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specparam</a>
<span class="navbar-text navbar-version pull-left"><b>2.0.0rc2</b></span>
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<section id="reference-and-reporting-information">
<h1>Reference and Reporting Information<a class="headerlink" href="#reference-and-reporting-information" title="Permalink to this heading">¶</a></h1>
<p>This page describes how to reference and report on using this method for parameterizing neural power spectra, and related information.</p>
<section id="table-of-contents">
<h2>Table of Contents<a class="headerlink" href="#table-of-contents" title="Permalink to this heading">¶</a></h2>
<nav class="contents local" id="contents">
<ul class="simple">
<li><p><a class="reference internal" href="#reference" id="id1">Reference</a></p></li>
<li><p><a class="reference internal" href="#example-applications" id="id2">Example Applications</a></p></li>
<li><p><a class="reference internal" href="#methods-reporting" id="id3">Methods Reporting</a></p></li>
<li><p><a class="reference internal" href="#reporting-template-example" id="id4">Reporting Template & Example</a></p></li>
<li><p><a class="reference internal" href="#checking-module-version" id="id5">Checking module version</a></p></li>
<li><p><a class="reference internal" href="#generating-methods-reports" id="id6">Generating Methods Reports</a></p></li>
</ul>
</nav>
<section id="reference">
<h3>Reference<a class="headerlink" href="#reference" title="Permalink to this heading">¶</a></h3>
<p>If you use this method, and/or want to refer to our approach, examples, and discussion points, please cite the following paper:</p>
<aside class="topic">
<p class="topic-title">Reference</p>
<p>Donoghue T, Haller M, Peterson EJ, Varma P, Sebastian P, Gao R, Noto T, Lara AH, Wallis JD,
Knight RT, Shestyuk A, Voytek B (2020). Parameterizing neural power spectra into periodic and aperiodic
components. Nature Neuroscience, 23, 1655-1665. DOI: 10.1038/s41593-020-00744-x</p>
</aside>
<p>Direct link: <a class="reference external" href="https://doi.org/10.1038/s41593-020-00744-x">https://doi.org/10.1038/s41593-020-00744-x</a></p>
</section>
<section id="example-applications">
<h3>Example Applications<a class="headerlink" href="#example-applications" title="Permalink to this heading">¶</a></h3>
<p>As well as reporting on the method, the full version of the paper includes simulation work as well as example analyses and applications.
The code for the simulations and applications is indexed and available in the
<a class="reference external" href="https://github.com/fooof-tools/Paper">Paper repository</a>.</p>
<p>You can also find the full list of articles that cite the <cite>Parameterizing Neural Power Spectra</cite> paper at this
<a class="reference external" href="https://scholar.google.com/scholar?cites=1871208307712966933&as_sdt=5,33&sciodt=0,33&hl=en">Google scholar link</a>.</p>
</section>
<section id="methods-reporting">
<h3>Methods Reporting<a class="headerlink" href="#methods-reporting" title="Permalink to this heading">¶</a></h3>
<p>If you use this module and the power spectrum model in your work, there is some information you should include in the methods section.</p>
<p>Specifically, we recommend including the following information in the methods section:</p>
<ul class="simple">
<li><p>The version number of the module that was used (for example 1.0.0)</p></li>
<li><p>The algorithm settings that were used</p>
<ul>
<li><p>You should report all public settings, even if default values are used</p></li>
</ul>
</li>
<li><p>The frequency range of the data that was fit</p></li>
</ul>
<p>In addition, we recommend that reports should include information on:</p>
<ul class="simple">
<li><p>Details of the data, including modality and any preprocessing steps applied</p></li>
<li><p>How power spectrum were generated, including the length of segments used to calculate spectra</p></li>
<li><p>If and how model goodness-of-fit measures were assessed</p></li>
</ul>
</section>
<section id="reporting-template-example">
<h3>Reporting Template & Example<a class="headerlink" href="#reporting-template-example" title="Permalink to this heading">¶</a></h3>
<p>To assist in reporting on using spectral parameterization, we have created some templates for reporting on spectral parameterization methods. There are also some utilities included in the code to collect the required information.</p>
<p>The following box is an example of what a methods report might look like (where all of the <em>X</em>’s should be filled in with the relevant information).</p>
<aside class="topic">
<p class="topic-title">Methods Report Template</p>
<p>Spectral parameterization, using the specparam Python tool (version <em>X.X.X</em>) was used to
parameterize neural power spectra. Settings for the algorithm were: peak width limits : <em>XX</em>;
max number of peaks : <em>XX</em>; minimum peak height : <em>XX</em>; peak threshold : <em>XX</em>; and aperiodic
mode : <em>XX</em>. Power spectra were parameterized across the frequency range <em>XX</em> to <em>XX</em> Hz.</p>
</aside>
</section>
<section id="checking-module-version">
<h3>Checking module version<a class="headerlink" href="#checking-module-version" title="Permalink to this heading">¶</a></h3>
<p>If you are not sure which version of the module you have installed, you can
check the <cite>__version__</cite> from Python, using the following code:</p>
<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="c1"># Check the version of the tool</span>
<span class="kn">from</span> <span class="nn">specparam</span> <span class="kn">import</span> <span class="n">__version__</span> <span class="k">as</span> <span class="n">specparam_version</span>
<span class="nb">print</span><span class="p">(</span><span class="s1">'Current specparam version:'</span><span class="p">,</span> <span class="n">specparam_version</span><span class="p">)</span>
</pre></div>
</div>
</section>
<section id="generating-methods-reports">
<h3>Generating Methods Reports<a class="headerlink" href="#generating-methods-reports" title="Permalink to this heading">¶</a></h3>
<p>As of version 1.0.0 there are code utilities to extract all required information for reporting, and for generating methods reports.</p>
<p>These utilities require a defined model object, such as <cite>SpectralModel</cite> or <cite>SpectralGroupModel</cite>, assumed to be called ‘model_obj’ in the following examples. This object will be used to extract all the relevant settings and any available meta-data for reporting.</p>
<p>The <a class="reference internal" href="generated/specparam.utils.reports.methods_report_info.html#specparam.utils.reports.methods_report_info" title="specparam.utils.reports.methods_report_info"><code class="xref py py-func docutils literal notranslate"><span class="pre">methods_report_info()</span></code></a> function can be used to print out the information you need for reporting:</p>
<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="c1"># Import the utility to print out information for reporting</span>
<span class="kn">from</span> <span class="nn">specparam.utils.reports</span> <span class="kn">import</span> <span class="n">methods_report_info</span>
<span class="c1"># Print out all the methods information for reporting</span>
<span class="n">methods_report_info</span><span class="p">(</span><span class="n">model_obj</span><span class="p">)</span>
</pre></div>
</div>
<p>The <a class="reference internal" href="generated/specparam.utils.reports.methods_report_text.html#specparam.utils.reports.methods_report_text" title="specparam.utils.reports.methods_report_text"><code class="xref py py-func docutils literal notranslate"><span class="pre">methods_report_text()</span></code></a> function can be used to print out an auto-generated methods report, like the one demonstrated above, with all available information filled:</p>
<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="c1"># Import the utility to print out information for reporting</span>
<span class="kn">from</span> <span class="nn">specparam.utils.reports</span> <span class="kn">import</span> <span class="n">methods_report_text</span>
<span class="c1"># Generate methods text, with methods information inserted</span>
<span class="n">methods_report_text</span><span class="p">(</span><span class="n">model_obj</span><span class="p">)</span>
</pre></div>
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