index.Rmd

---
title: A Reproducible Workflow exercise
author: Environment and Climate Change Canada, inSileco
date: 2021-03-01
output:
  html_document:
    toc: true
  pdf_document:
    toc: true
  word_document:
    toc: true
---

```{r setup, include = FALSE}
knitr::opts_chunk$set(
  echo = FALSE,
  fig.align = "center"
)
library(palmerpenguins)
data(penguins)

# The following objects are used as inline code within the text
n_individuals <- nrow(penguins)
n_species <- length(unique(penguins$species))
n_islands <- length(unique(penguins$island))
mean_flipper_length <- round(mean(penguins$flipper_length_mm, na.rm = TRUE),2)
```

# Section 1 title

## Subsection 1 title

*Lorem* **ipsum** ***dolor*** ~~sit~~ amet, consectetur adipiscing elit. Nulla eget ipsum a nulla maximus ornare. Nunc ut nibh orci. Phasellus lacinia velit sed tincidunt euismod. Morbi euismod, lectus et consectetur tristique, urna eros facilisis magna, faucibus condimentum leo dui a enim. Praesent massa velit, egestas et eros eget, ornare tincidunt nisl. Vestibulum mattis enim a enim mattis iaculis. Etiam ipsum tortor, vehicula pretium consequat at, pharetra non mauris. Nam ac facilisis libero. Donec ut arcu gravida, pellentesque eros in, tempor mi.

Numbered list of numbers

1. one
2. two
3. three

> A man who dares to waste one hour of time has not discovered the value of life.
![](img/lter_penguins.png)

Artistic drawing of palmer penguins.[^art]

```{r, echo = FALSE}
knitr::kable(penguins[1:20,])
```

[^art]: Artwork by \@allison_horst

## Subsection 2 title

The [penguins dataset](https://github.com/allisonhorst/palmerpenguins) contains data on `r n_individuals` individuals, `r n_species` species, and from `r n_islands` islands. Across individuals, the mean flipper length is `r mean_flipper_length` $mm$.


```{r, echo = FALSE}
plot(x = penguins$flipper_length_mm, y = penguins$body_mass_g, pch = 20, col = '#32c4c4',
     main = 'Penguin body mass as a function of flipper length',
     xlab = 'Flipper length (mm)', ylab = 'Body mass (g)')
```

```{r, child = "section2.Rmd"}
```