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  <div class="section" id="module-pebl.data">
<span id="data-pebl-dataset"></span><h1><tt class="xref py py-mod docutils literal"><span class="pre">data</span></tt> &#8211; Pebl Dataset<a class="headerlink" href="#module-pebl.data" title="Permalink to this headline"></a></h1>
<p>This module provides classes and functions for working with datasets.</p>
<div class="section" id="configuration-parameters">
<h2>Configuration Parameters<a class="headerlink" href="#configuration-parameters" title="Permalink to this headline"></a></h2>
<dl class="confparam">
<dt id="confparam-data.discretize">
<tt class="descname">data.discretize</tt><a class="headerlink" href="#confparam-data.discretize" title="Permalink to this definition"></a></dt>
<dd><p>Number of bins used to discretize data. Specify 0 to indicate that data should not be discretized.
default=0</p>
</dd></dl>

<dl class="confparam">
<dt id="confparam-data.filename">
<tt class="descname">data.filename</tt><a class="headerlink" href="#confparam-data.filename" title="Permalink to this definition"></a></dt>
<dd><p>File to read data from.
default=None</p>
</dd></dl>

<dl class="confparam">
<dt id="confparam-data.text">
<tt class="descname">data.text</tt><a class="headerlink" href="#confparam-data.text" title="Permalink to this definition"></a></dt>
<dd><p>The text of a dataset included in config file.
default=&#8217;&#8216;</p>
</dd></dl>

</div>
<div class="section" id="dataset-class">
<h2>Dataset class<a class="headerlink" href="#dataset-class" title="Permalink to this headline"></a></h2>
<dl class="class">
<dt id="pebl.data.Dataset">
<em class="property">class </em><tt class="descclassname">pebl.data.</tt><tt class="descname">Dataset</tt><big>(</big><em>observations</em>, <em>missing=None</em>, <em>interventions=None</em>, <em>variables=None</em>, <em>samples=None</em>, <em>skip_stats=False</em><big>)</big><a class="headerlink" href="#pebl.data.Dataset" title="Permalink to this definition"></a></dt>
<dd><p>Create a pebl Dataset instance.</p>
<p>A Dataset consists of the following data structures which are all
numpy.ndarray instances:</p>
<ul>
<li><dl class="first docutils">
<dt>observations: a 2D matrix of observed values. </dt>
<dd><ul class="first last simple">
<li>dimension 1 is over samples, dimension 2 is over variables.</li>
<li>observations[i,j] is the observed value for jth variable in the ith
sample.</li>
</ul>
</dd>
</dl>
</li>
<li><dl class="first docutils">
<dt>missing: a 2D binary mask for missing values</dt>
<dd><ul class="first last simple">
<li>missing[i,j] = 1 IFF observation[i,j] is missing</li>
</ul>
</dd>
</dl>
</li>
<li><dl class="first docutils">
<dt>interventions: a 2D binary mask for interventions</dt>
<dd><ul class="first last simple">
<li>interventions[i,j] = 1 IFF the jth variable was intervened upon in
the ith sample.</li>
</ul>
</dd>
</dl>
</li>
<li><p class="first">variables,samples: 1D array of variable or sample annotations</p>
</li>
</ul>
<p>This class provides a few public methods to manipulate datasets; one can
also use numpy functions/methods directly.</p>
<p>Required/Default values:</p>
<blockquote>
<div><ul class="simple">
<li>The only required argument is observations (a 2D numpy array).</li>
<li>If missing or interventions are not specified, they are assumed to
be all zeros (no missing values and no interventions).</li>
<li>If variables or samples are not specified, appropriate Variable or
Sample annotations are created with only the name attribute.</li>
</ul>
</div></blockquote>
<dl class="docutils">
<dt>Note:</dt>
<dd>If you alter Dataset.interventions or Dataset.missing, you must
call Dataset._calc_stats(). This is a terrible hack but it speeds
up pebl when used with datasets without interventions or missing
values (a common case).</dd>
</dl>
<dl class="method">
<dt id="pebl.data.Dataset.check_arities">
<tt class="descname">check_arities</tt><big>(</big><big>)</big><a class="headerlink" href="#pebl.data.Dataset.check_arities" title="Permalink to this definition"></a></dt>
<dd><p>Checks whether the specified airty &gt;= number of unique observations.</p>
<p>The check is only performed for discrete variables.</p>
<p>If this check fails, the CPT and other data structures would fail.
So, we should raise error while loading the data. Fail Early and Explicitly!</p>
</dd></dl>

<dl class="method">
<dt id="pebl.data.Dataset.discretize">
<tt class="descname">discretize</tt><big>(</big><em>includevars=None</em>, <em>excludevars=[]</em>, <em>numbins=3</em><big>)</big><a class="headerlink" href="#pebl.data.Dataset.discretize" title="Permalink to this definition"></a></dt>
<dd><p>Discretize (or bin) the data in-place.</p>
<p>This method is just an alias for pebl.discretizer.maximum_entropy_discretizer()
See the module documentation for pebl.discretizer for more information.</p>
</dd></dl>

<dl class="attribute">
<dt id="pebl.data.Dataset.has_interventions">
<tt class="descname">has_interventions</tt><a class="headerlink" href="#pebl.data.Dataset.has_interventions" title="Permalink to this definition"></a></dt>
<dd><p>Whether the dataset has any interventions.</p>
</dd></dl>

<dl class="attribute">
<dt id="pebl.data.Dataset.has_missing">
<tt class="descname">has_missing</tt><a class="headerlink" href="#pebl.data.Dataset.has_missing" title="Permalink to this definition"></a></dt>
<dd><p>Whether the dataset has any missing values.</p>
</dd></dl>

<dl class="attribute">
<dt id="pebl.data.Dataset.shape">
<tt class="descname">shape</tt><a class="headerlink" href="#pebl.data.Dataset.shape" title="Permalink to this definition"></a></dt>
<dd><p>The shape of the dataset as (number of samples, number of variables).</p>
</dd></dl>

<dl class="method">
<dt id="pebl.data.Dataset.subset">
<tt class="descname">subset</tt><big>(</big><em>variables=None</em>, <em>samples=None</em><big>)</big><a class="headerlink" href="#pebl.data.Dataset.subset" title="Permalink to this definition"></a></dt>
<dd><p>Returns a subset of the dataset (and metadata).</p>
<p>Specify the variables and samples for creating a subset of the data.
variables and samples should be a list of ids. If not specified, it is
assumed to be all variables or samples.</p>
<p>Some examples:</p>
<blockquote>
<div><ul class="simple">
<li>d.subset([3], [4])</li>
<li>d.subset([3,1,2])</li>
<li>d.subset(samples=[5,2,7,1])</li>
</ul>
</div></blockquote>
<p>Note: order matters! d.subset([3,1,2]) != d.subset([1,2,3])</p>
</dd></dl>

<dl class="method">
<dt id="pebl.data.Dataset.subset_byname">
<tt class="descname">subset_byname</tt><big>(</big><em>variables=None</em>, <em>samples=None</em><big>)</big><a class="headerlink" href="#pebl.data.Dataset.subset_byname" title="Permalink to this definition"></a></dt>
<dd><p>Returns a subset of the dataset (and metadata).</p>
<p>Same as Dataset.subset() except that variables and samples can be
specified by their names.</p>
<p>Some examples:</p>
<blockquote>
<div><ul class="simple">
<li>d.subset(variables=[&#8216;shh&#8217;, &#8216;genex&#8217;])</li>
<li>s.subset(samples=[&#8220;control%d&#8221; % i for i in xrange(10)])</li>
</ul>
</div></blockquote>
</dd></dl>

<dl class="method">
<dt id="pebl.data.Dataset.tofile">
<tt class="descname">tofile</tt><big>(</big><em>filename</em>, <em>*args</em>, <em>**kwargs</em><big>)</big><a class="headerlink" href="#pebl.data.Dataset.tofile" title="Permalink to this definition"></a></dt>
<dd><p>Write the data and metadata to file in a tab-delimited format.</p>
</dd></dl>

<dl class="method">
<dt id="pebl.data.Dataset.tostring">
<tt class="descname">tostring</tt><big>(</big><em>linesep='\n'</em>, <em>variable_header=True</em>, <em>sample_header=True</em><big>)</big><a class="headerlink" href="#pebl.data.Dataset.tostring" title="Permalink to this definition"></a></dt>
<dd><p>Return the data and metadata as a string in a tab-delimited format.</p>
<p>If variable_header is True, include variable names and type.
If sample_header is True, include sample names.
Both are True by default.</p>
</dd></dl>

</dd></dl>

</div>
<div class="section" id="functions">
<h2>Functions<a class="headerlink" href="#functions" title="Permalink to this headline"></a></h2>
<dl class="function">
<dt id="pebl.data.fromstring">
<tt class="descclassname">pebl.data.</tt><tt class="descname">fromstring</tt><big>(</big><em>stringrep</em>, <em>fieldsep='\t'</em><big>)</big><a class="headerlink" href="#pebl.data.fromstring" title="Permalink to this definition"></a></dt>
<dd><p>Parse the string representation of a dataset and return a Dataset instance.</p>
<p>See the documentation for fromfile() for information about file format.</p>
</dd></dl>

<dl class="function">
<dt id="pebl.data.fromfile">
<tt class="descclassname">pebl.data.</tt><tt class="descname">fromfile</tt><big>(</big><em>filename</em><big>)</big><a class="headerlink" href="#pebl.data.fromfile" title="Permalink to this definition"></a></dt>
<dd><p>Parse file and return a Dataset instance.</p>
<p>The data file is expected to conform to the following format</p>
<blockquote>
<div><ul class="simple">
<li>comment lines begin with &#8216;#&#8217; and are ignored.</li>
<li>The first non-comment line <em>must</em> specify variable annotations
separated by tab characters.</li>
<li>data lines specify the data values separated by tab characters.</li>
<li>data lines <em>can</em> include sample names</li>
</ul>
</div></blockquote>
<p>A data value specifies the observed numeric value, whether it&#8217;s missing and
whether it represents an intervention:</p>
<blockquote>
<div><ul class="simple">
<li>An &#8216;x&#8217; or &#8216;X&#8217; indicate that the value is missing</li>
<li>A &#8216;!&#8217; before or after the numeric value indicates an intervention</li>
</ul>
</div></blockquote>
<p>Variable annotations specify the name of the variable and, <em>optionally</em>,
the data type.</p>
<p>Examples include:</p>
<blockquote>
<div><ul>
<li><p class="first">Foo                     : just variable name</p>
</li>
<li><p class="first">Foo,continuous          : Foo is a continuous variable</p>
</li>
<li><p class="first">Foo,discrete(3)         : Foo is a discrete variable with arity of 3</p>
</li>
<li><dl class="first docutils">
<dt>Foo,class(normal,cancer): Foo is a class variable with arity of 2 and</dt>
<dd><p class="first last">values of either normal or cancer.</p>
</dd>
</dl>
</li>
</ul>
</div></blockquote>
</dd></dl>

<dl class="function">
<dt id="pebl.data.fromconfig">
<tt class="descclassname">pebl.data.</tt><tt class="descname">fromconfig</tt><big>(</big><big>)</big><a class="headerlink" href="#pebl.data.fromconfig" title="Permalink to this definition"></a></dt>
<dd><p>Create a Dataset from the configuration information.</p>
<p>Loads data and discretizes (if requested) based on configuration
parameters.</p>
</dd></dl>

<dl class="function">
<dt id="pebl.data.merge">
<tt class="descclassname">pebl.data.</tt><tt class="descname">merge</tt><big>(</big><em>datasets</em>, <em>axis=None</em><big>)</big><a class="headerlink" href="#pebl.data.merge" title="Permalink to this definition"></a></dt>
<dd><p>Merges multiple datasets.</p>
<p>datasets should be a list of Dataset objects.
axis should be either &#8216;variables&#8217; or &#8216;samples&#8217; and determines how the
datasets are merged.</p>
</dd></dl>

</div>
<div class="section" id="variable-and-sample-annotations">
<h2>Variable and sample annotations<a class="headerlink" href="#variable-and-sample-annotations" title="Permalink to this headline"></a></h2>
<dl class="class">
<dt id="pebl.data.Variable">
<em class="property">class </em><tt class="descclassname">pebl.data.</tt><tt class="descname">Variable</tt><big>(</big><em>name</em>, <em>*args</em><big>)</big><a class="headerlink" href="#pebl.data.Variable" title="Permalink to this definition"></a></dt>
<dd><p>Additional information about a variable.</p>
</dd></dl>

<dl class="class">
<dt id="pebl.data.DiscreteVariable">
<em class="property">class </em><tt class="descclassname">pebl.data.</tt><tt class="descname">DiscreteVariable</tt><big>(</big><em>name</em>, <em>param</em><big>)</big><a class="headerlink" href="#pebl.data.DiscreteVariable" title="Permalink to this definition"></a></dt>
<dd><p>A variable from a discrete domain.</p>
</dd></dl>

<dl class="class">
<dt id="pebl.data.ContinuousVariable">
<em class="property">class </em><tt class="descclassname">pebl.data.</tt><tt class="descname">ContinuousVariable</tt><big>(</big><em>name</em>, <em>param</em><big>)</big><a class="headerlink" href="#pebl.data.ContinuousVariable" title="Permalink to this definition"></a></dt>
<dd><p>A variable from a continuous domain.</p>
</dd></dl>

<dl class="class">
<dt id="pebl.data.ClassVariable">
<em class="property">class </em><tt class="descclassname">pebl.data.</tt><tt class="descname">ClassVariable</tt><big>(</big><em>name</em>, <em>param</em><big>)</big><a class="headerlink" href="#pebl.data.ClassVariable" title="Permalink to this definition"></a></dt>
<dd><p>A labeled, discrete variable.</p>
</dd></dl>

<dl class="class">
<dt id="pebl.data.Sample">
<em class="property">class </em><tt class="descclassname">pebl.data.</tt><tt class="descname">Sample</tt><big>(</big><em>name</em>, <em>*args</em><big>)</big><a class="headerlink" href="#pebl.data.Sample" title="Permalink to this definition"></a></dt>
<dd><p>Additional information about a sample.</p>
</dd></dl>

</div>
<div class="section" id="exceptions">
<h2>Exceptions<a class="headerlink" href="#exceptions" title="Permalink to this headline"></a></h2>
<dl class="exception">
<dt id="pebl.data.ParsingError">
<em class="property">exception </em><tt class="descclassname">pebl.data.</tt><tt class="descname">ParsingError</tt><a class="headerlink" href="#pebl.data.ParsingError" title="Permalink to this definition"></a></dt>
<dd><p>Error encountered while parsing an ill-formed datafile.</p>
</dd></dl>

<dl class="exception">
<dt id="pebl.data.IncorrectArityError">
<em class="property">exception </em><tt class="descclassname">pebl.data.</tt><tt class="descname">IncorrectArityError</tt><big>(</big><em>errors</em><big>)</big><a class="headerlink" href="#pebl.data.IncorrectArityError" title="Permalink to this definition"></a></dt>
<dd><p>Error encountered when the datafile speifies an incorrect variable arity.</p>
<p>If variable arity is specified, it should be greater than the number of
unique observation values for the variable.</p>
</dd></dl>

<dl class="exception">
<dt id="pebl.data.ClassVariableError">
<em class="property">exception </em><tt class="descclassname">pebl.data.</tt><tt class="descname">ClassVariableError</tt><a class="headerlink" href="#pebl.data.ClassVariableError" title="Permalink to this definition"></a></dt>
<dd><p>Error with a class variable.</p>
</dd></dl>

</div>
</div>


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  <h3><a href="index.html">Table Of Contents</a></h3>
  <ul>
<li><a class="reference internal" href="#"><tt class="docutils literal"><span class="pre">data</span></tt> &#8211; Pebl Dataset</a><ul>
<li><a class="reference internal" href="#configuration-parameters">Configuration Parameters</a></li>
<li><a class="reference internal" href="#dataset-class">Dataset class</a></li>
<li><a class="reference internal" href="#functions">Functions</a></li>
<li><a class="reference internal" href="#variable-and-sample-annotations">Variable and sample annotations</a></li>
<li><a class="reference internal" href="#exceptions">Exceptions</a></li>
</ul>
</li>
</ul>

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