Initialize 06-09-2023

.gitignore

+.Rproj.user
+.Rhistory
+.RData
+.Ruserdata
+
+/.quarto/

COVER LETTER.qmd

+---
+title: "COVER LETTER"
+editor: visual
+---
+
+# COVER LETTER
+
+`r lubridate::today()`
+
+Dr. XXX, Dr. YYY Editors {{< meta citation.container-title >}}
+
+Dear Dr. XXX, dear Dr. YYY,
+
+I wish to submit a research article for publication in {{< meta citation.container-title >}}, titled "{{< meta title >}}" The paper was coauthored by {{< meta author.name.id=hf >}} and {{< meta author.name.id=lh >}}.
+
+With the study presented here, we would like to contribute to the current discussion regarding the impact of artificial intelligence on medical education. In doing so, we have explicitly focused on
+
+We hope to be able to make a meaningful contribution to the current discussion with this study.
+
+Further, we believe that this paper will be of interest to the readership of your journal because it provides potentially useful information to identify skills that should be addressed in medical education. The results of this study could help guide future improvements in medical education.
+
+This manuscript has not been published or presented elsewhere in part or in entirety and is not under consideration by another journal. All study participants provided informed consent. We have read and understood your journal's policies, and we believe that neither the manuscript nor the study violates any of these. There are no conflicts of interest to declare.
+
+Thank you for your consideration. I look forward to hearing from you.
+
+Sincerely, Hendrik Friederichs
+
+Univ.-Prof. Dr. med. Hendrik Friederichs
+
+Professur für Medical Education, AG 7
+
+Medizinische Fakultät OWL
+
+Universität Bielefeld
+
+Universitätsstr. 25
+
+33615 Bielefeld
+
+Email: hendrik.friederichs\@uni-bielefeld.de

ChatGPT-CR.Rproj

+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX

README.md

+## A Quarto Manuscript Template
+
+This is a template repo for generating a manuscript from Quarto that accompanies the tutorial at: [Quarto Manuscripts: RStudio](https://quarto.org/docs/manuscripts/authoring/rstudio.html)
+
+I would like to use it as a template for scientific manuscripts in Medical Education.
\ No newline at end of file

Tables_and_figures.qmd

+---
+title: "Tables and figures"
+editor: visual
+---
+
+# TABLE(S) WITH CAPTION(S)
+
+(on individual pages)
+
+# FIGURES
+
+# FIGURE CAPTIONS
+
+(as a list)
+
+Figure 1: xxx
+
+Tabelle 1: xxx
+
+# Supplement
+
+Supplement Figure 1: xxx

_authordata.yml

+author:
+  - name:
+      given: Hendrik
+      family: Friederichs
+      literal: Hendrik Friederichs
+      dropping-particle: string
+      non-dropping-particle: string
+    url: https://ekvv.uni-bielefeld.de/pers_publ/publ/PersonDetail.jsp?personId=251340451
+    email: hendrik.friederichs@uni-bielefeld.de
+    orcid: 0000-0001-9671-5235
+    affiliations:
+      - ref: bi
+    attributes:
+      corresponding: true
+    equal-contributor: true
+    degrees: MD
+    roles: 
+      - conceptualization: lead
+      - data curation: supporting
+      - formal analysis: lead
+      - funding acquisition: lead
+      - investigation: lead
+      - methodology: lead
+      - project administration: lead
+      - resources: lead
+      - software: lead
+      - supervision: lead
+      - validation: lead
+      - visualization: lead
+      - writing - review & editing: lead
+      - writing - original draft: lead
+    id: hf
+  - name:
+      given: Lennart
+      family: Handke
+      literal: Lennart Handke
+      dropping-particle: string
+      non-dropping-particle: string
+    affiliations:
+      - ref: bi
+    orcid: 0000-2222-1111-3333
+    equal-contributor: true
+    id: lh
+#  - name:
+#      given: Nima
+#      family: Zandi
+#      literal: Nima Zandi
+#      dropping-particle: string
+#      non-dropping-particle: string
+#    affiliations:
+#      - ref: bi
+#    orcid: 0000-2222-1111-3333
+#    equal-contributor: false
+#  - name:
+#      given: Wolf Jonas
+#      family: Friederichs
+#      literal: Wolf Jonas Friederichs
+#      dropping-particle: string
+#      non-dropping-particle: string
+#    affiliations:
+#      - ref: aa
+#    orcid: 0000-0003-1733-7788
+#    equal-contributor: false
+#  - name:
+#      given: Maren
+#      family: März
+#      literal: Maren März
+#      dropping-particle: string
+#      non-dropping-particle: string
+#    affiliations:
+#      - ref: be
+#    orcid: 0000-0002-2661-5076
+#    equal-contributor: false
+    
+affiliations:
+  - id: bi
+    name: Universität Bielefeld, Medizinische Fakultät OWL
+    department: AG Medical Education
+    address: Universitätsstr. 25
+    city: Bielefeld
+    region: NRW
+    country: Deutschland
+    postal-code: 33615
+    url: https://www.uni-bielefeld.de/fakultaeten/medizin/
+    ror: https://ror.org/02hpadn98
+    isni: 0000000109449128
+#  - id: aa
+#    name: RWTH Aachen, Fakultät für Maschinenwesen, Aachen, Deutschland.
+#  - id: be
+#    name: Humboldt-Universität zu Berlin, Charité – Universitätsmedizin Berlin, Kooperationspartner der Freien Universität Berlin, Progress Test Medizin, Charitéplatz 1, Berlin, Deutschland.
\ No newline at end of file

_extensions/friederichs/AG_7/_extension.yml

+title: AG Medical Education Template
+author: Hendrik Friederichs
+version: 0.0.1
+contributes:
+  formats:
+    common:
+      # define below YAML configuration common to all formats
+      filters:
+        # You can include here Lua filters from your extension format 
+      shortcodes:
+        # You can include here Lua filters defining shortcodes from your extension
+      knitr:
+        opts_chunk:
+          echo: false
+      # Use a CSL file to style (https://www.zotero.org/styles/)
+      csl: apa.csl
+      link-citations: yes
+    pdf:
+      # define default configuration for the pdf version of your format
+      colorlinks: true
+      urlcolor: blue
+      fig-width: 6.5
+      fig-height: 4.5
+      mainfont: Verdana
+      # Content to add in header that your format is using
+      include-in-header: 
+        - include-in-header.tex
+      template-partials:
+        # Add here the partials your format is using
+        - "partials/before-body.tex"
+        - "partials/_authors.tex"
+        - "partials/_affiliations.tex"
+      format-resources:
+        # Add here the resources required for the PDF rendering
+        - logo.png
+    html:
+      # define default configuration for the html version of your format
+      number-sections: true
+      toc: true
+      theme: custom.scss
+

_extensions/friederichs/AG_7/bmc-medicine.csl

+<?xml version="1.0" encoding="utf-8"?>
+<style xmlns="http://purl.org/net/xbiblio/csl" version="1.0" default-locale="en-US">
+  <!-- Springer, generated from "springer" metadata at https://github.com/citation-style-language/journals -->
+  <info>
+    <title>BMC Medicine</title>
+    <id>http://www.zotero.org/styles/bmc-medicine</id>
+    <link href="http://www.zotero.org/styles/bmc-medicine" rel="self"/>
+    <link href="http://www.zotero.org/styles/biomed-central" rel="independent-parent"/>
+    <link href="http://www.springer.com/cda/content/document/cda_downloaddocument/Key_Style_Points_1.0.pdf" rel="documentation"/>
+    <link href="http://www.springer.com/cda/content/document/cda_downloaddocument/manuscript-guidelines-1.0.pdf" rel="documentation"/>
+    <category citation-format="numeric"/>
+    <category field="medicine"/>
+    <eissn>1741-7015</eissn>
+    <updated>2018-06-19T03:55:25+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>
+</style>

_extensions/friederichs/AG_7/include-in-header.tex

+\usepackage{orcidlink,fancyhdr,graphicx,xcolor,xstring,fontspec,mdframed}
+\usepackage[margin=1in]{geometry}
+\usepackage[onehalfspacing]{setspace}
+\usepackage[scale=2.5]{ccicons}
+\definecolor{SRXIVgreen}{RGB}{207, 250, 209}
+\newcommand\shortauthor{}
\ No newline at end of file

_extensions/friederichs/AG_7/partials/_affiliations.tex

+\textsuperscript{$it.number$}$if(it.name)$$it.name$$endif$$if(it.department)$, $it.department$$endif$$if(it.address)$, $it.address$$endif$$if(it.city)$, $it.city$$endif$$if(it.postal-code)$, $it.postal-code$$endif$$if(it.region)$, $it.region$$endif$$if(it.country)$, $it.country$$endif$$if(it.url)$, $it.url$$endif$
\ No newline at end of file

_extensions/friederichs/AG_7/partials/_authors.tex

+$it.name.literal$\textsuperscript{$for(it.affiliations)$$it.number$$sep$,$endfor$$if(it.attributes.equal-contributor)$\textsuperscript{\#}$endif$$if(it.attributes.corresponding)$*$endif$$if(it.attributes.deceased)$\dag$endif$$if(it.metadata.group)$\textpilcrow$endif$}$if(it.orcid)$~\orcidlink{$it.orcid$}$endif$
\ No newline at end of file

_extensions/friederichs/AG_7/partials/before-body.tex

+$-- Implements the frontmatter, title page, and abstract.
+$--
+$-- %%%% TODO %%%%%
+$-- Customize is needed, otherwise remove this partials to use Quarto default one
+$-- %%%%%%%%%%%%%%%%
+
+% set short author name
+\newcounter{nauthor}
+$for(by-author)$\stepcounter{nauthor}$endfor$
+\ifnum\thenauthor>2
+\renewcommand{\shortauthor}{$author/first$ et al. }
+\else 
+\renewcommand{\shortauthor}{${ for(by-author) }${ by-author.name.family }${ sep } \& ${ endfor } }
+\fi
+
+\pagestyle{fancy}
+\fancyhead[L]{$if(shorttitle)$$shorttitle$$else$\shortauthor$ if(year)$($year$)$else$(\the\year)$endif$$endif$}
+\fancyhead[R]{}
+\fancypagestyle{firstpage}{
+  \fancyhf{}% clear default for head and foot
+  \lhead{\href{https://www.uni-bielefeld.de/fakultaeten/medizin/}{\includegraphics[width = 40mm]{logo.png}}}
+  \chead{$printnote$}
+  \rhead{\$license-type$\AG Medical Education}
+  \lfoot{\color{gray}All authors have read and approved  this version  of the manuscript. \linebreak The manuscript was last updated on \today. \linebreak Alle Autoren haben diese Version des Manuskripts gelesen und genehmigt. \linebreak 
+Das Manuskript wurde zuletzt am \today\ aktualisiert.}
+}
+\begin{flushleft}
+\begin{spacing}{2.5}
+\thispagestyle{firstpage}
+\vspace*{0.1cm}
+{\huge{\textbf{$title$}}}
+\end{spacing}
+\vspace*{0.1cm}
+$by-author:_authors.tex()[, ]$
+\\
+\bigskip
+$by-affiliation:_affiliations.tex()[\\ ]$
+\\
+\bigskip
+*Correspondence: 
+$for(by-author)$
+$if(by-author.attributes.corresponding)$
+\href{mailto:$by-author.email$}{\color{black}$by-author.email$}
+$endif$
+$endfor$
+\\
+\bigskip
+\begin{spacing}{1}
+Cite as: \shortauthor$if(year)$($year$)$else$(\the\year)$endif$. $title$. \emph{AG Medical Education.} \\
+\end{spacing}
+$if(suppl-link)$
+  \vspace{1mm} Supplementary Materials: \href{$suppl-link$}{$suppl-link$} \\
+$endif$
+\vspace*{1cm}
+\end{flushleft}
+
+
+\newenvironment{abstractbox}
+  {}
+
+\surroundwithmdframed[
+  backgroundcolor=SRXIVgreen,
+  innertopmargin=10pt,
+  innerbottommargin=10pt,
+  linewidth=2pt,
+  linecolor=gray!30,
+  leftmargin=20pt,
+  rightmargin=20pt,
+  frametitle={\large{Abstract}},
+]{abstractbox}
+
+\begin{abstractbox}
+  $abstract$ 
+  $if(keywords)$
+  \\ \\
+  Keywords: \emph{${for(keywords)}${keywords}${sep}; ${endfor}}
+  $endif$ 
+\end{abstractbox}

_extensions/friederichs/AG_7/partials/graphics.tex

+$-- Provides image scaling and placement configuration.
+$--
+$-- %%%% TODO %%%%%
+$-- Customize is needed, otherwise remove this partials to use Quarto default one
+$-- %%%%%%%%%%%%%%%%
+$if(graphics)$
+\usepackage{graphicx}
+\makeatletter
+\def\maxwidth{\ifdim\Gin@nat@width>\linewidth\linewidth\else\Gin@nat@width\fi}
+\def\maxheight{\ifdim\Gin@nat@height>\textheight\textheight\else\Gin@nat@height\fi}
+\makeatother
+% Scale images if necessary, so that they will not overflow the page
+% margins by default, and it is still possible to overwrite the defaults
+% using explicit options in \includegraphics[width, height, ...]{}
+\setkeys{Gin}{width=\maxwidth,height=\maxheight,keepaspectratio}
+% Set default figure placement to htbp
+\makeatletter
+\def\fps@figure{htbp}
+\makeatother
+$endif$