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 CTMCStateSeq.zip 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".