calc.hycom

input PDT data output from <code><a rd-options="" href="/link/read.wc?package=HMMoce&version=1.0.0" data-mini-rdoc="HMMoce::read.wc">read.wc</a></code> and
<code><a rd-options="" href="/link/extract.pdt?package=HMMoce&version=1.0.0" data-mini-rdoc="HMMoce::extract.pdt">extract.pdt</a></code>

is the first part of the filename specified to the download 
function <code><a rd-options="" href="/link/get.env?package=HMMoce&version=1.0.0" data-mini-rdoc="HMMoce::get.env">get.env</a></code>. For example, if downloaded files were 
specific to a particular dataset, you may want to identify that with a name
like 'tuna' or 'shark1'. This results in a downloaded filename of, for 
example, 'tuna_date.nc'. This filename is required here so the calc 
function knows where to get the env data.

filename

directory of downloaded hycom (or other) data

hycom.dir

is integer for dimensions of raster::focal used to calculate 
sd() of temperature grid cell. Recommend focalDim = 9 for Hycom data at 
0.08deg resolution.

focalDim

vector of complete dates (from tag to pop by day) for data 
range. This should be in 'Date' format

dateVec

is logical indicating whether or not to use SE when using 
regression to predict temperature at specific depth levels.

use.se

Calculate Hycom profile likelihood surface

Improved analysis of marine animal movement data by implementing
a state-space hidden Markov model (HMM) to improve position estimates. Position
estimates are derived by comparing electronic tag data (from tags deployed on
marine animals, typically fish) to three-dimensional oceanographic data.

Camrin Braun

HMMoce

Improved Analysis of Marine Animal Movement Data Using Hidden
Markov Models

Benjamin Galuardi

Benjamin Jones

Martin Pedersen

calc.hycom function

input PDT data output from <code><a rd-options='' href='read.wc'>read.wc</a></code> and
<code><a rd-options='' href='extract.pdt'>extract.pdt</a></code>

is the first part of the filename specified to the download 
function <code><a rd-options='' href='get.env'>get.env</a></code>. For example, if downloaded files were 
specific to a particular dataset, you may want to identify that with a name
like 'tuna' or 'shark1'. This results in a downloaded filename of, for 
example, 'tuna_date.nc'. This filename is required here so the calc 
function knows where to get the env data.

calc.hycom: Hycom Profile LIkelihood

Description

Usage

Arguments

Value

See Also