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> | joseph.casillas@rutgers.edu | | <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[joseph.casillas@rutgers.edu] | | <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 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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] | | <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://www.jvcasillas.com/rmd_workshop/index.html] | ] .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 ] --- count: false class: title-slide-section-grey, middle # An advanced example --- count: false # Child and parent documents - Go to https://osf.io/cp9bs/ - Inspect the `docs` folder, then the `manuscript` folder -- - Click on `master.Rmd` and inspect the body of the document. How is it different from what we have already seen? -- - Go back and open the directory `includes`. Inspect the contents. -- - Specifically, navigate to the `sections` directory. Open some of the files. -- #### **Take away**: you can use 'child documents' to break up a large manuscript - the 'parent' or master document calls the child documents - the output is the same... a single word/pdf/html document - works well with dissertations (each child is a chapter) - useful when distractions are an issue --- count: false # Exercise ### knitr - Go back to the `papaja` document we created before - Create knitr code chunks and try the following commands (in different chunks). **Remember** you should always name your chunks! .pull-left[ Commands - `echo`: logical (TRUE/FALSE) - `eval`: 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') ] -- <br><br> .pull-right[ - hide/show code - evaluate/ignore code - format for code output - figure ouptions - normal or hi-def images - figure width in inches - figure height in inches - alignment of figure (most useful in html files) ] <style> .huge { font-size: 2.5em; } </style>