Re: [R] 'initial value not feasible' in constrOptim

2007-09-08 Thread Ingmar Visser
Hi, On Sep 7, 2007, at 11:00 PM, Yuchen Luo wrote: constrOptim(c(0.5,0.3,0.5), fit.error, fit.error.grr, ui=-1*ui,ci=-1*ci) and I am confronted with error message initial value not feasible I plug in the initial value of (0.5,0.3,0.5) to function fit.error and fit.error.grr and have

Re: [R] logical operators priority

2007-07-17 Thread Ingmar Visser
guide http://www.R-project.org/posting- guide.html and provide commented, minimal, self-contained, reproducible code. Ingmar Visser Department of Psychology, University of Amsterdam Roetersstraat 15 1018 WB Amsterdam The Netherlands t: +31-20-5256735 [[alternative HTML version deleted

Re: [R] R and Copula

2007-07-17 Thread Ingmar Visser
@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 and provide commented, minimal, self-contained, reproducible code. Ingmar Visser Department of Psychology, University of Amsterdam Roetersstraat 15 1018

Re: [R] help again

2007-07-03 Thread Ingmar Visser
On Jul 2, 2007, at 6:22 PM, umarporn charusombat wrote: hi i try to use arima and holtwinter to predict drought from 1895-2006 unless you have access to time-travel isn't this better called retrodiction? ingmar but i cannot read whole period of time and i try to do the exponent

Re: [R] fisher information matrix

2007-06-26 Thread Ingmar Visser
the posting guide http://www.R-project.org/posting- guide.html and provide commented, minimal, self-contained, reproducible code. Ingmar Visser Department of Psychology, University of Amsterdam Roetersstraat 15 1018 WB Amsterdam The Netherlands t: +31-20-5256735 [[alternative HTML version

Re: [R] meta-analysis in R

2007-06-21 Thread Ingmar Visser
://www.R-project.org/posting- guide.html and provide commented, minimal, self-contained, reproducible code. Ingmar Visser Department of Psychology, University of Amsterdam Roetersstraat 15 1018 WB Amsterdam The Netherlands t: +31-20-5256735 [[alternative HTML version deleted

Re: [R] How to solve difficult equations?

2007-04-25 Thread Ingmar Visser
/posting- guide.html and provide commented, minimal, self-contained, reproducible code. Ingmar Visser Department of Psychology, University of Amsterdam Roetersstraat 15 1018 WB Amsterdam The Netherlands t: +31-20-5256735 [[alternative HTML version deleted

[R] flexmix glm warning

2007-04-16 Thread Ingmar Visser
warnings: Warning messages: 1: non-integer #successes in a binomial glm! in: eval(expr, envir, enclos) 2: non-integer #successes in a binomial glm! in: eval(expr, envir, enclos) Any help with interpreting these warnings is welcome. Should I be worried about them? Best, Ingmar  Ingmar

Re: [R] Calling Optim() from C

2007-03-08 Thread Ingmar Visser
Section 6.8 of the writing R extensions manual mentions this: 6.8 Optimization The C code underlying optim can be accessed directly. The user needs to supply a function to compute the function to be minimized, of the type typedef double optimfn(int n, double *par, void *ex); And also vmmin()

[R] vectorized dmvnorm

2007-03-02 Thread Ingmar Visser
a vector with elements: dmvnorm(x[i,],y[i,],sig[,,i]) And/or is there another efficient of computing these without using loops: for(i in 1:3) print(dmvnorm(x[i,],y[i,],sig[,,i])) best, Ingmar Visser __ R-help@stat.math.ethz.ch mailing list https

Re: [R] circle fill problem

2007-02-08 Thread Ingmar Visser
Robin Mini, For those interested, googling for the 'orange packing problem' as it is known, or more officially the sphere packing problems gives you quite a few hits on these and similar problems. So at least the 3-d case the problem has been solved (I imagine the problem is easier in 2-d

[R] Efficient multinom probs

2007-01-05 Thread Ingmar Visser
Dear R-helpers, I need to compute probabilties of multinomial observations, eg by doing the following: y=sample(1:3,15,1) prob=matrix(runif(45),15) prob=prob/rowSums(prob) diag(prob[,y]) However, my question is whether this is the most efficient way to do this. In the call prob[,y] a whole

Re: [R] maximum likelihood estimation of 5 parameters

2007-01-05 Thread Ingmar Visser
Franco, You can provide lower and upper bounds on the parameters if you use optim with method=L-BFGS-B. Hth, Ingmar From: francogrex [EMAIL PROTECTED] Date: Fri, 5 Jan 2007 04:54:50 -0800 (PST) To: r-help@stat.math.ethz.ch Subject: [R] maximum likelihood estimation of 5 parameters Hi

Re: [R] Aggregate?

2006-12-08 Thread Ingmar Visser
It does that for me without errors ... (R 2.3.1 on Mac OSX 10.4.8) Best, Ingmar From: Gustaf Rydevik [EMAIL PROTECTED] Date: Fri, 8 Dec 2006 12:58:01 +0300 To: r-help@stat.math.ethz.ch Subject: [R] Aggregate? Hi All, I think i'm failing to undersatnd how aggregate() is supposed to

Re: [R] statistics help

2006-11-24 Thread Ingmar Visser
Dear Rohan, Why would you want to simulate these probabilities? As far as I can tell by your description these are all solvable analytically, see eg Kemeney, Mirkil, Snell Thompson, 1958, Finite Mathematical Structures. There are undoubtedly more recent publications that cover first passage

Re: [R] creating bins for a plot

2006-10-19 Thread Ingmar Visser
@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 and provide commented, minimal, self-contained, reproducible code. -- Ingmar Visser Department of Psychology, University of Amsterdam

[R] Barplot legend position

2006-10-13 Thread Ingmar Visser
Dear useRs, I'm trying to create a barplot like so: x=matrix(1:10,2,5) barplot(x,leg=c(left,right),besid=T) The legend is placed in default position topright, however the data are plotted there too. I tried controlling the legend position by adding x=topleft but this results in an error that x

Re: [R] Barplot legend position

2006-10-13 Thread Ingmar Visser
Thanks, this could work! However, the legend does not reproduce the color/shading used in the original barplot, are those available somehow? Best, Ingmar From: David Hajage [EMAIL PROTECTED] Date: Fri, 13 Oct 2006 14:11:21 +0200 To: Ingmar Visser [EMAIL PROTECTED] Cc: R-help@stat.math.ethz.ch

Re: [R] bimodal / trimodal

2006-10-10 Thread Ingmar Visser
Hi, If you want parametric modes you could fit mixtures with different numbers of components and select the best model with your favourite model-selection criterion. Various packages such as mclust and fitdistr may be helpful in doing this, the cluster task view has many more:

Re: [R] Linear model with hidden variables

2006-10-04 Thread Ingmar Visser
Richard, I'm not sure I fully understand your question but the flexmix package does mixtures of linear models which may be what you want. Hth, Ingmar From: Richard A. O'Keefe [EMAIL PROTECTED] Date: Wed, 4 Oct 2006 18:36:55 +1300 (NZDT) To: r-help@stat.math.ethz.ch Subject: [R] Linear model

Re: [R] Exponentiate a matrix

2006-09-22 Thread Ingmar Visser
://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Ingmar Visser Department of Psychology, University of Amsterdam Roetersstraat 15, 1018 WB Amsterdam The Netherlands

Re: [R] change the name of file

2006-07-24 Thread Ingmar Visser
Use paste(Data_,i, sep=) From: Robert Mcfadden [EMAIL PROTECTED] Date: Mon, 24 Jul 2006 11:06:38 +0200 To: r-help@stat.math.ethz.ch Subject: [R] change the name of file Dear R Users, Is it possible to make file names dependent on a changing variable? For instance. I generate random

Re: [R] parameter-restrictions in OPTIM

2006-05-29 Thread Ingmar Visser
You could reparametrize or use constrOptim, Hth, Ingmar From: Florian Staab [EMAIL PROTECTED] Date: Mon, 29 May 2006 12:08:59 +0200 To: r-help@stat.math.ethz.ch Subject: [R] parameter-restrictions in OPTIM Hallo, I'm trying to optimize a function A which calls another function B

Re: [R] flatten a list to a true list

2006-05-23 Thread Ingmar Visser
How about using c() ? c(list(a=1,b=2),list(c=3,d=4)) - L L L $a [1] 1 $b [1] 2 $c [1] 3 $d [1] 4 is.list(L) [1] TRUE How true of a list do you want? (-; Hth, ingmar From: Christian Hoffmann [EMAIL PROTECTED] Date: Tue, 23 May 2006 14:11:01 +0200 To: r-help@stat.math.ethz.ch Subject:

Re: [R] Precision in estimating log

2006-05-19 Thread Ingmar Visser
Googling for: What Every Computer Scientist should know about floating point arithmetic Gets you to a very enlightening pdf about these issues. Hth, ingmar From: Gichangi, Anthony [EMAIL PROTECTED] Date: Fri, 19 May 2006 14:25:51 +0200 To: R-help r-help@stat.math.ethz.ch Subject: [R]

[R] Calling R from C

2006-05-09 Thread Ingmar Visser
Dear R-helpers, I'm trying to transfer a loop from R code to C to improve performance using the .Call interface. However, I ran into problems before even getting started, and I hope (fear) I'm missing something completely obvious here. I use the following C function (passing an integer to the C

Re: [R] invalid variable type in model.frame within a function

2006-03-24 Thread Ingmar Visser
On Thu, 23 Mar 2006, Ingmar Visser wrote: Dear expeRts, I came across the following error in using model.frame: # make a data.frame jet=data.frame(y=rnorm(10),x1=rnorm(10),x2=rnorm(10),rvar=rnorm(10)) # spec of formula mf1=y~x1+x2 # make the model.frame mf=model.frame(formula=mf1

[R] invalid variable type in model.frame within a function

2006-03-23 Thread Ingmar Visser
Dear expeRts, I came across the following error in using model.frame: # make a data.frame jet=data.frame(y=rnorm(10),x1=rnorm(10),x2=rnorm(10),rvar=rnorm(10)) # spec of formula mf1=y~x1+x2 # make the model.frame mf=model.frame(formula=mf1,data=jet,weights=rvar) Which gives the desired output:

Re: [R] R package for computing state path using Viterbi algorithm

2006-03-22 Thread Ingmar Visser
Wuming, Have a look at the depmix package that implements the viterbi algorithm for hidden markov models (in discrete time). The function to use is posterior(...). The package includes a manual with a number of examples. Hth, Ingmar From: Wuming Gong [EMAIL PROTECTED] Date: Wed, 22 Mar 2006

Re: [R] Hessian from optim()

2006-03-21 Thread Ingmar Visser
Hello! Looking on how people use optim to get MLE I also noticed that one can use returned Hessian to get corresponding standard errors i.e. something like result - optim( snip , hessian=T) result$par # point estimates vc - solve(result$hessian) # var-cov matrix se -

Re: [R] discrete entropy is not rotation invariant?

2006-03-20 Thread Ingmar Visser
Hi Context, It seems to me that the changes in entropy are simply due to the binning. The usual entropy would be the limit of the discrete entropy when the number of bins goes to infinity. For the discrete entropy to be a useful approximation to the entropy the number of bins should be reasonably

Re: [R] anonymous postings

2006-03-04 Thread Ingmar Visser
, ingmar -- Ingmar Visser Department of Psychology, University of Amsterdam Roetersstraat 15, 1018 WB Amsterdam The Netherlands http://users.fmg.uva.nl/ivisser/ tel: +31-20-5256735 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman

Re: [R] any more direct-search optimization method in R

2006-02-28 Thread Ingmar Visser
If you have only boundary constraints on parameters you can use method L-BFGS in optim. Hth, ingmar From: Weijie Cai [EMAIL PROTECTED] Date: Tue, 28 Feb 2006 11:48:32 -0500 To: r-help@stat.math.ethz.ch Subject: [R] any more direct-search optimization method in R Hello list, I am

Re: [R] latent class modle for rater agreement

2006-02-10 Thread Ingmar Visser
Typing latent class on the R project search page gives you at least four packeges that do latent class models mmlcr, flexmix, gllm, depmix etc Hth, ingmar From: Lisa Wang [EMAIL PROTECTED] Organization: UHN\RIS Date: Thu, 09 Feb 2006 16:31:04 -0500 To: R-Help r-help@stat.math.ethz.ch

Re: [R] generating markov chain

2006-02-06 Thread Ingmar Visser
You can use the following, with x your transition matrix y=numeric(100) x=matrix(runif(16),4,4) for(i in 2:100) { y[i]=which(rmultinom(1, size = 1, prob = x[y[i-1], ])==1) } hth, ingmar -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Behalf Of Norman Goodacre Sent:

Re: [R] generating markov chain

2006-02-06 Thread Ingmar Visser
:37:13 -0800 To: Ingmar Visser [EMAIL PROTECTED] Cc: Norman Goodacre [EMAIL PROTECTED], r-help@stat.math.ethz.ch Subject: Re: [R] generating markov chain On 2/6/06, Ingmar Visser [EMAIL PROTECTED] wrote: You can use the following, with x your transition matrix y=numeric(100) x=matrix(runif

Re: [R] Making a markov transition matrix

2006-01-23 Thread Ingmar Visser
Ajay, On a similar note, there are two other packages as well for similar models: hmm.discnp for hidden Markov models of univariate discrete non-parametric distributions and depmix for hidden Markov models for multivariate data, ie gaussians, multinomials etc, and combinations of these hth, ingmar

Re: [R] multivariate markov switching

2006-01-13 Thread Ingmar Visser
I don't know the MS-VAR model. The graphical models page on the r-project site refers to a number of packages that deal with these types of models of which I don't know the specifics. The depmix package does multivariate hidden markov models. best, ingmar From: Carlo Fezzi [EMAIL PROTECTED]

Re: [R] Can I ask for the C code inside an R function using .C?

2006-01-13 Thread Ingmar Visser
You can download the source from any package from a CRAN mirror near you and the src directory will contain the source code of the included C and fortran functions. hth, ingmar From: Yingfu Xie [EMAIL PROTECTED] Date: Fri, 13 Jan 2006 17:04:43 +0100 To: r-help@stat.math.ethz.ch Subject: [R]

Re: [R] a series of 1's and -1's

2006-01-12 Thread Ingmar Visser
You could try to zip your data file and see whether there is a change in file size that you feel is significant in which case the series is not random (-: To be sure, there is no such thing as a positive test for randomness, only tests for specific deviations of randomness of which the runs.test

Re: [R] Finding all possible partitions of N units into k classe

2005-12-09 Thread Ingmar Visser
Can you tell us which package that function is in? Google on the r-project site nor on the www produced a hit. best, ingmar From: Ales Ziberna [EMAIL PROTECTED] Date: Fri, 9 Dec 2005 09:22:47 +0100 To: R-help r-help@stat.math.ethz.ch Subject: Re: [R] Finding all possible partitions of N units

Re: [R] Finding all possible partitions of N units into k classes

2005-12-08 Thread Ingmar Visser
combinations in the gtools package can be helpfull here, best, ingmar From: Ales Ziberna [EMAIL PROTECTED] Date: Thu, 8 Dec 2005 15:45:37 +0100 To: R-help r-help@stat.math.ethz.ch Subject: [R] Finding all possible partitions of N units into k classes Dear useRs! I would like to

Re: [R] how to construct an index or classify the cases with the combination of categorical and continuous variables

2005-12-05 Thread Ingmar Visser
/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Ingmar Visser Department of Psychology, University of Amsterdam Roetersstraat 15, 1018 WB Amsterdam The Netherlands http://users.fmg.uva.nl/ivisser/ tel: +31-20-5256735

Re: [R] bimodal data

2005-12-02 Thread Ingmar Visser
Hi Simone, It depends on what you want from the data ... A bimodal distribution can typically be modelled with a mixture distribution, where the assumption is that each of the modes corresponds to an underlying process generating those data. hth, ingmar Hi, Does anybody have a good tip of

[R] contrib pkg install problem on Windows with R2.2.0

2005-12-01 Thread Ingmar Visser
Dear R-helpers, I made the package depmix for fitting hidden markov models. After updating R to version 2.2.0 on my PC I got the following error when installing the package from a local directory. One of the C files includes the R.h file which apparently causes problems. I call R CMD INSTALL

Re: [R] contrib pkg install problem on Windows with R2.2.0

2005-12-01 Thread Ingmar Visser
Dear Uwe, I made the package depmix for fitting hidden markov models. After updating R to version 2.2.0 on my PC I got the following error when installing the package from a local directory. One of the C files includes the R.h file which apparently causes problems. I call R CMD INSTALL

[R] suppress checking chm files in R CMD check on Windows

2005-12-01 Thread Ingmar Visser
Dear R-helpers, When installing a source package I can suppress the compilation of .chm files by using the --docs=normal option. Is it also possible to suppress the creation and checking of .chm files when calling R CMD check ? best, ingmar __

[R] information matrix in random effects model

2005-10-31 Thread Ingmar Visser
random effects models, and is it possible to extract them somehow from the fitted objects? ingmar -- Ingmar Visser Department of Psychology Roetersstraat 15 (building A room 1009) 1018 WB Amsterdam tel.: +31-20-5256735 __ R-help@stat.math.ethz.ch mailing

[R] passing char to Fortran routine

2005-10-10 Thread Ingmar Visser
Hello all, I am using an existing Fortran routine that takes a single character string as argument. The routine echoes the argument that I provide. When working on OS X 3.9 there seems to be no problem, ie the Fortran routine nicely echoes my argument. However, I compiled the same package on a PC

Re: [R] Animation of Mandelbrot Set

2005-10-06 Thread Ingmar Visser
The binary version of caTools on CRAN (1.0) does not have the write.gif function but the source version (1.4) does ... hth, ingmar From: roger bos [EMAIL PROTECTED] Reply-To: roger bos [EMAIL PROTECTED] Date: Thu, 6 Oct 2005 08:14:42 -0400 To: Tuszynski, Jaroslaw W. [EMAIL PROTECTED] Cc:

Re: [R] regsubsets selection criterion

2005-09-27 Thread Ingmar Visser
Is there anyone who can tell me on which criterion is based the 'regsubsets' function ? the leaps help page says: cp or adjr2 or r2 is the value of the chosen model selection statistic for each model so each of these can be chosen as the selection statistic using the method argument hth,

Re: [R] hidden markov models

2005-09-26 Thread Ingmar Visser
Emilio, The depmix package on cran has multivariate distributions and the possibility of (linear) covariates on the parameters. If you have questions about its use feel free to contact me, best, ingmar visser On 9/26/05 6:29 PM, Dr. Emilio A. Laca [EMAIL PROTECTED] wrote: Dear R community

Re: [R] Help on optim

2005-09-21 Thread Ingmar Visser
Hi Manoj, AFAIK there is no way in R to optimize functions under general linear equality constraints (for inequality constraints there is constrOptim). In your case you could reparametrize such that you estimate weights w(1) ... w(n-1) and simply compute w(n) from those. Even so, it would be great

Re: [R] fitting distribution tails

2005-09-07 Thread Ingmar Visser
Not an R-response, but see this reference: Dolan CV, van der Maas HLJ, Molenaar PCM A framework for ML estimation of parameters of (mixtures of) common reaction time distributions given optional truncation or censoring  BEHAVIOR RESEARCH METHODS INSTRUMENTS COMPUTERS 34 (3): 304-323 AUG 2002

Re: [R] code for model-averaging by Akaike weights

2005-07-03 Thread Ingmar Visser
guide! http://www.R-project.org/posting-guide.html -- Ingmar Visser Department of Psychology, University of Amsterdam Roetersstraat 15, 1018 WB Amsterdam The Netherlands http://users.fmg.uva.nl/ivisser/ tel: +31-20-5256735 __ R-help@stat.math.ethz.ch

Re: [R] Linear Models with mean as Intercept.

2005-06-30 Thread Ingmar Visser
you could model: (y-mean(y))~x hth, ingmar From: Ghislain Vieilledent [EMAIL PROTECTED] Date: Thu, 30 Jun 2005 15:35:30 +0200 To: r-help@stat.math.ethz.ch Subject: [R] Linear Models with mean as Intercept. *** Questions *** How can I obtain a predictive model y=mean(y)+A(i) ?

[R] constraints

2005-05-21 Thread Ingmar Visser
Is there a package in R that handles general linear (in-)equality + box constrained optimization? If it is not there, could anyone advise me which way to go? And/or point me to packages that solve these problems partially? best, ingmar -- Ingmar Visser Department of Psychology, University

[R] constraint optimization

2005-05-16 Thread Ingmar Visser
in that case I could use constrOptim to fit the inequality constraints. Any help appreciated, best, ingmar -- Ingmar Visser Department of Psychology, University of Amsterdam Roetersstraat 15, 1018 WB Amsterdam The Netherlands http://users.fmg.uva.nl/ivisser/ tel: +31-20-5256735

[R] Rd.sty error

2005-05-03 Thread Ingmar Visser
seen this before and/or is it problematic? I'm not sure whether the output suffers from this but it does create a problem with R CMD check because tex produces a warning/error there. any hints are welcome, ingmar -- Ingmar Visser Department of Psychology, University of Amsterdam Roetersstraat 15

Re: [R] Rd.sty error

2005-05-03 Thread Ingmar Visser
on depmix-manual.pdf (47 pages, 270051 bytes). On 5/3/05 2:52 PM, Prof Brian Ripley [EMAIL PROTECTED] wrote: I don't see an error message here. And what is `texShop'? I think we need (a lot) more details of what you actually are doing. On Tue, 3 May 2005, Ingmar Visser wrote: I had

Re: [R] help files and vignettes

2005-04-29 Thread Ingmar Visser
On 4/29/05 7:48 AM, Uwe Ligges [EMAIL PROTECTED] wrote: Ingmar Visser wrote: Hi all, I'm writing a vignette for my package, and I would like to include some of the package help files in there as well. Is there an easy way of doing so? I tried using R CMD Rdconv to generate latex files from

[R] help files and vignettes

2005-04-28 Thread Ingmar Visser
that I have 6 or so .Rd files. Especially when updating them, adding functions and so forth, this process of generating the Rd2.tex files and then copying and pasting into the vignette source is quite tedious. In short, is there a faster way of doing this? best, ingmar -- Ingmar Visser Department

Re: [R] having problems with constrOptim

2005-04-09 Thread Ingmar Visser
@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 -- Ingmar Visser Department of Psychology, University of Amsterdam Roetersstraat 15, 1018 WB Amsterdam The Netherlands http://users.fmg.uva.nl/ivisser

Re: [R] error in kmeans

2005-04-01 Thread Ingmar Visser
/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Ingmar Visser Department of Psychology, University of Amsterdam Roetersstraat 15, 1018 WB Amsterdam The Netherlands http://users.fmg.uva.nl/ivisser/ tel: +31-20-5256735

Re: [R] non-derivative based optimization and standard errors.

2005-03-24 Thread Ingmar Visser
__ 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 -- Ingmar Visser Department of Psychology, University of Amsterdam Roetersstraat 15, 1018 WB Amsterdam

[R] Convert timeseries to transition matrix

2005-03-22 Thread Ingmar Visser
Meaning that there are two transitions from 1 to 1, two from 1 to 2, three from 2 to 1 and two from 2 to 2. Using for loops etc this is of course no problem, but I am curious whether there is a smarter solution. Any hints appreciated, Ingmar -- Ingmar Visser Department of Psychology, University

Re: [R] Convert timeseries to transition matrix

2005-03-22 Thread Ingmar Visser
-Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Ingmar Visser Sent: Tuesday, March 22, 2005 11:21 AM To: R-help@stat.math.ethz.ch Subject: [R] Convert timeseries to transition matrix Hi All, Does someone have an idea of how to cleverly convert

Re: [R] Positive log-likelihood in lme

2005-02-16 Thread Ingmar Visser
are privileged and/or confidenti...{{dropped}} __ 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 -- Ingmar Visser Roetersstraat 15 1018 WB

[R] error in building help files

2005-01-26 Thread Ingmar Visser
the help files makes the error disappear, but only removing the help file that I was working on does not ... I'm rather puzzled, which file is R CMD INSTALL looking for here? Has anyone come across this error before? best, ingmar visser ps: this is on OS X 10.3.7 and R 2.0.1 and R CMD INSTALL

[R] error in building help files

2005-01-26 Thread Ingmar Visser
the help files makes the error disappear, but only removing the help file that I was working on does not ... I'm rather puzzled, which file is R CMD INSTALL looking for here? Has anyone come across this error before? best, ingmar visser ps: this is on OS X 10.3.7 and R 2.0.1 and R CMD INSTALL

Re: [R] R packages on Mac

2005-01-07 Thread Ingmar Visser
hi Sam, Building source packages with C++ source code is no problem at all on Mac OS X if you simply follow the instructions in the FAQ. best and good luck with your new Mac, from a content MAC user, best, ingmar On 1/7/05 2:45 PM, Samuel Kemp [EMAIL PROTECTED] wrote: Hi, I am considering

Re: [R] Adding values to the end of a vector?

2005-01-04 Thread Ingmar Visser
The following works, but there may be more efficient ways to do this ... x=numeric(0) for(i in 1:5) { + x[length(x)+1]=i + } x [1] 1 2 3 4 5 Best, ingmar On 1/4/05 2:41 PM, Dan Bolser [EMAIL PROTECTED] wrote: I want to add values onto the end of a vector, for example... x - vector

Re: [R] R: optimisation

2004-12-15 Thread Ingmar Visser
There's also nlm for non-linear newton type minimization, best, ingmar On 12/15/04 3:48 PM, Clark Allan [EMAIL PROTECTED] wrote: hi all other than optim, optimise, and some other related optimisation functions are there any optimisation packages in R?

Re: [R] Cluster Analysis: Density-Based Method

2004-10-21 Thread Ingmar Visser
maybe ?kmeans is what you're looking for ... ingmar On 10/21/04 2:47 PM, Fernando Prass [EMAIL PROTECTED] wrote: Yes, but mclust don't have a density-based algorithm. Mclust have the algorithm BIC, that is a model-based method... Fernando Prass --- Kjetil Brinchmann Halvorsen [EMAIL

[R] meta.summaries and se's of effect sizes

2004-10-18 Thread Ingmar Visser
Hi All, I would like to use meta.summaries from package rmeta to do a meta-analysis. I have available effect sizes as r's (which could be easily transformed to effect sizes in terms of d's). My problem is that I'm not sure what the se's of these r's should be ... The r-values are themselves

[R] install failure Ruuid package on OS X

2004-10-11 Thread Ingmar Visser
Dear All, When installing the Ruuid package (from Bioconductor) from sources on my MAC (OS X 10.3.5, R version 2.0.0) I get the following errors: m00245:~ ivisser$ R CMD INSTALL -l /Users/ivisser/Library/R/library/ /Users/ivisser/Desktop/Ruuid * Installing *source* package 'Ruuid' ... loading

Re: [R] Bootstrap

2004-09-22 Thread Ingmar Visser
did you look at library(boot) ?boot On 9/22/04 9:19 AM, nmi13 [EMAIL PROTECTED] wrote: Dear Any, Can someone please inform me, if they have a code to estimate the varaince using bootstrap resampling method under a two stage cluster design. Thanks for all your help and time.

Re: [R] persiting complex R objects

2004-09-20 Thread Ingmar Visser
did you look at ?save ?load ??? ingmar On 9/20/04 1:00 PM, Richard Mott [EMAIL PROTECTED] wrote: Is there a method to save a large and complex R object (either as a binary or text file) so that it can be loaded and reused at a later time? Specifically, I am creating large lists (several

Re: [R] OS X specific question: help.start() won't launch

2004-08-19 Thread Ingmar Visser
Hi Dave, This has come up a couple of times recently. I don't remember by heart but searching the archives should help you find the answer. It's best to try R-SIG-MAC list archive. Bye, ingmar On 8/19/04 4:34 AM, David L. Van Brunt, Ph.D. [EMAIL PROTECTED] wrote: It's been a while since I used

Re: [R] linear constraint optim with bounds/reparametrization

2004-08-10 Thread Ingmar Visser
On 8/9/04 4:52 PM, Thomas Lumley [EMAIL PROTECTED] wrote: On Mon, 9 Aug 2004, Kahra Hannu wrote: 1) constrOptim does not work in this case because it only fits inequality constraints, ie A%*%theta = c --- I was struggling with the same problem a few weeks ago in

[R] linear constraint optim with bounds/reparametrization

2004-08-09 Thread Ingmar Visser
Hello All, I would like to optimize a (log-)likelihood function subject to a number of linear constraints between parameters. These constraints are equality constraints of the form A%*%theta=c, ie (1,1) %*% 0.8,0.2)^t = 1 meaning that these parameters should sum to one. Moreover, there are bounds

RE: [R] choosing constraints for function optim method=L-BFGS-B whenthey are in terms of other parameter values

2004-07-26 Thread Ingmar Visser
Hi Tom, I am not entirely sure what the problem, you haven't been very specific. If you want general linear constraints on your parameters, ie linear combinations of parameters summing to some value, constrOptim may be of help. hth, ingmar Ingmar Visser Developmental Processes Research Group

Re: [R] Block Bootstrap Simulation

2004-07-16 Thread Ingmar Visser
On 7/16/04 11:51 AM, Campbell [EMAIL PROTECTED] wrote: I don't want to use loop because a) the overhead and b) I'm comparing it with another technique that doesn't require a loop, and programming the simulation without the loop gave me an insight into the solution of the problem Is there a

Re: [R] Permutations

2004-07-15 Thread Ingmar Visser
On 7/14/04 7:42 PM, Jordi Altirriba Gutiérrez [EMAIL PROTECTED] wrote: 4 5 6 | 2 1 3 | 7 8 9 | 10 11 12 NO because it's an intra-block permutation of permutation 3 - - 10 1 7 | 4 8 7 | 5 6 12 | 3 2 9YES---Xth permutation 1 10 7 | 4 8 7 | 5 6 12 | 3 2 9NO because

[R] passing char's from C to Fortran (mac os x)

2004-07-05 Thread Ingmar Visser
anyone point me to a working example of passing characters from C to Fortran? Or tell me what's wrong in my code above? My platform is below, I use R CMD INSTALL to compile and install the complete package. thanks in advance, ingmar visser platform powerpc-apple-darwin6.8 arch powerpc os

[R] Mac OS X 10.2.8 versus 10.3.4 package load failure

2004-06-30 Thread Ingmar Visser
Hello All, I have built a package depmix and build a source package file from it for distribution. I have done all this on the following platform: platform powerpc-apple-darwin6.8 arch powerpc os darwin6.8 system powerpc, darwin6.8 status major1 minor

RE: [R] hidden markov models in R?

2004-06-20 Thread Ingmar Visser
Hi Cezar, Download and install the repeated package by Jim Lindsey and type ?hidden bye, ingmar Hi, friends! Has R estimation (library, for example) to do estimation in HMM? Thanks in advance, Cezar Freitas Estatistico - Comissao Permanente para

Re: [R] bus error macosx/off-topic

2004-05-17 Thread Ingmar Visser
On 5/13/04 12:46 PM, Prof Brian Ripley [EMAIL PROTECTED] wrote: On Thu, 13 May 2004, Ingmar Visser wrote: Dear Prof Ripley, Thanks for your answer. On 5/12/04 2:52 PM, Prof Brian Ripley [EMAIL PROTECTED] wrote: These normally occur (at that point) from having written off one end

Re: [R] bus error macosx/off-topic

2004-05-17 Thread Ingmar Visser
On 5/17/04 12:57 PM, Prof Brian Ripley [EMAIL PROTECTED] wrote: On Mon, 17 May 2004, Ingmar Visser wrote: On 5/13/04 12:46 PM, Prof Brian Ripley [EMAIL PROTECTED] wrote: On Thu, 13 May 2004, Ingmar Visser wrote: Dear Prof Ripley, Thanks for your answer. On 5/12/04 2:52 PM, Prof

Re: [R] bus error macosx/off-topic

2004-05-13 Thread Ingmar Visser
Dear Prof Ripley, Thanks for your answer. On 5/12/04 2:52 PM, Prof Brian Ripley [EMAIL PROTECTED] wrote: These normally occur (at that point) from having written off one end of an array. (If you are using .C/.Fortran, they try to copy back the arguments.) Compiling with bounds checking turned

[R] bus error macosx/off-topic

2004-05-12 Thread Ingmar Visser
out if that is what is happening while running R? Any hints greatly appreciated. Best, ingmar visser __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org

Re: [R] RAqua and gcc

2004-03-30 Thread Ingmar Visser
Hi Kosuke, The building R from sources FAQ (version from jan 31,2004, can't seem to find it on the web anymore), says that installing libwmf+iconv as part of the teTex system causes trouble between gcc and R. You may try removing it and install again. I succesfully installed from source files from

[R] Console/command line output

2004-03-30 Thread Ingmar Visser
Hi all, I am working on Macos x 10.3 (Panther) to build a package consisting of C/C++ code that is called from R. In the C/C++-sources I use several commands to print info to the console: std::cout info endl; and: Rprintf(info\n); Both work fine when R is run on the command line but

[R] Console output

2004-03-26 Thread Ingmar Visser
Hi all, I am working on Macos x 10.3 (Panther) to build a package consisting of C/C++ code that is called from R. In the C-sources I use several commands to print info to the console: I used two different ways: std::cout info\n; And Rprintf(info\n); Both work fine when R is run from the