Workflows

Jeff Stevens

2023-01-30

Review: Mental model of coding

Mental model of file directories

Directories/folders

File system

Structure of directories and files stored on your computer

/media/jstevens/data/jstevens/OneDrive/active_sync/teach/psyc_971--data_science_visualization_in_r/dpavir_2025/slides
├── 00_getting_started.html
├── 00_getting_started.qmd
├── 01_introduction.html
├── 01_introduction.qmd
├── 02_rstudio.html
├── 02_rstudio.qmd
├── 03_coding.html
├── 03_coding.qmd
├── 04_workflows.qmd
├── 04_workflows.rmarkdown
├── 05_rmarkdown.qmd
├── 06_datatypes.qmd
├── 07_datastructures.qmd
├── 08_importing.qmd
├── 09_validating.qmd
├── 10_selecting.qmd
├── 11_mutating.qmd
├── 12_piping.qmd
├── 13_filtering.qmd
├── 14_summarizing.qmd
├── 15_pivoting.qmd
├── 16_separating.qmd
├── 17_mergingcolumns.qmd
├── 18_mergingrows.qmd
├── 19_numbers.qmd
├── 20_strings.qmd
├── 21_patterns.qmd
├── 22_factors.qmd
├── 23_dates.qmd
├── 24_functions.qmd
├── 25_iteration.qmd
├── 26_grammar1.qmd
├── 27_grammar2.qmd
├── 28_themes.R
├── 28_themes.qmd
├── 29_color.qmd
├── 29_color_files
│   ├── figure-html
│   │   ├── unnamed-chunk-1-1.png
│   │   └── unnamed-chunk-2-1.png
│   └── libs
│       ├── clipboard
│       │   └── clipboard.min.js
│       ├── quarto-html
│       │   ├── popper.min.js
│       │   ├── quarto-html.min.css
│       │   ├── quarto-syntax-highlighting-dark.css
│       │   ├── tabby.min.js
│       │   ├── tippy.css
│       │   └── tippy.umd.min.js
│       └── revealjs
│           ├── dist
│           │   ├── reset.css
│           │   ├── reveal.css
│           │   ├── reveal.esm.js
│           │   ├── reveal.esm.js.map
│           │   ├── reveal.js
│           │   ├── reveal.js.map
│           │   └── theme
│           │       ├── fonts
│           │       │   ├── league-gothic
│           │       │   │   ├── LICENSE
│           │       │   │   ├── league-gothic.css
│           │       │   │   ├── league-gothic.eot
│           │       │   │   ├── league-gothic.ttf
│           │       │   │   └── league-gothic.woff
│           │       │   └── source-sans-pro
│           │       │       ├── LICENSE
│           │       │       ├── source-sans-pro-italic.eot
│           │       │       ├── source-sans-pro-italic.ttf
│           │       │       ├── source-sans-pro-italic.woff
│           │       │       ├── source-sans-pro-regular.eot
│           │       │       ├── source-sans-pro-regular.ttf
│           │       │       ├── source-sans-pro-regular.woff
│           │       │       ├── source-sans-pro-semibold.eot
│           │       │       ├── source-sans-pro-semibold.ttf
│           │       │       ├── source-sans-pro-semibold.woff
│           │       │       ├── source-sans-pro-semibolditalic.eot
│           │       │       ├── source-sans-pro-semibolditalic.ttf
│           │       │       ├── source-sans-pro-semibolditalic.woff
│           │       │       └── source-sans-pro.css
│           │       └── quarto.css
│           └── plugin
│               ├── highlight
│               │   ├── highlight.esm.js
│               │   ├── highlight.js
│               │   ├── monokai.css
│               │   ├── plugin.js
│               │   └── zenburn.css
│               ├── markdown
│               │   ├── markdown.esm.js
│               │   ├── markdown.js
│               │   └── plugin.js
│               ├── math
│               │   ├── katex.js
│               │   ├── math.esm.js
│               │   ├── math.js
│               │   ├── mathjax2.js
│               │   ├── mathjax3.js
│               │   └── plugin.js
│               ├── notes
│               │   ├── notes.esm.js
│               │   ├── notes.js
│               │   ├── plugin.js
│               │   └── speaker-view.html
│               ├── pdf-export
│               │   ├── pdfexport.js
│               │   └── plugin.yml
│               ├── quarto-line-highlight
│               │   ├── line-highlight.css
│               │   ├── line-highlight.js
│               │   └── plugin.yml
│               ├── quarto-support
│               │   ├── footer.css
│               │   ├── plugin.yml
│               │   └── support.js
│               ├── reveal-menu
│               │   ├── menu.css
│               │   ├── menu.js
│               │   ├── plugin.yml
│               │   ├── quarto-menu.css
│               │   └── quarto-menu.js
│               ├── search
│               │   ├── plugin.js
│               │   ├── search.esm.js
│               │   └── search.js
│               └── zoom
│                   ├── plugin.js
│                   ├── zoom.esm.js
│                   └── zoom.js
├── 30_histograms.R
├── 30_histograms_answers.R
├── 31_boxplots.R
├── 31_boxplots_answers.R
├── 32_barcharts.R
├── 32_barcharts_answers.R
├── 33_associations.R
├── 33_associations_answers.R
├── 34_timeseries.R
├── 34_timeseries_answers.R
├── 35_categories.R
├── 35_categories_answers.R
├── 36_axes.R
├── 36_axes_answers.R
├── 37_annotating.R
├── 37_annotating_answers.R
├── 38_overplotting.R
├── 38_overplotting_answers.R
├── 39_tables.Rmd
├── 39_tables.pdf
├── 39_tables.tex
├── 40_publications.qmd
├── 41_advrmarkdown.qmd
├── 42_quarto.qmd
├── 43_statistics.R
├── _freeze
│   └── 04_workflows
│       ├── execute-results
│       │   └── html.json
│       └── libs
│           ├── clipboard
│           │   └── clipboard.min.js
│           ├── quarto-html
│           │   ├── light-border.css
│           │   ├── popper.min.js
│           │   ├── quarto-html.min.css
│           │   ├── quarto-syntax-highlighting-dark.css
│           │   ├── tabby.min.js
│           │   ├── tippy.css
│           │   └── tippy.umd.min.js
│           └── revealjs
│               ├── dist
│               │   ├── reset.css
│               │   ├── reveal.css
│               │   ├── reveal.esm.js
│               │   ├── reveal.esm.js.map
│               │   ├── reveal.js
│               │   ├── reveal.js.map
│               │   └── theme
│               │       ├── fonts
│               │       │   ├── league-gothic
│               │       │   │   ├── LICENSE
│               │       │   │   ├── league-gothic.css
│               │       │   │   ├── league-gothic.eot
│               │       │   │   ├── league-gothic.ttf
│               │       │   │   └── league-gothic.woff
│               │       │   └── source-sans-pro
│               │       │       ├── LICENSE
│               │       │       ├── source-sans-pro-italic.eot
│               │       │       ├── source-sans-pro-italic.ttf
│               │       │       ├── source-sans-pro-italic.woff
│               │       │       ├── source-sans-pro-regular.eot
│               │       │       ├── source-sans-pro-regular.ttf
│               │       │       ├── source-sans-pro-regular.woff
│               │       │       ├── source-sans-pro-semibold.eot
│               │       │       ├── source-sans-pro-semibold.ttf
│               │       │       ├── source-sans-pro-semibold.woff
│               │       │       ├── source-sans-pro-semibolditalic.eot
│               │       │       ├── source-sans-pro-semibolditalic.ttf
│               │       │       ├── source-sans-pro-semibolditalic.woff
│               │       │       └── source-sans-pro.css
│               │       └── quarto.css
│               └── plugin
│                   ├── highlight
│                   │   ├── highlight.esm.js
│                   │   ├── highlight.js
│                   │   ├── monokai.css
│                   │   ├── plugin.js
│                   │   └── zenburn.css
│                   ├── markdown
│                   │   ├── markdown.esm.js
│                   │   ├── markdown.js
│                   │   └── plugin.js
│                   ├── math
│                   │   ├── katex.js
│                   │   ├── math.esm.js
│                   │   ├── math.js
│                   │   ├── mathjax2.js
│                   │   ├── mathjax3.js
│                   │   └── plugin.js
│                   ├── notes
│                   │   ├── notes.esm.js
│                   │   ├── notes.js
│                   │   ├── plugin.js
│                   │   └── speaker-view.html
│                   ├── pdf-export
│                   │   ├── pdfexport.js
│                   │   └── plugin.yml
│                   ├── quarto-line-highlight
│                   │   ├── line-highlight.css
│                   │   ├── line-highlight.js
│                   │   └── plugin.yml
│                   ├── quarto-support
│                   │   ├── footer.css
│                   │   ├── plugin.yml
│                   │   └── support.js
│                   ├── reveal-menu
│                   │   ├── menu.css
│                   │   ├── menu.js
│                   │   ├── plugin.yml
│                   │   ├── quarto-menu.css
│                   │   └── quarto-menu.js
│                   ├── search
│                   │   ├── plugin.js
│                   │   ├── search.esm.js
│                   │   └── search.js
│                   └── zoom
│                       ├── plugin.js
│                       ├── zoom.esm.js
│                       └── zoom.js
├── _quarto.yml
└── custom.scss

File managers

Apps/GUIs to interact with file system
- Windows File Explorer
- MacOS Finder

File managers

RStudio

Terminals

Interact with file system through prompt/command line
If not familiar with terminal, read primer for Windows or MacOS

Mental model of file directories

Paths

Convert tree structure to character string

exercises/01_introduction/rsconnect/documents/01_introduction.Rmd
/shinapps.io/jeffreyrstevens/01_introduction.dcf

Absolute paths

From root directory

Starts with drive letter or /
- Windows: C:\users\jeff\Documents\projects\dpavir_2023\R\
- Linux and MacOS: /home/jeff/projects/dpavir_2023/R/

Relative paths

From current directory

Starts with first subdirectory name
- If in projects/, relative path to R/ is dpavir_2023/R

Use relative paths!
Why?

Changing directories

Change directories with `cd`

/home/jeff/projects/dpavir_2023/

To move from dpavir_2023/ to rsconnect/, type
cd exercises/01_introduction/rsconnect/

Go backwards

Move backwards with `cd ..`

One set of .. for each directory going backwards
To move from rsconnect/ to 01_introduction/,
type cd ..
To move from 01_introduction/ to code/,
type cd ../../code/

Let’s try it!

Go to Files in RStudio
Add folder named test and a subfolder named R.
Go to Terminal.
Type ls or dir.
How do we go to test/?
How do we go back?
How do we go to test/R/?
How do we go back up to test/?

Mental model of file directories

Workflows

Project directory structure

Build a consistent directory structure
Why?
Consistency for you
Adapt structure to your needs or lab requirements
Consistency for the lab
Make a template directory

Working directories

Base directory for R session

View your working directory
- Console: getwd()
- RStudio: top of Console

What is your working directory?

RStudio Projects

Convenient system to:

Set working directory
Open files you had open before closing RStudio
Focus on relative paths
Enable version control

Use them! Always!

RStudio Projects

Let’s create an RStudio Project for this course

RStudio Projects

Create an RStudio Project in the existing test/ directory

Create your typical project structure
Use the terminal to change directories in your project

Project working directories

{here}: The package that sets your working directory to the RStudio Project root directory

read_csv(here("data/a.csv"))

Workflows

Review: Mental model of coding

Mental model of file directories

Directories/folders

File system

Structure of directories and files stored on your computer

File managers

File managers

Terminals

Mental model of file directories

Paths

Paths

Convert tree structure to character string

Absolute paths

From root directory

Relative paths

From current directory

Changing directories

Change directories with cd

Go backwards

Move backwards with cd ..

Let’s try it!

Mental model of file directories

Workflows

Project directory structure

Working directories

Base directory for R session

RStudio Projects

Convenient system to:

Use them! Always!

RStudio Projects

RStudio Projects

Project working directories

Mental model of file directories

Change directories with `cd`

Move backwards with `cd ..`