Spacing, Page Breaks, Formatting

In general the document with format each object chronologically. But some chuck options will modify the placement of an plot, table or image.

Bottom line: Markdown is not LaTeX. It was designed for HTML instead of LaTeX.

(Yihui Xie Explaining Markdown, Pandoc,formattting power on SO )[https://stackoverflow.com/a/17648350/9115822]

Main lesson

Using captions (fig.cap) treats plots, table or images differently and by default places one per page.

See ex_breaks.pdf and ex_no_breaks.pdf to see the difference.

Example of chronologically

Example of chronologically

Example of Captioned

Example of Captioned

Sidenote

There are options to set behaviour but they don’t work very well, as they dont seem to be strict.

knitr::opts_chunk$set(fig.pos = "t")

Where:

h , here; t , top; b , bottom; p , page of float

Table of Contents

---
title: "Example PDF Document"
author: "Ross"
date: "2018-07-02"
output:
  pdf_document:
    toc: true
    toc_depth: 2
---

Margin Control

Latex/Pandoc commands can be used in the first layer of the yaml. (First layer meaning the same indentation as title, date, etc.)

---
title: "Example PDF Document"
author: "Ross"
date: "2018-07-02"
geometry: margin=1.2in
---

Typeface / Font

This is a tricky one because there isn’t R and RMarkdown specific functions to modify the font…

All indications are that you have to use LaTeX.

\renewcommand{\familydefault}{\rmdefault}

(Some possibilities)[https://www.sharelatex.com/learn/Font_sizes,_families,_and_styles#Font_families]

Footnotes

Easy, using [^1] and a connected [^1]: blah:

Utinam accusata no sea, an nam solum omnium impedit, equidem propriae urbanitas per an. [^1]

[^1]: Lorem ipsum dolor sit amet, ius viris constituto mnesarchum ea, ius dicat inani iracundia ei, vim facer homero eirmod te. Nihil phaedrum qui eu.

Bibliographies and Citations

There are a bunch of ways to do this. I have included in ex_main.Rmd and example of a internal yaml reference, with citation and Bibliography at the end. A bit of a LaTeX learning curve.

A Reference

title: "Example PDF Document"
author: "Ross"
date: "2018-07-02"
references:
- id: fenner2012a
  title: One-click science marketing
  author:
  - family: Fenner
    given: Martin
  container-title: Nature Materials
  volume: 11
  URL: 'http://dx.doi.org/10.1038/nmat3283'
  DOI: 10.1038/nmat3283
  issue: 4
  publisher: Nature Publishing Group
  page: 261-263
  type: article-journal
  issued:
    year: 2012
    month: 3

A Citation

[@fenner2012a]

Automatically getting an attached bibliography at the end of document

# References

Page Numbers

By default a RMarkdown using the pdf_document output with have page numbers. Controlled in yaml with LaTeX command:

title: "Example PDF Document"
author: "Ross"
date: "2018-07-02"
header-includes:
  \pagenumbering{gobble}

Tables

If the data is in a data.frame, df or tibble class object then we can just print() the data to get a table.

Using the kable() function neatens it up with cell borders etc.

kableExtra::kable(head(iris))


Captioning a table, changes the formatting (centres and puts at bottom of page). See ex_table.pdf

Example of Tables

Example of Tables