update font spec and add equation example

01-intro.Rmd

 # Introduction {#intro}
 
 Background and introduction chapter
+
+Equation \@ref(eq:binom) is an example of how to make a referenced equation:
+
+\begin{equation} 
+  f\left(k\right) = \binom{n}{k} p^k\left(1-p\right)^{n-k}
+  (\#eq:binom)
+\end{equation} 
\ No newline at end of file

03-results-01.Rmd

 # First Results {#results-1}
 
-First results chapter.
+First results chapter with Figure \@ref(fig:fig1-chunk).
 
 (ref:mpg-plot) Car engine size versus fuel efficiency. The mpg data contains observations collected by the US Environmental Protection Agency on 38 models of car.
 
-```{r mpg,echo=FALSE,fig.cap ='(ref:mpg-plot)', fig.scap='Car engine size versus fuel efficiency',out.extra='',fig.align='center',cache=TRUE,warning=FALSE,fig.pos="H"}
+```{r fig1-chunk,echo=FALSE,fig.cap ='(ref:mpg-plot)', fig.scap='Car engine size versus fuel efficiency',out.extra='',fig.align='center',cache=TRUE,warning=FALSE,fig.pos="H"}
 ggplot(data = mpg) + 
   geom_point(mapping = aes(x = displ, y = hwy, color = class))
 ```
+
+> **Notes** The caption comes from the text following `(ref:fig1-caption)` and 
+this has to be all one line like so:
+
+>`(ref:mpg-plot) Car engine size versus fuel efficiency. The mpg data contains observations collected by the US Environmental Protection Agency on 38 models of car.`
+
+> Whilst the reference number to the figure itself comes from 
+the code chunk name `fig1-chunk` inside the referencing syntax `\@ref(fig:fig1-chunk)`.
\ No newline at end of file

_output.yml

 bookdown::pdf_book:
-  latex_engine: xelatex
+  latex_engine: pdflatex
   includes:
       in_header: tex-files/preamble.tex
       keep_tex: yes

tex-files/preamble.tex

 % Peamble - load all the packages
 \usepackage[none]{hyphenat}
-\usepackage[T1]{fontenc} % Use 8-bit encoding that has 256 glyphs
-\usepackage[default,osfigures,scale=0.95]{opensans} % Open sans font
+\usepackage[utf8]{inputenc} % For greek letters and othe unicode symbols
+\usepackage[scaled]{berasans} % Sans font
+\renewcommand*\familydefault{\sfdefault}  %% Only if the base font of the document is to be sans serif
 \usepackage{lmodern}
 \usepackage{lettrine} % The lettrine is the first enlarged letter at the beginning of the text
 \usepackage{appendix}