Re: [R] residual standard error in rlm (MASS package)
The 'r' in rlm is for 'robust', so it does not compute a residual sum of squares (which is not robust), but rather a robust estimate of the scale. That *is* what the help page ?summary.rlm says: sigma: The scale estimate. stddev: A scale estimate used for the standard errors. As to exactly what those scale esimates are, see the references or the code, but e.g. stddev is based on downweighting larger residuals. On Mon, 8 Dec 2008, Kari Ruohonen wrote: Hi, I would appreciate of someone could explain how the residual standard error is computed for rlm models (MASS package). Usually, one would expect to get the residual standard error by sqrt(sum((y-fitted(fm))^2)/(n-2)) where y is the response, fm a linear model with an intercept and slope for x and n the number of observations. This does not seem to work for rlm models and I am wondering what obvious am I missing here? Here is an example: x<-1:100 y <- c(2.37156056743079, 1.66644749462933, 6.33155723966817, 12.7709430358167, 11.124950273, 19.7839679181322, 15.4923741347280, 18.702397068068, 18.7599963836891, 16.5916430986993, 16.0653054434192, 25.4517287910774, 19.9306544701024, 25.3581170063305, 35.6823980984208, 25.8293557856092, 34.7021243077337, 31.5336533511445, 36.3599764020412, 44.6000402205419, 41.9899219097128, 45.4564141342995, 43.6061038794823, 48.7566542867736, 47.5504015095432, 54.8120780105412, 55.2620894365424, 53.223516997263, 59.5477081631011, 61.2390445046623, 62.3106323086734, 68.1104058608567, 62.399184797047, 73.9413640517595, 70.6710955288097, 74.5456476513766, 64.968260562374, 73.2318014155102, 73.7335636549196, 76.9362454490887, 80.2579421621043, 80.945827481932, 87.7805234941603, 90.0909966936097, 86.0620664696943, 90.3640690887434, 98.0965832886435, 96.789139334781, 102.114606626867, 98.3302535449148, 103.107825932103, 109.942412367491, 106.868253017023, 109.808738425258, 110.136050155862, 108.846488332796, 118.442973085485, 117.276921857816, 118.640871017018, 119.263784892266, 123.100214564588, 123.860590728955, 128.712228721465, 131.297848895423, 123.283516322512, 134.012585073241, 132.665302554315, 138.673423711638, 143.687124396642, 139.159598404340, 142.012045172451, 146.480644634549, 145.429104228138, 144.503524323636, 152.348091257061, 149.237135977337, 159.803973361884, 153.195835890301, 158.921034703569, 163.479578254736, 159.591944778941, 163.185119145309, 165.890510577093, 164.573471319534, 173.549321320816, 169.520130741843, 170.439532597426, 174.477604263110, 178.059609946662, 177.828073866105, 185.005760822296, 184.280998437732, 196.085419590290, 187.125508176825, 190.524627542992, 196.849299652848, 197.830377226055, 197.973198490102, 198.59328678419, 199.450725602621 ) # y originally generated with y<-2*x+rnorm(100,0,2) fm<-lm(y~x) rm<-rlm(y~x) fm.r<-sqrt(sum((y-fitted(fm))^2)/(n-2)) rm.r<-sqrt(sum((y-fitted(rm))^2)/(n-2)) print(matrix(c(fm.r,summary(fm)$sigma,rm.r,summary(rm)$sigma), ncol=2,byrow=T)) Output of this is: [,1] [,2] [1,] 1.900033 1.900033 [2,] 1.905847 1.595128 I.e. for the lm model the residual standard error from the summary.lm method matches exactly sqrt(sum((y-fitted(fm))^2)/(n-2)) but that for the summary.rlm model is somewhat smaller than sqrt(sum((y-fitted(rm))^2)/(n-2)). I am curious what causes this difference? My sessionInfo() R version 2.7.1 (2008-06-23) x86_64-pc-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] MASS_7.2-44 regards, Kari Ruohonen -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Compile Packages on vista
Remove all the blank spaces in your package's name and try again. Uwe Ligges Dominik Locher - bondsearch.ch wrote: Hi I'm trying to compile R packages on my vista (I'm very new on vista...). I installed Rtools, RExcel on a specific folder: c:\Rtools and gave full access. Unfortunately, I am still unable to compile any packages (may be still because of the security properties of vista). I checked several mailing list/forums/website but I did not found any solution. Does anybody have the same problem and found a solution? I've got the following error: ## R CMD install testPackage installing to 'D:\Rtmp' -- Making package testPackage adding build stamp to DESCRIPTION installing R files installing inst files find: `D:/Rtmp/ testPackage /doc': Permission denied find: `D:/Rtmp/ testPackage /unitTests': Permission denied make[2]: *** [D:/Rtmp/ testPackage /inst] Error 1 make[1]: *** [all] Error 2 make: *** [pkg- testPackage] Error 2 *** Installation of testPackage failed *** Removing 'D:/Rtmp/ testPackage Can't read D:/Rtmp/ testPackage /doc: Invalid argument at c:\Rtools\R\R-2.8.0/bin/i nstall line 411 Can't remove directory D:/Rtmp/ testPackage /doc: Directory not empty at c:\Rtools\ R\R-2.8.0/bin/install line 411 Can't read D:/Rtmp/ testPackage /unitTests: Invalid argument at c:\Rtools\R\R-2.8.0 /bin/install line 411 Can't remove directory D:/Rtmp/ testPackage /unitTests: Directory not empty at c:\R tools\R\R-2.8.0/bin/install line 411 Can't remove directory D:/Rtmp/ testPackage: Directory not empty at c:\Rtools\R\R- 2.8.0/bin/install line 411 Restoring previous 'D:/Rtmp/ testPackage' mv: cannot move `D:/Rtmp/00LOCK/ testPackage 'to `D:/Rtmp/ testPackage': Directory n ot empty Many thansk for your help. Best regards Dominik [[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] Logical inconsistency
Patrick Connolly wrote: > On Mon, 08-Dec-2008 at 02:05AM +0800, Berwin A Turlach wrote: > > |> G'day Wacek, > |> > |> On Sat, 06 Dec 2008 10:49:24 +0100 > |> Wacek Kusnierczyk <[EMAIL PROTECTED]> wrote: > |> > |> [] > |> > >> there is, in principle, no problem in having a high-level language > |> > >> perform the computation in a logically consistent way. > |> > > > |> > > Is this now supposed to be a "Radio Eriwan" joke? As another saying > |> > > goes: in theory there is no difference between theory and practice, > |> > > in practice there is. > |> > > |> > no joke, sorry to disappoint you. > |> > |> Apparently it is, you seem to be a comedian without knowing it. :) > > I think this guy's a riot! Self-effacing humour is not easy to do, > but he's really good at it. That wonderful phrase a bit further back > in this thread where he referred to his 'fiercely truculent' whining > is one deserving preservation. > > It's a shame the brilliance is lost somewhat by the use a keyboard > that has no key. I've found a lot of these wonderful musings > too much effort to read. I'm not familiar with exotic keyboard > layouts, but perhaps the Norwegian one uses for something mere > non-Nordics wouldn't understand. Pity that. > > sorry. i write so much nonsense i have no time to press the shift. if the lack of uppercase makes you skip my posts, the better for you. vQ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Logical inconsistency
Berwin A Turlach wrote: > > I am not surprised about CS guys never learning about these issues. As > long as you play around with data bases (their organisation &c), > sorting algorithms, artificial intelligence (at least when I attended a > lecture on this) you do not need to know about these issues. And, > unfortunately, it seems nowadays a lot of teaching is on a > "need-to-know" and "just-in-time" basis. > > It just became criminal when CS guys who were into compiler design > started to construct compilers that analysed the code and rearranged > the calculations based on an analysis that assumed infinite precision > arithmetic. Such compilers optimised away code that was designed to > deal with finite precision arithmetic. I believe this was one of the > motivations of Goldberg's article. > > you'd probably enjoy hacker's delight by warren [1], where tricks are presented that allow you to use computer arithmetic efficiently when you know the details of the representations. from the foreword by g.l. steele jr: "Many books on algorithms and data structures teach complicated techniques for sorting and searching, for maintaining hash tables and binary trees, for dealing with records and pointers. They overlook what can be done with very tiny pieces of data—bits and arrays of bits. It is amazing what can be done with just binary addition and subtraction and maybe some bitwise operations; the fact that the carry chain allows a single bit to affect all the bits to its left makes addition a peculiarly powerful data manipulation operation in ways that are not widely appreciated. Yes, there ought to be a book about these techniques. Now it is in your hands, and it's terrific. If you write optimizing compilers or high-performance code, you must read this book." vQ [1] http://www.hackersdelight.org/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Multivariate kernel density estimation
I would like to estimate a 95% highest density area for a multivariate parameter space (In the context of anova). Unfortunately I have only experience with univariate kernel density estimation, which is remarkebly easier :) Using Gibbs, i have sampled from a posterior distirbution of an Anova model with k means (mu) and 1 common residual variance (s2). The means are independent of eachother, but conditional on the residual variance. So now I have a data frame of say 10.000 iterations, and k+1 parameters. I am especially interested in the posterior distribution of the mu parameters, because I want to test the support for an inequalty constrained model (e.g. mu1 > mu2 > mu3). I wish to derive the multivariate 95% highest density parameter space for the mu parameters. For example, if I had a posterior distirbution with 2 means, this should somehow result in the circle or elipse that contains the 95% highest density area. Is something like this possible in R? All tips are welcome. -- View this message in context: http://www.nabble.com/Multivariate-kernel-density-estimation-tp20894766p20894766.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] Vars package - specification of VAR
Hello Bernd,
by definition, a VAR does only include **lagged endogenous** variables.
You might want consider SVAR() contained in the same package, or fit a
VECM (see CRAN package 'urca').
Best,
Bernhard
>Hi useRs,
>
>Been estimating a VAR with two variables, using VAR() of the
>package "vars".
>
>Perhaps I am missing something, but how can I include the
>present time t variables, i.e. for the set of equations to be:
>
>x(t) = a1*y(t) + a2*y(t-1) + a3*x(t-1) + ...
>Y(t) = a1*x(t) + a2*x(t-1) + a3*y(t-1) + ...
>
>The types available in function VAR() allow for seasonal
>dummies, time trends and constant term.
>
>But the terms
>
>a1*y(t)
>a1*x(t)
>
>always seem to be excluded by default, thus only lagged
>variables enter the right side.
>
>How can I specify VAR() such that a1*y(t) and a1*x(t) are included?
>Or would I have to estimate with lm() instead?
>
>Many thanks in advance,
>
>Bernd
>
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>
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[R] Permutation exact test to compare related series
I all, is there a way with R to perform an exact permutation test to replace the wilcoxon test to compare paired series and/or to perform pairwise multiple comparisons for related series after a Friedman test ? Thanks Gilles __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Taylor diagram
Csima Gabriella wrote:
Dear Everyone,
I wrote a Taylor diagram program in R, but it was not very general, so I was
happy to find the Taylor.diagram in the plotrix package.
On the other hand I can find many problems with the pos.cor=TRUE case, in other
words, when we use only the first quarter of the space (positive correlations).
(When we choose pos.cor=FALSE, the program seems to me perfect)
1.There is only one line around the (0,0) point:
I looked at this part of the program:
if (ref.sd) {
xcurve <- cos(seq(0, pi/2, by = 0.01)) * sd.r
ycurve <- sin(seq(0, pi/2, by = 0.01)) * sd.r
lines(xcurve, ycurve)
}
I have tried this part of the program (using sd.r=0 and naturally using a
plot(..)), it gave only one quarter circle and not a seq of them.
2. No lines helping to read the correlation easily at all.
Could you help me, how to correct the program to use as many sd, corr and rmse
line as I would like to?
Thank you very much for your help in advance!
Hi Gabriella,
Olivier Eterradossi wrote the version you prefer, and he may be able to
send you a fix. If not, I can probably have a look at it tomorrow night
and work something out. I'll check to see if you have gotten a reply then.
Jim
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Re: [R] About adf.test
Hello Kamlesh,
have a look at: fUnitRoots, tseries, urca, uroot
Best,
Bernhard
>
>Dear sir,
>
> I am a new user of R statistical package. I want to perform
>adf.test(augmented dickey fuller test), which packages I need
>to install in
>order to perform it. I am getting following message on my monitor.
>*x<-rnorm(1000)
>> adf.test(x)
>Error: could not find function "adf.test"
>
>*I am waiting for your response.
>
>Kamlesh Kumar.
>
>--
> Kamlesh Kumar
> Appt. No. - QQ420,
> Vila Universitaria, Campus de la UAB,
> 08193 Bellatera, Cerdanyola del Valles,
> Barcelona, Spain.
>
> [[alternative HTML version deleted]]
>
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>
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Re: [R] How to get Greenhouse-Geisser epsilons from anova?
Thank you for your help!
Sorry, for bothering you again..
I still have trouble combining within and between subject factors.
Interactions of within factors and D having only 2 levels work well.
How can I get the main effect of D? I have tried anova(mlmfitD, mlmfit).
With D having 3 levels I would expect the dfs to be 2 and 33. However,
the output states 84,24??
As long as the between factor has only 2 levels the between/within
interactions fit well with SPSS, but if D has 3 levels, the mismatch is
immense.
If I calculate the within effects with myma having not 12 subjects from
one group but for example 24 from 2 groups, the output treats it as if
all subjects came from the same group, for example for main effect A the
dfs are 1 and 35. SPSS puts out 1 and 33 which is what I would have
expected.. ..
Peter Dalgaard schrieb:
Nils Skotara wrote:
Thank you, this helped me a lot!
All within effects and interactions work well!
Sorry, but I still could not get how to include the between factor..
If I include D with 2 levels, then myma is 24 by 28. (another 12 by
28 for the
second group of subjects.)
mlmfitD <- lm(myma~D) is no problem, but whatever I tried afterwards
did not seem logical to me.
I am afraid I do not understand how to include the between factor. I
cannot include ~D into M or X because it has length 24 whereas the other
factors have 28...
Just do the same as before, but comparing mlmfitD to mlmfit:
anova(mlmfitD, mlmfit, X=~A+B, M=~A+B+C)
# or anova(mlmfitD, mlmfit, X=~1, M=~C), as long as things are balanced
gives the D:C interaction test (by testing whether the C contrasts
depend on D). The four-factor interaction is
anova(mlmfitD, mlmfit, X=~(A+B+C)^2, M=~A*B*C)
Zitat von Peter Dalgaard <[EMAIL PROTECTED]>:
Skotara wrote:
Dear Mr. Daalgard.
thank you very much for your reply, it helped me to progress a bit.
The following works fine:
dd <- expand.grid(C = 1:7, B= c("r", "l"), A= c("c", "f"))
myma <- as.matrix(myma) #myma is a 12 by 28 list
mlmfit <- lm(myma~1)
mlmfit0 <- update(mlmfit, ~0)
anova(mlmfit, mlmfit0, X= ~C+B, M = ~A+C+B, idata = dd,
test="Spherical"), which tests the main effect of A.
anova(mlmfit, mlmfit0, X= ~A+C, M = ~A+C+B, idata = dd,
test="Spherical"), which tests the main effect of B.
However, I can not figure out how this works for the other effects.
If I try:
anova(mlmfit, mlmfit0, X= ~A+B, M = ~A+C+B, idata = dd,
test="Spherical")
I get:
Fehler in function (object, ..., test = c("Pillai", "Wilks",
"Hotelling-Lawley", :
residuals have rank 1 < 4
dd$C is not a factor with that construction. It works for me after
dd$C <- factor(dd$C)
(The other message is nasty, though. It's slightly different in
R-patched:
> anova(mlmfit, mlmfit0, X= ~A+B, M = ~A+C+B, idata = dd,
test="Spherical")
Error in solve.default(Psi, B) :
system is computationally singular: reciprocal condition number =
2.17955e-34
but it shouldn't happen...
Looks like it is a failure of the internal Thin.row function. Ick!
)
I also don't know how I can calculate the various interactions..
My read is I should change the second argument mlmfit0, too, but I
can't
figure out how...
The "within" interactions should be straightforward, e.g.
M=~A*B*C
X=~A*B*C-A:B:C
etc.
The within/between interactions are otained from the similar tests of
the between factor(s)
e.g.
mlmfitD <- lm(myma~D)
and then
anova(mlmfitD, mlmfit,)
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[R] Re : Taylor diagram
Hi Gabriela, as suggested by Jim I'll have a look as soon as possible (but only tomorrow I'm afraid). Maybe you could provide me with a dataset of yours which shows the problem (use direct postin gt o my own address [EMAIL PROTECTED], instead of posting the data to Rlist) ? Thanks, Olivier -- Olivier ETERRADOSSI Maître-Assistant CMGD / Equipe "Propriétés Psycho-Sensorielles des Matériaux" Ecole des Mines d'Alès Hélioparc, 2 av. P. Angot, F-64053 PAU CEDEX 9 tel std: +33 (0)5.59.30.54.25 tel direct: +33 (0)5.59.30.90.35 fax: +33 (0)5.59.30.63.68 http://www.ema.fr __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Logical inconsistency
G'day Wacek, On Mon, 08 Dec 2008 13:13:33 +0100 Wacek Kusnierczyk <[EMAIL PROTECTED]> wrote: > Berwin A Turlach wrote: > > > > I am not surprised about CS guys never learning about these > > issues. As long as you play around with data bases (their > > organisation &c), sorting algorithms, artificial intelligence (at > > least when I attended a lecture on this) you do not need to know > > about these issues. And, unfortunately, it seems nowadays a lot of > > teaching is on a "need-to-know" and "just-in-time" basis. > > > > It just became criminal when CS guys who were into compiler design > > started to construct compilers that analysed the code and rearranged > > the calculations based on an analysis that assumed infinite > > precision arithmetic. Such compilers optimised away code that was > > designed to deal with finite precision arithmetic. I believe this > > was one of the motivations of Goldberg's article. > > > > > > you'd probably enjoy hacker's delight by warren [1], where tricks are > presented that allow you to use computer arithmetic efficiently when > you know the details of the representations. Unlikely, these days I am less interested in hacks but more in portable implementations. If it were to show that somethings I believe to be portable are actually not, then it could be of interest after all. Cheers, Berwin __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Legend and Main Title positioning
Thank you very much for your help! That code does exactly what I was looking for ( I don't have experience with lattice yet ) Ciao, Antje [EMAIL PROTECTED] schrieb: layout(matrix(c(1,2,3,4), nrow = 2, byrow = TRUE)) plot(rnorm(100)) plot(rnorm(200)) plot(rnorm(300)) plot(rnorm(400)) Now, I'd like to create a legend below each plot and generate a common title. How can I do that? If you are laying plots out in grids like this then lattice graphics are generally the way to go, but here's a solution based upon base graphics. The trick is to include extra potting space in your layout for the legends. The code is messy, since it requires you to manually specify which cell of the layout to plot into, but I'm sure guven some thought you can automate this. #4 space for plots, 4 for legends layout(matrix(1:8, nrow = 4, byrow = TRUE), heights=rep(c(3,1),4)) #Check the layout looks suitable layout.show(8) #Avoid clipping problems, and create space for your title par(xpd=TRUE, oma=c(0,0,2,0)) #First plot plot(rnorm(100)) #Move down and plot the first legend par(mfg=c(2,1)) legend(0,0, legend="foo", pch=1) #Repeat for the other plots and legends par(mfg=c(1,2)) plot(rnorm(200)) par(mfg=c(2,2)) legend(0,0, legend="bar", pch=1) par(mfg=c(3,1)) plot(rnorm(300)) par(mfg=c(4,1)) legend(0,0, legend="baz", pch=1) par(mfg=c(3,2)) plot(rnorm(400)) par(mfg=c(4,2)) legend(0,0, legend="quux", pch=1) #Title for all the plots title(main="4 plots", outer=TRUE) Regards, Richie. Mathematical Sciences Unit HSL ATTENTION: This message contains privileged and confidential information intended for the addressee(s) only. If this message was sent to you in error, you must not disseminate, copy or take any action in reliance on it and we request that you notify the sender immediately by return email. Opinions expressed in this message and any attachments are not necessarily those held by the Health and Safety Laboratory or any person connected with the organisation, save those by whom the opinions were expressed. Please note that any messages sent or received by the Health and Safety Laboratory email system may be monitored and stored in an information retrieval system. Scanned by MailMarshal - Marshal's comprehensive email content security solution. Download a free evaluation of MailMarshal at www.marshal.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] Logical inconsistency
G'day Wacek, On Sun, 07 Dec 2008 21:09:36 +0100 Wacek Kusnierczyk <[EMAIL PROTECTED]> wrote: > g'evening. Not the done thing. > c'mon, a person from central europe can't possibly be unaware of this > joke. I wouldn't call Norway central Europe, but then I also guess that you are not really Norwegian. > i know of a 60-page book collecting radio erewan jokes. deadly > serious. That would make you more of an expert in these kind of jokes than me. > > Classical Radio Eriwan stuff, and I thought this class of jokes have > > died out. > > apparently not, as long as there are people able to find them in > whatever they read. Not in whatever they read. There are necessary ingredients as you, as an expert on Radio Eriwan, should now. There has to be the phrase "in principle" and something self-contradictory. Plenty of things are written that could not possibly be interpreted as Radio Eriwan jokes. > > First, I think it is a rather ambitious jump in logic that a user is > > interested in stats because the user wants to see whether "8.3 - > > 7.3 > 1" is true. The only indication of the user being interested > > in stats would be that the user used R, which is used primarily for > > statistical analysis; > > that was my reasoning, good god! And as I said, probably a huge jump in logic and faith. > i'd agree that it's not a drawback to know how arithmetic is actually > done on computers (but hey, there is no unique standard here). but > many people i know (which certainly makes a poor statistic) would > prefer to be abstracted away from having to know that 8.8-7.8 > 1 is > true, less so why it is true. Well, these people should probably stick to pencil and paper. Or use an appropriate tool. As I mentioned to you in another thread, a good handyman does not blame his/her tools but selects the correct tool for the job. If I need dynamic memory allocation, I do not choose to use FORTRAN77 but some other language. If I need infinite precision arithmetic, then I do not choose R/Matlab/Scilab/Octave but some other tool. > not difficult at all to define an arithmetic where 1==0 is true, > document it in a man page, and refer to it when complaints come. > surely, an exotic example. You forget the bit that you first would have to convince some people that this is a useful arithmetic and have them start using it. And I am not convinced about the "not difficult" part anyway. > i know of cs guys who either have forgotten, or have never learned > (!). I am not surprised about CS guys never learning about these issues. As long as you play around with data bases (their organisation &c), sorting algorithms, artificial intelligence (at least when I attended a lecture on this) you do not need to know about these issues. And, unfortunately, it seems nowadays a lot of teaching is on a "need-to-know" and "just-in-time" basis. It just became criminal when CS guys who were into compiler design started to construct compilers that analysed the code and rearranged the calculations based on an analysis that assumed infinite precision arithmetic. Such compilers optimised away code that was designed to deal with finite precision arithmetic. I believe this was one of the motivations of Goldberg's article. Cheers, Berwin __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Reading txt file in R to run Random Intercept Model
>>> "Anamika Chaudhuri" <[EMAIL PROTECTED]> 08/12/2008 03:46:34 >>>
>I am using a random intercept model with SITEID as random and NAUSEA
as
>outcome.
Hardly surprising ;-)
More seriously, your data set fragment had only one level for SITEID. I
assume there were actually more levels?
S
***
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[R] Taylor diagram
Dear Everyone,
I wrote a Taylor diagram program in R, but it was not very general, so I was
happy to find the Taylor.diagram in the plotrix package.
On the other hand I can find many problems with the pos.cor=TRUE case, in other
words, when we use only the first quarter of the space (positive correlations).
(When we choose pos.cor=FALSE, the program seems to me perfect)
1.There is only one line around the (0,0) point:
I looked at this part of the program:
if (ref.sd) {
xcurve <- cos(seq(0, pi/2, by = 0.01)) * sd.r
ycurve <- sin(seq(0, pi/2, by = 0.01)) * sd.r
lines(xcurve, ycurve)
}
I have tried this part of the program (using sd.r=0 and naturally using a
plot(..)), it gave only one quarter circle and not a seq of them.
2. No lines helping to read the correlation easily at all.
Could you help me, how to correct the program to use as many sd, corr and rmse
line as I would like to?
Thank you very much for your help in advance!
Gabriella
[EMAIL PROTECTED]
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Re: [R] Permutation exact test to compare related series
Here's a paired-samples permutation test. Note that this does not obtain a
p-value based on all possible randomization orders, a test that by some
nomenclatures would be called a Randomization test and which I presume is
what you desire given the use of the word "exact" in your query.
Instead, the permutation test below it merely reshuffles the data randomly
many times; for small data sets this may achieve all possible randomization
orders, but for larger data sets it will more likely achieve only a subset
of all possible randomization orders. In any case, employing a large number
of randomization orders (set the "iterations" variable to something like
1e5) should provide a good approximation to the exact p-value. You can
always run the test several times to ensure all results are approximately
equal.
pairperm <- function(data1,data2,iterations,tails){
obs_diff = data1-data2 #create a vector of the difference scores
sim_diff = rep(0,length(data1)) #create an empty vector to be filled later
flip = rep(0,length(data1)) #create an empty vector to be filled later
all_data = as.data.frame(cbind(obs_diff,sim_diff,flip)) #create a table with
your difference scores and empty vectors as columns
obs_mean_diff = mean(all_data$obs_diff) #measure the observed mean
difference score
count = 1 #initialize counting variable
for(i in 1:iterations){ #start shuffling loop
all_data$flip = sample(c(-1,1),length(data1), replace=T) #randomly assign
cases to be flipped or not
all_data$sim_diff=all_data$obs_diff*all_data$flip #this flips the sign of
those cases marked for flip
sim_mean_diff = mean(all_data$sim_diff) #calculate the simulated mean
difference score
if(tails == 1){ #if one-tailed
if(obs_mean_diffwrote:
> I all,
> is there a way with R to perform an exact permutation test to replace the
> wilcoxon test to compare paired series and/or to perform pairwise multiple
> comparisons for related series after a Friedman test ?
> Thanks
> Gilles
>
> __
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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.
>
--
Mike Lawrence
Graduate Student
Department of Psychology
Dalhousie University
www.thatmike.com
Looking to arrange a meeting? Do so at:
http://www.timetomeet.info/with/mike/
~ Certainty is folly... I think. ~
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Re: [R] Questions on the results from glmmPQL(MASS)
Ben Bolker's response to a glmmPQL question below raises a question. Does the issue of bias with binomial data reported by Breslow (2003) remain valid with respect specifically to Ripley's treatment of PQL in glmmPQL? Breslow makes no reference to this particular implementation. He does discuss that of SAS GLIMMIX, but it does not work exactly as glmmPQL. I've compared results between binomial models between these two approaches, and they usually give compatible results. But they can diverge markedly in enough cases that I wish I understood just how they differ, so wonder if relative vulnerability to bias could be involved. BTW Ben refers Zhijie to a separate user group that focuses on mixed models. I knew nothing of this group. Following through on the link I found their archive, which included a fairly extensive thread on a question I posed to the regular R group in October. My question was forwarded, by Ben Bolker in fact (Wald F tests thread), for which I'm grateful. But I'm embarassed to say I only learned of the thread, even though I initiated it, because of this email. I just assumed no responses, other than R-News, and that was mostly questions to me about glmmPQL, rather than attempts to answer my own question. I'm clearly not the only one unaware of the mixed-models group, and a very sad choice for asking questions about glmmPQL. > Mark Fowler Population Ecology Division > Bedford Inst of Oceanography > Dept Fisheries & Oceans > Dartmouth NS Canada B2Y 4A2 Tel. (902) 426-3529 Fax (902) 426-9710 Email [EMAIL PROTECTED] Home Tel. (902) 461-0708 Home Email [EMAIL PROTECTED] -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Ben Bolker Sent: December 6, 2008 4:10 PM To: r-help@r-project.org Subject: Re: [R] Questions on the results from glmmPQL(MASS) zhijie zhang wrote: > > Dear Rusers, >I have used R,S-PLUS and SAS to analyze the sample data "bacteria" > in MASS package. Their results are listed below. > I have three questions, anybody can give me possible answers? > Q1:From the results, we see that R get 'NAs'for AIC,BIC and logLik, > while S-PLUS8.0 gave the exact values for them. Why? > This is a philosophical difference between S-PLUS and R. Since glmmPQL uses quasi-likelihood, technically there is no log-likelihood (hence no AIC nor BIC, which are based on the log-likelihood) for this model -- the argument is that one is limited to looking at Wald tests (testing the Z- or t-statistics, i.e. parameter estimates divided by estimated standard errors) for inference in this case. zhijie zhang wrote: > > Q2: The model to analyse the data is logity=b0+u+b1*trt+b2*I(week>2), > but the results for Random effects in R/SPLUS confused me. SAS may be clearer. > Random effects: > Formula: ~1 | ID >(Intercept) Residual > StdDev:1.410637 0.7800511 > Which is the random effect 'sigma'? I think it is "1.410637", but > what does "0.7800511" mean? That is, i want ot know how to explain/use > the above two data for Random effects. > The (Intercept) random effect is the variance in intercept across grouping factors . The residual (0.78) is (I believe) the individual-level error estimated for the underlying linear mixed model -- you can probably ignore this. zhijie zhang wrote: > > Q3:In SAS and other softwares, we can get *p*-values for the random > effect 'sigma', but i donot see the *p*-values in the results of > R/SPLUS. I have used attributes() to look for them, but no *p* values. > Anybody knows how to get *p*-values for the random effect 'sigma',. > Any suggestions or help are greatly appreciated. > #R Results:MASS' version 7.2-44; R version 2.7.2 > library(MASS) > summary(glmmPQL(y ~ trt + I(week > 2), random = ~ 1 | ID,family = > binomial, data = bacteria)) > > Linear mixed-effects model fit by maximum likelihood > Data: bacteria > AIC BIC logLik >NA NA NA > > Random effects: > Formula: ~1 | ID > (Intercept) Residual > StdDev:1.410637 0.7800511 > > Variance function: > Structure: fixed weights > Formula: ~invwt > Fixed effects: y ~ trt + I(week > 2) > Value Std.Error DF t-value > p-value > (Intercept) 3.4120140.5185033 169 6.580506 0. > trtdrug -1.247355 0.6440635 47 -1.936696 0.0588 > trtdrug+-0.7543270.6453978 47 -1.168779 0.2484 > I(week > 2)TRUE -1.607257 0.3583379 169 -4.485311 0. > Correlation: > (Intr) trtdrg trtdr+ > trtdrug -0.598 > trtdrug+-0.571 0.460 > I(week > 2)TRUE -0.537 0.047 -0.001 > > #S-PLUS8.0: The results are the same as R except the followings: > AIC BIClogLik > 1113.622 1133.984 -550.8111 > > #SAS9.1.3 > proc nlmixed data=b; > parms b0=-1 b1=1
[R] Transforming a string to a variable's name? help me newbie...
Dear all,
I'm a newbie in R.
I have a 45x2x2x8 design.
A dataframe stores the metadata of trials. And each trial has its own
data file: I used "read.table" to import every trial into R as a
dataframe (variable).
Now I dynamically ask R to retrieve trials that fit certain selection
criteria, so I use "subset", e.g.
tmptrialinfo <- subset(trialinfo, (Subject==24 & Filename=="v2msa8"))
The name of the dataframe / variable of an individual trial can be
obtained using:
paste("t",tmptrialinfo[1,2],tmptrialinfo[1,16],".gz",sep="")
Then I get a string:
"t24v2msa8.gz"
which is of the exact same name of the dataframe / variable of that
trial, which is:
t24v2msa8.gz
Can somebody tell me how can I change that string (obtained from
"paste()" above) to be a usable / manipulable variable name, so that I
can do something, such as:
(1)
tmptrial <- trialcompute(trialextract(
paste("t",tmptrialinfo[1,2],tmptrialinfo[1,16],".gz",sep="")
,tmptrialinfo[1,32],secs,sdm),secs,binsize)
instead of hardcoding:
(2)
tmptrial <-
trialcompute(trialextract(t24v2msa8.gz,tmptrialinfo[1,32],secs,sdm),secs,binsize)
Currently, 1) doesn't work...
Thanks in advance for your help!
Regards,
John
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] R - how to measure the distance?
Hi, I'm not sure that I fully understand your problem, so forgive me if my suggestion is irrelevant : maybe you should have a look to function geod.dist , in the oce package. Hope this helps. Olivier porzycka wrote: > > Hello, > I have been worked with R for 3 weeks. I have one problem. I could not > find the answer on it on web pages. I do not know how to measure the > shortes distance between point (Lon/Lat) and line. I used spatstat package > and distmap() but I want to calculate these distances only for particular > points without generate distance map. > > Thank you for all hints. > S.Porzycka > > __ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > > -- View this message in context: http://www.nabble.com/R---how-to-measure-the-distance--tp20879418p20897078.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] Permutation exact test to compare related series
Perhaps you will find useful code in the examples for freidman_test within package coin. They offer an implementation of the Wilcoxon- Nemenyi-McDonald-Thompson test. -- David Winsemius On Dec 8, 2008, at 6:15 AM, LE PAPE Gilles wrote: I all, is there a way with R to perform an exact permutation test to replace the wilcoxon test to compare paired series and/or to perform pairwise multiple comparisons for related series after a Friedman test ? Thanks Gilles __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] example of gladeXML - RGtk2
hello all, where I find a example or tutorial of RGtk2 package? I would like to know about the gladeXML functions in R. thanks in advance Cleber Borges __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Transforming a string to a variable's name? help me newbie...
On Dec 8, 2008, at 10:11 AM, tsunhin wong wrote:
Dear all,
I'm a newbie in R.
I have a 45x2x2x8 design.
A dataframe stores the metadata of trials. And each trial has its own
data file: I used "read.table" to import every trial into R as a
dataframe (variable).
Now I dynamically ask R to retrieve trials that fit certain selection
criteria, so I use "subset", e.g.
tmptrialinfo <- subset(trialinfo, (Subject==24 & Filename=="v2msa8"))
The name of the dataframe / variable of an individual trial can be
obtained using:
paste("t",tmptrialinfo[1,2],tmptrialinfo[1,16],".gz",sep="")
Then I get a string:
"t24v2msa8.gz"
which is of the exact same name of the dataframe / variable of that
trial, which is:
t24v2msa8.gz
Can somebody tell me how can I change that string (obtained from
"paste()" above) to be a usable / manipulable variable name, so that I
can do something, such as:
(1)
tmptrial <- trialcompute(trialextract(
paste("t",tmptrialinfo[1,2],tmptrialinfo[1,16],".gz",sep="")
,tmptrialinfo[1,32],secs,sdm),secs,binsize)
instead of hardcoding:
(2)
tmptrial <-
trialcompute
(trialextract(t24v2msa8.gz,tmptrialinfo[1,32],secs,sdm),secs,binsize)
It may have something to do with the semantics of trialextract about
which most useRs will know nothing (and I was unsuccessful in finding
a function by that name with an Rsitesearch). It seems strange that a
function would accept an unquoted reference to what is obviously a
file name. Perhaps you should be offering that code for inspection
rather than asking how to make a simple assignment. It is possible
that what you are really asking is answered by Faq 7.21:
http://cran.r-project.org/doc/FAQ/R-FAQ.html#How-can-I-turn-a-string-into-a-variable_003f
Currently, 1) doesn't work...
Saying "doesn't work" is not specific enough. What exactly was the
error message?
Thanks in advance for your help!
Regards,
John
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[R] multinomial losgitic regression--vglm()
Dear: I try to analysis multinomial logistic regression using vglm in VGAM package. However, I wonder how many levels of responses variable this command is suitable. I saw the examples in google search works for 3 levels, say 1,2,3. However, my response variable is more than 3 levels. Is it working for my case or have alternative approach? Many thanks! Xin [[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] ARMA models
Dear ALL: Could you please eamil me how to simulate Mixed Seasonal ARMA (p,q)x(P,Q)12 models [say ARMA(0,1)x(1,0)12 ]from R. With many thanks. Abou == AbouEl-Makarim Aboueissa, Ph.D. Assistant Professor of Statistics Department of Mathematics & Statistics University of Southern Maine 96 Falmouth Street P.O. Box 9300 Portland, ME 04104-9300 Tel: (207) 228-8389 Fax: (207) 780-5607 Email: [EMAIL PROTECTED] [EMAIL PROTECTED] http://www.usm.maine.edu/~aaboueissa/ Office: 301C Payson Smith [[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] Transforming a string to a variable's name? help me newbie...
?get
Sent from my iPhone
On Dec 8, 2008, at 7:11, "tsunhin wong" <[EMAIL PROTECTED]> wrote:
Dear all,
I'm a newbie in R.
I have a 45x2x2x8 design.
A dataframe stores the metadata of trials. And each trial has its own
data file: I used "read.table" to import every trial into R as a
dataframe (variable).
Now I dynamically ask R to retrieve trials that fit certain selection
criteria, so I use "subset", e.g.
tmptrialinfo <- subset(trialinfo, (Subject==24 & Filename=="v2msa8"))
The name of the dataframe / variable of an individual trial can be
obtained using:
paste("t",tmptrialinfo[1,2],tmptrialinfo[1,16],".gz",sep="")
Then I get a string:
"t24v2msa8.gz"
which is of the exact same name of the dataframe / variable of that
trial, which is:
t24v2msa8.gz
Can somebody tell me how can I change that string (obtained from
"paste()" above) to be a usable / manipulable variable name, so that I
can do something, such as:
(1)
tmptrial <- trialcompute(trialextract(
paste("t",tmptrialinfo[1,2],tmptrialinfo[1,16],".gz",sep="")
,tmptrialinfo[1,32],secs,sdm),secs,binsize)
instead of hardcoding:
(2)
tmptrial <-
trialcompute(
trialextract(t24v2msa8.gz,tmptrialinfo[1,32],secs,sdm),secs,binsize)
Currently, 1) doesn't work...
Thanks in advance for your help!
Regards,
John
__
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and provide commented, minimal, self-contained, reproducible code.
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[R] Save image as metafile
Hi, how can I save an image as a metafile? I know within windows you can do a right click and then 'save image as metafile' but I use Mac OS X...I know as well that mac users have a right click as well, but it does not work. Is there a command in R for saving images as metafiles? Regards, mentor -- View this message in context: http://www.nabble.com/Save-image-as-metafile-tp20894737p20894737.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] Query in Cuminc - stratification
Hello everyone,  I am a very new user of R and I have a query about the cuminc function in the package cmprsk. In particular I would like to verify that I am interpreting the output correctly when we have a stratification variable.  Hypothetical example:  group : fair hair, dark hair fstatus: 1=Relapse, 2=TRM, 0=censored strata: sex (M or F)  Our data would be split into:  Fair, male, relapse Dark,male, relapse Fair, female, relapse Dark, female, relapse  Fair, male, TRM Dark,male, TRM Fair, female, TRM Dark, female, TRM  Fair, male, censored Dark,male, censored Fair, female, censored Dark, female, censored  Am I correct in thinking that the 2 "Tests" which will be printed by R tell us (i) if there are significant differences between those with fair hair and those with dark hair as regards cumulative incidence of relapse [taking into account sex differences] (ii) if there are significant differences between those with fair hair and those with dark hair as regards cumulative incidence of TRM [taking into account sex differences] ? The âestâand âvarâvalues are the same regardless of whether we include a stratification variable or not.  If we do not include a stratification variable the âtestsâ results will be different to those when a stratification variable is included and they test (i) if there are significant differences between those with fair hair and those with dark hair as regards cumulative incidence of relapse (ii) if there are significant differences between those with fair hair and those with dark hair as regards cumulative incidence of TRM.  Just thought Iâd double check. Many thanks, Kim [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] statistics on "runs" of numbers
Dear R Users, Is there a package or some functionality in R which returns statistics on "runs" of numbers, i.e. series of numbers with similar qualities in a time series ? For example, the number of +ves,-ves, histograms on cumulations in runs, etc. ? Thanks in advance, Tolga Generally, this communication is for informational purposes only and it is not intended as an offer or solicitation for the purchase or sale of any financial instrument or as an official confirmation of any transaction. In the event you are receiving the offering materials attached below related to your interest in hedge funds or private equity, this communication may be intended as an offer or solicitation for the purchase or sale of such fund(s). All market prices, data and other information are not warranted as to completeness or accuracy and are subject to change without notice. Any comments or statements made herein do not necessarily reflect those of JPMorgan Chase & Co., its subsidiaries and affiliates. This transmission may contain information that is privileged, confidential, legally privileged, and/or exempt from disclosure under applicable law. If you are not the intended recipient, you are hereby notified that any disclosure, copying, distribution, or use of the information contained herein (including any reliance thereon) is STRICTLY PROHIBITED. Although this transmission and any attachments are believed to be free of any virus or other defect that might affect any computer system into which it is received and opened, it is the responsibility of the recipient to ensure that it is virus free and no responsibility is accepted by JPMorgan Chase & Co., its subsidiaries and affiliates, as applicable, for any loss or damage arising in any way from its use. If you received this transmission in error, please immediately contact the sender and destroy the material in its entirety, whether in electronic or hard copy format. Thank you. Please refer to http://www.jpmorgan.com/pages/disclosures for disclosures relating to UK legal entities. [[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] Transforming a string to a variable's name? help me newbie...
Dear Tsunhin,
Take a look at ?get
HTH,
Jorge
On Mon, Dec 8, 2008 at 10:11 AM, tsunhin wong <[EMAIL PROTECTED]> wrote:
> Dear all,
>
> I'm a newbie in R.
> I have a 45x2x2x8 design.
> A dataframe stores the metadata of trials. And each trial has its own
> data file: I used "read.table" to import every trial into R as a
> dataframe (variable).
>
> Now I dynamically ask R to retrieve trials that fit certain selection
> criteria, so I use "subset", e.g.
> tmptrialinfo <- subset(trialinfo, (Subject==24 & Filename=="v2msa8"))
>
> The name of the dataframe / variable of an individual trial can be
> obtained using:
> paste("t",tmptrialinfo[1,2],tmptrialinfo[1,16],".gz",sep="")
> Then I get a string:
> "t24v2msa8.gz"
> which is of the exact same name of the dataframe / variable of that
> trial, which is:
> t24v2msa8.gz
>
> Can somebody tell me how can I change that string (obtained from
> "paste()" above) to be a usable / manipulable variable name, so that I
> can do something, such as:
> (1)
> tmptrial <- trialcompute(trialextract(
> paste("t",tmptrialinfo[1,2],tmptrialinfo[1,16],".gz",sep="")
> ,tmptrialinfo[1,32],secs,sdm),secs,binsize)
> instead of hardcoding:
> (2)
> tmptrial <-
> trialcompute(trialextract(t24v2msa8.gz,tmptrialinfo[1,32],secs,sdm),secs,binsize)
>
> Currently, 1) doesn't work...
>
> Thanks in advance for your help!
>
> Regards,
>
> John
>
> __
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> 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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Re: [R] Transforming a string to a variable's name? help me newbie...
Thanks Jim and All!
It works:
tmptrial <- trialcompute(trialextract(
get(paste("t",tmptrialinfo[1,2],tmptrialinfo[1,16],".gz",sep="")) ,
tmptrialinfo[1,32],secs,sdm),secs,binsize)
Can I use "assign" instead? How should it be coded then?
Thanks!
- John
On Mon, Dec 8, 2008 at 10:40 AM, Jim Holtman <[EMAIL PROTECTED]> wrote:
> ?get
>
>
> Sent from my iPhone
>
> On Dec 8, 2008, at 7:11, "tsunhin wong" <[EMAIL PROTECTED]> wrote:
>
>> Dear all,
>>
>> I'm a newbie in R.
>> I have a 45x2x2x8 design.
>> A dataframe stores the metadata of trials. And each trial has its own
>> data file: I used "read.table" to import every trial into R as a
>> dataframe (variable).
>>
>> Now I dynamically ask R to retrieve trials that fit certain selection
>> criteria, so I use "subset", e.g.
>> tmptrialinfo <- subset(trialinfo, (Subject==24 & Filename=="v2msa8"))
>>
>> The name of the dataframe / variable of an individual trial can be
>> obtained using:
>> paste("t",tmptrialinfo[1,2],tmptrialinfo[1,16],".gz",sep="")
>> Then I get a string:
>> "t24v2msa8.gz"
>> which is of the exact same name of the dataframe / variable of that
>> trial, which is:
>> t24v2msa8.gz
>>
>> Can somebody tell me how can I change that string (obtained from
>> "paste()" above) to be a usable / manipulable variable name, so that I
>> can do something, such as:
>> (1)
>> tmptrial <- trialcompute(trialextract(
>> paste("t",tmptrialinfo[1,2],tmptrialinfo[1,16],".gz",sep="")
>> ,tmptrialinfo[1,32],secs,sdm),secs,binsize)
>> instead of hardcoding:
>> (2)
>> tmptrial <-
>> trialcompute(trialextract(t24v2msa8.gz,tmptrialinfo[1,32],secs,sdm),secs,binsize)
>>
>> Currently, 1) doesn't work...
>>
>> Thanks in advance for your help!
>>
>> Regards,
>>
>> John
>>
>> __
>> R-help@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> 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] legend at fixed distance form the bottom
I suggested the use of grconvertY if you want to place something exactly n
inches from the bottom, then grconvertY will give the user (or other)
coordinates that match, or if you want to place something exactly 10% of the
total device height from the bottom, etc.
What to do in replotting a graph afte a resize is usually tricky and requires
information that the program does not have and therefore has to guess at, that
is why it is safest to not depend on the computer doing the correct thing in a
resize and just tell the users to resize/set size before calling your function.
If you give a bit more detail on what you are trying to accomplish and what you
mean by fixed distance (number of inches, proportion of device height, margin
row, etc.) we may be better able to help.
--
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
[EMAIL PROTECTED]
801.408.8111
> -Original Message-
> From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
> project.org] On Behalf Of Christophe Genolini
> Sent: Saturday, December 06, 2008 7:08 AM
> To: Greg Snow
> Cc: r-help@r-project.org
> Subject: Re: [R] legend at fixed distance form the bottom
>
> Thanks for your answer.
>
> Unfortunatly, I can not create the graphice with the final size since I
> am writing a package in wich the user will have to chose between
> several
> graphics, and then he will have to export one. And they might be one
> graph, or 2x2, or 3x3...
>
> I check the grconvertY but I did not understand what you suggest. To
> me,
> the use of legend can not work since every length in the legend box
> (xlength, ylength, distance to axes) will change when resizing the
> graph. I was more expecting something like introduce the symbols used
> in
> the graph *in* the xlab. Is it possible ?
>
> Christophe
>
> > It is best to create the graphics device at the final size desired,
> then do the plotting and add the legend. For getting a fixed distance,
> look at the function grconvertY for one possibility.
> >
> > --
> > Gregory (Greg) L. Snow Ph.D.
> > Statistical Data Center
> > Intermountain Healthcare
> > [EMAIL PROTECTED]
> > 801.408.8111
> >
> >
> >
> >> -Original Message-
> >> From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
> >> project.org] On Behalf Of Christophe Genolini
> >> Sent: Friday, December 05, 2008 6:40 AM
> >> To: r-help@r-project.org
> >> Subject: [R] legend at fixed distance form the bottom
> >>
> >> Hi the list
> >>
> >> I would like to add a legend under a graph but at a fixed distance
> from
> >> the graphe. Is it possible ?
> >> More precisely, here is my code :
> >>
> >> --- 8<
> >> symboles <- c(3,4,5,6)
> >> dn <- rbind(matrix(rnorm(20),,5),matrix(rnorm(20,2),,5))
> >> listSymboles <- rep(symboles,each=2)
> >> matplot(t(dn),pch=listSymboles,type="b")
> >> legend("bottom", pch = unique(listSymboles), legend = c("ane",
> >> "cheval",
> >> "poney", "mule"), inset = c(0,-0.175), horiz = TRUE, xpd = NA)
> >> --- 8<
> >>
> >> But when I change the size of the graph, the legend is misplaced.
> >>
> >> Instead, I try to put some text in xlab, but I do not know how to
> get
> >> the +, x , V and other symbol.
> >> Does anyone got a solution ?
> >>
> >> Thanks a lot.
> >>
> >> Christophe
> >>
> >> __
> >> R-help@r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/r-help
> >> PLEASE do read the posting guide http://www.R-project.org/posting-
> >> guide.html
> >> and provide commented, minimal, self-contained, reproducible code.
> >>
> >
> >
>
> __
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> 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
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Re: [R] statistics on "runs" of numbers
rle(x) gives the run length encoding of x. rle(x>0) or rle(sign(x)) will do this for positive and negative values of x. albyn On Mon, Dec 08, 2008 at 03:24:50PM +, [EMAIL PROTECTED] wrote: > Dear R Users, > > Is there a package or some functionality in R which returns statistics on > "runs" of numbers, i.e. series of numbers with similar qualities in a time > series ? For example, the number of +ves,-ves, histograms on cumulations > in runs, etc. ? > > Thanks in advance, > Tolga > > > > Generally, this communication is for informational purposes only > and it is not intended as an offer or solicitation for the purchase > or sale of any financial instrument or as an official confirmation > of any transaction. In the event you are receiving the offering > materials attached below related to your interest in hedge funds or > private equity, this communication may be intended as an offer or > solicitation for the purchase or sale of such fund(s). All market > prices, data and other information are not warranted as to > completeness or accuracy and are subject to change without notice. > Any comments or statements made herein do not necessarily reflect > those of JPMorgan Chase & Co., its subsidiaries and affiliates. > > This transmission may contain information that is privileged, > confidential, legally privileged, and/or exempt from disclosure > under applicable law. If you are not the intended recipient, you > are hereby notified that any disclosure, copying, distribution, or > use of the information contained herein (including any reliance > thereon) is STRICTLY PROHIBITED. Although this transmission and any > attachments are believed to be free of any virus or other defect > that might affect any computer system into which it is received and > opened, it is the responsibility of the recipient to ensure that it > is virus free and no responsibility is accepted by JPMorgan Chase & > Co., its subsidiaries and affiliates, as applicable, for any loss > or damage arising in any way from its use. If you received this > transmission in error, please immediately contact the sender and > destroy the material in its entirety, whether in electronic or hard > copy format. Thank you. > Please refer to http://www.jpmorgan.com/pages/disclosures for > disclosures relating to UK legal entities. > [[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] statistics on "runs" of numbers
Many thanks, Tolga Albyn Jones <[EMAIL PROTECTED]> 08/12/2008 17:16 To [EMAIL PROTECTED] cc r-help@r-project.org Subject Re: [R] statistics on "runs" of numbers rle(x) gives the run length encoding of x. rle(x>0) or rle(sign(x)) will do this for positive and negative values of x. albyn On Mon, Dec 08, 2008 at 03:24:50PM +, [EMAIL PROTECTED] wrote: > Dear R Users, > > Is there a package or some functionality in R which returns statistics on > "runs" of numbers, i.e. series of numbers with similar qualities in a time > series ? For example, the number of +ves,-ves, histograms on cumulations > in runs, etc. ? > > Thanks in advance, > Tolga > > > > Generally, this communication is for informational purposes only > and it is not intended as an offer or solicitation for the purchase > or sale of any financial instrument or as an official confirmation > of any transaction. In the event you are receiving the offering > materials attached below related to your interest in hedge funds or > private equity, this communication may be intended as an offer or > solicitation for the purchase or sale of such fund(s). All market > prices, data and other information are not warranted as to > completeness or accuracy and are subject to change without notice. > Any comments or statements made herein do not necessarily reflect > those of JPMorgan Chase & Co., its subsidiaries and affiliates. > > This transmission may contain information that is privileged, > confidential, legally privileged, and/or exempt from disclosure > under applicable law. If you are not the intended recipient, you > are hereby notified that any disclosure, copying, distribution, or > use of the information contained herein (including any reliance > thereon) is STRICTLY PROHIBITED. Although this transmission and any > attachments are believed to be free of any virus or other defect > that might affect any computer system into which it is received and > opened, it is the responsibility of the recipient to ensure that it > is virus free and no responsibility is accepted by JPMorgan Chase & > Co., its subsidiaries and affiliates, as applicable, for any loss > or damage arising in any way from its use. If you received this > transmission in error, please immediately contact the sender and > destroy the material in its entirety, whether in electronic or hard > copy format. Thank you. > Please refer to http://www.jpmorgan.com/pages/disclosures for > disclosures relating to UK legal entities. >[[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. > Generally, this communication is for informational purposes only and it is not intended as an offer or solicitation for the purchase or sale of any financial instrument or as an official confirmation of any transaction. In the event you are receiving the offering materials attached below related to your interest in hedge funds or private equity, this communication may be intended as an offer or solicitation for the purchase or sale of such fund(s). All market prices, data and other information are not warranted as to completeness or accuracy and are subject to change without notice. Any comments or statements made herein do not necessarily reflect those of JPMorgan Chase & Co., its subsidiaries and affiliates. This transmission may contain information that is privileged, confidential, legally privileged, and/or exempt from disclosure under applicable law. If you are not the intended recipient, you are hereby notified that any disclosure, copying, distribution, or use of the information contained herein (including any reliance thereon) is STRICTLY PROHIBITED. Although this transmission and any attachments are believed to be free of any virus or other defect that might affect any computer system into which it is received and opened, it is the responsibility of the recipient to ensure that it is virus free and no responsibility is accepted by JPMorgan Chase & Co., its subsidiaries and affiliates, as applicable, for any loss or damage arising in any way from its use. If you received this transmission in error, please immediately contact the sender and destroy the material in its entirety, whether in electronic or hard copy format. Thank you. Please refer to http://www.jpmorgan.com/pages/disclosures for disclosures relating to UK legal entities. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] R 2.8.1 is scheduled for December 22
This is to announce that we plan to release R version 2.8.1 on Monday, December 22, 2008. Release procedures start Friday, December 12. Those directly involved should review the generic schedule at http://developer.r-project.org/release-checklist.html The source tarballs will be made available daily (barring build troubles) and the tarballs can be picked up at http://cran.r-project.org/src/base-prerelease/ a little later. Binary builds are expected to appear starting Monday 15 at the latest. For the Core Team Peter Dalgaard -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 ___ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-announce __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. ___ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-announce __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] partial correlation
Hej!
I have the following problem:
I would like to do partial correlations on non-parametric data. I checked
"pcor" (Computes the partial correlation between two variables given a set
of other variables) but I do not know how to change to a Spearman Rank
Correlation method [pcor(c("BCDNA","ImProd","A365"),var(PCor))]
Here's a glimpse of my data (data is raw data).
A436
A365
Chla
ImProd
BCDNA
0.001
0.003
0.624889
11.73023
0.776919
0.138
0.126
0.624889
27.29432
0.357468
0.075
0.056
0.624889
105.3115
0.429785
0.009
0.008
0.312444
55.2929
0.547752
0.005
0.002
0.624889
26.9638
0.738775
0.018
0.006
0.312444
31.14836
0.705814
0.02
0.018
2.22E-16
11.90303
0.755003
0.002
0.003
0.624889
7.829781
0.712091
0.047
0.044
1.523167
1.423823
0.710939
0.084
0.056
13.7085
1.533703
0.280171
Im really grateful for any help since I only recently started employing R.
Best regards,
JBL
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Re: [R] DLM - Covariates in the system equation
Hi Jens, I assume you are using package dlm. To add covariates to the system equation the workaround is to include psi in the state vector. Suppose your observation and system equations are as follow: Y[t] = F[t]theta[t] + v[t], v[t] ~ N[0,V] #observation equation theta[t] = G[t]theta[t-1] + Z[t]psi + w[t], w[t] ~ N[0,W] #system equation (Note that I wrote F[t]theta[t] instead of F'[t]theta[t], Z[t]psi instead of psi*Z[t], and G[t]theta[t-1] instead of simply theta[t-1]) Defining thetahat[t] = [theta[t]' psi']' Fhat[t] = [ F[t] 0 ] [ G[t] Z[t] ] Ghat[t] = [] [ 0 Id ] What = blockdiag(W, 0) you have a new DLM that satisfies your requirement. I hope this is clear enough for you to implement it in R. If not, please send a small example telling us what you want to do. By the way, questions about contributed packages should be addressed to the package maintainer first. Best, Giovanni Petris (author of package dlm) > Date: Mon, 08 Dec 2008 00:17:29 -0500 > From: [EMAIL PROTECTED] > Sender: [EMAIL PROTECTED] > Precedence: list > > Is there a way to add covariates to the system equation in a time-varying > approach: > > Y[t] = F'[t]theta[t] + v[t], v[t] ~ N[0,V] #observation equation > theta[t] = theta[t-1] + psi*Z[t] + w[t], w[t] ~ N[0,W] #system equation > > While F[t] is a matrix of regressors to capture the short term effect on > the response series Y, > Z[t] measures the long-term effect of either > (1) two policies by a step dummy or > (2) various policies with a continuous variable. > > I appreciate any kind of help! > Thanks in advance! > Jens > > __ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > > -- Giovanni Petris <[EMAIL PROTECTED]> Associate Professor Department of Mathematical Sciences University of Arkansas - Fayetteville, AR 72701 Ph: (479) 575-6324, 575-8630 (fax) http://definetti.uark.edu/~gpetris/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] gee niggles
I'm not sure if the gee package is still actively maintained, but I for one find it extremely useful. However, I've come across a few infelicities that I'm hoping could be resolved for future versions. Hope it's okay to list them all in one post! They are: (1) AR(1) models don't fit when clustsize = 1 for any subject, even if some subjects have clustsize > 1. (2) If the working correlation matrix has dimension less than 4x4, it doesn't get printed. (3) Using a "fixed" working correlation matrix stored in integer mode crashes R. To illustrate, generate some data: df <- data.frame(i = rep(1:5, each = 5), j = rep(1:5, 5), y = rep(rnorm(5), each = 5) + rnorm(25)) An AR(1) model fits fine to the full data: require(gee) gee(y ~ 1, id = i, df, corstr = "AR-M", Mv = 1) So also when some subjects have fewer observations than others: gee(y ~ 1, id = i, df, subset = j <= i + 1, corstr = "AR-M", Mv = 1) (1) However, when any subject (in this case, the first) has only 1 observation, gee bails out: gee(y ~ 1, id = i, df, subset = j <= i & j <= 2, corstr = "AR-M", Mv = 1) I see no particular reason an AR(1) working structure shouldn't be fit to these data. In fact, when (as here) there are at most two observations per subject, the AR(1) and exchangeable structures are equivalent, and the latter fits fine: gee(y ~ 1, id = i, df, subset = j <= i & j <= 2, corstr = "exchangeable") (2) This brings up the second niggle. When all cluster sizes are less than four, gee fits fine but the print method tries to extract elements of the working correlation matrix that don't exist (x$working.correlation[1:4, 1:4]): gee(y ~ 1, id = i, df, subset = j <= 3) (3) Finally, we might want to explicitly enter the identity matrix as the working correlation. If we do it this way gee(y ~ 1, id = i, df, corstr = "fixed", R = outer(1:5, 1:5, function(x, y) as.numeric(x == y))) then all is well, but like this # gee(y ~ 1, id = i, df, corstr = "fixed", R = outer(1:5, 1:5, function(x, y) as.integer(x == y))) # not run crashes R. I think it has to do with the correlation matrix being stored in integer mode: str(outer(1:5, 1:5, function(x, y) as.integer(x == y))) Presumably an explicit conversion to numeric mode would take care of this. Here's my sessionInfo(), in case it's of relevance: R version 2.7.2 (2008-08-25) i386-apple-darwin8.11.1 locale: en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] gee_4.13-13 Many thanks in advance! Daniel Farewell Cardiff University __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] how to fit nested random effects with LME
Dear experts I need to fit a model with nested random effects (cow within herd and season), and Im not sure how to do it with R. Using LME I know how to fit: cow within herd fit4 <- lme(milk ~ days + season + season*days , data=xxx, random = ~1 + days| herd/cow) How I can fit: cow within herd and season? In SAS I would write it: Proc mixed data=xxx; Class herd cow season; Model milk= days season days*season; Random intercept days/type=cssubject = cow(herd season) ; Thank for your help Maria _ Connect to the next generation of MSN Messenger http://imagine-msn.com/messenger/launch80/default.aspx?locale=en-us&source=wlmailtagline [[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 get Greenhouse-Geisser epsilons from anova?
Skotara wrote:
Thank you for your help!
Sorry, for bothering you again..
I still have trouble combining within and between subject factors.
Interactions of within factors and D having only 2 levels work well.
How can I get the main effect of D? I have tried anova(mlmfitD, mlmfit).
With D having 3 levels I would expect the dfs to be 2 and 33. However,
the output states 84,24??
That's not a main effect, it's a simultaneous test of all 28 components.
What you need is an analysis of the average of all
within-measurements. In principle that is obtained by X=~0, M=~1 or
T=matrix(1,1,28) but there's a bug that prevents it from working (fixed
in R-patched a couple of days ago).
As long as the between factor has only 2 levels the between/within
interactions fit well with SPSS, but if D has 3 levels, the mismatch is
immense.
If I calculate the within effects with myma having not 12 subjects from
one group but for example 24 from 2 groups, the output treats it as if
all subjects came from the same group, for example for main effect A the
dfs are 1 and 35. SPSS puts out 1 and 33 which is what I would have
expected.. ..
Hmm, there's a generic problem in that you can't get some of the
traditional ANOVA table F tests by comparing two models, and in your
case, SPSS is de facto using the residuals from a model with A:D
interaction when testing for A. It might help if you try
anova(mlmfitD, X=~..., M=~...)
Look at the (Intercept) line.
Peter Dalgaard schrieb:
Nils Skotara wrote:
Thank you, this helped me a lot!
All within effects and interactions work well!
Sorry, but I still could not get how to include the between factor..
If I include D with 2 levels, then myma is 24 by 28. (another 12 by
28 for the
second group of subjects.)
mlmfitD <- lm(myma~D) is no problem, but whatever I tried afterwards
did not seem logical to me.
I am afraid I do not understand how to include the between factor. I
cannot include ~D into M or X because it has length 24 whereas the other
factors have 28...
Just do the same as before, but comparing mlmfitD to mlmfit:
anova(mlmfitD, mlmfit, X=~A+B, M=~A+B+C)
# or anova(mlmfitD, mlmfit, X=~1, M=~C), as long as things are balanced
gives the D:C interaction test (by testing whether the C contrasts
depend on D). The four-factor interaction is
anova(mlmfitD, mlmfit, X=~(A+B+C)^2, M=~A*B*C)
Zitat von Peter Dalgaard <[EMAIL PROTECTED]>:
Skotara wrote:
Dear Mr. Daalgard.
thank you very much for your reply, it helped me to progress a bit.
The following works fine:
dd <- expand.grid(C = 1:7, B= c("r", "l"), A= c("c", "f"))
myma <- as.matrix(myma) #myma is a 12 by 28 list
mlmfit <- lm(myma~1)
mlmfit0 <- update(mlmfit, ~0)
anova(mlmfit, mlmfit0, X= ~C+B, M = ~A+C+B, idata = dd,
test="Spherical"), which tests the main effect of A.
anova(mlmfit, mlmfit0, X= ~A+C, M = ~A+C+B, idata = dd,
test="Spherical"), which tests the main effect of B.
However, I can not figure out how this works for the other effects.
If I try:
anova(mlmfit, mlmfit0, X= ~A+B, M = ~A+C+B, idata = dd,
test="Spherical")
I get:
Fehler in function (object, ..., test = c("Pillai", "Wilks",
"Hotelling-Lawley", :
residuals have rank 1 < 4
dd$C is not a factor with that construction. It works for me after
dd$C <- factor(dd$C)
(The other message is nasty, though. It's slightly different in
R-patched:
> anova(mlmfit, mlmfit0, X= ~A+B, M = ~A+C+B, idata = dd,
test="Spherical")
Error in solve.default(Psi, B) :
system is computationally singular: reciprocal condition number =
2.17955e-34
but it shouldn't happen...
Looks like it is a failure of the internal Thin.row function. Ick!
)
I also don't know how I can calculate the various interactions..
My read is I should change the second argument mlmfit0, too, but I
can't
figure out how...
The "within" interactions should be straightforward, e.g.
M=~A*B*C
X=~A*B*C-A:B:C
etc.
The within/between interactions are otained from the similar tests of
the between factor(s)
e.g.
mlmfitD <- lm(myma~D)
and then
anova(mlmfitD, mlmfit,)
--
O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B
c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K
(*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918
~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907
__
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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] Dates as x axis labels
Hello all, I wish to plot several hundred data groups in a boxplot(), with sensible labels on the x axis. For small datasets, this is possible by using the "names" parameter to the boxplot. However, for several hundred boxplots, boxplot() displays a tick on the x axis for every one. For my case, I am using Date objects from the chron package as the x labels. When passing a vector of Dates to plot() as the x values, plot() is intelligent enough to choose sensible major tick marks (e.g. the month name). Whereas boxplot() is picking arbitrary dates to show as the major tick marks. Does anybody know how to use Dates as labels in a boxplot() and have it use sensible values as the major tick marks? Note that I've tried using axis.Date() but it doesn't seem to do anything to a boxplot(). __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] legend at fixed distance form the bottom
Sorry, I will be more precise. Here is an example (simplified) of graph
I want :
8<
symboles <- c(3,4,5,6)
dn <- rbind(matrix(rnorm(20),5))
layout(matrix(c(1,1,1,2,2,3),3))
for(i in 1:3)
matplot(dn,type="b",xlab="+: a x: b ???: c ???: d",pch=symboles)
8<
But instead of ???, I want the "triangle" and the "losange".
So I try to use legend in order to get the losange and triangle :
--- 8<
for(i in 1:3){
matplot(dn,type="b",xlab="",pch=symboles)
legend("top", pch = unique(listSymboles),
legend = c("a","b","c","d"),
inset = c(0,1.1), horiz = TRUE, xpd = NA)
}
--- 8<
On the first plot, the legend is down, on the second, the legend is on a
correct position, on the third one, the legend in *on* the graduation.
So my problem is to plot either a legend at a fixed distance from the
graph or to put some symbol ("triangle", "losange" and all the other
since I might have more than 4 curves) in the xlab.
Any solution ?
Thanks
Christophe
I suggested the use of grconvertY if you want to place something exactly n
inches from the bottom, then grconvertY will give the user (or other)
coordinates that match, or if you want to place something exactly 10% of the
total device height from the bottom, etc.
What to do in replotting a graph afte a resize is usually tricky and requires
information that the program does not have and therefore has to guess at, that
is why it is safest to not depend on the computer doing the correct thing in a
resize and just tell the users to resize/set size before calling your function.
If you give a bit more detail on what you are trying to accomplish and what you
mean by fixed distance (number of inches, proportion of device height, margin
row, etc.) we may be better able to help.
--
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
[EMAIL PROTECTED]
801.408.8111
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
project.org] On Behalf Of Christophe Genolini
Sent: Saturday, December 06, 2008 7:08 AM
To: Greg Snow
Cc: r-help@r-project.org
Subject: Re: [R] legend at fixed distance form the bottom
Thanks for your answer.
Unfortunatly, I can not create the graphice with the final size since I
am writing a package in wich the user will have to chose between
several
graphics, and then he will have to export one. And they might be one
graph, or 2x2, or 3x3...
I check the grconvertY but I did not understand what you suggest. To
me,
the use of legend can not work since every length in the legend box
(xlength, ylength, distance to axes) will change when resizing the
graph. I was more expecting something like introduce the symbols used
in
the graph *in* the xlab. Is it possible ?
Christophe
It is best to create the graphics device at the final size desired,
then do the plotting and add the legend. For getting a fixed distance,
look at the function grconvertY for one possibility.
--
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
[EMAIL PROTECTED]
801.408.8111
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
project.org] On Behalf Of Christophe Genolini
Sent: Friday, December 05, 2008 6:40 AM
To: r-help@r-project.org
Subject: [R] legend at fixed distance form the bottom
Hi the list
I would like to add a legend under a graph but at a fixed distance
from
the graphe. Is it possible ?
More precisely, here is my code :
--- 8<
symboles <- c(3,4,5,6)
dn <- rbind(matrix(rnorm(20),,5),matrix(rnorm(20,2),,5))
listSymboles <- rep(symboles,each=2)
matplot(t(dn),pch=listSymboles,type="b")
legend("bottom", pch = unique(listSymboles), legend = c("ane",
"cheval",
"poney", "mule"), inset = c(0,-0.175), horiz = TRUE, xpd = NA)
--- 8<
But when I change the size of the graph, the legend is misplaced.
Instead, I try to put some text in xlab, but I do not know how to
get
the +, x , V and other symbol.
Does anyone got a solution ?
Thanks a lot.
Christophe
__
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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.
__
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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] Transforming a string to a variable's name? help me newbie...
In the long run it will probably make your life much easier to read all the
dataframes into one large list (and have the names of the elements be what your
currently name the dataframes), then you can just use regular list indexing
(using [[]] rather than $ in most cases) instead of having to worry about get
and assign and the risks/subtleties involved in using those.
Hope this helps,
--
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
[EMAIL PROTECTED]
801.408.8111
> -Original Message-
> From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
> project.org] On Behalf Of tsunhin wong
> Sent: Monday, December 08, 2008 8:45 AM
> To: Jim Holtman
> Cc: r-help@r-project.org
> Subject: Re: [R] Transforming a string to a variable's name? help me
> newbie...
>
> Thanks Jim and All!
>
> It works:
> tmptrial <- trialcompute(trialextract(
> get(paste("t",tmptrialinfo[1,2],tmptrialinfo[1,16],".gz",sep="")) ,
> tmptrialinfo[1,32],secs,sdm),secs,binsize)
>
> Can I use "assign" instead? How should it be coded then?
>
> Thanks!
>
> - John
>
> On Mon, Dec 8, 2008 at 10:40 AM, Jim Holtman <[EMAIL PROTECTED]>
> wrote:
> > ?get
> >
> >
> > Sent from my iPhone
> >
> > On Dec 8, 2008, at 7:11, "tsunhin wong" <[EMAIL PROTECTED]> wrote:
> >
> >> Dear all,
> >>
> >> I'm a newbie in R.
> >> I have a 45x2x2x8 design.
> >> A dataframe stores the metadata of trials. And each trial has its
> own
> >> data file: I used "read.table" to import every trial into R as a
> >> dataframe (variable).
> >>
> >> Now I dynamically ask R to retrieve trials that fit certain
> selection
> >> criteria, so I use "subset", e.g.
> >> tmptrialinfo <- subset(trialinfo, (Subject==24 &
> Filename=="v2msa8"))
> >>
> >> The name of the dataframe / variable of an individual trial can be
> >> obtained using:
> >> paste("t",tmptrialinfo[1,2],tmptrialinfo[1,16],".gz",sep="")
> >> Then I get a string:
> >> "t24v2msa8.gz"
> >> which is of the exact same name of the dataframe / variable of that
> >> trial, which is:
> >> t24v2msa8.gz
> >>
> >> Can somebody tell me how can I change that string (obtained from
> >> "paste()" above) to be a usable / manipulable variable name, so that
> I
> >> can do something, such as:
> >> (1)
> >> tmptrial <- trialcompute(trialextract(
> >> paste("t",tmptrialinfo[1,2],tmptrialinfo[1,16],".gz",sep="")
> >> ,tmptrialinfo[1,32],secs,sdm),secs,binsize)
> >> instead of hardcoding:
> >> (2)
> >> tmptrial <-
> >>
> trialcompute(trialextract(t24v2msa8.gz,tmptrialinfo[1,32],secs,sdm),sec
> s,binsize)
> >>
> >> Currently, 1) doesn't work...
> >>
> >> Thanks in advance for your help!
> >>
> >> Regards,
> >>
> >> John
> >>
> >> __
> >> R-help@r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/r-help
> >> PLEASE do read the posting guide
> >> http://www.R-project.org/posting-guide.html
> >> and provide commented, minimal, self-contained, reproducible code.
> >
>
> __
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-
> guide.html
> and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] legend at fixed distance form the bottom
Try this:
symboles <- c(3,4,5,6)
dn <- rbind(matrix(rnorm(20),5))
layout(matrix(c(1,1,1,2,2,3),3))
for(i in 1:3){
matplot(dn,type="b",xlab="",pch=symboles)
legend(grconvertX(0.5,'nfc'), grconvertY(0,'nfc'),
xjust=0.5, yjust=0,
pch = unique(symboles),
legend = c("a","b","c","d"),
horiz = TRUE, xpd = NA)
}
Does that do what you want? Or at least get you started in the correct
direction?
--
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
[EMAIL PROTECTED]
801.408.8111
> -Original Message-
> From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
> project.org] On Behalf Of Christophe Genolini
> Sent: Monday, December 08, 2008 11:28 AM
> To: Greg Snow
> Cc: r-help@r-project.org
> Subject: Re: [R] legend at fixed distance form the bottom
>
> Sorry, I will be more precise. Here is an example (simplified) of graph
> I want :
>
> 8<
>
> symboles <- c(3,4,5,6)
> dn <- rbind(matrix(rnorm(20),5))
> layout(matrix(c(1,1,1,2,2,3),3))
>
> for(i in 1:3)
> matplot(dn,type="b",xlab="+: a x: b ???: c ???: d",pch=symboles)
> 8<
>
> But instead of ???, I want the "triangle" and the "losange".
> So I try to use legend in order to get the losange and triangle :
>
> --- 8<
>
> for(i in 1:3){
> matplot(dn,type="b",xlab="",pch=symboles)
> legend("top", pch = unique(listSymboles),
> legend = c("a","b","c","d"),
> inset = c(0,1.1), horiz = TRUE, xpd = NA)
> }
>
> --- 8<
>
> On the first plot, the legend is down, on the second, the legend is on
> a
> correct position, on the third one, the legend in *on* the graduation.
> So my problem is to plot either a legend at a fixed distance from the
> graph or to put some symbol ("triangle", "losange" and all the other
> since I might have more than 4 curves) in the xlab.
>
> Any solution ?
>
> Thanks
>
> Christophe
>
>
>
>
>
> > I suggested the use of grconvertY if you want to place something
> exactly n inches from the bottom, then grconvertY will give the user
> (or other) coordinates that match, or if you want to place something
> exactly 10% of the total device height from the bottom, etc.
> >
> > What to do in replotting a graph afte a resize is usually tricky and
> requires information that the program does not have and therefore has
> to guess at, that is why it is safest to not depend on the computer
> doing the correct thing in a resize and just tell the users to
> resize/set size before calling your function.
> >
> > If you give a bit more detail on what you are trying to accomplish
> and what you mean by fixed distance (number of inches, proportion of
> device height, margin row, etc.) we may be better able to help.
> >
> > --
> > Gregory (Greg) L. Snow Ph.D.
> > Statistical Data Center
> > Intermountain Healthcare
> > [EMAIL PROTECTED]
> > 801.408.8111
> >
> >
> >
> >> -Original Message-
> >> From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
> >> project.org] On Behalf Of Christophe Genolini
> >> Sent: Saturday, December 06, 2008 7:08 AM
> >> To: Greg Snow
> >> Cc: r-help@r-project.org
> >> Subject: Re: [R] legend at fixed distance form the bottom
> >>
> >> Thanks for your answer.
> >>
> >> Unfortunatly, I can not create the graphice with the final size
> since I
> >> am writing a package in wich the user will have to chose between
> >> several
> >> graphics, and then he will have to export one. And they might be one
> >> graph, or 2x2, or 3x3...
> >>
> >> I check the grconvertY but I did not understand what you suggest. To
> >> me,
> >> the use of legend can not work since every length in the legend box
> >> (xlength, ylength, distance to axes) will change when resizing the
> >> graph. I was more expecting something like introduce the symbols
> used
> >> in
> >> the graph *in* the xlab. Is it possible ?
> >>
> >> Christophe
> >>
> >>
> >>> It is best to create the graphics device at the final size desired,
> >>>
> >> then do the plotting and add the legend. For getting a fixed
> distance,
> >> look at the function grconvertY for one possibility.
> >>
> >>> --
> >>> Gregory (Greg) L. Snow Ph.D.
> >>> Statistical Data Center
> >>> Intermountain Healthcare
> >>> [EMAIL PROTECTED]
> >>> 801.408.8111
> >>>
> >>>
> >>>
> >>>
> -Original Message-
> From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
> project.org] On Behalf Of Christophe Genolini
> Sent: Friday, December 05, 2008 6:40 AM
> To: r-help@r-project.org
> Subject: [R] legend at fixed distance form the bottom
>
> Hi the list
>
> I would like to add a legend under a graph but at a fixed distance
>
> >> from
> >>
> the graphe. Is it possible ?
> More precisely, here is my code :
>
> --- 8<
> symboles <- c(3,4,5,6)
> dn <- rbind(matrix(rnorm(20),,5),matrix(rnorm(20,2),,5))
> listSymboles <- rep(symboles,each=2)
> matplot(t(dn),pch=listSymboles,type="b")
> legend("bottom", pch = uni
[R] Clustering with Mahalanobis Distance
Dear R ExpeRts,
I'm having memory difficulties using mahalanobis distance to trying to cluster
in R. I was wondering if anyone has done it with a matrix of 6525x17 (or
something similar to that size). I have a matrix of 6525 genes and 17 samples.
I have my R memory increased to the max and am still getting "cannot allocate
vector of size" errors. My matrix "x" is actually a transpose of the original
matrix (as I want to cluster by samples and not genes). "y" is a vector of the
mean gene expression levels and "z" is the covariance matrix of "x" (I think
this is where the problem lies as the covariance matrix is enormous.
I can't really provide a reproducible example as I would have to attach my data
files, which I don't think anyone would appreciate.
rm(list=ls()) #removes everything from memory#
gc() #collects garbage#
memory.limit(size = 4095) #increases memory limit#
x <- as.matrix(read.table("x.txt", header=TRUE, row.names=1))
y <- as.matrix(read.table("y.txt", header=TRUE, row.names=1))
z <- as.matrix(read.table("z.txt", header=TRUE, row.names=1))
mal <- mahalanobis(x, y, z)
The ultimate goal is to run "hclust" with the mahalanobis distance matrix.
If anyone knows where I could find a more "memory friendly" function or any
advise as to what I might try to optimize my code, I would appreciate it.
sessionInfo() is below.
Many Thanks,
_
Patrick Richardson
Biostatistician - Program of Translational Medicine
Van Andel Research Institute - Webb Lab
333 Bostwick Avenue NE
Grand Rapids, MI 49503
R version 2.8.0 (2008-10-20)
i386-pc-mingw32
locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
States.1252;LC_MONETARY=English_United
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices datasets tcltk utils methods base
other attached packages:
[1] svSocket_0.9-5 svIO_0.9-5 R2HTML_1.59svMisc_0.9-5 svIDE_0.9-5
loaded via a namespace (and not attached):
[1] tools_2.8.0
This email message, including any attachments, is for th...{{dropped:9}}
__
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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] example of gladeXML - RGtk2
A good example of using glade with RGtk2 is the rattle package. See: http://rattle.togaware.com/ On Mon, Dec 8, 2008 at 8:15 AM, Cleber Nogueira Borges <[EMAIL PROTECTED]>wrote: > hello all, > > > where I find a example or tutorial of RGtk2 package? > I would like to know about the gladeXML functions in R. > > thanks in advance > > Cleber Borges > > __ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/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] lazy evaluation and scoping ?
I think actually it's both lazy evaluation and scoping. Here is how I
understand it.
Consider:
> flist <- vector("list",2) ## creates the empty list
> for(i in 1:2)slist[[i]] <- function()i
Now the RHS of the assignment is a function that returns the value of i.
That is:
> flist
function()i
[[2]]
function()i
So the question is: what will be the value of i when the function is
invoked? By R's lexical scoping rules it will be the value of i in the
enclosing environment of the function, which is the value of i in the
environment when the function is **defined** . This will be i = 2, the last
value of the for loop on exit. This is due to lazy evaluation -- the value
of i is not needed until the for() ends, as one can find by:
> sapply(flist,function(z)as.list(environment(z)))
$i
[1] 2
$i
[1] 2
Hence one gets the results you originally saw. Adding the force(i) statement
forces i to be evaluated separately at each iteration of the loop, thus
placing the current values of i at each iteration into each function's
enclosing environment.
HTH.
-- Bert Gunter
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On
Behalf Of Antonio, Fabio Di Narzo
Sent: Saturday, December 06, 2008 7:28 PM
To: Gabor Grothendieck
Cc: r-help@r-project.org
Subject: Re: [R] unexpected scoping behavior with functions created in a
loop
2008/12/6 Gabor Grothendieck <[EMAIL PROTECTED]>:
> The missing item is lazy evaluation. Try forcing the evaluation of i
> and then repeat:
>
> makeF <- function(i) { force(i); function() i }
Tnx! That works! Sometimes lazy evaluation + side effects is just too
much (complicated) for me:D
bests,
a.
>
>
> On Sat, Dec 6, 2008 at 9:22 PM, Antonio, Fabio Di Narzo
> <[EMAIL PROTECTED]> wrote:
>> Hi guys.
>> I recently stumbled on an unexpected behavior of R when using
>> functions created in a loop.
>> The problem is silly enough to me that I had hard time choosing a good
>> mail subject, not talking about searching in the archives...
>> After some experiments, I trimmed down the following minimal
>> reproducible example:
>> ###
>> makeF <- function(i) function() i
>>
>> fList <- list(makeF(1), makeF(2))
>> sapply(fList, do.call, list())
>> ##This works as expected (by me...):
>> #[1] 1 2
>>
>> ##Things go differently when creating functions in a for loop:
>> for(i in 1:2)
>> fList[[i]] <- makeF(i)
>> sapply(fList, do.call, list())
>> #[1] 2 2
>>
>> ##Same result with "lapply":
>> fList <- lapply(as.list(1:2), makeF)
>> sapply(fList, do.call, list())
>> #[1] 2 2
>> ###
>>
>> I evidently overlook some important detail, but I still can't get it.
>> Somebody can explain me what's happening there?
>> Bests,
>> antonio.
>>
>>> R.version
>> _
>> platform i686-pc-linux-gnu
>> arch i686
>> os linux-gnu
>> system i686, linux-gnu
>> status Patched
>> major 2
>> minor 8.0
>> year 2008
>> month 12
>> day04
>> svn rev47063
>> language R
>> version.string R version 2.8.0 Patched (2008-12-04 r47063)
>> --
>> Antonio, Fabio Di Narzo
>> Ph.D. student at
>> Department of Statistical Sciences
>> University of Bologna, Italy
>>
>> __
>> R-help@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>
>
--
Antonio, Fabio Di Narzo
Ph.D. student at
Department of Statistical Sciences
University of Bologna, Italy
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
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] partial correlation
not sure which library 'pcor' is in, but why don't you just use the ranks of
the variables and then perform the correlation on the ranks:
x<-sample(1:10,10,rep=T)
y<-x+ sample(1:10,10,rep=T)
cor(x,y)
cor(rank(x),rank(y))
HTH
david freedman
Jürg Brendan Logue wrote:
>
> Hej!
>
>
>
> I have the following problem:
>
>
>
> I would like to do partial correlations on non-parametric data. I checked
> "pcor" (Computes the partial correlation between two variables given a set
> of other variables) but I do not know how to change to a Spearman Rank
> Correlation method [pcor(c("BCDNA","ImProd","A365"),var(PCor))]
>
>
>
> Here's a glimpse of my data (data is raw data).
>
>
> A436
>
> A365
>
> Chla
>
> ImProd
>
> BCDNA
>
>
> 0.001
>
> 0.003
>
> 0.624889
>
> 11.73023
>
> 0.776919
>
>
> 0.138
>
> 0.126
>
> 0.624889
>
> 27.29432
>
> 0.357468
>
>
> 0.075
>
> 0.056
>
> 0.624889
>
> 105.3115
>
> 0.429785
>
>
> 0.009
>
> 0.008
>
> 0.312444
>
> 55.2929
>
> 0.547752
>
>
> 0.005
>
> 0.002
>
> 0.624889
>
> 26.9638
>
> 0.738775
>
>
> 0.018
>
> 0.006
>
> 0.312444
>
> 31.14836
>
> 0.705814
>
>
> 0.02
>
> 0.018
>
> 2.22E-16
>
> 11.90303
>
> 0.755003
>
>
> 0.002
>
> 0.003
>
> 0.624889
>
> 7.829781
>
> 0.712091
>
>
> 0.047
>
> 0.044
>
> 1.523167
>
> 1.423823
>
> 0.710939
>
>
> 0.084
>
> 0.056
>
> 13.7085
>
> 1.533703
>
> 0.280171
>
>
>
> Im really grateful for any help since I only recently started employing
> R.
>
>
>
> Best regards,
> JBL
>
>
>
>
>
>
>
>
>
>
>
>
> [[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.
>
>
-
David Freedman
Atlanta
--
View this message in context:
http://www.nabble.com/partial-correlation-tp20900010p20901761.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.
Re: [R] Save image as metafile
On Dec 8, 2008, at 7:51 AM, mentor_ wrote: Hi, how can I save an image as a metafile? I know within windows you can do a right click and then 'save image as metafile' but I use Mac OS X... Which means this question would be better posed on the Mac OS list. I know as well that mac users have a right click as well, but it does not work. Are you using the R.app? If so, then you need to focus on the quartz device window (by clicking on it or choosing it from the Window" pulldown menu) and choose Save as.. from the File menu. It will not offer to save it as a windows metafile, but rather does so as a pdf. In Preview you can open the pdf and then save as other formats, although wmf is not one of the options. If you prefer a tiff file, you could use Grab. Even LemkeSoft's GraphicConverter does not offer a WMF option, so it's probably a proprietary format that M$ is not documenting well or trying to restrict in some manner. To find out what devices are available, try: > capabilities() jpeg png tifftcltk X11 aqua http/ftp sockets libxml fifo clediticonv NLS TRUE TRUEFALSE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE profmemcairo FALSE TRUE So on my machine, a png device can get graphics output. That should provide all of the functionality of a wmf format and be much more cross-platform. Is there a command in R for saving images as metafiles? It would appear not, but why would it be necessary? What's wrong with the choice among jpeg, png, pdf or tiff? -- David Winsemius Regards, mentor -- View this message in context: http://www.nabble.com/Save-image-as-metafile-tp20894737p20894737.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Transforming a string to a variable's name? help me newbie...
I want to combine all dataframes into one large list too...
But each dataframe is a 35 columns x varying number of rows structure
(from 2000 to >9000 rows)
I have ~1500 dataframes of these to process, and that add up to >
1.5Gb of data...
Combining dataframes into a single one require me to transform each
single dataframe into one line, but I really don't have a good
solution for the varying number of rows scenario... And also, I don't
want to stall my laptop every time I run the data set: maybe I can do
that when my prof give me a ~ 4Gb ram desktop to run the script ;)
Thanks! :)
- John
On Mon, Dec 8, 2008 at 1:36 PM, Greg Snow <[EMAIL PROTECTED]> wrote:
> In the long run it will probably make your life much easier to read all the
> dataframes into one large list (and have the names of the elements be what
> your currently name the dataframes), then you can just use regular list
> indexing (using [[]] rather than $ in most cases) instead of having to worry
> about get and assign and the risks/subtleties involved in using those.
>
> Hope this helps,
>
> --
> Gregory (Greg) L. Snow Ph.D.
> Statistical Data Center
> Intermountain Healthcare
> [EMAIL PROTECTED]
> 801.408.8111
>
>
>> -Original Message-
>> From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
>> project.org] On Behalf Of tsunhin wong
>> Sent: Monday, December 08, 2008 8:45 AM
>> To: Jim Holtman
>> Cc: r-help@r-project.org
>> Subject: Re: [R] Transforming a string to a variable's name? help me
>> newbie...
>>
>> Thanks Jim and All!
>>
>> It works:
>> tmptrial <- trialcompute(trialextract(
>> get(paste("t",tmptrialinfo[1,2],tmptrialinfo[1,16],".gz",sep="")) ,
>> tmptrialinfo[1,32],secs,sdm),secs,binsize)
>>
>> Can I use "assign" instead? How should it be coded then?
>>
>> Thanks!
>>
>> - John
>>
>> On Mon, Dec 8, 2008 at 10:40 AM, Jim Holtman <[EMAIL PROTECTED]>
>> wrote:
>> > ?get
>> >
>> >
>> > Sent from my iPhone
>> >
>> > On Dec 8, 2008, at 7:11, "tsunhin wong" <[EMAIL PROTECTED]> wrote:
>> >
>> >> Dear all,
>> >>
>> >> I'm a newbie in R.
>> >> I have a 45x2x2x8 design.
>> >> A dataframe stores the metadata of trials. And each trial has its
>> own
>> >> data file: I used "read.table" to import every trial into R as a
>> >> dataframe (variable).
>> >>
>> >> Now I dynamically ask R to retrieve trials that fit certain
>> selection
>> >> criteria, so I use "subset", e.g.
>> >> tmptrialinfo <- subset(trialinfo, (Subject==24 &
>> Filename=="v2msa8"))
>> >>
>> >> The name of the dataframe / variable of an individual trial can be
>> >> obtained using:
>> >> paste("t",tmptrialinfo[1,2],tmptrialinfo[1,16],".gz",sep="")
>> >> Then I get a string:
>> >> "t24v2msa8.gz"
>> >> which is of the exact same name of the dataframe / variable of that
>> >> trial, which is:
>> >> t24v2msa8.gz
>> >>
>> >> Can somebody tell me how can I change that string (obtained from
>> >> "paste()" above) to be a usable / manipulable variable name, so that
>> I
>> >> can do something, such as:
>> >> (1)
>> >> tmptrial <- trialcompute(trialextract(
>> >> paste("t",tmptrialinfo[1,2],tmptrialinfo[1,16],".gz",sep="")
>> >> ,tmptrialinfo[1,32],secs,sdm),secs,binsize)
>> >> instead of hardcoding:
>> >> (2)
>> >> tmptrial <-
>> >>
>> trialcompute(trialextract(t24v2msa8.gz,tmptrialinfo[1,32],secs,sdm),sec
>> s,binsize)
>> >>
>> >> Currently, 1) doesn't work...
>> >>
>> >> Thanks in advance for your help!
>> >>
>> >> Regards,
>> >>
>> >> John
>> >>
>> >> __
>> >> R-help@r-project.org mailing list
>> >> https://stat.ethz.ch/mailman/listinfo/r-help
>> >> PLEASE do read the posting guide
>> >> http://www.R-project.org/posting-guide.html
>> >> and provide commented, minimal, self-contained, reproducible code.
>> >
>>
>> __
>> R-help@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide http://www.R-project.org/posting-
>> guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Save image as metafile
On Mon, 8 Dec 2008, David Winsemius wrote: On Dec 8, 2008, at 7:51 AM, mentor_ wrote: Hi, how can I save an image as a metafile? I know within windows you can do a right click and then 'save image as metafile' but I use Mac OS X... Which means this question would be better posed on the Mac OS list. I know as well that mac users have a right click as well, but it does not work. Are you using the R.app? If so, then you need to focus on the quartz device window (by clicking on it or choosing it from the Window" pulldown menu) and choose Save as.. from the File menu. It will not offer to save it as a windows metafile, but rather does so as a pdf. In Preview you can open the pdf and then save as other formats, although wmf is not one of the options. If you prefer a tiff file, you could use Grab. Even LemkeSoft's GraphicConverter does not offer a WMF option, so it's probably a proprietary format that M$ is not documenting well or trying to restrict in some manner. It is basically a set of calls to the (proprietary) Windows GDI. There seems to be no viable implementation on any other platform (except as a bitmap, but then there are lots of portable bitmap formats supported by R) To find out what devices are available, try: capabilities() jpeg png tifftcltk X11 aqua http/ftp sockets libxml fifo clediticonv NLS TRUE TRUEFALSE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE profmemcairo FALSE TRUE So on my machine, a png device can get graphics output. That should provide all of the functionality of a wmf format and be much more cross-platform. Not so: wmf is a primarily a vector format: however PDF is a good cross-platform substitute. Is there a command in R for saving images as metafiles? It would appear not, but why would it be necessary? What's wrong with the choice among jpeg, png, pdf or tiff? -- David Winsemius Regards, mentor -- View this message in context: http://www.nabble.com/Save-image-as-metafile-tp20894737p20894737.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. -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Transforming a string to a variable's name? help me newbie...
I really don't understand your concern. Something like:
> nms <- c('file1','file2','file3')
> my.data <- list()
> for (i in nms) my.data[[ i ]] <- read.table(i)
Will read in the files listed in the nms vector and put them into the list
my.data (each data frame is a single element of the list). This list will not
take up about the same amount of memory as if you read each file into a
dataframe in the global environment. And there is no transforming of data
frames (into 1 row or otherwise).
--
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
[EMAIL PROTECTED]
801.408.8111
> -Original Message-
> From: tsunhin wong [mailto:[EMAIL PROTECTED]
> Sent: Monday, December 08, 2008 1:34 PM
> To: Greg Snow
> Cc: Jim Holtman; r-help@r-project.org; [EMAIL PROTECTED]
> Subject: Re: [R] Transforming a string to a variable's name? help me
> newbie...
>
> I want to combine all dataframes into one large list too...
> But each dataframe is a 35 columns x varying number of rows structure
> (from 2000 to >9000 rows)
> I have ~1500 dataframes of these to process, and that add up to >
> 1.5Gb of data...
>
> Combining dataframes into a single one require me to transform each
> single dataframe into one line, but I really don't have a good
> solution for the varying number of rows scenario... And also, I don't
> want to stall my laptop every time I run the data set: maybe I can do
> that when my prof give me a ~ 4Gb ram desktop to run the script ;)
>
> Thanks! :)
>
> - John
>
> On Mon, Dec 8, 2008 at 1:36 PM, Greg Snow <[EMAIL PROTECTED]> wrote:
> > In the long run it will probably make your life much easier to read
> all the dataframes into one large list (and have the names of the
> elements be what your currently name the dataframes), then you can just
> use regular list indexing (using [[]] rather than $ in most cases)
> instead of having to worry about get and assign and the
> risks/subtleties involved in using those.
> >
> > Hope this helps,
> >
> > --
> > Gregory (Greg) L. Snow Ph.D.
> > Statistical Data Center
> > Intermountain Healthcare
> > [EMAIL PROTECTED]
> > 801.408.8111
> >
> >
> >> -Original Message-
> >> From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
> >> project.org] On Behalf Of tsunhin wong
> >> Sent: Monday, December 08, 2008 8:45 AM
> >> To: Jim Holtman
> >> Cc: r-help@r-project.org
> >> Subject: Re: [R] Transforming a string to a variable's name? help me
> >> newbie...
> >>
> >> Thanks Jim and All!
> >>
> >> It works:
> >> tmptrial <- trialcompute(trialextract(
> >> get(paste("t",tmptrialinfo[1,2],tmptrialinfo[1,16],".gz",sep="")) ,
> >> tmptrialinfo[1,32],secs,sdm),secs,binsize)
> >>
> >> Can I use "assign" instead? How should it be coded then?
> >>
> >> Thanks!
> >>
> >> - John
> >>
> >> On Mon, Dec 8, 2008 at 10:40 AM, Jim Holtman <[EMAIL PROTECTED]>
> >> wrote:
> >> > ?get
> >> >
> >> >
> >> > Sent from my iPhone
> >> >
> >> > On Dec 8, 2008, at 7:11, "tsunhin wong" <[EMAIL PROTECTED]> wrote:
> >> >
> >> >> Dear all,
> >> >>
> >> >> I'm a newbie in R.
> >> >> I have a 45x2x2x8 design.
> >> >> A dataframe stores the metadata of trials. And each trial has its
> >> own
> >> >> data file: I used "read.table" to import every trial into R as a
> >> >> dataframe (variable).
> >> >>
> >> >> Now I dynamically ask R to retrieve trials that fit certain
> >> selection
> >> >> criteria, so I use "subset", e.g.
> >> >> tmptrialinfo <- subset(trialinfo, (Subject==24 &
> >> Filename=="v2msa8"))
> >> >>
> >> >> The name of the dataframe / variable of an individual trial can
> be
> >> >> obtained using:
> >> >> paste("t",tmptrialinfo[1,2],tmptrialinfo[1,16],".gz",sep="")
> >> >> Then I get a string:
> >> >> "t24v2msa8.gz"
> >> >> which is of the exact same name of the dataframe / variable of
> that
> >> >> trial, which is:
> >> >> t24v2msa8.gz
> >> >>
> >> >> Can somebody tell me how can I change that string (obtained from
> >> >> "paste()" above) to be a usable / manipulable variable name, so
> that
> >> I
> >> >> can do something, such as:
> >> >> (1)
> >> >> tmptrial <- trialcompute(trialextract(
> >> >> paste("t",tmptrialinfo[1,2],tmptrialinfo[1,16],".gz",sep="")
> >> >> ,tmptrialinfo[1,32],secs,sdm),secs,binsize)
> >> >> instead of hardcoding:
> >> >> (2)
> >> >> tmptrial <-
> >> >>
> >>
> trialcompute(trialextract(t24v2msa8.gz,tmptrialinfo[1,32],secs,sdm),sec
> >> s,binsize)
> >> >>
> >> >> Currently, 1) doesn't work...
> >> >>
> >> >> Thanks in advance for your help!
> >> >>
> >> >> Regards,
> >> >>
> >> >> John
> >> >>
> >> >> __
> >> >> R-help@r-project.org mailing list
> >> >> https://stat.ethz.ch/mailman/listinfo/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.e
Re: [R] legend at fixed distance form the bottom
Thank you very much,
That's very close to what I want. Well, I would have love to let the
user manualy resize the graph, but I am not sur it is possible. So
that's enouth for me, thanks a lot.
Christophe
PS : with grconvertX(0.5,'nfc'), the legend is not center.
With grconvertX(0.535,'nfc'), it is almost center. Is it because the
left margin is larger than the right margin?
Try this:
symboles <- c(3,4,5,6)
dn <- rbind(matrix(rnorm(20),5))
layout(matrix(c(1,1,1,2,2,3),3))
for(i in 1:3){
matplot(dn,type="b",xlab="",pch=symboles)
legend(grconvertX(0.5,'nfc'), grconvertY(0,'nfc'),
xjust=0.5, yjust=0,
pch = unique(symboles),
legend = c("a","b","c","d"),
horiz = TRUE, xpd = NA)
}
Does that do what you want? Or at least get you started in the correct
direction?
--
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
[EMAIL PROTECTED]
801.408.8111
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
project.org] On Behalf Of Christophe Genolini
Sent: Monday, December 08, 2008 11:28 AM
To: Greg Snow
Cc: r-help@r-project.org
Subject: Re: [R] legend at fixed distance form the bottom
Sorry, I will be more precise. Here is an example (simplified) of graph
I want :
8<
symboles <- c(3,4,5,6)
dn <- rbind(matrix(rnorm(20),5))
layout(matrix(c(1,1,1,2,2,3),3))
for(i in 1:3)
matplot(dn,type="b",xlab="+: a x: b ???: c ???: d",pch=symboles)
8<
But instead of ???, I want the "triangle" and the "losange".
So I try to use legend in order to get the losange and triangle :
--- 8<
for(i in 1:3){
matplot(dn,type="b",xlab="",pch=symboles)
legend("top", pch = unique(listSymboles),
legend = c("a","b","c","d"),
inset = c(0,1.1), horiz = TRUE, xpd = NA)
}
--- 8<
On the first plot, the legend is down, on the second, the legend is on
a
correct position, on the third one, the legend in *on* the graduation.
So my problem is to plot either a legend at a fixed distance from the
graph or to put some symbol ("triangle", "losange" and all the other
since I might have more than 4 curves) in the xlab.
Any solution ?
Thanks
Christophe
I suggested the use of grconvertY if you want to place something
exactly n inches from the bottom, then grconvertY will give the user
(or other) coordinates that match, or if you want to place something
exactly 10% of the total device height from the bottom, etc.
What to do in replotting a graph afte a resize is usually tricky and
requires information that the program does not have and therefore has
to guess at, that is why it is safest to not depend on the computer
doing the correct thing in a resize and just tell the users to
resize/set size before calling your function.
If you give a bit more detail on what you are trying to accomplish
and what you mean by fixed distance (number of inches, proportion of
device height, margin row, etc.) we may be better able to help.
--
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
[EMAIL PROTECTED]
801.408.8111
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
project.org] On Behalf Of Christophe Genolini
Sent: Saturday, December 06, 2008 7:08 AM
To: Greg Snow
Cc: r-help@r-project.org
Subject: Re: [R] legend at fixed distance form the bottom
Thanks for your answer.
Unfortunatly, I can not create the graphice with the final size
since I
am writing a package in wich the user will have to chose between
several
graphics, and then he will have to export one. And they might be one
graph, or 2x2, or 3x3...
I check the grconvertY but I did not understand what you suggest. To
me,
the use of legend can not work since every length in the legend box
(xlength, ylength, distance to axes) will change when resizing the
graph. I was more expecting something like introduce the symbols
used
in
the graph *in* the xlab. Is it possible ?
Christophe
It is best to create the graphics device at the final size desired,
then do the plotting and add the legend. For getting a fixed
distance,
look at the function grconvertY for one possibility.
--
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
[EMAIL PROTECTED]
801.408.8111
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
project.org] On Behalf Of Christophe Genolini
Sent: Friday, December 05, 2008 6:40 AM
To: r-help@r-project.org
Subject: [R] legend at fixed distance form the bottom
Hi the list
I would like to add a legend under a graph but at a fixed distance
from
the graphe. Is it possible ?
More precisely, here is my code :
--- 8<
symboles <- c(3,4,5,6)
dn <- rbind(matrix(rnorm(20),,5),matrix(rnorm(20,2),,5))
listSymboles <- rep(symboles,each=2)
matplot(t(dn),pch=listSymbole
[R] Scan a folder for a given type of files
Dear R-users, I have found on the list several posts addressing the issue of getting data for a list of defined files. However, I found nothing about scanning a given folder and retrieving the list of, let's say, .txt files (I probably used the wrong keywords). Could someone tell me which posts or function help I should look at? Thanks in advance Sebastien __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Scan a folder for a given type of files
Sebastien, see ?list.files, especially the 'pattern' argument. For your particular case it is list.files(pattern="\\.txt$") You might want to use the 'ignore.case' argument as well. Gabor On Mon, Dec 8, 2008 at 10:53 PM, <[EMAIL PROTECTED]> wrote: > > > Dear R-users, > > I have found on the list several posts addressing the issue of getting data > for > a list of defined files. However, I found nothing about scanning a given > folder > and retrieving the list of, let's say, .txt files (I probably used the wrong > keywords). Could someone tell me which posts or function help I should look > at? > > Thanks in advance > > Sebastien > > __ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > -- Gabor Csardi <[EMAIL PROTECTED]> UNIL DGM __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Scan a folder for a given type of files
?files and the links therein. Seems like a most obvious keyword to me for asking about files ... Cheers, Bert Gunter -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of [EMAIL PROTECTED] Sent: Monday, December 08, 2008 1:54 PM To: r-help@r-project.org Subject: [R] Scan a folder for a given type of files Dear R-users, I have found on the list several posts addressing the issue of getting data for a list of defined files. However, I found nothing about scanning a given folder and retrieving the list of, let's say, .txt files (I probably used the wrong keywords). Could someone tell me which posts or function help I should look at? Thanks in advance Sebastien __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Multivariate kernel density estimation
Possible, yes (see fortune('Yoda')), but doing it can be a bit difficult.
Here is one approximation using an independent normal kernel in 2 dimensions:
kde.contour <- function(x,y=NULL, conf=0.95, xdiv=100, ydiv=100, kernel.sd ) {
xy <- xy.coords(x,y)
xr <- range(xy$x)
yr <- range(xy$y)
xr <- xr + c(-1,1)*0.1*diff(xr)
yr <- yr + c(-1,1)*0.1*diff(yr)
if(missing(kernel.sd)) {
kernel.sd <- c( diff(xr)/6, diff(yr)/6 )
} else if (length(kernel.sd)==1) {
kernel.sd <- rep(kernel.sd, 2)
}
xs <- seq(xr[1], xr[2], length.out=xdiv)
ys <- seq(yr[1], yr[2], length.out=ydiv)
mydf <- expand.grid( xx=xs, yy=ys )
tmpfun <- function(xx,yy) {
sum( dnorm(xx, xy$x, kernel.sd[1]) * dnorm(yy, xy$y,
kernel.sd[2]) )
}
z <- mapply(tmpfun, xx=mydf$xx, yy=mydf$yy)
sz <- sort(z, decreasing=TRUE)
cz <- cumsum(sz)
cz <- cz/cz[length(cz)]
cutoff <- sz[ which( cz > conf )[1] ]
plot(xy, xlab='x', ylab='y', xlim=xr, ylim=yr)
#contour( xs, ys, matrix(z, nrow=xdiv), add=TRUE, col='blue')
contour( xs, ys, matrix(z, nrow=xdiv), add=TRUE, col='red',
levels=cutoff, labels='')
invisible(NULL)
}
# test
kde.contour( rnorm(100), rnorm(100) )
# correlated data
my.xy <- MASS::mvrnorm(100, c(3,10), matrix( c(1,.8,.8,1), 2) )
kde.contour( my.xy, kernel.sd=.5 )
# compare to theoritical
lines(ellipse::ellipse( 0.8, scale=c(1,1), centre=c(3,10)), col='green')
# bimodal
new.xy <- rbind( MASS::mvrnorm(65, c(3,10), matrix( c(1,.6,.6,1),2) ),
MASS::mvrnorm(35, c(6, 7), matrix( c(1,.6,.6,1), 2) ) )
kde.contour( new.xy, kernel.sd=.75 )
For more than 2 dimensions it becomes more difficult (both to visualize and to
find the region, contour only works in 2 dimensions). You can also see that
the approximations are not great compared to the true theory, but possibly a
better kernel would improve that.
Hope this helps,
--
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
[EMAIL PROTECTED]
801.408.8111
> -Original Message-
> From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
> project.org] On Behalf Of Jeroen Ooms
> Sent: Monday, December 08, 2008 5:54 AM
> To: r-help@r-project.org
> Subject: [R] Multivariate kernel density estimation
>
>
> I would like to estimate a 95% highest density area for a multivariate
> parameter space (In the context of anova). Unfortunately I have only
> experience with univariate kernel density estimation, which is
> remarkebly
> easier :)
>
> Using Gibbs, i have sampled from a posterior distirbution of an Anova
> model
> with k means (mu) and 1 common residual variance (s2). The means are
> independent of eachother, but conditional on the residual variance. So
> now I
> have a data frame of say 10.000 iterations, and k+1 parameters.
>
> I am especially interested in the posterior distribution of the mu
> parameters, because I want to test the support for an inequalty
> constrained
> model (e.g. mu1 > mu2 > mu3). I wish to derive the multivariate 95%
> highest
> density parameter space for the mu parameters. For example, if I had a
> posterior distirbution with 2 means, this should somehow result in the
> circle or elipse that contains the 95% highest density area.
>
> Is something like this possible in R? All tips are welcome.
> --
> View this message in context: http://www.nabble.com/Multivariate-
> kernel-density-estimation-tp20894766p20894766.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] French IRC channel and mailing list ?
Dear all, For some time now, R is becomming more and more popular in more and more countries. France is for sure one of them, but french people being french one of the obstacle they might tackle is the lack of documentation and support in their native language. To offer this support in french an IRC channel (#Rfr on irc.freenode.net) was created some months ago, beside the official english channel #R. We (me (~juba) and Pierre-Yves Chibon (~pingou)) have to recognize that it has a very low activity right now but it's related to our lack of promotion about it. Another tool that could be useful to bring support in french (and other languages) would be dedicated mailing-lists. I've searched the archives to see if similar requests have already been made but couldn't manage to find one. So I would like to ask here the question, has there been any thought on the creation of dedicated R-help mailing-lists for the major languages such as Spanish, French, Chinese and others ? We had some thought about it and we actually think that it would be something useful for users to be able to receive some help (especially when their english is not really fluent). Thanks in advance for your answers, Sincerely, Pierre-Yves Chibon Julien Barnier __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Save image as metafile
On Dec 8, 2008, at 4:02 PM, Prof Brian Ripley wrote: On Mon, 8 Dec 2008, David Winsemius wrote: To find out what devices are available, try: capabilities() jpeg png tifftcltk X11 aqua http/ftp sockets libxml fifo clediticonv NLS TRUE TRUEFALSE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE profmemcairo FALSE TRUE So on my machine, a png device can get graphics output. That should provide all of the functionality of a wmf format and be much more cross-platform. Not so: wmf is a primarily a vector format: however PDF is a good cross-platform substitute. Thank you for the correction. I had conflated "lossless format" with "vector format". Perhaps the OP will be happier with pdf output. Will he be able to use cmd-S to bring up a Save as dialog if he is not running from R.app? -- David Winsemius Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] R and Scheme
I've read in many places that R semantics are based on Scheme semantics. As
a long-time Lisp user and implementor, I've tried to make this more precise,
and this is what I've found so far. I've excluded trivial things that
aren't basic semantic issues: support for arbitrary-precision integers;
subscripting; general style; etc. I would appreciate corrections or
additions from more experienced users of R -- I'm sure that some of the
points below simply reflect my ignorance.
==Similarities to Scheme==
R has first-class function closures. (i.e. correctly supports upward and
downward funarg).
R has a single namespace for functions and variables (Lisp-1).
==Important dissimilarities to Scheme (as opposed to other Lisps)==
R is not properly tail-recursive.
R does not have continuations or call-with-current-continuation or other
mechanisms for implementing coroutines, general iterators, and the like.
R supports keyword arguments.
==Similarities to Lisp and other dynamic languages, including Scheme==
R is runtime-typed and garbage-collected.
R supports nested read-eval-print loops for debugging etc.
R expressions are represented as user-manipulable data structures.
==Dissimilarities to all (modern) Lisps, including Scheme==
R has call-by-need, not call-by-object-value.
R does not have macros.
R objects are values, not pointers, so a<-1:10; b<-a; b[1]<-999; a[1] =>
999. Similarly, functions cannot modify the contents of their arguments.
There is no equivalent to set-car!/rplaca (not even pairlists and
expressions). For example, r<-pairlist(1,2); r[[1]]<-r does not create a
circular list. And in general there doesn't seem to be substructure sharing
at the semantic level (though there may be in the implementation).
R does not have multiple value return in the Lisp sense.
R assignment creates a new local variable on first assignment, dynamically.
So static analysis is not enough to determine variable reference (R is not
referentially transparent). Example: ff <- function(a){if (a) x<-1; x} ;
x<-99; ff(T) -> 1; ff(F) -> 99.
In R, most data types (including numeric vectors) do not have a standard
external representation which can be read back in without evaluation.
R coerces logicals to numbers and numbers to strings. Lisps are stricter
about automatic type conversion -- except that false a.k.a. NIL == () in
Lisps other than Scheme.
[[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] How to get Greenhouse-Geisser epsilons from anova?
Dear Peter and Nils,
I hesitate to repeat this (though I'm going to do it anyway!), but it's
quite simple to get these tests from Anova() in the car package. Here's an
example from ?Anova of a repeated-measures ANOVA with two within and two
between-subject factors:
-- snip ---
Anova> ## a multivariate linear model for repeated-measures data
Anova> ## See ?OBrienKaiser for a description of the data set used in this
example.
Anova>
Anova> phase <- factor(rep(c("pretest", "posttest", "followup"), c(5, 5,
5)),
Anova+ levels=c("pretest", "posttest", "followup"))
Anova> hour <- ordered(rep(1:5, 3))
Anova> idata <- data.frame(phase, hour)
Anova> idata
phase hour
1 pretest1
2 pretest2
3 pretest3
4 pretest4
5 pretest5
6 posttest1
7 posttest2
8 posttest3
9 posttest4
10 posttest5
11 followup1
12 followup2
13 followup3
14 followup4
15 followup5
Anova> mod.ok <- lm(cbind(pre.1, pre.2, pre.3, pre.4, pre.5,
Anova+ post.1, post.2, post.3, post.4, post.5,
Anova+ fup.1, fup.2, fup.3, fup.4, fup.5) ~
treatment*gender,
Anova+ data=OBrienKaiser)
Anova> (av.ok <- Anova(mod.ok, idata=idata, idesign=~phase*hour))
Type II Repeated Measures MANOVA Tests: Pillai test statistic
Df test stat approx F num Df den DfPr(>F)
treatment20.4809 4.6323 2 10 0.0376868 *
gender 10.2036 2.5558 1 10 0.1409735
treatment:gender 20.3635 2.8555 2 10 0.1044692
phase10.8505 25.6053 2 9 0.0001930
***
treatment:phase 20.6852 2.6056 4 20 0.0667354 .
gender:phase 10.0431 0.2029 2 9 0.8199968
treatment:gender:phase 20.3106 0.9193 4 20 0.4721498
hour 10.9347 25.0401 4 7 0.0003043
***
treatment:hour 20.3014 0.3549 8 16 0.9295212
gender:hour 10.2927 0.7243 4 7 0.6023742
treatment:gender:hour20.5702 0.7976 8 16 0.6131884
phase:hour 10.5496 0.4576 8 3 0.8324517
treatment:phase:hour 20.6637 0.2483 16 8 0.9914415
gender:phase:hour10.6950 0.8547 8 3 0.6202076
treatment:gender:phase:hour 20.7928 0.3283 16 8 0.9723693
---
Signif. codes: 0 *** 0.001 ** 0.01 * 0.05 . 0.1 1
Anova> summary(av.ok, multivariate=FALSE)
Univariate Type II Repeated-Measures ANOVA Assuming Sphericity
SS num Df Error SS den Df FPr(>F)
treatment 211.286 2 228.056 10 4.6323 0.037687
*
gender 58.286 1 228.056 10 2.5558 0.140974
treatment:gender130.241 2 228.056 10 2.8555 0.104469
phase 167.500 2 80.278 20 20.8651 1.274e-05
***
treatment:phase 78.668 4 80.278 20 4.8997 0.006426
**
gender:phase 1.668 2 80.278 20 0.2078 0.814130
treatment:gender:phase 10.221 4 80.278 20 0.6366 0.642369
hour106.292 4 62.500 40 17.0067 3.191e-08
***
treatment:hour1.161 8 62.500 40 0.0929 0.999257
gender:hour 2.559 4 62.500 40 0.4094 0.800772
treatment:gender:hour 7.755 8 62.500 40 0.6204 0.755484
phase:hour 11.083 8 96.167 80 1.1525 0.338317
treatment:phase:hour 6.262 16 96.167 80 0.3256 0.992814
gender:phase:hour 6.636 8 96.167 80 0.6900 0.699124
treatment:gender:phase:hour 14.155 16 96.167 80 0.7359 0.749562
---
Signif. codes: 0 *** 0.001 ** 0.01 * 0.05 . 0.1 1
Mauchly Tests for Sphericity
Test statistic p-value
phase 0.74927 0.27282
treatment:phase0.74927 0.27282
gender:phase 0.74927 0.27282
treatment:gender:phase 0.74927 0.27282
hour 0.06607 0.00760
treatment:hour 0.06607 0.00760
gender:hour0.06607 0.00760
treatment:gender:hour 0.06607 0.00760
phase:hour 0.00478 0.44939
treatment:phase:hour 0.00478 0.44939
gender:phase:hour 0.00478 0.44939
treatment:gender:phase:hour0.00478 0.44939
Greenhouse-Geisser and Huynh-Feldt Corrections
for Departure from Sphericity
GG eps Pr(>F[GG])
phase 0.79953 7.323e-05 ***
treatment:phase 0.799530.01223 *
gender:
Re: [R] R and Scheme
On Mon, 8 Dec 2008, Stavros Macrakis wrote:
I've read in many places that R semantics are based on Scheme semantics. As
a long-time Lisp user and implementor, I've tried to make this more precise,
and this is what I've found so far. I've excluded trivial things that
aren't basic semantic issues: support for arbitrary-precision integers;
subscripting; general style; etc. I would appreciate corrections or
additions from more experienced users of R -- I'm sure that some of the
points below simply reflect my ignorance.
==Similarities to Scheme==
R has first-class function closures. (i.e. correctly supports upward and
downward funarg).
R has a single namespace for functions and variables (Lisp-1).
==Important dissimilarities to Scheme (as opposed to other Lisps)==
R is not properly tail-recursive.
True at present. May be unavoidable since the language provides
access to the stack via things like sys.parent, but as it is rare to
look at anything other than the immediate calling environment and call
(outside of a debugging context) it may be possible to change that.
R does not have continuations or call-with-current-continuation or other
mechanisms for implementing coroutines, general iterators, and the like.
R supports keyword arguments.
==Similarities to Lisp and other dynamic languages, including Scheme==
R is runtime-typed and garbage-collected.
R supports nested read-eval-print loops for debugging etc.
R expressions are represented as user-manipulable data structures.
==Dissimilarities to all (modern) Lisps, including Scheme==
R has call-by-need, not call-by-object-value.
R does not have macros.
Those are related -- because of lazy evaluation one does macros are
not needed to achive semantic goals (see for example tryCatch). Being
able to define friendlier syntax would sometimes be nice though (see
tryCatch again).
R objects are values, not pointers, so a<-1:10; b<-a; b[1]<-999; a[1] =>
999. Similarly, functions cannot modify the contents of their arguments.
There is no equivalent to set-car!/rplaca (not even pairlists and
expressions). For example, r<-pairlist(1,2); r[[1]]<-r does not create a
circular list. And in general there doesn't seem to be substructure sharing
at the semantic level (though there may be in the implementation).
R does not have multiple value return in the Lisp sense.
R assignment creates a new local variable on first assignment, dynamically.
So static analysis is not enough to determine variable reference (R is not
referentially transparent). Example: ff <- function(a){if (a) x<-1; x} ;
x<-99; ff(T) -> 1; ff(F) -> 99.
Correct, and a fair nuisance for code analysis and compilation work.
I'm not sure how much would break if R adopted the conventions in
Python (or with Scheme's define as I recall) that referencing a not
yet initialized local variable is an error.
I'm not sure I would label this as meaning R is not referentially
transparent thoug -- that goes out the window with mutable bindings as
also available in Scheme.
In R, most data types (including numeric vectors) do not have a standard
external representation which can be read back in without evaluation.
The default print form is not readable in this sense but dput is
available for this purpose.
R coerces logicals to numbers and numbers to strings. Lisps are stricter
about automatic type conversion -- except that false a.k.a. NIL == () in
Lisps other than Scheme.
A more important difference may be that logicals can have three values
-- TRUE, FALSE and NA.
luke
[[alternative HTML version deleted]]
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--
Luke Tierney
Chair, Statistics and Actuarial Science
Ralph E. Wareham Professor of Mathematical Sciences
University of Iowa Phone: 319-335-3386
Department of Statistics andFax: 319-335-3017
Actuarial Science
241 Schaeffer Hall email: [EMAIL PROTECTED]
Iowa City, IA 52242 WWW: http://www.stat.uiowa.edu
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Re: [R] R and Scheme
A few comments interspersed.
On Mon, Dec 8, 2008 at 5:59 PM, Stavros Macrakis <[EMAIL PROTECTED]> wrote:
> I've read in many places that R semantics are based on Scheme semantics. As
> a long-time Lisp user and implementor, I've tried to make this more precise,
> and this is what I've found so far. I've excluded trivial things that
> aren't basic semantic issues: support for arbitrary-precision integers;
> subscripting; general style; etc. I would appreciate corrections or
> additions from more experienced users of R -- I'm sure that some of the
> points below simply reflect my ignorance.
>
> ==Similarities to Scheme==
>
> R has first-class function closures. (i.e. correctly supports upward and
> downward funarg).
>
> R has a single namespace for functions and variables (Lisp-1).
Environments can be used to create separate name spaces.
R packages can use the NAMESPACE file to set up their own namespace.
>
> ==Important dissimilarities to Scheme (as opposed to other Lisps)==
>
> R is not properly tail-recursive.
>
> R does not have continuations or call-with-current-continuation or other
> mechanisms for implementing coroutines, general iterators, and the like.
>
True although there is callCC but it just lets you jump right of a nested
sequence of calls.
> R supports keyword arguments.
>
> ==Similarities to Lisp and other dynamic languages, including Scheme==
>
> R is runtime-typed and garbage-collected.
>
> R supports nested read-eval-print loops for debugging etc.
>
> R expressions are represented as user-manipulable data structures.
>
> ==Dissimilarities to all (modern) Lisps, including Scheme==
>
> R has call-by-need, not call-by-object-value.
Call by need?
>
> R does not have macros.
You can create them. See:
Programmer's Niche: Macros in R
http://cran.r-project.org/doc/Rnews/Rnews_2001-3.pdf
>
> R objects are values, not pointers, so a<-1:10; b<-a; b[1]<-999; a[1] =>
> 999. Similarly, functions cannot modify the contents of their arguments.
>
a[1] is not 999 after the above completes (if that is what is meant by
a[1] => 999):
> a<-1:10; b<-a; b[1]<-999
> a
[1] 1 2 3 4 5 6 7 8 9 10
> There is no equivalent to set-car!/rplaca (not even pairlists and
> expressions). For example, r<-pairlist(1,2); r[[1]]<-r does not create a
> circular list. And in general there doesn't seem to be substructure sharing
> at the semantic level (though there may be in the implementation).
>
> R does not have multiple value return in the Lisp sense.
You can do this:
http://finzi.psych.upenn.edu/R/Rhelp02a/archive/36820.html
> R assignment creates a new local variable on first assignment, dynamically.
> So static analysis is not enough to determine variable reference (R is not
> referentially transparent). Example: ff <- function(a){if (a) x<-1; x} ;
> x<-99; ff(T) -> 1; ff(F) -> 99.
>
> In R, most data types (including numeric vectors) do not have a standard
> external representation which can be read back in without evaluation.
???
>
> R coerces logicals to numbers and numbers to strings. Lisps are stricter
> about automatic type conversion -- except that false a.k.a. NIL == () in
> Lisps other than Scheme.
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[R] How to display y-axis labels in Multcomp plot
Dear R-users, I'm currently using the multcomp package to produce plots of means with 95% confidence intervals i.e. mult<-glht(lm(response~treatment, data=statdata), linfct=mcp(treatment="Means")) plot(confint(mult,calpha = sig)) Unfortunately the y-axis on the plot appears to be fixed and hence if the labels on the y-axis (treatment levels) are too long, then they are not displayed in full on the plot. Of course I could always make the labels shorter but I was wondering if there was a way to make the position of the y-axis on the plot more flexible, such as in the scatterplot produced using xyplot function, that would allow me to view the labels in full. Thanks in advance for any advice! Simon -- View this message in context: http://www.nabble.com/How-to-display-y-axis-labels-in-Multcomp-plot-tp20904977p20904977.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] custom panel help in lattice
On Sun, Dec 7, 2008 at 9:37 AM, Jon Loehrke <[EMAIL PROTECTED]> wrote:
> Hi,
>
> I am having an issue with a custom panel for lattice. The problem
> comes when I try passing a groups argument.
>
> Here is the custom panel, a wrapper for smooth spline. I copied
> panel.loess and replaced the loess arguments with smooth.spline().
> [Note: I would like to use the cross-validation fitting properties of
> smooth.spline.]
>
> library(lattice)
>
> panel.smooth.spline<-function(x,y,w=NULL, df, spar = NULL, cv = FALSE,
>lwd=plot.line$lwd, lty=plot.line$lty,col, col.line=plot.line$col,
>type, horizontal=FALSE,... ){
>
>x <- as.numeric(x)
>y <- as.numeric(y)
>ok <- is.finite(x) & is.finite(y)
>if (sum(ok) < 1)
>return()
>if (!missing(col)) {
>if (missing(col.line))
>col.line <- col
>}
>plot.line <- trellis.par.get("plot.line")
>if (horizontal) {
>spline <- smooth.spline(y[ok], x[ok], ...)
>panel.lines(x = spline$y, y = spline$x, col = col.line,
>lty = lty, lwd = lwd, ...)
>}
>else {
>spline <- smooth.spline(x[ok], y[ok],...)
>panel.lines(x = spline$x, y = spline$y, col = col.line,
>lty = lty, lwd = lwd, ...)
>}
>}
>
>
> # Here is my test data frame
> set.seed(25)
> test<-data.frame(x=c(1:200), y=rnorm(200), groups=gl(4,200/4))
>
> # This call to xyplot works, but the smoother colors are not unique.
>
> xyplot(y~x|groups, data=test,
>panel=function(...){
>panel.xyplot(...)
>panel.smooth.spline(...)
>})
>
> # This call to xyplot doesn't work and results in an error "error
> using packet"
>
> xyplot(y~x|groups, data=test, groups=groups,
>panel=function(...){
>panel.xyplot(...)
>panel.smooth.spline(...)
>})
>
> I think this should be quite simple but I must be too simple minded.
> Thanks for any help.
You end up calling smooth.spline() with arguments it doesn't
recognize. One work-around is defining 'panel.smooth.spline' as
follows:
panel.smooth.spline <-
function(x, y,
w=NULL, df, spar = NULL, cv = FALSE,
lwd=plot.line$lwd, lty=plot.line$lty,col, col.line=plot.line$col,
type, horizontal=FALSE,... )
{
x <- as.numeric(x)
y <- as.numeric(y)
ok <- is.finite(x) & is.finite(y)
if (sum(ok) < 1)
return()
if (!missing(col)) {
if (missing(col.line))
col.line <- col
}
plot.line <- trellis.par.get("plot.line")
if (horizontal) {
spline <-
smooth.spline(y[ok], x[ok],
w=w, df=df, spar = spar, cv = cv)
panel.lines(x = spline$y, y = spline$x, col = col.line,
lty = lty, lwd = lwd, ...)
}
else {
spline <-
smooth.spline(x[ok], y[ok],
w=w, df=df, spar = spar, cv = cv)
panel.lines(x = spline$x, y = spline$y, col = col.line,
lty = lty, lwd = lwd, ...)
}
}
-Deepayan
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Re: [R] Identifying a subset of observations on a 3d-scatter plot using cloud()
On Sat, Dec 6, 2008 at 9:27 PM, Giam Xingli <[EMAIL PROTECTED]> wrote:
> Hello everyone,
>
> This is my first post to the mailing list, so I hope I am posting my message
> the correct way.
>
> I am trying to present my dataset in a 3d scatterplot using cloud() in the
> {lattice} package. I hope to explicitly identify a subset of my observations.
> The observations in this subset need to satisfy the following critera (values
> on x,y, and z axes above a certain cutoff value). It will be great if I can
> get advice on how to annotate the points representing the subset of
> observations with a different colour, and if possible, label the points.
>
For colors, you could try
cloud(z ~ x * y, ..., groups = (x > c1 & y > c2 & z > c3))
For interactive labeling, see ?panel.identify.cloud. Direct labeling
is also possible, but you need to write a panel function
('panel.3dtext' in the latticeExtra pacakge may help).
-Deepayan
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Re: [R] How to display y-axis labels in Multcomp plot
See ?par and note the 'mar' parameter
Here's an example:
library(multcomp)
labs <- c('short', 'medium', 'long')
treatment <- gl(3, 10, labels = labs)
response <- rnorm(30, mean=as.numeric(treatment))
mult <- glht(lm(response ~ treatment),
linfct=mcp(treatment='Means'))
par(mar=c(4,8,4,2))
plot(confint(mult))
hth,
Kingsford Jones
On Mon, Dec 8, 2008 at 5:06 PM, Metconnection <[EMAIL PROTECTED]> wrote:
>
> Dear R-users,
> I'm currently using the multcomp package to produce plots of means with 95%
> confidence intervals
> i.e.
>
> mult<-glht(lm(response~treatment, data=statdata),
> linfct=mcp(treatment="Means"))
> plot(confint(mult,calpha = sig))
>
> Unfortunately the y-axis on the plot appears to be fixed and hence if the
> labels on the y-axis (treatment levels) are too long, then they are not
> displayed in full on the plot. Of course I could always make the labels
> shorter but I was wondering if there was a way to make the position of the
> y-axis on the plot more flexible, such as in the scatterplot produced using
> xyplot function, that would allow me to view the labels in full.
>
> Thanks in advance for any advice!
> Simon
>
> --
> View this message in context:
> http://www.nabble.com/How-to-display-y-axis-labels-in-Multcomp-plot-tp20904977p20904977.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.
>
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and provide commented, minimal, self-contained, reproducible code.
[R] How to use different title in a loop
Hi all,
I want to draw n plots whose titles are "Main effect of X_i", i= 1,
2, ..., n, respectively.
More specifically, I use:
par(mfrow = c(n/2, 2))
for ( i in 1:n)
{
plot(1:J, y[i, 1: J], main = 'Main effect of X_i')
}
This gives me a series of plots with the common title with a letter i
in it, not the consecutive numbers I want.
Thanks in advance.
Xinxin
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[R] bayesm package not downloading via any mirror or repository
I am a pretty new R user, I am running the latest linux version on xandros,
updated with some extra debian packages, and I also run the latest windows
version, but prefer linux.
I am having trouble downloading "bayesm", it won't do it all from any of the
sites on the web, I resorted to this one,
http://packages.debian.org/unstable/math/r-cran-bayesm. and got slightly
further, but I think it is still not recognising a mirror. THis is my error
message:
> install.packages("bayesm")
Warning in install.packages("bayesm") : argument 'lib' is missing: using
/usr/local/lib/R/site-library
--- Please select a CRAN mirror for use in this session ---
Loading Tcl/Tk interface ... done
Warning in download.packages(unique(pkgs), destdir = tmpd, available =
available, :
no package 'bayesm' at the repositories
The package is certainly there.
It could be my version of linux, I know.
All I want to do is sample from a dirichlet prior, so I want rdirichlet and
ddirichlet commands basically. If anyone can help or suggest an alternate
package that would be great.
E
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Sent from the R help mailing list archive at Nabble.com.
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Re: [R] Scan a folder for a given type of files
Thanks Gabor Gábor Csárdi a écrit : > Sebastien, > > see ?list.files, especially the 'pattern' argument. For your > particular case it is > > list.files(pattern="\\.txt$") > > You might want to use the 'ignore.case' argument as well. > > Gabor > > On Mon, Dec 8, 2008 at 10:53 PM, <[EMAIL PROTECTED]> wrote: > >> Dear R-users, >> >> I have found on the list several posts addressing the issue of getting data >> for >> a list of defined files. However, I found nothing about scanning a given >> folder >> and retrieving the list of, let's say, .txt files (I probably used the wrong >> keywords). Could someone tell me which posts or function help I should look >> at? >> >> Thanks in advance >> >> Sebastien >> >> __ >> R-help@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/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 use different title in a loop
see ?paste
main = paste ("Main effect of ", variable)
> par(mfrow = c(n/2, 2))
> for ( i in 1:n)
> {
>plot(1:J, y[i, 1: J], main = 'Main effect of X_i')
> }
>
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Re: [R] Trouble with gridBase and inset plots
Hi
Lorenzo Isella wrote:
> Dear All,
> I ma having a trouble in generating a figure containing 3 insets with
> the gridBase package.
> I always get an error message of the kind:
>
> Error in gridPLT() : Figure region too small and/or viewport too large
>
> No matter which parameters I choose. The plots works nicely with two
> insets only, but when I try adding the third one, my troubles begin.
> I am probably doing something wrong in the generation of the 3rd inset
> and I paste below everything I do in this (a bit complicated) figure.
> Any suggestion is welcome.
The error means that you are creating a region that is too small. Try
setting the width and height of the PDF to something big and your code
might work and you might be able to see why the region is too small at
the default size. To get more help, you'll have to simplify your code
example and/or post some data so that we can run your code.
Paul
> Cheers
>
> Lorenzo
>
>
> pdf("./post-processing-plots/exploratory_research_figure_2.pdf")
> par( mar = c(4.5,5, 2, 1) + 0.1)
> plot(time[1:time_end],tot_num_150[1:time_end]/1e6,type="b",lwd=2,col="blue",lty=2,
> xlab=expression(paste(tau,"[s]")),
> ylab=expression(paste("N[",
> cm^{-3},"]")),cex.lab=1.6,ylim=range(c(7.4e7,1.43e8)),yaxt="n",cex.axis=1.4)
> #lines(time[1],ini_pop/1e6, "p",col="red",lwd=2,lty=1,pch=5 )
> lines(time[time_end],8.25e7, "p",col="red",lwd=2,lty=1,pch=5)
>
> axis(side=2, at=c( 7.4e7, 9.6e7, 1.18e8, 1.4e8),
> labels=expression(7.4%*%10^7, 9.6%*%10^7,
> 1.18%*%10^8,1.4%*%10^8),cex.lab=1.6,cex.axis=1.4)
> #axis(side=1,cex.axis=1.4)
> ## lines(time[1:time_end],
> N_approx[1:time_end],col="red",type="b",lwd=2,lty=1,pch=4)
> ## lines(time[1:time_end],
> N_approx2[1:time_end],col="black",type="b",lwd=2,lty=1,pch=2)
> ## lines(time[1:time_end],
> N_approx_beta1[1:time_end,2],col="brown",type="b",lwd=2,lty=1,pch=5)
> legend("topright",cex=1.2, c(expression("Simulation"),
> expression("Outlet measurement")),
> lwd=c(2,2),lty=c(2,0),pch = c(1,5),col=c("blue", "red"),box.lwd=0,box.lty=0,
> ,xjust = 1, yjust = 1)
> # abline(v=time[12],lwd=2,pch=2,lty=2)
> lines(c(time[14],time[14]), c(0,1.2e8),lwd=2,lty=2,pch=2)
> # legend(-0.2,9.2e7,cex=1.2,c(expression("numerical result for a
> 5m-long pipe")),bty="n")
> arrows(0.8, 9e7, time[14], tot_num_150[14]/1e6, length = 0.15,lwd=2)
> text(0.8,8.8e7,cex=1.2,"Final concentration for a")
> text(0.8,8.5e7,cex=1.2,"6.5m long transfer tube (LAT)")
>
> text(0.8,8e7,cex=1.2,"Final concentration for a")
> text(0.68,7.7e7,cex=1.2,"9m long transfer tube")
> text(0.8,7.4e7,cex=1.2,"(VELA)")
>
> text(1.3,1.24e8,cex=1.2,"Residence time for")
> text(1.3,1.21e8,cex=1.2,"a 6.5m long transfer tube")
>
>
> arrows(1.1, 7.7e7, time[21], 7.7e7, length = 0.,lwd=2)
> arrows( time[21], 7.7e7, time[21], tot_num_150[21]/1e6, length = 0.15,lwd=2)
>
>
>
> par( mar = c(0.,0., 0., 0.) )
>
>
> #1st inset
>
> vp <- baseViewports()
>pushViewport(vp$inner,vp$figure,vp$plot)
>pushViewport(viewport(x=-0.0,y=1.04,width=.4,height=.4,just=c(0,1)))
>
>par(fig=gridPLT(),new=F)
>
> #grid.rect(gp=gpar(lwd=0,col="red"))
>
>plot(D_mean,data_150[1, ]/log_factor*log(10)/1e6,"l",
> pch=1,col="black", lwd=2,xlab="",ylab=""
> ,cex.axis=1.,cex.lab=1.,log="x",xaxt="n",yaxt="n",
> ylim=range(c(0, 2.4e8)))
>
> ## axis(side=2, at=c( 0, 0.6e8, 1.2e8, 1.8e8, 2.4e8),
> ## labels=expression(0, 6%*%10^7, 1.2%*%10^8,
> 1.8%*%10^8,2.4%*%10^8),cex.lab=1.4,cex.axis=1.2)
>
>
> #2nd inset
>
> #vp <- baseViewports()
>pushViewport(vp$inner,vp$figure,vp$plot)
>pushViewport(viewport(x=0.5,y=0.65,width=.4,height=.4,just=c(0,1)))
>
>par(fig=gridPLT(),new=F)
>
> #grid.rect(gp=gpar(lwd=0,col="red"))
>
>plot(D_mean,data_150[21, ]/log_factor*log(10)/1e6,"l",lwd=2,
> pch=1,col="black",xlab="",ylab="", log="x"
> ,cex.axis=1.4,cex.lab=1.6,xaxt="n",yaxt="n",ylim=range(c(0, 2.4e8)))
>
>
>
> #3rd inset
>
> #vp <- baseViewports()
>pushViewport(vp$inner,vp$figure,vp$plot)
>pushViewport(viewport(x=0.25,y=0.7,width=.4,height=.4,just=c(0,1)))
>
>par(fig=gridPLT(),new=T)
>
> #grid.rect(gp=gpar(lwd=0,col="red"))
>
>plot(D_mean,data_150[14, ]/log_factor*log(10)/1e6,"l",lwd=2,
> pch=1,col="black",xlab="",ylab="", log="x"
> ,cex.axis=1.4,cex.lab=1.6,xaxt="n",yaxt="n",ylim=range(c(0, 2.4e8)))
>
>
> popViewport(3)
>
>
> dev.off()
>
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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.
--
Dr Paul Murrell
Department of Statistics
The University of Auckland
Private Bag 92019
Auckland
New Zealand
64 9 3737599 x85392
[EMAIL PROTECTED]
http://www.stat.auckland.ac.nz/~paul/
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[R] expected variable name error pos 98349 WInBUGS in R
> I am using a random intercept model with SITEID as random and NAUSEA as
> outcome.
>
> I tried using a dataset without missing values and changed my model
> statement accordingly but still get the same error. Follwoing in an excerpt.
> > anal.data <- read.table("nausea.txt", header=T, sep="\t")
> > list(names(anal.data))
> [[1]]
> [1] "SITEID" "NAUSEA"
> > #anal.data <- read.csv("simuldat.csv", header=T)
> > attach(anal.data)
> The following object(s) are masked from anal.data ( position 3 ) :
> NAUSEA SITEID
>
> The following object(s) are masked from anal.data ( position 4 ) :
> NAUSEA SITEID
> > data.bugs <-
> list("NAUSEA"=NAUSEA,"SITEID"=SITEID,"n.samples"=n.samples,"n.sites"=n.sites,"n.params"=n.params)
> > bugsData(data.bugs, fileName = "nauseadata.txt")
> > inits.bugs <- list("alpha"=rep(0,n.sites), "tau"=1)
> > bugsInits(list(inits.bugs), fileName = "nauseainit.txt")
> > modelCheck("nausea_random.txt") # check model file
> model is syntactically correct
> > modelData("nauseadata.txt") # read data file
> expected variable name error pos 98349
> *MODEL*
> model
> {
> for (i in 1:n.samples)
> {NAUSEA[i] ~ dbin(p[i],1)
> logit(p[i]) <- alpha[SITEID[i]]}
> #for(k in 1:n.params)
> #{b[k]~ dnorm(0.0,tau)}
> for (j in 1:n.sites)
> {alpha[j]~dnorm(0.0,1.0E-10)}
>
> tau ~ dgamma(0.001,0.001)
> }
> *Dataset:*
> SITEID NAUSEA
> 1 0
> 1 1
> 1 1
> 1 0
> 1 1
> 1 1
> 1 0
> 1 1
> 1 1
> 1 1
> 1 0
> 1 1
> 1 0
> 1 1
> 1 1
> 1 1
> 1 0
> 1 0
> 1 0
> 1 1
>
> -Anamika
>
[[alternative HTML version deleted]]
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[R] errors with compilation
Hi, i'm trying to compile R on a Cray XT3 using pgi/7.2.1 - CNL (compute node linux) The R version is 2.8.0 this is the option -enable-R-static-lib=yes --disable-R-shlib CPICFLAGS=fpic FPICFLAGS=fpic CXXPICFLAGS=fpic SHLIB_LDFLAGS=shared --with-x=no SHLIB_CXXLDFLAGS=shared --disable-BLAS-shlib CFLAGS="-g -O2 -Kieee" FFLAGS="-g -O2 -Kieee" CXXFLAGS="-g -O2 -Kieee" FCFLAGS="-g -O2 -Kieee" CC=cc F77=ftn CXX=CC FC=ftn R is now configured for x86_64-unknown-linux-gnu Source directory: . Installation directory:/lus/nid00036/jasont/R C compiler:cc -g -O2 -Kieee Fortran 77 compiler: ftn -g -O2 -Kieee C++ compiler: CC -g -O2 -Kieee Fortran 90/95 compiler:ftn -g -O2 -Kieee Obj-C compiler: gcc -g -O2 Interfaces supported: External libraries:readline Additional capabilities: PNG, JPEG, iconv, MBCS, NLS Options enabled: static R library, R profiling, Java Recommended packages: yes The error is : cc -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/ pcre -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H-g -O2 -Kieee -c pcre.c -o pcre.o /opt/cray/xt-asyncpe/1.2/bin/cc: INFO: linux target is being used PGC-W-0155-64-bit integral value truncated (/usr/include/wctype.h: 108) PGC-W-0155-64-bit integral value truncated (/usr/include/wctype.h: 109) PGC-W-0155-64-bit integral value truncated (/usr/include/wctype.h: 110) PGC-W-0155-64-bit integral value truncated (/usr/include/wctype.h: 111) PGC/x86-64 Linux 7.2-1: compilation completed with warnings cc -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/ pcre -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H-g -O2 -Kieee -c platform.c -o platform.o /opt/cray/xt-asyncpe/1.2/bin/cc: INFO: linux target is being used PGC-S-0037-Syntax error: Recovery attempted by deleting identifier FALSE (platform.c: 1657) PGC-S-0094-Illegal type conversion required (platform.c: 1661) PGC/x86-64 Linux 7.2-1: compilation completed with severe errors make[3]: *** [platform.o] Error 2 make[3]: Leaving directory `/lus/nid00036/jasont/R-2.8.0/src/main' make[2]: *** [R] Error 2 make[2]: Leaving directory `/lus/nid00036/jasont/R-2.8.0/src/main' make[1]: *** [R] Error 1 make[1]: Leaving directory `/lus/nid00036/jasont/R-2.8.0/src' make: *** [R] Error 1 Jason Tan Senior Computer Support Officer Western Australian Supercomputer Program (WASP) The University of Western Australia M024 35 Stirling Highway CRAWLEY WA 6009 Ph: +618 64888742 Fax: +618 6488 8088 Email: [EMAIL PROTECTED] Web: www.wasp.uwa.edu.au __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] error from running WinBUGS in R
Has anyone ever seen an error like this from running WinBUGS in R '> modelCompile(numChains=2) # compile model with 1 chain error for node p[3421] of type GraphLogit.Node node vetor contains undefined elements [[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] forestplot and x axis scale
Hello R users,
I would like to create several forestplots with the same X axis, so,
if you were to look at the plots lined up all the X axes would be
identical (and the different plots could be compared). Here is one
version of code I've used:
mytk10<-c(0.1, 0.5, 1, 2, 5, 10)
pdf(file = "myfile.pdf",
pointsize = 7, paper="letter", width=6, height=9)
forestplot(newcite,or,lcl,ucl,zero=0, graphwidth = unit(1.2,"inches"),
clip=c(log(0.1),log(10)), xlog=TRUE, xticks=mytk10, xlab="Odds Ratio",
col=meta.colors(box="darkblue",line="darkblue",zero="grey50"))
title(main = list("My title", col="darkblue", font=2))
dev.off()
--> I have changed the width of the pdf output and/or the graphwidth
specified in the forestplot function -- and depending on the length of
the text/table descriptions (in the matrix "newcite"), the X axis will
vary (when the text is long, the axis is shorter). I tried fixing the
axis at a relatively small size (using graphwidth), but it would still
be smaller when I was using data with long "newcite" text. Do I need
to fix the amount of text for display within "newcite"?
--> A second and less essential question: I've used mytk10 for the
axis tickmarks/labels - I'd prefer no decimal points for 1,2,5,and 10
- any way to adjust this?
Thanks in advance for any assistance!
Pam
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[R] How to add accuracy, sensitivity, specificity to logistic regression output?
Hi, Is there a way when doing logistic regression for the output to spit out accuracy, sensitivity, and specificity? I would like to know these basic measures for my model. 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] chron - when seconds data not included
I have date and time data which looks like this: [,1] [,2] [1,] "7/1/08" "9:19" [2,] "7/1/08" "9:58" [3,] "7/7/08" "15:47" [4,] "7/8/08" "10:03" [5,] "7/8/08" "10:32" [6,] "7/8/08" "15:22" [7,] "7/8/08" "15:27" [8,] "7/8/08" "15:40" [9,] "7/9/08" "10:25" [10,] "7/9/08" "10:27" I would like to use chron on it, so that I can calculate intervals in time. I can't seem to get chron to accept the time format that doesn't include seconds. Do I have to go through and append :00 on every line in order to use chron? -- View this message in context: http://www.nabble.com/chron---when-seconds-data-not-included-tp20908803p20908803.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] chron - when seconds data not included
On Mon, Dec 8, 2008 at 11:52 PM, Tubin <[EMAIL PROTECTED]> wrote:
>
> I have date and time data which looks like this:
>
> [,1] [,2]
> [1,] "7/1/08" "9:19"
> [2,] "7/1/08" "9:58"
> [3,] "7/7/08" "15:47"
> [4,] "7/8/08" "10:03"
> [5,] "7/8/08" "10:32"
> [6,] "7/8/08" "15:22"
> [7,] "7/8/08" "15:27"
> [8,] "7/8/08" "15:40"
> [9,] "7/9/08" "10:25"
> [10,] "7/9/08" "10:27"
>
> I would like to use chron on it, so that I can calculate intervals in time.
>
> I can't seem to get chron to accept the time format that doesn't include
> seconds. Do I have to go through and append :00 on every line in order to
> use chron?
That's one way:
m <- matrix( c("7/1/08","9:19",
"7/1/08","9:58",
"7/7/08","15:47",
"7/8/08","10:03",
"7/8/08","10:32",
"7/8/08","15:22",
"7/8/08","15:27",
"7/8/08","15:40",
"7/9/08","10:25",
"7/9/08","10:27"), nc = 2, byrow = TRUE)
chron(m[,1], paste(m[,2], 0, sep = ":"))
# another is to use as.chron
as.chron(apply(m, 1, paste, collapse = " "), "%m/%d/%y %H:%M")
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[R] Data Analysis Functions in R
Hi experts of R, Are there any functions in R to test a univariate series for long memory effects, structural breaks and time reversability? I've found for ARCH effects(ArchTest), for normal (Shapiro.test, KS.test(comparing with randn) and lillie.test) but not for the above mentioned. Where can I find a comprehensive list of functions available by type? Thank you Renato Costa -- View this message in context: http://www.nabble.com/Data-Analysis-Functions-in-R-tp20909079p20909079.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] R and Scheme
Luke Tierney wrote: R does not have macros. Those are related -- because of lazy evaluation one does macros are not needed to achive semantic goals (see for example tryCatch). Being able to define friendlier syntax would sometimes be nice though (see tryCatch again). Also for some practical purposes. For instance, it is pretty hard to loop over a set of variables and get the output labeled with the variable names for (y in list(systbt, diastbt)) plot (age, y) will (of course) plot both with a y axis labeled "y". A macro version of "for" could potentially create the expansion plot(age, systbt) plot(age, diastbt) and evaluate the result. (Presumably, this is already possible with a bit of sufficiently contorted code, but there's no user-friendly syntax for it that I know of.) In R, most data types (including numeric vectors) do not have a standard external representation which can be read back in without evaluation. The default print form is not readable in this sense but dput is available for this purpose. I think the point is that dput() is not always equivalent to the object - parsing dput output gives a different object from the original. Numeric vectors of length > 1 is the most obvious case, "expression" objects another (those can get terribly confusing at times). We currently have this sort of confusion > e <- substitute(x+a,list(a=c(1,2,3))) > e2 <- parse(text=deparse(e))[[1]] > e2 x + c(1, 2, 3) > e[[3]] [1] 1 2 3 > e2[[3]] c(1, 2, 3) > dput(e) x + c(1, 2, 3) > dput(e2) x + c(1, 2, 3) That is, deparse/reparse of an object can lead to a _different_ object that gets dput()'ed indistinguishably. I have occasionally been wondering whether it would be a good idea to have some sort of syntax primitive requesting parse-time evaluation. E.g. quote(x + .const(c(1,2,3))) would be equivalent to substitute(x+a,list(a=c(1,2,3))) -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] package "wmtsa": wavCWTPeaks error
I keep getting the following error when I look for minima in the series:
> aa.peak <- wavCWTPeaks (aa.tree)
Error in `row.names<-.data.frame`(`*tmp*`, value = c("1", "0")) :
invalid 'row.names' length
How can I work it around ?
Thank you.
Regards,
Maura
Alice Messenger ;-) chatti anche con gli amici di Windows Live Messenger e
tutti i telefonini TIM!
Vai su http://maileservizi.alice.it/alice_messenger/index.html?pmk=footer
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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] package "wmtsa": wavCWTPeaks error
Are the names of the rows the same as the time series that you are
using? I know that I am not being that helpful, but this seems like a
mismatch in the time series object. look at
length(rowname(your.data))
length(your.data[,1])
again it is always helpful to have reproducible code.
On Tue, Dec 9, 2008 at 1:39 AM, <[EMAIL PROTECTED]> wrote:
> I keep getting the following error when I look for minima in the series:
>
>> aa.peak <- wavCWTPeaks (aa.tree)
> Error in `row.names<-.data.frame`(`*tmp*`, value = c("1", "0")) :
> invalid 'row.names' length
>
> How can I work it around ?
>
> Thank you.
>
> Regards,
> Maura
>
>
> Alice Messenger ;-) chatti anche con gli amici di Windows Live Messenger e
> tutti i telefonini TIM!
> Vai su http://maileservizi.alice.it/alice_messenger/index.html?pmk=footer
>
> __
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
>
--
Stephen Sefick
Let's not spend our time and resources thinking about things that are
so little or so large that all they really do for us is puff us up and
make us feel like gods. We are mammals, and have not exhausted the
annoying little problems of being mammals.
-K. Mullis
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Re: [R] errors with compilation
Please try the R-patched.version of R (see the posting guide or the FAQ).
That seems to be about an error in the R 2.8.0 sources that was corrected
in October, and only happens if you do not ask for X11 support (which most
R users need, including it seems all the pre-release testers).
On Tue, 9 Dec 2008, Jason Tan wrote:
Hi,
i'm trying to compile R on a Cray XT3 using pgi/7.2.1 - CNL (compute node
linux)
The R version is 2.8.0
this is the option
-enable-R-static-lib=yes
--disable-R-shlib
/* The latter is the default */
CPICFLAGS=fpic
FPICFLAGS=fpic
CXXPICFLAGS=fpic
SHLIB_LDFLAGS=shared
--with-x=no
SHLIB_CXXLDFLAGS=shared
--disable-BLAS-shlib
Do you really need to set all these? And are you sure you know the
correct values? ('-shared' is standard on Linux.)
CFLAGS="-g -O2 -Kieee"
FFLAGS="-g -O2 -Kieee"
CXXFLAGS="-g -O2 -Kieee"
FCFLAGS="-g -O2 -Kieee"
CC=cc
F77=ftn
CXX=CC
FC=ftn
R is now configured for x86_64-unknown-linux-gnu
Source directory: .
Installation directory:/lus/nid00036/jasont/R
C compiler:cc -g -O2 -Kieee
Fortran 77 compiler: ftn -g -O2 -Kieee
C++ compiler: CC -g -O2 -Kieee
Fortran 90/95 compiler:ftn -g -O2 -Kieee
Obj-C compiler: gcc -g -O2
Interfaces supported:
External libraries:readline
Additional capabilities: PNG, JPEG, iconv, MBCS, NLS
Options enabled: static R library, R profiling, Java
Recommended packages: yes
The error is :
cc -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I.
-I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H
-g -O2 -Kieee -c pcre.c -o pcre.o
/opt/cray/xt-asyncpe/1.2/bin/cc: INFO: linux target is being used
PGC-W-0155-64-bit integral value truncated (/usr/include/wctype.h: 108)
PGC-W-0155-64-bit integral value truncated (/usr/include/wctype.h: 109)
PGC-W-0155-64-bit integral value truncated (/usr/include/wctype.h: 110)
PGC-W-0155-64-bit integral value truncated (/usr/include/wctype.h: 111)
PGC/x86-64 Linux 7.2-1: compilation completed with warnings
cc -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I.
-I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H
-g -O2 -Kieee -c platform.c -o platform.o
/opt/cray/xt-asyncpe/1.2/bin/cc: INFO: linux target is being used
PGC-S-0037-Syntax error: Recovery attempted by deleting identifier FALSE
(platform.c: 1657)
PGC-S-0094-Illegal type conversion required (platform.c: 1661)
PGC/x86-64 Linux 7.2-1: compilation completed with severe errors
make[3]: *** [platform.o] Error 2
make[3]: Leaving directory `/lus/nid00036/jasont/R-2.8.0/src/main'
make[2]: *** [R] Error 2
make[2]: Leaving directory `/lus/nid00036/jasont/R-2.8.0/src/main'
make[1]: *** [R] Error 1
make[1]: Leaving directory `/lus/nid00036/jasont/R-2.8.0/src'
make: *** [R] Error 1
Jason Tan
Senior Computer Support Officer
Western Australian Supercomputer Program (WASP)
The University of Western Australia
M024
35 Stirling Highway
CRAWLEY WA 6009
Ph: +618 64888742
Fax: +618 6488 8088
Email: [EMAIL PROTECTED]
Web: www.wasp.uwa.edu.au
__
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.
--
Brian D. Ripley, [EMAIL PROTECTED]
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax: +44 1865 272595
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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] errors with compilation
thanks. i noticed a syntax error. a missing semi colon.
any idea about the error below?
cc -I. -I../../../src/include -I../../../src/include -I/usr/local/
include -DHAVE_CONFIG_H -fPIC -g -O2 -c Rsock.c -o Rsock.o
/opt/cray/xt-asyncpe/1.2/bin/cc: INFO: linux target is being used
cc -I. -I../../../src/include -I../../../src/include -I/usr/local/
include -DHAVE_CONFIG_H -fPIC -g -O2 -c internet.c -o internet.o
/opt/cray/xt-asyncpe/1.2/bin/cc: INFO: linux target is being used
cc -I. -I../../../src/include -I../../../src/include -I/usr/local/
include -DHAVE_CONFIG_H -fPIC -g -O2 -c nanoftp.c -o nanoftp.o
/opt/cray/xt-asyncpe/1.2/bin/cc: INFO: linux target is being used
cc -I. -I../../../src/include -I../../../src/include -I/usr/local/
include -DHAVE_CONFIG_H -fPIC -g -O2 -c nanohttp.c -o nanohttp.o
/opt/cray/xt-asyncpe/1.2/bin/cc: INFO: linux target is being used
cc -I. -I../../../src/include -I../../../src/include -I/usr/local/
include -DHAVE_CONFIG_H -fPIC -g -O2 -c sock.c -o sock.o
/opt/cray/xt-asyncpe/1.2/bin/cc: INFO: linux target is being used
cc -I. -I../../../src/include -I../../../src/include -I/usr/local/
include -DHAVE_CONFIG_H -fPIC -g -O2 -c sockconn.c -o sockconn.o
/opt/cray/xt-asyncpe/1.2/bin/cc: INFO: linux target is being used
cc -shared -fPIC -L/usr/local/lib64 -o internet.so Rsock.o internet.o
nanoftp.o nanohttp.o sock.o sockconn.o
/opt/cray/xt-asyncpe/1.2/bin/cc: INFO: linux target is being used
/usr/bin/ld: /usr/lib64/libpthread.a(ptw-fcntl.o): relocation
R_X86_64_32 against `a local symbol' can not be used when making a
shared object; recompile with -fPIC
/usr/lib64/libpthread.a: could not read symbols: Bad value
make[4]: *** [internet.so] Error 2
jason
On 09/12/2008, at 4:50 PM, Prof Brian Ripley wrote:
Please try the R-patched.version of R (see the posting guide or the
FAQ).
That seems to be about an error in the R 2.8.0 sources that was
corrected in October, and only happens if you do not ask for X11
support (which most R users need, including it seems all the pre-
release testers).
On Tue, 9 Dec 2008, Jason Tan wrote:
Hi,
i'm trying to compile R on a Cray XT3 using pgi/7.2.1 - CNL
(compute node linux)
The R version is 2.8.0
this is the option
-enable-R-static-lib=yes
--disable-R-shlib
/* The latter is the default */
CPICFLAGS=fpic
FPICFLAGS=fpic
CXXPICFLAGS=fpic
SHLIB_LDFLAGS=shared
--with-x=no
SHLIB_CXXLDFLAGS=shared
--disable-BLAS-shlib
Do you really need to set all these? And are you sure you know the
correct values? ('-shared' is standard on Linux.)
CFLAGS="-g -O2 -Kieee"
FFLAGS="-g -O2 -Kieee"
CXXFLAGS="-g -O2 -Kieee"
FCFLAGS="-g -O2 -Kieee"
CC=cc
F77=ftn
CXX=CC
FC=ftn
R is now configured for x86_64-unknown-linux-gnu
Source directory: .
Installation directory:/lus/nid00036/jasont/R
C compiler:cc -g -O2 -Kieee
Fortran 77 compiler: ftn -g -O2 -Kieee
C++ compiler: CC -g -O2 -Kieee
Fortran 90/95 compiler:ftn -g -O2 -Kieee
Obj-C compiler: gcc -g -O2
Interfaces supported:
External libraries:readline
Additional capabilities: PNG, JPEG, iconv, MBCS, NLS
Options enabled: static R library, R profiling, Java
Recommended packages: yes
The error is :
cc -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/
pcre -I. -I../../src/include -I../../src/include -I/usr/local/
include -DHAVE_CONFIG_H -g -O2 -Kieee -c pcre.c -o pcre.o
/opt/cray/xt-asyncpe/1.2/bin/cc: INFO: linux target is being used
PGC-W-0155-64-bit integral value truncated (/usr/include/wctype.h:
108)
PGC-W-0155-64-bit integral value truncated (/usr/include/wctype.h:
109)
PGC-W-0155-64-bit integral value truncated (/usr/include/wctype.h:
110)
PGC-W-0155-64-bit integral value truncated (/usr/include/wctype.h:
111)
PGC/x86-64 Linux 7.2-1: compilation completed with warnings
cc -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/
pcre -I. -I../../src/include -I../../src/include -I/usr/local/
include -DHAVE_CONFIG_H -g -O2 -Kieee -c platform.c -o platform.o
/opt/cray/xt-asyncpe/1.2/bin/cc: INFO: linux target is being used
PGC-S-0037-Syntax error: Recovery attempted by deleting identifier
FALSE (platform.c: 1657)
PGC-S-0094-Illegal type conversion required (platform.c: 1661)
PGC/x86-64 Linux 7.2-1: compilation completed with severe errors
make[3]: *** [platform.o] Error 2
make[3]: Leaving directory `/lus/nid00036/jasont/R-2.8.0/src/main'
make[2]: *** [R] Error 2
make[2]: Leaving directory `/lus/nid00036/jasont/R-2.8.0/src/main'
make[1]: *** [R] Error 1
make[1]: Leaving directory `/lus/nid00036/jasont/R-2.8.0/src'
make: *** [R] Error 1
Jason Tan
Senior Computer Support Officer
Western Australian Supercomputer Program (WASP)
The University of Western Australia
M024
35 Stirling Highway
CRAWLEY WA 6009
Ph: +618 64888742
Fax: +618 6488 8088
Email: [EMAIL PROTECTED]
Web: www.wasp.uwa.edu.au
