Deploying to gh-pages from @ d4b47ff 🚀

manual.qmd

@@ -35,6 +35,9 @@ format:
     ## Rendering
     embed-resources: true
     fontsize: 12pt
+    mainfont: Arial
+    mathfont: LiberationMono
+    monofont: DejaVu Sans Mono
   pdf:
     toc: true
     margin-left: 2cm
@@ -52,9 +55,6 @@ crossref:
 engine: knitr
 output_dir: "docs"
 documentclass: article
-mainfont: Arial
-mathfont: LiberationMono
-monofont: DejaVu Sans Mono
 classoption: a4paper
 bibliography: resources/references.bib
 ---

manual.tex

@@ -21,9 +21,6 @@
 \usepackage{lmodern}
 \ifPDFTeX\else  
     % xetex/luatex font selection
-    \setmainfont[]{Arial}
-    \setmonofont[]{DejaVu Sans Mono}
-  \setmathfont[]{LiberationMono}
 \fi
 % Use upquote if available, for straight quotes in verbatim environments
 \IfFileExists{upquote.sty}{\usepackage{upquote}}{}
@@ -401,7 +398,7 @@ \subsection{Installing the and running the
    |- dataset2.xlsx
 \end{verbatim}
 
-\begin{tcolorbox}[enhanced jigsaw, titlerule=0mm, rightrule=.15mm, colbacktitle=quarto-callout-note-color!10!white, bottomrule=.15mm, toprule=.15mm, breakable, toptitle=1mm, bottomtitle=1mm, opacitybacktitle=0.6, title=\textcolor{quarto-callout-note-color}{\faInfo}\hspace{0.5em}{Note}, opacityback=0, coltitle=black, leftrule=.75mm, arc=.35mm, left=2mm, colback=white, colframe=quarto-callout-note-color-frame]
+\begin{tcolorbox}[enhanced jigsaw, toprule=.15mm, colback=white, colframe=quarto-callout-note-color-frame, coltitle=black, opacitybacktitle=0.6, breakable, opacityback=0, title=\textcolor{quarto-callout-note-color}{\faInfo}\hspace{0.5em}{Note}, arc=.35mm, toptitle=1mm, colbacktitle=quarto-callout-note-color!10!white, titlerule=0mm, bottomtitle=1mm, leftrule=.75mm, rightrule=.15mm, bottomrule=.15mm, left=2mm]
 
 In the above illustration, there are two example datasets
 (\texttt{dataset1.xlsx} and \texttt{dataset2.xlsx}). The datasets need
@@ -455,7 +452,7 @@ \subsection{Installing the and running the
 clicking the ``OK'' button. Shortly thereafter, the application will
 appear in a browser tab.
 
-\begin{tcolorbox}[enhanced jigsaw, titlerule=0mm, rightrule=.15mm, colbacktitle=quarto-callout-note-color!10!white, bottomrule=.15mm, toprule=.15mm, breakable, toptitle=1mm, bottomtitle=1mm, opacitybacktitle=0.6, title=\textcolor{quarto-callout-note-color}{\faInfo}\hspace{0.5em}{More specific information about the \texttt{deploy.bat} script}, opacityback=0, coltitle=black, leftrule=.75mm, arc=.35mm, left=2mm, colback=white, colframe=quarto-callout-note-color-frame]
+\begin{tcolorbox}[enhanced jigsaw, toprule=.15mm, colback=white, colframe=quarto-callout-note-color-frame, coltitle=black, opacitybacktitle=0.6, breakable, opacityback=0, title=\textcolor{quarto-callout-note-color}{\faInfo}\hspace{0.5em}{More specific information about the \texttt{deploy.bat} script}, arc=.35mm, toptitle=1mm, colbacktitle=quarto-callout-note-color!10!white, titlerule=0mm, bottomtitle=1mm, leftrule=.75mm, rightrule=.15mm, bottomrule=.15mm, left=2mm]
 
 The \texttt{deploy.bat} script performs the following:
 
@@ -902,7 +899,7 @@ \subsubsection{Validate input data}\label{validate-input-data}
   notes - this sheet is not processed or validated
 \end{itemize}
 
-\begin{tcolorbox}[enhanced jigsaw, titlerule=0mm, rightrule=.15mm, colbacktitle=quarto-callout-note-color!10!white, bottomrule=.15mm, toprule=.15mm, breakable, toptitle=1mm, bottomtitle=1mm, opacitybacktitle=0.6, title=\textcolor{quarto-callout-note-color}{\faInfo}\hspace{0.5em}{Note}, opacityback=0, coltitle=black, leftrule=.75mm, arc=.35mm, left=2mm, colback=white, colframe=quarto-callout-note-color-frame]
+\begin{tcolorbox}[enhanced jigsaw, toprule=.15mm, colback=white, colframe=quarto-callout-note-color-frame, coltitle=black, opacitybacktitle=0.6, breakable, opacityback=0, title=\textcolor{quarto-callout-note-color}{\faInfo}\hspace{0.5em}{Note}, arc=.35mm, toptitle=1mm, colbacktitle=quarto-callout-note-color!10!white, titlerule=0mm, bottomtitle=1mm, leftrule=.75mm, rightrule=.15mm, bottomrule=.15mm, left=2mm]
 
 All input data must be placed in the \texttt{/input} folder of the
 Project prior to starting the app.
@@ -1071,7 +1068,7 @@ \subsection{Stage 5 - Temporal
 thereafter aggregated up to Area and Whole of Harbour level trends as
 well.
 
-\begin{tcolorbox}[enhanced jigsaw, titlerule=0mm, rightrule=.15mm, colbacktitle=quarto-callout-note-color!10!white, bottomrule=.15mm, toprule=.15mm, breakable, toptitle=1mm, bottomtitle=1mm, opacitybacktitle=0.6, title=\textcolor{quarto-callout-note-color}{\faInfo}\hspace{0.5em}{Bayesian hierarchical models}, opacityback=0, coltitle=black, leftrule=.75mm, arc=.35mm, left=2mm, colback=white, colframe=quarto-callout-note-color-frame]
+\begin{tcolorbox}[enhanced jigsaw, toprule=.15mm, colback=white, colframe=quarto-callout-note-color-frame, coltitle=black, opacitybacktitle=0.6, breakable, opacityback=0, title=\textcolor{quarto-callout-note-color}{\faInfo}\hspace{0.5em}{Bayesian hierarchical models}, arc=.35mm, toptitle=1mm, colbacktitle=quarto-callout-note-color!10!white, titlerule=0mm, bottomtitle=1mm, leftrule=.75mm, rightrule=.15mm, bottomrule=.15mm, left=2mm]
 
 Hierarchical models are used to analyse data that are structured such
 that there are sampling units nested within higher order units in a
@@ -1473,7 +1470,7 @@ \subsection{Dashboard}\label{sec-dashboard}
 display. If the number of Log lines exceeds 10, a scroll bar will appear
 on the right side of the panel to help reviewing earlier Logs.
 
-\begin{tcolorbox}[enhanced jigsaw, rightrule=.15mm, left=2mm, bottomrule=.15mm, opacityback=0, toprule=.15mm, breakable, arc=.35mm, leftrule=.75mm, colback=white, colframe=quarto-callout-color-frame]
+\begin{tcolorbox}[enhanced jigsaw, toprule=.15mm, colback=white, leftrule=.75mm, colframe=quarto-callout-color-frame, bottomrule=.15mm, left=2mm, breakable, opacityback=0, rightrule=.15mm, arc=.35mm]
 
 Note
 
@@ -1495,7 +1492,7 @@ \subsection{Data}\label{sec-data}
 The Data page comprises two panels or subpages accessable by tabs named
 ``Raw data'' and ``Processed data'' at the top of the page.
 
-\begin{tcolorbox}[enhanced jigsaw, titlerule=0mm, rightrule=.15mm, colbacktitle=quarto-callout-note-color!10!white, bottomrule=.15mm, toprule=.15mm, breakable, toptitle=1mm, bottomtitle=1mm, opacitybacktitle=0.6, title=\textcolor{quarto-callout-note-color}{\faInfo}\hspace{0.5em}{Note}, opacityback=0, coltitle=black, leftrule=.75mm, arc=.35mm, left=2mm, colback=white, colframe=quarto-callout-note-color-frame]
+\begin{tcolorbox}[enhanced jigsaw, toprule=.15mm, colback=white, colframe=quarto-callout-note-color-frame, coltitle=black, opacitybacktitle=0.6, breakable, opacityback=0, title=\textcolor{quarto-callout-note-color}{\faInfo}\hspace{0.5em}{Note}, arc=.35mm, toptitle=1mm, colbacktitle=quarto-callout-note-color!10!white, titlerule=0mm, bottomtitle=1mm, leftrule=.75mm, rightrule=.15mm, bottomrule=.15mm, left=2mm]
 
 The contents of the Processed data subpage will not be revealed until
 the completion of Stage 3.
@@ -1561,7 +1558,7 @@ \subsubsection{Processed data panel}\label{processed-data-panel}
 compiled and processed data set. Descriptions of each field of these
 data are provided in the table below.
 
-\begin{tcolorbox}[enhanced jigsaw, titlerule=0mm, rightrule=.15mm, colbacktitle=quarto-callout-note-color!10!white, bottomrule=.15mm, toprule=.15mm, breakable, toptitle=1mm, bottomtitle=1mm, opacitybacktitle=0.6, title=\textcolor{quarto-callout-note-color}{\faInfo}\hspace{0.5em}{Note}, opacityback=0, coltitle=black, leftrule=.75mm, arc=.35mm, left=2mm, colback=white, colframe=quarto-callout-note-color-frame]
+\begin{tcolorbox}[enhanced jigsaw, toprule=.15mm, colback=white, colframe=quarto-callout-note-color-frame, coltitle=black, opacitybacktitle=0.6, breakable, opacityback=0, title=\textcolor{quarto-callout-note-color}{\faInfo}\hspace{0.5em}{Note}, arc=.35mm, toptitle=1mm, colbacktitle=quarto-callout-note-color!10!white, titlerule=0mm, bottomtitle=1mm, leftrule=.75mm, rightrule=.15mm, bottomrule=.15mm, left=2mm]
 
 This panel will not become active until the completion of Stage 3.
 
@@ -1821,7 +1818,7 @@ \subsubsection{Analysis overview}\label{analysis-overview}
 \textbf{Download trends as csv} button. Notes on Longitude and Latitude
 are as above.
 
-\begin{tcolorbox}[enhanced jigsaw, titlerule=0mm, rightrule=.15mm, colbacktitle=quarto-callout-important-color!10!white, bottomrule=.15mm, toprule=.15mm, breakable, toptitle=1mm, bottomtitle=1mm, opacitybacktitle=0.6, title=\textcolor{quarto-callout-important-color}{\faExclamation}\hspace{0.5em}{Important}, opacityback=0, coltitle=black, leftrule=.75mm, arc=.35mm, left=2mm, colback=white, colframe=quarto-callout-important-color-frame]
+\begin{tcolorbox}[enhanced jigsaw, toprule=.15mm, colback=white, colframe=quarto-callout-important-color-frame, coltitle=black, opacitybacktitle=0.6, breakable, opacityback=0, title=\textcolor{quarto-callout-important-color}{\faExclamation}\hspace{0.5em}{Important}, arc=.35mm, toptitle=1mm, colbacktitle=quarto-callout-important-color!10!white, titlerule=0mm, bottomtitle=1mm, leftrule=.75mm, rightrule=.15mm, bottomrule=.15mm, left=2mm]
 
 The routine behind this later button involves compiling together all
 posteriors across all scales and summarising each of them. These steps