Fit hidden Markov models using Template Model Builder (TMB): flexible state-dependent distributions, transition probability structures, random effects, and smoothing splines.
Install the package from Github using devtools,
devtools::install_github("r-glennie/hmmTMB")
To find help files for the methods implemented in the package, search for help using the name of the corresponding class, e.g.,
?MarkovChain
?Observation
?HMM
We describe functionalities of the package in two vignettes:
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'hmmTMB user guide': Overview of package functionalities using detailed examples based on animal movement data.
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'hmmTMB technical guide': Description of models and implementation.