From 806d9c687daffa2e84534d9a0272cdffa986b690 Mon Sep 17 00:00:00 2001
From: Ernest Guevarra <ernest@guevarra.io>
Date: Fri, 16 Feb 2024 15:36:00 +0000
Subject: [PATCH] add vignette placeholders

---
 .gitignore                                  |   1 +
 DESCRIPTION                                 |   5 +-
 docs/404.html                               |   9 ++
 docs/CODE_OF_CONDUCT.html                   |   9 ++
 docs/CONTRIBUTING.html                      |   9 ++
 docs/LICENSE.html                           |   9 ++
 docs/articles/codigo.html                   | 122 ++++++++++++++++++++
 docs/articles/icd11_foundation.html         | 121 +++++++++++++++++++
 docs/articles/index.html                    |  85 ++++++++++++++
 docs/authors.html                           |   9 ++
 docs/index.html                             |   9 ++
 docs/pkgdown.yml                            |   6 +-
 docs/reference/codigo.html                  |  13 ++-
 docs/reference/icd11_linearization_mms.html |  11 +-
 docs/reference/icd11_simple_table_mms.html  |  11 +-
 docs/reference/icd_authenticate.html        |  11 +-
 docs/reference/icd_autocode.html            |  11 +-
 docs/reference/icd_check.html               |  11 +-
 docs/reference/icd_get.html                 |  11 +-
 docs/reference/icd_search.html              |  11 +-
 docs/reference/icd_structure.html           |  11 +-
 docs/reference/icd_utils.html               |  11 +-
 docs/reference/icd_versions.html            |  11 +-
 docs/reference/index.html                   |  11 +-
 docs/search.json                            |   2 +-
 docs/sitemap.xml                            |   9 ++
 man/codigo.Rd                               |   2 +-
 pkgdown/_pkgdown.yml                        |  12 +-
 vignettes/.gitignore                        |   2 +
 vignettes/codigo.Rmd                        |  21 ++++
 vignettes/icd11_foundation.Rmd              |  19 +++
 31 files changed, 571 insertions(+), 24 deletions(-)
 create mode 100644 docs/articles/codigo.html
 create mode 100644 docs/articles/icd11_foundation.html
 create mode 100644 docs/articles/index.html
 create mode 100644 vignettes/.gitignore
 create mode 100644 vignettes/codigo.Rmd
 create mode 100644 vignettes/icd11_foundation.Rmd

diff --git a/.gitignore b/.gitignore
index d5a36a0..3eb10af 100644
--- a/.gitignore
+++ b/.gitignore
@@ -3,3 +3,4 @@
 .RData
 .Ruserdata
 .httr-oauth
+inst/doc
diff --git a/DESCRIPTION b/DESCRIPTION
index 8bd5a55..f3ce42d 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -3,7 +3,7 @@ Type: Package
 Title: Interface to the International Classification of Diseases (ICD) API
 Version: 0.0.0.9000
 Authors@R: c(
-    person("Anita", "Makori", email = "mark@brixtonhealth.com",
+    person("Anita", "Makori", email = "",
            role = c("aut", "cph")),
     person("Ernest", "Guevarra", 
            comment = c(ORCID = "0000-0002-4887-4415"), 
@@ -25,6 +25,8 @@ Imports:
 Suggests: 
     covr,
     httpuv,
+    knitr,
+    rmarkdown,
     spelling,
     testthat (>= 3.0.0)
 Encoding: UTF-8
@@ -35,3 +37,4 @@ Roxygen: list(markdown = TRUE)
 URL: https://oxford-ihtm.io/codigo/, https://github.com/OxfordIHTM/codigo
 BugReports: https://github.com/OxfordIHTM/codigo/issues
 Config/testthat/edition: 3
+VignetteBuilder: knitr
diff --git a/docs/404.html b/docs/404.html
index e46168c..48d350b 100644
--- a/docs/404.html
+++ b/docs/404.html
@@ -40,8 +40,17 @@
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
       <ul class="navbar-nav me-auto">
+<li class="nav-item">
+  <a class="nav-link" href="https://oxford-ihtm.io/codigo/articles/codigo.html">Get started</a>
+</li>
 <li class="nav-item">
   <a class="nav-link" href="https://oxford-ihtm.io/codigo/reference/index.html">Reference</a>
+</li>
+<li class="nav-item dropdown">
+  <a href="https://oxford-ihtm.io/codigo/#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
+  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
+    <a class="dropdown-item" href="https://oxford-ihtm.io/codigo/articles/icd11_foundation.html">ICD-11 Foundation</a>
+  </div>
 </li>
       </ul>
 <form class="form-inline my-2 my-lg-0" role="search">
diff --git a/docs/CODE_OF_CONDUCT.html b/docs/CODE_OF_CONDUCT.html
index a5d6026..2e356cb 100644
--- a/docs/CODE_OF_CONDUCT.html
+++ b/docs/CODE_OF_CONDUCT.html
@@ -19,7 +19,16 @@
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
       <ul class="navbar-nav me-auto"><li class="nav-item">
+  <a class="nav-link" href="articles/codigo.html">Get started</a>
+</li>
+<li class="nav-item">
   <a class="nav-link" href="reference/index.html">Reference</a>
+</li>
+<li class="nav-item dropdown">
+  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
+  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
+    <a class="dropdown-item" href="articles/icd11_foundation.html">ICD-11 Foundation</a>
+  </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
         <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
diff --git a/docs/CONTRIBUTING.html b/docs/CONTRIBUTING.html
index 5a73492..8eb173e 100644
--- a/docs/CONTRIBUTING.html
+++ b/docs/CONTRIBUTING.html
@@ -19,7 +19,16 @@
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
       <ul class="navbar-nav me-auto"><li class="nav-item">
+  <a class="nav-link" href="articles/codigo.html">Get started</a>
+</li>
+<li class="nav-item">
   <a class="nav-link" href="reference/index.html">Reference</a>
+</li>
+<li class="nav-item dropdown">
+  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
+  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
+    <a class="dropdown-item" href="articles/icd11_foundation.html">ICD-11 Foundation</a>
+  </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
         <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
diff --git a/docs/LICENSE.html b/docs/LICENSE.html
index bf736fe..512af9d 100644
--- a/docs/LICENSE.html
+++ b/docs/LICENSE.html
@@ -19,7 +19,16 @@
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
       <ul class="navbar-nav me-auto"><li class="nav-item">
+  <a class="nav-link" href="articles/codigo.html">Get started</a>
+</li>
+<li class="nav-item">
   <a class="nav-link" href="reference/index.html">Reference</a>
+</li>
+<li class="nav-item dropdown">
+  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
+  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
+    <a class="dropdown-item" href="articles/icd11_foundation.html">ICD-11 Foundation</a>
+  </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
         <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
diff --git a/docs/articles/codigo.html b/docs/articles/codigo.html
new file mode 100644
index 0000000..b6e47d8
--- /dev/null
+++ b/docs/articles/codigo.html
@@ -0,0 +1,122 @@
+<!DOCTYPE html>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<meta name="description" content="Interface to the International Classification of Diseases (ICD) API.
+">
+<title>Introduction to codigo • codigo</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous">
+<!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Introduction to codigo">
+<meta property="og:description" content="Interface to the International Classification of Diseases (ICD) API.
+">
+<meta property="og:image" content="https://oxford-ihtm.io/codigo/logo.png">
+<!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+</head>
+<body>
+    <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
+    
+
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-primary"><div class="container">
+    
+    <a class="navbar-brand me-2" href="../index.html">codigo</a>
+
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+
+    
+    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
+      <span class="navbar-toggler-icon"></span>
+    </button>
+
+    <div id="navbar" class="collapse navbar-collapse ms-3">
+      <ul class="navbar-nav me-auto">
+<li class="active nav-item">
+  <a class="nav-link" href="../articles/codigo.html">Get started</a>
+</li>
+<li class="nav-item">
+  <a class="nav-link" href="../reference/index.html">Reference</a>
+</li>
+<li class="nav-item dropdown">
+  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
+  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
+    <a class="dropdown-item" href="../articles/icd11_foundation.html">ICD-11 Foundation</a>
+  </div>
+</li>
+      </ul>
+<form class="form-inline my-2 my-lg-0" role="search">
+        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off">
+</form>
+
+      <ul class="navbar-nav">
+<li class="nav-item">
+  <a class="external-link nav-link" href="https://www.linkedin.com/company/international-health-and-tropical-medicine">
+    <span class="fab fa fab fa-linkedin fa-lg"></span>
+     
+  </a>
+</li>
+<li class="nav-item">
+  <a class="external-link nav-link" href="https://github.com/OxfordIHTM/codigo/" aria-label="github">
+    <span class="fab fa fab fa-github fa-lg"></span>
+     
+  </a>
+</li>
+      </ul>
+</div>
+
+    
+  </div>
+</nav><div class="container template-article">
+
+
+
+
+<div class="row">
+  <main id="main" class="col-md-9"><div class="page-header">
+      <img src="../logo.png" class="logo" alt=""><h1>Introduction to codigo</h1>
+            
+      
+      <small class="dont-index">Source: <a href="https://github.com/OxfordIHTM/codigo/blob/HEAD/vignettes/codigo.Rmd" class="external-link"><code>vignettes/codigo.Rmd</code></a></small>
+      <div class="d-none name"><code>codigo.Rmd</code></div>
+    </div>
+
+    
+    
+
+  </main>
+</div>
+
+
+
+    <footer><div class="pkgdown-footer-left">
+  <p></p>
+<p>Developed by Anita Makori, Ernest Guevarra.</p>
+</div>
+
+<div class="pkgdown-footer-right">
+  <p></p>
+<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+</div>
+
+    </footer>
+</div>
+
+  
+
+  
+
+  </body>
+</html>
diff --git a/docs/articles/icd11_foundation.html b/docs/articles/icd11_foundation.html
new file mode 100644
index 0000000..d7362ea
--- /dev/null
+++ b/docs/articles/icd11_foundation.html
@@ -0,0 +1,121 @@
+<!DOCTYPE html>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<meta name="description" content="codigo">
+<title>The ICD-11 Foundation and Linearization • codigo</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
+<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet">
+<script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous">
+<!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="The ICD-11 Foundation and Linearization">
+<meta property="og:description" content="codigo">
+<meta property="og:image" content="https://oxford-ihtm.io/codigo/logo.png">
+<!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+</head>
+<body>
+    <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
+    
+
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-primary"><div class="container">
+    
+    <a class="navbar-brand me-2" href="../index.html">codigo</a>
+
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+
+    
+    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
+      <span class="navbar-toggler-icon"></span>
+    </button>
+
+    <div id="navbar" class="collapse navbar-collapse ms-3">
+      <ul class="navbar-nav me-auto">
+<li class="nav-item">
+  <a class="nav-link" href="../articles/codigo.html">Get started</a>
+</li>
+<li class="nav-item">
+  <a class="nav-link" href="../reference/index.html">Reference</a>
+</li>
+<li class="active nav-item dropdown">
+  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
+  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
+    <a class="dropdown-item" href="../articles/icd11_foundation.html">ICD-11 Foundation</a>
+  </div>
+</li>
+      </ul>
+<form class="form-inline my-2 my-lg-0" role="search">
+        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off">
+</form>
+
+      <ul class="navbar-nav">
+<li class="nav-item">
+  <a class="external-link nav-link" href="https://www.linkedin.com/company/international-health-and-tropical-medicine">
+    <span class="fab fa fab fa-linkedin fa-lg"></span>
+     
+  </a>
+</li>
+<li class="nav-item">
+  <a class="external-link nav-link" href="https://github.com/OxfordIHTM/codigo/" aria-label="github">
+    <span class="fab fa fab fa-github fa-lg"></span>
+     
+  </a>
+</li>
+      </ul>
+</div>
+
+    
+  </div>
+</nav><div class="container template-article">
+
+
+
+
+<div class="row">
+  <main id="main" class="col-md-9"><div class="page-header">
+      <img src="../logo.png" class="logo" alt=""><h1>The ICD-11 Foundation and Linearization</h1>
+            
+      
+      <small class="dont-index">Source: <a href="https://github.com/OxfordIHTM/codigo/blob/HEAD/vignettes/icd11_foundation.Rmd" class="external-link"><code>vignettes/icd11_foundation.Rmd</code></a></small>
+      <div class="d-none name"><code>icd11_foundation.Rmd</code></div>
+    </div>
+
+    
+    
+<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://oxford-ihtm.io/codigo/">codigo</a></span><span class="op">)</span></span></code></pre></div>
+  </main>
+</div>
+
+
+
+    <footer><div class="pkgdown-footer-left">
+  <p></p>
+<p>Developed by Anita Makori, Ernest Guevarra.</p>
+</div>
+
+<div class="pkgdown-footer-right">
+  <p></p>
+<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+</div>
+
+    </footer>
+</div>
+
+  
+
+  
+
+  </body>
+</html>
diff --git a/docs/articles/index.html b/docs/articles/index.html
new file mode 100644
index 0000000..6972225
--- /dev/null
+++ b/docs/articles/index.html
@@ -0,0 +1,85 @@
+<!DOCTYPE html>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Articles • codigo</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Articles"><meta property="og:image" content="https://oxford-ihtm.io/codigo/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]--></head><body>
+    <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
+    
+
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-primary"><div class="container">
+    
+    <a class="navbar-brand me-2" href="../index.html">codigo</a>
+
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+
+    
+    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
+      <span class="navbar-toggler-icon"></span>
+    </button>
+
+    <div id="navbar" class="collapse navbar-collapse ms-3">
+      <ul class="navbar-nav me-auto"><li class="nav-item">
+  <a class="nav-link" href="../articles/codigo.html">Get started</a>
+</li>
+<li class="nav-item">
+  <a class="nav-link" href="../reference/index.html">Reference</a>
+</li>
+<li class="nav-item dropdown">
+  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
+  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
+    <a class="dropdown-item" href="../articles/icd11_foundation.html">ICD-11 Foundation</a>
+  </div>
+</li>
+      </ul><form class="form-inline my-2 my-lg-0" role="search">
+        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
+
+      <ul class="navbar-nav"><li class="nav-item">
+  <a class="external-link nav-link" href="https://www.linkedin.com/company/international-health-and-tropical-medicine">
+    <span class="fab fa fab fa-linkedin fa-lg"></span>
+     
+  </a>
+</li>
+<li class="nav-item">
+  <a class="external-link nav-link" href="https://github.com/OxfordIHTM/codigo/" aria-label="github">
+    <span class="fab fa fab fa-github fa-lg"></span>
+     
+  </a>
+</li>
+      </ul></div>
+
+    
+  </div>
+</nav><div class="container template-article-index">
+<div class="row">
+  <main id="main" class="col-md-9"><div class="page-header">
+      <img src="../logo.png" class="logo" alt=""><h1>Articles</h1>
+    </div>
+
+    <div class="section ">
+      <h3>All vignettes</h3>
+      <p class="section-desc"></p>
+
+      <dl><dt><a href="codigo.html">Introduction to codigo</a></dt>
+        <dd><p>Interface to the International Classification of Diseases (ICD) API.</p>
+        </dd><dt><a href="icd11_foundation.html">The ICD-11 Foundation and Linearization</a></dt>
+        <dd>
+      </dd></dl></div>
+  </main></div>
+
+
+    <footer><div class="pkgdown-footer-left">
+  <p></p><p>Developed by Anita Makori, Ernest Guevarra.</p>
+</div>
+
+<div class="pkgdown-footer-right">
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+</div>
+
+    </footer></div>
+
+  
+
+  
+
+  </body></html>
+
diff --git a/docs/authors.html b/docs/authors.html
index c066191..5c58679 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -19,7 +19,16 @@
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
       <ul class="navbar-nav me-auto"><li class="nav-item">
+  <a class="nav-link" href="articles/codigo.html">Get started</a>
+</li>
+<li class="nav-item">
   <a class="nav-link" href="reference/index.html">Reference</a>
+</li>
+<li class="nav-item dropdown">
+  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
+  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
+    <a class="dropdown-item" href="articles/icd11_foundation.html">ICD-11 Foundation</a>
+  </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
         <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
diff --git a/docs/index.html b/docs/index.html
index 0b18a05..0a6a11c 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -52,8 +52,17 @@
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
       <ul class="navbar-nav me-auto">
+<li class="nav-item">
+  <a class="nav-link" href="articles/codigo.html">Get started</a>
+</li>
 <li class="nav-item">
   <a class="nav-link" href="reference/index.html">Reference</a>
+</li>
+<li class="nav-item dropdown">
+  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
+  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
+    <a class="dropdown-item" href="articles/icd11_foundation.html">ICD-11 Foundation</a>
+  </div>
 </li>
       </ul>
 <form class="form-inline my-2 my-lg-0" role="search">
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index 92dfeab..a96e1ee 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -1,8 +1,10 @@
 pandoc: 3.1.1
 pkgdown: 2.0.7
 pkgdown_sha: ~
-articles: {}
-last_built: 2024-02-16T13:24Z
+articles:
+  codigo: codigo.html
+  icd11_foundation: icd11_foundation.html
+last_built: 2024-02-16T15:33Z
 urls:
   reference: https://oxford-ihtm.io/codigo/reference
   article: https://oxford-ihtm.io/codigo/articles
diff --git a/docs/reference/codigo.html b/docs/reference/codigo.html
index d130467..7ab80a9 100644
--- a/docs/reference/codigo.html
+++ b/docs/reference/codigo.html
@@ -28,8 +28,17 @@
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="active nav-item">
+      <ul class="navbar-nav me-auto"><li class="nav-item">
+  <a class="nav-link" href="../articles/codigo.html">Get started</a>
+</li>
+<li class="active nav-item">
   <a class="nav-link" href="../reference/index.html">Reference</a>
+</li>
+<li class="nav-item dropdown">
+  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
+  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
+    <a class="dropdown-item" href="../articles/icd11_foundation.html">ICD-11 Foundation</a>
+  </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
         <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
@@ -78,7 +87,7 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
     <div class="section level2">
     <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a></h2>
     <p><strong>Maintainer</strong>: Ernest Guevarra <a href="mailto:ernest@guevarra.io">ernest@guevarra.io</a> (<a href="https://orcid.org/0000-0002-4887-4415" class="external-link">ORCID</a>) [copyright holder]</p>
-<p>Authors:</p><ul><li><p>Anita Makori <a href="mailto:mark@brixtonhealth.com">mark@brixtonhealth.com</a> [copyright holder]</p></li>
+<p>Authors:</p><ul><li><p>Anita Makori [copyright holder]</p></li>
 </ul></div>
 
   </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
diff --git a/docs/reference/icd11_linearization_mms.html b/docs/reference/icd11_linearization_mms.html
index 56e8ddf..5a85dc4 100644
--- a/docs/reference/icd11_linearization_mms.html
+++ b/docs/reference/icd11_linearization_mms.html
@@ -18,8 +18,17 @@
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="active nav-item">
+      <ul class="navbar-nav me-auto"><li class="nav-item">
+  <a class="nav-link" href="../articles/codigo.html">Get started</a>
+</li>
+<li class="active nav-item">
   <a class="nav-link" href="../reference/index.html">Reference</a>
+</li>
+<li class="nav-item dropdown">
+  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
+  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
+    <a class="dropdown-item" href="../articles/icd11_foundation.html">ICD-11 Foundation</a>
+  </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
         <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
diff --git a/docs/reference/icd11_simple_table_mms.html b/docs/reference/icd11_simple_table_mms.html
index 1bbbfd4..2b3b01c 100644
--- a/docs/reference/icd11_simple_table_mms.html
+++ b/docs/reference/icd11_simple_table_mms.html
@@ -18,8 +18,17 @@
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="active nav-item">
+      <ul class="navbar-nav me-auto"><li class="nav-item">
+  <a class="nav-link" href="../articles/codigo.html">Get started</a>
+</li>
+<li class="active nav-item">
   <a class="nav-link" href="../reference/index.html">Reference</a>
+</li>
+<li class="nav-item dropdown">
+  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
+  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
+    <a class="dropdown-item" href="../articles/icd11_foundation.html">ICD-11 Foundation</a>
+  </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
         <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
diff --git a/docs/reference/icd_authenticate.html b/docs/reference/icd_authenticate.html
index 3e03bd6..a19a95e 100644
--- a/docs/reference/icd_authenticate.html
+++ b/docs/reference/icd_authenticate.html
@@ -18,8 +18,17 @@
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="active nav-item">
+      <ul class="navbar-nav me-auto"><li class="nav-item">
+  <a class="nav-link" href="../articles/codigo.html">Get started</a>
+</li>
+<li class="active nav-item">
   <a class="nav-link" href="../reference/index.html">Reference</a>
+</li>
+<li class="nav-item dropdown">
+  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
+  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
+    <a class="dropdown-item" href="../articles/icd11_foundation.html">ICD-11 Foundation</a>
+  </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
         <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
diff --git a/docs/reference/icd_autocode.html b/docs/reference/icd_autocode.html
index 5df9485..90f4d2c 100644
--- a/docs/reference/icd_autocode.html
+++ b/docs/reference/icd_autocode.html
@@ -18,8 +18,17 @@
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="active nav-item">
+      <ul class="navbar-nav me-auto"><li class="nav-item">
+  <a class="nav-link" href="../articles/codigo.html">Get started</a>
+</li>
+<li class="active nav-item">
   <a class="nav-link" href="../reference/index.html">Reference</a>
+</li>
+<li class="nav-item dropdown">
+  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
+  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
+    <a class="dropdown-item" href="../articles/icd11_foundation.html">ICD-11 Foundation</a>
+  </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
         <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
diff --git a/docs/reference/icd_check.html b/docs/reference/icd_check.html
index bd6dea3..cf63fe6 100644
--- a/docs/reference/icd_check.html
+++ b/docs/reference/icd_check.html
@@ -22,8 +22,17 @@
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="active nav-item">
+      <ul class="navbar-nav me-auto"><li class="nav-item">
+  <a class="nav-link" href="../articles/codigo.html">Get started</a>
+</li>
+<li class="active nav-item">
   <a class="nav-link" href="../reference/index.html">Reference</a>
+</li>
+<li class="nav-item dropdown">
+  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
+  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
+    <a class="dropdown-item" href="../articles/icd11_foundation.html">ICD-11 Foundation</a>
+  </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
         <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
diff --git a/docs/reference/icd_get.html b/docs/reference/icd_get.html
index 467b9f0..ec2434e 100644
--- a/docs/reference/icd_get.html
+++ b/docs/reference/icd_get.html
@@ -18,8 +18,17 @@
     </button>
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
-      <ul class="navbar-nav me-auto"><li class="active nav-item">
+      <ul class="navbar-nav me-auto"><li class="nav-item">
+  <a class="nav-link" href="../articles/codigo.html">Get started</a>
+</li>
+<li class="active nav-item">
   <a class="nav-link" href="../reference/index.html">Reference</a>
+</li>
+<li class="nav-item dropdown">
+  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
+  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
+    <a class="dropdown-item" href="../articles/icd11_foundation.html">ICD-11 Foundation</a>
+  </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
         <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
diff --git a/docs/reference/icd_search.html b/docs/reference/icd_search.html
index c7391b2..8fbd553 100644
--- a/docs/reference/icd_search.html
+++ b/docs/reference/icd_search.html
@@ -18,8 +18,17 @@
     </button>
 
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-      <ul class="navbar-nav me-auto"><li class="active nav-item">
+      <ul class="navbar-nav me-auto"><li class="nav-item">
+  <a class="nav-link" href="../articles/codigo.html">Get started</a>
+</li>
+<li class="active nav-item">
   <a class="nav-link" href="../reference/index.html">Reference</a>
+</li>
+<li class="nav-item dropdown">
+  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
+  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
+    <a class="dropdown-item" href="../articles/icd11_foundation.html">ICD-11 Foundation</a>
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diff --git a/docs/reference/icd_structure.html b/docs/reference/icd_structure.html
index 721d1bf..efc231c 100644
--- a/docs/reference/icd_structure.html
+++ b/docs/reference/icd_structure.html
@@ -18,8 +18,17 @@
     </button>
 
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-      <ul class="navbar-nav me-auto"><li class="active nav-item">
+      <ul class="navbar-nav me-auto"><li class="nav-item">
+  <a class="nav-link" href="../articles/codigo.html">Get started</a>
+</li>
+<li class="active nav-item">
   <a class="nav-link" href="../reference/index.html">Reference</a>
+</li>
+<li class="nav-item dropdown">
+  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
+  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
+    <a class="dropdown-item" href="../articles/icd11_foundation.html">ICD-11 Foundation</a>
+  </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
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diff --git a/docs/reference/icd_utils.html b/docs/reference/icd_utils.html
index 4338084..de06fd8 100644
--- a/docs/reference/icd_utils.html
+++ b/docs/reference/icd_utils.html
@@ -18,8 +18,17 @@
     </button>
 
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-      <ul class="navbar-nav me-auto"><li class="active nav-item">
+      <ul class="navbar-nav me-auto"><li class="nav-item">
+  <a class="nav-link" href="../articles/codigo.html">Get started</a>
+</li>
+<li class="active nav-item">
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+</li>
+<li class="nav-item dropdown">
+  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
+  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
+    <a class="dropdown-item" href="../articles/icd11_foundation.html">ICD-11 Foundation</a>
+  </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
         <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
diff --git a/docs/reference/icd_versions.html b/docs/reference/icd_versions.html
index 3d6052c..d45f086 100644
--- a/docs/reference/icd_versions.html
+++ b/docs/reference/icd_versions.html
@@ -18,8 +18,17 @@
     </button>
 
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-      <ul class="navbar-nav me-auto"><li class="active nav-item">
+      <ul class="navbar-nav me-auto"><li class="nav-item">
+  <a class="nav-link" href="../articles/codigo.html">Get started</a>
+</li>
+<li class="active nav-item">
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+</li>
+<li class="nav-item dropdown">
+  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
+  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
+    <a class="dropdown-item" href="../articles/icd11_foundation.html">ICD-11 Foundation</a>
+  </div>
 </li>
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diff --git a/docs/reference/index.html b/docs/reference/index.html
index 76fff3b..167f840 100644
--- a/docs/reference/index.html
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@@ -18,8 +18,17 @@
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-      <ul class="navbar-nav me-auto"><li class="active nav-item">
+      <ul class="navbar-nav me-auto"><li class="nav-item">
+  <a class="nav-link" href="../articles/codigo.html">Get started</a>
+</li>
+<li class="active nav-item">
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+</li>
+<li class="nav-item dropdown">
+  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
+  <div class="dropdown-menu" aria-labelledby="dropdown-articles">
+    <a class="dropdown-item" href="../articles/icd11_foundation.html">ICD-11 Foundation</a>
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diff --git a/docs/search.json b/docs/search.json
index d7562ff..0c42974 100644
--- a/docs/search.json
+++ b/docs/search.json
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General Public Licenses designed make sure freedom distribute copies free software (charge wish), receive source code can get want , can change software use pieces new free programs, know can things. protect rights, need prevent others denying rights asking surrender rights. Therefore, certain responsibilities distribute copies software, modify : responsibilities respect freedom others. example, distribute copies program, whether gratis fee, must pass recipients freedoms received. must make sure , , receive can get source code. must show terms know rights. Developers use GNU GPL protect rights two steps: (1) assert copyright software, (2) offer License giving legal permission copy, distribute /modify . developers’ authors’ protection, GPL clearly explains warranty free software. users’ authors’ sake, GPL requires modified versions marked changed, problems attributed erroneously authors previous versions. devices designed deny users access install run modified versions software inside , although manufacturer can . fundamentally incompatible aim protecting users’ freedom change software. systematic pattern abuse occurs area products individuals use, precisely unacceptable. Therefore, designed version GPL prohibit practice products. problems arise substantially domains, stand ready extend provision domains future versions GPL, needed protect freedom users. Finally, every program threatened constantly software patents. States allow patents restrict development use software general-purpose computers, , wish avoid special danger patents applied free program make effectively proprietary. prevent , GPL assures patents used render program non-free. precise terms conditions copying, distribution modification follow.","code":""},{"path":[]},{"path":"https://oxford-ihtm.io/codigo/LICENSE.html","id":"id_0-definitions","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"0. Definitions","title":"GNU General Public License","text":"“License” refers version 3 GNU General Public License. “Copyright” also means copyright-like laws apply kinds works, semiconductor masks. “Program” refers copyrightable work licensed License. licensee addressed “”. “Licensees” “recipients” may individuals organizations. “modify” work means copy adapt part work fashion requiring copyright permission, making exact copy. resulting work called “modified version” earlier work work “based ” earlier work. “covered work” means either unmodified Program work based Program. “propagate” work means anything , without permission, make directly secondarily liable infringement applicable copyright law, except executing computer modifying private copy. Propagation includes copying, distribution (without modification), making available public, countries activities well. “convey” work means kind propagation enables parties make receive copies. Mere interaction user computer network, transfer copy, conveying. interactive user interface displays “Appropriate Legal Notices” extent includes convenient prominently visible feature (1) displays appropriate copyright notice, (2) tells user warranty work (except extent warranties provided), licensees may convey work License, view copy License. interface presents list user commands options, menu, prominent item list meets criterion.","code":""},{"path":"https://oxford-ihtm.io/codigo/LICENSE.html","id":"id_1-source-code","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"1. Source Code","title":"GNU General Public License","text":"“source code” work means preferred form work making modifications . “Object code” means non-source form work. “Standard Interface” means interface either official standard defined recognized standards body, , case interfaces specified particular programming language, one widely used among developers working language. “System Libraries” executable work include anything, work whole, () included normal form packaging Major Component, part Major Component, (b) serves enable use work Major Component, implement Standard Interface implementation available public source code form. “Major Component”, context, means major essential component (kernel, window system, ) specific operating system () executable work runs, compiler used produce work, object code interpreter used run . “Corresponding Source” work object code form means source code needed generate, install, (executable work) run object code modify work, including scripts control activities. However, include work’s System Libraries, general-purpose tools generally available free programs used unmodified performing activities part work. example, Corresponding Source includes interface definition files associated source files work, source code shared libraries dynamically linked subprograms work specifically designed require, intimate data communication control flow subprograms parts work. Corresponding Source need include anything users can regenerate automatically parts Corresponding Source. Corresponding Source work source code form work.","code":""},{"path":"https://oxford-ihtm.io/codigo/LICENSE.html","id":"id_2-basic-permissions","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"2. Basic Permissions","title":"GNU General Public License","text":"rights granted License granted term copyright Program, irrevocable provided stated conditions met. License explicitly affirms unlimited permission run unmodified Program. output running covered work covered License output, given content, constitutes covered work. License acknowledges rights fair use equivalent, provided copyright law. may make, run propagate covered works convey, without conditions long license otherwise remains force. may convey covered works others sole purpose make modifications exclusively , provide facilities running works, provided comply terms License conveying material control copyright. thus making running covered works must exclusively behalf, direction control, terms prohibit making copies copyrighted material outside relationship . Conveying circumstances permitted solely conditions stated . Sublicensing allowed; section 10 makes unnecessary.","code":""},{"path":"https://oxford-ihtm.io/codigo/LICENSE.html","id":"id_3-protecting-users-legal-rights-from-anti-circumvention-law","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"3. Protecting Users’ Legal Rights From Anti-Circumvention Law","title":"GNU General Public License","text":"covered work shall deemed part effective technological measure applicable law fulfilling obligations article 11 WIPO copyright treaty adopted 20 December 1996, similar laws prohibiting restricting circumvention measures. convey covered work, waive legal power forbid circumvention technological measures extent circumvention effected exercising rights License respect covered work, disclaim intention limit operation modification work means enforcing, work’s users, third parties’ legal rights forbid circumvention technological measures.","code":""},{"path":"https://oxford-ihtm.io/codigo/LICENSE.html","id":"id_4-conveying-verbatim-copies","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"4. 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Conveying Modified Source Versions","title":"GNU General Public License","text":"may convey work based Program, modifications produce Program, form source code terms section 4, provided also meet conditions: ) work must carry prominent notices stating modified , giving relevant date. b) work must carry prominent notices stating released License conditions added section 7. requirement modifies requirement section 4 “keep intact notices”. c) must license entire work, whole, License anyone comes possession copy. License therefore apply, along applicable section 7 additional terms, whole work, parts, regardless packaged. License gives permission license work way, invalidate permission separately received . d) work interactive user interfaces, must display Appropriate Legal Notices; however, Program interactive interfaces display Appropriate Legal Notices, work need make . compilation covered work separate independent works, nature extensions covered work, combined form larger program, volume storage distribution medium, called “aggregate” compilation resulting copyright used limit access legal rights compilation’s users beyond individual works permit. Inclusion covered work aggregate cause License apply parts aggregate.","code":""},{"path":"https://oxford-ihtm.io/codigo/LICENSE.html","id":"id_6-conveying-non-source-forms","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"6. 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Regardless server hosts Corresponding Source, remain obligated ensure available long needed satisfy requirements. e) Convey object code using peer--peer transmission, provided inform peers object code Corresponding Source work offered general public charge subsection 6d. separable portion object code, whose source code excluded Corresponding Source System Library, need included conveying object code work. “User Product” either (1) “consumer product”, means tangible personal property normally used personal, family, household purposes, (2) anything designed sold incorporation dwelling. determining whether product consumer product, doubtful cases shall resolved favor coverage. particular product received particular user, “normally used” refers typical common use class product, regardless status particular user way particular user actually uses, expects expected use, product. product consumer product regardless whether product substantial commercial, industrial non-consumer uses, unless uses represent significant mode use product. “Installation Information” User Product means methods, procedures, authorization keys, information required install execute modified versions covered work User Product modified version Corresponding Source. information must suffice ensure continued functioning modified object code case prevented interfered solely modification made. convey object code work section , , specifically use , User Product, conveying occurs part transaction right possession use User Product transferred recipient perpetuity fixed term (regardless transaction characterized), Corresponding Source conveyed section must accompanied Installation Information. requirement apply neither third party retains ability install modified object code User Product (example, work installed ROM). requirement provide Installation Information include requirement continue provide support service, warranty, updates work modified installed recipient, User Product modified installed. 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Additional permissions applicable entire Program shall treated though included License, extent valid applicable law. additional permissions apply part Program, part may used separately permissions, entire Program remains governed License without regard additional permissions. convey copy covered work, may option remove additional permissions copy, part . (Additional permissions may written require removal certain cases modify work.) may place additional permissions material, added covered work, can give appropriate copyright permission. Notwithstanding provision License, material add covered work, may (authorized copyright holders material) supplement terms License terms: ) Disclaiming warranty limiting liability differently terms sections 15 16 License; b) Requiring preservation specified reasonable legal notices author attributions material Appropriate Legal Notices displayed works containing ; c) Prohibiting misrepresentation origin material, requiring modified versions material marked reasonable ways different original version; d) Limiting use publicity purposes names licensors authors material; e) Declining grant rights trademark law use trade names, trademarks, service marks; f) Requiring indemnification licensors authors material anyone conveys material (modified versions ) contractual assumptions liability recipient, liability contractual assumptions directly impose licensors authors. non-permissive additional terms considered “restrictions” within meaning section 10. Program received , part , contains notice stating governed License along term restriction, may remove term. license document contains restriction permits relicensing conveying License, may add covered work material governed terms license document, provided restriction survive relicensing conveying. add terms covered work accord section, must place, relevant source files, statement additional terms apply files, notice indicating find applicable terms. Additional terms, permissive non-permissive, may stated form separately written license, stated exceptions; requirements apply either way.","code":""},{"path":"https://oxford-ihtm.io/codigo/LICENSE.html","id":"id_8-termination","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"8. Termination","title":"GNU General Public License","text":"may propagate modify covered work except expressly provided License. attempt otherwise propagate modify void, automatically terminate rights License (including patent licenses granted third paragraph section 11). However, cease violation License, license particular copyright holder reinstated () provisionally, unless copyright holder explicitly finally terminates license, (b) permanently, copyright holder fails notify violation reasonable means prior 60 days cessation. Moreover, license particular copyright holder reinstated permanently copyright holder notifies violation reasonable means, first time received notice violation License (work) copyright holder, cure violation prior 30 days receipt notice. Termination rights section terminate licenses parties received copies rights License. rights terminated permanently reinstated, qualify receive new licenses material section 10.","code":""},{"path":"https://oxford-ihtm.io/codigo/LICENSE.html","id":"id_9-acceptance-not-required-for-having-copies","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"9. Acceptance Not Required for Having Copies","title":"GNU General Public License","text":"required accept License order receive run copy Program. Ancillary propagation covered work occurring solely consequence using peer--peer transmission receive copy likewise require acceptance. However, nothing License grants permission propagate modify covered work. actions infringe copyright accept License. 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Patents","title":"GNU General Public License","text":"“contributor” copyright holder authorizes use License Program work Program based. work thus licensed called contributor’s “contributor version”. contributor’s “essential patent claims” patent claims owned controlled contributor, whether already acquired hereafter acquired, infringed manner, permitted License, making, using, selling contributor version, include claims infringed consequence modification contributor version. purposes definition, “control” includes right grant patent sublicenses manner consistent requirements License. contributor grants non-exclusive, worldwide, royalty-free patent license contributor’s essential patent claims, make, use, sell, offer sale, import otherwise run, modify propagate contents contributor version. following three paragraphs, “patent license” express agreement commitment, however denominated, enforce patent (express permission practice patent covenant sue patent infringement). “grant” patent license party means make agreement commitment enforce patent party. convey covered work, knowingly relying patent license, Corresponding Source work available anyone copy, free charge terms License, publicly available network server readily accessible means, must either (1) cause Corresponding Source available, (2) arrange deprive benefit patent license particular work, (3) arrange, manner consistent requirements License, extend patent license downstream recipients. “Knowingly relying” means actual knowledge , patent license, conveying covered work country, recipient’s use covered work country, infringe one identifiable patents country reason believe valid. , pursuant connection single transaction arrangement, convey, propagate procuring conveyance , covered work, grant patent license parties receiving covered work authorizing use, propagate, modify convey specific copy covered work, patent license grant automatically extended recipients covered work works based . patent license “discriminatory” include within scope coverage, prohibits exercise , conditioned non-exercise one rights specifically granted License. may convey covered work party arrangement third party business distributing software, make payment third party based extent activity conveying work, third party grants, parties receive covered work , discriminatory patent license () connection copies covered work conveyed (copies made copies), (b) primarily connection specific products compilations contain covered work, unless entered arrangement, patent license granted, prior 28 March 2007. Nothing License shall construed excluding limiting implied license defenses infringement may otherwise available applicable patent law.","code":""},{"path":"https://oxford-ihtm.io/codigo/LICENSE.html","id":"id_12-no-surrender-of-others-freedom","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"12. No Surrender of Others’ Freedom","title":"GNU General Public License","text":"conditions imposed (whether court order, agreement otherwise) contradict conditions License, excuse conditions License. convey covered work satisfy simultaneously obligations License pertinent obligations, consequence may convey . example, agree terms obligate collect royalty conveying convey Program, way satisfy terms License refrain entirely conveying Program.","code":""},{"path":"https://oxford-ihtm.io/codigo/LICENSE.html","id":"id_13-use-with-the-gnu-affero-general-public-license","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"13. Use with the GNU Affero General Public License","title":"GNU General Public License","text":"Notwithstanding provision License, permission link combine covered work work licensed version 3 GNU Affero General Public License single combined work, convey resulting work. terms License continue apply part covered work, special requirements GNU Affero General Public License, section 13, concerning interaction network apply combination .","code":""},{"path":"https://oxford-ihtm.io/codigo/LICENSE.html","id":"id_14-revised-versions-of-this-license","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"14. Revised Versions of this License","title":"GNU General Public License","text":"Free Software Foundation may publish revised /new versions GNU General Public License time time. new versions similar spirit present version, may differ detail address new problems concerns. version given distinguishing version number. Program specifies certain numbered version GNU General Public License “later version” applies , option following terms conditions either numbered version later version published Free Software Foundation. Program specify version number GNU General Public License, may choose version ever published Free Software Foundation. Program specifies proxy can decide future versions GNU General Public License can used, proxy’s public statement acceptance version permanently authorizes choose version Program. Later license versions may give additional different permissions. However, additional obligations imposed author copyright holder result choosing follow later version.","code":""},{"path":"https://oxford-ihtm.io/codigo/LICENSE.html","id":"id_15-disclaimer-of-warranty","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"15. Disclaimer of Warranty","title":"GNU General Public License","text":"WARRANTY PROGRAM, EXTENT PERMITTED APPLICABLE LAW. EXCEPT OTHERWISE STATED WRITING COPYRIGHT HOLDERS /PARTIES PROVIDE PROGRAM “” WITHOUT WARRANTY KIND, EITHER EXPRESSED IMPLIED, INCLUDING, LIMITED , IMPLIED WARRANTIES MERCHANTABILITY FITNESS PARTICULAR PURPOSE. ENTIRE RISK QUALITY PERFORMANCE PROGRAM . PROGRAM PROVE DEFECTIVE, ASSUME COST NECESSARY SERVICING, REPAIR CORRECTION.","code":""},{"path":"https://oxford-ihtm.io/codigo/LICENSE.html","id":"id_16-limitation-of-liability","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"16. Limitation of Liability","title":"GNU General Public License","text":"EVENT UNLESS REQUIRED APPLICABLE LAW AGREED WRITING COPYRIGHT HOLDER, PARTY MODIFIES /CONVEYS PROGRAM PERMITTED , LIABLE DAMAGES, INCLUDING GENERAL, SPECIAL, INCIDENTAL CONSEQUENTIAL DAMAGES ARISING USE INABILITY USE PROGRAM (INCLUDING LIMITED LOSS DATA DATA RENDERED INACCURATE LOSSES SUSTAINED THIRD PARTIES FAILURE PROGRAM OPERATE PROGRAMS), EVEN HOLDER PARTY ADVISED POSSIBILITY DAMAGES.","code":""},{"path":"https://oxford-ihtm.io/codigo/LICENSE.html","id":"id_17-interpretation-of-sections-15-and-16","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"17. Interpretation of Sections 15 and 16","title":"GNU General Public License","text":"disclaimer warranty limitation liability provided given local legal effect according terms, reviewing courts shall apply local law closely approximates absolute waiver civil liability connection Program, unless warranty assumption liability accompanies copy Program return fee. END TERMS CONDITIONS","code":""},{"path":"https://oxford-ihtm.io/codigo/LICENSE.html","id":"how-to-apply-these-terms-to-your-new-programs","dir":"","previous_headings":"","what":"How to Apply These Terms to Your New Programs","title":"GNU General Public License","text":"develop new program, want greatest possible use public, best way achieve make free software everyone can redistribute change terms. , attach following notices program. safest attach start source file effectively state exclusion warranty; file least “copyright” line pointer full notice found. Also add information contact electronic paper mail. program terminal interaction, make output short notice like starts interactive mode: hypothetical commands show w show c show appropriate parts General Public License. course, program’s commands might different; GUI interface, use “box”. also get employer (work programmer) school, , sign “copyright disclaimer” program, necessary. information , apply follow GNU GPL, see <http://www.gnu.org/licenses/>. GNU General Public License permit incorporating program proprietary programs. program subroutine library, may consider useful permit linking proprietary applications library. want , use GNU Lesser General Public License instead License. first, please read <http://www.gnu.org/philosophy/--lgpl.html>.","code":"<one line to give the program's name and a brief idea of what it does.> Copyright (C) <year>  <name of author>  This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.  This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more details.  You should have received a copy of the GNU General Public License along with this program.  If not, see <http://www.gnu.org/licenses/>. <program>  Copyright (C) <year>  <name of author> This program comes with ABSOLUTELY NO WARRANTY; for details type 'show w'. This is free software, and you are welcome to redistribute it under certain conditions; type 'show c' for details."},{"path":"https://oxford-ihtm.io/codigo/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Anita Makori. Author, copyright holder. Ernest Guevarra. Author, maintainer, copyright holder.","code":""},{"path":"https://oxford-ihtm.io/codigo/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Anita Makori Ernest Guevarra (2024). codigo: Interface International Classification Diseases (ICD) API. R package version 0.0.9000. URL https://oxford-ihtm.io/codigo/","code":"@Manual{,   title = {codigo: Interface to the International Classification of Diseases (ICD) API},   author = {{Anita Makori} and {Ernest Guevarra}},   year = {2024},   note = {R package version 0.0.9000},   url = {https://oxford-ihtm.io/codigo/}, }"},{"path":"https://oxford-ihtm.io/codigo/index.html","id":"codigo-interface-to-the-international-classification-of-diseases-icd-api-","dir":"","previous_headings":"","what":"Interface to the International Classification of Diseases (ICD) API","title":"Interface to the International Classification of Diseases (ICD) API","text":"International Classification Diseases (ICD) serves broad range uses globally provides critical knowledge extent, causes consequences human disease death worldwide via data reported coded ICD. ICD API allows programmatic access ICD. HTTP based REST API. package provides functions interface ICD API.","code":""},{"path":"https://oxford-ihtm.io/codigo/index.html","id":"what-does-codigo-do","dir":"","previous_headings":"","what":"What does codigo do?","title":"Interface to the International Classification of Diseases (ICD) API","text":"Please note codigo still highly experimental undergoing lot development. Hence, functionalities described high likelihood changing interface approach aim stable working version. Currently, package provides functions authenticating ICD API. , plan develop functions wrap various available API endpoints.","code":""},{"path":"https://oxford-ihtm.io/codigo/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Interface to the International Classification of Diseases (ICD) API","text":"codigo yet CRAN. can install development version codigo GitHub : load codigo","code":"if(!require(remotes)) install.packages(\"remotes\") remotes::install_github(\"OxfordIHTM/codigo\") # load package library(codigo)"},{"path":[]},{"path":"https://oxford-ihtm.io/codigo/index.html","id":"authenticating-with-the-icd-api","dir":"","previous_headings":"Usage","what":"Authenticating with the ICD API","title":"Interface to the International Classification of Diseases (ICD) API","text":"ICD API uses OAuth2 authentication. package set utility functions support ICD API authentication specifications leading generation OAuth2 token. icd_oauth_client() function downstream user-facing function creates ICD OAuth2 client can used token retrieval future functions wrap ICD API entity linearization information retrieval. ICD OAuth2 client can generated follows: function uses built OAuth2 client created light use purposes package development testing. recommended intending use package programmatically performing high volume calls ICD API create access keys (client id client secret) using instructions. , access keys, perform following commands: OAuth2 client can now used various functions package require OAuth2 client authentication making requests ICD API.","code":"icd_oauth_client() ## Create your own OAuth client ---- my_oauth_client <- icd_oauth_client(   id = \"YOUR_CLIENT_ID\",   token_url = \"https://icdaccessmanagement.who.int/connect/token\",   secret = \"YOUR_CLIENT_SECRET\",   name = \"NAME_OF_YOUR_APP )"},{"path":"https://oxford-ihtm.io/codigo/index.html","id":"performing-a-basic-search","dir":"","previous_headings":"Usage","what":"Performing a basic search","title":"Interface to the International Classification of Diseases (ICD) API","text":"main feature ICD API ability search ICD 11 Foundation ICD 11 Linearization information regarding illness/disease. feature captured icd_search_foundation() function. example, colorectal cancer disease interest information available ICD 11 needed, following call can made: gives following output: output tibble created parsed JSON body text HTTP response ICD API.","code":"icd_search_foundation(\"colorectal cancer\", client = my_oauth_client) #> Release `2024-01` matches a known release for ICD-11. #> Language `en` is available for the release specified. #> # A tibble: 8 × 18 #>   id                    title stemId isLeaf postcoordinationAvai…¹ hasCodingNote #> * <chr>                 <chr> <chr>  <lgl>                   <int> <lgl>         #> 1 http://id.who.int/ic… Mali… http:… FALSE                       0 FALSE         #> 2 http://id.who.int/ic… Mali… http:… FALSE                       0 FALSE         #> 3 http://id.who.int/ic… Mali… http:… FALSE                       0 FALSE         #> 4 http://id.who.int/ic… Mali… http:… FALSE                       0 FALSE         #> 5 http://id.who.int/ic… Mali… http:… FALSE                       0 FALSE         #> 6 http://id.who.int/ic… Mali… http:… FALSE                       0 FALSE         #> 7 http://id.who.int/ic… Fami… http:… FALSE                       0 FALSE         #> 8 http://id.who.int/ic… Here… http:… FALSE                       0 FALSE         #> # ℹ abbreviated name: ¹​postcoordinationAvailability #> # ℹ 12 more variables: hasMaternalChapterLink <lgl>, #> #   hasPerinatalChapterLink <lgl>, matchingPVs <named list>, #> #   propertiesTruncated <lgl>, isResidualOther <lgl>, #> #   isResidualUnspecified <lgl>, chapter <chr>, score <dbl>, #> #   titleIsASearchResult <lgl>, titleIsTopScore <lgl>, entityType <int>, #> #   important <lgl>"},{"path":"https://oxford-ihtm.io/codigo/index.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Interface to the International Classification of Diseases (ICD) API","text":"find codigo package useful please cite using suggested citation provided call citation() function follows:","code":"citation(\"codigo\") #> To cite codigo in publications use: #>  #>   Anita Makori and Ernest Guevarra (2024). codigo: Interface to the #>   International Classification of Diseases (ICD) API. R package version #>   0.0.9000. URL https://oxford-ihtm.io/codigo/ #>  #> A BibTeX entry for LaTeX users is #>  #>   @Manual{, #>     title = {codigo: Interface to the International Classification of Diseases (ICD) API}, #>     author = {{Anita Makori} and {Ernest Guevarra}}, #>     year = {2024}, #>     note = {R package version 0.0.9000}, #>     url = {https://oxford-ihtm.io/codigo/}, #>   }"},{"path":"https://oxford-ihtm.io/codigo/index.html","id":"community-guidelines","dir":"","previous_headings":"","what":"Community guidelines","title":"Interface to the International Classification of Diseases (ICD) API","text":"Feedback, bug reports feature requests welcome; file issues seek support . like contribute package, please see contributing guidelines. project released Contributor Code Conduct. participating project agree abide terms.","code":""},{"path":"https://oxford-ihtm.io/codigo/reference/codigo.html","id":null,"dir":"Reference","previous_headings":"","what":"Interface to the International Classification of Diseases (ICD) API — codigo","title":"Interface to the International Classification of Diseases (ICD) API — codigo","text":"International Classification Diseases (ICD) serves broad range uses globally provides critical knowledge extent, causes consequences human disease death worldwide via data reported coded ICD. ICD API allows programmatic access ICD. HTTP based REST API. package provides functions interface ICD API.","code":""},{"path":[]},{"path":"https://oxford-ihtm.io/codigo/reference/codigo.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Interface to the International Classification of Diseases (ICD) API — codigo","text":"Maintainer: Ernest Guevarra ernest@guevarra.io (ORCID) [copyright holder] Authors: Anita Makori mark@brixtonhealth.com [copyright holder]","code":""},{"path":"https://oxford-ihtm.io/codigo/reference/icd.html","id":null,"dir":"Reference","previous_headings":"","what":"Interface to the International Classification of Diseases (ICD) API — icd","title":"Interface to the International Classification of Diseases (ICD) API — icd","text":"International Classification Diseases (ICD) serves broad range uses globally provides critical knowledge extent, causes consequences human disease death worldwide via data reported coded ICD. ICD API allows programmatic access ICD. HTTP based REST API. package provides functions interface ICD API.","code":""},{"path":[]},{"path":"https://oxford-ihtm.io/codigo/reference/icd.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Interface to the International Classification of Diseases (ICD) API — icd","text":"Maintainer: Ernest Guevarra ernest@guevarra.io (ORCID) [copyright holder] Authors: Anita Makori mark@brixtonhealth.com [copyright holder]","code":""},{"path":"https://oxford-ihtm.io/codigo/reference/icd11_linearization_mms.html","id":null,"dir":"Reference","previous_headings":"","what":"ICD-11 Mortality and Morbidity Linearization Outputs — icd11_linearization_mms","title":"ICD-11 Mortality and Morbidity Linearization Outputs — icd11_linearization_mms","text":"ICD-11 Mortality Morbidity Linearization Outputs","code":""},{"path":"https://oxford-ihtm.io/codigo/reference/icd11_linearization_mms.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"ICD-11 Mortality and Morbidity Linearization Outputs — icd11_linearization_mms","text":"","code":"icd11_linearization_mms"},{"path":"https://oxford-ihtm.io/codigo/reference/icd11_linearization_mms.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"ICD-11 Mortality and Morbidity Linearization Outputs — icd11_linearization_mms","text":"data frame 21 columns 36753 rows:","code":""},{"path":"https://oxford-ihtm.io/codigo/reference/icd11_linearization_mms.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"ICD-11 Mortality and Morbidity Linearization Outputs — icd11_linearization_mms","text":"https://icd..int/dev11/Downloads/Download?fileName=LinearizationMiniOutput-MMS-en.zip","code":""},{"path":"https://oxford-ihtm.io/codigo/reference/icd11_linearization_mms.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"ICD-11 Mortality and Morbidity Linearization Outputs — icd11_linearization_mms","text":"","code":"icd11_linearization_mms #> # A tibble: 36,753 × 21 #>    `Foundation URI`         Linearization (relea…¹ Code  BlockId Title ClassKind #>    <chr>                    <chr>                  <chr> <chr>   <chr> <chr>     #>  1 http://id.who.int/icd/e… http://id.who.int/icd… NA    NA      Cert… chapter   #>  2 http://id.who.int/icd/e… http://id.who.int/icd… NA    BlockL… - Ga… block     #>  3 http://id.who.int/icd/e… http://id.who.int/icd… NA    BlockL… - - … block     #>  4 http://id.who.int/icd/e… http://id.who.int/icd… 1A00  NA      - - … category  #>  5 http://id.who.int/icd/e… http://id.who.int/icd… 1A01  NA      - - … category  #>  6 http://id.who.int/icd/e… http://id.who.int/icd… 1A02  NA      - - … category  #>  7 http://id.who.int/icd/e… http://id.who.int/icd… 1A03  NA      - - … category  #>  8 http://id.who.int/icd/e… http://id.who.int/icd… 1A03… NA      - - … category  #>  9 http://id.who.int/icd/e… http://id.who.int/icd… 1A03… NA      - - … category  #> 10 http://id.who.int/icd/e… http://id.who.int/icd… 1A03… NA      - - … category  #> # ℹ 36,743 more rows #> # ℹ abbreviated name: ¹​`Linearization (release) URI` #> # ℹ 15 more variables: DepthInKind <chr>, IsResidual <chr>, #> #   PrimaryLocation <chr>, ChapterNo <chr>, BrowserLink <dbl>, iCatLink <dbl>, #> #   isLeaf <chr>, noOfNonResidualChildren <chr>, `Primary tabulation` <chr>, #> #   Grouping1 <chr>, Grouping2 <chr>, Grouping3 <chr>, Grouping4 <chr>, #> #   Grouping5 <chr>, Version <chr>"},{"path":"https://oxford-ihtm.io/codigo/reference/icd11_simple_table_mms.html","id":null,"dir":"Reference","previous_headings":"","what":"ICD-11 Mortality and Morbidity Simple Table Outputs — icd11_simple_table_mms","title":"ICD-11 Mortality and Morbidity Simple Table Outputs — icd11_simple_table_mms","text":"ICD-11 Mortality Morbidity Simple Table Outputs","code":""},{"path":"https://oxford-ihtm.io/codigo/reference/icd11_simple_table_mms.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"ICD-11 Mortality and Morbidity Simple Table Outputs — icd11_simple_table_mms","text":"","code":"icd11_simple_table_mms"},{"path":"https://oxford-ihtm.io/codigo/reference/icd11_simple_table_mms.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"ICD-11 Mortality and Morbidity Simple Table Outputs — icd11_simple_table_mms","text":"data frame 18 columns 36044 rows:","code":""},{"path":"https://oxford-ihtm.io/codigo/reference/icd11_simple_table_mms.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"ICD-11 Mortality and Morbidity Simple Table Outputs — icd11_simple_table_mms","text":"https://icdcdn..int/static/releasefiles/2024-01/SimpleTabulation-ICD-11-MMS-en.zip","code":""},{"path":"https://oxford-ihtm.io/codigo/reference/icd11_simple_table_mms.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"ICD-11 Mortality and Morbidity Simple Table Outputs — icd11_simple_table_mms","text":"","code":"icd11_simple_table_mms #> # A tibble: 36,044 × 18 #>    `Foundation URI`            `Linearization URI` Code  BlockId Title ClassKind #>    <chr>                       <chr>               <chr> <chr>   <chr> <chr>     #>  1 http://id.who.int/icd/enti… http://id.who.int/… NA    NA      Cert… chapter   #>  2 http://id.who.int/icd/enti… http://id.who.int/… NA    BlockL… - Ga… block     #>  3 http://id.who.int/icd/enti… http://id.who.int/… NA    BlockL… - - … block     #>  4 http://id.who.int/icd/enti… http://id.who.int/… 1A00  NA      - - … category  #>  5 http://id.who.int/icd/enti… http://id.who.int/… 1A01  NA      - - … category  #>  6 http://id.who.int/icd/enti… http://id.who.int/… 1A02  NA      - - … category  #>  7 http://id.who.int/icd/enti… http://id.who.int/… 1A03  NA      - - … category  #>  8 http://id.who.int/icd/enti… http://id.who.int/… 1A03… NA      - - … category  #>  9 http://id.who.int/icd/enti… http://id.who.int/… 1A03… NA      - - … category  #> 10 http://id.who.int/icd/enti… http://id.who.int/… 1A03… NA      - - … category  #> # ℹ 36,034 more rows #> # ℹ 12 more variables: DepthInKind <chr>, IsResidual <chr>, ChapterNo <chr>, #> #   BrowserLink <dbl>, isLeaf <chr>, `Primary tabulation` <chr>, #> #   Grouping1 <chr>, Grouping2 <chr>, Grouping3 <chr>, Grouping4 <chr>, #> #   Grouping5 <chr>, Version <chr>"},{"path":"https://oxford-ihtm.io/codigo/reference/icd_authenticate.html","id":null,"dir":"Reference","previous_headings":"","what":"OAuth2 authentication to ICD API — icd_oauth_client","title":"OAuth2 authentication to ICD API — icd_oauth_client","text":"OAuth2 authentication ICD API","code":""},{"path":"https://oxford-ihtm.io/codigo/reference/icd_authenticate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"OAuth2 authentication to ICD API — icd_oauth_client","text":"","code":"icd_oauth_client(   id = \"6fc8a1e4-4da9-43a8-bd0c-c164c0cb0ebd_3c7e272e-2f4b-46de-b127-df7454e36be8\",   token_url = \"https://icdaccessmanagement.who.int/connect/token\",   secret = \"OGIly8mTatQ2ILuhBTbviIp2FofWiQR3fj4HaPiGseE=\",   name = \"icd_client\",   ... )  icd_authenticate(   req,   client = icd_oauth_client(),   scope = \"icdapi_access\",   ... )"},{"path":"https://oxford-ihtm.io/codigo/reference/icd_authenticate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"OAuth2 authentication to ICD API — icd_oauth_client","text":"id Consumer key, also sometimes called client ID. token_url url used exchange unauthenticated authenticated token. secret Consumer secret, also sometimes called client secret. Despite name, necessarily need protected like password, .e. user still authenticate grant app permission access resources behalf. name Name application. used OAuth, used make easier identify different applications. ... parameters/arguments passed onto httr2::oauth_client() httr2::req_oauth_client_credentials() req request client OAuth2 client. Default call icd_oauth_client(). scope Scopes requested resource owner. Default \"icdapi_access\" specified ICD API documentation.","code":""},{"path":"https://oxford-ihtm.io/codigo/reference/icd_authenticate.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"OAuth2 authentication to ICD API — icd_oauth_client","text":"httr2_oauth_client class object.","code":""},{"path":"https://oxford-ihtm.io/codigo/reference/icd_authenticate.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"OAuth2 authentication to ICD API — icd_oauth_client","text":"","code":"icd_oauth_client() #> <httr2_oauth_client> #> name: icd_client #> id: 6fc8a1e4-4da9-43a8-bd0c-c164c0cb0ebd_3c7e272e-2f4b-46de-b127-df7454e36be8 #> secret: <REDACTED> #> token_url: https://icdaccessmanagement.who.int/connect/token #> auth: oauth_client_req_auth_header"},{"path":"https://oxford-ihtm.io/codigo/reference/icd_autocode.html","id":null,"dir":"Reference","previous_headings":"","what":"Perform autocoding — icd_autocode_foundation","title":"Perform autocoding — icd_autocode_foundation","text":"Perform autocoding","code":""},{"path":"https://oxford-ihtm.io/codigo/reference/icd_autocode.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Perform autocoding — icd_autocode_foundation","text":"","code":"icd_autocode_foundation(   q,   subtree = NULL,   release = NULL,   threshold = NULL,   api_version = c(\"v2\", \"v1\"),   language = \"en\",   tabular = TRUE,   verbose = TRUE,   base_url = \"https://id.who.int\",   client = icd_oauth_client(),   scope = \"icdapi_access\" )"},{"path":"https://oxford-ihtm.io/codigo/reference/icd_autocode.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Perform autocoding — icd_autocode_foundation","text":"q String. Text searched. character % end regarded wild card word. subtree string vector strings URIs. provided, search performed entities provided descendants. release string specifying release version Foundation search . specified, defaults latest release version. See available versions icd_versions. threshold numeric value 0 1 indicates similarity input text matched term. threshold minimum score included output. Default NULL use default value specified API. api_version Version API. Possible values v1 v2. example, provide value v2, API respond format version 2 API. Default v2. language ICD-API multi-lingual. changing header, may make API respond different languages. Languages available translations ICD-11 completes. values language codes en, es, zh, etc. Depending release_id specified, available languages vary. Default English (\"en\"). tabular Logical. output structured tibble? Default TRUE. verbose Logical. non-warning non-error messages printed? Default TRUE. base_url base URL API. Default uses API server https://id..int. using locally deployed server hosting ICD API server, specify URL instance . client OAuth2 client produced call icd_oauth_client(). scope Scopes requested resource owner. Default \"icdapi_access\" specified ICD API documentation.","code":""},{"path":"https://oxford-ihtm.io/codigo/reference/icd_autocode.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Perform autocoding — icd_autocode_foundation","text":"autocode","code":""},{"path":"https://oxford-ihtm.io/codigo/reference/icd_autocode.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Perform autocoding — icd_autocode_foundation","text":"","code":"icd_autocode_foundation(\"cholera\") #> Release `2024-01` matches a known release for ICD-11. #> Language `en` is available for the release specified. #> # A tibble: 1 × 6 #>   searchText matchingText foundationURI          matchLevel matchScore matchType #>   <chr>      <chr>        <chr>                       <int>      <int>     <int> #> 1 cholera    Cholera      http://id.who.int/icd…          0          1         0"},{"path":"https://oxford-ihtm.io/codigo/reference/icd_check.html","id":null,"dir":"Reference","previous_headings":"","what":"Checks for specified parameters supplied to search, autocode, and get\nfunctions — icd_check_release","title":"Checks for specified parameters supplied to search, autocode, and get\nfunctions — icd_check_release","text":"Checks specified parameters supplied search, autocode, get functions","code":""},{"path":"https://oxford-ihtm.io/codigo/reference/icd_check.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Checks for specified parameters supplied to search, autocode, and get\nfunctions — icd_check_release","text":"","code":"icd_check_release(release, verbose = TRUE)  icd_check_language(release = NULL, language, verbose = TRUE)"},{"path":"https://oxford-ihtm.io/codigo/reference/icd_check.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Checks for specified parameters supplied to search, autocode, and get\nfunctions — icd_check_release","text":"release string specifying release version ICD-11. verbose Logical. non-warning non-error messages printed? Default TRUE. language language codes en, es, zh, etc.","code":""},{"path":"https://oxford-ihtm.io/codigo/reference/icd_check.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Checks for specified parameters supplied to search, autocode, and get\nfunctions — icd_check_release","text":"message error release provided recognised . message warning language requested available release provided. icd_check_language(), returns character value character vector acceptable language codes.","code":""},{"path":"https://oxford-ihtm.io/codigo/reference/icd_check.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Checks for specified parameters supplied to search, autocode, and get\nfunctions — icd_check_release","text":"","code":"icd_check_release(\"2024-01\") #> Release `2024-01` matches a known release for ICD-11. try(icd_check_release(\"2025-01\")) #> Error in icd_check_release(\"2025-01\") :  #>   Release `2025-01` does not match any known release for ICD-11 #>        or ICD-10. Please verify and check with `icd_versions` and try again. icd_check_language(\"2024-01\", \"ar\") #> Release `2024-01` matches a known release for ICD-11. #> Language `ar` is available for the release specified. #> [1] \"ar\" icd_check_language(\"2024-01\", \"rr\") #> Release `2024-01` matches a known release for ICD-11. #> Warning: Language `rr` is not available for the release specified. Returning results for `en` (default). #> [1] \"en\" try(icd_check_language(\"2025-01\", \"ar\")) #> Error in icd_check_release(release, verbose = verbose) :  #>   Release `2025-01` does not match any known release for ICD-11 #>        or ICD-10. Please verify and check with `icd_versions` and try again."},{"path":"https://oxford-ihtm.io/codigo/reference/icd_get.html","id":null,"dir":"Reference","previous_headings":"","what":"Get information on various ICD 11 Foundation entities — icd_get_foundation","title":"Get information on various ICD 11 Foundation entities — icd_get_foundation","text":"Get information various ICD 11 Foundation entities","code":""},{"path":"https://oxford-ihtm.io/codigo/reference/icd_get.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get information on various ICD 11 Foundation entities — icd_get_foundation","text":"","code":"icd_get_foundation(   release = NULL,   api_version = c(\"v2\", \"v1\"),   language = \"en\",   tabular = TRUE,   verbose = TRUE,   base_url = \"https://id.who.int\",   client = icd_oauth_client(),   scope = \"icdapi_access\" )  icd_get_entity(   id,   release = NULL,   include = NULL,   api_version = c(\"v2\", \"v1\"),   language = \"en\",   base_url = \"https://id.who.int\",   client = icd_oauth_client(),   scope = \"icdapi_access\" )"},{"path":"https://oxford-ihtm.io/codigo/reference/icd_get.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get information on various ICD 11 Foundation entities — icd_get_foundation","text":"release string specifying release version Foundation search . specified, defaults latest release version. See available versions icd_versions. api_version Version API. Possible values v1 v2. example, provide value v2, API respond format version 2 API. Default v2. language ICD-API multi-lingual. changing header, may make API respond different languages. Languages available translations ICD-11 completes. values language codes en, es, zh, etc. Depending release_id specified, available languages vary. Default English (\"en\"). tabular Logical. output structured tibble? Default TRUE. verbose Logical. non-warning non-error messages printed? Default TRUE. base_url base URL API. Default uses API server https://id..int. using locally deployed server hosting ICD API server, specify URL instance . client OAuth2 client produced call icd_oauth_client(). scope Scopes requested resource owner. Default \"icdapi_access\" specified ICD API documentation. id Unique numerical identifier entity. include string vector strings optional property values included response. property values can included \"ancestor\", \"descendant\", \"diagnosticCriteria\". specified, properties included response.","code":""},{"path":"https://oxford-ihtm.io/codigo/reference/icd_get.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get information on various ICD 11 Foundation entities — icd_get_foundation","text":"list information specified ICD 11 Foundation top level entities.","code":""},{"path":"https://oxford-ihtm.io/codigo/reference/icd_get.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get information on various ICD 11 Foundation entities — icd_get_foundation","text":"","code":"icd_get_foundation() #> Release `2024-01` matches a known release for ICD-11. #> Language `en` is available for the release specified. #> New names: #> • `` -> `...8` #> # A tibble: 2 × 9 #>   `@context`   `@id` `title@language` `title@value` releaseId availableLanguages #>   <chr>        <chr> <chr>            <chr>         <chr>     <chr>              #> 1 http://id.w… http… en               WHO Family o… 2024-01   ar, cs, en, es, f… #> 2 http://id.w… http… en               WHO Family o… 2024-01   ar, cs, en, es, f… #> # ℹ 3 more variables: releaseDate <chr>, child <chr>, browserUrl <chr> icd_get_entity(id = \"1435254666\")     ## chapter #> Release `2024-01` matches a known release for ICD-11. #> Language `en` is available for the release specified. #> $`@context` #> [1] \"http://id.who.int/icd/contexts/contextForFoundationEntity.json\" #>  #> $`@id` #> [1] \"http://id.who.int/icd/entity/1435254666\" #>  #> $parent #> $parent[[1]] #> [1] \"http://id.who.int/icd/entity/455013390\" #>  #>  #> $child #> $child[[1]] #> [1] \"http://id.who.int/icd/entity/588616678\" #>  #> $child[[2]] #> [1] \"http://id.who.int/icd/entity/1904876434\" #>  #> $child[[3]] #> [1] \"http://id.who.int/icd/entity/979278646\" #>  #> $child[[4]] #> [1] \"http://id.who.int/icd/entity/1539889147\" #>  #> $child[[5]] #> [1] \"http://id.who.int/icd/entity/1412960686\" #>  #> $child[[6]] #> [1] \"http://id.who.int/icd/entity/1935092859\" #>  #> $child[[7]] #> [1] \"http://id.who.int/icd/entity/487269828\" #>  #> $child[[8]] #> [1] \"http://id.who.int/icd/entity/1000704511\" #>  #> $child[[9]] #> [1] \"http://id.who.int/icd/entity/1104303944\" #>  #> $child[[10]] #> [1] \"http://id.who.int/icd/entity/1585949804\" #>  #> $child[[11]] #> [1] \"http://id.who.int/icd/entity/1959883044\" #>  #> $child[[12]] #> [1] \"http://id.who.int/icd/entity/921595235\" #>  #> $child[[13]] #> [1] \"http://id.who.int/icd/entity/1251496839\" #>  #> $child[[14]] #> [1] \"http://id.who.int/icd/entity/1136802325\" #>  #> $child[[15]] #> [1] \"http://id.who.int/icd/entity/145723401\" #>  #> $child[[16]] #> [1] \"http://id.who.int/icd/entity/985510409\" #>  #> $child[[17]] #> [1] \"http://id.who.int/icd/entity/1646490591\" #>  #> $child[[18]] #> [1] \"http://id.who.int/icd/entity/1939815950\" #>  #> $child[[19]] #> [1] \"http://id.who.int/icd/entity/255141529\" #>  #> $child[[20]] #> [1] \"http://id.who.int/icd/entity/293771399\" #>  #> $child[[21]] #> [1] \"http://id.who.int/icd/entity/5960175\" #>  #> $child[[22]] #> [1] \"http://id.who.int/icd/entity/911707612\" #>  #> $child[[23]] #> [1] \"http://id.who.int/icd/entity/1965146397\" #>  #> $child[[24]] #> [1] \"http://id.who.int/icd/entity/142052508\" #>  #> $child[[25]] #> [1] \"http://id.who.int/icd/entity/1760597414\" #>  #> $child[[26]] #> [1] \"http://id.who.int/icd/entity/458687859\" #>  #> $child[[27]] #> [1] \"http://id.who.int/icd/entity/2143513892\" #>  #>  #> $browserUrl #> [1] \"https://icd.who.int/browse/2024-01/foundation/en#1435254666\" #>  #> $title #> $title$`@language` #> [1] \"en\" #>  #> $title$`@value` #> [1] \"Certain infectious or parasitic diseases\" #>  #>  #> $synonym #> $synonym[[1]] #> $synonym[[1]]$label #> $synonym[[1]]$label$`@language` #> [1] \"en\" #>  #> $synonym[[1]]$label$`@value` #> [1] \"infection NOS\" #>  #>  #>  #> $synonym[[2]] #> $synonym[[2]]$label #> $synonym[[2]]$label$`@language` #> [1] \"en\" #>  #> $synonym[[2]]$label$`@value` #> [1] \"infectious disease NOS\" #>  #>  #>  #> $synonym[[3]] #> $synonym[[3]]$label #> $synonym[[3]]$label$`@language` #> [1] \"en\" #>  #> $synonym[[3]]$label$`@value` #> [1] \"infection unknown\" #>  #>  #>  #> $synonym[[4]] #> $synonym[[4]]$label #> $synonym[[4]]$label$`@language` #> [1] \"en\" #>  #> $synonym[[4]]$label$`@value` #> [1] \"infection process NOS\" #>  #>  #>  #> $synonym[[5]] #> $synonym[[5]]$label #> $synonym[[5]]$label$`@language` #> [1] \"en\" #>  #> $synonym[[5]]$label$`@value` #> [1] \"infection by unspecified organism and of unspecified site\" #>  #>  #>  #>  #> $definition #> $definition$`@language` #> [1] \"en\" #>  #> $definition$`@value` #> [1] \"This chapter includes certain conditions caused by pathogenic organisms or microorganisms, such as bacteria, viruses, parasites or fungi.\" #>  #>  #> $exclusion #> $exclusion[[1]] #> $exclusion[[1]]$label #> $exclusion[[1]]$label$`@language` #> [1] \"en\" #>  #> $exclusion[[1]]$label$`@value` #> [1] \"Infection arising from device, implant or graft, not elsewhere classified\" #>  #>  #> $exclusion[[1]]$foundationReference #> [1] \"http://id.who.int/icd/entity/1612485599\" #>  #>  #>  #> $relatedEntitiesInPerinatalChapter #> $relatedEntitiesInPerinatalChapter[[1]] #> [1] \"http://id.who.int/icd/entity/911707612\" #>  #>  icd_get_entity(id = \"588616678\")      ## block; depth 1 #> Release `2024-01` matches a known release for ICD-11. #> Language `en` is available for the release specified. #> $`@context` #> [1] \"http://id.who.int/icd/contexts/contextForFoundationEntity.json\" #>  #> $`@id` #> [1] \"http://id.who.int/icd/entity/588616678\" #>  #> $parent #> $parent[[1]] #> [1] \"http://id.who.int/icd/entity/1435254666\" #>  #>  #> $child #> $child[[1]] #> [1] \"http://id.who.int/icd/entity/135352227\" #>  #> $child[[2]] #> [1] \"http://id.who.int/icd/entity/1834648119\" #>  #> $child[[3]] #> [1] \"http://id.who.int/icd/entity/30738976\" #>  #> $child[[4]] #> [1] \"http://id.who.int/icd/entity/730271848\" #>  #> $child[[5]] #> [1] \"http://id.who.int/icd/entity/2092703582\" #>  #> $child[[6]] #> [1] \"http://id.who.int/icd/entity/1688127370\" #>  #>  #> $browserUrl #> [1] \"https://icd.who.int/browse/2024-01/foundation/en#588616678\" #>  #> $title #> $title$`@language` #> [1] \"en\" #>  #> $title$`@value` #> [1] \"Gastroenteritis or colitis of infectious origin\" #>  #>  #> $relatedEntitiesInPerinatalChapter #> $relatedEntitiesInPerinatalChapter[[1]] #> [1] \"http://id.who.int/icd/entity/911707612\" #>  #>  icd_get_entity(id = \"1465325727\")     ## category; depth 1 #> Release `2024-01` matches a known release for ICD-11. #> Language `en` is available for the release specified. #> $`@context` #> [1] \"http://id.who.int/icd/contexts/contextForFoundationEntity.json\" #>  #> $`@id` #> [1] \"http://id.who.int/icd/entity/1465325727\" #>  #> $parent #> $parent[[1]] #> [1] \"http://id.who.int/icd/entity/30738976\" #>  #>  #> $browserUrl #> [1] \"https://icd.who.int/browse/2024-01/foundation/en#1465325727\" #>  #> $title #> $title$`@language` #> [1] \"en\" #>  #> $title$`@value` #> [1] \"Enteritis due to Norovirus\" #>  #>  #> $synonym #> $synonym[[1]] #> $synonym[[1]]$label #> $synonym[[1]]$label$`@language` #> [1] \"en\" #>  #> $synonym[[1]]$label$`@value` #> [1] \"acute gastroenteropathy due to Norwalk agent\" #>  #>  #>  #> $synonym[[2]] #> $synonym[[2]]$label #> $synonym[[2]]$label$`@language` #> [1] \"en\" #>  #> $synonym[[2]]$label$`@value` #> [1] \"viral gastroenteritis due to Norwalk agent\" #>  #>  #>  #> $synonym[[3]] #> $synonym[[3]]$label #> $synonym[[3]]$label$`@language` #> [1] \"en\" #>  #> $synonym[[3]]$label$`@value` #> [1] \"winter vomiting\" #>  #>  #>  #> $synonym[[4]] #> $synonym[[4]]$label #> $synonym[[4]]$label$`@language` #> [1] \"en\" #>  #> $synonym[[4]]$label$`@value` #> [1] \"epidemic winter vomiting disease\" #>  #>  #>  #> $synonym[[5]] #> $synonym[[5]]$label #> $synonym[[5]]$label$`@language` #> [1] \"en\" #>  #> $synonym[[5]]$label$`@value` #> [1] \"small round structured virus enteritis\" #>  #>  #>  #> $synonym[[6]] #> $synonym[[6]]$label #> $synonym[[6]]$label$`@language` #> [1] \"en\" #>  #> $synonym[[6]]$label$`@value` #> [1] \"epidemic vomiting syndrome\" #>  #>  #>  #> $synonym[[7]] #> $synonym[[7]]$label #> $synonym[[7]]$label$`@language` #> [1] \"en\" #>  #> $synonym[[7]]$label$`@value` #> [1] \"epidemic vomiting\" #>  #>  #>  #> $synonym[[8]] #> $synonym[[8]]$label #> $synonym[[8]]$label$`@language` #> [1] \"en\" #>  #> $synonym[[8]]$label$`@value` #> [1] \"epidemic nausea\" #>  #>  #>  #> $synonym[[9]] #> $synonym[[9]]$label #> $synonym[[9]]$label$`@language` #> [1] \"en\" #>  #> $synonym[[9]]$label$`@value` #> [1] \"epidemic viral gastroenteritis due to Norwalk virus\" #>  #>  #>  #> $synonym[[10]] #> $synonym[[10]]$label #> $synonym[[10]]$label$`@language` #> [1] \"en\" #>  #> $synonym[[10]]$label$`@value` #> [1] \"Noroviral enteritis\" #>  #>  #>  #>  #> $definition #> $definition$`@language` #> [1] \"en\" #>  #> $definition$`@value` #> [1] \"A disease of the gastrointestinal tract, caused by an infection with norovirus. This disease is characterised by acute onset of vomiting, non-haemorrhagic diarrhoea, and abdominal pain. Transmission is by ingestion of contaminated food or water, direct contact, or through fomites. Confirmation is by identification of norovirus.\" #>  #>  #> $longDefinition #> $longDefinition$`@language` #> [1] \"en\" #>  #> $longDefinition$`@value` #> [1] \"The official genus name Noroviruses which is the group of viruses previously described as “Norwalk-like viruses” are a group of related, single-stranded RNA, non-enveloped viruses. Noroviruses cause self-limiting explosive acute gastroenteritis that last for 24-48hours in humans. The most common symptoms of acute gastroenteritis are diarrhea, vomiting, and stomach pain.\" #>  #>  #> $relatedEntitiesInPerinatalChapter #> $relatedEntitiesInPerinatalChapter[[1]] #> [1] \"http://id.who.int/icd/entity/911707612\" #>  #>"},{"path":"https://oxford-ihtm.io/codigo/reference/icd_search.html","id":null,"dir":"Reference","previous_headings":"","what":"Search the foundation component of the ICD-11 — icd_search_foundation","title":"Search the foundation component of the ICD-11 — icd_search_foundation","text":"Search foundation component ICD-11","code":""},{"path":"https://oxford-ihtm.io/codigo/reference/icd_search.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Search the foundation component of the ICD-11 — icd_search_foundation","text":"","code":"icd_search_foundation(   q,   subtree = NULL,   chapter = NULL,   flexisearch = FALSE,   flat = TRUE,   properties = NULL,   release = NULL,   highlight = FALSE,   api_version = c(\"v2\", \"v1\"),   language = \"en\",   tabular = TRUE,   verbose = TRUE,   base_url = \"https://id.who.int\",   client = icd_oauth_client(),   scope = \"icdapi_access\" )"},{"path":"https://oxford-ihtm.io/codigo/reference/icd_search.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Search the foundation component of the ICD-11 — icd_search_foundation","text":"q String. Text searched. character % end regarded wild card word. subtree string vector strings URIs. provided, search performed entities provided descendants. chapter string vector strings chapter codes eg: c(\"01\", \"02\") provided, search performed chapters. flexisearch Logical. Default FALSE. Changes search mode flexible search. regular search mode, Coding Tool give results contain words used search. accepts different variants synonyms words essentially searches result contains components search. Whereas flexible search mode, results contain words typed. still try find best matching phrase may words search matched . recommended use flexible search regular search provide result. flat Logical. Default FALSE. set true search result entities provided nested data structure representing ICD-11 hierarchy. Otherwise listed flat list matches. properties string vector strings properties searched. default system  searches, \"Title\", \"Synonyms\", \"FullySpecifiedName\". valid values used : \"Title\", \"Synonym\", \"NarrowerTerm\", \"FullySpecifiedName\", \"Definition\", \"Exclusion\". release string specifying release version Foundation search . specified, defaults latest release version. See available versions icd_versions. highlight Logical. Default FALSE. set FALSE search result highlighting turned results contain special tags highlighting results found within text. api_version Version API. Possible values v1 v2. example, provide value v2, API respond format version 2 API. Default v2. language ICD-API multi-lingual. changing header, may make API respond different languages. Languages available translations ICD-11 completes. values language codes en, es, zh, etc. Depending release_id specified, available languages vary. Default English (\"en\"). tabular Logical. output structured tibble? Default TRUE. verbose Logical. non-warning non-error messages printed? Default TRUE. base_url base URL API. Default uses API server https://id..int. using locally deployed server hosting ICD API server, specify URL instance . client OAuth2 client produced call icd_oauth_client(). scope Scopes requested resource owner. Default \"icdapi_access\" specified ICD API documentation.","code":""},{"path":"https://oxford-ihtm.io/codigo/reference/icd_search.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Search the foundation component of the ICD-11 — icd_search_foundation","text":"tibble search results.","code":""},{"path":"https://oxford-ihtm.io/codigo/reference/icd_search.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Search the foundation component of the ICD-11 — icd_search_foundation","text":"","code":"icd_search_foundation(\"colorectal cancer\") #> Release `2024-01` matches a known release for ICD-11. #> Language `en` is available for the release specified. #> # A tibble: 8 × 18 #>   id                    title stemId isLeaf postcoordinationAvai…¹ hasCodingNote #> * <chr>                 <chr> <chr>  <lgl>                   <int> <lgl>         #> 1 http://id.who.int/ic… Mali… http:… FALSE                       0 FALSE         #> 2 http://id.who.int/ic… Mali… http:… FALSE                       0 FALSE         #> 3 http://id.who.int/ic… Mali… http:… FALSE                       0 FALSE         #> 4 http://id.who.int/ic… Mali… http:… FALSE                       0 FALSE         #> 5 http://id.who.int/ic… Mali… http:… FALSE                       0 FALSE         #> 6 http://id.who.int/ic… Mali… http:… FALSE                       0 FALSE         #> 7 http://id.who.int/ic… Fami… http:… FALSE                       0 FALSE         #> 8 http://id.who.int/ic… Here… http:… FALSE                       0 FALSE         #> # ℹ abbreviated name: ¹​postcoordinationAvailability #> # ℹ 12 more variables: hasMaternalChapterLink <lgl>, #> #   hasPerinatalChapterLink <lgl>, matchingPVs <named list>, #> #   propertiesTruncated <lgl>, isResidualOther <lgl>, #> #   isResidualUnspecified <lgl>, chapter <chr>, score <dbl>, #> #   titleIsASearchResult <lgl>, titleIsTopScore <lgl>, entityType <int>, #> #   important <lgl>"},{"path":"https://oxford-ihtm.io/codigo/reference/icd_search_foundation.html","id":null,"dir":"Reference","previous_headings":"","what":"Search the foundation component of the ICD-11 — icd_search_foundation","title":"Search the foundation component of the ICD-11 — icd_search_foundation","text":"Search foundation component ICD-11","code":""},{"path":"https://oxford-ihtm.io/codigo/reference/icd_search_foundation.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Search the foundation component of the ICD-11 — icd_search_foundation","text":"","code":"icd_search_foundation(   base_url = \"https://id.who.int/icd\",   client = icd_oauth_client(),   q = NULL,   flexisearch = FALSE,   flat = TRUE,   highlight = FALSE,   api_version = c(\"v2\", \"v1\"),   language = \"en\" )"},{"path":"https://oxford-ihtm.io/codigo/reference/icd_search_foundation.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Search the foundation component of the ICD-11 — icd_search_foundation","text":"base_url base URL API. Default uses API server https://id..int/icd/entity client OAuth2 client produced call icd_oauth_client() q String. Text searched. character % end regarded wild card word flexisearch Logical. Default FALSE. Changes search mode flexible search. regular search mode, Coding Tool give results contain words used search. accepts different variants synonyms words essentially searches result contains components search. Whereas flexible search mode, results contain words typed. still try find best matching phrase may words search matched . recommended use flexible search regular search provide result flat Logical. Default FALSE. set true search result entities provided nested data structure representing ICD-11 hierarchy. Otherwise listed flat list matches highlight Logical. Default FALSE. set FALSE search result highlighting turned results contain special tags highlighting results found within text api_version Version API. Possible values v1 v2. example, provide value v2, API respond format version 2 API. Default v2 language ICD-API multi-lingual. changing header, may make API respond different languages. Languages available translations ICD-11 completes. values language codes en, es, zh, etc. Depending release_id specified, available languages vary. Default English (\"en\").","code":""},{"path":"https://oxford-ihtm.io/codigo/reference/icd_search_foundation.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Search the foundation component of the ICD-11 — icd_search_foundation","text":"httr2_response object","code":""},{"path":"https://oxford-ihtm.io/codigo/reference/icd_search_foundation.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Search the foundation component of the ICD-11 — icd_search_foundation","text":"","code":"icd_search_foundation(q = \"cholera\") #> <httr2_response> #> GET #> https://id.who.int/icd/entity/search?q=cholera&useFlexisearch=false&flatResults=true&highlightingEnabled=false #> Status: 200 OK #> Content-Type: application/json #> Body: In memory (17590 bytes)"},{"path":"https://oxford-ihtm.io/codigo/reference/icd_structure.html","id":null,"dir":"Reference","previous_headings":"","what":"Structure ICD list and ICD search outputs — icd_structure_foundation","title":"Structure ICD list and ICD search outputs — icd_structure_foundation","text":"Structure ICD list ICD search outputs","code":""},{"path":"https://oxford-ihtm.io/codigo/reference/icd_structure.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Structure ICD list and ICD search outputs — icd_structure_foundation","text":"","code":"icd_structure_foundation(icd_list)  icd_structure_search(icd_search)  icd_structure_autocode(icd_autocode)"},{"path":"https://oxford-ihtm.io/codigo/reference/icd_structure.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Structure ICD list and ICD search outputs — icd_structure_foundation","text":"icd_list object produced call icd_get functions icd_search object produced call icd_search functions icd_autocode object produced call icd_autocode functions","code":""},{"path":"https://oxford-ihtm.io/codigo/reference/icd_structure.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Structure ICD list and ICD search outputs — icd_structure_foundation","text":"tibble structured ICD outputs.","code":""},{"path":"https://oxford-ihtm.io/codigo/reference/icd_structure.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Structure ICD list and ICD search outputs — icd_structure_foundation","text":"functions meant helper functions used within icd_get, icd_search, icd_autocode functions structure output responses.","code":""},{"path":"https://oxford-ihtm.io/codigo/reference/icd_structure.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Structure ICD list and ICD search outputs — icd_structure_foundation","text":"","code":"icd_list <- icd_get_foundation(tabular = FALSE) #> Release `2024-01` matches a known release for ICD-11. #> Language `en` is available for the release specified. icd_tbl_foundation <- icd_structure_foundation(icd_list) #> New names: #> • `` -> `...8` icd_structure_search(icd_search_foundation(\"cholera\", tabular = FALSE)) #> Release `2024-01` matches a known release for ICD-11. #> Language `en` is available for the release specified. #> # A tibble: 103 × 18 #>    id                   title stemId isLeaf postcoordinationAvai…¹ hasCodingNote #>  * <chr>                <chr> <chr>  <lgl>                   <int> <lgl>         #>  1 http://id.who.int/i… Chol… http:… FALSE                       0 FALSE         #>  2 http://id.who.int/i… Chol… http:… FALSE                       0 FALSE         #>  3 http://id.who.int/i… Chol… http:… FALSE                       0 FALSE         #>  4 http://id.who.int/i… Chol… http:… FALSE                       0 FALSE         #>  5 http://id.who.int/i… Chol… http:… FALSE                       0 FALSE         #>  6 http://id.who.int/i… Chol… http:… FALSE                       0 FALSE         #>  7 http://id.who.int/i… Chol… http:… FALSE                       0 FALSE         #>  8 http://id.who.int/i… Chol… http:… FALSE                       0 FALSE         #>  9 http://id.who.int/i… Chol… http:… FALSE                       0 FALSE         #> 10 http://id.who.int/i… Chol… http:… FALSE                       0 FALSE         #> # ℹ 93 more rows #> # ℹ abbreviated name: ¹​postcoordinationAvailability #> # ℹ 12 more variables: hasMaternalChapterLink <lgl>, #> #   hasPerinatalChapterLink <lgl>, matchingPVs <named list>, #> #   propertiesTruncated <lgl>, isResidualOther <lgl>, #> #   isResidualUnspecified <lgl>, chapter <chr>, score <dbl>, #> #   titleIsASearchResult <lgl>, titleIsTopScore <lgl>, entityType <int>, … icd_structure_autocode(icd_autocode_foundation(\"cholera\")) #> Release `2024-01` matches a known release for ICD-11. #> Language `en` is available for the release specified. #> # A tibble: 1 × 6 #>   searchText matchingText foundationURI          matchLevel matchScore matchType #>   <chr>      <chr>        <chr>                       <int>      <int>     <int> #> 1 cholera    Cholera      http://id.who.int/icd…          0          1         0"},{"path":"https://oxford-ihtm.io/codigo/reference/icd_utils.html","id":null,"dir":"Reference","previous_headings":"","what":"Utility functions for retrieving ICD parameters and definitions — icd_get_releases","title":"Utility functions for retrieving ICD parameters and definitions — icd_get_releases","text":"Utility functions retrieving ICD parameters definitions","code":""},{"path":"https://oxford-ihtm.io/codigo/reference/icd_utils.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Utility functions for retrieving ICD parameters and definitions — icd_get_releases","text":"","code":"icd_get_releases(icd = c(\"icd11\", \"icd10\"), latest = FALSE)  icd_get_languages(icd = c(\"icd11\", \"icd10\"), latest = FALSE)  icd_get_entities(class = NULL)"},{"path":"https://oxford-ihtm.io/codigo/reference/icd_utils.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Utility functions for retrieving ICD parameters and definitions — icd_get_releases","text":"icd character string available ICD classifications. Currently, can either \"icd10\" \"icd11\". Default \"icd11\". NULL, ICD classifications used (currently \"icd10\" \"icd11\"). latest Logical. TRUE, identifier latest release returned. Default FALSE. class character string code classes retrieve. can either \"chapter\", \"block\", \"category\". NULL (default), classes retrieved.","code":""},{"path":"https://oxford-ihtm.io/codigo/reference/icd_utils.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Utility functions for retrieving ICD parameters and definitions — icd_get_releases","text":"tibble ICD classification values corresponding release identifiers (icd_get_releases()). names list corresponding languages (icd_get_languages()). tibble entities definitions/titles classes (icd_get_entitties()).","code":""},{"path":"https://oxford-ihtm.io/codigo/reference/icd_utils.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Utility functions for retrieving ICD parameters and definitions — icd_get_releases","text":"","code":"icd_get_releases() #> # A tibble: 7 × 2 #>   Classification `Release ID` #>   <chr>          <chr>        #> 1 ICD-11         2024-01      #> 2 ICD-11         2023-01      #> 3 ICD-11         2022-02      #> 4 ICD-11         2021-05      #> 5 ICD-11         2020-09      #> 6 ICD-11         2019-04      #> 7 ICD-11         2018         icd_get_languages() #> $`ICD-11 - Release 2024-01` #>  [1] \"ar\" \"cs\" \"en\" \"es\" \"fr\" \"pt\" \"ru\" \"tr\" \"uz\" \"zh\" #>  #> $`ICD-11 - Release 2023-01` #> [1] \"ar\" \"en\" \"es\" \"fr\" \"ru\" \"tr\" \"zh\" #>  #> $`ICD-11 - Release 2022-02` #> [1] \"ar\"  \"en\"  \"es\"  \"fr\"  \" zh\" #>  #> $`ICD-11 - Release 2021-05` #> [1] \"ar\" \"en\" \"es\" \"zh\" #>  #> $`ICD-11 - Release 2020-09` #> [1] \"ar\" \"en\" \"es\" #>  #> $`ICD-11 - Release 2019-04` #> [1] \"en\" #>  #> $`ICD-11 - Release 2018` #> [1] \"en\" #>  icd_get_entities() #> # A tibble: 36,044 × 5 #>    entity_foundation entity_mms code   title                               class #>    <chr>             <chr>      <chr>  <chr>                               <chr> #>  1 1435254666        1435254666 NA     Certain infectious or parasitic di… chap… #>  2 588616678         588616678  NA     - Gastroenteritis or colitis of in… block #>  3 135352227         135352227  NA     - - Bacterial intestinal infections block #>  4 257068234         257068234  1A00   - - - Cholera                       cate… #>  5 416025325         416025325  1A01   - - - Intestinal infection due to … cate… #>  6 2080365623        2080365623 1A02   - - - Intestinal infections due to… cate… #>  7 344162786         344162786  1A03   - - - Intestinal infections due to… cate… #>  8 2099226249        2099226249 1A03.0 - - - - Enteropathogenic Escherich… cate… #>  9 408185629         408185629  1A03.1 - - - - Enterotoxigenic Escherichi… cate… #> 10 1828273122        1828273122 1A03.2 - - - - Enteroinvasive Escherichia… cate… #> # ℹ 36,034 more rows"},{"path":"https://oxford-ihtm.io/codigo/reference/icd_versions.html","id":null,"dir":"Reference","previous_headings":"","what":"Table of supported classifications and versions by the ICD API — icd_versions","title":"Table of supported classifications and versions by the ICD API — icd_versions","text":"Table supported classifications versions ICD API","code":""},{"path":"https://oxford-ihtm.io/codigo/reference/icd_versions.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Table of supported classifications and versions by the ICD API — icd_versions","text":"","code":"icd_versions"},{"path":"https://oxford-ihtm.io/codigo/reference/icd_versions.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Table of supported classifications and versions by the ICD API — icd_versions","text":"data frame 6 columns 11 rows: logical fields specify NA, indicates particular version release, particular field applicable relevant.","code":""},{"path":"https://oxford-ihtm.io/codigo/reference/icd_versions.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Table of supported classifications and versions by the ICD API — icd_versions","text":"https://icd..int/docs/icd-api/SupportedClassifications/","code":""},{"path":"https://oxford-ihtm.io/codigo/reference/icd_versions.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Table of supported classifications and versions by the ICD API — icd_versions","text":"","code":"icd_versions #> # A tibble: 11 × 6 #>    Classification `Release ID` Foundation MMS   ICF   Languages  #>    <chr>          <chr>        <lgl>      <lgl> <lgl> <list>     #>  1 ICD-11         2024-01      TRUE       TRUE  TRUE  <chr [10]> #>  2 ICD-11         2023-01      TRUE       TRUE  FALSE <chr [7]>  #>  3 ICD-11         2022-02      TRUE       TRUE  FALSE <chr [5]>  #>  4 ICD-11         2021-05      TRUE       TRUE  FALSE <chr [4]>  #>  5 ICD-11         2020-09      TRUE       TRUE  FALSE <chr [3]>  #>  6 ICD-11         2019-04      TRUE       TRUE  FALSE <chr [1]>  #>  7 ICD-11         2018         TRUE       TRUE  FALSE <chr [1]>  #>  8 ICD-10         2019         NA         NA    NA    <chr [1]>  #>  9 ICD-10         2016         NA         NA    NA    <chr [1]>  #> 10 ICD-10         2010         NA         NA    NA    <chr [1]>  #> 11 ICD-10         2008         NA         NA    NA    <chr [2]>"}]
+[{"path":[]},{"path":"https://oxford-ihtm.io/codigo/CODE_OF_CONDUCT.html","id":"our-pledge","dir":"","previous_headings":"","what":"Our Pledge","title":"Contributor Covenant Code of Conduct","text":"members, contributors, leaders pledge make participation community harassment-free experience everyone, regardless age, body size, visible invisible disability, ethnicity, sex characteristics, gender identity expression, level experience, education, socio-economic status, nationality, personal appearance, race, caste, color, religion, sexual identity orientation. pledge act interact ways contribute open, welcoming, diverse, inclusive, healthy community.","code":""},{"path":"https://oxford-ihtm.io/codigo/CODE_OF_CONDUCT.html","id":"our-standards","dir":"","previous_headings":"","what":"Our Standards","title":"Contributor Covenant Code of Conduct","text":"Examples behavior contributes positive environment community include: Demonstrating empathy kindness toward people respectful differing opinions, viewpoints, experiences Giving gracefully accepting constructive feedback Accepting responsibility apologizing affected mistakes, learning experience Focusing best just us individuals, overall community Examples unacceptable behavior include: use sexualized language imagery, sexual attention advances kind Trolling, insulting derogatory comments, personal political attacks Public private harassment Publishing others’ private information, physical email address, without explicit permission conduct reasonably considered inappropriate professional setting","code":""},{"path":"https://oxford-ihtm.io/codigo/CODE_OF_CONDUCT.html","id":"enforcement-responsibilities","dir":"","previous_headings":"","what":"Enforcement Responsibilities","title":"Contributor Covenant Code of Conduct","text":"Community leaders responsible clarifying enforcing standards acceptable behavior take appropriate fair corrective action response behavior deem inappropriate, threatening, offensive, harmful. Community leaders right responsibility remove, edit, reject comments, commits, code, wiki edits, issues, contributions aligned Code Conduct, communicate reasons moderation decisions appropriate.","code":""},{"path":"https://oxford-ihtm.io/codigo/CODE_OF_CONDUCT.html","id":"scope","dir":"","previous_headings":"","what":"Scope","title":"Contributor Covenant Code of Conduct","text":"Code Conduct applies within community spaces, also applies individual officially representing community public spaces. Examples representing community include using official e-mail address, posting via official social media account, acting appointed representative online offline event.","code":""},{"path":"https://oxford-ihtm.io/codigo/CODE_OF_CONDUCT.html","id":"enforcement","dir":"","previous_headings":"","what":"Enforcement","title":"Contributor Covenant Code of Conduct","text":"Instances abusive, harassing, otherwise unacceptable behavior may reported community leaders responsible enforcement ernest@guevarra.io. complaints reviewed investigated promptly fairly. community leaders obligated respect privacy security reporter incident.","code":""},{"path":"https://oxford-ihtm.io/codigo/CODE_OF_CONDUCT.html","id":"enforcement-guidelines","dir":"","previous_headings":"","what":"Enforcement Guidelines","title":"Contributor Covenant Code of Conduct","text":"Community leaders follow Community Impact Guidelines determining consequences action deem violation Code Conduct:","code":""},{"path":"https://oxford-ihtm.io/codigo/CODE_OF_CONDUCT.html","id":"id_1-correction","dir":"","previous_headings":"Enforcement Guidelines","what":"1. Correction","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Use inappropriate language behavior deemed unprofessional unwelcome community. Consequence: private, written warning community leaders, providing clarity around nature violation explanation behavior inappropriate. public apology may requested.","code":""},{"path":"https://oxford-ihtm.io/codigo/CODE_OF_CONDUCT.html","id":"id_2-warning","dir":"","previous_headings":"Enforcement Guidelines","what":"2. Warning","title":"Contributor Covenant Code of Conduct","text":"Community Impact: violation single incident series actions. Consequence: warning consequences continued behavior. interaction people involved, including unsolicited interaction enforcing Code Conduct, specified period time. includes avoiding interactions community spaces well external channels like social media. Violating terms may lead temporary permanent ban.","code":""},{"path":"https://oxford-ihtm.io/codigo/CODE_OF_CONDUCT.html","id":"id_3-temporary-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"3. Temporary Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: serious violation community standards, including sustained inappropriate behavior. Consequence: temporary ban sort interaction public communication community specified period time. public private interaction people involved, including unsolicited interaction enforcing Code Conduct, allowed period. Violating terms may lead permanent ban.","code":""},{"path":"https://oxford-ihtm.io/codigo/CODE_OF_CONDUCT.html","id":"id_4-permanent-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"4. Permanent Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Demonstrating pattern violation community standards, including sustained inappropriate behavior, harassment individual, aggression toward disparagement classes individuals. Consequence: permanent ban sort public interaction within community.","code":""},{"path":"https://oxford-ihtm.io/codigo/CODE_OF_CONDUCT.html","id":"attribution","dir":"","previous_headings":"","what":"Attribution","title":"Contributor Covenant Code of Conduct","text":"Code Conduct adapted Contributor Covenant, version 2.1, available https://www.contributor-covenant.org/version/2/1/code_of_conduct.html. Community Impact Guidelines inspired [Mozilla’s code conduct enforcement ladder][https://github.com/mozilla/inclusion]. answers common questions code conduct, see FAQ https://www.contributor-covenant.org/faq. Translations available https://www.contributor-covenant.org/translations.","code":""},{"path":[]},{"path":"https://oxford-ihtm.io/codigo/CONTRIBUTING.html","id":"bugs","dir":"","previous_headings":"","what":"Bugs","title":"Contributing","text":"Submit issue issues page","code":""},{"path":"https://oxford-ihtm.io/codigo/CONTRIBUTING.html","id":"code-contributions","dir":"","previous_headings":"","what":"Code contributions","title":"Contributing","text":"Fork repository Github account Clone version account machine account Make sure track progress upstream .e., version icd OxfordIHTM/icd, making changes make sure pull changes upstream either git fetch upstream merge later git pull upstream fetch merge one step Make changes new feature branch Please write test tests changes affect code just documentation Push changes account Submit pull request OxfordIHTM/icd","code":"git clone https://github.com/<yourgithubusername>/icd.git git remote add upstream https://github.com/OxfordIHTM/icd.git"},{"path":"https://oxford-ihtm.io/codigo/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"GNU General Public License","title":"GNU General Public License","text":"Version 3, 29 June 2007Copyright © 2007 Free Software Foundation, Inc. <http://fsf.org/> Everyone permitted copy distribute verbatim copies license document, changing allowed.","code":""},{"path":"https://oxford-ihtm.io/codigo/LICENSE.html","id":"preamble","dir":"","previous_headings":"","what":"Preamble","title":"GNU General Public License","text":"GNU General Public License free, copyleft license software kinds works. licenses software practical works designed take away freedom share change works. contrast, GNU General Public License intended guarantee freedom share change versions program–make sure remains free software users. , Free Software Foundation, use GNU General Public License software; applies also work released way authors. can apply programs, . speak free software, referring freedom, price. 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Protecting Users’ Legal Rights From Anti-Circumvention Law","title":"GNU General Public License","text":"covered work shall deemed part effective technological measure applicable law fulfilling obligations article 11 WIPO copyright treaty adopted 20 December 1996, similar laws prohibiting restricting circumvention measures. convey covered work, waive legal power forbid circumvention technological measures extent circumvention effected exercising rights License respect covered work, disclaim intention limit operation modification work means enforcing, work’s users, third parties’ legal rights forbid circumvention technological measures.","code":""},{"path":"https://oxford-ihtm.io/codigo/LICENSE.html","id":"id_4-conveying-verbatim-copies","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"4. 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Termination","title":"GNU General Public License","text":"may propagate modify covered work except expressly provided License. attempt otherwise propagate modify void, automatically terminate rights License (including patent licenses granted third paragraph section 11). However, cease violation License, license particular copyright holder reinstated () provisionally, unless copyright holder explicitly finally terminates license, (b) permanently, copyright holder fails notify violation reasonable means prior 60 days cessation. Moreover, license particular copyright holder reinstated permanently copyright holder notifies violation reasonable means, first time received notice violation License (work) copyright holder, cure violation prior 30 days receipt notice. 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Use with the GNU Affero General Public License","title":"GNU General Public License","text":"Notwithstanding provision License, permission link combine covered work work licensed version 3 GNU Affero General Public License single combined work, convey resulting work. terms License continue apply part covered work, special requirements GNU Affero General Public License, section 13, concerning interaction network apply combination .","code":""},{"path":"https://oxford-ihtm.io/codigo/LICENSE.html","id":"id_14-revised-versions-of-this-license","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"14. Revised Versions of this License","title":"GNU General Public License","text":"Free Software Foundation may publish revised /new versions GNU General Public License time time. new versions similar spirit present version, may differ detail address new problems concerns. version given distinguishing version number. Program specifies certain numbered version GNU General Public License “later version” applies , option following terms conditions either numbered version later version published Free Software Foundation. Program specify version number GNU General Public License, may choose version ever published Free Software Foundation. Program specifies proxy can decide future versions GNU General Public License can used, proxy’s public statement acceptance version permanently authorizes choose version Program. Later license versions may give additional different permissions. However, additional obligations imposed author copyright holder result choosing follow later version.","code":""},{"path":"https://oxford-ihtm.io/codigo/LICENSE.html","id":"id_15-disclaimer-of-warranty","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"15. Disclaimer of Warranty","title":"GNU General Public License","text":"WARRANTY PROGRAM, EXTENT PERMITTED APPLICABLE LAW. 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Interpretation of Sections 15 and 16","title":"GNU General Public License","text":"disclaimer warranty limitation liability provided given local legal effect according terms, reviewing courts shall apply local law closely approximates absolute waiver civil liability connection Program, unless warranty assumption liability accompanies copy Program return fee. END TERMS CONDITIONS","code":""},{"path":"https://oxford-ihtm.io/codigo/LICENSE.html","id":"how-to-apply-these-terms-to-your-new-programs","dir":"","previous_headings":"","what":"How to Apply These Terms to Your New Programs","title":"GNU General Public License","text":"develop new program, want greatest possible use public, best way achieve make free software everyone can redistribute change terms. , attach following notices program. safest attach start source file effectively state exclusion warranty; file least “copyright” line pointer full notice found. Also add information contact electronic paper mail. program terminal interaction, make output short notice like starts interactive mode: hypothetical commands show w show c show appropriate parts General Public License. course, program’s commands might different; GUI interface, use “box”. also get employer (work programmer) school, , sign “copyright disclaimer” program, necessary. information , apply follow GNU GPL, see <http://www.gnu.org/licenses/>. GNU General Public License permit incorporating program proprietary programs. program subroutine library, may consider useful permit linking proprietary applications library. want , use GNU Lesser General Public License instead License. first, please read <http://www.gnu.org/philosophy/--lgpl.html>.","code":"<one line to give the program's name and a brief idea of what it does.> Copyright (C) <year>  <name of author>  This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.  This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more details.  You should have received a copy of the GNU General Public License along with this program.  If not, see <http://www.gnu.org/licenses/>. <program>  Copyright (C) <year>  <name of author> This program comes with ABSOLUTELY NO WARRANTY; for details type 'show w'. This is free software, and you are welcome to redistribute it under certain conditions; type 'show c' for details."},{"path":"https://oxford-ihtm.io/codigo/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Anita Makori. Author, copyright holder. Ernest Guevarra. Author, maintainer, copyright holder.","code":""},{"path":"https://oxford-ihtm.io/codigo/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Anita Makori Ernest Guevarra (2024). codigo: Interface International Classification Diseases (ICD) API. R package version 0.0.9000. URL https://oxford-ihtm.io/codigo/","code":"@Manual{,   title = {codigo: Interface to the International Classification of Diseases (ICD) API},   author = {{Anita Makori} and {Ernest Guevarra}},   year = {2024},   note = {R package version 0.0.9000},   url = {https://oxford-ihtm.io/codigo/}, }"},{"path":"https://oxford-ihtm.io/codigo/index.html","id":"codigo-interface-to-the-international-classification-of-diseases-icd-api-","dir":"","previous_headings":"","what":"Interface to the International Classification of Diseases (ICD) API","title":"Interface to the International Classification of Diseases (ICD) API","text":"International Classification Diseases (ICD) serves broad range uses globally provides critical knowledge extent, causes consequences human disease death worldwide via data reported coded ICD. ICD API allows programmatic access ICD. HTTP based REST API. package provides functions interface ICD API.","code":""},{"path":"https://oxford-ihtm.io/codigo/index.html","id":"what-does-codigo-do","dir":"","previous_headings":"","what":"What does codigo do?","title":"Interface to the International Classification of Diseases (ICD) API","text":"Please note codigo still highly experimental undergoing lot development. Hence, functionalities described high likelihood changing interface approach aim stable working version. Currently, package provides functions authenticating ICD API. , plan develop functions wrap various available API endpoints.","code":""},{"path":"https://oxford-ihtm.io/codigo/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Interface to the International Classification of Diseases (ICD) API","text":"codigo yet CRAN. can install development version codigo GitHub : load codigo","code":"if(!require(remotes)) install.packages(\"remotes\") remotes::install_github(\"OxfordIHTM/codigo\") # load package library(codigo)"},{"path":[]},{"path":"https://oxford-ihtm.io/codigo/index.html","id":"authenticating-with-the-icd-api","dir":"","previous_headings":"Usage","what":"Authenticating with the ICD API","title":"Interface to the International Classification of Diseases (ICD) API","text":"ICD API uses OAuth2 authentication. package set utility functions support ICD API authentication specifications leading generation OAuth2 token. icd_oauth_client() function downstream user-facing function creates ICD OAuth2 client can used token retrieval future functions wrap ICD API entity linearization information retrieval. ICD OAuth2 client can generated follows: function uses built OAuth2 client created light use purposes package development testing. recommended intending use package programmatically performing high volume calls ICD API create access keys (client id client secret) using instructions. , access keys, perform following commands: OAuth2 client can now used various functions package require OAuth2 client authentication making requests ICD API.","code":"icd_oauth_client() ## Create your own OAuth client ---- my_oauth_client <- icd_oauth_client(   id = \"YOUR_CLIENT_ID\",   token_url = \"https://icdaccessmanagement.who.int/connect/token\",   secret = \"YOUR_CLIENT_SECRET\",   name = \"NAME_OF_YOUR_APP )"},{"path":"https://oxford-ihtm.io/codigo/index.html","id":"performing-a-basic-search","dir":"","previous_headings":"Usage","what":"Performing a basic search","title":"Interface to the International Classification of Diseases (ICD) API","text":"main feature ICD API ability search ICD 11 Foundation ICD 11 Linearization information regarding illness/disease. feature captured icd_search_foundation() function. example, colorectal cancer disease interest information available ICD 11 needed, following call can made: gives following output: output tibble created parsed JSON body text HTTP response ICD API.","code":"icd_search_foundation(\"colorectal cancer\", client = my_oauth_client) #> Release `2024-01` matches a known release for ICD-11. #> Language `en` is available for the release specified. #> # A tibble: 8 × 18 #>   id                    title stemId isLeaf postcoordinationAvai…¹ hasCodingNote #> * <chr>                 <chr> <chr>  <lgl>                   <int> <lgl>         #> 1 http://id.who.int/ic… Mali… http:… FALSE                       0 FALSE         #> 2 http://id.who.int/ic… Mali… http:… FALSE                       0 FALSE         #> 3 http://id.who.int/ic… Mali… http:… FALSE                       0 FALSE         #> 4 http://id.who.int/ic… Mali… http:… FALSE                       0 FALSE         #> 5 http://id.who.int/ic… Mali… http:… FALSE                       0 FALSE         #> 6 http://id.who.int/ic… Mali… http:… FALSE                       0 FALSE         #> 7 http://id.who.int/ic… Fami… http:… FALSE                       0 FALSE         #> 8 http://id.who.int/ic… Here… http:… FALSE                       0 FALSE         #> # ℹ abbreviated name: ¹​postcoordinationAvailability #> # ℹ 12 more variables: hasMaternalChapterLink <lgl>, #> #   hasPerinatalChapterLink <lgl>, matchingPVs <named list>, #> #   propertiesTruncated <lgl>, isResidualOther <lgl>, #> #   isResidualUnspecified <lgl>, chapter <chr>, score <dbl>, #> #   titleIsASearchResult <lgl>, titleIsTopScore <lgl>, entityType <int>, #> #   important <lgl>"},{"path":"https://oxford-ihtm.io/codigo/index.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Interface to the International Classification of Diseases (ICD) API","text":"find codigo package useful please cite using suggested citation provided call citation() function follows:","code":"citation(\"codigo\") #> To cite codigo in publications use: #>  #>   Anita Makori and Ernest Guevarra (2024). codigo: Interface to the #>   International Classification of Diseases (ICD) API. R package version #>   0.0.9000. URL https://oxford-ihtm.io/codigo/ #>  #> A BibTeX entry for LaTeX users is #>  #>   @Manual{, #>     title = {codigo: Interface to the International Classification of Diseases (ICD) API}, #>     author = {{Anita Makori} and {Ernest Guevarra}}, #>     year = {2024}, #>     note = {R package version 0.0.9000}, #>     url = {https://oxford-ihtm.io/codigo/}, #>   }"},{"path":"https://oxford-ihtm.io/codigo/index.html","id":"community-guidelines","dir":"","previous_headings":"","what":"Community guidelines","title":"Interface to the International Classification of Diseases (ICD) API","text":"Feedback, bug reports feature requests welcome; file issues seek support . like contribute package, please see contributing guidelines. project released Contributor Code Conduct. participating project agree abide terms.","code":""},{"path":"https://oxford-ihtm.io/codigo/reference/codigo.html","id":null,"dir":"Reference","previous_headings":"","what":"Interface to the International Classification of Diseases (ICD) API — codigo","title":"Interface to the International Classification of Diseases (ICD) API — codigo","text":"International Classification Diseases (ICD) serves broad range uses globally provides critical knowledge extent, causes consequences human disease death worldwide via data reported coded ICD. ICD API allows programmatic access ICD. HTTP based REST API. package provides functions interface ICD API.","code":""},{"path":[]},{"path":"https://oxford-ihtm.io/codigo/reference/codigo.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Interface to the International Classification of Diseases (ICD) API — codigo","text":"Maintainer: Ernest Guevarra ernest@guevarra.io (ORCID) [copyright holder] Authors: Anita Makori [copyright holder]","code":""},{"path":"https://oxford-ihtm.io/codigo/reference/icd.html","id":null,"dir":"Reference","previous_headings":"","what":"Interface to the International Classification of Diseases (ICD) API — icd","title":"Interface to the International Classification of Diseases (ICD) API — icd","text":"International Classification Diseases (ICD) serves broad range uses globally provides critical knowledge extent, causes consequences human disease death worldwide via data reported coded ICD. ICD API allows programmatic access ICD. HTTP based REST API. package provides functions interface ICD API.","code":""},{"path":[]},{"path":"https://oxford-ihtm.io/codigo/reference/icd.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Interface to the International Classification of Diseases (ICD) API — icd","text":"Maintainer: Ernest Guevarra ernest@guevarra.io (ORCID) [copyright holder] Authors: Anita Makori mark@brixtonhealth.com [copyright holder]","code":""},{"path":"https://oxford-ihtm.io/codigo/reference/icd11_linearization_mms.html","id":null,"dir":"Reference","previous_headings":"","what":"ICD-11 Mortality and Morbidity Linearization Outputs — icd11_linearization_mms","title":"ICD-11 Mortality and Morbidity Linearization Outputs — icd11_linearization_mms","text":"ICD-11 Mortality Morbidity Linearization Outputs","code":""},{"path":"https://oxford-ihtm.io/codigo/reference/icd11_linearization_mms.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"ICD-11 Mortality and Morbidity Linearization Outputs — icd11_linearization_mms","text":"","code":"icd11_linearization_mms"},{"path":"https://oxford-ihtm.io/codigo/reference/icd11_linearization_mms.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"ICD-11 Mortality and Morbidity Linearization Outputs — icd11_linearization_mms","text":"data frame 21 columns 36753 rows:","code":""},{"path":"https://oxford-ihtm.io/codigo/reference/icd11_linearization_mms.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"ICD-11 Mortality and Morbidity Linearization Outputs — icd11_linearization_mms","text":"https://icd..int/dev11/Downloads/Download?fileName=LinearizationMiniOutput-MMS-en.zip","code":""},{"path":"https://oxford-ihtm.io/codigo/reference/icd11_linearization_mms.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"ICD-11 Mortality and Morbidity Linearization Outputs — icd11_linearization_mms","text":"","code":"icd11_linearization_mms #> # A tibble: 36,753 × 21 #>    `Foundation URI`         Linearization (relea…¹ Code  BlockId Title ClassKind #>    <chr>                    <chr>                  <chr> <chr>   <chr> <chr>     #>  1 http://id.who.int/icd/e… http://id.who.int/icd… NA    NA      Cert… chapter   #>  2 http://id.who.int/icd/e… http://id.who.int/icd… NA    BlockL… - Ga… block     #>  3 http://id.who.int/icd/e… http://id.who.int/icd… NA    BlockL… - - … block     #>  4 http://id.who.int/icd/e… http://id.who.int/icd… 1A00  NA      - - … category  #>  5 http://id.who.int/icd/e… http://id.who.int/icd… 1A01  NA      - - … category  #>  6 http://id.who.int/icd/e… http://id.who.int/icd… 1A02  NA      - - … category  #>  7 http://id.who.int/icd/e… http://id.who.int/icd… 1A03  NA      - - … category  #>  8 http://id.who.int/icd/e… http://id.who.int/icd… 1A03… NA      - - … category  #>  9 http://id.who.int/icd/e… http://id.who.int/icd… 1A03… NA      - - … category  #> 10 http://id.who.int/icd/e… http://id.who.int/icd… 1A03… NA      - - … category  #> # ℹ 36,743 more rows #> # ℹ abbreviated name: ¹​`Linearization (release) URI` #> # ℹ 15 more variables: DepthInKind <chr>, IsResidual <chr>, #> #   PrimaryLocation <chr>, ChapterNo <chr>, BrowserLink <dbl>, iCatLink <dbl>, #> #   isLeaf <chr>, noOfNonResidualChildren <chr>, `Primary tabulation` <chr>, #> #   Grouping1 <chr>, Grouping2 <chr>, Grouping3 <chr>, Grouping4 <chr>, #> #   Grouping5 <chr>, Version <chr>"},{"path":"https://oxford-ihtm.io/codigo/reference/icd11_simple_table_mms.html","id":null,"dir":"Reference","previous_headings":"","what":"ICD-11 Mortality and Morbidity Simple Table Outputs — icd11_simple_table_mms","title":"ICD-11 Mortality and Morbidity Simple Table Outputs — icd11_simple_table_mms","text":"ICD-11 Mortality Morbidity Simple Table Outputs","code":""},{"path":"https://oxford-ihtm.io/codigo/reference/icd11_simple_table_mms.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"ICD-11 Mortality and Morbidity Simple Table Outputs — icd11_simple_table_mms","text":"","code":"icd11_simple_table_mms"},{"path":"https://oxford-ihtm.io/codigo/reference/icd11_simple_table_mms.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"ICD-11 Mortality and Morbidity Simple Table Outputs — icd11_simple_table_mms","text":"data frame 18 columns 36044 rows:","code":""},{"path":"https://oxford-ihtm.io/codigo/reference/icd11_simple_table_mms.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"ICD-11 Mortality and Morbidity Simple Table Outputs — icd11_simple_table_mms","text":"https://icdcdn..int/static/releasefiles/2024-01/SimpleTabulation-ICD-11-MMS-en.zip","code":""},{"path":"https://oxford-ihtm.io/codigo/reference/icd11_simple_table_mms.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"ICD-11 Mortality and Morbidity Simple Table Outputs — icd11_simple_table_mms","text":"","code":"icd11_simple_table_mms #> # A tibble: 36,044 × 18 #>    `Foundation URI`            `Linearization URI` Code  BlockId Title ClassKind #>    <chr>                       <chr>               <chr> <chr>   <chr> <chr>     #>  1 http://id.who.int/icd/enti… http://id.who.int/… NA    NA      Cert… chapter   #>  2 http://id.who.int/icd/enti… http://id.who.int/… NA    BlockL… - Ga… block     #>  3 http://id.who.int/icd/enti… http://id.who.int/… NA    BlockL… - - … block     #>  4 http://id.who.int/icd/enti… http://id.who.int/… 1A00  NA      - - … category  #>  5 http://id.who.int/icd/enti… http://id.who.int/… 1A01  NA      - - … category  #>  6 http://id.who.int/icd/enti… http://id.who.int/… 1A02  NA      - - … category  #>  7 http://id.who.int/icd/enti… http://id.who.int/… 1A03  NA      - - … category  #>  8 http://id.who.int/icd/enti… http://id.who.int/… 1A03… NA      - - … category  #>  9 http://id.who.int/icd/enti… http://id.who.int/… 1A03… NA      - - … category  #> 10 http://id.who.int/icd/enti… http://id.who.int/… 1A03… NA      - - … category  #> # ℹ 36,034 more rows #> # ℹ 12 more variables: DepthInKind <chr>, IsResidual <chr>, ChapterNo <chr>, #> #   BrowserLink <dbl>, isLeaf <chr>, `Primary tabulation` <chr>, #> #   Grouping1 <chr>, Grouping2 <chr>, Grouping3 <chr>, Grouping4 <chr>, #> #   Grouping5 <chr>, Version <chr>"},{"path":"https://oxford-ihtm.io/codigo/reference/icd_authenticate.html","id":null,"dir":"Reference","previous_headings":"","what":"OAuth2 authentication to ICD API — icd_oauth_client","title":"OAuth2 authentication to ICD API — icd_oauth_client","text":"OAuth2 authentication ICD API","code":""},{"path":"https://oxford-ihtm.io/codigo/reference/icd_authenticate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"OAuth2 authentication to ICD API — icd_oauth_client","text":"","code":"icd_oauth_client(   id = \"6fc8a1e4-4da9-43a8-bd0c-c164c0cb0ebd_3c7e272e-2f4b-46de-b127-df7454e36be8\",   token_url = \"https://icdaccessmanagement.who.int/connect/token\",   secret = \"OGIly8mTatQ2ILuhBTbviIp2FofWiQR3fj4HaPiGseE=\",   name = \"icd_client\",   ... )  icd_authenticate(   req,   client = icd_oauth_client(),   scope = \"icdapi_access\",   ... )"},{"path":"https://oxford-ihtm.io/codigo/reference/icd_authenticate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"OAuth2 authentication to ICD API — icd_oauth_client","text":"id Consumer key, also sometimes called client ID. token_url url used exchange unauthenticated authenticated token. secret Consumer secret, also sometimes called client secret. Despite name, necessarily need protected like password, .e. user still authenticate grant app permission access resources behalf. name Name application. used OAuth, used make easier identify different applications. ... parameters/arguments passed onto httr2::oauth_client() httr2::req_oauth_client_credentials() req request client OAuth2 client. Default call icd_oauth_client(). scope Scopes requested resource owner. Default \"icdapi_access\" specified ICD API documentation.","code":""},{"path":"https://oxford-ihtm.io/codigo/reference/icd_authenticate.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"OAuth2 authentication to ICD API — icd_oauth_client","text":"httr2_oauth_client class object.","code":""},{"path":"https://oxford-ihtm.io/codigo/reference/icd_authenticate.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"OAuth2 authentication to ICD API — icd_oauth_client","text":"","code":"icd_oauth_client() #> <httr2_oauth_client> #> name: icd_client #> id: 6fc8a1e4-4da9-43a8-bd0c-c164c0cb0ebd_3c7e272e-2f4b-46de-b127-df7454e36be8 #> secret: <REDACTED> #> token_url: https://icdaccessmanagement.who.int/connect/token #> auth: oauth_client_req_auth_header"},{"path":"https://oxford-ihtm.io/codigo/reference/icd_autocode.html","id":null,"dir":"Reference","previous_headings":"","what":"Perform autocoding — icd_autocode_foundation","title":"Perform autocoding — icd_autocode_foundation","text":"Perform autocoding","code":""},{"path":"https://oxford-ihtm.io/codigo/reference/icd_autocode.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Perform autocoding — icd_autocode_foundation","text":"","code":"icd_autocode_foundation(   q,   subtree = NULL,   release = NULL,   threshold = NULL,   api_version = c(\"v2\", \"v1\"),   language = \"en\",   tabular = TRUE,   verbose = TRUE,   base_url = \"https://id.who.int\",   client = icd_oauth_client(),   scope = \"icdapi_access\" )"},{"path":"https://oxford-ihtm.io/codigo/reference/icd_autocode.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Perform autocoding — icd_autocode_foundation","text":"q String. Text searched. character % end regarded wild card word. subtree string vector strings URIs. provided, search performed entities provided descendants. release string specifying release version Foundation search . specified, defaults latest release version. See available versions icd_versions. threshold numeric value 0 1 indicates similarity input text matched term. threshold minimum score included output. Default NULL use default value specified API. api_version Version API. Possible values v1 v2. example, provide value v2, API respond format version 2 API. Default v2. language ICD-API multi-lingual. changing header, may make API respond different languages. Languages available translations ICD-11 completes. values language codes en, es, zh, etc. Depending release_id specified, available languages vary. Default English (\"en\"). tabular Logical. output structured tibble? Default TRUE. verbose Logical. non-warning non-error messages printed? Default TRUE. base_url base URL API. Default uses API server https://id..int. using locally deployed server hosting ICD API server, specify URL instance . client OAuth2 client produced call icd_oauth_client(). scope Scopes requested resource owner. Default \"icdapi_access\" specified ICD API documentation.","code":""},{"path":"https://oxford-ihtm.io/codigo/reference/icd_autocode.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Perform autocoding — icd_autocode_foundation","text":"autocode","code":""},{"path":"https://oxford-ihtm.io/codigo/reference/icd_autocode.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Perform autocoding — icd_autocode_foundation","text":"","code":"icd_autocode_foundation(\"cholera\") #> Release `2024-01` matches a known release for ICD-11. #> Language `en` is available for the release specified. #> # A tibble: 1 × 6 #>   searchText matchingText foundationURI          matchLevel matchScore matchType #>   <chr>      <chr>        <chr>                       <int>      <int>     <int> #> 1 cholera    Cholera      http://id.who.int/icd…          0          1         0"},{"path":"https://oxford-ihtm.io/codigo/reference/icd_check.html","id":null,"dir":"Reference","previous_headings":"","what":"Checks for specified parameters supplied to search, autocode, and get\nfunctions — icd_check_release","title":"Checks for specified parameters supplied to search, autocode, and get\nfunctions — icd_check_release","text":"Checks specified parameters supplied search, autocode, get functions","code":""},{"path":"https://oxford-ihtm.io/codigo/reference/icd_check.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Checks for specified parameters supplied to search, autocode, and get\nfunctions — icd_check_release","text":"","code":"icd_check_release(release, verbose = TRUE)  icd_check_language(release = NULL, language, verbose = TRUE)"},{"path":"https://oxford-ihtm.io/codigo/reference/icd_check.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Checks for specified parameters supplied to search, autocode, and get\nfunctions — icd_check_release","text":"release string specifying release version ICD-11. verbose Logical. non-warning non-error messages printed? Default TRUE. language language codes en, es, zh, etc.","code":""},{"path":"https://oxford-ihtm.io/codigo/reference/icd_check.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Checks for specified parameters supplied to search, autocode, and get\nfunctions — icd_check_release","text":"message error release provided recognised . message warning language requested available release provided. icd_check_language(), returns character value character vector acceptable language codes.","code":""},{"path":"https://oxford-ihtm.io/codigo/reference/icd_check.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Checks for specified parameters supplied to search, autocode, and get\nfunctions — icd_check_release","text":"","code":"icd_check_release(\"2024-01\") #> Release `2024-01` matches a known release for ICD-11. try(icd_check_release(\"2025-01\")) #> Error in icd_check_release(\"2025-01\") :  #>   Release `2025-01` does not match any known release for ICD-11 #>        or ICD-10. Please verify and check with `icd_versions` and try again. icd_check_language(\"2024-01\", \"ar\") #> Release `2024-01` matches a known release for ICD-11. #> Language `ar` is available for the release specified. #> [1] \"ar\" icd_check_language(\"2024-01\", \"rr\") #> Release `2024-01` matches a known release for ICD-11. #> Warning: Language `rr` is not available for the release specified. Returning results for `en` (default). #> [1] \"en\" try(icd_check_language(\"2025-01\", \"ar\")) #> Error in icd_check_release(release, verbose = verbose) :  #>   Release `2025-01` does not match any known release for ICD-11 #>        or ICD-10. Please verify and check with `icd_versions` and try again."},{"path":"https://oxford-ihtm.io/codigo/reference/icd_get.html","id":null,"dir":"Reference","previous_headings":"","what":"Get information on various ICD 11 Foundation entities — icd_get_foundation","title":"Get information on various ICD 11 Foundation entities — icd_get_foundation","text":"Get information various ICD 11 Foundation entities","code":""},{"path":"https://oxford-ihtm.io/codigo/reference/icd_get.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get information on various ICD 11 Foundation entities — icd_get_foundation","text":"","code":"icd_get_foundation(   release = NULL,   api_version = c(\"v2\", \"v1\"),   language = \"en\",   tabular = TRUE,   verbose = TRUE,   base_url = \"https://id.who.int\",   client = icd_oauth_client(),   scope = \"icdapi_access\" )  icd_get_entity(   id,   release = NULL,   include = NULL,   api_version = c(\"v2\", \"v1\"),   language = \"en\",   base_url = \"https://id.who.int\",   client = icd_oauth_client(),   scope = \"icdapi_access\" )"},{"path":"https://oxford-ihtm.io/codigo/reference/icd_get.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get information on various ICD 11 Foundation entities — icd_get_foundation","text":"release string specifying release version Foundation search . specified, defaults latest release version. See available versions icd_versions. api_version Version API. Possible values v1 v2. example, provide value v2, API respond format version 2 API. Default v2. language ICD-API multi-lingual. changing header, may make API respond different languages. Languages available translations ICD-11 completes. values language codes en, es, zh, etc. Depending release_id specified, available languages vary. Default English (\"en\"). tabular Logical. output structured tibble? Default TRUE. verbose Logical. non-warning non-error messages printed? Default TRUE. base_url base URL API. Default uses API server https://id..int. using locally deployed server hosting ICD API server, specify URL instance . client OAuth2 client produced call icd_oauth_client(). scope Scopes requested resource owner. Default \"icdapi_access\" specified ICD API documentation. id Unique numerical identifier entity. include string vector strings optional property values included response. property values can included \"ancestor\", \"descendant\", \"diagnosticCriteria\". specified, properties included response.","code":""},{"path":"https://oxford-ihtm.io/codigo/reference/icd_get.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get information on various ICD 11 Foundation entities — icd_get_foundation","text":"list information specified ICD 11 Foundation top level entities.","code":""},{"path":"https://oxford-ihtm.io/codigo/reference/icd_get.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get information on various ICD 11 Foundation entities — icd_get_foundation","text":"","code":"icd_get_foundation() #> Release `2024-01` matches a known release for ICD-11. #> Language `en` is available for the release specified. #> New names: #> • `` -> `...8` #> # A tibble: 2 × 9 #>   `@context`   `@id` `title@language` `title@value` releaseId availableLanguages #>   <chr>        <chr> <chr>            <chr>         <chr>     <chr>              #> 1 http://id.w… http… en               WHO Family o… 2024-01   ar, cs, en, es, f… #> 2 http://id.w… http… en               WHO Family o… 2024-01   ar, cs, en, es, f… #> # ℹ 3 more variables: releaseDate <chr>, child <chr>, browserUrl <chr> icd_get_entity(id = \"1435254666\")     ## chapter #> Release `2024-01` matches a known release for ICD-11. #> Language `en` is available for the release specified. #> $`@context` #> [1] \"http://id.who.int/icd/contexts/contextForFoundationEntity.json\" #>  #> $`@id` #> [1] \"http://id.who.int/icd/entity/1435254666\" #>  #> $parent #> $parent[[1]] #> [1] \"http://id.who.int/icd/entity/455013390\" #>  #>  #> $child #> $child[[1]] #> [1] \"http://id.who.int/icd/entity/588616678\" #>  #> $child[[2]] #> [1] \"http://id.who.int/icd/entity/1904876434\" #>  #> $child[[3]] #> [1] \"http://id.who.int/icd/entity/979278646\" #>  #> $child[[4]] #> [1] \"http://id.who.int/icd/entity/1539889147\" #>  #> $child[[5]] #> [1] \"http://id.who.int/icd/entity/1412960686\" #>  #> $child[[6]] #> [1] \"http://id.who.int/icd/entity/1935092859\" #>  #> $child[[7]] #> [1] \"http://id.who.int/icd/entity/487269828\" #>  #> $child[[8]] #> [1] \"http://id.who.int/icd/entity/1000704511\" #>  #> $child[[9]] #> [1] \"http://id.who.int/icd/entity/1104303944\" #>  #> $child[[10]] #> [1] \"http://id.who.int/icd/entity/1585949804\" #>  #> $child[[11]] #> [1] \"http://id.who.int/icd/entity/1959883044\" #>  #> $child[[12]] #> [1] \"http://id.who.int/icd/entity/921595235\" #>  #> $child[[13]] #> [1] \"http://id.who.int/icd/entity/1251496839\" #>  #> $child[[14]] #> [1] \"http://id.who.int/icd/entity/1136802325\" #>  #> $child[[15]] #> [1] \"http://id.who.int/icd/entity/145723401\" #>  #> $child[[16]] #> [1] \"http://id.who.int/icd/entity/985510409\" #>  #> $child[[17]] #> [1] \"http://id.who.int/icd/entity/1646490591\" #>  #> $child[[18]] #> [1] \"http://id.who.int/icd/entity/1939815950\" #>  #> $child[[19]] #> [1] \"http://id.who.int/icd/entity/255141529\" #>  #> $child[[20]] #> [1] \"http://id.who.int/icd/entity/293771399\" #>  #> $child[[21]] #> [1] \"http://id.who.int/icd/entity/5960175\" #>  #> $child[[22]] #> [1] \"http://id.who.int/icd/entity/911707612\" #>  #> $child[[23]] #> [1] \"http://id.who.int/icd/entity/1965146397\" #>  #> $child[[24]] #> [1] \"http://id.who.int/icd/entity/142052508\" #>  #> $child[[25]] #> [1] \"http://id.who.int/icd/entity/1760597414\" #>  #> $child[[26]] #> [1] \"http://id.who.int/icd/entity/458687859\" #>  #> $child[[27]] #> [1] \"http://id.who.int/icd/entity/2143513892\" #>  #>  #> $browserUrl #> [1] \"https://icd.who.int/browse/2024-01/foundation/en#1435254666\" #>  #> $title #> $title$`@language` #> [1] \"en\" #>  #> $title$`@value` #> [1] \"Certain infectious or parasitic diseases\" #>  #>  #> $synonym #> $synonym[[1]] #> $synonym[[1]]$label #> $synonym[[1]]$label$`@language` #> [1] \"en\" #>  #> $synonym[[1]]$label$`@value` #> [1] \"infection NOS\" #>  #>  #>  #> $synonym[[2]] #> $synonym[[2]]$label #> $synonym[[2]]$label$`@language` #> [1] \"en\" #>  #> $synonym[[2]]$label$`@value` #> [1] \"infectious disease NOS\" #>  #>  #>  #> $synonym[[3]] #> $synonym[[3]]$label #> $synonym[[3]]$label$`@language` #> [1] \"en\" #>  #> $synonym[[3]]$label$`@value` #> [1] \"infection unknown\" #>  #>  #>  #> $synonym[[4]] #> $synonym[[4]]$label #> $synonym[[4]]$label$`@language` #> [1] \"en\" #>  #> $synonym[[4]]$label$`@value` #> [1] \"infection process NOS\" #>  #>  #>  #> $synonym[[5]] #> $synonym[[5]]$label #> $synonym[[5]]$label$`@language` #> [1] \"en\" #>  #> $synonym[[5]]$label$`@value` #> [1] \"infection by unspecified organism and of unspecified site\" #>  #>  #>  #>  #> $definition #> $definition$`@language` #> [1] \"en\" #>  #> $definition$`@value` #> [1] \"This chapter includes certain conditions caused by pathogenic organisms or microorganisms, such as bacteria, viruses, parasites or fungi.\" #>  #>  #> $exclusion #> $exclusion[[1]] #> $exclusion[[1]]$label #> $exclusion[[1]]$label$`@language` #> [1] \"en\" #>  #> $exclusion[[1]]$label$`@value` #> [1] \"Infection arising from device, implant or graft, not elsewhere classified\" #>  #>  #> $exclusion[[1]]$foundationReference #> [1] \"http://id.who.int/icd/entity/1612485599\" #>  #>  #>  #> $relatedEntitiesInPerinatalChapter #> $relatedEntitiesInPerinatalChapter[[1]] #> [1] \"http://id.who.int/icd/entity/911707612\" #>  #>  icd_get_entity(id = \"588616678\")      ## block; depth 1 #> Release `2024-01` matches a known release for ICD-11. #> Language `en` is available for the release specified. #> $`@context` #> [1] \"http://id.who.int/icd/contexts/contextForFoundationEntity.json\" #>  #> $`@id` #> [1] \"http://id.who.int/icd/entity/588616678\" #>  #> $parent #> $parent[[1]] #> [1] \"http://id.who.int/icd/entity/1435254666\" #>  #>  #> $child #> $child[[1]] #> [1] \"http://id.who.int/icd/entity/135352227\" #>  #> $child[[2]] #> [1] \"http://id.who.int/icd/entity/1834648119\" #>  #> $child[[3]] #> [1] \"http://id.who.int/icd/entity/30738976\" #>  #> $child[[4]] #> [1] \"http://id.who.int/icd/entity/730271848\" #>  #> $child[[5]] #> [1] \"http://id.who.int/icd/entity/2092703582\" #>  #> $child[[6]] #> [1] \"http://id.who.int/icd/entity/1688127370\" #>  #>  #> $browserUrl #> [1] \"https://icd.who.int/browse/2024-01/foundation/en#588616678\" #>  #> $title #> $title$`@language` #> [1] \"en\" #>  #> $title$`@value` #> [1] \"Gastroenteritis or colitis of infectious origin\" #>  #>  #> $relatedEntitiesInPerinatalChapter #> $relatedEntitiesInPerinatalChapter[[1]] #> [1] \"http://id.who.int/icd/entity/911707612\" #>  #>  icd_get_entity(id = \"1465325727\")     ## category; depth 1 #> Release `2024-01` matches a known release for ICD-11. #> Language `en` is available for the release specified. #> $`@context` #> [1] \"http://id.who.int/icd/contexts/contextForFoundationEntity.json\" #>  #> $`@id` #> [1] \"http://id.who.int/icd/entity/1465325727\" #>  #> $parent #> $parent[[1]] #> [1] \"http://id.who.int/icd/entity/30738976\" #>  #>  #> $browserUrl #> [1] \"https://icd.who.int/browse/2024-01/foundation/en#1465325727\" #>  #> $title #> $title$`@language` #> [1] \"en\" #>  #> $title$`@value` #> [1] \"Enteritis due to Norovirus\" #>  #>  #> $synonym #> $synonym[[1]] #> $synonym[[1]]$label #> $synonym[[1]]$label$`@language` #> [1] \"en\" #>  #> $synonym[[1]]$label$`@value` #> [1] \"acute gastroenteropathy due to Norwalk agent\" #>  #>  #>  #> $synonym[[2]] #> $synonym[[2]]$label #> $synonym[[2]]$label$`@language` #> [1] \"en\" #>  #> $synonym[[2]]$label$`@value` #> [1] \"viral gastroenteritis due to Norwalk agent\" #>  #>  #>  #> $synonym[[3]] #> $synonym[[3]]$label #> $synonym[[3]]$label$`@language` #> [1] \"en\" #>  #> $synonym[[3]]$label$`@value` #> [1] \"winter vomiting\" #>  #>  #>  #> $synonym[[4]] #> $synonym[[4]]$label #> $synonym[[4]]$label$`@language` #> [1] \"en\" #>  #> $synonym[[4]]$label$`@value` #> [1] \"epidemic winter vomiting disease\" #>  #>  #>  #> $synonym[[5]] #> $synonym[[5]]$label #> $synonym[[5]]$label$`@language` #> [1] \"en\" #>  #> $synonym[[5]]$label$`@value` #> [1] \"small round structured virus enteritis\" #>  #>  #>  #> $synonym[[6]] #> $synonym[[6]]$label #> $synonym[[6]]$label$`@language` #> [1] \"en\" #>  #> $synonym[[6]]$label$`@value` #> [1] \"epidemic vomiting syndrome\" #>  #>  #>  #> $synonym[[7]] #> $synonym[[7]]$label #> $synonym[[7]]$label$`@language` #> [1] \"en\" #>  #> $synonym[[7]]$label$`@value` #> [1] \"epidemic vomiting\" #>  #>  #>  #> $synonym[[8]] #> $synonym[[8]]$label #> $synonym[[8]]$label$`@language` #> [1] \"en\" #>  #> $synonym[[8]]$label$`@value` #> [1] \"epidemic nausea\" #>  #>  #>  #> $synonym[[9]] #> $synonym[[9]]$label #> $synonym[[9]]$label$`@language` #> [1] \"en\" #>  #> $synonym[[9]]$label$`@value` #> [1] \"epidemic viral gastroenteritis due to Norwalk virus\" #>  #>  #>  #> $synonym[[10]] #> $synonym[[10]]$label #> $synonym[[10]]$label$`@language` #> [1] \"en\" #>  #> $synonym[[10]]$label$`@value` #> [1] \"Noroviral enteritis\" #>  #>  #>  #>  #> $definition #> $definition$`@language` #> [1] \"en\" #>  #> $definition$`@value` #> [1] \"A disease of the gastrointestinal tract, caused by an infection with norovirus. This disease is characterised by acute onset of vomiting, non-haemorrhagic diarrhoea, and abdominal pain. Transmission is by ingestion of contaminated food or water, direct contact, or through fomites. Confirmation is by identification of norovirus.\" #>  #>  #> $longDefinition #> $longDefinition$`@language` #> [1] \"en\" #>  #> $longDefinition$`@value` #> [1] \"The official genus name Noroviruses which is the group of viruses previously described as “Norwalk-like viruses” are a group of related, single-stranded RNA, non-enveloped viruses. Noroviruses cause self-limiting explosive acute gastroenteritis that last for 24-48hours in humans. The most common symptoms of acute gastroenteritis are diarrhea, vomiting, and stomach pain.\" #>  #>  #> $relatedEntitiesInPerinatalChapter #> $relatedEntitiesInPerinatalChapter[[1]] #> [1] \"http://id.who.int/icd/entity/911707612\" #>  #>"},{"path":"https://oxford-ihtm.io/codigo/reference/icd_search.html","id":null,"dir":"Reference","previous_headings":"","what":"Search the foundation component of the ICD-11 — icd_search_foundation","title":"Search the foundation component of the ICD-11 — icd_search_foundation","text":"Search foundation component ICD-11","code":""},{"path":"https://oxford-ihtm.io/codigo/reference/icd_search.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Search the foundation component of the ICD-11 — icd_search_foundation","text":"","code":"icd_search_foundation(   q,   subtree = NULL,   chapter = NULL,   flexisearch = FALSE,   flat = TRUE,   properties = NULL,   release = NULL,   highlight = FALSE,   api_version = c(\"v2\", \"v1\"),   language = \"en\",   tabular = TRUE,   verbose = TRUE,   base_url = \"https://id.who.int\",   client = icd_oauth_client(),   scope = \"icdapi_access\" )"},{"path":"https://oxford-ihtm.io/codigo/reference/icd_search.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Search the foundation component of the ICD-11 — icd_search_foundation","text":"q String. Text searched. character % end regarded wild card word. subtree string vector strings URIs. provided, search performed entities provided descendants. chapter string vector strings chapter codes eg: c(\"01\", \"02\") provided, search performed chapters. flexisearch Logical. Default FALSE. Changes search mode flexible search. regular search mode, Coding Tool give results contain words used search. accepts different variants synonyms words essentially searches result contains components search. Whereas flexible search mode, results contain words typed. still try find best matching phrase may words search matched . recommended use flexible search regular search provide result. flat Logical. Default FALSE. set true search result entities provided nested data structure representing ICD-11 hierarchy. Otherwise listed flat list matches. properties string vector strings properties searched. default system  searches, \"Title\", \"Synonyms\", \"FullySpecifiedName\". valid values used : \"Title\", \"Synonym\", \"NarrowerTerm\", \"FullySpecifiedName\", \"Definition\", \"Exclusion\". release string specifying release version Foundation search . specified, defaults latest release version. See available versions icd_versions. highlight Logical. Default FALSE. set FALSE search result highlighting turned results contain special tags highlighting results found within text. api_version Version API. Possible values v1 v2. example, provide value v2, API respond format version 2 API. Default v2. language ICD-API multi-lingual. changing header, may make API respond different languages. Languages available translations ICD-11 completes. values language codes en, es, zh, etc. Depending release_id specified, available languages vary. Default English (\"en\"). tabular Logical. output structured tibble? Default TRUE. verbose Logical. non-warning non-error messages printed? Default TRUE. base_url base URL API. Default uses API server https://id..int. using locally deployed server hosting ICD API server, specify URL instance . client OAuth2 client produced call icd_oauth_client(). scope Scopes requested resource owner. Default \"icdapi_access\" specified ICD API documentation.","code":""},{"path":"https://oxford-ihtm.io/codigo/reference/icd_search.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Search the foundation component of the ICD-11 — icd_search_foundation","text":"tibble search results.","code":""},{"path":"https://oxford-ihtm.io/codigo/reference/icd_search.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Search the foundation component of the ICD-11 — icd_search_foundation","text":"","code":"icd_search_foundation(\"colorectal cancer\") #> Release `2024-01` matches a known release for ICD-11. #> Language `en` is available for the release specified. #> # A tibble: 8 × 18 #>   id                    title stemId isLeaf postcoordinationAvai…¹ hasCodingNote #> * <chr>                 <chr> <chr>  <lgl>                   <int> <lgl>         #> 1 http://id.who.int/ic… Mali… http:… FALSE                       0 FALSE         #> 2 http://id.who.int/ic… Mali… http:… FALSE                       0 FALSE         #> 3 http://id.who.int/ic… Mali… http:… FALSE                       0 FALSE         #> 4 http://id.who.int/ic… Mali… http:… FALSE                       0 FALSE         #> 5 http://id.who.int/ic… Mali… http:… FALSE                       0 FALSE         #> 6 http://id.who.int/ic… Mali… http:… FALSE                       0 FALSE         #> 7 http://id.who.int/ic… Fami… http:… FALSE                       0 FALSE         #> 8 http://id.who.int/ic… Here… http:… FALSE                       0 FALSE         #> # ℹ abbreviated name: ¹​postcoordinationAvailability #> # ℹ 12 more variables: hasMaternalChapterLink <lgl>, #> #   hasPerinatalChapterLink <lgl>, matchingPVs <named list>, #> #   propertiesTruncated <lgl>, isResidualOther <lgl>, #> #   isResidualUnspecified <lgl>, chapter <chr>, score <dbl>, #> #   titleIsASearchResult <lgl>, titleIsTopScore <lgl>, entityType <int>, #> #   important <lgl>"},{"path":"https://oxford-ihtm.io/codigo/reference/icd_search_foundation.html","id":null,"dir":"Reference","previous_headings":"","what":"Search the foundation component of the ICD-11 — icd_search_foundation","title":"Search the foundation component of the ICD-11 — icd_search_foundation","text":"Search foundation component ICD-11","code":""},{"path":"https://oxford-ihtm.io/codigo/reference/icd_search_foundation.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Search the foundation component of the ICD-11 — icd_search_foundation","text":"","code":"icd_search_foundation(   base_url = \"https://id.who.int/icd\",   client = icd_oauth_client(),   q = NULL,   flexisearch = FALSE,   flat = TRUE,   highlight = FALSE,   api_version = c(\"v2\", \"v1\"),   language = \"en\" )"},{"path":"https://oxford-ihtm.io/codigo/reference/icd_search_foundation.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Search the foundation component of the ICD-11 — icd_search_foundation","text":"base_url base URL API. Default uses API server https://id..int/icd/entity client OAuth2 client produced call icd_oauth_client() q String. Text searched. character % end regarded wild card word flexisearch Logical. Default FALSE. Changes search mode flexible search. regular search mode, Coding Tool give results contain words used search. accepts different variants synonyms words essentially searches result contains components search. Whereas flexible search mode, results contain words typed. still try find best matching phrase may words search matched . recommended use flexible search regular search provide result flat Logical. Default FALSE. set true search result entities provided nested data structure representing ICD-11 hierarchy. Otherwise listed flat list matches highlight Logical. Default FALSE. set FALSE search result highlighting turned results contain special tags highlighting results found within text api_version Version API. Possible values v1 v2. example, provide value v2, API respond format version 2 API. Default v2 language ICD-API multi-lingual. changing header, may make API respond different languages. Languages available translations ICD-11 completes. values language codes en, es, zh, etc. Depending release_id specified, available languages vary. Default English (\"en\").","code":""},{"path":"https://oxford-ihtm.io/codigo/reference/icd_search_foundation.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Search the foundation component of the ICD-11 — icd_search_foundation","text":"httr2_response object","code":""},{"path":"https://oxford-ihtm.io/codigo/reference/icd_search_foundation.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Search the foundation component of the ICD-11 — icd_search_foundation","text":"","code":"icd_search_foundation(q = \"cholera\") #> <httr2_response> #> GET #> https://id.who.int/icd/entity/search?q=cholera&useFlexisearch=false&flatResults=true&highlightingEnabled=false #> Status: 200 OK #> Content-Type: application/json #> Body: In memory (17590 bytes)"},{"path":"https://oxford-ihtm.io/codigo/reference/icd_structure.html","id":null,"dir":"Reference","previous_headings":"","what":"Structure ICD list and ICD search outputs — icd_structure_foundation","title":"Structure ICD list and ICD search outputs — icd_structure_foundation","text":"Structure ICD list ICD search outputs","code":""},{"path":"https://oxford-ihtm.io/codigo/reference/icd_structure.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Structure ICD list and ICD search outputs — icd_structure_foundation","text":"","code":"icd_structure_foundation(icd_list)  icd_structure_search(icd_search)  icd_structure_autocode(icd_autocode)"},{"path":"https://oxford-ihtm.io/codigo/reference/icd_structure.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Structure ICD list and ICD search outputs — icd_structure_foundation","text":"icd_list object produced call icd_get functions icd_search object produced call icd_search functions icd_autocode object produced call icd_autocode functions","code":""},{"path":"https://oxford-ihtm.io/codigo/reference/icd_structure.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Structure ICD list and ICD search outputs — icd_structure_foundation","text":"tibble structured ICD outputs.","code":""},{"path":"https://oxford-ihtm.io/codigo/reference/icd_structure.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Structure ICD list and ICD search outputs — icd_structure_foundation","text":"functions meant helper functions used within icd_get, icd_search, icd_autocode functions structure output responses.","code":""},{"path":"https://oxford-ihtm.io/codigo/reference/icd_structure.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Structure ICD list and ICD search outputs — icd_structure_foundation","text":"","code":"icd_list <- icd_get_foundation(tabular = FALSE) #> Release `2024-01` matches a known release for ICD-11. #> Language `en` is available for the release specified. icd_tbl_foundation <- icd_structure_foundation(icd_list) #> New names: #> • `` -> `...8` icd_structure_search(icd_search_foundation(\"cholera\", tabular = FALSE)) #> Release `2024-01` matches a known release for ICD-11. #> Language `en` is available for the release specified. #> # A tibble: 103 × 18 #>    id                   title stemId isLeaf postcoordinationAvai…¹ hasCodingNote #>  * <chr>                <chr> <chr>  <lgl>                   <int> <lgl>         #>  1 http://id.who.int/i… Chol… http:… FALSE                       0 FALSE         #>  2 http://id.who.int/i… Chol… http:… FALSE                       0 FALSE         #>  3 http://id.who.int/i… Chol… http:… FALSE                       0 FALSE         #>  4 http://id.who.int/i… Chol… http:… FALSE                       0 FALSE         #>  5 http://id.who.int/i… Chol… http:… FALSE                       0 FALSE         #>  6 http://id.who.int/i… Chol… http:… FALSE                       0 FALSE         #>  7 http://id.who.int/i… Chol… http:… FALSE                       0 FALSE         #>  8 http://id.who.int/i… Chol… http:… FALSE                       0 FALSE         #>  9 http://id.who.int/i… Chol… http:… FALSE                       0 FALSE         #> 10 http://id.who.int/i… Chol… http:… FALSE                       0 FALSE         #> # ℹ 93 more rows #> # ℹ abbreviated name: ¹​postcoordinationAvailability #> # ℹ 12 more variables: hasMaternalChapterLink <lgl>, #> #   hasPerinatalChapterLink <lgl>, matchingPVs <named list>, #> #   propertiesTruncated <lgl>, isResidualOther <lgl>, #> #   isResidualUnspecified <lgl>, chapter <chr>, score <dbl>, #> #   titleIsASearchResult <lgl>, titleIsTopScore <lgl>, entityType <int>, … icd_structure_autocode(icd_autocode_foundation(\"cholera\")) #> Release `2024-01` matches a known release for ICD-11. #> Language `en` is available for the release specified. #> # A tibble: 1 × 6 #>   searchText matchingText foundationURI          matchLevel matchScore matchType #>   <chr>      <chr>        <chr>                       <int>      <int>     <int> #> 1 cholera    Cholera      http://id.who.int/icd…          0          1         0"},{"path":"https://oxford-ihtm.io/codigo/reference/icd_utils.html","id":null,"dir":"Reference","previous_headings":"","what":"Utility functions for retrieving ICD parameters and definitions — icd_get_releases","title":"Utility functions for retrieving ICD parameters and definitions — icd_get_releases","text":"Utility functions retrieving ICD parameters definitions","code":""},{"path":"https://oxford-ihtm.io/codigo/reference/icd_utils.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Utility functions for retrieving ICD parameters and definitions — icd_get_releases","text":"","code":"icd_get_releases(icd = c(\"icd11\", \"icd10\"), latest = FALSE)  icd_get_languages(icd = c(\"icd11\", \"icd10\"), latest = FALSE)  icd_get_entities(class = NULL)"},{"path":"https://oxford-ihtm.io/codigo/reference/icd_utils.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Utility functions for retrieving ICD parameters and definitions — icd_get_releases","text":"icd character string available ICD classifications. Currently, can either \"icd10\" \"icd11\". Default \"icd11\". NULL, ICD classifications used (currently \"icd10\" \"icd11\"). latest Logical. TRUE, identifier latest release returned. Default FALSE. class character string code classes retrieve. can either \"chapter\", \"block\", \"category\". NULL (default), classes retrieved.","code":""},{"path":"https://oxford-ihtm.io/codigo/reference/icd_utils.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Utility functions for retrieving ICD parameters and definitions — icd_get_releases","text":"tibble ICD classification values corresponding release identifiers (icd_get_releases()). names list corresponding languages (icd_get_languages()). tibble entities definitions/titles classes (icd_get_entitties()).","code":""},{"path":"https://oxford-ihtm.io/codigo/reference/icd_utils.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Utility functions for retrieving ICD parameters and definitions — icd_get_releases","text":"","code":"icd_get_releases() #> # A tibble: 7 × 2 #>   Classification `Release ID` #>   <chr>          <chr>        #> 1 ICD-11         2024-01      #> 2 ICD-11         2023-01      #> 3 ICD-11         2022-02      #> 4 ICD-11         2021-05      #> 5 ICD-11         2020-09      #> 6 ICD-11         2019-04      #> 7 ICD-11         2018         icd_get_languages() #> $`ICD-11 - Release 2024-01` #>  [1] \"ar\" \"cs\" \"en\" \"es\" \"fr\" \"pt\" \"ru\" \"tr\" \"uz\" \"zh\" #>  #> $`ICD-11 - Release 2023-01` #> [1] \"ar\" \"en\" \"es\" \"fr\" \"ru\" \"tr\" \"zh\" #>  #> $`ICD-11 - Release 2022-02` #> [1] \"ar\"  \"en\"  \"es\"  \"fr\"  \" zh\" #>  #> $`ICD-11 - Release 2021-05` #> [1] \"ar\" \"en\" \"es\" \"zh\" #>  #> $`ICD-11 - Release 2020-09` #> [1] \"ar\" \"en\" \"es\" #>  #> $`ICD-11 - Release 2019-04` #> [1] \"en\" #>  #> $`ICD-11 - Release 2018` #> [1] \"en\" #>  icd_get_entities() #> # A tibble: 36,044 × 5 #>    entity_foundation entity_mms code   title                               class #>    <chr>             <chr>      <chr>  <chr>                               <chr> #>  1 1435254666        1435254666 NA     Certain infectious or parasitic di… chap… #>  2 588616678         588616678  NA     - Gastroenteritis or colitis of in… block #>  3 135352227         135352227  NA     - - Bacterial intestinal infections block #>  4 257068234         257068234  1A00   - - - Cholera                       cate… #>  5 416025325         416025325  1A01   - - - Intestinal infection due to … cate… #>  6 2080365623        2080365623 1A02   - - - Intestinal infections due to… cate… #>  7 344162786         344162786  1A03   - - - Intestinal infections due to… cate… #>  8 2099226249        2099226249 1A03.0 - - - - Enteropathogenic Escherich… cate… #>  9 408185629         408185629  1A03.1 - - - - Enterotoxigenic Escherichi… cate… #> 10 1828273122        1828273122 1A03.2 - - - - Enteroinvasive Escherichia… cate… #> # ℹ 36,034 more rows"},{"path":"https://oxford-ihtm.io/codigo/reference/icd_versions.html","id":null,"dir":"Reference","previous_headings":"","what":"Table of supported classifications and versions by the ICD API — icd_versions","title":"Table of supported classifications and versions by the ICD API — icd_versions","text":"Table supported classifications versions ICD API","code":""},{"path":"https://oxford-ihtm.io/codigo/reference/icd_versions.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Table of supported classifications and versions by the ICD API — icd_versions","text":"","code":"icd_versions"},{"path":"https://oxford-ihtm.io/codigo/reference/icd_versions.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Table of supported classifications and versions by the ICD API — icd_versions","text":"data frame 6 columns 11 rows: logical fields specify NA, indicates particular version release, particular field applicable relevant.","code":""},{"path":"https://oxford-ihtm.io/codigo/reference/icd_versions.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Table of supported classifications and versions by the ICD API — icd_versions","text":"https://icd..int/docs/icd-api/SupportedClassifications/","code":""},{"path":"https://oxford-ihtm.io/codigo/reference/icd_versions.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Table of supported classifications and versions by the ICD API — icd_versions","text":"","code":"icd_versions #> # A tibble: 11 × 6 #>    Classification `Release ID` Foundation MMS   ICF   Languages  #>    <chr>          <chr>        <lgl>      <lgl> <lgl> <list>     #>  1 ICD-11         2024-01      TRUE       TRUE  TRUE  <chr [10]> #>  2 ICD-11         2023-01      TRUE       TRUE  FALSE <chr [7]>  #>  3 ICD-11         2022-02      TRUE       TRUE  FALSE <chr [5]>  #>  4 ICD-11         2021-05      TRUE       TRUE  FALSE <chr [4]>  #>  5 ICD-11         2020-09      TRUE       TRUE  FALSE <chr [3]>  #>  6 ICD-11         2019-04      TRUE       TRUE  FALSE <chr [1]>  #>  7 ICD-11         2018         TRUE       TRUE  FALSE <chr [1]>  #>  8 ICD-10         2019         NA         NA    NA    <chr [1]>  #>  9 ICD-10         2016         NA         NA    NA    <chr [1]>  #> 10 ICD-10         2010         NA         NA    NA    <chr [1]>  #> 11 ICD-10         2008         NA         NA    NA    <chr [2]>"}]
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
index 6fe3606..17b5b40 100644
--- a/docs/sitemap.xml
+++ b/docs/sitemap.xml
@@ -12,6 +12,15 @@
   <url>
     <loc>https://oxford-ihtm.io/codigo/LICENSE.html</loc>
   </url>
+  <url>
+    <loc>https://oxford-ihtm.io/codigo/articles/codigo.html</loc>
+  </url>
+  <url>
+    <loc>https://oxford-ihtm.io/codigo/articles/icd11_foundation.html</loc>
+  </url>
+  <url>
+    <loc>https://oxford-ihtm.io/codigo/articles/index.html</loc>
+  </url>
   <url>
     <loc>https://oxford-ihtm.io/codigo/authors.html</loc>
   </url>
diff --git a/man/codigo.Rd b/man/codigo.Rd
index 9d22b85..3be37e6 100644
--- a/man/codigo.Rd
+++ b/man/codigo.Rd
@@ -27,7 +27,7 @@ Useful links:
 
 Authors:
 \itemize{
-  \item Anita Makori \email{mark@brixtonhealth.com} [copyright holder]
+  \item Anita Makori [copyright holder]
 }
 
 }
diff --git a/pkgdown/_pkgdown.yml b/pkgdown/_pkgdown.yml
index 7f8c244..5b1984d 100644
--- a/pkgdown/_pkgdown.yml
+++ b/pkgdown/_pkgdown.yml
@@ -17,15 +17,15 @@ navbar:
   bg: primary
   type: light
   structure:
-    left:  [home, reference, articles, news]
+    left:  [home, intro, reference, articles, news]
     right: [linkedin, github]
 
   components:
-    # articles:
-    #   text: Articles
-    #   menu:
-    #   - text: "Detecting haemoglobinaemia"
-    #     href: articles/haemoglobinaemia.html
+    articles:
+      text: Articles
+      menu:
+      - text: "ICD-11 Foundation"
+        href: articles/icd11_foundation.html
     #   - text: "Detecting inflammation"
     #     href: articles/inflammation.html
     #   - text: "Detecting iron deficiency"
diff --git a/vignettes/.gitignore b/vignettes/.gitignore
new file mode 100644
index 0000000..097b241
--- /dev/null
+++ b/vignettes/.gitignore
@@ -0,0 +1,2 @@
+*.html
+*.R
diff --git a/vignettes/codigo.Rmd b/vignettes/codigo.Rmd
new file mode 100644
index 0000000..43b815f
--- /dev/null
+++ b/vignettes/codigo.Rmd
@@ -0,0 +1,21 @@
+---
+title: "Introduction to codigo"
+description: >
+  Interface to the International Classification of Diseases (ICD) API.
+output: rmarkdown::html_vignette
+vignette: >
+  %\VignetteIndexEntry{Introduction to codigo}
+  %\VignetteEngine{knitr::rmarkdown}
+  %\VignetteEncoding{UTF-8}
+---
+
+```{r, include = FALSE}
+knitr::opts_chunk$set(
+  collapse = TRUE,
+  comment = "#>"
+)
+```
+
+```{r setup, echo = FALSE}
+library(codigo)
+```
diff --git a/vignettes/icd11_foundation.Rmd b/vignettes/icd11_foundation.Rmd
new file mode 100644
index 0000000..aaea1b0
--- /dev/null
+++ b/vignettes/icd11_foundation.Rmd
@@ -0,0 +1,19 @@
+---
+title: "The ICD-11 Foundation and Linearization"
+output: rmarkdown::html_vignette
+vignette: >
+  %\VignetteIndexEntry{The ICD-11 Foundation and Linearization}
+  %\VignetteEngine{knitr::rmarkdown}
+  %\VignetteEncoding{UTF-8}
+---
+
+```{r, include = FALSE}
+knitr::opts_chunk$set(
+  collapse = TRUE,
+  comment = "#>"
+)
+```
+
+```{r setup}
+library(codigo)
+```