Improved Analysis of Marine Animal Movement Data Using Hidden Markov Models


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Documentation for package ‘HMMoce’ version 1.0.0

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HMMoce-package 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
HMMoce HMMoce: an R package for improved analysis of marine animal movement data using hidden Markov models
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