deploy: efadfbc

01_0_transform_data_to_wide_format.html

@@ -154,27 +154,27 @@
 <p aria-level="2" class="caption" role="heading"><span class="caption-text">PIMMS models</span></p>
 <ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="01_1_train_Median.html">Median</a></li>
-<li class="toctree-l1"><a class="reference internal" href="01_1_train_CF.html">CF</a></li>
+<li class="toctree-l1"><a class="reference internal" href="01_1_train_DAE.html">DAE</a></li>
 <li class="toctree-l1"><a class="reference internal" href="01_1_train_KNN.html">KNN</a></li>
 <li class="toctree-l1"><a class="reference internal" href="01_1_train_VAE.html">VAE</a></li>
-<li class="toctree-l1"><a class="reference internal" href="01_1_train_DAE.html">DAE</a></li>
+<li class="toctree-l1"><a class="reference internal" href="01_1_train_CF.html">CF</a></li>
 </ul>
 <p aria-level="2" class="caption" role="heading"><span class="caption-text">R models</span></p>
 <ul class="nav bd-sidenav">
+<li class="toctree-l1"><a class="reference internal" href="01_1_train_NAGuideR_QRILC.html">QRILC</a></li>
+<li class="toctree-l1"><a class="reference internal" href="01_1_train_NAGuideR_IMPSEQ.html">IMPSEQ</a></li>
+<li class="toctree-l1"><a class="reference internal" href="01_1_transfer_NAGuideR_pred.html">transfer NAGuideR pred</a></li>
+<li class="toctree-l1"><a class="reference internal" href="01_1_train_NAGuideR_MICE-NORM.html">MICE-NORM</a></li>
 <li class="toctree-l1"><a class="reference internal" href="01_1_train_NAGuideR_IRM.html">IRM</a></li>
-<li class="toctree-l1"><a class="reference internal" href="01_1_train_NAGuideR_RF.html">RF</a></li>
+<li class="toctree-l1"><a class="reference internal" href="01_1_train_NAGuideR_MSIMPUTE_MNAR.html">MNAR</a></li>
+<li class="toctree-l1"><a class="reference internal" href="01_1_train_NAGuideR_ROWMEDIAN.html">ROWMEDIAN</a></li>
 <li class="toctree-l1"><a class="reference internal" href="01_1_train_NAGuideR_GSIMP.html">GSIMP</a></li>
-<li class="toctree-l1"><a class="reference internal" href="01_1_transfer_NAGuideR_pred.html">transfer NAGuideR pred</a></li>
-<li class="toctree-l1"><a class="reference internal" href="01_1_train_NAGuideR_IMPSEQ.html">IMPSEQ</a></li>
 <li class="toctree-l1"><a class="reference internal" href="01_1_train_NAGuideR_MLE.html">MLE</a></li>
-<li class="toctree-l1"><a class="reference internal" href="01_1_train_NAGuideR_KNN_IMPUTE.html">IMPUTE</a></li>
-<li class="toctree-l1"><a class="reference internal" href="01_1_train_NAGuideR_MICE-NORM.html">MICE-NORM</a></li>
-<li class="toctree-l1"><a class="reference internal" href="01_1_train_NAGuideR_SEQKNN.html">SEQKNN</a></li>
 <li class="toctree-l1"><a class="reference internal" href="01_1_train_NAGuideR_SVDMETHOD.html">SVDMETHOD</a></li>
-<li class="toctree-l1"><a class="reference internal" href="01_1_train_NAGuideR_ROWMEDIAN.html">ROWMEDIAN</a></li>
-<li class="toctree-l1"><a class="reference internal" href="01_1_train_NAGuideR_QRILC.html">QRILC</a></li>
+<li class="toctree-l1"><a class="reference internal" href="01_1_train_NAGuideR_SEQKNN.html">SEQKNN</a></li>
+<li class="toctree-l1"><a class="reference internal" href="01_1_train_NAGuideR_RF.html">RF</a></li>
+<li class="toctree-l1"><a class="reference internal" href="01_1_train_NAGuideR_KNN_IMPUTE.html">IMPUTE</a></li>
 <li class="toctree-l1"><a class="reference internal" href="01_1_train_NAGuideR_TRKNN.html">TRKNN</a></li>
-<li class="toctree-l1"><a class="reference internal" href="01_1_train_NAGuideR_MSIMPUTE_MNAR.html">MNAR</a></li>
 </ul>
 <p aria-level="2" class="caption" role="heading"><span class="caption-text">Imputation model comparison</span></p>
 <ul class="nav bd-sidenav">

01_1_train_CF.html

@@ -49,8 +49,8 @@
     <script>DOCUMENTATION_OPTIONS.pagename = '01_1_train_CF';</script>
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
-    <link rel="next" title="K- Nearest Neighbors (KNN)" href="01_1_train_KNN.html" />
-    <link rel="prev" title="Variational Autoencoder" href="01_1_train_Median.html" />
+    <link rel="next" title="NAGuide R methods" href="01_1_train_NAGuideR_QRILC.html" />
+    <link rel="prev" title="Variational Autoencoder" href="01_1_train_VAE.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
   </head>
@@ -154,27 +154,27 @@
 <p aria-level="2" class="caption" role="heading"><span class="caption-text">PIMMS models</span></p>
 <ul class="current nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="01_1_train_Median.html">Median</a></li>
-<li class="toctree-l1 current active"><a class="current reference internal" href="#">CF</a></li>
+<li class="toctree-l1"><a class="reference internal" href="01_1_train_DAE.html">DAE</a></li>
 <li class="toctree-l1"><a class="reference internal" href="01_1_train_KNN.html">KNN</a></li>
 <li class="toctree-l1"><a class="reference internal" href="01_1_train_VAE.html">VAE</a></li>
-<li class="toctree-l1"><a class="reference internal" href="01_1_train_DAE.html">DAE</a></li>
+<li class="toctree-l1 current active"><a class="current reference internal" href="#">CF</a></li>
 </ul>
 <p aria-level="2" class="caption" role="heading"><span class="caption-text">R models</span></p>
 <ul class="nav bd-sidenav">
+<li class="toctree-l1"><a class="reference internal" href="01_1_train_NAGuideR_QRILC.html">QRILC</a></li>
+<li class="toctree-l1"><a class="reference internal" href="01_1_train_NAGuideR_IMPSEQ.html">IMPSEQ</a></li>
+<li class="toctree-l1"><a class="reference internal" href="01_1_transfer_NAGuideR_pred.html">transfer NAGuideR pred</a></li>
+<li class="toctree-l1"><a class="reference internal" href="01_1_train_NAGuideR_MICE-NORM.html">MICE-NORM</a></li>
 <li class="toctree-l1"><a class="reference internal" href="01_1_train_NAGuideR_IRM.html">IRM</a></li>
-<li class="toctree-l1"><a class="reference internal" href="01_1_train_NAGuideR_RF.html">RF</a></li>
+<li class="toctree-l1"><a class="reference internal" href="01_1_train_NAGuideR_MSIMPUTE_MNAR.html">MNAR</a></li>
+<li class="toctree-l1"><a class="reference internal" href="01_1_train_NAGuideR_ROWMEDIAN.html">ROWMEDIAN</a></li>
 <li class="toctree-l1"><a class="reference internal" href="01_1_train_NAGuideR_GSIMP.html">GSIMP</a></li>
-<li class="toctree-l1"><a class="reference internal" href="01_1_transfer_NAGuideR_pred.html">transfer NAGuideR pred</a></li>
-<li class="toctree-l1"><a class="reference internal" href="01_1_train_NAGuideR_IMPSEQ.html">IMPSEQ</a></li>
 <li class="toctree-l1"><a class="reference internal" href="01_1_train_NAGuideR_MLE.html">MLE</a></li>
-<li class="toctree-l1"><a class="reference internal" href="01_1_train_NAGuideR_KNN_IMPUTE.html">IMPUTE</a></li>
-<li class="toctree-l1"><a class="reference internal" href="01_1_train_NAGuideR_MICE-NORM.html">MICE-NORM</a></li>
-<li class="toctree-l1"><a class="reference internal" href="01_1_train_NAGuideR_SEQKNN.html">SEQKNN</a></li>
 <li class="toctree-l1"><a class="reference internal" href="01_1_train_NAGuideR_SVDMETHOD.html">SVDMETHOD</a></li>
-<li class="toctree-l1"><a class="reference internal" href="01_1_train_NAGuideR_ROWMEDIAN.html">ROWMEDIAN</a></li>
-<li class="toctree-l1"><a class="reference internal" href="01_1_train_NAGuideR_QRILC.html">QRILC</a></li>
+<li class="toctree-l1"><a class="reference internal" href="01_1_train_NAGuideR_SEQKNN.html">SEQKNN</a></li>
+<li class="toctree-l1"><a class="reference internal" href="01_1_train_NAGuideR_RF.html">RF</a></li>
+<li class="toctree-l1"><a class="reference internal" href="01_1_train_NAGuideR_KNN_IMPUTE.html">IMPUTE</a></li>
 <li class="toctree-l1"><a class="reference internal" href="01_1_train_NAGuideR_TRKNN.html">TRKNN</a></li>
-<li class="toctree-l1"><a class="reference internal" href="01_1_train_NAGuideR_MSIMPUTE_MNAR.html">MNAR</a></li>
 </ul>
 <p aria-level="2" class="caption" role="heading"><span class="caption-text">Imputation model comparison</span></p>
 <ul class="nav bd-sidenav">
@@ -879,7 +879,7 @@ <h3>Training<a class="headerlink" href="#training" title="Permalink to this head
         background: #F44336;
     }
 </style>
-</div><div class="output text_html"></div><div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>suggested_lr.valley = 0.00437
+</div><div class="output text_html"></div><div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>suggested_lr.valley = 0.00759
 vaep.plotting - INFO     Saved Figures to runs/example/figures/collab_training
 </pre></div>
 </div>
@@ -911,25 +911,25 @@ <h3>Training<a class="headerlink" href="#training" title="Permalink to this head
   <tbody>
     <tr>
       <td>0</td>
-      <td>6.765793</td>
-      <td>6.017883</td>
+      <td>6.574684</td>
+      <td>5.951456</td>
       <td>00:00</td>
     </tr>
     <tr>
       <td>1</td>
-      <td>6.588053</td>
-      <td>5.816575</td>
+      <td>6.399632</td>
+      <td>5.564786</td>
       <td>00:00</td>
     </tr>
     <tr>
       <td>2</td>
-      <td>6.466160</td>
-      <td>5.728734</td>
+      <td>6.230272</td>
+      <td>5.380595</td>
       <td>00:00</td>
     </tr>
   </tbody>
-</table></div><img alt="_images/77f29face2a139e383af162930f170d19e47d1380d8baf4d0806ee2efed93489.png" src="_images/77f29face2a139e383af162930f170d19e47d1380d8baf4d0806ee2efed93489.png" />
-<img alt="_images/1b177133e6f13777d9f0f66b61dee6ce61e54f3ae5453c10df9b2b7c210b577a.png" src="_images/1b177133e6f13777d9f0f66b61dee6ce61e54f3ae5453c10df9b2b7c210b577a.png" />
+</table></div><img alt="_images/44778b14e4e023d7ef9d5d112b27230e3ad29e4891aea2e5b8007df2de41b21f.png" src="_images/44778b14e4e023d7ef9d5d112b27230e3ad29e4891aea2e5b8007df2de41b21f.png" />
+<img alt="_images/ea1869416bfac985849555290eb07e4cb481af04d1aef4e8b7bbc22d64dda444.png" src="_images/ea1869416bfac985849555290eb07e4cb481af04d1aef4e8b7bbc22d64dda444.png" />
 </div>
 </div>
 </section>
@@ -998,31 +998,31 @@ <h3>Predictions<a class="headerlink" href="#predictions" title="Permalink to thi
       <th>2019_12_18_14_35_Q-Exactive-HF-X-Orbitrap_6070</th>
       <th>GEMIN5</th>
       <td>30.946</td>
-      <td>28.577</td>
+      <td>28.639</td>
     </tr>
     <tr>
       <th>2020_02_28_12_27_Q-Exactive-HF-X-Orbitrap_6070</th>
       <th>AAR2</th>
       <td>27.248</td>
-      <td>28.408</td>
+      <td>28.256</td>
     </tr>
     <tr>
       <th>2020_02_13_03_11_Q-Exactive-HF-X-Orbitrap_6070</th>
       <th>ADAM10</th>
       <td>29.310</td>
-      <td>28.493</td>
+      <td>28.441</td>
     </tr>
     <tr>
       <th>2020_01_04_14_59_Q-Exactive-HF-X-Orbitrap_6070</th>
       <th>NDUFAF4</th>
       <td>24.352</td>
-      <td>28.344</td>
+      <td>28.221</td>
     </tr>
     <tr>
       <th>2020_05_27_13_57_Q-Exactive-HF-X-Orbitrap_6070</th>
       <th>EPN1</th>
       <td>29.250</td>
-      <td>28.408</td>
+      <td>28.403</td>
     </tr>
     <tr>
       <th>...</th>
@@ -1034,31 +1034,31 @@ <h3>Predictions<a class="headerlink" href="#predictions" title="Permalink to thi
       <th>2020_03_01_23_00_Q-Exactive-HF-X-Orbitrap_6070</th>
       <th>PRRC2B</th>
       <td>24.294</td>
-      <td>28.389</td>
+      <td>28.240</td>
     </tr>
     <tr>
       <th>2020_01_04_04_23_Q-Exactive-HF-X-Orbitrap_6070</th>
       <th>ARGLU1</th>
       <td>28.471</td>
-      <td>28.530</td>
+      <td>28.499</td>
     </tr>
     <tr>
       <th>2020_02_18_18_55_Q-Exactive-HF-X-Orbitrap_6070</th>
       <th>GBF1</th>
       <td>29.470</td>
-      <td>28.461</td>
+      <td>28.551</td>
     </tr>
     <tr>
       <th>2019_12_18_14_35_Q-Exactive-HF-X-Orbitrap_6070</th>
       <th>DENR</th>
       <td>27.902</td>
-      <td>28.319</td>
+      <td>28.190</td>
     </tr>
     <tr>
       <th>2020_05_12_21_07_Q-Exactive-HF-X-Orbitrap_6070</th>
       <th>SNRPF</th>
       <td>27.487</td>
-      <td>28.545</td>
+      <td>28.563</td>
     </tr>
   </tbody>
 </table>
@@ -1125,27 +1125,27 @@ <h3>Predictions<a class="headerlink" href="#predictions" title="Permalink to thi
       <th rowspan="5" valign="top">2019_12_18_14_35_Q-Exactive-HF-X-Orbitrap_6070</th>
       <th>ARAF</th>
       <td>23.248</td>
-      <td>28.340</td>
+      <td>28.239</td>
     </tr>
     <tr>
       <th>CENPH</th>
       <td>25.045</td>
-      <td>28.358</td>
+      <td>28.185</td>
     </tr>
     <tr>
       <th>CLPP</th>
       <td>27.745</td>
-      <td>28.407</td>
+      <td>28.272</td>
     </tr>
     <tr>
       <th>GNAI1</th>
       <td>24.335</td>
-      <td>28.365</td>
+      <td>28.217</td>
     </tr>
     <tr>
       <th>KIAA1143</th>
       <td>26.901</td>
-      <td>28.425</td>
+      <td>28.287</td>
     </tr>
     <tr>
       <th>...</th>
@@ -1157,27 +1157,27 @@ <h3>Predictions<a class="headerlink" href="#predictions" title="Permalink to thi
       <th rowspan="5" valign="top">2020_06_02_09_41_Q-Exactive-HF-X-Orbitrap_6070</th>
       <th>NUDT9</th>
       <td>27.658</td>
-      <td>28.579</td>
+      <td>28.536</td>
     </tr>
     <tr>
       <th>PTPN1</th>
       <td>29.024</td>
-      <td>28.618</td>
+      <td>28.678</td>
     </tr>
     <tr>
       <th>RDH13</th>
       <td>28.720</td>
-      <td>28.540</td>
+      <td>28.527</td>
     </tr>
     <tr>
       <th>RNASEH2C</th>
       <td>26.742</td>
-      <td>28.555</td>
+      <td>28.509</td>
     </tr>
     <tr>
       <th>SH3BGRL3</th>
       <td>29.162</td>
-      <td>28.737</td>
+      <td>28.828</td>
     </tr>
   </tbody>
 </table>
@@ -1451,8 +1451,8 @@ <h3>Validation data<a class="headerlink" href="#validation-data" title="Permalin
 <div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>Selected as truth to compare to: observed
 </pre></div>
 </div>
-<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>{&#39;CF&#39;: {&#39;MSE&#39;: 5.72873362862108,
-  &#39;MAE&#39;: 1.9245968625321523,
+<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>{&#39;CF&#39;: {&#39;MSE&#39;: 5.380595083910334,
+  &#39;MAE&#39;: 1.8528898122069692,
   &#39;N&#39;: 859,
   &#39;prop&#39;: 1.0}}
 </pre></div>
@@ -1476,8 +1476,8 @@ <h3>Test Datasplit<a class="headerlink" href="#test-datasplit" title="Permalink
 <div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>Selected as truth to compare to: observed
 </pre></div>
 </div>
-<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>{&#39;CF&#39;: {&#39;MSE&#39;: 6.107743219853425,
-  &#39;MAE&#39;: 2.005634316102109,
+<div class="output text_plain highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>{&#39;CF&#39;: {&#39;MSE&#39;: 5.740732289492064,
+  &#39;MAE&#39;: 1.9336526317271383,
   &#39;N&#39;: 859,
   &#39;prop&#39;: 1.0}}
 </pre></div>
@@ -1535,13 +1535,13 @@ <h3>Test Datasplit<a class="headerlink" href="#test-datasplit" title="Permalink
     <tr>
       <th rowspan="4" valign="top">CF</th>
       <th>MSE</th>
-      <td>5.729</td>
-      <td>6.108</td>
+      <td>5.381</td>
+      <td>5.741</td>
     </tr>
     <tr>
       <th>MAE</th>
-      <td>1.925</td>
-      <td>2.006</td>
+      <td>1.853</td>
+      <td>1.934</td>
     </tr>
     <tr>
       <th>N</th>
@@ -1622,7 +1622,7 @@ <h2>Config<a class="headerlink" href="#config" title="Permalink to this heading"
 
 <div class="prev-next-area">
     <a class="left-prev"
-       href="01_1_train_Median.html"
+       href="01_1_train_VAE.html"
        title="previous page">
       <i class="fa-solid fa-angle-left"></i>
       <div class="prev-next-info">
@@ -1631,11 +1631,11 @@ <h2>Config<a class="headerlink" href="#config" title="Permalink to this heading"
       </div>
     </a>
     <a class="right-next"
-       href="01_1_train_KNN.html"
+       href="01_1_train_NAGuideR_QRILC.html"
        title="next page">
       <div class="prev-next-info">
         <p class="prev-next-subtitle">next</p>
-        <p class="prev-next-title">K- Nearest Neighbors (KNN)</p>
+        <p class="prev-next-title">NAGuide R methods</p>
       </div>
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