<h2>File List</h2><div>
<p><a href="run_base_full_models.R">run_base_full_models.R</a> (MD5: adc930d6094b52c44838c1530c662920)</p>
<p><a href="base_model.txt">base_model.txt</a> (MD5: 36b6b952b0c31b1921cee7a53e48b83a)</p>
<p><a href="full_model.txt">full_model.txt</a> (MD5: 211e7b9afd6bc402f307653661e168ab)</p>
<p><a href="jags_data.Rd">jags_data.Rd</a> (MD5: b10e52de46c11eeb2477960681a631e6)</p>
<p><a href="viterbi_funs.R">viterbi_funs.R</a> (MD5: 7d6e8db0684738d8ea1722c95b8c7eba)</p>
</div><h2>Description</h2><div>
<p>The code included in run_base_full_models.R fits the 'base' and 'full' models described in the main text (Table 2). The base model (Model structure 2) is fitted with 5 states and fixed step length (FS). The full model (Model structure 9) is fitted with 6 states and time-varying step length (TS). The script then calls Viterbi_funs.R to estimate the Viterbi sequence of states based upon the posterior state-dependent parameter estimates. Running the script requires jags software (freely available at <a href="http://mcmc-jags.sourceforge.net/">http://mcmc-jags.sourceforge.net/</a>) and the r package 'R2jags'. Sample data, priors, and example R2jags fitting objects are supplied in jags_data.Rd which can be directly loaded into r. The text files contain the model structures in jags script. To run the script, place all the files into your r working directory.</p>
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