fit_hmm: Fits a Hidden Markov Model to estimate survival and detection...
In jBernardADFG/telprep: Quick and automatic processing of aerial telemetry data

Description Usage Arguments Value Examples

The function uses msm to fit the hidden Markov Model. In the output, live fish are in state 1 while expired fish are in state 2. For the emission matrices, outcome 1 relates fish movement information to the survival state: P(1) is the probabilty of no detection, P(2) is the probability that a fish moved, and P(3) is the probabilty that a fish stayed. Outcome 2 relates mortality sensor information to the survival state: P(1) is the probability of no detection, P(2) is the probability that the mortality signal is off, and P(3) is the probabilty that the morality signal is on.