calc.sst: Calculate SST-based likelihood

Description Usage Arguments Value See Also

View source: R/calc.sst.r

Description

calc.sst compares tag SST to remotely sensed SST and calculates likelihoods

Usage

1
calc.sst(tag.sst, filename, sst.dir, dateVec, focalDim = NULL, sens.err = 1)

Arguments

tag.sst

is data frame containing tag-collected SST data

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.

sst.dir

local directory where remote sensing SST downloads are stored

dateVec

is vector of dates from tag to pop-up in 1 day increments.

focalDim

is integer for dimensions of raster::focal used to calculate sd() of env grid cell. If left to NULL (default), this dimension will approximately incorporate 0.25 degrees.

sens.err

is numeric indicating the percent sensor error in the tag sst sensor. Default is 1.

Value

likelihood is raster brick of likelihood surfaces representing matches between tag-based sst and remotely sensed sst maps

See Also

calc.ohc


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