EcoMods Booklet
2022-06-09
Chapter 1 Hello and welcome to the EcoMods working group!
Figure 1.1: The EcoMods in 2020
In this document, you will (hopefully) find everything you need for your course / internship / thesis with us.
1.1 Very first things
The very first things you should do before starting your work are:
Mailinglists: subscribe to the CCTB and EcoMods mailing lists. Select CCTB and ecomod-cctb and register using your email address. These lists are used for announcements of talks or other important events.
Account: get an account in the CCTB server. Our IT support, Patrick Haag (patrick.haag(at)uni-wuerzburg.de), can do this for you.
Keys: get access to the building. Your student ID card needs to be unlocked to be able to use it as a key for all doors. Patrick will also help you with this.
Mattermost: remind your supervisor to send you an invitation link for our Mattermost. We use Mattermost for CCTB-wide communication. Be aware that the certificate for enabling https is self-signed. This means when you visit the Mattermost site for the first time, you will have to add it as an exception. Mattermost contains channels for different purposes like organizational stuff, lunch planning, working groups, etc. It is very similar to Slack, if you have used that before. There is also a Desktop App.
Meetings: save these time slots for obligatory participation:
- weekly CCTB seminar, Wednesdays 11:00-12:00
- weekly EcoMods lab meeting, Thursdays 13:30-15:00
Gathertown: we also have a CCTB Gathertown which is basically a virtual office space. It was used a lot during home office times, now, not as much anymore. But if you post on Mattermost that you would like to meet for a virtual coffee break, people will show up! You’ll find the link in the header of the town-square channel on Mattermost
IT questions: if you ever run into any IT-related problems that you cannot solve alone, post it in the Mattermost IT channel.
We hope that this document helps you to learn more about how to do Ecological Modeling and how to navigate life at the CCTB. If you have any questions, you can come by our offices or send us an email any time.
1.2 What you can find in this booklet
You’ll find information about the following topics:
Programming tools in Chapter 2
IT infrastructure in Chapter 3
Process based models in Chapter 4
Computational methods in Chapter 5
Project management in Chapter 6
Writing & Publishing in Chapter 7
We also gladly accept any suggestions on how to improve this guide, so let us (Figure 1.1) know if you feel that anything is missing! This document is under constant construction, so don’t wonder about missing parts. :)
1.3 How to edit this booklet
This booklet is written as bookdown document. This means, that it consists of several R Markdown files. To learn R markdown see section 2.1.1.4. The booklet is hosted on GitHub (see section 2.1.3.
Step: Clone the repository from GitHub.
Step: Open the .rmd file of the Chapter you would like to change.
Step: Do your changes.
Step: Commit your changes and push them on GitHub.
Step: Then the magic happens: via github actions the website will be updated, but this takes 5-10 Minutes (check the green dot!). This creates files that are pushed automatically. Therefore, don’t work within the Repo while waiting and pull the changes before you go on editing.
Don’t forget to add links, citations, figures etc in a nice and organized way. Check text for typos and readability and be sure that a beginner can understand it.
1.4 Missing sections and TODOs within this booklet
If you find any missing topics, collect them here or write a TODO at the appropriate part.
1.4.1 TODOs Juliano
Juliano, do you have scripts for these points below that I could link?
Playing with R Codes - Intro R - First Models - Intro Ecological Functions and Simulations Exercise - First Functions and Simulations - Shiny