03-projects.knit

class: title-slide
count: false

.title[
  # 03 - Projects
]
.subtitle[
  ## Open Science Tools
]

.author[
  ### Claudio Zandonella & Davide Massidda
]

.institute[

]

---

class: center, middle, inverse

# Step II: Project Structure

---

# Project Structure

---

# Project Structure

---

# Project Structure

.pull-left-30[

---
# Project Structure

.pull-left-30[

## Data

]

---
# Project Structure

.pull-left-30[

## Data

.my-code-block[
```
- data/
    |-- data-raw/
    |-- cache/
    |-- output/
```
]

.li-small[
{{content}}
]
]

- Data in input are **`read-only`**
- Share data in **machine readable format** (no `.pdf`)
- Add data **documentation** (`data-README`) 
- Add data **license**

---
# Project Structure

.pull-left-30[

## Code

.li-small[
{{content}}
]
]

### Functional Style

- `analysis/` - Scripts used for running the analysis
- `src/` - Scripts with definition of custom functions
---

# Project Structure

.pull-left-30[

## Documents

]

---

# Project Structure

.pull-left-30[

## Documents

.my-code-block[
```
- documents/
    |-- paper/
    |-- presentation/
    |-- report/
```
]

.li-small[
{{content}}
]
]

- Use dynamic documents (e.g., Rmarkdown, Jupyter Notebook)
- ![](images/03-projects/logo-quarto.png) &nbsp;&nbsp; https://quarto.org/

---
# Project Structure

.pull-left-30[

## README

.li-small[
{{content}}
]
]

- Title and Authors
- Description
- Project Structure
- Getting Started
  - Requirements
  - Installation/Run Analysis
- Other
  - Citation
  - Acknowledgements

---
# Project Structure

.pull-left-30[

## README

.li-small[
- Title and Authors
- Description
- Project Structure
- Getting Started
  - Requirements
  - Installation/Run Analysis
- Other
  - Citation
  - Acknowledgements
  
https://gitlab.inf.unibz.it/URS/builthub/eu27materials
]
]

---
# Project Structure

.pull-left-30[

## LICENSE

.center[
{{content}}
]
]

*Without license all rights are reserved!*

---
# Project Structure

.pull-left-30[

## LICENSE

.center[
*Without license all rights are reserved!*
]

.li-small[
- Software open-source license (e.g., MIT, Apache, GNU GPL) https://choosealicense.com/licenses/
- Materials Creative Commons Licenses &nbsp;&nbsp; <img style="width:7em" src="images/03-projects/cc-by-sa.png" class="inline-img"> https://creativecommons.org/about/cclicenses/
- Open data license
]

{{content}}
]

Extra - Aaron Swartz [Story](https://en.wikipedia.org/wiki/Aaron_Swartz) (
[Documentary](https://www.youtube.com/watch?v=M85UvH0TRPc))

---
# Project Structure

.pull-left-30[

## LICENSE

.move-up-70[
<img src="images/03-projects/cc-piramid.png" width="40%" style="display: block; margin: auto;" />
]
]

---
# Project Structure

.pull-left-30[

## Naming Conventions
]
---
# Project Structure

.pull-left-30[

## Naming Conventions

.li-small[
- Use meaningful names
.bad-code[

```r
"untitled.R" # not meaningful name
```
]
.good-code[

```r
"analysis-experiment-A.R" # clear descriptive name
```
]
]
]

---
# Project Structure

.pull-left-30[

## Naming Conventions

.li-small[
- Use meaningful names
- Prefer lower-case names (`my-file.txt` &nbsp; vs &nbsp; `My-File.txt`)
]
]

---
# Project Structure

.pull-left-30[

## Naming Conventions

.li-small[
- Use meaningful names
- Prefer lower-case names
- Specify files extension
]
]
---
# Project Structure

.pull-left-30[

## Naming Conventions

.li-small[
- Use meaningful names
- Prefer lower-case names
- Specify files extension
- Avoid spaces
.bad-code[

```r
"I like to/mess things up.txt" # Your machine is gonna hate you 
```
]
.good-code[

```r
"path-to/my-file.txt"
```
]
]
]

---
# Project Structure

.pull-left-30[

## Naming Conventions

.li-small[
- Use meaningful names
- Prefer lower-case names
- Specify files extension
- Avoid spaces
- Avoid special characters
.bad-code[

```r
"brûlée-recipe.txt" # surely a good recipe for troubles
```
]
.good-code[

```r
"brulee-reciepe.txt" # use only basic Latin characters
```
]
]
]
---
# Project Structure

.pull-left-30[

## Advantages

]

---
# Project Structure

.pull-left-30[

## Advantages

.li-small[
- Ready to share and collaborate
- Centralize the analysis
]
]

---
# Project Structure

.pull-left-30[

## Advantages

.li-small[
- Ready to share and collaborate
- Centralize the analysis
- Configuration files for project settings
]
]
---
# Project Structure

.pull-left-30[

## Advantages

.li-small[
- Ready to share and collaborate
- Centralize the analysis
- Configuration files for project settings
- **Working directory** and **relative paths**
.bad-code[

```r
# absolute path
"/Users/<username>/Desktop/my-project/data/my-data.csv"
```
]
.good-code[

```r
# relative path
"data/my-data.csv"
```
]
]
]

---
# Extra: The Garden of Forking Paths

.pull-left-50[
### Unix

.li-small[
- `"/"` (forward slash) to separate directories
.code-compact[

```r
"my-project/data/my-data.csv"
```
]
- `"/"` indicates root-directory
.code-compact[
.code-small[

```r
# Mac
"/Users/<username>/Desktop/my-project/data/my-data.csv"
# Linux
"/home/<username>/Desktop/my-project/data/my-data.csv"
```
]]
- `"~"` indicates home-directory `"/Users/<username>/"` - MacOS; `"/home/<username>/"` - Linux
.code-compact[

```r
"~/Desktop/my-project/data/my-data.csv"
```
]
]
]
.pull-right-50[
### Windows Systems

.li-small[
- `"\"` (backslash) to separate directories
.code-compact[

```r
"my-project\\data\\my-data.csv"
```
]
- `"C:\"` indicates root-directory
.code-compact[

```r
"C:\\Users\\<username>\\Desktop\\my-project\\data\\my-data.csv"
```
]
- `"~"` indicates Documents directory
]

### Other Commands

.li-small[
- `"."` current working directory
- `".."` parent folder
]

]

---
class: inverse, middle, center

# RStudio Projects

---
# RStudio Projects: New Project
--

.pull-left-50[
*“File > New Project”*

<img src="images/03-projects/new-proj-1.png" width="80%" style="display: block; margin: auto;" />
]
.pull-right-50[
{{content}}
]

--
Create project options...

<img src="images/03-projects/new-proj-2.png" width="80%" style="display: block; margin: auto;" />
---
# RStudio Projects: New Project

.pull-left-50[
Project templates

<img src="images/03-projects/new-proj-3.png" width="80%" style="display: block; margin: auto;" />
]
.pull-right-50[
{{content}}
]

--
Project specifications

---
# RStudio Projects: Features

.pull-left-50[
.li-small[
- Working Directory and File Paths

]
]
.pull-right-50[

]

> Always use forward slash `"/"`

--
- `<project-name>.Rproj`

---
# RStudio Projects: Features

.pull-left-50[
.li-small[
- Working Directory and File Paths

> Always use forward slash `"/"`

- `<project-name>.Rproj`

]
]
.pull-right-50[
.li-small[
- Project settings

<img src="images/03-projects/proj-options.png" width="60%" style="display: block; margin: auto;" />
]
]
---
# RStudio Projects: Features

.no-border[
#### Suggested global settings
]
--

.pull-left-50[
.li-small[
- Always start in a new empty environment

<img src="images/03-projects/general-options.png" width="75%" style="display: block; margin: auto;" />
]
]
.pull-right-50[
.li-small[
{{content}}
]
]

- *“UTF-8”* encoding

<img src="images/03-projects/settings-UTF8.png" width="75%" style="display: block; margin: auto;" />
---
# RStudio Projects: Features

.no-border[
#### `.Rprofile`
]

.pull-left-50[

{{content}}
]
.pull-right-50[

]

--
<img src="images/03-projects/restart-session.png" width="75%" style="display: block; margin: auto;" />

---
# RStudio Projects: Features

.no-border[
#### `.Rprofile`
]

.pull-left-50[

]
.pull-right-50[

My `.Rprofile`

]
---
class: inverse, center, middle

# Like having multiple office desks!

## Moving to the next step...