Submission project Github microcredential

.gitignore

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+.Rproj.user
+*.Rproj

README.md

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-# Micro-credentials Project
-
-If you found this repository and is not registered in [our micro-credential]() please read more in the last topic.
-
-You should **fork this repository** and in collaboration with a colleague that is also part of the micro-credential course. You develop the project together.
-The project is simple, and consists of creating a repository for documenting concepts, best practices, examples and a cheat-sheet on using Git & GitHub.
-
-Your repository must contain a **folder structure, a README file, a gitignore file, a license**. All files must be developed in markdown (MD), you can find more information about [MD here](https://www.markdownguide.org/cheat-sheet/) and about [Liascript](https://liascript.github.io/), a MD dialect. You can add images and printscreens if you want.
-
-<span style="color:mediumBlue"> **Think about and inform yourself via internet resources about a useful folder structure in the repository, and cite your sources (2,3, as you see fit)**.</span>
-
-
-Define the your collaboration strategy considering:
-----------------------------------------------------
-
-1. Both should work in different branches
-
-    a. A minimum of 3 branches must be available (main, partner1 and partner2), if necessary more branches can be created.
-
-    b. The delivered project should be the final merged version.
-
-    c. You can merge directly or using branch pull request if you want someone to review.
-
-2. A minimum of 10 commits per person must be seen in the history.
-
-3. You need to have at least two solved conflicts in the history, one by each person.
-
-4. You need to revert at least on commit.
-
-5. Include examples in your documents, you can decide where and how this fits better.
-
-6. Search for other Git commands, that were not introduced in the course, choose one or more that you agree could be useful in your work and include in the documentation.
-
-7. You must have at least one tag in your project.
-
-8. Review and communicate with each other using GitHub-issues.
-
-9. Work as much as possible using command line.
-
-Delivery
------------
-
-Once with the final version you must <span style="color:mediumBlue">make a pull request</span> to this repository.
-
-
-**Micro-credential |** Reproducible Data Analysis: an Essential Capability in Modern Science
--------------------------------------------------------------------------------------------------
-
-This project is part the first evaluation of the micro-credetial that is offered by [VIB](https://vib.be/en#/) and [UGent](https://www.ugent.be/en) with the aim to improve data analysis reproducbility in science. A micro-credential is like a mini-diploma that you have followed a course and learnd a new skill that is valuable for your carrear. If you are interested to register you can find more detais in the [UGent registration page](https://studiekiezer.ugent.be/2025/micro-credential-reproducible-data-analysis-an-essential-capability-in-modern-science-en).
+# README
+
+This repository is made as an assignment for the UGent/VIB course "Reproducible Data Analysis".
+The repository must contain the following files
+
+- [`cheat-sheet.md`](./doc/cheat-sheet.md) a file with useful git commands
+- [`best-practices.md`](./doc/best-practices.md) a file with some best practices using Git and GitHub
+- [`concepts-git-github.md`](./doc/best-practices.md) a file important concepts of Git and GitHub explained
+- [`examples.md`](./doc/examples.m) a file in which some examples are illustrated
+
+
+The folder structure was inspired by [this webpage](https://coderefinery.github.io/reproducible-research/organizing-projects/) and 
+[this webpage](https://medium.com/code-factory-berlin/github-repository-structure-best-practices-248e6effc405).
+
+The folder structure can be visualized as follows:
+
+```
+├── Data \
+│   ├── processed-data \
+│   └── raw-data \
+├── doc \
+│   ├── best-practices.md \
+│   ├── cheat-sheet.md \
+│   ├── concepts-git-github.MD \
+│   └── examples.md \
+│   └── images \
+├── figures \
+├── README.md \
+└── LICENSE \
+├── src \
+└── tests \
+```

doc/best-practices.md

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+
+- Always save the files before commiting 
+- When commiting, always include a meaningful message. This should be clarify how was the issue addressed i.e. specify the changes/updates, why was it changed, effects due to change, limitations of the change (if not entirely final version)
+- Keep the timeline as clear as possible 
+- include a README file with general description about the project and instructions
+- Always make sure that there is only one .git repo in your folder. 
+- when collaborating, make sure that you always synchronize first with `git pull` and `git push` once you have made the required changes
+- when you give the branch a name, it is interesting to add your initials so it is clear that you are working on it
+- Always close all the  files when moving between branches
+- 

doc/cheat-sheet.md

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+# Git Commands Cheat Sheet
+
+
+## Check documentation
+
+- `git <command> --help`  => see the documentation for a git command.
+
+
+## Git Configuration
+
+- `git config --global --list`     => check global configurations
+- `git config --global user.name "<your name>"` => set user name
+- `git config --global user.email "<your email>"` => set user email
+
+
+## Git Workflow
+
+- `git status`                => check the status of the files in the current branch
+- `git add <files/folders>`   => stage files/folders of choice
+- `git add --all`             => stage all files/folders in the repository
+- `git add .`                 => stage all files/folders in the repository
+- `git restore --staged "<file>`  => remove file from the staging area
+
+
+
+- `git commit -m "<message>`  => commit the staged files/folders with a message
+- `git commit`               => commit the staged files/folders with, a text 
+                                 editor will open for a multiline comment 
+
+## Check versions and changes
+
+- `git log`                => get a list of all the commits in the current branch
+- `git log <file name>`    => get a list of all the commits for a specific file in the current branch
+- `git log --abrev-commit` => get a list of all the commits with an abbreviated commit references
+- `git log -n 3`           => get a list of the last three commits 
+
+- `git reflog show`        => view an ordered list of the commits that HEAD has pointed to
+
+- `git diff <old commit> <new commit>`  => create diff between two commits
+- `git show <old commit> <new commit>`  => shows the two file next to each other between two commits
+
+
+## Connect with remote repository
+
+- `git remote add origin [email protected]:ddebeer/<repository name>.git` 
+  => "make a bridge" between local and remote repository (using ssh)
+- `git push --set-upstream origin main`  => first push: to create a branch upstream (on the remote repository)
+- `git push -u origin main`              => push form origin (local repository) the branch main
+- `git push`   => send the latest version of the commit history to the remote repository
+
+
+## reverting and restoring
+
+- `git revert <commit ID>` => creates a new commit that is the same as the chosen one
+
+
+## Collaborating 
+
+- `git clone <ssh remote>` => creates a local repositor, creates "the bridge" and pulls the complete project (commit history)
+
+
+## Tagging
+
+- `HEAD` is the most recent commit, hence the HEAD changes with every new commit
+- `git tag <name>`   => give the current commit a name of choice: a "tag"
+- `git tag <name>`   => give the current commit a name of choice: a "tag"
+- `git tag <name> <commit ID>`  => give the commit of choice a name.
+- `git push --tags`  => push all the tags to the remote repository
+- `git tag -d <name>` => delete the tag  BUT not on github, should be deleted manually.
+
+
+## Branching
+
+- `git branch <branch name>`   => creates a new branch with a chosen name
+- `git chekcout <branch name>` => jumps to the chosen branch, new commits are
+                                  added to that branch.
+- `git chekcout HEAD`          => jumps to the most recent commit 
+
+- `git branch -l`              => list the local branches
+- `git branch -a`              => list all branches, local and remote
+- `git branch -b <new branch>` => create a new branch and jump to it immediately.
+
+
+- `git push --set-upstream origin <branch name>`  => push new branch and create a corresponding branch remote
+- `git push --al`              => push all commits of all local branches
+
+- `git chekcout <commit ID>`   => jumps to the chosen commit (i.e., travel in time)
+- `git switch -c <new branch>` => create a new branch after traveling to a commit (in the path).
+
+- `git log --graph --all`    => give a visual overview of all the branches
+
+
+## merging
+
+- `git merge <branch names>` => tries to merge the (HEAD of the) chosen branch with
+                                the (HEAD of the) currently active branch. If merging
+                                automatically is not possible, conflicts will need
+                                to be resolved and commited.
+
+- `git branch -d <branch name>` => delete a branch
+
+