---
title: "References in R Markdown"
author: "Harald Schilly"
date: "`r Sys.Date()`"
site: "bookdown::bookdown_site"
output:
  bookdown::html_document2: default
---

# Introduction

Using RMarkdown's bookdown rendering, long documents with LaTeX-style references can be rendered.
More information here: [bookdown: Authoring Books and Technical Documents with R Markdown](https://bookdown.org/yihui/bookdown/)

\begin{equation}
  E = m c^2 (\#eq:emc2)
\end{equation}

# Examples

## Example 1

Let's start with a simple Formula:

\begin{equation}
  f\left(k\right) = \binom{n}{k} p^k\left(1-p\right)^{n-k}
  (\#eq:binom)
\end{equation}

The equation \@ref(eq:binom) is well known.

## Example 2

Another well known formula is the following:

```{theorem, pyth, name="Pythagorean theorem"}
For a right triangle, if $c$ denotes the length of the hypotenuse
and $a$ and $b$ denote the lengths of the other two sides, we have

\begin{equation}
a^2 + b^2 = c^2
(\#eq:pyth)
\end{equation}
```

Which is this equation:

# Fill up

A normal paragraph.

(ref:foo) A scatterplot of the data `cars` using **base** R graphics.

```{r foo, fig.cap='(ref:foo)'}
plot(cars)  # a scatterplot
```

More text ...

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## Python code

```{r setup,  include=FALSE}
library(reticulate)
use_python("/usr/bin/python3")
```

```{python}
import numpy as np
import pandas as pd
x = np.random.randn(1000)
pd.Series(x).describe()
```

### Plotting with Python

```{python}
import seaborn
seaborn.set('paper')
import numpy as np
import matplotlib.pyplot as plt
xx = np.linspace(0, 10, 100)
yy = np.exp(0.1 * -xx) * np.sin(2 * xx)
plt.plot(xx, yy)
plt.grid(True)
plt.show()
```

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# Testing reference links

First check if you know about theorem \@ref(thm:pyth) with the formula \@ref(eq:pyth), that famous equation \@ref(eq:emc2) and then look up what \@ref(eq:binom) is about!

... and don't forget the figure \@ref(fig:foo)!

# More information

- https://bookdown.org/yihui/bookdown/
- in particular about references: https://bookdown.org/yihui/bookdown/markdown-extensions-by-bookdown.html#equations
- and theorems: https://bookdown.org/yihui/bookdown/markdown-extensions-by-bookdown.html#theorems
