calc.hycom: Hycom Profile LIkelihood

In HMMoce: Improved Analysis of Marine Animal Movement Data Using Hidden Markov Models

Description

Calculate Hycom profile likelihood surface

Usage

calc.hycom(pdt, filename, hycom.dir, focalDim = 9, dateVec, use.se = TRUE)

Arguments

pdt	input PDT data output from read.wc and extract.pdt
filename	is the first part of the filename specified to the download function get.env. 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.
hycom.dir	directory of downloaded hycom (or other) data
focalDim	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.
dateVec	vector of complete dates (from tag to pop by day) for data range. This should be in 'Date' format
use.se	is logical indicating whether or not to use SE when using regression to predict temperature at specific depth levels.

Value

a raster brick of Hycom profile likelihood

See Also

calc.hycom.par

HMMoce documentation built on Nov. 17, 2017, 5:57 a.m.