These are the materials for a workshop run by Palaeoverse at the 4th Crossing the Paleontological-Ecological Gap (CPEG) Meeting & 3rd Conservation Paleobiology Symposium in Zurich in July, 2025.

Follow this helpful checklist to contribute to these workshop materials.

1. The README.md file in the repository should include information about the workshop (e.g. who it is run by, where and when, funding support, etc) and archiving information (see below).
2. The index.qmd file in the top-level of the directory represents the landing page for the workshop materials. There is placeholder text in the file, so just update accordingly! Note that whatever title you list in the header will be used for the navigation menu in the workshop website. The order attribute should be updated to place this workshop in the desired location in the navigation menu. The oldest workshop (UCL 2023) has order: 99, the next oldest workshop (NAPC 2024) has order: 98, etc. You should assign your workshop with the highest order value less than 100 that has yet to be used (you can check the files in the workshop website repository if counting is too hard).
3. Each unit of the workshop should have a designated folder (with an informative name). Within each unit folder, you should have an index.qmd file. This is the landing file you should populate for the given unit. As with the root index.qmd file, the title in this file will be used in the navigation menu.
4. In order to ensure that the units are listed in the desired order in the navigation menu, the order attribute in the YAML of each index.qmd file should be updated to reflect the desired order of the units (e.g. the index.qmd file in the first unit should have order: 1, the index.qmd file in the second unit should have order: 2, etc).
5. (optional) Within each unit folder, you can also have other .qmd files if you need to organize your content across multiple pages. You should again use the order attribute to determine the order of these pages in the navigation menu. You are welcome to also include other materials in these unit folders, including, but not limited to, images, scripts, and data files. You can structure your materials as you please, but in general, we recommend being organised - this means having a dedicated folder structure such as materials/data. When linking between pages, linking to other materials, or including images, make sure to use relative paths instead of absolute paths. You may also use full URLs if linking to external materials or including external images.

When you are happy with the content in your individual workshop repository, you'll want to deploy it to the workshop website. Fortunately for you, we've developed a GitHub Actions workflow that will automatically copy your materials into our general workshop website repository and a separate Github Actions workflow that will then render the new files and regenerate the website and host it on GitHub Pages.

In order to start this syncing process, you will need to add a super secret SSH key to your repository settings. You can follow these steps to add the key as a repository secret:

1. While looking at the landing page for your GitHub repository, click on the 'Settings' tab at the top of the page (settings for the repository, not the account settings; it should have a gear icon). If you don't see this tab, you'll need to get someone with admin access to help.
2. On the left-hand side pane click on 'Secrets and variables' and then on 'Actions'.
3. Click on the green 'New repository secret' button.
4. Under 'Name' put 'SSH_DEPLOY_KEY'. Under 'Secret' put the contents of the id_github_workshop file (it's located in the Palaeoverse Google Drive in the Workshop folder).
5. Click the green 'Add secret' button.
6. Click the 'Actions' tab at the top (it has a play button icon).
7. Click on the most recent (closest to the top) workflow run, then on the top right, click the 'Rerun all jobs' button. If a prompt appears, click the green 'Rerun all jobs' button.

Now sit back and relax while all of your hard work is copied to the website repository and the workshop website is updated! Once the SSH key is set, any time you update materials in your repository, the workflows will again run and automatically update the workshop website. Once you push your changes to GitHub, the full website updating and rendering process should normally take ~5-10 minutes.

Note: We strongly recommend that you wait to add this SSH key secret to your repository until you are somewhat ready for your materials to be published to the website. Once the secret is in place, all changes will be copied and published automatically to the public website.

These materials are archived on Zenodo:

2025-CPEG-workshop ├── .github │ └── workflows │ └── copy.yml -- copies files to the main workshop repository ├── 01_introduction -- materials for the introduction of the workshop │ ├── index.qmd -- landing page │ └── workshop_intro_cpeg.qmd -- slides ├── 02_workflow -- materials for the reproducible workflow module │ ├── index.qmd -- landing page │ └── rproj_github.qmd -- slides ├── 03_acquisition -- materials for the data acquisition workflow module │ ├── index.qmd -- landing page │ ├── cenozoic_crocs_raw.csv -- data for module │ └── CPEGDataAcquisition.pdf -- slides ├── 04_exploration -- materials for the data exploration and cleaning module │ ├── index.qmd -- landing page │ └── cenozoic_crocs.csv -- data for module ├── 05_harmonization -- materials for the data harmonization module │ ├── index.qmd -- landing page │ └── ... -- various data files and figures for the module ├── 06_archiving -- materials for the data archiving module │ ├── index.qmd -- landing page │ └── CPEGArchivingPublishing.pdf -- slides ├── 07_wrap-up -- materials for the workshop wrap-up │ └── index.qmd -- landing page ├── images -- use this folder for storing images needed for one or more pages │ ├── logo.png -- Palaeoverse logo │ └── ... -- various other images ├── .gitignore ├── LICENSE ├── README.md ├── index.qmd -- workshop home page └── workshop.Rproj -- Rproject file for RStudio