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R package for downloading eReefs marine model output from NCI and plotting.

An R package has been created to help R users to access and visualise eReefs marine model outputs. The package contains a few useful functions to make accessing eReefs and other CSIRO-EMS output files easier, and is available through https://github.com/AIMS/ereefs.

These functions rely on the netcdf4 package, which works best under Linux or MacOS. The functions provided here should work under Windows for locally-stored files, but will also work for OPeNDAP-served netcdf files under Linux or MacOS.

To install the “ereefs” package, copy and paste the following two lines into R:

install.packages("devtools")
devtools::install_github("BarbaraRobson/ereefs")

The package includes:

Functions to extract time-series from eReefs netcdf files

get_ereefs_ts()
get_ereefs_depth_integrated_ts ()
get_ereefs_depth_specified_ts()
get_ereefs_bottom_ts()

Functions to produce maps or animations of eReefs model outputs

map_ereefs()
map_ereefs_movie()
plot_map()

Function to calculate optical plume class from modelled surface reflectances

plume_class()

Functions to extract profiles and vertical slices

get_ereefs_profile()
get_ereefs_slice()

Functions to plot profiles

plot_ereefs_profile()
plot_ereefs_zvt()

Functions to convert outputs to GIS formats

poly2sp()
sp2raster()