-
lucas.longour_ird.fr authoredlucas.longour_ird.fr authored
index.html 14.14 KiB
<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
<meta charset="utf-8">
<meta name="generator" content="quarto-1.1.251">
<meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
<title>Mapping and spatial analyses in R for One Health studies</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 -1.6em;
vertical-align: middle;
}
</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="./">
<link href="./01-introduction.html" rel="next">
<script src="site_libs/quarto-html/quarto.js"></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.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.min.css" rel="stylesheet" id="quarto-bootstrap" data-mode="light">
<script id="quarto-search-options" type="application/json">{
"location": "sidebar",
"copy-button": false,
"collapse-after": 3,
"panel-placement": "start",
"type": "textbox",
"limit": 20,
"language": {
"search-no-results-text": "No results",
"search-matching-documents-text": "matching documents",
"search-copy-link-title": "Copy link to search",
"search-hide-matches-text": "Hide additional matches",
"search-more-match-text": "more match in this document",
"search-more-matches-text": "more matches in this document",
"search-clear-button-title": "Clear",
"search-detached-cancel-button-title": "Cancel",
"search-submit-button-title": "Submit"
}
}</script>
<style>html{ scroll-behavior: smooth; }</style>
<link rel="stylesheet" href="styles.css">
</head>
<body class="nav-sidebar floating">
<div id="quarto-search-results"></div>
<header id="quarto-header" class="headroom fixed-top">
<nav class="quarto-secondary-nav" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
<div class="container-fluid d-flex justify-content-between">
<h1 class="quarto-secondary-nav-title">Mapping and spatial analyses in R for One Health studies</h1>
<button type="button" class="quarto-btn-toggle btn" aria-label="Show secondary navigation">
<i class="bi bi-chevron-right"></i>
</button>
</div>
</nav>
</header>
<!-- content -->
<div id="quarto-content" class="quarto-container page-columns page-rows-contents page-layout-article">
<!-- sidebar -->
<nav id="quarto-sidebar" class="sidebar collapse sidebar-navigation floating overflow-auto">
<div class="pt-lg-2 mt-2 text-left sidebar-header">
<div class="sidebar-title mb-0 py-0">
<a href="./">Mapping and spatial analyses in R for One Health studies</a>
<div class="sidebar-tools-main">
<a href="https://forge.ird.fr/espace-dev/personnels/longour/geohealth/documentation/rspatial-for-onehealth" title="Source Code" class="sidebar-tool px-1"><i class="bi bi-git"></i></a>
</div>
</div>
</div>
<div class="mt-2 flex-shrink-0 align-items-center">
<div class="sidebar-search">
<div id="quarto-search" class="" title="Search"></div>
</div>
</div>
<div class="sidebar-menu-container">
<ul class="list-unstyled mt-1">
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="./index.html" class="sidebar-item-text sidebar-link active">Preface</a>
</div>
</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="./01-introduction.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">1</span> <span class="chapter-title">Introduction</span></a>
</div>
</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="./02-data_acquisition.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">2</span> <span class="chapter-title">Data Acquisition</span></a>
</div>
</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="./03-vector_data.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">3</span> <span class="chapter-title">Using vector data</span></a>
</div>
</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="./04-raster_data.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">4</span> <span class="chapter-title">Using raster data</span></a>
</div>
</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="./05-mapping_with_r.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">5</span> <span class="chapter-title">Mapping With R</span></a>
</div>
</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="./07-basic_statistics.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">6</span> <span class="chapter-title">Basic statistics for spatial analysis</span></a>
</div>
</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="./references.html" class="sidebar-item-text sidebar-link">References</a>
</div>
</li>
</ul>
</div>
</nav>
<!-- margin-sidebar -->
<div id="quarto-margin-sidebar" class="sidebar margin-sidebar">
<nav id="TOC" role="doc-toc" class="toc-active">
<h2 id="toc-title">Table of contents</h2>
<ul>
<li><a href="#preface" id="toc-preface" class="nav-link active" data-scroll-target="#preface">Preface</a></li>
</ul>
</nav>
</div>
<!-- main -->
<main class="content" id="quarto-document-content">
<header id="title-block-header" class="quarto-title-block default">
<div class="quarto-title">
<h1 class="title d-none d-lg-block">Mapping and spatial analyses in R for One Health studies</h1>
<p class="subtitle lead">GeoHealth Training Series</p>
</div>
<div class="quarto-title-meta">
</div>
</header>
<section id="preface" class="level1 unnumbered">
<p><img src="img/geohealth_banner.jpeg" title="Mapping and spatial analyses in R for One Health studies" class="quarto-cover-image img-fluid"></p><h1 class="unnumbered">Preface</h1>
<p>This training is designed for people interested in using R for mapping and spatial analysis for applications in the various fields related to “one health” approaches. R is an open source software widely used by the scientific community for data analysis and which is becoming an interesting choice for cartography and spatial analysis, as a Geographic Information System.</p>
<p>This training was first prepared to be given from 28th November to 2nd December 2022, in Phnom Penh Cambodia, by the GeoHealth team under the French National Research Institute for Sustainable Development (IRD) and the Institut Pasteur du Cambodge (IPC), in the frame of:</p>
<ul>
<li><p>the OHSEA Project (One Health in Practices in South-East Asia), funded by the FSPI (Solidarity Fund for Innovative Projects) under the French Ministry for Europe and Foreign Affairs,</p></li>
<li><p>the Dissemination activities of the EASIMES (Environment Analysis and Surveillance to Improve Malaria Elimination Strategy) Project funded by the Global Fund RAI2E.</p></li>
</ul>
<p>Conception: It was first designed from the courses “<a href="https://rcarto.github.io/geomatique_avec_r/">Géomatique avec R</a>” and “<a href="https://rcarto.github.io/cartographie_avec_r/">Cartographie avec R</a>” by Timothée Giraud and Hugues Pecout. It was then translated and its examples were adapted for Cambodia and health applications.</p>
<p><strong>Development team</strong>:<br>
<em>Coordination</em>: Vincent Herbreteau, Florian Girond and Lucas Longour<br>
<em>Implementation in R with Quarto</em>: Lucas Longour and Sokeang Hoeun<br>
<em>Core of the tutorial</em>: Timothée Giraud and Hugues Pecout<br>
<em>Development of examples on Cambodia</em>: Vincent Herbreteau, Lucas Longour and Sokeang Hoeun<br>
<em>OSM extract chapter</em>: Lucas Longour<br>
<em>Geostatistics chapter</em>: Léa Douchet</p>
<p><a href="https://e1.pcloud.link/publink/show?code=XZQ60YZxwN09vWJ8bmuSivWezhuG8u94lCV" class="btn btn-primary btn-sm" role="button">Download the training data</a></p>
<hr>
<div class="quarto-figure quarto-figure-left">
<figure class="figure">
<p><img src="img/by-nc-sa.png" class="img-fluid figure-img"></p>
<p></p><figcaption class="figure-caption">Creative Commons License</figcaption><p></p>
</figure>
</div>
<p>The online version of this document licensed under the <a href="http://creativecommons.org/licenses/by-nc-sa/4.0/">Creative Commons Attribution-NonCommercial-ShareAlike 4.0</a>.</p>
</section>
</main> <!-- /main -->
<script id="quarto-html-after-body" type="application/javascript">
window.document.addEventListener("DOMContentLoaded", function (event) {
const toggleBodyColorMode = (bsSheetEl) => {
const mode = bsSheetEl.getAttribute("data-mode");
const bodyEl = window.document.querySelector("body");
if (mode === "dark") {
bodyEl.classList.add("quarto-dark");
bodyEl.classList.remove("quarto-light");
} else {
bodyEl.classList.add("quarto-light");
bodyEl.classList.remove("quarto-dark");
}
}
const toggleBodyColorPrimary = () => {
const bsSheetEl = window.document.querySelector("link#quarto-bootstrap");
if (bsSheetEl) {
toggleBodyColorMode(bsSheetEl);
}
}
toggleBodyColorPrimary();
const icon = "";
const anchorJS = new window.AnchorJS();
anchorJS.options = {
placement: 'right',
icon: icon
};
anchorJS.add('.anchored');
const clipboard = new window.ClipboardJS('.code-copy-button', {
target: function(trigger) {
return trigger.previousElementSibling;
}
});
clipboard.on('success', 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", "Copied!");
setTimeout(function() {
button.setAttribute("title", currentTitle);
button.classList.remove('code-copy-button-checked');
}, 1000);
// clear code selection
e.clearSelection();
});
function tippyHover(el, contentFn) {
const config = {
allowHTML: true,
content: contentFn,
maxWidth: 500,
delay: 100,
arrow: false,
appendTo: function(el) {
return el.parentElement;
},
interactive: true,
interactiveBorder: 10,
theme: 'quarto',
placement: 'bottom-start'
};
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);
return note.innerHTML;
});
}
var bibliorefs = window.document.querySelectorAll('a[role="doc-biblioref"]');
for (var i=0; i<bibliorefs.length; i++) {
const ref = bibliorefs[i];
const cites = ref.parentNode.getAttribute('data-cites').split(' ');
tippyHover(ref, function() {
var popup = window.document.createElement('div');
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;
});
}
var localhostRegex = new RegExp(/^(?:http|https):\/\/localhost\:?[0-9]*\//);
var filterRegex = new RegExp('/' + window.location.host + '/');
var isInternal = (href) => {
return filterRegex.test(href) || localhostRegex.test(href);
}
// Inspect non-navigation links and adorn them if external
var links = window.document.querySelectorAll('a:not(.nav-link):not(.navbar-brand):not(.toc-action):not(.sidebar-link):not(.sidebar-item-toggle):not(.pagination-link):not(.no-external)');
for (var i=0; i<links.length; i++) {
const link = links[i];
if (!isInternal(link.href)) {
// target, if specified
link.setAttribute("target", "_blank");
}
}
});
</script>
<nav class="page-navigation">
<div class="nav-page nav-page-previous">
</div>
<div class="nav-page nav-page-next">
<a href="./01-introduction.html" class="pagination-link">
<span class="nav-page-text"><span class="chapter-number">1</span> <span class="chapter-title">Introduction</span></span> <i class="bi bi-arrow-right-short"></i>
</a>
</div>
</nav>
</div> <!-- /content -->
<footer class="footer">
<div class="nav-footer">
<div class="nav-footer-left">UMR 228 ESPACE-DEV</div>
<div class="nav-footer-right"><img src="img/ird_footer.png" height="50"></div>
</div>
</footer>
<script src="site_libs/quarto-html/zenscroll-min.js"></script>
</body></html>