From 107c5c338881f8c1f1cbf542102a9129ce63cb7f Mon Sep 17 00:00:00 2001
From: "Luke W. Johnston" <lwjohnst@gmail.com>
Date: Fri, 8 Mar 2024 15:28:24 +0100
Subject: [PATCH] docs: add bib and csl files

---
 vignettes/design.Rmd     |   3 +
 vignettes/references.bib |  14 ++
 vignettes/vancouver.csl  | 351 +++++++++++++++++++++++++++++++++++++++
 3 files changed, 368 insertions(+)
 create mode 100644 vignettes/references.bib
 create mode 100644 vignettes/vancouver.csl

diff --git a/vignettes/design.Rmd b/vignettes/design.Rmd
index f8ee92b..1c51473 100644
--- a/vignettes/design.Rmd
+++ b/vignettes/design.Rmd
@@ -1,6 +1,8 @@
 ---
 title: "Design"
 output: rmarkdown::html_vignette
+bibliography: references.bib
+csl: vancouver.csl
 vignette: >
   %\VignetteIndexEntry{design}
   %\VignetteEngine{knitr::rmarkdown}
@@ -147,3 +149,4 @@ The exclusion criteria are:
     date.
 
 ## References
+
diff --git a/vignettes/references.bib b/vignettes/references.bib
new file mode 100644
index 0000000..0829492
--- /dev/null
+++ b/vignettes/references.bib
@@ -0,0 +1,14 @@
+@Article{Isaksen2023,
+  author    = {Isaksen, Anders Aasted and Sandbæk, Annelli and Bjerg, Lasse},
+  journal   = {Clinical Epidemiology},
+  title     = {Validation of Register-Based Diabetes Classifiers in Danish Data},
+  year      = {2023},
+  issn      = {1179-1349},
+  month     = may,
+  pages     = {569--581},
+  volume    = {Volume 15},
+  doi       = {10.2147/clep.s407019},
+  publisher = {Informa UK Limited},
+}
+
+@Comment{jabref-meta: databaseType:bibtex;}
diff --git a/vignettes/vancouver.csl b/vignettes/vancouver.csl
new file mode 100644
index 0000000..edbb69b
--- /dev/null
+++ b/vignettes/vancouver.csl
@@ -0,0 +1,351 @@
+<?xml version="1.0" encoding="utf-8"?>
+<style xmlns="http://purl.org/net/xbiblio/csl" class="in-text" version="1.0" demote-non-dropping-particle="sort-only" page-range-format="minimal">
+  <info>
+    <title>Vancouver</title>
+    <id>http://www.zotero.org/styles/vancouver</id>
+    <link href="http://www.zotero.org/styles/vancouver" rel="self"/>
+    <link href="http://www.nlm.nih.gov/bsd/uniform_requirements.html" rel="documentation"/>
+    <author>
+      <name>Michael Berkowitz</name>
+      <email>mberkowi@gmu.edu</email>
+    </author>
+    <contributor>
+      <name>Sean Takats</name>
+      <email>stakats@gmu.edu</email>
+    </contributor>
+    <contributor>
+      <name>Sebastian Karcher</name>
+    </contributor>
+    <category citation-format="numeric"/>
+    <category field="medicine"/>
+    <summary>Vancouver style as outlined by International Committee of Medical Journal Editors Uniform Requirements for Manuscripts Submitted to Biomedical Journals: Sample References</summary>
+    <updated>2014-09-06T16:03:01+00:00</updated>
+    <rights license="http://creativecommons.org/licenses/by-sa/3.0/">This work is licensed under a Creative Commons Attribution-ShareAlike 3.0 License</rights>
+  </info>
+  <locale xml:lang="en">
+    <date form="text" delimiter=" ">
+      <date-part name="year"/>
+      <date-part name="month" form="short" strip-periods="true"/>
+      <date-part name="day"/>
+    </date>
+    <terms>
+      <term name="collection-editor" form="long">
+        <single>editor</single>
+        <multiple>editors</multiple>
+      </term>
+      <term name="presented at">presented at</term>
+      <term name="available at">available from</term>
+      <term name="section" form="short">sect.</term>
+    </terms>
+  </locale>
+  <locale xml:lang="fr">
+    <date form="text" delimiter=" ">
+      <date-part name="day"/>
+      <date-part name="month" form="short" strip-periods="true"/>
+      <date-part name="year"/>
+    </date>
+  </locale>
+  <macro name="author">
+    <names variable="author">
+      <name sort-separator=" " initialize-with="" name-as-sort-order="all" delimiter=", " delimiter-precedes-last="always"/>
+      <label form="long" prefix=", "/>
+      <substitute>
+        <names variable="editor"/>
+      </substitute>
+    </names>
+  </macro>
+  <macro name="editor">
+    <names variable="editor" suffix=".">
+      <name sort-separator=" " initialize-with="" name-as-sort-order="all" delimiter=", " delimiter-precedes-last="always"/>
+      <label form="long" prefix=", "/>
+    </names>
+  </macro>
+  <macro name="chapter-marker">
+    <choose>
+      <if type="chapter paper-conference entry-dictionary entry-encyclopedia" match="any">
+        <text term="in" text-case="capitalize-first"/>
+      </if>
+    </choose>
+  </macro>
+  <macro name="publisher">
+    <choose>
+      <!--discard publisher info for articles-->
+      <if type="article-journal article-magazine article-newspaper" match="none">
+        <group delimiter=": " suffix=";">
+          <choose>
+            <if type="thesis">
+              <text variable="publisher-place" prefix="[" suffix="]"/>
+            </if>
+            <else-if type="speech"/>
+            <else>
+              <text variable="publisher-place"/>
+            </else>
+          </choose>
+          <text variable="publisher"/>
+        </group>
+      </if>
+    </choose>
+  </macro>
+  <macro name="access">
+    <choose>
+      <if variable="URL">
+        <group delimiter=": ">
+          <text term="available at" text-case="capitalize-first"/>
+          <text variable="URL"/>
+        </group>
+      </if>
+    </choose>
+  </macro>
+  <macro name="accessed-date">
+    <choose>
+      <if variable="URL">
+        <group prefix="[" suffix="]" delimiter=" ">
+          <text term="cited" text-case="lowercase"/>
+          <date variable="accessed" form="text"/>
+        </group>
+      </if>
+    </choose>
+  </macro>
+  <macro name="container-title">
+    <choose>
+      <if type="article-journal article-magazine chapter paper-conference article-newspaper review review-book entry-dictionary entry-encyclopedia" match="any">
+        <group suffix="." delimiter=" ">
+          <choose>
+            <if type="article-journal review review-book" match="any">
+              <text variable="container-title" form="short" strip-periods="true"/>
+            </if>
+            <else>
+              <text variable="container-title" strip-periods="true"/>
+            </else>
+          </choose>
+          <choose>
+            <if variable="URL">
+              <text term="internet" prefix="[" suffix="]" text-case="capitalize-first"/>
+            </if>
+          </choose>
+        </group>
+        <text macro="edition" prefix=" "/>
+      </if>
+      <!--add event-name and event-place once they become available-->
+      <else-if type="bill legislation" match="any">
+        <group delimiter=", ">
+          <group delimiter=". ">
+            <text variable="container-title"/>
+            <group delimiter=" ">
+              <text term="section" form="short" text-case="capitalize-first"/>
+              <text variable="section"/>
+            </group>
+          </group>
+          <text variable="number"/>
+        </group>
+      </else-if>
+      <else-if type="speech">
+        <group delimiter=": " suffix=";">
+          <group delimiter=" ">
+            <text variable="genre" text-case="capitalize-first"/>
+            <text term="presented at"/>
+          </group>
+          <text variable="event"/>
+        </group>
+      </else-if>
+      <else>
+        <group delimiter=", " suffix=".">
+          <choose>
+            <if variable="collection-title" match="none">
+              <group delimiter=" ">
+                <label variable="volume" form="short" text-case="capitalize-first"/>
+                <text variable="volume"/>
+              </group>
+            </if>
+          </choose>
+          <text variable="container-title"/>
+        </group>
+      </else>
+    </choose>
+  </macro>
+  <macro name="title">
+    <text variable="title"/>
+    <choose>
+      <if type="article-journal article-magazine chapter paper-conference article-newspaper review review-book entry-dictionary entry-encyclopedia" match="none">
+        <choose>
+          <if variable="URL">
+            <text term="internet" prefix=" [" suffix="]" text-case="capitalize-first"/>
+          </if>
+        </choose>
+        <text macro="edition" prefix=". "/>
+      </if>
+    </choose>
+    <choose>
+      <if type="thesis">
+        <text variable="genre" prefix=" [" suffix="]"/>
+      </if>
+    </choose>
+  </macro>
+  <macro name="edition">
+    <choose>
+      <if is-numeric="edition">
+        <group delimiter=" ">
+          <number variable="edition" form="ordinal"/>
+          <text term="edition" form="short"/>
+        </group>
+      </if>
+      <else>
+        <text variable="edition" suffix="."/>
+      </else>
+    </choose>
+  </macro>
+  <macro name="date">
+    <choose>
+      <if type="article-journal article-magazine article-newspaper review review-book" match="any">
+        <group suffix=";" delimiter=" ">
+          <date variable="issued" form="text"/>
+          <text macro="accessed-date"/>
+        </group>
+      </if>
+      <else-if type="bill legislation" match="any">
+        <group delimiter=", ">
+          <date variable="issued" delimiter=" ">
+            <date-part name="month" form="short" strip-periods="true"/>
+            <date-part name="day"/>
+          </date>
+          <date variable="issued">
+            <date-part name="year"/>
+          </date>
+        </group>
+      </else-if>
+      <else-if type="report">
+        <date variable="issued" delimiter=" ">
+          <date-part name="year"/>
+          <date-part name="month" form="short" strip-periods="true"/>
+        </date>
+        <text macro="accessed-date" prefix=" "/>
+      </else-if>
+      <else-if type="patent">
+        <group suffix=".">
+          <group delimiter=", ">
+            <text variable="number"/>
+            <date variable="issued">
+              <date-part name="year"/>
+            </date>
+          </group>
+          <text macro="accessed-date" prefix=" "/>
+        </group>
+      </else-if>
+      <else-if type="speech">
+        <group delimiter="; ">
+          <group delimiter=" ">
+            <date variable="issued" delimiter=" ">
+              <date-part name="year"/>
+              <date-part name="month" form="short" strip-periods="true"/>
+              <date-part name="day"/>
+            </date>
+            <text macro="accessed-date"/>
+          </group>
+          <text variable="event-place"/>
+        </group>
+      </else-if>
+      <else>
+        <group suffix=".">
+          <date variable="issued">
+            <date-part name="year"/>
+          </date>
+          <text macro="accessed-date" prefix=" "/>
+        </group>
+      </else>
+    </choose>
+  </macro>
+  <macro name="pages">
+    <choose>
+      <if type="article-journal article-magazine article-newspaper review review-book" match="any">
+        <text variable="page" prefix=":"/>
+      </if>
+      <else-if type="book" match="any">
+        <text variable="number-of-pages" prefix=" "/>
+        <choose>
+          <if is-numeric="number-of-pages">
+            <label variable="number-of-pages" form="short" prefix=" " plural="never"/>
+          </if>
+        </choose>
+      </else-if>
+      <else>
+        <group prefix=" " delimiter=" ">
+          <label variable="page" form="short" plural="never"/>
+          <text variable="page"/>
+        </group>
+      </else>
+    </choose>
+  </macro>
+  <macro name="journal-location">
+    <choose>
+      <if type="article-journal article-magazine review review-book" match="any">
+        <text variable="volume"/>
+        <text variable="issue" prefix="(" suffix=")"/>
+      </if>
+    </choose>
+  </macro>
+  <macro name="collection-details">
+    <choose>
+      <if type="article-journal article-magazine article-newspaper review review-book" match="none">
+        <choose>
+          <if variable="collection-title">
+            <group delimiter=" " prefix="(" suffix=")">
+              <names variable="collection-editor" suffix=".">
+                <name sort-separator=" " initialize-with="" name-as-sort-order="all" delimiter=", " delimiter-precedes-last="always"/>
+                <label form="long" prefix=", "/>
+              </names>
+              <group delimiter="; ">
+                <text variable="collection-title"/>
+                <group delimiter=" ">
+                  <label variable="volume" form="short"/>
+                  <text variable="volume"/>
+                </group>
+              </group>
+            </group>
+          </if>
+        </choose>
+      </if>
+    </choose>
+  </macro>
+  <macro name="report-details">
+    <choose>
+      <if type="report">
+        <text variable="number" prefix="Report No.: "/>
+      </if>
+    </choose>
+  </macro>
+  <citation collapse="citation-number">
+    <sort>
+      <key variable="citation-number"/>
+    </sort>
+    <layout prefix="(" suffix=")" delimiter=",">
+      <text variable="citation-number"/>
+    </layout>
+  </citation>
+  <bibliography et-al-min="7" et-al-use-first="6" second-field-align="flush">
+    <layout>
+      <text variable="citation-number" suffix=". "/>
+      <group delimiter=". " suffix=". ">
+        <text macro="author"/>
+        <text macro="title"/>
+      </group>
+      <group delimiter=" " suffix=". ">
+        <group delimiter=": ">
+          <text macro="chapter-marker"/>
+          <group delimiter=" ">
+            <text macro="editor"/>
+            <text macro="container-title"/>
+          </group>
+        </group>
+        <text macro="publisher"/>
+        <group>
+          <text macro="date"/>
+          <text macro="journal-location"/>
+          <text macro="pages"/>
+        </group>
+      </group>
+      <text macro="collection-details" suffix=". "/>
+      <text macro="report-details" suffix=". "/>
+      <text macro="access"/>
+    </layout>
+  </bibliography>
+</style>