HMMoce                  HMMoce: an R package for 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
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
getCtr                  Get specified contour coordinates
hmm.filter              HMM filter functions
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
