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Release 0.6.5 (#176)
* Prepare to release 0.6.5 * Update docs * Update docs * Update typo statsitics
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strategy:
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fail-fast: false
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matrix:
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platform: [ubuntu-latest, macos-latest, windows-latest]
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python-version: ["3.8", "3.9", "3.10", "3.11"]
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platform: [ubuntu-latest, windows-latest] # macos-latest
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python-version: ["3.9", "3.10", "3.11"]
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runs-on: ${{ matrix.platform }}
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sleep_statistics
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Hypnogram
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simulate_hypnogram
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EpochByEpochAgreement
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SleepStatsAgreement
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Spectral analyses
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-----------------

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# Sphinx build info version 1
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# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
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config: 489cdac284cc185cfdae105616c5af8a
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config: f80ed99698c532d7a1c5d14ebdacc629
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tags: 645f666f9bcd5a90fca523b33c5a78b7

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<head>
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<meta charset="utf-8" />
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<meta name="viewport" content="width=device-width, initial-scale=1.0" />
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<title>Overview: module code &#8212; yasa 0.6.4 documentation</title>
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<title>Overview: module code &#8212; yasa 0.6.5 documentation</title>
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<link rel="stylesheet" type="text/css" href="../_static/pygments.css" />
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</button>
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<a class="navbar-brand" href="../index.html"><span><img src="../_static/yasa_128x128.png"></span>
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yasa</a>
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<span class="navbar-text navbar-version pull-left"><b>0.6.4</b></span>
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<span class="navbar-text navbar-version pull-left"><b>0.6.5</b></span>
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</div>
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<h1>All modules for which code is available</h1>
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<ul><li><a href="yasa/detection.html">yasa.detection</a></li>
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<li><a href="yasa/evaluation.html">yasa.evaluation</a></li>
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<li><a href="yasa/heart.html">yasa.heart</a></li>
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<li><a href="yasa/hypno.html">yasa.hypno</a></li>
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<li><a href="yasa/others.html">yasa.others</a></li>

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<meta name="viewport" content="width=device-width, initial-scale=1.0" />
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<title>yasa.detection &#8212; yasa 0.6.4 documentation</title>
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<title>yasa.detection &#8212; yasa 0.6.5 documentation</title>
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</button>
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<a class="navbar-brand" href="../../index.html"><span><img src="../../_static/yasa_128x128.png"></span>
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yasa</a>
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<span class="navbar-text navbar-version pull-left"><b>0.6.4</b></span>
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<span class="navbar-text navbar-version pull-left"><b>0.6.5</b></span>
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<span class="sd">- GitHub: https://github.com/raphaelvallat/yasa</span>
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<span class="sd">- License: BSD 3-Clause License</span>
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<span class="sd">&quot;&quot;&quot;</span>
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<span class="kn">import</span> <span class="nn">mne</span>
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<span class="kn">import</span> <span class="nn">logging</span>
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<span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>

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<title>yasa.heart &#8212; yasa 0.6.4 documentation</title>
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<title>yasa.heart &#8212; yasa 0.6.5 documentation</title>
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<a class="navbar-brand" href="../../index.html"><span><img src="../../_static/yasa_128x128.png"></span>
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yasa</a>
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<span class="navbar-text navbar-version pull-left"><b>0.6.5</b></span>
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<span class="sd">Author: Dr Raphael Vallat &lt;[email protected]&gt;, UC Berkeley.</span>
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<span class="sd">Date: May 2022</span>
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<span class="sd">&quot;&quot;&quot;</span>
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<span class="kn">import</span> <span class="nn">logging</span>
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<span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
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<span class="kn">import</span> <span class="nn">pandas</span> <span class="k">as</span> <span class="nn">pd</span>

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<title>yasa.hypno &#8212; yasa 0.6.4 documentation</title>
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<title>yasa.hypno &#8212; yasa 0.6.5 documentation</title>
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<a class="navbar-brand" href="../../index.html"><span><img src="../../_static/yasa_128x128.png"></span>
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<span class="navbar-text navbar-version pull-left"><b>0.6.5</b></span>
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<span></span><span class="sd">&quot;&quot;&quot;</span>
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<span class="sd">Hypnogram-related functions and class.</span>
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<span class="sd">&quot;&quot;&quot;</span>
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<span class="kn">from</span> <span class="nn">yasa.io</span> <span class="kn">import</span> <span class="n">set_log_level</span>
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<span class="kn">from</span> <span class="nn">yasa.plotting</span> <span class="kn">import</span> <span class="n">plot_hypnogram</span>
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<span class="kn">from</span> <span class="nn">yasa.sleepstats</span> <span class="kn">import</span> <span class="n">transition_matrix</span>
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<span class="kn">from</span> <span class="nn">yasa.evaluation</span> <span class="kn">import</span> <span class="n">EpochByEpochAgreement</span>
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<span class="n">__all__</span> <span class="o">=</span> <span class="p">[</span>
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<span class="sd"> Name: Stage, dtype: int16</span>
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<span class="sd"> &quot;&quot;&quot;</span>
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<span class="c1"># Return as int16 (-32768 to 32767) to reduce memory usage</span>
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<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">hypno</span><span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">mapping</span><span class="p">)</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">int16</span><span class="p">)</span></div>
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<span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">hypno</span><span class="o">.</span><span class="n">cat</span><span class="o">.</span><span class="n">rename_categories</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">mapping</span><span class="p">)</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">int16</span><span class="p">)</span></div>
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<div class="viewcode-block" id="Hypnogram.consolidate_stages"><a class="viewcode-back" href="../../generated/yasa.Hypnogram.html#yasa.Hypnogram.consolidate_stages">[docs]</a> <span class="k">def</span> <span class="nf">consolidate_stages</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">new_n_stages</span><span class="p">):</span>
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<span class="sd">&quot;&quot;&quot;Reduce the number of stages in a hypnogram to match actigraphy or wearables.</span>
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<span class="n">scorer</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">scorer</span><span class="p">,</span>
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<div class="viewcode-block" id="Hypnogram.evaluate"><a class="viewcode-back" href="../../generated/yasa.Hypnogram.html#yasa.Hypnogram.evaluate">[docs]</a> <span class="k">def</span> <span class="nf">evaluate</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">obs_hyp</span><span class="p">):</span>
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<span class="sd">&quot;&quot;&quot;Evaluate agreement between two hypnograms of the same sleep session.</span>
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<span class="sd"> For example, the reference hypnogram (i.e., ``self``) might be a manually-scored hypnogram</span>
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<span class="sd"> and the reference hypnogram (i.e., ``ref_hyp``) might be a hypnogram from actigraphy, a</span>
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<span class="sd"> wearable device, or an automated scorer (e.g., :py:meth:`yasa.SleepStaging.predict`).</span>
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<span class="sd"> Parameters</span>
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<span class="sd"> ----------</span>
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<span class="sd"> self : :py:class:`yasa.Hypnogram`</span>
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<span class="sd"> Reference or ground-truth hypnogram.</span>
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<span class="sd"> obs_hyp : :py:class:`yasa.Hypnogram`</span>
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<span class="sd"> The observed or to-be-evaluated hypnogram.</span>
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<span class="sd"> Returns</span>
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<span class="sd"> -------</span>
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<span class="sd"> ebe : :py:class:`yasa.EpochByEpochAgreement`</span>
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<span class="sd"> See :py:class:`~yasa.EpochByEpochAgreement` documentation for more detail.</span>
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<span class="sd"> Examples</span>
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<span class="sd"> --------</span>
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<span class="sd"> &gt;&gt;&gt; from yasa import simulate_hypnogram</span>
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<span class="sd"> &gt;&gt;&gt; hyp_a = simulate_hypnogram(tib=90, scorer=&quot;AASM&quot;, seed=8)</span>
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<span class="sd"> &gt;&gt;&gt; hyp_b = hyp_a.simulate_similar(scorer=&quot;YASA&quot;, seed=9)</span>
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<span class="sd"> &gt;&gt;&gt; ebe = hyp_a.evaluate(hyp_b)</span>
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<span class="sd"> &gt;&gt;&gt; ebe.get_agreement().round(3)</span>
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<span class="sd"> accuracy 0.550</span>
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<span class="sd"> balanced_acc 0.355</span>
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<span class="sd"> kappa 0.227</span>
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<span class="sd"> mcc 0.231</span>
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<span class="sd"> precision 0.515</span>
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<span class="sd"> recall 0.550</span>
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<span class="sd"> fbeta 0.524</span>
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<span class="sd"> Name: agreement, dtype: float64</span>
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<span class="sd"> &quot;&quot;&quot;</span>
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<span class="k">return</span> <span class="n">EpochByEpochAgreement</span><span class="p">([</span><span class="bp">self</span><span class="p">],</span> <span class="p">[</span><span class="n">obs_hyp</span><span class="p">])</span></div>
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<div class="viewcode-block" id="Hypnogram.find_periods"><a class="viewcode-back" href="../../generated/yasa.Hypnogram.html#yasa.Hypnogram.find_periods">[docs]</a> <span class="k">def</span> <span class="nf">find_periods</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">threshold</span><span class="o">=</span><span class="s2">&quot;5min&quot;</span><span class="p">,</span> <span class="n">equal_length</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span>
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<span class="sd">&quot;&quot;&quot;Find sequences of consecutive values exceeding a certain duration in hypnogram.</span>
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<span></span><span class="sd">&quot;&quot;&quot;</span>
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<span class="sd">This file contains several helper functions to manipulate 1D and 2D EEG data.</span>
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<span class="sd">&quot;&quot;&quot;</span>
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<span class="kn">import</span> <span class="nn">logging</span>
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<span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
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<span class="kn">from</span> <span class="nn">scipy.interpolate</span> <span class="kn">import</span> <span class="n">interp1d</span>

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