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\documentclass[
]{amnestyreport}
\renewcommand{\thesection}{\Alph{section}}
\usepackage{booktabs}
\usepackage{longtable}
\usepackage{array}
\usepackage{multirow}
\usepackage{wrapfig}
\usepackage{float}
\usepackage{colortbl}
\usepackage{pdflscape}
\usepackage{tabu}
\usepackage{threeparttable}
\usepackage{threeparttablex}
\usepackage[normalem]{ulem}
\usepackage{makecell}
\usepackage{xcolor}
\title{RMarkdown report example}
\subtitle{An example report for Amnesty output}
\titleimage{BoschFragment}
\titleimagecaption{The Garden of Earthly Delights is the modern title
given to a triptych oil painting on oak panel painted by the Early
Netherlandish master Hieronymus Bosch, between 1490 and 1510, when Bosch
was between 40 and 60 years old. It has been housed in the Museo del
Prado in Madrid, Spain since 1939.\\
\textcopyright{} Image: Public domain.\\
\textcopyright{} Caption: Wikipedia contributors, 2023, released under
Creative Commons Attribution-ShareAlike License 4.0}
\copyrightyear{2023}
\firstpublicationyear{2022}
\reportindex{ABXC/AAAA/2022}
\blurb{This sample output of Rmarkdown with TeX shows the general
commands and options of the amnestyinternational TeX class. It is based
on the text by Jule Krueger.}

\addbibresource{examplereferences.bib}

\begin{document}
\frontmatter
\maketitle


\tableofcontents
\mainmatter

\begin{AmnestyGlossary}[10em]
Commute &
Commute means to replace a punishment, usually a death sentence, with a less severe one. For example, Amnesty called for the USA to commute to time served the 35-year jail sentence of whistleblower Chelsea Manning, who had been arrested after leaking classified government material
\\
Crimes against humanity &
When certain acts---including murder, torture and slavery---form part of a widespread attack on a civilian population by a state or organization. Unlike war crimes, they can take place at times of peace as well as during conflict. The Rwandan genocide of 1994 is one example of a crime against humanity.
\\
Extrajudicial executions &
Unlawful killings ordered by a government, or committed with its knowledge and support. They can be carried out by the military, police, or by civilians working with government forces. For example, Hamas forces in Gaza committed serious human rights abuses, including extrajudicial executions, torture and abductions, during the 2014 Gaza/Israel conflict.
\\
Freedom of expression &
The right to seek, receive and share information and ideas, without fear or interference. It is closely linked with freedom of association (the right to meet with anyone you choose, for example, to form and join clubs, societies or trade unions) and the right to take part in a peaceful assembly, such as a demonstration or public meeting.
\\
Immunity (from prosecution) &
Allows an accused person to avoid prosecution for a crime because of their job or office. Amnesty International is opposed to immunity. For example, Amnesty has called for the rejection of immunity in the Central African Republic so that people who committed crimes during conflict there are brought to justice.
\\
Impunity &
Impunity is when people who have committed crimes avoid punishment. For example, there is a ‘culture of impunity’ among police in the Philippines, who are able to torture people without fear of being punished. Amnesty calls for these people to be tried and sentenced fairly, according to the law.
\\
Prisoner of conscience &
A prisoner of conscience is someone who is imprisoned because of who they are (sexual orientation, ethnic, national or social origin, language, birth, colour, sex or economic status) or their religious, political or other beliefs, and who hasn’t used or advocated violence. For example, Dr Mohammed al-Roken is a current prisoner of conscience in the United Arab Emirates, jailed for 10 years following a deeply unfair trial.
\\
War crimes &
War crimes are serious crimes committed during armed conflicts, which could include murdering prisoners of war, killing hostages, torture and destroying towns and villages. A recent example is in the Ukraine, where there is overwhelming evidence of ongoing war crimes, including torture and summary killings of prisoners.
\\
\end{AmnestyGlossary}

From
\url{https://www.amnesty.org/en/latest/campaigns/2015/07/beginners-guide-human-rights-jargon/}

\clearpage

\section*{Introduction to the
appendix}\label{introduction-to-the-appendix}
\addcontentsline{toc}{section}{Introduction to the appendix}

This appendix accompanies the Amnesty International report ``\emph{Some
Amnesty Report Title}''. The report used an innovative mixed-methods
research approach to capture the experiences of survivors of violence
from multiple perspectives. The mixed-methods approach involved
interviews with survivors and experts; desk research, including reviews
of existing literature
\citep[See][]{SecondRef2022}\textsuperscript{,}\citep[See
also][p.12]{FirstRef2023} and media articles
\citep[p.~23]{FirstRef2023}; formal requests to relevant officials for
public information access; and quantitative analysis of a representative
sample of court judgments.

This appendix provides more detail on each aspect of the quantitative
research methodology, in-depth empirical analysis of the judgment data,
and a codebook that describes the manual coding procedure employed. The
data that Amnesty International extracted from these cases on judgments,
defendants and victims is publicly available at \url{https://data.link}.

\autoref{sec:methodology} describes how court decisions on ~violence
were identified and selected for analysis. \autoref{sec:results}
analyses the data from the judgments. Empirical analysis was performed
using the R programming language for statistical computing.
\autoref{sec:codebook} explains the rules used to manually code data
from judgments (codebooks) as well as the data available to the public.

\clearpage

\section{\texorpdfstring{Research methodology
\label{sec:methodology}}{Research methodology }}\label{research-methodology}

This section describes the steps taken in the research methodology. We
are using the R built-in iris data to compute an example table and
figure in \autoref{sec:results} below. \clearpage

\section{\texorpdfstring{Empirical analysis
\label{sec:results}}{Empirical analysis }}\label{empirical-analysis}

This section conducts the empirical analysis and results. Irises are
beautiful flowers that come in different types, shapes and sizes. In
this report, we look at different species of irises in terms of petal
size.\footnote{This is how you can add a footnote. Some footnotes are very long, and some are several lines log, but this is OK. Just make sure the indentation is right.}

There are a total of 150 iris flower specimen in the built-in
\textbf{iris} data.

\subsection{Subsection with a table
example}\label{subsection-with-a-table-example}

We are make an example table from the built-in \textit{iris} data (see
\autoref{tab:species}). The \emph{kableExtra} package is used to
emphasize the last line

\begin{table}[!ht]

\caption{\label{tab:make an example table from iris data}\label{tab:species}Frequency distribution of iris species.}
\centering
\begin{tabular}[t]{lrr}
\toprule
\textbf{Species} & \textbf{Number of species} & \textbf{(\%)}\\
\midrule
setosa & 50 & 33.33\\
versicolor & 50 & 33.33\\
virginica & 50 & 33.33\\
\textbf{Total} & \textbf{150} & \textbf{100.00}\\
\bottomrule
\end{tabular}
\end{table}
\FloatBarrier

\subsection{Subsection with a figure
example}\label{subsection-with-a-figure-example}

We are using the \textit{ggplot2} package to make an example figure from
the built-in iris data. As can be seen in
\autoref{fig:species-petal-size}, the virginica species of iris has the
largest petal size in comparison to the other two iris species. Note
that it is recommended to use both color and line shape to convey the
same information for the benefit of color blind users.

\begin{figure}

{\centering \includegraphics{sample_files/figure-latex/make an example figure from iris data-1} 

}

\caption{\label{fig:species-petal-size}Distribution of petal length and petal width, by iris species.}\label{fig:make an example figure from iris data}
\end{figure}

We use viridis scale optimized for color blind users both for the
discrete (\autoref{fig:species-petal-size}) and continuous
(\autoref{fig:petal-size-sepal-size}) scales.

\begin{figure}

{\centering \includegraphics{sample_files/figure-latex/unnamed-chunk-1-1} 

}

\caption{\label{fig:petal-size-sepal-size}Distribution of petal and sepal sizes}\label{fig:unnamed-chunk-1}
\end{figure}

\clearpage

\section{\texorpdfstring{Data and codebooks
\label{sec:codebook}}{Data and codebooks }}\label{data-and-codebooks}

\subsection{A subsection heading}\label{a-subsection-heading}

\subsubsection{A subsubsection heading}\label{a-subsubsection-heading}

\paragraph{A subsubsubsection heading}\label{a-subsubsubsection-heading}

The custom formatting does add a line break after a subsubsubsection
heading as Amnesty style requires.

\paragraph{Type of iris species
(Species)}\label{type-of-iris-species-species}

This variable indicates the different botanical types of iris species.

\begin{description}
\item[\textbf{setosa:}] The iris belongs to the botanical species of setosa. 
\item[\textbf{versicolor:}]  The iris belongs to the botanical species of versicolor. 
\item[\textbf{virginica:}] The iris belongs to the botanical species of virginica. 
\end{description}

An example of a quotation

\begin{quote}
All human beings are born free and equal in dignity and rights. They are
endowed with reason and conscience and should act towards one another in
a spirit of brotherhood.

\attribution{Universal Declaration of Human Rights}
\end{quote}

\backmatter
\end{document}