get.env: Download and Read Oceanographic Data

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

Description

get.env accesses oceanographic data like sea surface temperature from a remote server and downloads the temporal and spatial extent of interest for further use

Usage

get.env(uniqueDates = NULL, filename = NULL, type = NULL,
  spatLim = NULL, resol = NULL, save.dir = getwd(), sst.type = NULL,
  depLevels = NULL)

Arguments

uniqueDates	is a POSIXct vector of desired dates
filename	is first part of the filename specified to the download function. 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'.
type	is a character string indicating whether you're after sea surface temperature 'sst', hybrid coordinate ocean model 'hycom', or world ocean atlas 'woa' data
spatLim	is a list of spatial limits as list(xmin, xmax, ymin, ymax)
resol	is character describing the desired resolution in degrees if type = 'woa', otherwise NULL. Choices are 'one' or 'quarter'.
save.dir	is the directory to save the downloaded data to
sst.type	is character indicating type of desired SST product. Choices are currently Optimum Interpolation ('oi') https://www.ncdc.noaa.gov/oisst or a high-resolution composite ('ghr') https://www.ghrsst.org/.
depLevels	is an integer describing which depth levels to download from Hycom (e.g. 1=surface). Default is NULL and all levels are downloaded.

Value

nothing, just downloads the data to your local machine

Examples

## Not run: 
# Not run to prevent actual data download
sp.lim <- list(lonmin = -82, lonmax = -25, latmin = 15, latmax = 50)
# FOR OI SST DATA
get.env(as.Date('2015-10-01'), filename='oisst', type = 'sst', 
sst.type='oi', spatLim = sp.lim, save.dir = tempdir())

# FOR HYCOM DATA
get.env(as.Date('2015-10-01'), filename='hycom', type = 'hycom', 
spatLim = sp.lim, save.dir = tempdir())

# FOR WORLD OCEAN ATLAS DATA
get.env(type = 'woa', resol = 'quarter', save.dir = woa.dir)

## End(Not run)

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