Man pages for HMMoce
Improved Analysis of Marine Animal Movement Data Using Hidden Markov Models

calc.errEllCalculates error ellipses around input locations
calc.gpe2Calculate Light Likelihood from GPE2 Output
calc.hycomHycom Profile LIkelihood
calc.hycom.parHycom Profile LIkelihood in Parallel
calc.locsCalculate Position-based Likelihood
calc.ohcCalculate Ocean Heat Content (OHC) likelihood surface
calc.ohc.parOHC Likelihood in Parallel
calc.paramCalculates movement parameters used for behavior kernels
calc.srssCalculate Position-based Likelihood from SRSS
calc.sstCalculate SST-based likelihood
calc.sst.parCalculate SST-based likelihood in parallel
calc.trackCalculate most probable track from state estimates
calc.woaCalculate WOA profile in parallel
calc.woa.parCalculate WOA profile likelihood in parallel
expmaxExpectation-maximization framework for state-switching
extract.pdtExtract PDT from Wildlife Computers tag data
extract.woaExtract temperatures from World Ocean Atlas
findDateFormatDetermine date format of vector
gausskernCreate Gaussian Kernel
get.bath.dataDownload bathymetry data
getCtrGet specified contour coordinates
get.envDownload and Read Oceanographic Data
get.ghr.sstDownload GHR Sea Surface Temperature (SST) data
get.hycomDownload HYCOM data
get.nll.funNegative Log likelihood of parameters
get.oi.sstDownload OI Sea Surface Temperature (SST) data
get.woaDownload World Ocean Atlas Climatology
hmm.filterHMM filter functions
HMMoceHMMoce: an R package for improved analysis of marine animal...
hmm.smootherSmoother recursion over filtered state estimates
likint3Calculate density function and integrate between limits
liksrssCalculate density function and integrate between limits
make.LCombine individual source likelihoods
makePar'makePar' gets parameters for subsequent filter/smoother
mask.LMask L likelihood
meshgridCreates grid from matrices
plotHMMPlot track results of HMMoce
plotRDPlot RD results
read.wcRead and format tag data
removePacificRemove Pacific Ocean data from N. Atlantic analyses
repmatRepeat your matrix?
resample.gridResample likelihood rasters to common resolution/extent
resample.grid.parResample likelihood rasters to common resolution/extent
setup.gridSetup the discrete spatial grid for the HMM
setup.grid.rasterSetup the discrete spatial grid for the HMM
setup.locs.gridSetup the discrete spatial grid for the HMM
simplifyLocsSimplifies locations to one per day
HMMoce documentation built on Nov. 17, 2017, 5:57 a.m.