somehow, then call hist:
hist(xprocess,breaks=breaks,...)
} else {
# use breaks give in calling argument
hist(xprocess,...)
}
}
But, those of you who know R better than I do have already spotted that
is.null(breaks) just won't work. Neither does exists or missing.
I can think of ways to do this involving new arguments with new names --
like histbreaks or something -- but that seems inelegant.
Is there a way to do what I am trying to do here?
Thanks.
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Re: [R] ) Error in eval(expr, envir, enclos) : object '' not found
It looks like your column name has periods in it somewhere. Is your header separated by something other than commas? look at: names(data.sex) or test by age %in% names(data.sex) -- Jonathan P. Daily Technician - USGS Leetown Science Center 11649 Leetown Road Kearneysville WV, 25430 (304) 724-4480 Is the room still a room when its empty? Does the room, the thing itself have purpose? Or do we, what's the word... imbue it. - Jubal Early, Firefly r-help-boun...@r-project.org wrote on 03/23/2011 09:31:40 AM: [image removed] [R] ) Error in eval(expr, envir, enclos) : object '' not found mipplor to: r-help 03/23/2011 10:11 AM Sent by: r-help-boun...@r-project.org datafilename=E:/my documents/r/sex/bysex1.csv data.sex=read.table(datafilename,header=T) data.sex y.sex.age.region.c.n 1 1980,F,A,N,-18.15,13.61 2 1980,F,A,N,-18.61,13.04 3 1980,F,A,N,-18.81,12.32 41990,F,A,N,-21.12,11.7 5 1990,F,A,N,-20.77,11.58 61990,F,A,N,-21.6,13.34 71990,F,A,N,-21.78,12.6 model.anova-aov(c~age*sex,data=data.sex) Error in eval(expr, envir, enclos) : object 'age' not found i just wanna do a anova test. but the error message is as above,,, what should i do to shoot this problem ? Should i define the age? -- View this message in context: http://r.789695.n4.nabble.com/Error- in-eval-expr-envir-enclos-object-not-found-tp3399503p3399503.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] memory increasing
1) What kind of file is a .dta? 2) Do you have more RAM than R is using? Check this with ?memory.limit 3) Are you on a 64 bit OS with 64 bit R? I can tell you that starting R with --max-mem-size= may help, but you probably want to look into R interfaces with databases first. -- Jonathan P. Daily Technician - USGS Leetown Science Center 11649 Leetown Road Kearneysville WV, 25430 (304) 724-4480 Is the room still a room when its empty? Does the room, the thing itself have purpose? Or do we, what's the word... imbue it. - Jubal Early, Firefly r-help-boun...@r-project.org wrote on 03/22/2011 10:17:13 AM: [image removed] [R] memory increasing graziella to: r-help 03/22/2011 10:33 AM Sent by: r-help-boun...@r-project.org Dear All, I am an Italian researcher in Economics. I work with large sample data. I need to increase the memory in R-project in order to upload a file .dta. How can I do this? Thank you. graziella -- View this message in context: http://r.789695.n4.nabble.com/memory- increasing-tp3396511p3396511.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] Understanding tryCatch
tryCatch will only execute it's error function on errors. If you are getting warnings, you may find it helpful to set: options(warn = 2) ?options tryCatch(warning(!), error = function(x) print(Error!)) -- Jonathan P. Daily Technician - USGS Leetown Science Center 11649 Leetown Road Kearneysville WV, 25430 (304) 724-4480 Is the room still a room when its empty? Does the room, the thing itself have purpose? Or do we, what's the word... imbue it. - Jubal Early, Firefly r-help-boun...@r-project.org wrote on 03/18/2011 03:04:41 PM: [image removed] [R] Understanding tryCatch steven mosher to: r-help 03/18/2011 03:07 PM Sent by: r-help-boun...@r-project.org I've read the help and the archives on tryCatch but I'm still stuggling trying to understand how it works exactly and how I can use it to get the result I need. I have a data.frame of urls which point to 11 .zip files. Basically I use RCurl to get the list of files from a ftp and then reduce that directory dump to the 11 zip files I want to download. Its easy enough to do that in a loop over the elements in data.frame. The problem is that the site is very inconsistent. All 11 files will download, but I will get random warnings that the size of some of the files does not match what was downloaded. So at the end of the loop I may get 5 warnings about the file size not matching. These files, when tried a second or third time, will eventually download properly. What I want to do is record which files had this download warning. [[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] a question
What operating system are you working with? On windows, making it run by double clicking on it from explorer is not going to work. You will probably have to write a batch file that invokes Rterm or Rscript (see documentation for which you want to use). So if your script file is myscript.r, you could use Rterm myscript.r so long as the R executable directory is in the search path. On linux, make sure to start your script starts with #!/usr/bin/env Rscript, and make it executable (i.e. chmod +x myscript.r). Now it should run when you type ./myscript.r HTH, Jon -- Jonathan P. Daily Technician - USGS Leetown Science Center 11649 Leetown Road Kearneysville WV, 25430 (304) 724-4480 Is the room still a room when its empty? Does the room, the thing itself have purpose? Or do we, what's the word... imbue it. - Jubal Early, Firefly r-help-boun...@r-project.org wrote on 03/16/2011 06:18:09 AM: [image removed] [R] a question Jeela Mohammadian to: r-help 03/16/2011 08:59 AM Sent by: r-help-boun...@r-project.org Hi, I must seek a favour regarding of R project, can we make an application out of R. I mean a small application that automatically runs and do the estimation automatically. Because the things I do is that I copy codes from script to work book and then it runs and gives the output. can it be done automatically? I will appreaciate if you could answer. Best Regards Jeela [[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] Scope of variable?
?cat
cat prints text, and returns an invisible NULL. Also, it is general
practice to assign values using '-' even inside of functions, for reasons
detailed in ?-
--
Jonathan P. Daily
Technician - USGS Leetown Science Center
11649 Leetown Road
Kearneysville WV, 25430
(304) 724-4480
Is the room still a room when its empty? Does the room,
the thing itself have purpose? Or do we, what's the word... imbue it.
- Jubal Early, Firefly
r-help-boun...@r-project.org wrote on 03/16/2011 07:41:36 AM:
[image removed]
[R] Scope of variable?
Ravi Kulkarni
to:
r-help
03/16/2011 09:07 AM
Sent by:
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I know this is a very elementary question... I could not find a solution
looking at old posts.
I am unable to access a variable outside the scope of a for loop, even
when
the variable was defined before the loop:
haar - function() {
a = c(1.4560773, 2.3752412, 0.9798882, 3.0909252, 2.3986487, 1.8581543)
for (i in c(1:100)) {
m = matrix(rnorm(36)+1i*rnorm(36),6)
qrm = qr(m)
Q = qr.Q(qrm)
eival = eigen(Q, only.values=T)
ph = Arg(eival$values)
v = Mod(ph)
a = cat(a,v)
}
hist(a)
}
The hist command does not plot because a is null there.
How do I plot a? I tried using
assign(a, a, envir = .GlobalEnv)
but that does not help either... Neither did using -
Any help is most welcome.
Ravi
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[R] (no subject)
I was wondering if there is a way to get read in a single keystroke at a time in R as a string, akin to ncurses-style interfaces. I looked into readLines, readChar, etc. using stdin, but these all require the use of an end of line. Has anyone ever had need to do this or have any ideas on how to do this? Thanks, Jon PS I apologize if this double-sends, but I am having mail client issues. -- Jonathan P. Daily Technician - USGS Leetown Science Center 11649 Leetown Road Kearneysville WV, 25430 (304) 724-4480 Is the room still a room when its empty? Does the room, the thing itself have purpose? Or do we, what's the word... imbue it. - Jubal Early, Firefly __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Keyboard Input
I apologize for being unclear in my original post. What I am trying to achieve is to capture the stdin() connection and read in a single keystroke - including arrow keys and the like - without having to have to use the return key each time. My goal is to create a small UI for rapidly looking through the results of a large simulation. As I think about it more, though, it is probably going to be easier to dump the data into files and look through it outside of R. Thanks anyways, Jon -- Jonathan P. Daily Technician - USGS Leetown Science Center 11649 Leetown Road Kearneysville WV, 25430 (304) 724-4480 Is the room still a room when its empty? Does the room, the thing itself have purpose? Or do we, what's the word... imbue it. - Jubal Early, Firefly Bert Gunter gunter.ber...@gene.com wrote on 03/15/2011 10:08:51 AM: [image removed] Re: [R] (no subject) Bert Gunter to: Jonathan P Daily 03/15/2011 10:08 AM Cc: r-help ?strsplit x - ThisIsaString y- strsplit(x,) This gives a list, which you can convert to a vector by unlist(y) Incidentally, you could have found out about strsplit via R's help.search(character string) (or similar) or even googling R string function . Please use R's native Help capabilities before posting to the list. (I will grant that the unlist() trick may not be that easy to find). Also, it's often worthwhile searching the Help archives first. Peter Dalgaard answered this same question here a day or two ago. Cheers, Bert On Tue, Mar 15, 2011 at 6:35 AM, Jonathan P Daily jda...@usgs.gov wrote: I was wondering if there is a way to get read in a single keystroke at a time in R as a string, akin to ncurses-style interfaces. I looked into readLines, readChar, etc. using stdin, but these all require the use of an end of line. Has anyone ever had need to do this or have any ideas on how to do this? Thanks, Jon PS I apologize if this double-sends, but I am having mail client issues. -- Jonathan P. Daily Technician - USGS Leetown Science Center 11649 Leetown Road Kearneysville WV, 25430 (304) 724-4480 Is the room still a room when its empty? Does the room, the thing itself have purpose? Or do we, what's the word... imbue it. - Jubal Early, Firefly __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Bert Gunter Genentech Nonclinical Biostatistics __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] indeterminate for loop
?while
You don't want a for loop. You need a while loop.
--
Jonathan P. Daily
Technician - USGS Leetown Science Center
11649 Leetown Road
Kearneysville WV, 25430
(304) 724-4480
Is the room still a room when its empty? Does the room,
the thing itself have purpose? Or do we, what's the word... imbue it.
- Jubal Early, Firefly
r-help-boun...@r-project.org wrote on 03/15/2011 10:14:21 AM:
[image removed]
[R] indeterminate for loop
lm609
to:
r-help
03/15/2011 10:16 AM
Sent by:
r-help-boun...@r-project.org
Hello,
I have written a 'for' loop which on the first run makes nearest
neighbour
calculations for my dataset 'A' in relation to dataset 'B', then based
on
these results, some of the rows from A are moved into dataset B, and the
calculation is repeated on the remaining rows in A. Therefore a smaller
and
smaller amount of data is analysed as the loop proceeds, since A is
losing
rows each time. The results of the calculation change as less data is
used,
but not in a predictable way, therefore the end point of the loop is
indeterminate.
The script is long and the datasets big, but a simplified example where
'A'
and 'B' are datasets, and the function 'ndist2' calculates 'x' is...
for (i in 1:100)
{
C - data.frame(ndist2(B,A))
C1 - subset(C, x = min(C$x))
B - rbind(B, C1)
A - subset(C, x min(C$x))
}
So eventually A runs out.
Currently, I let the loop run until a warning comes up which effectively
says no more data, and at this point it is finished.
What I would now like to do is place this loop inside another loop in
order
to run through multiple datasets, but I can't do this when the script
produces a warning message at the end of each dataset.
Is there any way I can overcome this problem?
Thanks for your help,
Louise
__
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Re: [R] Keyboard Input
Solved. Thanks. -- Jonathan P. Daily Technician - USGS Leetown Science Center 11649 Leetown Road Kearneysville WV, 25430 (304) 724-4480 Is the room still a room when its empty? Does the room, the thing itself have purpose? Or do we, what's the word... imbue it. - Jubal Early, Firefly Gabor Grothendieck ggrothendi...@gmail.com wrote on 03/15/2011 10:38:34 AM: [image removed] Re: [R] Keyboard Input Gabor Grothendieck to: Jonathan P Daily 03/15/2011 10:38 AM Cc: Bert Gunter, r-help On Tue, Mar 15, 2011 at 10:29 AM, Jonathan P Daily jda...@usgs.gov wrote: I apologize for being unclear in my original post. What I am trying to achieve is to capture the stdin() connection and read in a single keystroke - including arrow keys and the like - without having to have to use the return key each time. My goal is to create a small UI for rapidly looking through the results of a large simulation. As I think about it more, though, it is probably going to be easier to dump the data into files and look through it outside of R. See: http://r.789695.n4.nabble.com/detecting-a-key-press-td2324938.html -- Statistics Software Consulting GKX Group, GKX Associates Inc. tel: 1-877-GKX-GROUP email: ggrothendieck at gmail.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] tryCatch - Continuing for/next loop after error
--
Jonathan P. Daily
Technician - USGS Leetown Science Center
11649 Leetown Road
Kearneysville WV, 25430
(304) 724-4480
Is the room still a room when its empty? Does the room,
the thing itself have purpose? Or do we, what's the word... imbue it.
- Jubal Early, Firefly
r-help-boun...@r-project.org wrote on 03/10/2011 03:51:15 AM:
[image removed]
[R] tryCatch - Continuing for/next loop after error
Costas
to:
r-help
03/10/2011 03:53 AM
Sent by:
r-help-boun...@r-project.org
Please respond to costas.vorlow
Dear all,
I am not sure I understand fully the functionality of tryCatch and
try commands and how these are used to continue a for/next loop if an
error occurs within the loop.
Can somebody point me to material (or share some code) with more
extensive examples than the ones in the help/FAQ pages?
Do explain my problem in more detail:
for (i in 100:1000)
{
## do some other stuff
dataset-head(data,i)
tryCatch(estimatemodel(dataset))
if estimatemodel returns an error (i.e. via a call to stop()), then this
should break out of the loop:
tryCatch(estimatemodel(dataset), error = function() break)
if you want to skip to the next iteration, use:
tryCatch(estimatemodel(dataset), error = function() next)
}
My for/next loop reads in data (increasing the dataset by one point at
every loop run) and then estimates a model. When the problem is
computationally singular, the loop exits. I want to continue the loop
and register an error estimation value for that step. However when I
use use the try tryCatch(estimatemodel(data)) (where estimatemodel() is
a wrapper function calling the model estimation and optimization
routines), the problem still persists.
Is this the correct way to use tryCatch (or try) or should these go
inside the actual code bits (i.e., in a more low level fashion) that
conduct the optimization and model estimation?
Apologies if this is not clear enough.
Best,
Costas
__
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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] tryCatch - Continuing for/next loop after error
Wow, I had a major brain fart there. The function after error was supposed
to accept an argument, and next won't do anything there because inside the
function there is no loop. Also, the first argument of tryCatch is an
expression, so do the assignment there. Corrections inline below:
--
Jonathan P. Daily
Technician - USGS Leetown Science Center
11649 Leetown Road
Kearneysville WV, 25430
(304) 724-4480
Is the room still a room when its empty? Does the room,
the thing itself have purpose? Or do we, what's the word... imbue it.
- Jubal Early, Firefly
Nipesh Bajaj bajaj141...@gmail.com wrote on 03/10/2011 10:21:38 AM:
[image removed]
Re: [R] tryCatch - Continuing for/next loop after error
Nipesh Bajaj
to:
Jonathan P Daily
03/10/2011 10:21 AM
Cc:
r-help
Hi Jonathan, I was also trying to understand this tryCatch function on
my own problem. Here is mine:
fn1 - function(x) {
if(as.integer(x) == 5) {
stop(stop)
}
return(x+5)
}
res - matrix(NA, 5, 7)
for(i in 1:5) {
for(j in 1:7) {
res[i,j] - tryCatch(fn1(j), error = function() next)
}
}
for(i in 1:5) { for(j in 1:7) {
tryCatch(res[i,j] - fn1(j), error = function(x) x)
} }
I was expecting while completion of these loops, the 5th column of
'res' will have NA values. However I got some error:
Error in value[[3L]](cond) : unused argument(s) (cond)
What is the actual problem here?
Thanks,
On Thu, Mar 10, 2011 at 7:19 PM, Jonathan P Daily jda...@usgs.gov
wrote:
--
Jonathan P. Daily
Technician - USGS Leetown Science Center
11649 Leetown Road
Kearneysville WV, 25430
(304) 724-4480
Is the room still a room when its empty? Does the room,
the thing itself have purpose? Or do we, what's the word... imbue
it.
- Jubal Early, Firefly
r-help-boun...@r-project.org wrote on 03/10/2011 03:51:15 AM:
[image removed]
[R] tryCatch - Continuing for/next loop after error
Costas
to:
r-help
03/10/2011 03:53 AM
Sent by:
r-help-boun...@r-project.org
Please respond to costas.vorlow
Dear all,
I am not sure I understand fully the functionality of tryCatch and
try commands and how these are used to continue a for/next loop if
an
error occurs within the loop.
Can somebody point me to material (or share some code) with more
extensive examples than the ones in the help/FAQ pages?
Do explain my problem in more detail:
for (i in 100:1000)
{
## do some other stuff
dataset-head(data,i)
tryCatch(estimatemodel(dataset))
if estimatemodel returns an error (i.e. via a call to stop()), then
this
should break out of the loop:
tryCatch(estimatemodel(dataset), error = function() break)
if you want to skip to the next iteration, use:
tryCatch(estimatemodel(dataset), error = function() next)
}
My for/next loop reads in data (increasing the dataset by one point
at
every loop run) and then estimates a model. When the problem is
computationally singular, the loop exits. I want to continue the loop
and register an error estimation value for that step. However when
I
use use the try tryCatch(estimatemodel(data)) (where estimatemodel()
is
a wrapper function calling the model estimation and optimization
routines), the problem still persists.
Is this the correct way to use tryCatch (or try) or should these go
inside the actual code bits (i.e., in a more low level fashion) that
conduct the optimization and model estimation?
Apologies if this is not clear enough.
Best,
Costas
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] tryCatch - Continuing for/next loop after error
I did not know that. When reading the help topic for the first time
myself, I think I assumed that it returned no value since it had no Value
section, and I haven't used it in a way that it would return a value.
--
Jonathan P. Daily
Technician - USGS Leetown Science Center
11649 Leetown Road
Kearneysville WV, 25430
(304) 724-4480
Is the room still a room when its empty? Does the room,
the thing itself have purpose? Or do we, what's the word... imbue it.
- Jubal Early, Firefly
William Dunlap wdun...@tibco.com wrote on 03/10/2011 11:29:59 AM:
[image removed]
RE: [R] tryCatch - Continuing for/next loop after error
William Dunlap
to:
Jonathan P Daily, Nipesh Bajaj
03/10/2011 11:30 AM
Cc:
r-help
-Original Message-
From: r-help-boun...@r-project.org
[mailto:r-help-boun...@r-project.org] On Behalf Of Jonathan P Daily
Sent: Thursday, March 10, 2011 7:49 AM
To: Nipesh Bajaj
Cc: r-help@r-project.org
Subject: Re: [R] tryCatch - Continuing for/next loop after error
Wow, I had a major brain fart there. The function after error
was supposed
to accept an argument, and next won't do anything there
because inside the
function there is no loop. Also, the first argument of tryCatch is an
expression, so do the assignment there. Corrections inline below:
The stuff about the error handle requiring an argument and
not being able to call next() from outside of a loop is true,
but you do not need to do the assignment inside the main expression
of tryCatch(). I find it clearer if you do the assignment outside
of tryCatch() so the main expression can return one thing and the
error handler can return something else. You can use this in an
*apply() function or a for loop, while the assignment-in-tryCatch()
won't work in a *apply() call. E.g., suppose we have a function
that only works on positive odd integers:
o - function (x) {
stopifnot(x%%2 == 1, x0)
(x - 1)/2
}
Then you can use tryCatch to flag the bad inputs with a code
that tells you about the bad input:
sapply(1:5, function(i)tryCatch(o(i), error=function(e)-1000-i))
[1] 0 -1002 1 -1004 2
or with a for loop where you don't have to prefill the output
vector with any particular values:
value - numeric(5)
for(i in 1:5) value[i] - tryCatch(o(i), error=function(e)-1000-i)
value
[1] 0 -1002 1 -1004 2
To do that with with an assignment in the main expression of tryCatch
would require something like
value - -1000 -(1:5)
for(i in 1:5) tryCatch(value[i] - o(i), error=function(e)NULL)
value
[1] 0 -1002 1 -1004 2
which seems to me uglier and harder to follow since value's entries
are filled in different parts of the code.
Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com
--
Jonathan P. Daily
Technician - USGS Leetown Science Center
11649 Leetown Road
Kearneysville WV, 25430
(304) 724-4480
Is the room still a room when its empty? Does the room,
the thing itself have purpose? Or do we, what's the word...
imbue it.
- Jubal Early, Firefly
Nipesh Bajaj bajaj141...@gmail.com wrote on 03/10/2011 10:21:38 AM:
[image removed]
Re: [R] tryCatch - Continuing for/next loop after error
Nipesh Bajaj
to:
Jonathan P Daily
03/10/2011 10:21 AM
Cc:
r-help
Hi Jonathan, I was also trying to understand this tryCatch
function on
my own problem. Here is mine:
fn1 - function(x) {
if(as.integer(x) == 5) {
stop(stop)
}
return(x+5)
}
res - matrix(NA, 5, 7)
for(i in 1:5) {
for(j in 1:7) {
res[i,j] - tryCatch(fn1(j), error = function() next)
}
}
for(i in 1:5) { for(j in 1:7) {
tryCatch(res[i,j] - fn1(j), error = function(x) x)
} }
I was expecting while completion of these loops, the 5th column of
'res' will have NA values. However I got some error:
Error in value[[3L]](cond) : unused argument(s) (cond)
What is the actual problem here?
Thanks,
On Thu, Mar 10, 2011 at 7:19 PM, Jonathan P Daily jda...@usgs.gov
wrote:
--
Jonathan P. Daily
Technician - USGS Leetown Science Center
11649 Leetown Road
Kearneysville WV, 25430
(304) 724-4480
Is the room still a room when its empty? Does the room,
the thing itself have purpose? Or do we, what's the
word... imbue
it.
- Jubal Early, Firefly
r-help-boun...@r-project.org wrote on 03/10/2011 03:51:15 AM:
[image removed]
[R] tryCatch - Continuing for/next loop after error
Costas
to:
r-help
03/10/2011 03:53 AM
Sent by:
r-help-boun...@r-project.org
Please respond to costas.vorlow
Re: [R] sum of variables in function
How about:
x - rnorm(1000)
fn - function(k) sum(x[1:k]*(x[k+1] + x[k+2]))
vals - sapply(1:100, fn)
vals
--
Jonathan P. Daily
Technician - USGS Leetown Science Center
11649 Leetown Road
Kearneysville WV, 25430
(304) 724-4480
Is the room still a room when its empty? Does the room,
the thing itself have purpose? Or do we, what's the word... imbue it.
- Jubal Early, Firefly
r-help-boun...@r-project.org wrote on 03/10/2011 08:49:25 AM:
[image removed]
[R] sum of variables in function
beatleb
to:
r-help
03/10/2011 01:15 PM
Sent by:
r-help-boun...@r-project.org
Dear R users,
Probably, this is quite a simpe question, but I do not find the proper
way
to obtain want I need. To explain the problem, I constructed a simple
example.
Suppose I have the following function:
try1-function(x){
y-x[1:2]
z-x[3:4]
y[1]*(z[1]+z[2])+y[2]*(z[1]+z[2])
}
This function will be part of a for loop. This is what I like to obtain
for
every k:
if k=2
try1-function(x){
y-x[1:2]
z-x[3:4]
y[1]*(z[1]+z[2])+y[2]*(z[1]+z[2])
}
if k=3
try1-function(x){
y-x[1:3]
z-x[4:5]
y[1]*(z[1]+z[2])+y[2]*(z[1]+z[2])+y[3]*(z[1]+z[2])
}
if k=4
try1-function(x){
y-x[1:3]
z-x[4:5]
y[1]*(z[1]+z[2])+y[2]*(z[1]+z[2])+y[3]*(z[1]+z[2])+y[4]*(z[1]+z[2])
}
Assume that k will be quite high, for example 100.
The problem isn't in defining a for loop, or in defining the appropriate
y
or z, but in the line starting with
y[1]. The values of the variables are still unknown, which causes that I
am
not able to create this sum.
I really hope that there is somebody in the audience that can help me.
--
View this message in context: http://r.789695.n4.nabble.com/sum-of-
variables-in-function-tp3345888p3345888.html
Sent from the R help mailing list archive at Nabble.com.
__
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PLEASE do read the posting guide
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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] Complex sampling?
--
Jonathan P. Daily
Technician - USGS Leetown Science Center
11649 Leetown Road
Kearneysville WV, 25430
(304) 724-4480
Is the room still a room when its empty? Does the room,
the thing itself have purpose? Or do we, what's the word... imbue it.
- Jubal Early, Firefly
r-help-boun...@r-project.org wrote on 03/09/2011 01:01:32 PM:
[image removed]
[R] Complex sampling?
Hosack, Michael
to:
r-help@R-project.org
03/09/2011 01:04 PM
Sent by:
r-help-boun...@r-project.org
-Original Message-
From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-
project.org]
On Behalf Of Hosack, Michael
Sent: Wednesday, March 09, 2011 7:34 AM
To: r-help at R-project.org
Subject: [R] Complex sampling?
R users,
I am trying to generate a randomized weekday survey schedule that
ensures
even coverage of weekdays in
the sample, where the distribution of variable DOW is random with
respect
to WEEK. To accomplish this I need
to randomly sample without replacement two weekdays per week for each
of
27 weeks (only 5 are shown).
This seems simple enough, sampling without replacement.
However,
I need to sample from a sequence (3:7) that needs to be completely
depleted and replenished until the
final selection is made. Here is an example of what I want to do,
beginning at WEEK 1. I would prefer to do
this without using a loop, if possible.
sample frame: [3,4,5,6,7] -- [4,5,6] -- [4],[1,2,3,(4),5,6] --
[1,2,4,5,6] -- for each WEEK in dataframe
OK, now you have me completely lost. Sorry, but I have no clue as
to what you just did here. I looks like you are trying to describe
some transformation/algorithm but I don't follow it.
I could not reply to this email because it not been delivered to my
inbox, so I had to copy it from the forum.
I apologize for the confusion, this would take less than a minute to
explain in conversation but an hour
to explain well in print. Two DOW_NUMs will be selected randomly
without replacement from the vector 3:7 for each WEEK. When this
vector is reduced to a single integer that integer will be selected
This is what doesn't make sense to me. You sample two values from 3:7
without replacement. Then this sample of two is turned into one by a
mechanism you have not specified. Are these averaged? Lets assume you
assign this mechanism to fun(x1) where x1 is the sample.
and the vector will be restored and a single integer will then be
selected that differs from the prior selected integer (i.e. cannot
sample the same day twice in the same week).
so then you want to sample twice from 3:7 again such that fun(x2) !=
fun(x1)?
If so, then this might be what you need.
vals - matrix(,5,2)
pairs - expand.grid(3:7, 3:7)
for(i in 1:5)
{
vals[i,1] - fun(sample(pairs))
vals[i,2] - fun(sample(pairs[fun(pairs) != vals[i,1])))
}
Or something similar.
This process will be
repeated until two DOW_NUM have been assigned for each WEEK. That
process is what I attempted to illustrate in my original message.
This is beyond my current coding capabilities.
Randomly sample 2 DOW_NUM without replacement from each WEEK ( () = no
two
identical DOW_NUM can be sampled
in the same WEEK)
sample = {3,7}, {5,6}, {4,3}, {1,5}, -- for each WEEK in dataframe
So, are you sampling from [3,4,5,6,7], or [1,2,4,5,6], or ...? Can
you show an 'example' of what you would like to end up given your data
below?
Thanks you,
Mike
DATE DOW DOW_NUM WEEK
2 2011-05-02 Mon 31
3 2011-05-03 Tue 41
4 2011-05-04 Wed 51
5 2011-05-05 Thu 61
6 2011-05-06 Fri 71
9 2011-05-09 Mon 32
10 2011-05-10 Tue 42
11 2011-05-11 Wed 52
12 2011-05-12 Thu 62
13 2011-05-13 Fri 72
16 2011-05-16 Mon 33
17 2011-05-17 Tue 43
18 2011-05-18 Wed 53
19 2011-05-19 Thu 63
20 2011-05-20 Fri 73
23 2011-05-23 Mon 34
24 2011-05-24 Tue 44
25 2011-05-25 Wed 54
26 2011-05-26 Thu 64
27 2011-05-27 Fri 74
30 2011-05-30 Mon 35
31 2011-05-31 Tue 45
32 2011-06-01 Wed 55
33 2011-06-02 Thu 65
34 2011-06-03 Fri 75
DF -
structure(list(DATE = structure(c(15096, 15097, 15098, 15099,
15100, 15103, 15104, 15105, 15106, 15107, 15110, 15111, 15112,
15113, 15114, 15117, 15118, 15119, 15120, 15121, 15124, 15125,
15126, 15127, 15128), class = Date), DOW = c(Mon, Tue,
Wed, Thu, Fri, Mon, Tue, Wed, Thu, Fri, Mon,
Tue, Wed, Thu, Fri, Mon, Tue, Wed, Thu, Fri,
Mon, Tue, Wed, Thu, Fri), DOW_NUM = c(3, 4, 5, 6, 7,
3, 4, 5, 6, 7, 3, 4, 5, 6, 7, 3, 4, 5, 6, 7, 3, 4, 5, 6, 7),
WEEK = c(1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 4,
4, 4, 4
Re: [R] generate 3 distinct random samples without replacement
would this work? s - sample(d1, 300, F) D - data.frame(a = s[1:100], b = s[101:200], c = s[201:300]) -- Jonathan P. Daily Technician - USGS Leetown Science Center 11649 Leetown Road Kearneysville WV, 25430 (304) 724-4480 Is the room still a room when its empty? Does the room, the thing itself have purpose? Or do we, what's the word... imbue it. - Jubal Early, Firefly r-help-boun...@r-project.org wrote on 03/07/2011 02:17:19 PM: [image removed] [R] generate 3 distinct random samples without replacement Cesar Hincapié to: r-help 03/07/2011 03:06 PM Sent by: r-help-boun...@r-project.org Hello: I wonder if I could get a little help with random sampling in R. I have a vector of length 7375. I would like to draw 3 distinct random samples, each of length 100 without replacement. I have tried the following: d1 - 1:7375 set.seed(7) i - sample(d1, 100, replace=F) s1 - sort(d1[i]) s1 d2 - d1[-i] set.seed(77) j - sample(d2, 100, replace=F) s2 - sort(d2[j]) s2 d3 - d2[-j] set.seed(777) k - sample(d3, 100, replace=F) s3 - sort(d3[k]) s3 D - data.frame(a=s1,b=s2,c=s3) However, s2 is only 97 elements long, and s3, only 96 long. I would appreciate any suggestions on a better approach. I'm also curious to know why my second and third samples are less than 100 elements in length. Thanks for your time and consideration, Cesar A. Hincapié, DC, MHSc Research Fellow, Division of Health Care and Outcomes Research, Toronto Western Research Institute PhD Candidate in Epidemiology, Dalla Lana School of Public Health, University of Toronto e. cesar.hinca...@utoronto.ca [[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] Probabilities greather than 1 in HIST
If you read ?hist, you will answer your own question.
The issue in your code is the parameter prob = T, which does nothing. By
default, hist reports density.
--
Jonathan P. Daily
Technician - USGS Leetown Science Center
11649 Leetown Road
Kearneysville WV, 25430
(304) 724-4480
Is the room still a room when its empty? Does the room,
the thing itself have purpose? Or do we, what's the word... imbue it.
- Jubal Early, Firefly
r-help-boun...@r-project.org wrote on 03/03/2011 09:03:21 AM:
[image removed]
[R] Probabilities greather than 1 in HIST
jpmaroco
to:
r-help
03/03/2011 10:13 AM
Sent by:
r-help-boun...@r-project.org
Dear all,
I am a newbie in R and could not find help on this problem. I am trying
to
plot an histogram with probabilities in the y axis. This is the code I
am
using:
#TLC uniform
n=30
mi=1; mx=6
nrep=1000
xbar=rep(0,nrep)
for (i in 1:nrep) {xbar[i]=mean(runif(n,min=mi,max=mx))}
hist(xbar,prob=TRUE,breaks=Sturges,xlim=c(1,6),main=paste(n =,n),
xlab=Média, ylab=Probabilidade)
curve(dnorm(x,mean=mean(xbar),sd=sd(xbar)),add=TRUE,lwd=2,col=red)
The problem is that I am getting greater than 1 probabilities in the Y
axis?
Is there a way to correct this?
Many thanks in advance.
Joao
--
View this message in context: http://r.789695.n4.nabble.com/
Probabilities-greather-than-1-in-HIST-tp388p388.html
Sent from the R help mailing list archive at Nabble.com.
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Re: [R] Vector manipulations
Is this what you want? I don't know what your v looks like, but this won't work if there are cases in which v won't sum to exactly x. x - 20 v - sample(0:1, 100, T) w - v[1:which(cumsum(v)==x)] -- Jonathan P. Daily Technician - USGS Leetown Science Center 11649 Leetown Road Kearneysville WV, 25430 (304) 724-4480 Is the room still a room when its empty? Does the room, the thing itself have purpose? Or do we, what's the word... imbue it. - Jubal Early, Firefly r-help-boun...@r-project.org wrote on 03/02/2011 10:42:12 AM: [image removed] [R] Vector manipulations Benjamin Hartley to: r-help 03/02/2011 11:08 AM Sent by: r-help-boun...@r-project.org I have a question regarding the most efficient way to select a substring of a vector: I have a vector of value v, and I want to select a subspace of this vector called w such that: w=v[1:n] where sum(w) = x I am interested in what you thing would be the most efficient way to do this - I would like to avoid slowing down my simulations as much as possible. Thank you very much for any help that anyone is able to give. [[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] bootstrap resampling - simplified
I will point out again that sampling a five-fold replicate of 1:20 is not the same as resampling with replacement, although I made an error in reporting probabilities - the P(x2 = 1 | x1 = 1) = 4/99 and not 4/100. When sampling with replacement, P(x2 = 1 | x1 = 1) = P(x2 = 1 | x1 != 1) = 1/20. -- Jonathan P. Daily Technician - USGS Leetown Science Center 11649 Leetown Road Kearneysville WV, 25430 (304) 724-4480 Is the room still a room when its empty? Does the room, the thing itself have purpose? Or do we, what's the word... imbue it. - Jubal Early, Firefly r-help-boun...@r-project.org wrote on 03/02/2011 01:05:01 PM: [image removed] Re: [R] bootstrap resampling - simplified Vokey, John to: r-help 03/02/2011 01:07 PM Sent by: r-help-boun...@r-project.org On 2011-03-02, at 4:00 AM, r-help-requ...@r-project.org wrote: Hello there, I have a problem concerning bootstrapping in R - especially focusing on the resampling part of it. I try to sum it up in a simplified way so that I would not confuse anybody. I have a small database consisting of 20 observations (basically numbers from 1 to 20, I mean: 1, 2, 3, 4, 5, ... 18, 19, 20). I would like to resample this database many times for the bootstrap process with the following conditions. Firstly, every resampled database should also include 20 observations. Secondly, when selecting a number from the above-mentioned 20 numbers, you can do this selection with replacement. The difficult part comes now: one number can be selected only maximum 5 times. In order to make this clear I show you a couple of examples. So the resampled databases might be like the following ones: (1st database) 1,2,1,2,1,2,1,2,1,2,3,3,3,3,3,4,4,4,4,4 4 different numbers are chosen (1, 2, 3, 4), each selected - for the maximum possible - 5 times. (2nd database) 1,8,8,6,8,8,8,2,3,4,5,6,6,6,6,7,19,1,1,1 Two numbers - 8 and 6 - selected 5 times (the maximum possible times), number 1 selected 4 times, the others selected less than 4 times. (3rd database) 1,1,2,2,3,3,4,4,9,9,9,10,10,13,10,9,3,9,2,1 Number 9 chosen for the maximum possible 5 times, number 10, 3, 2, 1 chosen for 3 times, number 4 selected twice and number 13 selectedonly once. ... Anybody knows how to implement my tricky condition into one of the R functions - that one number can be selected only 5 times at most? Are 'boot' and 'bootstrap' packages capable of managing this? I guess they are, I just couldn't figure it out yet... Thanks very much! Best regards, Laszlo Bodnar Laszlo, Create a vector consisting of 5 of each number. Then, for each sample, scramble the order of the items in the vector, and select the first 20. -- Please avoid sending me Word or PowerPoint attachments. See http://www.gnu.org/philosophy/no-word-attachments.html -Dr. John R. Vokey __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] bootstrap resampling - simplified
I apologize if I was not clear in my response. I only mentioned x1, x2 in my example, but I did not clarify that I also knew that P(x6 = 1 | x1..5 = 1) = 0 in the original request. I also see that if he meant that he wanted to sample with replacement from the set of sequences that sample(rep(1:20, 5), 20) is fine for generating said sequences. My interpretation was that the sequences themselves should be sampling with replacement until frequency hits 5, whereupon it is not replaced. Hence my suggestion of: bigsamp - sample(1:20, 100, T) idx - sort(unlist(sapply(1:20, function(x) which(bigsamp == x)[1:5])))[1:20] samp - bigsamp[idx] I apologize for my lack of clarity, though after reading the original post I'm not sure which solution the OP was looking for. Cheers, Jon -- Jonathan P. Daily Technician - USGS Leetown Science Center 11649 Leetown Road Kearneysville WV, 25430 (304) 724-4480 Is the room still a room when its empty? Does the room, the thing itself have purpose? Or do we, what's the word... imbue it. - Jubal Early, Firefly Bert Gunter gunter.ber...@gene.com wrote on 03/02/2011 02:42:40 PM: [image removed] Re: [R] bootstrap resampling - simplified Bert Gunter to: Jonathan P Daily 03/02/2011 02:42 PM Cc: Vokey, John, r-help, r-help-bounces Folks: On Wed, Mar 2, 2011 at 10:32 AM, Jonathan P Daily jda...@usgs.gov wrote: I will point out again that sampling a five-fold replicate of 1:20 is not the same as resampling with replacement, -- Correct. In sampling with replacement from 1:20 there is positive probability of getting all 1's or all 2's, etc. The poster specifically said that he wanted 0 probability of such results. So, obviously, the poster does NOT want to sample with replacement from 1:20. What he does want (I think) is a re-sample of size n from the set of all **vectors** of length 20, each element of which is an integer from 1 to 20, and for which no individual values occur more than 5 times in the vector. Of course I'm just interpreting/paraphrasing the original post (if I got it right), but I think doing so makes the nature of the task clearer: one needs to find some way to sample with replacement from the space of all such **sequences**. I think it is now clear that one may do so by rejection sampling: i.e. sample with replacement from 1:20 and throw away any sequences that fail the at most 5 criterion. The sequences that remain are samples of size 1 from the population of sequences that satisfy the poster's criteria (in theory, anyway; this might tax a pseudo RNG in practice). A collection of n such sequences is a bootstrap sample from this population. I **think** that's what the poster wants -- and what others have already provided. However, maybe this clarifies why it works. If I have made any error in this, **Please** post a message pointing out my error. I sometimes get confused about this stuff, too. Cheers, Bert although I made an error in reporting probabilities - the P(x2 = 1 | x1 = 1) = 4/99 and not 4/100. When sampling with replacement, P(x2 = 1 | x1 = 1) = P(x2 = 1 | x1 != 1) = 1/20. -- Jonathan P. Daily Technician - USGS Leetown Science Center 11649 Leetown Road Kearneysville WV, 25430 (304) 724-4480 Is the room still a room when its empty? Does the room, the thing itself have purpose? Or do we, what's the word... imbue it. - Jubal Early, Firefly r-help-boun...@r-project.org wrote on 03/02/2011 01:05:01 PM: [image removed] Re: [R] bootstrap resampling - simplified Vokey, John to: r-help 03/02/2011 01:07 PM Sent by: r-help-boun...@r-project.org On 2011-03-02, at 4:00 AM, r-help-requ...@r-project.org wrote: Hello there, I have a problem concerning bootstrapping in R - especially focusing on the resampling part of it. I try to sum it up in a simplified way so that I would not confuse anybody. I have a small database consisting of 20 observations (basically numbers from 1 to 20, I mean: 1, 2, 3, 4, 5, ... 18, 19, 20). I would like to resample this database many times for the bootstrap process with the following conditions. Firstly, every resampled database should also include 20 observations. Secondly, when selecting a number from the above-mentioned 20 numbers, you can do this selection with replacement. The difficult part comes now: one number can be selected only maximum 5 times. In order to make this clear I show you a couple of examples. So the resampled databases might be like the following ones: (1st database) 1,2,1,2,1,2,1,2,1,2,3,3,3,3,3,4,4,4,4,4 4 different numbers are chosen (1, 2, 3, 4), each selected - for the maximum possible - 5 times. (2nd database) 1,8,8,6,8,8,8,2,3,4,5,6,6,6,6,7,19,1,1,1 Two numbers - 8 and 6 - selected 5 times (the maximum
Re: [R] bootstrap resampling question
I'm not sure that is equivalent to sampling with replacement, since if the
first draw is 1, then the probability that the next draw will be one is
4/100 instead of the 1/20 it would be in sampling with replacement. I
think the way to do this would be what Greg suggested - something like:
bigsamp - sample(1:20, 100, T)
idx - sort(unlist(sapply(1:20, function(x) which(bigsamp ==
x)[1:5])))[1:20]
samp - bigsamp[idx]
--
Jonathan P. Daily
Technician - USGS Leetown Science Center
11649 Leetown Road
Kearneysville WV, 25430
(304) 724-4480
Is the room still a room when its empty? Does the room,
the thing itself have purpose? Or do we, what's the word... imbue it.
- Jubal Early, Firefly
r-help-boun...@r-project.org wrote on 03/01/2011 09:37:31 AM:
[image removed]
Re: [R] bootstrap resampling question
Giovanni Petris
to:
Bodnar Laszlo EB_HU
03/01/2011 11:58 AM
Sent by:
r-help-boun...@r-project.org
Cc:
'r-help@r-project.org'
A simple way of sampling with replacement from 1:20, with the additional
constraint that each number can be selected at most five times is
sample(rep(1:20, 5), 20)
HTH,
Giovanni
On Tue, 2011-03-01 at 11:30 +0100, Bodnar Laszlo EB_HU wrote:
Hello there,
I have a problem concerning bootstrapping in R - especially
focusing on the resampling part of it. I try to sum it up in a
simplified way so that I would not confuse anybody.
I have a small database consisting of 20 observations (basically
numbers from 1 to 20, I mean: 1, 2, 3, 4, 5, ... 18, 19, 20).
I would like to resample this database many times for the
bootstrap process with the following two conditions. The resampled
databases should also have 20 observations and you can select each
of the previously mentioned 20 numbers with replacement. I guess it
is obvious so far. Now the more difficult second condition is that
one number can be selected only maximum 5 times. In order to make
this clear I try to show you an example. So there can be resampled
databases like the following ones:
(1st database) 1,2,1,2,1,2,1,2,1,2,3,3,3,3,3,4,4,4,4,4
(4 different numbers are chosen, each selected 5 times)
(2nd database) 1,8,8,6,8,8,8,2,3,4,5,6,6,6,6,7,19,1,1,1
(Two numbers - 8 and 6 - selected 5 times, number 1 selected
four times, the others selected less than 4 times)
My very first guess that came to my mind whilst thinking about the
problem was the sample function where there are settings like
replace=TRUE and prob=... where you can create a probability vector
i.e. how much should be the probability of selecting a number. So I
tried to calculate probabilities first. I thought the problem can
basically described as a k-combination with repetitions.
Unfortunately the only thing I could calculate so far is the total
number of all possible selections which amounts to 137 846 527 049.
Anybody knows how to implement my second tricky condition into
one of the R functions? Are 'boot' and 'bootstrap' packages capable
of managing this? I guess they are, I just couldn't figure it out yet...
Thanks very much! Best regards,
Laszlo Bodnar
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tartalmazhat. Amennyiben nem Ön a levél címzettje akkor a levél
tartalmának közlése, reprodukálása, másolása, vagy egyéb más úton
történő terjesztése, felhasználása szigorúan tilos. Amennyiben
tévedésből kapta meg ezt az üzenetet kérjük azonnal értesítse az
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- eljuttatásáért, valamint semmilyen késésért, kapcsolat
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vagy annak megbízhatatlanságából eredő kárért.
Az üzenetek EBH-n kívüli küldője vagy címzettje tudomásul veszi és
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--
Giovanni Petris gpet...@uark.edu
Associate Professor
Department of Mathematical Sciences
University of Arkansas - Fayetteville, AR 72701
Ph: (479) 575-6324, 575-8630 (fax)
http://definetti.uark.edu/~gpetris/
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Re: [R] Variable names AS variable names?
To access a variable by a character string name, try
for(code in codes)
{
dat - get(code)
[stuff]
}
Other options include ?assign if you need to manipulate the original, or
?with to use the subject of codes as an environment.
--
Jonathan P. Daily
Technician - USGS Leetown Science Center
11649 Leetown Road
Kearneysville WV, 25430
(304) 724-4480
Is the room still a room when its empty? Does the room,
the thing itself have purpose? Or do we, what's the word... imbue it.
- Jubal Early, Firefly
r-help-boun...@r-project.org wrote on 02/25/2011 12:33:32 PM:
[image removed]
Re: [R] Variable names AS variable names?
Noah Silverman
to:
02/25/2011 12:35 PM
Sent by:
r-help-boun...@r-project.org
Cc:
r-help
My actual code is several things with adaptive filtering. This will
require accessing data sporadically. The loop was just a quick example
for the e-mail.
One application is to work with online (streaming) data. If I get a new
data point in for code a1, I'll need to be able to reference the
matrix named a1.
On 2/25/11 12:23 AM, David Winsemius wrote:
On Feb 25, 2011, at 1:55 AM, Noah Silverman wrote:
How can I dynamically use a variable as the name for another
variable?
I realize this sounds cryptic, so an example is best:
#Start with an array of codes
codes - c(a1, b24, q99)
Is there some reason not to use list(a1, b24, q99)? If not then:
lapply(codes, somefun)
#Each code has a corresponding matrix (could be vector)
a1 - matrix(rnorm(100), nrow=10)
b24 - matrix(rnorm(100), nrow=10)
q99 - matrix(rnorm(100), nrow=10)
#Now, I want to loop through all the codes and do something with each
matrix
for(code in codes){
#here is where I'm stuck. I don't want the value of code, but the
variable who's name is the value of code
}
Any suggestions?
-N
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David Winsemius, MD
West Hartford, CT
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Re: [R] Running code sequentially from separate scripts (but not functions)
If you are just wanting to run them once, you can just do: source(code1.r) source(code2.r) source(code3.r) or place the file names in a vector, say 'filenames' and: sapply(filenames, source) If you want to use them multiple times, try: run1 - parse(code1.r) run2 - parse(code2.r) run3 - parse(code3.r) # Use this to run anytime eval(run1) eval(run2) eval(run3) -- Jonathan P. Daily Technician - USGS Leetown Science Center 11649 Leetown Road Kearneysville WV, 25430 (304) 724-4480 Is the room still a room when its empty? Does the room, the thing itself have purpose? Or do we, what's the word... imbue it. - Jubal Early, Firefly r-help-boun...@r-project.org wrote on 02/24/2011 10:21:47 AM: [image removed] [R] Running code sequentially from separate scripts (but not functions) Dimitri Liakhovitski to: r-help 02/24/2011 10:24 AM Sent by: r-help-boun...@r-project.org Hello! I am wondering if it's possible to run - in sequence - code that is stored in several R scripts. For example: Script in the file code1.r contains the code: a = 3; b = 5; c = a + b Script in the file code2.r contains the code: d = 10; e = d - c Script in the file code3.r contains the code: result=e/a I understand that I could write those 3 scripts as 3 functions and source them from another script. But maybe there is a way of having them run one by one as such? Thanks a lot! -- Dimitri Liakhovitski Ninah Consulting www.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-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] create dummy variables by for loop
See inline below.
--
Jonathan P. Daily
Technician - USGS Leetown Science Center
11649 Leetown Road
Kearneysville WV, 25430
(304) 724-4480
Is the room still a room when its empty? Does the room,
the thing itself have purpose? Or do we, what's the word... imbue it.
- Jubal Early, Firefly
r-help-boun...@r-project.org wrote on 02/24/2011 01:23:54 PM:
[image removed]
[R] create dummy variables by for loop
Changbin Du
to:
r-help@r-project.org
02/24/2011 01:25 PM
Sent by:
r-help-boun...@r-project.org
HI, Dear R community,
I try to create 100 dummy variables like the following:
ack$id_1 - (ack$ID==1)*1
ack$id_2 - (ack$ID==2)*1
..
.
ack$id_100 - (ack$ID==100)*1
I used the following codes:
for(i in 1:100){
ack$id_[i] - (ack$ID==i)*1
}
This doesn't do what you think it does. when i = 1, it assigns the result
of (ack$ID==1)*1 to the first element of ack$id_
If you want ack$id_i to be created, try:
ack[[paste(id, i, sep = _)]] - (ack$ID==i)*1
But only one column is created, can anyone help me?
Thanks a lot!
--
Sincerely,
Changbin
--
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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 string to call/manipulate an object
If you are looping through and have the names of the files as characters,
say in ticker.names - c(IBM, ...), you may be able to do this using:
for(nam in ticker.names)
{
[snip...]
eval(parse(text = paste('colnames(', nam, ') - c(
open,high,low,close,vol)', sep = '')))
}
HTH,
Jon
--
Jonathan P. Daily
Technician - USGS Leetown Science Center
11649 Leetown Road
Kearneysville WV, 25430
(304) 724-4480
Is the room still a room when its empty? Does the room,
the thing itself have purpose? Or do we, what's the word... imbue it.
- Jubal Early, Firefly
r-help-boun...@r-project.org wrote on 02/23/2011 10:23:35 AM:
[image removed]
Re: [R] Using string to call/manipulate an object
Kushan Thakkar
to:
David Winsemius
02/23/2011 10:55 AM
Sent by:
r-help-boun...@r-project.org
Cc:
r-help
@Scott:
I can't just use
colnames(IBM) - c(open,high,low,close,vol)
I have nearly 100 tickers stored in an vector and I am looping through
them.
Its not a good idea to hardcode all of them.
@David:
Column names is just an example. I have a long script that takes in an
xts
object and performs a series of manipulation. I want to to be able to
run
the same program on a series of xts objects through a loop. For that I
need
to be able to able to dynamically point/refer to those xts object inside
my
loop.
On Wed, Feb 23, 2011 at 8:58 AM, David Winsemius
dwinsem...@comcast.netwrote:
On Feb 23, 2011, at 8:55 AM, Kushan Thakkar wrote:
I am using getSymbols function from quantmod package to get price
data
from
internet.
Currently I have:
my.ticker - IBM
getSymbols(my.ticker,src=google)
This creates an xts object named my.ticker which contains historical
price
data for IBM.
How can I call and manipulating this xts object using my original
string
my.ticker?
I want to do:
colnames(my.ticker) - c(open,high,low,close,vol)
If you want to change the colnames (an attribute) of the object now
named
IBM in your global environment, then look a:
?attributes
?attr
However, this does not work as my.ticker refers to the string IBM
rather
than the xts object called IBM.
Out of desperation, I have also tried:
colnames(paste(my.ticker)) - c(open,high,low,close,vol)
colnames(as.xts(my.ticker)) - c(open,high,low,close,vol)
But why are you do this??? It already has a perfectly servicable set
of
names:
colnames(get(my.ticker))
[1] IBM.Open IBM.High IBM.LowIBM.Close IBM.Volume
--
David.
Thanks
Kushan
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PLEASE do read the posting guide
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David Winsemius, MD
West Hartford, CT
[[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] R script HELP!
It looks to me like when you assign ID_min and ID_max that you want them to be vectors. In R, this is accomplished by ?c. Example: ID_min - c(976834501, 290018099.3145, 1000) -- Jonathan P. Daily Technician - USGS Leetown Science Center 11649 Leetown Road Kearneysville WV, 25430 (304) 724-4480 Is the room still a room when its empty? Does the room, the thing itself have purpose? Or do we, what's the word... imbue it. - Jubal Early, Firefly r-help-boun...@r-project.org wrote on 02/18/2011 08:21:36 AM: [image removed] [R] R script HELP! whizevans to: r-help 02/18/2011 08:49 AM Sent by: r-help-boun...@r-project.org The following is my R script which I am struggling with to assess ICESat data..perhaps it is the ID_min or ID_max that is wrong? I don't know, any help would be greatly appreciated :( # OPTIONS - CHANGE THESE VARIABLES IF NEEDED\par ##\par \par icesatfile - 'C:/Users/Whiz/My_Documents/Year3/GY3072/ICESat_GLAS/IDLreadGLASWF/ out_wf_GLA01_09030918_r5947_031_L2E.dat'\par \par plotdir - 'C:/Users/Whiz/My_Documents/Year3/GY3072/ICESat_GLAS/PLOT'\par \par \par \par ID_min - 976834501 290018099.3145 1000 #231741042 # specify range of waveforms to be plotted, -1 means all\par ID_max - 976834506 290018101.2895 1000 @@@note only one ID used @@@\par \par \par \par noise - 0.05 # values below NOISE will be disregarded in the waveform fitting\par sdthres - 0.02 # threshold for a standard deviation of volt measurements indicating the presence of a signal\par \par fit_waveform_model - TRUE # set to TRUE this activates the Gaussian waveform model fitting and plotting\par #fit_waveform_select - c(976834501 290018099.3145 1000) # gives the Unique ID for which the model fitting will be activated\par \par #\par # END OF OPTIONS\par -- View this message in context: http://r.789695.n4.nabble.com/R- script-HELP-tp3312644p3312644.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] R script HELP!
Well, this script only shows the option settings, so I assumed that the string being used as your infile was formatted for R. As for how it will have to look for R to read it in, there are many ways to do this - I would start by reading R Data Import/Export that ships with every copy of R. As for scripts and their default writing methods AFAIR Rscript writes to stdout, though if you want it to save your modified data in some other format than a text dump, look at the various methods of exporting data... again in the aforementioned R Data Import/Export. -- Jonathan P. Daily Technician - USGS Leetown Science Center 11649 Leetown Road Kearneysville WV, 25430 (304) 724-4480 Is the room still a room when its empty? Does the room, the thing itself have purpose? Or do we, what's the word... imbue it. - Jubal Early, Firefly r-help-boun...@r-project.org wrote on 02/18/2011 10:29:55 AM: [image removed] Re: [R] R script HELP! whizevans to: r-help 02/18/2011 11:06 AM Sent by: r-help-boun...@r-project.org OK thanks Jonathon, I will have a go. Is the plotdir file technically my output file? Or what is this otherwise? Also, having never used R script before, is it not very good at reading data, may I have to alter my input file in excel first? Thanks -- View this message in context: http://r.789695.n4.nabble.com/R- script-HELP-tp3312644p3312898.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] CDF of Sample Quantile
If I understand this, you have a value x, or a vector of values x, and you want to know the CDF that this value is drawn from a normal distribution? I assume you are drawing from rnorm for your simulations, so look at the other functions listed when you ?rnorm. HTH -- Jonathan P. Daily Technician - USGS Leetown Science Center 11649 Leetown Road Kearneysville WV, 25430 (304) 724-4480 Is the room still a room when its empty? Does the room, the thing itself have purpose? Or do we, what's the word... imbue it. - Jubal Early, Firefly r-help-boun...@r-project.org wrote on 02/14/2011 09:58:09 AM: [image removed] [R] CDF of Sample Quantile Bentley Coffey to: r-help 02/14/2011 01:58 PM Sent by: r-help-boun...@r-project.org I need to calculate the probability that a sample quantile will exceed a threshold given the size of the iid sample and the parameters describing the distribution of each observation (normal, in my case). I can compute the probability with brute force simulation: simulate a size N sample, apply R's quantile() function on it, compare it to the threshold, replicate this MANY times, and count the number of times the sample quantile exceeded the threshold (dividing by the total number of replications yields the probability of interest). The problem is that the number of replications required to get sufficient precision (3 digits say) is so HUGE that this takes FOREVER. I have to perform this task so much in my script (searching over the sample size and repeated for several different distribution parameters) that it takes too many hours to run. I've searched for pre-existing code to do this in R and haven't found anything. Perhaps I'm missing something. Is anyone aware of an R function to compute this probability? I've tried writing my own code using the fact that R's quantile() function is a linear combination of 2 order statistics. Basically, I wrote down the mathematical form of the joint pdf for the 2 order statistics (a function of the sample size and the distribution parameters) then performed a pseudo-Monte Carlo integration (i.e. using Halton Draws rather than R's random draws) over the region where the sample quantile exceeds the threshold. In theory, this should work and it takes about 1000 times fewer clock cycles to compute than the Brute Force approach. My problem is that there is a significant discrepancy between the results using Brute Force and using this more efficient approach that I have coded up. I believe that the problem is numerical error but it could be some programming bug; regardless, I have been unable to locate the source of this problem and have spent over 20 hours trying to identify it this weekend. Please, somebody help!!! So, again, my question: is there code in R for quickly evaluating the CDF of a Sample Quantile given the sample size and the parameters governing the distribution of each iid point in the sample? Grateful for any help, Bentley [[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] help - the condition has length 1 and only the first element will be used
The issue here is that if only accepts a single True/False argument. Try
these functions:
?ifelse
?all
?any
--
Jonathan P. Daily
Technician - USGS Leetown Science Center
11649 Leetown Road
Kearneysville WV, 25430
(304) 724-4480
Is the room still a room when its empty? Does the room,
the thing itself have purpose? Or do we, what's the word... imbue it.
- Jubal Early, Firefly
r-help-boun...@r-project.org wrote on 02/10/2011 09:07:40 AM:
[image removed]
[R] help - the condition has length 1 and only the first element
will be used
Bodnar Laszlo EB_HU
to:
'r-help@r-project.org'
02/10/2011 10:25 AM
Sent by:
r-help-boun...@r-project.org
Hello there,
I don't know if I'm addressing my question to the right e-mail
address, I hope I do. Actually I have a little problem concerning
writing a code in R. I try to briefly sum up my problem.
As you can see below, I created the functions Equation1 and
Equation2 with some conditions.
Equation1 -function(x){
if (x=0.25) y -1-4*x
if (x0.25) y -0
y
}
Equation2 -function(x){
if (x=0.25)y -4*x
if (x0.25 x=0.5) y -2-4*x
if (x0.5) y -0
y
}
And then I generated a sequence of numbers from 0 to 1 using
the following code:
x -seq(0,1,0.05)
What I intended to do was to create 3 columns like below. In
the first column you can find all the x values I created just before
using the seq procedure and in the next 2 columns you can see all
the calculated values of functions Equation1 and Equation2 respectively.
x Egyenlet1 Egyenlet2
0.00 1.000.00
0.05 0.800.20
0.10 0.600.40
0.15 0.400.60
0.20 0.200.80
0.25 0.001.00
0.30 0.000.80
0.35 0.000.60
0.40 0.000.40
0.45 0.000.20
0.50 0.000.00
0.55 0.000.00
0.60 0.000.00
0.65 0.000.00
0.70 0.000.00
0.75 0.000.00
0.80 0.000.00
0.85 0.000.00
0.90 0.000.00
0.95 0.000.00
1.00 0.000.00
Unfortunately I didn't know how to create these columns.
Whenever I tried to send the following codes into R:
Equation1(x) or Equation1(x) (remember x representing the
values from 0 to 1)
...I instantaneously got a warning message saying:
[1] 1.0 0.8 0.6 0.4 0.2 0.0 -0.2 -0.4 -0.6 -0.8 -1.0
-1.2 -1.4 -1.6 -1.8 -2.0 -2.2 -2.4 -2.6 -2.8 -3.0
Warning messages:
1: In if (x = 0.25) y - 1 - 4 * x :
the condition has length 1 and only the first element will be
used
2: In if (x 0.25) y - 0 :
the condition has length 1 and only the first element will be
used
Could somebody please help me with this? I would greatly
appreciate if somebody would reply.
Thank you very much and have a pleasant day!
Best regards,
Laszlo
Ez az e-mail és az összes hozzá tartozó csatolt melléklet
titkos és/vagy jogilag, szakmailag vagy más módon védett
információt tartalmazhat. Amennyiben nem Ã?n a levél cÃmzettje
akkor a levél tartalmának közlése, reprodukálása, másolása,
vagy egyéb más úton történÅ? terjesztése, felhasználása
szigorúan tilos. Amennyiben tévedésbÅ?l kapta meg ezt az
üzenetet kérjük azonnal értesÃtse az üzenet küldÅ?jét. Az
Erste Bank Hungary Zrt. (EBH) nem vállal felelÅ?sséget az
információ teljes és pontos - cÃmzett(ek)hez történÅ? -
eljuttatásáért, valamint semmilyen késésért, kapcsolat
megszakadásból eredÅ? hibáért, vagy az információ
felhasználásából vagy annak megbÃzhatatlanságából eredÅ?
kárért.
Az üzenetek EBH-n kÃvüli küldÅ?je vagy cÃmzettje tudomásul
veszi és hozzájárul, hogy az üzenetekhez más banki alkalmazott
is hozzáférhet az EBH folytonos munkamenetének biztosÃtása
érdekében.
This e-mail and any attached files are confidential
and/...{{dropped:19}}
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PLEASE do read the posting guide
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and provide commented, minimal, self-contained
Re: [R] R-/Text-editor for Windows?
Well, AutoHotKey [1] is a free program/scripting language that runs
scripts to perform basic window handling, file I/O, and program execution.
It also allows you to bind the running of these scripts to keys or
mouse-strokes with the option of making each window-specific. NppToR is
actually a compiled AutoHotKey script designed to do Notepad++ specific
things. For example, one of my generic, slower, user-unfriendly scripts
is:
TestConsole()
{
IfWinNotExist, ahk_class Console_2_Main,
{
Run, C:\Documents and Settings\jdaily\Console2\Console.exe
-t R
WinWait, ahk_class Console_2_Main,
}
}
ActivateConsole()
{
TestConsole()
WinActivate, ahk_class Console_2_Main,
WinWaitActive, ahk_class Console_2_Main,
}
#1::
WinGetActiveTitle, editor
old_clipboard = %clipboard%
Send, {CTRLDOWN}c{CTRLUP}
ActivateConsole()
Send, {CTRLDOWN}{END}{CTRLUP}{RETURN}
WinActivate, %editor%,
clipboard = %old_clipboard%
return
What it does when I press the Super+1 is assign the current window to a
variable editor, backup my current clipboard, and copy my highlighted
text. Then it checks to see if Console [2] is active and opens console
with R if not open. It pastes the copied text and reactivates editor,
restoring my old clipboard. Its nice because it works whether I'm in
Geany, Notepad, MSword, etc., but I didn't bother doing any checking to
make sure console's active tab is R. This could easily be solved if you
just use RTerm/RGui by replacing all the instances of Console with the
appropriate R executable.
[1]www.autohotkey.com
[2]sourceforge.net/projects/console
--
Jonathan P. Daily
Technician - USGS Leetown Science Center
11649 Leetown Road
Kearneysville WV, 25430
(304) 724-4480
Is the room still a room when its empty? Does the room,
the thing itself have purpose? Or do we, what's the word... imbue it.
- Jubal Early, Firefly
Liviu Andronic landronim...@gmail.com wrote on 01/29/2011 04:08:46 AM:
[image removed]
Re: [R] R-/Text-editor for Windows?
Liviu Andronic
to:
Jonathan P Daily
01/29/2011 04:09 AM
Cc:
Sascha Vieweg, r-help, r-help-bounces
Hello
On Fri, Jan 28, 2011 at 8:03 PM, Jonathan P Daily jda...@usgs.gov
wrote:
Geany also handles a ton of filetypes, but lacks a direct interface to
R
in the windows version - I wrote an AutoHotKey script that did this
for me
in about 5 minutes.
Could you please expand on that? I prefer to use Geany when working on
Linux, but I always found it annoying the Windows limitation.
Thank you
Liviu
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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] R-/Text-editor for Windows?
Notepad ++ handles just about anything and has an accompanying program NppToR to make passing scripts easier. Geany also handles a ton of filetypes, but lacks a direct interface to R in the windows version - I wrote an AutoHotKey script that did this for me in about 5 minutes. On the other hand, geany is cross platform. As always, EMACS + ESS and Vim are also options. -- Jonathan P. Daily Technician - USGS Leetown Science Center 11649 Leetown Road Kearneysville WV, 25430 (304) 724-4480 Is the room still a room when its empty? Does the room, the thing itself have purpose? Or do we, what's the word... imbue it. - Jubal Early, Firefly r-help-boun...@r-project.org wrote on 01/28/2011 01:55:25 PM: [image removed] [R] R-/Text-editor for Windows? Sascha Vieweg to: r-help 01/28/2011 01:57 PM Sent by: r-help-boun...@r-project.org Tinn-R (http://www.sciviews.org/Tinn-R/) is one of the topmost suggestions when googling an R-(text-)editor for Windows. However, to me it appears dissappointing that Tinn-R does not handle utf-8 (mac-roman, or any other) encoded R-scripts or, in general, text files. Besides Emacs and the R built-in editor, could you recommend a good editor for Windows, even some commmercial for a small price? (For a comparison, TextMate for OS X is 35 USD and does a great job on all plain text and code related issues, not only R.) Thanks, *S* -- Sascha Vieweg, saschav...@gmail.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] Quantile Regression: Extracting Residuals
Try looking here: ?rq.object ?residuals R has excellent documentation that can answer many such questions with less than a minute of reading. -- Jonathan P. Daily Technician - USGS Leetown Science Center 11649 Leetown Road Kearneysville WV, 25430 (304) 724-4480 Is the room still a room when its empty? Does the room, the thing itself have purpose? Or do we, what's the word... imbue it. - Jubal Early, Firefly r-help-boun...@r-project.org wrote on 01/19/2011 11:30:49 AM: [image removed] [R] Quantile Regression: Extracting Residuals Thanaset to: r-help 01/19/2011 02:12 PM Sent by: r-help-boun...@r-project.org Dear R users Is there a way to obtain the residuals from a model fitted by quantile regression? Thank you. Thanaset -- View this message in context: http://r.789695.n4.nabble.com/ Quantile-Regression-Extracting-Residuals-tp3225423p3225423.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] Question about histogram
Because a histogram is descriptive and makes no assumptions about what it describes? Attaching a probability to the bars assumes that some random draw is being made. Suppose my data is a count of computers running a particular OS. What would be the value in reporting this as a probability that a randomly chosen computer is running Ubuntu? Density is more universal, IMO. -- Jonathan P. Daily Technician - USGS Leetown Science Center 11649 Leetown Road Kearneysville WV, 25430 (304) 724-4480 Is the room still a room when its empty? Does the room, the thing itself have purpose? Or do we, what's the word... imbue it. - Jubal Early, Firefly r-help-boun...@r-project.org wrote on 01/13/2011 01:37:01 PM: [image removed] [R] Question about histogram Longe to: r-help 01/13/2011 03:11 PM Sent by: r-help-boun...@r-project.org Dear list, I'm new to R, please bear with my silly questions. I'm trying to get an understanding of why the results I get from a call to hist() are not as I thought I would get. When I use the parameter freq=FALSE, I think the plot will contain bars that none of them is larger than 1, because they're probabilities. But for my code, the bars exceeded 1. The actual data seems immaterial. I tried with dummy data: hist(runif(1000), freq=FALSE) and the histogram includes bars well over 1 in height. The man page says that freq=FALSE produces densities, so that the total area is 1. Clearly if all the values are between 0 and 1, as is the case here, some of the bars stand out above 1, for the area to be 1. I thought that it is the sum of the bar heights that would be 1, so that the bars reflect probabilities for each interval, rather than densities. So, the answer to my question would be because it's densities, not probabilities, but then the question is, why densities and not probabilities? Regards, L. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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 wrap a long line in R scripts?
a - rey lo ong charrr Although the indentation is just personal preference. -- Jonathan P. Daily Technician - USGS Leetown Science Center 11649 Leetown Road Kearneysville WV, 25430 (304) 724-4480 Is the room still a room when its empty? Does the room, the thing itself have purpose? Or do we, what's the word... imbue it. - Jubal Early, Firefly __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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 wrap a long line in R scripts?
To elaborate, expressions and any explicit enclosures can also be simply split between lines. Often, this is done without space issues just for clarity. EX: vec - c(LETTERS[1:5], 1:5, letters[1:5]) plot(X, Y, main = A plot, xlab = X Values, ylab = Response, lty = 1, pch = 5, cex = .75) num - ((a1 + a2 + a3)/b1 + (a4 + a5 + a6)/b2) / b3 -- Jonathan P. Daily Technician - USGS Leetown Science Center 11649 Leetown Road Kearneysville WV, 25430 (304) 724-4480 Is the room still a room when its empty? Does the room, the thing itself have purpose? Or do we, what's the word... imbue it. - Jubal Early, Firefly r-help-boun...@r-project.org wrote on 01/10/2011 09:04:23 AM: [image removed] Re: [R] how to wrap a long line in R scripts? Jonathan P Daily to: Tutu2008 01/10/2011 09:09 AM Sent by: r-help-boun...@r-project.org Cc: r-help, r-help-bounces a - rey lo ong charrr Although the indentation is just personal preference. -- Jonathan P. Daily Technician - USGS Leetown Science Center 11649 Leetown Road Kearneysville WV, 25430 (304) 724-4480 Is the room still a room when its empty? Does the room, the thing itself have purpose? Or do we, what's the word... imbue it. - Jubal Early, Firefly __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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 wrap a long line in R scripts?
Oops! Good catch. I have been coding in python and R recently and now I'm mixing conventions ... R's automatic line wrapping and Python's auto-catenation given a line wrap (via '\'). A better solution would be: a - paste(rey lo, ong charrr, sep = ) print(a) -- Jonathan P. Daily Technician - USGS Leetown Science Center 11649 Leetown Road Kearneysville WV, 25430 (304) 724-4480 Is the room still a room when its empty? Does the room, the thing itself have purpose? Or do we, what's the word... imbue it. - Jubal Early, Firefly r-help-boun...@r-project.org wrote on 01/10/2011 09:51:28 AM: [image removed] Re: [R] how to wrap a long line in R scripts? Keith Jewell to: r-help 01/10/2011 09:54 AM Sent by: r-help-boun...@r-project.org Jonathan P Daily jda...@usgs.gov wrote in message news:of588e803b.869e9aff-on85257814.004d298d-85257814.004d4...@usgs.gov... a - rey lo ong charrr Although the indentation is just personal preference. -- Jonathan P. Daily Technician - USGS Leetown Science Center 11649 Leetown Road Kearneysville WV, 25430 (304) 724-4480 Is the room still a room when its empty? Does the room, the thing itself have purpose? Or do we, what's the word... imbue it. - Jubal Early, Firefly Did you test that? Printing a to see the result so the commands are - a - rey lo ong charrr a Pasting directly into Rgui a - rey lo + ong charrr a [1] rey lo\nong charrr Saving to file 'test.r' and sourcing source(C:\\Documents and Settings\\jewell\\Desktop\\test.r, echo=TRUE) a - rey lo + ong charrr a [1] rey lo\nong charrr I don't think this is what the OP wanted. I guess he wants rey loong charrr I don't know the answer (other than, as suggested by Peter Ehlers) to build it bit by bit. KJ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] matrices call a function element-wise
IIRC, R is perfectly able to call matrices as vectors, so you might be
able to do this:
FT - function(i) fisher.test(matrix(c(A[i],B[i],C[i],D[i]),2))
E - sapply(1:100, FT)
Though I don't know how much time you will save.
--
Jonathan P. Daily
Technician - USGS Leetown Science Center
11649 Leetown Road
Kearneysville WV, 25430
(304) 724-4480
Is the room still a room when its empty? Does the room,
the thing itself have purpose? Or do we, what's the word... imbue it.
- Jubal Early, Firefly
r-help-boun...@r-project.org wrote on 01/03/2011 09:57:14 AM:
[image removed]
[R] matrices call a function element-wise
zhaoxing731
to:
R-help
01/03/2011 01:46 PM
Sent by:
r-help-boun...@r-project.org
Hello
I have 4 1000*1000 matrix A,B,C,D. I want to use the corresponding
element of the 4 matrices. Using the for loop as follow:
E-o
for (i in 1:1000)
{for (j in 1:1000)
{
E-fisher.test(matrix(c(A[i][j],B[i][j],C[i][j],D[i][j]),
2))#call fisher.test for every element
}
}
It is so time-consuming
Need vectorization
Yours sincerely
ZhaoXing
Department of Health Statistics
West China School of Public Health
Sichuan University
No.17 Section 3, South Renmin Road
Chengdu, Sichuan 610041
P.R.China
[[alternative HTML version deleted]]
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8O?lW2aQE;3,4sH]A?Cb7QSJOd?
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Re: [R] randomForest speed improvements
Have you tried adjusting:
mtry - the number of parameters to try per tree
ntree - the number of trees grown
keep.forest - logical on whether to store tree
Specifically, I found huge improvements in speed by switching keep.forest
to FALSE in the past when I didn't actually need the forest post analysis.
--
Jonathan P. Daily
Technician - USGS Leetown Science Center
11649 Leetown Road
Kearneysville WV, 25430
(304) 724-4480
Is the room still a room when its empty? Does the room,
the thing itself have purpose? Or do we, what's the word... imbue it.
- Jubal Early, Firefly
r-help-boun...@r-project.org wrote on 01/03/2011 02:59:29 PM:
[image removed]
[R] randomForest speed improvements
apresley
to:
r-help
01/03/2011 03:03 PM
Sent by:
r-help-boun...@r-project.org
Hi there,
We're trying to use randomForest to do some predictions. The
test-harness
for our code is pretty straightforward:
library ('randomForest');
data202 - read.csv (random.csv, header=TRUE);
x- data202[1:5,1:6];
y- data202[1:5,8];
y- y[,drop=TRUE];
x2 - data202[50001:6,1:6];
y2 - data202[50001:6,8];
y2 - y2[,drop=TRUE];
RFobject - randomForest(x,y,na.action=na.roughfix);
p - predict (RFobject, x2);
In this case, the CSV contains 10 columns, of which 1-6 are numeric in
nature (day of week, week of month, etc...) and column 8 is the target
(sales, a numeric number).
randomForest does fine with the data, our issue is how long it takes. In
this case, about 5,000 rows of data seems to take just a few seconds,
but
going to 50,000 rows doesn't take 5x the time, it takes perhaps 30 or 40
minutes.
We've downloaded and tried RT-Rank, which is a multi-threaded version of
RandomForest, and this seems to produce the same (or slightly better)
predictions, but also gets done fairly quickly.
What can we do to improve the speed of this data computation? The
system
we're on is a dual quad-core Intel CPU @ 2.33Ghz, and with 16GB of RAM
...
we're using the stock R RPM for CentOS 5.5.
Thanks!
--
Anthony
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Re: [R] Windows editor suggestions - autosave
I can also suggest the following: Notepad++ has an AutoSave plugin, a slew of other useful features, and a Scintilla editor. If you use other languages, it is also extensible and has almost no learning curve. NppToR is a background application that allows you to pass lines or files straight from your editor to an R console. Notepad++: notepad-plus-plus.org NppToR: sourceforge.net/projects/npptor/ I can also suggest Geany, another Scintilla-powered editor. In the plugins list, Save Actions has a autosave feature. While Geany doesn't have a native R interface in Windows (I wrote one for myself in AutoHotKey in about 2 mins), it has a ton of other options and is cross-platform. Geany: www.geany.org -- Jonathan P. Daily Technician - USGS Leetown Science Center 11649 Leetown Road Kearneysville WV, 25430 (304) 724-4480 Is the room still a room when its empty? Does the room, the thing itself have purpose? Or do we, what's the word... imbue it. - Jubal Early, Firefly r-help-boun...@r-project.org wrote on 12/29/2010 11:32:40 AM: [image removed] [R] Windows editor suggestions - autosave Michael Conklin to: R-help 12/29/2010 11:35 AM Sent by: r-help-boun...@r-project.org I am looking for advice on an editor to use with R (windows) that has an autosave feature. I typically write scripts using the RGui (and tried TinnR yesterday) but I am having continuing problems with BSODs (non R related) and have in the past have had issues with R crashes and would really like a system that does not require me to remember to hit the save button on my script every 10 minutes so that I can avoid redoing everything. W. Michael Conklin Chief Methodologist Google Voice: (612) 56STATS MarketTools, Inc. | www.markettools.com 6465 Wayzata Blvd | Suite 170 | St. Louis Park, MN 55426. PHONE: 952.417.4719 | CELL: 612.201.8978 This email and attachment(s) may contain confidential and/or proprietary information and is intended only for the intended addressee(s) or its authorized agent(s). Any disclosure, printing, copying or use of such information is strictly prohibited. If this email and/or attachment(s) were received in error, please immediately notify the sender and delete all copies __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Faster way to do it??...using apply?
I don't know if it's any faster, but it is also possible this way: y - ifelse(x ==1, round(runif(x)), sign(x)) -- Jonathan P. Daily Technician - USGS Leetown Science Center 11649 Leetown Road Kearneysville WV, 25430 (304) 724-4480 Is the room still a room when its empty? Does the room, the thing itself have purpose? Or do we, what's the word... imbue it. - Jubal Early, Firefly r-help-boun...@r-project.org wrote on 12/28/2010 12:48:04 PM: [image removed] Re: [R] Faster way to do it??...using apply? Henrique Dallazuanna to: M.Ribeiro 12/28/2010 12:51 PM Sent by: r-help-boun...@r-project.org Cc: r-help Try this indeed replace(replace(x, x == 1, sample(0:1, sum(x == 1), rep = TRUE)), x == 2, 1) On Tue, Dec 28, 2010 at 3:14 PM, M.Ribeiro mresende...@yahoo.com.br wrote: Hi Henrique, Thanks for the fast answer, The only problem in your code, which I think I didn't mention in my message is that I would like one different random sampling procedure for each 1 in my vector The way it was written, it samples only once and replace by every 1: x = as.matrix(c(1,1,1,1,1,1,1,1,1,1,1,1,1,1,1)) replace(replace(x, x == 1, sample(0:1, 1)), x == 2, 1) [,1] [1,]1 [2,]1 [3,]1 [4,]1 [5,]1 [6,]1 [7,]1 [8,]1 [9,]1 [10,]1 [11,]1 [12,]1 [13,]1 [14,]1 [15,]1 Thanks -- View this message in context: http://r.789695.n4.nabble.com/Faster-way-to-do-it-using-apply- tp3166161p3166203.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Fitting a Triangular Distribution to Bivariate Data
I don't know if any specific package has a triangular distribution, but I know you can fit a model using first degree b-splines with a single knot. library(splines) ?bs x - 1:100 y - rnorm(100, ifelse(x 50, x, 100-x), 15) fit - lm(y ~ bs(x, knots = 50, degree = 1)) -- Jonathan P. Daily Technician - USGS Leetown Science Center 11649 Leetown Road Kearneysville WV, 25430 (304) 724-4480 Is the room still a room when its empty? Does the room, the thing itself have purpose? Or do we, what's the word... imbue it. - Jubal Early, Firefly r-help-boun...@r-project.org wrote on 12/22/2010 01:19:16 PM: [image removed] [R] Fitting a Triangular Distribution to Bivariate Data David Bapst to: r-help 12/22/2010 04:04 PM Sent by: r-help-boun...@r-project.org Hello, I have some xy data which clearly shows a non-monotonic, peaked triangular trend. You can get an idea of what it looks like with: x-1:20 y-c(2*x[1:10]+1,-2*x[11:20]+42) I've tried fitting a quadratic, but it just doesn't the data-structure with the break point adequately. Is there anyway to fit a triangular or 'tent' function to my data in R? Some sample code would be appreciated; I'm not new to R, but I sometimes have difficulty understanding the model-fitting functions (finally figured out how to extrapolate with predict() today!) Thanks! -Dave Bapst, UChicago __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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 optimize function parameters?
Without an example, I'm not sure how much help I can be. Does your
Variogram calculation return a single value that could be minimized? Or
could it be coerced to be so?
I would suggest, if you haven't done so, a look at ?nlm and ?nlminb.
Alternatively, the CRAN package 'optimx' serves as a wrapper to many
optimization algorithms and offers methods to compare them side-by-side.
Good luck,
Jon
--
Jonathan P. Daily
Technician - USGS Leetown Science Center
11649 Leetown Road
Kearneysville WV, 25430
(304) 724-4480
Is the room still a room when its empty? Does the room,
the thing itself have purpose? Or do we, what's the word... imbue it.
- Jubal Early, Firefly
r-help-boun...@r-project.org wrote on 12/20/2010 09:39:49 AM:
[image removed]
[R] How to optimize function parameters?
zbynek.jano...@gmail.com
to:
r-help
12/20/2010 10:43 AM
Sent by:
r-help-boun...@r-project.org
Hi,
I have a dataset and I want to fit a function to it.
The function is variogram model (http://en.wikipedia.org/wiki/Variogram)
The variogram model is defined by three parameters and I want them to be
automatically optimized for real time data.
I tried to use gafit {gafit} for this, but there are some data
configuration, where optimal results given by gafit() are negative,
which is
not correct and cannot be used for further calculating. gafit() does not
enable me to set a range of possible results (at least I did not
succeded in
doing so), therefore I am looking for another solution (Powell´s
gradient
descent possibly?).
Can anyone give me a hint where to look?
Thanks
Zbynek
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Re: [R] How to optimize function parameters?
If you can somehow add the sign of the output to the root square error, nlm, nlminb, and many options within optimx accept bounds. -- Jonathan P. Daily Technician - USGS Leetown Science Center 11649 Leetown Road Kearneysville WV, 25430 (304) 724-4480 Is the room still a room when its empty? Does the room, the thing itself have purpose? Or do we, what's the word... imbue it. - Jubal Early, Firefly r-help-boun...@r-project.org wrote on 12/20/2010 01:13:53 PM: [image removed] Re: [R] How to optimize function parameters? zbynek.jano...@gmail.com to: r-help 12/20/2010 02:35 PM Sent by: r-help-boun...@r-project.org Thanks for your suggestions, I will certainly look at that To answer your question... I can calculate root square error between empirical data a those predicted by model (I used this to optimize the parameters using gafit()). -- View this message in context: http://r.789695.n4.nabble.com/How-to- optimize-function-parameters-tp3095603p3095938.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] Alter plot point size by value of the plot value
Assuming your plot values are X and Y: cex.val - 1 + (Y 1E-6)*.5 - (Y 1E-3)*.5 plot(X, Y, cex = cex.val) -- Jonathan P. Daily Technician - USGS Leetown Science Center 11649 Leetown Road Kearneysville WV, 25430 (304) 724-4480 Is the room still a room when its empty? Does the room, the thing itself have purpose? Or do we, what's the word... imbue it. - Jubal Early, Firefly r-help-boun...@r-project.org wrote on 12/17/2010 11:58:07 AM: [image removed] [R] Alter plot point size by value of the plot value Douglas Scheftner to: r-help 12/17/2010 12:00 PM Sent by: r-help-boun...@r-project.org R folks, I am trying to create a mhtplot plot that will alter the point size via the plot point value.The size of the point should change via a set criteria such as: if point value 10^-6 size 3x else if 10^-3 point value 10^-6 size 2x else point value 10^-3 size is x I consider myself an R newbie, and I am assuming that I could do this via some sort of function to change the parameter cex value of the plot, but I do not even know where to begin. I have searched for something similar to this, but have not had any luck. Is it possible to write a function that will alter the cex value via the plot value. Any suggestions? Thanks in advance, Doug __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Integrate two function in R
As a minor plug for my favorite non stat-based mathematics software, sagemath also has a rudimentary R interface built-in -- Jonathan P. Daily Technician - USGS Leetown Science Center 11649 Leetown Road Kearneysville WV, 25430 (304) 724-4480 Is the room still a room when its empty? Does the room, the thing itself have purpose? Or do we, what's the word... imbue it. - Jubal Early, Firefly r-help-boun...@r-project.org wrote on 12/16/2010 09:11:33 AM: [image removed] Re: [R] Integrate two function in R Kjetil Halvorsen to: Ben Bolker 12/16/2010 09:13 AM Sent by: r-help-boun...@r-project.org Cc: r-help see inline. On Thu, Dec 16, 2010 at 10:11 AM, Ben Bolker bbol...@gmail.com wrote: Alaios alaios at yahoo.com writes: Hello I have two function in R like g(x)=2x-3 and s(x)=5x^2+2 and I want to find the integrafl of the g(x)*s(x) inside the interval of [a,b] Analytically or numerically? It sounds like you want the answer analytically, in which case R can't do it, but it is an easy integral g(x)*s(x) = 10*x^3-15*x^2+4*x-6 indefinite integral = 10/3*x^4 -15/3*x^3 + 4/2*x^2 - 6*x + C evaluate between a and b or if you can't do this (although this is a very basic integral) you can try it on Wolfram alpha/the Mathematica integrator (google for it) Or a free software alternative: sage http://www.sagemath.org/ kjetil use ?integrate (surprisingly enough) for 1-D numerical integration __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Help about nlminb function
How are we supposed to help you if we have no idea how you are using it? Did you read the PORT documentation? Did you look at the control parameters outlined in the function help page? Often times for me a return of the initial conditions is an issue with either inappropriate tolerance or having variables on very different scales. Since you did not follow the posting guide (important part *'d below), my only suggestion is to ?nlminb -- Jonathan P. Daily Technician - USGS Leetown Science Center 11649 Leetown Road Kearneysville WV, 25430 (304) 724-4480 Is the room still a room when its empty? Does the room, the thing itself have purpose? Or do we, what's the word... imbue it. - Jubal Early, Firefly r-help-boun...@r-project.org wrote on 12/15/2010 08:53:39 AM: [image removed] [R] Help about nlminb function kamel gaanoun to: r-help 12/15/2010 08:56 AM Sent by: r-help-boun...@r-project.org Hi Everyone, Can anyone help me resolve a problem that i'm having with nlminb. The problem is that it stops after just one iteration and returns the same values as start ones. Thank you very much for your help. Sincerely. -- Kamel Gaanoun (+33) (0)6.76.04.65.77 [[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] Help about nlminb function
Your function is evaluating to Inf. Is this expected behavior? I don't know what starting values you are using, but it looks like the initial values evaluate to Inf. If this is also true for values near your initial conditions then I am not surprised the optimization returns initial values. Try changing parametres[,3] -- Jonathan P. Daily Technician - USGS Leetown Science Center 11649 Leetown Road Kearneysville WV, 25430 (304) 724-4480 Is the room still a room when its empty? Does the room, the thing itself have purpose? Or do we, what's the word... imbue it. - Jubal Early, Firefly kamel gaanoun kamel.gaan...@gmail.com wrote on 12/15/2010 09:22:57 AM: [image removed] Re: [R] Help about nlminb function kamel gaanoun to: Jonathan P Daily 12/15/2010 09:23 AM Cc: r-help, r-help-bounces I appologize for the lack of information in my previous mail, but it is my first one. Yes I red -in part- the Port documentation to learn what does the message X-convergence (3) mean. so this is my nlminb and the results : res1-nlminb(parametres[,3], V, lower=c(rep(0.01, 18), rep(0.01, 3), rep(-Inf, 6)), upper=c(rep(Inf, 18), rep(0.99, 3), rep(Inf, 6)), control = list(maxit=1000) ) Results : res1 $par [1] 1.000 1.000 1.000 1.000 1.000 1.000 1.000 [8] 1.000 1.000 1.000 1.000 1.000 1.000 1.000 [15] 1.000 1.000 1.000 1.000 0.6899225 0.7993528 0.6480687 [22] 0.000 0.000 0.000 0.000 0.000 0.000 $objective [1] Inf $convergence [1] 0 $message [1] X-convergence (3) $iterations [1] 1 $evaluations function gradient 2 27 So as you see, it stops after just one iteration but it is converging. Thanks 2010/12/15 Jonathan P Daily jda...@usgs.gov How are we supposed to help you if we have no idea how you are using it? Did you read the PORT documentation? Did you look at the control parameters outlined in the function help page? Often times for me a return of the initial conditions is an issue with either inappropriate tolerance or having variables on very different scales. Since you did not follow the posting guide (important part *'d below), my only suggestion is to ?nlminb -- Jonathan P. Daily Technician - USGS Leetown Science Center 11649 Leetown Road Kearneysville WV, 25430 (304) 724-4480 Is the room still a room when its empty? Does the room, the thing itself have purpose? Or do we, what's the word... imbue it. - Jubal Early, Firefly r-help-boun...@r-project.org wrote on 12/15/2010 08:53:39 AM: [image removed] [R] Help about nlminb function kamel gaanoun to: r-help 12/15/2010 08:56 AM Sent by: r-help-boun...@r-project.org Hi Everyone, Can anyone help me resolve a problem that i'm having with nlminb. The problem is that it stops after just one iteration and returns the same values as start ones. Thank you very much for your help. Sincerely. -- Kamel Gaanoun (+33) (0)6.76.04.65.77 [[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. ** -- Kamel Gaanoun (+33) (0)6.76.04.65.77 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Integration with LaTex and LyX
?Sweave LyX is a bit harder, although you can probably export LyX docs to a *.tex and Sweave those fairly painlessly. -- Jonathan P. Daily Technician - USGS Leetown Science Center 11649 Leetown Road Kearneysville WV, 25430 (304) 724-4480 Is the room still a room when its empty? Does the room, the thing itself have purpose? Or do we, what's the word... imbue it. - Jubal Early, Firefly r-help-boun...@r-project.org wrote on 12/13/2010 10:27:43 AM: [image removed] [R] Integration with LaTex and LyX Eduardo de Oliveira Horta to: r-help 12/13/2010 10:29 AM Sent by: r-help-boun...@r-project.org Hello, Are there any packages which allow for a good integration between R and LaTex / LyX? I'm interested mainly in automatic (automagic?) imports of plots/graphics. Thanks in advance and best regards, Eduardo de Oliveira Horta [[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] string
?paste collapse = T may be necessary. -- Jonathan P. Daily Technician - USGS Leetown Science Center 11649 Leetown Road Kearneysville WV, 25430 (304) 724-4480 Is the room still a room when its empty? Does the room, the thing itself have purpose? Or do we, what's the word... imbue it. - Jubal Early, Firefly r-help-boun...@r-project.org wrote on 12/07/2010 10:11:41 AM: [image removed] [R] string Benoit Wastine to: r-help 12/07/2010 10:14 AM Sent by: r-help-boun...@r-project.org Hi, I'm running R 2.11 Does anyone know if it possible to transform one character vector to one character string ? Many thanks Benoit -- Benoit Wastine Laboratoire des Sciences du Climat et de l’Environnement (LSCE/IPSL) CEA-CNRS-UVSQ CE Saclay Orme des merisiers Bât 703 - Pte 13A 91191 Gif sur Yvette Cedex France Tel : 33 (0)1 69 08 21 97 Fax : 33 (0)1 69 08 77 16 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] More elegant magnitude method
I have a need to find the order of number to get a scaling parameter as a
power of 10. I have a function that works *so far*, but it is ugly and
probably buggy. In the interest of avoiding code-based outliers in my
data, I thought I would ask if anyone here has a better way.
scl - function(x){
+ length(charToRaw(format(trunc(x), scientific = F)))-1}
a - 123456789
b - 1E15
c - 12.345
scl(a)
[1] 8
scl(b)
[1] 15
scl(c)
[1] 1
Thanks
--
Jonathan P. Daily
Technician - USGS Leetown Science Center
11649 Leetown Road
Kearneysville WV, 25430
(304) 724-4480
Is the room still a room when its empty? Does the room,
the thing itself have purpose? Or do we, what's the word... imbue it.
- Jubal Early, Firefly
__
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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] More elegant magnitude method
What a brain fart...
Thanks!
--
Jonathan P. Daily
Technician - USGS Leetown Science Center
11649 Leetown Road
Kearneysville WV, 25430
(304) 724-4480
Is the room still a room when its empty? Does the room,
the thing itself have purpose? Or do we, what's the word... imbue it.
- Jubal Early, Firefly
David Winsemius dwinsem...@comcast.net wrote on 12/07/2010 02:50:34 PM:
[image removed]
Re: [R] More elegant magnitude method
David Winsemius
to:
Jonathan P Daily
12/07/2010 02:50 PM
Cc:
r-help
On Dec 7, 2010, at 2:43 PM, Jonathan P Daily wrote:
I have a need to find the order of number to get a scaling parameter
as a
power of 10. I have a function that works *so far*, but it is ugly and
probably buggy. In the interest of avoiding code-based outliers in my
data, I thought I would ask if anyone here has a better way.
scl - function(x){
+ length(charToRaw(format(trunc(x), scientific = F)))-1}
a - 123456789
b - 1E15
c - 12.345
scl(a)
[1] 8
scl(b)
[1] 15
scl(c)
[1] 1
scl- function(x) trunc(log(x,10))
scl(a)
[1] 8
scl(b)
[1] 15
scl(c)
[1] 1
Seems mathematically clearer.
--
David Winsemius, MD
West Hartford, CT
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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Re: [R] Optimize multiple variable sets
Correct me if I'm wrong, but isn't the minimal x value in your example the
same regardless of what positive coefficient you apply to x? If that is
the case, you would expect the same min(x) for each iteration.
i.e. in the interval [0,1] the minimum x value of x^2 + x is the same as
x^2 + 1*x, at x = 0.
--
Jonathan P. Daily
Technician - USGS Leetown Science Center
11649 Leetown Road
Kearneysville WV, 25430
(304) 724-4480
Is the room still a room when its empty? Does the room,
the thing itself have purpose? Or do we, what's the word... imbue it.
- Jubal Early, Firefly
r-help-boun...@r-project.org wrote on 12/06/2010 07:00:57 AM:
[image removed]
[R] Optimize multiple variable sets
sandra lag
to:
r-help
12/06/2010 08:54 AM
Sent by:
r-help-boun...@r-project.org
Hi,
I usually use optimize function for ML Estimation. Now I´ve got a
data frame with many sets, but I can´t save estimates each time I
run the code for each data set (I´m using a for loop with my
loglikelihood function and works ok but when I apply another for loop
to:
optimize(my.loglikelihood.function[i], int=c(0.0001,10))
it doesn´t work;
alternatively, using optimize inside the for loop (like in the
example below), it returns always the same value, which is not expected:
data-matrix(c(1,1,1, 2,2,2, 3,3,3, 4,4,4), nrow=3, ncol=4)
c-dim(data)[2]
results-vector(length=c)
for (i in 1:c){
f-function(x){
x^2+x*sum(data[,i])
}
results[i]-optimize(f,int=c(0.0001,10))[1] #minimum
}
#results
Can someone please indicate me if there´s a different function/ way
to do so? (with no need of initial parameter values)
Thanks! Sandra
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Re: [R] Optimize multiple variable sets
I suppose I should have been more clear. I saw that her interval did not include the actual minimum, but I was asking if (and if, why) she was expecting the minimum x value to be different for each run. If the y value were returned the same on each run that would be puzzling. As for the returned x issue, you are correct that it is a 'tol' issue: reducing tol to something reasonably low approximates the min fairly well. -- Jonathan P. Daily Technician - USGS Leetown Science Center 11649 Leetown Road Kearneysville WV, 25430 (304) 724-4480 Is the room still a room when its empty? Does the room, the thing itself have purpose? Or do we, what's the word... imbue it. - Jubal Early, Firefly peter dalgaard pda...@gmail.com wrote on 12/06/2010 09:39:43 AM: [image removed] Re: [R] Optimize multiple variable sets peter dalgaard to: Jonathan P Daily 12/06/2010 09:39 AM Cc: sandra lag, r-help, r-help-bounces On Dec 6, 2010, at 15:15 , Jonathan P Daily wrote: Correct me if I'm wrong, but isn't the minimal x value in your example the same regardless of what positive coefficient you apply to x? If that is the case, you would expect the same min(x) for each iteration. i.e. in the interval [0,1] the minimum x value of x^2 + x is the same as x^2 + 1*x, at x = 0. You're wrong --- slightly. The returned $minimum is the x, the y is $objective. But the interval given doesn't bracket the minimum, as you'll clearly see if you put int=c(-10,10). The only puzzling bit is that optimize() doesn't actually return the left endpoint, but rather the first evaluation point inside the interval. The rather wide tolerance of .Machine$double.eps^0.25 == 0.0001220703 probably plays a role in this. -- Peter Dalgaard Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Email: pd@cbs.dk Priv: pda...@gmail.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] rpart results - problem after oversampling
Short answer: Not really. Slightly longer answer: from what I remember of partitioning methods, a given split is made at either a single observation or between two consecutive observations. In your case, I estimate rpart would have split on that particular point... except that there are 6 of them now. So the choice of which 6 to split is arbitrary. (Someone with more knowledge of rpart's guts feel free to correct me). -- Jonathan P. Daily Technician - USGS Leetown Science Center 11649 Leetown Road Kearneysville WV, 25430 (304) 724-4480 Is the room still a room when its empty? Does the room, the thing itself have purpose? Or do we, what's the word... imbue it. - Jubal Early, Firefly r-help-boun...@r-project.org wrote on 12/02/2010 05:34:23 AM: [image removed] [R] rpart results - problem after oversampling Mederos, Vicente (Santander) to: r-help@r-project.org 12/02/2010 05:36 AM Sent by: r-help-boun...@r-project.org Hi all, I am trying to predict a target variable that takes values 0 or 1 using the rpart command. In my initial dataset I have few positive observations of the target variable; therefore I have oversampled the rare event by a multiple of 6 (i.e. from 762 to 4572). However, in my results, I end up with a number of positives in one of the terminal nodes that is not divisible by 6. As I have the same observation repeated 6 times, shouldn't all of them follow the same branch of the tree and go to the same terminal node? Thanks for your help, Vicente Emails aren't always secure, and they may be intercepted or changed after they've been sent. Santander doesn't accept liability if this happens. If you think someone may have interfered with this email, please get in touch with the sender another way. This message doesn't create or change any contract. Santander doesn't accept responsibility for damage caused by any viruses contained in this email or its attachments. Emails may be monitored. If you've received this email by mistake, please let the sender know at once that it's gone to the wrong person and then destroy it without copying, using, or telling anyone about its contents. Santander UK plc (SAN UK) Reg. No. 2294747 and Abbey National Treasury Services plc (ANTS) Reg. No. 2338548 are registered in England and have their Registered Offices at 2 Triton Square, Regent's Place, London, NW1 3AN. www.santander.co.uk SAN UK and ANTS are authorised and regulated by the Financial Services Authority (Reg. No. 106054 and 146003 respectively). SAN UK advises on mortgages, a limited range of life assurance, pension and collective investment scheme products and acts as an insurance intermediary for general insurance. Santander and the flame logo are registered trademarks. Ref:[PDB#1-4] [[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] Sequence for repeated numbers
Try this: ord - order(grade) ID - Id[ord] grade - grade[ord] sequence - unlist(sapply(table(grade), FUN = function(x) 1:x), use.names = F) And as a general tip, it is much easier to work with related values like ID and grade if they are in a data frame. Such as: dat - data.frame(ID, grade) dat - dat[order(grade),] -- Jonathan P. Daily Technician - USGS Leetown Science Center 11649 Leetown Road Kearneysville WV, 25430 (304) 724-4480 Is the room still a room when its empty? Does the room, the thing itself have purpose? Or do we, what's the word... imbue it. - Jubal Early, Firefly r-help-boun...@r-project.org wrote on 12/01/2010 11:08:06 AM: [image removed] [R] Sequence for repeated numbers Luana Marotta to: r-help, r-help-request 12/01/2010 11:09 AM Sent by: r-help-boun...@r-project.org Hello fellows, I would like to create a sequence for repeated numbers in a dataset. For example: ID - c(1:20) grade - c(4,4,4,5,5,7,7,7,7,8,8,8,9,9,9,9,9,10,10,10) Data: ID Grade 1 4 2 4 3 4 4 5 5 5 6 7 7 7 8 7 9 7 (...) I would like to create a variable sequence: Data: ID GradeSequence: 1 4 1 2 4 2 3 4 3 4 5 1 5 5 2 6 7 1 7 7 2 8 7 3 9 7 4 Any help is very much appreciate! Thank you, Luana Marotta [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Two dimensional Array defined on intevals
Does this work for you? g - function(x,y) ifelse(x .5, 0, 2) + ifelse(y .5, 1, 2) -- Jonathan P. Daily Technician - USGS Leetown Science Center 11649 Leetown Road Kearneysville WV, 25430 (304) 724-4480 Is the room still a room when its empty? Does the room, the thing itself have purpose? Or do we, what's the word... imbue it. - Jubal Early, Firefly r-help-boun...@r-project.org wrote on 11/29/2010 11:37:41 AM: [image removed] [R] Two dimensional Array defined on intevals Leon Adams to: r-help 11/29/2010 11:39 AM Sent by: r-help-boun...@r-project.org Hi I am new to R and am trying to set up a two-dimensional array/matrix with the elements defined by the function similar to below. Been trying to use outer with apply but can't seem to get the indexing quite right. Is their a simple way of accomplishing this task ?? - / | 1 x 0.5 y 0.5 | / 2 x 0.5 y 0.5 / G(x,y) = \ \ | 3 x 0.5 y 0.5 | \ 4 x 0.5 y 0.5 - -- Thanks in advance Leon Adams [[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] Population abundance, change point
I agree that SiZer is not the ultimate answer to all changepoint analysis, but that is why there are so many changepoint detection methods used. I will clarify, though, that my understanding of SiZer (which may be wrong) was that the smoothing splines are just a vessel for finding the changepoints, and made no assumptions about the continuity of the changepoint itself. One thing that would certainly help, especially with the confidence intervals about 0, is some bandwidth selection standard, though choosing that standard would be a difficult process to say the least. -- Jonathan P. Daily Technician - USGS Leetown Science Center 11649 Leetown Road Kearneysville WV, 25430 (304) 724-4480 Is the room still a room when its empty? Does the room, the thing itself have purpose? Or do we, what's the word... imbue it. - Jubal Early, Firefly Gavin Simpson gavin.simp...@ucl.ac.uk wrote on 11/24/2010 09:15:55 AM: [image removed] Re: [R] Population abundance, change point Gavin Simpson to: Jonathan P Daily 11/24/2010 09:16 AM Cc: Mike Marchywka, r-help, r-help-bounces, carusonm Please respond to gavin.simpson On Wed, 2010-11-17 at 09:17 -0500, Jonathan P Daily wrote: Indeed I have looked into various non-standard changepoint analysis methods. I figured the OP was more interested in traditional methods since you have to spend less time justifying your methodology. Wavelets are one potential nontraditional method, as is Significant Zero Crossings (R package SiZer), which fits arbitrary-degree smoothing splines over a range of bandwidth parameters and looks for changes. ...By looking to see if the derivative of the fitted curve is different from 0 (given a suitable confidence interval on the derivative. My problem with all of this is that these data are time series and SiZeR doesn't take this into account (AFAICS) when computing the confidence intervals - they are certainly too narrow for examples I have run. Also, if these things are using splines, aren't we already assuming that the underlying function is smooth and not a discontinuity? So which technique the OP chooses will depend on how they think about the type of change taking place at the changepoint - a point I think you made earlier Jonathan. Don't mean to be too negative, this has been a very useful discussion that I am coming to late after a spot of time in the field. All the best, G With large communities of abundance counts, another approach that is gaining popularity is the community-level indicator taxa analysis (TITAN), though that is not useful to the OP. -- Jonathan P. Daily Technician - USGS Leetown Science Center 11649 Leetown Road Kearneysville WV, 25430 (304) 724-4480 Is the room still a room when its empty? Does the room, the thing itself have purpose? Or do we, what's the word... imbue it. - Jubal Early, Firefly Mike Marchywka marchy...@hotmail.com wrote on 11/17/2010 09:11:11 AM: [image removed] RE: [R] Population abundance, change point Mike Marchywka to: jdaily, carusonm 11/17/2010 09:11 AM Cc: r-help, r-help-bounces To: carus...@gmail.com From: jda...@usgs.gov Date: Wed, 17 Nov 2010 08:45:01 -0500 CC: r-help@r-project.org; r-help-boun...@r-project.org Subject: Re: [R] Population abundance, change point There are really no set ways to determine a changepoint, since a changepoint depends completely on what you decide. Recursive partitioning will fit a best changepoint, but it will pretty much always fit one. This If you are open to newer ideas, have you looked at wavelets at all? these come up on googel along with R. Also with aonly a few points, even 20-30, you coldconsider exhasiutvely fitting slopes to all 2^n subsets and plowing throgh the histograms looking for anything that may be publishable or illuminating about your data. Fitting to your own model or null hypotheses would make interesting contrasts of course, populations remained the same after atrazine spill or asteroid hit etc. function can be found in the package rpart: fit - rpart(count ~ year, control = list(maxdepth = 1)) summary(fit) However this measure offers no level of confidence. This is where packages like strucchange and party come into use, as they provide measures of confidence. Alternatively, you could look into regression-based methods where the changepoint is some parameter. Piecewise regression, for instance, is as simple as fitting a spline of degree 1 and changepoint X: library(splines) fit - lm(count ~ bs(year, knots = X, degree = 1)) plot(year, count) lines(year, fitted(fit)) Then you can fit a regression at each
Re: [R] Population abundance, change point
I understand that smoothing splines produce continuous models, however the end product of SiZer is not a single model that is then used in any predictive manner. Rather, the end product is a map of potential changepoint locations along a gradient. Are you suggesting that SiZer would not find a changepoint at the Aswan Dam? If so, I would argue against that conclusion. If your point is that pulling one underlying spline model used to create a SiZer map out and trying to draw conclusions from that model is ineffective, you are absolutely right. I tend to think of SiZer outputs more akin to tree outputs than piecewise regression outputs. -- Jonathan P. Daily Technician - USGS Leetown Science Center 11649 Leetown Road Kearneysville WV, 25430 (304) 724-4480 Is the room still a room when its empty? Does the room, the thing itself have purpose? Or do we, what's the word... imbue it. - Jubal Early, Firefly Gavin Simpson gavin.simp...@ucl.ac.uk wrote on 11/24/2010 12:09:15 PM: [image removed] Re: [R] Population abundance, change point Gavin Simpson to: Jonathan P Daily 11/24/2010 12:09 PM Cc: r-help, carusonm Please respond to gavin.simpson On Wed, 2010-11-24 at 10:59 -0500, Jonathan P Daily wrote: I agree that SiZer is not the ultimate answer to all changepoint analysis, but that is why there are so many changepoint detection methods used. I will clarify, though, that my understanding of SiZer (which may be wrong) was that the smoothing splines are just a vessel for finding the changepoints, and made no assumptions about the continuity of the changepoint itself. But by the nature of using splines, they *you) are positing a model for what the changepoint looks like. If you model the classic Nile data with a spline model (say using gam()) then it will suggest that there was a smooth transition from high flow before the dam at Aswan was built to lower flow afterwards. Other techniques that posit a discontinuity as a changepoint would fit two, effectively flat [slope 0], linear lines either side of the point when the dam was built. If you didn't know a dam was built and all you fitted was a spline to the data, that would likely influence how you interpreted the change. One thing that would certainly help, especially with the confidence intervals about 0, is some bandwidth selection standard, though choosing that standard would be a difficult process to say the least. That won't help with the lack of independence in the residuals, which will result in deflated CI on the derivatives, hence more wiggles seem significant... Oh the joy. Also, there has to be a point where with siZer you are just looking at pattern in noise at the small bandwidth end of things... I'll get off my soap box about now! ;-) Cheers, G -- Jonathan P. Daily Technician - USGS Leetown Science Center 11649 Leetown Road Kearneysville WV, 25430 (304) 724-4480 Is the room still a room when its empty? Does the room, the thing itself have purpose? Or do we, what's the word... imbue it. - Jubal Early, Firefly Gavin Simpson gavin.simp...@ucl.ac.uk wrote on 11/24/2010 09:15:55 AM: [image removed] Re: [R] Population abundance, change point Gavin Simpson to: Jonathan P Daily 11/24/2010 09:16 AM Cc: Mike Marchywka, r-help, r-help-bounces, carusonm Please respond to gavin.simpson On Wed, 2010-11-17 at 09:17 -0500, Jonathan P Daily wrote: Indeed I have looked into various non-standard changepoint analysis methods. I figured the OP was more interested in traditional methods since you have to spend less time justifying your methodology. Wavelets are one potential nontraditional method, as is Significant Zero Crossings (R package SiZer), which fits arbitrary-degree smoothing splines over a range of bandwidth parameters and looks for changes. ...By looking to see if the derivative of the fitted curve is different from 0 (given a suitable confidence interval on the derivative. My problem with all of this is that these data are time series and SiZeR doesn't take this into account (AFAICS) when computing the confidence intervals - they are certainly too narrow for examples I have run. Also, if these things are using splines, aren't we already assuming that the underlying function is smooth and not a discontinuity? So which technique the OP chooses will depend on how they think about the type of change taking place at the changepoint - a point I think you made earlier Jonathan. Don't mean to be too negative, this has been a very useful discussion that I am coming to late after a spot of time in the field. All the best, G With large communities of abundance counts
Re: [R] Check for is.object
I think you want the function ?exists if(!exists(NewObject)) -- Jonathan P. Daily Technician - USGS Leetown Science Center 11649 Leetown Road Kearneysville WV, 25430 (304) 724-4480 Is the room still a room when its empty? Does the room, the thing itself have purpose? Or do we, what's the word... imbue it. - Jubal Early, Firefly r-help-boun...@r-project.org wrote on 11/22/2010 10:14:51 AM: [image removed] [R] Check for is.object Santosh Srinivas to: r-help 11/22/2010 10:17 AM Sent by: r-help-boun...@r-project.org Hello, I am trying to recursively append some data from multiple files into a common object For this, I am using in a loop NewObject - rbind(NewObject,tempObject) For the first loop, obviously there is no NewObject ... so I wanted to do NewObject - tempObject[0,] Now when it loops again I want to put the statement do NewObject - tempObject[0,] inside a if statement ... so that it does I can skip it once NewObject has been initialized. But, is.object doesn't seem to work. What is the alternative check that I can do? And is there a better way to achieve what I want? Thanks, S __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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 constraint minimization
Does ?constrOptim look as though it will handle your needs? -- Jonathan P. Daily Technician - USGS Leetown Science Center 11649 Leetown Road Kearneysville WV, 25430 (304) 724-4480 Is the room still a room when its empty? Does the room, the thing itself have purpose? Or do we, what's the word... imbue it. - Jubal Early, Firefly r-help-boun...@r-project.org wrote on 11/19/2010 02:51:46 PM: [image removed] [R] question about constraint minimization dhacade...@gmail.com to: r-help 11/19/2010 03:15 PM Sent by: r-help-boun...@r-project.org Hi, I am a beginner of R. There is a question about constraint minimization. A function, y=f(x1,x2,x3x12), needs to be minimized. There are 3 requirements for the minimization: (1) x2+x3+...+x12=1.5 (x1 is excluded); (2) x1=x3=x4; (3) x1, x3 and x5 are in the range of -1~0, respectively. The rest variables (x2, x4, x6, x7, , x12) are in the range of 0~1, respectively. The optim function is used. And part of my input is as follow, where xx1r represents the x12: xx1r=1.5-x[2]-x[1]-x[1]-x[3]-x[4]-x[5]-x[6]-x[7]-x[8]-x[9] start=rnorm(9) up=1:9/1:9*1 lo=1:9/1:9*-1 out=optim(start,f,lower=lo,upper=up,method=L-BFGS-B,hessian=TRUE, control=list(trace=6,maxit=1000)) There are two problems in this input. the up and lo only define a range of -1~1 for x1 to x11, which can not meet the requirement (3). In addition, there is not any constraint imposed on x12. I have no idea how to specify a matrix that can impose different constraints on individual variables in a function. Any suggestion is highly appreciated. Best, Hao -- View this message in context: http://r.789695.n4.nabble.com/ question-about-constraint-minimization-tp3050880p3050880.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] predict() an rpart() model: how to ignore missing levels in a factor
I don't think that, considering the mechanism behind recursive partitioning, that there is any way for you to ignore the crop factor if it is not in the original test set. What decision should be made if, for instance, the next split in a decision tree were on crops and output was 5 for apples, 6 for bananas, and you had an instance of jicamas? It can't ignore the crop factor at that point since the next decision hinges on it. What I think you can do, however, is pre-trim your test set by testing whether each factor is present in the first set with something like (UNTESTED): test.set - test.set[test.set$crop %in% original.set$crop,] -- Jonathan P. Daily Technician - USGS Leetown Science Center 11649 Leetown Road Kearneysville WV, 25430 (304) 724-4480 Is the room still a room when its empty? Does the room, the thing itself have purpose? Or do we, what's the word... imbue it. - Jubal Early, Firefly r-help-boun...@r-project.org wrote on 11/18/2010 12:35:41 PM: [image removed] [R] predict() an rpart() model: how to ignore missing levels in a factor jamessc to: r-help 11/18/2010 12:37 PM Sent by: r-help-boun...@r-project.org I am using an algorigm to split my data set into two random sections repeatedly and constuct a model using rpart() on one, test on the other and average out the results. One of my variables is a factor(crop) where each crop type has a code. Some crop types occur infrequently or singly. when the data set is randomly split, it may be that the first data set has a crop type which is not present in the second and so using predict() I get the error: Error in model.frame.default(Terms, newdata, na.action = na.action, xlev = attr(object, : factor 'factor(c2001)' has new level(s) 13, 24, 35 where c2001 is the crop. I would like the predict function to ignore these records. is there a command which will allow this as part of the predict() function? With those with a small number of records (eg. 3-4), I would hope some of the models would have the right balance to allow a prediction to be made. -- View this message in context: http://r.789695.n4.nabble.com/predict- an-rpart-model-how-to-ignore-missing-levels-in-a-factor-tp3049218p3049218.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] Population abundance, change point
There are really no set ways to determine a changepoint, since a changepoint depends completely on what you decide. Recursive partitioning will fit a best changepoint, but it will pretty much always fit one. This function can be found in the package rpart: fit - rpart(count ~ year, control = list(maxdepth = 1)) summary(fit) However this measure offers no level of confidence. This is where packages like strucchange and party come into use, as they provide measures of confidence. Alternatively, you could look into regression-based methods where the changepoint is some parameter. Piecewise regression, for instance, is as simple as fitting a spline of degree 1 and changepoint X: library(splines) fit - lm(count ~ bs(year, knots = X, degree = 1)) plot(year, count) lines(year, fitted(fit)) Then you can fit a regression at each year and compare. Alternatively, since count data is often noisy, you could easily substitute quantile regression for linear regression to much of the same effect (assuming whatever tau you decide, I used 0.8 but this is arbitrary): library(splines) library(quantreg) fit - rq(count ~ bs(year, knots = X, degree = 1), tau = 0.8) plot(year, count) lines(year, fitted(fit)) -- Jonathan P. Daily Technician - USGS Leetown Science Center 11649 Leetown Road Kearneysville WV, 25430 (304) 724-4480 Is the room still a room when its empty? Does the room, the thing itself have purpose? Or do we, what's the word... imbue it. - Jubal Early, Firefly r-help-boun...@r-project.org wrote on 11/16/2010 05:30:49 PM: [image removed] [R] Population abundance, change point Nicholas M. Caruso to: r-help 11/16/2010 05:32 PM Sent by: r-help-boun...@r-project.org I am trying to understand my population abundance data and am looking into analyses of change point to try and determine, at approximately what point do populations begin to change (either decline or increasing). Can anyone offer suggestions on ways to go about this? I have looked into bcp and strucchange packages but am not completely convinced that these are appropriate for my data. Here is an example of what type of data I have Year of survey (continuous variable) 1960 - 2009 (there are gaps in the surveys (e.g., there were no surveys from 2002-2004) Relative abundance of salamanders during the survey periods Thanks for your help, Nick -- Nicholas M Caruso Graduate Student CLFS-Biology 4219 Biology-Psychology Building University of Maryland, College Park, MD 20742-5815 -- I learned something of myself in the woods today, and walked out pleased for having made the acquaintance. [[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] Population abundance, change point
Indeed I have looked into various non-standard changepoint analysis methods. I figured the OP was more interested in traditional methods since you have to spend less time justifying your methodology. Wavelets are one potential nontraditional method, as is Significant Zero Crossings (R package SiZer), which fits arbitrary-degree smoothing splines over a range of bandwidth parameters and looks for changes. With large communities of abundance counts, another approach that is gaining popularity is the community-level indicator taxa analysis (TITAN), though that is not useful to the OP. -- Jonathan P. Daily Technician - USGS Leetown Science Center 11649 Leetown Road Kearneysville WV, 25430 (304) 724-4480 Is the room still a room when its empty? Does the room, the thing itself have purpose? Or do we, what's the word... imbue it. - Jubal Early, Firefly Mike Marchywka marchy...@hotmail.com wrote on 11/17/2010 09:11:11 AM: [image removed] RE: [R] Population abundance, change point Mike Marchywka to: jdaily, carusonm 11/17/2010 09:11 AM Cc: r-help, r-help-bounces To: carus...@gmail.com From: jda...@usgs.gov Date: Wed, 17 Nov 2010 08:45:01 -0500 CC: r-help@r-project.org; r-help-boun...@r-project.org Subject: Re: [R] Population abundance, change point There are really no set ways to determine a changepoint, since a changepoint depends completely on what you decide. Recursive partitioning will fit a best changepoint, but it will pretty much always fit one. This If you are open to newer ideas, have you looked at wavelets at all? these come up on googel along with R. Also with aonly a few points, even 20-30, you coldconsider exhasiutvely fitting slopes to all 2^n subsets and plowing throgh the histograms looking for anything that may be publishable or illuminating about your data. Fitting to your own model or null hypotheses would make interesting contrasts of course, populations remained the same after atrazine spill or asteroid hit etc. function can be found in the package rpart: fit - rpart(count ~ year, control = list(maxdepth = 1)) summary(fit) However this measure offers no level of confidence. This is where packages like strucchange and party come into use, as they provide measures of confidence. Alternatively, you could look into regression-based methods where the changepoint is some parameter. Piecewise regression, for instance, is as simple as fitting a spline of degree 1 and changepoint X: library(splines) fit - lm(count ~ bs(year, knots = X, degree = 1)) plot(year, count) lines(year, fitted(fit)) Then you can fit a regression at each year and compare. Alternatively, since count data is often noisy, you could easily substitute quantile regression for linear regression to much of the same effect (assuming whatever tau you decide, I used 0.8 but this is arbitrary): library(splines) library(quantreg) fit - rq(count ~ bs(year, knots = X, degree = 1), tau = 0.8) plot(year, count) lines(year, fitted(fit)) -- Jonathan P. Daily Technician - USGS Leetown Science Center 11649 Leetown Road Kearneysville WV, 25430 (304) 724-4480 Is the room still a room when its empty? Does the room, the thing itself have purpose? Or do we, what's the word... imbue it. - Jubal Early, Firefly r-help-boun...@r-project.org wrote on 11/16/2010 05:30:49 PM: [image removed] [R] Population abundance, change point Nicholas M. Caruso to: r-help 11/16/2010 05:32 PM Sent by: r-help-boun...@r-project.org I am trying to understand my population abundance data and am looking into analyses of change point to try and determine, at approximately what point do populations begin to change (either decline or increasing). Can anyone offer suggestions on ways to go about this? I have looked into bcp and strucchange packages but am not completely convinced that these are appropriate for my data. Here is an example of what type of data I have Year of survey (continuous variable) 1960 - 2009 (there are gaps in the surveys (e.g., there were no surveys from 2002-2004) Relative abundance of salamanders during the survey periods Thanks for your help, Nick -- Nicholas M Caruso Graduate Student CLFS-Biology 4219 Biology-Psychology Building University of Maryland, College Park, MD 20742-5815 -- I learned something of myself in the woods today, and walked out pleased for having made the acquaintance. [[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
Re: [R] help on IDE
Each IDE is going to have its own setup that will also usually depend on what type of computer you are running. EMACS, for instance, requires a pre-existing R install with the 'ess' package (packages are usually installed inside R). Geany, on the other hand, requires an R install and, in some cases, a custom Run command. Linux systems also often ship language specific IDEs with dependency checks on R, but not always. -- Jonathan P. Daily Technician - USGS Leetown Science Center 11649 Leetown Road Kearneysville WV, 25430 (304) 724-4480 Is the room still a room when its empty? Does the room, the thing itself have purpose? Or do we, what's the word... imbue it. - Jubal Early, Firefly r-help-boun...@r-project.org wrote on 11/17/2010 01:41:39 PM: [image removed] [R] help on IDE Partha Sinha to: r-help 11/17/2010 01:50 PM Sent by: r-help-boun...@r-project.org I am new comer in R.There r few IDE like Tinn R,VIM etc.I mean How to use them? Do I need to install R and then install them to use or they can work alone? Also does one install packages on R or IDEs? Can I call/use the package from IDEs? regards Parth -- Socrates, proclaimed: I came to know one thing; that I know nothing. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Anyone can help with this question
assuming your data takes the form of locationlatitudelongitude string num num string2 num num try: sub - dat[sample.int(length(dat$location), 1000),] -- Jonathan P. Daily Technician - USGS Leetown Science Center 11649 Leetown Road Kearneysville WV, 25430 (304) 724-4480 Is the room still a room when its empty? Does the room, the thing itself have purpose? Or do we, what's the word... imbue it. - Jubal Early, Firefly r-help-boun...@r-project.org wrote on 11/16/2010 12:13:57 PM: [image removed] [R] Anyone can help with this question Mariana to: r-help 11/16/2010 02:22 PM Sent by: r-help-boun...@r-project.org Hi there: I am a total beginner in R, and I have a simple question: I have a table with thousands of lines that represent locations, and two columns: latitude and longitude. I need to randomly sample 1000 lines. How do I do it? I know the command sample, but it samples elements independently, not lines. If there is a better place for me to ask that type of question, please let me know. Thanks a lot, Mariana (from Brazil) -- View this message in context: http://r.789695.n4.nabble.com/Anyone- can-help-with-this-question-tp3045265p3045265.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] Null values in R
Would ?is.null be what you are looking for? -- Jonathan P. Daily Technician - USGS Leetown Science Center 11649 Leetown Road Kearneysville WV, 25430 (304) 724-4480 Is the room still a room when its empty? Does the room, the thing itself have purpose? Or do we, what's the word... imbue it. - Jubal Early, Firefly From: Raji raji.sanka...@gmail.com To: r-help@r-project.org Date: 11/15/2010 09:58 AM Subject: [R] Null values in R Sent by: r-help-boun...@r-project.org Hi R-helpers , can you please let me know the methods in which NULL values can be handled in R? Are there any generic commands/functions that can be given in a workspace,so that the NULL values occuring in that workspace (for any datasets that are loaded , any output that is calculated) , are considered in the same way? Thanks in advance. -- View this message in context: http://r.789695.n4.nabble.com/Null-values-in-R-tp3043184p3043184.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] external R scripts
It would be possible to call other R scripts using calls to ?system or ?system2 and ?Rscript, provided you formatted what you passed as [args] and how your scripts handled [args]. -- Jonathan P. Daily Technician - USGS Leetown Science Center 11649 Leetown Road Kearneysville WV, 25430 (304) 724-4480 Is the room still a room when its empty? Does the room, the thing itself have purpose? Or do we, what's the word... imbue it. - Jubal Early, Firefly From: Maas James Dr (MED) j.m...@uea.ac.uk To: r-help@r-project.org r-help@r-project.org Date: 11/10/2010 08:42 AM Subject: [R] external R scripts Sent by: r-help-boun...@r-project.org Is it possible to send data from an executing R script, to external R script files, on linux in this case, get that external R script to execute, and pass results back to the central script? If so what commands should I be looking at? I've googled for R and external, stuff like that but no luck. The reason for the question is that I need to generate simulation data, then perform several different analyses on the same data set, then collate the results. All individual analyses can be done sequentially, or perhaps more quickly by doing the individual analyses simultaneously if I pass them to external functions. Thanks J === Dr. Jim Maas University of East Anglia [[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] maptools package
I know the default plot() method expects dat$x and dat$y to exist and be equal if you simply try plot(dat) Try looking at methods(plot) to see if there is a specified method from maptools, then check documentation on ?plot.methodfrommaptools Otherwise, check spb for $x and $y objects. -- Jonathan P. Daily Technician - USGS Leetown Science Center 11649 Leetown Road Kearneysville WV, 25430 (304) 724-4480 Is the room still a room when its empty? Does the room, the thing itself have purpose? Or do we, what's the word... imbue it. - Jubal Early, Firefly From: Aleksandr Andreev aleksandr.andr...@gmail.com To: r-help@r-project.org Date: 11/10/2010 01:10 PM Subject: [R] maptools package Sent by: r-help-boun...@r-project.org A few years back, I wrote some code to plot maps with the maptools package. Now I am trying to reproduce my results, only to find out that maptools has been updated and my code no longer works. I've been able to fix the first part of it by forcing spb - maptools:::read.shape(/home/sasha/Documents/maps/spb.shp) (as read.shape has been deprecated) but now when I do plot(spb, xlab=Longitude, ylab=Latitude, main=Map of St Petersburg, Russia) I get the message Error in xy.coords(x, y, xlabel, ylabel, log) : 'x' is a list, but does not have components 'x' and 'y' What's the new syntax that I'm supposed to use? I'm using R version 2.12.0 (2010-10-15) on x86_64-pc-linux-gnu (64-bit) Thanks, Aleksandr Andreev Graduate Student - Department of Economics University of North Carolina at Chapel Hill Mobile: +1 303 507 93 88 Skype: typiconman __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Random Sample
Use set.seed() -- Jonathan P. Daily Technician - USGS Leetown Science Center 11649 Leetown Road Kearneysville WV, 25430 (304) 724-4480 Is the room still a room when its empty? Does the room, the thing itself have purpose? Or do we, what's the word... imbue it. - Jubal Early, Firefly From: Xiaoxi Gao rhel...@hotmail.com To: R Help r-help@r-project.org Date: 11/08/2010 03:59 PM Subject: [R] Random Sample Sent by: r-help-boun...@r-project.org Hello R users, Here is my question about generating random sample. How to set the random seed to recreate the same random numbers? For example, 10 random numbers is generated from N(0,1), then runif(10) is used.What if I want to get the same 10 random numbers when I run runif(10) again? Is it possible?I think .Random.seed should be used here. Thanks. Xiaoxi [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] improve R memory under linux
A very small script should fit just fine in an email: what are you trying to do? Likely, you are assigning many small variables in some loop. Even if you have 4GB of RAM available, if R assigns 3.99 GB of it and then then a call comes in to assign something of size .02, it will tell you it can't allocate an object of size .02. -- Jonathan P. Daily Technician - USGS Leetown Science Center 11649 Leetown Road Kearneysville WV, 25430 (304) 724-4480 Is the room still a room when its empty? Does the room, the thing itself have purpose? Or do we, what's the word... imbue it. - Jubal Early, Firefly From: ricardo souza ricsouz...@yahoo.com.br To: r-help@r-project.org Date: 11/05/2010 11:29 AM Subject: [R] improve R memory under linux Sent by: r-help-boun...@r-project.org Dear all, I am using ubuntu linux 32 with 4 Gb. I am running a very small script and I always got the same error message: CAN NOT ALLOCATE A VECTOR OF SIZE 231.8 Mb. I have reading carefully the instruction in ?Memory. Using the function gc() I got very low numbers of memory (please sea below). I know that it has been posted several times at r-help ( http://tolstoy.newcastle.edu.au/R/help/05/06/7565.html#7627qlink2). However I did not find yet the solution to improve my memory issue in Linux. Somebody cold please give some instruction how to improve my memory under linux? gc() used (Mb) gc trigger (Mb) max used (Mb) Ncells 170934 4.6 35 9.4 35 9.4 Vcells 195920 1.5 786432 6.0 781384 6.0 INCREASING THE R MEMORY FOLLOWING THE INSTRUCTION IN ?Memory I started R with: R --min-vsize=10M --max-vsize=4G --min-nsize=500k --max-nsize=900M gc() used (Mb) gc trigger (Mb) limit (Mb) max used (Mb) Ncells 130433 3.5 50 13.4 25200 50 13.4 Vcells 81138 0.71310720 10.0 NA 499143 3.9 It increased but not so much! Please, please let me know. I have read all r-help about this matter, but not solution. Thanks for your attention! Ricardo [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] subsets, %in%
Any logical value can be negatively compared using ! does: subset(dat, !(dat$ID %in% someID)) provide what you need? -- Jonathan P. Daily Technician - USGS Leetown Science Center 11649 Leetown Road Kearneysville WV, 25430 (304) 724-4480 Is the room still a room when its empty? Does the room, the thing itself have purpose? Or do we, what's the word... imbue it. - Jubal Early, Firefly From: mp.sylves...@gmail.com To: r-help@r-project.org Date: 11/05/2010 02:21 PM Subject: [R] subsets, %in% Sent by: r-help-boun...@r-project.org Hi, I have a question about %in% and subsettin data frames. Say I need to keep ID 1,2,4,5, 10 from the data frame dat. I can do: dat - data.frame(ID = 1:10, var = 1:10) someID - c(1,2,4,5,10) subset(dat, dat$ID %in% someID) Is there a quick way to do the opposite, ie to do a subset that contains all ID but someID? Something like %not in%, which would *remove* lines with ID in someID? I am asking because I need this in a more complex example where there are multiple lines with the same ID (data in long format) and I need to remove selected ID. thanks, MP [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] cross-validation for choosing regression trees
Forgive me if I misunderstand your goals but I have no idea what you are trying to determine or what your data is. I can say, however, that setting mindev to 0 has always overfit data for me, and that you are more than likely looking at a situation in which that 1 node tree is more accurate. Also, if you look at ?cv.tree, the default function to use is prune.tree(). Perhaps prune.tree() is trimming down to that terminal node? If you want an alternative look at CART methods that may account for some of your issues, I would recommend the packages 'rpart' and 'party', as they may be more informative. -- Jonathan P. Daily Technician - USGS Leetown Science Center 11649 Leetown Road Kearneysville WV, 25430 (304) 724-4480 Is the room still a room when its empty? Does the room, the thing itself have purpose? Or do we, what's the word... imbue it. - Jubal Early, Firefly From: Shiyao Liu lsy...@iastate.edu To: r-help@r-project.org Date: 11/03/2010 09:04 PM Subject: [R] cross-validation for choosing regression trees Sent by: r-help-boun...@r-project.org Dear All, We came across a problem when using the tree package to analyze our data set. First, in the tree function, if we use the default value mindev=0.01, the resulting regression tree has a single node. So, we set mindev=0, and obtain a tree with 931 terminal nodes. However, when we further use the cv.tree function to run a 10-fold cross-validation, the error message is: Error in prune.tree(list(frame = list(var = 1L, n = 6676, dev = 3.28220789569792, : can not prune singlenode tree. Is the cv.tree function respecting the mindev chosen in the tree function or what else might be wrong? Thanks, Shiyao [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] memory allocation problem
The optim function is very resource hungry. I have had similar problems in
the past when dealing with extremely large datasets.
What is perhaps happening is that each 'step' of the optimization
algorithm stores some info so that it can compare to the next 'step', and
while the original vector may only be a few Mb of data, over many
iterations a huge amount memory is allocated to the optimization steps.
Maybe look at the control options under ?optim, particularly stuff like
trace, fnscale, ndeps, etc. that may cut down on the amount of data being
stored each step as well as the number of steps needed.
Good luck!
--
Jonathan P. Daily
Technician - USGS Leetown Science Center
11649 Leetown Road
Kearneysville WV, 25430
(304) 724-4480
Is the room still a room when its empty? Does the room,
the thing itself have purpose? Or do we, what's the word... imbue it.
- Jubal Early, Firefly
From:
Lorenzo Cattarino l.cattar...@uq.edu.au
To:
David Winsemius dwinsem...@comcast.net, Peter Langfelder
peter.langfel...@gmail.com
Cc:
r-help@r-project.org
Date:
11/03/2010 03:26 AM
Subject:
Re: [R] memory allocation problem
Sent by:
r-help-boun...@r-project.org
Thanks for all your suggestions,
This is what I get after removing all the other (not useful) objects and
run my code:
getsizes()
[,1]
org_results 47240832
myfun 11672
getsizes4176
SS 3248
coeff168
NA NA
NA NA
NA NA
NA NA
NA NA
est_coeff - optim(coeff,SS, steps=org_results$no.steps,
Range=org_results$Range, H1=org_results$H1, H2=org_results$H2,
p=org_results$p)
Error: cannot allocate vector of size 5.0 Mb
In addition: Warning messages:
1: In optim(coeff, SS, steps = org_results$no.steps, Range =
org_results$Range, :
Reached total allocation of 4055Mb: see help(memory.size)
2: In optim(coeff, SS, steps = org_results$no.steps, Range =
org_results$Range, :
Reached total allocation of 4055Mb: see help(memory.size)
3: In optim(coeff, SS, steps = org_results$no.steps, Range =
org_results$Range, :
Reached total allocation of 4055Mb: see help(memory.size)
4: In optim(coeff, SS, steps = org_results$no.steps, Range =
org_results$Range, :
Reached total allocation of 4055Mb: see help(memory.size)
It seems that R is using all the default availabe memory (4 GB, which is
the RAM of my processor).
memory.limit()
[1] 4055
memory.size()
[1] 4049.07
My dataframe has a size of 47240832 bytes, or about 45 Mb. So it should
not be a problem in terms of memory usage?
I do not understand what is going on.
Thanks for your help anyway
Lorenzo
-Original Message-
From: David Winsemius [mailto:dwinsem...@comcast.net]
Sent: Wednesday, 3 November 2010 12:48 PM
To: Lorenzo Cattarino
Cc: r-help@r-project.org
Subject: Re: [R] memory allocation problem
Restart your computer. (Yeah, I know that what the help-desk always
says.)
Start R before doing anything else.
Then run your code in a clean session. Check ls() oafter starte up to
make sure you don't have a bunch f useless stuff in your .Rdata
file. Don't load anything that is not germane to this problem. Use
this function to see what sort of space issues you might have after
loading objects:
getsizes - function() {z - sapply(ls(envir=globalenv()),
function(x) object.size(get(x)))
(tmp - as.matrix(rev(sort(z))[1:10]))}
Then run your code.
--
David.
On Nov 2, 2010, at 10:13 PM, Lorenzo Cattarino wrote:
I would also like to include details on my R version
version _
platform x86_64-pc-mingw32
arch x86_64
os mingw32
system x86_64, mingw32
status
major 2
minor 11.1
year 2010
month 05
day31
svn rev52157
language R
version.string R version 2.11.1 (2010-05-31)
from FAQ 2.9
(http://cran.r-project.org/bin/windows/base/rw-FAQ.html#There-seems-to-b
e-a-limit-on-the-memory-it-uses_0021
http://cran.r-project.org/bin/windows/base/rw-FAQ.html#There-seems-to-b
e-a-limit-on-the-memory-it-uses_0021 ) it says that:
For a 64-bit build, the default is the amount of RAM
So in my case the amount of RAM would be 4 GB. R should be able to
allocate a vector of size 5 Mb without me typing any command (either
as
memory.limit() or appended string in the target path), is that right?
From: Lorenzo Cattarino
Sent: Wednesday, 3 November 2010 10:55 AM
To: 'r-help@r-project.org'
Subject: memory allocation problem
I forgot to mention that I am using windows 7 (64-bit) and the R
version
2.11.1 (64-bit)
From: Lorenzo Cattarino
I am trying to run a non linear parameter optimization using the
function optim() and I have problems regarding memory allocation.
My data are in a dataframe with 9 columns. There are 656100 rows.
head(org_results)
comb.id p
Re: [R] optim works on command-line but not inside a function
As the error message says, the values of your function must be finite in
order to run the algorithm.
Some part of your loop is passing arguments (inits maybe... you only tried
(0,0) in the CLI example) that cause IRT.llZetaLambdaCorrNan to be
infinite.
--
Jonathan P. Daily
Technician - USGS Leetown Science Center
11649 Leetown Road
Kearneysville WV, 25430
(304) 724-4480
Is the room still a room when its empty? Does the room,
the thing itself have purpose? Or do we, what's the word... imbue it.
- Jubal Early, Firefly
From:
Damokun dmroi...@students.cs.uu.nl
To:
r-help@r-project.org
Date:
11/03/2010 10:19 AM
Subject:
[R] optim works on command-line but not inside a function
Sent by:
r-help-boun...@r-project.org
Dear all,
I am trying to optimize a logistic function using optim, inside the
following functions:
#Estimating a and b from thetas and outcomes by ML
IRT.estimate.abFromThetaX - function(t, X, inits, lw=c(-Inf,-Inf),
up=rep(Inf,2)){
optRes - optim(inits, method=L-BFGS-B, fn=IRT.llZetaLambdaCorrNan,
gr=IRT.gradZL,
lower=lw, upper=up, t=t, X=X)
c(optRes$par[2], -(optRes$par[1]/optRes$par[2]) )
}
#Estimating a and b from thetas and outcomes by ML, avoiding 0*log(0)
IRT.estimate.abFromThetaX2 - function(tar, Xes, inits, lw=c(-Inf,-Inf),
up=rep(Inf,2)){
optRes - optim(inits, method=L-BFGS-B, fn=IRT.llZetaLambdaCorrNan,
gr=IRT.gradZL,
lower=lw, upper=up, t=tar, X=Xes)
c(optRes$par[2], -(optRes$par[1]/optRes$par[2]) )
}
The problem is that this does not work:
IRT.estimate.abFromThetaX(sx, st, c(0,0))
Error in optim(inits, method = L-BFGS-B, fn = IRT.llZetaLambdaCorrNan, :
L-BFGS-B needs finite values of 'fn'
But If I try the same optim call on the command line, with the same data,
it
works fine:
optRes - optim(c(0,0), method=L-BFGS-B, fn=IRT.llZetaLambdaCorrNan,
+ gr=IRT.gradZL,
+ lower=c(-Inf, -Inf), upper=c(Inf, Inf), t=st, X=sx)
optRes
$par
[1] -0.6975157 0.7944972
$convergence
[1] 0
$message
[1] CONVERGENCE: REL_REDUCTION_OF_F = FACTR*EPSMCH
Does anyone have an idea what this could be, and what I could try to avoid
this error? I tried bounding the parameters, with lower=c(-10, -10) and
upper=... but that made no difference.
Thanks,
Diederik Roijers
Utrecht University MSc student.
--
PS: the other functions I am using are:
#IRT.p is the function that represents the probability
#of a positive outcome of an item with difficulty b,
#discriminativity a, in combination with a student with
#competence theta.
IRT.p - function(theta, a, b){
epow - exp(-a*(theta-b))
result - 1/(1+epow)
result
}
# = IRT.p^-1 ; for usage in the loglikelihood
IRT.oneOverP - function(theta, a, b){
epow - exp(-a*(theta-b))
result - (1+epow)
result
}
# = (1-IRT.p)^-1 ; for usage in the loglikelihood
IRT.oneOverPneg - function(theta, a, b){
epow - exp(a*(theta-b))
result - (1+epow)
result
}
#simulation-based sample generation of thetas and outcomes
#based on a given a and b. (See IRT.p) The sample-size is n
IRT.generateSample - function(a, b, n){
x-rnorm(n, mean=b, sd=b/2)
t-IRT.p(x,a,b)
ch-runif(length(t))
t[t=ch]=1
t[tch]=0
cbind(x,t)
}
#This loglikelihood function is based on the a and be parameters,
#and requires thetas as input in X, and outcomes in t
#prone to give NaN errors due to 0*log(0)
IRT.logLikelihood2 - function(params, t, X){
pos- sum(t * log(IRT.p(X,params[1],params[2])))
neg- sum( (1-t) * log( (1-IRT.p(X,params[1],params[2])) ) )
-pos-neg
}
#Avoiding NaN problems due to 0*log(0)
#otherwise equivalent to IRT.logLikelihood2
IRT.logLikelihood2CorrNan - function(params, t, X){
pos- sum(t * log(IRT.oneOverP(X,params[1],params[2])))
neg- sum((1-t) * log(IRT.oneOverPneg(X,params[1],params[2])))
-pos-neg
}
#IRT.p can also be espressed in terms of z and l
#where z=-ab and l=a - makes it a standard logit function
IRT.pZL - function(theta, z, l){
epow - exp(-(z+l*theta))
result - 1/(1+epow)
result
}
#as IRT.oneOverP but now for IRT.pZL
IRT.pZLepos - function(theta, z, l){
epow - exp(-(z+l*theta))
result - (1+epow)
result
}
#as IRT.oneOverPneg but now for IRT.pZL
IRT.pZLeneg - function(theta, z, l){
epow - exp(z+l*theta)
result - (1+epow)
result
}
#The loglikelihood of IRT, but now expressed in terms of z and l
IRT.llZetaLambda - function(params, t, X){
pos- sum(t * log(IRT.pZL( X,params[1],params[2]) ))
neg- sum( (1-t) * log( (1-IRT.pZL(X,params[1],params[2] )) ) )
-pos-neg
}
#Same as IRT.logLikelihood2CorrNan but for IRT.llZetaLambda
IRT.llZetaLambdaCorrNan - function(params, t, X){
pos - sum(t * log(IRT.pZLepos( X,params[1],params[2]) ))
neg - sum((1-t) * log(IRT.pZLeneg(X,params[1],params[2]) ))
pos+neg
}
#Gradient of IRT.llZetaLambda
IRT.gradZL - function(params, t, X){
res-numeric(length(params
Re: [R] programming questions
For data frames you can also use with() in your example: with(d, exists(z)) -- Jonathan P. Daily Technician - USGS Leetown Science Center 11649 Leetown Road Kearneysville WV, 25430 (304) 724-4480 Is the room still a room when its empty? Does the room, the thing itself have purpose? Or do we, what's the word... imbue it. - Jubal Early, Firefly From: ivo welch ivo.we...@gmail.com To: Erik Iverson er...@ccbr.umn.edu Cc: r-help r-h...@stat.math.ethz.ch Date: 11/03/2010 02:20 PM Subject: Re: [R] programming questions Sent by: r-help-boun...@r-project.org yikes. this is all my fault. it was the first thing that I ever defined when I started using R. is.defined - function(name) exists(as.character(substitute(name))) I presume there is something much better... /iaw On Wed, Nov 3, 2010 at 2:12 PM, Erik Iverson er...@ccbr.umn.edu wrote: ivo welch wrote: quick programming questions. I want to turn on more errors. there are two traps I occasionally fall into. * I wonder why R thinks that a variable is always defined in a data frame. is.defined(d) [1] FALSE d= data.frame( x=1:5, y=1:5 ) is.defined(d$z) [1] TRUE is.defined(nonexisting$garbage) [1] TRUE Which package/version of R is the 'is.defined' function in? I don't seem to have it here on 2.11.1, which I know is not the latest version of R. What does 'defined' mean? this is a bit unfortunate for me, because subsequent errors become less clear. right now, I need to do '(is.defined(d) and !is.null(d$z))' to check that my function inputs are valid. It would be nicer if one could just write if (is.defined(d$z). z %in% names(d) ? * is there a way to turn off automatic recycling? I would rather get an error than unexpected recycling. I can force recycling with rep() when I need to. regards, /iaw Ivo Welch (ivo.we...@brown.edu, ivo.we...@gmail.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. [[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 script on linux?
What is the error message? -- Jonathan P. Daily Technician - USGS Leetown Science Center 11649 Leetown Road Kearneysville WV, 25430 (304) 724-4480 Is the room still a room when its empty? Does the room, the thing itself have purpose? Or do we, what's the word... imbue it. - Jubal Early, Firefly From: gokhanocakoglu ocako...@uludag.edu.tr To: r-help@r-project.org Date: 11/02/2010 09:11 AM Subject: Re: [R] R script on linux? Sent by: r-help-boun...@r-project.org I can't run the script the program doesn't work... -- View this message in context: http://r.789695.n4.nabble.com/R-script-on-linux-tp3023650p3023670.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] R script on linux?
Alternatively, you can simply prefix all scripts with
#! /path/to/R/Rscript
...
where the path is usually /usr/bin/
This info is in the manual that comes packaged with R under, conveniently,
the scripting section. I assumed that he was getting some error message.
Likely, the script was not created executable, in which case the terminal
command chmod +x myscript.R will do it.
--
Jonathan P. Daily
Technician - USGS Leetown Science Center
11649 Leetown Road
Kearneysville WV, 25430
(304) 724-4480
Is the room still a room when its empty? Does the room,
the thing itself have purpose? Or do we, what's the word... imbue it.
- Jubal Early, Firefly
From:
Thomas Levine thomas.lev...@gmail.com
To:
Jonathan P Daily jda...@usgs.gov
Cc:
gokhanocakoglu ocako...@uludag.edu.tr, r-help@r-project.org,
r-help-boun...@r-project.org
Date:
11/02/2010 02:24 PM
Subject:
Re: [R] R script on linux?
Open a terminal, then run these two commands.
cd /home/the/directory/with/your/script
R
Then run this in R
source('yourscript.R')
Tom
2010/11/2 Jonathan P Daily jda...@usgs.gov:
What is the error message?
--
Jonathan P. Daily
Technician - USGS Leetown Science Center
11649 Leetown Road
Kearneysville WV, 25430
(304) 724-4480
Is the room still a room when its empty? Does the room,
the thing itself have purpose? Or do we, what's the word... imbue it.
- Jubal Early, Firefly
From:
gokhanocakoglu ocako...@uludag.edu.tr
To:
r-help@r-project.org
Date:
11/02/2010 09:11 AM
Subject:
Re: [R] R script on linux?
Sent by:
r-help-boun...@r-project.org
I can't run the script the program doesn't work...
--
View this message in context:
http://r.789695.n4.nabble.com/R-script-on-linux-tp3023650p3023670.html
Sent from the R help mailing list archive at Nabble.com.
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[R] Possible memory leak in loop.
I was trying to use memory.size() to determine whether a code loop I am executing created a memory leak, since one replicate of the simulation takes 670.98 seconds according to proc.time(), while 5 replicates takes 170762 seconds. So I set it up as: memA - memory.size() looping code... memB - memory.size() memA returns as 9.3, and memB returns 11.3. I'm not familiar with fluctuation patterns in RAM usage (if there are any). Does anyone with more experience know if this is indicative of a memory leak? Thanks, Jon -- Jonathan P. Daily Technician - USGS Leetown Science Center 11649 Leetown Road Kearneysville WV, 25430 (304) 724-4480 Is the room still a room when its empty? Does the room, the thing itself have purpose? Or do we, what's the word... imbue it. - Jubal Early, Firefly [[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] Possible memory leak in loop.
Thank you, I will give that a try. -- Jonathan P. Daily Technician - USGS Leetown Science Center 11649 Leetown Road Kearneysville WV, 25430 (304) 724-4480 Is the room still a room when its empty? Does the room, the thing itself have purpose? Or do we, what's the word... imbue it. - Jubal Early, Firefly From: jim holtman jholt...@gmail.com To: Jonathan P Daily jda...@usgs.gov Cc: r-help@r-project.org Date: 11/01/2010 09:48 AM Subject: Re: [R] Possible memory leak in loop. If you are running on Windows, you might want to use 'perfmon' to look at the memory usage of the process over time. You might also want to put calls to memory.size in your looping code to see if there are things you are doing in the code that might temporarily use a lot of space and maybe fragment memory. On Mon, Nov 1, 2010 at 8:35 AM, Jonathan P Daily jda...@usgs.gov wrote: I was trying to use memory.size() to determine whether a code loop I am executing created a memory leak, since one replicate of the simulation takes 670.98 seconds according to proc.time(), while 5 replicates takes 170762 seconds. So I set it up as: memA - memory.size() looping code... memB - memory.size() memA returns as 9.3, and memB returns 11.3. I'm not familiar with fluctuation patterns in RAM usage (if there are any). Does anyone with more experience know if this is indicative of a memory leak? Thanks, Jon -- Jonathan P. Daily Technician - USGS Leetown Science Center 11649 Leetown Road Kearneysville WV, 25430 (304) 724-4480 Is the room still a room when its empty? Does the room, the thing itself have purpose? Or do we, what's the word... imbue it. - Jubal Early, Firefly [[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. -- 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] Zoom in in a plot
In that case you may wish to look into the rggobi package, which provides an R interface to the ggobi tools. I haven't used it much, but it has a lot of interactive options. -- Jonathan P. Daily Technician - USGS Leetown Science Center 11649 Leetown Road Kearneysville WV, 25430 (304) 724-4480 Is the room still a room when its empty? Does the room, the thing itself have purpose? Or do we, what's the word... imbue it. - Jubal Early, Firefly From: Alaios ala...@yahoo.com To: Greg Snow greg.s...@imail.org, Rhelp r-help@r-project.org Date: 10/27/2010 02:21 AM Subject: Re: [R] Zoom in in a plot Sent by: r-help-boun...@r-project.org Actually I want to see how close are some point to a line segment so I want to use some zoom lenses and zoom in and out into different parts of the plot and see how some places look like. Best Regards From: Greg Snow greg.s...@imail.org Sent: Tue, October 26, 2010 6:47:32 PM Subject: RE: [R] Zoom in in a plot For a quick exploration of the plot you can use the zoomplot function in the TeachingDemos package. But for production graphs it is better to explicitly set the xlim and ylim parameters in creating the plot up front. -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r- project.org] On Behalf Of Alaios Sent: Tuesday, October 26, 2010 9:31 AM To: Rhelp Subject: [R] Zoom in in a plot in a simple plot. When i do plot is it possible to zoom in or out or this is not possible at all? Best 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. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Best IDE for R
I noticed that nabble link presented Notepad++ as having to copy/paste into the editor. There is a companion to NP++, though, that allows line/file passing directly to an R console, auto-completion, and a bunch of other goodies called NppToR. -- Jonathan P. Daily Technician - USGS Leetown Science Center 11649 Leetown Road Kearneysville WV, 25430 (304) 724-4480 Is the room still a room when its empty? Does the room, the thing itself have purpose? Or do we, what's the word... imbue it. - Jubal Early, Firefly From: Dennis Murphy djmu...@gmail.com To: Santosh Srinivas santosh.srini...@gmail.com Cc: r-help@r-project.org Date: 10/27/2010 09:03 AM Subject: Re: [R] Best IDE for R Sent by: r-help-boun...@r-project.org Hi: This topic came up a couple of days ago: http://r.789695.n4.nabble.com/R-file-td3009812.html#a3009812 HTH, Dennis On Wed, Oct 27, 2010 at 4:01 AM, Santosh Srinivas santosh.srini...@gmail.com wrote: Dear R-Group, I am looking for suggestions for the best IDE for R. Best is obviously subjective but I need just the basic features that should function well (and I looked through the threads already). - Proper integration with R 2.11.1 - Good key shortcuts ... similar to the R Gui - Manageability of Projects, etc. - Neat formatting features I tried Revolution R but it seems huge in size for something my basic needs and keep throwing up configuration problems. I tried Komodo. It works fine but having problems with proper integration into R and unable to do debugging. Any help? Thanks, S __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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. [[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] Best IDE for R
I can second using Geany as an IDE. Another large plus for it is that it is cross platform (I work in both Windows and Linux), cross environment (I also code in Python/Sage), very customizable, and even has a version on PortableApps for windows so you can take a customized version around on a USB stick with ease. -- Jonathan P. Daily Technician - USGS Leetown Science Center 11649 Leetown Road Kearneysville WV, 25430 (304) 724-4480 Is the room still a room when its empty? Does the room, the thing itself have purpose? Or do we, what's the word... imbue it. - Jubal Early, Firefly From: Liviu Andronic landronim...@gmail.com To: Lee Hachadoorian lee.hachadooria...@gmail.com Cc: r-h...@stat.math.ethz.ch Date: 10/27/2010 02:45 PM Subject: Re: [R] Best IDE for R Sent by: r-help-boun...@r-project.org On Wed, Oct 27, 2010 at 4:05 PM, Lee Hachadoorian lee.hachadooria...@gmail.com wrote: For an R-enabled text editor, I would suggest Tinn-R for Windows or RGedit (a gedit plugin) for Linux/Gnome-desktop. Since both are just text editors, they will work with whatever version R you have installed (criteria 1). RGedit is pretty spare: basically just console integration and keyboard shortcuts to send code (current line, selection, defined blocks) to the console. Criteria 1 Y 2 basic 3 N 4 N For Linux and Mac, I usually suggest Geany [1] as an alternative to Gedit. Geany is an intuitive IDE that can send commands to rterm in the integrated virtual terminal emulator. It provides various features for project management, source highlighting, code folding, etc. Regards Liviu [1] http://www.r-bloggers.com/integrating-r-with-geany/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Reading in a tab delimitated file
A call to read.table(..., sep = , ...) reads in any length of whitespace as the delimiter. On your sample text it read in a 2 column dataframe. -- Jonathan P. Daily Technician - USGS Leetown Science Center 11649 Leetown Road Kearneysville WV, 25430 (304) 724-4480 Is the room still a room when its empty? Does the room, the thing itself have purpose? Or do we, what's the word... imbue it. - Jubal Early, Firefly From: Ùukasz Ræcùawowicz lukasz.reclawow...@gmail.com To: amindlessbrain jillianrowe91...@gmail.com Cc: r-help@r-project.org Date: 10/26/2010 09:34 AM Subject: Re: [R] Reading in a tab delimitated file Sent by: r-help-boun...@r-project.org 2010/10/26 amindlessbrain jillianrowe91...@gmail.com (I'm not sure why the disease column isn't showing up as a tab here, but it is sep by \t in my file. You've got a double tab space, I don't know is there a prettier way, but paste this: pd-read.delim(new_treat.txt,sep=) -- Mi³ego dnia [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Reading in a tab delimitated file
Right, I forgot to mention to use header = T. -- Jonathan P. Daily Technician - USGS Leetown Science Center 11649 Leetown Road Kearneysville WV, 25430 (304) 724-4480 Is the room still a room when its empty? Does the room, the thing itself have purpose? Or do we, what's the word... imbue it. - Jubal Early, Firefly From: Henrique Dallazuanna www...@gmail.com To: amindlessbrain jillianrowe91...@gmail.com Cc: r-help@r-project.org Date: 10/26/2010 11:08 AM Subject: Re: [R] Reading in a tab delimitated file Sent by: r-help-boun...@r-project.org Try this: Lines - SampleIDDisease E-CBIL-28-raw-cel-1435145228.cel1 E-CBIL-28-raw-cel-1435145451.cel2 E-CBIL-28-raw-cel-1435145479.cel2 E-CBIL-28-raw-cel-1435145132.cel3 E-CBIL-28-raw-cel-1435145417.cel3 E-CBIL-28-raw-cel-1435145301.cel2 E-CBIL-28-raw-cel-1435145558.cel1 E-CBIL-28-raw-cel-1435145073.cel3 E-CBIL-28-raw-cel-1435145196.cel2 E-CBIL-28-raw-cel-1435145511.cel1 E-CBIL-28-raw-cel-1435145336.cel3 E-CBIL-28-raw-cel-1435145260.cel2 E-CBIL-28-raw-cel-1435145167.cel2 E-CBIL-28-raw-cel-1435145387.cel3 E-CBIL-28-raw-cel-1435145099.cel3 DF - read.table(textConnection(Lines), header = TRUE) On Tue, Oct 26, 2010 at 10:35 AM, amindlessbrain jillianrowe91...@gmail.com wrote: Hi all, I have a total newbie question, but I could really use some help. I need to read in this file: SampleIDDisease E-CBIL-28-raw-cel-1435145228.cel1 E-CBIL-28-raw-cel-1435145451.cel2 E-CBIL-28-raw-cel-1435145479.cel2 E-CBIL-28-raw-cel-1435145132.cel3 E-CBIL-28-raw-cel-1435145417.cel3 E-CBIL-28-raw-cel-1435145301.cel2 E-CBIL-28-raw-cel-1435145558.cel1 E-CBIL-28-raw-cel-1435145073.cel3 E-CBIL-28-raw-cel-1435145196.cel2 E-CBIL-28-raw-cel-1435145511.cel1 E-CBIL-28-raw-cel-1435145336.cel3 E-CBIL-28-raw-cel-1435145260.cel2 E-CBIL-28-raw-cel-1435145167.cel2 E-CBIL-28-raw-cel-1435145387.cel3 E-CBIL-28-raw-cel-1435145099.cel3 (I'm not sure why the disease column isn't showing up as a tab here, but it is sep by \t in my file. I've tried several variations on these: pd - read.AnnotatedDataFrame (new_treat.txt , header = TRUE , sep=\t, row.names = SampleID, colClasses = c(Disease = character)) And I keep on getting this error: Error in read.table(filename, sep = sep, header = header, quote = quote, : more columns than column names Any help would be very very very appreciated! Thanks! -- View this message in context: http://r.789695.n4.nabble.com/Reading-in-a-tab-delimitated-file-tp3013620p3013620.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[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] Zoom in in a plot
I think that this would be possible if you save the graph to a scalable format. Try looking into: ?postscript ?xfig ?pdf -- Jonathan P. Daily Technician - USGS Leetown Science Center 11649 Leetown Road Kearneysville WV, 25430 (304) 724-4480 Is the room still a room when its empty? Does the room, the thing itself have purpose? Or do we, what's the word... imbue it. - Jubal Early, Firefly From: Alaios ala...@yahoo.com To: Rhelp r-help@r-project.org Date: 10/26/2010 11:32 AM Subject: [R] Zoom in in a plot Sent by: r-help-boun...@r-project.org in a simple plot. When i do plot is it possible to zoom in or out or this is not possible at all? Best 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. [[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] anomalies with the loess() function
?loess use this instead: fit - loess(b~a) lines(a, predict(fit)) -- Jonathan P. Daily Technician - USGS Leetown Science Center 11649 Leetown Road Kearneysville WV, 25430 (304) 724-4480 Is the room still a room when its empty? Does the room, the thing itself have purpose? Or do we, what's the word... imbue it. - Jubal Early, Firefly From: Federico Bonofiglio bonori...@gmail.com To: r-help@r-project.org Date: 10/26/2010 02:38 PM Subject: [R] anomalies with the loess() function Sent by: r-help-boun...@r-project.org Hello Masters, I run the loess() function to obtain local weighted regressions, given lowess() can't handle NAs, but I don't improve significantly my situation.., actually loess() performance leave me much puzzled I attach my easy experiment below #--SCRIPT-- #I explore the functionalities of lowess() loess() #because I have encountered problems in execute local weighted regressions #with lowess() (in presence of NAs) with loess() (always!!!) #I generate 2 fictious vectors a-sample(c(sample(1:1000,100),rep(NA,50))) b-sample(c(sample(1:1000,100),rep(NA,50))) #lm() has no problems..can handle the missing values plot(a,b) abline(lm(b~a),col=red,lwd=2) #loess return a plain mess like it would go dizzed with ordering or something. #Off course lowess() turns useless in presence of NAs, I don't even try it. lines(loess(b~a)) #I get rid off NAs and compare lowess() loess() performance, expecting to #obtain the same result as both functions implement local weighted regressions a-na.omit(a) b-na.omit(b) #check out the evidence.something's wrong with loess()??? par(mfrow=c(1,2)) plot(a,b) lines(lowess(a,b),col=red)#if NAs are excluded lowess() runs regularly plot(a,b) lines(loess(b~a),col=red)#.but loess() keeps messing all over...!!??? [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] lowess() won't handle NAs
Try using the loess() function instead - it has an na.action parameter that should be able to handle your problem. -- Jonathan P. Daily Technician - USGS Leetown Science Center 11649 Leetown Road Kearneysville WV, 25430 (304) 724-4480 Is the room still a room when its empty? Does the room, the thing itself have purpose? Or do we, what's the word... imbue it. - Jubal Early, Firefly [[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] Passing rq models to Fstats
I have seen literature on using a combination of the 'strucchange' and 'segmented' packages to find and fit piecewise linear models. I have been trying to apply the same methods to quantile regression from the quantreg package, but am having issues using a rq object where the function assumes a lm. Has anyone had this issue? -- Jonathan P. Daily Technician - USGS Leetown Science Center 11649 Leetown Road Kearneysville WV, 25430 (304) 724-4480 Is the room still a room when its empty? Does the room, the thing itself have purpose? Or do we, what's the word... imbue it. - Jubal Early, Firefly [[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.
