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diff --git a/macros/latex/contrib/amnestyreport/sample.tex b/macros/latex/contrib/amnestyreport/sample.tex
index ff6dcb2f23..a72d70fd8e 100644
--- a/macros/latex/contrib/amnestyreport/sample.tex
+++ b/macros/latex/contrib/amnestyreport/sample.tex
@@ -1,5 +1,45 @@
\documentclass[
-]{amnestyreport}
+ freefonts, nologo]{amnestyreport}
+\usepackage{color}
+\usepackage{fancyvrb}
+\newcommand{\VerbBar}{|}
+\newcommand{\VERB}{\Verb[commandchars=\\\{\}]}
+\DefineVerbatimEnvironment{Highlighting}{Verbatim}{commandchars=\\\{\}}
+% Add ',fontsize=\small' for more characters per line
+\usepackage{framed}
+\definecolor{shadecolor}{RGB}{248,248,248}
+\newenvironment{Shaded}{\begin{snugshade}}{\end{snugshade}}
+\newcommand{\AlertTok}[1]{\textcolor[rgb]{0.94,0.16,0.16}{#1}}
+\newcommand{\AnnotationTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textbf{\textit{#1}}}}
+\newcommand{\AttributeTok}[1]{\textcolor[rgb]{0.13,0.29,0.53}{#1}}
+\newcommand{\BaseNTok}[1]{\textcolor[rgb]{0.00,0.00,0.81}{#1}}
+\newcommand{\BuiltInTok}[1]{#1}
+\newcommand{\CharTok}[1]{\textcolor[rgb]{0.31,0.60,0.02}{#1}}
+\newcommand{\CommentTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textit{#1}}}
+\newcommand{\CommentVarTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textbf{\textit{#1}}}}
+\newcommand{\ConstantTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{#1}}
+\newcommand{\ControlFlowTok}[1]{\textcolor[rgb]{0.13,0.29,0.53}{\textbf{#1}}}
+\newcommand{\DataTypeTok}[1]{\textcolor[rgb]{0.13,0.29,0.53}{#1}}
+\newcommand{\DecValTok}[1]{\textcolor[rgb]{0.00,0.00,0.81}{#1}}
+\newcommand{\DocumentationTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textbf{\textit{#1}}}}
+\newcommand{\ErrorTok}[1]{\textcolor[rgb]{0.64,0.00,0.00}{\textbf{#1}}}
+\newcommand{\ExtensionTok}[1]{#1}
+\newcommand{\FloatTok}[1]{\textcolor[rgb]{0.00,0.00,0.81}{#1}}
+\newcommand{\FunctionTok}[1]{\textcolor[rgb]{0.13,0.29,0.53}{\textbf{#1}}}
+\newcommand{\ImportTok}[1]{#1}
+\newcommand{\InformationTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textbf{\textit{#1}}}}
+\newcommand{\KeywordTok}[1]{\textcolor[rgb]{0.13,0.29,0.53}{\textbf{#1}}}
+\newcommand{\NormalTok}[1]{#1}
+\newcommand{\OperatorTok}[1]{\textcolor[rgb]{0.81,0.36,0.00}{\textbf{#1}}}
+\newcommand{\OtherTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{#1}}
+\newcommand{\PreprocessorTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textit{#1}}}
+\newcommand{\RegionMarkerTok}[1]{#1}
+\newcommand{\SpecialCharTok}[1]{\textcolor[rgb]{0.81,0.36,0.00}{\textbf{#1}}}
+\newcommand{\SpecialStringTok}[1]{\textcolor[rgb]{0.31,0.60,0.02}{#1}}
+\newcommand{\StringTok}[1]{\textcolor[rgb]{0.31,0.60,0.02}{#1}}
+\newcommand{\VariableTok}[1]{\textcolor[rgb]{0.00,0.00,0.00}{#1}}
+\newcommand{\VerbatimStringTok}[1]{\textcolor[rgb]{0.31,0.60,0.02}{#1}}
+\newcommand{\WarningTok}[1]{\textcolor[rgb]{0.56,0.35,0.01}{\textbf{\textit{#1}}}}
\renewcommand{\thesection}{\Alph{section}}
\usepackage{booktabs}
\usepackage{longtable}
@@ -75,65 +115,188 @@ From
\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.
+\section*{Introduction}\label{introduction}
+\addcontentsline{toc}{section}{Introduction}
+
+In this document we discuss the use of \texttt{amnestyreport.cls}, and
+accompanying \texttt{R} package \& \texttt{pandoc} template for writing
+Amnesty International Reports.
+
+You can either use an \texttt{Rnw} file with \LaTeX~syntax, or an
+\texttt{Rmd} file with R Markdown syntax. In both cases you need:
+
+\begin{itemize}
+\tightlist
+\item
+ The \LaTeX~class file \texttt{amnestyreport.cls},
+\item
+ A properly installed \texttt{R} package \texttt{amnestyreportR},
+\item
+ Optionally Amnesty International fonts and logo (see below).
+\end{itemize}
+
+If you use R Markdown syntax rather than \LaTeX~syntax, you also need
+
+\begin{itemize}
+\tightlist
+\item
+ The \texttt{pandoc} template \texttt{amnestytemplate.tex}
+\end{itemize}
+
+\subsection*{A note about the fonts and
+logos}\label{a-note-about-the-fonts-and-logos}
+\addcontentsline{toc}{subsection}{A note about the fonts and logos}
+
+If you have an established relationship with Amnesty International, you
+may use their fonts and logos in your report. You need to install the
+fonts, and the file with the logo (rename it to
+\texttt{Amnesty\_logo.png}). Otherwise you need the options
+\texttt{freefonts,\ nologo} in your preamble for \LaTeX~or the line
+\texttt{classoption:\ freefonts,\ nologo} in the RMD preamble.
+
+\subsection*{Rmd premable example}\label{rmd-premable-example}
+\addcontentsline{toc}{subsection}{Rmd premable example}
+
+If you use Rmd, you need to specify in your preamble that
+
+\begin{itemize}
+\tightlist
+\item
+ You are using the template \texttt{amnestytemplate.tex} rather than
+ the generic \texttt{pandoc} template;
+\item
+ You are using \texttt{xelatex} (or \texttt{lualatex}) rather than a
+ 8-bit engine \texttt{podflatex}.
+\end{itemize}
+
+For example this file has the following preamble:
+
+\begin{verbatim}
+---
+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.\n\n
+\\textcopyright{} Image: Public domain.\n\n
+\\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."
+
+output:
+ pdf_document:
+ template: amnestytemplate.tex
+ latex_engine: xelatex
+ toc: true
+ keep_tex: true
+ citation_package: natbib
+classoption: freefonts, nologo
+header-includes:
+ - \renewcommand{\thesection}{\Alph{section}}
+bibliography: "examplereferences.bib"
+---
+\end{verbatim}
\clearpage
-\section{\texorpdfstring{Research methodology
-\label{sec:methodology}}{Research methodology }}\label{research-methodology}
+\section{\texorpdfstring{Cross-references and bibliography
+\label{cross-ref}}{Cross-references and bibliography }}\label{cross-references-and-bibliography}
+
+You can use the standard \LaTeX~and R Markdown facilities for
+references.
+
+The package uses \texttt{biblatex} with the \texttt{bibtex} backend for
+citations to provide footnote citations,
+\citep[See][]{SecondRef2022}\textsuperscript{,}\citep[See
+also][12]{FirstRef2023} and \citep[23]{FirstRef2023}. However, due to
+idiosyncrasies of \texttt{pandoc} we need to specify \texttt{natbib} as
+the citation engine in the preamble. Never mind biblatex warnings during
+the processing.
-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
+Below in \autoref{sec:figures_tables} we show the examples of tables and
+figures provided by the package.
-\section{\texorpdfstring{Empirical analysis
-\label{sec:results}}{Empirical analysis }}\label{empirical-analysis}
+\section{\texorpdfstring{Figures and tables
+\label{sec:figures_tables}}{Figures and tables }}\label{figures-and-tables}
-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
+\subsection{Inline expressions}\label{inline-expressions}
+
+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.
+We define the variable \texttt{N\_iris} and use it inline in the
+following example:
+
+\begin{Shaded}
+\begin{Highlighting}[]
+\NormalTok{N\_iris }\OtherTok{\textless{}{-}} \FunctionTok{nrow}\NormalTok{(iris)}
+\end{Highlighting}
+\end{Shaded}
+
+There are a total of 150 (coded as
+\texttt{`}\texttt{r N\_iris}\texttt{`}) iris flower specimen in the
+built-in \textbf{iris} data.
+
+\subsection{A table}\label{a-table}
+
+Here is an example of a table using \texttt{kable} package and
+\texttt{amnesty\_table} function:
+
+\begin{Shaded}
+\begin{Highlighting}[]
+\NormalTok{iris }\SpecialCharTok{\%\textgreater{}\%}
+ \FunctionTok{count}\NormalTok{(Species) }\SpecialCharTok{\%\textgreater{}\%}
+ \FunctionTok{mutate}\NormalTok{(}\AttributeTok{percent =}\NormalTok{ n}\SpecialCharTok{/}\FunctionTok{sum}\NormalTok{(n)}\SpecialCharTok{*}\DecValTok{100}\NormalTok{) }\SpecialCharTok{\%\textgreater{}\%}
+ \FunctionTok{bind\_rows}\NormalTok{(}\FunctionTok{summarise}\NormalTok{(., }\FunctionTok{across}\NormalTok{(}\FunctionTok{where}\NormalTok{(is.numeric), sum),}
+ \FunctionTok{across}\NormalTok{(}\FunctionTok{where}\NormalTok{(is.factor), }\SpecialCharTok{\textasciitilde{}}\StringTok{\textquotesingle{}Total\textquotesingle{}}\NormalTok{))) }\SpecialCharTok{\%\textgreater{}\%}
+ \FunctionTok{amnesty\_table}\NormalTok{(}\AttributeTok{row.names =} \ConstantTok{FALSE}\NormalTok{,}
+ \AttributeTok{align =} \StringTok{"lrr"}\NormalTok{,}
+ \AttributeTok{caption=}\StringTok{"}\SpecialCharTok{\textbackslash{}\textbackslash{}}\StringTok{label\{tab:species\}}
+\StringTok{ Frequency distribution of iris species."}\NormalTok{,}
+ \AttributeTok{position=}\StringTok{"!ht"}\NormalTok{,}
+ \AttributeTok{col.names =} \FunctionTok{c}\NormalTok{(}\StringTok{"Species"}\NormalTok{, }\StringTok{"Number of species"}\NormalTok{, }\StringTok{"(\%)"}\NormalTok{),}
+ \AttributeTok{digits=}\DecValTok{2}\NormalTok{) }\SpecialCharTok{\%\textgreater{}\%}
+\NormalTok{ kableExtra}\SpecialCharTok{::}\FunctionTok{row\_spec}\NormalTok{(}\DecValTok{4}\NormalTok{, }\AttributeTok{bold=}\ConstantTok{TRUE}\NormalTok{)}
+\end{Highlighting}
+\end{Shaded}
+
+We can typeset it with sideways caption using
+\texttt{\textbackslash{}sideTableCaptions}: \sideTableCaptions
+
+\begin{table}[!ht]
-\subsection{Subsection with a table
-example}\label{subsection-with-a-table-example}
+\caption{\label{tab:example_table}\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}
-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
+Alternatively, we can typeset it with normal captions using
+\texttt{\textbackslash{}normalTableCaptions}: \normalTableCaptions
\begin{table}[!ht]
-\caption{\label{tab:make an example table from iris data}\label{tab:species}Frequency distribution of iris species.}
+\caption{\label{tab:example_table_1}\label{tab:species1}
+ Frequency distribution of iris species.}
\centering
\begin{tabular}[t]{lrr}
\toprule
@@ -146,10 +309,27 @@ virginica & 50 & 33.33\\
\bottomrule
\end{tabular}
\end{table}
+
\FloatBarrier
-\subsection{Subsection with a figure
-example}\label{subsection-with-a-figure-example}
+\subsection{Figures}\label{figures}
+
+Normally the figures are prepared in separate \LaTeX~runs. This might be
+very slow, so you may want to use the draft mode for the editing runs.
+Before making the figures, you need to issue the \texttt{R} command
+\texttt{setup\_amnesty\_plots(options=...,\ draft=...)}. The
+\texttt{options} are those that are passed to \LaTeX~class; if you do
+not have Amnesty International fonts, use \texttt{freefonts}. The
+\texttt{draft} can be either \texttt{TRUE} or \texttt{FALSE} (for quick
+plots). For example
+
+\begin{Shaded}
+\begin{Highlighting}[]
+\FunctionTok{setup\_amnesty\_plots}\NormalTok{() }\CommentTok{\# You have Amnesty fonts and logo}
+\FunctionTok{setup\_amnesty\_plots}\NormalTok{(}\AttributeTok{options=}\StringTok{\textquotesingle{}freefonts, nologo\textquotesingle{}}\NormalTok{) }\CommentTok{\# No Amnesty fonts}
+\FunctionTok{setup\_amnesty\_plots}\NormalTok{(}\AttributeTok{draft=}\ConstantTok{TRUE}\NormalTok{) }\CommentTok{\# Draft mode}
+\end{Highlighting}
+\end{Shaded}
We are using the \textit{ggplot2} package to make an example figure from
the built-in iris data. As can be seen in
@@ -160,30 +340,31 @@ 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}
+{\centering \includegraphics{sample_files/figure-latex/species-petal-size-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}
+\caption{Distribution of petal length and petal width, by iris species.}\label{fig:species-petal-size}
\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.
+(\autoref{fig:petal-size-sepal-size}) scales. We also use
+\texttt{\textbackslash{}sideFigureCaptions} to typeset the caption on
+the side \sideFigureCaptions
\begin{figure}
-{\centering \includegraphics{sample_files/figure-latex/unnamed-chunk-1-1}
+{\centering \includegraphics{sample_files/figure-latex/petal-size-sepal-size-1}
}
-\caption{\label{fig:petal-size-sepal-size}Distribution of petal and sepal sizes}\label{fig:unnamed-chunk-1}
+\caption{Distribution of petal and sepal sizes}\label{fig:petal-size-sepal-size}
\end{figure}
\clearpage
-\section{\texorpdfstring{Data and codebooks
-\label{sec:codebook}}{Data and codebooks }}\label{data-and-codebooks}
+\section{Other typographic features}\label{other-typographic-features}
\subsection{A subsection heading}\label{a-subsection-heading}
@@ -191,8 +372,8 @@ discrete (\autoref{fig:species-petal-size}) and continuous
\paragraph{A subsubsubsection heading}\label{a-subsubsubsection-heading}
-The custom formatting does add a line break after a subsubsubsection
-heading as Amnesty style requires.
+We have line break after a subsubsubsection heading as Amnesty style
+requires.
\paragraph{Type of iris species
(Species)}\label{type-of-iris-species-species}
@@ -205,7 +386,7 @@ This variable indicates the different botanical types of iris species.
\item[\textbf{virginica:}] The iris belongs to the botanical species of virginica.
\end{description}
-An example of a quotation
+An example of a quotation.
\begin{quote}
All human beings are born free and equal in dignity and rights. They are