feat(repo): Add journal extension
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14 changed files with 6579 additions and 28 deletions
19
_extensions/quarto-journals/elsevier/_extension.yml
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19
_extensions/quarto-journals/elsevier/_extension.yml
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title: Elsevier Journal Format
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author: Charles Teague
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version: 0.4.2
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quarto-required: ">=1.2.198"
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contributes:
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formats:
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common:
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date-format: full
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filters:
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- elsevier.lua
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pdf:
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documentclass: elsarticle
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template-partials: ["partials/before-body.tex", "partials/title.tex"]
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format-resources:
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- elsarticle.cls
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cite-method: natbib
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number-sections: true
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html:
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theme: styles/elsevier.scss
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1598
_extensions/quarto-journals/elsevier/bib/elsarticle-harv.bst
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_extensions/quarto-journals/elsevier/bib/elsarticle-harv.bst
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1535
_extensions/quarto-journals/elsevier/bib/elsarticle-num-names.bst
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1535
_extensions/quarto-journals/elsevier/bib/elsarticle-num-names.bst
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1509
_extensions/quarto-journals/elsevier/bib/elsarticle-num.bst
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_extensions/quarto-journals/elsevier/bib/elsarticle-num.bst
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239
_extensions/quarto-journals/elsevier/bib/elsevier-harvard.csl
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_extensions/quarto-journals/elsevier/bib/elsevier-harvard.csl
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<?xml version="1.0" encoding="utf-8"?>
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<style xmlns="http://purl.org/net/xbiblio/csl" class="in-text" version="1.0" demote-non-dropping-particle="never" default-locale="en-US">
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<info>
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<title>Elsevier - Harvard (with titles)</title>
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<id>http://www.zotero.org/styles/elsevier-harvard</id>
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<link href="http://www.zotero.org/styles/elsevier-harvard" rel="self"/>
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<link href="http://www.zotero.org/styles/ecology-letters" rel="template"/>
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<link href="http://www.elsevier.com/journals/biological-conservation/0006-3207/guide-for-authors#68000" rel="documentation"/>
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<author>
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<name>David Kaplan</name>
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<email>david.kaplan@ird.fr</email>
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</author>
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<contributor>
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<name>Simon Kornblith</name>
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<email>simon@simonster.com</email>
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</contributor>
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<contributor>
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<name>Bruce D'Arcus</name>
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</contributor>
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<contributor>
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<name>Curtis M. Humphrey</name>
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</contributor>
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<contributor>
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<name>Richard Karnesky</name>
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<email>karnesky+zotero@gmail.com</email>
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<uri>http://arc.nucapt.northwestern.edu/Richard_Karnesky</uri>
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</contributor>
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<contributor>
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<name>Sebastian Karcher</name>
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</contributor>
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<category citation-format="author-date"/>
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<category field="biology"/>
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<category field="generic-base"/>
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<updated>2019-01-22T15:57:12+00:00</updated>
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<rights license="http://creativecommons.org/licenses/by-sa/3.0/">This work is licensed under a Creative Commons Attribution-ShareAlike 3.0 License</rights>
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</info>
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<macro name="container">
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<choose>
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<if type="chapter paper-conference" match="any">
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<text term="in" prefix=", " suffix=": "/>
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<names variable="editor translator" delimiter=", " suffix=", ">
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<name name-as-sort-order="all" sort-separator=", " initialize-with="." delimiter=", " delimiter-precedes-last="always"/>
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<label form="short" text-case="capitalize-first" prefix=" (" suffix=")"/>
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</names>
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<group delimiter=", ">
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<text variable="container-title" text-case="title"/>
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<text variable="collection-title" text-case="title"/>
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</group>
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</if>
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<else-if type="bill book graphic legal_case legislation motion_picture report song" match="any">
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<group prefix=", " delimiter=", ">
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<text variable="container-title"/>
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<text variable="collection-title"/>
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</group>
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</else-if>
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<else>
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<group prefix=". " delimiter=", ">
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<text variable="container-title" form="short"/>
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<text variable="collection-title"/>
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</group>
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</else>
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</choose>
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</macro>
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<macro name="author">
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<names variable="author">
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<name name-as-sort-order="all" sort-separator=", " initialize-with="." delimiter=", " delimiter-precedes-last="always"/>
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<label form="short" prefix=" (" suffix=")" text-case="capitalize-first"/>
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<substitute>
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<names variable="editor"/>
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<names variable="translator"/>
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<text macro="title"/>
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</substitute>
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</names>
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</macro>
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<macro name="author-short">
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<names variable="author">
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<name form="short" and="text" delimiter=", " initialize-with=". "/>
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<substitute>
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<names variable="editor"/>
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<names variable="translator"/>
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<choose>
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<if type="bill book graphic legal_case legislation motion_picture report song" match="any">
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<text variable="title" form="short" font-style="italic"/>
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</if>
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<else>
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<text variable="title" form="short" quotes="true"/>
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</else>
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</choose>
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</substitute>
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</names>
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</macro>
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<macro name="access">
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<choose>
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<if variable="DOI">
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<text variable="DOI" prefix="https://doi.org/"/>
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</if>
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<else-if type="webpage post-weblog" match="any">
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<group delimiter=" ">
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<text value="URL"/>
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<text variable="URL"/>
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<group prefix="(" suffix=").">
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<text term="accessed" suffix=" "/>
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<date variable="accessed">
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<date-part name="month" form="numeric" suffix="."/>
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<date-part name="day" suffix="."/>
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<date-part name="year" form="short"/>
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</date>
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</group>
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</group>
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</else-if>
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</choose>
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</macro>
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<macro name="title">
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<choose>
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<if type="report thesis" match="any">
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<text variable="title"/>
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<group prefix=" (" suffix=")" delimiter=" ">
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<text variable="genre"/>
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<text variable="number" prefix="No. "/>
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</group>
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</if>
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<else-if type="bill book graphic legal_case legislation motion_picture report song speech" match="any">
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<text variable="title"/>
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<text macro="edition" prefix=", "/>
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</else-if>
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<else-if type="webpage">
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<text variable="title"/>
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<text value="WWW Document" prefix=" [" suffix="]"/>
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</else-if>
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<else>
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<text variable="title"/>
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</else>
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</choose>
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</macro>
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<macro name="publisher">
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<group delimiter=", ">
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<text variable="publisher"/>
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<text variable="publisher-place"/>
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</group>
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</macro>
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<macro name="event">
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<choose>
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<if variable="event">
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<text term="presented at" text-case="capitalize-first" suffix=" "/>
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<text variable="event"/>
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</if>
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</choose>
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</macro>
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<macro name="issued">
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<choose>
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<if variable="issued">
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<date variable="issued">
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<date-part name="year"/>
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</date>
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</if>
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<else>
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<text term="no date" form="short"/>
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</else>
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</choose>
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</macro>
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<macro name="edition">
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<group delimiter=" ">
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<choose>
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<if is-numeric="edition">
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<number variable="edition" form="ordinal"/>
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</if>
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<else>
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<text variable="edition" suffix="."/>
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</else>
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</choose>
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<text value="ed"/>
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</group>
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</macro>
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<macro name="locators">
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<choose>
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<if type="article-journal article-magazine article-newspaper" match="any">
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<group prefix=" " delimiter=", ">
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<group>
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<text variable="volume"/>
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</group>
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<text variable="page"/>
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</group>
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</if>
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<else-if type="bill book graphic legal_case legislation motion_picture report song thesis" match="any">
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<group delimiter=", " prefix=". ">
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<text macro="event"/>
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<text macro="publisher"/>
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</group>
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</else-if>
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<else-if type="chapter paper-conference" match="any">
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<group delimiter=", " prefix=". ">
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<text macro="event"/>
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<text macro="publisher"/>
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<group>
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<label variable="page" form="short" suffix=" "/>
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<text variable="page"/>
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</group>
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</group>
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</else-if>
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<else-if type="patent">
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<text variable="number" prefix=". "/>
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</else-if>
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</choose>
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</macro>
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<citation et-al-min="3" et-al-use-first="1" disambiguate-add-givenname="true" disambiguate-add-year-suffix="true" collapse="year" cite-group-delimiter=", ">
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<sort>
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<key macro="author"/>
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<key macro="issued" sort="descending"/>
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</sort>
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<layout prefix="(" suffix=")" delimiter="; ">
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<group delimiter=", ">
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<text macro="author-short"/>
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<text macro="issued"/>
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<group delimiter=" ">
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<label variable="locator" form="short"/>
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<text variable="locator"/>
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</group>
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</group>
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</layout>
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</citation>
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<bibliography hanging-indent="true" entry-spacing="0" line-spacing="1">
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<sort>
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<key macro="author"/>
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<key macro="issued" sort="descending"/>
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</sort>
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<layout>
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<group suffix=".">
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<text macro="author" suffix=","/>
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<text macro="issued" prefix=" "/>
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<group prefix=". ">
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<text macro="title"/>
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<text macro="container"/>
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<text macro="locators"/>
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</group>
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</group>
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<text macro="access" prefix=". "/>
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</layout>
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</bibliography>
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</style>
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1379
_extensions/quarto-journals/elsevier/elsarticle.cls
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_extensions/quarto-journals/elsevier/elsarticle.cls
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171
_extensions/quarto-journals/elsevier/elsevier.lua
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_extensions/quarto-journals/elsevier/elsevier.lua
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-- cite style constants
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local kBibStyleDefault = 'number'
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local kBibStyles = { 'number', 'numbername', 'authoryear' }
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local kBibStyleAuthYr = 'elsarticle-harv'
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local kBibStyleNumber = 'elsarticle-num'
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local kBibStyleNumberName = 'elsarticle-num-names'
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local kBibStyleUnknown = kBibStyleNumberName
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-- layout and style
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local kFormatting = pandoc.List({ 'preprint', 'review', 'doubleblind' })
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local kModels = pandoc.List({ '1p', '3p', '5p' })
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local kLayouts = pandoc.List({ 'onecolumn', 'twocolumn' })
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local function setBibStyle(meta, style)
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if meta['biblio-style'] == nil then
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meta['biblio-style'] = style
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quarto.doc.add_format_resource('bib/' .. style .. '.bst')
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end
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end
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local function hasClassOption(meta, option)
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if meta['classoption'] == nil then
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return false
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end
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for i, v in ipairs(meta['classoption']) do
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if v[1].text == option then
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return true
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end
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end
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return false
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end
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local function addClassOption(meta, option)
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if meta['classoption'] == nil then
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meta['classoption'] = pandoc.List({})
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end
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if not hasClassOption(meta, option) then
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meta['classoption']:insert({ pandoc.Str(option) })
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end
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end
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local function printList(list)
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local result = ''
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local sep = ''
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for i, v in ipairs(list) do
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result = result .. sep .. v
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sep = ', '
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end
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return result
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end
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local bibstyle = kBibStyleDefault
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return {
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{
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Meta = function(meta)
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-- If citeproc is being used, switch to the proper
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-- CSL file
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if quarto.doc.cite_method() == 'citeproc' and meta['csl'] == nil then
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meta['csl'] = quarto.utils.resolve_path('bib/elsevier-harvard.csl')
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end
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if quarto.doc.is_format("pdf") then
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-- read the journal settings
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local journal = meta['journal']
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local citestyle = nil
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local formatting = nil
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local model = nil
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local layout = nil
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local name = nil
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if journal ~= nil then
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citestyle = journal['cite-style']
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formatting = journal['formatting']
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model = journal['model']
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layout = journal['layout']
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name = journal['name']
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end
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-- process the site style
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if citestyle ~= nil then
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citestyle = pandoc.utils.stringify(citestyle)
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else
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citestyle = kBibStyleDefault
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end
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-- capture the bibstyle
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bibstyle = citestyle
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if citestyle == 'numbername' then
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setBibStyle(meta, kBibStyleNumberName)
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addClassOption(meta, 'number')
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elseif citestyle == 'authoryear' then
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setBibStyle(meta, kBibStyleAuthYr)
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addClassOption(meta, 'authoryear')
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elseif citestyle == 'number' then
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setBibStyle(meta, kBibStyleNumber)
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addClassOption(meta, 'number')
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elseif citestyle == 'super' then
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addClassOption(meta, 'super')
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setBibStyle(meta, kBibStyleNumber)
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else
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error("Unknown journal cite-style " .. citestyle .. "\nPlease use one of " .. printList(kBibStyles))
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setBibStyle(meta, kBibStyleUnknown)
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end
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-- process the layout
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if formatting ~= nil then
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formatting = pandoc.utils.stringify(formatting)
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if kFormatting:includes(formatting) then
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addClassOption(meta, formatting)
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else
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error("Unknown journal formatting " .. formatting .. "\nPlease use one of " .. printList(kFormatting))
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end
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end
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-- process the type
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if model ~= nil then
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model = pandoc.utils.stringify(model)
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if kModels:includes(model) then
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addClassOption(meta, model)
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else
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error("Unknown journal model " .. model .. "\nPlease use one of " .. printList(kModels))
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end
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end
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-- 5p models should be two column always
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if model == '5p' and layout == nil then
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layout = 'twocolumn'
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end
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-- process the type
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if layout ~= nil then
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layout = pandoc.utils.stringify(layout)
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if kLayouts:includes(layout) then
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addClassOption(meta, layout)
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if layout == 'twocolumn' then
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quarto.doc.include_file('in-header', 'partials/_two-column-longtable.tex')
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end
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else
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error("Unknown journal layout " .. layout .. "\nPlease use one of " .. printList(kLayouts))
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end
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end
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-- process the name
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if name ~= nil then
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name = pandoc.utils.stringify(name)
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quarto.doc.include_text('in-header', '\\journal{' .. name .. '}')
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end
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end
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return meta
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end
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},
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{
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Cite = function(cite)
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if bibstyle == 'number' then
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-- If we are numbered, force citations into normal mode
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-- as the author styles don't make sense
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for i, v in ipairs(cite.citations) do
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v.mode = 'NormalCitation'
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end
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return cite
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end
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end,
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}
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}
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\usepackage{float}
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\makeatletter
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\let\oldlt\longtable
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\let\endoldlt\endlongtable
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\def\longtable{\@ifnextchar[\longtable@i \longtable@ii}
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\def\longtable@i[#1]{\begin{figure}[H]
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\onecolumn
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\begin{minipage}{0.5\textwidth}
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\oldlt[#1]
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}
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\def\longtable@ii{\begin{figure}[H]
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\onecolumn
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\begin{minipage}{0.5\textwidth}
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\oldlt
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}
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\def\endlongtable{\endoldlt
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\end{minipage}
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\twocolumn
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\end{figure}}
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\makeatother
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\begin{frontmatter}
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\title{$title$$if(subtitle)$ \\\large{$subtitle$} $endif$}
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$for(by-author)$\author[$for(by-author.affiliations)$$it.number$$sep$,$endfor$]{$by-author.name.literal$%
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$if(by-author.attributes.corresponding)$\corref{cor1}$endif$%
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$if(by-author.note.text)$\fnref{fn$by-author.note.number$}$endif$}
|
||||
$if(by-author.email)$ \ead{$by-author.email$} $endif$
|
||||
$endfor$
|
||||
$for(by-affiliation)$
|
||||
\affiliation[$it.number$]{organization={$it.name$$if(it.department)$, $it.department$$endif$},$if(it.address)$addressline={$it.address$}$endif$$if(it.city)$$if(it.address)$,$endif$city={$it.city$}$endif$$if(it.country)$$if(it.city)$,$elseif(it.address)$,$endif$country={$it.country$},countrysep={,}$endif$$if(it.postal-code)$$if(it.country)$,$elseif(it.city)$,$elseif(it.address)$,$endif$postcode={$it.postal-code$}$endif$,postcodesep={}}
|
||||
$endfor$
|
||||
|
||||
\cortext[cor1]{Corresponding author}
|
||||
$for(by-author)$
|
||||
$if(by-author.note.text)$\fntext[fn$by-author.note.number$]{$by-author.note.text$}$endif$
|
||||
$endfor$
|
||||
|
||||
$if(abstract)$
|
||||
\begin{abstract}
|
||||
$abstract$
|
||||
\end{abstract}
|
||||
$endif$
|
||||
|
||||
$if(journal.graphical-abstract)$\begin{graphicalabstract}
|
||||
$journal.graphical-abstract$
|
||||
\end{graphicalabstract}
|
||||
$endif$
|
||||
|
||||
$if(journal.highlights)$\begin{highlights}
|
||||
$for(journal.highlights)$\item $it$$endfor$
|
||||
\end{highlights}
|
||||
$endif$
|
||||
|
||||
$if(keywords)$
|
||||
\begin{keyword}
|
||||
$for(keywords/allbutlast)$$keywords$ \sep $endfor$
|
||||
$for(keywords/last)$$keywords$$endfor$
|
||||
\end{keyword}
|
||||
$endif$
|
||||
\end{frontmatter}
|
||||
|
||||
1
_extensions/quarto-journals/elsevier/partials/title.tex
Normal file
1
_extensions/quarto-journals/elsevier/partials/title.tex
Normal file
|
|
@ -0,0 +1 @@
|
|||
\setlength{\parindent}{6pt}
|
||||
|
|
@ -0,0 +1 @@
|
|||
/*-- scss:defaults --*/
|
||||
35
_quarto-article.yml
Normal file
35
_quarto-article.yml
Normal file
|
|
@ -0,0 +1,35 @@
|
|||
project:
|
||||
type: manuscript
|
||||
output-dir: 04-outputs
|
||||
render:
|
||||
- article.qmd
|
||||
|
||||
manuscript:
|
||||
article: article.qmd
|
||||
# resources:
|
||||
# - 02-data/processed/extracted.csv
|
||||
|
||||
format:
|
||||
elsevier-html: default
|
||||
docx:
|
||||
echo: false
|
||||
number-sections: true
|
||||
reference-doc: 02-data/supplementary/justified.docx
|
||||
# filters:
|
||||
# - pandoc-to-zotero-live
|
||||
elsevier-pdf:
|
||||
echo: false
|
||||
number-sections: true
|
||||
html:
|
||||
comments:
|
||||
hypothesis: true
|
||||
jats: default
|
||||
|
||||
# (other formats)
|
||||
# pdf: default
|
||||
|
||||
execute:
|
||||
freeze: true
|
||||
|
||||
|
||||
|
||||
31
_quarto-workingpaper.yml
Normal file
31
_quarto-workingpaper.yml
Normal file
|
|
@ -0,0 +1,31 @@
|
|||
project:
|
||||
title: "Key terms and definitions"
|
||||
output-dir: 04-outputs
|
||||
render:
|
||||
- presentation_summary.md
|
||||
- notes.qmd
|
||||
- meeting_eoy.qmd
|
||||
- scoping_review.qmd
|
||||
|
||||
toc: true
|
||||
format:
|
||||
html:
|
||||
code-fold: true
|
||||
code-tools: true
|
||||
embed-resources: true
|
||||
fig-format: svg
|
||||
link-external-icon: true
|
||||
number-sections: false
|
||||
reference-links: true
|
||||
theme: darkly
|
||||
docx:
|
||||
echo: false
|
||||
number-sections: true
|
||||
reference-doc: 02-data/supplementary/justified.docx
|
||||
filters:
|
||||
- pandoc-to-zotero-live
|
||||
- docx-landscape
|
||||
pdf:
|
||||
echo: false
|
||||
number-sections: true
|
||||
pdf-engine: tectonic
|
||||
28
_quarto.yml
28
_quarto.yml
|
|
@ -1,33 +1,5 @@
|
|||
project:
|
||||
title: "Key terms and definitions"
|
||||
output-dir: 04-outputs
|
||||
render:
|
||||
- presentation_summary.md
|
||||
- notes.qmd
|
||||
- meeting_eoy.qmd
|
||||
- scoping_review.qmd
|
||||
|
||||
toc: true
|
||||
format:
|
||||
html:
|
||||
code-fold: true
|
||||
code-tools: true
|
||||
embed-resources: true
|
||||
fig-format: svg
|
||||
link-external-icon: true
|
||||
number-sections: false
|
||||
reference-links: true
|
||||
theme: darkly
|
||||
docx:
|
||||
echo: false
|
||||
number-sections: true
|
||||
reference-doc: 02-data/supplementary/justified.docx
|
||||
filters:
|
||||
- pandoc-to-zotero-live
|
||||
pdf:
|
||||
echo: false
|
||||
number-sections: true
|
||||
pdf-engine: tectonic
|
||||
|
||||
bibliography: 02-data/intermediate/zotero-library.bib
|
||||
csl: /home/marty/documents/library/utilities/styles/APA-7.csl
|
||||
|
|
|
|||
Loading…
Reference in a new issue