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

Michael Sumner mdsumner at gmail.com
Fri Sep 18 16:23:04 CEST 2015

The crux is hdf4, the format once you bunzip2 these files, and while geo
metadata is unstandard the L3m variants are trivially longlat complete
global grids on Atlantic view.

Raster/rgdal makes it easy though manual and installing hdf4 for GDAL is
easy on ubuntu, but  non existent for R on windows, due to zlib license I

It sucks, and be apprised NASA is moving to Netcdf4 just to complicate life
further. L3m is simplish relatively in the new regime, but on windows you
must compile for yourself.


On Friday, September 18, 2015, 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
> 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 (
> 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
> and from
> 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.
> All the best,
> Antônio Olinto
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Michael Sumner
Software and Database Engineer
Australian Antarctic Division
Hobart, Australia
e-mail: mdsumner at gmail.com

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