---
title: "Basic R markdown"
author: "author"
date: "1/28/2021"
output: html_document
bibliography: bibtex.bib
weight: 1
type: docs
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

## R Markdown

This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see <http://rmarkdown.rstudio.com>.

When you click the **Knit** button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this:

```{r cars}
summary(cars)
```



## Math 

$$\sum(a+b)$$

Inline math $\sum(a+b)$. 

## Including Plots

You can also embed plots, for example:

```{r pressure, echo=FALSE}
plot(pressure)
```

Note that the `echo = FALSE` parameter was added to the code chunk to prevent printing of the R code that generated the plot.

## Violin Plot with `ggplot2`

```{r}
# Library
library(ggplot2)
# create a dataset
data <- data.frame(
  name=c( rep("A",500), rep("B",500), rep("B",500), rep("C",20), rep('D', 100)  ),
  value=c( rnorm(500, 10, 5), rnorm(500, 13, 1), rnorm(500, 18, 1), rnorm(20, 25, 4), rnorm(100, 12, 1) )
)

# Most basic violin chart
p <- ggplot(data, aes(x=name, y=value, fill=name)) + # fill=name allow to automatically dedicate a color for each group
  geom_violin()
p
```

## Violin Plot with interactive plot (plotly)

```{r, message=FALSE}
library(plotly)
ggplotly(p)
```

Add references [@R-2021]. 

## References