Creating reports with RMarkdown
Printing tables
There are several packages that allow the output of data structures in form of HTML or LaTeX tables. They mostly differ in flexibility.
Here I use the packages:
- knitr
- xtable
- pander
For HTML documents
---
title: "Printing Tables"
author: "Martin Schmelzer"
date: "29 Juli 2016"
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
library(knitr)
library(xtable)
library(pander)
df <- mtcars[1:4,1:4]
```
# Print tables using `kable`
```{r, 'kable'}
kable(df)
```
# Print tables using `xtable`
```{r, 'xtable', results='asis'}
print(xtable(df), type="html")
```
# Print tables using `pander`
```{r, 'pander'}
pander(df)
```
For PDF documents
---
title: "Printing Tables"
author: "Martin Schmelzer"
date: "29 Juli 2016"
output: pdf_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
library(knitr)
library(xtable)
library(pander)
df <- mtcars[1:4,1:4]
```
# Print tables using `kable`
```{r, 'kable'}
kable(df)
```
# Print tables using `xtable`
```{r, 'xtable', results='asis'}
print(xtable(df, caption="My Table"))
```
# Print tables using `pander`
```{r, 'pander'}
pander(df)
```
How can I stop xtable printing the comment ahead of each table?
options(xtable.comment = FALSE)
Including LaTeX Preample Commands
There are two possible ways of including LaTeX preamble commands (e.g. \usepackage) in a RMarkdown document.
1. Using the YAML option header-includes:
---
title: "Including LaTeX Preample Commands in RMarkdown"
header-includes:
- \renewcommand{\familydefault}{cmss}
- \usepackage[cm, slantedGreek]{sfmath}
- \usepackage[T1]{fontenc}
output: pdf_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE, external=T)
```
# Section 1
As you can see, this text uses the Computer Moden Font!
2. Including External Commands with includes, in_header
---
title: "Including LaTeX Preample Commands in RMarkdown"
output:
pdf_document:
includes:
in_header: includes.tex
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE, external=T)
```
# Section 1
As you can see, this text uses the Computer Modern Font!Here, the content of includes.tex are the same three commands we included with header-includes.
Writing a whole new template
A possible third option is to write your own LaTex template and include it with template. But this covers a lot more of the structure than only the preamble.
---
title: "My Template"
author: "Martin Schmelzer"
output:
pdf_document:
template: myTemplate.tex
---Including bibliographies
A bibtex catalogue cna easily be included with the YAML option bibliography:. A certain style for the bibliography can be added with biblio-style:.
The references are added at the end of the document.
---
title: "Including Bibliography"
author: "John Doe"
output: pdf_document
bibliography: references.bib
---
# Abstract
@R_Core_Team_2016
# References