hmm_survival: Use a Hidden Markov Model to determine the living status of...
In jBernardADFG/telprep: Quick and automatic processing of aerial telemetry data

Description Usage Arguments Value Examples

This function is a wrapper calling org_dat_msm, fit_hmm, get_viterbi, and extract_results. See the help files for these functions for more information.

1	hmm_survival(best_detects, t_star = 1, cl = 0.95)

`best_detects`	Output of `get_locations` or `get_best_locations`.
`t_star`	The distance in km at which a fish is considered to have stayed in place between detection periods.
`cl`	The desired confidence level.

Returns a list where $results provides a summary of the fit HMM and $viterbi returns a data.frame where the most likely path of survival states (i.e. the viterbi path) is added to the best_detects (1 means alive whereas 2 means expired). $viterbi can be input into make_plot.