README.md

In BigelowLab/neracooscrawler: A limited THREDDS crawler for programmatically working with the OpeNDAP data offerings from http://www.neracoos.org/thredds/catalog/GMRI/SATELLITE/NASA/catalog.xml

NERACOOS Crawler

NERACOOS provides OpeNDAP access to data from within R. neracooscrawler package provides basic THREDDS crawling facilties. The idea is to programmatically search the OpeNDAP offerings at NERACOOS.

This package is nearly identical to obpgcrawler but is configured specifically for the NERACOOS offerings. Windows users are able to use the crawler to identify resources, but are unable to use the OpeNDAP services. To circumvent that issue, this package provides utlitiy functions for downloading files to a local drive.

Requirements

R >= 3.0

threddscrawler

Installation

It is easy to install with devtools

library(devtools)
install_github("btupper/neracooscrawler")

Useage

Most users will only use the MODISA_query(). An equivalent MURSST_query() is under development.

# get all of the monthly CHL in a 2 year period
x <- MODISA_query(what = 'within', date_filter = as.POSIXct(c("2008-01-01", "2011-12-31")),
    greplargs = list(pattern="MO_CHL_chlor_a_4km", fixed = TRUE))

head(x, n = 2) ; cat("..............\n\n"); tail(x, n = 2)
# $A20080012008031.L3m_MO_CHL_chlor_a_4km.nc
# Reference Class: "DatasetsRefClass"
#   verbose_mode: FALSE
#   url: http://www.neracoos.org/thredds/catalog/GMRI/SATELLITE/NASA/MODISA_NESHELF/MODISA/L3SMI/2008/001/A20080012008031.L3m_MO_CHL_chlor_a_4km.nc
#   children: dataSize date
#   datasets: NA
# 
# $A20080322008060.L3m_MO_CHL_chlor_a_4km.nc
# Reference Class: "DatasetsRefClass"
#   verbose_mode: FALSE
#   url: http://www.neracoos.org/thredds/catalog/GMRI/SATELLITE/NASA/MODISA_NESHELF/MODISA/L3SMI/2008/032/A20080322008060.L3m_MO_CHL_chlor_a_4km.nc
#   children: dataSize date
#   datasets: NA
# 
# ..............
# 
# $A20113052011334.L3m_MO_CHL_chlor_a_4km.nc
# Reference Class: "DatasetsRefClass"
#   verbose_mode: FALSE
#   url: http://www.neracoos.org/thredds/catalog/GMRI/SATELLITE/NASA/MODISA_NESHELF/MODISA/L3SMI/2011/305/A20113052011334.L3m_MO_CHL_chlor_a_4km.nc
#   children: dataSize date
#   datasets: NA
# 
# $A20113352011365.L3m_MO_CHL_chlor_a_4km.nc
# Reference Class: "DatasetsRefClass"
#   verbose_mode: FALSE
#   url: http://www.neracoos.org/thredds/catalog/GMRI/SATELLITE/NASA/MODISA_NESHELF/MODISA/L3SMI/2011/335/A20113352011365.L3m_MO_CHL_chlor_a_4km.nc
#   children: dataSize date
#   datasets: NA

For Windows users who cannot access OpeNDAP resources, we provide a download function. Taking the example above we can download on or more of these datasets.

ok <- MODISA_download(x[1:3], dest = "/Users/ben/Downloads")
ok
# /Users/ben/Downloads/A20080012008031.L3m_MO_CHL_chlor_a_4km.nc 
#                                                           TRUE 
# /Users/ben/Downloads/A20080322008060.L3m_MO_CHL_chlor_a_4km.nc 
#                                                           TRUE 
# /Users/ben/Downloads/A20080612008091.L3m_MO_CHL_chlor_a_4km.nc 
#                                                           TRUE 

BigelowLab/neracooscrawler documentation built on May 5, 2019, 2:44 p.m.