Re: [R] How to re-combine values based on an index?
Thank you I believe that is just what I was looking for. Brian On Dec 2, 2012, at 12:37 AM, Berend Hasselman [via R] ml-node+s789695n4651599...@n4.nabble.com wrote: On 02-12-2012, at 06:06, Brian Feeny wrote: Thank you for your response, here is a better example of what I am trying to do: data(iris) index_setosa - which(iris$Species == setosa) iris_setosa - data.frame() iris_setosa[index_setosa,] -iris[index_setosa,] iris_others - data.frame() iris_others[-index_setosa,] - iris[-index_setosa,] Change you example to make it actually do something data(iris) index_setosa - which(iris$Species == setosa) iris_setosa -iris[index_setosa,] head(iris_setosa) # iris_others - data.frame() # iris_others[-index_setosa,] - iris[-index_setosa,] iris_others - iris[-index_setosa,] head(iris_others) tail(iris_others) The head() and tail() calls are for checking. Combine the two like this z - rbind(iris_setosa,iris_others) head(z) tail(z) Berend So the idea would be that iris_setosa is a dataframe of size 150, with 50 observations of setosa, using their original same indices, and 100 observations of NA. Likewise iris_others would be 100 observations of species besides setosa, using their original indices, and there would be 50 NA's. The above doesn't work. When I execute it, I am left with iris_setosa having 0 columns, I wish it to have all the original columns of iris. That said, once I get past the above (being able to split them out and keep original indices), I wish to be able to combine iris_setosa and iris_others so that iris_combined is a data frame with no NA's and all the original data. Does this make sense? So I am basically taking a dataframe, splitting it based on some criteria, and working on the two split dataframes separately, and then I wish to recombine. Brian So at this point, I have iris_setosa a dataframe of size On Dec 1, 2012, at 11:34 PM, William Dunlap wrote: newdataset[testindex] = testset[testindex] object 'dataset' not found Is that really what R printed? I get newdataset[testindex] = testset[testindex] Error in newdataset[testindex] = testset[testindex] : object 'newdataset' not found but perhaps you have a different problem. Copy and paste (and read) the error message you got. Bill Dunlap Spotfire, TIBCO Software wdunlap tibco.com -Original Message- From: [hidden email] [mailto:[hidden email]] On Behalf Of Brian Feeny Sent: Saturday, December 01, 2012 8:04 PM To: [hidden email] Subject: [R] How to re-combine values based on an index? I am able to split my df into two like so: dataset - trainset index - 1:nrow(dataset) testindex - sample(index, trunc(length(index)*30/100)) trainset - dataset[-testindex,] testset - dataset[testindex,-1] So I have the index information, how could I re-combine the data using that back into a single df? I tried what I thought might work, but failed with: newdataset[testindex] = testset[testindex] object 'dataset' not found newdataset[-testindex] = trainset[-testindex] object 'dataset' not found Brian __ [hidden email] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ [hidden email] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ [hidden email] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. If you reply to this email, your message will be added to the discussion below: http://r.789695.n4.nabble.com/How-to-re-combine-values-based-on-an-index-tp4651594p4651599.html To unsubscribe from How to re-combine values based on an index?, click here. NAML -- View this message in context: http://r.789695.n4.nabble.com/How-to-re-combine-values-based-on-an-index-tp4651594p4651600.html Sent from the R help mailing list archive at Nabble.com. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Line numbers with errors and warnings?
What I mean is how do I get the R compilation or execution process to spit out a line number with errors and warnings? I should not have mentioned ESS, that is a distraction. option(error=browser) is a help. But it still does not say what piece of code caused the error. This is costing me a lot of time chasing down errors in mine and others code... Worik On Sat, Dec 1, 2012 at 1:47 PM, Duncan Murdoch murdoch.dun...@gmail.comwrote: On 12-11-30 7:15 PM, Worik R wrote: How? This is a script I am running under ess on Emacs I've never used ESS. You'll need to ask someone on the ESS list. Duncan Murdoch (Useful information optuion(error=recover) cheers Worik On Sat, Dec 1, 2012 at 12:34 PM, Duncan Murdoch murdoch.dun...@gmail.com mailto:murdoch.duncan@gmail.**commurdoch.dun...@gmail.com wrote: On 12-11-30 4:22 PM, Worik R wrote: Is it possible to get a line number with an error report? Yes, if the error occurs in code that has line number information. You get line number info by default if you use source(). If the error is deeply buried in code that doesn't have the info (as it may be in your case), then the suggestions to use options(error=recover) will offer you a stack trace that shows you which high level code called the function reporting the problem. Duncan Murdoch I have a long script and an error: Error in `[.xts`(x, xsubset) : subscript out of bounds It would be very helpful, and save a lot of time, if there was some indication in the error message which line the error was. I can find it using binary search but that is a painful process. cheers Worik [[alternative HTML version deleted]] __**__ R-help@r-project.org mailto:R-help@r-project.org mailing list https://stat.ethz.ch/mailman/_**_listinfo/r-helphttps://stat.ethz.ch/mailman/__listinfo/r-help https://stat.ethz.ch/mailman/**listinfo/r-helphttps://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/__**posting-guide.htmlhttp://www.R-project.org/__posting-guide.html http://www.R-project.org/**posting-guide.htmlhttp://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] How can i change the number of iterations in lme function
lme2-lme(y~ age + time + timeDay,data= DF, random=~time |id/timeDay) Error in lme.formula(y ~ age + time + timeDay, data = DF, random = ~time | : nlminb problem, convergence error code = 1 message = iteration limit reached without convergence (10) [[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] Nightingale’s Rose chart-any suggestion?
On 11/30/2012 11:24 PM, Henry Smith wrote: Hello, Everyone. Does anyone know how to create a Nightingale’s Rose chart by using R? Hopefully, the graph could be displayed like this: http://mbostock.github.com/protovis/ex/crimea-rose.html Hi Henry, I cited Florence in a paper with Anupam Tyagi as a predecessor of a novel type of chart, but the recently added radial.pie (plotrix) function might give you a close enough approximation. Jim __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] x axis labels
On 12/02/2012 09:49 AM, apprentice wrote: Hi, I have a problem with plotting my data as a histogram using barplot2. I am plotting the x axis using axis(). I want to label only every fifth bar and not all of them as they get too busy but I don't know how to do it. I was trying to set the labels for the axis using at=seq(min value, max value, by=5) but that leads to labels not being under the right bars but just sort of spread around. Does anyone know how to do it properly? Hi Barbara, Two ways I can think of. Get the bar positions from the call to barplot2: barpos-barplot2(...) Try barp in the plotrix package. By default the bars or groups are spaced at integer values and you get the bar positions returned as well. Jim __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] instrumental variables regression using ivreg (AER) or tsls (sem)
On Thu, 29 Nov 2012, Ranjan Maitra wrote: Dear friends, I am trying to understand and implement instrumental variables regression using R. I found a small (simple) example here which purportedly illustrates the mechanics (using 2-stage least-squares): http://www.r-bloggers.com/a-simple-instrumental-variables-problem/ The 1st stage regression is not quite correct in this example. My understanding is that he wants to use distance as an instrument for education and all other variables as instruments for themselves. However, the rest of the instruments have been erroneously left out of the 1st stage in his example. Basically, here are the R commands (reproducible example) from that site: # -- begin R library(AER) library(lmtest) data(CollegeDistance) cd.d-CollegeDistance simple.ed.1s- lm(education ~ distance,data=cd.d) This should be: simple.ed.1s- lm(education ~ urban + gender + ethnicity + unemp + distance, data=cd.d) cd.d$ed.pred- predict(simple.ed.1s) simple.ed.2s- lm(wage ~ urban + gender + ethnicity + unemp + ed.pred , data=cd.d) And then the same estimates could be obtained in ivreg() as: m - ivreg(wage ~ urban + gender + ethnicity + unemp + education | urban + gender + ethnicity + unemp + distance, data = CollegeDistance) Or in tsls() as: m2 - tsls(wage ~ urban + gender + ethnicity + unemp + education, ~ urban + gender + ethnicity + unemp + distance, data = CollegeDistance) Best, Z # -- end R This yields the following summary: summary(simple.ed.2s) Call: lm(formula = wage ~ urban + gender + ethnicity + unemp + ed.pred, data = cd.d) Residuals: Min 1Q Median 3Q Max -3.1692 -0.8294 0.1502 0.8482 3.9537 Coefficients: Estimate Std. Error t value Pr(|t|) (Intercept) -2.053604 1.675314 -1.226 0.2203 urbanyes -0.013588 0.046403 -0.293 0.7697 genderfemale -0.086700 0.036909 -2.349 0.0189 * ethnicityafam -0.566524 0.051686 -10.961 2e-16 *** ethnicityhispanic -0.529088 0.048429 -10.925 2e-16 *** unemp 0.145806 0.006969 20.922 2e-16 *** ed.pred0.774340 0.120372 6.433 1.38e-10 *** --- Signif. codes: 0 ?***? 0.001 ?**? 0.01 ?*? 0.05 ?.? 0.1 ? ? 1 Residual standard error: 1.263 on 4732 degrees of freedom Multiple R-squared: 0.1175, Adjusted R-squared: 0.1163 F-statistic: 105 on 6 and 4732 DF, p-value: 2.2e-16 Question: Assuming that the above illustration is correct, I was wondering how I could mimic these calculations using the ivreg () in AER or tsls () in sem? Any suggestions? Many thanks in advance, and best wishes, Ranjan -- Important Notice: This mailbox is ignored: e-mails are set to be deleted on receipt. For those needing to send personal or professional e-mail, please use appropriate addresses. FREE ONLINE PHOTOSHARING - Share your photos online with your friends and family! Visit http://www.inbox.com/photosharing to find out more! __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] [mgcv][gam] Manually defining my own knots?
Hi Andrew, mgcv matches the knots to the smooth arguments by name. If an element of 'knots' has no name it will be ignored. The following will do what you want... dumb.example = gam(y~s(x,k=3),knots=list(x=dumb.knots)) best, Simon On 29/11/12 23:44, Andrew Crane-Droesch wrote: Dear List, I'm using GAMs in a multiple imputation project, and I want to be able to combine the parameter estimates and covariance matrices from each completed dataset's fitted model in the end. In order to do this, I need the knots to be uniform for each model with partially-imputed data. I want to specify these knots based on the quantiles of the unique values of the non-missing original data, ignoring the NA's. When I fit the GAM with the imputed data included, I don't want mgcv to use the data that it is supplied to figure out the knots, because this will lead to un-comparable results when the many fitted models are combined. Here is a caricatured example of what I want to do: #Random data x = runif(1000,0,1) y = (log(x^2)+x^3)/sin(x) example = gam(y~s(x)) plot(example) #But I want to define my own knots dumb.knots = c(.7,.8,.9) dumb.example = gam(y~s(x,k=3),knots=list(dumb.knots)) plot(dumb.example) dumb.example2 = gam(y~s(x,k=3)) plot(dumb.example2) Dumb example 1 is the same as dumb example 2, but it shouldn't be. Once I figure out how to do this, I'll take the fitted coefficients from each model and average them, then take the vcv's from each model and average them, and add a correction to account for within and between imputation variability, then plug them into a gamObject$coeffient and gamObject$Vp matrix, plot/summarize, and have my result. Comments welcome on whether or not this would be somehow incorrect would be welcome as well. Still have a lot to learn! Thanks, Andrew [[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 can i change the number of iterations in lme function
On 02-12-2012, at 10:15, Haris Rhrlp wrote: lme2-lme(y~ age + time + timeDay,data= DF, random=~time |id/timeDay) Error in lme.formula(y ~ age + time + timeDay, data = DF, random = ~time | : nlminb problem, convergence error code = 1 message = iteration limit reached without convergence (10) Assuming you are using package nlme. Have you tried ?lmeControl and seen the msMaxIter and/or msMaxEval arguments. You can set these with the control argument of lme. Reading and browsing the help of a package really can be quite helpful. Berend __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] cubic spline
but definitely *no* need to use a function from an extra CRAN package .. as someone else ``erronously'' suggested. Except that Matlab's interp1() 'cubic' method does not use cubic spline interpolation, but Moler's 'pchip' approach, a piecewise cubic Hermite interpolation. Thus the results are different: % Matlab: interp1(X, Y, 11, 'cubic') %= 5.8000 interp1(X, Y, 15, 'cubic') %= 5. # R: spfun - splinefun( X, Y, natural) spfun(11)#= 5.785714 spfun(15)#= 4.928571 spfun - splinefun( X, Y, monoH.FC) spfun(11)#= 5.8 spfun(15)#= 5.0 Unfortunately, if the points are not monotonic, the 'monoH.FC' method does not exactly agree with the 'pchip' approach, i.e. does not in general return the same results. By the way, pchip() in package 'pracma' implements Moler's approach and does return the same (interpolation and extrapolation) results as interp1() with the 'cubic' option in Matlab. Hans Werner Martin Maechler maechler at stat.math.ethz.ch writes: David Winsemius dwinsemius at comcast.net on Sat, 1 Dec 2012 09:25:42 -0700 writes: On Dec 1, 2012, at 5:09 AM, Steve Stephenson wrote: Hallo, I'm facing a problem and I would really appreciate your support. I have to translate some Matalb code in R that I don't know very well but I would like to. I have to interpolate 5 point with a cubic spline function and then I expect my function returns the Y value as output a specific X value inside the evaluation range. Let's suppose that: 1- *X = [-10, -5, 0, 5, 10]* 2 - *Y = [12, 10, 8, 7, 6]* 3 - *I have to interpolate with a cubic spline assuming x=11* In Matlab I used this function: *y = interp1(X, Y, x, cubic); * How can I do the same in R? Many thanks in advance for your reply and support! splinefun( x = c(-10, -5, 0, 5, 10), y = c(12, 10, 8, 7, 6), method=natural)(11) [1] 5.785714 Yes, indeed, or simple spline() but definitely *no* need to use a function from an extra CRAN package .. as someone else ``erronously'' suggested. Note that spline() and splinefun() together with approx() and approxfun() are among the several hundred functions that were already part of pre-alpha R, i.e., before R had a version number or *any* packages ... and yes, the README then started with the two lines | R Source Code (Tue Jun 20 14:33:47 NZST 1995) | Copyright 1993, 1994, 1995 by Robert Gentleman and Ross Ihaka and it would be *really* *really* great if people did not add stuff to their packages that has been part of R for longer than they have even heard of R. Martin Maechler, ETH Zurich __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Line numbers with errors and warnings?
Hi, On Sun, Dec 2, 2012 at 12:31 AM, Worik R wor...@gmail.com wrote: What I mean is how do I get the R compilation or execution process to spit out a line number with errors and warnings? As Duncan mentioned already, you can't *always* get a line number. You can, however, usually get enough context around the failing call for you to be able to smoke the problem out. option(error=browser) is a help. But it still does not say what piece of code caused the error. I typically run with a slightly different setting: R options(error=utils:::dump.frames) Whenever my script throws an error, after I'm done cursing at it I then wonder where this error happened, so I call: R traceback() And you'll see the details of the stack that just blew up, starting (or ending, can't remember) with the call itself, then the parent call, and its parent, etc. all the way up to the top most call (likely the line in your script itself). If that's not enough information for me to figure out how to fix the code in my script, I'll then call: R debugger() and this will then give me (more or less) the same information that `traceback` showed (but in reverse order (which is why I never remember the order of traceback)) and you are asked at what point you'd like to enter the exploded wreckage to explore (via picking a number) ... this way you can poke at the local variables until you see what went wrong. Your error: Error in `[.xts`(x, xsubset) : subscript out of bounds Is suggesting that you are trying to index an `xts` object with an illegal value -- can you find the part in your code that's trying to do this in your own script? You can put a call to `browser()` before that part and explore the value of the subscript vs. the length of your xts object to see what the problem is. If you can't find this point, then take the traceback/debugger route. This is costing me a lot of time chasing down errors in mine and others code... ... which is typical when your wading in uncharted territory. As you get a better feel of how to resolve these issues, your time-to-fix these things will get better, so ... stay strong. -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Line numbers with errors and warnings?
Le dimanche 02 décembre 2012 à 06:02 -0500, Steve Lianoglou a écrit : Hi, On Sun, Dec 2, 2012 at 12:31 AM, Worik R wor...@gmail.com wrote: What I mean is how do I get the R compilation or execution process to spit out a line number with errors and warnings? Indeed, I often suffer from the same problem when debugging R code too. This is a real issue for me. As Duncan mentioned already, you can't *always* get a line number. You can, however, usually get enough context around the failing call for you to be able to smoke the problem out. What are the cases where you cannot get line numbers? Duncan said source()ed code comes with line numbers, but what's the more general rule? option(error=browser) is a help. But it still does not say what piece of code caused the error. I typically run with a slightly different setting: R options(error=utils:::dump.frames) Whenever my script throws an error, after I'm done cursing at it I then wonder where this error happened, so I call: R traceback() And you'll see the details of the stack that just blew up, starting (or ending, can't remember) with the call itself, then the parent call, and its parent, etc. all the way up to the top most call (likely the line in your script itself). If that's not enough information for me to figure out how to fix the code in my script, I'll then call: R debugger() and this will then give me (more or less) the same information that `traceback` showed (but in reverse order (which is why I never remember the order of traceback)) and you are asked at what point you'd like to enter the exploded wreckage to explore (via picking a number) ... this way you can poke at the local variables until you see what went wrong. This is very useful of course to find the problematic function, but quite often I end up wondering what exact command triggered an error. For example, subscript out of bounds is hard to match to a precise `[' use in a whole function. Even when using browser(), sometimes you cannot know where you are in the function. So the line number, or the contents of the last line, would be relevant information. Your error: Error in `[.xts`(x, xsubset) : subscript out of bounds Is suggesting that you are trying to index an `xts` object with an illegal value -- can you find the part in your code that's trying to do this in your own script? You can put a call to `browser()` before that part and explore the value of the subscript vs. the length of your xts object to see what the problem is. If you can't find this point, then take the traceback/debugger route. This is costing me a lot of time chasing down errors in mine and others code... ... which is typical when your wading in uncharted territory. As you get a better feel of how to resolve these issues, your time-to-fix these things will get better, so ... stay strong. Of course experience helps, but without the most relevant information (line number) you productivity is always affected... ;-) Regards __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Line numbers with errors and warnings?
On 12-12-02 12:31 AM, Worik R wrote:
What I mean is how do I get the R compilation or execution process to
spit out a line number with errors and warnings?
I should not have mentioned ESS, that is a distraction.
I think ESS is not a distraction here, it is the cause of the problem.
If you source() your code, R will (by default) record line numbers. ESS
apparently doesn't send code to R using source(). (Or perhaps it does,
and you aren't looking in the right place for it?)
For example, in Windows, if I put this code into the clipboard:
f - function() {
stop(this is the error)
}
g - function() {
f()
}
g()
then run source(clipboard) followed by traceback(), this is what I see:
source(clipboard)
Error in f() (from clipboard#2) : this is the error
traceback()
7: stop(this is the error) at clipboard#2
6: f() at clipboard#6
5: g() at clipboard#9
4: eval(expr, envir, enclos)
3: eval(ei, envir)
2: withVisible(eval(ei, envir))
1: source(clipboard)
You can ignore entries 1 to 4; they are part of source(). Entries 5, 6,
and 7 each tell the line of the script where they were parsed.
Duncan Murdoch
option(error=browser) is a help. But it still does not say what piece
of code caused the error.
This is costing me a lot of time chasing down errors in mine and others
code...
Worik
On Sat, Dec 1, 2012 at 1:47 PM, Duncan Murdoch murdoch.dun...@gmail.com
mailto:murdoch.dun...@gmail.com wrote:
On 12-11-30 7:15 PM, Worik R wrote:
How?
This is a script I am running under ess on Emacs
I've never used ESS. You'll need to ask someone on the ESS list.
Duncan Murdoch
(Useful information optuion(error=recover)
cheers
Worik
On Sat, Dec 1, 2012 at 12:34 PM, Duncan Murdoch
murdoch.dun...@gmail.com mailto:murdoch.dun...@gmail.com
mailto:murdoch.duncan@gmail.__com
mailto:murdoch.dun...@gmail.com wrote:
On 12-11-30 4:22 PM, Worik R wrote:
Is it possible to get a line number with an error report?
Yes, if the error occurs in code that has line number
information.
You get line number info by default if you use source().
If the
error is deeply buried in code that doesn't have the info
(as it may
be in your case), then the suggestions to use
options(error=recover)
will offer you a stack trace that shows you which high
level code
called the function reporting the problem.
Duncan Murdoch
I have a long script and an error:
Error in `[.xts`(x, xsubset) : subscript out of bounds
It would be very helpful, and save a lot of time, if
there was some
indication in the error message which line the error was.
I can find it using binary search but that is a painful
process.
cheers
Worik
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] Line numbers with errors and warnings?
On 12-12-02 8:33 AM, Milan Bouchet-Valat wrote: Le dimanche 02 décembre 2012 à 06:02 -0500, Steve Lianoglou a écrit : Hi, On Sun, Dec 2, 2012 at 12:31 AM, Worik R wor...@gmail.com wrote: What I mean is how do I get the R compilation or execution process to spit out a line number with errors and warnings? Indeed, I often suffer from the same problem when debugging R code too. This is a real issue for me. As Duncan mentioned already, you can't *always* get a line number. You can, however, usually get enough context around the failing call for you to be able to smoke the problem out. What are the cases where you cannot get line numbers? Duncan said source()ed code comes with line numbers, but what's the more general rule? The general rule is that parse() needs to be called with the srcfile argument set to a srcfile object. source() does that by default. Duncan Murdoch option(error=browser) is a help. But it still does not say what piece of code caused the error. I typically run with a slightly different setting: R options(error=utils:::dump.frames) Whenever my script throws an error, after I'm done cursing at it I then wonder where this error happened, so I call: R traceback() And you'll see the details of the stack that just blew up, starting (or ending, can't remember) with the call itself, then the parent call, and its parent, etc. all the way up to the top most call (likely the line in your script itself). If that's not enough information for me to figure out how to fix the code in my script, I'll then call: R debugger() and this will then give me (more or less) the same information that `traceback` showed (but in reverse order (which is why I never remember the order of traceback)) and you are asked at what point you'd like to enter the exploded wreckage to explore (via picking a number) ... this way you can poke at the local variables until you see what went wrong. This is very useful of course to find the problematic function, but quite often I end up wondering what exact command triggered an error. For example, subscript out of bounds is hard to match to a precise `[' use in a whole function. Even when using browser(), sometimes you cannot know where you are in the function. So the line number, or the contents of the last line, would be relevant information. Your error: Error in `[.xts`(x, xsubset) : subscript out of bounds Is suggesting that you are trying to index an `xts` object with an illegal value -- can you find the part in your code that's trying to do this in your own script? You can put a call to `browser()` before that part and explore the value of the subscript vs. the length of your xts object to see what the problem is. If you can't find this point, then take the traceback/debugger route. This is costing me a lot of time chasing down errors in mine and others code... ... which is typical when your wading in uncharted territory. As you get a better feel of how to resolve these issues, your time-to-fix these things will get better, so ... stay strong. Of course experience helps, but without the most relevant information (line number) you productivity is always affected... ;-) Regards __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Getting all possible contingency tables
Thanks Ted (and other) for your suggestion. Here I have implemented
following:
Tab - matrix(c(8, 10, 12, 6), nr = 2)
Simu_Number - 5
Tab_Simulate - vector(list, length = Simu_Number)
for (i in 1:Simu_Number) {
Tab_Simulate[[i]] - matrix(rmultinom(1, sum(Tab), rep(0.25,
4)), nrow = 2) ## All Cells have equal probability
}
Sample_ChiSq - sapply(Tab_Simulate, function(x) {
Statistic -
sum((chisq.test(as.table(x))$observed -
chisq.test(as.table(x))$expected)^2/chisq.test(as.table(x))$expected)
return(Statistic)
})
length(Sample_ChiSq[Sample_ChiSq qchisq(0.95, 1)])/Simu_Number
hist(Sample_ChiSq, freq = FALSE)
lines(dchisq(seq(min(Sample_ChiSq), max(Sample_ChiSq), by = 0.5), 1))
However I think I am making some serious mistake as histogram did not
match the density curve.
Can somebody help me where I am making mistake?
Thanks and regards,
On 01-12-2012 21:45, (Ted Harding) wrote:
You will need to be clear about whether you are conditioning on
the marginal totals as well as on the overall total. As stated,
you are only asking for the overall total (36) to be fixed.
In that case, one possible (and by no means unique) approach
would be to:
[A]: Choose any four random integers a,b,c,d that add up to 36
(even there, you still have to make a choice about what distribution
to adopt for the random integers).
[B]: Place the results into the 2x2 matrix; then evaluate chi-squared.
[C]: Repeat until you have enough cases.
Example (using equiprobable multinomial to generate 4 random integers)
Tab - matrix(rmultinom(1,36,c(1,1,1,1)/4), nrow=2)
A more specific choice would be to fix the row and column probablilties
(but not the sample row and column totals), e.g.:
P.row1 - 0.25 ; P.row2 - 1 - P.row1
P.col1 - 0.50 ; P.col2 - 1 - P.col1
Then, adopting the hypothesis of independence between rows and columns:
P11 - P.row1*P.col1
P21 - P.row2*P.col1
P12 - P.row1*P.col2
P22 - P.row2*P.col2
Tab - matrix(rmultinom(1,36,c(P11,P21,P12,P22)), nrow=2)
On the other hand, if you want to also fix the sample row margins
and column margins, then your sampled table needs to be generated
using a hypergeometric distribution, (which is the basis of the
fisher.test mentioned by Bert Gunter). Since explaining how to
do this is a bit mjore complicated than the above, please first
confirm what constraints (e.g. only total count; row-margins
only; col-margins only; both row- col-margins) you wich to impose.
Hoping this helps,
Ted.
On 01-Dec-2012 14:28:24 Christofer Bogaso wrote:
Thanks Bert for your reply.
I am trying to understand/visualize the Sample Chi-Squared Statistic's
Null distribution. Therefore I need all possible Contingency tables
under Independence case.
What could be better way to visualize that?
Thanks and regards,
On 01 December 2012 20:03:00, Bert Gunter wrote:
Christopher:
Don't do this!
If I understand you correctly, you want FIsher's exact test. This is
already available in R, using far smarter algorithms then you would. See:
?fisher.test
-- Bert
On Sat, Dec 1, 2012 at 5:48 AM, Christofer Bogaso
bogaso.christo...@gmail.com mailto:bogaso.christo...@gmail.com wrote:
Thanks John for your reply. However still not clear how I should
proceed.
My goal is to generate all possible contingency tables. Basically
I want to see the distribution of Chi-squared Statistic under
independence (NULL).
So I was thinking if I can generate all possible permutation of
integer numbers having sum equal to (8 + 10 + 12 + 6) = 36. Is
there any R function to do that?
Thanks and regards,
On 01-12-2012 18:39, John Kane wrote:
Are you basically asking for all possible permutations of the
table? If so see ?permn in the combinat package.
John Kane
Kingston ON Canada
-Original Message-
From:bogaso.christo...@gmail.com
mailto:bogaso.christo...@gmail.com
Sent: Sat, 01 Dec 2012 18:10:15 +0545
To:r-help@r-project.org mailto:r-help@r-project.org
Subject: [R] Getting all possible contingency tables
Hello all,
Let say I have 2-way contingency table:
Tab - matrix(c(8, 10, 12, 6), nr = 2)
and the Chi-squared test could not reject the independence:
chisq.test(Tab)
Pearson's Chi-squared test with Yates'
continuity correction
data: Tab
X-squared = 1.0125, df = 1, p-value = 0.3143
However I want to get all possible contingency tables
under this
independence scenario (one of them would obviously be the
given table
as, we could not reject the independence), and for each
such table I
want to
Re: [R] reading json tables
On 12/1/2012 4:08 PM, Duncan Temple Lang wrote: Hi Michael The problem is that the content of the .js file is not JSON, but actual JavaScript code. You could use something like the following tt = readLines(http://mbostock.github.com/protovis/ex/wheat.js;) txt = c([, gsub(;, ,, gsub(var [a-zA-Z]+ = , , tt)), ]) tmp = paste(txt, collapse = \n) tmp = gsub(([a-zA-Z]+):, '\\1:', tmp) o = fromJSON(tmp) data = structure(o[1:2], names = c(wheat, monarch)) Basically, this removes the 'var variable name =' part replaces the ; with a , to separate elements quotes the names of the fields, e.g. year, wheat, wages puts the two global data objects into a top-level array ([]) container This isn't ideal (as the regular expressions are not sufficiently specific and could modify the actual values incorrectly). However, it does the job for this particular file. Thanks for this, Duncan I hadn't understood that the data had to be pure JSON. The actual result I want is two data frames, wheat and monarch, whereas fromJSON returns a list of lists. I'll try to figure that part out. -Michael -- Michael Friendly Email: friendly AT yorku DOT ca Professor, Psychology Dept. Chair, Quantitative Methods York University Voice: 416 736-2100 x66249 Fax: 416 736-5814 4700 Keele StreetWeb: http://www.datavis.ca Toronto, ONT M3J 1P3 CANADA __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help 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 json tables
Hi Michael The actual result I want is two data frames, wheat and monarch, whereas fromJSON returns a list of lists. I'll try to figure that part out. do.call(rbind, data[[1]]) will do the job, but there are elements in each of data[[1]] and data[[2]] that are incomplete and which need to be filled in with NAs before rbinding. Best, D. On 12/2/12 6:26 AM, Michael Friendly wrote: On 12/1/2012 4:08 PM, Duncan Temple Lang wrote: Hi Michael The problem is that the content of the .js file is not JSON, but actual JavaScript code. You could use something like the following tt = readLines(http://mbostock.github.com/protovis/ex/wheat.js;) txt = c([, gsub(;, ,, gsub(var [a-zA-Z]+ = , , tt)), ]) tmp = paste(txt, collapse = \n) tmp = gsub(([a-zA-Z]+):, '\\1:', tmp) o = fromJSON(tmp) data = structure(o[1:2], names = c(wheat, monarch)) Basically, this removes the 'var variable name =' part replaces the ; with a , to separate elements quotes the names of the fields, e.g. year, wheat, wages puts the two global data objects into a top-level array ([]) container This isn't ideal (as the regular expressions are not sufficiently specific and could modify the actual values incorrectly). However, it does the job for this particular file. Thanks for this, Duncan I hadn't understood that the data had to be pure JSON. The actual result I want is two data frames, wheat and monarch, whereas fromJSON returns a list of lists. I'll try to figure that part out. -Michael __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Line numbers with errors and warnings?
Le dimanche 02 décembre 2012 à 09:02 -0500, Duncan Murdoch a écrit : On 12-12-02 8:33 AM, Milan Bouchet-Valat wrote: Le dimanche 02 décembre 2012 à 06:02 -0500, Steve Lianoglou a écrit : Hi, On Sun, Dec 2, 2012 at 12:31 AM, Worik R wor...@gmail.com wrote: What I mean is how do I get the R compilation or execution process to spit out a line number with errors and warnings? Indeed, I often suffer from the same problem when debugging R code too. This is a real issue for me. As Duncan mentioned already, you can't *always* get a line number. You can, however, usually get enough context around the failing call for you to be able to smoke the problem out. What are the cases where you cannot get line numbers? Duncan said source()ed code comes with line numbers, but what's the more general rule? The general rule is that parse() needs to be called with the srcfile argument set to a srcfile object. source() does that by default. OK. But isn't it technically possible to compute a line number even when no source file is present? If you call fix() on any function, you will get something like a source file even if srcfile was not set. So it could make sense to have a line number referring to what you would see in fix(). Or at least, the last executed line when calling browser() or when using options(error=recover), like gdb does. This could be especially useful for packages that were not installed with keep.source=TRUE. It could even help getting more useful error messages on R-help... Regards Duncan Murdoch option(error=browser) is a help. But it still does not say what piece of code caused the error. I typically run with a slightly different setting: R options(error=utils:::dump.frames) Whenever my script throws an error, after I'm done cursing at it I then wonder where this error happened, so I call: R traceback() And you'll see the details of the stack that just blew up, starting (or ending, can't remember) with the call itself, then the parent call, and its parent, etc. all the way up to the top most call (likely the line in your script itself). If that's not enough information for me to figure out how to fix the code in my script, I'll then call: R debugger() and this will then give me (more or less) the same information that `traceback` showed (but in reverse order (which is why I never remember the order of traceback)) and you are asked at what point you'd like to enter the exploded wreckage to explore (via picking a number) ... this way you can poke at the local variables until you see what went wrong. This is very useful of course to find the problematic function, but quite often I end up wondering what exact command triggered an error. For example, subscript out of bounds is hard to match to a precise `[' use in a whole function. Even when using browser(), sometimes you cannot know where you are in the function. So the line number, or the contents of the last line, would be relevant information. Your error: Error in `[.xts`(x, xsubset) : subscript out of bounds Is suggesting that you are trying to index an `xts` object with an illegal value -- can you find the part in your code that's trying to do this in your own script? You can put a call to `browser()` before that part and explore the value of the subscript vs. the length of your xts object to see what the problem is. If you can't find this point, then take the traceback/debugger route. This is costing me a lot of time chasing down errors in mine and others code... ... which is typical when your wading in uncharted territory. As you get a better feel of how to resolve these issues, your time-to-fix these things will get better, so ... stay strong. Of course experience helps, but without the most relevant information (line number) you productivity is always affected... ;-) Regards __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Getting all possible contingency tables
On 02-Dec-2012 14:17:20 Christofer Bogaso wrote:
Thanks Ted (and other) for your suggestion. Here I have implemented
following:
Tab - matrix(c(8, 10, 12, 6), nr = 2)
Simu_Number - 5
Tab_Simulate - vector(list, length = Simu_Number)
for (i in 1:Simu_Number) {
Tab_Simulate[[i]] - matrix(rmultinom(1, sum(Tab), rep(0.25,
4)), nrow = 2) ## All Cells have equal probability
}
Sample_ChiSq - sapply(Tab_Simulate, function(x) {
Statistic -
sum((chisq.test(as.table(x))$observed -
chisq.test(as.table(x))$expected)^2/chisq.test(as.table(x))$expected)
return(Statistic)
})
length(Sample_ChiSq[Sample_ChiSq qchisq(0.95, 1)])/Simu_Number
hist(Sample_ChiSq, freq = FALSE)
lines(dchisq(seq(min(Sample_ChiSq), max(Sample_ChiSq), by = 0.5), 1))
However I think I am making some serious mistake as histogram did not
match the density curve.
Can somebody help me where I am making mistake?
Thanks and regards,
[the remainder (copies of previous posts) snipped]
The reasons for the mis-match are:
A: that you have put the curve in the wrong place, by not
supplying x-coordinates to lines(), so that it plots its
points at x = 1,2,3,4,...
B: that you need to multiply the plotted density by the width
of the histogram cells, so as to match the density curve to the
discrete density of the histogram. It will also then look better
when the chis-squared curve is plotted at the mid-points of the cells.
Hence, try something like:
hist(Sample_ChiSq, freq = FALSE, breaks=0.5*(0:40))
x0 - 0.25+0.5*(0:20)
lines(x0,dchisq(x0,1))
Hoping this helps,
Ted.
-
E-Mail: (Ted Harding) ted.hard...@wlandres.net
Date: 02-Dec-2012 Time: 15:02:45
This message was sent by XFMail
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to use doSMP(revoIPC) with R 2.15.x version
On 29.11.2012 17:56, 박상규 wrote:
Hello,
I'd like to use package 'doSMP'. But I can only found source codes in the CRAN.
I tried to build source code using 'r CMD build doSMP' in the source directory,
the following error is shown:
ERROR: dependencies 'foreach', 'iterators', 'revoIPC' are not available for pack
age 'doSMP'
So, i tried to install dependency packages. But I failed to install revoIPC
with following error:
install.packages('revoIPC')
Installing package(s) into ‘C:/Program Files/R/R-2.15.2/library’
(as ‘lib’ is unspecified)
Warning in install.packages :
package ‘revoIPC’ is not available (for R version 2.15.2)
Could you let me know how to use it in R ver2.15.x ?
See
https://stat.ethz.ch/pipermail/r-help/2012-January/301664.html
Uwe Ligges
Thanks in advance,
[[alternative HTML version deleted]]
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[R] overlapping graphs in logarithmic y-axis
dear useRs, i want to overlap graphs of two matrices in such a way that the y-axis of graph should be logarithmic against normal x-axis. i am, unsuccessfully, trying the followings matplot(mata, log=mata,type = l, col=red)lines(mata, log=matb,type = l, col=yellow) could you please help me out on it?? thanks in advanceregards eliza [[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] Getting all possible contingency tables
Thanks Ted for your correction. I was depressed thinking that I did not
understand the theory. However now it comes as just a plotting mistake!
Thanks,
On 02 December 2012 20:47:48, (Ted Harding) wrote:
On 02-Dec-2012 14:17:20 Christofer Bogaso wrote:
Thanks Ted (and other) for your suggestion. Here I have implemented
following:
Tab - matrix(c(8, 10, 12, 6), nr = 2)
Simu_Number - 5
Tab_Simulate - vector(list, length = Simu_Number)
for (i in 1:Simu_Number) {
Tab_Simulate[[i]] - matrix(rmultinom(1, sum(Tab), rep(0.25,
4)), nrow = 2) ## All Cells have equal probability
}
Sample_ChiSq - sapply(Tab_Simulate, function(x) {
Statistic -
sum((chisq.test(as.table(x))$observed -
chisq.test(as.table(x))$expected)^2/chisq.test(as.table(x))$expected)
return(Statistic)
})
length(Sample_ChiSq[Sample_ChiSq qchisq(0.95, 1)])/Simu_Number
hist(Sample_ChiSq, freq = FALSE)
lines(dchisq(seq(min(Sample_ChiSq), max(Sample_ChiSq), by = 0.5), 1))
However I think I am making some serious mistake as histogram did not
match the density curve.
Can somebody help me where I am making mistake?
Thanks and regards,
[the remainder (copies of previous posts) snipped]
The reasons for the mis-match are:
A: that you have put the curve in the wrong place, by not
supplying x-coordinates to lines(), so that it plots its
points at x = 1,2,3,4,...
B: that you need to multiply the plotted density by the width
of the histogram cells, so as to match the density curve to the
discrete density of the histogram. It will also then look better
when the chis-squared curve is plotted at the mid-points of the cells.
Hence, try something like:
hist(Sample_ChiSq, freq = FALSE, breaks=0.5*(0:40))
x0 - 0.25+0.5*(0:20)
lines(x0,dchisq(x0,1))
Hoping this helps,
Ted.
-
E-Mail: (Ted Harding) ted.hard...@wlandres.net
Date: 02-Dec-2012 Time: 15:02:45
This message was sent by XFMail
-
__
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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] overlapping graphs in logarithmic y-axis
On 02.12.2012 16:19, eliza botto wrote: dear useRs, i want to overlap graphs of two matrices in such a way that the y-axis of graph should be logarithmic against normal x-axis. i am, unsuccessfully, trying the followings matplot(mata, log=mata,type = l, col=red)lines(mata, log=matb,type = l, col=yellow) This cannot wok for several reasons, inclusing typos, and is not reproducible for us given we do not know about mata. Anyway, fixing your typos and the specification of the argument log, we get: matplot(mata, log=y, type = l, col = red) and overlay the red with yellow lines, although it makes no sense: matplot(mata, type = l, col = yellow, add = TRUE) Uwe Ligges could you please help me out on it?? thanks in advanceregards eliza [[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] Stripchart colors don't vary after I sort a data frame
On 28.11.2012 18:27, Thomas Levine wrote:
# Hi,
# This plot has two colors.
overflow - read.csv('http://chainsaw.thomaslevine.com/overflow.csv',
stringsAsFactors = F)
png('original.png')
stripchart(overflow$precipi ~ overflow$after.9.am, method='stack', pch =
22, bg = overflow$overflow + 1, vertical = T, col = 0)
dev.off()
# I wanted continuous bands of color, so I sorted the data frame.
# But after sorting, it only had one color.
overflow.sorted - overflow[order(overflow$overflow),]
png('sorted.png')
stripchart(overflow.sorted$precipi ~ overflow.sorted$after.9.am,
method='stack', pch = 22, bg = overflow.sorted$overflow + 1, vertical =
T, col = 0)
dev.off()
# What's wrong?
All red are hidden by the black strips, perhaps you want to order it the
other way round, i.e.:
overflow.sorted - overflow[order(rev(overflow$overflow)),]
do not understand the data and you aim well enough after 5 seconds,
hence it may not be what you aim at...
Uwe Ligges
# Here are all of the files.
# http://chainsaw.thomaslevine.com/overflow.csv
# http://chainsaw.thomaslevine.com/original.png
# http://chainsaw.thomaslevine.com/sorted.png
# Thanks
# Tom
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Re: [R] overlapping graphs in logarithmic y-axis
Dear ligges,thankyou very much. Actually majority of the questions i asked on this forum were without sense, as quoted by majority of experts. i actually wanted to over lap mata and matb. by replacing your code with matb, it worked!!! thankseliza Date: Sun, 2 Dec 2012 16:53:24 +0100 From: lig...@statistik.tu-dortmund.de To: eliza_bo...@hotmail.com CC: r-help@r-project.org Subject: Re: [R] overlapping graphs in logarithmic y-axis On 02.12.2012 16:19, eliza botto wrote: dear useRs, i want to overlap graphs of two matrices in such a way that the y-axis of graph should be logarithmic against normal x-axis. i am, unsuccessfully, trying the followings matplot(mata, log=mata,type = l, col=red)lines(mata, log=matb,type = l, col=yellow) This cannot wok for several reasons, inclusing typos, and is not reproducible for us given we do not know about mata. Anyway, fixing your typos and the specification of the argument log, we get: matplot(mata, log=y, type = l, col = red) and overlay the red with yellow lines, although it makes no sense: matplot(mata, type = l, col = yellow, add = TRUE) Uwe Ligges could you please help me out on it?? thanks in advanceregards eliza [[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] overlapping graphs in logarithmic y-axis
On 02.12.2012 17:03, eliza botto wrote: Dear ligges,thankyou very much. Actually majority of the questions i asked on this forum were without sense IOnm this case the reason is that you do not ask the question precisely. Your exampole had matplot(mata, .) lines(mata, ) Please just be more specific, try to avoid errors that are not subject of your question, then people can help much better and understand what you are actually going to do. Also,m provide toy matrices. Uwe Ligges , as quoted by majority of experts. i actually wanted to over lap mata and matb. by replacing your code with matb, it worked!!! thankseliza Date: Sun, 2 Dec 2012 16:53:24 +0100 From: lig...@statistik.tu-dortmund.de To: eliza_bo...@hotmail.com CC: r-help@r-project.org Subject: Re: [R] overlapping graphs in logarithmic y-axis On 02.12.2012 16:19, eliza botto wrote: dear useRs, i want to overlap graphs of two matrices in such a way that the y-axis of graph should be logarithmic against normal x-axis. i am, unsuccessfully, trying the followings matplot(mata, log=mata,type = l, col=red)lines(mata, log=matb,type = l, col=yellow) This cannot wok for several reasons, inclusing typos, and is not reproducible for us given we do not know about mata. Anyway, fixing your typos and the specification of the argument log, we get: matplot(mata, log=y, type = l, col = red) and overlay the red with yellow lines, although it makes no sense: matplot(mata, type = l, col = yellow, add = TRUE) Uwe Ligges could you please help me out on it?? thanks in advanceregards eliza [[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. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Plot from a jpeg
On 27.11.2012 22:38, bgnumis wrote: Hi all, I know that I can for instance draw to plots in one using nf-layout(matrix(c(1,2),1,2,byrow=FALSE)) Imagine I have 3 files: plot1.jpeg plot2.jpeg plot3.jpeg Anyone knows if I can read them and put on one colum and three rows reading directly from the jpeg file? Yes, there are many packages around, One idea: download.file(http://www.user2007.org/photos/r-cake.jpg;, jpfile - tempfile(), mode=wb) library(ReadImages) jp - read.jpeg(jpfile) par(mfrow=c(3,1)) plot(jp) plot(jp) plot(jp) Best, Uwe Ligges Many Thanks [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] simple subset question
Hi, Consider the small dataset below, I want to subset by two variables in one line but it wont work...it works though if I subset separately. I have to be missing something obvious that I did not realize before while using subset.. fish - structure(list(IDWeek = c(27L, 28L, 29L, 30L, 31L, 32L, 33L, 34L, 35L, 36L, 37L, 38L, 39L, 40L, 41L, 42L, 43L, 44L, 45L, 46L, 47L, 48L, 49L, 50L, 51L, 52L, 27L, 28L, 29L, 30L, 31L, 32L, 33L, 34L, 35L, 36L, 37L, 38L, 39L, 40L, 41L, 42L, 43L, 44L, 45L, 46L, 47L, 48L, 49L, 50L, 51L, 52L), Total = c(0L, 0L, 326L, 1735L, 1807L, 2208L, 3883L, 8820L, 6060L, 19326L, 63158L, 100718L, 53015L, 91689L, 152629L, 122708L, 61293L, 15574L, 86538L, 75365L, 303259L, 19691L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 161L, 321L, 1000L, 4425L, 13202L, 19726L, 30518L, 84949L, 157260L, 145691L, 85801L, 62044L, 44439L, 23272L, 22391L, 20159L, 14854L, 35379L, 31142L, 7736L, 13221L, 4894L), Fry = c(0L, 0L, 326L, 1735L, 1807L, 2208L, 3883L, 8759L, 6060L, 19326L, 63119L, 100524L, 52582L, 88170L, 145564L, 111416L, 38233L, 5248L, 17826L, 11038L, 34008L, 215L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 161L, 321L, 1000L, 4425L, 13055L, 19488L, 30518L, 84818L, 156909L, 144786L, 84207L, 57720L, 31049L, 6858L, 1616L, 719L, 364L, 49L, 0L, 0L, 0L, 0L), Smolt = c(0L, 0L, 0L, 0L, 0L, 0L, 0L, 62L, 0L, 0L, 38L, 195L, 433L, 3518L, 7067L, 11290L, 23058L, 10327L, 68712L, 64328L, 269248L, 19479L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 147L, 238L, 0L, 131L, 351L, 905L, 1592L, 4324L, 13391L, 16414L, 20774L, 19444L, 14491L, 35330L, 31142L, 7736L, 13221L, 4894L), FryEq = c(0L, 0L, 326L, 1735L, 1807L, 2208L, 3883L, 8864L, 6060L, 19326L, 63185L, 100854L, 53318L, 94151L, 157576L, 130610L, 77432L, 22805L, 134639L, 120393L, 491733L, 33327L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 161L, 321L, 1000L, 4425L, 13306L, 19894L, 30518L, 85042L, 157506L, 146328L, 86914L, 65073L, 53812L, 34763L, 36931L, 33769L, 24998L, 60110L, 52938L, 13149L, 22476L, 8319L), Year = c(2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L)), .Names = c(IDWeek, Total, Fry, Smolt, FryEq, Year), row.names = c(NA, 52L), class = data.frame) fish # Subset to get the max Total for 2012 x - subset(winter,Year==2012 Total==max(Total));b # How come one line doesn't work? # It works if I subset the year first and then get the Total max from it xx - subset(winter,Year==2012) xxx - subset(xx,Total==max(Total));xxx xxx Felipe D. Carrillo Supervisory Fishery Biologist Department of the Interior US Fish Wildlife Service California, USA http://www.fws.gov/redbluff/rbdd_jsmp.aspx [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] simple subset question
shouldn't you just change b to x and winter to fish? :) On Sun, Dec 2, 2012 at 12:21 PM, Felipe Carrillo mazatlanmex...@yahoo.comwrote: Hi, Consider the small dataset below, I want to subset by two variables in one line but it wont work...it works though if I subset separately. I have to be missing something obvious that I did not realize before while using subset.. fish - structure(list(IDWeek = c(27L, 28L, 29L, 30L, 31L, 32L, 33L, 34L, 35L, 36L, 37L, 38L, 39L, 40L, 41L, 42L, 43L, 44L, 45L, 46L, 47L, 48L, 49L, 50L, 51L, 52L, 27L, 28L, 29L, 30L, 31L, 32L, 33L, 34L, 35L, 36L, 37L, 38L, 39L, 40L, 41L, 42L, 43L, 44L, 45L, 46L, 47L, 48L, 49L, 50L, 51L, 52L), Total = c(0L, 0L, 326L, 1735L, 1807L, 2208L, 3883L, 8820L, 6060L, 19326L, 63158L, 100718L, 53015L, 91689L, 152629L, 122708L, 61293L, 15574L, 86538L, 75365L, 303259L, 19691L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 161L, 321L, 1000L, 4425L, 13202L, 19726L, 30518L, 84949L, 157260L, 145691L, 85801L, 62044L, 44439L, 23272L, 22391L, 20159L, 14854L, 35379L, 31142L, 7736L, 13221L, 4894L), Fry = c(0L, 0L, 326L, 1735L, 1807L, 2208L, 3883L, 8759L, 6060L, 19326L, 63119L, 100524L, 52582L, 88170L, 145564L, 111416L, 38233L, 5248L, 17826L, 11038L, 34008L, 215L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 161L, 321L, 1000L, 4425L, 13055L, 19488L, 30518L, 84818L, 156909L, 144786L, 84207L, 57720L, 31049L, 6858L, 1616L, 719L, 364L, 49L, 0L, 0L, 0L, 0L), Smolt = c(0L, 0L, 0L, 0L, 0L, 0L, 0L, 62L, 0L, 0L, 38L, 195L, 433L, 3518L, 7067L, 11290L, 23058L, 10327L, 68712L, 64328L, 269248L, 19479L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 147L, 238L, 0L, 131L, 351L, 905L, 1592L, 4324L, 13391L, 16414L, 20774L, 19444L, 14491L, 35330L, 31142L, 7736L, 13221L, 4894L), FryEq = c(0L, 0L, 326L, 1735L, 1807L, 2208L, 3883L, 8864L, 6060L, 19326L, 63185L, 100854L, 53318L, 94151L, 157576L, 130610L, 77432L, 22805L, 134639L, 120393L, 491733L, 33327L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 161L, 321L, 1000L, 4425L, 13306L, 19894L, 30518L, 85042L, 157506L, 146328L, 86914L, 65073L, 53812L, 34763L, 36931L, 33769L, 24998L, 60110L, 52938L, 13149L, 22476L, 8319L), Year = c(2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L)), .Names = c(IDWeek, Total, Fry, Smolt, FryEq, Year), row.names = c(NA, 52L), class = data.frame) fish # Subset to get the max Total for 2012 x - subset(winter,Year==2012 Total==max(Total));b # How come one line doesn't work? # It works if I subset the year first and then get the Total max from it xx - subset(winter,Year==2012) xxx - subset(xx,Total==max(Total));xxx xxx Felipe D. Carrillo Supervisory Fishery Biologist Department of the Interior US Fish Wildlife Service California, USA http://www.fws.gov/redbluff/rbdd_jsmp.aspx [[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] simple subset question
On Dec 2, 2012, at 9:21 AM, Felipe Carrillo wrote: Hi, Consider the small dataset below, I want to subset by two variables in one line but it wont work...it works though if I subset separately. I have to be missing something obvious that I did not realize before while using subset.. fish - structure(list(IDWeek = c(27L, 28L, 29L, 30L, 31L, 32L, 33L, 34L, 35L, 36L, 37L, 38L, 39L, 40L, 41L, 42L, 43L, 44L, 45L, 46L, 47L, 48L, 49L, 50L, 51L, 52L, 27L, 28L, 29L, 30L, 31L, 32L, 33L, 34L, 35L, 36L, 37L, 38L, 39L, 40L, 41L, 42L, 43L, 44L, 45L, 46L, 47L, 48L, 49L, 50L, 51L, 52L), Total = c(0L, 0L, 326L, 1735L, 1807L, 2208L, 3883L, 8820L, 6060L, 19326L, 63158L, 100718L, 53015L, 91689L, 152629L, 122708L, 61293L, 15574L, 86538L, 75365L, 303259L, 19691L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 161L, 321L, 1000L, 4425L, 13202L, 19726L, 30518L, 84949L, 157260L, 145691L, 85801L, 62044L, 44439L, 23272L, 22391L, 20159L, 14854L, 35379L, 31142L, 7736L, 13221L, 4894L), Fry = c(0L, 0L, 326L, 1735L, 1807L, 2208L, 3883L, 8759L, 6060L, 19326L, 63119L, 100524L, 52582L, 88170L, 145564L, 111416L, 38233L, 5248L, 17826L, 11038L, 34008L, 215L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 161L, 321L, 1000L, 4425L, 13055L, 19488L, 30518L, 84818L, 156909L, 144786L, 84207L, 57720L, 31049L, 6858L, 1616L, 719L, 364L, 49L, 0L, 0L, 0L, 0L), Smolt = c(0L, 0L, 0L, 0L, 0L, 0L, 0L, 62L, 0L, 0L, 38L, 195L, 433L, 3518L, 7067L, 11290L, 23058L, 10327L, 68712L, 64328L, 269248L, 19479L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 147L, 238L, 0L, 131L, 351L, 905L, 1592L, 4324L, 13391L, 16414L, 20774L, 19444L, 14491L, 35330L, 31142L, 7736L, 13221L, 4894L), FryEq = c(0L, 0L, 326L, 1735L, 1807L, 2208L, 3883L, 8864L, 6060L, 19326L, 63185L, 100854L, 53318L, 94151L, 157576L, 130610L, 77432L, 22805L, 134639L, 120393L, 491733L, 33327L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 161L, 321L, 1000L, 4425L, 13306L, 19894L, 30518L, 85042L, 157506L, 146328L, 86914L, 65073L, 53812L, 34763L, 36931L, 33769L, 24998L, 60110L, 52938L, 13149L, 22476L, 8319L), Year = c(2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L)), .Names = c(IDWeek, Total, Fry, Smolt, FryEq, Year), row.names = c(NA, 52L), class = data.frame) fish # Subset to get the max Total for 2012 x - subset(winter,Year==2012 Total==max(Total));b # How come one line doesn't work? # It works if I subset the year first and then get the Total max from it xx - subset(winter,Year==2012) xxx - subset(xx,Total==max(Total));xxx xxx Try instead either of these one step operations: xxx - max( subset(fish, Year==2012 )$Total) ;xxx [1] 303259 xxx - max( subset(fish, Year==2012 , Total) ) ;xxx [1] 303259 -- David Winsemius, MD Alameda, CA, USA __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] simple subset question
On Sun, Dec 2, 2012 at 5:21 PM, Felipe Carrillo mazatlanmex...@yahoo.com wrote: Hi, Consider the small dataset below, I want to subset by two variables in one line but it wont work...it works though if I subset separately. I have to be missing something obvious that I did not realize before while using subset.. fish - structure(list(IDWeek = c(27L, 28L, 29L, 30L, 31L, 32L, 33L, 34L, 35L, 36L, 37L, 38L, 39L, 40L, 41L, 42L, 43L, 44L, 45L, 46L, 47L, 48L, 49L, 50L, 51L, 52L, 27L, 28L, 29L, 30L, 31L, 32L, 33L, 34L, 35L, 36L, 37L, 38L, 39L, 40L, 41L, 42L, 43L, 44L, 45L, 46L, 47L, 48L, 49L, 50L, 51L, 52L), Total = c(0L, 0L, 326L, 1735L, 1807L, 2208L, 3883L, 8820L, 6060L, 19326L, 63158L, 100718L, 53015L, 91689L, 152629L, 122708L, 61293L, 15574L, 86538L, 75365L, 303259L, 19691L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 161L, 321L, 1000L, 4425L, 13202L, 19726L, 30518L, 84949L, 157260L, 145691L, 85801L, 62044L, 44439L, 23272L, 22391L, 20159L, 14854L, 35379L, 31142L, 7736L, 13221L, 4894L), Fry = c(0L, 0L, 326L, 1735L, 1807L, 2208L, 3883L, 8759L, 6060L, 19326L, 63119L, 100524L, 52582L, 88170L, 145564L, 111416L, 38233L, 5248L, 17826L, 11038L, 34008L, 215L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 161L, 321L, 1000L, 4425L, 13055L, 19488L, 30518L, 84818L, 156909L, 144786L, 84207L, 57720L, 31049L, 6858L, 1616L, 719L, 364L, 49L, 0L, 0L, 0L, 0L), Smolt = c(0L, 0L, 0L, 0L, 0L, 0L, 0L, 62L, 0L, 0L, 38L, 195L, 433L, 3518L, 7067L, 11290L, 23058L, 10327L, 68712L, 64328L, 269248L, 19479L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 147L, 238L, 0L, 131L, 351L, 905L, 1592L, 4324L, 13391L, 16414L, 20774L, 19444L, 14491L, 35330L, 31142L, 7736L, 13221L, 4894L), FryEq = c(0L, 0L, 326L, 1735L, 1807L, 2208L, 3883L, 8864L, 6060L, 19326L, 63185L, 100854L, 53318L, 94151L, 157576L, 130610L, 77432L, 22805L, 134639L, 120393L, 491733L, 33327L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 161L, 321L, 1000L, 4425L, 13306L, 19894L, 30518L, 85042L, 157506L, 146328L, 86914L, 65073L, 53812L, 34763L, 36931L, 33769L, 24998L, 60110L, 52938L, 13149L, 22476L, 8319L), Year = c(2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L)), .Names = c(IDWeek, Total, Fry, Smolt, FryEq, Year), row.names = c(NA, 52L), class = data.frame) fish # Subset to get the max Total for 2012 x - subset(winter,Year==2012 Total==max(Total));b # How come one line doesn't work? Works fine for me if I change winter to fish here. subset(fish,Year==2012 Total==max(Total)) IDWeek Total Fry Smolt FryEq Year 21 47 303259 34008 269248 491733 2012 # It works if I subset the year first and then get the Total max from it xx - subset(winter,Year==2012) xxx - subset(xx,Total==max(Total));xxx xxx Felipe D. Carrillo Supervisory Fishery Biologist Department of the Interior US Fish Wildlife Service California, USA http://www.fws.gov/redbluff/rbdd_jsmp.aspx [[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] simple subset question
Hi, Felipe, two typos? See below! On Sun, 2 Dec 2012, Felipe Carrillo wrote: Hi, Consider the small dataset below, I want to subset by two variables in one line but it wont work...it works though if I subset separately. I have to be missing something obvious that I did not realize before while using subset.. fish - structure(list(IDWeek = c(27L, 28L, 29L, 30L, 31L, 32L, 33L, ... [snip] 2011L)), .Names = c(IDWeek, Total, Fry, Smolt, FryEq, Year), row.names = c(NA, 52L), class = data.frame) fish # Subset to get the max Total for 2012 x - subset(winter,Year==2012 Total==max(Total));b # How come one line doesn't work? Don't you want *fish* instead of *winter* and *x* instead of *b*, as in x - subset( fish,Year==2012 Total==max(Total));x ? Hth -- Gerrit # It works if I subset the year first and then get the Total max from it xx - subset(winter,Year==2012) xxx - subset(xx,Total==max(Total));xxx xxx __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] How to calculate mean of every nth time series data with zoo or xts ?
Hello, I have 1-minute time series stock data and I'd like to calculate mean of every n-th candle data of m-days. result = c(mean of 1th data, mean of 2nd data, ...) mean of 1th data = (1th data of 2012-1-1 + 1th data of 2012-1-2 + 1th data of 2012-1-3) / 3 mean of 2nd data = (2nd data of 2012-1-1 + 2nd data of 2012-1-2 + 2nd data of 2012-1-3) / 3 ... Could you let me know the fastest method ? Thanks in advance, [[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] missed values
It's simpler, easier, and more correct to use zoo::na.approx.
R library(zoo)
R dat1-read.table(text=
+date value
+ 80 2006-10 0.1577647
+ 81 2006-11 NaN
+ 82 2006-12 NaN
+ 83 2007-01 NaN
+ 84 2007-02 NaN
+ 85 2007-03 0.2956429,
+ header=TRUE,stringsAsFactors=FALSE)
R dat1$valnew - na.approx(dat1$value, as.yearmon(dat1$date))
R dat1
date valuevalnew
80 2006-10 0.1577647 0.1577647
81 2006-11 NaN 0.1853403
82 2006-12 NaN 0.2129160
83 2007-01 NaN 0.2404916
84 2007-02 NaN 0.2680673
85 2007-03 0.2956429 0.2956429
Best,
--
Joshua Ulrich | about.me/joshuaulrich
FOSS Trading | www.fosstrading.com
On Fri, Nov 30, 2012 at 11:28 AM, arun smartpink...@yahoo.com wrote:
Hi,
May be this helps:
dat1-read.table(text=
---data---
,header=TRUE,stringsAsFactors=FALSE)
library(zoo)
dat1$date-as.yearmon(dat1$date,format=%Y-%m)
lm1-lm(value~date,dat1)
dat2-data.frame(date=dat1[,1])
dat1$fit-predict(lm1,newdata=dat2)
dat1-within(dat1,{newvalue-ifelse(is.na(value)==T,fit,value)})
dat1new-dat1[,c(1:2,4)]
dat1new[80:86,]
# date value newvalue
#80 Oct 2006 0.1577647 0.1577647
#81 Nov 2006 NaN 0.2782320
#82 Dec 2006 NaN 0.2773986
#83 Jan 2007 NaN 0.2765651
#84 Feb 2007 NaN 0.2757317
#85 Mar 2007 0.2956429 0.2956429
#86 Apr 2007 0.3767500 0.3767500
A.K.
- Original Message -
From: Vasilchenko Aleksander vasilchenko@gmail.com
To: arun smartpink...@yahoo.com
Cc:
Sent: Friday, November 30, 2012 8:22 AM
Subject: Re: [R] missed values
date value
snip
80 2006-10 0.1577647
81 2006-11 NaN
82 2006-12 NaN
83 2007-01 NaN
84 2007-02 NaN
85 2007-03 0.2956429
snip
I want to obtain these values by linear interpolation between 80
2006-10 0.1577647 and 85 2007-03 0.2956429
81 2006-11 NaN
82 2006-12 NaN
83 2007-01 NaN
84 2007-02 NaN
This time series has only one such block, but there can be several
such blocks in general
thanks
__
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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] simple subset question
Sorry, I was trying it to subset from a bigger dataset called 'winter' and forgot to change the variable names when I asked the question. David W suggestion works but the strange part is that I am still getting an error message with : x - subset(fish,Year==2012 Total==max(Total));x I get: [1] IDWeek Total Fry Smolt FryEq Year 0 rows (or 0-length row.names) I will start a fresh session to see if that helps...Thank you all Felipe D. Carrillo Supervisory Fishery Biologist Department of the Interior US Fish Wildlife Service California, USA http://www.fws.gov/redbluff/rbdd_jsmp.aspx From: R. Michael Weylandt michael.weyla...@gmail.com To: Felipe Carrillo mazatlanmex...@yahoo.com Cc: r-help@r-project.org r-help@r-project.org Sent: Sunday, December 2, 2012 9:42 AM Subject: Re: [R] simple subset question On Sun, Dec 2, 2012 at 5:21 PM, Felipe Carrillo mazatlanmex...@yahoo.com wrote: Hi, Consider the small dataset below, I want to subset by two variables in one line but it wont work...it works though if I subset separately. I have to be missing something obvious that I did not realize before while using subset.. fish - structure(list(IDWeek = c(27L, 28L, 29L, 30L, 31L, 32L, 33L, 34L, 35L, 36L, 37L, 38L, 39L, 40L, 41L, 42L, 43L, 44L, 45L, 46L, 47L, 48L, 49L, 50L, 51L, 52L, 27L, 28L, 29L, 30L, 31L, 32L, 33L, 34L, 35L, 36L, 37L, 38L, 39L, 40L, 41L, 42L, 43L, 44L, 45L, 46L, 47L, 48L, 49L, 50L, 51L, 52L), Total = c(0L, 0L, 326L, 1735L, 1807L, 2208L, 3883L, 8820L, 6060L, 19326L, 63158L, 100718L, 53015L, 91689L, 152629L, 122708L, 61293L, 15574L, 86538L, 75365L, 303259L, 19691L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 161L, 321L, 1000L, 4425L, 13202L, 19726L, 30518L, 84949L, 157260L, 145691L, 85801L, 62044L, 44439L, 23272L, 22391L, 20159L, 14854L, 35379L, 31142L, 7736L, 13221L, 4894L), Fry = c(0L, 0L, 326L, 1735L, 1807L, 2208L, 3883L, 8759L, 6060L, 19326L, 63119L, 100524L, 52582L, 88170L, 145564L, 111416L, 38233L, 5248L, 17826L, 11038L, 34008L, 215L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 161L, 321L, 1000L, 4425L, 13055L, 19488L, 30518L, 84818L, 156909L, 144786L, 84207L, 57720L, 31049L, 6858L, 1616L, 719L, 364L, 49L, 0L, 0L, 0L, 0L), Smolt = c(0L, 0L, 0L, 0L, 0L, 0L, 0L, 62L, 0L, 0L, 38L, 195L, 433L, 3518L, 7067L, 11290L, 23058L, 10327L, 68712L, 64328L, 269248L, 19479L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 147L, 238L, 0L, 131L, 351L, 905L, 1592L, 4324L, 13391L, 16414L, 20774L, 19444L, 14491L, 35330L, 31142L, 7736L, 13221L, 4894L), FryEq = c(0L, 0L, 326L, 1735L, 1807L, 2208L, 3883L, 8864L, 6060L, 19326L, 63185L, 100854L, 53318L, 94151L, 157576L, 130610L, 77432L, 22805L, 134639L, 120393L, 491733L, 33327L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 161L, 321L, 1000L, 4425L, 13306L, 19894L, 30518L, 85042L, 157506L, 146328L, 86914L, 65073L, 53812L, 34763L, 36931L, 33769L, 24998L, 60110L, 52938L, 13149L, 22476L, 8319L), Year = c(2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L)), .Names = c(IDWeek, Total, Fry, Smolt, FryEq, Year), row.names = c(NA, 52L), class = data.frame) fish # Subset to get the max Total for 2012 x - subset(winter,Year==2012 Total==max(Total));b # How come one line doesn't work? Works fine for me if I change winter to fish here. subset(fish,Year==2012 Total==max(Total)) IDWeek Total Fry Smolt FryEq Year 21 47 303259 34008 269248 491733 2012 # It works if I subset the year first and then get the Total max from it xx - subset(winter,Year==2012) xxx - subset(xx,Total==max(Total));xxx xxx Felipe D. Carrillo Supervisory Fishery Biologist Department of the Interior US Fish Wildlife Service California, USA http://www.fws.gov/redbluff/rbdd_jsmp.aspx [[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] How to calculate mean of every nth time series data with zoo or xts ?
Hello, You should include a data example, using ?dput. Anyway, making up some data, t1 - as.POSIXct(2012-1-1 0:0:0) t2 - as.POSIXct(2012-1-4 0:0:0) d - seq(t1, t2, by = 1 min) x - rnorm(length(d)) z - zoo(x, d) aggregate(z, list(format(index(z), %H:%M)), FUN = mean) Hope this helps, Rui Barradas Em 02-12-2012 18:09, 박상규 escreveu: Hello, I have 1-minute time series stock data and I'd like to calculate mean of every n-th candle data of m-days. result = c(mean of 1th data, mean of 2nd data, ...) mean of 1th data = (1th data of 2012-1-1 + 1th data of 2012-1-2 + 1th data of 2012-1-3) / 3 mean of 2nd data = (2nd data of 2012-1-1 + 2nd data of 2012-1-2 + 2nd data of 2012-1-3) / 3 ... Could you let me know the fastest method ? Thanks in advance, [[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] simple subset question
Works with the small dataset (2 years) but I get the error message with the whole dataset (12 years of data). I am going to have to check what's wrong with it...Thanks Felipe D. Carrillo Supervisory Fishery Biologist Department of the Interior US Fish Wildlife Service California, USA http://www.fws.gov/redbluff/rbdd_jsmp.aspx From: arun smartpink...@yahoo.com To: Felipe Carrillo mazatlanmex...@yahoo.com Cc: R help r-help@r-project.org; R. Michael Weylandt michael.weyla...@gmail.com Sent: Sunday, December 2, 2012 10:29 AM Subject: Re: [R] simple subset question Hi, I am getting this: x-subset(fish,Year==2012 Total==max(Total)) x # IDWeek Total Fry Smolt FryEq Year #21 47 303259 34008 269248 491733 2012 A.K. - Original Message - From: Felipe Carrillo mazatlanmex...@yahoo.com To: R. Michael Weylandt michael.weyla...@gmail.com Cc: r-help@r-project.org r-help@r-project.org Sent: Sunday, December 2, 2012 1:25 PM Subject: Re: [R] simple subset question Sorry, I was trying it to subset from a bigger dataset called 'winter' and forgot to change the variable names when I asked the question. David W suggestion works but the strange part is that I am still getting an error message with : x - subset(fish,Year==2012 Total==max(Total));x I get: [1] IDWeek Total Fry Smolt FryEq Year 0 rows (or 0-length row.names) I will start a fresh session to see if that helps...Thank you all Felipe D. Carrillo Supervisory Fishery Biologist Department of the Interior US Fish Wildlife Service California, USA http://www.fws.gov/redbluff/rbdd_jsmp.aspx From: R. Michael Weylandt michael.weyla...@gmail.com To: Felipe Carrillo mazatlanmex...@yahoo.com Cc: r-help@r-project.org r-help@r-project.org Sent: Sunday, December 2, 2012 9:42 AM Subject: Re: [R] simple subset question On Sun, Dec 2, 2012 at 5:21 PM, Felipe Carrillo mazatlanmex...@yahoo.com wrote: Hi, Consider the small dataset below, I want to subset by two variables in one line but it wont work...it works though if I subset separately. I have to be missing something obvious that I did not realize before while using subset.. fish - structure(list(IDWeek = c(27L, 28L, 29L, 30L, 31L, 32L, 33L, 34L, 35L, 36L, 37L, 38L, 39L, 40L, 41L, 42L, 43L, 44L, 45L, 46L, 47L, 48L, 49L, 50L, 51L, 52L, 27L, 28L, 29L, 30L, 31L, 32L, 33L, 34L, 35L, 36L, 37L, 38L, 39L, 40L, 41L, 42L, 43L, 44L, 45L, 46L, 47L, 48L, 49L, 50L, 51L, 52L), Total = c(0L, 0L, 326L, 1735L, 1807L, 2208L, 3883L, 8820L, 6060L, 19326L, 63158L, 100718L, 53015L, 91689L, 152629L, 122708L, 61293L, 15574L, 86538L, 75365L, 303259L, 19691L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 161L, 321L, 1000L, 4425L, 13202L, 19726L, 30518L, 84949L, 157260L, 145691L, 85801L, 62044L, 44439L, 23272L, 22391L, 20159L, 14854L, 35379L, 31142L, 7736L, 13221L, 4894L), Fry = c(0L, 0L, 326L, 1735L, 1807L, 2208L, 3883L, 8759L, 6060L, 19326L, 63119L, 100524L, 52582L, 88170L, 145564L, 111416L, 38233L, 5248L, 17826L, 11038L, 34008L, 215L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 161L, 321L, 1000L, 4425L, 13055L, 19488L, 30518L, 84818L, 156909L, 144786L, 84207L, 57720L, 31049L, 6858L, 1616L, 719L, 364L, 49L, 0L, 0L, 0L, 0L), Smolt = c(0L, 0L, 0L, 0L, 0L, 0L, 0L, 62L, 0L, 0L, 38L, 195L, 433L, 3518L, 7067L, 11290L, 23058L, 10327L, 68712L, 64328L, 269248L, 19479L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 147L, 238L, 0L, 131L, 351L, 905L, 1592L, 4324L, 13391L, 16414L, 20774L, 19444L, 14491L, 35330L, 31142L, 7736L, 13221L, 4894L), FryEq = c(0L, 0L, 326L, 1735L, 1807L, 2208L, 3883L, 8864L, 6060L, 19326L, 63185L, 100854L, 53318L, 94151L, 157576L, 130610L, 77432L, 22805L, 134639L, 120393L, 491733L, 33327L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 161L, 321L, 1000L, 4425L, 13306L, 19894L, 30518L, 85042L, 157506L, 146328L, 86914L, 65073L, 53812L, 34763L, 36931L, 33769L, 24998L, 60110L, 52938L, 13149L, 22476L, 8319L), Year = c(2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L)), .Names = c(IDWeek, Total, Fry, Smolt, FryEq, Year), row.names = c(NA, 52L), class = data.frame) fish # Subset to get the max Total for 2012 x - subset(winter,Year==2012 Total==max(Total));b # How come one line doesn't work? Works fine for me if I change winter to fish here. subset(fish,Year==2012 Total==max(Total)) IDWeek Total Fry Smolt FryEq Year 21 47 303259 34008 269248 491733 2012 # It works if I subset the year first and then get the Total max from it xx - subset(winter,Year==2012) xxx - subset(xx,Total==max(Total));xxx xxx Felipe D. Carrillo Supervisory Fishery Biologist Department of the Interior US Fish Wildlife Service California, USA
Re: [R] simple subset question
On Sun, Dec 2, 2012 at 6:46 PM, Felipe Carrillo mazatlanmex...@yahoo.com wrote: Works with the small dataset (2 years) but I get the error message with the whole dataset (12 years of data). I am going to have to check what's wrong with it...Thanks Off the cuff guess: there's a NA in Total so max(Total) is NA which throws a wrench in `==`. MW __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] simple subset question
I am still getting an error message with : x - subset(fish,Year==2012 Total==max(Total));x I get: [1] IDWeek Total FrySmolt FryEq Year 0 rows (or 0-length row.names) The above is not an error message. It says that there are no rows satisfying your criteria. Note that Total==max(Total) returns a TRUE for each row in which the Total value equals the maximum Total value over all the years in the data. Are you looking for the maximum value of Total in each year? tmp - transform(fish, YearlyMaxTotal = ave(Total, Year, FUN=max)) subset(tmp, Total==YearlyMaxTotal) IDWeek TotalFry Smolt FryEq Year YearlyMaxTotal 21 47 303259 34008 269248 491733 2012 303259 39 39 157260 156909351 157506 2011 157260 subset(tmp, Total==YearlyMaxTotal Year==2012) IDWeek Total Fry Smolt FryEq Year YearlyMaxTotal 21 47 303259 34008 269248 491733 2012 303259 Bill Dunlap Spotfire, TIBCO Software wdunlap tibco.com -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Felipe Carrillo Sent: Sunday, December 02, 2012 10:47 AM To: arun Cc: R help Subject: Re: [R] simple subset question Works with the small dataset (2 years) but I get the error message with the whole dataset (12 years of data). I am going to have to check what's wrong with it...Thanks Felipe D. Carrillo Supervisory Fishery Biologist Department of the Interior US Fish Wildlife Service California, USA http://www.fws.gov/redbluff/rbdd_jsmp.aspx From: arun smartpink...@yahoo.com To: Felipe Carrillo mazatlanmex...@yahoo.com Cc: R help r-help@r-project.org; R. Michael Weylandt michael.weyla...@gmail.com Sent: Sunday, December 2, 2012 10:29 AM Subject: Re: [R] simple subset question Hi, I am getting this: x-subset(fish,Year==2012 Total==max(Total)) x # IDWeek Total Fry Smolt FryEq Year #21 47 303259 34008 269248 491733 2012 A.K. - Original Message - From: Felipe Carrillo mazatlanmex...@yahoo.com To: R. Michael Weylandt michael.weyla...@gmail.com Cc: r-help@r-project.org r-help@r-project.org Sent: Sunday, December 2, 2012 1:25 PM Subject: Re: [R] simple subset question Sorry, I was trying it to subset from a bigger dataset called 'winter' and forgot to change the variable names when I asked the question. David W suggestion works but the strange part is that I am still getting an error message with : x - subset(fish,Year==2012 Total==max(Total));x I get: [1] IDWeek Total Fry Smolt FryEq Year 0 rows (or 0-length row.names) I will start a fresh session to see if that helps...Thank you all Felipe D. Carrillo Supervisory Fishery Biologist Department of the Interior US Fish Wildlife Service California, USA http://www.fws.gov/redbluff/rbdd_jsmp.aspx From: R. Michael Weylandt michael.weyla...@gmail.com To: Felipe Carrillo mazatlanmex...@yahoo.com Cc: r-help@r-project.org r-help@r-project.org Sent: Sunday, December 2, 2012 9:42 AM Subject: Re: [R] simple subset question On Sun, Dec 2, 2012 at 5:21 PM, Felipe Carrillo mazatlanmex...@yahoo.com wrote: Hi, Consider the small dataset below, I want to subset by two variables in one line but it wont work...it works though if I subset separately. I have to be missing something obvious that I did not realize before while using subset.. fish - structure(list(IDWeek = c(27L, 28L, 29L, 30L, 31L, 32L, 33L, 34L, 35L, 36L, 37L, 38L, 39L, 40L, 41L, 42L, 43L, 44L, 45L, 46L, 47L, 48L, 49L, 50L, 51L, 52L, 27L, 28L, 29L, 30L, 31L, 32L, 33L, 34L, 35L, 36L, 37L, 38L, 39L, 40L, 41L, 42L, 43L, 44L, 45L, 46L, 47L, 48L, 49L, 50L, 51L, 52L), Total = c(0L, 0L, 326L, 1735L, 1807L, 2208L, 3883L, 8820L, 6060L, 19326L, 63158L, 100718L, 53015L, 91689L, 152629L, 122708L, 61293L, 15574L, 86538L, 75365L, 303259L, 19691L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 161L, 321L, 1000L, 4425L, 13202L, 19726L, 30518L, 84949L, 157260L, 145691L, 85801L, 62044L, 44439L, 23272L, 22391L, 20159L, 14854L, 35379L, 31142L, 7736L, 13221L, 4894L), Fry = c(0L, 0L, 326L, 1735L, 1807L, 2208L, 3883L, 8759L, 6060L, 19326L, 63119L, 100524L, 52582L, 88170L, 145564L, 111416L, 38233L, 5248L, 17826L, 11038L, 34008L, 215L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 161L, 321L, 1000L, 4425L, 13055L, 19488L, 30518L, 84818L, 156909L, 144786L, 84207L, 57720L, 31049L, 6858L, 1616L, 719L, 364L, 49L, 0L, 0L, 0L, 0L), Smolt = c(0L, 0L, 0L, 0L, 0L, 0L, 0L, 62L, 0L, 0L, 38L, 195L, 433L, 3518L, 7067L, 11290L, 23058L, 10327L, 68712L, 64328L, 269248L, 19479L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 147L, 238L, 0L, 131L, 351L, 905L, 1592L, 4324L, 13391L, 16414L, 20774L, 19444L, 14491L, 35330L, 31142L, 7736L, 13221L, 4894L), FryEq = c(0L, 0L, 326L, 1735L, 1807L, 2208L, 3883L, 8864L, 6060L, 19326L, 63185L, 100854L, 53318L, 94151L, 157576L, 130610L, 77432L, 22805L, 134639L, 120393L, 491733L, 33327L, 0L,
Re: [R] Line numbers with errors and warnings?
On 12-12-02 9:52 AM, Milan Bouchet-Valat wrote: Le dimanche 02 décembre 2012 à 09:02 -0500, Duncan Murdoch a écrit : On 12-12-02 8:33 AM, Milan Bouchet-Valat wrote: Le dimanche 02 décembre 2012 à 06:02 -0500, Steve Lianoglou a écrit : Hi, On Sun, Dec 2, 2012 at 12:31 AM, Worik R wor...@gmail.com wrote: What I mean is how do I get the R compilation or execution process to spit out a line number with errors and warnings? Indeed, I often suffer from the same problem when debugging R code too. This is a real issue for me. As Duncan mentioned already, you can't *always* get a line number. You can, however, usually get enough context around the failing call for you to be able to smoke the problem out. What are the cases where you cannot get line numbers? Duncan said source()ed code comes with line numbers, but what's the more general rule? The general rule is that parse() needs to be called with the srcfile argument set to a srcfile object. source() does that by default. OK. But isn't it technically possible to compute a line number even when no source file is present? Yes, you don't really need to have a file present, you just need a srcfile object. For example, on Windows when you use source(clipboard), there's no file, just the system clipboard. If you call fix() on any function, you will get something like a source file even if srcfile was not set. Yes, and then you can call source on that object, and you'll get line number information attached, relative to whatever you sourced. So it could make sense to have a line number referring to what you would see in fix(). Or at least, the last executed line when calling browser() or when using options(error=recover), like gdb does. The thing is that if you didn't attach the line number information to the code, then it's not there. R can't figure out after the fact where the code came from. It needs to have the debug info in place when it runs it. How could R figure out where some expression came from that it happens to be executing? Using eval() on a constructed expression in a function is not all that uncommon, but to the evaluator, it looks just like any other evaluation. This could be especially useful for packages that were not installed with keep.source=TRUE. It could even help getting more useful error messages on R-help... If you're debugging a package, then why not install it with keep.source=TRUE? Duncan Murdoch __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] simple subset question
Using my whole dataset I get: library(plyr) ddply(winter,Year,summarise,maxTotal=max(Total)) fish - structure(list(Year = 2002:2012, maxTotal = c(1464311L, 1071051L, 714837L, 2115018L, 850491L, 207537L, 321195L, 935599L, 194429L, 157260L, 303259L)), .Names = c(Year, maxTotal), row.names = c(NA, -11L), class = data.frame) I only want to extract the max Total for 2012 and want the whole row like this: IDWeek Total Fry Smolt FryEq Year 21 47 303259 34008 269248 491733 2012 My whole dataset is too big to post it so thanks for your help and will try to figure out why subset returns an empty row Felipe D. Carrillo Supervisory Fishery Biologist Department of the Interior US Fish Wildlife Service California, USA http://www.fws.gov/redbluff/rbdd_jsmp.aspx From: William Dunlap wdun...@tibco.com To: Felipe Carrillo mazatlanmex...@yahoo.com; arun smartpink...@yahoo.com Cc: R help r-help@r-project.org Sent: Sunday, December 2, 2012 11:00 AM Subject: RE: [R] simple subset question I am still getting an error message with : x - subset(fish,Year==2012 Total==max(Total));x I get: [1] IDWeek Total Fry Smolt FryEq Year 0 rows (or 0-length row.names) The above is not an error message. It says that there are no rows satisfying your criteria. Note that Total==max(Total) returns a TRUE for each row in which the Total value equals the maximum Total value over all the years in the data. Are you looking for the maximum value of Total in each year? tmp - transform(fish, YearlyMaxTotal = ave(Total, Year, FUN=max)) subset(tmp, Total==YearlyMaxTotal) IDWeek Total Fry Smolt FryEq Year YearlyMaxTotal 21 47 303259 34008 269248 491733 2012 303259 39 39 157260 156909 351 157506 2011 157260 subset(tmp, Total==YearlyMaxTotal Year==2012) IDWeek Total Fry Smolt FryEq Year YearlyMaxTotal 21 47 303259 34008 269248 491733 2012 303259 Bill Dunlap Spotfire, TIBCO Software wdunlap tibco.com -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Felipe Carrillo Sent: Sunday, December 02, 2012 10:47 AM To: arun Cc: R help Subject: Re: [R] simple subset question Works with the small dataset (2 years) but I get the error message with the whole dataset (12 years of data). I am going to have to check what's wrong with it...Thanks Felipe D. Carrillo Supervisory Fishery Biologist Department of the Interior US Fish Wildlife Service California, USA http://www.fws.gov/redbluff/rbdd_jsmp.aspx From: arun smartpink...@yahoo.com To: Felipe Carrillo mazatlanmex...@yahoo.com Cc: R help r-help@r-project.org; R. Michael Weylandt michael.weyla...@gmail.com Sent: Sunday, December 2, 2012 10:29 AM Subject: Re: [R] simple subset question Hi, I am getting this: x-subset(fish,Year==2012 Total==max(Total)) x # IDWeek Total Fry Smolt FryEq Year #21 47 303259 34008 269248 491733 2012 A.K. - Original Message - From: Felipe Carrillo mazatlanmex...@yahoo.com To: R. Michael Weylandt michael.weyla...@gmail.com Cc: r-help@r-project.org r-help@r-project.org Sent: Sunday, December 2, 2012 1:25 PM Subject: Re: [R] simple subset question Sorry, I was trying it to subset from a bigger dataset called 'winter' and forgot to change the variable names when I asked the question. David W suggestion works but the strange part is that I am still getting an error message with : x - subset(fish,Year==2012 Total==max(Total));x I get: [1] IDWeek Total Fry Smolt FryEq Year 0 rows (or 0-length row.names) I will start a fresh session to see if that helps...Thank you all Felipe D. Carrillo Supervisory Fishery Biologist Department of the Interior US Fish Wildlife Service California, USA http://www.fws.gov/redbluff/rbdd_jsmp.aspx From: R. Michael Weylandt michael.weyla...@gmail.com To: Felipe Carrillo mazatlanmex...@yahoo.com Cc: r-help@r-project.org r-help@r-project.org Sent: Sunday, December 2, 2012 9:42 AM Subject: Re: [R] simple subset question On Sun, Dec 2, 2012 at 5:21 PM, Felipe Carrillo mazatlanmex...@yahoo.com wrote: Hi, Consider the small dataset below, I want to subset by two variables in one line but it wont work...it works though if I subset separately. I have to be missing something obvious that I did not realize before while using subset.. fish - structure(list(IDWeek = c(27L, 28L, 29L, 30L, 31L, 32L, 33L, 34L, 35L, 36L, 37L, 38L, 39L, 40L, 41L, 42L, 43L, 44L, 45L, 46L, 47L, 48L, 49L, 50L, 51L, 52L, 27L, 28L, 29L, 30L, 31L, 32L, 33L, 34L, 35L, 36L, 37L, 38L, 39L, 40L, 41L, 42L, 43L, 44L, 45L, 46L, 47L, 48L, 49L, 50L, 51L, 52L), Total = c(0L, 0L, 326L, 1735L, 1807L, 2208L, 3883L, 8820L, 6060L, 19326L, 63158L, 100718L, 53015L, 91689L, 152629L, 122708L, 61293L, 15574L, 86538L, 75365L, 303259L, 19691L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 161L, 321L, 1000L, 4425L, 13202L,
Re: [R] e1071 SVM: Cross-validation error confusion matrix
What do you mean by accuracy? Proportion classified correctly is not a good index of accuracy if that's the problem. Frank rahul143 wrote Hi, I ran two svm models in R e1071 package: the first without cross-validation and the second with 10-fold cross-validation. I used the following syntax: #Model 1: Without cross-validation: svm.model - svm(Response ~ ., data=data.df, type=C-classification, kernel=linear, cost=1) predict - fitted(svm.model) cm - table(predict, data.df$Response) cm #Model2: With 10-fold cross-validation: svm.model2 - svm(Response ~ ., data=data.df, type=C-classification, kernel=linear, cost=1, cross=10) predict2 - fitted(svm.model2) cm2 - table(predict2, data.df$Response) cm2 However, when I compare cm and cm2, I notice that the confusion matrices are identical although the accuracy of each model is diffent. What am I doing wrong? Thanks for you help, - Frank Harrell Department of Biostatistics, Vanderbilt University -- View this message in context: http://r.789695.n4.nabble.com/e1071-SVM-Cross-validation-error-confusion-matrix-tp4651652p4651692.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] simple subset question
The reason I suggested the alternative that I did was because your code could fail when the max(Total) value was not in the subset where Year==2012. -- David On Dec 2, 2012, at 11:34 AM, Felipe Carrillo wrote: Using my whole dataset I get: library(plyr) ddply(winter,Year,summarise,maxTotal=max(Total)) fish - structure(list(Year = 2002:2012, maxTotal = c(1464311L, 1071051L, 714837L, 2115018L, 850491L, 207537L, 321195L, 935599L, 194429L, 157260L, 303259L)), .Names = c(Year, maxTotal), row.names = c(NA, -11L), class = data.frame) I only want to extract the max Total for 2012 and want the whole row like this: IDWeek Total Fry Smolt FryEq Year 21 47 303259 34008 269248 491733 2012 My whole dataset is too big to post it so thanks for your help and will try to figure out why subset returns an empty row Felipe D. Carrillo Supervisory Fishery Biologist Department of the Interior US Fish Wildlife Service California, USA http://www.fws.gov/redbluff/rbdd_jsmp.aspx From: William Dunlap wdun...@tibco.com To: Felipe Carrillo mazatlanmex...@yahoo.com; arun smartpink...@yahoo.com Cc: R help r-help@r-project.org Sent: Sunday, December 2, 2012 11:00 AM Subject: RE: [R] simple subset question I am still getting an error message with : x - subset(fish,Year==2012 Total==max(Total));x I get: [1] IDWeek Total FrySmolt FryEq Year 0 rows (or 0-length row.names) The above is not an error message. It says that there are no rows satisfying your criteria. Note that Total==max(Total) returns a TRUE for each row in which the Total value equals the maximum Total value over all the years in the data. Are you looking for the maximum value of Total in each year? tmp - transform(fish, YearlyMaxTotal = ave(Total, Year, FUN=max)) subset(tmp, Total==YearlyMaxTotal) IDWeek TotalFry Smolt FryEq Year YearlyMaxTotal 2147 303259 34008 269248 491733 2012303259 3939 157260 156909351 157506 2011157260 subset(tmp, Total==YearlyMaxTotal Year==2012) IDWeek Total Fry Smolt FryEq Year YearlyMaxTotal 2147 303259 34008 269248 491733 2012303259 Bill Dunlap Spotfire, TIBCO Software wdunlap tibco.com -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org ] On Behalf Of Felipe Carrillo Sent: Sunday, December 02, 2012 10:47 AM To: arun Cc: R help Subject: Re: [R] simple subset question Works with the small dataset (2 years) but I get the error message with the whole dataset (12 years of data). I am going to have to check what's wrong with it...Thanks Felipe D. Carrillo Supervisory Fishery Biologist Department of the Interior US Fish Wildlife Service California, USA http://www.fws.gov/redbluff/rbdd_jsmp.aspx From: arun smartpink...@yahoo.com To: Felipe Carrillo mazatlanmex...@yahoo.com Cc: R help r-help@r-project.org; R. Michael Weylandt michael.weyla...@gmail.com Sent: Sunday, December 2, 2012 10:29 AM Subject: Re: [R] simple subset question Hi, I am getting this: x-subset(fish,Year==2012 Total==max(Total)) x # IDWeek Total Fry Smolt FryEq Year #21 47 303259 34008 269248 491733 2012 A.K. - Original Message - From: Felipe Carrillo mazatlanmex...@yahoo.com To: R. Michael Weylandt michael.weyla...@gmail.com Cc: r-help@r-project.org r-help@r-project.org Sent: Sunday, December 2, 2012 1:25 PM Subject: Re: [R] simple subset question Sorry, I was trying it to subset from a bigger dataset called 'winter' and forgot to change the variable names when I asked the question. David W suggestion works but the strange part is that I am still getting an error message with : x - subset(fish,Year==2012 Total==max(Total));x I get: [1] IDWeek Total FrySmolt FryEq Year 0 rows (or 0-length row.names) I will start a fresh session to see if that helps...Thank you all Felipe D. Carrillo Supervisory Fishery Biologist Department of the Interior US Fish Wildlife Service California, USA http://www.fws.gov/redbluff/rbdd_jsmp.aspx From: R. Michael Weylandt michael.weyla...@gmail.com To: Felipe Carrillo mazatlanmex...@yahoo.com Cc: r-help@r-project.org r-help@r-project.org Sent: Sunday, December 2, 2012 9:42 AM Subject: Re: [R] simple subset question On Sun, Dec 2, 2012 at 5:21 PM, Felipe Carrillo mazatlanmex...@yahoo.com wrote: Hi, Consider the small dataset below, I want to subset by two variables in one line but it wont work...it works though if I subset separately. I have to be missing something obvious that I did not realize before while using subset.. fish - structure(list(IDWeek = c(27L, 28L, 29L, 30L, 31L, 32L, 33L, 34L, 35L, 36L, 37L, 38L, 39L, 40L, 41L, 42L, 43L, 44L, 45L, 46L, 47L, 48L, 49L, 50L, 51L, 52L, 27L, 28L, 29L, 30L, 31L, 32L, 33L, 34L, 35L, 36L, 37L, 38L, 39L, 40L, 41L, 42L, 43L, 44L, 45L, 46L, 47L, 48L, 49L, 50L, 51L, 52L), Total = c(0L, 0L, 326L, 1735L, 1807L, 2208L, 3883L, 8820L, 6060L, 19326L, 63158L, 100718L, 53015L, 91689L,
Re: [R] simple subset question
I also thought that I could use it but ggplot didn't like it by itself,,,it wants to whole rowI guess it is hard to understand because I didn't post all the ggplot code of what I am trying to accomplish. The strangest thing is that ddply can extract all my Totals by year but when I try to subset only one year out of my whole dataset, it returns empty rows it regardless of what year I am subsetting. I am doing a few tests to see what's going on Felipe D. Carrillo Supervisory Fishery Biologist Department of the Interior US Fish Wildlife Service California, USA http://www.fws.gov/redbluff/rbdd_jsmp.aspx From: David Winsemius dwinsem...@comcast.net To: Felipe Carrillo mazatlanmex...@yahoo.com Cc: William Dunlap wdun...@tibco.com; arun smartpink...@yahoo.com; R help r-help@r-project.org Sent: Sunday, December 2, 2012 11:54 AM Subject: Re: [R] simple subset question The reason I suggested the alternative that I did was because your code could fail when the max(Total) value was not in the subset where Year==2012. --David On Dec 2, 2012, at 11:34 AM, Felipe Carrillo wrote: Using my whole dataset I get: library(plyr) ddply(winter,Year,summarise,maxTotal=max(Total)) fish - structure(list(Year = 2002:2012, maxTotal = c(1464311L, 1071051L, 714837L, 2115018L, 850491L, 207537L, 321195L, 935599L, 194429L, 157260L, 303259L)), .Names = c(Year, maxTotal), row.names = c(NA, -11L), class = data.frame) I only want to extract the max Total for 2012 and want the whole row like this: IDWeek Total Fry Smolt FryEq Year 21 47 303259 34008 269248 491733 2012 My whole dataset is too big to post it so thanks for your help and will try to figure out why subset returns an empty row Felipe D. Carrillo Supervisory Fishery Biologist Department of the Interior US Fish Wildlife Service California, USA http://www.fws.gov/redbluff/rbdd_jsmp.aspx From: William Dunlap wdun...@tibco.com To: Felipe Carrillo mazatlanmex...@yahoo.com; arun smartpink...@yahoo.com Cc: R help r-help@r-project.org Sent: Sunday, December 2, 2012 11:00 AM Subject: RE: [R] simple subset question I am still getting an error message with : x - subset(fish,Year==2012 Total==max(Total));x I get: [1] IDWeek Total Fry Smolt FryEq Year 0 rows (or 0-length row.names) The above is not an error message. It says that there are no rows satisfying your criteria. Note that Total==max(Total) returns a TRUE for each row in which the Total value equals the maximum Total value over all the years in the data. Are you looking for the maximum value of Total in each year? tmp - transform(fish, YearlyMaxTotal = ave(Total, Year, FUN=max)) subset(tmp, Total==YearlyMaxTotal) IDWeek Total Fry Smolt FryEq Year YearlyMaxTotal 21 47 303259 34008 269248 491733 2012 303259 39 39 157260 156909 351 157506 2011 157260 subset(tmp, Total==YearlyMaxTotal Year==2012) IDWeek Total Fry Smolt FryEq Year YearlyMaxTotal 21 47 303259 34008 269248 491733 2012 303259 Bill Dunlap Spotfire, TIBCO Software wdunlap tibco.com -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Felipe Carrillo Sent: Sunday, December 02, 2012 10:47 AM To: arun Cc: R help Subject: Re: [R] simple subset question Works with the small dataset (2 years) but I get the error message with the whole dataset (12 years of data). I am going to have to check what's wrong with it...Thanks Felipe D. Carrillo Supervisory Fishery Biologist Department of the Interior US Fish Wildlife Service California, USA http://www.fws.gov/redbluff/rbdd_jsmp.aspx From: arun smartpink...@yahoo.com To: Felipe Carrillo mazatlanmex...@yahoo.com Cc: R help r-help@r-project.org; R. Michael Weylandt michael.weyla...@gmail.com Sent: Sunday, December 2, 2012 10:29 AM Subject: Re: [R] simple subset question Hi, I am getting this: x-subset(fish,Year==2012 Total==max(Total)) x # IDWeek Total Fry Smolt FryEq Year #21 47 303259 34008 269248 491733 2012 A.K. - Original Message - From: Felipe Carrillo mazatlanmex...@yahoo.com To: R. Michael Weylandt michael.weyla...@gmail.com Cc: r-help@r-project.org r-help@r-project.org Sent: Sunday, December 2, 2012 1:25 PM Subject: Re: [R] simple subset question Sorry, I was trying it to subset from a bigger dataset called 'winter' and forgot to change the variable names when I asked the question. David W suggestion works but the strange part is that I am still getting an error message with : x - subset(fish,Year==2012 Total==max(Total));x I get: [1] IDWeek Total Fry Smolt FryEq Year 0 rows (or 0-length row.names) I will start a fresh session to see if that helps...Thank you all Felipe D. Carrillo Supervisory Fishery Biologist Department of the Interior US Fish Wildlife Service California, USA
Re: [R] Line numbers with errors and warnings?
Le dimanche 02 décembre 2012 à 14:21 -0500, Duncan Murdoch a écrit : On 12-12-02 9:52 AM, Milan Bouchet-Valat wrote: Le dimanche 02 décembre 2012 à 09:02 -0500, Duncan Murdoch a écrit : On 12-12-02 8:33 AM, Milan Bouchet-Valat wrote: Le dimanche 02 décembre 2012 à 06:02 -0500, Steve Lianoglou a écrit : Hi, On Sun, Dec 2, 2012 at 12:31 AM, Worik R wor...@gmail.com wrote: What I mean is how do I get the R compilation or execution process to spit out a line number with errors and warnings? Indeed, I often suffer from the same problem when debugging R code too. This is a real issue for me. As Duncan mentioned already, you can't *always* get a line number. You can, however, usually get enough context around the failing call for you to be able to smoke the problem out. What are the cases where you cannot get line numbers? Duncan said source()ed code comes with line numbers, but what's the more general rule? The general rule is that parse() needs to be called with the srcfile argument set to a srcfile object. source() does that by default. OK. But isn't it technically possible to compute a line number even when no source file is present? Yes, you don't really need to have a file present, you just need a srcfile object. For example, on Windows when you use source(clipboard), there's no file, just the system clipboard. If you call fix() on any function, you will get something like a source file even if srcfile was not set. Yes, and then you can call source on that object, and you'll get line number information attached, relative to whatever you sourced. So it could make sense to have a line number referring to what you would see in fix(). Or at least, the last executed line when calling browser() or when using options(error=recover), like gdb does. The thing is that if you didn't attach the line number information to the code, then it's not there. R can't figure out after the fact where the code came from. It needs to have the debug info in place when it runs it. How could R figure out where some expression came from that it happens to be executing? Using eval() on a constructed expression in a function is not all that uncommon, but to the evaluator, it looks just like any other evaluation. OK. This could be especially useful for packages that were not installed with keep.source=TRUE. It could even help getting more useful error messages on R-help... If you're debugging a package, then why not install it with keep.source=TRUE? Of course. I just wondered whether this step could possibly be avoided. It can be useful to have debugging details when casual users report a bug, without reinstalling the package. Not a big deal, though. Regards __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] cubic spline
Dear all, many thanks for your answer and support!! Steve -- View this message in context: http://r.789695.n4.nabble.com/cubic-spline-tp4651537p4651698.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] What is ts command for?
Hello, i'm here to have an explenation about time series I have to analize a time series of a stock prices and i don't understand the meaning of ts .. i load, for instance mps - get.hist.quote(instrument = bmps.mi , quote=Close, start=2006-01-01, end=2012-09-30, compression=d) and i get a value mps(zoo) ... if i run mps i get this : http://r.789695.n4.nabble.com/file/n4651620/Immagine.png isn't that a time series already? why do i have to transform it with ts or read.ts? I don't get the point Thank you for your availability Have a good day -- View this message in context: http://r.789695.n4.nabble.com/What-is-ts-command-for-tp4651620.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] function stays in loop
function - function(p){
i - 2
r - 0
while(i p) {
q - (p/i)
while(q=1) {
q=(q-1)
}
if (q==0) {
r=1
} else
i=i+1
}
return(r)
}
This function stays in some kind of loop when I enter 4 as a function value.
It immediately returns 0 when I inter 3 though.
I don't seem te get why it does not give me just a result. Can someone tell
me why it stays in a loop?
Kind regards,
Michiel
--
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and provide commented, minimal, self-contained, reproducible code.
[R] Fwd: How to calculate different groups of varialbes importance level?
Dear R user! I have a small question! I have calculated the relative importance of the variables. However I would like to compare the relative importance of two different groups of variables (i.e Strategy and industry) For example let me say that strategy has 2 sub varialbes and industry has four different variables! Can I simply add the importance of those four industry variables importance over each other and say that the importance level of industry is the total of those four varibales' importance? Can I also do the same thing and add the importance of two strategic variables and have a strategic level importance? After these simple calculation, can I compare the importance of those groups? Thanks for the kind help Best regards -- Solmaz Filiz KARABAG -- Solmaz Filiz KARABAG [[alternative HTML version deleted]] -- Solmaz Filiz KARABAG [[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] Daily Time Series, patterns.
HI, I guess you can check library(forecast). You could also use ?stl(), though not sure whether this will help you in this case. For e.g. set.seed(5) quantity-sample(c(120:220,NA),699,replace=TRUE) Date=seq(as.Date(2011-01-01),len=699,by=1 day) dat3-data.frame(Date=Date,quantity=quantity) library(zoo) z - zooreg(dat3[,2], frequency = 7) plot(stl(na.approx(z),per)) A.K. - Original Message - From: mekbatub mekba...@gmail.com To: r-help@r-project.org Cc: Sent: Saturday, December 1, 2012 8:00 PM Subject: Re: [R] Daily Time Series, patterns. Hi Arun, thx for Your reply. thats interesting, but its not what I mean. I know that there is some patterns in data, example: the highest value of the sale is on Monday, and the smallest on Wednesday and so on, there might be trend also I am trying to build forecasting model that will include patterns like that, for example forecast to next 5 days. So i think I can say that is weekly sesonality, i believe the metod to make correct model is to decompose time series like there. http://otexts.com/fppfigs/elecequip_stl.png http://otexts.com/fppfigs/elecequip_stl.png Do You think I am right? In any case, I have big problem to do this in R. -- View this message in context: http://r.789695.n4.nabble.com/Daily-Time-Series-patterns-tp4651569p4651591.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 setting up crossed data
Hello, and thanks for your time reading this. I'm trying to test
interactions of my dataset, in which the all of the factors are within the
same column.
TypeVol
1 CMass -4.598
2 BBack -4.605
3 BMass -4.602
4 CMass -4.601
5 CBack -4.605
6 CMass -4.604
7 CMass -4.602
8 CMass -4.604
9 CBack -4.605
10 BBack -4.503
11 CMass -4.605
Im attempting to determine the interaction effects of B or C on Mass and
Back
Looking for a set up as such Volume ~ CorB + MassorBack + CorB:MassorBack
is there an easy way to arrange the data so I can have the factors in column
1 broken down as I'd like?
Here if my current setup of the situation, In which I don't consider the
interactions. please forgive the armature coding.
if (T) {
#Arrange all data in a 2 column matrix as such: [Tissue Type, Measure]
measure = matrix(NA,4812,2)
measure=data.frame(measure)
for (i in a:b) {
#loads threshold factor
measure[,1] = data[,1]
#loads ith threshold
measure[,2] = data[,i]
measure$X1=factor(measure$X1, levels =
c('CMass','BMass','CBack','BBack'))
measure.aov= aov(X2 ~ X1,data = measure)
#prints results
print(TukeyHSD(measure.aov, order= TRUE, conf.level = .995))
}
}
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Re: [R] CreateThread failure since R 2.15.2 (32-bit)
I tried with Java 1.6.0_20 and 1.7.0_09. It actually doesn't matter what command I'm running with system. Any command will fail with the same error message. But for the example I posted, yes, I was using ls from Rtools. I found that I can only reproduce this with R 2.15.2+ 32-bit on Windows 32-bit. There are no issues with R 2.15.2+ 32-bit on Windows 64-bit. Best regards, Martin -- View this message in context: http://r.789695.n4.nabble.com/CreateThread-failure-since-R-2-15-2-32-bit-tp4651411p4651651.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] simple subset question
Hi, I am getting this: x-subset(fish,Year==2012 Total==max(Total)) x # IDWeek Total Fry Smolt FryEq Year #21 47 303259 34008 269248 491733 2012 A.K. - Original Message - From: Felipe Carrillo mazatlanmex...@yahoo.com To: R. Michael Weylandt michael.weyla...@gmail.com Cc: r-help@r-project.org r-help@r-project.org Sent: Sunday, December 2, 2012 1:25 PM Subject: Re: [R] simple subset question Sorry, I was trying it to subset from a bigger dataset called 'winter' and forgot to change the variable names when I asked the question. David W suggestion works but the strange part is that I am still getting an error message with : x - subset(fish,Year==2012 Total==max(Total));x I get: [1] IDWeek Total Fry Smolt FryEq Year 0 rows (or 0-length row.names) I will start a fresh session to see if that helps...Thank you all Felipe D. Carrillo Supervisory Fishery Biologist Department of the Interior US Fish Wildlife Service California, USA http://www.fws.gov/redbluff/rbdd_jsmp.aspx From: R. Michael Weylandt michael.weyla...@gmail.com To: Felipe Carrillo mazatlanmex...@yahoo.com Cc: r-help@r-project.org r-help@r-project.org Sent: Sunday, December 2, 2012 9:42 AM Subject: Re: [R] simple subset question On Sun, Dec 2, 2012 at 5:21 PM, Felipe Carrillo mazatlanmex...@yahoo.com wrote: Hi, Consider the small dataset below, I want to subset by two variables in one line but it wont work...it works though if I subset separately. I have to be missing something obvious that I did not realize before while using subset.. fish - structure(list(IDWeek = c(27L, 28L, 29L, 30L, 31L, 32L, 33L, 34L, 35L, 36L, 37L, 38L, 39L, 40L, 41L, 42L, 43L, 44L, 45L, 46L, 47L, 48L, 49L, 50L, 51L, 52L, 27L, 28L, 29L, 30L, 31L, 32L, 33L, 34L, 35L, 36L, 37L, 38L, 39L, 40L, 41L, 42L, 43L, 44L, 45L, 46L, 47L, 48L, 49L, 50L, 51L, 52L), Total = c(0L, 0L, 326L, 1735L, 1807L, 2208L, 3883L, 8820L, 6060L, 19326L, 63158L, 100718L, 53015L, 91689L, 152629L, 122708L, 61293L, 15574L, 86538L, 75365L, 303259L, 19691L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 161L, 321L, 1000L, 4425L, 13202L, 19726L, 30518L, 84949L, 157260L, 145691L, 85801L, 62044L, 44439L, 23272L, 22391L, 20159L, 14854L, 35379L, 31142L, 7736L, 13221L, 4894L), Fry = c(0L, 0L, 326L, 1735L, 1807L, 2208L, 3883L, 8759L, 6060L, 19326L, 63119L, 100524L, 52582L, 88170L, 145564L, 111416L, 38233L, 5248L, 17826L, 11038L, 34008L, 215L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 161L, 321L, 1000L, 4425L, 13055L, 19488L, 30518L, 84818L, 156909L, 144786L, 84207L, 57720L, 31049L, 6858L, 1616L, 719L, 364L, 49L, 0L, 0L, 0L, 0L), Smolt = c(0L, 0L, 0L, 0L, 0L, 0L, 0L, 62L, 0L, 0L, 38L, 195L, 433L, 3518L, 7067L, 11290L, 23058L, 10327L, 68712L, 64328L, 269248L, 19479L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 147L, 238L, 0L, 131L, 351L, 905L, 1592L, 4324L, 13391L, 16414L, 20774L, 19444L, 14491L, 35330L, 31142L, 7736L, 13221L, 4894L), FryEq = c(0L, 0L, 326L, 1735L, 1807L, 2208L, 3883L, 8864L, 6060L, 19326L, 63185L, 100854L, 53318L, 94151L, 157576L, 130610L, 77432L, 22805L, 134639L, 120393L, 491733L, 33327L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 161L, 321L, 1000L, 4425L, 13306L, 19894L, 30518L, 85042L, 157506L, 146328L, 86914L, 65073L, 53812L, 34763L, 36931L, 33769L, 24998L, 60110L, 52938L, 13149L, 22476L, 8319L), Year = c(2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2012L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L, 2011L)), .Names = c(IDWeek, Total, Fry, Smolt, FryEq, Year), row.names = c(NA, 52L), class = data.frame) fish # Subset to get the max Total for 2012 x - subset(winter,Year==2012 Total==max(Total));b # How come one line doesn't work? Works fine for me if I change winter to fish here. subset(fish,Year==2012 Total==max(Total)) IDWeek Total Fry Smolt FryEq Year 21 47 303259 34008 269248 491733 2012 # It works if I subset the year first and then get the Total max from it xx - subset(winter,Year==2012) xxx - subset(xx,Total==max(Total));xxx xxx Felipe D. Carrillo Supervisory Fishery Biologist Department of the Interior US Fish Wildlife Service California, USA http://www.fws.gov/redbluff/rbdd_jsmp.aspx [[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
Re: [R] How to calculate mean of every nth time series data with zoo or xts ?
Hi, You could use: set.seed(5) dat1-data.frame(Date=seq(from=as.POSIXct(2012-11-01 00:00:00),to=as.POSIXct(2012-11-03 23:59:00), by=1 min),col2=rnorm(4320,0,1)) library(xts) dat2-xts(dat1[,-1],order.by=dat1[,1]) res-ave(dat2[,1],format(index(dat2),%H:%M),FUN=mean) #or res-tapply(dat2[,1],format(index(dat2),%H:%M),FUN=mean) head(res) # 00:00 00:01 00:02 00:03 00:04 00:05 #-0.50875473 0.07165023 -0.35019421 0.44377065 0.61380169 0.21490898 A.K. - Original Message - From: 박상규 birdfir...@naver.com To: r-help@r-project.org Cc: Sent: Sunday, December 2, 2012 1:09 PM Subject: [R] How to calculate mean of every nth time series data with zoo or xts ? Hello, I have 1-minute time series stock data and I'd like to calculate mean of every n-th candle data of m-days. result = c(mean of 1th data, mean of 2nd data, ...) mean of 1th data = (1th data of 2012-1-1 + 1th data of 2012-1-2 + 1th data of 2012-1-3) / 3 mean of 2nd data = (2nd data of 2012-1-1 + 2nd data of 2012-1-2 + 2nd data of 2012-1-3) / 3 ... Could you let me know the fastest method ? Thanks in advance, [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Warning message: In scan(file, what, nmax...)
Dear R-users, When i try - Data1-read.table(/Users/kama/Analysis/GDP10.csv,header=TRUE,sep=;) i am getting this error: Warning message: In scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : number of items read is not a multiple of the number of columns I wonder what Iam doing wrong. i guess it is something simple, however, i do not understand the help-function in R. Thank you, Regards, Faradj Stockholm university Department of Political Science -- View this message in context: http://r.789695.n4.nabble.com/Warning-message-In-scan-file-what-nmax-tp4651689.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] Repeated-measures anova with a within-subject covariate (or varying slopes random-effects?)
Dear all, I am having quite a hard time in trying to figure out how to correctly spell out a model in R (a repeated-measures anova with a within-subject covariate, I guess). Even though I have read in the posting guide that statistical advice may or may not get an answer on this list, I decided to try it anyway, hoping not to incur in somebody's ire for misusing the tool. For the sake of clarity, I will explain the problem. We conducted an experiment measuring average response times in a cognitive task. The task has two types of stimuli (stim1, stim2) and was performed in a 6-run session, where subjects performed the task under condition A on odd-numbered runs and under condition B on even-numbered runs. Thus, the temporal sequence of the runs was the following: - run 1: cond A - run 2: cond B - run 3: cond A - run 4: cond B - run 5: cond A - run 6: cond B where for each run and for each subject, an average RT was collected for stim1 and for stim2. After collecting and plotting the data, an approximately linear decrease in RT from run1 to run6 was apparent in most subjects (practice effect: subjects become better and faster with time). Now, I am struggling with how to properly specify a model to perform the group analysis by taking into account this confounding practice effect, so that the real effects of interest (the main effect of condition, and the interaction of condition and stimulus type) can be better assessed. I used a dataframe in long format, with `subj', `rt' (response time), `stim' (stim1, stim2), `cond' (A, B), and `run' (1 to 6) as columns, where `run' is coded as an integer so that it can be used for modeling a linear trend. The R command I tried is: rt.aov - aov(rt ~ run + stim * cond + Error(subj /(run + stim * cond)), data=rt.df) but I am not at all sure that the error term is correctly specified. Furthermore, we have also collected data on an additional batch of subjects that performed the task in the 6-run session but with the order of conditions A and B reversed (A on even-numbered runs and B on odd-numbered runs); now, if we wanted to analyze the data from the two groups of subjects together, by including a between-subjects group factor (groupAB, groupBA), would the model specification become something like the following? rt.aov - aov(rt ~ run + group * stim * cond + Error(subj /(run + stim * cond)), data=rt.df) Perhaps should lme() be used instead (and with which formula?)? Many thanks in advance to anybody who'd be so kind to offer their advice or tip on this. I have scoured the web and some textbooks for a few days now, but to little avail. very best giuseppe -- Giuseppe Pagnoni Dip. Scienze Biomediche, Metaboliche e Neuroscienze Sezione Fisiologia e Neuroscienze Univ. di Modena e Reggio Emilia Via Campi 287 I-41125 Modena, Italy Tel: +39-059-205-5742 Fax: +39-059-205-5363 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Change case of factor in data frame
I am trying to write a function to change the case of all of the text in a
data frame to lower case. I do not have foreknowledge of the data frame
names or the data types of each column.
It seems that if one references the data frame by index, then it returns
class data.frame but if it is referenced by name, it returns class
factor or whatever the column actually is:
dat[1] returns class data.frame but
dat$name returns class factor
The problem is that, when one applies the tolower() and toupper() functions,
dat$name will return a column of lower/uppercase returns (now class
character) but dat[1] will return an array of factor level indexes.
Specifying dat[1] as.character during the function call does not work (e.g.
tolower(as.character(dat[1]))).
So, I would loop over the column names, but I can not figure out how to
generically call them:
tst=names(dat);
dat$(tst[1]) returns an error
dat[tst[1]] returns class data.frame again
Thank you in advance!
change_case-function(dat,wcase){
# change case
res=sapply(dat,class); # get classes
ind-res=='character';
dat[ind]-switch(wcase,
'lower'=tolower(dat[ind]),
'upper'=toupper(dat[ind])
)
rm(ind);
ind-res=='factor';
dat[ind]-switch(wcase,
'lower'=factor(tolower(as.character(dat[ind]))),
'upper'=factor(toupper(as.character(dat[ind])))
)
return(dat);
}
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[R] marginal structural modeling
Does anyone know an R package that implements marginal structural modeling as described by Jamie Robins? A similar question was asked of the list approximately two-years ago and it does not appear that anyone responded. Thanks, John Sorkin John David Sorkin M.D., Ph.D. Chief, Biostatistics and Informatics University of Maryland School of Medicine Division of Gerontology Baltimore VA Medical Center 10 North Greene Street GRECC (BT/18/GR) Baltimore, MD 21201-1524 (Phone) 410-605-7119 (Fax) 410-605-7913 (Please call phone number above prior to faxing) Confidentiality Statement: This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] simple subset question
Hi, From the ddply() output, you could get the whole row by: fish1 - structure(list(Year = 2002:2012, maxTotal = c(1464311L, 1071051L, 714837L, 2115018L, 850491L, 207537L, 321195L, 935599L, 194429L, 157260L, 303259L)), .Names = c(Year, maxTotal), row.names = c(NA, -11L), class = data.frame) fish[fish[,2]%in%fish1[,2][fish1[,1]==2012],] #fish (or winter) is your original dataset # IDWeek Total Fry Smolt FryEq Year #21 47 303259 34008 269248 491733 2012 A.K. From: Felipe Carrillo mazatlanmex...@yahoo.com To: William Dunlap wdun...@tibco.com; arun smartpink...@yahoo.com Cc: R help r-help@r-project.org Sent: Sunday, December 2, 2012 2:34 PM Subject: Re: [R] simple subset question Using my whole dataset I get: library(plyr) ddply(winter,Year,summarise,maxTotal=max(Total)) fish - structure(list(Year = 2002:2012, maxTotal = c(1464311L, 1071051L, 714837L, 2115018L, 850491L, 207537L, 321195L, 935599L, 194429L, 157260L, 303259L)), .Names = c(Year, maxTotal), row.names = c(NA, -11L), class = data.frame) I only want to extract the max Total for 2012 and want the whole row like this: IDWeek Total Fry Smolt FryEq Year 21 47 303259 34008 269248 491733 2012 My whole dataset is too big to post it so thanks for your help and will try to figure out why subset returns an empty row Felipe D. Carrillo Supervisory Fishery Biologist Department of the Interior US Fish Wildlife Service California, USA http://www.fws.gov/redbluff/rbdd_jsmp.aspx From: William Dunlap wdun...@tibco.com To: Felipe Carrillo mazatlanmex...@yahoo.com; arun smartpink...@yahoo.com Cc: R help r-help@r-project.org Sent: Sunday, December 2, 2012 11:00 AM Subject: RE: [R] simple subset question I am still getting an error message with : x - subset(fish,Year==2012 Total==max(Total));x I get: [1] IDWeek Total Fry Smolt FryEq Year 0 rows (or 0-length row.names) The above is not an error message. It says that there are no rows satisfying your criteria. Note that Total==max(Total) returns a TRUE for each row in which the Total value equals the maximum Total value over all the years in the data. Are you looking for the maximum value of Total in each year? tmp - transform(fish, YearlyMaxTotal = ave(Total, Year, FUN=max)) subset(tmp, Total==YearlyMaxTotal) IDWeek Total Fry Smolt FryEq Year YearlyMaxTotal 21 47 303259 34008 269248 491733 2012 303259 39 39 157260 156909 351 157506 2011 157260 subset(tmp, Total==YearlyMaxTotal Year==2012) IDWeek Total Fry Smolt FryEq Year YearlyMaxTotal 21 47 303259 34008 269248 491733 2012 303259 Bill Dunlap Spotfire, TIBCO Software wdunlap tibco.com -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Felipe Carrillo Sent: Sunday, December 02, 2012 10:47 AM To: arun Cc: R help Subject: Re: [R] simple subset question Works with the small dataset (2 years) but I get the error message with the whole dataset (12 years of data). I am going to have to check what's wrong with it...Thanks Felipe D. Carrillo Supervisory Fishery Biologist Department of the Interior US Fish Wildlife Service California, USA http://www.fws.gov/redbluff/rbdd_jsmp.aspx From: arun smartpink...@yahoo.com To: Felipe Carrillo mazatlanmex...@yahoo.com Cc: R help r-help@r-project.org; R. Michael Weylandt michael.weyla...@gmail.com Sent: Sunday, December 2, 2012 10:29 AM Subject: Re: [R] simple subset question Hi, I am getting this: x-subset(fish,Year==2012 Total==max(Total)) x # IDWeek Total Fry Smolt FryEq Year #21 47 303259 34008 269248 491733 2012 A.K. - Original Message - From: Felipe Carrillo mazatlanmex...@yahoo.com To: R. Michael Weylandt michael.weyla...@gmail.com Cc: r-help@r-project.org r-help@r-project.org Sent: Sunday, December 2, 2012 1:25 PM Subject: Re: [R] simple subset question Sorry, I was trying it to subset from a bigger dataset called 'winter' and forgot to change the variable names when I asked the question. David W suggestion works but the strange part is that I am still getting an error message with : x - subset(fish,Year==2012 Total==max(Total));x I get: [1] IDWeek Total Fry Smolt FryEq Year 0 rows (or 0-length row.names) I will start a fresh session to see if that helps...Thank you all Felipe D. Carrillo Supervisory Fishery Biologist Department of the Interior US Fish Wildlife Service California, USA http://www.fws.gov/redbluff/rbdd_jsmp.aspx From: R. Michael Weylandt michael.weyla...@gmail.com To: Felipe Carrillo mazatlanmex...@yahoo.com Cc: r-help@r-project.org r-help@r-project.org Sent: Sunday, December 2, 2012 9:42 AM Subject: Re: [R] simple subset question On Sun, Dec 2, 2012 at 5:21 PM, Felipe Carrillo mazatlanmex...@yahoo.com wrote: Hi, Consider the small dataset below, I want to subset by
Re: [R] Line numbers with errors and warnings?
Gentleman, This thread has been of great interest. Perhaps I missed part of it, but do far I have not seen an example of code that has line numbers that demonstrates how one can (in some instances) recover the line number of an error. Can I impose upon the people who contributed to this thread to post example code? The question if very important, and the discussion about solutions has been somewhat abstract to this point. Thank you, John John David Sorkin M.D., Ph.D. Chief, Biostatistics and Informatics University of Maryland School of Medicine Division of Gerontology Baltimore VA Medical Center 10 North Greene Street GRECC (BT/18/GR) Baltimore, MD 21201-1524 (Phone) 410-605-7119 (Fax) 410-605-7913 (Please call phone number above prior to faxing) Milan Bouchet-Valat nalimi...@club.fr 12/2/2012 4:00 PM Le dimanche 02 décembre 2012 à 14:21 -0500, Duncan Murdoch a écrit : On 12-12-02 9:52 AM, Milan Bouchet-Valat wrote: Le dimanche 02 décembre 2012 à 09:02 -0500, Duncan Murdoch a écrit : On 12-12-02 8:33 AM, Milan Bouchet-Valat wrote: Le dimanche 02 décembre 2012 à 06:02 -0500, Steve Lianoglou a écrit : Hi, On Sun, Dec 2, 2012 at 12:31 AM, Worik R wor...@gmail.com wrote: What I mean is how do I get the R compilation or execution process to spit out a line number with errors and warnings? Indeed, I often suffer from the same problem when debugging R code too. This is a real issue for me. As Duncan mentioned already, you can't *always* get a line number. You can, however, usually get enough context around the failing call for you to be able to smoke the problem out. What are the cases where you cannot get line numbers? Duncan said source()ed code comes with line numbers, but what's the more general rule? The general rule is that parse() needs to be called with the srcfile argument set to a srcfile object. source() does that by default. OK. But isn't it technically possible to compute a line number even when no source file is present? Yes, you don't really need to have a file present, you just need a srcfile object. For example, on Windows when you use source(clipboard), there's no file, just the system clipboard. If you call fix() on any function, you will get something like a source file even if srcfile was not set. Yes, and then you can call source on that object, and you'll get line number information attached, relative to whatever you sourced. So it could make sense to have a line number referring to what you would see in fix(). Or at least, the last executed line when calling browser() or when using options(error=recover), like gdb does. The thing is that if you didn't attach the line number information to the code, then it's not there. R can't figure out after the fact where the code came from. It needs to have the debug info in place when it runs it. How could R figure out where some expression came from that it happens to be executing? Using eval() on a constructed expression in a function is not all that uncommon, but to the evaluator, it looks just like any other evaluation. OK. This could be especially useful for packages that were not installed with keep.source=TRUE. It could even help getting more useful error messages on R-help... If you're debugging a package, then why not install it with keep.source=TRUE? Of course. I just wondered whether this step could possibly be avoided. It can be useful to have debugging details when casual users report a bug, without reinstalling the package. Not a big deal, though. Regards __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Confidentiality Statement: This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Line numbers with errors and warnings?
On 12-12-02 5:02 PM, John Sorkin wrote:
Gentleman,
This thread has been of great interest. Perhaps I missed part of it, but
do far I have not seen an example of code that has line numbers that
demonstrates how one can (in some instances) recover the line number of
an error. Can I impose upon the people who contributed to this thread to
post example code? The question if very important, and the discussion
about solutions has been somewhat abstract to this point.
From my post this morning:
For example, in Windows, if I put this code into the clipboard:
f - function() {
stop(this is the error)
}
g - function() {
f()
}
g()
then run source(clipboard) followed by traceback(), this is what I see:
source(clipboard)
Error in f() (from clipboard#2) : this is the error
traceback()
7: stop(this is the error) at clipboard#2
6: f() at clipboard#6
5: g() at clipboard#9
4: eval(expr, envir, enclos)
3: eval(ei, envir)
2: withVisible(eval(ei, envir))
1: source(clipboard)
You can ignore entries 1 to 4; they are part of source(). Entries 5, 6,
and 7 each tell the line of the script where they were parsed.
Duncan Murdoch
Thank you,
John
John David Sorkin M.D., Ph.D.
Chief, Biostatistics and Informatics
University of Maryland School of Medicine Division of Gerontology
Baltimore VA Medical Center
10 North Greene Street
GRECC (BT/18/GR)
Baltimore, MD 21201-1524
(Phone) 410-605-7119
(Fax) 410-605-7913 (Please call phone number above prior to faxing)
Milan Bouchet-Valat nalimi...@club.fr 12/2/2012 4:00 PM
Le dimanche 02 décembre 2012 à 14:21 -0500, Duncan Murdoch a écrit :
On 12-12-02 9:52 AM, Milan Bouchet-Valat wrote:
Le dimanche 02 décembre 2012 à 09:02 -0500, Duncan Murdoch a écrit :
On 12-12-02 8:33 AM, Milan Bouchet-Valat wrote:
Le dimanche 02 décembre 2012 à 06:02 -0500, Steve Lianoglou a écrit :
Hi,
On Sun, Dec 2, 2012 at 12:31 AM, Worik R wor...@gmail.com wrote:
What I mean is how do I get the R compilation or execution
process to spit
out a line number with errors and warnings?
Indeed, I often suffer from the same problem when debugging R
code too.
This is a real issue for me.
As Duncan mentioned already, you can't *always* get a line
number. You
can, however, usually get enough context around the failing call for
you to be able to smoke the problem out.
What are the cases where you cannot get line numbers? Duncan said
source()ed code comes with line numbers, but what's the more general
rule?
The general rule is that parse() needs to be called with the srcfile
argument set to a srcfile object. source() does that by default.
OK. But isn't it technically possible to compute a line number even
when
no source file is present?
Yes, you don't really need to have a file present, you just need a
srcfile object. For example, on Windows when you use
source(clipboard), there's no file, just the system clipboard.
If you call fix() on any function, you will
get something like a source file even if srcfile was not set.
Yes, and then you can call source on that object, and you'll get line
number information attached, relative to whatever you sourced.
So it
could make sense to have a line number referring to what you would see
in fix(). Or at least, the last executed line when calling browser() or
when using options(error=recover), like gdb does.
The thing is that if you didn't attach the line number information to
the code, then it's not there. R can't figure out after the fact where
the code came from. It needs to have the debug info in place when it
runs it. How could R figure out where some expression came from that it
happens to be executing? Using eval() on a constructed expression in a
function is not all that uncommon, but to the evaluator, it looks just
like any other evaluation.
OK.
This could be especially useful for packages that were not installed
with keep.source=TRUE. It could even help getting more useful error
messages on R-help...
If you're debugging a package, then why not install it with
keep.source=TRUE?
Of course. I just wondered whether this step could possibly be avoided.
It can be useful to have debugging details when casual users report a
bug, without reinstalling the package. Not a big deal, though.
Regards
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Re: [R] simple subset question
Actually, I dput(winter) and is not that big.so here is the whole thing I am trying to accomplish. winter - structure(list(IDWeek = c(27L, 28L, 29L, 30L, 31L, 32L, 33L, 34L, 35L, 36L, 37L, 38L, 39L, 40L, 41L, 42L, 43L, 44L, 45L, 46L, 47L, 48L, 49L, 50L, 51L, 52L, 27L, 28L, 29L, 30L, 31L, 32L, 33L, 34L, 35L, 36L, 37L, 38L, 39L, 40L, 41L, 42L, 43L, 44L, 45L, 46L, 47L, 48L, 49L, 50L, 51L, 52L, 27L, 28L, 29L, 30L, 31L, 32L, 33L, 34L, 35L, 36L, 37L, 38L, 39L, 40L, 41L, 42L, 43L, 44L, 45L, 46L, 47L, 48L, 49L, 50L, 51L, 52L, 27L, 28L, 29L, 30L, 31L, 32L, 33L, 34L, 35L, 36L, 37L, 38L, 39L, 40L, 41L, 42L, 43L, 44L, 45L, 46L, 47L, 48L, 49L, 50L, 51L, 52L, 27L, 28L, 29L, 30L, 31L, 32L, 33L, 34L, 35L, 36L, 37L, 38L, 39L, 40L, 41L, 42L, 43L, 44L, 45L, 46L, 47L, 48L, 49L, 50L, 51L, 52L, 27L, 28L, 29L, 30L, 31L, 32L, 33L, 34L, 35L, 36L, 37L, 38L, 39L, 40L, 41L, 42L, 43L, 44L, 45L, 46L, 47L, 48L, 49L, 50L, 51L, 52L, 27L, 28L, 29L, 30L, 31L, 32L, 33L, 34L, 35L, 36L, 37L, 38L, 39L, 40L, 41L, 42L, 43L, 44L, 45L, 46L, 47L, 48L, 49L, 50L, 51L, 52L, 27L, 28L, 29L, 30L, 31L, 32L, 33L, 34L, 35L, 36L, 37L, 38L, 39L, 40L, 41L, 42L, 43L, 44L, 45L, 46L, 47L, 48L, 49L, 50L, 51L, 52L, 27L, 28L, 29L, 30L, 31L, 32L, 33L, 34L, 35L, 36L, 37L, 38L, 39L, 40L, 41L, 42L, 43L, 44L, 45L, 46L, 47L, 48L, 49L, 50L, 51L, 52L, 27L, 28L, 29L, 30L, 31L, 32L, 33L, 34L, 35L, 36L, 37L, 38L, 39L, 40L, 41L, 42L, 43L, 44L, 45L, 46L, 47L, 48L, 49L, 50L, 51L, 52L, 27L, 28L, 29L, 30L, 31L, 32L, 33L, 34L, 35L, 36L, 37L, 38L, 39L, 40L, 41L, 42L, 43L, 44L, 45L, 46L, 47L, 48L, 49L, 50L, 51L, 52L), Total = c(0L, 0L, 326L, 1735L, 1807L, 2208L, 3883L, 8820L, 6060L, 19326L, 63158L, 100718L, 53015L, 91689L, 152629L, 122708L, 61293L, 15574L, 86538L, 75365L, 303259L, 19691L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 161L, 321L, 1000L, 4425L, 13202L, 19726L, 30518L, 84949L, 157260L, 145691L, 85801L, 62044L, 44439L, 23272L, 22391L, 20159L, 14854L, 35379L, 31142L, 7736L, 13221L, 4894L, 0L, 460L, 1129L, 1757L, 11105L, 27730L, 55769L, 12298L, 32964L, 80110L, 160507L, 74134L, 101736L, 138355L, 107873L, 53806L, 194429L, 7596L, 55497L, 30336L, 18392L, 22291L, 16850L, 16567L, 14799L, 7909L, 93L, 329L, 363L, 2762L, 5573L, 33466L, 96762L, 340947L, 612835L, 347972L, 526506L, 656981L, 344181L, 145465L, 150543L, 935599L, 32789L, 15092L, 7288L, 9889L, 6945L, 5138L, 6299L, 3095L, 108227L, 1191L, 0L, 0L, 132L, 227L, 2157L, 7558L, 16459L, 87220L, 321195L, 209299L, 110807L, 112024L, 128058L, 74373L, 41531L, 15111L, 21890L, 15060L, 22538L, 12443L, 11052L, 3907L, 2640L, 2745L, 3936L, 17593L, 0L, 0L, 10775L, 4166L, 4958L, 16221L, 29401L, 34951L, 33188L, 146044L, 105007L, 185297L, 159682L, 207537L, 140694L, 128275L, 44274L, 27079L, 18928L, 10437L, 29984L, 18395L, 25846L, 4573L, 31995L, 3679L, 707L, 2390L, 8860L, 24430L, 40885L, 72792L, 205521L, 344493L, 662973L, 526409L, 631953L, 850491L, 842678L, 445987L, 558152L, 332032L, 174326L, 80601L, 48696L, 98571L, 103563L, 149469L, 78081L, 182478L, 2158L, 16566L, 0L, 868L, 2044L, 4064L, 6049L, 9399L, 13304L, 45172L, 242155L, 476864L, 712534L, 1058409L, 2115018L, 1510342L, 1138213L, 333192L, 158820L, 94379L, 348882L, 39290L, 29701L, 47258L, 69837L, 7884L, 49338L, 22168L, 0L, 147L, 1231L, 3216L, 5021L, 18462L, 37441L, 64669L, 136590L, 338523L, 559448L, 714837L, 358037L, 180910L, 291943L, 222708L, 163801L, 39109L, 23247L, 15726L, 38701L, 5795L, 12509L, 18721L, 822L, 6674L, 765L, 1753L, 6226L, 9727L, 22033L, 50472L, 67863L, 100909L, 276699L, 239609L, 416465L, 845073L, 1071051L, 571656L, 409021L, 451331L, 167006L, 68069L, 250439L, 104641L, 76062L, 35261L, 55883L, 16064L, 11058L, 8872L, 9346L, 24760L, 41699L, 40032L, 80576L, 152208L, 171888L, 292862L, 522669L, 441518L, 858538L, 906010L, 1464311L, 1334433L, 542204L, 211514L, 64507L, 94830L, 100663L, 116931L, 83139L, 46268L, 14455L, 22811L, 47446L, 54224L), Fry = c(0L, 0L, 326L, 1735L, 1807L, 2208L, 3883L, 8759L, 6060L, 19326L, 63119L, 100524L, 52582L, 88170L, 145564L, 111416L, 38233L, 5248L, 17826L, 11038L, 34008L, 215L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 161L, 321L, 1000L, 4425L, 13055L, 19488L, 30518L, 84818L, 156909L, 144786L, 84207L, 57720L, 31049L, 6858L, 1616L, 719L, 364L, 49L, 0L, 0L, 0L, 0L, 0L, 460L, 1129L, 1757L, 11105L, 27730L, 55769L, 12109L, 32638L, 79547L, 158892L, 72867L, 96249L, 130695L, 88837L, 32531L, 65746L, 1885L, 4188L, 680L, 100L, 109L, 0L, 0L, 0L, 0L, 93L, 329L, 363L, 2762L, 5573L, 33466L, 96694L, 339394L, 611967L, 345807L, 522991L, 645886L, 327353L, 118537L, 109158L, 419571L, 6691L, 456L, 133L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 132L, 227L, 2157L, 7558L, 16459L, 87220L, 320684L, 207921L, 110221L, 110021L, 123153L, 63829L, 23982L, 5090L, 4183L, 374L, 439L, 78L, 67L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 10775L, 4166L, 4958L, 16221L, 29401L, 34851L, 32933L, 145103L, 105007L, 182715L, 153781L, 201622L, 129968L, 87997L, 17235L, 3401L, 1343L, 397L, 316L, 37L, 0L, 0L, 0L, 0L, 707L, 2390L, 8860L, 24430L, 40885L, 72792L, 205521L, 343593L, 658875L, 523360L, 627333L, 847147L, 837189L, 429016L, 523436L,
[R] Problem with figures
I am having problem making ggplot2, tikzDevice, and knitr working together.
I used a very simple example:
---example.Rnw-
\documentclass[preview]{standalone}
\begin{document}
\begin{figure}
fig1,eval=TRUE,echo=FALSE,dev='tikz'=
library(ggplot2)
qplot(displ, hwy, data = mpg, colour = factor(cyl))
@
\end{figure}
\end{document}
-
I got ... ! == Fatal error occurred, no output PDF file produced!
label: fig1 (with options)
List of 3
$ eval: logi TRUE
$ echo: logi FALSE
$ dev : chr tikz
Error in process_file(text, output) :
Quitting from lines 6-8: (test_Rnw.Rnw) Error in
getMetricsFromLatex(TeXMetrics) :
TeX was unable to calculate metrics for the following string
or character:
hwy
Common reasons for failure include:
* The string contains a character which is special to LaTeX unless
escaped properly, such as % or $.
* The string makes use of LaTeX commands provided by a package and
the tikzDevice was not told to load the package.
The contents of the LaTeX log of the aborted run have been printed above,
it may contain additional details as to why the metric calculation failed.
Calls: knit - process_file
Execution halted
Best,
Shige
[[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] Line numbers with errors and warnings?
Similar to Duncan's example, if you have a script test.R which looks like so:
start script =
a1 - 1:10
a2 - 101:122
plot(a1, a1)
plot(a1, a2)
end script ==
You can source it one way:
R source('test.R', keep.source=TRUE)
Error in xy.coords(x, y, xlabel, ylabel, log) :
'x' and 'y' lengths differ
R traceback()
8: stop('x' and 'y' lengths differ)
7: xy.coords(x, y, xlabel, ylabel, log)
6: plot.default(a1, a2)
5: plot(a1, a2) at test.R#4 ### - Error is on line 4
4: eval(expr, envir, enclos)
3: eval(ei, envir)
2: withVisible(eval(ei, envir))
1: source(test.R, keep.source = TRUE)
If you `source(test.R, keep.source=FALSE)`, you will see that the
line number is not reported.
Also:
R library(devtools)
R options(keep.source=TRUE)
R install_github(BadPackage, lianos)
R plot.me(1:10)
Error in xy.coords(x, y, xlabel, ylabel, log) :
'x' and 'y' lengths differ
R traceback()
5: stop('x' and 'y' lengths differ)
4: xy.coords(x, y, xlabel, ylabel, log)
3: plot.default(x, c(x, 0), pch = 16)
2: plot(x, c(x, 0), pch = 16) at test.R#4 - BAM
1: plot.me(1:10)
HTH,
-steve
On Sun, Dec 2, 2012 at 5:08 PM, Duncan Murdoch murdoch.dun...@gmail.com wrote:
On 12-12-02 5:02 PM, John Sorkin wrote:
Gentleman,
This thread has been of great interest. Perhaps I missed part of it, but
do far I have not seen an example of code that has line numbers that
demonstrates how one can (in some instances) recover the line number of
an error. Can I impose upon the people who contributed to this thread to
post example code? The question if very important, and the discussion
about solutions has been somewhat abstract to this point.
From my post this morning:
For example, in Windows, if I put this code into the clipboard:
f - function() {
stop(this is the error)
}
g - function() {
f()
}
g()
then run source(clipboard) followed by traceback(), this is what I see:
source(clipboard)
Error in f() (from clipboard#2) : this is the error
traceback()
7: stop(this is the error) at clipboard#2
6: f() at clipboard#6
5: g() at clipboard#9
4: eval(expr, envir, enclos)
3: eval(ei, envir)
2: withVisible(eval(ei, envir))
1: source(clipboard)
You can ignore entries 1 to 4; they are part of source(). Entries 5, 6,
and 7 each tell the line of the script where they were parsed.
Duncan Murdoch
Thank you,
John
John David Sorkin M.D., Ph.D.
Chief, Biostatistics and Informatics
University of Maryland School of Medicine Division of Gerontology
Baltimore VA Medical Center
10 North Greene Street
GRECC (BT/18/GR)
Baltimore, MD 21201-1524
(Phone) 410-605-7119
(Fax) 410-605-7913 (Please call phone number above prior to faxing)
Milan Bouchet-Valat nalimi...@club.fr 12/2/2012 4:00 PM
Le dimanche 02 décembre 2012 à 14:21 -0500, Duncan Murdoch a écrit :
On 12-12-02 9:52 AM, Milan Bouchet-Valat wrote:
Le dimanche 02 décembre 2012 à 09:02 -0500, Duncan Murdoch a écrit :
On 12-12-02 8:33 AM, Milan Bouchet-Valat wrote:
Le dimanche 02 décembre 2012 à 06:02 -0500, Steve Lianoglou a écrit
:
Hi,
On Sun, Dec 2, 2012 at 12:31 AM, Worik R wor...@gmail.com wrote:
What I mean is how do I get the R compilation or execution
process to spit
out a line number with errors and warnings?
Indeed, I often suffer from the same problem when debugging R
code too.
This is a real issue for me.
As Duncan mentioned already, you can't *always* get a line
number. You
can, however, usually get enough context around the failing call
for
you to be able to smoke the problem out.
What are the cases where you cannot get line numbers? Duncan said
source()ed code comes with line numbers, but what's the more
general
rule?
The general rule is that parse() needs to be called with the
srcfile
argument set to a srcfile object. source() does that by default.
OK. But isn't it technically possible to compute a line number even
when
no source file is present?
Yes, you don't really need to have a file present, you just need a
srcfile object. For example, on Windows when you use
source(clipboard), there's no file, just the system clipboard.
If you call fix() on any function, you will
get something like a source file even if srcfile was not set.
Yes, and then you can call source on that object, and you'll get line
number information attached, relative to whatever you sourced.
So it
could make sense to have a line number referring to what you would
see
in fix(). Or at least, the last executed line when calling browser()
or
when using options(error=recover), like gdb does.
The thing is that if you didn't attach the line number information to
the code, then it's not there. R can't figure out after the fact where
the code came from. It needs to have the debug info in place when it
runs it. How could R figure out where some expression came from that
it
happens to
Re: [R] simple subset question
As David W. guessed. The maximum is in year 2005 not 2012 so no row from 2012 matches the maximum. subset(winter,Year==2012 Total==max(Total)) [1] IDWeek Total FrySmolt FryEq Year 0 rows (or 0-length row.names) winter[which(winter$Total==max(winter$Total)),] IDWeek Total Fry Smolt FryEq Year 195 39 2115018 2083214 31805 2137281 2005 Change to subset(winter, Year==2012 Total==max(Total[Year==2012])) IDWeek Total Fry Smolt FryEq Year 21 47 303259 34008 269248 491733 2012 -- David L Carlson Associate Professor of Anthropology Texas AM University College Station, TX 77843-4352 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-bounces@r- project.org] On Behalf Of Felipe Carrillo Sent: Sunday, December 02, 2012 4:40 PM To: arun Cc: R help Subject: Re: [R] simple subset question Actually, I dput(winter) and is not that big.so here is the whole thing I am trying to accomplish. winter - structure(list(IDWeek = c(27L, 28L, 29L, 30L, 31L, 32L, 33L, 34L, 35L, 36L, 37L, 38L, 39L, 40L, 41L, 42L, 43L, 44L, 45L, 46L, 47L, 48L, 49L, 50L, 51L, 52L, 27L, 28L, 29L, 30L, 31L, 32L, 33L, 34L, 35L, 36L, 37L, 38L, 39L, 40L, 41L, 42L, 43L, 44L, 45L, 46L, 47L, 48L, 49L, 50L, 51L, 52L, 27L, 28L, 29L, 30L, 31L, 32L, 33L, 34L, 35L, 36L, 37L, 38L, 39L, 40L, 41L, 42L, 43L, 44L, 45L, 46L, 47L, 48L, 49L, 50L, 51L, 52L, 27L, 28L, 29L, 30L, 31L, 32L, 33L, 34L, 35L, 36L, 37L, 38L, 39L, 40L, 41L, 42L, 43L, 44L, 45L, 46L, 47L, 48L, 49L, 50L, 51L, 52L, 27L, 28L, 29L, 30L, 31L, 32L, 33L, 34L, 35L, 36L, 37L, 38L, 39L, 40L, 41L, 42L, 43L, 44L, 45L, 46L, 47L, 48L, 49L, 50L, 51L, 52L, 27L, 28L, 29L, 30L, 31L, 32L, 33L, 34L, 35L, 36L, 37L, 38L, 39L, 40L, 41L, 42L, 43L, 44L, 45L, 46L, 47L, 48L, 49L, 50L, 51L, 52L, 27L, 28L, 29L, 30L, 31L, 32L, 33L, 34L, 35L, 36L, 37L, 38L, 39L, 40L, 41L, 42L, 43L, 44L, 45L, 46L, 47L, 48L, 49L, 50L, 51L, 52L, 27L, 28L, 29L, 30L, 31L, 32L, 33L, 34L, 35L, 36L, 37L, 38L, 39L, 40L, 41L, 42L, 43L, 44L, 45L, 46L, 47L, 48L, 49L, 50L, 51L, 52L, 27L, 28L, 29L, 30L, 31L, 32L, 33L, 34L, 35L, 36L, 37L, 38L, 39L, 40L, 41L, 42L, 43L, 44L, 45L, 46L, 47L, 48L, 49L, 50L, 51L, 52L, 27L, 28L, 29L, 30L, 31L, 32L, 33L, 34L, 35L, 36L, 37L, 38L, 39L, 40L, 41L, 42L, 43L, 44L, 45L, 46L, 47L, 48L, 49L, 50L, 51L, 52L, 27L, 28L, 29L, 30L, 31L, 32L, 33L, 34L, 35L, 36L, 37L, 38L, 39L, 40L, 41L, 42L, 43L, 44L, 45L, 46L, 47L, 48L, 49L, 50L, 51L, 52L), Total = c(0L, 0L, 326L, 1735L, 1807L, 2208L, 3883L, 8820L, 6060L, 19326L, 63158L, 100718L, 53015L, 91689L, 152629L, 122708L, 61293L, 15574L, 86538L, 75365L, 303259L, 19691L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 161L, 321L, 1000L, 4425L, 13202L, 19726L, 30518L, 84949L, 157260L, 145691L, 85801L, 62044L, 44439L, 23272L, 22391L, 20159L, 14854L, 35379L, 31142L, 7736L, 13221L, 4894L, 0L, 460L, 1129L, 1757L, 11105L, 27730L, 55769L, 12298L, 32964L, 80110L, 160507L, 74134L, 101736L, 138355L, 107873L, 53806L, 194429L, 7596L, 55497L, 30336L, 18392L, 22291L, 16850L, 16567L, 14799L, 7909L, 93L, 329L, 363L, 2762L, 5573L, 33466L, 96762L, 340947L, 612835L, 347972L, 526506L, 656981L, 344181L, 145465L, 150543L, 935599L, 32789L, 15092L, 7288L, 9889L, 6945L, 5138L, 6299L, 3095L, 108227L, 1191L, 0L, 0L, 132L, 227L, 2157L, 7558L, 16459L, 87220L, 321195L, 209299L, 110807L, 112024L, 128058L, 74373L, 41531L, 15111L, 21890L, 15060L, 22538L, 12443L, 11052L, 3907L, 2640L, 2745L, 3936L, 17593L, 0L, 0L, 10775L, 4166L, 4958L, 16221L, 29401L, 34951L, 33188L, 146044L, 105007L, 185297L, 159682L, 207537L, 140694L, 128275L, 44274L, 27079L, 18928L, 10437L, 29984L, 18395L, 25846L, 4573L, 31995L, 3679L, 707L, 2390L, 8860L, 24430L, 40885L, 72792L, 205521L, 344493L, 662973L, 526409L, 631953L, 850491L, 842678L, 445987L, 558152L, 332032L, 174326L, 80601L, 48696L, 98571L, 103563L, 149469L, 78081L, 182478L, 2158L, 16566L, 0L, 868L, 2044L, 4064L, 6049L, 9399L, 13304L, 45172L, 242155L, 476864L, 712534L, 1058409L, 2115018L, 1510342L, 1138213L, 333192L, 158820L, 94379L, 348882L, 39290L, 29701L, 47258L, 69837L, 7884L, 49338L, 22168L, 0L, 147L, 1231L, 3216L, 5021L, 18462L, 37441L, 64669L, 136590L, 338523L, 559448L, 714837L, 358037L, 180910L, 291943L, 222708L, 163801L, 39109L, 23247L, 15726L, 38701L, 5795L, 12509L, 18721L, 822L, 6674L, 765L, 1753L, 6226L, 9727L, 22033L, 50472L, 67863L, 100909L, 276699L, 239609L, 416465L, 845073L, 1071051L, 571656L, 409021L, 451331L, 167006L, 68069L, 250439L, 104641L, 76062L, 35261L, 55883L, 16064L, 11058L, 8872L, 9346L, 24760L, 41699L, 40032L, 80576L, 152208L, 171888L, 292862L, 522669L, 441518L, 858538L, 906010L, 1464311L, 1334433L, 542204L, 211514L, 64507L, 94830L, 100663L, 116931L, 83139L, 46268L, 14455L, 22811L, 47446L, 54224L), Fry = c(0L, 0L, 326L, 1735L, 1807L, 2208L, 3883L, 8759L, 6060L, 19326L, 63119L, 100524L, 52582L, 88170L, 145564L, 111416L, 38233L, 5248L, 17826L, 11038L, 34008L, 215L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
[R] Object Browser
Dear all, I have tried all the popular R IDE or editors like Eclipse, Komodo, JGR, Revolution... They all have fancy fucntions like auto completion, syntax highlight BUT, I JUST WANT A OBJECT BROWSER! The easiest way to view objects in R console is fix(), but you have no global view of all the objects in the workspace. Revolution has the best object browser so far, but this thing is way too big... Eclipse all has automatically object browser, but you can't only see the basic summary info. and it's really tricky to configure StatET. Jgr is very handy, when you double click the object name, you can view the object in a spreadsheet like using fix(), but you have to press the Refresh button each time you want to see the updated objects... So, is there any thing like the combination of eclipse and Jgr? If not, I am interested to develope something to fulfill this simple but very important function. But right now I have no idea where to start. Any suggestions? Peter - TO GET MORE DETAILS CLICK HERE -- View this message in context: http://r.789695.n4.nabble.com/Object-Browser-tp4651647.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Can you turn a string into a (working) symbol?
Dear folks--
Suppose I have an expression that evaluates to a string, and that that
string, were it not a character vector, would be a symbol. I would like a
function, call it doppel(), that will take that expression as an argument
and produce something that functions exactly like the symbol would have if I
typed it in the place of the function of the expression. It should go as
far along the path to evaluation as the symbol would have, and then stop,
and be available for subsequent manipulation. For example, if
aa - 3.1416
bb - function(x) {x^2}
r - 2
xx - c(aa, bb)
out - doppel(xx[1])*doppel(xx[2])(r)
Then out should be 13.3664
Or similarly, after
doppel(paste(a, a, sep='')) - 3
aa
typing aa should return 3.
Is there such a function? Can there be?
I thought as.symbol would do this, but it does not.
as.symbol (xx[1])*as.symbol (xx[2])(r)
Error: attempt to apply non-function
-
--
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and provide commented, minimal, self-contained, reproducible code.
[R] Conjoint Analysis in R??
Pls advise how I can use R in conjoint analysis?? regds Faisal Afzal Siddiqui Karachi, Pakistan Looking for last minute shopping deals? - TO GET MORE DETAILS CLICK HERE -- View this message in context: http://r.789695.n4.nabble.com/Conjoint-Analysis-in-R-tp4651650.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] postForm() in RCurl and library RHTMLForms
Hi RUsers, Suppose I want to see the data on the website url - http://www.nseindia.com/content/indices/ind_histvalues.htm; for the index SP CNX NIFTY for dates FromDate=01-11-2010,ToDate=02-11-2010 then read the html table from the page using readHTMLtable() I am using this code webpage - postForm(url,.params=list( FromDate=01-11-2010, ToDate=02-11-2010, IndexType=SP CNX NIFTY, Indicesdata=Get Details), .opts=list(useragent = getOption(HTTPUserAgent))) But it doesn't give me desired result Also I was trying to use the function getHTMLFormDescription from the package RHTMLForms but there we can't use the argument .opts=list(useragent = getOption(HTTPUserAgent)) which is needed for this particular website - TO GET MORE DETAILS CLICK HERE -- View this message in context: http://r.789695.n4.nabble.com/postForm-in-RCurl-and-library-RHTMLForms-tp4651655.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] Stepwise analysis with fixed variables
Hello, How can I run a backward stepwise regression with part of the variables fixed, while the others participate in the backward stepwise analysis? Thank you - TO GET MORE DETAILS CLICK HERE -- View this message in context: http://r.789695.n4.nabble.com/Stepwise-analysis-with-fixed-variables-tp4651636.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] Reading PDF files
I need to do text mining on PDF files. I understand there is a readPDF command in tm that can be used. Have read the 2008 posts on converting PDF files to text by Tony Breyal and others. Wondering if the procedure has been standardized in any tutorial or otherwise? Being new to R, I was able to follow only part of the discussion. Any way to get a set of step by step instructions appropriate for my level? I am an ageing academic who has worked mostly with SAS and MATLAB. - TO GET MORE DETAILS CLICK HERE -- View this message in context: http://r.789695.n4.nabble.com/Reading-PDF-files-tp4651657.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] Problems with nls
I'm trying to fit the Bass Diffusion Model using the nls function in R but I'm running into a strange problem. The model has either two or three parameters, depending on how it's parameterized, p (coefficient of innovation), q (coefficient of immitation), and sometimes m (maximum market share). Regardless of how I parameterize the model I get an error saying that the step factor has decreased below it's minimum. I have tried re-setting the minimum in nls.controls but that doesn't seem to fix the problem. Likewise, I have run through a variety of start values in the past few days, all to no avail. Looking at the trace output it appears that R believes I always have one more parameter than I actually have (i.e. when the model is parameterized with p and q R seems to be seeing three parameters, when m is also included R seems to be seeing four). My experience with nls is limited, can someone explain to me why it's doing this? I've included the data set I'm working with (published in Michalakelis et al. 2008) and some example code. ## Assign relevant variables adoption - c(167000,273000,531000,938000,2056452,3894103,5932090,7963742,9314687,10469060,11393302,11976340) time - seq(from = 1,to = 12, by = 1) ## Models Bass.Model - adoption ~ ((p + q)^2/p) * (exp(-(p + q) * time)/((q / p) * exp(-(p + q) * time) + 1)^2) ## Starting Parameters Bass.Params - list(p = 0.1, q = 0.1) ## Model fitting - TO GET MORE DETAILS CLICK HERE -- View this message in context: http://r.789695.n4.nabble.com/Problems-with-nls-tp4651641.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] postForm() in RCurl and library RHTMLForms
Hi RUsers, Suppose I want to see the data on the website url - http://www.nseindia.com/content/indices/ind_histvalues.htm; for the index SP CNX NIFTY for dates FromDate=01-11-2010,ToDate=02-11-2010 then read the html table from the page using readHTMLtable() I am using this code webpage - postForm(url,.params=list( FromDate=01-11-2010, ToDate=02-11-2010, IndexType=SP CNX NIFTY, Indicesdata=Get Details), .opts=list(useragent = getOption(HTTPUserAgent))) But it doesn't give me desired result Also I was trying to use the function getHTMLFormDescription from the package RHTMLForms but there we can't use the argument .opts=list(useragent = getOption(HTTPUserAgent)) which is needed for this particular website Thanks and Regard - TO GET MORE DETAILS CLICK HERE -- View this message in context: http://r.789695.n4.nabble.com/postForm-in-RCurl-and-library-RHTMLForms-tp4651644.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] Sullivan, Timmerman and White 1999: TA rules, and R
Friends I am trying to save myself some tedious work. I am processing a paper from The Journal Of Finance * Vol. LIV, No. 5 October 1999 by Sullivan, Timmerman and White. Data-Snooping, Technical Trading Rule Performance, and the Bootstrap I am aiming to reproduce their results using the same TA rules as they used. They describe the rules they use in English and I am in the process of trying to programme them into R. But if some one has already done this it would save me a pile of work. It would be nice to just grab some rules from the TTR package, but because of the way STW describe the rules it is quite a lot of work to calculate what parameters to use. So I am clutching at a straw here: If anybody could point me in a better direction than slogging through the English text and trying to match that with the TTR docs I would be grateful cheers - TO GET MORE DETAILS CLICK HERE -- View this message in context: http://r.789695.n4.nabble.com/Sullivan-Timmerman-and-White-1999-TA-rules-and-R-tp4651658.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] e1071 SVM: Cross-validation error confusion matrix
Hi, I ran two svm models in R e1071 package: the first without cross-validation and the second with 10-fold cross-validation. I used the following syntax: #Model 1: Without cross-validation: svm.model - svm(Response ~ ., data=data.df, type=C-classification, kernel=linear, cost=1) predict - fitted(svm.model) cm - table(predict, data.df$Response) cm #Model2: With 10-fold cross-validation: svm.model2 - svm(Response ~ ., data=data.df, type=C-classification, kernel=linear, cost=1, cross=10) predict2 - fitted(svm.model2) cm2 - table(predict2, data.df$Response) cm2 However, when I compare cm and cm2, I notice that the confusion matrices are identical although the accuracy of each model is diffent. What am I doing wrong? Thanks for you help, - TO GET MORE DETAILS CLICK HERE -- View this message in context: http://r.789695.n4.nabble.com/e1071-SVM-Cross-validation-error-confusion-matrix-tp4651652.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] Problems of metafile plots when converting word to pdf file
Hi all, I copy metafile boxplot from R to Word. Then save as Pdf file. But I found there are some unexpected black lines in some plots within this PDF file. Please give me some advice how to get rid of these black lines in PDF files. Thanks a lot, Jim - TO GET MORE DETAILS CLICK HERE -- View this message in context: http://r.789695.n4.nabble.com/Problems-of-metafile-plots-when-converting-word-to-pdf-file-tp4651659.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] RMySQL install on windows
I have been trying to install RMySQL on Windows 7 following the procedure at: http://biostat.mc.vanderbilt.edu/wiki/Main/RMySQL I think I have properly installed RTools and created a proper Renviron.site file saying: MYSQL_HOME=C:/Program Files/MySQL/MySQL Server 5.5 When I try to install the packages from source, I get warnings that suggest I'm still not quite with the program yet. There are comments about POSIX paths that I don't quite grasp. Can anyone give me additional hints? There seems to be a libmysql.dll in the /lib subdirectory although the install seems to be looking in the /bin directory for a file of similar name. Is this something that has changed with recent versions of MySQL that should be fixed in the RMySQL package or is it something I can work around by hand or by properly setting some environmental variable? Thanks, - -- View this message in context: http://r.789695.n4.nabble.com/RMySQL-install-on-windows-tp4651660.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] Object Browser
What's the best object browser? Dear all, I have tried all the popular R IDE or editors like Eclipse, Komodo, JGR, Revolution... They all have fancy fucntions like auto completion, syntax highlight BUT, I JUST WANT A OBJECT BROWSER! The easiest way to view objects in R console is fix(), but you have no global view of all the objects in the workspace. Revolution has the best object browser so far, but this thing is way too big... Eclipse all has automatically object browser, but you can't only see the basic summary info. and it's really tricky to configure StatET. Jgr is very handy, when you double click the object name, you can view the object in a spreadsheet like using fix(), but you have to press the Refresh button each time you want to see the updated objects... So, is there any thing like the combination of eclipse and Jgr? If not, I am interested to develope something to fulfill this simple but very important function. But right now I have no idea where to start. Any suggestions? - TO GET MORE DETAILS CLICK HERE -- View this message in context: http://r.789695.n4.nabble.com/Object-Browser-tp4651654.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] Linking C/C++ GUI to R.dll
Hi, I am in the process of linking a C/C++ application to the R.dll directly. I have obtained the R source code and compiled it successfully. I have also successfully linked the R.dll directly into our application and have made calls successfully into the R.dll that are included in the sample rtest.c and in the Writing R Extensions - The R API. The R functionality that we are interested in embedding into our application is the data analysis and graphics. However, I did not see any references to this in the R API section of the documentation. Is this functionality available from our C/C++ application via the R.dll? If so, how do we access this functionality? Thank you, - TO GET MORE DETAILS CLICK HERE -- View this message in context: http://r.789695.n4.nabble.com/Linking-C-C-GUI-to-R-dll-tp4651661.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] Sullivan, Timmerman and White 1999: TA rules, and R
Friends I am trying to save myself some tedious work. I am processing a paper from The Journal Of Finance * Vol. LIV, No. 5 October 1999 by Sullivan, Timmerman and White. Data-Snooping, Technical Trading Rule Performance, and the Bootstrap I am aiming to reproduce their results using the same TA rules as they used. They describe the rules they use in English and I am in the process of trying to programme them into R. But if some one has already done this it would save me a pile of work. It would be nice to just grab some rules from the TTR package, but because of the way STW describe the rules it is quite a lot of work to calculate what parameters to use. So I am clutching at a straw here: If anybody could point me in a better direction than slogging through the English text and trying to match that with the TTR docs I would be grateful - TO GET MORE DETAILS CLICK HERE -- View this message in context: http://r.789695.n4.nabble.com/Sullivan-Timmerman-and-White-1999-TA-rules-and-R-tp4651656.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] residual and null deviance of an lme object with correlation structure
Hello, I am attempting to calculate the residual and null deviance of an lme object that includes a corAR1 correlation structure. I tried deviance(lme.object) and it only returned NULL. Can anyone help? Thank you. - TO GET MORE DETAILS CLICK HERE -- View this message in context: http://r.789695.n4.nabble.com/residual-and-null-deviance-of-an-lme-object-with-correlation-structure-tp4651662.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] finding index of maximum value in vector
I found: max.col(matrix(c(1,3,2),nrow=1)) Is there a more concise/elegant way? Thanks, - TO GET MORE DETAILS CLICK HERE -- View this message in context: http://r.789695.n4.nabble.com/finding-index-of-maximum-value-in-vector-tp4651663.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] Fitting binomial lmer-model, high deviance and low logLik
Hello I have a problem when fitting a mixed generalised linear model with the lmer-function in the Matrix package, version 0.98-7. I have a respons variable (sfox) that is 1 or 0, whether a roe deer fawn is killed or not by red fox. This is expected to be related to e.g. the density of red fox (roefoxratio) or other variables. In addition, we account for family effects by adding the mother (fam) of the fawns as random factor. I want to use AIC to select the best model (if no other model selection criterias are suggested). the syntax looks like this: mod - lmer(sfox ~ roefoxratio + (1|fam), data=manu2, family=binomial) The output looks ok, except that the deviance is extremely high (1.798e+308). mod Generalized linear mixed model fit using PQL Formula: sfox ~ roefoxratio + (1 | fam) Data: manu2 Family: binomial(logit link) AIC BIC logLik deviance 1.797693e+308 1.797693e+308 -8.988466e+307 1.797693e+308 Random effects: GroupsNameVarianceStd.Dev. fam (Intercept) 17.149 4.1412 # of obs: 128, groups: fam, 58 Estimated scale (compare to 1) 0.5940245 - TO GET MORE DETAILS CLICK HERE -- View this message in context: http://r.789695.n4.nabble.com/Fitting-binomial-lmer-model-high-deviance-and-low-logLik-tp4651668.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] Hmisc latex cell background color
Dear latex/R-Sweavers,
Using the codel below, I can color text in individual cells for latex
output.
Is there a similar way to get a background shading? My attempts failed
because I did not get the closing brace at the right place with Hmisc/latex.
library(Hmisc)
x - as.data.frame(diag(rnorm(3),nrow=3))
cellTex - matrix(rep(, NROW(x) * NCOL(x)), nrow=NROW(x))
cellTex[2,2] - \color{red}
ct - latex(x, cellTexCmds = cellTex,numeric.dollar=FALSE)
ct$style - color
dvi(ct)
-
TO GET MORE DETAILS CLICK HERE
--
View this message in context:
http://r.789695.n4.nabble.com/Hmisc-latex-cell-background-color-tp4651664.html
Sent from the R help mailing list archive at Nabble.com.
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] Kalman Filter Forecast using 'SSPIR'
Dear R Users, I am new to state-space modeling. I am using SSPIR package for Kalman Filter. I have a data set containing one dependent variable and 7 independent variables with 250 data points. I want to use Kalman Filter for forecast the future values of the dependent variable using a multiple regression framework. I have used ssm function to produce the state space (SS) object, but I am bit confused that how can I predict the future values. Thanks a lot in advance. - TO GET MORE DETAILS CLICK HERE -- View this message in context: http://r.789695.n4.nabble.com/Kalman-Filter-Forecast-using-SSPIR-tp4651666.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] Fitting binomial lmer-model, high deviance and low logLik
Hello I have a problem when fitting a mixed generalised linear model with the lmer-function in the Matrix package, version 0.98-7. I have a respons variable (sfox) that is 1 or 0, whether a roe deer fawn is killed or not by red fox. This is expected to be related to e.g. the density of red fox (roefoxratio) or other variables. In addition, we account for family effects by adding the mother (fam) of the fawns as random factor. I want to use AIC to select the best model (if no other model selection criterias are suggested). the syntax looks like this: mod - lmer(sfox ~ roefoxratio + (1|fam), data=manu2, family=binomial) The output looks ok, except that the deviance is extremely high (1.798e+308). mod Generalized linear mixed model fit using PQL Formula: sfox ~ roefoxratio + (1 | fam) Data: manu2 Family: binomial(logit link) AIC BIC logLik deviance 1.797693e+308 1.797693e+308 -8.988466e+307 1.797693e+308 Random effects: GroupsNameVarianceStd.Dev. fam (Intercept) 17.149 4.1412 # of obs: 128, groups: fam, 58 Estimated scale (compare to 1) 0.5940245 - TO GET MORE DETAILS CLICK HERE -- View this message in context: http://r.789695.n4.nabble.com/Fitting-binomial-lmer-model-high-deviance-and-low-logLik-tp4651669.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] How to simulate correlated data
Hello there, I would like to simulate X --Normal (20, 5) Y-- Normal (40, 10) and the correlation between X and Y is 0.6. How do I do it in R? Thank you very much - TO GET MORE DETAILS CLICK HERE -- View this message in context: http://r.789695.n4.nabble.com/How-to-simulate-correlated-data-tp4651667.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] concatenating expressions and standard text
Hi all, is it possible to concatenate expressions and basic text when for instance labeling axis of a plot? I would like to see something like the concatenation of expression(C[0]) and for case 1 on my x axis. Obviously a plot(x, y, xlab=paste(expression(C[0]), in case1)) will not work. Thank you in advance, - TO GET MORE DETAILS CLICK HERE -- View this message in context: http://r.789695.n4.nabble.com/concatenating-expressions-and-standard-text-tp4651670.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] superimpose density line over hist
Romain == Romain Francois [hidden email] on Tue, 13 Dec 2005 15:40:59 +0100 writes: Romain A few comments : Romain - your code should be reproductible, otherwise it is useless. (that Romain recommandation is on the posting guide) Romain - that question is a top ten question on that list, go to the archive Romain and you will find answers. (also posting guide) Romain BTW, it should be a FAQ and what about an example of overlaying in hist Romain help page ? What about the following one --- do also note the comments though! set.seed(14) x - rchisq(100, df = 4) ## Comparing data with a model distribution should be done with qqplot()! qqplot(x, qchisq(ppoints(x), df = 4)); abline(0,1, col = 2, lty = 2) ## if you really insist on using hist() ... : hist(x, prob = TRUE, ylim = c(0, 0.2)) curve(dchisq(x, df = 4), col = 2, lty = 2, lwd = 2, add = TRUE) - TO GET MORE DETAILS CLICK HERE -- View this message in context: http://r.789695.n4.nabble.com/Re-superimpose-density-line-over-hist-tp4651671.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Labeling a range of bars in barplot?
Marc Schwartz (via MN) wrote: On Tue, 2005-12-13 at 10:53 +, Dan Bolser wrote: Hi, I am plotting a distribution of (ordered) values as a barplot. I would like to label groups of bars together to highlight aspects of the distribution. The label for the group should be the range of values in those bars. As this is hard to describe, here is an example; - TO GET MORE DETAILS CLICK HERE -- View this message in context: http://r.789695.n4.nabble.com/Re-Labeling-a-range-of-bars-in-barplot-tp4651672.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] model selection with spg and AIC (or, convert list to fitted model object)
Dear Ravi,
Thank you so much for the help. I switched to using the optimx function
but I continue to use the spg method (for the most part) because I found
that only spg consistently converges give different datasets. I also
decided to use AIC rather that a likelihood ratio test.
I have a new question. I would like to construct 95% confidence
intervals for the parameter estimates from the best model. From a
previous R Help thread, you said that it was a bad idea to use the
Hessian matrix computed from optim/optimx or hessian() [numDeriv
package] when the optimization is constrained and parameter estimates
are on the boundary because the MLE is likely at a local minimum:
http://tolstoy.newcastle.edu.au/R/e15/help/11/09/6673.html
In the same thread, you suggest using the Hessian matrix from augmented
Lagrangian optimization with auglag() [alabama package] (with some
caveats). I would like to construct 95% CI with auglag, but I don't
understand how to write the inequality constraints (hin) function.
Could you please help me write the hin function?
Below is R code for my MLE problem, using data that results in parameter
estimates on the boundary, and my unsuccessful attempt at auglag()
optimization. Note: I have gradient functions for NLL1 and NLL2 but
they're very large and don't seem to improve optimization, so they are
not included here. I can supply them if needed for the auglag()
function. Also, I am running R 2.15.2 on a Windows 7 64-bit machine.
##
library(optimx)
library(alabama)
# define multinomial distribution
dmnom2 - function(x,prob,log=FALSE) {
r - lgamma(sum(x) + 1) + sum(x * log(prob) - lgamma(x + 1))
if (log) r else exp(r)
}
# data frame y
y - structure(list(t = c(0.167, 0.5, 1, 12, 18, 24, 36), n1 = c(1L,
1L, 1L, 8L, 9L, 10L, 12L), n2 = c(0L, 1L, 2L, 6L, 5L, 3L, 2L),
n3 = c(13L, 12L, 11L, 0L, 0L, 1L, 0L)), .Names = c(t, n1,
n2, n3), class = data.frame, row.names = 36:42)
# Negative log-likelihood functions
NLL1 - function(par, y) {
p1 - par[1]
p2 - p1
mu1 - par[2]
mu2 - mu1
t - y$t
n1 - y$n1
n2 - y$n2
n3 - y$n3
P1 - (p1*((-1 + exp(sqrt((mu1 + mu2 + p1 + p2)^2 -
4*(mu2*p1 + mu1*(mu2 + p2)))*t))*((-mu2)*(mu2 - p1 + p2) +
mu1*(mu2 + 2*p2)) - mu2*sqrt((mu1 + mu2 + p1 + p2)^2 -
4*(mu2*p1 + mu1*(mu2 + p2))) -
exp(sqrt((mu1 + mu2 + p1 + p2)^2 - 4*(mu2*p1 + mu1*(mu2 + p2)))*t)*
mu2*sqrt((mu1 + mu2 + p1 + p2)^2 - 4*(mu2*p1 + mu1*(mu2 + p2))) +
2*exp((1/2)*(mu1 + mu2 + p1 + p2 + sqrt((mu1 + mu2 + p1 + p2)^2 -
4*(mu2*p1 + mu1*(mu2 + p2*t)*mu2*
sqrt((mu1 + mu2 + p1 + p2)^2 - 4*(mu2*p1 + mu1*(mu2 + p2)/
exp((1/2)*(mu1 + mu2 + p1 + p2 + sqrt((mu1 + mu2 + p1 + p2)^2 -
4*(mu2*p1 + mu1*(mu2 + p2*t)/(2*(mu2*p1 + mu1*(mu2 + p2))*
sqrt((mu1 + mu2 + p1 + p2)^2 - 4*(mu2*p1 + mu1*(mu2 + p2
P2 - (p2*((-1 + exp(sqrt((mu1 + mu2 + p1 + p2)^2 -
4*(mu2*p1 + mu1*(mu2 + p2)))*t))*(-mu1^2 + 2*mu2*p1 +
mu1*(mu2 - p1 + p2)) - mu1*sqrt((mu1 + mu2 + p1 + p2)^2 -
4*(mu2*p1 + mu1*(mu2 + p2))) -
exp(sqrt((mu1 + mu2 + p1 + p2)^2 - 4*(mu2*p1 + mu1*(mu2 + p2)))*t)*
mu1*sqrt((mu1 + mu2 + p1 + p2)^2 - 4*(mu2*p1 + mu1*(mu2 + p2))) +
2*exp((1/2)*(mu1 + mu2 + p1 + p2 + sqrt((mu1 + mu2 + p1 + p2)^2 -
4*(mu2*p1 + mu1*(mu2 + p2*t)*mu1*
sqrt((mu1 + mu2 + p1 + p2)^2 - 4*(mu2*p1 + mu1*(mu2 + p2)/
exp((1/2)*(mu1 + mu2 + p1 + p2 + sqrt((mu1 + mu2 + p1 + p2)^2 -
4*(mu2*p1 + mu1*(mu2 + p2*t)/(2*(mu2*p1 + mu1*(mu2 + p2))*
sqrt((mu1 + mu2 + p1 + p2)^2 - 4*(mu2*p1 + mu1*(mu2 + p2
P3 - 1 - P1 - P2
p.all - c(P1, P2, P3)
if(all(p.all 0 p.all 1)) -sum(dmnom2(c(n1, n2, n3), prob =
p.all, log = TRUE)) else 1e07
}
NLL2 - function(par, y) {
p1 - par[1]
p2 - par[2]
mu1 - par[3]
mu2 - par[4]
t - y$t
n1 - y$n1
n2 - y$n2
n3 - y$n3
P1 - (p1*((-1 + exp(sqrt((mu1 + mu2 + p1 + p2)^2 -
4*(mu2*p1 + mu1*(mu2 + p2)))*t))*((-mu2)*(mu2 - p1 + p2) +
mu1*(mu2 + 2*p2)) - mu2*sqrt((mu1 + mu2 + p1 + p2)^2 -
4*(mu2*p1 + mu1*(mu2 + p2))) -
exp(sqrt((mu1 + mu2 + p1 + p2)^2 - 4*(mu2*p1 + mu1*(mu2 + p2)))*t)*
mu2*sqrt((mu1 + mu2 + p1 + p2)^2 - 4*(mu2*p1 + mu1*(mu2 + p2))) +
2*exp((1/2)*(mu1 + mu2 + p1 + p2 + sqrt((mu1 + mu2 + p1 + p2)^2 -
4*(mu2*p1 + mu1*(mu2 + p2*t)*mu2*
sqrt((mu1 + mu2 + p1 + p2)^2 - 4*(mu2*p1 + mu1*(mu2 + p2)/
exp((1/2)*(mu1 + mu2 + p1 + p2 + sqrt((mu1 + mu2 + p1 + p2)^2 -
4*(mu2*p1 + mu1*(mu2 + p2*t)/(2*(mu2*p1 + mu1*(mu2 + p2))*
sqrt((mu1 + mu2 + p1 + p2)^2 - 4*(mu2*p1 + mu1*(mu2 + p2
P2 - (p2*((-1 + exp(sqrt((mu1 + mu2 + p1 + p2)^2 -
4*(mu2*p1 + mu1*(mu2 + p2)))*t))*(-mu1^2 + 2*mu2*p1 +
mu1*(mu2 - p1 + p2)) -
[R] R beginner
Dear R-help group, I'm a R beginner and I find difficulty in manipulating R. Could you send to me a support that helps me to be familiar with R. Thank you in advance Sincerely, [[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] problem with convergence in mle2/optim function
Dear Berend,
Thank you so much for your help! I was able to write the gradient
function for my NLL function. For you're and others' possible interest,
here is my final gradient function:
Following from my description of the problem below, gr.p1, gr.p2,
gr.mu1, and gr.mu2 are the (very large) gradient equations of NLL2,
below, with respect to the parameters p1, p2, mu1, and mu2,
respectively. The gradient function is:
# Gradient function of NLL1
grr - function(par, y){
p1 - par[1]
p2 - par[2]
mu1 - par[3]
mu2 - par[4]
t - y[,1]
n1 - y[,2]
n2 - y[,3]
n3 - y[,4]
gr.p1 -
gr.p2 -
gr.mu1 -
gr.mu2 -
gr.mat - matrix(c(gr.p1, gr.p2, gr.mu1, gr.mu2), ncol = 4)
-colSums(gr.mat)
}
I verified this gradient function with numerical approximation with the
grad() function [numDeriv package].
Thanks again.
Adam Zeilinger
On 10/10/2012 3:57 AM, Berend Hasselman wrote:
On 10-10-2012, at 00:21, Adam Zeilinger wrote:
Dear R help,
Thanks again for the responses. I increased the lower constraint to:
lower = list(p1 = 0.0001, p2 = 0.0001, mu1 = 0.0001, mu2 = 0.0001).
I also included an upper box constraint of:
upper = list(p1 = Inf, p2 = Inf, mu1 = p1t, mu2 = p2t).
Making these changes improved the rate of convergence among stochastic
simulation runs, but I still had convergence problems.
I found success in switching from mle2/optim to spg (BB package). So far, spg
has produced similarly precise estimates as L-BFGS-B and consistently provides
parameter estimates.
If anyone is interested, here is the new objective function and spg call,
instead of my previous objective function and mle2 call. All other parts of my
reproducible code are the same as I've previously supplied:
##
library(BB)
# Objective function for spg()
NLL2 - function(par, y){
p1 - par[1]
p2 - par[2]
mu1 - par[3]
mu2 - par[4]
t - y$tv
n1 - y$n1
n2 - y$n2
n3 - y$n3
P1 - (p1*((-1 + exp(sqrt((mu1 + mu2 + p1 + p2)^2 -
4*(mu2*p1 + mu1*(mu2 + p2)))*t))*((-mu2)*(mu2 - p1 + p2) +
mu1*(mu2 + 2*p2)) - mu2*sqrt((mu1 + mu2 + p1 + p2)^2 -
4*(mu2*p1 + mu1*(mu2 + p2))) -
exp(sqrt((mu1 + mu2 + p1 + p2)^2 - 4*(mu2*p1 + mu1*(mu2 + p2)))*t)*
mu2*sqrt((mu1 + mu2 + p1 + p2)^2 - 4*(mu2*p1 + mu1*(mu2 + p2))) +
2*exp((1/2)*(mu1 + mu2 + p1 + p2 + sqrt((mu1 + mu2 + p1 + p2)^2 -
4*(mu2*p1 + mu1*(mu2 + p2*t)*mu2*
sqrt((mu1 + mu2 + p1 + p2)^2 - 4*(mu2*p1 + mu1*(mu2 + p2)/
exp((1/2)*(mu1 + mu2 + p1 + p2 + sqrt((mu1 + mu2 + p1 + p2)^2 -
4*(mu2*p1 + mu1*(mu2 + p2*t)/(2*(mu2*p1 + mu1*(mu2 + p2))*
sqrt((mu1 + mu2 + p1 + p2)^2 - 4*(mu2*p1 + mu1*(mu2 + p2
P2 - (p2*((-1 + exp(sqrt((mu1 + mu2 + p1 + p2)^2 -
4*(mu2*p1 + mu1*(mu2 + p2)))*t))*(-mu1^2 + 2*mu2*p1 +
mu1*(mu2 - p1 + p2)) - mu1*sqrt((mu1 + mu2 + p1 + p2)^2 -
4*(mu2*p1 + mu1*(mu2 + p2))) -
exp(sqrt((mu1 + mu2 + p1 + p2)^2 - 4*(mu2*p1 + mu1*(mu2 + p2)))*t)*
mu1*sqrt((mu1 + mu2 + p1 + p2)^2 - 4*(mu2*p1 + mu1*(mu2 + p2))) +
2*exp((1/2)*(mu1 + mu2 + p1 + p2 + sqrt((mu1 + mu2 + p1 + p2)^2 -
4*(mu2*p1 + mu1*(mu2 + p2*t)*mu1*
sqrt((mu1 + mu2 + p1 + p2)^2 - 4*(mu2*p1 + mu1*(mu2 + p2)/
exp((1/2)*(mu1 + mu2 + p1 + p2 + sqrt((mu1 + mu2 + p1 + p2)^2 -
4*(mu2*p1 + mu1*(mu2 + p2*t)/(2*(mu2*p1 + mu1*(mu2 + p2))*
sqrt((mu1 + mu2 + p1 + p2)^2 - 4*(mu2*p1 + mu1*(mu2 + p2
P3 - 1 - P1 - P2
p.all - c(P1, P2, P3)
#cat(NLL.free p.all {P1,P2,P3}\n)
#print(matrix(p.all, ncol=3))
-sum(dmnom2(c(n1, n2, n3), prob = p.all, log = TRUE))
}
par - c(p1t, p2t, mu1t, mu2t)
spg.fit - spg(par = par, fn = NLL2, y = yt,
lower = c(0.001, 0.001, 0.001, 0.001),
control = list(maxit = 5000))
My next problem is that spg takes about twice as long as L-BFGS-B to converge.
The spg help file strongly suggests the use of an exact gradient function to
improve speed. But I am having trouble writing a gradient function. Here is
what I have so far:
I derived the gradient function by taking the derivative of my NLL equation
with respect to each parameter. My NLL equation is the probability mass
function of the trinomial distribution. Here is some reproducible code:
#
library(Ryacas)
p1 - Sym(p1); p2 - Sym(p2); mu1 - Sym(mu1); mu2 - Sym(mu2)
t - Sym(t); n1 - Sym(n1); n2 - Sym(n2); n3 - Sym(n3)
P1.symb - ((p1*((-1 + exp(sqrt((mu1 + mu2 + p1 + p2)^2 -
4*(mu2*p1 + mu1*(mu2 + p2)))*t))*((-mu2)*(mu2 - p1 + p2) +
mu1*(mu2 + 2*p2)) - mu2*sqrt((mu1 + mu2 + p1 + p2)^2 -
4*(mu2*p1 + mu1*(mu2 + p2))) -
exp(sqrt((mu1 + mu2 + p1 + p2)^2 - 4*(mu2*p1 + mu1*(mu2 + p2)))*t)*
mu2*sqrt((mu1 + mu2 + p1 + p2)^2 - 4*(mu2*p1 + mu1*(mu2 + p2))) +
2*exp((1/2)*(mu1 + mu2 + p1 + p2 + sqrt((mu1 + mu2 + p1 + p2)^2 -
4*(mu2*p1 + mu1*(mu2 +
Re: [R] Warning message: In scan(file, what, nmax...)
In addition, I tried Data1-read.table(/Users/kama/Analysis/GDP10.csv, sep=\t, fill=TRUE) the result: *** caught segfault *** address 0xd020, cause 'memory not mapped' Possible actions: 1: abort (with core dump, if enabled) 2: normal R exit 3: exit R without saving workspace 4: exit R saving workspace -- View this message in context: http://r.789695.n4.nabble.com/Warning-message-In-scan-file-what-nmax-tp4651689p4651712.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Warning message: In scan(file, what, nmax...)
Also tries this: x-count.fields(/Users/kama/Analysis/GDP10.csv, sep=\t) x [1] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 [38] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 [75] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 [112] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 [149] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 [186] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 [223] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 [260] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 [297] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 [334] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 [371] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 [408] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 [445] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 [482] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 [519] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 [556] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 [593] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 [630] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 [667] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 [704] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 [741] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 [778] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 [815] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 [852] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 [889] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 [926] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 [963] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 [1000] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 [1037] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 [1074] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 [] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 [1148] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 [1185] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 [1222] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 However, it is not clear for me what is wrong with my data. .. -- View this message in context: http://r.789695.n4.nabble.com/Warning-message-In-scan-file-what-nmax-tp4651689p4651715.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] simple subset question
I finally see what you and David W mean...I was under the assumption that by subsetting Year==2012 it would also extract the max for that year.I guess I have to review 'subset' again :) Thank you much Felipe D. Carrillo Supervisory Fishery Biologist Department of the Interior US Fish Wildlife Service California, USA http://www.fws.gov/redbluff/rbdd_jsmp.aspx From: David L Carlson dcarl...@tamu.edu To: 'Felipe Carrillo' mazatlanmex...@yahoo.com; 'arun' smartpink...@yahoo.com Cc: 'R help' r-help@r-project.org Sent: Sunday, December 2, 2012 2:54 PM Subject: RE: [R] simple subset question As David W. guessed. The maximum is in year 2005 not 2012 so no row from 2012 matches the maximum. subset(winter,Year==2012 Total==max(Total)) [1] IDWeek Total Fry Smolt FryEq Year 0 rows (or 0-length row.names) winter[which(winter$Total==max(winter$Total)),] IDWeek Total Fry Smolt FryEq Year 195 39 2115018 2083214 31805 2137281 2005 Change to subset(winter, Year==2012 Total==max(Total[Year==2012])) IDWeek Total Fry Smolt FryEq Year 21 47 303259 34008 269248 491733 2012 -- David L Carlson Associate Professor of Anthropology Texas AM University College Station, TX 77843-4352 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-bounces@r- project.org] On Behalf Of Felipe Carrillo Sent: Sunday, December 02, 2012 4:40 PM To: arun Cc: R help Subject: Re: [R] simple subset question Actually, I dput(winter) and is not that big.so here is the whole thing I am trying to accomplish. winter - structure(list(IDWeek = c(27L, 28L, 29L, 30L, 31L, 32L, 33L, 34L, 35L, 36L, 37L, 38L, 39L, 40L, 41L, 42L, 43L, 44L, 45L, 46L, 47L, 48L, 49L, 50L, 51L, 52L, 27L, 28L, 29L, 30L, 31L, 32L, 33L, 34L, 35L, 36L, 37L, 38L, 39L, 40L, 41L, 42L, 43L, 44L, 45L, 46L, 47L, 48L, 49L, 50L, 51L, 52L, 27L, 28L, 29L, 30L, 31L, 32L, 33L, 34L, 35L, 36L, 37L, 38L, 39L, 40L, 41L, 42L, 43L, 44L, 45L, 46L, 47L, 48L, 49L, 50L, 51L, 52L, 27L, 28L, 29L, 30L, 31L, 32L, 33L, 34L, 35L, 36L, 37L, 38L, 39L, 40L, 41L, 42L, 43L, 44L, 45L, 46L, 47L, 48L, 49L, 50L, 51L, 52L, 27L, 28L, 29L, 30L, 31L, 32L, 33L, 34L, 35L, 36L, 37L, 38L, 39L, 40L, 41L, 42L, 43L, 44L, 45L, 46L, 47L, 48L, 49L, 50L, 51L, 52L, 27L, 28L, 29L, 30L, 31L, 32L, 33L, 34L, 35L, 36L, 37L, 38L, 39L, 40L, 41L, 42L, 43L, 44L, 45L, 46L, 47L, 48L, 49L, 50L, 51L, 52L, 27L, 28L, 29L, 30L, 31L, 32L, 33L, 34L, 35L, 36L, 37L, 38L, 39L, 40L, 41L, 42L, 43L, 44L, 45L, 46L, 47L, 48L, 49L, 50L, 51L, 52L, 27L, 28L, 29L, 30L, 31L, 32L, 33L, 34L, 35L, 36L, 37L, 38L, 39L, 40L, 41L, 42L, 43L, 44L, 45L, 46L, 47L, 48L, 49L, 50L, 51L, 52L, 27L, 28L, 29L, 30L, 31L, 32L, 33L, 34L, 35L, 36L, 37L, 38L, 39L, 40L, 41L, 42L, 43L, 44L, 45L, 46L, 47L, 48L, 49L, 50L, 51L, 52L, 27L, 28L, 29L, 30L, 31L, 32L, 33L, 34L, 35L, 36L, 37L, 38L, 39L, 40L, 41L, 42L, 43L, 44L, 45L, 46L, 47L, 48L, 49L, 50L, 51L, 52L, 27L, 28L, 29L, 30L, 31L, 32L, 33L, 34L, 35L, 36L, 37L, 38L, 39L, 40L, 41L, 42L, 43L, 44L, 45L, 46L, 47L, 48L, 49L, 50L, 51L, 52L), Total = c(0L, 0L, 326L, 1735L, 1807L, 2208L, 3883L, 8820L, 6060L, 19326L, 63158L, 100718L, 53015L, 91689L, 152629L, 122708L, 61293L, 15574L, 86538L, 75365L, 303259L, 19691L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 161L, 321L, 1000L, 4425L, 13202L, 19726L, 30518L, 84949L, 157260L, 145691L, 85801L, 62044L, 44439L, 23272L, 22391L, 20159L, 14854L, 35379L, 31142L, 7736L, 13221L, 4894L, 0L, 460L, 1129L, 1757L, 11105L, 27730L, 55769L, 12298L, 32964L, 80110L, 160507L, 74134L, 101736L, 138355L, 107873L, 53806L, 194429L, 7596L, 55497L, 30336L, 18392L, 22291L, 16850L, 16567L, 14799L, 7909L, 93L, 329L, 363L, 2762L, 5573L, 33466L, 96762L, 340947L, 612835L, 347972L, 526506L, 656981L, 344181L, 145465L, 150543L, 935599L, 32789L, 15092L, 7288L, 9889L, 6945L, 5138L, 6299L, 3095L, 108227L, 1191L, 0L, 0L, 132L, 227L, 2157L, 7558L, 16459L, 87220L, 321195L, 209299L, 110807L, 112024L, 128058L, 74373L, 41531L, 15111L, 21890L, 15060L, 22538L, 12443L, 11052L, 3907L, 2640L, 2745L, 3936L, 17593L, 0L, 0L, 10775L, 4166L, 4958L, 16221L, 29401L, 34951L, 33188L, 146044L, 105007L, 185297L, 159682L, 207537L, 140694L, 128275L, 44274L, 27079L, 18928L, 10437L, 29984L, 18395L, 25846L, 4573L, 31995L, 3679L, 707L, 2390L, 8860L, 24430L, 40885L, 72792L, 205521L, 344493L, 662973L, 526409L, 631953L, 850491L, 842678L, 445987L, 558152L, 332032L, 174326L, 80601L, 48696L, 98571L, 103563L, 149469L, 78081L, 182478L, 2158L, 16566L, 0L, 868L, 2044L, 4064L, 6049L, 9399L, 13304L, 45172L, 242155L, 476864L, 712534L, 1058409L, 2115018L, 1510342L, 1138213L, 333192L, 158820L, 94379L, 348882L, 39290L, 29701L, 47258L, 69837L, 7884L, 49338L, 22168L, 0L, 147L, 1231L, 3216L, 5021L, 18462L, 37441L, 64669L, 136590L, 338523L, 559448L, 714837L, 358037L, 180910L, 291943L, 222708L, 163801L, 39109L, 23247L, 15726L, 38701L, 5795L, 12509L, 18721L, 822L, 6674L, 765L, 1753L,
Re: [R] Problem with figures
On 12-12-02 5:42 PM, Shige Song wrote:
I am having problem making ggplot2, tikzDevice, and knitr working together.
I used a very simple example:
I don't use knitr so I can't really help, but you didn't tell us how you
passed this file to knitr, so maybe nobody can. However, if you were
using Sweave, you would need to mention that the code chunk produces a
figure (using fig=TRUE in the = header).
Duncan Murdoch
---example.Rnw-
\documentclass[preview]{standalone}
\begin{document}
\begin{figure}
fig1,eval=TRUE,echo=FALSE,dev='tikz'=
library(ggplot2)
qplot(displ, hwy, data = mpg, colour = factor(cyl))
@
\end{figure}
\end{document}
-
I got ... ! == Fatal error occurred, no output PDF file produced!
label: fig1 (with options)
List of 3
$ eval: logi TRUE
$ echo: logi FALSE
$ dev : chr tikz
Error in process_file(text, output) :
Quitting from lines 6-8: (test_Rnw.Rnw) Error in
getMetricsFromLatex(TeXMetrics) :
TeX was unable to calculate metrics for the following string
or character:
hwy
Common reasons for failure include:
* The string contains a character which is special to LaTeX unless
escaped properly, such as % or $.
* The string makes use of LaTeX commands provided by a package and
the tikzDevice was not told to load the package.
The contents of the LaTeX log of the aborted run have been printed above,
it may contain additional details as to why the metric calculation failed.
Calls: knit - process_file
Execution halted
Best,
Shige
[[alternative HTML version deleted]]
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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] Can you turn a string into a (working) symbol?
I believe I answered this a few weeks ago at this link:
https://stat.ethz.ch/pipermail/r-help/2012-November/328053.html and
following.
Michael
On Sun, Dec 2, 2012 at 2:43 PM, rahul143 rk204...@gmail.com wrote:
Dear folks--
Suppose I have an expression that evaluates to a string, and that that
string, were it not a character vector, would be a symbol. I would like a
function, call it doppel(), that will take that expression as an argument
and produce something that functions exactly like the symbol would have if I
typed it in the place of the function of the expression. It should go as
far along the path to evaluation as the symbol would have, and then stop,
and be available for subsequent manipulation. For example, if
aa - 3.1416
bb - function(x) {x^2}
r - 2
xx - c(aa, bb)
out - doppel(xx[1])*doppel(xx[2])(r)
Then out should be 13.3664
Or similarly, after
doppel(paste(a, a, sep='')) - 3
aa
typing aa should return 3.
Is there such a function? Can there be?
I thought as.symbol would do this, but it does not.
as.symbol (xx[1])*as.symbol (xx[2])(r)
Error: attempt to apply non-function
-
--
View this message in context:
http://r.789695.n4.nabble.com/Can-you-turn-a-string-into-a-working-symbol-tp4651634.html
Sent from the R help mailing list archive at Nabble.com.
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.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] RMySQL install on windows
On Sun, Dec 2, 2012 at 11:35 AM, rahul143 rk204...@gmail.com wrote: I have been trying to install RMySQL on Windows 7 following the procedure at: http://biostat.mc.vanderbilt.edu/wiki/Main/RMySQL I think I have properly installed RTools and created a proper Renviron.site file saying: MYSQL_HOME=C:/Program Files/MySQL/MySQL Server 5.5 When I try to install the packages from source, I get warnings that suggest I'm still not quite with the program yet. There are comments about POSIX paths that I don't quite grasp. Can anyone give me additional hints? There seems to be a libmysql.dll in the /lib subdirectory although the install seems to be looking in the /bin directory for a file of similar name. Is this something that has changed with recent versions of MySQL that should be fixed in the RMySQL package or is it something I can work around by hand or by properly setting some environmental variable? There likely has been some change in the location of the dll's in various versions of MySQL. See: http://www.mail-archive.com/r-help@r-project.org/msg185838.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] Problem with figures
Easiest way: copy and paste the code into Rstudio and hit compile pdf.
From the command line, I believe you can do knit2pdf example.Rnw.
Shige
On Sun, Dec 2, 2012 at 6:12 PM, Duncan Murdoch murdoch.dun...@gmail.comwrote:
On 12-12-02 5:42 PM, Shige Song wrote:
I am having problem making ggplot2, tikzDevice, and knitr working
together.
I used a very simple example:
I don't use knitr so I can't really help, but you didn't tell us how you
passed this file to knitr, so maybe nobody can. However, if you were using
Sweave, you would need to mention that the code chunk produces a figure
(using fig=TRUE in the = header).
Duncan Murdoch
---**example.Rnw---**--
\documentclass[preview]{**standalone}
\begin{document}
\begin{figure}
fig1,eval=TRUE,echo=FALSE,**dev='tikz'=
library(ggplot2)
qplot(displ, hwy, data = mpg, colour = factor(cyl))
@
\end{figure}
\end{document}
--**--**
-
I got ... ! == Fatal error occurred, no output PDF file produced!
label: fig1 (with options)
List of 3
$ eval: logi TRUE
$ echo: logi FALSE
$ dev : chr tikz
Error in process_file(text, output) :
Quitting from lines 6-8: (test_Rnw.Rnw) Error in
getMetricsFromLatex(**TeXMetrics) :
TeX was unable to calculate metrics for the following string
or character:
hwy
Common reasons for failure include:
* The string contains a character which is special to LaTeX unless
escaped properly, such as % or $.
* The string makes use of LaTeX commands provided by a package and
the tikzDevice was not told to load the package.
The contents of the LaTeX log of the aborted run have been printed above,
it may contain additional details as to why the metric calculation failed.
Calls: knit - process_file
Execution halted
Best,
Shige
[[alternative HTML version deleted]]
__**
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https://stat.ethz.ch/mailman/**listinfo/r-helphttps://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/**
posting-guide.html 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
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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] finding index of maximum value in vector
?which.max On Mon, Dec 3, 2012 at 3:44 AM, rahul143 rk204...@gmail.com wrote: I found: max.col(matrix(c(1,3,2),nrow=1)) Is there a more concise/elegant way? Thanks, - TO GET MORE DETAILS CLICK HERE -- View this message in context: http://r.789695.n4.nabble.com/finding-index-of-maximum-value-in-vector-tp4651663.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.
