[R-sig-Geo] SST and chlorophyll data extraction in R

Ben Tupper btupper at bigelow.org
Fri Sep 18 16:08:36 CEST 2015


On Sep 18, 2015, at 9:39 AM, Antonio Silva <aolinto.lst at gmail.com> wrote:

> Dear R-Sig-Geo fellows
> This is my first post to this list. My name is Antonio Olinto and I work as
> researcher at Fisheries Institute, São Paulo, Brazil.
> Well, I'd like to hear suggestions on how to proceed in R to extract sea
> surface temperature and chlorophyll concentration data and calculate some
> statistics from MODIS/AQUA data in a given area.
> I used to do this in QGIS but available statistical parameters are limited
> and I had to work with one image at a time. I found a reference to a
> package named satin (
> https://www.r-project.org/conferences/useR-2009/slides/Villalobos+GonzalezRodriguez.pdf)
> but it seems it's not available anymore.
> I have several  *.L3m_MO_SST_4.bz2 and *.L3m_MO_CHL_chlor_a_4km.bz2 files
> obtained from
> http://podaac.jpl.nasa.gov/dataset/MODIS_AQUA_L3_SST_THERMAL_MONTHLY_4KM_DAYTIME
> and from http://oceandata.sci.gsfc.nasa.gov/MODISA/Mapped/Monthly/4km/chlor/
> I also have a shapefile with the boundaries of the area of interest. I'd
> like to have some statistics (maximum, minimum, mean, quantiles, ect.) of
> both variables in this area.
> Any indication of tutorials, sites or packages will be welcome.  Thanks in
> advance.

You might give this package a try: https://github.com/btupper/spnc It's essentially a wrapper around ncdf4, sp and raster and we have it configured for a couple of different data sources including Ocean Color's new netcdf files.  It won't handle the .bz2 files though, just the .nc.   It is very much in it's "beta" stage, but it works well for us.

If it works for you, you can also try https://github.com/btupper/obpgcrawler to simplify downloads from the Ocean Color resources using their THREDDS framework.  


> All the best,
> Antônio Olinto
> 	[[alternative HTML version deleted]]
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Ben Tupper
Bigelow Laboratory for Ocean Sciences
60 Bigelow Drive, P.O. Box 380
East Boothbay, Maine 04544

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