| 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 |
