similar to: hmm.discnp or other?

Hi all, I am using a discrete Hidden Markov Model with discrete observations in order to detect a sequence of integers. I am using the "hmm.discnp" package. I am using the following code: signature <- c(-89, -98, -90, -84, -77, -75, -64, -60, -58, -55, -56, -57, -57, -63, -77, -81, -82, -91, -85, -89, -93) quant <- length(-110:-6) # Initialize and train the hmm with the

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

If I actually finished writing this module, would any of you use it? Would you wish it did something else/different than what's described below? Any comments or suggestions on its proposed usage, intent, or syntax are welcome! (An alternative, better name would also be appreciated) -Aaron NAME R::Wrapper - Wrapper around the RS-Perl R module SYNOPSIS #!/usr/bin/perl -w

I've posted a message twice to this list, and never seen it appear yet ... perhaps this one will go through ... ? -- Aaron J. Mackey, Ph.D. Dept. of Biology, Goddard 212 University of Pennsylvania email: amackey at pcbi.upenn.edu 415 S. University Avenue office: 215-898-1205 Philadelphia, PA 19104-6017 fax: 215-746-6697

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,

On Fedora Core Linux 4, I have a cron job that causes R to update all packages and install new ones. Lately, I notice in the log that some packages fail to install. These are ones that assume X is running. For example, the pbatR install requires tcltk to be loaded, and then the install fails because in a cron job, there is no DISPLAY environment. I suppose the same happens if you try to

On Fedora Core Linux 4, I have a cron job that causes R to update all packages and install new ones. Lately, I notice in the log that some packages fail to install. These are ones that assume X is running. For example, the pbatR install requires tcltk to be loaded, and then the install fails because in a cron job, there is no DISPLAY environment. I suppose the same happens if you try to

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

I have not devoted time to setting up ROracle since binaries are not available and it seems to require some effort to compile (see http://cran.r-project.org/web/packages/ROracle/index.html). On the other hand, RODBC worked more or less magically once I set up the data sources. What is your success using ROracle and why would it be preferable to RODBC ? -Avram On Thursday, September 11,

Dear R users, I am looking for the source code of the implementation of ppr (Projection Pursuit Regression) in R. It will be great if citations of the source papers on which the implementation is based, are also provided. Thank you, Arvind Iyer, Grad student, Deptt. of Biomedical Engineering Viterbi School of Engineering University of Southern California, Los Angeles [[alternative HTML

Hi All Please see the Rprofile file which i have modified as follows and after that when I start R then I see that R says to me "TRUE" for all the packages implying that all loaded at once. But when i try to use commands as simple as help("lm"), it doesnt work nor any of the menu "Packages" is not working. Although the regression using lm ( Y ~ X ) is working

Network Operations Specialist The University of Southern California (USC), founded in 1880, is the largest private employer in the City of Los Angeles and proud recipient of Time Magazine's College of the Year 2000. USC offers competitive pay and an outstanding benefits package. **PLEASE NOTE THAT THIS POSITION IS LOCATED IN Marina del Rey, California** The USC Viterbi School of

Perhaps you noticed that LLVM gained a new optimizing register allocator yesterday (r130568). Linear scan is going away, and RAGreedy is the new default for optimizing builds. Hopefully, you noticed because your binaries were suddenly 2% smaller and 10% faster*. Some noticed because LLVM started crashing or miscompiling their code. Greedy replaces a fairly big chunk of the code generator, so

On Mar 1, 2008, at 3:40 AM, Richard Warburton wrote: >> Also, LLVM benefits quite a bit from mod/ref info for function. I >> don't know if you've thought about it at all, but it is an important >> problem. If you're interested, my thesis describes these issues in >> detail. > > I'll peruse this, are there any other relevant, LLVM specific texts >

Hi, In support of reproducible research at my Institute, I seek an approach to re-creating the R environments in which an analysis has been conducted. By which I mean, the exact version of R and the exact version of all packages used in a particular R session. I am seeking comments/criticism of this as a goal, and of the following outline of an approach: === When all the steps to an workflow

There's got to be a better way to use order() on a matrix than this: > y 2L-035-3 2L-081-23 2L-143-18 2L-189-1 2R-008-5 2R-068-15 3L-113-4 3L-173-2 398 1 1 2 2 1 1 2 2 857 1 1 2 2 1 2 2 2 911 1 1 2 2 1 2 2 2 383 1 1

Chris Lattner wrote: > I'm fine with starting simple and generalizing it out from there. I'd > actually recommend against trying to implement a maximally precise > dependence analyzer without a client. With no client, there is no way > to test that you're getting correct results and whether the > improvements in precision are actually useful. > > I'd

I have code and documentation that don't match, but R CMD check didn't flag it. in mspath.R mspath <- function(formula, # formula with observed Markov states ~ observation times (required) qmatrix, # matrix of 1s and 0s with indices of allowed transitions (diagonal is ignored) (required) misc = FALSE, ematrix = NULL, # matrix

On Mar 18, 2008, at 9:21 AM, Wojciech Matyjewicz wrote: > Hi, > >> Cool! I think the most critical part of this is to get a good >> interface for dependence analysis. There are lots of interesting >> implementations that have various time/space tradeoffs. >> >> For example, it would be great if Omega was available as an option, >> even if the compiler