title: Authors and affiliations in the YAML of RMarkdown
body: <p>I know this question was already asked in the past in this forum (<a href="https://www.google.es/url?sa=t&amp;rct=j&amp;q=&amp;esrc=s&amp;source=web&amp;cd=1&amp;cad=rja&amp;uact=8&amp;ved=2ahUKEwjRvauGlZjeAhXMx4UKHWBeDkMQFjAAegQICRAB&amp;url=https%3A%2F%2Fstackoverflow.com%2Fquestions%2F29532214%2Fadd-author-affiliation-in-r-markdown-beamer-presentation&amp;usg=AOvVaw35DvCYdCbXc9f8BcMfBJcK" rel="noreferrer">1</a>, <a href="https://www.google.es/url?sa=t&amp;rct=j&amp;q=&amp;esrc=s&amp;source=web&amp;cd=1&amp;cad=rja&amp;uact=8&amp;ved=2ahUKEwjRvauGlZjeAhXMx4UKHWBeDkMQrAIoADAAegQICRAK&amp;url=https%3A%2F%2Fstackoverflow.com%2Fquestions%2F46136924%2Fhow-to-add-multiple-authors-and-multiple-affiliations-in-rmarkdown&amp;usg=AOvVaw2FPil8dlHRXtngIGreNHsn" rel="noreferrer">2</a>, <a href="https://www.google.es/url?sa=t&amp;rct=j&amp;q=&amp;esrc=s&amp;source=web&amp;cd=1&amp;cad=rja&amp;uact=8&amp;ved=2ahUKEwjRvauGlZjeAhXMx4UKHWBeDkMQrAIoAjAAegQICRAM&amp;url=https%3A%2F%2Fstackoverflow.com%2Fquestions%2F26043807%2Fmultiple-authors-and-subtitles-in-rmarkdown-yaml&amp;usg=AOvVaw07zhr4PUpxbfI9WwIuJRW-" rel="noreferrer">3</a>). Before you mark this as duplicated, I tried all the answers with no success. Most of the questions were asked long ago, and some updates related with <code>pandoc</code> might affect nowadays results.</p>
  
  <p>The issue is that I am writing a scientific paper using RMarkdown, and would like to export the results either in HTML, PDF or Word files.</p>
  
  <p>More importantly is that <strong>there are 12 authors</strong> signing the papers. <strong>Some of the authors present more than one affiliation</strong>, and <strong>some authors presenting the same affiliation</strong>.</p>
  
  <p>My question is very clear: How can I edit the YAML to include all the authors with all the affiliations in the YAML in order to export to different formats (HTML, PDF, DOC)?</p>
  
  <p>I tried this YAML:</p>
  
  <pre><code>---
  title: "My title"
  author:
    - name: Mario Modesto-Mata^1,2^
      email: paleomariomm@gmail.com
    - name: Christopher^1^
    - name: Seaghán Mhartain^2^
    - name: Rita Yuri Ynoue^1^
  address:
    - code: 1
      address: Instituto de Astronomía, Geofísica e Ciências Atmosféricas, Universidade de São Paulo
    - code: 2
      address: Faculdade de Medicina, Universidade de São Paulo
  date: "1 October 2018"
  output: 
    pdf_document: 
      number_sections: yes
      toc: yes
      toc_depth: 4
    word_document:
      toc: yes
    html_document:
      css: Scripts accesorios/estiloboton.css
      number_sections: yes
      theme: sandstone
      toc: yes
      toc_depth: 4
  bibliography: references.bib
  csl: science.csl
  ---
  </code></pre>
  
  <h1>PDF output</h1>
  
  <p>This is what I see when I export to PDF the <code>.Rmd</code> file:</p>
  
  <p><a href="https://i.stack.imgur.com/41Feh.png" rel="noreferrer"><img src="https://i.stack.imgur.com/41Feh.png" alt="enter image description here"></a></p>
  
  <p>Instead of the authors, I see <code>true</code> and no affiliations.</p>
  
  <h1>HTML output</h1>
  
  <p>I see the authors and not all the affiliation numbers. The affiliations themselves remain hidden.</p>
  
  <p><a href="https://i.stack.imgur.com/Ln75w.png" rel="noreferrer"><img src="https://i.stack.imgur.com/Ln75w.png" alt="enter image description here"></a></p>
  
  <h1>DOCX output</h1>
  
  <p>Neither names nor affiliations appear in the final Word file.</p>
  
  <h1>My system</h1>
  
  <p>I am using the latest RStudio version (Version 1.1.453), running on Linux Mint 19 Cinnamon.</p>
  
  <h1>UPDATE: original example</h1>
  
  <pre><code>---
  title: "My title"
  author:
    - Mario Modesto-Mata:
        email: paleomariomm@gmail.com
        institute: [cenieh, ucl1, ppex]
        correspondence: true
    - M. Christopher Dean:
      institute: [ucl2, nhm]
    - Yuliet Quintino:
      institute: ubu
    - Rebeca García-González:
      institute: ubu
    - Rodrigo S. Lacruz:
      institute: nyu
    - Timothy G. Bromage:
      institute: nyu
    - Cecilia García-Campos:
      institute: [cenieh, ucl1]
    - Marina Martínez de Pinillos:
      institute: cenieh
    - Laura Martín-Francés:
      institute: [bor, cenieh]
    - María Martinón-Torres:
      institute: [cenieh, ucl1]
    - Eudald Carbonell:
      institute: [iphes, urv]
    - Juan Luis Arsuaga:
      institute: [isciii, ucm]
    - José María Bermúdez de Castro:
      institute: [cenieh, ucl1]
  institute:
    - cenieh: Centro Nacional de Investigación sobre la Evolución Humana (CENIEH), Paseo Sierra de Atapuerca 3, 09002, Burgos, Spain
    - ucl1: Department of Anthropology, University College London, London, WC1H 0BW, UK
    - ucl2: Department of Cell and Developmental Biology, University College London, Gower Street, London, WC1E 6BT, UK
    - ubu: Laboratorio de Evolución Humana, Unierisdad de Burgos, Edificio I+D+i, Burgos, Spain
    - ppex: Equipo Primeros Pobladores de Extremadura, Casa de Cultura Rodríguez Moñino, Cáceres, Spain
    - nhm: Centre for Human Evolution Research (CHER), Department of Earth Sciences, Natural History Museum, London, SW7 5BD, UK
    - nyu: New York University
    - bor: De la Préhistoire à l'Actuel - Culture, Environnement et Anthropologie, University of Bordeaux, CNRS, MCC, PACE, UMR 5199 F_33615, Pessac Cedex, France
    - iphes: Institut Català de Paleoecologia Humana i Evolució Social (IPHES), Zona Educacional 4, Campus Sescelades, Edifici W3, Universitat Rovira i Virgili, Tarragona, Spain
    - urv: Àrea de Prehistòria, Universitat Rovira i Virgili, Avinguda de Catalunya 35, 43002, Tarragona, Spain
    - isciii: Centro mixto UCM-ISCIII de Evolución y Comportamiento humanos, Madrid, Spain
    - ucm: Departamento de Geodinámica, Estratigrafía y Paleontología, Facultad de Ciencias Geológicas, Universidad Complutense de Madrid, Spain
  date: "1 October 2018"
  output: 
    pdf_document: 
      number_sections: yes
      toc: yes
      toc_depth: 4
      pandoc_args:
        - '--lua-filter=scholarly-metadata.lua'
        - '--lua-filter=author-info-blocks.lua'
    html_document:
      css: Scripts accesorios/estiloboton.css
      number_sections: yes
      theme: sandstone
      toc: yes
      toc_depth: 4
    word_document:
      toc: yes
      pandoc_args:
        - '--lua-filter=scholarly-metadata.lua'
        - '--lua-filter=author-info-blocks.lua'
  bibliography: references.bib
  csl: science.csl
  ---
  </code></pre>