calc.ohc: Calculate Ocean Heat Content (OHC) likelihood surface

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

Description

Compare tag data to OHC grid and calculate likelihoods

Usage

calc.ohc(pdt, filename, isotherm = "", ohc.dir, dateVec, bathy = TRUE,
  use.se = TRUE)

Arguments

pdt	input PDT data see 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.
isotherm	default ” in which isotherm is calculated on the fly based on daily tag data. Otherwise, numeric isotherm constraint can be specified (e.g. 20 deg C).
ohc.dir	directory of downloaded hycom (or other) data
dateVec	is vector of dates from tag to pop-up in 1 day increments.
bathy	is logical indicating whether or not a bathymetric mask should be applied
use.se	is logical indicating whether or not to use SE when using regression to predict temperature at specific depth levels.

Value

likelihood is raster brick of likelihood surfaces representing estimated position based on tag-based OHC compared to calculated OHC using HYCOM

References

Luo J, Ault JS, Shay LK, Hoolihan JP, Prince ED, Brown C a., Rooker JR (2015) Ocean Heat Content Reveals Secrets of Fish Migrations. PLoS One 10:e0141101

See Also

calc.woa

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