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am-03-reference-management.Rmd
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am-03-reference-management.Rmd
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---
title: "Week 3 - Reference Management with Zotero"
---
<script defer data-domain="rbtl-fs22.github.io/website" src="https://plausible.io/js/plausible.js"></script>
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
# Introduction
We are using the Zotero reference manager to organize and collaborate on our reference libraries.
## Prerequisites
We assume that you have:
1. Completed Assignment 1 & 2 of this course. If you have not, follow the instructions here:
- Assignment 1: https://rbtl-fs22.github.io/website/am-01-hello-github.html
- Assignment 2: https://rbtl-fs22.github.io/website/am-02-hello-rstudio.html
## Learning Objectives
In this unit, you will learn to:
1. Create a Zotero Account
2. Add references to Zotero using the Zotero Connector browser add-on
3. Setup a common citekey
4. Use the autopin functionality to update citekeys
## Terminology
**Open Source**
- Open Data Handbook Glossary http://opendatahandbook.org/glossary/en/terms/open-source/
- FORRT (Framework for Open and Reproducible Research Training) Glossary: https://forrt.org/glossary/open-source-software/
- Open Source Inititiative Definition: https://opensource.org/osd
# Tasks
## 1. Setup Zotero Account
1. Open https://www.zotero.org/user/login/
2. Click on "Register for a free account"
3. Chose username, email, and password
4. Click "Register"
5. Open your email and verify your account
## 2. Join GHE Group Library
1. Login into Zotero: https://www.zotero.org/user/login/
2. Open GHE Group Library: https://www.zotero.org/groups/4609540/rbtl
3. Click on "Join" button
4. Wait for group admin to confirm your membership or contact Lars if you require immediate access
## 3. Install Zotero Desktop Client
1. Open https://www.zotero.org/download/
2. Download Zotero for your operating system
3. Install Zotero
## 4. Watch the Video and setup Zotero Preferences
The following video provides instruction to:
1. Install Zotero Connector for the Firefox browser: https://www.zotero.org/
2. Add references:
- https://www.tandfonline.com/doi/full/10.1080/00031305.2017.1375989
- https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005510
2. Install Better BibTeX for Zotero Add-on: https://retorque.re/zotero-better-bibtex/installation/
3. Edit the Zotero CiteKey preferences to the following:
`[auth:lower][year][veryshorttitle1_0:lower]`
4. Change setting for CityKey autoping delay, also listed here:
- Open Zotero
- Open Zotero Preferences
- Click "Advanced" tab
- At the bottom of the window under "Advanced Configuration", click: "Config Editor"
- Click "I accept the risk!"
- In the search bar, search for "autopin"
- Double click into the field under "Value"
- In the new windows with the title "Enter integer value" change value from 0 to 2
- Click "OK"
# Video
<iframe width="560" height="400" src="https://www.youtube.com/embed/yWlSeqhZCNM" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
# Acknowledgements
The settings that are used in these instructions are inspired by [Cortex Futura: How to install Zotero, BetterBibTex and Zotfile](https://www.youtube.com/watch?v=Nm5BsfMfO9M).