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 |