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---
title: "EcoMods Booklet"
author: "The EcoMods, Würzburg"
date: "`r Sys.Date()`"
site: bookdown::bookdown_site
documentclass: book
bibliography: [book.bib, packages.bib]
url: https://cctb-ecomods.github.io/Ecomods-Booklet
cover-image: booklet_pictures/workingGroup_2021.jpg
description: |
This is HowTo of the CCTB Würzburg EcoMods members.
link-citations: yes
github-repo: CCTB-Ecomods/Ecomods-Booklet
editor_options:
markdown:
wrap: 72
---
# Hello and welcome to the EcoMods working group!
```{r EcoMods, fig.cap="The EcoMods in 2020", echo=FALSE}
knitr::include_graphics("booklet_pictures/workingGroup_2021.jpg")
```
In this document, you will (hopefully) find everything you need for your
course / internship / thesis with us.
## Very first things
The very first things you should do before starting your work are:
- **Mailinglists**: subscribe to the CCTB and EcoMods [mailing
lists](https://lists.uni-wuerzburg.de). 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](https://cctb-intern.biologie.uni-wuerzburg.de). 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](https://about.mattermost.com/download/#mattermostApps).
- **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.
## What you can find in this booklet
You'll find information about the following topics:
- **Programming tools** in Chapter \@ref(programming-tools)
- **IT infrastructure** in Chapter \@ref(it-infrastructure)
- **Process based models** in Chapter \@ref(process-based-models)
- **Computational methods** in Chapter \@ref(computational-methods)
- **Project management** in Chapter \@ref(project-management)
- **Writing & Publishing** in Chapter \@ref(writing-publishing)
We also gladly accept any suggestions on how to improve this guide, so
let us (Figure \@ref(fig:EcoMods)) know if you feel that anything is
missing! This document is under constant construction, so don't wonder
about missing parts. :)
## 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
\@ref(rmd). The booklet is hosted on
[GitHub](https://github.com/CCTB-Ecomods/Ecomods-Booklet) (see section
\@ref(version-control).
1. Step: Clone the repository from GitHub.
2. Step: Open the .rmd file of the Chapter you would like to change.
3. Step: Do your changes.
4. Step: Commit your changes and push them on GitHub.
5. 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.
## Missing sections and TODOs within this booklet
If you find any missing topics, collect them here or write a *TODO* at
the appropriate part.
### 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
### TODOs Anne
- improve sections \@ref(sensitivity-analyses) and
\@ref(parameter-optimization)
- add more language tips \@ref(language-tips)
###