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<!DOCTYPE html>
<html lang="" xml:lang="">
<head>
<title>Is Your Code Ready for Publication?</title>
<meta charset="utf-8" />
<script src="assets/header-attrs-2.9.2/header-attrs.js"></script>
<link href="assets/remark-css-0.0.1/hygge.css" rel="stylesheet" />
<link href="assets/remark-css-0.0.1/rutgers.css" rel="stylesheet" />
<link href="assets/remark-css-0.0.1/rutgers-fonts.css" rel="stylesheet" />
</head>
<body>
<textarea id="source">
class: center, middle, inverse, title-slide
# Is Your Code Ready for Publication?
## A Practical Guide to R Markdown
### <p>Joseph V. Casillas</p>
### <p>From Proposal to Publication:</br> Pathways to Open Science | 07-16-2021</p>
---
class: middle
# Hi! 👋🏼
.Large[
| | |
| ----------------------------------: | :-------------------------------------- |
| <svg aria-hidden="true" role="img" viewBox="0 0 512 512" style="height:1em;width:1em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:red;overflow:visible;position:relative;"><path d="M476 3.2L12.5 270.6c-18.1 10.4-15.8 35.6 2.2 43.2L121 358.4l287.3-253.2c5.5-4.9 13.3 2.6 8.6 8.3L176 407v80.5c0 23.6 28.5 32.9 42.5 15.8L282 426l124.6 52.2c14.2 6 30.4-2.9 33-18.2l72-432C515 7.8 493.3-6.8 476 3.2z"/></svg> | [email protected] |
| <svg aria-hidden="true" role="img" viewBox="0 0 512 512" style="height:1em;width:1em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:red;overflow:visible;position:relative;"><path d="M459.37 151.716c.325 4.548.325 9.097.325 13.645 0 138.72-105.583 298.558-298.558 298.558-59.452 0-114.68-17.219-161.137-47.106 8.447.974 16.568 1.299 25.34 1.299 49.055 0 94.213-16.568 130.274-44.832-46.132-.975-84.792-31.188-98.112-72.772 6.498.974 12.995 1.624 19.818 1.624 9.421 0 18.843-1.3 27.614-3.573-48.081-9.747-84.143-51.98-84.143-102.985v-1.299c13.969 7.797 30.214 12.67 47.431 13.319-28.264-18.843-46.781-51.005-46.781-87.391 0-19.492 5.197-37.36 14.294-52.954 51.655 63.675 129.3 105.258 216.365 109.807-1.624-7.797-2.599-15.918-2.599-24.04 0-57.828 46.782-104.934 104.934-104.934 30.213 0 57.502 12.67 76.67 33.137 23.715-4.548 46.456-13.32 66.599-25.34-7.798 24.366-24.366 44.833-46.132 57.827 21.117-2.273 41.584-8.122 60.426-16.243-14.292 20.791-32.161 39.308-52.628 54.253z"/></svg> | [@jvcasill](https://twitter.com/jvcasill) |
| <svg aria-hidden="true" role="img" viewBox="0 0 512 512" style="height:1em;width:1em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:red;overflow:visible;position:relative;"><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"/></svg> | https://github.com/jvcasillas/rmd_workshop |
| <svg aria-hidden="true" role="img" viewBox="0 0 512 512" style="height:1em;width:1em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:red;overflow:visible;position:relative;"><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"/></svg> | https://www.jvcasillas.com/rmd_workshop/index.html |
]
---
count: false
background-image: url(https://raw.githubusercontent.com/jvcasillas/media/master/rstats/memes/rstats_cult.png)
background-size: contain
---
exclude: true
count: false
class: center, middle
background-color: #fd9426
<iframe src="https://wall.sli.do/event/ba48cucz" width="1000" height="600" style="border:none;"></iframe>
---
class: middle, center
## About that title...
--
# .grey[Is your code ready for publication?]
--
.huge[.RUred[Yes!]]
---
class: middle
# What are we going to do today?
--
.Large[
1. What is RMarkdown and why should I use it?
2. Hands on examples
]
---
class: title-slide-section-red
background-image: url(https://cdn-images-1.medium.com/max/1600/1*gYQhlM7v6GyRuxaL8JtPIQ.png), url(https://upload.wikimedia.org/wikipedia/commons/thumb/4/48/Markdown-mark.svg/2000px-Markdown-mark.svg.png), url(https://www.rstudio.com/wp-content/uploads/2017/05/rmarkdown.png), url(https://upload.wikimedia.org/wikipedia/commons/thumb/7/7d/Tab_plus.svg/2000px-Tab_plus.svg.png), url(https://upload.wikimedia.org/wikipedia/commons/thumb/c/cf/Kennzeichnung_für_Äquivalenzglied.svg/2000px-Kennzeichnung_für_Äquivalenzglied.svg.png)
background-position: 5% 60%, 43% 60%, 95% 60%, 27% 60%, 62% 63%
background-size: 250px, 250px, 375px, 100px, 175px
# Let's go!
---
class: middle, center
background-image: url(https://raw.githubusercontent.com/jvcasillas/stats-illustrations/master/rstats-artwork/exploder.gif)
background-size: 200px
background-position: 50% 75%
# What is R?
---
class: middle, center
background-image: url(https://upload.wikimedia.org/wikipedia/commons/thumb/4/48/Markdown-mark.svg/2000px-Markdown-mark.svg.png)
background-size: 500px
background-position: 50% 25%
<br><br><br>
<br><br><br>
<br><br><br>
# What is markdown?
---
class: middle
# What is markdown?
.big[
- Markdown is a language used to format text
- Rather than click a button to format (like in word), you use markdown
syntax
- Lightweight markup language (like HTML but simple)
- Easy to read and write because it uses simple tags (e.g. #)
]
---
.pull-left[
# Raw markdown
<br><br><br><br>
.big[
```
# This is a section header
This is **bold** text.
This is *italic* text.
- This is
- a list
1. This is a
2. numbered list
```
]
]
--
.pull-right[
# Rendered markdown
<br><br>
## This is a section header
This is **.black[bold]** text.
This is *italic* text.
- This is
- a list
1. This is a
2. numbered list
]
---
class: middle
background-image: url(https://raw.githubusercontent.com/jvcasillas/stats-illustrations/master/rstats-artwork/rmarkdown_rockstar.png)
background-size: contain
background-position: 110% 50%
# What is</br>R Markdown?
.footnote[
Artwork by [@allison_horst](https://github.com/allisonhorst/stats-illustrations)
]
---
background-image: url(https://learn.r-journalism.com/publishing/rmarkdown/images/rmdfiles.png)
background-position: 95% 50%
# What is R Markdown?
.big[
- An authoring format that combines markdown syntax
and R code (R + markdown)
]
--
.big[
- An R Markdown file consists of 3 components...
- front matter
- plain text
- R code
]
--
.big[
- How does it do that?
]
---
background-image: url(https://cdn-images-1.medium.com/max/1600/1*gYQhlM7v6GyRuxaL8JtPIQ.png), url(https://upload.wikimedia.org/wikipedia/commons/thumb/4/48/Markdown-mark.svg/2000px-Markdown-mark.svg.png), url(https://www.rstudio.com/wp-content/uploads/2017/05/rmarkdown.png), url(https://upload.wikimedia.org/wikipedia/commons/thumb/7/7d/Tab_plus.svg/2000px-Tab_plus.svg.png), url(https://upload.wikimedia.org/wikipedia/commons/thumb/c/cf/Kennzeichnung_für_Äquivalenzglied.svg/2000px-Kennzeichnung_für_Äquivalenzglied.svg.png), url(http://hexb.in/vector/knitr.svg)
background-position: 18% 15%, 50% 20%, 88% 8%, 35% 20%, 65% 13%, 50% 85%
background-size: 200px, 200px, 275px, 100px, 175px, 275px
---
background-color: #f2f2f2
background-image: url(./assets/img/how_it_works.png)
background-size: contain
.big[
.RUred[`knitr` *knits* text and R code from an Rmd file<br>into an md file]
]
--
.footnote[
.big[
.blue[`pandoc` converts the md file to a desired output]
]
]
---
background-image: url(https://raw.githubusercontent.com/jvcasillas/stats-illustrations/master/rstats-artwork/rmarkdown_wizards.png)
background-size: contain
---
class: middle
# Why should you care?
---
background-image: url(https://raw.githubusercontent.com/jvcasillas/stats-illustrations/master/rstats-artwork/reproducibility_court.png)
background-size: contain
---
class: center, middle
# Why should you care?
### An RMardown file is a **dynamic document** that is fully reproducible
--
### It can be regenerated automatically whenever the R code or data changes
--
### It allows you to easily share your results
--
### It allows others to see exactly what you did
---
class: middle
# But how does it work?
--
.pull-left[
## Let's find out
### But first...
]
--
.pull-right[
## Installations
### You should have...
- R ✅
- RStudio ✅
- Some packages ❓
]
---
class: middle
background-image: url(https://github.com/jvcasillas/stats-illustrations/blob/master/rstats-artwork/tidyverse_celestial.png?raw=true)
background-size: contain
background-position: 100% 50%
```
install.packages("rmarkdown")
install.packages("knitr")
install.packages("tidyverse")
install.packages("here")
install.packages("broom")
install.packages("tinytex")
```
---
class: title-slide-section-red, middle
background-image: url(https://raw.githubusercontent.com/jvcasillas/stats-illustrations/master/rstats-artwork/rainbowr.gif)
background-position: 85% 50%
background-size: 200px
# Exercise I - Getting started
<!--
(template, first knit)
-->
---
count: false
background-image: url(./assets/img/new_rmd.gif)
background-size: 800px
background-position: 50% 50%
# Exercise I - Getting started
---
# Exercise I - Getting started
.large[
- Open RStudio
- File > New file > RMarkdown (then click "ok")
- Select all (cmd + a) and delete everything
- Type "hello world"
- Click "knit" (You will be asked to save. Save the file as `my_ex.Rmd` to your desktop)
- Add the following:
- a section header
- bold text
- an ordered list
- an unordered list
- a link to your favorite website
]
---
# Exercise I - Getting started
### Key ideas
.big[
- R Markdown files are just text files that end with **.Rmd**
- Markdown syntax!
- **knit** the Rmd file to get a specific output
]
---
exclude: true
count: false
class: center, middle
background-color: #fd9426
<iframe src="https://wall.sli.do/event/ba48cucz" width="1000" height="600" style="border:none;"></iframe>
---
class: title-slide-section-red, middle
background-image: url(https://coda.newjobs.com/api/imagesproxy/ms/cms/content30/images/greys-anatomy.jpg)
background-size: 300px
background-position: 95% 50%
# Anatomy of an Rmd document
<!--
(yaml, text, chunks)
-->
---
# Exercise II - Anatomy of an Rmd
.big[
- Add YAML front matter to `my_ex.Rmd`
- Add code chunks
- Knit to html
]
---
# Exercise II - Anatomy of an Rmd
### Key ideas
.big[
- **YAML** front matter is where we set things up, i.e., `output: html_document`
- Code **chunks**:
````
```{r, ex-chunk}
# R code here
2 + 2
```
````
- We ~~can~~ should name code chunks
- We can generate different output documents according to our needs
]
---
exclude: true
count: false
class: center, middle
background-color: #fd9426
<iframe src="https://wall.sli.do/event/ba48cucz" width="1000" height="600" style="border:none;"></iframe>
---
background-image: url(https://raw.githubusercontent.com/jvcasillas/media/master/rstats/memes/rstats_rmd.png)
background-size: contain
---
class: title-slide-section-red, middle
background-image: url(./assets/img/chunky_monkey.png)
background-size: 350px
background-position: 95% 50%
# Exercise III <br>More about chunks
<!--
(echo, eval, include)
-->
---
# Exercise III - More about chunks
### Chunk options
.big[
- `echo`: logical (TRUE/FALSE)
- `eval`: logical (TRUE/FALSE)
- `include`: logical (TRUE/FALSE)
]
---
# Exercise III - More about chunks
### Key ideas
.big[
- Code chunks have (many!) options
- We can take advantage of them to show/hide/evaluate/include R code
- Arguments are separated by commas
]
---
exclude: true
count: false
class: center, middle
background-color: #fd9426
<iframe src="https://wall.sli.do/event/ba48cucz" width="1000" height="600" style="border:none;"></iframe>
---
class: title-slide-section-red, middle
background-image: url(https://media.tenor.com/images/6beac3b4d75a09f9df7ad46458a9c5bb/tenor.gif)
background-size: 350px
background-position: 90% 50%
# Exercise IV - In-line code
<!--
(calculator math, objects)
-->
---
# Exercise IV - In-line code
.big[
- In-line calculations
- Printings objects
- Reporting results
]
---
# Exercise IV - In-line code
### Key ideas
.pull-left[
.big[
- We can use the power of the R console in prose
- Two plus two = 4
```r
Two plus two = `r 2 + 2`
```
- We can calculate summary statistics: The mean mpg is 20.090625
```r
The mean mpg is `r mean(mtcars$mpg)`
```
]
]
.pull-right[
.big[
- We can print most R objects: The mean mpg is 20.090625
```r
the_mean <- mean(mtcars$mpg)
The mean mpg is `r the_mean`
```
]
]
---
exclude: true
count: false
class: center, middle
background-color: #fd9426
<iframe src="https://wall.sli.do/event/ba48cucz" width="1000" height="600" style="border:none;"></iframe>
---
background-image: url(https://raw.githubusercontent.com/jvcasillas/stats-illustrations/master/rstats-artwork/r_first_then.png)
background-size: contain
---
# What's next?
### Publishing
.big[
- Plots and tables
- Writing results
- Different outputs
- References
- APA format with `papaja`
]
.footnote[
For these exercises we will use a `example_project`
Available here: https://www.jvcasillas.com/rmd_workshop/assets/example_project.zip
]
---
exclude: true
background-image: url(https://raw.githubusercontent.com/jvcasillas/stats-illustrations/master/rstats-artwork/presenting_monster.png)
background-size: contain
background-position: 50% 50%
---
exclude: true
background-image: url(https://raw.githubusercontent.com/tidyverse/ggplot2/master/man/figures/logo.png)
background-size: 225px
background-position: 95% 15%
# Exercise V - Plots and tables
<!--
(fig chunk options, results="asis")
-->
### Important chunk options
.big[
- .lightgrey[`echo`: logical (TRUE/FALSE)]
- .lightgrey[`eval`: logical (TRUE/FALSE)]
- .lightgrey[`include`: logical (TRUE/FALSE)]
- `results`: character ('hide', 'asis', etc.)
- figure options
- `fig.retina`: numeric (1 or 2)
- `fig.width`: numeric
- `fig.height`: numeric
- `fig.align`: character ('left', 'right', 'center')
]
.footnote[
For these exercises we will use a `example_project`
Available here: https://www.jvcasillas.com/rmd_workshop/assets/example_project.zip
]
---
exclude: true
# Publishing
.big[
- Different outputs
- Formatting
- References
- APA format with `papaja`
]
.footnote[
For these exercises we will use a `example_project`
Available here: https://www.jvcasillas.com/rmd_workshop/assets/example_project.zip
]
---
class: middle
background-image: url(./assets/img/rmd_01.png)
background-size: contain
background-position: 100% 50%
.pull-left[
.big[
RMarkdown allows you to write simple text documents that can be
converted to many differnt output formats
- HTML
- PDF
- Word
- HTML5 slides
- websites/blogs
- Beamer
- Tufte handouts
- Books
- dashboards
]
]
---
count: false
background-image: url(https://raw.githubusercontent.com/jvcasillas/media/master/rstats/memes/os_heartbreak.png)
background-size: contain
---
count: false
background-image: url(https://raw.githubusercontent.com/jvcasillas/stats-illustrations/master/rstats-artwork/r_rollercoaster.png)
background-size: contain
---
# More resources
.big[
- [Reproducible reports with RMarkdown](https://rmarkdown-shilaan.netlify.app/)
- [Boost Your R Markdown Skills](https://raukr-boost-rmd-skills.netlify.app/#1)
- [R Markdown for scientists](https://rmd4sci.njtierney.com)
- [All the chunk options!](https://yihui.org/knitr/options/)
- [All about papaja](http://frederikaust.com/papaja_man/)
]
---
count: false
background-image: url(https://www.r-project.org/Rlogo.png), url(./assets/img/prohibited.png), url(https://www.mcdwayne.com/wp-content/uploads/2018/05/I-love-markdown-syntax-language.png)
background-size: 200px, 350px, contain
background-position: 0% 80%, 66% 26%, 60% 60%
background-color: #e6e6e6
---
count: false
class: title-slide-final
background-image: url(https://github.com/jvcasillas/ru_xaringan/raw/master/img/logo/ru_shield.png), url(https://raw.githubusercontent.com/jvcasillas/stats-illustrations/master/rstats-artwork/rainbowr.gif)
background-size: 70px, 175px
background-position: 15% 15%, 95% 0%
<br>
# Thank you!
<br><br><br><br><br>
.Large[
| | |
| ----------------------------------: | :-------------------------------------- |
| <svg aria-hidden="true" role="img" viewBox="0 0 512 512" style="height:1em;width:1em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:red;overflow:visible;position:relative;"><path d="M476 3.2L12.5 270.6c-18.1 10.4-15.8 35.6 2.2 43.2L121 358.4l287.3-253.2c5.5-4.9 13.3 2.6 8.6 8.3L176 407v80.5c0 23.6 28.5 32.9 42.5 15.8L282 426l124.6 52.2c14.2 6 30.4-2.9 33-18.2l72-432C515 7.8 493.3-6.8 476 3.2z"/></svg> | .lightgrey[[email protected]] |
| <svg aria-hidden="true" role="img" viewBox="0 0 512 512" style="height:1em;width:1em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:red;overflow:visible;position:relative;"><path d="M459.37 151.716c.325 4.548.325 9.097.325 13.645 0 138.72-105.583 298.558-298.558 298.558-59.452 0-114.68-17.219-161.137-47.106 8.447.974 16.568 1.299 25.34 1.299 49.055 0 94.213-16.568 130.274-44.832-46.132-.975-84.792-31.188-98.112-72.772 6.498.974 12.995 1.624 19.818 1.624 9.421 0 18.843-1.3 27.614-3.573-48.081-9.747-84.143-51.98-84.143-102.985v-1.299c13.969 7.797 30.214 12.67 47.431 13.319-28.264-18.843-46.781-51.005-46.781-87.391 0-19.492 5.197-37.36 14.294-52.954 51.655 63.675 129.3 105.258 216.365 109.807-1.624-7.797-2.599-15.918-2.599-24.04 0-57.828 46.782-104.934 104.934-104.934 30.213 0 57.502 12.67 76.67 33.137 23.715-4.548 46.456-13.32 66.599-25.34-7.798 24.366-24.366 44.833-46.132 57.827 21.117-2.273 41.584-8.122 60.426-16.243-14.292 20.791-32.161 39.308-52.628 54.253z"/></svg> | .lightgrey[@jvcasill] |
| <svg aria-hidden="true" role="img" viewBox="0 0 512 512" style="height:1em;width:1em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:red;overflow:visible;position:relative;"><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"/></svg> | .lightgrey[https://github.com/jvcasillas/rmd_workshop] |
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]
.left[.footnote[.large[Hint: continue for more tips, tricks, and exercises!]]]
---
count: false
# More tips and tricks
### Efficiency
- For costly computations, large object, etc., it is a good idea to cache
- the option is `cache=TRUE`
- knitr won't rerun the chunk unless it is changed
- Saving large objects
- instead of refitting slow models every time you knit your document you can run the model once and save the output to an rds file
- use `saveRDS(model_object, PATH_WHERE_YOU_WANT_IT)`
- see `example_project` [here](https://github.com/jvcasillas/rmd_workshop/blob/master/assets/example_project.zip?raw=true) for a concrete example
### Common mistakes
- "It worked before and now I get an error!"
- Happens often when you do not restart your R session regularly
- Why? What happens when you knit?
new R session > set working directory to location of Rmd file > execute code chunks in order
- Pro tip: change RStudio default settings to not save sessions and not restore from Rdata (Preferences > General, under `Workspace` and `History`)
---
count: false
class: title-slide-section-grey, middle
# Writing reproducible scientific reports with papaja
---
count: false
# papaja
### Overview
- When publishing you have to adhere to the standards of the journal
- This is a pain in the neck
- Journals in Psychology use APA format and accept LaTeX, PDF, word,
and other file formats
- Most journals in linguistics accept (require) APA format and usually
only .docx (word) files (i.e., SSLA)
- If you ~~hate~~ dislike word this is annoying
---
count: false
# papaja
### What is papaja?
- An R package that formats documents (pdf, .docx) in APA format
- Basically it provides a template and helper functions for academic
writing
- It also provides templates for revision response letters
### Purpose?
- Simplify paper formatting
- The idea is that you don't have to worry about the little things
so you can 'just write'
- Because it uses RMarkdown you can integrate r code and create
reproducible reports
---
count: false
# papaja
### Why should I use it?
- Obvious benefits of using RMarkdown (reproducibility, flexibility, integration with github)
- Fast, easy
- Pandoc citations
1. Create a .bib file with references (more on this later)
2. Automatically generate references section in APA format
- Pre-prints
--
count: false
### How does it work?
- Install papaja
- Open new template
- Write and knit
- If you know RMarkdown, you know papaja
---
count: false
class: title-slide-section-grey, middle
# A simple example
---
count: false
background-image: url(./assets/img/papaja_1.png)
background-size: 400px
background-position: 99% 50%
# Exercise I
- If you haven't already, install `papaja`:
`remotes::install_github("crsh/papaja")`
- (Probably not necessary but...) restart RStudio
--
- Click the new file icon (white square with a green ".green[+]")
- Select `R Markdown...` > `From template` > `APA article (6th edition)`
- A template will open automatically. Inspect the file.
What is familiar? What is different?
--
- Save the file in `manuscript` and click "Knit" (probably get an error)
--
- Look for this section of the YAML front matter...
```
documentclass : "apa6"
classoption : "man"
output : papaja::apa6_word
---
```
- change **papaja::apa6_pdf** to .green[papaja::apa6_word] and knit
--
.pull-left[
- Make changes to the text and re-Knit
- Add r chunks
1. with simple math (i.e., 2 + 2)
2. with a plot using `ggplot2`
]
--
.pull-right[
</br>
- Open and inspect the .bib file
- Try to cite it in the text and re-Knit
]