deploy: 2c67655

.buildinfo

@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 4efea0e36b6414411d20c7ff672ac55f
+config: 37341b2db80fe12eb750b88ba76a4dd1
 tags: 645f666f9bcd5a90fca523b33c5a78b7

_downloads/2932d6ac7842b6d781c27c5737ae52fa/plot_marginal_cumulative_incidence_estimation.ipynb

@@ -22,7 +22,7 @@
       "cell_type": "markdown",
       "metadata": {},
       "source": [
-        "Since we know the true distribution of the data, we can compute the\ntheoretical cumulative incidence functions (CIFs) by integrating the hazard\nfunctions. The CIFs are the probability of experiencing the event of interest\nbefore time t, given that the subject has not experienced any other event\nbefore time t.\n\nThe following function computes the [hazard function of a Weibull\ndistribution](https://en.wikipedia.org/wiki/Weibull_distribution):\n\n"
+        "Since we know the true distribution of the data, we can compute the\ntheoretical cumulative incidence functions (CIFs) by integrating the hazard\nfunctions. The CIFs are the probability of experiencing the event of interest\nbefore time t, given that the subject has not experienced any other event\nbefore time t.\n\nThe following function computes the hazard function of a [Weibull\ndistribution](https://en.wikipedia.org/wiki/Weibull_distribution):\n\n"
       ]
     },
     {
@@ -136,7 +136,7 @@
       "name": "python",
       "nbconvert_exporter": "python",
       "pygments_lexer": "ipython3",
-      "version": "3.10.12"
+      "version": "3.10.13"
     }
   },
   "nbformat": 4,

_downloads/878bb6ffe7fba36a0655277b8151e4cd/plot_marginal_cumulative_incidence_estimation.py

@@ -82,8 +82,8 @@
 # before time t, given that the subject has not experienced any other event
 # before time t.
 #
-# The following function computes the [hazard function of a Weibull
-# distribution](https://en.wikipedia.org/wiki/Weibull_distribution):
+# The following function computes the hazard function of a `Weibull
+# distribution <https://en.wikipedia.org/wiki/Weibull_distribution>`_:
 
 
 def weibull_hazard(t, shape=1.0, scale=1.0, **ignored_kwargs):

_sources/auto_examples/plot_marginal_cumulative_incidence_estimation.rst.txt

@@ -121,8 +121,8 @@ functions. The CIFs are the probability of experiencing the event of interest
 before time t, given that the subject has not experienced any other event
 before time t.
 
-The following function computes the [hazard function of a Weibull
-distribution](https://en.wikipedia.org/wiki/Weibull_distribution):
+The following function computes the hazard function of a `Weibull
+distribution <https://en.wikipedia.org/wiki/Weibull_distribution>`_:
 
 .. GENERATED FROM PYTHON SOURCE LINES 87-100
 
@@ -368,7 +368,7 @@ the large time horizons:
 
 .. rst-class:: sphx-glr-timing
 
-   **Total running time of the script:** ( 0 minutes  30.220 seconds)
+   **Total running time of the script:** (0 minutes 26.655 seconds)
 
 
 .. _sphx_glr_download_auto_examples_plot_marginal_cumulative_incidence_estimation.py:

_sources/auto_examples/sg_execution_times.rst.txt

@@ -6,8 +6,8 @@
 
 Computation times
 =================
-**00:30.220** total execution time for **auto_examples** files:
+**00:26.655** total execution time for **auto_examples** files:
 
 +---------------------------------------------------------------------------------------------------------------------------------------+-----------+--------+
-| :ref:`sphx_glr_auto_examples_plot_marginal_cumulative_incidence_estimation.py` (``plot_marginal_cumulative_incidence_estimation.py``) | 00:30.220 | 0.0 MB |
+| :ref:`sphx_glr_auto_examples_plot_marginal_cumulative_incidence_estimation.py` (``plot_marginal_cumulative_incidence_estimation.py``) | 00:26.655 | 0.0 MB |
 +---------------------------------------------------------------------------------------------------------------------------------------+-----------+--------+

_static/basic.css

@@ -237,6 +237,10 @@ a.headerlink {
     visibility: hidden;
 }
 
+a:visited {
+    color: #551A8B;
+}
+
 h1:hover > a.headerlink,
 h2:hover > a.headerlink,
 h3:hover > a.headerlink,
@@ -670,6 +674,16 @@ dd {
     margin-left: 30px;
 }
 
+.sig dd {
+    margin-top: 0px;
+    margin-bottom: 0px;
+}
+
+.sig dl {
+    margin-top: 0px;
+    margin-bottom: 0px;
+}
+
 dl > dd:last-child,
 dl > dd:last-child > :last-child {
     margin-bottom: 0;
@@ -738,6 +752,14 @@ abbr, acronym {
     cursor: help;
 }
 
+.translated {
+    background-color: rgba(207, 255, 207, 0.2)
+}
+
+.untranslated {
+    background-color: rgba(255, 207, 207, 0.2)
+}
+
 /* -- code displays --------------------------------------------------------- */
 
 pre {

_static/documentation_options.js

@@ -1,5 +1,4 @@
-var DOCUMENTATION_OPTIONS = {
-    URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
+const DOCUMENTATION_OPTIONS = {
     VERSION: '0.1.0',
     LANGUAGE: 'en',
     COLLAPSE_INDEX: false,

_static/searchtools.js

@@ -57,12 +57,12 @@ const _removeChildren = (element) => {
 const _escapeRegExp = (string) =>
   string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string
 
-const _displayItem = (item, searchTerms) => {
+const _displayItem = (item, searchTerms, highlightTerms) => {
   const docBuilder = DOCUMENTATION_OPTIONS.BUILDER;
-  const docUrlRoot = DOCUMENTATION_OPTIONS.URL_ROOT;
   const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX;
   const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX;
   const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY;
+  const contentRoot = document.documentElement.dataset.content_root;
 
   const [docName, title, anchor, descr, score, _filename] = item;
 
@@ -75,20 +75,24 @@ const _displayItem = (item, searchTerms) => {
     if (dirname.match(/\/index\/$/))
       dirname = dirname.substring(0, dirname.length - 6);
     else if (dirname === "index/") dirname = "";
-    requestUrl = docUrlRoot + dirname;
+    requestUrl = contentRoot + dirname;
     linkUrl = requestUrl;
   } else {
     // normal html builders
-    requestUrl = docUrlRoot + docName + docFileSuffix;
+    requestUrl = contentRoot + docName + docFileSuffix;
     linkUrl = docName + docLinkSuffix;
   }
   let linkEl = listItem.appendChild(document.createElement("a"));
   linkEl.href = linkUrl + anchor;
   linkEl.dataset.score = score;
   linkEl.innerHTML = title;
-  if (descr)
+  if (descr) {
     listItem.appendChild(document.createElement("span")).innerHTML =
       " (" + descr + ")";
+    // highlight search terms in the description
+    if (SPHINX_HIGHLIGHT_ENABLED)  // set in sphinx_highlight.js
+      highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted"));
+  }
   else if (showSearchSummary)
     fetch(requestUrl)
       .then((responseData) => responseData.text())
@@ -97,6 +101,9 @@ const _displayItem = (item, searchTerms) => {
           listItem.appendChild(
             Search.makeSearchSummary(data, searchTerms)
           );
+        // highlight search terms in the summary
+        if (SPHINX_HIGHLIGHT_ENABLED)  // set in sphinx_highlight.js
+          highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted"));
       });
   Search.output.appendChild(listItem);
 };
@@ -115,14 +122,15 @@ const _finishSearch = (resultCount) => {
 const _displayNextItem = (
   results,
   resultCount,
-  searchTerms
+  searchTerms,
+  highlightTerms,
 ) => {
   // results left, load the summary and display it
   // this is intended to be dynamic (don't sub resultsCount)
   if (results.length) {
-    _displayItem(results.pop(), searchTerms);
+    _displayItem(results.pop(), searchTerms, highlightTerms);
     setTimeout(
-      () => _displayNextItem(results, resultCount, searchTerms),
+      () => _displayNextItem(results, resultCount, searchTerms, highlightTerms),
       5
     );
   }
@@ -360,7 +368,7 @@ const Search = {
     // console.info("search results:", Search.lastresults);
 
     // print the results
-    _displayNextItem(results, results.length, searchTerms);
+    _displayNextItem(results, results.length, searchTerms, highlightTerms);
   },
 
   /**

_static/sg_gallery-dataframe.css

@@ -19,6 +19,7 @@ table.dataframe {
   color: var(--sg-text-color);
   font-size: 12px;
   table-layout: fixed;
+  width: auto;
 }
 table.dataframe thead {
   border-bottom: 1px solid var(--sg-text-color);

_static/sphinx_highlight.js

@@ -29,14 +29,19 @@ const _highlight = (node, addItems, text, className) => {
       }
 
       span.appendChild(document.createTextNode(val.substr(pos, text.length)));
+      const rest = document.createTextNode(val.substr(pos + text.length));
       parent.insertBefore(
         span,
         parent.insertBefore(
-          document.createTextNode(val.substr(pos + text.length)),
+          rest,
           node.nextSibling
         )
       );
       node.nodeValue = val.substr(0, pos);
+      /* There may be more occurrences of search term in this node. So call this
+       * function recursively on the remaining fragment.
+       */
+      _highlight(rest, addItems, text, className);
 
       if (isInSVG) {
         const rect = document.createElementNS(
@@ -140,5 +145,10 @@ const SphinxHighlight = {
   },
 };
 
-_ready(SphinxHighlight.highlightSearchWords);
-_ready(SphinxHighlight.initEscapeListener);
+_ready(() => {
+  /* Do not call highlightSearchWords() when we are on the search page.
+   * It will highlight words from the *previous* search query.
+   */
+  if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords();
+  SphinxHighlight.initEscapeListener();
+});

api.html

@@ -28,19 +28,19 @@
 <link rel="preload" as="font" type="font/woff2" crossorigin href="_static/vendor/fontawesome/6.1.2/webfonts/fa-brands-400.woff2" />
 <link rel="preload" as="font" type="font/woff2" crossorigin href="_static/vendor/fontawesome/6.1.2/webfonts/fa-regular-400.woff2" />
 
-    <link rel="stylesheet" type="text/css" href="_static/pygments.css" />
-    <link rel="stylesheet" type="text/css" href="_static/sg_gallery.css" />
-    <link rel="stylesheet" type="text/css" href="_static/sg_gallery-binder.css" />
-    <link rel="stylesheet" type="text/css" href="_static/sg_gallery-dataframe.css" />
-    <link rel="stylesheet" type="text/css" href="_static/sg_gallery-rendered-html.css" />
+    <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=a746c00c" />
+    <link rel="stylesheet" type="text/css" href="_static/sg_gallery.css?v=61a4c737" />
+    <link rel="stylesheet" type="text/css" href="_static/sg_gallery-binder.css?v=f4aeca0c" />
+    <link rel="stylesheet" type="text/css" href="_static/sg_gallery-dataframe.css?v=2082cf3c" />
+    <link rel="stylesheet" type="text/css" href="_static/sg_gallery-rendered-html.css?v=1277b6f3" />
 
   <!-- Pre-loaded scripts that we'll load fully later -->
   <link rel="preload" as="script" href="_static/scripts/bootstrap.js?digest=e353d410970836974a52" />
 <link rel="preload" as="script" href="_static/scripts/pydata-sphinx-theme.js?digest=e353d410970836974a52" />
 
-    <script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
-    <script src="_static/doctools.js"></script>
-    <script src="_static/sphinx_highlight.js"></script>
+    <script src="_static/documentation_options.js?v=38b66d78"></script>
+    <script src="_static/doctools.js?v=888ff710"></script>
+    <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script>DOCUMENTATION_OPTIONS.pagename = 'api';</script>
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
@@ -327,11 +327,11 @@
                 <article class="bd-article" role="main">
 
   <section id="api">
-<h1>API<a class="headerlink" href="#api" title="Permalink to this heading">#</a></h1>
+<h1>API<a class="headerlink" href="#api" title="Link to this heading">#</a></h1>
 <p>This page lists all the public functions and classes of the <cite>hazardous</cite>
 package:</p>
 <section id="estimators">
-<h2>Estimators<a class="headerlink" href="#estimators" title="Permalink to this heading">#</a></h2>
+<h2>Estimators<a class="headerlink" href="#estimators" title="Link to this heading">#</a></h2>
 <table class="autosummary longtable table autosummary">
 <tbody>
 <tr class="row-odd"><td><p><a class="reference internal" href="generated/hazardous.GradientBoostingIncidence.html#hazardous.GradientBoostingIncidence" title="hazardous.GradientBoostingIncidence"><code class="xref py py-obj docutils literal notranslate"><span class="pre">GradientBoostingIncidence</span></code></a></p></td>
@@ -341,7 +341,7 @@ <h2>Estimators<a class="headerlink" href="#estimators" title="Permalink to this
 </table>
 </section>
 <section id="metrics">
-<h2>Metrics<a class="headerlink" href="#metrics" title="Permalink to this heading">#</a></h2>
+<h2>Metrics<a class="headerlink" href="#metrics" title="Link to this heading">#</a></h2>
 <table class="autosummary longtable table autosummary">
 <tbody>
 <tr class="row-odd"><td><p><a class="reference internal" href="generated/hazardous.metrics.brier_score_survival.html#hazardous.metrics.brier_score_survival" title="hazardous.metrics.brier_score_survival"><code class="xref py py-obj docutils literal notranslate"><span class="pre">metrics.brier_score_survival</span></code></a></p></td>
@@ -360,7 +360,7 @@ <h2>Metrics<a class="headerlink" href="#metrics" title="Permalink to this headin
 </table>
 </section>
 <section id="datasets">
-<h2>Datasets<a class="headerlink" href="#datasets" title="Permalink to this heading">#</a></h2>
+<h2>Datasets<a class="headerlink" href="#datasets" title="Link to this heading">#</a></h2>
 <table class="autosummary longtable table autosummary">
 <tbody>
 <tr class="row-odd"><td><p><a class="reference internal" href="generated/hazardous.data.make_synthetic_competing_weibull.html#hazardous.data.make_synthetic_competing_weibull" title="hazardous.data.make_synthetic_competing_weibull"><code class="xref py py-obj docutils literal notranslate"><span class="pre">data.make_synthetic_competing_weibull</span></code></a></p></td>
@@ -370,7 +370,7 @@ <h2>Datasets<a class="headerlink" href="#datasets" title="Permalink to this head
 </table>
 </section>
 <section id="inverse-probability-censoring-weight">
-<h2>Inverse Probability Censoring Weight<a class="headerlink" href="#inverse-probability-censoring-weight" title="Permalink to this heading">#</a></h2>
+<h2>Inverse Probability Censoring Weight<a class="headerlink" href="#inverse-probability-censoring-weight" title="Link to this heading">#</a></h2>
 <table class="autosummary longtable table autosummary">
 <tbody>
 <tr class="row-odd"><td><p><a class="reference internal" href="generated/hazardous.IPCWEstimator.html#hazardous.IPCWEstimator" title="hazardous.IPCWEstimator"><code class="xref py py-obj docutils literal notranslate"><span class="pre">IPCWEstimator</span></code></a></p></td>
@@ -475,7 +475,7 @@ <h2>Inverse Probability Censoring Weight<a class="headerlink" href="#inverse-pro
 
         <div class="footer-item">
   <p class="sphinx-version">
-    Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 7.0.1.
+    Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 7.2.6.
     <br/>
   </p>
 </div>

auto_examples/index.html

@@ -28,19 +28,19 @@
 <link rel="preload" as="font" type="font/woff2" crossorigin href="../_static/vendor/fontawesome/6.1.2/webfonts/fa-brands-400.woff2" />
 <link rel="preload" as="font" type="font/woff2" crossorigin href="../_static/vendor/fontawesome/6.1.2/webfonts/fa-regular-400.woff2" />
 
-    <link rel="stylesheet" type="text/css" href="../_static/pygments.css" />
-    <link rel="stylesheet" type="text/css" href="../_static/sg_gallery.css" />
-    <link rel="stylesheet" type="text/css" href="../_static/sg_gallery-binder.css" />
-    <link rel="stylesheet" type="text/css" href="../_static/sg_gallery-dataframe.css" />
-    <link rel="stylesheet" type="text/css" href="../_static/sg_gallery-rendered-html.css" />
+    <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=a746c00c" />
+    <link rel="stylesheet" type="text/css" href="../_static/sg_gallery.css?v=61a4c737" />
+    <link rel="stylesheet" type="text/css" href="../_static/sg_gallery-binder.css?v=f4aeca0c" />
+    <link rel="stylesheet" type="text/css" href="../_static/sg_gallery-dataframe.css?v=2082cf3c" />
+    <link rel="stylesheet" type="text/css" href="../_static/sg_gallery-rendered-html.css?v=1277b6f3" />
 
   <!-- Pre-loaded scripts that we'll load fully later -->
   <link rel="preload" as="script" href="../_static/scripts/bootstrap.js?digest=e353d410970836974a52" />
 <link rel="preload" as="script" href="../_static/scripts/pydata-sphinx-theme.js?digest=e353d410970836974a52" />
 
-    <script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js"></script>
-    <script src="../_static/doctools.js"></script>
-    <script src="../_static/sphinx_highlight.js"></script>
+    <script src="../_static/documentation_options.js?v=38b66d78"></script>
+    <script src="../_static/doctools.js?v=888ff710"></script>
+    <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script>DOCUMENTATION_OPTIONS.pagename = 'auto_examples/index';</script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
@@ -315,7 +315,7 @@
                 <article class="bd-article" role="main">
 
   <section id="example-gallery">
-<h1>Example gallery<a class="headerlink" href="#example-gallery" title="Permalink to this heading">#</a></h1>
+<h1>Example gallery<a class="headerlink" href="#example-gallery" title="Link to this heading">#</a></h1>
 <p>Below is a gallery of examples on how to use <cite>hazardous</cite> for predictive
 competive risk analysis problems.</p>
 <div class="sphx-glr-thumbnails"><div class="sphx-glr-thumbcontainer" tooltip="This example demonstrates how to estimate the marginal cumulative incidence using hazardous.Gra..."><img alt="" src="../_images/sphx_glr_plot_marginal_cumulative_incidence_estimation_thumb.png" />
@@ -415,7 +415,7 @@ <h1>Example gallery<a class="headerlink" href="#example-gallery" title="Permalin
 
         <div class="footer-item">
   <p class="sphinx-version">
-    Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 7.0.1.
+    Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 7.2.6.
     <br/>
   </p>
 </div>