Data & Workflows

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04

# Data & Workflows

## R Markdown for Medicine

### Alison Hill &#183; RStudio

#### [rmd4medicine.netlify.com/](https://rmd4medicine.netlify.com/)

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#

# Go here and log in (free):

https://rstd.io/rmd4medicine-cloud

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<div class="my-footer">https://rstd.io/rmd4medicine-cloud</div>

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1

# Hygiene

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# Philosophy

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### Less

# 🐭
]

.pull-right[

### More

# 🎹
]

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.pull-left[
![](https://raw.githubusercontent.com/hadley/r4ds/master/screenshots/rstudio-workspace.png)
]

.pull-right[
#

In RStudio: _Tools > Global Options_

]

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# Restart R early & often

.pull-left[
#

In RStudio: _Session > Restart R_
]

.pull-right[
#

`Cmd/Ctrl` + `Shift` + `F10` (Mac)   
or  
`Ctrl` + `Shift` + `F10` (Windows/Linux)

]

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# Reknit up to...

.pull-left[
#

![](images/rstudio-runabove.png)

]

.pull-right[
#

Place cursor anywhere in your doc then:

`Command` + `Option` + `P` (Mac)  
or  
`Ctrl`+`Alt`+`P`  (Windows/Linux)
]

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#

# Not recommended

```r
rm(list = ls())
```

.footnote[https://whattheyforgot.org/save-source.html#rm-list-ls]

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2

# Projects

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# R projects

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.pull-left[
#

_File > New Project..._
<img src="images/rstudio-new.png" width="2056" />
]
--

.pull-right[
#

Pick one
<img src="images/rstudio-newproj.png" width="1773" />
]

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#

Equivalent to:
_File > New Project...>_ New or Existing

```r
library(usethis)
create_project(here::here())
```

.footnote[https://usethis.r-lib.org/reference/create_package.html]

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.pull-left[
#

_File > New File > R Markdown..._
<img src="images/rstudio-newfile.png" width="2037" />
]
--

.pull-right[
#

Fill in, can leave as HTML
<img src="images/rstudio-newrmd.png" width="1768" />
]

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.pull-left[
#

![](images/rstudio-freshrmd.png)
]

.pull-right[
#

![](images/rstudio-blankrmd.png)
]

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# Live code demo

We make our first R project from scratch with a single R Markdown file inside.

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3

# External files

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???

save a local copy, keep raw data raw

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# File paths

.pull-left[

###

```r
"~/mm/nope.csv"
setwd("/haha/good/luck/")
setwd('c:\iamyournightmare\!')
setwd("C:\user\oh\no")
setwd("path/that/only/works/on/my/machine")
```

###

```r
mockdata <- read_csv(
 here::here("data/mockdata.csv")
 )
```

]

.pull-right[
<div class="figure" style="text-align: center">
<img src="images/horst_here.png" alt="Art by Allison Horst" width="90%" />
Art by Allison Horst
</div>
]

https://whattheyforgot.org/project-oriented-workflow.html#setwd

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4

# Bibliography

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See [citations](http://rmarkdown.rstudio.com/authoring_bibliographies_and_citations.html#citations)

.pull-right[
Generates these in-text citation styles:

1. Blah blah [see @R-blogdown, pp. 33-35; also @R-knitr, ch. 1].

2. Blah blah [@R-blogdown, pp. 33-35].

3. Blah blah [@R-blogdown; @R-knitr].

4. Yihui says blah [-@R-blogdown].

5. @R-blogdown says blah.

]

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# Your turn

### Choose your adventure

1. Take `04-manuscript.Rmd` and add in the tables and figures in code chunks, with code chunk options that make sense. 🧶 __Knit__ and/or run chunks interactively as you work.

1. Play with knitting to different output formats. Try to figure out valid output options for each format you can add to your YAML.

1. Go to https://github.com/thomasp85/scico and try knitting with different palette names. Pick a favorite.

__Too much?__ Look at `04-manuscript-alison.Rmd`, 🧶 __Knit__. Then do 2 and 3 above.

__Not enough?__ See next slide for building a graphical user interface for parameters.

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# Your turn

### Extra: Play more with parameters

.pull-left[

From `03-draft.Rmd`

```yaml
---
params:
  palette: berlin
---
```

]

.pull-right[

Try in `04-manuscript.Rmd`

```yaml
---
params:
  palette:
    input: select
    label: 'scico palette:'
    choices:
    - berlin
    - roma
    - cork
    - grayC
    selected: roma
---
```
]

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# If we have time...

.pull-left[

Open & Knit:

`analyis/presentations/slides.Rmd`

```yaml
---
output:
  beamer_presentation:
    slide_level: 2.0
  powerpoint_presentation: default
  revealjs::revealjs_presentation: default
---
```
]

.pull-right[

![](04-data-workflows_files/figure-html/unnamed-chunk-17-1.gif)

]

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# Time to wrap-up!

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!

# Extension formats

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# Dashboards

https://jenthompson.me/examples/progressdash.html

https://jenthompson.me/2018/02/09/flexdashboards-monitoring/

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# Presentations

https://bookdown.org/yihui/rmarkdown/presentations.html

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!

# Cheatsheets!

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.left-column[

# 📌

]

.right-column[

_Help > Cheatsheets > RStudio IDE_

<a href="https://www.rstudio.com/resources/cheatsheets/#ide" target="_blank"><img src="https://442r58kc8ke1y38f62ssb208-wpengine.netdna-ssl.com/wp-content/uploads/2018/08/rstudio-ide.png" width="50%" /></a>
]

.footnote[https://www.rstudio.com/resources/cheatsheets/#ide]

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.left-column[
# 📌
]

.right-column[
_Help > Cheatsheets > R Markdown Cheat Sheet_

<a href="https://www.rstudio.com/resources/cheatsheets/#rmarkdown" target="_blank"><img src="https://442r58kc8ke1y38f62ssb208-wpengine.netdna-ssl.com/wp-content/uploads/2018/08/rmarkdown-2.0.png" width="50%" /></a>
]

.footnote[https://www.rstudio.com/resources/cheatsheets/#rmarkdown]

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.left-column[
# 📌
]

.right-column[
_Help > Cheatsheets > R Markdown Reference Guide_

]

.footnote[https://www.rstudio.com/wp-content/uploads/2015/03/rmarkdown-reference.pdf]

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!

# Book!

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.left-column[
# 📖
]

.right-column[

<a href="https://bookdown.org/yihui/rmarkdown/" target="_blank"><img src="https://bookdown.org/yihui/rmarkdown/images/cover.png" width="40%" /></a>
]

.footnote[https://bookdown.org/yihui/rmarkdown/]

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!

# Websites!

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.left-column[
# 🔗
]

.right-column[

<a href="https://rmarkdown.rstudio.com/" target="_blank"><img src="images/rmarkdown-site.png" width="80%" /></a>
]

.footnote[https://rmarkdown.rstudio.com/]

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.left-column[
# 🔗
]

.right-column[

<a href="https://rmarkdown.rstudio.com/docs/" target="_blank"><img src="images/rmarkdowndocs-site.png" width="80%" /></a>
]

.footnote[https://rmarkdown.rstudio.com/docs/]

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.left-column[
# 🎯
]

.right-column[

<a href="https://community.rstudio.com/c/R-Markdown" target="_blank"><img src="images/rmarkdowncommunity-site.png" width="80%" /></a>
]

.footnote[https://community.rstudio.com/c/R-Markdown]

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.left-column[
# 🤖
]

.right-column[

<a href="https://rmarkdown.rstudio.com/lesson-6.html" target="_blank"><img src="https://raw.githubusercontent.com/rstudio/rmarkdown/gh-pages/lesson-images/params-1-hawaii.png" width="80%" /></a>
]

.footnote[https://bookdown.org/yihui/rmarkdown/parameterized-reports.html, 
https://rmarkdown.rstudio.com/lesson-6.html]

---

# More

+ [`redoc` 📦](https://noamross.github.io/redoc/)

+ [`spelling` 📦](https://docs.ropensci.org/spelling/)

+ [`wordcountaddin` 📦](https://github.com/benmarwick/wordcountaddin)

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# Thank you!

Thanks to Peter Higgins & Daniel Chen for all their hard work