similar to: hmm.discnp hidden markov model

(I think) I'd like to use the hmm.discnp package for a simple discrete, two-state HMM, but my training data is irregularly shaped (i.e. the observation chains are of varying length). Additionally, I do not see how to label the state of the observations given to the hmm() function. Ultimately, I'd like to 1) train the hmm on labeled data, 2) use viterbi() to calculate optimal labeling of

Hi folks, I'm pleased to introduce a new package called ?aphid?, for analysis with profile hidden Markov models in R. The package contains functions for multiple and pairwise sequence alignment for both nucleic acids and proteins (preferably in the DNAbin or AAbin format), model building, parameter optimization (Baum Welch and Viterbi training), plotting, file import & export,

Hi folks, I'm pleased to introduce a new package called ?aphid?, for analysis with profile hidden Markov models in R. The package contains functions for multiple and pairwise sequence alignment for both nucleic acids and proteins (preferably in the DNAbin or AAbin format), model building, parameter optimization (Baum Welch and Viterbi training), plotting, file import & export,

Dear list, This question is about Hidden Markov Model. Given a transition matrix, an emission matrix and a sequence of observed symbols (actually, nucleotide sequences, A, T, C and G), I hope to predict the sequence of state by Viterbi algorithm. I searched R repository for related packages. msm package has function viterbi.msm (as well as very good document), but it only works for

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

R Community - I am attempting to fit a model as described in Hampton, Bossaerts, and O'doherty (J. Neuroscience) 2006. They use a bayesian hidden markov model to model the Reversal Learning data. I have tried using HMM and depmixS4 with no success. My data is a Reversal Learning Task in which there are 3 sets of patterns over 3 blocks. The participant receives incorrect or correct

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 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

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

Hi, Is there a package that will estimate simple Markov models and hidden Markov models for discrete time processes in R? Thanks in advance, David -- =============================================================== David Kaplan, Ph.D. Professor Department of Educational Psychology University of Wisconsin - Madison Educational Sciences, Room, 1061 1025 W. Johnson Street Madison, WI 53706

Hi this is my first post. I am trying to run a simulation for a computer playing Von Neumann poker and adjusting it's expectation of an opponent's behavior according to how the opponent plays. This program involves random generation of "hands" and shifting of parameters. However, when I run the code, no errors come up, but the program doesn't do anything. Could someone

Hi, I am new to R and need help with rpart. I am trying to create a classification tree using rpart. In order to plot the reults I use the plot function and the text function to label the plot of the tree dendrogram with text. The documentation of text.rpart says : "For the "class" method, label="yval" results in the factor levels being used, "yprob" results

Hello All, Am I misreading the documentation? The text.rpart documentation says: "label a column name of x$frame; values of this will label the nodes. For the "class" method, label="yval" results in the factor levels being used, "yprob" results in the probability of the winning factor level being used, and ?specific yval level? results in the probability of

Hi, I am trying to use the rpart library with my own set of functions on a survival object. I get an immeadiate segmentation fault when i try calling rpart with my list of functions. I get the same problem with the logrank example from Therneau,s S-rpart library though their anova example works. Should I report this as a bug, as even if my functions are structured improperly, that should lead to

I tried using rpart, as below, and got this error message "rpart Error in yval[, 1] : incorrect number of dimensions". Thinking it might somehow be related to the large number of missing values, I tried using complete data, but with the same result. Does anyone know what may be going on, and how to fix it? I have traced two similar error messages in the Archive, but following the

Hi Prof. Williams, thanks for your suggestion. The updated code is below. It turns out it was a matter of displaying the second column in yval to get the number of N and subtracting it from the n column in the frame to get the number of Y remaining in a binary example. once this is added now the function returns the rules along with Y and N count affected by the resulting rule. I am ccing

Hi R-users, I have a collection of dataframes and know how to build a string that refers to it, in this example, name_infra_alg_inc. Then, I have a character string yval, which the user can select from a drop down list. It contains the column names of the dataframes. assign(paste(name_infra_alg_inc, "ci", sep="."), ci(get(name_infra_alg_inc)[[yval]], confidence=0.95)) My

Hello, I am in the process of writing a Perl program to carry out and analyze large numbers of regressions using R as the regression engine, and I am using Statistics::R to create the communication bridge between the two programs. Statistics::R creates a pipe between R and Perl and uses Rterm.exe (hidden during run-time) to carry out the R commands. This communication bridge works well for

Full_Name: Bill Wheeler Version: 2.0.1 OS: Windows 2000 Submission from: (NULL) (67.130.36.229) The program to reproduce the error is below. I am calling rpart with a user-defined split function for a binary response variable and one continuous independent variable. The split function works for some datasets but not others. The error is: Error in "$<-.data.frame"(`*tmp*`,

Hi, I am using the rpart package to build a classification tree. I did manage to build a tree with data on a previous project. However, when attampting to build a tree on a project I am working on, I seem to be getting the error shown below: > nhg3.rp <- rpart(profitresp ~., nhg3, method="class") > plot(nhg3.rp, branch=0.4, uniform=T); text(nhg3.rp, digits=3) Error in