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nhsengland · Jul 3, 2024 · 22f5ca1 · 22f5ca1
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diff --git a/404.html b/404.html
@@ -14,7 +14,7 @@
 
 
       <link rel="icon" href="/assets/NHS.svg">
-      <meta name="generator" content="mkdocs-1.6.0, mkdocs-material-9.5.27">
+      <meta name="generator" content="mkdocs-1.6.0, mkdocs-material-9.5.28">
 
 
 
@@ -561,7 +561,7 @@ <h1>404 - Not found</h1>
     <script id="__config" type="application/json">{"base": "/", "features": ["navigation.instant", "navigation.tracking", "navigation.tabs", "navigation.tabs.sticky", "toc.integrate", "navigation.top", "search.suggest", "search.highlight", "search.share", "navigation.footer", "content.action.view", "content.action.edit", "content.code.copy"], "search": "/assets/javascripts/workers/search.b8dbb3d2.min.js", "translations": {"clipboard.copied": "Copied to clipboard", "clipboard.copy": "Copy to clipboard", "search.result.more.one": "1 more on this page", "search.result.more.other": "# more on this page", "search.result.none": "No matching documents", "search.result.one": "1 matching document", "search.result.other": "# matching documents", "search.result.placeholder": "Type to start searching", "search.result.term.missing": "Missing", "select.version": "Select version"}}</script>
 
 
-      <script src="/assets/javascripts/bundle.ad660dcc.min.js"></script>
+      <script src="/assets/javascripts/bundle.fe8b6f2b.min.js"></script>
 
 
   </body>

diff --git a/assets/javascripts/bundle.ad660dcc.min.js → assets/javascripts/bundle.fe8b6f2b.min.js b/assets/javascripts/bundle.ad660dcc.min.js → assets/javascripts/bundle.fe8b6f2b.min.js
diff --git a/...ts/javascripts/bundle.ad660dcc.min.js.map → ...ts/javascripts/bundle.fe8b6f2b.min.js.map b/...ts/javascripts/bundle.ad660dcc.min.js.map → ...ts/javascripts/bundle.fe8b6f2b.min.js.map
diff --git a/functions/index.html b/functions/index.html
@@ -16,7 +16,7 @@
 
 
       <link rel="icon" href="../assets/NHS.svg">
-      <meta name="generator" content="mkdocs-1.6.0, mkdocs-material-9.5.27">
+      <meta name="generator" content="mkdocs-1.6.0, mkdocs-material-9.5.28">
 
 
 
@@ -1488,7 +1488,7 @@ <h2 id="src.utils.functions.scale_numeric_features" class="doc doc-heading">
     <script id="__config" type="application/json">{"base": "..", "features": ["navigation.instant", "navigation.tracking", "navigation.tabs", "navigation.tabs.sticky", "toc.integrate", "navigation.top", "search.suggest", "search.highlight", "search.share", "navigation.footer", "content.action.view", "content.action.edit", "content.code.copy"], "search": "../assets/javascripts/workers/search.b8dbb3d2.min.js", "translations": {"clipboard.copied": "Copied to clipboard", "clipboard.copy": "Copy to clipboard", "search.result.more.one": "1 more on this page", "search.result.more.other": "# more on this page", "search.result.none": "No matching documents", "search.result.one": "1 matching document", "search.result.other": "# matching documents", "search.result.placeholder": "Type to start searching", "search.result.term.missing": "Missing", "select.version": "Select version"}}</script>
 
 
-      <script src="../assets/javascripts/bundle.ad660dcc.min.js"></script>
+      <script src="../assets/javascripts/bundle.fe8b6f2b.min.js"></script>
 
 
   </body>

diff --git a/getting_started/index.html b/getting_started/index.html
@@ -18,7 +18,7 @@
 
 
       <link rel="icon" href="../assets/NHS.svg">
-      <meta name="generator" content="mkdocs-1.6.0, mkdocs-material-9.5.27">
+      <meta name="generator" content="mkdocs-1.6.0, mkdocs-material-9.5.28">
 
 
 
@@ -737,7 +737,7 @@ <h3 id="1-extracting-the-data">1. Extracting the data</h3>
 <p>Example:</p>
 <div class="language-text highlight"><pre><span></span><code><span id="__span-1-1"><a id="__codelineno-1-1" name="__codelineno-1-1" href="#__codelineno-1-1"></a>extract_data.py /path/to/data/  -o /data/extracted_data --event_tables labevents vitalsign --sample 1000 --lazy --labitems labitems.txt
 </span></code></pre></div>
-<p>This command will read from the /data/mimic directory and extract relevant events from the MIMIC-IV hosp/labevents.csv and ed/vitalsign.csv for 1000 stays. Output files will be saved under the <code>/data/extracted_data</code> folder.</p>
+<p>This command will read from the <code>/data/mimic</code> directory and extract relevant events from the MIMIC-IV hosp/labevents.csv and ed/vitalsign.csv for 1000 stays. Output files will be saved under the <code>/data/extracted_data</code> folder.</p>
 <h3 id="2-preparing-the-data">2. Preparing the data</h3>
 <p>Once these core files have been downloaded, run <code>prepare_data.py</code> to create a dictionary (key = hadm_id, values = dataframes of preprocessed data) for model training and evaluation. The resulting file will be called <strong><code>processed_data.pkl</code></strong> and is required for downstream analysis scripts.</p>
 <p>Usage:
@@ -867,7 +867,7 @@ <h2 id="general-tips">General Tips</h2>
     <script id="__config" type="application/json">{"base": "..", "features": ["navigation.instant", "navigation.tracking", "navigation.tabs", "navigation.tabs.sticky", "toc.integrate", "navigation.top", "search.suggest", "search.highlight", "search.share", "navigation.footer", "content.action.view", "content.action.edit", "content.code.copy"], "search": "../assets/javascripts/workers/search.b8dbb3d2.min.js", "translations": {"clipboard.copied": "Copied to clipboard", "clipboard.copy": "Copy to clipboard", "search.result.more.one": "1 more on this page", "search.result.more.other": "# more on this page", "search.result.none": "No matching documents", "search.result.one": "1 matching document", "search.result.other": "# matching documents", "search.result.placeholder": "Type to start searching", "search.result.term.missing": "Missing", "select.version": "Select version"}}</script>
 
 
-      <script src="../assets/javascripts/bundle.ad660dcc.min.js"></script>
+      <script src="../assets/javascripts/bundle.fe8b6f2b.min.js"></script>
 
 
   </body>

diff --git a/index.html b/index.html
@@ -16,7 +16,7 @@
 
 
       <link rel="icon" href="assets/NHS.svg">
-      <meta name="generator" content="mkdocs-1.6.0, mkdocs-material-9.5.27">
+      <meta name="generator" content="mkdocs-1.6.0, mkdocs-material-9.5.28">
 
 
 
@@ -731,7 +731,7 @@ <h2 id="running-experiments">Running experiments</h2>
     <script id="__config" type="application/json">{"base": ".", "features": ["navigation.instant", "navigation.tracking", "navigation.tabs", "navigation.tabs.sticky", "toc.integrate", "navigation.top", "search.suggest", "search.highlight", "search.share", "navigation.footer", "content.action.view", "content.action.edit", "content.code.copy"], "search": "assets/javascripts/workers/search.b8dbb3d2.min.js", "translations": {"clipboard.copied": "Copied to clipboard", "clipboard.copy": "Copy to clipboard", "search.result.more.one": "1 more on this page", "search.result.more.other": "# more on this page", "search.result.none": "No matching documents", "search.result.one": "1 matching document", "search.result.other": "# matching documents", "search.result.placeholder": "Type to start searching", "search.result.term.missing": "Missing", "select.version": "Select version"}}</script>
 
 
-      <script src="assets/javascripts/bundle.ad660dcc.min.js"></script>
+      <script src="assets/javascripts/bundle.fe8b6f2b.min.js"></script>
 
 
   </body>

diff --git a/mimiciv/index.html b/mimiciv/index.html
@@ -18,7 +18,7 @@
 
 
       <link rel="icon" href="../assets/NHS.svg">
-      <meta name="generator" content="mkdocs-1.6.0, mkdocs-material-9.5.27">
+      <meta name="generator" content="mkdocs-1.6.0, mkdocs-material-9.5.28">
 
 
 
@@ -2680,7 +2680,7 @@ <h2 id="src.utils.mimiciv.read_stays_table" class="doc doc-heading">
     <script id="__config" type="application/json">{"base": "..", "features": ["navigation.instant", "navigation.tracking", "navigation.tabs", "navigation.tabs.sticky", "toc.integrate", "navigation.top", "search.suggest", "search.highlight", "search.share", "navigation.footer", "content.action.view", "content.action.edit", "content.code.copy"], "search": "../assets/javascripts/workers/search.b8dbb3d2.min.js", "translations": {"clipboard.copied": "Copied to clipboard", "clipboard.copy": "Copy to clipboard", "search.result.more.one": "1 more on this page", "search.result.more.other": "# more on this page", "search.result.none": "No matching documents", "search.result.one": "1 matching document", "search.result.other": "# matching documents", "search.result.placeholder": "Type to start searching", "search.result.term.missing": "Missing", "select.version": "Select version"}}</script>
 
 
-      <script src="../assets/javascripts/bundle.ad660dcc.min.js"></script>
+      <script src="../assets/javascripts/bundle.fe8b6f2b.min.js"></script>
 
 
   </body>

diff --git a/preprocessing/index.html b/preprocessing/index.html
@@ -18,7 +18,7 @@
 
 
       <link rel="icon" href="../assets/NHS.svg">
-      <meta name="generator" content="mkdocs-1.6.0, mkdocs-material-9.5.27">
+      <meta name="generator" content="mkdocs-1.6.0, mkdocs-material-9.5.28">
 
 
 
@@ -1393,7 +1393,7 @@ <h2 id="src.utils.preprocessing.process_text_to_embeddings" class="doc doc-headi
 </span><span id="__span-0-172"><a id="__codelineno-0-172" name="__codelineno-0-172"></a>        <span class="n">hadm_id</span> <span class="o">=</span> <span class="n">row</span><span class="p">[</span><span class="s2">&quot;hadm_id&quot;</span><span class="p">]</span>
 </span><span id="__span-0-173"><a id="__codelineno-0-173" name="__codelineno-0-173"></a>        <span class="n">text</span> <span class="o">=</span> <span class="n">row</span><span class="p">[</span><span class="s2">&quot;subtext&quot;</span><span class="p">]</span>
 </span><span id="__span-0-174"><a id="__codelineno-0-174" name="__codelineno-0-174"></a>
-</span><span id="__span-0-175"><a id="__codelineno-0-175" name="__codelineno-0-175"></a>        <span class="c1"># Turn text into sentences</span>
+</span><span id="__span-0-175"><a id="__codelineno-0-175" name="__codelineno-0-175"></a>        <span class="c1"># Tokenize text into sentences</span>
 </span><span id="__span-0-176"><a id="__codelineno-0-176" name="__codelineno-0-176"></a>        <span class="n">doc</span> <span class="o">=</span> <span class="n">nlp</span><span class="p">(</span><span class="n">text</span><span class="p">)</span>
 </span><span id="__span-0-177"><a id="__codelineno-0-177" name="__codelineno-0-177"></a>        <span class="n">sentences</span> <span class="o">=</span> <span class="p">[</span><span class="n">sent</span><span class="o">.</span><span class="n">text</span> <span class="k">for</span> <span class="n">sent</span> <span class="ow">in</span> <span class="n">doc</span><span class="o">.</span><span class="n">sents</span><span class="p">]</span>
 </span><span id="__span-0-178"><a id="__codelineno-0-178" name="__codelineno-0-178"></a>
@@ -1981,7 +1981,7 @@ <h2 id="src.utils.preprocessing.transform_race" class="doc doc-heading">
     <script id="__config" type="application/json">{"base": "..", "features": ["navigation.instant", "navigation.tracking", "navigation.tabs", "navigation.tabs.sticky", "toc.integrate", "navigation.top", "search.suggest", "search.highlight", "search.share", "navigation.footer", "content.action.view", "content.action.edit", "content.code.copy"], "search": "../assets/javascripts/workers/search.b8dbb3d2.min.js", "translations": {"clipboard.copied": "Copied to clipboard", "clipboard.copy": "Copy to clipboard", "search.result.more.one": "1 more on this page", "search.result.more.other": "# more on this page", "search.result.none": "No matching documents", "search.result.one": "1 matching document", "search.result.other": "# matching documents", "search.result.placeholder": "Type to start searching", "search.result.term.missing": "Missing", "select.version": "Select version"}}</script>
 
 
-      <script src="../assets/javascripts/bundle.ad660dcc.min.js"></script>
+      <script src="../assets/javascripts/bundle.fe8b6f2b.min.js"></script>
 
 
   </body>

diff --git a/scripts/gen_ref_pages.py b/scripts/gen_ref_pages.py
diff --git a/search/search_index.json b/search/search_index.json
diff --git a/sitemap.xml.gz b/sitemap.xml.gz