Antarctic and Southern Ocean Science
This article is about R packages that are relevant to Antarctic and
Southern Ocean science. It includes packages in various states of
maturity, including some in planning or very early stages of
development.
Antarctic and Southern Ocean science covers a diverse range of topics
within the geosciences, life sciences, physical sciences, and humanities
and social sciences. This article is not intended to be an exhaustive
list of packages that are relevant to all of those fields, but rather a
synopsis of packages that are for one reason or another of particular
interest to Antarctic and Southern Ocean researchers. The definition of
“particular interest” is of course largely arbitrary. Packages listed
here are generally expected to be at a useful stage of development, or
if not, are seeking engagement/input from the wider community.
Contributions are welcome\! Please [submit an
issue](https://github.com/SCAR/ropensci/issues) , or make a contribution
(see the [contribution guidelines](/ropensci/task_view/CONTRIBUTING.md) ). If you have an
issue with one of the packages discussed below, please contact the
maintainer of that package.
Many thanks to contributors, including Scott Chamberlain, Michael
Sumner, Grant Humphries, Hsun-yi Hsieh, and Anton Van de Putte.
### Taxonomic Data
The Register of Antarctic Marine Species (RAMS) is the authoritative
taxonomic database for Antarctic marine organisms. RAMS is part of the
World Register of Marine Species (WoRMS).
- [worrms](https://cran.rstudio.com/web/packages/worrms/index.html) client for the
[WoRMS](http://www.marinespecies.org/) API. Contains mostly
taxonomic data, but also trait data.
- [taxize](https://cran.rstudio.com/web/packages/taxize/index.html) provides access to 20ish
sources of taxonomic data sources, including WoRMS. It has
consistent data outputs and function interfaces across the different
data sources so that you don’t need to tailor your code to different
taxonomic data providers.
RAMS is currently being extended to cover non-marine taxa, which will
become the Register of Antarctic Species (RAS). Hopefully this will
remain covered by `worrms` and the server-side infrastructure hosted by
VLIZ. There is also the
[biotaxa](https://github.com/hhsieh/biotaxa_Rpackage) package in
development for working with RAS (visualising and predicting the growth
in taxonomic diversity over time).
For more detail on R packages dealing with taxonomy in general, see the
[rOpenSci taxonomy task view](https://github.com/ropensci/taxonomy) .
### Mapping
Mapping is a very common task, and in an Antarctic/Southern Ocean
context brings with it particular issues including dealing with
projection properties at high latitudes, coping with data that crosses
the 180°E line, adding commonly-desired features such as ocean fronts,
management boundaries, sea ice extent, stations and other geographic
features, and common contextual layers such as bathymetry.
- [SOmap](https://github.com/AustralianAntarcticDivision/SOmap) is in
development, but aims to provide straightforward mapping functions
for Southern Ocean (polar stereographic) maps, along with
commonly-used management and contextual layers such as MPA
boundaries and ocean fronts.
- [antanym](https://github.com/SCAR/antanym) provides geographic place
name data from the SCAR Composite Gazetteer of Antarctica, with
plans to extend the coverage to subantarctic and informal gazetteers
at a later date.
- [orsifronts](https://cran.rstudio.com/web/packages/orsifronts/index.html) provides the
commonly-used Orsi et al. (1995) definitions of the major Southern
Ocean fronts.
- [graticule](https://cran.rstudio.com/web/packages/graticule/index.html) creates graticule
lines (lines of longitude and latitude) and labels for maps.
- [palr](https://cran.rstudio.com/web/packages/palr/index.html) provides colour palettes for
data, based on some well known remotely sensed data sets for sea ice
concentration, sea surface temperature and chlorophyll- *a* .
- there is some Antarctic-related mapping functionality in
[prtools](https://github.com/pierreroudier/prtools) ,
[atlasr](https://github.com/jiho/atlasr) ,
[CCAMLRGIS](https://github.com/ccamlr/CCAMLRGIS) , and
[sospatial](https://github.com/AustralianAntarcticDivision/sospatial)
.
### Environmental Data
- [blueant](https://github.com/AustralianAntarcticDivision/blueant)
and its companion package
[bowerbird](https://github.com/AustralianAntarcticDivision/bowerbird)
provide a mechanism to download a range of environmental data
including satellite-derived sea ice, sea surface temperature,
topography, ocean colour (chlorophyll- *a* ), and meteorological
data from various providers. Many of these data sets can be read and
manipulated with [raster](https://cran.rstudio.com/web/packages/raster/index.html) and similar
packages: the [spatial task
view](https://cran.r-project.org/web/views/Spatial.html) is a good
resource here.
- the [PolarWatch](https://polarwatch.noaa.gov/) project aims to
enable data discovery and broader use of high-latitude ocean remote
sensing data sets. The dedicated ERDDAP server
(https://polarwatch.noaa.gov/erddap) is accessible to R users with
[rerddap](https://cran.rstudio.com/web/packages/rerddap/index.html).
- [rsoi](https://cran.rstudio.com/web/packages/rsoi/index.html) downloads the most up to date
Southern Oscillation Index, Oceanic Nino Index, and North Pacific
Gyre Oscillation data.
### Oceanography
- satellite reflectance data are a common basis for estimating
chlorophyll- *a* and other phytoplankton parameters at ocean-basin
scales. Global products are widely available; however,
Southern-Ocean specific algorithms are likely to provide better
estimates in these regions. [croc](https://github.com/sosoc/croc)
implements the Johnson et al. (2013) Southern Ocean algorithm.
- more broadly, [oce](https://cran.rstudio.com/web/packages/oce/index.html) provides a wide
range of tools for reading, processing, and displaying oceanographic
data, including measurements from Argo floats and CTD casts,
sectional data, sea-level time series, and coastline and topographic
data.
- [fda.oce](https://github.com/EPauthenet/fda.oce) provides functional
data analysis of oceanographic profiles for front detection, water
mass identification, unsupervised or supervised classification,
model comparison, data calibration, and more.
### Biodiversity data
- [robis](https://cran.rstudio.com/web/packages/robis/index.html) for marine data,
[rgbif](https://cran.rstudio.com/web/packages/rgbif/index.html) for global biodiversity data.
[spocc](https://cran.rstudio.com/web/packages/spocc/index.html) wraps these and other
occurrence data providers with a consistent interface (but not
necessarily the full functionality of provider-specific packages,
where they exist).
- [obistools](https://github.com/iobis/obistools) and
[scrubr](https://cran.rstudio.com/web/packages/scrubr/index.html) for quality-checking
occurrence data.
- a package for the data behind the [Mapping Application for Penguin
Populations and Projected Dynamics
(MAPPPD)](http://www.penguinmap.com/) is in planning: contact [Grant
Humphries](mailto:grwhumphries@blackbawks.net) .
- diet data [sohungry](https://github.com/SCAR/sohungry) and
allometric equations [solong](https://github.com/SCAR/solong)
### Animal tracking
Tracking of animals using satellite, GPS, or light-level geolocation
tags is common, and there are many R packages that can help with this.
See the [spatiotemporal task
view](https://cloud.r-project.org/web/views/SpatioTemporal.html) for a
more complete list. Of particular interest may be:
- [TwilightFree](https://github.com/ABindoff/TwilightFree) provides a
method for processing light-level geolocation data that is robust to
noise (sensor shading and obscuration) and may be particularly
suitable for Southern Ocean applications.
- [foieGras](https://cran.rstudio.com/web/packages/foieGras/index.html) fits continuous-time
random walk and correlated random walk state-space models to filter
Argos satellite location data.
- [availability](https://github.com/AustralianAntarcticDivision/availability)
estimates the geographic space available to animals based on
telemetry data.
### Miscellaneous
Packages that may be of interest but don’t yet fit neatly into another
category.
- [distancetocoast](https://github.com/mdsumner/distancetocoast)
provides “distance to coastline” data for longitude and latitude
coordinates.
CRAN packages: