Re: [R] convolution of the double exponential distribution
Hi David,
you can even increase the precision of these computations by changing
the variables
DefaultNrFFTGridPointsExponent (default: 12 - 2^12 grid points) and
TruncQuantile
(default: 1e-5) in our package distr; see
distroptions()
You can for instance use
distroptions(DefaultNrFFTGridPointsExponent, 14)
and
distroptions(TruncQuantile, 1e-8)
We checked our algorithm in case of Binomial, Poisson, Normal and
Exponential distributions and found a very high precision; confer
Section 5 of
http://www.stamats.de/comp.pdf
Moreover, for n-fold convolutions you can also use the function
convpow which can be found under
http://www.uni-bayreuth.de/departments/math/org/mathe7/DISTR/nFoldConvolution.R
hth,
Matthias
Ravi, Duncan, and Matthias,
Thank you very much for the helpful replies. For convolutions with 2 or
3 copies, I found that the CDFs from the distr package closely match the
analytic results from this paper:
K. Singh, M. Xie, and W. E. Strawderman, Combining Information From
Independent Sources Through Confidence Distributions, Annals of
Statistics 33, no. 1 (2005): 159-183.
That gives me confidence that the package will also work well for higher
copy numbers. At least for me, using the package is much more convenient
than programming all the needed integrals into R.
David
___
David R. Bickel http://davidbickel.com
Research Scientist
Pioneer Hi-Bred International (DuPont)
Bioinformatics and Exploratory Research
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Johnston, IA 50131-0184
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[EMAIL PROTECTED], [EMAIL PROTECTED]
| -Original Message-
| From: Matthias Kohl [mailto:[EMAIL PROTECTED]
| Sent: Friday, December 23, 2005 9:09 AM
| To: Bickel, David
| Cc: Duncan Murdoch; r-help@stat.math.ethz.ch
| Subject: Re: [R] convolution of the double exponential distribution
|
| Duncan Murdoch schrieb:
|
| On 12/22/2005 7:56 PM, Bickel, David wrote:
|
|
| Is there any R function that computes the convolution of the double
| exponential distribution?
|
| If not, is there a good way to integrate ((q+x)^n)*exp(-2x)
| over x from
| 0 to Inf for any value of q and for any positive integer n?
| I need to
| perform the integration within a function with q and n as
| arguments. The
| function integrate() is giving me this message:
|
| evaluation of function gave a result of wrong length
|
|
|
| Under the substitution of y = q+x, that looks like a gamma integral.
| The x = 0 to Inf range translates into y = q to Inf, so
| you'll need an
| incomplete gamma function, such as pgamma. Be careful to get the
| constant multiplier right.
|
| Duncan Murdoch
|
| __
| R-help@stat.math.ethz.ch mailing list
| https://stat.ethz.ch/mailman/listinfo/r-help
| PLEASE do read the posting guide!
| http://www.R-project.org/posting-guide.html
|
|
|
| Hi,
|
| you can use our package distr.
|
| require(distr)
| ## define double exponential distribution
| loc - 0 # location parameter
| sca - 1 # scale parameter
|
| rfun - function(n){ loc + scale * ifelse(runif(n) 0.5, 1,
| -1) * rexp(n) }
| body(rfun) - substitute({ loc + scale * ifelse(runif(n)
| 0.5, 1, -1) *
| rexp(n) },
| list(loc = loc, scale = sca))
|
| dfun - function(x){ exp(-abs(x-loc)/scale)/(2*scale) }
| body(dfun) - substitute({ exp(-abs(x-loc)/scale)/(2*scale)
| }, list(loc
| = loc, scale = sca))
|
| pfun - function(x){ 0.5*(1 +
| sign(x-loc)*(1-exp(-abs(x-loc)/scale))) }
| body(pfun) - substitute({ 0.5*(1 +
| sign(x-loc)*(1-exp(-abs(x-loc)/scale))) },
| list(loc = loc, scale = sca))
|
| qfun - function(x){ loc - scale*sign(x-0.5)*log(1 - 2*abs(x-0.5)) }
| body(qfun) - substitute({ loc - scale*sign(x-0.5)*log(1 -
| 2*abs(x-0.5)) },
| list(loc = loc, scale = sca))
|
| D1 - new(AbscontDistribution, r = rfun, d = dfun, p =
| pfun, q = qfun)
| plot(D1)
|
| D2 - D1 + D1 # convolution based on FFT
| plot(D2)
|
| hth,
| Matthias
|
| --
| StaMatS - Statistik + Mathematik Service
| Dipl.Math.(Univ.) Matthias Kohl
| www.stamats.de
|
This communication is for use by the intended recipient and ...{{dropped}}
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Dipl.Math.(Univ.) Matthias Kohl
Gottlieb-Keim-Straße 60
95448 Bayreuth
Phone: +49 921 50736 457
E-Mail: [EMAIL PROTECTED]
www.stamats.de
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Re: [R] R on Mandriva 2006
On Τετ, Δεκέμβριος 28, 2005 9:11, Paolo Bulla wrote: Hello anyone, I'm trying to install R on Mandriva 2006 distribution via rpm file with the line urpmi R-2.0.0-1mdk.i586.rpm but I got an error message saying that the file is not accessible due to some info problem. I also tried with a source code in R-2.1.1.tar but I think that there is some problem concerning the new version of gcc (4.x), so I downgraded it to gcc 3.4.5 but it does not work either. Could anyone help me with this installation, please? Thanks, Paolo -- Paolo Bulla Istituto di Metodi Quantitativi Universitΰ L. Bocconi Tel. +39 02.5836.5651 viale Isonzo 25 20136 Milano [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Ioannis C. Dimakos, Ph.D. University of Patras Department of Elementary Education Patras, GR-26500 GREECE http://www.elemedu.upatras.gr/dimakos/ http://yannishome.port5.com/ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] [Fwd: Re: R on Mandriva 2006]
Apologies for the empty post that went to the list... On Τετ, Δεκέμβριος 28, 2005 9:11, Paolo Bulla wrote: Hello anyone, I'm trying to install R on Mandriva 2006 distribution via rpm file with the line urpmi R-2.0.0-1mdk.i586.rpm ^^ This is an older rpm that Michele Alzeta contributed for Mandrake 10.0 (and that was a long time ago, before Mandrakesoft merged with Connectiva to become Mandriva). And it is for R-2.0.0 In my experience with Mandrake distros, I have found it is easy to download the most recent sources and compile your own version of R. I also tried with a source code in R-2.1.1.tar but I think that there is ^^^ Unless you have a typo, this is also an older version of R. Get the newer sources and recompile. I don't know if Michele is still active in maintaining R for Mandrake. But he has a site for R and Mandrake in italian and this may provide some first clues. HTH, Ioannis -- Ioannis C. Dimakos, Ph.D. University of Patras Department of Elementary Education Patras, GR-26500 GREECE http://www.elemedu.upatras.gr/dimakos/ http://yannishome.port5.com/ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Which cluster function can be used to cluster a correlaiton matrix?
Hi, I'd got a matrix of correaltion values. Which cluster method can I use to cluster it? Best Regards... __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R on Mandriva 2006
Please consult the posting guide and use a current version of R, 2.2.1. If that does not work, please report the information the posting guide requests, including the exact problems you found. R 2.2.1 should have no problem with gcc4, but versions predating the release of gcc4 may well do. On Wed, 28 Dec 2005, Paolo Bulla wrote: Hello anyone, I'm trying to install R on Mandriva 2006 distribution via rpm file with the line urpmi R-2.0.0-1mdk.i586.rpm but I got an error message saying that the file is not accessible due to some info problem. I also tried with a source code in R-2.1.1.tar but I think that there is some problem concerning the new version of gcc (4.x), so I downgraded it to gcc 3.4.5 but it does not work either. Could anyone help me with this installation, please? Thanks, Paolo -- Paolo Bulla Istituto di Metodi Quantitativi Università L. Bocconi Tel. +39 02.5836.5651 viale Isonzo 25 20136 Milano [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- 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@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Omegahat sjava
I am trying to download and install Omegahat Sjava (http://www.omegahat.org/RSJava) to be able to call R from within Java. The install instructions are as follows: cd $RHOME/src/library unzip SJava_0.69-0.zip cd SJava ./configure.win $RHOME cd $RHOME/src/gnuwin32 make pkg-SJava However, my command prompt won't recognize unzip,./configure.win, or make. What should I do to make this work? Neil Eastep. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Which cluster function can be used to cluster a correlaiton matrix?
Vincent == Vincent Deng [EMAIL PROTECTED] on Wed, 28 Dec 2005 17:34:27 +0800 writes: Vincent Hi, I'd got a matrix of correaltion values. Which Vincent cluster method can I use to cluster it? almost everyone. The clue is to transform correlations to dissimilarities. There are several choices for that, and it depends on the context what you should do. If 'Cx' is your correlation matrix, reasonable possibilities are Dx - as.dist(1 - Cx) Dx - as.dist(1 - abs(Cx)) Dx - as.dist(sqrt(1 - Cx^2)) and then use hclust(), agnes(), pam(), [the latter two from package 'cluster'], ... with 'Dx' as dissimilarity __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Omegahat sjava
Neil Eastep wrote: I am trying to download and install Omegahat Sjava (http://www.omegahat.org/RSJava) to be able to call R from within Java. The install instructions are as follows: cd $RHOME/src/library unzip SJava_0.69-0.zip cd SJava ./configure.win $RHOME cd $RHOME/src/gnuwin32 make pkg-SJava However, my command prompt won't recognize unzip,./configure.win, or make. What should I do to make this work? Please read the whole page you cited above and install the required tools. Which tools are required to build packages from source is also described in the R Installation and Administration manual. Perhaps you can live with the CRAN package rJava (there is a binary Windows version available). Uwe Ligges Neil Eastep. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Which cluster function can be used to cluster a correlaiton matrix?
Vincent Deng wrote: Hi, I'd got a matrix of correaltion values. Which cluster method can I use to cluster it? library(Hmisc) ?varclus __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Open a new script from R command prompt
Hi, (this is a minor irritation), is it possible for me to call R's editor from the R command prompt (I searched for script but that didn't yield anything). (The mouse-file-new-script route is a minor irritation ) __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] segmetation fault
Hey, I don;t know if anyone has come across this error before... I am running R on the terminal of my MAC OS X 10.3.4 and I have written C code and compiled it using R CMD SHLIB mycode.c There were no problems in compiling so I now have mycode.o and mycode.so. I used dyn.load(mycode.so) and again, no problems. But when I try to use the code .C(mycode,x) I get the error Segmentation fault and R shuts down. Any ideas as to where my problem could be? Any ideas or help would be appreciated! Thanks, Elizabeth Lawson - Ring in the New Year with Photo Calendars. Add photos, events, holidays, whatever. [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] [Fwd: Re: R on Mandriva 2006]
Hi Ioannis and Paolo, As Ioannis recommends getting the last R source (R-2.2.1) is better and does not require much effort. If you want the compilation to go smoothly on Mandriva 2006 you should first use drakconf to download and install: gfortran readline blas which are not installed by default by the powerpack (or free) distribution. Then follow the basic Unix/Linux intructions (to compile from sources) on the R Installation and Administration Manual (ie, tar -xvzf R-2.2.1.tar.gz, cd R-2.2.1, ./configure, make, make check, make install). Mandriva 2006 uses gcc-4.0.1, etc. On my machine (Intel PIV) all the tests went fine. Christophe. Ioannis Dimakos a écrit : Apologies for the empty post that went to the list... On Τετ, Δεκέμβριος 28, 2005 9:11, Paolo Bulla wrote: Hello anyone, I'm trying to install R on Mandriva 2006 distribution via rpm file with the line urpmi R-2.0.0-1mdk.i586.rpm ^^ This is an older rpm that Michele Alzeta contributed for Mandrake 10.0 (and that was a long time ago, before Mandrakesoft merged with Connectiva to become Mandriva). And it is for R-2.0.0 In my experience with Mandrake distros, I have found it is easy to download the most recent sources and compile your own version of R. I also tried with a source code in R-2.1.1.tar but I think that there is ^^^ Unless you have a typo, this is also an older version of R. Get the newer sources and recompile. I don't know if Michele is still active in maintaining R for Mandrake. But he has a site for R and Mandrake in italian and this may provide some first clues. HTH, Ioannis __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] parameterization of factor in R
Dear Prof Brian Ripley and Graves, Thank you for your replies. MASS has been very helpful! Oana From: Spencer Graves [EMAIL PROTECTED] To: Prof Brian Ripley [EMAIL PROTECTED] CC: Oana Mocila [EMAIL PROTECTED], r-help@stat.math.ethz.ch Subject: Re: [R] parameterization of factor in R Date: Tue, 27 Dec 2005 12:27:05 -0800 If you are not familiar with MASS (Modern Applied Statistics with S, 4th ed, Venables and Ripley 2002, Springer), I can assure you it is an excellent reference for learning R. There are many books on R that I have not read, but among the books in my personal library, I refer to MASS fairly frequently. If it is beyond your budget and not in a local library, I encourage you to investigate the possibility of having that library obtain a copy. If the library needs justification, please explain what you know of the book, how it became recommended for you, the problems you hope it will help you solve, etc. Spencer Graves Prof Brian Ripley wrote: ?contr.sum And Chapter 6 of MASS would have explained all this to you, so if you have further questions please consult it. On Tue, 27 Dec 2005, Oana Mocila wrote: I encountered this problem with parameterization in R: I have two factors in a regression. how about if I want to set constraint so that for each factor, the sum of their coefficients equals to zero(instead of choosing a reference category)? for example, I have factor(variable) A(with three categories) and factor(variable) B(with 4 categories), and I want to parameterize so that the sum of the three coefficients of A = 0, and sum of the four coefficients of B = 0? I mean how to do it in R? -- Spencer Graves, PhD Senior Development Engineer PDF Solutions, Inc. 333 West San Carlos Street Suite 700 San Jose, CA 95110, USA [EMAIL PROTECTED] www.pdf.com http://www.pdf.com Tel: 408-938-4420 Fax: 408-280-7915 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] segmetation fault
Elizabeth Lawson Wrote:
Hey,
I don;t know if anyone has come across this error before...
More times than I care to remember.
I am running R on the terminal of my MAC OS X 10.3.4 and I have
written
C code and compiled it using
R CMD SHLIB mycode.c
There were no problems in compiling so I now have mycode.o and
mycode.so.
A segmentation fault occurs when you try to access memory you didn't
allocate for your use (see below). In other words, you are trying to
use memory outside the segment allocated to your program (which, if
allowed, could result in corrupting memory being used by other
programs--which brings back unhappy memories of days gone by when an
error in one program could crash the whole system). So these kinds of
problems will not show up at compile time...only when you actually run
the program.
I used dyn.load(mycode.so) and again, no problems. But when I try
to
use the code .C(mycode,x) I get the error Segmentation fault and R
shuts
down. Any ideas as to where my problem could be?
When I run into a segmentation fault, it is usually because I am trying
to access an element of an array that is beyond what I have allocated,
as in...
int main()
{
int *a;
a = (int*) malloc(3*sizeof(int));
printf(Fasten your seatbelts...\n);
a[4000] = 12;
return(0);
}
One less obvious way this can happen is forgetting to initialize your
arrays to the proper length before passing a reference to them to your C
function.
If you still are having trouble, you could post a small snippet of code
that recreates the error for us to examine.
HTH,
Eric
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Re: [R] Open a new script from R command prompt
Are you talking about Rgui on Windows? Use the shortcut, Alt-F-N. -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Ronnie Babigumira Sent: Wednesday, December 28, 2005 9:21 AM To: R Help Subject: [R] Open a new script from R command prompt Hi, (this is a minor irritation), is it possible for me to call R's editor from the R command prompt (I searched for script but that didn't yield anything). (The mouse-file-new-script route is a minor irritation ) __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] lme X lmer results
On 12/26/05, Ronaldo Reis-Jr. [EMAIL PROTECTED] wrote: Hi, this is not a new doubt, but is a doubt that I cant find a good response. Look this output: m.lme - lme(Yvar~Xvar,random=~1|Plot1/Plot2/Plot3) anova(m.lme) numDF denDF F-value p-value (Intercept) 1 860 210.2457 .0001 Xvar1 2 1.2352 0.3821 summary(m.lme) Linear mixed-effects model fit by REML Data: NULL AIC BIClogLik 5416.59 5445.256 -2702.295 Random effects: Formula: ~1 | Plot1 (Intercept) StdDev: 0.000745924 Formula: ~1 | Plot2 %in% Plot1 (Intercept) StdDev: 0.000158718 Formula: ~1 | Plot3 %in% Plot2 %in% Plot1 (Intercept) Residual StdDev: 0.000196583 5.216954 Fixed effects: Yvar ~ Xvar Value Std.Error DF t-value p-value (Intercept)2.3545454 0.2487091 860 9.467066 0. XvarFactor20.3909091 0.3517278 2 1.111397 0.3821 Number of Observations: 880 Number of Groups: Plot1 Plot2 %in% Plot1 4 8 Plot3 %in% Plot2 %in% Plot1 20 This is the correct result, de correct denDF for Xvar. I make this using lmer. m.lmer - lmer(Yvar~Xvar+(1|Plot1)+(1|Plot1:Plot2)+(1|Plot3)) anova(m.lmer) Analysis of Variance Table Df Sum Sq Mean Sq Denom F value Pr(F) Xvar 1 33.62 33.62 878.00 1.2352 0.2667 summary(m.lmer) Linear mixed-effects model fit by REML Formula: Yvar ~ Xvar + (1 | Plot1) + (1 | Plot1:Plot2) + (1 | Plot3) AIC BIClogLik MLdeviance REMLdeviance 5416.59 5445.27 -2702.295 5402.698 5404.59 Random effects: GroupsNameVariance Std.Dev. Plot3 (Intercept) 1.3608e-08 0.00011665 Plot1:Plot2 (Intercept) 1.3608e-08 0.00011665 Plot1 (Intercept) 1.3608e-08 0.00011665 Residual 2.7217e+01 5.21695390 # of obs: 880, groups: Plot3, 20; Plot1:Plot2, 8; Plot1, 4 Fixed effects: Estimate Std. Error DF t value Pr(|t|) (Intercept) 2.354550.24871 878 9.4671 2e-16 *** XvarFactor2 0.390910.35173 878 1.1114 0.2667 --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 Look the wrong P value, I know that it is wrong because the DF used. But, In this case, the result is not correct. Dont have any difference of the result using random effects with lmer and using a simple analyses with lm. You are assuming that there is a correct value of the denominator degrees of freedom. I don't believe there is. The statistic that is quoted there doesn't have exactly an F distribution so there is no correct degrees of freedom. One thing you can do with lmer is to form a Markov Chain Monte Carlo sample from the posterior distribution of the parameters so you can check to see whether the value of zero is in the middle of the distribution of XvarFactor2 or not. It would be possible for me to recreate in lmer the rules used in lme for calculating denominator degrees of freedom associated with terms of the random effects. However, the class of models fit by lmer is larger than the class of models fit by lme (at least as far as the structure of the random-effects terms goes). In particular lmer allows for random effects associated with crossed or partially crossed grouping factors and the rules for denominator degrees of freedom in lme only apply cleanly to nested grouping factors. I would prefer to have a set of rules that would apply to the general case. Right now I would prefer to devote my time to other aspects of lmer - in particular I am still working on code for generalized linear mixed models using a supernodal Cholesky factorization. I am willing to put this aside and code up the rules for denominator degrees of freedom with nested grouping factors BUT first I want someone to show me an example demonstrating that there really is a problem. The example must show that the p-value calculated in the anova table or the parameter estimates table for lmer is seriously wrong compared to an empirical p-value - obtained from simulation under the null distribution or through MCMC sampling or something like that. Saying that Software XYZ says there are n denominator d.f. and lmer says there are m does NOT count as an example. I will readily concede that the denominator degrees of freedom reported by lmer are wrong but so are the degrees of freedom reported by Software XYZ because there is no right answer (in general - in a few simple balanced designs there may be a right answer). m.lm - lm(Yvar~Xvar) anova(m.lm) Analysis of Variance Table Response: Nadultos Df Sum Sq Mean Sq F value Pr(F) Xvar 133.633.6 1.2352 0.2667 Residuals 878 23896.227.2 summary(m.lm) Call: lm(formula = Yvar ~ Xvar) Residuals: Min 1Q Median 3Q Max -2.7455 -2.3545 -1.7455 0.2545
Re: [R] lme X lmer results
On 12/28/05, Douglas Bates [EMAIL PROTECTED] miswrote: It would be possible for me to recreate in lmer the rules used in lme for calculating denominator degrees of freedom associated with terms of the random effects. I should have written fixed effects, not random effects at the end of that sentence. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Axis/Ticks/Scale
Dear All, Apologies for this simple question and thanks in advance for any help given. Suppose I wanted to plot 1 million observations and produce the command plot(rnorm(100)) The labels of the xaxis are 0, e+00 2 e+05 etc. These are clearly not very attractive (The plots are for a PhD. thesis). I would like the axes to be 0,2,4,6,8,10 with a *10^5 on the right hand side. Is there a simple command for this? Best Wishes Roger __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Axis/Ticks/Scale
Here is one way to do it with a smaller set of data, but the 'range' is the same: x - c(1,1000,100) y - pretty(range(x)) y [1] 0e+00 2e+05 4e+05 6e+05 8e+05 1e+06 plot(x,1:3,xaxt='n', xlab=X * 10^5) axis(1, at=y, labels=y/10) On 12/28/05, [EMAIL PROTECTED] [EMAIL PROTECTED] wrote: Dear All, Apologies for this simple question and thanks in advance for any help given. Suppose I wanted to plot 1 million observations and produce the command plot(rnorm(100)) The labels of the xaxis are 0, e+00 2 e+05 etc. These are clearly not very attractive (The plots are for a PhD. thesis). I would like the axes to be 0,2,4,6,8,10 with a *10^5 on the right hand side. Is there a simple command for this? Best Wishes Roger __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Jim Holtman Cincinnati, OH +1 513 247 0281 What the problem you are trying to solve? [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Axis/Ticks/Scale
Try this: x - c(1, 1e6); y - 0:1 par(mar = c(5, 4, 4, 5) + 0.1) # make room at the right plot(x, y, axes = FALSE) box() axis(2) axis(1, at = 0:5 * 2 * 1e5, labels = 0:5 * 2) mtext(text = expression(phantom(0)%*%10^5), side = 1, line = 1, at = 11.0 * 1e5) Peter Ehlers [EMAIL PROTECTED] wrote: Dear All, Apologies for this simple question and thanks in advance for any help given. Suppose I wanted to plot 1 million observations and produce the command plot(rnorm(100)) The labels of the xaxis are 0, e+00 2 e+05 etc. These are clearly not very attractive (The plots are for a PhD. thesis). I would like the axes to be 0,2,4,6,8,10 with a *10^5 on the right hand side. Is there a simple command for this? Best Wishes Roger __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Axis/Ticks/Scale
On Wed, 2005-12-28 at 20:15 +, [EMAIL PROTECTED] wrote: Dear All, Apologies for this simple question and thanks in advance for any help given. Suppose I wanted to plot 1 million observations and produce the command plot(rnorm(100)) The labels of the xaxis are 0, e+00 2 e+05 etc. These are clearly not very attractive (The plots are for a PhD. thesis). I would like the axes to be 0,2,4,6,8,10 with a *10^5 on the right hand side. Is there a simple command for this? Best Wishes Roger See ?plotmath for some additional examples and there are some others in the list archives. set.seed(1) x - rnorm(100) # Now do the plot, but leave the x axis blank plot(x, xaxt = n) # Set the x axis label tick marks x.at - seq(0, 10, 2) * 10 ^ 5 # Create the expressions for the tick mark labels # Using parse() takes the character vectors from paste() # and converts them to expressions for use in plotmath x.lab - parse(text = paste(seq(0, 10, 2), %*% 10^5)) # Now do the axis labels axis(1, at = x.at, labels = x.lab) HTH, Marc Schwartz __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] segmetation fault and abort trap
Sorry, one more thing. Sometimes if crashes with Abort trap and sometimes it
crashes with Segmentation fault. Help!
Thanks!
Elizabeth Lawson [EMAIL PROTECTED] wrote:
I fixed the problem that I was having with the segmentation error and can
load it with dyn.load.
I have one more problem now that I don't understand. I am using the .C in a for
loop
for( i in 1:ncol(L.D)){
new[,i]-.C(mycode,as.double(L.D[,i]))
}
It crashes at different places each time I try to run it. So I tried
i-1
then running
new[,i]-.C(mycode,as.double(L.D[,i]))
repeatedly.
It works for 3-6 times then will crash with the error
abort trap
What does this mean?
Why does it work sometimes and not others?
Any suggestions?
Thanks,
Elizabeth Lawson
Kort, Eric wrote:
Elizabeth Lawson Wrote:
Hey,
I don;t know if anyone has come across this error before...
More times than I care to remember.
I am running R on the terminal of my MAC OS X 10.3.4 and I have
written
C code and compiled it using
R CMD SHLIB mycode.c
There were no problems in compiling so I now have mycode.o and
mycode.so.
A segmentation fault occurs when you try to access memory you didn't
allocate for your use (see below). In other words, you are trying to
use memory outside the segment allocated to your program (which, if
allowed, could result in corrupting memory being used by other
programs--which brings back unhappy memories of days gone by when an
error in one program could crash the whole system). So these kinds of
problems will not show up at compile time...only when you actually run
the program.
I used dyn.load(mycode.so) and again, no problems. But when I try
to
use the code .C(mycode,x) I get the error Segmentation fault and R
shuts
down. Any ideas as to where my problem could be?
When I run into a segmentation fault, it is usually because I am trying
to access an element of an array that is beyond what I have allocated,
as in...
int main()
{
int *a;
a = (int*) malloc(3*sizeof(int));
printf(Fasten your seatbelts...\n);
a[4000] = 12;
return(0);
}
One less obvious way this can happen is forgetting to initialize your
arrays to the proper length before passing a reference to them to your C
function.
If you still are having trouble, you could post a small snippet of code
that recreates the error for us to examine.
HTH,
Eric
This email message, including any attachments, is for the so...{{dropped}}
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[R] FW: R and read.irts
I have never worked with R before so I am
sorry if this is a bad question but I've
tried and tried ( all day ) and I can't figure this
problem out. I have the code below and I included the
data file as an attachment.
The code works in term of reading in the data
correctly but when the graph gets
created, the xaxis is really strangely/incorrectly
labelled. I have been trying
to understand this Posixct stuff in R but
I think this is where my knowledge is lacking and is maybe causing the
problem ?
Thank you very much.
I am using R in windows but through cygwin if that matters
but I doubt it does. Thanks again.
Mark
-
postscript(file=burp.ps)
library(quadprog)
library(zoo)
library(tseries)
temp-read.irts('~/ml/research/data/highfreq.dat',format=%H:%M:%S,tz=
GMT,sep=,,header=FALSE,row.names=NULL,
col.names=c(transdate,transprice,transamount))
temp
plot(temp,type=l,xlab=Time,ylab=NULL,main=NULL,ylim=NULL)
-
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Re: [R] R and read.irts
I thought r-help let you
attach asci files but
I don't think it does now
so below is a sample of my data set.
Thanks again.
09:40:08.5238,67.00,33
09:40:09.1968,67.00,2
09:40:09.7945,67.00,2
09:40:09.7975,67.00,2
09:40:09.8318,66.99,-3
09:40:17.6335,66.95,3
09:41:09.3393,66.95,6
09:41:11.1482,66.95,-1
09:42:07.4552,66.90,-5
09:42:12.5823,66.85,-5
09:42:14.4329,66.80,-2
09:42:16.2443,66.75,-2
09:43:04.1058,66.70,-2
09:44:16.2121,66.65,-6
09:44:21.5150,66.60,-7
09:44:25.6575,66.57,-2
09:44:29.5285,66.55,-8
09:44:33.2789,66.54,-2
09:44:38.5528,66.55,1
09:44:39.2230,66.55,1
09:44:59.7104,66.58,12
09:45:00.7885,66.59,2
09:45:10.8272,66.62,1
09:45:11.6823,66.65,1
09:45:13.2348,66.75,7
09:45:14.4443,66.74,1
09:45:16.3109,66.75,2
09:45:18.3270,66.80,1
09:45:42.1371,66.86,-6
09:45:44.5825,66.80,-5
09:46:15.3339,66.97,1
09:46:15.9808,66.97,2
09:46:20.8899,67.00,5
09:46:31.2155,67.03,2
09:46:31.2191,67.00,-10
09:46:32.8894,67.03,-6
09:46:44.0140,67.50,53
09:46:56.0595,67.45,-1
09:46:57.2567,67.46,2
09:48:06.0436,67.30,6
09:48:07.7098,67.29,1
09:48:08.9179,67.26,-3
09:48:09.6386,67.26,-1
09:48:09.6518,67.26,-1
09:48:28.6469,67.26,-2
09:48:29.7615,67.25,-5
09:48:30.0150,67.25,-2
09:48:30.0286,67.26,2
09:48:31.3576,67.25,-3
09:48:31.3691,67.25,-1
09:48:31.6511,67.26,2
09:48:33.2846,67.26,10
09:48:33.8989,67.25,-4
09:48:34.9265,67.26,10
09:48:54.3861,67.26,3
09:48:56.2098,67.23,-3
09:48:59.0664,67.20,-1
09:49:27.1401,67.20,-1
09:49:33.7843,67.10,-2
09:50:01.0211,67.00,-7
09:50:01.8044,67.00,-1
09:50:18.6195,67.00,1
09:50:43.9515,67.01,3
09:50:44.2924,67.01,6
09:50:45.4829,67.01,5
09:50:49.1846,67.05,10
09:51:17.9104,67.05,7
09:51:20.3488,67.09,2
09:51:41.7684,67.09,-2
09:51:43.1375,67.09,-2
09:51:47.7718,67.09,1
09:51:48.4666,67.10,1
09:51:49.2406,67.10,2
09:52:14.1491,67.10,3
09:52:19.8536,67.05,-1
09:52:48.1685,67.09,1
09:53:45.2387,67.08,-1
09:53:51.6611,67.08,-2
09:53:54.0639,67.09,3
09:55:07.0671,66.99,5
09:55:12.5074,66.90,-7
-Original Message-
From: Mark Leeds
Sent: Wednesday, December 28, 2005 6:42 PM
To: 'r-help@stat.math.ethz.ch'
Subject: FW: R and read.irts
I have never worked with R before so I am
sorry if this is a bad question but I've
tried and tried ( all day ) and I can't figure this
problem out. I have the code below and I included the
data file as an attachment.
The code works in term of reading in the data
correctly but when the graph gets
created, the xaxis is really strangely/incorrectly
labelled. I have been trying
to understand this Posixct stuff in R but
I think this is where my knowledge is lacking and is maybe causing the
problem ?
Thank you very much.
I am using R in windows but through cygwin if that matters
but I doubt it does. Thanks again.
Mark
-
postscript(file=burp.ps)
library(quadprog)
library(zoo)
library(tseries)
temp-read.irts('~/ml/research/data/highfreq.dat',format=%H:%M:%S,tz=
GMT,sep=,,header=FALSE,row.names=NULL,
col.names=c(transdate,transprice,transamount))
temp
plot(temp,type=l,xlab=Time,ylab=NULL,main=NULL,ylim=NULL)
-
**
This email and any files transmitted with it are confidentia...{{dropped}}
__
R-help@stat.math.ethz.ch mailing list
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PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] FW: R and read.irts
The attachment did not come through.
Look at R News 4/1 in general for info on dates and times and
if you still have a problem repost running this and placing its
output into the body of your post so we can see what your
data look like.
Lines - readLines(myfile) # read in lines without parsing them
dput(head(Lines)) # display first few lines in a way easy to read back in
On 12/28/05, Mark Leeds [EMAIL PROTECTED] wrote:
I have never worked with R before so I am
sorry if this is a bad question but I've
tried and tried ( all day ) and I can't figure this
problem out. I have the code below and I included the
data file as an attachment.
The code works in term of reading in the data
correctly but when the graph gets
created, the xaxis is really strangely/incorrectly
labelled. I have been trying
to understand this Posixct stuff in R but
I think this is where my knowledge is lacking and is maybe causing the
problem ?
Thank you very much.
I am using R in windows but through cygwin if that matters
but I doubt it does. Thanks again.
Mark
-
postscript(file=burp.ps)
library(quadprog)
library(zoo)
library(tseries)
temp-read.irts('~/ml/research/data/highfreq.dat',format=%H:%M:%S,tz=
GMT,sep=,,header=FALSE,row.names=NULL,
col.names=c(transdate,transprice,transamount))
temp
plot(temp,type=l,xlab=Time,ylab=NULL,main=NULL,ylim=NULL)
-
**
This email and any files transmitted with it are confident...{{dropped}}
__
R-help@stat.math.ethz.ch mailing list
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PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R and read.irts
I guess we are posting at the same time since I got this after
I posted a prior reply. Anyways, try this and also review the
R News article I mentioned previously as well as the zoo vignette
[i.e. library(zoo); vignette(zoo) ]
library(zoo)
library(chron)
z - read.zoo(myfile, FUN = times, sep = ,, col.names = letters[1:3])
plot(z)
On 12/28/05, Mark Leeds [EMAIL PROTECTED] wrote:
I thought r-help let you
attach asci files but
I don't think it does now
so below is a sample of my data set.
Thanks again.
09:40:08.5238,67.00,33
09:40:09.1968,67.00,2
09:40:09.7945,67.00,2
09:40:09.7975,67.00,2
09:40:09.8318,66.99,-3
09:40:17.6335,66.95,3
09:41:09.3393,66.95,6
09:41:11.1482,66.95,-1
09:42:07.4552,66.90,-5
09:42:12.5823,66.85,-5
09:42:14.4329,66.80,-2
09:42:16.2443,66.75,-2
09:43:04.1058,66.70,-2
09:44:16.2121,66.65,-6
09:44:21.5150,66.60,-7
09:44:25.6575,66.57,-2
09:44:29.5285,66.55,-8
09:44:33.2789,66.54,-2
09:44:38.5528,66.55,1
09:44:39.2230,66.55,1
09:44:59.7104,66.58,12
09:45:00.7885,66.59,2
09:45:10.8272,66.62,1
09:45:11.6823,66.65,1
09:45:13.2348,66.75,7
09:45:14.4443,66.74,1
09:45:16.3109,66.75,2
09:45:18.3270,66.80,1
09:45:42.1371,66.86,-6
09:45:44.5825,66.80,-5
09:46:15.3339,66.97,1
09:46:15.9808,66.97,2
09:46:20.8899,67.00,5
09:46:31.2155,67.03,2
09:46:31.2191,67.00,-10
09:46:32.8894,67.03,-6
09:46:44.0140,67.50,53
09:46:56.0595,67.45,-1
09:46:57.2567,67.46,2
09:48:06.0436,67.30,6
09:48:07.7098,67.29,1
09:48:08.9179,67.26,-3
09:48:09.6386,67.26,-1
09:48:09.6518,67.26,-1
09:48:28.6469,67.26,-2
09:48:29.7615,67.25,-5
09:48:30.0150,67.25,-2
09:48:30.0286,67.26,2
09:48:31.3576,67.25,-3
09:48:31.3691,67.25,-1
09:48:31.6511,67.26,2
09:48:33.2846,67.26,10
09:48:33.8989,67.25,-4
09:48:34.9265,67.26,10
09:48:54.3861,67.26,3
09:48:56.2098,67.23,-3
09:48:59.0664,67.20,-1
09:49:27.1401,67.20,-1
09:49:33.7843,67.10,-2
09:50:01.0211,67.00,-7
09:50:01.8044,67.00,-1
09:50:18.6195,67.00,1
09:50:43.9515,67.01,3
09:50:44.2924,67.01,6
09:50:45.4829,67.01,5
09:50:49.1846,67.05,10
09:51:17.9104,67.05,7
09:51:20.3488,67.09,2
09:51:41.7684,67.09,-2
09:51:43.1375,67.09,-2
09:51:47.7718,67.09,1
09:51:48.4666,67.10,1
09:51:49.2406,67.10,2
09:52:14.1491,67.10,3
09:52:19.8536,67.05,-1
09:52:48.1685,67.09,1
09:53:45.2387,67.08,-1
09:53:51.6611,67.08,-2
09:53:54.0639,67.09,3
09:55:07.0671,66.99,5
09:55:12.5074,66.90,-7
-Original Message-
From: Mark Leeds
Sent: Wednesday, December 28, 2005 6:42 PM
To: 'r-help@stat.math.ethz.ch'
Subject: FW: R and read.irts
I have never worked with R before so I am
sorry if this is a bad question but I've
tried and tried ( all day ) and I can't figure this
problem out. I have the code below and I included the
data file as an attachment.
The code works in term of reading in the data
correctly but when the graph gets
created, the xaxis is really strangely/incorrectly
labelled. I have been trying
to understand this Posixct stuff in R but
I think this is where my knowledge is lacking and is maybe causing the
problem ?
Thank you very much.
I am using R in windows but through cygwin if that matters
but I doubt it does. Thanks again.
Mark
-
postscript(file=burp.ps)
library(quadprog)
library(zoo)
library(tseries)
temp-read.irts('~/ml/research/data/highfreq.dat',format=%H:%M:%S,tz=
GMT,sep=,,header=FALSE,row.names=NULL,
col.names=c(transdate,transprice,transamount))
temp
plot(temp,type=l,xlab=Time,ylab=NULL,main=NULL,ylim=NULL)
-
**
This email and any files transmitted with it are confidentia...{{dropped}}
__
R-help@stat.math.ethz.ch mailing list
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PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
__
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PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Show graph integrated to GUI
Hi, Thank you for information.. I tried the TechingDemos package. But it seems that the window which contains slider control and graph window is separated. What I want to do is show slider control and graph in one window simultaneiously. It is possible ? Chihiro Kuraya Gregory Snow [EMAIL PROTECTED] wrote: The slider function in the TeachingDemos and relax packages (same function is in both packages you can use either) provides a way to do this using a Tk window. There are also several functions in the TechingDemos package that use a lower level interface to a Tk window that you can look at their source code as an example to build your own (examples include: vis.gamma, rotate.persp, and run.power.examp). 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] On Behalf Of Chihiro Kuraya Sent: Saturday, December 24, 2005 9:53 PM To: r-help@stat.math.ethz.ch Subject: [R] Show graph integrated to GUI Hi all, It it posssible to show graph which is integrated to some GUI (e.g. TclTk or R-wxPython). I want to make an application by R, for example, like the following picture: http://www.natch.co.uk/downloads/SigJenny/SJnScreenShot.gif Regards, Chihiro Kuraya -- STOP HIV/AIDS. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Show graph integrated to GUI
Try the example in ?tkrplot in package tkrplot. That shows a tcl-based plot interactively modified by a slider all in a single window. On 12/28/05, Chihiro Kuraya [EMAIL PROTECTED] wrote: Hi, Thank you for information.. I tried the TechingDemos package. But it seems that the window which contains slider control and graph window is separated. What I want to do is show slider control and graph in one window simultaneiously. It is possible ? Chihiro Kuraya Gregory Snow [EMAIL PROTECTED] wrote: The slider function in the TeachingDemos and relax packages (same function is in both packages you can use either) provides a way to do this using a Tk window. There are also several functions in the TechingDemos package that use a lower level interface to a Tk window that you can look at their source code as an example to build your own (examples include: vis.gamma, rotate.persp, and run.power.examp). 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] On Behalf Of Chihiro Kuraya Sent: Saturday, December 24, 2005 9:53 PM To: r-help@stat.math.ethz.ch Subject: [R] Show graph integrated to GUI Hi all, It it posssible to show graph which is integrated to some GUI (e.g. TclTk or R-wxPython). I want to make an application by R, for example, like the following picture: http://www.natch.co.uk/downloads/SigJenny/SJnScreenShot.gif Regards, Chihiro Kuraya -- STOP HIV/AIDS. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] trouble with S4 methods for group Summary
Hello. This question concerns the Methods package. I have created a new class and am trying to set a method for it for S4 group generic Summary. I have run into some signature problems. An example: setClass(track, representation(x=numeric, y=character)) [1] track setGeneric(max, group=Summary) [1] max setMethod(Summary, signature(x=track), function(x, ..., na.rm) callGeneric([EMAIL PROTECTED], ..., na.rm)) [1] Summary dd-new(track, x=c(1,2), y=abc) max(dd) [1] -Inf Warning message: no finite arguments to max; returning -Inf showMethods(max) Function max: na.rm = ANY na.rm = track na.rm = missing (inherited from na.rm = ANY) As you can see from the above, the method I tried to set for max (via Summary) was defined for the formal argument na.rm not x. This makes sense because the standardGeneric created for max only allows methods to be defined for argument na.rm max standardGeneric for max defined from package base belonging to group(s): Summary function (..., na.rm = FALSE) standardGeneric(max) environment: 0x19447a28 Methods may be defined for arguments: na.rm However, group Summary purports to allow you to define methods for arguments x and na.rm. Summary groupGenericFunction for Summary defined from package base function (x, ..., na.rm = FALSE) stop(function 'Summary' is a group generic; do not call it directly, domain = NA) environment: 0x16aef098 Methods may be defined for arguments: x, na.rm How does this work? Can someone point me to where I am going wrong, and explain how to define S4 methods for group Summary for argument x? Perhaps I need to do more in my setGeneric call? Thanks in advance. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
