Using the goodenuffR package

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<div class="footer-small">https://github.com/mjfrigaard/csuc-data-journalism</div>

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# Using the `goodenuffR` package
#.fancy[Everything...in its right place]

.large[by Martin Frigaard]

Written: October 21 2021

Updated: November 30 2021

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 [Created using the "λέξις" theme](https://jhelvy.github.io/lexis/index.html#what-does-%CE%BB%CE%AD%CE%BE%CE%B9%CF%82-mean)
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## `goodenuffR` = good enuff practices in R computing

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# Outline

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### 1) The Problem

### 2) A Solution

### 3) Installation

### 4) Quick Start
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### 5) Package functions

+ `goodenuff_code()`  
+ `goodenuff_collab()`  
+ `goodenuff_data()`   
+ `goodenuff_doc()`  
+ `goodenuff_results()`
+ `goodenuff_files()`

### 6) Using `goodenuffR`

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# The Problem

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> *Where is my stuff?*

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### [THE VERGE: FILE NOT FOUND](https://www.theverge.com/22684730/students-file-folder-directory-structure-education-gen-z)

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# The Problem

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> *Store stuff in a particular place*

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# The Problem

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> *Most soul-destroying "bug" when trying to learn programming*

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# A Solution: `goodenuffR`!

### Based on the excellent paper, [*Good enough practices in scientific computing*](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005510)

by Greg Wilson, Jennifer Bryan, Karen Cranston, Justin Kitzes, Lex Nederbragt, Tracy K. Teal

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# A Solution

#### The paper focuses on...

> *"a minimum set of tools and techniques that we believe every researcher can and should consider adopting"*

#### Specifically

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+ Data management

+ Software

+ Collaboration

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+ Project organization

+ Tracking changes

+ Manuscripts

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# A Solution

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#### `goodenuffR` focuses on:

+ Data management

+ Project organization

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#### Specifically

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# Installation

### Available on GitHub here:

https://github.com/mjfrigaard/goodenuffR

### Install `goodenuffR` using the code below:

```r
install.packages("devtools")
devtools::install_github("mjfrigaard/goodenuffR")
```

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# Quick Start

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### In a fresh RStudio Session

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# Quick Start

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### 1) Install `devtools`, then install and load `goodenuffR`

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# Quick Start

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### 2) Enter a project name

### 3) Enter the folder path for your project

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```r
goodenuffR::goodenuff_project(
  project_name = "my awesome project", 
  folder_path = "/Users/mjfrigaard/Projects")
```

#### TIP: *use `getwd()` in the Console or `pwd` in the Terminal to locate current folder*

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# Quick Start

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### RStudio will open a new session for your project

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# Quick Start

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### 4) Run

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```r
goodenuffR::goodenuff_files()
```

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# Quick Start

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### Now you're good (enuff) to go!

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# Package functions

#### `goodenuff_code()`

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### Paper

- *readable, reusable, and testable* 
- *short, single-purpose functions with clearly-defined inputs and outputs*
- *name all files to reflect their content or function*

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### `goodenuffR`

```r
goodenuffR::goodenuff_code()
# └── code
#    ├── 01-import.R
#    ├── 02-tidy.R
#    ├── 03-wrangle.R
#    ├── 04-visualize.R
#    ├── 05-model.R
#    ├── 06-communicate.R
#    └── runall.R
```

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# Package functions

#### `goodenuff_code()`

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### Paper

- *Place a brief explanatory comment at the start of every program*

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### `goodenuffR`

Each `code` file has a header:

```r
#=======================
# This is code to create:
# Authored by and feedback to:
# MIT License
# Version:
#=======================
```

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# Package functions

#### `goodenuff_collab()`

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### Paper

- *Make the project citable* 
- *Make the license explicit*
- *Create an overview of your project*
- *Make dependencies and requirements explicit*

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### `goodenuffR`

```r
goodenuffR::goodenuff_collab()
# └── CITATION
# └── LICENSE
# └── README.Rmd
# └── requirements.txt
```

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# Package functions

#### `goodenuff_data()`

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### Paper

- *Save the raw data*
- *Record all the steps used to process data*

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### `goodenuffR`

```r
goodenuffR::goodenuff_data()
# data
# ├── README.md
# └── raw
```

*Folder for keeping `raw/` data separate from other data files*

*Document in `README.md`*

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# Package functions

### `goodenuff_data()` (BONUS!)

`data/README.md` provides some guidance on storing and documenting data.

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```
# Project Data

For guidance please see:
https://help.osf.io/hc/en-us/articles/360019739054-How-to-Make-a-Data-Dictionary

## Additional Resources

1. Sharing data
http://bit.ly/data-4-sharing  
2. Data in spreadsheets
http://bit.ly/data-in-sheets  
3. External data (https://r-pkgs.org/)
https://r-pkgs.org/data.html

source: 
https://swcarpentry.github.io/good-enough-practices-in-scientific-computing/
```

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# Package functions

#### `goodenuff_doc()`

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### Paper

- *Put text documents associated with the project in the `doc` directory*
- *Add a file called `CHANGELOG.txt` to the project's docs subfolder*
- *a running lab notebook describing various ideas for the project and how these were implemented*

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### `goodenuffR`

```r
goodenuffR::goodenuff_doc() 
# docs
# ├── changelog.txt
# ├── manuscript.Rmd
# └── notebook.Rmd
```

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# Package functions

#### `goodenuff_results()`

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### Paper

- *Put raw data and metadata in a `data/` directory and files generated during cleanup and analysis in a `results/` directory*

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### `goodenuffR`

```r
goodenuffR::goodenuff_results()
# results
# ├── figures
# ├── manuscript
# └── tables
```

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# Package functions

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#### `goodenuff_files()`

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## BONUS: RMarkdown Template

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### `goodenuffR` also comes with a `rmarkdown` template:

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# Thank you!

## Feedback to

### - `@mjfrigaard` on Github and Twitter

### - `mjfrigaard(at)pm.me` email