├── .github └── workflows │ └── publish.yml ├── .gitignore ├── Collaborative-RStudio-GitHub.Rproj ├── LICENSE-CODE.md ├── LICENSE.md ├── README.md ├── _quarto.yml ├── assets ├── LMU-OSC_favicon.jpg ├── LMU-OSC_logo.jpg ├── clone-button.png ├── colour_picker.png ├── command-line.png ├── comment-and-merge.png ├── commit.png ├── copy-params_tmpl.png ├── create-fork.png ├── create-pull-request.png ├── created-pull-request.png ├── edit-file.png ├── files-changed.png ├── files-tab.png ├── final-push.png ├── fork-button.png ├── fork-process.png ├── git-project.png ├── knit.png ├── new-overview.png ├── new-project.png ├── open-shell.png ├── paste-url.png ├── plot.png ├── pull-request-button.png ├── pull.png ├── push-github.png ├── push-rstudio.png ├── rename-copy.png ├── skulls.png ├── stage.png ├── success-commit.png └── version-control-project.png ├── clone.md ├── commit.md ├── custom.scss ├── fork.md ├── gif.gif ├── gif ├── tmp-51.gif ├── tmp-52.gif ├── tmp-53.gif ├── tmp-54.gif ├── tmp-55.gif ├── tmp-56.gif ├── tmp-57.gif ├── tmp-58.gif ├── tmp-59.gif ├── tmp-60.gif ├── tmp-61.gif ├── tmp-62.gif ├── tmp-63.gif ├── tmp-64.gif ├── tmp-65.gif ├── tmp-66.gif ├── tmp-67.gif ├── tmp-68.gif ├── tmp-69.gif ├── tmp-70.gif ├── tmp-71.gif ├── tmp-72.gif ├── tmp-73.gif ├── tmp-74.gif ├── tmp-75.gif ├── tmp-76.gif ├── tmp-77.gif ├── tmp-78.gif ├── tmp-79.gif ├── tmp-80.gif ├── tmp-81.gif ├── tmp-82.gif ├── tmp-83.gif ├── tmp-84.gif ├── tmp-85.gif ├── tmp-86.gif ├── tmp-87.gif ├── tmp-88.gif ├── tmp-89.gif ├── tmp-90.gif ├── tmp-91.gif ├── tmp-92.gif ├── tmp-93.gif ├── tmp-94.gif ├── tmp-95.gif ├── tmp-96.gif ├── tmp-97.gif ├── tmp-98.gif └── tmp-99.gif ├── index.md ├── matomo-analytics.html ├── merge.md ├── params ├── Jose_params.R ├── Luz_params.R ├── Sarah_params.R ├── anas_krystallinus.R ├── malika_rocks.R └── params_copy.R ├── plot_trait_evolution.Rmd ├── pull-request.md ├── pull-upstream.md ├── push.md └── styles.css /.github/workflows/publish.yml: -------------------------------------------------------------------------------- 1 | on: 2 | workflow_dispatch: 3 | push: 4 | branches: main 5 | 6 | name: Quarto Publish 7 | 8 | jobs: 9 | build-deploy: 10 | runs-on: ubuntu-latest 11 | permissions: 12 | contents: write 13 | steps: 14 | - name: Check out repository 15 | uses: actions/checkout@v4 16 | 17 | - name: Install libcurl 18 | run: | 19 | sudo apt-get install libcurl4-openssl-dev 20 | 21 | - name: Set up Quarto 22 | uses: quarto-dev/quarto-actions/setup@v2 23 | 24 | - name: Install R 25 | uses: r-lib/actions/setup-r@v2 26 | with: 27 | r-version: '4.4.0' 28 | 29 | - name: Install R Packages 30 | uses: r-lib/actions/setup-r-dependencies@v2 31 | with: 32 | cache-version: 1 33 | packages: | 34 | any::rmarkdown 35 | any::dplyr 36 | ggplot2@3.5.1 37 | plotly@4.10.4 38 | any::sessioninfo 39 | 40 | - name: Render and Publish 41 | uses: quarto-dev/quarto-actions/publish@v2 42 | with: 43 | target: gh-pages 44 | env: 45 | GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} 46 | -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | # History files 2 | .Rhistory 3 | .Rapp.history 4 | 5 | # Session Data files 6 | .RData 7 | .RDataTmp 8 | 9 | # User-specific files 10 | .Ruserdata 11 | 12 | # Example code in package build process 13 | *-Ex.R 14 | 15 | # Output files from R CMD build 16 | /*.tar.gz 17 | 18 | # Output files from R CMD check 19 | /*.Rcheck/ 20 | 21 | # RStudio files 22 | .Rproj.user/ 23 | 24 | # produced vignettes 25 | vignettes/*.html 26 | vignettes/*.pdf 27 | 28 | # OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3 29 | .httr-oauth 30 | 31 | # knitr and R markdown default cache directories 32 | *_cache/ 33 | /cache/ 34 | 35 | # Temporary files created by R markdown 36 | *.utf8.md 37 | *.knit.md 38 | 39 | # R Environment Variables 40 | .Renviron 41 | 42 | # pkgdown site 43 | docs/ 44 | 45 | # translation temp files 46 | po/*~ 47 | 48 | # RStudio Connect folder 49 | rsconnect/ 50 | 51 | # Quarto 52 | /.quarto/ 53 | 54 | # Future-proofing: ignore commonly included files that should not be tracked 55 | # Inspired by usethis::git_vaccinate() options 56 | .DS_Store 57 | .Rproj.user 58 | .httr-oauth 59 | .quarto 60 | _site/ 61 | -------------------------------------------------------------------------------- /Collaborative-RStudio-GitHub.Rproj: -------------------------------------------------------------------------------- 1 | Version: 1.0 2 | 3 | RestoreWorkspace: Default 4 | SaveWorkspace: Default 5 | AlwaysSaveHistory: Default 6 | 7 | EnableCodeIndexing: Yes 8 | UseSpacesForTab: Yes 9 | NumSpacesForTab: 2 10 | Encoding: UTF-8 11 | 12 | RnwWeave: knitr 13 | LaTeX: pdfLaTeX 14 | 15 | AutoAppendNewline: Yes 16 | StripTrailingWhitespace: Yes 17 | -------------------------------------------------------------------------------- /LICENSE-CODE.md: -------------------------------------------------------------------------------- 1 | # Creative Commons Zero v1.0 Universal 2 | 3 | CREATIVE COMMONS CORPORATION IS NOT A LAW FIRM AND DOES NOT PROVIDE LEGAL SERVICES. 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For the avoidance of doubt, this paragraph does not form part of the public licenses. 170 | > 171 | > Creative Commons may be contacted at creativecommons.org. -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # Collaborative coding with GitHub and RStudio 2 | 3 | ## About this work 4 | This work was originally created by [Anna Krystalli](https://github.com/annakrystalli) from [RSE-Sheffield](https://github.com/RSE-Sheffield) under a [MIT licence](https://github.com/lmu-osc/Collaborative-RStudio-GitHub/blob/master/LICENSE) ([original repository](https://github.com/RSE-Sheffield/collaborative_github_exercise)). It was subsequently adapted by [Malika Ihle](https://ox.ukrn.org/people/#MalikaIhle) from [Reproducible Research Oxford](https://ox.ukrn.org/), with the contributions of [Adam Kenny](https://github.com/Kennyanthro). It is now maintained by [Malika Ihle](https://www.osc.uni-muenchen.de/about_us/coordinator/index.html) at the [LMU Open Science Center](https://www.osc.uni-muenchen.de/index.html). The overview image is from [Dumitru Uzun](https://duzun.me/tips/git). The exercice is based on the [research](http://eprints.whiterose.ac.uk/99452/1/Bright%20et%20al.%202016_SelfArchive.pdf) of [Jen Bright](https://twitter.com/MorphobeakGeek) who also kindly provided the gifs used in the exercice. You are free to use, copy, modify, distribute this work for your own projects. 5 | 6 | 7 | This session follows-up from the [Introduction to RStudio, Git, and GitHub](https://lmu-osc.github.io/Introduction-RStudio-Git-GitHub/) and is accompanied by this 10 min introductory [videorecording](https://osf.io/dcqt9/). 8 | 9 | *** 10 | 11 | ## Overview of the exercice 12 | 13 | In this session, you will 14 | * **fork** a GitHub repository (i.e. copy a collaborator's repository to your own GitHub account) 15 | * **clone** it locally (i.e. copy it to your computer while maintaining a connection to your remote (GitHub) version) 16 | * create a new file locally and **commit** it to your local repository (i.e. save the file locally in your version control system) 17 | * **push** your changes to your GitHub version (i.e. synchronise your local changes with your remote repository) 18 | * contribute a file to the original repository by making a **pull request** (i.e. request your collaborator, the owner of the original repository, to fetch your proposed changes and merge them into the original repository) 19 | * observe the outcome of all contributions merged by your collaborator 20 | * **pull the upstream repository into your fork** (i.e. update your fork to reflect all the changes that happened in your collaborator's original repository) 21 | 22 | 23 |
24 | 25 | In this example, the file you will contribute is required to simulate the evolutionary trajectory of an imaginary bird species’ body size. We will use RStudio and GitHub to collate all species files and plot them all up together at the end. We will also discover the skull and beak shapes associated with each species you contributed (after they 'evolved' through a simple brownian motion model which assumes steps to progress completely at random). 26 | 27 | ![](gif.gif) 28 | 29 | *** 30 | 31 | ## Step-by-step tutorial 32 | The material is self-paced and it is necessary that you work through the sections in order. 33 | 34 | * [Fork](./fork.md) - Copy your collaborator's repository 35 | * [Clone](./clone.md) - Copy your repository locally 36 | * [Commit](./commit.md) - Make changes and save them locally 37 | * [Push](./push.md) - Update your remote repository with your local changes 38 | * [Pull request](./pull-request.md) - Ask your collaborator to integrate your changes in their repository 39 | * [Merged results](./merge.md) - Observe the merge of all contributions 40 | * [Pull the upstream repository into your fork](./pull-upstream.md) - Update your fork with all contributions made to the original repository 41 | 42 | *** 43 | -------------------------------------------------------------------------------- /_quarto.yml: -------------------------------------------------------------------------------- 1 | project: 2 | type: website 3 | 4 | 5 | 6 | website: 7 | title: "" 8 | page-footer: 9 | center: "Copyright, 2024 Open Science Center at LMU Munich" 10 | border: false 11 | search: 12 | location: sidebar 13 | repo-url: https://github.com/lmu-osc/Collaborative-RStudio-GitHub 14 | repo-actions: [edit, issue] 15 | page-navigation: true 16 | favicon: assets/LMU-OSC_favicon.jpg 17 | margin-header: | 18 | ![](/assets/LMU-OSC_logo.jpg){width="175"} 19 | navbar: 20 | left: 21 | - href: index.md 22 | 23 | sidebar: 24 | style: docked 25 | contents: 26 | - text: "Home" 27 | href: index.md 28 | - section: "Tutorial" 29 | contents: 30 | - href: fork.md 31 | text: "Fork a Repo" 32 | - href: clone.md 33 | text: "Clone a Repo" 34 | - href: commit.md 35 | text: "Commit to a Project" 36 | - href: push.md 37 | text: "Push 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11 | 12 | 13 | 2. **RStudio**: create a new project 14 | 15 | ![](./assets/new-project.png) 16 | 17 |
18 | 19 | 20 | 3. **RStudio**: select `Checkout a project from a version control repository` 21 | 22 | ![](./assets/version-control-project.png) 23 | 24 |
25 | 26 | 27 | 4. **RStudio**: select `Clone a project from a Git repository` 28 | 29 | ![](./assets/git-project.png) 30 | 31 |
32 | 33 | 34 | 5. **RStudio**: paste the URL of **your** GitHub repository into 'Repository URL'. Do not locate this new Git repository in the folder created in the first tutorial (i.e. so that each folder has its own Git database). Click `Create Project`. Your password will be requested. 35 | 36 | ![](./assets/paste-url.png) 37 | 38 |
39 | 40 | 41 | 6. **RStudio**: Click on the Files tab to check that it contains all the files from the GitHub repository 42 | 43 | ![](./assets/files-tab.png) 44 | 45 | *** 46 | 47 | -------------------------------------------------------------------------------- /commit.md: -------------------------------------------------------------------------------- 1 | --- 2 | title: Commit changes locally 3 | --- 4 | 5 | *** 6 | To avoid conflict during this collaborative coding exercice (i.e. contributors editing the same line of code at the same time), today, we will work on different files altogether. To avoid conflict in future projects, no tool will be able to replace good communication. However, GitHub offers tools to help that communication, called [GitHub issues](https://guides.github.com/features/issues/). And if need be, you could still [resolve conflicts using the command line](https://docs.github.com/en/free-pro-team@latest/github/collaborating-with-issues-and-pull-requests/resolving-a-merge-conflict-using-the-command-line). Today, to avoid conflict, you will copy a template file and edit your own copy. 7 | 8 | 1. **RStudio**: select `params/params_tmpl.R` and click on 'More', 'Copy', and give it the name of your imaginary species or your name. **Please to not overwrite or edit the file `params/params_tmpl.R`.** 9 | 10 | ![](./assets/copy-params_tmpl.png) 11 | ![](./assets/rename-copy.png) 12 | 13 |
14 | 15 | 16 | 2. **RStudio**: edit your `.R` script 17 | 18 | ![](./assets/edit-file.png) 19 | 20 | The parameters each participants need to supply are: 21 | 22 | - **`sig2`:** A numeric value greater than 0 but smaller than 5. A numerical value doesn't have quotaiton marks around it. 23 | 24 | - **`species.name`:** a character string e.g. `"anas_krystallinus"`. Try to create a species name out of your name! A string has quotation marks around it in R. 25 | 26 | - **`color`:** e.g. `"red"`, `"#FFFFFF"`. This code or string should have quotation marks around it. 27 | 28 | (optional) If you want, you can use the RStudio colour picker to select a color. If you don't have it installed, type `install.packages("colourpicker")` in your console. 29 | 30 | 31 | 32 |
33 | 34 | 35 | 3. **RStudio**: save your file and in the Git tab, tick the box next to *** **your new script ONLY** *** to stage your file and click 'commit'. 36 | 37 | ![](./assets/stage.png) 38 | 39 |
40 | 41 | 42 | 4. **RStudio**: supply a descriptive message of the commit and click `commit` 43 | 44 | ![](./assets/commit.png) 45 | 46 | 47 | *** 48 | 49 | -------------------------------------------------------------------------------- /custom.scss: -------------------------------------------------------------------------------- 1 | /*-- scss:defaults --*/ 2 | // Base document colors 3 | $navbar-bg: #009933; 4 | $link-color: #006426; 5 | $sidebar-hl: #006426; 6 | -------------------------------------------------------------------------------- /fork.md: -------------------------------------------------------------------------------- 1 | --- 2 | title: Fork a GitHub repository 3 | --- 4 | 5 | *** 6 | 1. **GitHub**: go to [https://github.com/lmu-osc/Collaborative-RStudio-GitHub](https://github.com/lmu-osc/Collaborative-RStudio-GitHub). 7 | 8 |
9 | 10 | 11 | 2. **GitHub**: click on `Fork`. GitHub is creating your own copy of the repository in your GitHub account. Forks are linked and traceable. 12 | 13 | ![](./assets/fork-button.png) 14 | 15 |
16 | 17 | 3. **GitHub**: click on the green button 'create fork' with the default settings. 18 | 19 | 20 | 21 |
22 | 23 | 4. **GitHub**: you should now have a fork of this repository in your own GitHub account. 24 | 25 | ![](./assets/fork-process.png) 26 | 27 |
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repository](https://github.com/RSE-Sheffield/collaborative_github_exercise)). It was subsequently adapted by [Malika Ihle](https://ox.ukrn.org/people/#MalikaIhle) during her time at [Reproducible Research Oxford](https://ox.ukrn.org/), with the contributions of [Adam Kenny](https://github.com/Kennyanthro). It is now maintained by [Malika Ihle](https://www.osc.uni-muenchen.de/about_us/coordinator/index.html) at the [LMU Open Science Center](https://www.osc.uni-muenchen.de/index.html). The overview image is from [Dumitru Uzun](https://duzun.me/tips/git). The exercice is based on the [research](http://eprints.whiterose.ac.uk/99452/1/Bright%20et%20al.%202016_SelfArchive.pdf) of [Jen Bright](https://twitter.com/MorphobeakGeek) who also kindly provided the gifs used in the exercice. You are free to use, copy, modify, distribute this work for your own projects. 7 | 8 | 9 | This session follows-up from the [Introduction to RStudio, Git, and GitHub](https://lmu-osc.github.io/Introduction-RStudio-Git-GitHub/) and is accompanied by this 10 min introductory [videorecording](https://osf.io/dcqt9/). 10 | 11 | *** 12 | 13 | ## Overview of the exercice 14 | 15 | In this session, you will 16 | 17 | * **fork** a GitHub repository (i.e. copy a collaborator's repository to your own GitHub account) 18 | * **clone** it locally (i.e. copy it to your computer while maintaining a connection to your remote (GitHub) version) 19 | * create a new file locally and **commit** it to your local repository (i.e. save the file locally in your version control system) 20 | * **push** your changes to your GitHub version (i.e. synchronise your local changes with your remote repository) 21 | * contribute a file to the original repository by making a **pull request** (i.e. request your collaborator, the owner of the original repository, to fetch your proposed changes and merge them into the original repository) 22 | * observe the outcome of all contributions merged by your collaborator 23 | * **pull the upstream repository into your fork** (i.e. update your fork to reflect all the changes that happened in your collaborator's original repository) 24 | 25 | 26 |
27 | 28 | In this example, the file you will contribute is required to simulate the evolutionary trajectory of an imaginary bird species’ beak size. We will use RStudio and GitHub to collate all species files and plot them all up together at the end. We will also discover the skull and beak shapes associated with each species you contributed (after they 'evolved' through a simple brownian motion model which assumes steps to progress completely at random). 29 | 30 | ![](gif.gif) 31 | 32 | 33 | *** 34 | 35 | ## Step-by-step tutorial 36 | The material is self-paced and it is necessary that you work through the sections in order. 37 | 38 | * [Fork](./fork.md) - Copy your collaborator's repository 39 | * [Clone](./clone.md) - Copy your repository locally 40 | * [Commit](./commit.md) - Make changes and save them locally 41 | * [Push](./push.md) - Update your remote repository with your local changes 42 | * [Pull request](./pull-request.md) - Ask your collaborator to integrate your changes in their repository 43 | * [Merged results](./merge.md) - Observe the merge of all contributions 44 | * [Pull the upstream repository into your fork](./pull-upstream.md) - Update your fork with all contributions made to the original repository 45 | 46 | *** 47 | -------------------------------------------------------------------------------- /matomo-analytics.html: -------------------------------------------------------------------------------- 1 | 2 | 15 | 16 | -------------------------------------------------------------------------------- /merge.md: -------------------------------------------------------------------------------- 1 | --- 2 | title: Observe the merged contributions 3 | --- 4 | 5 | *** 6 | 7 | **!!! If the session is live!!!**: go see your collaborator merge your pull request! Most likely it will be a thumbs up and result in a merge! But your collaborator might also request a correction if they spot an error. 8 | 9 | 10 |
11 | 12 | 13 | 14 | **If you are following this tutorial on your own asynchronously**: These are the steps of the merge: 15 | 16 |
17 | 18 | 1. **Collaborator's screen - GitHub**: In their pull request tab, they will inspect the files you changed and ensure that the parameters were inputted correctly so as to not break down their code down the line. 19 | 20 | ![](./assets/files-changed.png) 21 | 22 |
23 | 24 | 2. **Collaborator's screen - GitHub**: They will navigate back to the conversation tab of your pull request to write some comments, merge your pull request, and confirm the merge. 25 | 26 | ![](./assets/comment-and-merge.png) 27 | 28 |
29 | 30 | 3. **Collaborator's screen - RStudio**: They will pull their GitHub repository into their local repository. 31 | 32 | ![](./assets/pull.png) 33 | 34 |
35 | 36 | 37 | 4. **Collaborator's screen - RStudio**: They will knit the Rmarkdown file `plot-trait-evolution.Rmd` which sources all the contributed files. Knitting a Rmarkdown file means rendering the Rmarkdown code (that integrate R code and Markdown code) into a defined format, here a html file. This file generates plots and figures based on the parameters that were contributed. 38 | 39 | ![](./assets/knit.png) 40 | 41 |
42 | 43 | 44 | 5. **Collaborator's screen - RStudio**: If all packages needed to run this script and to knit the file into a html page are installed, this file will generate plots and figures based on the parameters that were contributed. 45 | 46 | ![](./assets/plot.png) 47 | ![](./assets/skulls.png) 48 | 49 | 50 | 51 |
52 | 53 | This is how one can integrate data and code to a common repository shared amongst collaborators! 54 | 55 | 56 | *** 57 | 58 | -------------------------------------------------------------------------------- /params/Jose_params.R: -------------------------------------------------------------------------------- 1 | # !! PLEASE DO NOT EDIT THIS FILE !! 2 | # ** make a copy and edit that instead ** 3 | # ________________________________________________ 4 | # input parameters 5 | 6 | # sigma2: 0 < value < 5 7 | sig2 <- 2 8 | 9 | # e.g. "anas_krystallinus" 10 | #elena = starlight, lux = light; isenberg = iron mountain, fer = iron, mont = mountain 11 | species.name <- "jose_luxmont" 12 | 13 | # my colors: c("#6B8E23", "#00688B", "#FFB90F") 14 | color <- "#FFB90F" 15 | 16 | # tip: pick a color using rstudio colour picker. 17 | # Addins > Colour Picker (to install: install.packages("colourpicker")) 18 | -------------------------------------------------------------------------------- /params/Luz_params.R: -------------------------------------------------------------------------------- 1 | # !! PLEASE DO NOT EDIT THIS FILE !! 2 | # ** make a copy and edit that instead ** 3 | # ________________________________________________ 4 | # input parameters 5 | 6 | # sigma2: 0 < value < 5 7 | sig2 <- 2.5 8 | 9 | # e.g. "anas_krystallinus" 10 | #elena = starlight, lux = light; isenberg = iron mountain, fer = iron, mont = mountain 11 | species.name <- "lux_fermonta" 12 | 13 | # my colors: c("#6B8E23", "#00688B", "#FFB90F") 14 | color <- "#00688B" 15 | 16 | # tip: pick a color using rstudio colour picker. 17 | # Addins > Colour Picker (to install: install.packages("colourpicker")) 18 | -------------------------------------------------------------------------------- /params/Sarah_params.R: -------------------------------------------------------------------------------- 1 | # !! PLEASE DO NOT EDIT THIS FILE !! 2 | # ** make a copy and edit that instead ** 3 | # ________________________________________________ 4 | # input parameters 5 | 6 | # sigma2: 0 < value < 5 7 | sig2 <- 3 8 | 9 | # e.g. "anas_krystallinus" 10 | #elena = starlight, lux = light; isenberg = iron mountain, fer = iron, mont = mountain 11 | species.name <- "lupus_castri" 12 | 13 | # my colors: c("#6B8E23", "#00688B", "#FFB90F") 14 | color <- "#551A8B" 15 | 16 | # tip: pick a color using rstudio colour picker. 17 | # Addins > Colour Picker (to install: install.packages("colourpicker")) 18 | -------------------------------------------------------------------------------- /params/anas_krystallinus.R: -------------------------------------------------------------------------------- 1 | # !! PLEASE DO NOT EDIT THIS FILE !! 2 | # ** make a copy and edit that instead ** 3 | # ________________________________________________ 4 | # input parameters 5 | 6 | # sigma2: 0 < value < 5 7 | sig2 <- 0.8 8 | 9 | # e.g. "anas_krystallinus" 10 | species.name <- "anas_krystallinus" 11 | 12 | # e.g. "orange" 13 | color <- "orange" 14 | 15 | # tip: pick a color at using rstudio colour picker. Addins > Colour Picker 16 | -------------------------------------------------------------------------------- /params/malika_rocks.R: -------------------------------------------------------------------------------- 1 | # !! PLEASE DO NOT EDIT THIS FILE !! 2 | # ** make a copy and edit that instead ** 3 | # ________________________________________________ 4 | # input parameters 5 | 6 | # sigma2: 0 < value < 5 7 | sig2 <- 3.5 8 | 9 | # e.g. "anas_krystallinus" 10 | species.name <- "malika_rocks" 11 | 12 | # e.g. "red" 13 | color <- "#311DB3" 14 | 15 | # tip: pick a color using rstudio colour picker. 16 | # Addins > Colour Picker (to install: install.packages("colourpicker")) 17 | -------------------------------------------------------------------------------- /params/params_copy.R: -------------------------------------------------------------------------------- 1 | # !! PLEASE DO NOT EDIT THIS FILE !! 2 | # ** make a copy and edit that instead ** 3 | # ________________________________________________ 4 | # input parameters 5 | 6 | # sigma2: 0 < value < 5 7 | sig2 <- 3 8 | 9 | # e.g. "anas_krystallinus" 10 | #elena = starlight, lux = light; isenberg = iron mountain, fer = iron, mont = mountain 11 | species.name <- "lux_fermonta" 12 | 13 | # my colors: c("#6B8E23", "#00688B", "#FFB90F") 14 | color <- "#00688B" 15 | 16 | # tip: pick a color using rstudio colour picker. 17 | # Addins > Colour Picker (to install: install.packages("colourpicker")) 18 | -------------------------------------------------------------------------------- /plot_trait_evolution.Rmd: -------------------------------------------------------------------------------- 1 | --- 2 | output: 3 | html_document: 4 | theme: cerulean 5 | pdf_document: default 6 | --- 7 | 8 | # **Evolutionary lottery of skull and beak morphology** 9 | 10 |
11 | 12 | > [**Beak and skull shapes in birds of prey ("raptors") are strongly coupled and largely controlled by size.**](http://eprints.whiterose.ac.uk/99452/1/Bright%20et%20al.%202016_SelfArchive.pdf) 13 | 14 | gif provided by the awesome **Jen Bright** [**\@MorphobeakGeek**](https://twitter.com/MorphobeakGeek)! 15 | 16 | ![](gif.gif) 17 | 18 | In this exercise we will **use a github repo** to collaboratively collate and *simulate evolutionary trajectories for each participants' species* ***body size*** using a simple brownian motion evolutionary model. This assumes evolutionary steps to progress comletely at random. You could say: 19 | 20 | #### it's a bit of lottery! 21 | 22 |
23 | 24 | Each participant has **created and contributed a file** specifying the parameters required to simulate and plot their species evolutionary trajectory. We've collect all participants' files in the master repo. Next we need to simulate species trajectories plot them up. 25 | 26 | Participants will then get to **see the skull and beak shape** corresponding to their species relative body size! 27 | 28 | ------------------------------------------------------------------------ 29 | 30 | ### setup 31 | 32 | First we load the required packages and create some objects to compile data on trait evolution for each species. 33 | 34 | ```{r warning=F, message=FALSE} 35 | library(dplyr) 36 | library(ggplot2) #3.5.1 37 | library(plotly) #4.10.4 38 | set.seed(1) 39 | 40 | t <- 0:100 # generate time vector 41 | dt <- NULL # generate object to compile time-series data 42 | cols <- NULL # generate object to compile trendline colours 43 | ``` 44 | 45 | ------------------------------------------------------------------------ 46 | 47 | ### Simulate trait evolution, iterate over all species files in `params/` folder 48 | 49 | We'll use the parameters supplied in your scripts to generate brownian trait evolution trendline for each species. 50 | 51 | ```{r} 52 | #getting the file names for everything except the template that has undefined values 53 | spp.files <- dir("params/")[dir("params/") != "params_tmpl.R"] 54 | 55 | for(spp in spp.files){ 56 | # source parameters for each species 57 | source(file.path("params", spp)) 58 | 59 | # generate trait evolution time-series and compile plotting data 60 | dt <- rbind(dt, data.frame(t, 61 | trait = c(0, rnorm(n = length(t) - 1, sd = sqrt(sig2)) |> cumsum()), 62 | species = species.name)) 63 | cols <- c(cols, color) 64 | } 65 | 66 | ``` 67 | 68 | 69 | ### Plot trait evolution timeseries 70 | 71 | Use the data generated to plot all species. 72 | 73 | ```{r fig.width = 9} 74 | 75 | # Specify the order of species based on the order of colors in cols to stop a mismatch in colours 76 | dt$species <- factor(dt$species, levels = unique(dt$species)) 77 | 78 | # Create the ggplot object 79 | p <- ggplot(data = dt, aes(x = t, y = trait, group = species, colour = species)) + 80 | geom_line() + 81 | scale_colour_manual(values = cols) 82 | 83 | # Plot the results 84 | ggplotly(p) 85 | ``` 86 | 87 |
88 | 89 | ------------------------------------------------------------------------ 90 | 91 | ## **Skulls!** find the skull associated with your species: 92 | 93 |
94 | 95 | Skulls are organised from **largest** to **smallest**. The largest skulls are **vulture-like**, (e.g. **no. 50, the Andean condor** [*Vultur gryphus*](https://en.wikipedia.org/wiki/Andean_condor)) and the smallest are **falconet-like**, (e.g. **no. 1 Collared falconet** [*Microhierax caerulescens*](https://en.wikipedia.org/wiki/Collared_falconet)) 96 | 97 | ```{r, echo=FALSE, results='asis'} 98 | skull <- dt[dt$t == 100,] 99 | skull <- skull[order(skull$trait, decreasing = T),] 100 | 101 | gf <- list.files("gif/") 102 | 103 | if(length(gf) > 0){ 104 | max.x <- max(abs(dt$trait)) 105 | breaks <- seq(-max.x, max.x, length.out = 51) 106 | bins <- cut(skull$trait, breaks = breaks, include.lowest = T, labels = F) 107 | 108 | for(i in 1:nrow(skull)){ 109 | cat("### **No: ",bins[i], "** ***", as.character(skull$species[i]),"***", "\n", "\n", sep = "") 110 | cat("![](gif/", gf[bins[i]], ")", "\n", "\n", sep = "") 111 | } 112 | } 113 | ``` 114 | 115 | 116 | ### Session Info 117 | 118 | ```{r} 119 | sessioninfo::session_info() 120 | ``` 121 | -------------------------------------------------------------------------------- /pull-request.md: -------------------------------------------------------------------------------- 1 | --- 2 | title: Create a pull request to ask your collaborator to merge your fork to the original repository 3 | --- 4 | 5 | *** 6 | 7 | 1. **GitHub**: in your repository, click on '**contribute**' and '**open pull request**' 8 | 9 | ![](./assets/pull-request-button.png) 10 | 11 |
12 | 13 | 14 | 2. **GitHub**: **make sure the base repository is the LMU Open Science Center's original one and the head fork is yours**, both set on their main branch (these repositories should only have one branch anyway called 'main'. Branches are diverging versions of a file *within* a repository - we will not cover this concept today). Check that your requested merge does not create any conflict. In addition, **write an informative message**, explaining your changes to your collaborator, the author of the original repository. Click on `Create pull request` 15 | 16 | ![](./assets/create-pull-request.png) 17 | 18 |
19 | 20 | 21 | 3. **GitHub**: you can now see a conversation tab around your pull request in the repository of the original owner: 22 | 23 | 24 | 25 | 26 | *** 27 | 28 | -------------------------------------------------------------------------------- /pull-upstream.md: -------------------------------------------------------------------------------- 1 | --- 2 | title: Pull upstream repository into your fork 3 | --- 4 | 5 | *** 6 | 7 | To integrate all the contributions made to the original repository into your local repository, you may think that you could first integrate the changes from the original repository into your fork (your GitHub version) and then pull your fork (to update your local copy), but this is not possible. You will need to shortcircuit this by pulling the original repository into your local repository directly (and then push the local new changes to your remote version on GitHub). This means that this operation needs to happen locally, in RStudio. Because you will not be pulling from your fork (your remote GitHub) but from the original repository, and that this isn't a daily operation, you do not have a shortcut for this in RStudio. This operation needs to be instructed in the command line, in the Terminal tab of RStudio. 8 | 9 | 1. **RStudio**: go to the Terminal tab of Rstudio 10 | 11 | 2. **Terminal**: first make sure you are on the branch you wish to receive the modifications (today we didn't create branches other than the default one called 'main') by typing: 12 | 13 | ```bash 14 | git checkout main 15 | ``` 16 | 17 | 18 | 4. **Terminal**: type the command to pull the original repository and branch you wish to obtain locally which has the format: `git pull git@github.com:ORIGINAL_OWNER/ORIGINAL_REPOSITORY.git` where you would replace original owner and repository to the appropriate names. Here: 19 | 20 | ```bash 21 | git pull git@github.com:lmu-osc/Collaborative-RStudio-GitHub.git 22 | ``` 23 | 24 | 25 | ![](./assets/command-line.png) 26 | 27 | 6. **RStudio**: check in the Files tab that the new contributions appeared. 28 | 29 | 7. **RStudio**: push those local changes to your GitHub repository (you can do this from the command line by typing `git push`) 30 | 31 | ![](./assets/final-push.png) 32 | 33 | 34 | You are done! 35 | 36 | *** 37 | 38 | -------------------------------------------------------------------------------- /push.md: -------------------------------------------------------------------------------- 1 | --- 2 | title: "Push your local changes to your remote repository" 3 | --- 4 | 5 | *** 6 | 7 | 1. **RStudio**: push your changes to GitHub by clicking, in the Git tab, the green arrow pointing up and entering your password. 8 | 9 | ![](./assets/push-rstudio.png) 10 | 11 | when successful you should get this pop up box which you can close: 12 | 13 | 14 | 15 | 16 |
17 | 18 | 19 | 2. **GitHub**: verify that your changes were integrated in your GitHub repository by refreshing your GitHub repository webpage and looking into the params folder to see if your file is there. 20 | 21 | *** 22 | 23 | -------------------------------------------------------------------------------- /styles.css: -------------------------------------------------------------------------------- 1 | /* css styles */ 2 | 3 | .nav-page .nav-page-text { 4 | font-size: 15pt; 5 | } 6 | --------------------------------------------------------------------------------