├── README.md
├── _config.yml
└── task_view
    ├── Antarctic.ctv
    ├── Antarctic.html
    ├── CONTRIBUTING.md
    ├── Makefile
    ├── README.md
    ├── antarctic.md
    ├── buildxml.R
    ├── checkurls.R
    └── process.R


/README.md:
--------------------------------------------------------------------------------
 1 | # ropensci
 2 | 
 3 | ## Background
 4 | 
 5 | Collaboration and reproducibility are [fundamental to Antarctic and Southern Ocean science](https://doi.org/10.1038/d41586-018-05369-6), and fit seamlessly with the [Antarctic Treaty's](https://www.ats.aq/e/ats.htm) provision that "to the greatest extent feasible and practicable ... scientific observations and results from Antarctica shall be exchanged and made freely available".
 6 | 
 7 | [rOpenSci](https://ropensci.org/) is a a non-profit initiative founded in 2011 that promotes open and reproducible research using shared data and reusable software. This is achieved by promoting R software tools that lower the barriers to working with scientific data sources, creating social infrastructure through a welcoming and diverse community, and building the capacity of software users and developers.
 8 | 
 9 | Software development to support Antarctic data usage is growing, but still lags behind the available data, and some common tasks are still more difficult than we would like. Starting in late 2017, the [Scientific Committee on Antarctic Research](https://www.scar.org/) has been collaborating with rOpenSci to strengthen the Antarctic and Southern Ocean R/science communities. Our focus is on data and tasks that are common or even unique to Antarctic and Southern Ocean science, including supporting the development of R packages to meet Antarctic science needs, guides for R users and developers, active fora for open discussions, and strengthening connections with the broader science world. This collaboration has been coordinated through the [Expert Group on Antarctic Biodiversity Informatics](https://www.scar.org/science/egabi/abi/).
10 | 
11 | ## Get involved
12 | 
13 | Please get involved!
14 | 
15 | - contribute your Antarctic R knowledge, your Antarctic [use case](https://discuss.ropensci.org/c/usecases) for a package, or ask a question in the dedicated [Antarctic and Southern Ocean](https://discuss.ropensci.org/c/antarctic) category of rOpenSci's discussion forum,
16 | 
17 | - make [a suggestion](https://discuss.ropensci.org/c/antarctic) — perhaps for Antarctic-related functionality that you feel is missing from the current R ecosystem?
18 | 
19 | - contribute an Antarctic R package, or improve the documentation or code of an existing one. See the [task view](https://github.com/SCAR/ropensci/tree/master/task_view) as a starting point,
20 | 
21 | - join the #antarctic rOpenSci Slack channel for R users and developers &mdash; contact us at <antarctic@ropensci.org> for an invitation to join. Slack is a great space in which to have conversations with the rOpenSci community, or to give us feedback in a less-public manner,
22 | 
23 | - participate in the [broader rOpenSci community](https://ropensci.org/community/). Follow on [Twitter](https://twitter.com/rOpenSci), read the [blog](https://ropensci.org/blog/), and check out the [ecosystem of R packages](https://ropensci.org/packages/).
24 | 
25 | 
26 | The administrative contacts for this initiative are Ben Raymond, Sara Labrousse, Michael Sumner, and Jess Melbourne-Thomas. Contact us via <antarctic@ropensci.org>, or find us on Slack or Twitter.
27 | 
28 | See also [this blog post](https://ropensci.org/blog/2018/11/13/antarctic/) which includes a short demonstration of a few early packages from this community.
29 | 
30 | ---
31 | 
32 | <div style="width:30%; margin-left:auto; margin-right:auto;">
33 | <img align="left" style="width:45%;" src="https://avatars1.githubusercontent.com/u/22830629?s=200&v=4" alt="SCAR logo" />
34 | <img align="right" style="width:45%;" src="https://raw.githubusercontent.com/ropensci/logos/master/icon_short_color.png" alt="rOpenSci logo" />
35 | </div>
36 | 
37 | 


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/_config.yml:
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1 | theme: jekyll-theme-minimal


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/task_view/Antarctic.ctv:
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 1 | <CRANTaskView>
 2 |   <name>Antarctic</name>
 3 |   <topic>Antarctic and Southern Ocean Science</topic>
 4 |   <maintainer email="ben.raymond@aad.gov.au">Ben Raymond</maintainer>
 5 |   <version>2021-03-09</version>
 6 |   <info>
 7 |     <p>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.</p>
 8 |     <p>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.</p>
 9 |     <p>Contributions are welcome! Please <a href="https://github.com/SCAR/ropensci/issues">submit an issue</a>, or make a contribution (see the <a href="CONTRIBUTING.md">contribution guidelines</a>). If you have an issue with one of the packages discussed below, please contact the maintainer of that package.</p>
10 |     <p>Many thanks to contributors, including Scott Chamberlain, Michael Sumner, Grant Humphries, Hsun-yi Hsieh, and Anton Van de Putte.</p>
11 |     <h3 id="taxonomic-data">Taxonomic Data</h3>
12 |     <p>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).</p>
13 |     <ul>
14 |     <li><pkg>worrms</pkg> client for the <a href="http://www.marinespecies.org/">WoRMS</a> API. Contains mostly taxonomic data, but also trait data.</li>
15 |     <li><pkg>taxize</pkg> 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.</li>
16 |     </ul>
17 |     <p>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 <code>worrms</code> and the server-side infrastructure hosted by VLIZ. There is also the <a href="https://github.com/hhsieh/biotaxa_Rpackage">biotaxa</a> package in development for working with RAS (visualising and predicting the growth in taxonomic diversity over time).</p>
18 |     <p>For more detail on R packages dealing with taxonomy in general, see the <a href="https://github.com/ropensci/taxonomy">rOpenSci taxonomy task view</a>.</p>
19 |     <h3 id="mapping">Mapping</h3>
20 |     <p>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.</p>
21 |     <ul>
22 |     <li><p><a href="https://github.com/AustralianAntarcticDivision/SOmap">SOmap</a> 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.</p></li>
23 |     <li><p><a href="https://github.com/SCAR/antanym">antanym</a> 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.</p></li>
24 |     <li><p><pkg>orsifronts</pkg> provides the commonly-used Orsi et al. (1995) definitions of the major Southern Ocean fronts.</p></li>
25 |     <li><p><pkg>graticule</pkg> creates graticule lines (lines of longitude and latitude) and labels for maps.</p></li>
26 |     <li><p><pkg>palr</pkg> provides colour palettes for data, based on some well known remotely sensed data sets for sea ice concentration, sea surface temperature and chlorophyll-<em>a</em>.</p></li>
27 |     <li><p>there is some Antarctic-related mapping functionality in <a href="https://github.com/pierreroudier/prtools">prtools</a>, <a href="https://github.com/jiho/atlasr">atlasr</a>, <a href="https://github.com/ccamlr/CCAMLRGIS">CCAMLRGIS</a>, and <a href="https://github.com/AustralianAntarcticDivision/sospatial">sospatial</a>.</p></li>
28 |     </ul>
29 |     <h3 id="environmental-data">Environmental Data</h3>
30 |     <ul>
31 |     <li><p><a href="https://github.com/AustralianAntarcticDivision/blueant">blueant</a> and its companion package <a href="https://github.com/AustralianAntarcticDivision/bowerbird">bowerbird</a> provide a mechanism to download a range of environmental data including satellite-derived sea ice, sea surface temperature, topography, ocean colour (chlorophyll-<em>a</em>), and meteorological data from various providers. Many of these data sets can be read and manipulated with <pkg>raster</pkg> and similar packages: the <a href="https://cran.r-project.org/web/views/Spatial.html">spatial task view</a> is a good resource here.</p></li>
32 |     <li><p>the <a href="https://polarwatch.noaa.gov/">PolarWatch</a> 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 <pkg>rerddap</pkg>.</p></li>
33 |     <li><p><pkg>rsoi</pkg> downloads the most up to date Southern Oscillation Index, Oceanic Nino Index, and North Pacific Gyre Oscillation data.</p></li>
34 |     </ul>
35 |     <h3 id="oceanography">Oceanography</h3>
36 |     <ul>
37 |     <li><p>satellite reflectance data are a common basis for estimating chlorophyll-<em>a</em> 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. <a href="https://github.com/sosoc/croc">croc</a> implements the Johnson et al. (2013) Southern Ocean algorithm.</p></li>
38 |     <li><p>more broadly, <pkg>oce</pkg> 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.</p></li>
39 |     <li><p><a href="https://github.com/EPauthenet/fda.oce">fda.oce</a> provides functional data analysis of oceanographic profiles for front detection, water mass identification, unsupervised or supervised classification, model comparison, data calibration, and more.</p></li>
40 |     </ul>
41 |     <h3 id="biodiversity-data">Biodiversity data</h3>
42 |     <ul>
43 |     <li><p><pkg>robis</pkg> for marine data, <pkg>rgbif</pkg> for global biodiversity data. <pkg>spocc</pkg> wraps these and other occurrence data providers with a consistent interface (but not necessarily the full functionality of provider-specific packages, where they exist).</p></li>
44 |     <li><p><a href="https://github.com/iobis/obistools">obistools</a> and <pkg>scrubr</pkg> for quality-checking occurrence data.</p></li>
45 |     <li><p>a package for the data behind the <a href="http://www.penguinmap.com/">Mapping Application for Penguin Populations and Projected Dynamics (MAPPPD)</a> is in planning: contact <a href="mailto:grwhumphries@blackbawks.net">Grant Humphries</a>.</p></li>
46 |     <li><p>diet data <a href="https://github.com/SCAR/sohungry">sohungry</a> and allometric equations <a href="https://github.com/SCAR/solong">solong</a></p></li>
47 |     </ul>
48 |     <h3 id="animal-tracking">Animal tracking</h3>
49 |     <p>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 <a href="https://cloud.r-project.org/web/views/SpatioTemporal.html">spatiotemporal task view</a> for a more complete list. Of particular interest may be:</p>
50 |     <ul>
51 |     <li><p><a href="https://github.com/ABindoff/TwilightFree">TwilightFree</a> 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.</p></li>
52 |     <li><p><pkg>foieGras</pkg> fits continuous-time random walk and correlated random walk state-space models to filter Argos satellite location data.</p></li>
53 |     <li><p><a href="https://github.com/AustralianAntarcticDivision/availability">availability</a> estimates the geographic space available to animals based on telemetry data.</p></li>
54 |     </ul>
55 |     <h3 id="miscellaneous">Miscellaneous</h3>
56 |     <p>Packages that may be of interest but don’t yet fit neatly into another category.</p>
57 |     <ul>
58 |     <li><a href="https://github.com/mdsumner/distancetocoast">distancetocoast</a> provides “distance to coastline” data for longitude and latitude coordinates.</li>
59 |     </ul>
60 |   </info>
61 |   <packagelist>
62 |     <pkg>foieGras</pkg>
63 |     <pkg>graticule</pkg>
64 |     <pkg>oce</pkg>
65 |     <pkg>orsifronts</pkg>
66 |     <pkg>palr</pkg>
67 |     <pkg>raster</pkg>
68 |     <pkg>rerddap</pkg>
69 |     <pkg>rgbif</pkg>
70 |     <pkg>robis</pkg>
71 |     <pkg>rsoi</pkg>
72 |     <pkg>scrubr</pkg>
73 |     <pkg>spocc</pkg>
74 |     <pkg>taxize</pkg>
75 |     <pkg>worrms</pkg>
76 |   </packagelist>
77 |   <links>
78 |     <a href="https://github.com/ropensci/taxonomy">taxonomy task view</a>
79 |     <a href="https://cran.r-project.org/web/views/Spatial.html">spatial task view</a>
80 |     <a href="https://cloud.r-project.org/web/views/SpatioTemporal.html">spatiotemporal task view</a>
81 |   </links>
82 | </CRANTaskView>
83 | 


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/task_view/Antarctic.html:
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  1 | <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
  2 | <html xmlns="http://www.w3.org/1999/xhtml">
  3 | <head>
  4 | <title>CRAN Task View: Antarctic and Southern Ocean Science</title>
  5 | <link rel="stylesheet" type="text/css" href="../CRAN_web.css">
  6 | <meta http-equiv="content-type" content="text/html; charset=UTF-8">
  7 | <meta name="citation_title" content="CRAN Task View: Antarctic and Southern Ocean Science">
  8 | <meta name="citation_author" content="Ben Raymond">
  9 | <meta name="citation_publication_date" content="2021-03-09">
 10 | <meta name="citation_public_url" content="https://CRAN.R-project.org/view=Antarctic">
 11 | <meta name="DC.title" content="CRAN Task View: Antarctic and Southern Ocean Science">
 12 | <meta name="DC.creator" content="Ben Raymond">
 13 | <meta name="DC.issued" content="2021-03-09">
 14 | <meta name="DC.identifier" content="https://CRAN.R-project.org/view=Antarctic">
 15 | </head>
 16 | <body>
 17 |   <h2>Antarctic and Southern Ocean Science</h2>
 18 |   <div>
 19 |       <p>
 20 |         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.
 21 |       </p>
 22 |       <p>
 23 |         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.
 24 |       </p>
 25 |       <p>
 26 |         Contributions are welcome! Please
 27 |         <a href="https://github.com/SCAR/ropensci/issues">
 28 |           submit an issue
 29 |         </a>, or make a contribution (see the
 30 |         <a href="CONTRIBUTING.md">
 31 |           contribution guidelines
 32 |         </a>). If you have an issue with one of the packages discussed below, please contact the maintainer of that package.
 33 |       </p>
 34 |       <p>
 35 |         Many thanks to contributors, including Scott Chamberlain, Michael Sumner, Grant Humphries, Hsun-yi Hsieh, and Anton Van de Putte.
 36 |       </p>
 37 |       <h3 id="taxonomic-data">
 38 |         Taxonomic Data
 39 |       </h3>
 40 |       <p>
 41 |         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).
 42 |       </p>
 43 |       <ul>
 44 | <li>
 45 | <a href="../packages/worrms/index.html">worrms</a>
 46 |           client for the
 47 |           <a href="http://www.marinespecies.org/">
 48 |             WoRMS
 49 |           </a>
 50 |           API. Contains mostly taxonomic data, but also trait data.
 51 |         </li>
 52 |         <li>
 53 | <a href="../packages/taxize/index.html">taxize</a>
 54 |           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.
 55 |         </li>
 56 |       </ul>
 57 | <p>
 58 |         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
 59 | <tt>worrms</tt>
 60 |         and the server-side infrastructure hosted by VLIZ. There is also the
 61 |         <a href="https://github.com/hhsieh/biotaxa_Rpackage">
 62 |           biotaxa
 63 |         </a>
 64 |         package in development for working with RAS (visualising and predicting the growth in taxonomic diversity over time).
 65 |       </p>
 66 |       <p>
 67 |         For more detail on R packages dealing with taxonomy in general, see the
 68 |         <a href="https://github.com/ropensci/taxonomy">
 69 |           rOpenSci taxonomy task view
 70 |         </a>.
 71 |       </p>
 72 |       <h3 id="mapping">
 73 |         Mapping
 74 |       </h3>
 75 |       <p>
 76 |         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.
 77 |       </p>
 78 |       <ul>
 79 | <li>
 80 |           <p>
 81 |             <a href="https://github.com/AustralianAntarcticDivision/SOmap">
 82 |               SOmap
 83 |             </a>
 84 |             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.
 85 |           </p>
 86 |         </li>
 87 |         <li>
 88 |           <p>
 89 |             <a href="https://github.com/SCAR/antanym">
 90 |               antanym
 91 |             </a>
 92 |             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.
 93 |           </p>
 94 |         </li>
 95 |         <li>
 96 |           <p>
 97 | <a href="../packages/orsifronts/index.html">orsifronts</a>
 98 |             provides the commonly-used Orsi et al. (1995) definitions of the major Southern Ocean fronts.
 99 |           </p>
100 |         </li>
101 |         <li>
102 |           <p>
103 | <a href="../packages/graticule/index.html">graticule</a>
104 |             creates graticule lines (lines of longitude and latitude) and labels for maps.
105 |           </p>
106 |         </li>
107 |         <li>
108 |           <p>
109 | <a href="../packages/palr/index.html">palr</a>
110 |             provides colour palettes for data, based on some well known remotely sensed data sets for sea ice concentration, sea surface temperature and chlorophyll-
111 |             <em>
112 |               a
113 |             </em>.
114 |           </p>
115 |         </li>
116 |         <li>
117 |           <p>
118 |             there is some Antarctic-related mapping functionality in
119 |             <a href="https://github.com/pierreroudier/prtools">
120 |               prtools
121 |             </a>,
122 |             <a href="https://github.com/jiho/atlasr">
123 |               atlasr
124 |             </a>,
125 |             <a href="https://github.com/ccamlr/CCAMLRGIS">
126 |               CCAMLRGIS
127 |             </a>, and
128 |             <a href="https://github.com/AustralianAntarcticDivision/sospatial">
129 |               sospatial
130 |             </a>.
131 |           </p>
132 |         </li>
133 |       </ul>
134 | <h3 id="environmental-data">
135 |         Environmental Data
136 |       </h3>
137 |       <ul>
138 | <li>
139 |           <p>
140 |             <a href="https://github.com/AustralianAntarcticDivision/blueant">
141 |               blueant
142 |             </a>
143 |             and its companion package
144 |             <a href="https://github.com/AustralianAntarcticDivision/bowerbird">
145 |               bowerbird
146 |             </a>
147 |             provide a mechanism to download a range of environmental data including satellite-derived sea ice, sea surface temperature, topography, ocean colour (chlorophyll-
148 |             <em>
149 |               a
150 |             </em>), and meteorological data from various providers. Many of these data sets can be read and manipulated with
151 | <a href="../packages/raster/index.html">raster</a>
152 |             and similar packages: the
153 |             <a href="https://cran.r-project.org/web/views/Spatial.html">
154 |               spatial task view
155 |             </a>
156 |             is a good resource here.
157 |           </p>
158 |         </li>
159 |         <li>
160 |           <p>
161 |             the
162 |             <a href="https://polarwatch.noaa.gov/">
163 |               PolarWatch
164 |             </a>
165 |             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
166 | <a href="../packages/rerddap/index.html">rerddap</a>.
167 |           </p>
168 |         </li>
169 |         <li>
170 |           <p>
171 | <a href="../packages/rsoi/index.html">rsoi</a>
172 |             downloads the most up to date Southern Oscillation Index, Oceanic Nino Index, and North Pacific Gyre Oscillation data.
173 |           </p>
174 |         </li>
175 |       </ul>
176 | <h3 id="oceanography">
177 |         Oceanography
178 |       </h3>
179 |       <ul>
180 | <li>
181 |           <p>
182 |             satellite reflectance data are a common basis for estimating chlorophyll-
183 |             <em>
184 |               a
185 |             </em>
186 |             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.
187 |             <a href="https://github.com/sosoc/croc">
188 |               croc
189 |             </a>
190 |             implements the Johnson et al. (2013) Southern Ocean algorithm.
191 |           </p>
192 |         </li>
193 |         <li>
194 |           <p>
195 |             more broadly,
196 | <a href="../packages/oce/index.html">oce</a>
197 |             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.
198 |           </p>
199 |         </li>
200 |         <li>
201 |           <p>
202 |             <a href="https://github.com/EPauthenet/fda.oce">
203 |               fda.oce
204 |             </a>
205 |             provides functional data analysis of oceanographic profiles for front detection, water mass identification, unsupervised or supervised classification, model comparison, data calibration, and more.
206 |           </p>
207 |         </li>
208 |       </ul>
209 | <h3 id="biodiversity-data">
210 |         Biodiversity data
211 |       </h3>
212 |       <ul>
213 | <li>
214 |           <p>
215 | <a href="../packages/robis/index.html">robis</a>
216 |             for marine data,
217 | <a href="../packages/rgbif/index.html">rgbif</a>
218 |             for global biodiversity data.
219 | <a href="../packages/spocc/index.html">spocc</a>
220 |             wraps these and other occurrence data providers with a consistent interface (but not necessarily the full functionality of provider-specific packages, where they exist).
221 |           </p>
222 |         </li>
223 |         <li>
224 |           <p>
225 |             <a href="https://github.com/iobis/obistools">
226 |               obistools
227 |             </a>
228 |             and
229 | <a href="../packages/scrubr/index.html">scrubr</a>
230 |             for quality-checking occurrence data.
231 |           </p>
232 |         </li>
233 |         <li>
234 |           <p>
235 |             a package for the data behind the
236 |             <a href="http://www.penguinmap.com/">
237 |               Mapping Application for Penguin Populations and Projected Dynamics (MAPPPD)
238 |             </a>
239 |             is in planning: contact
240 |             <a href="mailto:grwhumphries@blackbawks.net">
241 |               Grant Humphries
242 |             </a>.
243 |           </p>
244 |         </li>
245 |         <li>
246 |           <p>
247 |             diet data
248 |             <a href="https://github.com/SCAR/sohungry">
249 |               sohungry
250 |             </a>
251 |             and allometric equations
252 |             <a href="https://github.com/SCAR/solong">
253 |               solong
254 |             </a>
255 |           </p>
256 |         </li>
257 |       </ul>
258 | <h3 id="animal-tracking">
259 |         Animal tracking
260 |       </h3>
261 |       <p>
262 |         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
263 |         <a href="https://cloud.r-project.org/web/views/SpatioTemporal.html">
264 |           spatiotemporal task view
265 |         </a>
266 |         for a more complete list. Of particular interest may be:
267 |       </p>
268 |       <ul>
269 | <li>
270 |           <p>
271 |             <a href="https://github.com/ABindoff/TwilightFree">
272 |               TwilightFree
273 |             </a>
274 |             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.
275 |           </p>
276 |         </li>
277 |         <li>
278 |           <p>
279 | <a href="../packages/foieGras/index.html">foieGras</a>
280 |             fits continuous-time random walk and correlated random walk state-space models to filter Argos satellite location data.
281 |           </p>
282 |         </li>
283 |         <li>
284 |           <p>
285 |             <a href="https://github.com/AustralianAntarcticDivision/availability">
286 |               availability
287 |             </a>
288 |             estimates the geographic space available to animals based on telemetry data.
289 |           </p>
290 |         </li>
291 |       </ul>
292 | <h3 id="miscellaneous">
293 |         Miscellaneous
294 |       </h3>
295 |       <p>
296 |         Packages that may be of interest but don’t yet fit neatly into another category.
297 |       </p>
298 |       <ul>
299 | <li>
300 |           <a href="https://github.com/mdsumner/distancetocoast">
301 |             distancetocoast
302 |           </a>
303 |           provides “distance to coastline” data for longitude and latitude coordinates.
304 |         </li>
305 |       </ul>
306 | </div>
307 | 
308 |   <h3>CRAN packages:</h3>
309 |   <ul>
310 | <li><a href="../packages/foieGras/index.html">foieGras</a></li>
311 |     <li><a href="../packages/graticule/index.html">graticule</a></li>
312 |     <li><a href="../packages/oce/index.html">oce</a></li>
313 |     <li><a href="../packages/orsifronts/index.html">orsifronts</a></li>
314 |     <li><a href="../packages/palr/index.html">palr</a></li>
315 |     <li><a href="../packages/raster/index.html">raster</a></li>
316 |     <li><a href="../packages/rerddap/index.html">rerddap</a></li>
317 |     <li><a href="../packages/rgbif/index.html">rgbif</a></li>
318 |     <li><a href="../packages/robis/index.html">robis</a></li>
319 |     <li><a href="../packages/rsoi/index.html">rsoi</a></li>
320 |     <li><a href="../packages/scrubr/index.html">scrubr</a></li>
321 |     <li><a href="../packages/spocc/index.html">spocc</a></li>
322 |     <li><a href="../packages/taxize/index.html">taxize</a></li>
323 |     <li><a href="../packages/worrms/index.html">worrms</a></li>
324 |   </ul>
325 | <h3>Related links:</h3>
326 |   <ul>
327 | <li><a href="https://github.com/ropensci/taxonomy">
328 |   taxonomy task view
329 | </a></li>
330 |     <li><a href="https://cran.r-project.org/web/views/Spatial.html">
331 |   spatial task view
332 | </a></li>
333 |     <li><a href="https://cloud.r-project.org/web/views/SpatioTemporal.html">
334 |   spatiotemporal task view
335 | </a></li>
336 |   </ul>
337 | </body>
338 | </html>
339 | 


--------------------------------------------------------------------------------
/task_view/CONTRIBUTING.md:
--------------------------------------------------------------------------------
 1 | Thanks for your contribution!
 2 | 
 3 | ## Edit the task view:
 4 | 
 5 | ### Requirements:
 6 | 
 7 | * R
 8 | * `make`
 9 | * [`pandoc`](http://johnmacfarlane.net/pandoc/installing.html)
10 | 
11 | If you don't want to or can't install these things, then just edit the `antarctic.md` file, and submit a pull request.
12 | 
13 | ### Steps
14 | 
15 | 1. Fork this repo
16 | 2. Edit the [antarctic.md](https://github.com/SCAR/ropensci/blob/master/task_view/antarctic.md) file. If the package you are adding is on CRAN, add a the package name within `<pkg></pkg>` tags (use `<ohat></ohat>` for OmegaHat packages, `<rforge></rforge>` for [RForge](https://r-forge.r-project.org/), and `<bioc></bioc>` for [Bioconductor](http://www.bioconductor.org/) packages). If it's not on CRAN, put it markdown link syntax: `[display-text](url)` (e.g., `[rgbif](https://github.com/ropensci/rgbif) (not on CRAN)`). If there is a non-CRAN source repository available, add it as a link in parentheses after the package name (e.g., `<pkg>rgbif</pkg> ([GitHub](https://github.com/ropensci/rgbif))`). Note that GitHub is written in camel case.
17 | 3. On the command line type `make` and press enter, which creates the `Antarctic.ctv`, `Antarctic.html`, and `README.md` files.
18 | 4. Check to make sure the `.ctv` file is correct. In the console output from `make check`, you should get:
19 | 
20 |     ```coffee
21 |     $`Packages in <info> but not in <packagelist>`
22 |     character(0)
23 | 
24 |     $`Packages in <packagelist> but not in <info>`
25 |     character(0)
26 | 
27 |     $`Packages in <packagelist> but not in repos`
28 |     character(0)
29 |     ```
30 | 
31 |     If you don't, follow the error messages to fix. If you can't figure out how to fix, just send the PR anyway, and the maintainer will fix.
32 | 
33 |     If you changed anything in the `antarctic.md` file, repeat step 3 to remake files. If everything was fine, proceed.
34 | 	5. Push back up to your account, then [submit a pull request](https://github.com/SCAR/ropensci/pulls)
35 | 	
36 | ## Submit an issue
37 | 
38 | If you just want to submit an issue, then go to the [issues page](https://github.com/SCAR/ropensci/issues?state=open) and do that. Please list as much of the following as possible: package name, repository, development URL, description/details.
39 | 


--------------------------------------------------------------------------------
/task_view/Makefile:
--------------------------------------------------------------------------------
 1 | all: README.md
 2 | 
 3 | Antarctic.ctv: antarctic.md buildxml.R
 4 | 	pandoc -w html -o Antarctic.ctv antarctic.md
 5 | 	R -e 'source("buildxml.R")'
 6 | 
 7 | Antarctic.html: Antarctic.ctv
 8 | 	R -e 'if(!require("ctv")) install.packages("ctv", repos = "https://cran.rstudio.com/"); ctv::ctv2html("Antarctic.ctv"); source("process.R")'
 9 | 
10 | README.md: Antarctic.html
11 | 	pandoc -w gfm -o README.md Antarctic.html
12 | 	sed -i.tmp -e 's|( \[|(\[|g' README.md
13 | 	sed -i.tmp -e 's| : |: |g' README.md
14 | 	sed -i.tmp -e 's|../packages/|https://cran.rstudio.com/web/packages/|g' README.md
15 | 	# sed -i.tmp -e '4s/.*/| | |\n|---|---|/' README.md
16 | 	#sed -i.tmp -e '4i/*Do not edit this README by hand. See \[CONTRIBUTING.md\]\(CONTRIBUTING.md\).*\n/' README.md
17 | 	rm *.tmp
18 | 
19 | README.html: README.md
20 | 	pandoc --from=gfm -o README.html README.md
21 | 
22 | check:
23 | 	R -e 'if(!require("ctv")) install.packages("ctv", repos = "https://cran.rstudio.com/"); print(ctv::check_ctv_packages("Antarctic.ctv", repos = "https://cran.rstudio.com/"))'
24 | 
25 | checkurls:
26 | 	R -e 'source("checkurls.R")'
27 | 	
28 | 


--------------------------------------------------------------------------------
/task_view/README.md:
--------------------------------------------------------------------------------
  1 | ## Antarctic and Southern Ocean Science
  2 | 
  3 | <div>
  4 | 
  5 | This article is about R packages that are relevant to Antarctic and
  6 | Southern Ocean science. It includes packages in various states of
  7 | maturity, including some in planning or very early stages of
  8 | development.
  9 | 
 10 | Antarctic and Southern Ocean science covers a diverse range of topics
 11 | within the geosciences, life sciences, physical sciences, and humanities
 12 | and social sciences. This article is not intended to be an exhaustive
 13 | list of packages that are relevant to all of those fields, but rather a
 14 | synopsis of packages that are for one reason or another of particular
 15 | interest to Antarctic and Southern Ocean researchers. The definition of
 16 | “particular interest” is of course largely arbitrary. Packages listed
 17 | here are generally expected to be at a useful stage of development, or
 18 | if not, are seeking engagement/input from the wider community.
 19 | 
 20 | Contributions are welcome\! Please [submit an
 21 | issue](https://github.com/SCAR/ropensci/issues) , or make a contribution
 22 | (see the [contribution guidelines](CONTRIBUTING.md) ). If you have an
 23 | issue with one of the packages discussed below, please contact the
 24 | maintainer of that package.
 25 | 
 26 | Many thanks to contributors, including Scott Chamberlain, Michael
 27 | Sumner, Grant Humphries, Hsun-yi Hsieh, and Anton Van de Putte.
 28 | 
 29 | ### Taxonomic Data
 30 | 
 31 | The Register of Antarctic Marine Species (RAMS) is the authoritative
 32 | taxonomic database for Antarctic marine organisms. RAMS is part of the
 33 | World Register of Marine Species (WoRMS).
 34 | 
 35 |   - [worrms](https://cran.rstudio.com/web/packages/worrms/index.html) client for the
 36 |     [WoRMS](http://www.marinespecies.org/) API. Contains mostly
 37 |     taxonomic data, but also trait data.
 38 |   - [taxize](https://cran.rstudio.com/web/packages/taxize/index.html) provides access to 20ish
 39 |     sources of taxonomic data sources, including WoRMS. It has
 40 |     consistent data outputs and function interfaces across the different
 41 |     data sources so that you don’t need to tailor your code to different
 42 |     taxonomic data providers.
 43 | 
 44 | RAMS is currently being extended to cover non-marine taxa, which will
 45 | become the Register of Antarctic Species (RAS). Hopefully this will
 46 | remain covered by `worrms` and the server-side infrastructure hosted by
 47 | VLIZ. There is also the
 48 | [biotaxa](https://github.com/hhsieh/biotaxa_Rpackage) package in
 49 | development for working with RAS (visualising and predicting the growth
 50 | in taxonomic diversity over time).
 51 | 
 52 | For more detail on R packages dealing with taxonomy in general, see the
 53 | [rOpenSci taxonomy task view](https://github.com/ropensci/taxonomy) .
 54 | 
 55 | ### Mapping
 56 | 
 57 | Mapping is a very common task, and in an Antarctic/Southern Ocean
 58 | context brings with it particular issues including dealing with
 59 | projection properties at high latitudes, coping with data that crosses
 60 | the 180°E line, adding commonly-desired features such as ocean fronts,
 61 | management boundaries, sea ice extent, stations and other geographic
 62 | features, and common contextual layers such as bathymetry.
 63 | 
 64 |   - [SOmap](https://github.com/AustralianAntarcticDivision/SOmap) is in
 65 |     development, but aims to provide straightforward mapping functions
 66 |     for Southern Ocean (polar stereographic) maps, along with
 67 |     commonly-used management and contextual layers such as MPA
 68 |     boundaries and ocean fronts.
 69 | 
 70 |   - [antanym](https://github.com/SCAR/antanym) provides geographic place
 71 |     name data from the SCAR Composite Gazetteer of Antarctica, with
 72 |     plans to extend the coverage to subantarctic and informal gazetteers
 73 |     at a later date.
 74 | 
 75 |   - [orsifronts](https://cran.rstudio.com/web/packages/orsifronts/index.html) provides the
 76 |     commonly-used Orsi et al. (1995) definitions of the major Southern
 77 |     Ocean fronts.
 78 | 
 79 |   - [graticule](https://cran.rstudio.com/web/packages/graticule/index.html) creates graticule
 80 |     lines (lines of longitude and latitude) and labels for maps.
 81 | 
 82 |   - [palr](https://cran.rstudio.com/web/packages/palr/index.html) provides colour palettes for
 83 |     data, based on some well known remotely sensed data sets for sea ice
 84 |     concentration, sea surface temperature and chlorophyll- *a* .
 85 | 
 86 |   - there is some Antarctic-related mapping functionality in
 87 |     [prtools](https://github.com/pierreroudier/prtools) ,
 88 |     [atlasr](https://github.com/jiho/atlasr) ,
 89 |     [CCAMLRGIS](https://github.com/ccamlr/CCAMLRGIS) , and
 90 |     [sospatial](https://github.com/AustralianAntarcticDivision/sospatial)
 91 |     .
 92 | 
 93 | ### Environmental Data
 94 | 
 95 |   - [blueant](https://github.com/AustralianAntarcticDivision/blueant)
 96 |     and its companion package
 97 |     [bowerbird](https://github.com/AustralianAntarcticDivision/bowerbird)
 98 |     provide a mechanism to download a range of environmental data
 99 |     including satellite-derived sea ice, sea surface temperature,
100 |     topography, ocean colour (chlorophyll- *a* ), and meteorological
101 |     data from various providers. Many of these data sets can be read and
102 |     manipulated with [raster](https://cran.rstudio.com/web/packages/raster/index.html) and similar
103 |     packages: the [spatial task
104 |     view](https://cran.r-project.org/web/views/Spatial.html) is a good
105 |     resource here.
106 | 
107 |   - the [PolarWatch](https://polarwatch.noaa.gov/) project aims to
108 |     enable data discovery and broader use of high-latitude ocean remote
109 |     sensing data sets. The dedicated ERDDAP server
110 |     (https://polarwatch.noaa.gov/erddap) is accessible to R users with
111 |     [rerddap](https://cran.rstudio.com/web/packages/rerddap/index.html).
112 | 
113 |   - [rsoi](https://cran.rstudio.com/web/packages/rsoi/index.html) downloads the most up to date
114 |     Southern Oscillation Index, Oceanic Nino Index, and North Pacific
115 |     Gyre Oscillation data.
116 | 
117 | ### Oceanography
118 | 
119 |   - satellite reflectance data are a common basis for estimating
120 |     chlorophyll- *a* and other phytoplankton parameters at ocean-basin
121 |     scales. Global products are widely available; however,
122 |     Southern-Ocean specific algorithms are likely to provide better
123 |     estimates in these regions. [croc](https://github.com/sosoc/croc)
124 |     implements the Johnson et al. (2013) Southern Ocean algorithm.
125 | 
126 |   - more broadly, [oce](https://cran.rstudio.com/web/packages/oce/index.html) provides a wide
127 |     range of tools for reading, processing, and displaying oceanographic
128 |     data, including measurements from Argo floats and CTD casts,
129 |     sectional data, sea-level time series, and coastline and topographic
130 |     data.
131 | 
132 |   - [fda.oce](https://github.com/EPauthenet/fda.oce) provides functional
133 |     data analysis of oceanographic profiles for front detection, water
134 |     mass identification, unsupervised or supervised classification,
135 |     model comparison, data calibration, and more.
136 | 
137 | ### Biodiversity data
138 | 
139 |   - [robis](https://cran.rstudio.com/web/packages/robis/index.html) for marine data,
140 |     [rgbif](https://cran.rstudio.com/web/packages/rgbif/index.html) for global biodiversity data.
141 |     [spocc](https://cran.rstudio.com/web/packages/spocc/index.html) wraps these and other
142 |     occurrence data providers with a consistent interface (but not
143 |     necessarily the full functionality of provider-specific packages,
144 |     where they exist).
145 | 
146 |   - [obistools](https://github.com/iobis/obistools) and
147 |     [scrubr](https://cran.rstudio.com/web/packages/scrubr/index.html) for quality-checking
148 |     occurrence data.
149 | 
150 |   - a package for the data behind the [Mapping Application for Penguin
151 |     Populations and Projected Dynamics
152 |     (MAPPPD)](http://www.penguinmap.com/) is in planning: contact [Grant
153 |     Humphries](mailto:grwhumphries@blackbawks.net) .
154 | 
155 |   - diet data [sohungry](https://github.com/SCAR/sohungry) and
156 |     allometric equations [solong](https://github.com/SCAR/solong)
157 | 
158 | ### Animal tracking
159 | 
160 | Tracking of animals using satellite, GPS, or light-level geolocation
161 | tags is common, and there are many R packages that can help with this.
162 | See the [spatiotemporal task
163 | view](https://cloud.r-project.org/web/views/SpatioTemporal.html) for a
164 | more complete list. Of particular interest may be:
165 | 
166 |   - [TwilightFree](https://github.com/ABindoff/TwilightFree) provides a
167 |     method for processing light-level geolocation data that is robust to
168 |     noise (sensor shading and obscuration) and may be particularly
169 |     suitable for Southern Ocean applications.
170 | 
171 |   - [foieGras](https://cran.rstudio.com/web/packages/foieGras/index.html) fits continuous-time
172 |     random walk and correlated random walk state-space models to filter
173 |     Argos satellite location data.
174 | 
175 |   - [availability](https://github.com/AustralianAntarcticDivision/availability)
176 |     estimates the geographic space available to animals based on
177 |     telemetry data.
178 | 
179 | ### Miscellaneous
180 | 
181 | Packages that may be of interest but don’t yet fit neatly into another
182 | category.
183 | 
184 |   - [distancetocoast](https://github.com/mdsumner/distancetocoast)
185 |     provides “distance to coastline” data for longitude and latitude
186 |     coordinates.
187 | 
188 | </div>
189 | 
190 | ### CRAN packages:
191 | 
192 |   - [foieGras](https://cran.rstudio.com/web/packages/foieGras/index.html)
193 |   - [graticule](https://cran.rstudio.com/web/packages/graticule/index.html)
194 |   - [oce](https://cran.rstudio.com/web/packages/oce/index.html)
195 |   - [orsifronts](https://cran.rstudio.com/web/packages/orsifronts/index.html)
196 |   - [palr](https://cran.rstudio.com/web/packages/palr/index.html)
197 |   - [raster](https://cran.rstudio.com/web/packages/raster/index.html)
198 |   - [rerddap](https://cran.rstudio.com/web/packages/rerddap/index.html)
199 |   - [rgbif](https://cran.rstudio.com/web/packages/rgbif/index.html)
200 |   - [robis](https://cran.rstudio.com/web/packages/robis/index.html)
201 |   - [rsoi](https://cran.rstudio.com/web/packages/rsoi/index.html)
202 |   - [scrubr](https://cran.rstudio.com/web/packages/scrubr/index.html)
203 |   - [spocc](https://cran.rstudio.com/web/packages/spocc/index.html)
204 |   - [taxize](https://cran.rstudio.com/web/packages/taxize/index.html)
205 |   - [worrms](https://cran.rstudio.com/web/packages/worrms/index.html)
206 | 
207 | ### Related links:
208 | 
209 |   - [taxonomy task view](https://github.com/ropensci/taxonomy)
210 |   - [spatial task
211 |     view](https://cran.r-project.org/web/views/Spatial.html)
212 |   - [spatiotemporal task
213 |     view](https://cloud.r-project.org/web/views/SpatioTemporal.html)
214 | 


--------------------------------------------------------------------------------
/task_view/antarctic.md:
--------------------------------------------------------------------------------
 1 | 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.
 2 | 
 3 | 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.
 4 | 
 5 | Contributions are welcome! Please [submit an issue](https://github.com/SCAR/ropensci/issues), or make a contribution (see the [contribution guidelines](CONTRIBUTING.md)). If you have an issue with one of the packages discussed below, please contact the maintainer of that package.
 6 | 
 7 | Many thanks to contributors, including Scott Chamberlain, Michael Sumner, Grant Humphries, Hsun-yi Hsieh, and Anton Van de Putte.
 8 | 
 9 | 
10 | ### Taxonomic Data
11 | 
12 | 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).
13 | 
14 | - <pkg>worrms</pkg> client for the [WoRMS](http://www.marinespecies.org/) API. Contains mostly taxonomic data, but also trait data. 
15 | - <pkg>taxize</pkg> 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.
16 | 
17 | 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).
18 | 
19 | For more detail on R packages dealing with taxonomy in general, see the [rOpenSci taxonomy task view](https://github.com/ropensci/taxonomy).
20 | 
21 | 
22 | ### Mapping
23 | 
24 | 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&deg;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.
25 | 
26 | - [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.
27 | 
28 | - [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.
29 | 
30 | - <pkg>orsifronts</pkg> provides the commonly-used Orsi et al. (1995) definitions of the major Southern Ocean fronts.
31 | 
32 | - <pkg>graticule</pkg> creates graticule lines (lines of longitude and latitude) and labels for maps.
33 | 
34 | - <pkg>palr</pkg> provides colour palettes for data, based on some well known remotely sensed data sets for sea ice concentration, sea surface temperature and chlorophyll-*a*.
35 | 
36 | - 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).
37 | 
38 | ### Environmental Data
39 | 
40 | - [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 <pkg>raster</pkg> and similar packages: the [spatial task view](https://cran.r-project.org/web/views/Spatial.html) is a good resource here.
41 | 
42 | - 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 <pkg>rerddap</pkg>.
43 | 
44 | - <pkg>rsoi</pkg> downloads the most up to date Southern Oscillation Index, Oceanic Nino Index, and North Pacific Gyre Oscillation data.
45 | 
46 | 
47 | ### Oceanography
48 | 
49 | - 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.
50 | 
51 | - more broadly, <pkg>oce</pkg> 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.
52 | 
53 | - [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.
54 | 
55 | ### Biodiversity data
56 | 
57 | - <pkg>robis</pkg> for marine data, <pkg>rgbif</pkg> for global biodiversity data. <pkg>spocc</pkg> wraps these and other occurrence data providers with a consistent interface (but not necessarily the full functionality of provider-specific packages, where they exist).
58 | 
59 | - [obistools](https://github.com/iobis/obistools) and <pkg>scrubr</pkg> for quality-checking occurrence data.
60 | 
61 | - 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).
62 | 
63 | - diet data [sohungry](https://github.com/SCAR/sohungry) and allometric equations [solong](https://github.com/SCAR/solong)
64 | 
65 | ### Animal tracking
66 | 
67 | 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:
68 | 
69 | - [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.
70 | 
71 | - <pkg>foieGras</pkg> fits continuous-time random walk and correlated random walk state-space models to filter Argos satellite location data.
72 | 
73 | - [availability](https://github.com/AustralianAntarcticDivision/availability) estimates the geographic space available to animals based on telemetry data.
74 | 
75 | ### Miscellaneous
76 | 
77 | Packages that may be of interest but don't yet fit neatly into another category.
78 | 
79 | - [distancetocoast](https://github.com/mdsumner/distancetocoast) provides "distance to coastline" data for longitude and latitude coordinates.
80 | 


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/task_view/buildxml.R:
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 1 | if(!require("stringr")) install.packages("stringr", repos="https://cran.rstudio.com")
 2 | template <- readLines("Antarctic.ctv")
 3 | pattern <- "pkg>[[:alnum:]]+[[:alnum:].]*[[:alnum:]]+"
 4 | out <- paste0(template, collapse = " ")
 5 | pkgs <- stringr::str_extract_all(out, pattern)[[1]]
 6 | pkgs <- unique(gsub("^pkg>", "", pkgs))
 7 | priority <- c()
 8 | pkgs <- pkgs[ !pkgs %in% priority] # remove priority packages
 9 | pkgs <- lapply(as.list(sort(pkgs)), function(x) list(package=x))
10 | output <-
11 | c(paste0('<CRANTaskView>
12 |   <name>Antarctic</name>
13 |   <topic>Antarctic and Southern Ocean Science</topic>
14 |   <maintainer email="ben.raymond@aad.gov.au">Ben Raymond</maintainer>
15 |   <version>',Sys.Date(),'</version>'),
16 |   '  <info>',
17 |   paste0("    ",template),
18 |   '  </info>',
19 |   '  <packagelist>',
20 |   # list priority packages explicitly
21 |   ## uncommment this line once there is somthing in "priority" list, above
22 |   ##paste0('    <pkg priority="core">', priority, '</pkg>', collapse = "\n"),
23 |   # add all other packages from `pkgs`
24 |   paste0('    <pkg>', unlist(unname(pkgs)), '</pkg>', collapse = "\n"),
25 |   '  </packagelist>',
26 |   '  <links>',
27 |   '    <a href="https://github.com/ropensci/taxonomy">taxonomy task view</a>',
28 |   '    <a href="https://cran.r-project.org/web/views/Spatial.html">spatial task view</a>',
29 |   '    <a href="https://cloud.r-project.org/web/views/SpatioTemporal.html">spatiotemporal task view</a>',
30 |   '  </links>',
31 |   '</CRANTaskView>')
32 | 
33 | writeLines(output, "Antarctic.ctv")
34 | 


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/task_view/checkurls.R:
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 1 | if (!require("httr")) {
 2 |     install.packages("httr", repos = "https://cran.rstudio.com/")
 3 | }
 4 | 
 5 | extract_urls <- function(file, ...) {
 6 |     f <- rawToChar(readBin(file, what = "raw", n = 1e7L))
 7 |     x <- "(http|ftp|https)://([\\w_-]+(?:(?:\\.[\\w_-]+)+))([\\w.,@?^=%&:/~+#-]*[\\w@?^=%&/~+#-])?"
 8 |     # Credit: http://stackoverflow.com/questions/6038061/regular-expression-to-find-urls-within-a-string
 9 |     m <- regmatches(f, gregexpr(x, f, perl=TRUE))[[1]]
10 |     m
11 | }
12 | 
13 | check_one <- function(url, ...) {
14 |     r <- try(httr::HEAD(url, ...), silent = TRUE)
15 |     if (inherits(r, "try-error")) {
16 |         list(url1 = url, 
17 |              url2 = NA_character_, 
18 |              redirect = NA, 
19 |              error = NA, 
20 |              status = NA_real_
21 |              )
22 |     } else {
23 |         list(url1 = url, 
24 |              url2 = r$url, 
25 |              redirect = !identical(url, r$url), 
26 |              error = http_error(r), 
27 |              status = status_code(r)
28 |              )
29 |     }
30 | }
31 | 
32 | check_urls <- function(urls, ...) {
33 |     check <- lapply(urls, check_one, ...)
34 |     out <- do.call("rbind.data.frame", c(check, stringsAsFactors = FALSE, make.row.names = FALSE))
35 |     return(structure(out, class = c("url_check", "data.frame")))
36 | }
37 | 
38 | print.url_check <- function(x, ...) {
39 |     f <- is.na(x[["url2"]])
40 |     r <- x[["redirect"]]
41 |     e <- x[["error"]]
42 |     s <- x[["status"]] != 200
43 |     print.data.frame(x[ (f | r | e | s) ,, drop = FALSE])
44 |     invisible(x)
45 | }
46 | 
47 | u <- extract_urls("antarctic.md")
48 | print(ch <- check_urls(u))
49 | 


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/task_view/process.R:
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 1 | if(!require("xml2")) install.packages("xml2", repos = "http://cran.rstudio.com/")
 2 | x <- xml2::read_html("Antarctic.html")
 3 | 
 4 | # remove table
 5 | tab <- xml2::xml_find_first(x, "//table")
 6 | xml2::xml_remove(tab)
 7 | 
 8 | # strip cran task view h2
 9 | h2 <- xml2::xml_find_first(x, '//h2[contains(text(), "CRAN Task View: Antarctic and Southern Ocean Science")]')
10 | xml2::xml_text(h2) <- "Antarctic and Southern Ocean Science"
11 | 
12 | # write
13 | xml2::write_html(x, "Antarctic.html")
14 | 


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