manuscript.Rmd

---
title: "Awesome manuscript about Iris"
author: "`r Sys.info()['user']`"
date: "Compiled on `r date()` by `r Sys.info()['user']`"
output: 
  bookdown::html_document2: 
    fig_caption: yes
    toc: yes
    toc_float: yes
    toc_depth: 4
---

```{r setup_chunk, echo = F}
# Set some options
knitr::opts_chunk$set(echo = FALSE,
                      message = FALSE,
                      warning = FALSE,
                      fig.width = 5,
                      fig.height = 3)

# Load some packages
suppressPackageStartupMessages({
  library(startR)
  library(here)
  library(ggplot2)
  })
```

# Introduction

In this awesome manuscript, we show that there is a correlation between sepal length and sepal width for three species of *Iris spp.*. The three species are:

```{r load_data}
iris <- read.csv(file = here("raw_data", "iris.csv"))
```


# Methods

We fit a linear model with sepal width as a function of sepal length:

$$
SW = mSL + b
$$

# Results

Figure \@ref(fig:plot) shows that larger petals are lighter.

```{r plot, fig.cap = "Relationship between sepal width (gr) and sepal length (cm) for three *Iris spp*."}
ggplot(data = iris,
       mapping = aes(x = Sepal.Length, y = Sepal.Width)) +
  geom_point(mapping = aes(color = Species)) +
  geom_smooth(method = "lm") +
  ggtheme_plot() +
  labs(x = "Sepal Length (cm)",
       y = "Sepal Width (gr)") +
  scale_color_brewer(palette = "Set1")
```

# So what?

Yeah, that's about it.