exercises.knit

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.title[
  # Exercises
]
.subtitle[
  ## Open Science Tools
]

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

.institute[

]

---
## Attchment Study

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#### Aim

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Evaluate the relationship between attachment towards the mother and social emotional problems in children in the 3rd and 4th year of primary school.
]

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#### Data
]

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- `id`: Children id code
- `grade`: Children school grade (`3` and `4`)
- `gender`: Children gender<br>(`0` = Male; `1` = Female)
- `ssm*` (from 1 to 15): Mother Security Scale (SS) items
- `sdq*` (from 1 to 25): Strength and Difficulties Questionnaire items
]
]
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####  Mother Security Scale (SS)

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- 15 items on a 4-point likert scale (1-2-3-4)
- Total given by the **average**
- **Invert scores items 1, 3, 4, 9, 10, 13, and 15**
]

#### Strength and Difficulties Questionnaire (SDQ)

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- 25 items on a 3-point likert scale (0-1-2)
- Total given by the **sum** 
- **Invert scores items s 7, 11, 14, 21, 25**
]

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Subscales:
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- **Emotion**	=	3, 8, 13, 16, 24
- **Conduct**	=	5, 7, 12, 18, 22
- **Hyper**	=	2, 10, 15, 21, 25
- **Peer**	=	6, 11, 14, 19, 23
- **Prosoc**	=	1, 4, 9, 17, 20
]
]
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Summary scores:
]
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- **Internalizing** = emotion + peer
- **Externalizing** = hyper + conduct
]
]
]
]

---
## Step I: Sharing Materials

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#### For Coding Pinguins 🐧

.li-small[
1. Create your Profile in OSF
1. Create a new project
1. Fill in summary information and WiKi section
1. Upload the project files
1. Get the DOI
1. Add contributors to the project
1. Share an anonymized link
]
]

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#### For Coding Monkeys 🐒

.li-small[
1. Explore the OSF Preprint service
1. Explore the OSF Registries service
1. Explore the SF Add-on section
1. Is an anonymized link really anonymous?
]
]

---
## Step II: Project Structure

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#### For Coding Pinguins 🐧

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1. Create a RStudio Project
1. Use a proper project structure
1. Add a `README.md` file
1. Add a `LICENSE`
]
]

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#### For Coding Monkeys 🐒

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1. Set recommended global options
1. Use the `.Rprofile` to load libraries
1. Use the `.Rprofile` to set ggplot default theme
1. Create a second project and see what happens when you switch between them
]
]

---
## Step III: Sharing Data

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#### For Coding Pinguins 🐧

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1. Use an appropriate data format (and encoding)
1. Write a `README.md` for the data
]
]

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#### For Coding Monkeys 🐒

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1. Pivot data from wide to long format
1. Create multiple table in a relational structure
1. Use join operations
1. Create a `CITATION.cff` file
]
]

---
## Step IV: Coding [with] Style

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#### For Coding Pinguins 🐧

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1. Reframe code following good practices
1. Define custom functions to be DRY
1. Wrap analysis steps into functions
1. Provide minimal documentation
]
]

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#### For Coding Monkeys 🐒

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1. Provide full documentation
1. Write Unit tests
1. Use R-package project structure
]
]

---
## Step V: Terminal

```bash
$ docker run -it --rm claudiozandonella/my-ubuntu:1.0.0
```

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#### For Coding Pinguins 🐧

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1. Explore the `arca` folder 
1. Create a new directory
1. Create a new file
1. Copy a file
1. Move a file
1. Remove a file
]
]

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#### For Coding Monkeys 🐒

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1. Rename a file
1. Write inside a file
1. Use Nano text editor
1. Copy a directory and its content
1. Move a directory and its content
1. Remove a directory and its content
]
]

---
## Step VI: Versioning

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#### For Coding Pinguins 🐧

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1. Use git to track project development
1. Create commits
1. Move to a previous commit
1. Create an experimental branch
]
]

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#### For Coding Monkeys 🐒

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1. Do everything from command line
1. Experiment with different undoing commits commands
1. Merge two branches
1. Create a conflict
]
]

---
## Step VII: GitHub

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#### For Coding Pinguins 🐧

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1. Create an **empty** remote repository
1. Push changes to the remote
1. Collaborate on a colleague repository
]
]

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#### For Coding Monkeys 🐒

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1. Open an Issue
1. Create a Pull Request
1. Get a DOI with Zenodo
1. Ignore all files in a sub folder except one
]
]

---
## Step VIII: Workflows

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#### For Coding Pinguins 🐧

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1. Divide code into `src` and `analysis` scripts
1. Use `targets` to run the analysis 
1. Document the analysis workflow
1. Create a report using `targets` results
]
]

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#### For Coding Monkeys 🐒

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1. Use `targets` with custom `script` and `store` paths
1. Load all targets in the `.Rprofile`
1. Read branching documentation
1. Which random seed is used by `targets`?
]
]

---
## Step IX: Literate Programming

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#### For Coding Pinguins 🐧

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1. Move from RMarkdown to Quarto
1. Try `trackdown` (CRAN version)
]
]

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#### For Coding Monkeys 🐒

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1. Try `trackdown` (GitHub version)
]
]

---
## Step X: Requirements

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#### For Coding Pinguins 🐧

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1. Use `renv` to track package versions
1. Write documentation on ho to install the required dependencies
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]

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#### For Coding Monkeys 🐒

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1. Use `.renvignore` to avoid tracking *old/experimental* scripts
1. Use `DESCRIPTION` field to force tracking packages
]
]

---
## Step XI: Containerization

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#### For Coding Pinguins 🐧

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1. Run the `claudiozandonella/my-ubuntu` container
1. Access the terminal of the container
1. Stop/restart the container 
1. Remove the container
]
]

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#### For Coding Monkeys 🐒

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1. Do everything using the command line
1. Create a `Dockerfile` copying new files into the container
1. Attach a bind-mount 
1. Attach a named-volume
]
]

---
## Step XII: Rocker

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#### For Coding Pinguins 🐧

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1. Crete a container for the analysis
1. Document how to run the container and the analysis
1. Run the analysis from the container
]
]

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#### For Coding Monkeys 🐒

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1. The container should also include all the required dependencies
1. The container should also run the analysis at build
1. Publish the Docker in Docker Hub
]
]

---
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# God Progammer Mode Achieved!