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neuropsychology · Aug 6, 2024 · ec1feb1 · ec1feb1
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diff --git a/.doctrees/environment.pickle b/.doctrees/environment.pickle
diff --git a/.doctrees/examples/bio_custom/bio_custom.doctree b/.doctrees/examples/bio_custom/bio_custom.doctree
diff --git a/.doctrees/examples/bio_eventrelated/bio_eventrelated.doctree b/.doctrees/examples/bio_eventrelated/bio_eventrelated.doctree
diff --git a/.doctrees/examples/ecg_generate_12leads/ecg_generate_12leads.doctree b/.doctrees/examples/ecg_generate_12leads/ecg_generate_12leads.doctree
diff --git a/.doctrees/examples/ecg_heartbeats/ecg_heartbeats.doctree b/.doctrees/examples/ecg_heartbeats/ecg_heartbeats.doctree
diff --git a/.doctrees/examples/eda_peaks/eda_peaks.doctree b/.doctrees/examples/eda_peaks/eda_peaks.doctree
diff --git a/.doctrees/examples/eeg_complexity/eeg_complexity.doctree b/.doctrees/examples/eeg_complexity/eeg_complexity.doctree
diff --git a/.doctrees/examples/eeg_microstates/eeg_microstates.doctree b/.doctrees/examples/eeg_microstates/eeg_microstates.doctree
diff --git a/.doctrees/examples/eeg_power/eeg_power.doctree b/.doctrees/examples/eeg_power/eeg_power.doctree
diff --git a/.doctrees/examples/eog_analyze/eog_analyze.doctree b/.doctrees/examples/eog_analyze/eog_analyze.doctree
diff --git a/.doctrees/examples/misc_epochs_create/misc_epochs_create.doctree b/.doctrees/examples/misc_epochs_create/misc_epochs_create.doctree
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diff --git a/.doctrees/examples/signal_simulation/signal_simulation.doctree b/.doctrees/examples/signal_simulation/signal_simulation.doctree
diff --git a/.doctrees/functions/benchmark.doctree b/.doctrees/functions/benchmark.doctree
diff --git a/.doctrees/functions/bio.doctree b/.doctrees/functions/bio.doctree
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diff --git a/_images/p_signal_surrogate1.png b/_images/p_signal_surrogate1.png
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diff --git a/_modules/neurokit2/ecg/ecg_peaks.html b/_modules/neurokit2/ecg/ecg_peaks.html
@@ -399,7 +399,9 @@ <h1>Source code for neurokit2.ecg.ecg_peaks</h1><div class="highlight"><pre>
 
 <span class="sd">    * **neurokit** (default): QRS complexes are detected based on the steepness of the absolute</span>
 <span class="sd">      gradient of the ECG signal. Subsequently, R-peaks are detected as local maxima in</span>
-<span class="sd">      the QRS complexes. Unpublished, but see https://github.com/neuropsychology/NeuroKit/issues/476</span>
+<span class="sd">      the QRS complexes. The method is unpublished, but see: (i) https://github.com/neuropsychology/NeuroKit/issues/476 </span>
+<span class="sd">      for discussion of this algorithm; and (ii) https://doi.org/10.21105/joss.02621 for the original validation of</span>
+<span class="sd">      this algorithm.</span>
 <span class="sd">    * **pantompkins1985**: Algorithm by Pan &amp; Tompkins (1985).</span>
 <span class="sd">    * **hamilton2002**: Algorithm by Hamilton (2002).</span>
 <span class="sd">    * **zong2003**: Algorithm by Zong et al. (2003).</span>

diff --git a/examples/bio_custom/bio_custom.html b/examples/bio_custom/bio_custom.html
@@ -495,7 +495,7 @@ <h2>The Default NeuroKit processing pipeline<a class="headerlink" href="#the-def
 </div>
 </div>
 <div class="cell_output docutils container">
-<img alt="../../_images/3f35dd775f19984b31530ad8ca033c275e0f1a911eefc8e9123e3bb4aa6718c3.png" src="../../_images/3f35dd775f19984b31530ad8ca033c275e0f1a911eefc8e9123e3bb4aa6718c3.png" />
+<img alt="../../_images/a911330592b1704f72dac65e1441052bc0b0217b84706d00bbf5bdd60715ddce.png" src="../../_images/a911330592b1704f72dac65e1441052bc0b0217b84706d00bbf5bdd60715ddce.png" />
 </div>
 </div>
 </section>
@@ -543,7 +543,7 @@ <h2>Building your own <code class="docutils literal notranslate"><span class="pr
 </div>
 </div>
 <div class="cell_output docutils container">
-<img alt="../../_images/d1d28987108e446c6abfd80bd0b6f9f7f954969a3669068d35b0973766e60303.png" src="../../_images/d1d28987108e446c6abfd80bd0b6f9f7f954969a3669068d35b0973766e60303.png" />
+<img alt="../../_images/5e2957af3613ba994ef11a8834653e04625b92faf978eacf69ad2b428df29051.png" src="../../_images/5e2957af3613ba994ef11a8834653e04625b92faf978eacf69ad2b428df29051.png" />
 </div>
 </div>
 </section>
@@ -635,7 +635,7 @@ <h2>Customize even more!<a class="headerlink" href="#customize-even-more" title=
 </div>
 </div>
 <div class="cell_output docutils container">
-<img alt="../../_images/f4365ff9b4c87fc883a376a6b62e8166632781e44516f97def594c9c5e060819.png" src="../../_images/f4365ff9b4c87fc883a376a6b62e8166632781e44516f97def594c9c5e060819.png" />
+<img alt="../../_images/80a3360dd47fc5f8fd024942056a9f28137905a5b287744ac91daa0776f1a465.png" src="../../_images/80a3360dd47fc5f8fd024942056a9f28137905a5b287744ac91daa0776f1a465.png" />
 </div>
 </div>
 <p>This doesn’t look bad :) <strong>Can you do better?</strong></p>

diff --git a/examples/bio_eventrelated/bio_eventrelated.html b/examples/bio_eventrelated/bio_eventrelated.html
@@ -530,7 +530,7 @@ <h2>Find Events<a class="headerlink" href="#find-events" title="Link to this hea
 </div>
 </div>
 <div class="cell_output docutils container">
-<img alt="../../_images/4aba064195a36ec2868bc77d575d370aea08dc6a817c0386a295308757748ebc.png" src="../../_images/4aba064195a36ec2868bc77d575d370aea08dc6a817c0386a295308757748ebc.png" />
+<img alt="../../_images/cc0b84a971cd33eb90a68546db92709f7a3f2af2d14c594713a79615f73ccb7a.png" src="../../_images/cc0b84a971cd33eb90a68546db92709f7a3f2af2d14c594713a79615f73ccb7a.png" />
 </div>
 </div>
 <p>The output of <a class="reference external" href="https://neuropsychology.github.io/NeuroKit/functions/functions_events.html#events-plot">events_plot()</a> shows the corresponding events in the signal, with the blue dashed line representing a Negative event and red dashed line representing a Neutral event.</p>
@@ -641,11 +641,11 @@ <h2>Manually Extract Event Related Features<a class="headerlink" href="#manually
 </div>
 </div>
 <div class="cell_output docutils container">
-<div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>C:\Users\runneradmin\AppData\Local\Temp\ipykernel_7256\4246861920.py:12: FutureWarning: The behavior of obj[i:j] with a float-dtype index is deprecated. In a future version, this will be treated as positional instead of label-based. For label-based slicing, use obj.loc[i:j] instead
+<div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>C:\Users\runneradmin\AppData\Local\Temp\ipykernel_3184\4246861920.py:12: FutureWarning: The behavior of obj[i:j] with a float-dtype index is deprecated. In a future version, this will be treated as positional instead of label-based. For label-based slicing, use obj.loc[i:j] instead
   ecg_mean = epoch[&quot;ECG_Rate&quot;][0:4].mean()  # Mean heart rate in the 0-4 seconds
-C:\Users\runneradmin\AppData\Local\Temp\ipykernel_7256\4246861920.py:18: FutureWarning: The behavior of obj[i:j] with a float-dtype index is deprecated. In a future version, this will be treated as positional instead of label-based. For label-based slicing, use obj.loc[i:j] instead
+C:\Users\runneradmin\AppData\Local\Temp\ipykernel_3184\4246861920.py:18: FutureWarning: The behavior of obj[i:j] with a float-dtype index is deprecated. In a future version, this will be treated as positional instead of label-based. For label-based slicing, use obj.loc[i:j] instead
   rsp_rate = epoch[&quot;RSP_Rate&quot;][0:6].mean()  # Longer window for RSP that has a slower dynamic
-C:\Users\runneradmin\AppData\Local\Temp\ipykernel_7256\4246861920.py:24: FutureWarning: The behavior of obj[i:j] with a float-dtype index is deprecated. In a future version, this will be treated as positional instead of label-based. For label-based slicing, use obj.loc[i:j] instead
+C:\Users\runneradmin\AppData\Local\Temp\ipykernel_3184\4246861920.py:24: FutureWarning: The behavior of obj[i:j] with a float-dtype index is deprecated. In a future version, this will be treated as positional instead of label-based. For label-based slicing, use obj.loc[i:j] instead
   scr_max = epoch[&quot;SCR_Amplitude&quot;][0:6].max()  # Maximum SCR peak
 </pre></div>
 </div>

diff --git a/examples/ecg_generate_12leads/ecg_generate_12leads.html b/examples/ecg_generate_12leads/ecg_generate_12leads.html
@@ -481,7 +481,7 @@ <h2>Normal Multi-lead ECG<a class="headerlink" href="#normal-multi-lead-ecg" tit
 </div>
 </div>
 <div class="cell_output docutils container">
-<img alt="../../_images/0746e10715a9de777e7ccd636b5f531b39f37248280328d71701cbbe2ca29f03.png" src="../../_images/0746e10715a9de777e7ccd636b5f531b39f37248280328d71701cbbe2ca29f03.png" />
+<img alt="../../_images/067235a6922762f3a234cef8b4abbe118a44116e17e8640029fc3d371f26e5ea.png" src="../../_images/067235a6922762f3a234cef8b4abbe118a44116e17e8640029fc3d371f26e5ea.png" />
 </div>
 </div>
 </section>
@@ -513,7 +513,7 @@ <h2>Abnormal Multi-lead ECG<a class="headerlink" href="#abnormal-multi-lead-ecg"
 </div>
 </div>
 <div class="cell_output docutils container">
-<img alt="../../_images/f9da93aadea1e1d21fe18c77618ff599b5ad5469006c0080c15741ca571a92cf.png" src="../../_images/f9da93aadea1e1d21fe18c77618ff599b5ad5469006c0080c15741ca571a92cf.png" />
+<img alt="../../_images/d23ad7c07afaf6cb8d8d7a641fc7b1d3ef9f5ee916ab296ec8f81b5a333919d2.png" src="../../_images/d23ad7c07afaf6cb8d8d7a641fc7b1d3ef9f5ee916ab296ec8f81b5a333919d2.png" />
 </div>
 </div>
 </section>

diff --git a/examples/ecg_heartbeats/ecg_heartbeats.html b/examples/ecg_heartbeats/ecg_heartbeats.html
@@ -520,7 +520,7 @@ <h2>Extract R-peaks location<a class="headerlink" href="#extract-r-peaks-locatio
 </div>
 </div>
 <div class="cell_output docutils container">
-<img alt="../../_images/614f306e4c3b1f9267255fec0162491951743969c21f3272a281e4ed1e0f1683.png" src="../../_images/614f306e4c3b1f9267255fec0162491951743969c21f3272a281e4ed1e0f1683.png" />
+<img alt="../../_images/cfd4321e5dfe76a6c4cfbdcac301e03707c80e9d1ee08062dfdb48c7dc94f9ba.png" src="../../_images/cfd4321e5dfe76a6c4cfbdcac301e03707c80e9d1ee08062dfdb48c7dc94f9ba.png" />
 </div>
 </div>
 <p>Once that we know where the R-peaks are located, we can create windows of signal around them (of a length of for instance 1 second, ranging from 400 ms before the R-peak), which we can refer to as <em>epochs</em>.</p>
@@ -536,7 +536,7 @@ <h2>Segment the signal around the heart beats<a class="headerlink" href="#segmen
 </div>
 </div>
 <div class="cell_output docutils container">
-<img alt="../../_images/3bb9b34639607f42c8e8af2d03deafd84c5ad4fb13ca77b1ce9ef267f1efc5a0.png" src="../../_images/3bb9b34639607f42c8e8af2d03deafd84c5ad4fb13ca77b1ce9ef267f1efc5a0.png" />
+<img alt="../../_images/731b1227637623d51d3e5ef751e4c1613e67fac59fdbc00ff9d4527a719c6d64.png" src="../../_images/731b1227637623d51d3e5ef751e4c1613e67fac59fdbc00ff9d4527a719c6d64.png" />
 </div>
 </div>
 <p>This create a dictionary of dataframes for each ‘epoch’ (in this case, each heart beat).</p>
@@ -592,36 +592,36 @@ <h3>Custom colors and legend<a class="headerlink" href="#custom-colors-and-legen
   <tbody>
     <tr>
       <th>0</th>
-      <td>-0.201741</td>
-      <td>138</td>
+      <td>-0.171613</td>
+      <td>145</td>
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       <td>-0.300000</td>
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+      <td>-0.165996</td>
+      <td>146</td>
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+      <td>147</td>
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+      <td>-0.154247</td>
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+      <td>-0.147958</td>
+      <td>149</td>
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@@ -706,123 +706,123 @@ <h3>Custom colors and legend<a class="headerlink" href="#custom-colors-and-legen
   <tbody>
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       <th>-0.300000</th>
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-      <td>-0.133132</td>
-      <td>-0.134888</td>
-      <td>-0.134908</td>
-      <td>-0.139741</td>
-      <td>-0.137998</td>
-      <td>-0.142197</td>
-      <td>-0.138135</td>
-      <td>-0.133675</td>
+      <td>-0.171613</td>
+      <td>-0.134621</td>
+      <td>-0.139992</td>
+      <td>-0.132925</td>
+      <td>-0.136068</td>
+      <td>-0.135397</td>
+      <td>-0.136384</td>
+      <td>-0.127918</td>
+      <td>-0.130730</td>
+      <td>-0.134260</td>
       <td>...</td>
-      <td>-0.130146</td>
-      <td>-0.159835</td>
-      <td>-0.103471</td>
-      <td>-0.223781</td>
-      <td>-0.120153</td>
-      <td>-0.139750</td>
-      <td>-0.134874</td>
-      <td>-0.140533</td>
-      <td>-0.135164</td>
-      <td>-0.129830</td>
+      <td>-0.140481</td>
+      <td>-0.172995</td>
+      <td>-0.025607</td>
+      <td>-0.330808</td>
+      <td>-0.109664</td>
+      <td>-0.141837</td>
+      <td>-0.134080</td>
+      <td>-0.129938</td>
+      <td>-0.137441</td>
+      <td>-0.133026</td>
     </tr>
     <tr>
       <th>-0.295977</th>
-      <td>-0.196297</td>
-      <td>-0.137900</td>
-      <td>-0.132140</td>
-      <td>-0.134249</td>
-      <td>-0.134512</td>
-      <td>-0.138890</td>
-      <td>-0.137228</td>
-      <td>-0.141015</td>
-      <td>-0.137116</td>
-      <td>-0.132538</td>
+      <td>-0.165996</td>
+      <td>-0.133087</td>
+      <td>-0.138649</td>
+      <td>-0.131986</td>
+      <td>-0.135087</td>
+      <td>-0.134586</td>
+      <td>-0.135515</td>
+      <td>-0.126972</td>
+      <td>-0.129928</td>
+      <td>-0.133527</td>
       <td>...</td>
-      <td>-0.128919</td>
-      <td>-0.158315</td>
-      <td>-0.103030</td>
-      <td>-0.223309</td>
-      <td>-0.119796</td>
-      <td>-0.139018</td>
-      <td>-0.133899</td>
-      <td>-0.139143</td>
-      <td>-0.134507</td>
-      <td>-0.128933</td>
+      <td>-0.139150</td>
+      <td>-0.171946</td>
+      <td>-0.024954</td>
+      <td>-0.330345</td>
+      <td>-0.109227</td>
+      <td>-0.140678</td>
+      <td>-0.133018</td>
+      <td>-0.128910</td>
+      <td>-0.136207</td>
+      <td>-0.131844</td>
     </tr>
     <tr>
       <th>-0.291954</th>
-      <td>-0.190793</td>
-      <td>-0.136233</td>
-      <td>-0.130996</td>
-      <td>-0.133499</td>
-      <td>-0.133966</td>
-      <td>-0.137865</td>
-      <td>-0.136340</td>
-      <td>-0.139719</td>
-      <td>-0.135931</td>
-      <td>-0.131265</td>
+      <td>-0.160230</td>
+      <td>-0.131344</td>
+      <td>-0.137023</td>
+      <td>-0.130898</td>
+      <td>-0.133974</td>
+      <td>-0.133661</td>
+      <td>-0.134568</td>
+      <td>-0.125933</td>
+      <td>-0.129000</td>
+      <td>-0.132651</td>
       <td>...</td>
-      <td>-0.127491</td>
-      <td>-0.156553</td>
-      <td>-0.102401</td>
-      <td>-0.222694</td>
-      <td>-0.119281</td>
-      <td>-0.138202</td>
-      <td>-0.132748</td>
-      <td>-0.137551</td>
-      <td>-0.133741</td>
-      <td>-0.127984</td>
+      <td>-0.137637</td>
+      <td>-0.170751</td>
+      <td>-0.024271</td>
+      <td>-0.329715</td>
+      <td>-0.108697</td>
+      <td>-0.139322</td>
+      <td>-0.131813</td>
+      <td>-0.127790</td>
+      <td>-0.134847</td>
+      <td>-0.130519</td>
     </tr>
     <tr>
       <th>-0.287931</th>
-      <td>-0.185175</td>
-      <td>-0.134409</td>
-      <td>-0.129637</td>
-      <td>-0.132592</td>
-      <td>-0.133239</td>
-      <td>-0.136637</td>
-      <td>-0.135288</td>
-      <td>-0.138267</td>
-      <td>-0.134542</td>
-      <td>-0.129813</td>
+      <td>-0.154247</td>
+      <td>-0.129353</td>
+      <td>-0.135055</td>
+      <td>-0.129610</td>
+      <td>-0.132692</td>
+      <td>-0.132575</td>
+      <td>-0.133490</td>
+      <td>-0.124770</td>
+      <td>-0.127906</td>
+      <td>-0.131604</td>
       <td>...</td>
-      <td>-0.125809</td>
-      <td>-0.154496</td>
-      <td>-0.101551</td>
-      <td>-0.221904</td>
-      <td>-0.118577</td>
-      <td>-0.137248</td>
-      <td>-0.131348</td>
-      <td>-0.135694</td>
-      <td>-0.132811</td>
-      <td>-0.126913</td>
+      <td>-0.135872</td>
+      <td>-0.169380</td>
+      <td>-0.023528</td>
+      <td>-0.328884</td>
+      <td>-0.108049</td>
+      <td>-0.137719</td>
+      <td>-0.130428</td>
+      <td>-0.126547</td>
+      <td>-0.133335</td>
+      <td>-0.129022</td>
     </tr>
     <tr>
       <th>-0.283908</th>
-      <td>-0.179371</td>
-      <td>-0.132391</td>
-      <td>-0.127983</td>
-      <td>-0.131465</td>
-      <td>-0.132300</td>
-      <td>-0.135177</td>
-      <td>-0.134019</td>
-      <td>-0.136616</td>
-      <td>-0.132904</td>
-      <td>-0.128115</td>
+      <td>-0.147958</td>
+      <td>-0.127058</td>
+      <td>-0.132679</td>
+      <td>-0.128056</td>
+      <td>-0.131189</td>
+      <td>-0.131269</td>
+      <td>-0.132207</td>
+      <td>-0.123433</td>
+      <td>-0.126592</td>
+      <td>-0.130343</td>
       <td>...</td>
-      <td>-0.123801</td>
-      <td>-0.152071</td>
-      <td>-0.100442</td>
-      <td>-0.220903</td>
-      <td>-0.117648</td>
-      <td>-0.136078</td>
-      <td>-0.129616</td>
-      <td>-0.133485</td>
-      <td>-0.131648</td>
-      <td>-0.125630</td>
+      <td>-0.133770</td>
+      <td>-0.167792</td>
+      <td>-0.022670</td>
+      <td>-0.327802</td>
+      <td>-0.107248</td>
+      <td>-0.135815</td>
+      <td>-0.128824</td>
+      <td>-0.125138</td>
+      <td>-0.131629</td>
+      <td>-0.127314</td>
     </tr>
   </tbody>
 </table>
@@ -850,7 +850,7 @@ <h3>Custom colors and legend<a class="headerlink" href="#custom-colors-and-legen
 </div>
 </div>
 <div class="cell_output docutils container">
-<img alt="../../_images/2b5605187e4d86c3e71ac2c3f1c878c1f29c377b9b22f602e70d0f2276da45d1.png" src="../../_images/2b5605187e4d86c3e71ac2c3f1c878c1f29c377b9b22f602e70d0f2276da45d1.png" />
+<img alt="../../_images/5648b41fa08b760a33ca402772dc07581a4ca8ec7feb5191f66ed69988676514.png" src="../../_images/5648b41fa08b760a33ca402772dc07581a4ca8ec7feb5191f66ed69988676514.png" />
 </div>
 </div>
 </section>