similar to: Hmm Topology restriction

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

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

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 binomial covariate (HS). I am trying to compute confidence intervals using the following code, where fmms4s is the model:

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 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, I'm a newbie to the world of HMMs and HMMs in R. I've had a look at the hmm package and the RHmm package but I couldn't see anything straightforward on how a labelled sequential dataset with observed values and underlying states might be used to construct and train a HMM based on that data and no pre-computed values for the transition, emission or initial state distributions. Does

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

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

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

Dear R- Users, I am unable to install R packages over the internet. Below is my session information. My guess is that this may be a proxy issue. I have set the http_proxy_user : my user id(network id) : password (machine password) . The error I get is as below > install.packages("MASS") Warning: unable to access index for repository

Thank you for your prompt answer. The breathing signal observations are the amplitude values as a function of time and phase. According to our model the hidden states are the different breathing types. Subjects, whose respiratiion process is regular, are likely to breathe, keeping the same cycle pattern/type, for many consecutive cycles. therefore dwelling in the same hidden state. The more

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

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

Hello list, I am dealing with a noisy function (gradient,hessian not available) with simple boundary constraints (x_i>0). I've tried constrOptim() using nelder mead to minimize it but it is way too slow and the returned results are not satisfying. simulated annealing is so hard to tune and it always crashes R program in my case. I wonder if there are any packages or functions can do

Can anybody, please, explain me how many parameter are estimated using randomLCA? For examples, model "dentistry.lca2random" estimate 1 scale (or variance, b_j) parameter and 2 position parameters (a_cj)? Doesn't it? Do I need at least 4 diagnostic tests for such a model? What happens if I specify options blocksize and byclass? How many diagnostic tests (or rater) I need?

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

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 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

Hi r-help, I have been using your RHmm package for some time and have recently had to try using the package for a new dataset. Basically I have a dataset with a number of discrete observation variables that change over time, and I would love to try modeling them using a HMM. Basically I was wondering if RHmm can be used to model a multivariate discrete HMM, i.e., the observations are a vector