Improved Analysis of Marine Animal Movement Data Using Hidden Markov Models

calc.errEll | Calculates error ellipses around input locations |

calc.gpe2 | Calculate Light Likelihood from GPE2 Output |

calc.hycom | Hycom Profile LIkelihood |

calc.hycom.par | Hycom Profile LIkelihood in Parallel |

calc.locs | Calculate Position-based Likelihood |

calc.ohc | Calculate Ocean Heat Content (OHC) likelihood surface |

calc.ohc.par | OHC Likelihood in Parallel |

calc.param | Calculates movement parameters used for behavior kernels |

calc.srss | Calculate Position-based Likelihood from SRSS |

calc.sst | Calculate SST-based likelihood |

calc.sst.par | Calculate SST-based likelihood in parallel |

calc.track | Calculate most probable track from state estimates |

calc.woa | Calculate WOA profile in parallel |

calc.woa.par | Calculate WOA profile likelihood in parallel |

expmax | Expectation-maximization framework for state-switching |

extract.pdt | Extract PDT from Wildlife Computers tag data |

extract.woa | Extract temperatures from World Ocean Atlas |

findDateFormat | Determine date format of vector |

gausskern | Create Gaussian Kernel |

get.bath.data | Download bathymetry data |

getCtr | Get specified contour coordinates |

get.env | Download and Read Oceanographic Data |

get.ghr.sst | Download GHR Sea Surface Temperature (SST) data |

get.hycom | Download HYCOM data |

get.nll.fun | Negative Log likelihood of parameters |

get.oi.sst | Download OI Sea Surface Temperature (SST) data |

get.woa | Download World Ocean Atlas Climatology |

hmm.filter | HMM filter functions |

HMMoce | HMMoce: an R package for improved analysis of marine animal... |

hmm.smoother | Smoother recursion over filtered state estimates |

likint3 | Calculate density function and integrate between limits |

liksrss | Calculate density function and integrate between limits |

make.L | Combine individual source likelihoods |

makePar | 'makePar' gets parameters for subsequent filter/smoother |

mask.L | Mask L likelihood |

meshgrid | Creates grid from matrices |

plotHMM | Plot track results of HMMoce |

plotRD | Plot RD results |

read.wc | Read and format tag data |

removePacific | Remove Pacific Ocean data from N. Atlantic analyses |

repmat | Repeat your matrix? |

resample.grid | Resample likelihood rasters to common resolution/extent |

resample.grid.par | Resample likelihood rasters to common resolution/extent |

setup.grid | Setup the discrete spatial grid for the HMM |

setup.grid.raster | Setup the discrete spatial grid for the HMM |

setup.locs.grid | Setup the discrete spatial grid for the HMM |

simplifyLocs | Simplifies locations to one per day |

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