From 69b10803c786c5203492628f07ac524e6d2beb11 Mon Sep 17 00:00:00 2001
From: Stephan Schiffels <stephan_schiffels@eva.mpg.de>
Date: Tue, 24 Oct 2023 16:20:08 +0200
Subject: [PATCH] added authors and set reference side layout

---
 Quarto_intro.qmd   |   2 +
 docs/poseidon.html |  14 ++
 index.tex          | 561 ---------------------------------------------
 poseidon.qmd       |   8 +-
 4 files changed, 22 insertions(+), 563 deletions(-)
 delete mode 100644 index.tex

diff --git a/Quarto_intro.qmd b/Quarto_intro.qmd
index b612c46..54f40c1 100644
--- a/Quarto_intro.qmd
+++ b/Quarto_intro.qmd
@@ -5,6 +5,8 @@ date: "10/23/2023"
 editor: visual
 bibliography: references.bib
 toc: true
+reference-location: margin
+citation-location: margin
 ---
 
 In this introduction to quarto, you will be shown the basics in how to set up a website and a book. For more detailed information, I highly recommend checking out the [website](https://quarto.org) and also watch the [introduction tutorial](https://youtu.be/_f3latmOhew).
diff --git a/docs/poseidon.html b/docs/poseidon.html
index 2717f73..5a145a5 100644
--- a/docs/poseidon.html
+++ b/docs/poseidon.html
@@ -6,6 +6,8 @@
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
+<meta name="author" content="Ayshin Ghalichi &amp; CLemens Schmid">
+<meta name="dcterms.date" content="2023-10-19">
 
 <title>Computational Methods for human population genetics and ancient DNA - 2&nbsp; Genotype and context data management with Poseidon</title>
 <style>
@@ -212,7 +214,19 @@ <h1 class="title"><span class="chapter-number">2</span>&nbsp; <span class="chapt
 
 <div class="quarto-title-meta">
 
+    <div>
+    <div class="quarto-title-meta-heading">Author</div>
+    <div class="quarto-title-meta-contents">
+             <p>Ayshin Ghalichi &amp; CLemens Schmid </p>
+          </div>
+  </div>
     
+    <div>
+    <div class="quarto-title-meta-heading">Published</div>
+    <div class="quarto-title-meta-contents">
+      <p class="date">October 19, 2023</p>
+    </div>
+  </div>
   
     
   </div>
diff --git a/index.tex b/index.tex
deleted file mode 100644
index 6624254..0000000
--- a/index.tex
+++ /dev/null
@@ -1,561 +0,0 @@
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-\usepackage{amsmath,amssymb}
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-    % xetex/luatex font selection
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-% Use upquote if available, for straight quotes in verbatim environments
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-% Make \paragraph and \subparagraph free-standing
-\ifx\paragraph\undefined\else
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-  \renewcommand{\paragraph}[1]{\oldparagraph{#1}\mbox{}}
-\fi
-\ifx\subparagraph\undefined\else
-  \let\oldsubparagraph\subparagraph
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-\fi
-
-
-\providecommand{\tightlist}{%
-  \setlength{\itemsep}{0pt}\setlength{\parskip}{0pt}}\usepackage{longtable,booktabs,array}
-\usepackage{calc} % for calculating minipage widths
-% Correct order of tables after \paragraph or \subparagraph
-\usepackage{etoolbox}
-\makeatletter
-\patchcmd\longtable{\par}{\if@noskipsec\mbox{}\fi\par}{}{}
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-% Allow footnotes in longtable head/foot
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-\makesavenoteenv{longtable}
-\usepackage{graphicx}
-\makeatletter
-\def\maxwidth{\ifdim\Gin@nat@width>\linewidth\linewidth\else\Gin@nat@width\fi}
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-\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, ...]{}
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-% Set default figure placement to htbp
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-\AtBeginDocument{%
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-\else
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-\fi
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-  \renewcommand*\tablename{Table}
-\else
-  \newcommand\tablename{Table}
-\fi
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-\@ifpackageloaded{float}{}{\usepackage{float}}
-\floatstyle{ruled}
-\@ifundefined{c@chapter}{\newfloat{codelisting}{h}{lop}}{\newfloat{codelisting}{h}{lop}[chapter]}
-\floatname{codelisting}{Listing}
-\newcommand*\listoflistings{\listof{codelisting}{List of Listings}}
-\makeatother
-\makeatletter
-\@ifpackageloaded{caption}{}{\usepackage{caption}}
-\@ifpackageloaded{subcaption}{}{\usepackage{subcaption}}
-\makeatother
-\makeatletter
-\@ifpackageloaded{tcolorbox}{}{\usepackage[skins,breakable]{tcolorbox}}
-\makeatother
-\makeatletter
-\@ifundefined{shadecolor}{\definecolor{shadecolor}{rgb}{.97, .97, .97}}
-\makeatother
-\makeatletter
-\makeatother
-\makeatletter
-\makeatother
-\ifLuaTeX
-  \usepackage{selnolig}  % disable illegal ligatures
-\fi
-\IfFileExists{bookmark.sty}{\usepackage{bookmark}}{\usepackage{hyperref}}
-\IfFileExists{xurl.sty}{\usepackage{xurl}}{} % add URL line breaks if available
-\urlstyle{same} % disable monospaced font for URLs
-\hypersetup{
-  pdftitle={Computational Methods for human population genetics and ancient DNA},
-  pdfauthor={Various enthusiasts at the MPI-EVA},
-  colorlinks=true,
-  linkcolor={blue},
-  filecolor={Maroon},
-  citecolor={Blue},
-  urlcolor={Blue},
-  pdfcreator={LaTeX via pandoc}}
-
-\title{Computational Methods for human population genetics and ancient
-DNA}
-\author{Various enthusiasts at the MPI-EVA}
-\date{2023-09-21}
-
-\begin{document}
-\maketitle
-\ifdefined\Shaded\renewenvironment{Shaded}{\begin{tcolorbox}[boxrule=0pt, sharp corners, breakable, borderline west={3pt}{0pt}{shadecolor}, frame hidden, enhanced, interior hidden]}{\end{tcolorbox}}\fi
-
-\renewcommand*\contentsname{Table of contents}
-{
-\hypersetup{linkcolor=}
-\setcounter{tocdepth}{2}
-\tableofcontents
-}
-\bookmarksetup{startatroot}
-
-\hypertarget{preface}{%
-\chapter*{Preface}\label{preface}}
-\addcontentsline{toc}{chapter}{Preface}
-
-\markboth{Preface}{Preface}
-
-This book summarises prepared mini-courses for various computational
-tools and methods in the field of human archaeogenetic data analysis,
-with a particular emphasis on population genetics.
-
-The chapters are contributed by different authors, as indicated in the
-Yaml-frontmatter of each chapter's \texttt{.qmd} source file.
-
-\bookmarksetup{startatroot}
-
-\hypertarget{introduction-to-quarto}{%
-\chapter{Introduction to Quarto}\label{introduction-to-quarto}}
-
-In this introduction to quarto, you will be shown the basics in how to
-set up a website and a book. For more detailed information, I highly
-recommend checking out the \href{https://quarto.org}{website} and also
-watch the \href{https://youtu.be/_f3latmOhew}{introduction tutorial}.
-
-\hypertarget{setting-up}{%
-\section{Setting up}\label{setting-up}}
-
-Quarto is the ``next generation'' of R Markdown and is usable on
-different tools.
-
-\includegraphics[width=3.125in,height=\textheight]{img/quarto_intro/Picture 1.png}
-
-Here, we will describe how to set up your environment to use Quarto in
-\textbf{RStudio}, and VSCode.
-
-Quarto in general is set up to be very intuitive and user friendly. And
-while it is possible to set up different documents simultaneously, those
-can also easily be set up to in just the way you need for whatever
-occasion. So, for either communicating your results to collaborators,
-discuss code with your supervisor, setting up a website or writing your
-paper, to just name some scenarios, quarto comes in quite handy. So,
-let's begin:
-
-\hypertarget{rstudio}{%
-\section{RStudio}\label{rstudio}}
-
-For this, you have to
-\href{https://posit.co/download/rstudio-desktop/}{download} RStudio
-first. If you have done this already, we can get started.
-
-\hypertarget{getting-started}{%
-\subsection{Getting started}\label{getting-started}}
-
-First, we have to install the quarto package using the following command
-in our console:
-
-\texttt{install.packages("quarto")}
-
-Now we are ready to set up a quarto document.
-
-For this we open a new project and select the quarto document we want to
-create. You can choose to set up a git repository as well. For
-practicality, I usually also tick the box visual markdown editor.
-
-\includegraphics[width=3.125in,height=\textheight]{img/quarto_intro/Screenshot 2023-10-11 at 11.34.16.png}
-
-The new project will look like this:
-
-\includegraphics{img/quarto_intro/Screenshot 2023-10-11 at 11.39.43.png}
-
-\hypertarget{universal-instructions}{%
-\subsection{Universal instructions}\label{universal-instructions}}
-
-When setting up your document, quarto will always provide you with some
-presets. So first, we will have a look into the .qmd files, for they are
-handled the same way, regardless the format you are setting up (website,
-book, presentation, etc.).
-
-\hypertarget{render-save}{%
-\subsubsection{Render \& save}\label{render-save}}
-
-If we now click on render, we will be provided with the preview of our
-final version if the project in the viewer.
-
-\textbf{Important: Do not mistake ``save'' with ``render''.} Just by
-saving, your document did not get rendered automatically,
-\textbf{unless} you tick the box ``\textbf{Render on Save}''. You have
-to tick that box on each .qmd file individually though.
-
-\includegraphics[width=3.125in,height=\textheight]{img/quarto_intro/Screenshot 2023-10-11 at 14.12.45.png}
-
-\hypertarget{visual-and-source}{%
-\subsubsection{Visual and Source}\label{visual-and-source}}
-
-If you have chosen the \textbf{Visual} option on your toolbar, the
-preview will mostly resemble your .qmd files. If you are more
-comfortable with the R markdown optics, you can switch to
-\textbf{Source.}
-
-In the \textbf{Source} version, you can write up your document in LaTeX.
-
-\includegraphics[width=4.16667in,height=\textheight]{img/quarto_intro/Screenshot_3.png}
-
-\hypertarget{qmd-files}{%
-\subsubsection{.qmd files}\label{qmd-files}}
-
-Quarto will automatically provide you with two \textbf{.qmd files}, as
-well as a \textbf{.yml file}.
-
-The .qmd files respond to the individual pages of your website or
-chapter of your book or pages of your presentation, etc. You can shape
-them individually or define the layout for all of them in the .yml file,
-to which we will get later.
-
-In your .qmd files you also find a yaml at the top of your document,
-separated by
-
--\/-\/-
-
--\/-\/-
-
-Within these, you can define the outline of .qmd file
-\textbf{individually}, starting with the page header. Other options, you
-might be using in the future are:
-
-\texttt{author:\ Jessi\ Doe}
-
--\textgreater{} will add an author underneath the header
-
-\texttt{execute:\ \ \ \ echo:\ true}
-
--\textgreater{} if \textgreater true\textless, code will be visible
-
-\texttt{toc:true}
-
--\textgreater{} if \textgreater true\textless, a table of content will
-be automatically added
-
-\texttt{bibliography:\ your\_references.bib}
-
--\textgreater{} file or list of files for your references
-
-It is crucial to stick to the spacing. Otherwise, an error will occur.
-
-\hypertarget{insert}{%
-\paragraph{Insert}\label{insert}}
-
-If you click \texttt{Insert}, you will realize, quarto provides you with
-a lot of options and shortcuts as well. So by just selecting on your
-chosen item to insert, it will be added to the document, while you are
-also provided with options on the appearance (in the case of
-figure/images or tables, etc). We will here have a brief look into how
-to work with \textbf{R code} and how to use the \textbf{reference}
-option.
-
-\hypertarget{r-code}{%
-\paragraph{R code}\label{r-code}}
-
-To add R code to your file, you select \texttt{Insert}, select
-\texttt{Code\ Cell} and choose the kind of code you want to insert. In
-this case, \texttt{R}. There are some things to keep in mind though.
-
-Depending on how you have set up your .qmd file (or your .yml), your
-code will be visible or not on your website. To check your output, you
-can click the green arrow for the latest bit of code or the grey arrow
-above a bar to run the previous code.
-
-\includegraphics[width=4.16667in,height=\textheight]{img/quarto_intro/Screenshot 2023-10-11 at 15.04.31.png}
-
-But in case there are some chunks of code, you do not want to show all
-the time, there are some nice sets.
-
-So if we just load the library \texttt{tidyverse}, for example, the
-additional information regardless and it will be also visible on our
-website.
-
-\includegraphics{img/quarto_intro/Screenshot 2023-10-11 at 14.49.43.png}
-
-To avoid this, we can set up a code chunk, looking like this:
-
-\includegraphics{img/quarto_intro/Screenshot 2023-10-11 at 14.55.13.png}
-
-This will prevent the output of this code chunk to be depicted on your
-website, while the package is otherwise active and can be used in the
-following R code. This is, by the way, true for all R code and data sets
-you will use: they will be active in your document and can be used in
-different code chunks, once provided.
-
-A code block included in your document could look like the following.
-Here I used the option
-
-\texttt{code-fold:\ true} so the code can be extended. This option is
-only available in html though.
-
-\includegraphics[width=4.16667in,height=\textheight]{img/quarto_intro/Screenshot 2023-10-17 at 17.05.28.png}
-
-\hypertarget{references}{%
-\paragraph{References}\label{references}}
-
-Depending on which citation program you are using, quarto is able to
-connect to it (\href{https://www.zotero.org}{Zotero} works, for
-example). So, when selecting to insert a \texttt{Citation}, you can
-choose to simply add a reference from your program.
-
-Alternatively, you are provided with some options to choose from:
-
-\includegraphics[width=2.08333in,height=\textheight]{img/quarto_intro/Screenshot 2023-10-11 at 15.09.41.png}
-
-In your source code and your website, a citation will be depicted as
-follows:
-
-\includegraphics{img/quarto_intro/Screenshot 2023-10-11 at 15.12.57.png}
-
-The citation will also automatically be added to a
-\texttt{references.bib} as well as to a \texttt{references.qmd} and is
-therefore available on your website on the page ``References'', which
-also will be created automatically.
-
-\hypertarget{render-your-document}{%
-\subsection{Render your document}\label{render-your-document}}
-
-When done with setting up your documents, you would like to have the
-actual output. Depending on the \texttt{format} you set in your .yml
-file, your output can be a \texttt{html}, \texttt{pdf},
-\texttt{MS\ Word}, \texttt{OpenOffice}, or \texttt{ePUB} file. To create
-those, the terminal in your RStudio Project is used.
-
-By using the command:\\
-\texttt{quarto\ render}
-
-all formats you predefined in your .yml file will be rendered.
-
-In case you are only interested in one format to be rendered, you can
-specify your command:
-
-\texttt{quarto\ render\ -to\ pdf}
-
-Your rendered document should now look like this:
-
-\includegraphics{img/quarto_intro/Screenshot 2023-10-17 at 14.15.05.png}
-
-\hypertarget{quarto-website}{%
-\subsection{Quarto website}\label{quarto-website}}
-
-In the provided .qmd files, the index is also the first page of your
-website. As you might have noticed, quarto already sets up a navbar as
-well as a search function on your website.
-
-\includegraphics[width=2.08333in,height=\textheight]{img/quarto_intro/Screenshot 2023-10-11 at 14.09.08.png}
-
-\hypertarget{yml-files}{%
-\subsubsection{.yml files}\label{yml-files}}
-
-While your .qmd files contain information about one page, the .yml file
-defines the overall looks of the website.
-
-Here, you can define the type of your project (in this case a website),
-you can change the name of the website (\texttt{Title}), define your
-navbar (which shall be your landing page and in what order your pages
-shall be set up) or the overall appearance of your website in general
-(\texttt{theme}, \texttt{css}, \texttt{toc}, \texttt{backgroundcolor},
-etc.). For different styles and layouts, check out the quarto
-\href{https://quarto.org/docs/reference/formats/html.html}{website}
-again.
-
-\includegraphics[width=2.08333in,height=\textheight]{img/quarto_intro/Screenshot 2023-10-12 at 11.25.37.png}
-
-\hypertarget{quarto-book}{%
-\subsection{Quarto book}\label{quarto-book}}
-
-The setup of the .yml file in a quarto book is slightly different than
-that of the website. So here are some general remarks about them.
-
-\hypertarget{yml-files-1}{%
-\subsubsection{.yml files}\label{yml-files-1}}
-
-We see, for example, that instead of a navbar, we find
-\texttt{chapters}. Those will appear in the listed order in your book.
-
-We also already get provided with a \texttt{bibliography} and the
-responding .bib file. If you have other .bib files, those can be
-included in your references, by just adding them to
-\texttt{bibliography}.
-
-\includegraphics[width=2.08333in,height=\textheight]{img/quarto_intro/Screenshot 2023-10-12 at 11.41.30.png}
-
-\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_
-
-With this, you should at least have some ideas on how you can use quarto
-in your daily work routine. Happy coding and please feel free to contact
-me for any remarks or questions. I am happy to try and help.
-
-\hypertarget{vscode}{%
-\section{VSCode}\label{vscode}}
-
-Much of the concepts as described in the RStudio tutorial above apply
-equally well to using Quarto in VSCode, just with a different interface
-to execute them.
-
-Here we will describe how to set up VSCode and Quarto, and how to
-preview and render Quarto objects within the VSCode interface.
-
-To understand about more about the details of which files to edit etc.,
-please see the RStudio description above.
-
-\hypertarget{getting-started-1}{%
-\subsection{Getting Started}\label{getting-started-1}}
-
-\begin{enumerate}
-\def\labelenumi{\arabic{enumi}.}
-\tightlist
-\item
-  Install the Quarto CLI tool for your operating system from the
-  \href{https://quarto.org/docs/get-started/}{Quarto Website}
-\item
-  Install the
-  \href{https://marketplace.visualstudio.com/items?itemName=quarto.quarto}{VSCode
-  Quarto extension}
-\end{enumerate}
-
-\hypertarget{using-quarto}{%
-\subsection{Using Quarto}\label{using-quarto}}
-
-The basic workflow is as follows:
-
-\begin{enumerate}
-\def\labelenumi{\arabic{enumi}.}
-\tightlist
-\item
-  Create or modify \texttt{.qmd} objects etc as described above in the
-  Rstudio section about \protect\hyperlink{qmd-files}{Quarto markdown
-  files}
-\item
-  Within VSCode, make sure you've opened it in the repository containing
-  all the files
-\item
-  Press ctrl + shift + p to bring up your command palette
-
-  \begin{enumerate}
-  \def\labelenumii{\arabic{enumii}.}
-  \tightlist
-  \item
-    To preview a local `live' version of HTML or website versions, you
-    can type \texttt{Quarto:\ preview}. To close the live preview, press
-    ctrl+c in the VSCode terminal.
-  \item
-    To render all the files e.g.~final HTML and/or PDF versions, you can
-    type \texttt{Quarto:\ Render\ Project}, where you will be given
-    different options depending on the formats defined in the
-    \texttt{\_quarto.yml} file.
-  \end{enumerate}
-\end{enumerate}
-
-For further VSCode integrations, just type \texttt{Quarto:} into your
-command palette and explore all the options.
-
-\bookmarksetup{startatroot}
-
-\hypertarget{references-1}{%
-\chapter*{References}\label{references-1}}
-\addcontentsline{toc}{chapter}{References}
-
-\markboth{References}{References}
-
-\hypertarget{refs}{}
-\begin{CSLReferences}{0}{0}
-\end{CSLReferences}
-
-
-
-\end{document}
diff --git a/poseidon.qmd b/poseidon.qmd
index fed89c1..3d5094e 100644
--- a/poseidon.qmd
+++ b/poseidon.qmd
@@ -1,9 +1,13 @@
 ---
+title: "Genotype and context data management with Poseidon"
+author: "Ayshin Ghalichi & CLemens Schmid"
+date: "10/19/2023"
+bibliography: references.bib
+toc: true
 reference-location: margin
 citation-location: margin
----
 
-# Genotype and context data management with Poseidon
+---
 
 Poseidon is an open computational framework to enable standardised and FAIR (@Wilkinson2016) handling of genotypes with their highly relevant context information.