846 lines
No EOL
35 KiB
HTML
846 lines
No EOL
35 KiB
HTML
<!DOCTYPE html>
|
||
<html xmlns="http://www.w3.org/1999/xhtml" lang="fr" xml:lang="fr"><head>
|
||
|
||
<meta charset="utf-8">
|
||
<meta name="generator" content="quarto-1.7.22">
|
||
|
||
<meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
|
||
|
||
<meta name="author" content="Louis Lacoste">
|
||
|
||
<title>Bilan semaine 25 2025 : 16 juin - 20 juin – Suivi de la thèse</title>
|
||
<style>
|
||
code{white-space: pre-wrap;}
|
||
span.smallcaps{font-variant: small-caps;}
|
||
div.columns{display: flex; gap: min(4vw, 1.5em);}
|
||
div.column{flex: auto; overflow-x: auto;}
|
||
div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;}
|
||
ul.task-list{list-style: none;}
|
||
ul.task-list li input[type="checkbox"] {
|
||
width: 0.8em;
|
||
margin: 0 0.8em 0.2em -1em; /* quarto-specific, see https://github.com/quarto-dev/quarto-cli/issues/4556 */
|
||
vertical-align: middle;
|
||
}
|
||
/* CSS for citations */
|
||
div.csl-bib-body { }
|
||
div.csl-entry {
|
||
clear: both;
|
||
margin-bottom: 0em;
|
||
}
|
||
.hanging-indent div.csl-entry {
|
||
margin-left:2em;
|
||
text-indent:-2em;
|
||
}
|
||
div.csl-left-margin {
|
||
min-width:2em;
|
||
float:left;
|
||
}
|
||
div.csl-right-inline {
|
||
margin-left:2em;
|
||
padding-left:1em;
|
||
}
|
||
div.csl-indent {
|
||
margin-left: 2em;
|
||
}</style>
|
||
|
||
|
||
<script src="../../site_libs/quarto-nav/quarto-nav.js"></script>
|
||
<script src="../../site_libs/quarto-nav/headroom.min.js"></script>
|
||
<script src="../../site_libs/clipboard/clipboard.min.js"></script>
|
||
<script src="../../site_libs/quarto-search/autocomplete.umd.js"></script>
|
||
<script src="../../site_libs/quarto-search/fuse.min.js"></script>
|
||
<script src="../../site_libs/quarto-search/quarto-search.js"></script>
|
||
<meta name="quarto:offset" content="../../">
|
||
<script src="../../site_libs/quarto-html/quarto.js" type="module"></script>
|
||
<script src="../../site_libs/quarto-html/tabsets/tabsets.js" type="module"></script>
|
||
<script src="../../site_libs/quarto-html/popper.min.js"></script>
|
||
<script src="../../site_libs/quarto-html/tippy.umd.min.js"></script>
|
||
<script src="../../site_libs/quarto-html/anchor.min.js"></script>
|
||
<link href="../../site_libs/quarto-html/tippy.css" rel="stylesheet">
|
||
<link href="../../site_libs/quarto-html/quarto-syntax-highlighting-7b4406b7675125bc2ba204020e191172.css" rel="stylesheet" id="quarto-text-highlighting-styles">
|
||
<script src="../../site_libs/bootstrap/bootstrap.min.js"></script>
|
||
<link href="../../site_libs/bootstrap/bootstrap-icons.css" rel="stylesheet">
|
||
<link href="../../site_libs/bootstrap/bootstrap-b7709e3ceabf99e2647fc5ea1b9a158c.min.css" rel="stylesheet" append-hash="true" id="quarto-bootstrap" data-mode="light">
|
||
<script id="quarto-search-options" type="application/json">{
|
||
"location": "navbar",
|
||
"copy-button": false,
|
||
"collapse-after": 3,
|
||
"panel-placement": "end",
|
||
"type": "overlay",
|
||
"limit": 50,
|
||
"keyboard-shortcut": [
|
||
"f",
|
||
"/",
|
||
"s"
|
||
],
|
||
"show-item-context": false,
|
||
"language": {
|
||
"search-no-results-text": "Pas de résultats",
|
||
"search-matching-documents-text": "documents trouvés",
|
||
"search-copy-link-title": "Copier le lien vers la recherche",
|
||
"search-hide-matches-text": "Cacher les correspondances additionnelles",
|
||
"search-more-match-text": "correspondance de plus dans ce document",
|
||
"search-more-matches-text": "correspondances de plus dans ce document",
|
||
"search-clear-button-title": "Effacer",
|
||
"search-text-placeholder": "",
|
||
"search-detached-cancel-button-title": "Annuler",
|
||
"search-submit-button-title": "Envoyer",
|
||
"search-label": "Recherche"
|
||
}
|
||
}</script>
|
||
|
||
<script>window.backupDefine = window.define; window.define = undefined;</script><script src="https://cdn.jsdelivr.net/npm/katex@latest/dist/katex.min.js"></script>
|
||
<script>document.addEventListener("DOMContentLoaded", function () {
|
||
var mathElements = document.getElementsByClassName("math");
|
||
var macros = [];
|
||
for (var i = 0; i < mathElements.length; i++) {
|
||
var texText = mathElements[i].firstChild;
|
||
if (mathElements[i].tagName == "SPAN") {
|
||
katex.render(texText.data, mathElements[i], {
|
||
displayMode: mathElements[i].classList.contains('display'),
|
||
throwOnError: false,
|
||
macros: macros,
|
||
fleqn: false
|
||
});
|
||
}}});
|
||
</script>
|
||
<script>window.define = window.backupDefine; window.backupDefine = undefined;</script><link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/katex@latest/dist/katex.min.css">
|
||
|
||
<script type="text/javascript">
|
||
const typesetMath = (el) => {
|
||
if (window.MathJax) {
|
||
// MathJax Typeset
|
||
window.MathJax.typeset([el]);
|
||
} else if (window.katex) {
|
||
// KaTeX Render
|
||
var mathElements = el.getElementsByClassName("math");
|
||
var macros = [];
|
||
for (var i = 0; i < mathElements.length; i++) {
|
||
var texText = mathElements[i].firstChild;
|
||
if (mathElements[i].tagName == "SPAN") {
|
||
window.katex.render(texText.data, mathElements[i], {
|
||
displayMode: mathElements[i].classList.contains('display'),
|
||
throwOnError: false,
|
||
macros: macros,
|
||
fleqn: false
|
||
});
|
||
}
|
||
}
|
||
}
|
||
}
|
||
window.Quarto = {
|
||
typesetMath
|
||
};
|
||
</script>
|
||
|
||
</head>
|
||
|
||
<body class="nav-fixed quarto-light">
|
||
|
||
<div id="quarto-search-results"></div>
|
||
<header id="quarto-header" class="headroom fixed-top quarto-banner">
|
||
<nav class="navbar navbar-expand-lg " data-bs-theme="dark">
|
||
<div class="navbar-container container-fluid">
|
||
<div class="navbar-brand-container mx-auto">
|
||
<a class="navbar-brand" href="../../index.html">
|
||
<span class="navbar-title">Suivi de la thèse</span>
|
||
</a>
|
||
</div>
|
||
<div id="quarto-search" class="" title="Recherche"></div>
|
||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbarCollapse" aria-controls="navbarCollapse" role="menu" aria-expanded="false" aria-label="Basculer la navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
|
||
<span class="navbar-toggler-icon"></span>
|
||
</button>
|
||
<div class="collapse navbar-collapse" id="navbarCollapse">
|
||
<ul class="navbar-nav navbar-nav-scroll me-auto">
|
||
<li class="nav-item">
|
||
<a class="nav-link" href="../../index.html"> <i class="bi bi-journals" role="img">
|
||
</i>
|
||
<span class="menu-text">Liste des semaines</span></a>
|
||
</li>
|
||
</ul>
|
||
<ul class="navbar-nav navbar-nav-scroll ms-auto">
|
||
<li class="nav-item compact">
|
||
<a class="nav-link" href="https://git.polarolouis.fr/polarolouis/these-recap-hebdo"> <i class="bi bi-git" role="img" aria-label="Dépôt Git du journal">
|
||
</i>
|
||
<span class="menu-text"></span></a>
|
||
</li>
|
||
</ul>
|
||
</div> <!-- /navcollapse -->
|
||
<div class="quarto-navbar-tools">
|
||
</div>
|
||
</div> <!-- /container-fluid -->
|
||
</nav>
|
||
</header>
|
||
<!-- content -->
|
||
<header id="title-block-header" class="quarto-title-block default page-columns page-full">
|
||
<div class="quarto-title-banner page-columns page-full">
|
||
<div class="quarto-title column-body">
|
||
<h1 class="title">Bilan semaine 25 2025 : 16 juin - 20 juin</h1>
|
||
<div class="quarto-categories">
|
||
<div class="quarto-category">colBiSBM</div>
|
||
<div class="quarto-category">inférence</div>
|
||
<div class="quarto-category">GNN</div>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
|
||
<div class="quarto-title-meta-author">
|
||
<div class="quarto-title-meta-heading">Auteur·rice</div>
|
||
<div class="quarto-title-meta-heading">Affiliation</div>
|
||
|
||
<div class="quarto-title-meta-contents">
|
||
<p class="author">Louis Lacoste <a href="mailto:louis.lacoste@agroparistech.fr" class="quarto-title-author-email"><i class="bi bi-envelope"></i></a> <a href="https://orcid.org/0009-0004-0178-9821" class="quarto-title-author-orcid"> <img src="data:image/png;base64,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"></a></p>
|
||
</div>
|
||
<div class="quarto-title-meta-contents">
|
||
<p class="affiliation">
|
||
MIA Paris-Saclay, INRAE, AgroParisTech, Université Paris-Saclay
|
||
</p>
|
||
</div>
|
||
</div>
|
||
|
||
<div class="quarto-title-meta">
|
||
|
||
|
||
<div>
|
||
<div class="quarto-title-meta-heading">Date de publication</div>
|
||
<div class="quarto-title-meta-contents">
|
||
<p class="date">20 juin 2025</p>
|
||
</div>
|
||
</div>
|
||
|
||
<div>
|
||
<div class="quarto-title-meta-heading">Modifié</div>
|
||
<div class="quarto-title-meta-contents">
|
||
<p class="date-modified">22 octobre 2025</p>
|
||
</div>
|
||
</div>
|
||
|
||
</div>
|
||
|
||
|
||
</header><div id="quarto-content" class="quarto-container page-columns page-rows-contents page-layout-article page-navbar">
|
||
<!-- sidebar -->
|
||
<!-- margin-sidebar -->
|
||
<div id="quarto-margin-sidebar" class="sidebar margin-sidebar">
|
||
<nav id="TOC" role="doc-toc" class="toc-active">
|
||
<h2 id="toc-title">Sur cette page</h2>
|
||
|
||
<ul>
|
||
<li><a href="#todo-list" id="toc-todo-list" class="nav-link active" data-scroll-target="#todo-list">TODO List</a>
|
||
<ul class="collapse">
|
||
<li><a href="#inférence-et-microbes" id="toc-inférence-et-microbes" class="nav-link" data-scroll-target="#inférence-et-microbes">Inférence et microbes</a></li>
|
||
</ul></li>
|
||
<li><a href="#lecture-en-cours" id="toc-lecture-en-cours" class="nav-link" data-scroll-target="#lecture-en-cours">Lecture en cours</a>
|
||
<ul class="collapse">
|
||
<li><a href="#ot" id="toc-ot" class="nav-link" data-scroll-target="#ot">OT</a></li>
|
||
<li><a href="#inférence-de-graphes" id="toc-inférence-de-graphes" class="nav-link" data-scroll-target="#inférence-de-graphes">Inférence de graphes</a></li>
|
||
</ul></li>
|
||
<li><a href="#a-discuter" id="toc-a-discuter" class="nav-link" data-scroll-target="#a-discuter">A discuter</a>
|
||
<ul class="collapse">
|
||
<li><a href="#inférence" id="toc-inférence" class="nav-link" data-scroll-target="#inférence">Inférence</a></li>
|
||
</ul></li>
|
||
</ul>
|
||
</nav>
|
||
</div>
|
||
<!-- main -->
|
||
<main class="content quarto-banner-title-block" id="quarto-document-content">
|
||
|
||
|
||
|
||
|
||
|
||
<section id="todo-list" class="level2">
|
||
<h2 class="anchored" data-anchor-id="todo-list">TODO List</h2>
|
||
<ul>
|
||
<li><p>Pour clustering de collections sur données réelles :<br>
|
||
→ L’intuition de Pierre semble être confirmé, les dissimilarités semblent arrêter de varier sensiblement pour de grandes valeurs <span class="math inline">(Q_1,Q_2)</span>.</p>
|
||
<ul>
|
||
<li>✅ Si plusieurs clustering possibles les tester et sélectionner le meilleur</li>
|
||
<li>✅ Ré-ajuster les bonnes partitions.</li>
|
||
<li>❓Je n’arrive plus à reproduire le bug pour l’inférence…</li>
|
||
</ul></li>
|
||
<li><p>✅ <strong>Oui c’est bien le cas</strong> Clustering descendant & ascendant : vérifier qu’au cours du temps le <span class="math inline">BICL_{asc} \geq BICL_{desc}</span></p></li>
|
||
<li><p>Creuser et explorer avec easy16s !</p></li>
|
||
<li><p>✅ Comparer les perfs du VAE sur Baldock avec colBiSBM par exemple</p></li>
|
||
</ul>
|
||
<table>
|
||
<caption>
|
||
AUC values for colBiSBM and VGAE models across cities
|
||
</caption>
|
||
<thead>
|
||
<tr>
|
||
<th style="empty-cells: hide;border-bottom:hidden;" colspan="1">
|
||
</th>
|
||
<th style="border-bottom:hidden;padding-bottom:0; padding-left:3px;padding-right:3px;text-align: center; " colspan="2">
|
||
<div style="border-bottom: 1px solid #ddd; padding-bottom: 5px; ">
|
||
AUC
|
||
</div>
|
||
</th>
|
||
</tr>
|
||
<tr>
|
||
<th style="text-align:left;">
|
||
City
|
||
</th>
|
||
<th style="text-align:right;">
|
||
colBiSBM
|
||
</th>
|
||
<th style="text-align:right;">
|
||
Untuned VGAE
|
||
</th>
|
||
</tr>
|
||
</thead>
|
||
<tbody>
|
||
<tr>
|
||
<td style="text-align:left;">
|
||
Bristol
|
||
</td>
|
||
<td style="text-align:right;">
|
||
0.798
|
||
</td>
|
||
<td style="text-align:right;">
|
||
0.755
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td style="text-align:left;">
|
||
Edinburgh
|
||
</td>
|
||
<td style="text-align:right;">
|
||
0.836
|
||
</td>
|
||
<td style="text-align:right;">
|
||
0.774
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td style="text-align:left;">
|
||
Leeds
|
||
</td>
|
||
<td style="text-align:right;">
|
||
0.854
|
||
</td>
|
||
<td style="text-align:right;">
|
||
0.760
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td style="text-align:left;">
|
||
Reading
|
||
</td>
|
||
<td style="text-align:right;">
|
||
0.867
|
||
</td>
|
||
<td style="text-align:right;">
|
||
0.740
|
||
</td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
<ul>
|
||
<li><p>Dé-bugger les simulations :</p>
|
||
<ul>
|
||
<li>⌛ Inférence : Relancer simus d’inférence avec n = 240 pour voir si la qualité augmenter (se rassurer). En fait on est déjà à 240, j’ai relancé avec M = 4 au lieu de M = 2. En attente résultats MIGALE -> BUG, dois creuser mais juste des problèmes techniques -> Visiblement il y a d’autres problèmes que juste le plan de parallélisation.
|
||
<ul>
|
||
<li>✅ <strong>Non ça n’a pas l’air d’être ça</strong>. Vérifier si problème de version tidyverse pour vapply sur l’<strong>inférence</strong>.</li>
|
||
<li>⌛Bon le bug ne se reproduit plus… les jobs sont juste trop longs (> 120h) j’ai relancé, il ne reste que 182/972 conditions.</li>
|
||
</ul></li>
|
||
</ul></li>
|
||
<li><p>✅ <strong>Il suffisait de faire la màj soit même…</strong> Si problème de parallélisation vient de pb de version <em>future.callr</em> le signaler à MIGALE.</p></li>
|
||
<li><p>Kmeans sur la densité des réseaux subdoré pour pré-partitionner et <em>clusteriser</em>. Car densités déséquilibrées.</p></li>
|
||
</ul>
|
||
<div id="ref-kmeans-vae" class="quarto-float quarto-figure quarto-figure-center anchored">
|
||
<figure class="quarto-float quarto-float-ref figure">
|
||
<div aria-describedby="ref-kmeans-vae-caption-0ceaefa1-69ba-4598-a22c-09a6ac19f8ca">
|
||
<ul>
|
||
<li>Faire GNN-VAE Doré et sub-Doré avec kmeans et clustering sur l’espace latent J’ai commencé à regarder un peu</li>
|
||
</ul>
|
||
</div>
|
||
<figcaption class="quarto-float-caption-bottom quarto-float-caption quarto-float-ref quarto-uncaptioned" id="ref-kmeans-vae-caption-0ceaefa1-69ba-4598-a22c-09a6ac19f8ca">
|
||
Reference 1
|
||
</figcaption>
|
||
</figure>
|
||
</div>
|
||
<section id="inférence-et-microbes" class="level3">
|
||
<h3 class="anchored" data-anchor-id="inférence-et-microbes">Inférence et microbes</h3>
|
||
<ul>
|
||
<li>Lancer <em>colBiSBM</em> sur <span class="math inline">OTU\times Sample</span> → problème du chargement en mémoire des données à voir</li>
|
||
<li>Lancer <em>colSBM</em> sur <span class="math inline">OTU\times OTU</span></li>
|
||
<li>Creuser <a href="https://raw.githubusercontent.com/cregouby/R-toulouse-tabnet/main/Tabnet_RR2023_fr_pdf.pdf">TabNet</a> de Christophe Regouby et les <a href="https://github.com/cregouby/Tutoriel_torch">exercices</a></li>
|
||
<li>Regarder <strong>SPARTA</strong> Rennes</li>
|
||
<li>Lire Papiers compositional data (Aitchison et al. intro)</li>
|
||
<li>Lire article multi-niveaux Saint-Clair</li>
|
||
<li>Demander à JA si elle connaît des réseaux d’interactions connus par les experts (idée d’intégrer une connaissance experte et de voir les différences de structure par rapport à celle attendue)</li>
|
||
<li>Ecrire et étudier les modèles pour différents niveaux taxonomiques. <span class="math display">\begin{align*}
|
||
i \rightarrow &~N^1_i \subseteq N^2_i \subseteq N^3_i & \text{Taxonomie}\\
|
||
Z^0_i \overset{?}{=} & Z^1_i \overset{?}{=} Z^2_i \overset{?}{=} Z^3_i & \text{Groupes fonctionnels}
|
||
\end{align*}</span></li>
|
||
</ul>
|
||
</section>
|
||
</section>
|
||
<section id="lecture-en-cours" class="level2">
|
||
<h2 class="anchored" data-anchor-id="lecture-en-cours">Lecture en cours</h2>
|
||
<section id="ot" class="level3">
|
||
<h3 class="anchored" data-anchor-id="ot">OT</h3>
|
||
<ul>
|
||
<li>⌛ <span class="citation" data-cites="mazeletUnsupervisedLearningOptimal">Mazelet, Flamary, et Thirion (<a href="#ref-mazeletUnsupervisedLearningOptimal" role="doc-biblioref">s. d.</a>)</span> Intéressant pour le transport optimal entre graphes de tailles différentes</li>
|
||
<li>⌛ <span class="citation" data-cites="nennaLecture2Entropic">Nenna (<a href="#ref-nennaLecture2Entropic" role="doc-biblioref">s. d.b</a>)</span> Pour comprendre le problème d’OT régularisé pour l’entropie.</li>
|
||
<li>⌛ <span class="citation" data-cites="nennaLecture1Monge">Nenna (<a href="#ref-nennaLecture1Monge" role="doc-biblioref">s. d.a</a>)</span></li>
|
||
</ul>
|
||
</section>
|
||
<section id="inférence-de-graphes" class="level3">
|
||
<h3 class="anchored" data-anchor-id="inférence-de-graphes">Inférence de graphes</h3>
|
||
<ul>
|
||
<li>✅ <span class="citation" data-cites="matchadoNetworkAnalysisMethods2021b">Matchado et al. (<a href="#ref-matchadoNetworkAnalysisMethods2021b" role="doc-biblioref">2021</a>)</span> ➡️ Nos données étant compositionnelles il faut utiliser:
|
||
<ul>
|
||
<li>CCLasso et SparCC</li>
|
||
<li>HARMONIES pour zéro inflation (Binomiale négative), COZINE centered log ratio transformation compositionnalité, zéro inflation et forte précision</li>
|
||
<li>MixMPLN pour générer K réseaux issus de K Poisson log Normal</li>
|
||
<li>mLDM peut enlever les arêtes indirectes.</li>
|
||
</ul></li>
|
||
<li>NetComi agrège plusieurs méthodes tout en permettant l’analyse différentielle !</li>
|
||
</ul>
|
||
<p>Si pas compositionnelles :</p>
|
||
<ul>
|
||
<li>Meta-Network pour arêtes indirectes et non linéaires</li>
|
||
<li>Environmentally-Driven Edge detection pour corriger les effets de l’environnement</li>
|
||
</ul>
|
||
</section>
|
||
</section>
|
||
<section id="a-discuter" class="level2">
|
||
<h2 class="anchored" data-anchor-id="a-discuter">A discuter</h2>
|
||
<section id="inférence" class="level3">
|
||
<h3 class="anchored" data-anchor-id="inférence">Inférence</h3>
|
||
<ul>
|
||
<li>pbs : variance, bcp de zero, covariables, offset et taxonomie (Reseaux arretes differents niveaux : Genre, OTU …)</li>
|
||
</ul>
|
||
<blockquote class="blockquote">
|
||
<p>Combine networks at different taxonomic levels</p>
|
||
</blockquote>
|
||
<ul>
|
||
<li>Inférence + GREMLINS</li>
|
||
</ul>
|
||
|
||
|
||
|
||
</section>
|
||
</section>
|
||
|
||
<div id="quarto-appendix" class="default"><section class="quarto-appendix-contents" role="doc-bibliography" id="quarto-bibliography"><h2 class="anchored quarto-appendix-heading">Les références</h2><div id="refs" class="references csl-bib-body hanging-indent" data-entry-spacing="0" role="list">
|
||
<div id="ref-matchadoNetworkAnalysisMethods2021b" class="csl-entry" role="listitem">
|
||
Matchado, Monica Steffi, Michael Lauber, Sandra Reitmeier, Tim Kacprowski, Jan Baumbach, Dirk Haller, et Markus List. 2021. <span>« Network Analysis Methods for Studying Microbial Communities: <span>A</span> Mini Review »</span>. <em>Computational and Structural Biotechnology Journal</em> 19 (janvier): 2687‑98. <a href="https://doi.org/10.1016/j.csbj.2021.05.001">https://doi.org/10.1016/j.csbj.2021.05.001</a>.
|
||
</div>
|
||
<div id="ref-mazeletUnsupervisedLearningOptimal" class="csl-entry" role="listitem">
|
||
Mazelet, Sonia, Rémi Flamary, et Bertrand Thirion. s. d. <span>« Unsupervised <span>Learning</span> for <span>Optimal Transport</span> Plan Prediction Between Unbalanced Graphs »</span>.
|
||
</div>
|
||
<div id="ref-nennaLecture1Monge" class="csl-entry" role="listitem">
|
||
Nenna, Luca. s. d.a. <span>« Lecture 1 <span>Monge</span> and <span>Kantorovich</span> Problems: From Primal to Dual »</span>.
|
||
</div>
|
||
<div id="ref-nennaLecture2Entropic" class="csl-entry" role="listitem">
|
||
———. s. d.b. <span>« Lecture 2: <span>Entropic Optimal Transport</span> »</span>.
|
||
</div>
|
||
</div></section></div></main> <!-- /main -->
|
||
<script id="quarto-html-after-body" type="application/javascript">
|
||
window.document.addEventListener("DOMContentLoaded", function (event) {
|
||
const icon = "";
|
||
const anchorJS = new window.AnchorJS();
|
||
anchorJS.options = {
|
||
placement: 'right',
|
||
icon: icon
|
||
};
|
||
anchorJS.add('.anchored');
|
||
const isCodeAnnotation = (el) => {
|
||
for (const clz of el.classList) {
|
||
if (clz.startsWith('code-annotation-')) {
|
||
return true;
|
||
}
|
||
}
|
||
return false;
|
||
}
|
||
const onCopySuccess = function(e) {
|
||
// button target
|
||
const button = e.trigger;
|
||
// don't keep focus
|
||
button.blur();
|
||
// flash "checked"
|
||
button.classList.add('code-copy-button-checked');
|
||
var currentTitle = button.getAttribute("title");
|
||
button.setAttribute("title", "Copié");
|
||
let tooltip;
|
||
if (window.bootstrap) {
|
||
button.setAttribute("data-bs-toggle", "tooltip");
|
||
button.setAttribute("data-bs-placement", "left");
|
||
button.setAttribute("data-bs-title", "Copié");
|
||
tooltip = new bootstrap.Tooltip(button,
|
||
{ trigger: "manual",
|
||
customClass: "code-copy-button-tooltip",
|
||
offset: [0, -8]});
|
||
tooltip.show();
|
||
}
|
||
setTimeout(function() {
|
||
if (tooltip) {
|
||
tooltip.hide();
|
||
button.removeAttribute("data-bs-title");
|
||
button.removeAttribute("data-bs-toggle");
|
||
button.removeAttribute("data-bs-placement");
|
||
}
|
||
button.setAttribute("title", currentTitle);
|
||
button.classList.remove('code-copy-button-checked');
|
||
}, 1000);
|
||
// clear code selection
|
||
e.clearSelection();
|
||
}
|
||
const getTextToCopy = function(trigger) {
|
||
const codeEl = trigger.previousElementSibling.cloneNode(true);
|
||
for (const childEl of codeEl.children) {
|
||
if (isCodeAnnotation(childEl)) {
|
||
childEl.remove();
|
||
}
|
||
}
|
||
return codeEl.innerText;
|
||
}
|
||
const clipboard = new window.ClipboardJS('.code-copy-button:not([data-in-quarto-modal])', {
|
||
text: getTextToCopy
|
||
});
|
||
clipboard.on('success', onCopySuccess);
|
||
if (window.document.getElementById('quarto-embedded-source-code-modal')) {
|
||
const clipboardModal = new window.ClipboardJS('.code-copy-button[data-in-quarto-modal]', {
|
||
text: getTextToCopy,
|
||
container: window.document.getElementById('quarto-embedded-source-code-modal')
|
||
});
|
||
clipboardModal.on('success', onCopySuccess);
|
||
}
|
||
var localhostRegex = new RegExp(/^(?:http|https):\/\/localhost\:?[0-9]*\//);
|
||
var mailtoRegex = new RegExp(/^mailto:/);
|
||
var filterRegex = new RegExp('/' + window.location.host + '/');
|
||
var isInternal = (href) => {
|
||
return filterRegex.test(href) || localhostRegex.test(href) || mailtoRegex.test(href);
|
||
}
|
||
// Inspect non-navigation links and adorn them if external
|
||
var links = window.document.querySelectorAll('a[href]:not(.nav-link):not(.navbar-brand):not(.toc-action):not(.sidebar-link):not(.sidebar-item-toggle):not(.pagination-link):not(.no-external):not([aria-hidden]):not(.dropdown-item):not(.quarto-navigation-tool):not(.about-link)');
|
||
for (var i=0; i<links.length; i++) {
|
||
const link = links[i];
|
||
if (!isInternal(link.href)) {
|
||
// undo the damage that might have been done by quarto-nav.js in the case of
|
||
// links that we want to consider external
|
||
if (link.dataset.originalHref !== undefined) {
|
||
link.href = link.dataset.originalHref;
|
||
}
|
||
}
|
||
}
|
||
function tippyHover(el, contentFn, onTriggerFn, onUntriggerFn) {
|
||
const config = {
|
||
allowHTML: true,
|
||
maxWidth: 500,
|
||
delay: 100,
|
||
arrow: false,
|
||
appendTo: function(el) {
|
||
return el.parentElement;
|
||
},
|
||
interactive: true,
|
||
interactiveBorder: 10,
|
||
theme: 'quarto',
|
||
placement: 'bottom-start',
|
||
};
|
||
if (contentFn) {
|
||
config.content = contentFn;
|
||
}
|
||
if (onTriggerFn) {
|
||
config.onTrigger = onTriggerFn;
|
||
}
|
||
if (onUntriggerFn) {
|
||
config.onUntrigger = onUntriggerFn;
|
||
}
|
||
window.tippy(el, config);
|
||
}
|
||
const noterefs = window.document.querySelectorAll('a[role="doc-noteref"]');
|
||
for (var i=0; i<noterefs.length; i++) {
|
||
const ref = noterefs[i];
|
||
tippyHover(ref, function() {
|
||
// use id or data attribute instead here
|
||
let href = ref.getAttribute('data-footnote-href') || ref.getAttribute('href');
|
||
try { href = new URL(href).hash; } catch {}
|
||
const id = href.replace(/^#\/?/, "");
|
||
const note = window.document.getElementById(id);
|
||
if (note) {
|
||
return note.innerHTML;
|
||
} else {
|
||
return "";
|
||
}
|
||
});
|
||
}
|
||
const xrefs = window.document.querySelectorAll('a.quarto-xref');
|
||
const processXRef = (id, note) => {
|
||
// Strip column container classes
|
||
const stripColumnClz = (el) => {
|
||
el.classList.remove("page-full", "page-columns");
|
||
if (el.children) {
|
||
for (const child of el.children) {
|
||
stripColumnClz(child);
|
||
}
|
||
}
|
||
}
|
||
stripColumnClz(note)
|
||
if (id === null || id.startsWith('sec-')) {
|
||
// Special case sections, only their first couple elements
|
||
const container = document.createElement("div");
|
||
if (note.children && note.children.length > 2) {
|
||
container.appendChild(note.children[0].cloneNode(true));
|
||
for (let i = 1; i < note.children.length; i++) {
|
||
const child = note.children[i];
|
||
if (child.tagName === "P" && child.innerText === "") {
|
||
continue;
|
||
} else {
|
||
container.appendChild(child.cloneNode(true));
|
||
break;
|
||
}
|
||
}
|
||
if (window.Quarto?.typesetMath) {
|
||
window.Quarto.typesetMath(container);
|
||
}
|
||
return container.innerHTML
|
||
} else {
|
||
if (window.Quarto?.typesetMath) {
|
||
window.Quarto.typesetMath(note);
|
||
}
|
||
return note.innerHTML;
|
||
}
|
||
} else {
|
||
// Remove any anchor links if they are present
|
||
const anchorLink = note.querySelector('a.anchorjs-link');
|
||
if (anchorLink) {
|
||
anchorLink.remove();
|
||
}
|
||
if (window.Quarto?.typesetMath) {
|
||
window.Quarto.typesetMath(note);
|
||
}
|
||
if (note.classList.contains("callout")) {
|
||
return note.outerHTML;
|
||
} else {
|
||
return note.innerHTML;
|
||
}
|
||
}
|
||
}
|
||
for (var i=0; i<xrefs.length; i++) {
|
||
const xref = xrefs[i];
|
||
tippyHover(xref, undefined, function(instance) {
|
||
instance.disable();
|
||
let url = xref.getAttribute('href');
|
||
let hash = undefined;
|
||
if (url.startsWith('#')) {
|
||
hash = url;
|
||
} else {
|
||
try { hash = new URL(url).hash; } catch {}
|
||
}
|
||
if (hash) {
|
||
const id = hash.replace(/^#\/?/, "");
|
||
const note = window.document.getElementById(id);
|
||
if (note !== null) {
|
||
try {
|
||
const html = processXRef(id, note.cloneNode(true));
|
||
instance.setContent(html);
|
||
} finally {
|
||
instance.enable();
|
||
instance.show();
|
||
}
|
||
} else {
|
||
// See if we can fetch this
|
||
fetch(url.split('#')[0])
|
||
.then(res => res.text())
|
||
.then(html => {
|
||
const parser = new DOMParser();
|
||
const htmlDoc = parser.parseFromString(html, "text/html");
|
||
const note = htmlDoc.getElementById(id);
|
||
if (note !== null) {
|
||
const html = processXRef(id, note);
|
||
instance.setContent(html);
|
||
}
|
||
}).finally(() => {
|
||
instance.enable();
|
||
instance.show();
|
||
});
|
||
}
|
||
} else {
|
||
// See if we can fetch a full url (with no hash to target)
|
||
// This is a special case and we should probably do some content thinning / targeting
|
||
fetch(url)
|
||
.then(res => res.text())
|
||
.then(html => {
|
||
const parser = new DOMParser();
|
||
const htmlDoc = parser.parseFromString(html, "text/html");
|
||
const note = htmlDoc.querySelector('main.content');
|
||
if (note !== null) {
|
||
// This should only happen for chapter cross references
|
||
// (since there is no id in the URL)
|
||
// remove the first header
|
||
if (note.children.length > 0 && note.children[0].tagName === "HEADER") {
|
||
note.children[0].remove();
|
||
}
|
||
const html = processXRef(null, note);
|
||
instance.setContent(html);
|
||
}
|
||
}).finally(() => {
|
||
instance.enable();
|
||
instance.show();
|
||
});
|
||
}
|
||
}, function(instance) {
|
||
});
|
||
}
|
||
let selectedAnnoteEl;
|
||
const selectorForAnnotation = ( cell, annotation) => {
|
||
let cellAttr = 'data-code-cell="' + cell + '"';
|
||
let lineAttr = 'data-code-annotation="' + annotation + '"';
|
||
const selector = 'span[' + cellAttr + '][' + lineAttr + ']';
|
||
return selector;
|
||
}
|
||
const selectCodeLines = (annoteEl) => {
|
||
const doc = window.document;
|
||
const targetCell = annoteEl.getAttribute("data-target-cell");
|
||
const targetAnnotation = annoteEl.getAttribute("data-target-annotation");
|
||
const annoteSpan = window.document.querySelector(selectorForAnnotation(targetCell, targetAnnotation));
|
||
const lines = annoteSpan.getAttribute("data-code-lines").split(",");
|
||
const lineIds = lines.map((line) => {
|
||
return targetCell + "-" + line;
|
||
})
|
||
let top = null;
|
||
let height = null;
|
||
let parent = null;
|
||
if (lineIds.length > 0) {
|
||
//compute the position of the single el (top and bottom and make a div)
|
||
const el = window.document.getElementById(lineIds[0]);
|
||
top = el.offsetTop;
|
||
height = el.offsetHeight;
|
||
parent = el.parentElement.parentElement;
|
||
if (lineIds.length > 1) {
|
||
const lastEl = window.document.getElementById(lineIds[lineIds.length - 1]);
|
||
const bottom = lastEl.offsetTop + lastEl.offsetHeight;
|
||
height = bottom - top;
|
||
}
|
||
if (top !== null && height !== null && parent !== null) {
|
||
// cook up a div (if necessary) and position it
|
||
let div = window.document.getElementById("code-annotation-line-highlight");
|
||
if (div === null) {
|
||
div = window.document.createElement("div");
|
||
div.setAttribute("id", "code-annotation-line-highlight");
|
||
div.style.position = 'absolute';
|
||
parent.appendChild(div);
|
||
}
|
||
div.style.top = top - 2 + "px";
|
||
div.style.height = height + 4 + "px";
|
||
div.style.left = 0;
|
||
let gutterDiv = window.document.getElementById("code-annotation-line-highlight-gutter");
|
||
if (gutterDiv === null) {
|
||
gutterDiv = window.document.createElement("div");
|
||
gutterDiv.setAttribute("id", "code-annotation-line-highlight-gutter");
|
||
gutterDiv.style.position = 'absolute';
|
||
const codeCell = window.document.getElementById(targetCell);
|
||
const gutter = codeCell.querySelector('.code-annotation-gutter');
|
||
gutter.appendChild(gutterDiv);
|
||
}
|
||
gutterDiv.style.top = top - 2 + "px";
|
||
gutterDiv.style.height = height + 4 + "px";
|
||
}
|
||
selectedAnnoteEl = annoteEl;
|
||
}
|
||
};
|
||
const unselectCodeLines = () => {
|
||
const elementsIds = ["code-annotation-line-highlight", "code-annotation-line-highlight-gutter"];
|
||
elementsIds.forEach((elId) => {
|
||
const div = window.document.getElementById(elId);
|
||
if (div) {
|
||
div.remove();
|
||
}
|
||
});
|
||
selectedAnnoteEl = undefined;
|
||
};
|
||
// Handle positioning of the toggle
|
||
window.addEventListener(
|
||
"resize",
|
||
throttle(() => {
|
||
elRect = undefined;
|
||
if (selectedAnnoteEl) {
|
||
selectCodeLines(selectedAnnoteEl);
|
||
}
|
||
}, 10)
|
||
);
|
||
function throttle(fn, ms) {
|
||
let throttle = false;
|
||
let timer;
|
||
return (...args) => {
|
||
if(!throttle) { // first call gets through
|
||
fn.apply(this, args);
|
||
throttle = true;
|
||
} else { // all the others get throttled
|
||
if(timer) clearTimeout(timer); // cancel #2
|
||
timer = setTimeout(() => {
|
||
fn.apply(this, args);
|
||
timer = throttle = false;
|
||
}, ms);
|
||
}
|
||
};
|
||
}
|
||
// Attach click handler to the DT
|
||
const annoteDls = window.document.querySelectorAll('dt[data-target-cell]');
|
||
for (const annoteDlNode of annoteDls) {
|
||
annoteDlNode.addEventListener('click', (event) => {
|
||
const clickedEl = event.target;
|
||
if (clickedEl !== selectedAnnoteEl) {
|
||
unselectCodeLines();
|
||
const activeEl = window.document.querySelector('dt[data-target-cell].code-annotation-active');
|
||
if (activeEl) {
|
||
activeEl.classList.remove('code-annotation-active');
|
||
}
|
||
selectCodeLines(clickedEl);
|
||
clickedEl.classList.add('code-annotation-active');
|
||
} else {
|
||
// Unselect the line
|
||
unselectCodeLines();
|
||
clickedEl.classList.remove('code-annotation-active');
|
||
}
|
||
});
|
||
}
|
||
const findCites = (el) => {
|
||
const parentEl = el.parentElement;
|
||
if (parentEl) {
|
||
const cites = parentEl.dataset.cites;
|
||
if (cites) {
|
||
return {
|
||
el,
|
||
cites: cites.split(' ')
|
||
};
|
||
} else {
|
||
return findCites(el.parentElement)
|
||
}
|
||
} else {
|
||
return undefined;
|
||
}
|
||
};
|
||
var bibliorefs = window.document.querySelectorAll('a[role="doc-biblioref"]');
|
||
for (var i=0; i<bibliorefs.length; i++) {
|
||
const ref = bibliorefs[i];
|
||
const citeInfo = findCites(ref);
|
||
if (citeInfo) {
|
||
tippyHover(citeInfo.el, function() {
|
||
var popup = window.document.createElement('div');
|
||
citeInfo.cites.forEach(function(cite) {
|
||
var citeDiv = window.document.createElement('div');
|
||
citeDiv.classList.add('hanging-indent');
|
||
citeDiv.classList.add('csl-entry');
|
||
var biblioDiv = window.document.getElementById('ref-' + cite);
|
||
if (biblioDiv) {
|
||
citeDiv.innerHTML = biblioDiv.innerHTML;
|
||
}
|
||
popup.appendChild(citeDiv);
|
||
});
|
||
return popup.innerHTML;
|
||
});
|
||
}
|
||
}
|
||
});
|
||
</script>
|
||
</div> <!-- /content -->
|
||
|
||
|
||
|
||
|
||
</body></html> |