Supplement 1. R code for fitting the individual-specific HMMs and HSMMs, for computing the HSMM residuals, for fitting the hierarchical HSMM, and observations for one of the bison, as well as an updated more efficient version of the code.

File List (Older version) 1_individual_specific_HMMs_and_HSMMs.r (md5: 480705d7fbaa10185b499a13c72dff91) 2_residuals_for_HSMMs.r (md5: f49e03aedde8c09cad8325ce72b87a8b) (Older version) 3_hierarchical_HSMM.r (md5: c5e3234dcbc9a81079411c26e85892d2) 4_obs.txt (md5: b5eea7bba207da7711801939d10da124) <b>Revised, more efficient code. Received and published 5 February 2015:</b> 1_individual_specific_HMMs_and_HSMMs_revised.r.R (MD5: c4ec48927645e403ed9e3c6b7df22f9f) 3_hierarchical_HSMM_revised.r.R (MD5: 5f11bc3831bd8c7a93f7560d304e6f56) Description The supplements give R implementations of the methods described in the paper. The first supplement gives R code for fitting individual-specific HMMs and HSMMs. The second supplement gives R code for computing residuals for fitted HSMMs. The third supplement gives R code for fitting the hierarchical HSMM described in Section 5 of the main manuscript. The fourth supplement gives an example bivariate time series, the step lengths and turning angles for one of the bison considered in the main manuscript, that can be analyzed using the first supplement.