similar to: passing char to Fortran routine

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 --docs="normal" depmix and I get the following error: make[3]: *** No rule to make target

Hi All, I was updating my help pages for a package when all of a sudden I got the following error when using R CMD INSTALL: >>> Building/Updating help pages for package 'depmix' Formats: text html latex example Error in load(zfile, envir = envir) : error reading from connection Removing all the help files makes the error disappear, but only removing the help file that I

Hi, When running R CMD check I'm getting a number of errors that I don't quite follow and don't know where to start looking for an answer, any hints appreciated. R CMD check trunk * checking for working latex ... OK * using log directory '/Users/ivisser/Documents/projects/ depmixProject/depmixNew/rforge/depmix/trunk.Rcheck' * using R version 2.6.2 (2008-02-08) * checking

Hello All, In some package I use a c-routine which calls a fortran routine which expects a char-string as input. As per the writing R-extensions manual, the Fortran routine is declared in C as: void F77_NAME (setoptions) (char **option); and then it is calles as follows: char **option; option = new char*[1]; option[0] = new char[256]; option[0] = strcpy(option[0],"Iteration

Dear R community, I am looking for an R package or other software to study hidden Markov models. I need to be able to incorporate multivariate emissions and covariates for the transition probabilities. The msm package seems almost perfect for my purpose, but I do not think it allows multivariate emissions. I will be grateful for your suggestions. All the best, -- Emilio A. Laca One

Hi All, Does someone have an idea of how to cleverly convert a categorical timeseries into a transition matrix? Ie, I have something like: x<- c(1,1,2,1,1,2,2,2,1,2), And I want a matrix with counts and/or probabilities: > tr <- matrix(c(2,3,2,2),2,2) > tr [,1] [,2] [1,] 2 2 [2,] 3 2 Meaning that there are two transitions from 1 to 1, two from 1 to 2, three from 2 to 1

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 matches multiple formal arguments. Leaving out the legend

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 of Amsterdam Roetersstraat 15, 1018 WB Amsterdam The Netherlands http://users.fmg.uva.nl/ivisser/ tel:

Hi All, I'm building a package using C/C++ and Fortran code which usually runs fine. However I do get occasional bus errors around the time of exiting one of the C functions. Where do I need to be looking to solve this problem? Do bus errors stem from unmapped memory exceptions? How can I find out if that is what is happening while running R? Any hints greatly appreciated. Best, ingmar

We are trying to build a human respiration model. Preliminary analysis of some breathing signals has shown that humans breathe through switching among a finite number of patterns. Hidden Markov seems to be the right approach. Since most of our code is written in R scripting language, finding an R package implementing an HMM that we can use for our prototype would be very helpful. I have been

Dear R-help, I'm trying to load the fGarch package and keep running into problems with tcltk: After succesfully instaling fGarch (and dependencies) I get: >library(fGarch) Loading required package: fBasics Loading required package: fImport Loading required package: fSeries Loading required package: robustbase Loading required package: fCalendar Loading required package: MASS Loading

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 neither works when running Raqau (I did check the preference boxes

Dear R-help, I'm facing a problem with defining a repeated measures anova with weighted data. Here's the code to reproduce the problem: # generate some data seed=11 rtrep <- data.frame(rt=rnorm(100),ti=rep(1:5,20),subj=gl (20,5,100),we=runif(100)) # model with within factor for subjects/repeated measurements, no problem aov(rt~ti + Error(subj/ti),data=rtrep) #model with weights

Dear helpers, is there any possible that transition (in depmixS4) is in scale of two variable, e.g transition=~scale(x1,x2)? If it can be, how transition of two variable (covariate time) can be worked in depmixS4-hidden markov model for time series. Many thanks, nglthu -- View this message in context: http://r.789695.n4.nabble.com/depmixS4-transition-tp4572726p4572726.html Sent from the R help

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 .Rd files but I am not sure how to include these into a .Rnw file (ie the vignette source). The resulting file from Rdconv do not readily compile using latex ... The other option I

I use the lme function from the nlme library (or alternatively from the Matrix library) to estimate a random effects model. Both functions return the covariance matrix of the estimated parameters. I have the following question: Is it possible to retrieve the information matrix of such a model (ie from the fitted object)? In particular, the information matrix can be computed as a sum of individual

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 matrix is computed which seems a bit of a waste. Is there maybe a vectorized version of dmultinom which

depmixS4 has reached some form of maturity and therefore we have bumped its version number to 1.0-0 which is now on CRAN: http://cran.r-project.org/web/packages/depmixS4/index.html depmixS4 fits hidden (latent) Markov models of multivariate, mixed categorical and continuous data, otherwise known as dependent mixture models. Responses or observations can be modeled using GLMs, and additionally

depmixS4 has reached some form of maturity and therefore we have bumped its version number to 1.0-0 which is now on CRAN: http://cran.r-project.org/web/packages/depmixS4/index.html depmixS4 fits hidden (latent) Markov models of multivariate, mixed categorical and continuous data, otherwise known as dependent mixture models. Responses or observations can be modeled using GLMs, and additionally

I had written a vignette and included a \usepackage{Rd} command to make it possible to include latex'ed Rd files in the vignette. However, when loading Rd.sty texShop produces the following error: l. 180 ...d}[1]{\ifmmode\bm{#1}\else\textbf{#1}\fi} This is on Max OS X 3.9 and R 2.0.1 Has anyone seen this before and/or is it problematic? I'm not sure whether the output suffers from this