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Software for State Sequence Analysis, as in Levin, Lefebvre and Perkins (2012)

This page contains Matlab and R code packages implementing State Sequence Analysis, an approach proposed in the paper to analyzing continuous-time Markov chain dynamics by computing maximum probability state sequences. The Matlab code also includes scripts to analyze each of the three examples in the paper. The R code package includes the HIV example.

To use the Matlab code, download either the or the CTMCStateSeq.tar_.gz file below. Uncompress the archive, and you will obtain a directory called CTMCStateSeq which contains the files in the distribution. A REAMDE.txt file in the distribution provides further information and instructions.

To use the R package, download the archive CTMCStateSeq_1.0.tar_.gz. In a Linux/Unix environment, you can install it using a command like "R CMD install ctmcSSA_1.0.tar.gz".

CTMCStateSeq.tar_.gz : Matlab Code Package (archived with tar and gzip)8.78 KB : Matlab Code Package (compressed)12.69 KB
CTMCStateSeq_1.0.tar_.gz : R Code Package (archived with tar and gzip)10.29 KB