Old package used in van der Kirk et al. (2014). Here for reproducibility purposes. There are many, better R packages to fit HMMs to animal movement data now.
https://besjournals.onlinelibrary.wiley.com/doi/full/10.1111/1365-2656.12290
Flexible, user-friendly Hidden (Semi) Markov Models for animal movement data (Langrock et al. 2012)
This package is intended to take the maximum likelihood methodology for HMM and HSMM animal movement models of Langrock et al. (2012) and make it accessible to ecologists. Further, it works for an arbitrary number of hidden states, arbitrary number of observation distributions, and arbitrary observation distributions. This aids model comparison via AIC and there are several functions for graphical goodness of fit checking.
The code is also now more efficient.
Before installing the package, install it's dependencies: numDeriv pscl CircStats psych VGAM
If bootstrapping, install foreach snow doSNOW
Things to add:
- Profile likelihood CIs?
- Random effects, maybe via ADMB
- covariate-dependent state transitions
- mid-residuals for discrete distributions