Fit HMM and HSMM animal movement models

Distributions | Parameter transformations and distribution functions |

dlnorm3 | Shifted lognormal pdf |

dshiftnegbin | Shifted negative binomial pdf |

dshiftpois | Shifted Poisson pdf |

dwrpnorm | Wrapped normal pdf |

dzanegbin | Zero-altered Negative Binomial PDF |

gen.Gamma | Generate t.p.m. to approximate HSMM with HMM |

HMM.plot | Plot a move.HMM object |

HSMM.plot | Plot a move.HSMM object |

move.HMM.ACF | ACF plot |

move.HMM.Altman | Altman plot |

move.HMM.CI | Add confidence intervals to a move.HMM object |

move.HMM.dwell.plot | Dwell Plot |

move.HMM.lalphabeta | Compute forward and backwards probabilities |

move.HMM.mle | Fit a Hidden Markov Model (HMM) via maximum likelihood |

move.HMM.mllk | Compute negative log likelihood of HMM |

move.HMM.mllk.full | Compute negative log likelihood of HMM using all parameters |

move.HMM-package | Fit hidden Markov models and hidden semi-Markov... |

move.HMM.pn2pw | Transform parameters to the working scale |

move.HMM.psresid | Compute and plot pseudoresiduals |

move.HMM.pw2pn | Transform parameters back to real scale |

move.HMM.simulate | Simulate data from a hidden markov model |

move.HMM.state_probs | Compute conditional and posterior state probabilities |

move.HMM.viterbi | Assign states using the Viterbi algorithm |

move.HSMM.ACF | ACF plot |

move.HSMM.Altman | Altman plot |

move.HSMM.CI | Add confidence intervals to a move.HSMM object |

move.HSMM.dwell.plot | Dwell Plot |

move.HSMM.lalphabeta | Compute forward and backwards probabilities for a move.HSMM... |

move.HSMM.mle | Fit a Hidden Semi Markov Model (HSMM) via maximum likelihood |

move.HSMM.mllk | Compute negative log likelihood of HSMM |

move.HSMM.mllk.full | Compute negative log likelihood of HSMM using all parameters |

move.HSMM.pn2pw | Transform parameters to the working scale |

move.HSMM.psresid | Compute and plot pseudoresiduals |

move.HSMM.pw2pn | Transform parameters back to real scale |

move.HSMM.simulate | Simulate data from a hidden semi markov model |

move.HSMM.state_probs | Compute conditional and posterior state probabilities |

move.HSMM.viterbi | Assign states using the Viterbi algorithm |

plnorm3 | Shifted lognormal cdf |

print.move.HMM | Print a move.HMM object |

print.move.HSMM | Print a move.HSMM object |

pshiftnegbin | Shifted negative binomial cdf |

pshiftpois | Shifted Poisson cdf |

pwrpcauchy | Wrapped cauchy cdf |

pwrpnorm | Wrapped normal cdf |

pzanegbin | Zero-altered Negative Binomial CDF |

qlnorm3 | Shifted lognormal quantile function |

rlnorm3 | Shifted lognormal random number generation |

rshiftnegbin | Generate random deviates shifted negative binomial pdf |

rshiftpois | Generate random deviates shifted Poisson pdf |

rwrpcauchy | Wrapped cauchy random number generation |

rwrpnorm | Wrapped normal random number generation |

rzanegbin | Zero-altered Negative Binomial random number generation |

stationaryDist | Calculate the stationary distribution from the t.p.m. |

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