GithubShortIntro

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# <span style=" font-weight: bold;    color: white !important;border-radius: 4px; padding-right: 4px; padding-left: 4px; background-color: #0091ad !important;font-size: 80px;" >Git &amp; Github</span>

# <span style=" font-weight: bold;    color: white !important;border-radius: 4px; padding-right: 4px; padding-left: 4px; background-color: #0091ad !important;font-size: 60px;" >A short intro</span>

<br>
<h2><span style=" font-weight: bold;    color: white !important;border-radius: 4px; padding-right: 4px; padding-left: 4px; background-color: #2e6f95 !important;" >Miriam Lerma</span></h2>

<h3><span style=" font-weight: bold;    color: white !important;border-radius: 4px; padding-right: 4px; padding-left: 4px; background-color: #455e89 !important;" >October 2021</span></h3>

---

# Intro

- [Git](#git)
- [Github](#github)
- [Reproducibility](#repro)
- [Git+Github](#git_github)
- [Organice projects](#organize)

---
name: git
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# 1. Git

---

## 1.2. Git

**Git** is a version control software (VCS-Version control system).

- The advantages of using **version control** is that you can modify your code/analyses and have a safe backup.
In you **repository** you can have always the latest version

- It also allows you to have the history of changes that you have done to your **repository** and be able to trace back to old files. 
You can go back to older version on your projects

- You repository can be only local if you dont want to put it online

**Cons**:

- It takes some time to get use to it

- It was developed by programmers so its usually not very intuitive to use

---

## 1.3. Install

- To dowload :<br>
Webpage: [git](https://git-scm.com/)

- Select your OS (operating system):<br>
[Windows](https://happygitwithr.com/install-git.html#install-git-windows)<br>
[macOS](https://happygitwithr.com/install-git.html#macos)<br>
[Linux](https://happygitwithr.com/install-git.html#linux)

- The installation is very different between computers
- You only need to install it once

---
name: github
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# 2. Github

---

## 2.1. What is GitHub

[Github](https://github.com/): is a provider of internet hosting for software development and version control using git <br>

However, it is not the only one and there are many other platforms to host repositories. <br>

For example: [gitlab](https://about.gitlab.com/)
<img src="https://about.gitlab.com/images/press/press-kit-icon.svg" height="80" style="display: block; margin: auto;" />

Which one to use? Discussion between [Github o Gitlab](https://rachelcarmena.github.io/2018/12/12/how-to-teach-git.html)

---

## 2.1. Why Github

- It allows you to have a backup of your project online
- Allows collaboration 
- Simplifies remote work

---

## 2.2. To use GitHub

You need to register [Github](https://github.com/) <br>

---

## 2.3. Create an user name

You can register using your email <br>
<img src="https://raw.githubusercontent.com/MiriamLL/Curso_CIAD/main/Figuras/Github2.png" height="250" style="display: block; margin: auto;" />

**Recommended**
- Use a similar name that the one from your publications, so people can easily find you and trust your repository
- Select a name that you feel comfortable to use in the future
- Short names are preferred than long names
- Separate name using _ or -

[Click here for further reading](https://happygitwithr.com/github-acct.html)

---

## 2.4. Create a repository

There are many ways to create a repository, using the **+** symbol next to your picture is one.

---

## 2.5. Make a public repository

In the description of your repository, you can select if you want to make it public or private. You can change it later if you want to.

---

## 2.6. Upload files in your repository

- There are also many ways to upload files. Initially you can just **upload an existing file**

---

## 2.7. Repository

Select your files, **commit changes** and there is your repository.

To share it, you can go to setting and add the email of the person you want to share it with.

---

# 3. Reproducibility

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# 3.1. Share

- Work locally, share globally.

You can collaborate with many people working on the same projects.

---

## 3.1. Share

But not only that! you can help your future **you** to be replicate your analyses.

... or your students, employees, etc...

---

## 3.3. Reproducibility crisis

This has been quoted a reproducibility crisis.

- [<svg aria-hidden="true" role="img" viewBox="0 0 576 512" style="height:1em;width:1.12em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:red;overflow:visible;position:relative;"><path d="M549.655 124.083c-6.281-23.65-24.787-42.276-48.284-48.597C458.781 64 288 64 288 64S117.22 64 74.629 75.486c-23.497 6.322-42.003 24.947-48.284 48.597-11.412 42.867-11.412 132.305-11.412 132.305s0 89.438 11.412 132.305c6.281 23.65 24.787 41.5 48.284 47.821C117.22 448 288 448 288 448s170.78 0 213.371-11.486c23.497-6.321 42.003-24.171 48.284-47.821 11.412-42.867 11.412-132.305 11.412-132.305s0-89.438-11.412-132.305zm-317.51 213.508V175.185l142.739 81.205-142.739 81.201z"/></svg> Ted talk](https://www.youtube.com/watch?v=FpCrY7x5nEE)
]

.pull-right[
<img src="https://www.nature.com/news/polopoly_fs/7.36716.1469695923!/image/reproducibility-graphic-online1.jpeg_gen/derivatives/landscape_630/reproducibility-graphic-online1.jpeg" height="300" style="display: block; margin: auto;" />
]
.right[Source: [nature](https://www.nature.com/news/1-500-scientists-lift-the-lid-on-reproducibility-1.19970)]

---

## 3.4. Reproducibility crisis

There is low reproducibility in ecology ([Culina 2020](https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3000763))

- **73%** from published papers (between 2015 and 2019, n = 346) do not include code
- **5%** not all the code
- **1%** no data
- **21%** almost reproducible (26% do not use free software, 56% do not include data set, y 46% not version of the software)

<img src="https://media.eurekalert.org/multimedia_prod/pub/web/238857_web.jpg" height="300" style="display: block; margin: auto;" />
.right[ Source: [@Culina](https://twitter.com/antica_c/status/1288382890636709888)]

---

## 3.5. Old code

.pull-left[
Interestingly, the low reproducibility does not apply to only to work form other scientist but also their **own** research.

Lack of documentation and old programs were the main problems to reproduce research from 10 years ago
]
.pull-right[
- [Ten years reproducibility challenge](https://rescience.github.io/ten-years/)

Source: [nature](https://www.nature.com/articles/d41586-020-02462-7)
]

---

## 3.6. Gradient of reproducibility

---

# 4.  Git + Github

---

## 4.1. Git + Github

You can share projects, code, workflows.

Ho I do it is by:
- Creating an R project
- Having  git installed
- Having git connected : [introduce yourself to git](https://happygitwithr.com/hello-git.html)
- Having a github account

To read more:
- [Cheat Sheets](https://levelup.gitconnected.com/understanding-git-a-beginners-guide-containing-cheat-sheets-resources-b50c9c01a107)
- [What is version control](https://www.atlassian.com/git/tutorials/what-is-version-control)
- [How to teach git](https://rachelcarmena.github.io/2018/12/12/how-to-teach-git.html)

---

## 4.2. R projects

Instead of uploading file by file, you can connect your git to an R project in RStudio.

**RStudio** is an Integrated Development Environment (IDE) for R, a programming language for statistical computing and graphics.

Note that you can have R scripts and SQL queries in RStudio.

---

## 4.3. Version control

Very briefly:

- On R Studio you can select the project option of having a version control.

---

## 4.4. Clone

- You copy the link that you created online in your repository

---

## 4.5. Repositorio

- You paste the link on your git repository.

---

## 4.6. Pestaña

- If it works you will have the following icons.

---

## 4.7. Pull

Now you can either download everything that was in the repository

This screen will appear
<img src="https://raw.githubusercontent.com/MiriamLL/Curso_CIAD/main/Figuras/Git06-pull.png" height="200" style="display: block; margin: auto;" />

---

## 4.8. Stage & Commit

You can then change the files, and add a commit.

**Important**

Every time we make a commit git storage it with a 40-digit unique code. It is important to add the commit message to be able to identify the change in the future. It is very unlikely that we will remember the 40-digit code!

If you have an older project you can click on the history and see what I mean.

---

## 4.9. Push

Now to upload it to github and make the latest version available to collaborators you need to click on **push**.

This screen will appear
<img src="https://raw.githubusercontent.com/MiriamLL/Curso_CIAD/main/Figuras/Git09-push.png" height="300" style="display: block; margin: auto;" />

---

# 5.  Organize

---

## 5.1. Naming things

I share my repository...

What are all those files in the repository?

**Difficult names**:

- Final December Introduction.pdf  
- Model.xlsx  
- Figure12.png  
--

- Final December Introduction-2.pdf    
- Models.txt   
- Figure1234.docx  
--

- Final December Introduction-2_Final.pdf   
--

- Final December Introduction-2_Final-Rev.pdf

Source: [Stephanie Orellana](https://sporella.github.io/nombrar_cosas/#3), [Jenny Bryan](http://www2.stat.duke.edu/~rcs46/lectures_2015/01-markdown-git/slides/naming-slides/naming-slides.pdf)

---

## 5.2. Good names

- Use key words
- No special characters  
- No punctuation, use "_" to separate names with more than one word
- **Avoid** : Using similar key words for files with different contents

You can easily understand what the files contents are.
- 01_Introduction.docx  
- 02_Analisis_ANOVA.Rmd

Using something numeric at the beginning allows you to order by default, and the best its include zeros. 
If we do not include zeros at the beginning, it would not line with the 10.

- 01_Introduction.docx  
- 02_Discussion.docx  
- 03_Tables.docx

---

# Keen to learn more?

.left[- Happy git:    
[<svg aria-hidden="true" role="img" viewBox="0 0 576 512" style="height:1em;width:1.12em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:#D6F8FF;overflow:visible;position:relative;"><path d="M542.22 32.05c-54.8 3.11-163.72 14.43-230.96 55.59-4.64 2.84-7.27 7.89-7.27 13.17v363.87c0 11.55 12.63 18.85 23.28 13.49 69.18-34.82 169.23-44.32 218.7-46.92 16.89-.89 30.02-14.43 30.02-30.66V62.75c.01-17.71-15.35-31.74-33.77-30.7zM264.73 87.64C197.5 46.48 88.58 35.17 33.78 32.05 15.36 31.01 0 45.04 0 62.75V400.6c0 16.24 13.13 29.78 30.02 30.66 49.49 2.6 149.59 12.11 218.77 46.95 10.62 5.35 23.21-1.94 23.21-13.46V100.63c0-5.29-2.62-10.14-7.27-12.99z"/></svg> Happy Git by Jennifer Bryan](https://happygitwithr.com/)<br>
- Tutorials   
[<svg aria-hidden="true" role="img" viewBox="0 0 576 512" style="height:1em;width:1.12em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:#D6F8FF;overflow:visible;position:relative;"><path d="M549.655 124.083c-6.281-23.65-24.787-42.276-48.284-48.597C458.781 64 288 64 288 64S117.22 64 74.629 75.486c-23.497 6.322-42.003 24.947-48.284 48.597-11.412 42.867-11.412 132.305-11.412 132.305s0 89.438 11.412 132.305c6.281 23.65 24.787 41.5 48.284 47.821C117.22 448 288 448 288 448s170.78 0 213.371-11.486c23.497-6.321 42.003-24.171 48.284-47.821 11.412-42.867 11.412-132.305 11.412-132.305s0-89.438-11.412-132.305zm-317.51 213.508V175.185l142.739 81.205-142.739 81.201z"/></svg> RLadiesFreiburg](https://www.youtube.com/watch?v=tSse0KPgSoQ&t=1s)
- Image by
[Unsplash by Adam Gonzales](https://unsplash.com/@adamgonzales)]

.right[This material is all accessible in <br>
my [<svg aria-hidden="true" role="img" viewBox="0 0 512 512" style="height:1em;width:1em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:#D6F8FF;overflow:visible;position:relative;"><path d="M432,320H400a16,16,0,0,0-16,16V448H64V128H208a16,16,0,0,0,16-16V80a16,16,0,0,0-16-16H48A48,48,0,0,0,0,112V464a48,48,0,0,0,48,48H400a48,48,0,0,0,48-48V336A16,16,0,0,0,432,320ZM488,0h-128c-21.37,0-32.05,25.91-17,41l35.73,35.73L135,320.37a24,24,0,0,0,0,34L157.67,377a24,24,0,0,0,34,0L435.28,133.32,471,169c15,15,41,4.5,41-17V24A24,24,0,0,0,488,0Z"/></svg>github](https://github.com/MiriamLL/Curso_CIAD/)
and my [<svg aria-hidden="true" role="img" viewBox="0 0 512 512" style="height:1em;width:1em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:#D6F8FF;overflow:visible;position:relative;"><path d="M432,320H400a16,16,0,0,0-16,16V448H64V128H208a16,16,0,0,0,16-16V80a16,16,0,0,0-16-16H48A48,48,0,0,0,0,112V464a48,48,0,0,0,48,48H400a48,48,0,0,0,48-48V336A16,16,0,0,0,432,320ZM488,0h-128c-21.37,0-32.05,25.91-17,41l35.73,35.73L135,320.37a24,24,0,0,0,0,34L157.67,377a24,24,0,0,0,34,0L435.28,133.32,471,169c15,15,41,4.5,41-17V24A24,24,0,0,0,488,0Z"/></svg>blog](https://www.miriam-lerma.com/materiales.html)

[<svg aria-hidden="true" role="img" viewBox="0 0 576 512" style="height:1em;width:1.12em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:#D6F8FF;overflow:visible;position:relative;"><path d="M280.37 148.26L96 300.11V464a16 16 0 0 0 16 16l112.06-.29a16 16 0 0 0 15.92-16V368a16 16 0 0 1 16-16h64a16 16 0 0 1 16 16v95.64a16 16 0 0 0 16 16.05L464 480a16 16 0 0 0 16-16V300L295.67 148.26a12.19 12.19 0 0 0-15.3 0zM571.6 251.47L488 182.56V44.05a12 12 0 0 0-12-12h-56a12 12 0 0 0-12 12v72.61L318.47 43a48 48 0 0 0-61 0L4.34 251.47a12 12 0 0 0-1.6 16.9l25.5 31A12 12 0 0 0 45.15 301l235.22-193.74a12.19 12.19 0 0 1 15.3 0L530.9 301a12 12 0 0 0 16.9-1.6l25.5-31a12 12 0 0 0-1.7-16.93z"/></svg> Home ](https://www.miriam-lerma.com)

[<svg aria-hidden="true" role="img" viewBox="0 0 448 512" style="height:1em;width:0.88em;vertical-align:-0.125em;margin-left:auto;margin-right:auto;font-size:inherit;fill:#D6F8FF;overflow:visible;position:relative;"><path d="M424.4 214.7L72.4 6.6C43.8-10.3 0 6.1 0 47.9V464c0 37.5 40.7 60.1 72.4 41.3l352-208c31.4-18.5 31.5-64.1 0-82.6z"/></svg> Start ](https://miriamll.github.io/git_pres/GitGithubZenodo#1)
]