About reproducibility

## .font140[<svg viewBox="0 0 581 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M581 226.6C581 119.1 450.9 32 290.5 32S0 119.1 0 226.6C0 322.4 103.3 402 239.4 418.1V480h99.1v-61.5c24.3-2.7 47.6-7.4 69.4-13.9L448 480h112l-67.4-113.7c54.5-35.4 88.4-84.9 88.4-139.7zm-466.8 14.5c0-73.5 98.9-133 220.8-133s211.9 40.7 211.9 133c0 50.1-26.5 85-70.3 106.4-2.4-1.6-4.7-2.9-6.4-3.7-10.2-5.2-27.8-10.5-27.8-10.5s86.6-6.4 86.6-92.7-90.6-87.9-90.6-87.9h-199V361c-74.1-21.5-125.2-67.1-125.2-119.9zm225.1 38.3v-55.6c57.8 0 87.8-6.8 87.8 27.3 0 36.5-38.2 28.3-87.8 28.3zm-.9 72.5H365c10.8 0 18.9 11.7 24 19.2-16.1 1.9-33 2.8-50.6 2.9v-22.1z"></path></svg>eproducible Workflows]

<br>

.instructors[
  .font180[Increase Everyday Efficiency]
  <br><br><br>
  .authors140[David Beauchesne & Kevin Cazelles]
  <br><br>
  March 02, 2021
  <br>
  .font200[
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  [<svg viewBox="0 0 448 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M448 73.143v45.714C448 159.143 347.667 192 224 192S0 159.143 0 118.857V73.143C0 32.857 100.333 0 224 0s224 32.857 224 73.143zM448 176v102.857C448 319.143 347.667 352 224 352S0 319.143 0 278.857V176c48.125 33.143 136.208 48.572 224 48.572S399.874 209.143 448 176zm0 160v102.857C448 479.143 347.667 512 224 512S0 479.143 0 438.857V336c48.125 33.143 136.208 48.572 224 48.572S399.874 369.143 448 336z"></path></svg>](https://github.com/inSilecoInc/workshop_reproducibility/raw/gh-pages/data_and_script.zip)
  
  ]
]

![deploy workshop](https://github.com/inSilecoInc/workshop_reproducibility/workflows/deploy%20workshop/badge.svg)

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---

# Learning objectives

![:custom_hr]()

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---

# Learning objectives

<br>

### 1. Understand the importance of reproducible research.

### 2. Understand how R can be useful for reproducible research.

### 3. Set up a minimal reproducible workflow.

### 4. Create a simple R Markdown document including a reproducible analysis.

---

# <svg viewBox="0 0 512 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M256 8C119.043 8 8 119.083 8 256c0 136.997 111.043 248 248 248s248-111.003 248-248C504 119.083 392.957 8 256 8zm0 110c23.196 0 42 18.804 42 42s-18.804 42-42 42-42-18.804-42-42 18.804-42 42-42zm56 254c0 6.627-5.373 12-12 12h-88c-6.627 0-12-5.373-12-12v-24c0-6.627 5.373-12 12-12h12v-64h-12c-6.627 0-12-5.373-12-12v-24c0-6.627 5.373-12 12-12h64c6.627 0 12 5.373 12 12v100h12c6.627 0 12 5.373 12 12v24z"></path></svg> Reproducible research

![:custom_hr]()

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???

Comments

---
# Reproducible research ✋

<br>

## Reproducibility

<br>

## Reproducibility vs. Replicability

<br>

## Reproducibility vs. Replicability vs. Generalizability

---
# Terminology is not clear yet...

- Various terms with different meanings

---
# Terminology is not clear yet...

## Reproducible vs. Replicable

### **no distinction** (A)

### **distinction** :
- for some (B1):
  - *reproducible*: authors provide data + computer code to re-create the results.
  - *replicable*: new study same scientific findings as another study, collecting new
  data and new analyses.
--

- for others (B2): opposite definitions

???

similar methods but could be different

---
# Terminology is not clear yet...

## Reproducible vs. Replicable

---
# Terminology is being clarified

---
# Terminology is being clarified

> We define **reproducibility** to mean **computational reproducibility**—
obtaining consistent computational results using the same **input data**, computational steps, methods, **code**, and conditions of analysis;

> and **replicability** to mean obtaining **consistent results across studies aimed at answering the
same scientific question**, each of which has obtained its own data.

> In short, reproducibility involves the original data and code; replicability involves
new data collection and similar methods used by previous studies.

???

1. good practices
2. robustness of a finding science

---
# Terminology is being clarified

> A third concept, **generalizability**, refers to the **extent that results of a study apply** in other contexts or populations that differ from the original one.

???

what the scope of the finding. There is a study on stressor that affect 
the mortality of a given bird species. Then I think studying this on a second 
bird species and I don't find any significance. Then studies may very well be replicable 
but it is not generalizabe to the second bird species.

---
# Reproducibility is tied to computer science

<br>

### **1. Scientific studies should be replicable (Material & Methods)**

<br>

### **2. With the help of technologies scientific studies should now be reproducible (Research compendium)**

???

It's a topic about research but quickly due to its nature we are talking about technologies.

---
# How do we produce knowledge?

???

similar with report

---
# How do we produce knowledge?

---
# How do we produce knowledge?

---
# How do we produce knowledge?

???

only retrieve data!!not carry out experiment
getting more complex in terms of computataional steps.

---
# How do we produce knowledge?

---
# How do we produce knowledge?

---
# How do we produce knowledge?

???

circle : science bringing new tools and with new tools more complex science.

---
# How do we produce knowledge?

## Analyzing data has become increasingly complex

<br>

## - more and more <svg viewBox="0 0 640 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M255.03 261.65c6.25 6.25 16.38 6.25 22.63 0l11.31-11.31c6.25-6.25 6.25-16.38 0-22.63L253.25 192l35.71-35.72c6.25-6.25 6.25-16.38 0-22.63l-11.31-11.31c-6.25-6.25-16.38-6.25-22.63 0l-58.34 58.34c-6.25 6.25-6.25 16.38 0 22.63l58.35 58.34zm96.01-11.3l11.31 11.31c6.25 6.25 16.38 6.25 22.63 0l58.34-58.34c6.25-6.25 6.25-16.38 0-22.63l-58.34-58.34c-6.25-6.25-16.38-6.25-22.63 0l-11.31 11.31c-6.25 6.25-6.25 16.38 0 22.63L386.75 192l-35.71 35.72c-6.25 6.25-6.25 16.38 0 22.63zM624 416H381.54c-.74 19.81-14.71 32-32.74 32H288c-18.69 0-33.02-17.47-32.77-32H16c-8.8 0-16 7.2-16 16v16c0 35.2 28.8 64 64 64h512c35.2 0 64-28.8 64-64v-16c0-8.8-7.2-16-16-16zM576 48c0-26.4-21.6-48-48-48H112C85.6 0 64 21.6 64 48v336h512V48zm-64 272H128V64h384v256z"></path></svg> steps

<br>

## - each step has a certain risk of user error.

Recognized in the 80's/90's by [Jon Claerbout](https://en.wikipedia.org/wiki/Jon_Claerbout) and this led to [Redoc](https://ieeexplore.ieee.org/document/881708).

---
# How do we produce knowledge?

## "Publish or perish" system urges scientists to work (too) fast

<br>

## and to adopt "questionable research practices"
  - p-value hacking,
  - cherry picking,
  - Hypothesizing After Results are Known (HARKing).

???

also covid money or ego

---
# Why does reproducibility matter?

.font80[<svg viewBox="0 0 384 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M369.9 97.9L286 14C277 5 264.8-.1 252.1-.1H48C21.5 0 0 21.5 0 48v416c0 26.5 21.5 48 48 48h288c26.5 0 48-21.5 48-48V131.9c0-12.7-5.1-25-14.1-34zM332.1 128H256V51.9l76.1 76.1zM48 464V48h160v104c0 13.3 10.7 24 24 24h104v288H48z"></path></svg> Open Science Collaboration (2015). [Estimating the reproducibility of psychological science.](https://science.sciencemag.org/content/349/6251/aac4716)]

---
# Why does reproducibility matter?

???

might very well expect that for ecology

---
# Why does reproducibility matter?

.font80[<svg viewBox="0 0 384 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M369.9 97.9L286 14C277 5 264.8-.1 252.1-.1H48C21.5 0 0 21.5 0 48v416c0 26.5 21.5 48 48 48h288c26.5 0 48-21.5 48-48V131.9c0-12.7-5.1-25-14.1-34zM332.1 128H256V51.9l76.1 76.1zM48 464V48h160v104c0 13.3 10.7 24 24 24h104v288H48z"></path></svg> Fang & Casadevall. (2011) [Retracted Science and the Retraction Index.](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3187237/)]

---
# Why does reproducibility matter?

<br>

### **Reproducible Research leads to scientific findings more robust/reliable by minimizing user errors**

---
# Reproducible workflows

---
# Reproducible workflows

<img src="img/workflow3.png" width="55%" style="display: block; margin: auto;" />
--

### .font120[<svg viewBox="0 0 512 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M500.33 0h-47.41a12 12 0 0 0-12 12.57l4 82.76A247.42 247.42 0 0 0 256 8C119.34 8 7.9 119.53 8 256.19 8.1 393.07 119.1 504 256 504a247.1 247.1 0 0 0 166.18-63.91 12 12 0 0 0 .48-17.43l-34-34a12 12 0 0 0-16.38-.55A176 176 0 1 1 402.1 157.8l-101.53-4.87a12 12 0 0 0-12.57 12v47.41a12 12 0 0 0 12 12h200.33a12 12 0 0 0 12-12V12a12 12 0 0 0-12-12z"></path></svg> **Reproducible workflows** / **Research compendia**]

---
# Reproducible workflows

### .font140[**Can do**? make research findings more robust/reliable.]

### .font140[**How**? by adopting good coding practices.]

### .font140[**Require**? making data and code open.]

### .font140[**Collateral benefits**]

- "**Open science**" movement:
    - [Open Science Framework](https://osf.io/)
    - [rOpenSci](https://ropensci.org/)

- re-usage of code can lead to an increase of efficiency;
  - improved coding skills;

???

DB and I have developed coding skills for this.

---
# How to reproduce studies

### .font140[Reproducibility will not solve all issues]

> Unfortunately, the mere reproducibility of computational results is
> insufficient to address the replication crisis because even a reproducible
> analysis can suffer from many problems—confounding from omitted variables,
> poor study design, missing data—that threaten the validity and useful
> interpretation of the results.

.font80[<svg viewBox="0 0 384 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M369.9 97.9L286 14C277 5 264.8-.1 252.1-.1H48C21.5 0 0 21.5 0 48v416c0 26.5 21.5 48 48 48h288c26.5 0 48-21.5 48-48V131.9c0-12.7-5.1-25-14.1-34zM332.1 128H256V51.9l76.1 76.1zM48 464V48h160v104c0 13.3 10.7 24 24 24h104v288H48z"></path></svg> Leek & Peng (2015).
[Opinion: Reproducible research can still be wrong: Adopting a prevention approach](https://doi.org/10.1073/pnas.1421412111)]

---
# How to reproduce studies

### .font140[**Obstacle**: it takes **a lot** of time]

> It is also important to recognize that there are costs and barriers to shifting to a practice
of reproducible research, particularly when the culture does not recognize the value of
developing this new paradigm or the effort that can be required to develop or learn to use
suitable tools. This is of particular concern to young people who need to earn tenure
or secure a permanent position.

.font80[<svg viewBox="0 0 384 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M369.9 97.9L286 14C277 5 264.8-.1 252.1-.1H48C21.5 0 0 21.5 0 48v416c0 26.5 21.5 48 48 48h288c26.5 0 48-21.5 48-48V131.9c0-12.7-5.1-25-14.1-34zM332.1 128H256V51.9l76.1 76.1zM48 464V48h160v104c0 13.3 10.7 24 24 24h104v288H48z"></path></svg> Stodden et al. (2013).
[Setting the default to reproducible: Reproducibility in Computational and Experimental Mathematics](http://ethics.iit.edu/eelibrary/node/15429)]

???

I've spent a lot of time on making my studies reproducible but not even sure sb re-run my code, not even sure it'll be useful. What is sure is that I didn't spend that time on other papers and I am "more proud of what I have done". But so far, without a system shift, it could be regarded as a virtue. I am very happy to see DFO is taking this very seriously and understood the collateral benefits. Yes it pays off. There is less technical obstacle, there are better practice. You can do more.

---

# Questions?

![:custom_hr]()

## .font150[<svg viewBox="0 0 512 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M256 8C119.043 8 8 119.083 8 256c0 136.997 111.043 248 248 248s248-111.003 248-248C504 119.083 392.957 8 256 8zm0 448c-110.532 0-200-89.431-200-200 0-110.495 89.472-200 200-200 110.491 0 200 89.471 200 200 0 110.53-89.431 200-200 200zm107.244-255.2c0 67.052-72.421 68.084-72.421 92.863V300c0 6.627-5.373 12-12 12h-45.647c-6.627 0-12-5.373-12-12v-8.659c0-35.745 27.1-50.034 47.579-61.516 17.561-9.845 28.324-16.541 28.324-29.579 0-17.246-21.999-28.693-39.784-28.693-23.189 0-33.894 10.977-48.942 29.969-4.057 5.12-11.46 6.071-16.666 2.124l-27.824-21.098c-5.107-3.872-6.251-11.066-2.644-16.363C184.846 131.491 214.94 112 261.794 112c49.071 0 101.45 38.304 101.45 88.8zM298 368c0 23.159-18.841 42-42 42s-42-18.841-42-42 18.841-42 42-42 42 18.841 42 42z"></path></svg>]

---

# A minimal reproducible workflow with <svg viewBox="0 0 581 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M581 226.6C581 119.1 450.9 32 290.5 32S0 119.1 0 226.6C0 322.4 103.3 402 239.4 418.1V480h99.1v-61.5c24.3-2.7 47.6-7.4 69.4-13.9L448 480h112l-67.4-113.7c54.5-35.4 88.4-84.9 88.4-139.7zm-466.8 14.5c0-73.5 98.9-133 220.8-133s211.9 40.7 211.9 133c0 50.1-26.5 85-70.3 106.4-2.4-1.6-4.7-2.9-6.4-3.7-10.2-5.2-27.8-10.5-27.8-10.5s86.6-6.4 86.6-92.7-90.6-87.9-90.6-87.9h-199V361c-74.1-21.5-125.2-67.1-125.2-119.9zm225.1 38.3v-55.6c57.8 0 87.8-6.8 87.8 27.3 0 36.5-38.2 28.3-87.8 28.3zm-.9 72.5H365c10.8 0 18.9 11.7 24 19.2-16.1 1.9-33 2.8-50.6 2.9v-22.1z"></path></svg>

![:custom_hr]()

## <svg viewBox="0 0 448 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M448 73.143v45.714C448 159.143 347.667 192 224 192S0 159.143 0 118.857V73.143C0 32.857 100.333 0 224 0s224 32.857 224 73.143zM448 176v102.857C448 319.143 347.667 352 224 352S0 319.143 0 278.857V176c48.125 33.143 136.208 48.572 224 48.572S399.874 209.143 448 176zm0 160v102.857C448 479.143 347.667 512 224 512S0 479.143 0 438.857V336c48.125 33.143 136.208 48.572 224 48.572S399.874 369.143 448 336z"></path></svg> &nbsp; <svg viewBox="0 0 448 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M190.5 66.9l22.2-22.2c9.4-9.4 24.6-9.4 33.9 0L441 239c9.4 9.4 9.4 24.6 0 33.9L246.6 467.3c-9.4 9.4-24.6 9.4-33.9 0l-22.2-22.2c-9.5-9.5-9.3-25 .4-34.3L311.4 296H24c-13.3 0-24-10.7-24-24v-32c0-13.3 10.7-24 24-24h287.4L190.9 101.2c-9.8-9.3-10-24.8-.4-34.3z"></path></svg> &nbsp; <svg viewBox="0 0 581 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M581 226.6C581 119.1 450.9 32 290.5 32S0 119.1 0 226.6C0 322.4 103.3 402 239.4 418.1V480h99.1v-61.5c24.3-2.7 47.6-7.4 69.4-13.9L448 480h112l-67.4-113.7c54.5-35.4 88.4-84.9 88.4-139.7zm-466.8 14.5c0-73.5 98.9-133 220.8-133s211.9 40.7 211.9 133c0 50.1-26.5 85-70.3 106.4-2.4-1.6-4.7-2.9-6.4-3.7-10.2-5.2-27.8-10.5-27.8-10.5s86.6-6.4 86.6-92.7-90.6-87.9-90.6-87.9h-199V361c-74.1-21.5-125.2-67.1-125.2-119.9zm225.1 38.3v-55.6c57.8 0 87.8-6.8 87.8 27.3 0 36.5-38.2 28.3-87.8 28.3zm-.9 72.5H365c10.8 0 18.9 11.7 24 19.2-16.1 1.9-33 2.8-50.6 2.9v-22.1z"></path></svg> &nbsp; <svg viewBox="0 0 448 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M190.5 66.9l22.2-22.2c9.4-9.4 24.6-9.4 33.9 0L441 239c9.4 9.4 9.4 24.6 0 33.9L246.6 467.3c-9.4 9.4-24.6 9.4-33.9 0l-22.2-22.2c-9.5-9.5-9.3-25 .4-34.3L311.4 296H24c-13.3 0-24-10.7-24-24v-32c0-13.3 10.7-24 24-24h287.4L190.9 101.2c-9.8-9.3-10-24.8-.4-34.3z"></path></svg> &nbsp; <svg viewBox="0 0 640 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M512.1 191l-8.2 14.3c-3 5.3-9.4 7.5-15.1 5.4-11.8-4.4-22.6-10.7-32.1-18.6-4.6-3.8-5.8-10.5-2.8-15.7l8.2-14.3c-6.9-8-12.3-17.3-15.9-27.4h-16.5c-6 0-11.2-4.3-12.2-10.3-2-12-2.1-24.6 0-37.1 1-6 6.2-10.4 12.2-10.4h16.5c3.6-10.1 9-19.4 15.9-27.4l-8.2-14.3c-3-5.2-1.9-11.9 2.8-15.7 9.5-7.9 20.4-14.2 32.1-18.6 5.7-2.1 12.1.1 15.1 5.4l8.2 14.3c10.5-1.9 21.2-1.9 31.7 0L552 6.3c3-5.3 9.4-7.5 15.1-5.4 11.8 4.4 22.6 10.7 32.1 18.6 4.6 3.8 5.8 10.5 2.8 15.7l-8.2 14.3c6.9 8 12.3 17.3 15.9 27.4h16.5c6 0 11.2 4.3 12.2 10.3 2 12 2.1 24.6 0 37.1-1 6-6.2 10.4-12.2 10.4h-16.5c-3.6 10.1-9 19.4-15.9 27.4l8.2 14.3c3 5.2 1.9 11.9-2.8 15.7-9.5 7.9-20.4 14.2-32.1 18.6-5.7 2.1-12.1-.1-15.1-5.4l-8.2-14.3c-10.4 1.9-21.2 1.9-31.7 0zm-10.5-58.8c38.5 29.6 82.4-14.3 52.8-52.8-38.5-29.7-82.4 14.3-52.8 52.8zM386.3 286.1l33.7 16.8c10.1 5.8 14.5 18.1 10.5 29.1-8.9 24.2-26.4 46.4-42.6 65.8-7.4 8.9-20.2 11.1-30.3 5.3l-29.1-16.8c-16 13.7-34.6 24.6-54.9 31.7v33.6c0 11.6-8.3 21.6-19.7 23.6-24.6 4.2-50.4 4.4-75.9 0-11.5-2-20-11.9-20-23.6V418c-20.3-7.2-38.9-18-54.9-31.7L74 403c-10 5.8-22.9 3.6-30.3-5.3-16.2-19.4-33.3-41.6-42.2-65.7-4-10.9.4-23.2 10.5-29.1l33.3-16.8c-3.9-20.9-3.9-42.4 0-63.4L12 205.8c-10.1-5.8-14.6-18.1-10.5-29 8.9-24.2 26-46.4 42.2-65.8 7.4-8.9 20.2-11.1 30.3-5.3l29.1 16.8c16-13.7 34.6-24.6 54.9-31.7V57.1c0-11.5 8.2-21.5 19.6-23.5 24.6-4.2 50.5-4.4 76-.1 11.5 2 20 11.9 20 23.6v33.6c20.3 7.2 38.9 18 54.9 31.7l29.1-16.8c10-5.8 22.9-3.6 30.3 5.3 16.2 19.4 33.2 41.6 42.1 65.8 4 10.9.1 23.2-10 29.1l-33.7 16.8c3.9 21 3.9 42.5 0 63.5zm-117.6 21.1c59.2-77-28.7-164.9-105.7-105.7-59.2 77 28.7 164.9 105.7 105.7zm243.4 182.7l-8.2 14.3c-3 5.3-9.4 7.5-15.1 5.4-11.8-4.4-22.6-10.7-32.1-18.6-4.6-3.8-5.8-10.5-2.8-15.7l8.2-14.3c-6.9-8-12.3-17.3-15.9-27.4h-16.5c-6 0-11.2-4.3-12.2-10.3-2-12-2.1-24.6 0-37.1 1-6 6.2-10.4 12.2-10.4h16.5c3.6-10.1 9-19.4 15.9-27.4l-8.2-14.3c-3-5.2-1.9-11.9 2.8-15.7 9.5-7.9 20.4-14.2 32.1-18.6 5.7-2.1 12.1.1 15.1 5.4l8.2 14.3c10.5-1.9 21.2-1.9 31.7 0l8.2-14.3c3-5.3 9.4-7.5 15.1-5.4 11.8 4.4 22.6 10.7 32.1 18.6 4.6 3.8 5.8 10.5 2.8 15.7l-8.2 14.3c6.9 8 12.3 17.3 15.9 27.4h16.5c6 0 11.2 4.3 12.2 10.3 2 12 2.1 24.6 0 37.1-1 6-6.2 10.4-12.2 10.4h-16.5c-3.6 10.1-9 19.4-15.9 27.4l8.2 14.3c3 5.2 1.9 11.9-2.8 15.7-9.5 7.9-20.4 14.2-32.1 18.6-5.7 2.1-12.1-.1-15.1-5.4l-8.2-14.3c-10.4 1.9-21.2 1.9-31.7 0zM501.6 431c38.5 29.6 82.4-14.3 52.8-52.8-38.5-29.6-82.4 14.3-52.8 52.8z"></path></svg> &nbsp; <svg viewBox="0 0 448 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M190.5 66.9l22.2-22.2c9.4-9.4 24.6-9.4 33.9 0L441 239c9.4 9.4 9.4 24.6 0 33.9L246.6 467.3c-9.4 9.4-24.6 9.4-33.9 0l-22.2-22.2c-9.5-9.5-9.3-25 .4-34.3L311.4 296H24c-13.3 0-24-10.7-24-24v-32c0-13.3 10.7-24 24-24h287.4L190.9 101.2c-9.8-9.3-10-24.8-.4-34.3z"></path></svg> &nbsp; <svg viewBox="0 0 384 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M369.9 97.9L286 14C277 5 264.8-.1 252.1-.1H48C21.5 0 0 21.5 0 48v416c0 26.5 21.5 48 48 48h288c26.5 0 48-21.5 48-48V131.9c0-12.7-5.1-25-14.1-34zM332.1 128H256V51.9l76.1 76.1zM48 464V48h160v104c0 13.3 10.7 24 24 24h104v288H48z"></path></svg> &nbsp; <svg viewBox="0 0 448 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M190.5 66.9l22.2-22.2c9.4-9.4 24.6-9.4 33.9 0L441 239c9.4 9.4 9.4 24.6 0 33.9L246.6 467.3c-9.4 9.4-24.6 9.4-33.9 0l-22.2-22.2c-9.5-9.5-9.3-25 .4-34.3L311.4 296H24c-13.3 0-24-10.7-24-24v-32c0-13.3 10.7-24 24-24h287.4L190.9 101.2c-9.8-9.3-10-24.8-.4-34.3z"></path></svg> &nbsp; <svg viewBox="0 0 512 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M370.72 133.28C339.458 104.008 298.888 87.962 255.848 88c-77.458.068-144.328 53.178-162.791 126.85-1.344 5.363-6.122 9.15-11.651 9.15H24.103c-7.498 0-13.194-6.807-11.807-14.176C33.933 94.924 134.813 8 256 8c66.448 0 126.791 26.136 171.315 68.685L463.03 40.97C478.149 25.851 504 36.559 504 57.941V192c0 13.255-10.745 24-24 24H345.941c-21.382 0-32.09-25.851-16.971-40.971l41.75-41.749zM32 296h134.059c21.382 0 32.09 25.851 16.971 40.971l-41.75 41.75c31.262 29.273 71.835 45.319 114.876 45.28 77.418-.07 144.315-53.144 162.787-126.849 1.344-5.363 6.122-9.15 11.651-9.15h57.304c7.498 0 13.194 6.807 11.807 14.176C478.067 417.076 377.187 504 256 504c-66.448 0-126.791-26.136-171.315-68.685L48.97 471.03C33.851 486.149 8 475.441 8 454.059V320c0-13.255 10.745-24 24-24z"></path></svg>

???

Questions??

---
# A reproducible workflow?

## There are clear benefits of using a reproducible workflow!

???
click and change all values... will certainly lead to errors...
Avoid re-doing every by hand! Instead, set up your repository.

---
# A reproducibility spectrum

.font80[<svg viewBox="0 0 384 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M369.9 97.9L286 14C277 5 264.8-.1 252.1-.1H48C21.5 0 0 21.5 0 48v416c0 26.5 21.5 48 48 48h288c26.5 0 48-21.5 48-48V131.9c0-12.7-5.1-25-14.1-34zM332.1 128H256V51.9l76.1 76.1zM48 464V48h160v104c0 13.3 10.7 24 24 24h104v288H48z"></path></svg> Peng. (2011).
[Reproducible Research in Computational Science.](https://science.sciencemag.org/content/334/6060/1226)]

### Towards full reproducibility, technologies are getting more complex

- entire pipeline in a versioned repository

- record all version(s) of software(s) used in the workflow

- run code without being impacted by OS or hardware

???

You quickly get benefits!

Before making the topics more complex that needed.
We are aiming at given you a sense of this!!

---
# You might not be that far!

### <svg viewBox="0 0 581 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M581 226.6C581 119.1 450.9 32 290.5 32S0 119.1 0 226.6C0 322.4 103.3 402 239.4 418.1V480h99.1v-61.5c24.3-2.7 47.6-7.4 69.4-13.9L448 480h112l-67.4-113.7c54.5-35.4 88.4-84.9 88.4-139.7zm-466.8 14.5c0-73.5 98.9-133 220.8-133s211.9 40.7 211.9 133c0 50.1-26.5 85-70.3 106.4-2.4-1.6-4.7-2.9-6.4-3.7-10.2-5.2-27.8-10.5-27.8-10.5s86.6-6.4 86.6-92.7-90.6-87.9-90.6-87.9h-199V361c-74.1-21.5-125.2-67.1-125.2-119.9zm225.1 38.3v-55.6c57.8 0 87.8-6.8 87.8 27.3 0 36.5-38.2 28.3-87.8 28.3zm-.9 72.5H365c10.8 0 18.9 11.7 24 19.2-16.1 1.9-33 2.8-50.6 2.9v-22.1z"></path></svg> is suitable for Reproducibility

- open source (no license-related issues)

- strong community actively engaged in making science more reproducible

- A large diversity of package for reproducibility purposes
  - packages to improve the workflow

- [rOpenSci](https://ropensci.org/)

???

community ==> made of R user
and so are Python and Julia

---
# You might not be that far!

### One well-structured folder! [Download it](https://github.com/inSilecoInc/workshop_reproducibility/raw/main/demo/min_workflow.zip).

```sh
.
├── data
├── ms
├── output
├── R
└── README.md
```

<br>

---
# You might not be that far!

- 📁 `R` : R code (`.R` files)

- functions, scripts ...
  - data retrieval, statistical analysis, figure

<br>

- 📁 `data` :

- input/raw data
  - processed data
  - data may be archived on line (e.g. Dryad) and may be accessed via a script (see [rdryad](https://docs.ropensci.org/rdryad/))

---
# You might not be that far!

- 📁 `output` (`fig` `tab`):

- figures
  - tables

<br>

- 📁 `ms` (`doc`)

- main manuscript
  - Supplementary Information (SI)

---
# You might not be that far!

## Follow 3 simple rules!

### 1. The folder must be self contained

- think of the root of the folder as the root of the system
  - ~~C:\user/data\dat0001.txt~~
  - but this system is not isolated (e.g. remote)
  - does not mean everything will be shared / added in the research compendium

---
# You might not be that far!

## Follow 3 simple rules!

### 2. document massively

- your datasets (could be a link to relevant documentation)
  - your functions and scripts
  - and the tricks you've used that won't be clear to others (that includes future yourself!)

---
# You might not be that far!

## Follow 3 simple rules!

### 3. Keep track of all versions you've used

- R version (and other software)
  - Package versions

.font80[<svg viewBox="0 0 384 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M369.9 97.9L286 14C277 5 264.8-.1 252.1-.1H48C21.5 0 0 21.5 0 48v416c0 26.5 21.5 48 48 48h288c26.5 0 48-21.5 48-48V131.9c0-12.7-5.1-25-14.1-34zM332.1 128H256V51.9l76.1 76.1zM48 464V48h160v104c0 13.3 10.7 24 24 24h104v288H48z"></path></svg> Sandve et al. [Ten Simple Rules for Reproducible Computational
Research](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003285)]

---
# You might not be that far! 💻

## A minimal workflow with this folder

### 1. Add data / edit code

### 2. source R function / render your manuscript / `pipeline()`

### 3. repeat until your entire analysis is completed!

<br>

## Zip this folder <svg viewBox="0 0 448 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M190.5 66.9l22.2-22.2c9.4-9.4 24.6-9.4 33.9 0L441 239c9.4 9.4 9.4 24.6 0 33.9L246.6 467.3c-9.4 9.4-24.6 9.4-33.9 0l-22.2-22.2c-9.5-9.5-9.3-25 .4-34.3L311.4 296H24c-13.3 0-24-10.7-24-24v-32c0-13.3 10.7-24 24-24h287.4L190.9 101.2c-9.8-9.3-10-24.8-.4-34.3z"></path></svg> research compendium.

???

80% of the job is done !

---

# Questions?

![:custom_hr]()

---
class: inverse, center, middle

# Reproducible documents in reproducible workflows

![:custom_hr]()

## <svg viewBox="0 0 448 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M448 73.143v45.714C448 159.143 347.667 192 224 192S0 159.143 0 118.857V73.143C0 32.857 100.333 0 224 0s224 32.857 224 73.143zM448 176v102.857C448 319.143 347.667 352 224 352S0 319.143 0 278.857V176c48.125 33.143 136.208 48.572 224 48.572S399.874 209.143 448 176zm0 160v102.857C448 479.143 347.667 512 224 512S0 479.143 0 438.857V336c48.125 33.143 136.208 48.572 224 48.572S399.874 369.143 448 336z"></path></svg> &nbsp; <svg viewBox="0 0 448 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M190.5 66.9l22.2-22.2c9.4-9.4 24.6-9.4 33.9 0L441 239c9.4 9.4 9.4 24.6 0 33.9L246.6 467.3c-9.4 9.4-24.6 9.4-33.9 0l-22.2-22.2c-9.5-9.5-9.3-25 .4-34.3L311.4 296H24c-13.3 0-24-10.7-24-24v-32c0-13.3 10.7-24 24-24h287.4L190.9 101.2c-9.8-9.3-10-24.8-.4-34.3z"></path></svg> &nbsp; <svg viewBox="0 0 581 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M581 226.6C581 119.1 450.9 32 290.5 32S0 119.1 0 226.6C0 322.4 103.3 402 239.4 418.1V480h99.1v-61.5c24.3-2.7 47.6-7.4 69.4-13.9L448 480h112l-67.4-113.7c54.5-35.4 88.4-84.9 88.4-139.7zm-466.8 14.5c0-73.5 98.9-133 220.8-133s211.9 40.7 211.9 133c0 50.1-26.5 85-70.3 106.4-2.4-1.6-4.7-2.9-6.4-3.7-10.2-5.2-27.8-10.5-27.8-10.5s86.6-6.4 86.6-92.7-90.6-87.9-90.6-87.9h-199V361c-74.1-21.5-125.2-67.1-125.2-119.9zm225.1 38.3v-55.6c57.8 0 87.8-6.8 87.8 27.3 0 36.5-38.2 28.3-87.8 28.3zm-.9 72.5H365c10.8 0 18.9 11.7 24 19.2-16.1 1.9-33 2.8-50.6 2.9v-22.1z"></path></svg> &nbsp; <svg viewBox="0 0 448 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M190.5 66.9l22.2-22.2c9.4-9.4 24.6-9.4 33.9 0L441 239c9.4 9.4 9.4 24.6 0 33.9L246.6 467.3c-9.4 9.4-24.6 9.4-33.9 0l-22.2-22.2c-9.5-9.5-9.3-25 .4-34.3L311.4 296H24c-13.3 0-24-10.7-24-24v-32c0-13.3 10.7-24 24-24h287.4L190.9 101.2c-9.8-9.3-10-24.8-.4-34.3z"></path></svg> &nbsp; <svg viewBox="0 0 640 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M512.1 191l-8.2 14.3c-3 5.3-9.4 7.5-15.1 5.4-11.8-4.4-22.6-10.7-32.1-18.6-4.6-3.8-5.8-10.5-2.8-15.7l8.2-14.3c-6.9-8-12.3-17.3-15.9-27.4h-16.5c-6 0-11.2-4.3-12.2-10.3-2-12-2.1-24.6 0-37.1 1-6 6.2-10.4 12.2-10.4h16.5c3.6-10.1 9-19.4 15.9-27.4l-8.2-14.3c-3-5.2-1.9-11.9 2.8-15.7 9.5-7.9 20.4-14.2 32.1-18.6 5.7-2.1 12.1.1 15.1 5.4l8.2 14.3c10.5-1.9 21.2-1.9 31.7 0L552 6.3c3-5.3 9.4-7.5 15.1-5.4 11.8 4.4 22.6 10.7 32.1 18.6 4.6 3.8 5.8 10.5 2.8 15.7l-8.2 14.3c6.9 8 12.3 17.3 15.9 27.4h16.5c6 0 11.2 4.3 12.2 10.3 2 12 2.1 24.6 0 37.1-1 6-6.2 10.4-12.2 10.4h-16.5c-3.6 10.1-9 19.4-15.9 27.4l8.2 14.3c3 5.2 1.9 11.9-2.8 15.7-9.5 7.9-20.4 14.2-32.1 18.6-5.7 2.1-12.1-.1-15.1-5.4l-8.2-14.3c-10.4 1.9-21.2 1.9-31.7 0zm-10.5-58.8c38.5 29.6 82.4-14.3 52.8-52.8-38.5-29.7-82.4 14.3-52.8 52.8zM386.3 286.1l33.7 16.8c10.1 5.8 14.5 18.1 10.5 29.1-8.9 24.2-26.4 46.4-42.6 65.8-7.4 8.9-20.2 11.1-30.3 5.3l-29.1-16.8c-16 13.7-34.6 24.6-54.9 31.7v33.6c0 11.6-8.3 21.6-19.7 23.6-24.6 4.2-50.4 4.4-75.9 0-11.5-2-20-11.9-20-23.6V418c-20.3-7.2-38.9-18-54.9-31.7L74 403c-10 5.8-22.9 3.6-30.3-5.3-16.2-19.4-33.3-41.6-42.2-65.7-4-10.9.4-23.2 10.5-29.1l33.3-16.8c-3.9-20.9-3.9-42.4 0-63.4L12 205.8c-10.1-5.8-14.6-18.1-10.5-29 8.9-24.2 26-46.4 42.2-65.8 7.4-8.9 20.2-11.1 30.3-5.3l29.1 16.8c16-13.7 34.6-24.6 54.9-31.7V57.1c0-11.5 8.2-21.5 19.6-23.5 24.6-4.2 50.5-4.4 76-.1 11.5 2 20 11.9 20 23.6v33.6c20.3 7.2 38.9 18 54.9 31.7l29.1-16.8c10-5.8 22.9-3.6 30.3 5.3 16.2 19.4 33.2 41.6 42.1 65.8 4 10.9.1 23.2-10 29.1l-33.7 16.8c3.9 21 3.9 42.5 0 63.5zm-117.6 21.1c59.2-77-28.7-164.9-105.7-105.7-59.2 77 28.7 164.9 105.7 105.7zm243.4 182.7l-8.2 14.3c-3 5.3-9.4 7.5-15.1 5.4-11.8-4.4-22.6-10.7-32.1-18.6-4.6-3.8-5.8-10.5-2.8-15.7l8.2-14.3c-6.9-8-12.3-17.3-15.9-27.4h-16.5c-6 0-11.2-4.3-12.2-10.3-2-12-2.1-24.6 0-37.1 1-6 6.2-10.4 12.2-10.4h16.5c3.6-10.1 9-19.4 15.9-27.4l-8.2-14.3c-3-5.2-1.9-11.9 2.8-15.7 9.5-7.9 20.4-14.2 32.1-18.6 5.7-2.1 12.1.1 15.1 5.4l8.2 14.3c10.5-1.9 21.2-1.9 31.7 0l8.2-14.3c3-5.3 9.4-7.5 15.1-5.4 11.8 4.4 22.6 10.7 32.1 18.6 4.6 3.8 5.8 10.5 2.8 15.7l-8.2 14.3c6.9 8 12.3 17.3 15.9 27.4h16.5c6 0 11.2 4.3 12.2 10.3 2 12 2.1 24.6 0 37.1-1 6-6.2 10.4-12.2 10.4h-16.5c-3.6 10.1-9 19.4-15.9 27.4l8.2 14.3c3 5.2 1.9 11.9-2.8 15.7-9.5 7.9-20.4 14.2-32.1 18.6-5.7 2.1-12.1-.1-15.1-5.4l-8.2-14.3c-10.4 1.9-21.2 1.9-31.7 0zM501.6 431c38.5 29.6 82.4-14.3 52.8-52.8-38.5-29.6-82.4 14.3-52.8 52.8z"></path></svg> &nbsp; <svg viewBox="0 0 448 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M190.5 66.9l22.2-22.2c9.4-9.4 24.6-9.4 33.9 0L441 239c9.4 9.4 9.4 24.6 0 33.9L246.6 467.3c-9.4 9.4-24.6 9.4-33.9 0l-22.2-22.2c-9.5-9.5-9.3-25 .4-34.3L311.4 296H24c-13.3 0-24-10.7-24-24v-32c0-13.3 10.7-24 24-24h287.4L190.9 101.2c-9.8-9.3-10-24.8-.4-34.3z"></path></svg> &nbsp; [<svg viewBox="0 0 384 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M369.9 97.9L286 14C277 5 264.8-.1 252.1-.1H48C21.5 0 0 21.5 0 48v416c0 26.5 21.5 48 48 48h288c26.5 0 48-21.5 48-48V131.9c0-12.7-5.1-25-14.1-34zM332.1 128H256V51.9l76.1 76.1zM48 464V48h160v104c0 13.3 10.7 24 24 24h104v288H48z"></path></svg>]() &nbsp; <svg viewBox="0 0 448 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M190.5 66.9l22.2-22.2c9.4-9.4 24.6-9.4 33.9 0L441 239c9.4 9.4 9.4 24.6 0 33.9L246.6 467.3c-9.4 9.4-24.6 9.4-33.9 0l-22.2-22.2c-9.5-9.5-9.3-25 .4-34.3L311.4 296H24c-13.3 0-24-10.7-24-24v-32c0-13.3 10.7-24 24-24h287.4L190.9 101.2c-9.8-9.3-10-24.8-.4-34.3z"></path></svg> &nbsp; <svg viewBox="0 0 512 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M370.72 133.28C339.458 104.008 298.888 87.962 255.848 88c-77.458.068-144.328 53.178-162.791 126.85-1.344 5.363-6.122 9.15-11.651 9.15H24.103c-7.498 0-13.194-6.807-11.807-14.176C33.933 94.924 134.813 8 256 8c66.448 0 126.791 26.136 171.315 68.685L463.03 40.97C478.149 25.851 504 36.559 504 57.941V192c0 13.255-10.745 24-24 24H345.941c-21.382 0-32.09-25.851-16.971-40.971l41.75-41.749zM32 296h134.059c21.382 0 32.09 25.851 16.971 40.971l-41.75 41.75c31.262 29.273 71.835 45.319 114.876 45.28 77.418-.07 144.315-53.144 162.787-126.849 1.344-5.363 6.122-9.15 11.651-9.15h57.304c7.498 0 13.194 6.807 11.807 14.176C478.067 417.076 377.187 504 256 504c-66.448 0-126.791-26.136-171.315-68.685L48.97 471.03C33.851 486.149 8 475.441 8 454.059V320c0-13.255 10.745-24 24-24z"></path></svg>

---

# Building reproducible workflows

## Dynamic documents

- Creating dynamic documents to automate workflows
  - Code & text living together

## Markup language

- Rendering text using tags to format document
  - LaTex, HTML <svg viewBox="0 0 384 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M0 32l34.9 395.8L191.5 480l157.6-52.2L384 32H0zm308.2 127.9H124.4l4.1 49.4h175.6l-13.6 148.4-97.9 27v.3h-1.1l-98.7-27.3-6-75.8h47.7L138 320l53.5 14.5 53.7-14.5 6-62.2H84.3L71.5 112.2h241.1l-4.4 47.7z"></path></svg>, Markdown <svg viewBox="0 0 640 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M593.8 59.1H46.2C20.7 59.1 0 79.8 0 105.2v301.5c0 25.5 20.7 46.2 46.2 46.2h547.7c25.5 0 46.2-20.7 46.1-46.1V105.2c0-25.4-20.7-46.1-46.2-46.1zM338.5 360.6H277v-120l-61.5 76.9-61.5-76.9v120H92.3V151.4h61.5l61.5 76.9 61.5-76.9h61.5v209.2zm135.3 3.1L381.5 256H443V151.4h61.5V256H566z"></path></svg>
  - Forget word! <svg viewBox="0 0 512 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M256 8C119.034 8 8 119.033 8 256s111.034 248 248 248 248-111.034 248-248S392.967 8 256 8zm130.108 117.892c65.448 65.448 70 165.481 20.677 235.637L150.47 105.216c70.204-49.356 170.226-44.735 235.638 20.676zM125.892 386.108c-65.448-65.448-70-165.481-20.677-235.637L361.53 406.784c-70.203 49.356-170.226 44.736-235.638-20.676z"></path></svg> <svg viewBox="0 0 384 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M369.9 97.9L286 14C277 5 264.8-.1 252.1-.1H48C21.5 0 0 21.5 0 48v416c0 26.5 21.5 48 48 48h288c26.5 0 48-21.5 48-48V131.9c0-12.7-5.1-25-14.1-34zM332.1 128H256V51.9l76.1 76.1zM48 464V48h160v104c0 13.3 10.7 24 24 24h104v288H48zm220.1-208c-5.7 0-10.6 4-11.7 9.5-20.6 97.7-20.4 95.4-21 103.5-.2-1.2-.4-2.6-.7-4.3-.8-5.1.3.2-23.6-99.5-1.3-5.4-6.1-9.2-11.7-9.2h-13.3c-5.5 0-10.3 3.8-11.7 9.1-24.4 99-24 96.2-24.8 103.7-.1-1.1-.2-2.5-.5-4.2-.7-5.2-14.1-73.3-19.1-99-1.1-5.6-6-9.7-11.8-9.7h-16.8c-7.8 0-13.5 7.3-11.7 14.8 8 32.6 26.7 109.5 33.2 136 1.3 5.4 6.1 9.1 11.7 9.1h25.2c5.5 0 10.3-3.7 11.6-9.1l17.9-71.4c1.5-6.2 2.5-12 3-17.3l2.9 17.3c.1.4 12.6 50.5 17.9 71.4 1.3 5.3 6.1 9.1 11.6 9.1h24.7c5.5 0 10.3-3.7 11.6-9.1 20.8-81.9 30.2-119 34.5-136 1.9-7.6-3.8-14.9-11.6-14.9h-15.8z"></path></svg> .font60[as much as allowed by collaborators]

## Computing language

- Code for analyses and figures
  - <svg viewBox="0 0 581 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M581 226.6C581 119.1 450.9 32 290.5 32S0 119.1 0 226.6C0 322.4 103.3 402 239.4 418.1V480h99.1v-61.5c24.3-2.7 47.6-7.4 69.4-13.9L448 480h112l-67.4-113.7c54.5-35.4 88.4-84.9 88.4-139.7zm-466.8 14.5c0-73.5 98.9-133 220.8-133s211.9 40.7 211.9 133c0 50.1-26.5 85-70.3 106.4-2.4-1.6-4.7-2.9-6.4-3.7-10.2-5.2-27.8-10.5-27.8-10.5s86.6-6.4 86.6-92.7-90.6-87.9-90.6-87.9h-199V361c-74.1-21.5-125.2-67.1-125.2-119.9zm225.1 38.3v-55.6c57.8 0 87.8-6.8 87.8 27.3 0 36.5-38.2 28.3-87.8 28.3zm-.9 72.5H365c10.8 0 18.9 11.7 24 19.2-16.1 1.9-33 2.8-50.6 2.9v-22.1z"></path></svg>, Python <svg viewBox="0 0 448 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M439.8 200.5c-7.7-30.9-22.3-54.2-53.4-54.2h-40.1v47.4c0 36.8-31.2 67.8-66.8 67.8H172.7c-29.2 0-53.4 25-53.4 54.3v101.8c0 29 25.2 46 53.4 54.3 33.8 9.9 66.3 11.7 106.8 0 26.9-7.8 53.4-23.5 53.4-54.3v-40.7H226.2v-13.6h160.2c31.1 0 42.6-21.7 53.4-54.2 11.2-33.5 10.7-65.7 0-108.6zM286.2 404c11.1 0 20.1 9.1 20.1 20.3 0 11.3-9 20.4-20.1 20.4-11 0-20.1-9.2-20.1-20.4.1-11.3 9.1-20.3 20.1-20.3zM167.8 248.1h106.8c29.7 0 53.4-24.5 53.4-54.3V91.9c0-29-24.4-50.7-53.4-55.6-35.8-5.9-74.7-5.6-106.8.1-45.2 8-53.4 24.7-53.4 55.6v40.7h106.9v13.6h-147c-31.1 0-58.3 18.7-66.8 54.2-9.8 40.7-10.2 66.1 0 108.6 7.6 31.6 25.7 54.2 56.8 54.2H101v-48.8c0-35.3 30.5-66.4 66.8-66.4zm-6.7-142.6c-11.1 0-20.1-9.1-20.1-20.3.1-11.3 9-20.4 20.1-20.4 11 0 20.1 9.2 20.1 20.4s-9 20.3-20.1 20.3z"></path></svg>, Julia, Matlab, C++, ...
  - Forget excel! <svg viewBox="0 0 512 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M256 8C119.034 8 8 119.033 8 256s111.034 248 248 248 248-111.034 248-248S392.967 8 256 8zm130.108 117.892c65.448 65.448 70 165.481 20.677 235.637L150.47 105.216c70.204-49.356 170.226-44.735 235.638 20.676zM125.892 386.108c-65.448-65.448-70-165.481-20.677-235.637L361.53 406.784c-70.203 49.356-170.226 44.736-235.638-20.676z"></path></svg> <svg viewBox="0 0 384 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M369.9 97.9L286 14C277 5 264.8-.1 252.1-.1H48C21.5 0 0 21.5 0 48v416c0 26.5 21.5 48 48 48h288c26.5 0 48-21.5 48-48V131.9c0-12.7-5.1-25-14.1-34zM332.1 128H256V51.9l76.1 76.1zM48 464V48h160v104c0 13.3 10.7 24 24 24h104v288H48zm212-240h-28.8c-4.4 0-8.4 2.4-10.5 6.3-18 33.1-22.2 42.4-28.6 57.7-13.9-29.1-6.9-17.3-28.6-57.7-2.1-3.9-6.2-6.3-10.6-6.3H124c-9.3 0-15 10-10.4 18l46.3 78-46.3 78c-4.7 8 1.1 18 10.4 18h28.9c4.4 0 8.4-2.4 10.5-6.3 21.7-40 23-45 28.6-57.7 14.9 30.2 5.9 15.9 28.6 57.7 2.1 3.9 6.2 6.3 10.6 6.3H260c9.3 0 15-10 10.4-18L224 320c.7-1.1 30.3-50.5 46.3-78 4.7-8-1.1-18-10.3-18z"></path></svg> .font60[as much as humanly possible]

---

# Markdown

![:custom_hr]()

## .font200[<svg viewBox="0 0 640 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M593.8 59.1H46.2C20.7 59.1 0 79.8 0 105.2v301.5c0 25.5 20.7 46.2 46.2 46.2h547.7c25.5 0 46.2-20.7 46.1-46.1V105.2c0-25.4-20.7-46.1-46.2-46.1zM338.5 360.6H277v-120l-61.5 76.9-61.5-76.9v120H92.3V151.4h61.5l61.5 76.9 61.5-76.9h61.5v209.2zm135.3 3.1L381.5 256H443V151.4h61.5V256H566z"></path></svg>]

---

# <svg viewBox="0 0 640 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M593.8 59.1H46.2C20.7 59.1 0 79.8 0 105.2v301.5c0 25.5 20.7 46.2 46.2 46.2h547.7c25.5 0 46.2-20.7 46.1-46.1V105.2c0-25.4-20.7-46.1-46.2-46.1zM338.5 360.6H277v-120l-61.5 76.9-61.5-76.9v120H92.3V151.4h61.5l61.5 76.9 61.5-76.9h61.5v209.2zm135.3 3.1L381.5 256H443V151.4h61.5V256H566z"></path></svg> Markdown

## The genesis

HTML markup is complex:

```html
<!DOCTYPE html>
<html>
    <body>
        <h1>Section header</h1>
        <p>Paragraph</p>
    </body>
</html>
```

---

# <svg viewBox="0 0 640 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M593.8 59.1H46.2C20.7 59.1 0 79.8 0 105.2v301.5c0 25.5 20.7 46.2 46.2 46.2h547.7c25.5 0 46.2-20.7 46.1-46.1V105.2c0-25.4-20.7-46.1-46.2-46.1zM338.5 360.6H277v-120l-61.5 76.9-61.5-76.9v120H92.3V151.4h61.5l61.5 76.9 61.5-76.9h61.5v209.2zm135.3 3.1L381.5 256H443V151.4h61.5V256H566z"></path></svg> Markdown

## The genesis

In comes markdown, a lightweight markup language:

> Markdown is a text-to-HTML conversion tool for web writers. Markdown allows you to write using an easy-to-read, easy-to-write plain text format, then convert it to structurally valid XHTML (or HTML).

> The overriding design goal for Markdown’s formatting syntax is to make it as readable as possible. .font90[[John Gruber, 2004](https://daringfireball.net/projects/markdown/)]

---

# <svg viewBox="0 0 640 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M593.8 59.1H46.2C20.7 59.1 0 79.8 0 105.2v301.5c0 25.5 20.7 46.2 46.2 46.2h547.7c25.5 0 46.2-20.7 46.1-46.1V105.2c0-25.4-20.7-46.1-46.2-46.1zM338.5 360.6H277v-120l-61.5 76.9-61.5-76.9v120H92.3V151.4h61.5l61.5 76.9 61.5-76.9h61.5v209.2zm135.3 3.1L381.5 256H443V151.4h61.5V256H566z"></path></svg> Markdown

## The genesis

```html
<!DOCTYPE html>
<html>
    <body>
        <h1>Section header</h1>
        <p>Paragraphe</p>
    </body>
</html>
```
]

Paragraph
```
]

---

# <svg viewBox="0 0 640 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M593.8 59.1H46.2C20.7 59.1 0 79.8 0 105.2v301.5c0 25.5 20.7 46.2 46.2 46.2h547.7c25.5 0 46.2-20.7 46.1-46.1V105.2c0-25.4-20.7-46.1-46.2-46.1zM338.5 360.6H277v-120l-61.5 76.9-61.5-76.9v120H92.3V151.4h61.5l61.5 76.9 61.5-76.9h61.5v209.2zm135.3 3.1L381.5 256H443V151.4h61.5V256H566z"></path></svg> Markdown

## Variants

- Original developers (John Gruber and Aaron Swartz) did not continue developing Markdown after its release in 2004

- Avid enthusiasts took care of that. The results: many variants.
  - [GitHub Flavored Markdown (GFM)](https://docs.github.com/en/github/writing-on-github)
  - [Kramdown](https://kramdown.gettalong.org/)
  - [Markdown Extra](https://michelf.ca/projects/php-markdown/extra/)
  - [Multi Markdow](https://github.com/fletcher/MultiMarkdown/wiki/MultiMarkdown-Syntax-Guide#math-support)
  - [Pandoc's Markdown](https://pandoc.org/MANUAL.html)

- [CommonMark](https://commonmark.org/) is addressing standardizing issues with Markdown.

---

# <svg viewBox="0 0 640 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M593.8 59.1H46.2C20.7 59.1 0 79.8 0 105.2v301.5c0 25.5 20.7 46.2 46.2 46.2h547.7c25.5 0 46.2-20.7 46.1-46.1V105.2c0-25.4-20.7-46.1-46.2-46.1zM338.5 360.6H277v-120l-61.5 76.9-61.5-76.9v120H92.3V151.4h61.5l61.5 76.9 61.5-76.9h61.5v209.2zm135.3 3.1L381.5 256H443V151.4h61.5V256H566z"></path></svg> Markdown

## Pandoc's Markdown

**Why?**

- <svg viewBox="0 0 581 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M581 226.6C581 119.1 450.9 32 290.5 32S0 119.1 0 226.6C0 322.4 103.3 402 239.4 418.1V480h99.1v-61.5c24.3-2.7 47.6-7.4 69.4-13.9L448 480h112l-67.4-113.7c54.5-35.4 88.4-84.9 88.4-139.7zm-466.8 14.5c0-73.5 98.9-133 220.8-133s211.9 40.7 211.9 133c0 50.1-26.5 85-70.3 106.4-2.4-1.6-4.7-2.9-6.4-3.7-10.2-5.2-27.8-10.5-27.8-10.5s86.6-6.4 86.6-92.7-90.6-87.9-90.6-87.9h-199V361c-74.1-21.5-125.2-67.1-125.2-119.9zm225.1 38.3v-55.6c57.8 0 87.8-6.8 87.8 27.3 0 36.5-38.2 28.3-87.8 28.3zm-.9 72.5H365c10.8 0 18.9 11.7 24 19.2-16.1 1.9-33 2.8-50.6 2.9v-22.1z"></path></svg> uses it through [R Markdown](https://rmarkdown.rstudio.com/lesson-8.html) .font60[much more on this later]

**What is Pandoc?**

> a universal document converter

> <svg viewBox="0 0 640 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M593.8 59.1H46.2C20.7 59.1 0 79.8 0 105.2v301.5c0 25.5 20.7 46.2 46.2 46.2h547.7c25.5 0 46.2-20.7 46.1-46.1V105.2c0-25.4-20.7-46.1-46.2-46.1zM338.5 360.6H277v-120l-61.5 76.9-61.5-76.9v120H92.3V151.4h61.5l61.5 76.9 61.5-76.9h61.5v209.2zm135.3 3.1L381.5 256H443V151.4h61.5V256H566z"></path></svg> <svg viewBox="0 0 448 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M190.5 66.9l22.2-22.2c9.4-9.4 24.6-9.4 33.9 0L441 239c9.4 9.4 9.4 24.6 0 33.9L246.6 467.3c-9.4 9.4-24.6 9.4-33.9 0l-22.2-22.2c-9.5-9.5-9.3-25 .4-34.3L311.4 296H24c-13.3 0-24-10.7-24-24v-32c0-13.3 10.7-24 24-24h287.4L190.9 101.2c-9.8-9.3-10-24.8-.4-34.3z"></path></svg> <i>LaTeX</i> <svg viewBox="0 0 448 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M190.5 66.9l22.2-22.2c9.4-9.4 24.6-9.4 33.9 0L441 239c9.4 9.4 9.4 24.6 0 33.9L246.6 467.3c-9.4 9.4-24.6 9.4-33.9 0l-22.2-22.2c-9.5-9.5-9.3-25 .4-34.3L311.4 296H24c-13.3 0-24-10.7-24-24v-32c0-13.3 10.7-24 24-24h287.4L190.9 101.2c-9.8-9.3-10-24.8-.4-34.3z"></path></svg> <svg viewBox="0 0 384 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M369.9 97.9L286 14C277 5 264.8-.1 252.1-.1H48C21.5 0 0 21.5 0 48v416c0 26.5 21.5 48 48 48h288c26.5 0 48-21.5 48-48V131.9c0-12.7-5.1-25-14.1-34zM332.1 128H256V51.9l76.1 76.1zM48 464V48h160v104c0 13.3 10.7 24 24 24h104v288H48zm250.2-143.7c-12.2-12-47-8.7-64.4-6.5-17.2-10.5-28.7-25-36.8-46.3 3.9-16.1 10.1-40.6 5.4-56-4.2-26.2-37.8-23.6-42.6-5.9-4.4 16.1-.4 38.5 7 67.1-10 23.9-24.9 56-35.4 74.4-20 10.3-47 26.2-51 46.2-3.3 15.8 26 55.2 76.1-31.2 22.4-7.4 46.8-16.5 68.4-20.1 18.9 10.2 41 17 55.8 17 25.5 0 28-28.2 17.5-38.7zm-198.1 77.8c5.1-13.7 24.5-29.5 30.4-35-19 30.3-30.4 35.7-30.4 35zm81.6-190.6c7.4 0 6.7 32.1 1.8 40.8-4.4-13.9-4.3-40.8-1.8-40.8zm-24.4 136.6c9.7-16.9 18-37 24.7-54.7 8.3 15.1 18.9 27.2 30.1 35.5-20.8 4.3-38.9 13.1-54.8 19.2zm131.6-5s-5 6-37.3-7.8c35.1-2.6 40.9 5.4 37.3 7.8z"></path></svg>
<br/>
> <svg viewBox="0 0 640 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M593.8 59.1H46.2C20.7 59.1 0 79.8 0 105.2v301.5c0 25.5 20.7 46.2 46.2 46.2h547.7c25.5 0 46.2-20.7 46.1-46.1V105.2c0-25.4-20.7-46.1-46.2-46.1zM338.5 360.6H277v-120l-61.5 76.9-61.5-76.9v120H92.3V151.4h61.5l61.5 76.9 61.5-76.9h61.5v209.2zm135.3 3.1L381.5 256H443V151.4h61.5V256H566z"></path></svg> <svg viewBox="0 0 448 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M190.5 66.9l22.2-22.2c9.4-9.4 24.6-9.4 33.9 0L441 239c9.4 9.4 9.4 24.6 0 33.9L246.6 467.3c-9.4 9.4-24.6 9.4-33.9 0l-22.2-22.2c-9.5-9.5-9.3-25 .4-34.3L311.4 296H24c-13.3 0-24-10.7-24-24v-32c0-13.3 10.7-24 24-24h287.4L190.9 101.2c-9.8-9.3-10-24.8-.4-34.3z"></path></svg> <svg viewBox="0 0 384 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M369.9 97.9L286 14C277 5 264.8-.1 252.1-.1H48C21.5 0 0 21.5 0 48v416c0 26.5 21.5 48 48 48h288c26.5 0 48-21.5 48-48V131.9c0-12.7-5.1-25-14.1-34zM332.1 128H256V51.9l76.1 76.1zM48 464V48h160v104c0 13.3 10.7 24 24 24h104v288H48zm220.1-208c-5.7 0-10.6 4-11.7 9.5-20.6 97.7-20.4 95.4-21 103.5-.2-1.2-.4-2.6-.7-4.3-.8-5.1.3.2-23.6-99.5-1.3-5.4-6.1-9.2-11.7-9.2h-13.3c-5.5 0-10.3 3.8-11.7 9.1-24.4 99-24 96.2-24.8 103.7-.1-1.1-.2-2.5-.5-4.2-.7-5.2-14.1-73.3-19.1-99-1.1-5.6-6-9.7-11.8-9.7h-16.8c-7.8 0-13.5 7.3-11.7 14.8 8 32.6 26.7 109.5 33.2 136 1.3 5.4 6.1 9.1 11.7 9.1h25.2c5.5 0 10.3-3.7 11.6-9.1l17.9-71.4c1.5-6.2 2.5-12 3-17.3l2.9 17.3c.1.4 12.6 50.5 17.9 71.4 1.3 5.3 6.1 9.1 11.6 9.1h24.7c5.5 0 10.3-3.7 11.6-9.1 20.8-81.9 30.2-119 34.5-136 1.9-7.6-3.8-14.9-11.6-14.9h-15.8z"></path></svg>
<br/>
> <svg viewBox="0 0 384 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M0 32l34.9 395.8L191.5 480l157.6-52.2L384 32H0zm308.2 127.9H124.4l4.1 49.4h175.6l-13.6 148.4-97.9 27v.3h-1.1l-98.7-27.3-6-75.8h47.7L138 320l53.5 14.5 53.7-14.5 6-62.2H84.3L71.5 112.2h241.1l-4.4 47.7z"></path></svg> <svg viewBox="0 0 448 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M190.5 66.9l22.2-22.2c9.4-9.4 24.6-9.4 33.9 0L441 239c9.4 9.4 9.4 24.6 0 33.9L246.6 467.3c-9.4 9.4-24.6 9.4-33.9 0l-22.2-22.2c-9.5-9.5-9.3-25 .4-34.3L311.4 296H24c-13.3 0-24-10.7-24-24v-32c0-13.3 10.7-24 24-24h287.4L190.9 101.2c-9.8-9.3-10-24.8-.4-34.3z"></path></svg> <svg viewBox="0 0 640 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M593.8 59.1H46.2C20.7 59.1 0 79.8 0 105.2v301.5c0 25.5 20.7 46.2 46.2 46.2h547.7c25.5 0 46.2-20.7 46.1-46.1V105.2c0-25.4-20.7-46.1-46.2-46.1zM338.5 360.6H277v-120l-61.5 76.9-61.5-76.9v120H92.3V151.4h61.5l61.5 76.9 61.5-76.9h61.5v209.2zm135.3 3.1L381.5 256H443V151.4h61.5V256H566z"></path></svg>
<br/>
> **...**

---

# .font200[<svg viewBox="0 0 581 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M581 226.6C581 119.1 450.9 32 290.5 32S0 119.1 0 226.6C0 322.4 103.3 402 239.4 418.1V480h99.1v-61.5c24.3-2.7 47.6-7.4 69.4-13.9L448 480h112l-67.4-113.7c54.5-35.4 88.4-84.9 88.4-139.7zm-466.8 14.5c0-73.5 98.9-133 220.8-133s211.9 40.7 211.9 133c0 50.1-26.5 85-70.3 106.4-2.4-1.6-4.7-2.9-6.4-3.7-10.2-5.2-27.8-10.5-27.8-10.5s86.6-6.4 86.6-92.7-90.6-87.9-90.6-87.9h-199V361c-74.1-21.5-125.2-67.1-125.2-119.9zm225.1 38.3v-55.6c57.8 0 87.8-6.8 87.8 27.3 0 36.5-38.2 28.3-87.8 28.3zm-.9 72.5H365c10.8 0 18.9 11.7 24 19.2-16.1 1.9-33 2.8-50.6 2.9v-22.1z"></path></svg>]

![:custom_hr]()

---

# <img src="img/knitr.png" style="vertical-align: middle;margin:10px" width="50px"></img> knitr

[`knitr`](https://cran.r-project.org/package=knitr) .font90[01/2012 (0.1) &nbsp; // &nbsp; 01/2021 (1.3.1)]

> Elegant, flexible, and fast dynamic report generation with R .font80[([Yihui Xie, creator](https://yihui.org/knitr/))]

- `knitr` executes code embedded in a dynamic document and "knits" it back into the document.

---

# <img src="img/rmarkdown.png" style="vertical-align: middle;margin:10px" width="50px"></img> R Markdown

[`rmarkdown`](https://cran.r-project.org/package=rmarkdown) .font90[09/2014 (0.3.3) &nbsp; // &nbsp; 02/2021 (2.7)]

> Convert R Markdown documents into a variety of formats.

---

# Questions?

![:custom_hr]()

---

# <img src="img/rmarkdown.png" style="vertical-align: middle;margin:10px" width="50px"></img> Basic anatomy

![:custom_hr]()

## .font160[**YAML** + <svg viewBox="0 0 640 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M593.8 59.1H46.2C20.7 59.1 0 79.8 0 105.2v301.5c0 25.5 20.7 46.2 46.2 46.2h547.7c25.5 0 46.2-20.7 46.1-46.1V105.2c0-25.4-20.7-46.1-46.2-46.1zM338.5 360.6H277v-120l-61.5 76.9-61.5-76.9v120H92.3V151.4h61.5l61.5 76.9 61.5-76.9h61.5v209.2zm135.3 3.1L381.5 256H443V151.4h61.5V256H566z"></path></svg> + <svg viewBox="0 0 581 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M581 226.6C581 119.1 450.9 32 290.5 32S0 119.1 0 226.6C0 322.4 103.3 402 239.4 418.1V480h99.1v-61.5c24.3-2.7 47.6-7.4 69.4-13.9L448 480h112l-67.4-113.7c54.5-35.4 88.4-84.9 88.4-139.7zm-466.8 14.5c0-73.5 98.9-133 220.8-133s211.9 40.7 211.9 133c0 50.1-26.5 85-70.3 106.4-2.4-1.6-4.7-2.9-6.4-3.7-10.2-5.2-27.8-10.5-27.8-10.5s86.6-6.4 86.6-92.7-90.6-87.9-90.6-87.9h-199V361c-74.1-21.5-125.2-67.1-125.2-119.9zm225.1 38.3v-55.6c57.8 0 87.8-6.8 87.8 27.3 0 36.5-38.2 28.3-87.8 28.3zm-.9 72.5H365c10.8 0 18.9 11.7 24 19.2-16.1 1.9-33 2.8-50.6 2.9v-22.1z"></path></svg>]

---

# <img src="img/rmarkdown.png" style="vertical-align: middle;margin:10px" width="50px"></img> Basic anatomy

## R Markdown file

.pull-left[
- A <svg viewBox="0 0 640 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M593.8 59.1H46.2C20.7 59.1 0 79.8 0 105.2v301.5c0 25.5 20.7 46.2 46.2 46.2h547.7c25.5 0 46.2-20.7 46.1-46.1V105.2c0-25.4-20.7-46.1-46.2-46.1zM338.5 360.6H277v-120l-61.5 76.9-61.5-76.9v120H92.3V151.4h61.5l61.5 76.9 61.5-76.9h61.5v209.2zm135.3 3.1L381.5 256H443V151.4h61.5V256H566z"></path></svg> file written with (<svg viewBox="0 0 581 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M581 226.6C581 119.1 450.9 32 290.5 32S0 119.1 0 226.6C0 322.4 103.3 402 239.4 418.1V480h99.1v-61.5c24.3-2.7 47.6-7.4 69.4-13.9L448 480h112l-67.4-113.7c54.5-35.4 88.4-84.9 88.4-139.7zm-466.8 14.5c0-73.5 98.9-133 220.8-133s211.9 40.7 211.9 133c0 50.1-26.5 85-70.3 106.4-2.4-1.6-4.7-2.9-6.4-3.7-10.2-5.2-27.8-10.5-27.8-10.5s86.6-6.4 86.6-92.7-90.6-87.9-90.6-87.9h-199V361c-74.1-21.5-125.2-67.1-125.2-119.9zm225.1 38.3v-55.6c57.8 0 87.8-6.8 87.8 27.3 0 36.5-38.2 28.3-87.8 28.3zm-.9 72.5H365c10.8 0 18.9 11.7 24 19.2-16.1 1.9-33 2.8-50.6 2.9v-22.1z"></path></svg>) has the extension `.Rmd` (capital optional)

- Structured in three parts:
  - .font80[**YAML**]: Metadata / front matter
  - <svg viewBox="0 0 640 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M593.8 59.1H46.2C20.7 59.1 0 79.8 0 105.2v301.5c0 25.5 20.7 46.2 46.2 46.2h547.7c25.5 0 46.2-20.7 46.1-46.1V105.2c0-25.4-20.7-46.1-46.2-46.1zM338.5 360.6H277v-120l-61.5 76.9-61.5-76.9v120H92.3V151.4h61.5l61.5 76.9 61.5-76.9h61.5v209.2zm135.3 3.1L381.5 256H443V151.4h61.5V256H566z"></path></svg>: Text / document content
  - <svg viewBox="0 0 581 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M581 226.6C581 119.1 450.9 32 290.5 32S0 119.1 0 226.6C0 322.4 103.3 402 239.4 418.1V480h99.1v-61.5c24.3-2.7 47.6-7.4 69.4-13.9L448 480h112l-67.4-113.7c54.5-35.4 88.4-84.9 88.4-139.7zm-466.8 14.5c0-73.5 98.9-133 220.8-133s211.9 40.7 211.9 133c0 50.1-26.5 85-70.3 106.4-2.4-1.6-4.7-2.9-6.4-3.7-10.2-5.2-27.8-10.5-27.8-10.5s86.6-6.4 86.6-92.7-90.6-87.9-90.6-87.9h-199V361c-74.1-21.5-125.2-67.1-125.2-119.9zm225.1 38.3v-55.6c57.8 0 87.8-6.8 87.8 27.3 0 36.5-38.2 28.3-87.8 28.3zm-.9 72.5H365c10.8 0 18.9 11.7 24 19.2-16.1 1.9-33 2.8-50.6 2.9v-22.1z"></path></svg>: Code chunks .font70[(optional)]
]

---

# <img src="img/rmarkdown.png" style="vertical-align: middle;margin:10px" width="50px"></img> Basic anatomy

## Exporting .font80[*a.k.a.* knitting 🧶]

.pull-left[
- `knitr` executes the code and converts `.Rmd` to `.md`
- Pandoc renders the `.md` file to the output format you want.
]

---

# <img src="img/rmarkdown.png" style="vertical-align: middle;margin:10px" width="50px"></img> Basic anatomy

## Exporting .font80[*a.k.a.* knitting 🧶]

### `rmarkdown::render()`

- Use [`render()`](https://www.rdocumentation.org/packages/rmarkdown/versions/2.6/topics/render) from the [`rmarkdown`](https://cran.r-project.org/package=rmarkdown) package
- Generates the desired output from the `.Rmd` file

Main arguments:

```md
input: name of file to render
output_format: one or more output formats, as specified in the YAML header.
               "all" exports all the specified formats (optional).
output_file: name of output file (optional).
```

Minimal example:

```r
rmarkdown::render(input = "myrmd.Rmd")
```

---

# Metadata

![:custom_hr]()

## .font160[**YAML**]

---

# .font60[**YAML**] Metadata

- Contains the metadata of the document
- Starts and ends with three hyphens (---)
- Comes first in the `.Rmd` file
- Sets *Pandoc* document options with `key: value` (.font60[**YAML**] syntax)
- Available options depend on the output format .font90[(see `?html_document `, `?pdf_document`, `?word_document`)]

<br/>

Minimal .font60[**YAML**] metadata for <svg viewBox="0 0 384 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M369.9 97.9L286 14C277 5 264.8-.1 252.1-.1H48C21.5 0 0 21.5 0 48v416c0 26.5 21.5 48 48 48h288c26.5 0 48-21.5 48-48V131.9c0-12.7-5.1-25-14.1-34zM332.1 128H256V51.9l76.1 76.1zM48 464V48h160v104c0 13.3 10.7 24 24 24h104v288H48zm250.2-143.7c-12.2-12-47-8.7-64.4-6.5-17.2-10.5-28.7-25-36.8-46.3 3.9-16.1 10.1-40.6 5.4-56-4.2-26.2-37.8-23.6-42.6-5.9-4.4 16.1-.4 38.5 7 67.1-10 23.9-24.9 56-35.4 74.4-20 10.3-47 26.2-51 46.2-3.3 15.8 26 55.2 76.1-31.2 22.4-7.4 46.8-16.5 68.4-20.1 18.9 10.2 41 17 55.8 17 25.5 0 28-28.2 17.5-38.7zm-198.1 77.8c5.1-13.7 24.5-29.5 30.4-35-19 30.3-30.4 35.7-30.4 35zm81.6-190.6c7.4 0 6.7 32.1 1.8 40.8-4.4-13.9-4.3-40.8-1.8-40.8zm-24.4 136.6c9.7-16.9 18-37 24.7-54.7 8.3 15.1 18.9 27.2 30.1 35.5-20.8 4.3-38.9 13.1-54.8 19.2zm131.6-5s-5 6-37.3-7.8c35.1-2.6 40.9 5.4 37.3 7.8z"></path></svg> PDF output:

```yaml
---
output: pdf_document
---
```

---

# .font60[**YAML**] Metadata

## Document information

Title, author and date options

```yaml
---
title: "My document title"
date: "01-03-2021"
author: Me, you, them
output: pdf_document
---
```

---

# .font60[**YAML**] Metadata

## Document options: table of content

- To include a table of contents, use `toc: true`
- To specify the depth of the table of contents, use `toc_depth = depth`

```yaml
---
title: "My document title"
date: "01-03-2021"
author: Me, you, them
output:
  pdf_document:
    toc: true
    toc_depth: 2
---
```

.font90[
<svg viewBox="0 0 576 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M569.517 440.013C587.975 472.007 564.806 512 527.94 512H48.054c-36.937 0-59.999-40.055-41.577-71.987L246.423 23.985c18.467-32.009 64.72-31.951 83.154 0l239.94 416.028zM288 354c-25.405 0-46 20.595-46 46s20.595 46 46 46 46-20.595 46-46-20.595-46-46-46zm-43.673-165.346l7.418 136c.347 6.364 5.609 11.346 11.982 11.346h48.546c6.373 0 11.635-4.982 11.982-11.346l7.418-136c.375-6.874-5.098-12.654-11.982-12.654h-63.383c-6.884 0-12.356 5.78-11.981 12.654z"></path></svg> Be sure to respect indentation, either 2 spaces or tabulations
]

---

# .font60[**YAML**] Metadata

## Document options: section numbers

- To include numbered sections, use `number_sections: true`

```yaml
---
title: "My document title"
date: "01-03-2021"
author: Me, you, them
output:
  pdf_document:
    toc: true
    toc_depth: 2
    number_sections: true
---
```

.font90[
<svg viewBox="0 0 576 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M569.517 440.013C587.975 472.007 564.806 512 527.94 512H48.054c-36.937 0-59.999-40.055-41.577-71.987L246.423 23.985c18.467-32.009 64.72-31.951 83.154 0l239.94 416.028zM288 354c-25.405 0-46 20.595-46 46s20.595 46 46 46 46-20.595 46-46-20.595-46-46-46zm-43.673-165.346l7.418 136c.347 6.364 5.609 11.346 11.982 11.346h48.546c6.373 0 11.635-4.982 11.982-11.346l7.418-136c.375-6.874-5.098-12.654-11.982-12.654h-63.383c-6.884 0-12.356 5.78-11.981 12.654z"></path></svg> To avoid numbering a section, use `{-}` at the end of the section title

```md
# Section title {-}
```
]

---

# .font60[**YAML**] Metadata

## Document options: figures options

- To specify default figure size, use `fig_width: size` and `fig_height = size`
- To include figure captions, use `fig_caption: true`

```yaml
---
title: "My document title"
date: "01-03-2021"
author: Me, you, them
output:
  pdf_document:
    toc: true
    toc_depth: 2
    number_sections: true
    fig_width: 6
    fig_height: 6
    fig_caption: true
---
```

---

# .font60[**YAML**] Metadata

## Document options: additional options

- There is a wide variety of [.font60[**YAML**] options](https://rstudio.com/wp-content/uploads/2016/03/rmarkdown-cheatsheet-2.0.pdf) available

.font90[
```yaml
---
title: "My document title"
date: "01-03-2021"
author: Me, you, them
abstract: "The objective of our work was to ..."
fontfamily: fourier
linestretch: 1
fontsize: 10pt
geometry: margin=1in
urlcolor: red
citecolor: blue
output:
  pdf_document:
    toc: true
  html_document:
    toc: true
  word_document:
    toc: true
---
```
]

---

# Questions?

![:custom_hr]()

---

# Text

![:custom_hr]()

## .font160[<svg viewBox="0 0 640 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M593.8 59.1H46.2C20.7 59.1 0 79.8 0 105.2v301.5c0 25.5 20.7 46.2 46.2 46.2h547.7c25.5 0 46.2-20.7 46.1-46.1V105.2c0-25.4-20.7-46.1-46.2-46.1zM338.5 360.6H277v-120l-61.5 76.9-61.5-76.9v120H92.3V151.4h61.5l61.5 76.9 61.5-76.9h61.5v209.2zm135.3 3.1L381.5 256H443V151.4h61.5V256H566z"></path></svg>]

---

# <svg viewBox="0 0 640 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M593.8 59.1H46.2C20.7 59.1 0 79.8 0 105.2v301.5c0 25.5 20.7 46.2 46.2 46.2h547.7c25.5 0 46.2-20.7 46.1-46.1V105.2c0-25.4-20.7-46.1-46.2-46.1zM338.5 360.6H277v-120l-61.5 76.9-61.5-76.9v120H92.3V151.4h61.5l61.5 76.9 61.5-76.9h61.5v209.2zm135.3 3.1L381.5 256H443V151.4h61.5V256H566z"></path></svg> Text formatting

---

# <svg viewBox="0 0 640 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M593.8 59.1H46.2C20.7 59.1 0 79.8 0 105.2v301.5c0 25.5 20.7 46.2 46.2 46.2h547.7c25.5 0 46.2-20.7 46.1-46.1V105.2c0-25.4-20.7-46.1-46.2-46.1zM338.5 360.6H277v-120l-61.5 76.9-61.5-76.9v120H92.3V151.4h61.5l61.5 76.9 61.5-76.9h61.5v209.2zm135.3 3.1L381.5 256H443V151.4h61.5V256H566z"></path></svg> Document formatting

## Titles

.pull-left[
.font80[
```md
# Header 1
## Header 2
### Header 3
#### Header 4
##### Header 5
###### Header 6
```
]
]

.pull-right[
.font80[
# Header 1
## Header 2
### Header 3
#### Header 4
##### Header 5
###### Header 6
]
]

---

# <svg viewBox="0 0 640 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M593.8 59.1H46.2C20.7 59.1 0 79.8 0 105.2v301.5c0 25.5 20.7 46.2 46.2 46.2h547.7c25.5 0 46.2-20.7 46.1-46.1V105.2c0-25.4-20.7-46.1-46.2-46.1zM338.5 360.6H277v-120l-61.5 76.9-61.5-76.9v120H92.3V151.4h61.5l61.5 76.9 61.5-76.9h61.5v209.2zm135.3 3.1L381.5 256H443V151.4h61.5V256H566z"></path></svg> Document formatting

## Paragraph

a paragraph
```
]
]

a paragraph
]
]

---

# <svg viewBox="0 0 640 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M593.8 59.1H46.2C20.7 59.1 0 79.8 0 105.2v301.5c0 25.5 20.7 46.2 46.2 46.2h547.7c25.5 0 46.2-20.7 46.1-46.1V105.2c0-25.4-20.7-46.1-46.2-46.1zM338.5 360.6H277v-120l-61.5 76.9-61.5-76.9v120H92.3V151.4h61.5l61.5 76.9 61.5-76.9h61.5v209.2zm135.3 3.1L381.5 256H443V151.4h61.5V256H566z"></path></svg> Document formatting

## Lists

.font80[You must include an empty line between the beginning of the list and the preceding paragraph]

- Element 1
- Element 2
- Element 3
- Element 4
```
]
]

- Element 1
- Element 2
- Element 3
- Element 4]
]

---

# <svg viewBox="0 0 640 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M593.8 59.1H46.2C20.7 59.1 0 79.8 0 105.2v301.5c0 25.5 20.7 46.2 46.2 46.2h547.7c25.5 0 46.2-20.7 46.1-46.1V105.2c0-25.4-20.7-46.1-46.2-46.1zM338.5 360.6H277v-120l-61.5 76.9-61.5-76.9v120H92.3V151.4h61.5l61.5 76.9 61.5-76.9h61.5v209.2zm135.3 3.1L381.5 256H443V151.4h61.5V256H566z"></path></svg> Document formatting

## Numbered lists

.font80[No matter the order, <svg viewBox="0 0 640 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M593.8 59.1H46.2C20.7 59.1 0 79.8 0 105.2v301.5c0 25.5 20.7 46.2 46.2 46.2h547.7c25.5 0 46.2-20.7 46.1-46.1V105.2c0-25.4-20.7-46.1-46.2-46.1zM338.5 360.6H277v-120l-61.5 76.9-61.5-76.9v120H92.3V151.4h61.5l61.5 76.9 61.5-76.9h61.5v209.2zm135.3 3.1L381.5 256H443V151.4h61.5V256H566z"></path></svg> automatically adjusts the list numbers.]

1. Element 1
2. Element 2
6. Element 3
7. Element 4
```
]
]

1. Element 1
2. Element 2
6. Element 3
7. Element 4
]
]

---

# <svg viewBox="0 0 640 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M593.8 59.1H46.2C20.7 59.1 0 79.8 0 105.2v301.5c0 25.5 20.7 46.2 46.2 46.2h547.7c25.5 0 46.2-20.7 46.1-46.1V105.2c0-25.4-20.7-46.1-46.2-46.1zM338.5 360.6H277v-120l-61.5 76.9-61.5-76.9v120H92.3V151.4h61.5l61.5 76.9 61.5-76.9h61.5v209.2zm135.3 3.1L381.5 256H443V151.4h61.5V256H566z"></path></svg> Document formatting

## List indentations

1. Element 1
  - Element 1.1
  - Element 1.2
7. Element 2
  8. Element 2.1
  9. Element 2.2
```
]
]

1. Element 1
  - Element 1.1
  - Element 1.2
7. Element 2
  8. Element 2.1
  9. Element 2.2
]
]

---

# <svg viewBox="0 0 640 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M593.8 59.1H46.2C20.7 59.1 0 79.8 0 105.2v301.5c0 25.5 20.7 46.2 46.2 46.2h547.7c25.5 0 46.2-20.7 46.1-46.1V105.2c0-25.4-20.7-46.1-46.2-46.1zM338.5 360.6H277v-120l-61.5 76.9-61.5-76.9v120H92.3V151.4h61.5l61.5 76.9 61.5-76.9h61.5v209.2zm135.3 3.1L381.5 256H443V151.4h61.5V256H566z"></path></svg> Document formatting

## New numbered lists

.font80[To start a new numbered list (*i.e.* reinitialize numbers), use the tag `` with an empty line before and afterthe tag]

1. Element 1
2. Element 2

6. Element 3
7. Element 4
```
]
]

1. Element 1
2. Element 2

6. Element 3
7. Element 4
]
]

---

# <svg viewBox="0 0 640 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M593.8 59.1H46.2C20.7 59.1 0 79.8 0 105.2v301.5c0 25.5 20.7 46.2 46.2 46.2h547.7c25.5 0 46.2-20.7 46.1-46.1V105.2c0-25.4-20.7-46.1-46.2-46.1zM338.5 360.6H277v-120l-61.5 76.9-61.5-76.9v120H92.3V151.4h61.5l61.5 76.9 61.5-76.9h61.5v209.2zm135.3 3.1L381.5 256H443V151.4h61.5V256H566z"></path></svg> Citations

To add citations, use the `>` before the text

```md
> This is a citation

>> This is also a citation
```

> This is a citation

>> This is also a citation

---

# <svg viewBox="0 0 640 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M593.8 59.1H46.2C20.7 59.1 0 79.8 0 105.2v301.5c0 25.5 20.7 46.2 46.2 46.2h547.7c25.5 0 46.2-20.7 46.1-46.1V105.2c0-25.4-20.7-46.1-46.2-46.1zM338.5 360.6H277v-120l-61.5 76.9-61.5-76.9v120H92.3V151.4h61.5l61.5 76.9 61.5-76.9h61.5v209.2zm135.3 3.1L381.5 256H443V151.4h61.5V256H566z"></path></svg> Footnotes

To add footnotes, use:

1. The tag `[^footnote]` in the text
2. Description of the footnote anywhere later in the text

```md
Ecosystem-based management[^ebm] seeks to address systemic management, monitoring and assessment issues for the environment

...

[^ebm]: See Christensen *et al.* 1996 for a detailed description of ecosystem-based management
```

Ecosystem-based management[^ebm] seeks to address systemic management, monitoring and assessment issues for the environment

...

---

# <svg viewBox="0 0 640 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M593.8 59.1H46.2C20.7 59.1 0 79.8 0 105.2v301.5c0 25.5 20.7 46.2 46.2 46.2h547.7c25.5 0 46.2-20.7 46.1-46.1V105.2c0-25.4-20.7-46.1-46.2-46.1zM338.5 360.6H277v-120l-61.5 76.9-61.5-76.9v120H92.3V151.4h61.5l61.5 76.9 61.5-76.9h61.5v209.2zm135.3 3.1L381.5 256H443V151.4h61.5V256H566z"></path></svg> Images

To insert a figure, use: `![](path_to_figure)`

```md
![inSileco](img/logo.png)
```

.pull-left[
<figure>
  <img title="inSileco" src="img/logo.png" width="140px"></img>
  <figcaption>inSileco</figcaption>
</figure>
]

it is not possible to specify dimensions of figures using <svg viewBox="0 0 640 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M593.8 59.1H46.2C20.7 59.1 0 79.8 0 105.2v301.5c0 25.5 20.7 46.2 46.2 46.2h547.7c25.5 0 46.2-20.7 46.1-46.1V105.2c0-25.4-20.7-46.1-46.2-46.1zM338.5 360.6H277v-120l-61.5 76.9-61.5-76.9v120H92.3V151.4h61.5l61.5 76.9 61.5-76.9h61.5v209.2zm135.3 3.1L381.5 256H443V151.4h61.5V256H566z"></path></svg>

**Solutions**:

- [`html`](https://www.w3schools.com/tags/att_img_width.asp) syntax for <svg viewBox="0 0 384 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M0 32l34.9 395.8L191.5 480l157.6-52.2L384 32H0zm308.2 127.9H124.4l4.1 49.4h175.6l-13.6 148.4-97.9 27v.3h-1.1l-98.7-27.3-6-75.8h47.7L138 320l53.5 14.5 53.7-14.5 6-62.2H84.3L71.5 112.2h241.1l-4.4 47.7z"></path></svg>
- [`latex`](https://www.overleaf.com/learn/latex/Inserting_Images) syntax for <svg viewBox="0 0 384 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M369.9 97.9L286 14C277 5 264.8-.1 252.1-.1H48C21.5 0 0 21.5 0 48v416c0 26.5 21.5 48 48 48h288c26.5 0 48-21.5 48-48V131.9c0-12.7-5.1-25-14.1-34zM332.1 128H256V51.9l76.1 76.1zM48 464V48h160v104c0 13.3 10.7 24 24 24h104v288H48zm250.2-143.7c-12.2-12-47-8.7-64.4-6.5-17.2-10.5-28.7-25-36.8-46.3 3.9-16.1 10.1-40.6 5.4-56-4.2-26.2-37.8-23.6-42.6-5.9-4.4 16.1-.4 38.5 7 67.1-10 23.9-24.9 56-35.4 74.4-20 10.3-47 26.2-51 46.2-3.3 15.8 26 55.2 76.1-31.2 22.4-7.4 46.8-16.5 68.4-20.1 18.9 10.2 41 17 55.8 17 25.5 0 28-28.2 17.5-38.7zm-198.1 77.8c5.1-13.7 24.5-29.5 30.4-35-19 30.3-30.4 35.7-30.4 35zm81.6-190.6c7.4 0 6.7 32.1 1.8 40.8-4.4-13.9-4.3-40.8-1.8-40.8zm-24.4 136.6c9.7-16.9 18-37 24.7-54.7 8.3 15.1 18.9 27.2 30.1 35.5-20.8 4.3-38.9 13.1-54.8 19.2zm131.6-5s-5 6-37.3-7.8c35.1-2.6 40.9 5.4 37.3 7.8z"></path></svg>
- Use <svg viewBox="0 0 581 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M581 226.6C581 119.1 450.9 32 290.5 32S0 119.1 0 226.6C0 322.4 103.3 402 239.4 418.1V480h99.1v-61.5c24.3-2.7 47.6-7.4 69.4-13.9L448 480h112l-67.4-113.7c54.5-35.4 88.4-84.9 88.4-139.7zm-466.8 14.5c0-73.5 98.9-133 220.8-133s211.9 40.7 211.9 133c0 50.1-26.5 85-70.3 106.4-2.4-1.6-4.7-2.9-6.4-3.7-10.2-5.2-27.8-10.5-27.8-10.5s86.6-6.4 86.6-92.7-90.6-87.9-90.6-87.9h-199V361c-74.1-21.5-125.2-67.1-125.2-119.9zm225.1 38.3v-55.6c57.8 0 87.8-6.8 87.8 27.3 0 36.5-38.2 28.3-87.8 28.3zm-.9 72.5H365c10.8 0 18.9 11.7 24 19.2-16.1 1.9-33 2.8-50.6 2.9v-22.1z"></path></svg> to plot figure as matrix and set dimensions with code chunk options (more on this later)
]

---

# <svg viewBox="0 0 640 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M593.8 59.1H46.2C20.7 59.1 0 79.8 0 105.2v301.5c0 25.5 20.7 46.2 46.2 46.2h547.7c25.5 0 46.2-20.7 46.1-46.1V105.2c0-25.4-20.7-46.1-46.2-46.1zM338.5 360.6H277v-120l-61.5 76.9-61.5-76.9v120H92.3V151.4h61.5l61.5 76.9 61.5-76.9h61.5v209.2zm135.3 3.1L381.5 256H443V151.4h61.5V256H566z"></path></svg> Hyperlinks

## Text as hyperlink

To insert a hyperlink, use: `[text](url)`

```md
Click [here](https://rmarkdown.rstudio.com/) to visit the `rmarkdown` website
```

Click [here](https://rmarkdown.rstudio.com/) to visit the `rmarkdown` website

---

# <svg viewBox="0 0 640 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M593.8 59.1H46.2C20.7 59.1 0 79.8 0 105.2v301.5c0 25.5 20.7 46.2 46.2 46.2h547.7c25.5 0 46.2-20.7 46.1-46.1V105.2c0-25.4-20.7-46.1-46.2-46.1zM338.5 360.6H277v-120l-61.5 76.9-61.5-76.9v120H92.3V151.4h61.5l61.5 76.9 61.5-76.9h61.5v209.2zm135.3 3.1L381.5 256H443V151.4h61.5V256H566z"></path></svg> Hyperlinks

## External image

To insert an external image, use: `![](url_to_image)`

```md
![](https://media.giphy.com/media/MkGyW2cOH7uhO/giphy.gif)
```

![](https://media.giphy.com/media/MkGyW2cOH7uhO/giphy.gif)

.font90[
<svg viewBox="0 0 576 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M569.517 440.013C587.975 472.007 564.806 512 527.94 512H48.054c-36.937 0-59.999-40.055-41.577-71.987L246.423 23.985c18.467-32.009 64.72-31.951 83.154 0l239.94 416.028zM288 354c-25.405 0-46 20.595-46 46s20.595 46 46 46 46-20.595 46-46-20.595-46-46-46zm-43.673-165.346l7.418 136c.347 6.364 5.609 11.346 11.982 11.346h48.546c6.373 0 11.635-4.982 11.982-11.346l7.418-136c.375-6.874-5.098-12.654-11.982-12.654h-63.383c-6.884 0-12.356 5.78-11.981 12.654z"></path></svg> Beware that not all graphics can be loaded in a pdf and that images should be loaded locally for pdf documents.
]

---

# <svg viewBox="0 0 640 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M593.8 59.1H46.2C20.7 59.1 0 79.8 0 105.2v301.5c0 25.5 20.7 46.2 46.2 46.2h547.7c25.5 0 46.2-20.7 46.1-46.1V105.2c0-25.4-20.7-46.1-46.2-46.1zM338.5 360.6H277v-120l-61.5 76.9-61.5-76.9v120H92.3V151.4h61.5l61.5 76.9 61.5-76.9h61.5v209.2zm135.3 3.1L381.5 256H443V151.4h61.5V256H566z"></path></svg> Hyperlinks

## Image as hyperlink

To use an image as an external link, use: `[![](url_to_image)](url)`

.font70[
```md
[![](https://media.giphy.com/media/MkGyW2cOH7uhO/giphy.gif)](https://www.bloomberg.com/graphics/2020-us-election-results)
```
]

[![](https://media.giphy.com/media/MkGyW2cOH7uhO/giphy.gif)](https://www.bloomberg.com/graphics/2020-us-election-results)

---

# <svg viewBox="0 0 640 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M593.8 59.1H46.2C20.7 59.1 0 79.8 0 105.2v301.5c0 25.5 20.7 46.2 46.2 46.2h547.7c25.5 0 46.2-20.7 46.1-46.1V105.2c0-25.4-20.7-46.1-46.2-46.1zM338.5 360.6H277v-120l-61.5 76.9-61.5-76.9v120H92.3V151.4h61.5l61.5 76.9 61.5-76.9h61.5v209.2zm135.3 3.1L381.5 256H443V151.4h61.5V256H566z"></path></svg> Hyperlinks

## Link to section

To add a link to a text section:

- Add dentifier tag to section with `# Section {#tag}` (can be higher level sections).

```md
# Introduction {#intro}
```

- Refer to it in the text using `[text](tag)`

```md
This was discussed in the [introduction](#intro)
```

---

# <svg viewBox="0 0 640 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M593.8 59.1H46.2C20.7 59.1 0 79.8 0 105.2v301.5c0 25.5 20.7 46.2 46.2 46.2h547.7c25.5 0 46.2-20.7 46.1-46.1V105.2c0-25.4-20.7-46.1-46.2-46.1zM338.5 360.6H277v-120l-61.5 76.9-61.5-76.9v120H92.3V151.4h61.5l61.5 76.9 61.5-76.9h61.5v209.2zm135.3 3.1L381.5 256H443V151.4h61.5V256H566z"></path></svg> Tables

The simplest way to make tables in markdown:

- `|` seperates columns
- `-` identify headers
- `:` specifies text alignment

```md
| Left | Center | Right |
| :--- | :----: | ----: |
| 12   | 100    | 1     |
| 13   | 214    | 43    |
| 14   | 234    | 10    |
```
]

.pull-right[
| Left | Center | Right |
| :--- | :----: | ----: |
| 12   | 100    | 1     |
| 13   | 214    | 43    |
| 14   | 234    | 10    |
]

<br/>
.font90[For more options, you can create your tables directly using <svg viewBox="0 0 581 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M581 226.6C581 119.1 450.9 32 290.5 32S0 119.1 0 226.6C0 322.4 103.3 402 239.4 418.1V480h99.1v-61.5c24.3-2.7 47.6-7.4 69.4-13.9L448 480h112l-67.4-113.7c54.5-35.4 88.4-84.9 88.4-139.7zm-466.8 14.5c0-73.5 98.9-133 220.8-133s211.9 40.7 211.9 133c0 50.1-26.5 85-70.3 106.4-2.4-1.6-4.7-2.9-6.4-3.7-10.2-5.2-27.8-10.5-27.8-10.5s86.6-6.4 86.6-92.7-90.6-87.9-90.6-87.9h-199V361c-74.1-21.5-125.2-67.1-125.2-119.9zm225.1 38.3v-55.6c57.8 0 87.8-6.8 87.8 27.3 0 36.5-38.2 28.3-87.8 28.3zm-.9 72.5H365c10.8 0 18.9 11.7 24 19.2-16.1 1.9-33 2.8-50.6 2.9v-22.1z"></path></svg> and export them in a code chunk using the [`knitr::kable`](https://cran.r-project.org/package=knitr) function and [`kableExtra`](https://cran.r-project.org/package=kableExtra) package.

See this [website](https://cran.r-project.org/web/packages/kableExtra/vignettes/awesome_table_in_html.html) for more.]

---

# <svg viewBox="0 0 640 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M593.8 59.1H46.2C20.7 59.1 0 79.8 0 105.2v301.5c0 25.5 20.7 46.2 46.2 46.2h547.7c25.5 0 46.2-20.7 46.1-46.1V105.2c0-25.4-20.7-46.1-46.2-46.1zM338.5 360.6H277v-120l-61.5 76.9-61.5-76.9v120H92.3V151.4h61.5l61.5 76.9 61.5-76.9h61.5v209.2zm135.3 3.1L381.5 256H443V151.4h61.5V256H566z"></path></svg> Mathematical equations and symbols

Mathematical equations and symbols can be incorporated in the text using `$L^AT_EX$` [syntax](https://en.wikibooks.org/wiki/LaTeX/Mathematics) and `$` tags.

- Use single `$` for inline equations and symbols: `$math$`
- Use double `$$` for equation blocks: <code>$$equation block$$ </code>

$$E = mc^2$$,

where $E$ is energy, $m$ is mass,
and $c$ is the speed of light.
```
]

`$$E = mc^2$$`

where `$E$` is energy, `$m$` is mass,
and `$c$` is the speed of light.
]
]

---

# Questions?

![:custom_hr]()

---

#  <svg viewBox="0 0 640 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M278.9 511.5l-61-17.7c-6.4-1.8-10-8.5-8.2-14.9L346.2 8.7c1.8-6.4 8.5-10 14.9-8.2l61 17.7c6.4 1.8 10 8.5 8.2 14.9L293.8 503.3c-1.9 6.4-8.5 10.1-14.9 8.2zm-114-112.2l43.5-46.4c4.6-4.9 4.3-12.7-.8-17.2L117 256l90.6-79.7c5.1-4.5 5.5-12.3.8-17.2l-43.5-46.4c-4.5-4.8-12.1-5.1-17-.5L3.8 247.2c-5.1 4.7-5.1 12.8 0 17.5l144.1 135.1c4.9 4.6 12.5 4.4 17-.5zm327.2.6l144.1-135.1c5.1-4.7 5.1-12.8 0-17.5L492.1 112.1c-4.8-4.5-12.4-4.3-17 .5L431.6 159c-4.6 4.9-4.3 12.7.8 17.2L523 256l-90.6 79.7c-5.1 4.5-5.5 12.3-.8 17.2l43.5 46.4c4.5 4.9 12.1 5.1 17 .6z"></path></svg> Code chunks

## The <svg viewBox="0 0 581 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M581 226.6C581 119.1 450.9 32 290.5 32S0 119.1 0 226.6C0 322.4 103.3 402 239.4 418.1V480h99.1v-61.5c24.3-2.7 47.6-7.4 69.4-13.9L448 480h112l-67.4-113.7c54.5-35.4 88.4-84.9 88.4-139.7zm-466.8 14.5c0-73.5 98.9-133 220.8-133s211.9 40.7 211.9 133c0 50.1-26.5 85-70.3 106.4-2.4-1.6-4.7-2.9-6.4-3.7-10.2-5.2-27.8-10.5-27.8-10.5s86.6-6.4 86.6-92.7-90.6-87.9-90.6-87.9h-199V361c-74.1-21.5-125.2-67.1-125.2-119.9zm225.1 38.3v-55.6c57.8 0 87.8-6.8 87.8 27.3 0 36.5-38.2 28.3-87.8 28.3zm-.9 72.5H365c10.8 0 18.9 11.7 24 19.2-16.1 1.9-33 2.8-50.6 2.9v-22.1z"></path></svg>  part

---

# <svg viewBox="0 0 640 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M278.9 511.5l-61-17.7c-6.4-1.8-10-8.5-8.2-14.9L346.2 8.7c1.8-6.4 8.5-10 14.9-8.2l61 17.7c6.4 1.8 10 8.5 8.2 14.9L293.8 503.3c-1.9 6.4-8.5 10.1-14.9 8.2zm-114-112.2l43.5-46.4c4.6-4.9 4.3-12.7-.8-17.2L117 256l90.6-79.7c5.1-4.5 5.5-12.3.8-17.2l-43.5-46.4c-4.5-4.8-12.1-5.1-17-.5L3.8 247.2c-5.1 4.7-5.1 12.8 0 17.5l144.1 135.1c4.9 4.6 12.5 4.4 17-.5zm327.2.6l144.1-135.1c5.1-4.7 5.1-12.8 0-17.5L492.1 112.1c-4.8-4.5-12.4-4.3-17 .5L431.6 159c-4.6 4.9-4.3 12.7.8 17.2L523 256l-90.6 79.7c-5.1 4.5-5.5 12.3-.8 17.2l43.5 46.4c4.5 4.9 12.1 5.1 17 .6z"></path></svg> Code chunks

````md
This text is written in markdown

```{r}
library(tibble)
data(iris)
head(iris)
```
````

- <svg viewBox="0 0 576 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M569.517 440.013C587.975 472.007 564.806 512 527.94 512H48.054c-36.937 0-59.999-40.055-41.577-71.987L246.423 23.985c18.467-32.009 64.72-31.951 83.154 0l239.94 416.028zM288 354c-25.405 0-46 20.595-46 46s20.595 46 46 46 46-20.595 46-46-20.595-46-46-46zm-43.673-165.346l7.418 136c.347 6.364 5.609 11.346 11.982 11.346h48.546c6.373 0 11.635-4.982 11.982-11.346l7.418-136c.375-6.874-5.098-12.654-11.982-12.654h-63.383c-6.884 0-12.356 5.78-11.981 12.654z"></path></svg> `r` between brackets `{}`, why is that?
- Where is the <svg viewBox="0 0 581 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M581 226.6C581 119.1 450.9 32 290.5 32S0 119.1 0 226.6C0 322.4 103.3 402 239.4 418.1V480h99.1v-61.5c24.3-2.7 47.6-7.4 69.4-13.9L448 480h112l-67.4-113.7c54.5-35.4 88.4-84.9 88.4-139.7zm-466.8 14.5c0-73.5 98.9-133 220.8-133s211.9 40.7 211.9 133c0 50.1-26.5 85-70.3 106.4-2.4-1.6-4.7-2.9-6.4-3.7-10.2-5.2-27.8-10.5-27.8-10.5s86.6-6.4 86.6-92.7-90.6-87.9-90.6-87.9h-199V361c-74.1-21.5-125.2-67.1-125.2-119.9zm225.1 38.3v-55.6c57.8 0 87.8-6.8 87.8 27.3 0 36.5-38.2 28.3-87.8 28.3zm-.9 72.5H365c10.8 0 18.9 11.7 24 19.2-16.1 1.9-33 2.8-50.6 2.9v-22.1z"></path></svg> code and the <svg viewBox="0 0 640 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M593.8 59.1H46.2C20.7 59.1 0 79.8 0 105.2v301.5c0 25.5 20.7 46.2 46.2 46.2h547.7c25.5 0 46.2-20.7 46.1-46.1V105.2c0-25.4-20.7-46.1-46.2-46.1zM338.5 360.6H277v-120l-61.5 76.9-61.5-76.9v120H92.3V151.4h61.5l61.5 76.9 61.5-76.9h61.5v209.2zm135.3 3.1L381.5 256H443V151.4h61.5V256H566z"></path></svg> section?

---

# <svg viewBox="0 0 640 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M278.9 511.5l-61-17.7c-6.4-1.8-10-8.5-8.2-14.9L346.2 8.7c1.8-6.4 8.5-10 14.9-8.2l61 17.7c6.4 1.8 10 8.5 8.2 14.9L293.8 503.3c-1.9 6.4-8.5 10.1-14.9 8.2zm-114-112.2l43.5-46.4c4.6-4.9 4.3-12.7-.8-17.2L117 256l90.6-79.7c5.1-4.5 5.5-12.3.8-17.2l-43.5-46.4c-4.5-4.8-12.1-5.1-17-.5L3.8 247.2c-5.1 4.7-5.1 12.8 0 17.5l144.1 135.1c4.9 4.6 12.5 4.4 17-.5zm327.2.6l144.1-135.1c5.1-4.7 5.1-12.8 0-17.5L492.1 112.1c-4.8-4.5-12.4-4.3-17 .5L431.6 159c-4.6 4.9-4.3 12.7.8 17.2L523 256l-90.6 79.7c-5.1 4.5-5.5 12.3-.8 17.2l43.5 46.4c4.5 4.9 12.1 5.1 17 .6z"></path></svg> Code chunks

### Code

```r
library(tibble)
data(iris)
head(iris)
```

### Print output

```
#>   Sepal.Length Sepal.Width Petal.Length Petal.Width Species
#> 1          5.1         3.5          1.4         0.2  setosa
#> 2          4.9         3.0          1.4         0.2  setosa
#> 3          4.7         3.2          1.3         0.2  setosa
#> 4          4.6         3.1          1.5         0.2  setosa
#> 5          5.0         3.6          1.4         0.2  setosa
#> 6          5.4         3.9          1.7         0.4  setosa
```

---

# <svg viewBox="0 0 640 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M278.9 511.5l-61-17.7c-6.4-1.8-10-8.5-8.2-14.9L346.2 8.7c1.8-6.4 8.5-10 14.9-8.2l61 17.7c6.4 1.8 10 8.5 8.2 14.9L293.8 503.3c-1.9 6.4-8.5 10.1-14.9 8.2zm-114-112.2l43.5-46.4c4.6-4.9 4.3-12.7-.8-17.2L117 256l90.6-79.7c5.1-4.5 5.5-12.3.8-17.2l-43.5-46.4c-4.5-4.8-12.1-5.1-17-.5L3.8 247.2c-5.1 4.7-5.1 12.8 0 17.5l144.1 135.1c4.9 4.6 12.5 4.4 17-.5zm327.2.6l144.1-135.1c5.1-4.7 5.1-12.8 0-17.5L492.1 112.1c-4.8-4.5-12.4-4.3-17 .5L431.6 159c-4.6 4.9-4.3 12.7.8 17.2L523 256l-90.6 79.7c-5.1 4.5-5.5 12.3-.8 17.2l43.5 46.4c4.5 4.9 12.1 5.1 17 .6z"></path></svg> Code chunks
.pull-left[

### Code

```r
library(ggplot2)
data(iris)
ggplot(
      data=iris,
      aes(x = Sepal.Length,
          y = Sepal.Width)
  ) +
geom_point(
  aes(color=Species, shape=Species)
) +
xlab("Sepal Length") +
ylab("Sepal Width") +
ggtitle("Sepal Length-Width")
```
]

<img src="index_files/figure-html/unnamed-chunk-26-1.png" style="display: block; margin: auto;" />
]

---

# <svg viewBox="0 0 640 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M278.9 511.5l-61-17.7c-6.4-1.8-10-8.5-8.2-14.9L346.2 8.7c1.8-6.4 8.5-10 14.9-8.2l61 17.7c6.4 1.8 10 8.5 8.2 14.9L293.8 503.3c-1.9 6.4-8.5 10.1-14.9 8.2zm-114-112.2l43.5-46.4c4.6-4.9 4.3-12.7-.8-17.2L117 256l90.6-79.7c5.1-4.5 5.5-12.3.8-17.2l-43.5-46.4c-4.5-4.8-12.1-5.1-17-.5L3.8 247.2c-5.1 4.7-5.1 12.8 0 17.5l144.1 135.1c4.9 4.6 12.5 4.4 17-.5zm327.2.6l144.1-135.1c5.1-4.7 5.1-12.8 0-17.5L492.1 112.1c-4.8-4.5-12.4-4.3-17 .5L431.6 159c-4.6 4.9-4.3 12.7.8 17.2L523 256l-90.6 79.7c-5.1 4.5-5.5 12.3-.8 17.2l43.5 46.4c4.5 4.9 12.1 5.1 17 .6z"></path></svg> Code chunks

```r
library(leaflet)
leaflet(height=400, width=400) %>%
  addTiles() %>%
  addMarkers(lng=174.768, lat=-36.852,
             popup="The birthplace of R")
```
]

<div id="htmlwidget-bb1b6f172de2e3bec2c6" style="width:400px;height:400px;" class="leaflet html-widget"></div>
<script type="application/json" data-for="htmlwidget-bb1b6f172de2e3bec2c6">{"x":{"options":{"crs":{"crsClass":"L.CRS.EPSG3857","code":null,"proj4def":null,"projectedBounds":null,"options":{}}},"calls":[{"method":"addTiles","args":["//{s}.tile.openstreetmap.org/{z}/{x}/{y}.png",null,null,{"minZoom":0,"maxZoom":18,"tileSize":256,"subdomains":"abc","errorTileUrl":"","tms":false,"noWrap":false,"zoomOffset":0,"zoomReverse":false,"opacity":1,"zIndex":1,"detectRetina":false,"attribution":"© <a href=\"http://openstreetmap.org\">OpenStreetMap<\/a> contributors, <a href=\"http://creativecommons.org/licenses/by-sa/2.0/\">CC-BY-SA<\/a>"}]},{"method":"addMarkers","args":[-36.852,174.768,null,null,null,{"interactive":true,"draggable":false,"keyboard":true,"title":"","alt":"","zIndexOffset":0,"opacity":1,"riseOnHover":false,"riseOffset":250},"The birthplace of R",null,null,null,null,{"interactive":false,"permanent":false,"direction":"auto","opacity":1,"offset":[0,0],"textsize":"10px","textOnly":false,"className":"","sticky":true},null]}],"limits":{"lat":[-36.852,-36.852],"lng":[174.768,174.768]}},"evals":[],"jsHooks":[]}</script>
]

---

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```r
library(rbokeh)
p <- figure() %>%
  ly_points(Sepal.Length, Sepal.Width,
    data = iris,
    color = Species, glyph = Species,
    hover = list(Sepal.Length, Sepal.Width))
p
```
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]

---

# <svg viewBox="0 0 640 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M278.9 511.5l-61-17.7c-6.4-1.8-10-8.5-8.2-14.9L346.2 8.7c1.8-6.4 8.5-10 14.9-8.2l61 17.7c6.4 1.8 10 8.5 8.2 14.9L293.8 503.3c-1.9 6.4-8.5 10.1-14.9 8.2zm-114-112.2l43.5-46.4c4.6-4.9 4.3-12.7-.8-17.2L117 256l90.6-79.7c5.1-4.5 5.5-12.3.8-17.2l-43.5-46.4c-4.5-4.8-12.1-5.1-17-.5L3.8 247.2c-5.1 4.7-5.1 12.8 0 17.5l144.1 135.1c4.9 4.6 12.5 4.4 17-.5zm327.2.6l144.1-135.1c5.1-4.7 5.1-12.8 0-17.5L492.1 112.1c-4.8-4.5-12.4-4.3-17 .5L431.6 159c-4.6 4.9-4.3 12.7.8 17.2L523 256l-90.6 79.7c-5.1 4.5-5.5 12.3-.8 17.2l43.5 46.4c4.5 4.9 12.1 5.1 17 .6z"></path></svg> Inline code chunks

### <svg viewBox="0 0 640 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M278.9 511.5l-61-17.7c-6.4-1.8-10-8.5-8.2-14.9L346.2 8.7c1.8-6.4 8.5-10 14.9-8.2l61 17.7c6.4 1.8 10 8.5 8.2 14.9L293.8 503.3c-1.9 6.4-8.5 10.1-14.9 8.2zm-114-112.2l43.5-46.4c4.6-4.9 4.3-12.7-.8-17.2L117 256l90.6-79.7c5.1-4.5 5.5-12.3.8-17.2l-43.5-46.4c-4.5-4.8-12.1-5.1-17-.5L3.8 247.2c-5.1 4.7-5.1 12.8 0 17.5l144.1 135.1c4.9 4.6 12.5 4.4 17-.5zm327.2.6l144.1-135.1c5.1-4.7 5.1-12.8 0-17.5L492.1 112.1c-4.8-4.5-12.4-4.3-17 .5L431.6 159c-4.6 4.9-4.3 12.7.8 17.2L523 256l-90.6 79.7c-5.1 4.5-5.5 12.3-.8 17.2l43.5 46.4c4.5 4.9 12.1 5.1 17 .6z"></path></svg> Syntax

We studied `` `r
length(levels(iris$Species))` `` iris species and took
measurements on `` `r
nrow(iris)` `` flowers.

We found that Iris virginica had the longest sepal with a mean of
`` `r
mean(subset(iris,Species=="virginica")$Sepal.Length)`
`` millimeters!

### <svg viewBox="0 0 384 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M288 248v28c0 6.6-5.4 12-12 12H108c-6.6 0-12-5.4-12-12v-28c0-6.6 5.4-12 12-12h168c6.6 0 12 5.4 12 12zm-12 72H108c-6.6 0-12 5.4-12 12v28c0 6.6 5.4 12 12 12h168c6.6 0 12-5.4 12-12v-28c0-6.6-5.4-12-12-12zm108-188.1V464c0 26.5-21.5 48-48 48H48c-26.5 0-48-21.5-48-48V48C0 21.5 21.5 0 48 0h204.1C264.8 0 277 5.1 286 14.1L369.9 98c9 8.9 14.1 21.2 14.1 33.9zm-128-80V128h76.1L256 51.9zM336 464V176H232c-13.3 0-24-10.7-24-24V48H48v416h288z"></path></svg> Output

````md
This text is written in markdown.

We studied 3 iris species and took measurements on 150 flowers.

We found that Iris virginica had the longest sepal with a mean of 6.588 millimeters!
````

---

# Questions?

![:custom_hr]()

---

# Exercise

![:custom_hr]()

---

# Exercise

## Context

- *The goal of the exercise is to apply what we have seen today to generate a dynamic document using R Markdown.*

- *To do this, we will use data on Palmer penguins from [Dr. Kristen Gorman](https://www.uaf.edu/cfos/people/faculty/detail/kristen-gorman.php) and the [Palmer Station, Antarctica LTER](https://pal.lternet.edu/).*

- *Data are available through the [`palmerpenguin`](https://github.com/allisonhorst/palmerpenguins) R package.*

```r
library(palmerpenguins)
data(package = 'palmerpenguins')
```

---

# Exercise

## Context

```r
head(penguins)
#> # A tibble: 6 x 8
#>   species island bill_length_mm bill_depth_mm flipper_length_… body_mass_g sex  
#>   <fct>   <fct>           <dbl>         <dbl>            <int>       <int> <fct>
#> 1 Adelie  Torge…           39.1          18.7              181        3750 male 
#> 2 Adelie  Torge…           39.5          17.4              186        3800 fema…
#> 3 Adelie  Torge…           40.3          18                195        3250 fema…
#> 4 Adelie  Torge…           NA            NA                 NA          NA <NA> 
#> 5 Adelie  Torge…           36.7          19.3              193        3450 fema…
#> 6 Adelie  Torge…           39.3          20.6              190        3650 male 
#> # … with 1 more variable: year <int>
```

---

# Exercise

## Task

**2)** Create a new R Markdown document (`.rmd`)

**3)** Write a .font80[**YAML**] header including the document title, the authors, the date, and output formats html, pdf and word with a table of content for each

**4)** Include a single section (level 1) and two subsections (level 2)
]

---

# Exercise

## Task

- Add paragraphs including normal and formatted text (italic, bold)

- Add artwork from @allison_horst on palmer penguins found on the `palmerpenguins` R Package GitHub repository (https://github.com/allisonhorst/palmerpenguins) as a local image (for pdf output).

- Add a footnote to the artwork that states: *"Artwork by @allison_horst"*

- Add a code chunk that loads the `palmerpenguins` package and `penguins` dataset. Generate a table with to visualize the first 20 lines of the dataset.
]

---

# Exercise

## Task

- Copy the following text and use inline code chunks to fill in the blanks:

> The penguins dataset contains data on \_\_\_\_ individuals, \_\_\_\_ species, and from \_\_\_\_ islands. Across individuals, the mean flipper length is \_\_\_\_.

- In the previous text, add a hyperlink to the `palmerpenguins` R Package GitHub repository when a user clicks on [penguins dataset](https://github.com/allisonhorst/palmerpenguins);

- Add a code chunk that generates a scatterplot of flipper length on the x-axis and body mass on the y-axis.

**7)** Render `.html`, `.pdf` and `.docx` documents.
]

---
# Exercise

## Task

```r
install.packages("tinytex")
tinytex::install_tinytex()
```

---

# Exercise

## Solution

Load solution file here: [<svg viewBox="0 0 448 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M448 73.143v45.714C448 159.143 347.667 192 224 192S0 159.143 0 118.857V73.143C0 32.857 100.333 0 224 0s224 32.857 224 73.143zM448 176v102.857C448 319.143 347.667 352 224 352S0 319.143 0 278.857V176c48.125 33.143 136.208 48.572 224 48.572S399.874 209.143 448 176zm0 160v102.857C448 479.143 347.667 512 224 512S0 479.143 0 438.857V336c48.125 33.143 136.208 48.572 224 48.572S399.874 369.143 448 336z"></path></svg>](https://github.com/inSilecoInc/workshop_reproducibility/blob/main/exercise1.rmd)

---

# <svg viewBox="0 0 512 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M505.12019,19.09375c-1.18945-5.53125-6.65819-11-12.207-12.1875C460.716,0,435.507,0,410.40747,0,307.17523,0,245.26909,55.20312,199.05238,128H94.83772c-16.34763.01562-35.55658,11.875-42.88664,26.48438L2.51562,253.29688A28.4,28.4,0,0,0,0,264a24.00867,24.00867,0,0,0,24.00582,24H127.81618l-22.47457,22.46875c-11.36521,11.36133-12.99607,32.25781,0,45.25L156.24582,406.625c11.15623,11.1875,32.15619,13.15625,45.27726,0l22.47457-22.46875V488a24.00867,24.00867,0,0,0,24.00581,24,28.55934,28.55934,0,0,0,10.707-2.51562l98.72834-49.39063c14.62888-7.29687,26.50776-26.5,26.50776-42.85937V312.79688c72.59753-46.3125,128.03493-108.40626,128.03493-211.09376C512.07526,76.5,512.07526,51.29688,505.12019,19.09375ZM384.04033,168A40,40,0,1,1,424.05,128,40.02322,40.02322,0,0,1,384.04033,168Z"></path></svg> Chunk options

---

# <svg viewBox="0 0 640 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M278.9 511.5l-61-17.7c-6.4-1.8-10-8.5-8.2-14.9L346.2 8.7c1.8-6.4 8.5-10 14.9-8.2l61 17.7c6.4 1.8 10 8.5 8.2 14.9L293.8 503.3c-1.9 6.4-8.5 10.1-14.9 8.2zm-114-112.2l43.5-46.4c4.6-4.9 4.3-12.7-.8-17.2L117 256l90.6-79.7c5.1-4.5 5.5-12.3.8-17.2l-43.5-46.4c-4.5-4.8-12.1-5.1-17-.5L3.8 247.2c-5.1 4.7-5.1 12.8 0 17.5l144.1 135.1c4.9 4.6 12.5 4.4 17-.5zm327.2.6l144.1-135.1c5.1-4.7 5.1-12.8 0-17.5L492.1 112.1c-4.8-4.5-12.4-4.3-17 .5L431.6 159c-4.6 4.9-4.3 12.7.8 17.2L523 256l-90.6 79.7c-5.1 4.5-5.5 12.3-.8 17.2l43.5 46.4c4.5 4.9 12.1 5.1 17 .6z"></path></svg> Code chunk options

- Multiple options separated by commas
  `{r option1=value, option2=value}`

- Label your code chunk!
<img height="160px" width="160px" src="https://d33wubrfki0l68.cloudfront.net/6fcddff214345601f998805adce94ab0e21d8615/2a098/screenshots/rmarkdown-chunk-nav.png"></img>

]

.font90[
````md
```{r dispIris, option1=value, option2=value}
library(tibble)
data(iris)
head(iris)
```
````
]
]

---

# <svg viewBox="0 0 640 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M278.9 511.5l-61-17.7c-6.4-1.8-10-8.5-8.2-14.9L346.2 8.7c1.8-6.4 8.5-10 14.9-8.2l61 17.7c6.4 1.8 10 8.5 8.2 14.9L293.8 503.3c-1.9 6.4-8.5 10.1-14.9 8.2zm-114-112.2l43.5-46.4c4.6-4.9 4.3-12.7-.8-17.2L117 256l90.6-79.7c5.1-4.5 5.5-12.3.8-17.2l-43.5-46.4c-4.5-4.8-12.1-5.1-17-.5L3.8 247.2c-5.1 4.7-5.1 12.8 0 17.5l144.1 135.1c4.9 4.6 12.5 4.4 17-.5zm327.2.6l144.1-135.1c5.1-4.7 5.1-12.8 0-17.5L492.1 112.1c-4.8-4.5-12.4-4.3-17 .5L431.6 159c-4.6 4.9-4.3 12.7.8 17.2L523 256l-90.6 79.7c-5.1 4.5-5.5 12.3-.8 17.2l43.5 46.4c4.5 4.9 12.1 5.1 17 .6z"></path></svg> Code chunk options

Chunk output can be customised with [numerous options](https://yihui.name/knitr/options/):

```r
str(knitr::opts_chunk$get())
#> List of 54
#>  $ eval         : logi TRUE
#>  $ echo         : logi TRUE
#>  $ results      : chr "markup"
#>  $ tidy         : logi FALSE
#>  $ tidy.opts    : NULL
#>  $ collapse     : logi TRUE
#>  $ prompt       : logi FALSE
#>  $ comment      : chr "#>"
#>  $ highlight    : logi TRUE
#>  $ strip.white  : logi TRUE
#>  $ size         : chr "normalsize"
#>  $ background   : chr "#F7F7F7"
#>  $ cache        : logi FALSE
#>  $ cache.path   : chr "index_cache/html/"
#>  $ cache.vars   : NULL
#>  $ cache.lazy   : logi TRUE
#>  $ dependson    : NULL
#>  $ autodep      : logi FALSE
#>  $ cache.rebuild: logi FALSE
#>  $ fig.keep     : chr "high"
#>  $ fig.show     : chr "asis"
#>  $ fig.align    : chr "center"
#>  $ fig.path     : chr "index_files/figure-html/"
#>  $ dev          : chr "png"
#>  $ dev.args     : NULL
#>  $ dpi          : num 108
#>  $ fig.ext      : NULL
#>  $ fig.width    : num 6
#>  $ fig.height   : num 4.5
#>  $ fig.env      : chr "figure"
#>  $ fig.cap      : NULL
#>  $ fig.scap     : NULL
#>  $ fig.lp       : chr "fig:"
#>  $ fig.subcap   : NULL
#>  $ fig.pos      : chr ""
#>  $ out.width    : NULL
#>  $ out.height   : NULL
#>  $ out.extra    : NULL
#>  $ fig.retina   : num 1
#>  $ external     : logi TRUE
#>  $ sanitize     : logi FALSE
#>  $ interval     : num 1
#>  $ aniopts      : chr "controls,loop"
#>  $ warning      : logi FALSE
#>  $ error        : logi FALSE
#>  $ message      : logi FALSE
#>  $ render       : NULL
#>  $ ref.label    : NULL
#>  $ child        : NULL
#>  $ engine       : chr "R"
#>  $ split        : logi FALSE
#>  $ include      : logi TRUE
#>  $ purl         : logi TRUE
#>  $ width        : num 120
```

---

# <svg viewBox="0 0 640 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M278.9 511.5l-61-17.7c-6.4-1.8-10-8.5-8.2-14.9L346.2 8.7c1.8-6.4 8.5-10 14.9-8.2l61 17.7c6.4 1.8 10 8.5 8.2 14.9L293.8 503.3c-1.9 6.4-8.5 10.1-14.9 8.2zm-114-112.2l43.5-46.4c4.6-4.9 4.3-12.7-.8-17.2L117 256l90.6-79.7c5.1-4.5 5.5-12.3.8-17.2l-43.5-46.4c-4.5-4.8-12.1-5.1-17-.5L3.8 247.2c-5.1 4.7-5.1 12.8 0 17.5l144.1 135.1c4.9 4.6 12.5 4.4 17-.5zm327.2.6l144.1-135.1c5.1-4.7 5.1-12.8 0-17.5L492.1 112.1c-4.8-4.5-12.4-4.3-17 .5L431.6 159c-4.6 4.9-4.3 12.7.8 17.2L523 256l-90.6 79.7c-5.1 4.5-5.5 12.3-.8 17.2l43.5 46.4c4.5 4.9 12.1 5.1 17 .6z"></path></svg> Code chunk options

## Default options

````md
```{r}
head(iris)
```
````

]

```r
head(iris)
#>   Sepal.Length Sepal.Width Petal.Length Petal.Width Species
#> 1          5.1         3.5          1.4         0.2  setosa
#> 2          4.9         3.0          1.4         0.2  setosa
#> 3          4.7         3.2          1.3         0.2  setosa
#> 4          4.6         3.1          1.5         0.2  setosa
#> 5          5.0         3.6          1.4         0.2  setosa
#> 6          5.4         3.9          1.7         0.4  setosa
```

]

---

# <svg viewBox="0 0 640 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M278.9 511.5l-61-17.7c-6.4-1.8-10-8.5-8.2-14.9L346.2 8.7c1.8-6.4 8.5-10 14.9-8.2l61 17.7c6.4 1.8 10 8.5 8.2 14.9L293.8 503.3c-1.9 6.4-8.5 10.1-14.9 8.2zm-114-112.2l43.5-46.4c4.6-4.9 4.3-12.7-.8-17.2L117 256l90.6-79.7c5.1-4.5 5.5-12.3.8-17.2l-43.5-46.4c-4.5-4.8-12.1-5.1-17-.5L3.8 247.2c-5.1 4.7-5.1 12.8 0 17.5l144.1 135.1c4.9 4.6 12.5 4.4 17-.5zm327.2.6l144.1-135.1c5.1-4.7 5.1-12.8 0-17.5L492.1 112.1c-4.8-4.5-12.4-4.3-17 .5L431.6 159c-4.6 4.9-4.3 12.7.8 17.2L523 256l-90.6 79.7c-5.1 4.5-5.5 12.3-.8 17.2l43.5 46.4c4.5 4.9 12.1 5.1 17 .6z"></path></svg> Code chunk options

## Option `echo`

````md
```{r echo = FALSE}
head(iris)
```
````

]

- Display results but not code.
- Useful to present results to people not interested by the code.
- Use `echo = -1` to hide only the first line of a code chunk.

---

# <svg viewBox="0 0 640 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M278.9 511.5l-61-17.7c-6.4-1.8-10-8.5-8.2-14.9L346.2 8.7c1.8-6.4 8.5-10 14.9-8.2l61 17.7c6.4 1.8 10 8.5 8.2 14.9L293.8 503.3c-1.9 6.4-8.5 10.1-14.9 8.2zm-114-112.2l43.5-46.4c4.6-4.9 4.3-12.7-.8-17.2L117 256l90.6-79.7c5.1-4.5 5.5-12.3.8-17.2l-43.5-46.4c-4.5-4.8-12.1-5.1-17-.5L3.8 247.2c-5.1 4.7-5.1 12.8 0 17.5l144.1 135.1c4.9 4.6 12.5 4.4 17-.5zm327.2.6l144.1-135.1c5.1-4.7 5.1-12.8 0-17.5L492.1 112.1c-4.8-4.5-12.4-4.3-17 .5L431.6 159c-4.6 4.9-4.3 12.7.8 17.2L523 256l-90.6 79.7c-5.1 4.5-5.5 12.3-.8 17.2l43.5 46.4c4.5 4.9 12.1 5.1 17 .6z"></path></svg> Code chunk options

## Option `eval`

.pull-left[
### <svg viewBox="0 0 640 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M278.9 511.5l-61-17.7c-6.4-1.8-10-8.5-8.2-14.9L346.2 8.7c1.8-6.4 8.5-10 14.9-8.2l61 17.7c6.4 1.8 10 8.5 8.2 14.9L293.8 503.3c-1.9 6.4-8.5 10.1-14.9 8.2zm-114-112.2l43.5-46.4c4.6-4.9 4.3-12.7-.8-17.2L117 256l90.6-79.7c5.1-4.5 5.5-12.3.8-17.2l-43.5-46.4c-4.5-4.8-12.1-5.1-17-.5L3.8 247.2c-5.1 4.7-5.1 12.8 0 17.5l144.1 135.1c4.9 4.6 12.5 4.4 17-.5zm327.2.6l144.1-135.1c5.1-4.7 5.1-12.8 0-17.5L492.1 112.1c-4.8-4.5-12.4-4.3-17 .5L431.6 159c-4.6 4.9-4.3 12.7.8 17.2L523 256l-90.6 79.7c-5.1 4.5-5.5 12.3-.8 17.2l43.5 46.4c4.5 4.9 12.1 5.1 17 .6z"></path></svg> Syntax
````md
```{r eval = FALSE}
head(iris)
```
````
]

.pull-right[
### <svg viewBox="0 0 384 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M288 248v28c0 6.6-5.4 12-12 12H108c-6.6 0-12-5.4-12-12v-28c0-6.6 5.4-12 12-12h168c6.6 0 12 5.4 12 12zm-12 72H108c-6.6 0-12 5.4-12 12v28c0 6.6 5.4 12 12 12h168c6.6 0 12-5.4 12-12v-28c0-6.6-5.4-12-12-12zm108-188.1V464c0 26.5-21.5 48-48 48H48c-26.5 0-48-21.5-48-48V48C0 21.5 21.5 0 48 0h204.1C264.8 0 277 5.1 286 14.1L369.9 98c9 8.9 14.1 21.2 14.1 33.9zm-128-80V128h76.1L256 51.9zM336 464V176H232c-13.3 0-24-10.7-24-24V48H48v416h288z"></path></svg> Output

```r
head(iris)
```
]

- Code is not evaluated.
- Useful to show exemple code.
- Use `eval = -1` to evaluate every line of a code chunk except the first.

---

# <svg viewBox="0 0 640 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M278.9 511.5l-61-17.7c-6.4-1.8-10-8.5-8.2-14.9L346.2 8.7c1.8-6.4 8.5-10 14.9-8.2l61 17.7c6.4 1.8 10 8.5 8.2 14.9L293.8 503.3c-1.9 6.4-8.5 10.1-14.9 8.2zm-114-112.2l43.5-46.4c4.6-4.9 4.3-12.7-.8-17.2L117 256l90.6-79.7c5.1-4.5 5.5-12.3.8-17.2l-43.5-46.4c-4.5-4.8-12.1-5.1-17-.5L3.8 247.2c-5.1 4.7-5.1 12.8 0 17.5l144.1 135.1c4.9 4.6 12.5 4.4 17-.5zm327.2.6l144.1-135.1c5.1-4.7 5.1-12.8 0-17.5L492.1 112.1c-4.8-4.5-12.4-4.3-17 .5L431.6 159c-4.6 4.9-4.3 12.7.8 17.2L523 256l-90.6 79.7c-5.1 4.5-5.5 12.3-.8 17.2l43.5 46.4c4.5 4.9 12.1 5.1 17 .6z"></path></svg> Code chunk options

## Option `include`

]

- Code is evaluated but no output (code, results and figures) is displayed.
- Useful in setup options and package installation.

---

# <svg viewBox="0 0 640 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M278.9 511.5l-61-17.7c-6.4-1.8-10-8.5-8.2-14.9L346.2 8.7c1.8-6.4 8.5-10 14.9-8.2l61 17.7c6.4 1.8 10 8.5 8.2 14.9L293.8 503.3c-1.9 6.4-8.5 10.1-14.9 8.2zm-114-112.2l43.5-46.4c4.6-4.9 4.3-12.7-.8-17.2L117 256l90.6-79.7c5.1-4.5 5.5-12.3.8-17.2l-43.5-46.4c-4.5-4.8-12.1-5.1-17-.5L3.8 247.2c-5.1 4.7-5.1 12.8 0 17.5l144.1 135.1c4.9 4.6 12.5 4.4 17-.5zm327.2.6l144.1-135.1c5.1-4.7 5.1-12.8 0-17.5L492.1 112.1c-4.8-4.5-12.4-4.3-17 .5L431.6 159c-4.6 4.9-4.3 12.7.8 17.2L523 256l-90.6 79.7c-5.1 4.5-5.5 12.3-.8 17.2l43.5 46.4c4.5 4.9 12.1 5.1 17 .6z"></path></svg> Code chunk options

## Option `results`

```r
1 + 1
2 + 2
#> [1] 2
#> [1] 4
```
]

- Hold all results in a code chunk and display them at the end.

---

# <svg viewBox="0 0 640 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M278.9 511.5l-61-17.7c-6.4-1.8-10-8.5-8.2-14.9L346.2 8.7c1.8-6.4 8.5-10 14.9-8.2l61 17.7c6.4 1.8 10 8.5 8.2 14.9L293.8 503.3c-1.9 6.4-8.5 10.1-14.9 8.2zm-114-112.2l43.5-46.4c4.6-4.9 4.3-12.7-.8-17.2L117 256l90.6-79.7c5.1-4.5 5.5-12.3.8-17.2l-43.5-46.4c-4.5-4.8-12.1-5.1-17-.5L3.8 247.2c-5.1 4.7-5.1 12.8 0 17.5l144.1 135.1c4.9 4.6 12.5 4.4 17-.5zm327.2.6l144.1-135.1c5.1-4.7 5.1-12.8 0-17.5L492.1 112.1c-4.8-4.5-12.4-4.3-17 .5L431.6 159c-4.6 4.9-4.3 12.7.8 17.2L523 256l-90.6 79.7c-5.1 4.5-5.5 12.3-.8 17.2l43.5 46.4c4.5 4.9 12.1 5.1 17 .6z"></path></svg> Code chunk options

## Option `results`

- Hide results but not plots

]

```r
1 + 1
ggplot(data = iris,
       aes(x = Petal.Length,
           y = Petal.Width)) +
  geom_point()
```

<img src="index_files/figure-html/unnamed-chunk-40-1.png" width="432" style="display: block; margin: auto;" />
]

---

# <svg viewBox="0 0 640 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M278.9 511.5l-61-17.7c-6.4-1.8-10-8.5-8.2-14.9L346.2 8.7c1.8-6.4 8.5-10 14.9-8.2l61 17.7c6.4 1.8 10 8.5 8.2 14.9L293.8 503.3c-1.9 6.4-8.5 10.1-14.9 8.2zm-114-112.2l43.5-46.4c4.6-4.9 4.3-12.7-.8-17.2L117 256l90.6-79.7c5.1-4.5 5.5-12.3.8-17.2l-43.5-46.4c-4.5-4.8-12.1-5.1-17-.5L3.8 247.2c-5.1 4.7-5.1 12.8 0 17.5l144.1 135.1c4.9 4.6 12.5 4.4 17-.5zm327.2.6l144.1-135.1c5.1-4.7 5.1-12.8 0-17.5L492.1 112.1c-4.8-4.5-12.4-4.3-17 .5L431.6 159c-4.6 4.9-4.3 12.7.8 17.2L523 256l-90.6 79.7c-5.1 4.5-5.5 12.3-.8 17.2l43.5 46.4c4.5 4.9 12.1 5.1 17 .6z"></path></svg> Code chunk options

## Options `fig.height` & `fig.width`

- width and height of the plot in inches
- Note that options are separated by commas

---

# <svg viewBox="0 0 640 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M278.9 511.5l-61-17.7c-6.4-1.8-10-8.5-8.2-14.9L346.2 8.7c1.8-6.4 8.5-10 14.9-8.2l61 17.7c6.4 1.8 10 8.5 8.2 14.9L293.8 503.3c-1.9 6.4-8.5 10.1-14.9 8.2zm-114-112.2l43.5-46.4c4.6-4.9 4.3-12.7-.8-17.2L117 256l90.6-79.7c5.1-4.5 5.5-12.3.8-17.2l-43.5-46.4c-4.5-4.8-12.1-5.1-17-.5L3.8 247.2c-5.1 4.7-5.1 12.8 0 17.5l144.1 135.1c4.9 4.6 12.5 4.4 17-.5zm327.2.6l144.1-135.1c5.1-4.7 5.1-12.8 0-17.5L492.1 112.1c-4.8-4.5-12.4-4.3-17 .5L431.6 159c-4.6 4.9-4.3 12.7.8 17.2L523 256l-90.6 79.7c-5.1 4.5-5.5 12.3-.8 17.2l43.5 46.4c4.5 4.9 12.1 5.1 17 .6z"></path></svg> Code chunk options

## Option `fig.cap`

---

# <svg viewBox="0 0 640 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M278.9 511.5l-61-17.7c-6.4-1.8-10-8.5-8.2-14.9L346.2 8.7c1.8-6.4 8.5-10 14.9-8.2l61 17.7c6.4 1.8 10 8.5 8.2 14.9L293.8 503.3c-1.9 6.4-8.5 10.1-14.9 8.2zm-114-112.2l43.5-46.4c4.6-4.9 4.3-12.7-.8-17.2L117 256l90.6-79.7c5.1-4.5 5.5-12.3.8-17.2l-43.5-46.4c-4.5-4.8-12.1-5.1-17-.5L3.8 247.2c-5.1 4.7-5.1 12.8 0 17.5l144.1 135.1c4.9 4.6 12.5 4.4 17-.5zm327.2.6l144.1-135.1c5.1-4.7 5.1-12.8 0-17.5L492.1 112.1c-4.8-4.5-12.4-4.3-17 .5L431.6 159c-4.6 4.9-4.3 12.7.8 17.2L523 256l-90.6 79.7c-5.1 4.5-5.5 12.3-.8 17.2l43.5 46.4c4.5 4.9 12.1 5.1 17 .6z"></path></svg> Code chunk options

## What output each option suppresses?

Option             | Run code | Show code | Output | Plots | Messages | Warnings
-------------------|:--------:|:---------:|:------:|:-----:|:--------:|:-------:
`eval = FALSE`     |<svg viewBox="0 0 352 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M242.72 256l100.07-100.07c12.28-12.28 12.28-32.19 0-44.48l-22.24-22.24c-12.28-12.28-32.19-12.28-44.48 0L176 189.28 75.93 89.21c-12.28-12.28-32.19-12.28-44.48 0L9.21 111.45c-12.28 12.28-12.28 32.19 0 44.48L109.28 256 9.21 356.07c-12.28 12.28-12.28 32.19 0 44.48l22.24 22.24c12.28 12.28 32.2 12.28 44.48 0L176 322.72l100.07 100.07c12.28 12.28 32.2 12.28 44.48 0l22.24-22.24c12.28-12.28 12.28-32.19 0-44.48L242.72 256z"></path></svg>|         |<svg viewBox="0 0 352 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M242.72 256l100.07-100.07c12.28-12.28 12.28-32.19 0-44.48l-22.24-22.24c-12.28-12.28-32.19-12.28-44.48 0L176 189.28 75.93 89.21c-12.28-12.28-32.19-12.28-44.48 0L9.21 111.45c-12.28 12.28-12.28 32.19 0 44.48L109.28 256 9.21 356.07c-12.28 12.28-12.28 32.19 0 44.48l22.24 22.24c12.28 12.28 32.2 12.28 44.48 0L176 322.72l100.07 100.07c12.28 12.28 32.2 12.28 44.48 0l22.24-22.24c12.28-12.28 12.28-32.19 0-44.48L242.72 256z"></path></svg>|<svg viewBox="0 0 352 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M242.72 256l100.07-100.07c12.28-12.28 12.28-32.19 0-44.48l-22.24-22.24c-12.28-12.28-32.19-12.28-44.48 0L176 189.28 75.93 89.21c-12.28-12.28-32.19-12.28-44.48 0L9.21 111.45c-12.28 12.28-12.28 32.19 0 44.48L109.28 256 9.21 356.07c-12.28 12.28-12.28 32.19 0 44.48l22.24 22.24c12.28 12.28 32.2 12.28 44.48 0L176 322.72l100.07 100.07c12.28 12.28 32.2 12.28 44.48 0l22.24-22.24c12.28-12.28 12.28-32.19 0-44.48L242.72 256z"></path></svg>|<svg viewBox="0 0 352 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M242.72 256l100.07-100.07c12.28-12.28 12.28-32.19 0-44.48l-22.24-22.24c-12.28-12.28-32.19-12.28-44.48 0L176 189.28 75.93 89.21c-12.28-12.28-32.19-12.28-44.48 0L9.21 111.45c-12.28 12.28-12.28 32.19 0 44.48L109.28 256 9.21 356.07c-12.28 12.28-12.28 32.19 0 44.48l22.24 22.24c12.28 12.28 32.2 12.28 44.48 0L176 322.72l100.07 100.07c12.28 12.28 32.2 12.28 44.48 0l22.24-22.24c12.28-12.28 12.28-32.19 0-44.48L242.72 256z"></path></svg>|<svg viewBox="0 0 352 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M242.72 256l100.07-100.07c12.28-12.28 12.28-32.19 0-44.48l-22.24-22.24c-12.28-12.28-32.19-12.28-44.48 0L176 189.28 75.93 89.21c-12.28-12.28-32.19-12.28-44.48 0L9.21 111.45c-12.28 12.28-12.28 32.19 0 44.48L109.28 256 9.21 356.07c-12.28 12.28-12.28 32.19 0 44.48l22.24 22.24c12.28 12.28 32.2 12.28 44.48 0L176 322.72l100.07 100.07c12.28 12.28 32.2 12.28 44.48 0l22.24-22.24c12.28-12.28 12.28-32.19 0-44.48L242.72 256z"></path></svg>
`include = FALSE`  | |<svg viewBox="0 0 352 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M242.72 256l100.07-100.07c12.28-12.28 12.28-32.19 0-44.48l-22.24-22.24c-12.28-12.28-32.19-12.28-44.48 0L176 189.28 75.93 89.21c-12.28-12.28-32.19-12.28-44.48 0L9.21 111.45c-12.28 12.28-12.28 32.19 0 44.48L109.28 256 9.21 356.07c-12.28 12.28-12.28 32.19 0 44.48l22.24 22.24c12.28 12.28 32.2 12.28 44.48 0L176 322.72l100.07 100.07c12.28 12.28 32.2 12.28 44.48 0l22.24-22.24c12.28-12.28 12.28-32.19 0-44.48L242.72 256z"></path></svg>|<svg viewBox="0 0 352 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M242.72 256l100.07-100.07c12.28-12.28 12.28-32.19 0-44.48l-22.24-22.24c-12.28-12.28-32.19-12.28-44.48 0L176 189.28 75.93 89.21c-12.28-12.28-32.19-12.28-44.48 0L9.21 111.45c-12.28 12.28-12.28 32.19 0 44.48L109.28 256 9.21 356.07c-12.28 12.28-12.28 32.19 0 44.48l22.24 22.24c12.28 12.28 32.2 12.28 44.48 0L176 322.72l100.07 100.07c12.28 12.28 32.2 12.28 44.48 0l22.24-22.24c12.28-12.28 12.28-32.19 0-44.48L242.72 256z"></path></svg>|<svg viewBox="0 0 352 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M242.72 256l100.07-100.07c12.28-12.28 12.28-32.19 0-44.48l-22.24-22.24c-12.28-12.28-32.19-12.28-44.48 0L176 189.28 75.93 89.21c-12.28-12.28-32.19-12.28-44.48 0L9.21 111.45c-12.28 12.28-12.28 32.19 0 44.48L109.28 256 9.21 356.07c-12.28 12.28-12.28 32.19 0 44.48l22.24 22.24c12.28 12.28 32.2 12.28 44.48 0L176 322.72l100.07 100.07c12.28 12.28 32.2 12.28 44.48 0l22.24-22.24c12.28-12.28 12.28-32.19 0-44.48L242.72 256z"></path></svg>|<svg viewBox="0 0 352 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M242.72 256l100.07-100.07c12.28-12.28 12.28-32.19 0-44.48l-22.24-22.24c-12.28-12.28-32.19-12.28-44.48 0L176 189.28 75.93 89.21c-12.28-12.28-32.19-12.28-44.48 0L9.21 111.45c-12.28 12.28-12.28 32.19 0 44.48L109.28 256 9.21 356.07c-12.28 12.28-12.28 32.19 0 44.48l22.24 22.24c12.28 12.28 32.2 12.28 44.48 0L176 322.72l100.07 100.07c12.28 12.28 32.2 12.28 44.48 0l22.24-22.24c12.28-12.28 12.28-32.19 0-44.48L242.72 256z"></path></svg>|<svg viewBox="0 0 352 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M242.72 256l100.07-100.07c12.28-12.28 12.28-32.19 0-44.48l-22.24-22.24c-12.28-12.28-32.19-12.28-44.48 0L176 189.28 75.93 89.21c-12.28-12.28-32.19-12.28-44.48 0L9.21 111.45c-12.28 12.28-12.28 32.19 0 44.48L109.28 256 9.21 356.07c-12.28 12.28-12.28 32.19 0 44.48l22.24 22.24c12.28 12.28 32.2 12.28 44.48 0L176 322.72l100.07 100.07c12.28 12.28 32.2 12.28 44.48 0l22.24-22.24c12.28-12.28 12.28-32.19 0-44.48L242.72 256z"></path></svg>
`echo = FALSE`     |  |<svg viewBox="0 0 352 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M242.72 256l100.07-100.07c12.28-12.28 12.28-32.19 0-44.48l-22.24-22.24c-12.28-12.28-32.19-12.28-44.48 0L176 189.28 75.93 89.21c-12.28-12.28-32.19-12.28-44.48 0L9.21 111.45c-12.28 12.28-12.28 32.19 0 44.48L109.28 256 9.21 356.07c-12.28 12.28-12.28 32.19 0 44.48l22.24 22.24c12.28 12.28 32.2 12.28 44.48 0L176 322.72l100.07 100.07c12.28 12.28 32.2 12.28 44.48 0l22.24-22.24c12.28-12.28 12.28-32.19 0-44.48L242.72 256z"></path></svg>|     |    |      |
`results = "hide"` |        |        |<svg viewBox="0 0 352 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M242.72 256l100.07-100.07c12.28-12.28 12.28-32.19 0-44.48l-22.24-22.24c-12.28-12.28-32.19-12.28-44.48 0L176 189.28 75.93 89.21c-12.28-12.28-32.19-12.28-44.48 0L9.21 111.45c-12.28 12.28-12.28 32.19 0 44.48L109.28 256 9.21 356.07c-12.28 12.28-12.28 32.19 0 44.48l22.24 22.24c12.28 12.28 32.2 12.28 44.48 0L176 322.72l100.07 100.07c12.28 12.28 32.2 12.28 44.48 0l22.24-22.24c12.28-12.28 12.28-32.19 0-44.48L242.72 256z"></path></svg>|     |        |
`fig.show = "hide"`|        |       |     | <svg viewBox="0 0 352 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M242.72 256l100.07-100.07c12.28-12.28 12.28-32.19 0-44.48l-22.24-22.24c-12.28-12.28-32.19-12.28-44.48 0L176 189.28 75.93 89.21c-12.28-12.28-32.19-12.28-44.48 0L9.21 111.45c-12.28 12.28-12.28 32.19 0 44.48L109.28 256 9.21 356.07c-12.28 12.28-12.28 32.19 0 44.48l22.24 22.24c12.28 12.28 32.2 12.28 44.48 0L176 322.72l100.07 100.07c12.28 12.28 32.2 12.28 44.48 0l22.24-22.24c12.28-12.28 12.28-32.19 0-44.48L242.72 256z"></path></svg>|      |
`message = FALSE`  |          |           |        |       |<svg viewBox="0 0 352 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M242.72 256l100.07-100.07c12.28-12.28 12.28-32.19 0-44.48l-22.24-22.24c-12.28-12.28-32.19-12.28-44.48 0L176 189.28 75.93 89.21c-12.28-12.28-32.19-12.28-44.48 0L9.21 111.45c-12.28 12.28-12.28 32.19 0 44.48L109.28 256 9.21 356.07c-12.28 12.28-12.28 32.19 0 44.48l22.24 22.24c12.28 12.28 32.2 12.28 44.48 0L176 322.72l100.07 100.07c12.28 12.28 32.2 12.28 44.48 0l22.24-22.24c12.28-12.28 12.28-32.19 0-44.48L242.72 256z"></path></svg>|
`warning = FALSE`  |          |           |        |       |          |<svg viewBox="0 0 352 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M242.72 256l100.07-100.07c12.28-12.28 12.28-32.19 0-44.48l-22.24-22.24c-12.28-12.28-32.19-12.28-44.48 0L176 189.28 75.93 89.21c-12.28-12.28-32.19-12.28-44.48 0L9.21 111.45c-12.28 12.28-12.28 32.19 0 44.48L109.28 256 9.21 356.07c-12.28 12.28-12.28 32.19 0 44.48l22.24 22.24c12.28 12.28 32.2 12.28 44.48 0L176 322.72l100.07 100.07c12.28 12.28 32.2 12.28 44.48 0l22.24-22.24c12.28-12.28 12.28-32.19 0-44.48L242.72 256z"></path></svg>

Table from [R for Data Science](https://r4ds.had.co.nz/r-markdown.html#chunk-options)

---

# <svg viewBox="0 0 640 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M278.9 511.5l-61-17.7c-6.4-1.8-10-8.5-8.2-14.9L346.2 8.7c1.8-6.4 8.5-10 14.9-8.2l61 17.7c6.4 1.8 10 8.5 8.2 14.9L293.8 503.3c-1.9 6.4-8.5 10.1-14.9 8.2zm-114-112.2l43.5-46.4c4.6-4.9 4.3-12.7-.8-17.2L117 256l90.6-79.7c5.1-4.5 5.5-12.3.8-17.2l-43.5-46.4c-4.5-4.8-12.1-5.1-17-.5L3.8 247.2c-5.1 4.7-5.1 12.8 0 17.5l144.1 135.1c4.9 4.6 12.5 4.4 17-.5zm327.2.6l144.1-135.1c5.1-4.7 5.1-12.8 0-17.5L492.1 112.1c-4.8-4.5-12.4-4.3-17 .5L431.6 159c-4.6 4.9-4.3 12.7.8 17.2L523 256l-90.6 79.7c-5.1 4.5-5.5 12.3-.8 17.2l43.5 46.4c4.5 4.9 12.1 5.1 17 .6z"></path></svg> Code chunk options

## Global code chunk options

### Setup

You can change the default chunk options for all following chunks in your document.

````md
```{r include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  cache = TRUE,
  comment = "#>",
  fig.width = 6,
  fig.align = "center"
)
```
````

---

# Questions?

![:custom_hr]()

---

# Bibliography and citations

![:custom_hr]()

---

# Bibliography

## Bibliographic files

- Bibliographies are typically included to a `.Rmd` document using an external bibliographic file

- *Pandoc* can use a wide variety of [bibliographic files](https://rmarkdown.rstudio.com/authoring_bibliographies_and_citations.html#Specifying_a_Bibliography) to manage bibliographies and citations.

- For scientific writing, we recommend using a `mybiblio.bib` file in BiBTeX format, which you can export from your favorite reference manager software (*e.g.* [Zotero](https://www.zotero.org/), [<svg viewBox="0 0 640 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M624.6 325.2c-12.3-12.4-29.7-19.2-48.4-17.2-43.3-1-49.7-34.9-37.5-98.8 22.8-57.5-14.9-131.5-87.4-130.8-77.4.7-81.7 82-130.9 82-48.1 0-54-81.3-130.9-82-72.9-.8-110.1 73.3-87.4 130.8 12.2 63.9 5.8 97.8-37.5 98.8-21.2-2.3-37 6.5-53 22.5-19.9 19.7-19.3 94.8 42.6 102.6 47.1 5.9 81.6-42.9 61.2-87.8-47.3-103.7 185.9-106.1 146.5-8.2-.1.1-.2.2-.3.4-26.8 42.8 6.8 97.4 58.8 95.2 52.1 2.1 85.4-52.6 58.8-95.2-.1-.2-.2-.3-.3-.4-39.4-97.9 193.8-95.5 146.5 8.2-4.6 10-6.7 21.3-5.7 33 4.9 53.4 68.7 74.1 104.9 35.2 17.8-14.8 23.1-65.6 0-88.3zm-303.9-19.1h-.6c-43.4 0-62.8-37.5-62.8-62.8 0-34.7 28.2-62.8 62.8-62.8h.6c34.7 0 62.8 28.1 62.8 62.8 0 25-19.2 62.8-62.8 62.8z"></path></svg> Mendeley](https://www.mendeley.com/), [EndNote](https://endnote.com/))

- Note that bibliographic metadata can be included in the [YAML header](https://rmarkdown.rstudio.com/authoring_bibliographies_and_citations.html#Inline_References). We however do not recommend using this strategy, unless you wish to cite few references.

---

# Bibliography

## `.bib` file

```md
@article{galbraith2012,
  author = {Galbraith, Peter S. and Larouche, Pierre and Chass{\'e}, Jo{\"e}l and Petrie, Brian},
  title = {Sea-Surface Temperature in Relation to Air Temperature in the {{Gulf}} of {{St}}. {{Lawrence}}: {{Interdecadal}} Variability and Long Term Trends},
  journal = {Deep Sea Research Part II: Topical Studies in Oceanography},
  volume = {77-80},
  pages = {10--20},
  year = {2012},
  doi = {10.1016/j.dsr2.2012.04.001},
  series = {Satellite {{Oceanography}} and {{Climate Change}}}
}
```

- Use the citation key `galbraith2012` for in-text citations (more on this later)

---

# Bibliography

## Include to `.Rmd`

- Include a bibliography to a `.Rmd` in the .font60[**YAML**] header using the `bibliography` option

```yaml
---
title: "My document title"
date: "01-03-2021"
author: Me, you, them
output: pdf_document
bibliography: mybiblio.bib
---
```

.font90[
<svg viewBox="0 0 576 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M569.517 440.013C587.975 472.007 564.806 512 527.94 512H48.054c-36.937 0-59.999-40.055-41.577-71.987L246.423 23.985c18.467-32.009 64.72-31.951 83.154 0l239.94 416.028zM288 354c-25.405 0-46 20.595-46 46s20.595 46 46 46 46-20.595 46-46-20.595-46-46-46zm-43.673-165.346l7.418 136c.347 6.364 5.609 11.346 11.982 11.346h48.546c6.373 0 11.635-4.982 11.982-11.346l7.418-136c.375-6.874-5.098-12.654-11.982-12.654h-63.383c-6.884 0-12.356 5.78-11.981 12.654z"></path></svg> Be sure that the path to your `.bib` file is well identified.
]

---

# Bibliography

## Placement

- A bibliography will be added at the end of the document by default. Use an appropriate header at the end and you are good to go.

```md
...that will revolutionize the way we think about science.

# References
```

- If you wish to include text after the bibliography, such as an appendix, your can use the `<div id="refs"></div>` HTML tag (see [here](https://bookdown.org/yihui/rmarkdown-cookbook/bibliography.html) for more on this):

```md
...that will revolutionize the way we think about science.

# References

# Appendix
```

---

# Bibliography

## Citation syntax

- Use citation key with `@` to refer to a reference: `@id`

---

# Bibliography

## Styling

- By default, pandoc uses the Chicago author-date format
- You can use another style by specifying CSL style files with the the `csl` option in the .font60[**YAML**] header.
- CSL files contain bibliographic and citation formatting informations.
- There are hundreds of styles available on [GitHub](https://github.com/citation-style-language/styles) and scientific journals often provide their own CSL file.

```yaml
---
title: "My document title"
date: "01-03-2021"
author: Me, you, them
output: pdf_document
bibliography: mybiblio.bib
csl: mystyle.csl
---
```

.font90[
<svg viewBox="0 0 576 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M569.517 440.013C587.975 472.007 564.806 512 527.94 512H48.054c-36.937 0-59.999-40.055-41.577-71.987L246.423 23.985c18.467-32.009 64.72-31.951 83.154 0l239.94 416.028zM288 354c-25.405 0-46 20.595-46 46s20.595 46 46 46 46-20.595 46-46-20.595-46-46-46zm-43.673-165.346l7.418 136c.347 6.364 5.609 11.346 11.982 11.346h48.546c6.373 0 11.635-4.982 11.982-11.346l7.418-136c.375-6.874-5.098-12.654-11.982-12.654h-63.383c-6.884 0-12.356 5.78-11.981 12.654z"></path></svg> Be sure that the path to your `.csl` file is well identified.
]

---

# Questions?

![:custom_hr]()

---

# Customizing documents

![:custom_hr]()

---

# Customizing documents

## <svg viewBox="0 0 384 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M0 32l34.9 395.8L191.5 480l157.6-52.2L384 32H0zm308.2 127.9H124.4l4.1 49.4h175.6l-13.6 148.4-97.9 27v.3h-1.1l-98.7-27.3-6-75.8h47.7L138 320l53.5 14.5 53.7-14.5 6-62.2H84.3L71.5 112.2h241.1l-4.4 47.7z"></path></svg> Themes

- There are 12 custom themes available in `rmarkdown`, and multiple others available through numerous R packages. See [here](https://www.datadreaming.org/post/r-markdown-theme-gallery/) and [here](https://cran.r-project.org/web/packages/prettydoc/vignettes/tactile.html) for examples.

```yaml
---
title: Awesome report
author: Me, You, Them
date: 2021-03-01
output:
  html_document:
    theme: lumen
---
```

---

# Customizing documents

## <svg viewBox="0 0 384 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M369.9 97.9L286 14C277 5 264.8-.1 252.1-.1H48C21.5 0 0 21.5 0 48v416c0 26.5 21.5 48 48 48h288c26.5 0 48-21.5 48-48V131.9c0-12.7-5.1-25-14.1-34zM332.1 128H256V51.9l76.1 76.1zM48 464V48h160v104c0 13.3 10.7 24 24 24h104v288H48zm250.2-143.7c-12.2-12-47-8.7-64.4-6.5-17.2-10.5-28.7-25-36.8-46.3 3.9-16.1 10.1-40.6 5.4-56-4.2-26.2-37.8-23.6-42.6-5.9-4.4 16.1-.4 38.5 7 67.1-10 23.9-24.9 56-35.4 74.4-20 10.3-47 26.2-51 46.2-3.3 15.8 26 55.2 76.1-31.2 22.4-7.4 46.8-16.5 68.4-20.1 18.9 10.2 41 17 55.8 17 25.5 0 28-28.2 17.5-38.7zm-198.1 77.8c5.1-13.7 24.5-29.5 30.4-35-19 30.3-30.4 35.7-30.4 35zm81.6-190.6c7.4 0 6.7 32.1 1.8 40.8-4.4-13.9-4.3-40.8-1.8-40.8zm-24.4 136.6c9.7-16.9 18-37 24.7-54.7 8.3 15.1 18.9 27.2 30.1 35.5-20.8 4.3-38.9 13.1-54.8 19.2zm131.6-5s-5 6-37.3-7.8c35.1-2.6 40.9 5.4 37.3 7.8z"></path></svg> Templates

- Specify a LaTeX template `.tex` file to use pre-specified document formatting guidelines. See [here](https://www.overleaf.com/latex/templates) for many templates. Many scientific journals provide LaTeX templates.
- Download the desired template and refer to it in the .font80[**YAML**] header.

```yaml
---
title: Awesome report
author: Me, You, Them
date: 2021-03-01
output:
  pdf_document:
    template: my_template.tex
---
```

---

# <svg viewBox="0 0 448 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M448 360V24c0-13.3-10.7-24-24-24H96C43 0 0 43 0 96v320c0 53 43 96 96 96h328c13.3 0 24-10.7 24-24v-16c0-7.5-3.5-14.3-8.9-18.7-4.2-15.4-4.2-59.3 0-74.7 5.4-4.3 8.9-11.1 8.9-18.6zM128 134c0-3.3 2.7-6 6-6h212c3.3 0 6 2.7 6 6v20c0 3.3-2.7 6-6 6H134c-3.3 0-6-2.7-6-6v-20zm0 64c0-3.3 2.7-6 6-6h212c3.3 0 6 2.7 6 6v20c0 3.3-2.7 6-6 6H134c-3.3 0-6-2.7-6-6v-20zm253.4 250H96c-17.7 0-32-14.3-32-32 0-17.6 14.4-32 32-32h285.4c-1.9 17.1-1.9 46.9 0 64z"></path></svg> The `down` universe

- [`bookdown`](https://bookdown.org/): Write a notebook
- [`csasdown`](https://github.com/pbs-assess/csasdown): Write a CSAS document
- [`thesisdown`](https://github.com/ismayc/thesisdown): Write a thesis
- [`rticles`](https://github.com/rstudio/rticles): Write a scientific article
- [`posterdown`](https://github.com/brentthorne/posterdown): Create a poster
- [`xaringan`](https://github.com/yihui/xaringan): Create nice presentation
- [`vitae`](https://github.com/mitchelloharawild/vitae): Build a CV
- [`blogdown`](https://bookdown.org/yihui/blogdown/): Generate a blog
- [`pkgdown`](https://pkgdown.r-lib.org/): Generate R package documentation

---

# Wrapping up

![:custom_hr]()

---

# Wrapping up

✔️ **Document your document**: use YAML to set up meaningful metadata

✔️ **Style your document**: use YAML to add options to your chosen output format

✔️ **Organize your text**: use markdown headers with `#`

✔️ **Organize your code**: use `knitr` chunk labels

✔️ **Style your text**: use markdown **bold**, *italics*, <svg viewBox="0 0 512 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M48 48a48 48 0 1 0 48 48 48 48 0 0 0-48-48zm0 160a48 48 0 1 0 48 48 48 48 0 0 0-48-48zm0 160a48 48 0 1 0 48 48 48 48 0 0 0-48-48zm448 16H176a16 16 0 0 0-16 16v32a16 16 0 0 0 16 16h320a16 16 0 0 0 16-16v-32a16 16 0 0 0-16-16zm0-320H176a16 16 0 0 0-16 16v32a16 16 0 0 0 16 16h320a16 16 0 0 0 16-16V80a16 16 0 0 0-16-16zm0 160H176a16 16 0 0 0-16 16v32a16 16 0 0 0 16 16h320a16 16 0 0 0 16-16v-32a16 16 0 0 0-16-16z"></path></svg> bullets, <svg viewBox="0 0 512 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M61.77 401l17.5-20.15a19.92 19.92 0 0 0 5.07-14.19v-3.31C84.34 356 80.5 352 73 352H16a8 8 0 0 0-8 8v16a8 8 0 0 0 8 8h22.83a157.41 157.41 0 0 0-11 12.31l-5.61 7c-4 5.07-5.25 10.13-2.8 14.88l1.05 1.93c3 5.76 6.29 7.88 12.25 7.88h4.73c10.33 0 15.94 2.44 15.94 9.09 0 4.72-4.2 8.22-14.36 8.22a41.54 41.54 0 0 1-15.47-3.12c-6.49-3.88-11.74-3.5-15.6 3.12l-5.59 9.31c-3.72 6.13-3.19 11.72 2.63 15.94 7.71 4.69 20.38 9.44 37 9.44 34.16 0 48.5-22.75 48.5-44.12-.03-14.38-9.12-29.76-28.73-34.88zM496 224H176a16 16 0 0 0-16 16v32a16 16 0 0 0 16 16h320a16 16 0 0 0 16-16v-32a16 16 0 0 0-16-16zm0-160H176a16 16 0 0 0-16 16v32a16 16 0 0 0 16 16h320a16 16 0 0 0 16-16V80a16 16 0 0 0-16-16zm0 320H176a16 16 0 0 0-16 16v32a16 16 0 0 0 16 16h320a16 16 0 0 0 16-16v-32a16 16 0 0 0-16-16zM16 160h64a8 8 0 0 0 8-8v-16a8 8 0 0 0-8-8H64V40a8 8 0 0 0-8-8H32a8 8 0 0 0-7.14 4.42l-8 16A8 8 0 0 0 24 64h8v64H16a8 8 0 0 0-8 8v16a8 8 0 0 0 8 8zm-3.91 160H80a8 8 0 0 0 8-8v-16a8 8 0 0 0-8-8H41.32c3.29-10.29 48.34-18.68 48.34-56.44 0-29.06-25-39.56-44.47-39.56-21.36 0-33.8 10-40.46 18.75-4.37 5.59-3 10.84 2.8 15.37l8.58 6.88c5.61 4.56 11 2.47 16.12-2.44a13.44 13.44 0 0 1 9.46-3.84c3.33 0 9.28 1.56 9.28 8.75C51 248.19 0 257.31 0 304.59v4C0 316 5.08 320 12.09 320z"></path></svg> lists, hyperlinks, ...

✔️ **Style your output**: use `knitr` chunk options

✔️ **Add a bibliography**: use `@id`, `mybiblio.bib`, `mystyle.csl`

✔️ **Customize your documents**: use themes and templates, or other tools

✔️ **Export your document**: use `rmarkdown::render()`

✔️ **Enjoy a simplified life** .font50[most of the time]

---

# Exercise

![:custom_hr]()

---

# Exercise

## Context

- *The goal of the exercise is to apply what we have seen today to update the dynamic document with generated yesterday using R Markdown.*

- *We will thus begin where we left off yesterday, i.e. with the `.rmd` you created.*

---

# Exercise

## Task

**2)** Give the labels `table` and `figure` to the code chunks;

**3)** Modify code chunk options so that the code is not visible in the report;

**4)** Modify `figure` code chunk options to set figure size and include a caption;

**5)** Format `table` using `knitr::kable`. For more advanced users, you can use the [`kableExtra`](https://cran.r-project.org/package=kableExtra) R Package to format the table

**6)** Using your reference manager, export a bibliographic file in BiBTeX format titled `mybiblio.bib` and store it in the same folder as your `.rmd` file;

**7)** Include `mybiblio.bib` to the .font80[**YAML**] header;

**8)** Within the document body, add citations from your bibliographic files using proper citation keys `@id`;
]

---

# Exercise

## Task

.font90[
**9)** Change the default citation format (Chicago style) for the format from *The American Naturalist*:

- Download the `csl` file from [https://www.zotero.org/styles](https://www.zotero.org/styles) and store it in the same folder as your `.rmd` file

- Include `new-style.csl` to the .font80[**YAML**] header

**10)** Add a section header at the end for your reference list

**11)** For the html document output, use the `lumen` theme

**12)** Render `.html`, `.pdf` and `.docx` documents.
]

---

# Exercise

## Solution

---

# <svg viewBox="0 0 512 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M502.63 214.63l-45.25-45.25c-6-6-14.14-9.37-22.63-9.37H384V80c0-26.51-21.49-48-48-48H176c-26.51 0-48 21.49-48 48v80H77.25c-8.49 0-16.62 3.37-22.63 9.37L9.37 214.63c-6 6-9.37 14.14-9.37 22.63V320h128v-16c0-8.84 7.16-16 16-16h32c8.84 0 16 7.16 16 16v16h128v-16c0-8.84 7.16-16 16-16h32c8.84 0 16 7.16 16 16v16h128v-82.75c0-8.48-3.37-16.62-9.37-22.62zM320 160H192V96h128v64zm64 208c0 8.84-7.16 16-16 16h-32c-8.84 0-16-7.16-16-16v-16H192v16c0 8.84-7.16 16-16 16h-32c-8.84 0-16-7.16-16-16v-16H0v96c0 17.67 14.33 32 32 32h448c17.67 0 32-14.33 32-32v-96H384v16z"></path></svg> Towards the gold standard

![:custom_hr]()

???

A word about setting up those tools depending on the environment.
A word about that all are not needed.

---
# Gold standard

.font80[<svg viewBox="0 0 384 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M369.9 97.9L286 14C277 5 264.8-.1 252.1-.1H48C21.5 0 0 21.5 0 48v416c0 26.5 21.5 48 48 48h288c26.5 0 48-21.5 48-48V131.9c0-12.7-5.1-25-14.1-34zM332.1 128H256V51.9l76.1 76.1zM48 464V48h160v104c0 13.3 10.7 24 24 24h104v288H48z"></path></svg> Peng. (2011).
[Reproducible Research in Computational Science.](https://science.sciencemag.org/content/334/6060/1226)]

### Towards full reproducibility, technologies are getting more complex

---
# Gold standard

<br>

???

A tool box of software
Coding a lot

---
# Version control ✋

### **I've changed something... not sure what... but it no longer works!**

<br>

### **Keep track of code changes!**

- to talk about the same piece of code

- to easily go back in time

- to tag code versions

---
# Version control

### Local versioning

---
# Version control

### Centralized version control

---
# Version control with Git

### Distributed version control such as Git

<br>

- [GitKraken](https://www.gitkraken.com/)
- [GitHub Desktop](https://desktop.github.com/)
- R Studio

---
# Version control with Git + GitHub/Gitlab

### e.g. The [<svg viewBox="0 0 496 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M165.9 397.4c0 2-2.3 3.6-5.2 3.6-3.3.3-5.6-1.3-5.6-3.6 0-2 2.3-3.6 5.2-3.6 3-.3 5.6 1.3 5.6 3.6zm-31.1-4.5c-.7 2 1.3 4.3 4.3 4.9 2.6 1 5.6 0 6.2-2s-1.3-4.3-4.3-5.2c-2.6-.7-5.5.3-6.2 2.3zm44.2-1.7c-2.9.7-4.9 2.6-4.6 4.9.3 2 2.9 3.3 5.9 2.6 2.9-.7 4.9-2.6 4.6-4.6-.3-1.9-3-3.2-5.9-2.9zM244.8 8C106.1 8 0 113.3 0 252c0 110.9 69.8 205.8 169.5 239.2 12.8 2.3 17.3-5.6 17.3-12.1 0-6.2-.3-40.4-.3-61.4 0 0-70 15-84.7-29.8 0 0-11.4-29.1-27.8-36.6 0 0-22.9-15.7 1.6-15.4 0 0 24.9 2 38.6 25.8 21.9 38.6 58.6 27.5 72.9 20.9 2.3-16 8.8-27.1 16-33.7-55.9-6.2-112.3-14.3-112.3-110.5 0-27.5 7.6-41.3 23.6-58.9-2.6-6.5-11.1-33.3 2.6-67.9 20.9-6.5 69 27 69 27 20-5.6 41.5-8.5 62.8-8.5s42.8 2.9 62.8 8.5c0 0 48.1-33.6 69-27 13.7 34.7 5.2 61.4 2.6 67.9 16 17.7 25.8 31.5 25.8 58.9 0 96.5-58.9 104.2-114.8 110.5 9.2 7.9 17 22.9 17 46.4 0 33.7-.3 75.4-.3 83.6 0 6.5 4.6 14.4 17.3 12.1C428.2 457.8 496 362.9 496 252 496 113.3 383.5 8 244.8 8zM97.2 352.9c-1.3 1-1 3.3.7 5.2 1.6 1.6 3.9 2.3 5.2 1 1.3-1 1-3.3-.7-5.2-1.6-1.6-3.9-2.3-5.2-1zm-10.8-8.1c-.7 1.3.3 2.9 2.3 3.9 1.6 1 3.6.7 4.3-.7.7-1.3-.3-2.9-2.3-3.9-2-.6-3.6-.3-4.3.7zm32.4 35.6c-1.6 1.3-1 4.3 1.3 6.2 2.3 2.3 5.2 2.6 6.5 1 1.3-1.3.7-4.3-1.3-6.2-2.2-2.3-5.2-2.6-6.5-1zm-11.4-14.7c-1.6 1-1.6 3.6 0 5.9 1.6 2.3 4.3 3.3 5.6 2.3 1.6-1.3 1.6-3.9 0-6.2-1.4-2.3-4-3.3-5.6-2z"></path></svg>](https://github.com/inSilecoInc/workshop_reproducibility) repository for this workshop !

???

push and pull
show repo
git log 
git pulll

---
# Use a pipeline toolkit: [GNU Make](https://www.gnu.org/software/make/manual/make.html)

### 1. Create a file `makefile` (or `Makefile`) [<svg viewBox="0 0 384 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M369.9 97.9L286 14C277 5 264.8-.1 252.1-.1H48C21.5 0 0 21.5 0 48v416c0 26.5 21.5 48 48 48h288c26.5 0 48-21.5 48-48V131.9c0-12.7-5.1-25-14.1-34zM332.1 128H256V51.9l76.1 76.1zM48 464V48h160v104c0 13.3 10.7 24 24 24h104v288H48z"></path></svg>](https://raw.githubusercontent.com/inSilecoInc/workshop_reproducibility/main/demo/makefile)

### 2. Write down what it needs to do (steps of your workflow)

```sh
all: ms code
	
ms: code ms/ms.Rmd 
	Rscript -e 'rmarkdown::render("ms/ms.Rmd")'

code: 
	Rscript -e 'lapply(list.files("R", full.names = TRUE), source); pipeline()'
```

### 3. Use `make` command e.g. `make` or `make ms`

???

Not R-specific

---
# Use a pipeline toolkit: [targets](https://www.gnu.org/software/make/manual/make.html)

> The targets package is a Make-like pipeline toolkit for Statistics and data science in R.

<br>

]

<img src="https://docs.ropensci.org/targets/reference/figures/logo.png" width="85%" style="display: block; margin: auto;" />
]

---
# Use a pipeline toolkit: [targets](https://www.gnu.org/software/make/manual/make.html)

### 1. Create a `_targets.R` file at the root of your repository [<svg viewBox="0 0 512 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M464 128H272l-54.63-54.63c-6-6-14.14-9.37-22.63-9.37H48C21.49 64 0 85.49 0 112v288c0 26.51 21.49 48 48 48h416c26.51 0 48-21.49 48-48V176c0-26.51-21.49-48-48-48zm0 272H48V112h140.12l54.63 54.63c6 6 14.14 9.37 22.63 9.37H464v224z"></path></svg>](https://github.com/inSilecoInc/workshop_reproducibility/raw/main/demo/targets_workflow.zip)

```r
library(targets)
library(tarchetypes)
rsrc <- lapply(list.files("R", full.names = TRUE), source)
options(tidyverse.quiet = TRUE)
tar_option_set(packages = c("weathercan", "tidyverse"))
list(
  tar_target(data, get_data()),
  tar_target(tab1, create_tab1(data)),
  tar_target(fig1, create_fig1(data)),
  tar_render(report, "ms/ms.Rmd")
)
```

### 2. use `tar_make()`

---
# Structure your repo as an R package

## Why?

### 1. Because the structure of an R package is very relevant for research compendia

### 2. Because R developers created great packages to develop packages!

---
# Structure your repo as an R package

## Basic structure of an R package

```sh
.
├── DESCRIPTION
├── doc
├── data
├── LICENSE
├── man
├── NAMESPACE
├── R
├── README.md
├── tests
└── vignettes
```

---
# Structure your repo as an R package

## Basic structure of an R package

```sh
.
├── DESCRIPTION # includes info about package versions
├── doc         # include a website
├── data
├── LICENSE     # always good to specify a license
├── man         # document function
├── NAMESPACE   # no need
├── R
├── README.md
├── tests       # test your code
└── vignettes   # include your ms
```

---
# Make a R package !

## Is it an overkill?

### **NO!**

- Jim Hester (2018) [You can make a package in 20 minutes](https://rstudio.com/resources/rstudioconf-2018/you-can-make-a-package-in-20-minutes-jim-hester/)

- The collection of packages for developers makes every steps easy

- This is a very good avenue to go further

???

Yes... it might be a steep learning curve but it's worth it.

---
# Make a R package !

## Benefit from popular development tools

---
# Make a R package !

### It structures your workflow

```R
library(devtools)
# load all functions
load_all()
# document functions and edit Namespace
document()
# test functions
test()
# check the package integrity
check()
```

???

shared workflow

---
# Make a R package !

## Benefit from popular development tools

---
# Make a R package !

> usethis is a workflow package: it automates repetitive tasks that arise during project setup and development, both for R packages and non-package projects.

```R
library(usethis)
usethis::use_gpl_license()
usethis::use_citation()
```

---
# Manage your dependencies

## Different R versions, different results!

```R
# R 3.6
df <- data.frame(fact = rep(c("F1", "F2"), each = 5), val = runif(10))
plot(val ~ fact, data = df)   # works
# R 4.0
df <- data.frame(fact = rep(c("F1", "F2"), each = 5), val = runif(10))
plot(val ~ fact, data = df)   # does not work
```

---
# Manage your dependencies

---
# Manage your dependencies

## Save all dependencies in renv.lock and install them later seamlessly

```R
renv::init()
renv::snapshot()
# later (on another device)
renv::restore()
```

---
# Continuous Integration (CI)

## Check your code on a freshly installed machine

<br>

## Again, with an R package, everything goes smoothly

```R
usethis::use_github_action_check_standard()
```

???

start thinking about OS agnosticism

---
# Use a container with [Docker <svg viewBox="0 0 640 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M349.9 236.3h-66.1v-59.4h66.1v59.4zm0-204.3h-66.1v60.7h66.1V32zm78.2 144.8H362v59.4h66.1v-59.4zm-156.3-72.1h-66.1v60.1h66.1v-60.1zm78.1 0h-66.1v60.1h66.1v-60.1zm276.8 100c-14.4-9.7-47.6-13.2-73.1-8.4-3.3-24-16.7-44.9-41.1-63.7l-14-9.3-9.3 14c-18.4 27.8-23.4 73.6-3.7 103.8-8.7 4.7-25.8 11.1-48.4 10.7H2.4c-8.7 50.8 5.8 116.8 44 162.1 37.1 43.9 92.7 66.2 165.4 66.2 157.4 0 273.9-72.5 328.4-204.2 21.4.4 67.6.1 91.3-45.2 1.5-2.5 6.6-13.2 8.5-17.1l-13.3-8.9zm-511.1-27.9h-66v59.4h66.1v-59.4zm78.1 0h-66.1v59.4h66.1v-59.4zm78.1 0h-66.1v59.4h66.1v-59.4zm-78.1-72.1h-66.1v60.1h66.1v-60.1z"></path></svg>](https://www.docker.com/)

> Containers are a standardized unit of software that allows developers to
> isolate their app from its environment, solving the “it works on my machine”
> headache.

###  docker allows you

- to create images (via dockerfiles)

- to use images!

<br>

```sh
$ docker run --rm -ti rocker/r-base
```

Run your code directly in the container!

---
# Holepunch

> `holepunch` will read the contents of your R project on GitHub, create a DESCRIPTION file with all dependencies, write a Dockerfile, add a badge to your README, and build a Docker image. Once these 4 steps are complete, any reader can click the badge and within minutes, be dropped into a free, live, RStudio server.

### - Uses [Binder](https://mybinder.org/) (GitHub repo ==> Docker image) + RStudio server.

### - Example: <svg viewBox="0 0 496 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M165.9 397.4c0 2-2.3 3.6-5.2 3.6-3.3.3-5.6-1.3-5.6-3.6 0-2 2.3-3.6 5.2-3.6 3-.3 5.6 1.3 5.6 3.6zm-31.1-4.5c-.7 2 1.3 4.3 4.3 4.9 2.6 1 5.6 0 6.2-2s-1.3-4.3-4.3-5.2c-2.6-.7-5.5.3-6.2 2.3zm44.2-1.7c-2.9.7-4.9 2.6-4.6 4.9.3 2 2.9 3.3 5.9 2.6 2.9-.7 4.9-2.6 4.6-4.6-.3-1.9-3-3.2-5.9-2.9zM244.8 8C106.1 8 0 113.3 0 252c0 110.9 69.8 205.8 169.5 239.2 12.8 2.3 17.3-5.6 17.3-12.1 0-6.2-.3-40.4-.3-61.4 0 0-70 15-84.7-29.8 0 0-11.4-29.1-27.8-36.6 0 0-22.9-15.7 1.6-15.4 0 0 24.9 2 38.6 25.8 21.9 38.6 58.6 27.5 72.9 20.9 2.3-16 8.8-27.1 16-33.7-55.9-6.2-112.3-14.3-112.3-110.5 0-27.5 7.6-41.3 23.6-58.9-2.6-6.5-11.1-33.3 2.6-67.9 20.9-6.5 69 27 69 27 20-5.6 41.5-8.5 62.8-8.5s42.8 2.9 62.8 8.5c0 0 48.1-33.6 69-27 13.7 34.7 5.2 61.4 2.6 67.9 16 17.7 25.8 31.5 25.8 58.9 0 96.5-58.9 104.2-114.8 110.5 9.2 7.9 17 22.9 17 46.4 0 33.7-.3 75.4-.3 83.6 0 6.5 4.6 14.4 17.3 12.1C428.2 457.8 496 362.9 496 252 496 113.3 383.5 8 244.8 8zM97.2 352.9c-1.3 1-1 3.3.7 5.2 1.6 1.6 3.9 2.3 5.2 1 1.3-1 1-3.3-.7-5.2-1.6-1.6-3.9-2.3-5.2-1zm-10.8-8.1c-.7 1.3.3 2.9 2.3 3.9 1.6 1 3.6.7 4.3-.7.7-1.3-.3-2.9-2.3-3.9-2-.6-3.6-.3-4.3.7zm32.4 35.6c-1.6 1.3-1 4.3 1.3 6.2 2.3 2.3 5.2 2.6 6.5 1 1.3-1.3.7-4.3-1.3-6.2-2.2-2.3-5.2-2.6-6.5-1zm-11.4-14.7c-1.6 1-1.6 3.6 0 5.9 1.6 2.3 4.3 3.3 5.6 2.3 1.6-1.3 1.6-3.9 0-6.2-1.4-2.3-4-3.3-5.6-2z"></path></svg> [HomogenFishOntario](https://github.com/McCannLab/HomogenFishOntario)!

---
# Archive your code/data with [Zenodo](https://zenodo.org/)

---
class: inverse, center, middle

# <svg viewBox="0 0 512 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M256 8C119.043 8 8 119.083 8 256c0 136.997 111.043 248 248 248s248-111.003 248-248C504 119.083 392.957 8 256 8zm0 110c23.196 0 42 18.804 42 42s-18.804 42-42 42-42-18.804-42-42 18.804-42 42-42zm56 254c0 6.627-5.373 12-12 12h-88c-6.627 0-12-5.373-12-12v-24c0-6.627 5.373-12 12-12h12v-64h-12c-6.627 0-12-5.373-12-12v-24c0-6.627 5.373-12 12-12h64c6.627 0 12 5.373 12 12v100h12c6.627 0 12 5.373 12 12v24z"></path></svg> Resources

![:custom_hr]()

---
# Resources <svg viewBox="0 0 512 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M326.612 185.391c59.747 59.809 58.927 155.698.36 214.59-.11.12-.24.25-.36.37l-67.2 67.2c-59.27 59.27-155.699 59.262-214.96 0-59.27-59.26-59.27-155.7 0-214.96l37.106-37.106c9.84-9.84 26.786-3.3 27.294 10.606.648 17.722 3.826 35.527 9.69 52.721 1.986 5.822.567 12.262-3.783 16.612l-13.087 13.087c-28.026 28.026-28.905 73.66-1.155 101.96 28.024 28.579 74.086 28.749 102.325.51l67.2-67.19c28.191-28.191 28.073-73.757 0-101.83-3.701-3.694-7.429-6.564-10.341-8.569a16.037 16.037 0 0 1-6.947-12.606c-.396-10.567 3.348-21.456 11.698-29.806l21.054-21.055c5.521-5.521 14.182-6.199 20.584-1.731a152.482 152.482 0 0 1 20.522 17.197zM467.547 44.449c-59.261-59.262-155.69-59.27-214.96 0l-67.2 67.2c-.12.12-.25.25-.36.37-58.566 58.892-59.387 154.781.36 214.59a152.454 152.454 0 0 0 20.521 17.196c6.402 4.468 15.064 3.789 20.584-1.731l21.054-21.055c8.35-8.35 12.094-19.239 11.698-29.806a16.037 16.037 0 0 0-6.947-12.606c-2.912-2.005-6.64-4.875-10.341-8.569-28.073-28.073-28.191-73.639 0-101.83l67.2-67.19c28.239-28.239 74.3-28.069 102.325.51 27.75 28.3 26.872 73.934-1.155 101.96l-13.087 13.087c-4.35 4.35-5.769 10.79-3.783 16.612 5.864 17.194 9.042 34.999 9.69 52.721.509 13.906 17.454 20.446 27.294 10.606l37.106-37.106c59.271-59.259 59.271-155.699.001-214.959z"></path></svg>

.font80[<svg viewBox="0 0 496 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M165.9 397.4c0 2-2.3 3.6-5.2 3.6-3.3.3-5.6-1.3-5.6-3.6 0-2 2.3-3.6 5.2-3.6 3-.3 5.6 1.3 5.6 3.6zm-31.1-4.5c-.7 2 1.3 4.3 4.3 4.9 2.6 1 5.6 0 6.2-2s-1.3-4.3-4.3-5.2c-2.6-.7-5.5.3-6.2 2.3zm44.2-1.7c-2.9.7-4.9 2.6-4.6 4.9.3 2 2.9 3.3 5.9 2.6 2.9-.7 4.9-2.6 4.6-4.6-.3-1.9-3-3.2-5.9-2.9zM244.8 8C106.1 8 0 113.3 0 252c0 110.9 69.8 205.8 169.5 239.2 12.8 2.3 17.3-5.6 17.3-12.1 0-6.2-.3-40.4-.3-61.4 0 0-70 15-84.7-29.8 0 0-11.4-29.1-27.8-36.6 0 0-22.9-15.7 1.6-15.4 0 0 24.9 2 38.6 25.8 21.9 38.6 58.6 27.5 72.9 20.9 2.3-16 8.8-27.1 16-33.7-55.9-6.2-112.3-14.3-112.3-110.5 0-27.5 7.6-41.3 23.6-58.9-2.6-6.5-11.1-33.3 2.6-67.9 20.9-6.5 69 27 69 27 20-5.6 41.5-8.5 62.8-8.5s42.8 2.9 62.8 8.5c0 0 48.1-33.6 69-27 13.7 34.7 5.2 61.4 2.6 67.9 16 17.7 25.8 31.5 25.8 58.9 0 96.5-58.9 104.2-114.8 110.5 9.2 7.9 17 22.9 17 46.4 0 33.7-.3 75.4-.3 83.6 0 6.5 4.6 14.4 17.3 12.1C428.2 457.8 496 362.9 496 252 496 113.3 383.5 8 244.8 8zM97.2 352.9c-1.3 1-1 3.3.7 5.2 1.6 1.6 3.9 2.3 5.2 1 1.3-1 1-3.3-.7-5.2-1.6-1.6-3.9-2.3-5.2-1zm-10.8-8.1c-.7 1.3.3 2.9 2.3 3.9 1.6 1 3.6.7 4.3-.7.7-1.3-.3-2.9-2.3-3.9-2-.6-3.6-.3-4.3.7zm32.4 35.6c-1.6 1.3-1 4.3 1.3 6.2 2.3 2.3 5.2 2.6 6.5 1 1.3-1.3.7-4.3-1.3-6.2-2.2-2.3-5.2-2.6-6.5-1zm-11.4-14.7c-1.6 1-1.6 3.6 0 5.9 1.6 2.3 4.3 3.3 5.6 2.3 1.6-1.3 1.6-3.9 0-6.2-1.4-2.3-4-3.3-5.6-2z"></path></svg> Casajus N., Dray S., Gimenez O., Guéry L., Guilhaumon F. & Schiettekatte N. M. D. (2020) Formation FRB CESAB / GDR ECOSTAT : Bonnes pratiques pour une recherche reproductible en écologie numérique (Version 2020). Zenodo. http://doi.org/10.5281/zenodo.4262978.]

## Reproducibility

- [Barba-group reproducibility syllabus](https://medium.com/hackernoon/barba-group-reproducibility-syllabus-e3757ee635cf#.h603izuwo)
- [What does research reproducibility mean?](https://stm.sciencemag.org/content/8/341/341ps12.full)
- [Retracted Science and the Retraction Index](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3187237/)
- [Questionable research practices in ecology and evolution](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0200303)
- [An interesting GiHub thread](https://github.com/ReScience/ReScience-article/issues/5)
- [Ten Simple Rules for Reproducible Computational
Research](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003285)

## Open Science Framework

- [COS: Strategic Plan, v2.0](https://docs.google.com/document/d/1sqz3appQ73vqa6fP1Gy8KK8HZpotoSGaiJC1XQuvREI/edit)
- [50 cancer studies](https://www.sciencemag.org/news/2018/07/plan-replicate-50-high-impact-cancer-papers-shrinks-just-18)
- [Reproducibility Project: Cancer Biology](https://elifesciences.org/collections/9b1e83d1/reproducibility-project-cancer-biology)

## Research Compendium

- [rOpenSci](https://ropensci.org/)
- [rOpenSci Packages: Development, Maintenance, and Peer Review](https://devguide.ropensci.org/index.html)
- [R for Reproducible Scientific Analysis](https://swcarpentry.github.io/r-novice-gapminder/)
- [Reproducible Analysis With R](https://nceas.github.io/sasap-training/materials/reproducible_research_in_r_fairbanks/)
- [Formation FRB-Cesab & GDR EcoStat (fr)](https://frbcesab.github.io/datatoolbox/index.html#1)
- [Research Compendium](https://research-compendium.science/) landing page
- [rrrpkg](https://github.com/ropensci/rrrpkg)
- [rrtools](https://github.com/benmarwick/rrtools)

## R Markdown

### 🇬🇧

- [R Markdown: The Definitive Guide](https://bookdown.org/yihui/rmarkdown/)
- [R Markdown Cookbook](https://bookdown.org/yihui/rmarkdown-cookbook/)
- [Touchdown your research with R Markdown](https://insileco.github.io/ResearchDown/#1)
- [R MarkdownReference Guide](https://rstudio.com/wp-content/uploads/2015/03/rmarkdown-reference.pdf)
- [Writing dynamic and reproducible documents](https://frbcesab.github.io/datatoolbox/courses/rmarkdown/index.html)

### 🇫🇷

- [Utiliser R Markdown pour créer des documents dynamiques](https://kevcaz.github.io/Rmarkdowndocfr/)
- https://nicolascasajus.fr/mastering-markdown/#67

---
# inSileco

- <svg viewBox="0 0 496 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M336.5 160C322 70.7 287.8 8 248 8s-74 62.7-88.5 152h177zM152 256c0 22.2 1.2 43.5 3.3 64h185.3c2.1-20.5 3.3-41.8 3.3-64s-1.2-43.5-3.3-64H155.3c-2.1 20.5-3.3 41.8-3.3 64zm324.7-96c-28.6-67.9-86.5-120.4-158-141.6 24.4 33.8 41.2 84.7 50 141.6h108zM177.2 18.4C105.8 39.6 47.8 92.1 19.3 160h108c8.7-56.9 25.5-107.8 49.9-141.6zM487.4 192H372.7c2.1 21 3.3 42.5 3.3 64s-1.2 43-3.3 64h114.6c5.5-20.5 8.6-41.8 8.6-64s-3.1-43.5-8.5-64zM120 256c0-21.5 1.2-43 3.3-64H8.6C3.2 212.5 0 233.8 0 256s3.2 43.5 8.6 64h114.6c-2-21-3.2-42.5-3.2-64zm39.5 96c14.5 89.3 48.7 152 88.5 152s74-62.7 88.5-152h-177zm159.3 141.6c71.4-21.2 129.4-73.7 158-141.6h-108c-8.8 56.9-25.6 107.8-50 141.6zM19.3 352c28.6 67.9 86.5 120.4 158 141.6-24.4-33.8-41.2-84.7-50-141.6h-108z"></path></svg> inSileco website 🚧 https://insilecoinc.github.io/ 🚧
- <svg viewBox="0 0 496 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M165.9 397.4c0 2-2.3 3.6-5.2 3.6-3.3.3-5.6-1.3-5.6-3.6 0-2 2.3-3.6 5.2-3.6 3-.3 5.6 1.3 5.6 3.6zm-31.1-4.5c-.7 2 1.3 4.3 4.3 4.9 2.6 1 5.6 0 6.2-2s-1.3-4.3-4.3-5.2c-2.6-.7-5.5.3-6.2 2.3zm44.2-1.7c-2.9.7-4.9 2.6-4.6 4.9.3 2 2.9 3.3 5.9 2.6 2.9-.7 4.9-2.6 4.6-4.6-.3-1.9-3-3.2-5.9-2.9zM244.8 8C106.1 8 0 113.3 0 252c0 110.9 69.8 205.8 169.5 239.2 12.8 2.3 17.3-5.6 17.3-12.1 0-6.2-.3-40.4-.3-61.4 0 0-70 15-84.7-29.8 0 0-11.4-29.1-27.8-36.6 0 0-22.9-15.7 1.6-15.4 0 0 24.9 2 38.6 25.8 21.9 38.6 58.6 27.5 72.9 20.9 2.3-16 8.8-27.1 16-33.7-55.9-6.2-112.3-14.3-112.3-110.5 0-27.5 7.6-41.3 23.6-58.9-2.6-6.5-11.1-33.3 2.6-67.9 20.9-6.5 69 27 69 27 20-5.6 41.5-8.5 62.8-8.5s42.8 2.9 62.8 8.5c0 0 48.1-33.6 69-27 13.7 34.7 5.2 61.4 2.6 67.9 16 17.7 25.8 31.5 25.8 58.9 0 96.5-58.9 104.2-114.8 110.5 9.2 7.9 17 22.9 17 46.4 0 33.7-.3 75.4-.3 83.6 0 6.5 4.6 14.4 17.3 12.1C428.2 457.8 496 362.9 496 252 496 113.3 383.5 8 244.8 8zM97.2 352.9c-1.3 1-1 3.3.7 5.2 1.6 1.6 3.9 2.3 5.2 1 1.3-1 1-3.3-.7-5.2-1.6-1.6-3.9-2.3-5.2-1zm-10.8-8.1c-.7 1.3.3 2.9 2.3 3.9 1.6 1 3.6.7 4.3-.7.7-1.3-.3-2.9-2.3-3.9-2-.6-3.6-.3-4.3.7zm32.4 35.6c-1.6 1.3-1 4.3 1.3 6.2 2.3 2.3 5.2 2.6 6.5 1 1.3-1.3.7-4.3-1.3-6.2-2.2-2.3-5.2-2.6-6.5-1zm-11.4-14.7c-1.6 1-1.6 3.6 0 5.9 1.6 2.3 4.3 3.3 5.6 2.3 1.6-1.3 1.6-3.9 0-6.2-1.4-2.3-4-3.3-5.6-2z"></path></svg> https://github.com/inSilecoInc
- <svg viewBox="0 0 512 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M172.2 226.8c-14.6-2.9-28.2 8.9-28.2 23.8V301c0 10.2 7.1 18.4 16.7 22 18.2 6.8 31.3 24.4 31.3 45 0 26.5-21.5 48-48 48s-48-21.5-48-48V120c0-13.3-10.7-24-24-24H24c-13.3 0-24 10.7-24 24v248c0 89.5 82.1 160.2 175 140.7 54.4-11.4 98.3-55.4 109.7-109.7 17.4-82.9-37-157.2-112.5-172.2zM209 0c-9.2-.5-17 6.8-17 16v31.6c0 8.5 6.6 15.5 15 15.9 129.4 7 233.4 112 240.9 241.5.5 8.4 7.5 15 15.9 15h32.1c9.2 0 16.5-7.8 16-17C503.4 139.8 372.2 8.6 209 0zm.3 96c-9.3-.7-17.3 6.7-17.3 16.1v32.1c0 8.4 6.5 15.3 14.8 15.9 76.8 6.3 138 68.2 144.9 145.2.8 8.3 7.6 14.7 15.9 14.7h32.2c9.3 0 16.8-8 16.1-17.3-8.4-110.1-96.5-198.2-206.6-206.7z"></path></svg> https://github.com/inSileco/inSileco.github.io

- David Beauchesne [<svg viewBox="0 0 512 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M464 64H48C21.49 64 0 85.49 0 112v288c0 26.51 21.49 48 48 48h416c26.51 0 48-21.49 48-48V112c0-26.51-21.49-48-48-48zm0 48v40.805c-22.422 18.259-58.168 46.651-134.587 106.49-16.841 13.247-50.201 45.072-73.413 44.701-23.208.375-56.579-31.459-73.413-44.701C106.18 199.465 70.425 171.067 48 152.805V112h416zM48 400V214.398c22.914 18.251 55.409 43.862 104.938 82.646 21.857 17.205 60.134 55.186 103.062 54.955 42.717.231 80.509-37.199 103.053-54.947 49.528-38.783 82.032-64.401 104.947-82.653V400H48z"></path></svg>](mailto:david.beauchesne@hotmail.com)
- Kevin Cazelles [<svg viewBox="0 0 512 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M464 64H48C21.49 64 0 85.49 0 112v288c0 26.51 21.49 48 48 48h416c26.51 0 48-21.49 48-48V112c0-26.51-21.49-48-48-48zm0 48v40.805c-22.422 18.259-58.168 46.651-134.587 106.49-16.841 13.247-50.201 45.072-73.413 44.701-23.208.375-56.579-31.459-73.413-44.701C106.18 199.465 70.425 171.067 48 152.805V112h416zM48 400V214.398c22.914 18.251 55.409 43.862 104.938 82.646 21.857 17.205 60.134 55.186 103.062 54.955 42.717.231 80.509-37.199 103.053-54.947 49.528-38.783 82.032-64.401 104.947-82.653V400H48z"></path></svg>](mailto:kevin.cazelles@gmail.com)
- Steve Vissault [<svg viewBox="0 0 512 512" style="height:1em;fill:currentColor;position:relative;display:inline-block;top:.1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M464 64H48C21.49 64 0 85.49 0 112v288c0 26.51 21.49 48 48 48h416c26.51 0 48-21.49 48-48V112c0-26.51-21.49-48-48-48zm0 48v40.805c-22.422 18.259-58.168 46.651-134.587 106.49-16.841 13.247-50.201 45.072-73.413 44.701-23.208.375-56.579-31.459-73.413-44.701C106.18 199.465 70.425 171.067 48 152.805V112h416zM48 400V214.398c22.914 18.251 55.409 43.862 104.938 82.646 21.857 17.205 60.134 55.186 103.062 54.955 42.717.231 80.509-37.199 103.053-54.947 49.528-38.783 82.032-64.401 104.947-82.653V400H48z"></path></svg>](s.vissault@yahoo.fr)