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<div class="section" id="dataone-r-client-package">
<h1>DataONE R Client Package<a class="headerlink" href="#dataone-r-client-package" title="Permalink to this headline">¶</a></h1>
<div class="section" id="synopsis">
<h2>Synopsis<a class="headerlink" href="#synopsis" title="Permalink to this headline">¶</a></h2>
<p>Environmental scientists commonly use the <a class="reference external" href="http://www.r-project.org">R Project</a> software system for
statistical analysis and modeling. The R framework is a flexible statistical
computing environment with robust, extensive packages to perform a large
variety of analysis and modeling tasks. Because R is open source and
extensible, it has been widely adopted by the environmental science community,
and it is easy to extend to provide new analysis capabilities.</p>
<p>The <a class="reference internal" href="#dataone-r-client-package">DataONE R Client Package</a> is an R package that provides access to the
DataONE services that are present at Coordinating Nodes and Member Nodes. The
tool will allow an R user to easily load the d1r package (using <a class="reference external" href="http://cran.r-project.org">CRAN</a>) and
then use functions in R to search the DataONE system, locate data of interest,
load that data into the R environment, process it using R’s various tools, and
then upload derived data and metadata back into DataONE.</p>
<p>By targeting R in the Investigator Toolkit, we enable a wide variety of
scientists to harness data within the network of Member Nodes, and to
reference the data sets within their R scripts using their unique identifiers
from DataONE. This allows anyone to execute the R script from a paper or
analysis, and the <cite>dataone</cite> library handles the details of finding and accessing
the data needed for analysis or visualization.</p>
</div>
<div class="section" id="user-stories">
<h2>User stories<a class="headerlink" href="#user-stories" title="Permalink to this headline">¶</a></h2>
<ul>
<li><p class="first">A scientist with R on their system can easily install d1r from <a class="reference external" href="http://cran.r-project.org">CRAN</a></p>
</li>
<li><p class="first">A scientist can load a data object using its DataONE identifier from the
DataONE system into R for further processing by other R functions. The
data objects supported should minimally include:</p>
<blockquote>
<div><ul class="simple">
<li>Data Tables in CSV and other delimited formats</li>
<li>NetCDF files</li>
<li>Raster images in various formats</li>
</ul>
</div></blockquote>
</li>
<li><p class="first">A scientist can use d1r to search for data based on critical metadata,
including title, creator, keywords, abstract, spatial location, temporal
coverage, taxonomic coverage, and other relevant fields</p>
</li>
<li><p class="first">A scientist can load all of the supported data objects into R by using the
metadata found in a metadata search without directly knowing the
identifiers for individual data objects</p>
</li>
<li><p class="first">Given a data object loaded from DataONE into R, a scientist can display
the science metadata associated with that object from within the R system
(this might include a link to an external web URI that provides a nice
human readable version of the metadata too)</p>
</li>
<li><p class="first">A scientist can authenticate with the DataONE system in order to establish
their identity to access restricted objects and services</p>
</li>
<li><p class="first">A scientist can upload an R dataframe as a data set with associated
science and system metadata for that object from within the R environment</p>
</li>
</ul>
</div>
<div class="section" id="package-design">
<h2>Package design<a class="headerlink" href="#package-design" title="Permalink to this headline">¶</a></h2>
<div class="section" id="classes-fields-and-methods">
<h3>Classes, fields, and methods<a class="headerlink" href="#classes-fields-and-methods" title="Permalink to this headline">¶</a></h3>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">All of the classes and methods in R are inverted (ie, classes don’t
contain methods per se, instead, methods are specialized to work on
particular classes, and the class is generally passed in as the first
parameter of the method call. So, all signatures below need to have an
added parameter for this object to be passed in.</p>
</div>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">This design is out of date, and instead follows the design in DataPackage.
The R package mainly follows and uses the Java implementation, so does not
need to reimplement this structure. Probably can delete this section, but
leaving for now until DataPackage design is completed.</p>
</div>
<ul>
<li><dl class="first docutils">
<dt>D1Client</dt>
<dd><ul class="first last">
<li><dl class="first docutils">
<dt>Fields</dt>
<dd><ul class="first last simple">
<li>endpoint</li>
<li>username</li>
<li>cli <D1Client></li>
<li>token <AuthToken></li>
</ul>
</dd>
</dl>
</li>
<li><dl class="first docutils">
<dt>Constructors</dt>
<dd><ul class="first last simple">
<li>D1Client(CN_URI)</li>
</ul>
</dd>
</dl>
</li>
<li><dl class="first docutils">
<dt>Methods</dt>
<dd><ul class="first last simple">
<li>login(username, password): AuthToken</li>
<li>logout()</li>
<li>getEndpoint(): String</li>
<li>getPackage(pid): DataPackage</li>
<li>getUsername(): String</li>
<li>getToken(): AuthToken</li>
<li>search(): ResultSet</li>
<li>resolve(pid): [MemberNodeURI]</li>
</ul>
</dd>
</dl>
</li>
</ul>
</dd>
</dl>
</li>
<li><dl class="first docutils">
<dt>DataPackage</dt>
<dd><ul class="first last">
<li><dl class="first docutils">
<dt>Fields</dt>
<dd><ul class="first last simple">
<li>identifier</li>
<li>scimeta</li>
<li>sysmeta</li>
<li>[dataObject]</li>
</ul>
</dd>
</dl>
</li>
<li><dl class="first docutils">
<dt>Constructors</dt>
<dd><ul class="first last simple">
<li>DataPackage(identifier, scimeta, sysmeta)</li>
</ul>
</dd>
</dl>
</li>
<li><dl class="first docutils">
<dt>Methods</dt>
<dd><ul class="first last simple">
<li>addData(DataObject): DataPackage</li>
<li>getDataObjectCount(): int</li>
<li>getDataObject(index): DataObject</li>
<li>getTitle(): String</li>
<li>getCreator(): String</li>
<li>getDisplayURL(): String</li>
</ul>
</dd>
</dl>
</li>
</ul>
</dd>
</dl>
</li>
<li><dl class="first docutils">
<dt>DataObject</dt>
<dd><ul class="first last">
<li><dl class="first docutils">
<dt>Fields</dt>
<dd><ul class="first last simple">
<li>sysmeta</li>
<li>databytes</li>
</ul>
</dd>
</dl>
</li>
<li><dl class="first docutils">
<dt>Constructors</dt>
<dd><ul class="first last simple">
<li>DataObject(Identifier, SystemMetadata, databytes)</li>
</ul>
</dd>
</dl>
</li>
<li><p class="first">Methods</p>
</li>
</ul>
</dd>
</dl>
</li>
</ul>
</div>
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<h3><a href="../index.html">Table Of Contents</a></h3>
<ul>
<li><a class="reference internal" href="#">DataONE R Client Package</a><ul>
<li><a class="reference internal" href="#synopsis">Synopsis</a></li>
<li><a class="reference internal" href="#user-stories">User stories</a></li>
<li><a class="reference internal" href="#package-design">Package design</a><ul>
<li><a class="reference internal" href="#classes-fields-and-methods">Classes, fields, and methods</a></li>
</ul>
</li>
</ul>
</li>
</ul>
<h3>Related Topics</h3>
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<li><a href="../index.html">Documentation Overview</a><ul>
<li><a href="index.html"><no title></a><ul>
<li><a href="itk-analysis.html">Analysis and Modeling Tools</a><ul>
<li>Previous: <a href="itk-analysis.html" title="previous chapter">Analysis and Modeling Tools</a></li>
<li>Next: <a href="itk-matlab.html" title="next chapter">Matlab</a></li>
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<p>This material is based upon work supported by the National Science Foundation
under Grant Numbers <a href="http://www.nsf.gov/awardsearch/showAward?AWD_ID=0830944">083094</a> and <a href="http://www.nsf.gov/awardsearch/showAward?AWD_ID=1430508">1430508</a>.</p>
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