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class: title-slide
count: false

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

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

.institute[

]

---

class: center, middle, inverse

# Step II: Project Structure

---

# Project Structure

--

.code-small[
.pull-left-50[
```
- Tesi Magistrale/
      |- Data Analysis/
            |- 10052018.R
            |- 16052018.R
            |- Analisi preliminari.docx
            |- DataAnlysis.R
            |- Grafici.3D.R
            |- Limitation.R
            |- Marginal effects m10.png
            |- Marginal effects m2.png
            |- ModelsAnalysis.R
            |- Parameters m10.png
            |- Parameters m2.png
            |- Plots.R
            |- Posterior Predicto Ext Int.png
            |- PreparazioneDataset.r
            |- Prior Probabilities 2.png
            |- Prior Probabilities.png
            |- Prior probabilities 3.png
            |- Sample_analysis.R
            |- Variables Relative Frequencies.png
            |- Warm-up Iteractions.png
            |- claudio.xls
            |- d.conmeans.rda
            |- d.correct.rda
            |- d.finale.rda
            |- d.girato.rda
```
]
.pull-right-50[
```


            |- d.noNA.rda
            |- d.selez.rda
            |- data.CSV
            |- ext~base.rda
            |- ext~ssm+ssp.rda
            |- ext~ssm.bis.rda
            |- ext~ssm.rda
            |- ext~ssm_ssp.rda
            |- ext~ssp.rda
            |- int1.png
            |- int2.png
            |- int~base.rda
            |- int~ssm+ssp.rda
            |- int~ssm.rda
            |- int~ssm_ssp.bis.rda
            |- int~ssm_ssp.rda
            |- int~ssp.rda
            |- int~ssp_ssm.rda
            |- m1.txt
            |- naquest0.1.pdf
            |- naquest01.R
            |- note_claudio.R
            |- sample_studies.csv
            |- studies_table.csv
```
]
]

---

# Project Structure


.code-small[
.pull-left-50[
```
- Tesi Magistrale/
      |- Data Analysis/
*           |- 10052018.R
*           |- 16052018.R
            |- Analisi preliminari.docx
            |- DataAnlysis.R
            |- Grafici.3D.R
            |- Limitation.R
            |- Marginal effects m10.png
            |- Marginal effects m2.png
            |- ModelsAnalysis.R
            |- Parameters m10.png
            |- Parameters m2.png
            |- Plots.R
            |- Posterior Predicto Ext Int.png
            |- PreparazioneDataset.r
            |- Prior Probabilities 2.png
            |- Prior Probabilities.png
            |- Prior probabilities 3.png
            |- Sample_analysis.R
            |- Variables Relative Frequencies.png
            |- Warm-up Iteractions.png
            |- claudio.xls
*           |- d.conmeans.rda
*           |- d.correct.rda
*           |- d.finale.rda
*           |- d.girato.rda
```
]
.pull-right-50[
```


*           |- d.noNA.rda
*           |- d.selez.rda
            |- data.CSV
            |- ext~base.rda
            |- ext~ssm+ssp.rda
            |- ext~ssm.bis.rda
            |- ext~ssm.rda
            |- ext~ssm_ssp.rda
            |- ext~ssp.rda
            |- int1.png
            |- int2.png
            |- int~base.rda
            |- int~ssm+ssp.rda
            |- int~ssm.rda
*           |- int~ssm_ssp.bis.rda
*           |- int~ssm_ssp.rda
            |- int~ssp.rda
            |- int~ssp_ssm.rda
            |- m1.txt
            |- naquest0.1.pdf
            |- naquest01.R
            |- note_claudio.R
            |- sample_studies.csv
            |- studies_table.csv
```
]
]

---

# Project Structure

--

.pull-left-30[

&lt;br&gt;


```r
- my-project/
    |
    |-- data/
    |-- analysis/
    |-- documents/
    |-- src/
    |-- README
    |-- LICENSE
```
]
.pull-right-70[
]

---
# Project Structure

.pull-left-30[

&lt;br&gt;


```r
- my-project/
    |
*   |-- data/
    |-- analysis/
    |-- documents/
    |-- src/
    |-- README
    |-- LICENSE
```
]
.pull-right-70[

## Data

]

---
# Project Structure

.pull-left-30[

&lt;br&gt;


```r
- my-project/
    |
*   |-- data/
    |-- analysis/
    |-- documents/
    |-- src/
    |-- README
    |-- LICENSE
```
]
.pull-right-70[

## Data

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

&lt;br&gt;

.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[

&lt;br&gt;


```r
- my-project/
    |
    |-- data/
*   |-- analysis/
    |-- documents/
*   |-- src/
    |-- README
    |-- LICENSE
```
]
.pull-right-70[

## Code

&lt;br&gt;

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

--

### Functional Style

{{content}}

--

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

# Project Structure

.pull-left-30[

&lt;br&gt;


```r
- my-project/
    |
    |-- data/
    |-- analysis/
*   |-- documents/
    |-- src/
    |-- README
    |-- LICENSE
```
]
.pull-right-70[

## Documents

]

---

# Project Structure

.pull-left-30[

&lt;br&gt;


```r
- my-project/
    |
    |-- data/
    |-- analysis/
*   |-- documents/
    |-- src/
    |-- README
    |-- LICENSE
```
]
.pull-right-70[

## Documents

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

&lt;br&gt;

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

--

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

---
# Project Structure

.pull-left-30[

&lt;br&gt;


```r
- my-project/
    |
    |-- data/
    |-- analysis/
    |-- documents/
    |-- src/
*   |-- README
    |-- LICENSE
```
]
.pull-right-70[

## README

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

--

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

---
# Project Structure

.pull-left-30[

&lt;br&gt;


```r
- my-project/
    |
    |-- data/
    |-- analysis/
    |-- documents/
    |-- src/
*   |-- README
    |-- LICENSE
```
]
.pull-right-70[

## 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[

&lt;br&gt;


```r
- my-project/
    |
    |-- data/
    |-- analysis/
    |-- documents/
    |-- src/
    |-- README
*   |-- LICENSE
```
]
.pull-right-70[

## LICENSE

.center[
{{content}}
]
]

--

*Without license all rights are reserved!*

---
# Project Structure

.pull-left-30[

&lt;br&gt;


```r
- my-project/
    |
    |-- data/
    |-- analysis/
    |-- documents/
    |-- src/
    |-- README
*   |-- LICENSE
```
]
.pull-right-70[

## LICENSE

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

&lt;br&gt;

.li-small[
- Software open-source license (e.g., MIT, Apache, GNU GPL)&lt;br&gt;https://choosealicense.com/licenses/
- Materials Creative Commons Licenses &amp;nbsp;&amp;nbsp; &lt;img style="width:7em" src="images/03-projects/cc-by-sa.png" class="inline-img"&gt;&lt;br&gt;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[

&lt;br&gt;


```r
- my-project/
    |
    |-- data/
    |-- analysis/
    |-- documents/
    |-- src/
    |-- README
*   |-- LICENSE
```
]
.pull-right-70[

## LICENSE

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

---
# Project Structure

.pull-left-30[

&lt;br&gt;


```r
- my-project/
    |
    |-- data/
    |-- analysis/
    |-- documents/
    |-- src/
    |-- README
    |-- LICENSE
```
]
.pull-right-70[

## Naming Conventions
]
---
# Project Structure

.pull-left-30[

&lt;br&gt;


```r
- my-project/
    |
    |-- data/
    |-- analysis/
    |-- documents/
    |-- src/
    |-- README
    |-- LICENSE
```
]
.pull-right-70[

## 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[

&lt;br&gt;


```r
- my-project/
    |
    |-- data/
    |-- analysis/
    |-- documents/
    |-- src/
    |-- README
    |-- LICENSE
```
]
.pull-right-70[

## Naming Conventions

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

---
# Project Structure

.pull-left-30[

&lt;br&gt;


```r
- my-project/
    |
    |-- data/
    |-- analysis/
    |-- documents/
    |-- src/
    |-- README
    |-- LICENSE
```
]
.pull-right-70[

## Naming Conventions

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

.pull-left-30[

&lt;br&gt;


```r
- my-project/
    |
    |-- data/
    |-- analysis/
    |-- documents/
    |-- src/
    |-- README
    |-- LICENSE
```
]
.pull-right-70[

## 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[

&lt;br&gt;


```r
- my-project/
    |
    |-- data/
    |-- analysis/
    |-- documents/
    |-- src/
    |-- README
    |-- LICENSE
```
]
.pull-right-70[

## 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[

&lt;br&gt;


```r
- my-project/
    |
    |-- data/
    |-- analysis/
    |-- documents/
    |-- src/
    |-- README
    |-- LICENSE
```
]
.pull-right-70[

## Advantages

]

---
# Project Structure

.pull-left-30[

&lt;br&gt;


```r
- my-project/
    |
    |-- data/
    |-- analysis/
    |-- documents/
    |-- src/
    |-- README
    |-- LICENSE
```
]
.pull-right-70[

## Advantages

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

---
# Project Structure

.pull-left-30[

&lt;br&gt;


```r
- my-project/
    |
    |-- data/
    |-- analysis/
    |-- documents/
    |-- src/
    |-- README
    |-- LICENSE
```
]
.pull-right-70[

## Advantages

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

.pull-left-30[

&lt;br&gt;


```r
- my-project/
    |
    |-- data/
    |-- analysis/
    |-- documents/
    |-- src/
    |-- README
    |-- LICENSE
```
]
.pull-right-70[

## 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/&lt;username&gt;/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/&lt;username&gt;/Desktop/my-project/data/my-data.csv"
# Linux
"/home/&lt;username&gt;/Desktop/my-project/data/my-data.csv"
```
]]
- `"~"` indicates home-directory  &lt;br&gt;`"/Users/&lt;username&gt;/"` - MacOS; `"/home/&lt;username&gt;/"` - 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\\&lt;username&gt;\\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 &gt; New Project”*

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

--
Create project options...

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

.pull-left-50[
Project templates

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

--
Project specifications

&lt;img src="images/03-projects/new-proj-4.png" width="80%" style="display: block; margin: auto;" /&gt;

---
# RStudio Projects: Features

--

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

&lt;img src="images/03-projects/proj-wd.png" width="80%" style="display: block; margin: auto;" /&gt;

{{content}}

]
]
.pull-right-50[

]

--

&gt; Always use forward slash `"/"`

{{content}}

--
- `&lt;project-name&gt;.Rproj`

&lt;img src="images/03-projects/rproj-file.png" width="80%" style="display: block; margin: auto;" /&gt;

---
# RStudio Projects: Features

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

&lt;img src="images/03-projects/proj-wd.png" width="80%" style="display: block; margin: auto;" /&gt;

&gt; Always use forward slash `"/"`

- `&lt;project-name&gt;.Rproj`

&lt;img src="images/03-projects/rproj-file.png" width="80%" style="display: block; margin: auto;" /&gt;

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

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

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

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

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

--

- *“UTF-8”* encoding

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

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

.pull-left-50[

&lt;img src="images/03-projects/hidden-files.png" width="75%" style="display: block; margin: auto;" /&gt;

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

]

--

&lt;img src="images/03-projects/rprofile.png" width="75%" style="display: block; margin: auto;" /&gt;

{{content}}

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

---
# RStudio Projects: Features

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

.pull-left-50[

&lt;img src="images/03-projects/hidden-files.png" width="75%" style="display: block; margin: auto;" /&gt;

&lt;img src="images/03-projects/rprofile.png" width="75%" style="display: block; margin: auto;" /&gt;

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

]
.pull-right-50[

My `.Rprofile`

&lt;img src="images/03-projects/my-rprofile.png" width="75%" style="display: block; margin: auto;" /&gt;

]
---
class: inverse, center, middle


# Like having multiple office desks!

## Moving to the next step...
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