similar to: error in building help files

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, 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

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, 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 (using all the tools provided in the R for windows faq), and the routine only echoes the first letter

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:

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

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, 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

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

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

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 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

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

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

On Tue, 30 May 2023 17:43:31 +0000 Heather Lucas <hlucas2 at lsu.edu> wrote: > Hello, > > I've been enjoying using the "Mixture and Hidden Markov Models in R" > by Visser & Speekenbrink to learn how to apply these analyses to my > own data using depmixS4. > > I currently have a fitted 4-state mixture model with three emissions > variables and one

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

Hello, I tried to fit a poisson distribution but looking at the function fitdistr() it does not optimize lambda but simply estimates the mean of the data and returns it as lambda. I'm a bit confused because I was expecting an optimization of this parameter to gain a good fit... If I would use mle() of stats4 package or mle2() of bbmle package, I would have to write the function by myself

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-helpers & Friedrich Leisch, I'm trying to fit a mixture of regression models on attached data set by doing the following: agl <- read.table("agl.txt") mod1 <- flexmix(resp~gng+csc|Subject,data=agl, model=FLXglm(family="binomial"),k=2) The result is a (varying) number of the following warnings: Warning messages: 1: non-integer #successes in a

Hello All, Does anyone know of a package that performs constraint-based clusters? Ideally the package could perform "Time-Ordered Clustering", a technique applied in a recent journal article by Runger, Nelson, Harnish (using MS Excel). Quote, "in our specific implementation of constrained clustering, the clustering algorithm remains agglomerative and hierarchical, but observations