Preparation and installation

Last updated on 2023-01-05 | Edit this page

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Zotero, Zotero Connector, Zutilo, Better Bibtex for Zotero, Better notes for Zotero and text editing in R Cloud

Go to Zotero.org and download the relevant Zotero desktop version and connector for your PC, Mac or Linux machine. We are going to use Zutillo add-on to Zotero and SR Accelerator in order to get an overview of our field of research.

Download the zutilo. xpi file from Zutilo’s GitHub releases page. Then go to Tools-> Add-ons in Zotero. Click on the gear button in the upper right area of the Add-ons Manager window and install the Add-on from the file. Then select the downloaded zutilo. Note that this should not be done in Mozilla. Most other web browsers should work. Do same procedure with Better notes for Zotero and Better bibtex for zotero.

You will need a google account, or a GitHub account in order to be able to use the cloud service of RStudio called Posit. If you need digital privacy, you may download R and R Studio to your desktop instead. In this case, you do not have to make a user id for login.

Academic preparation In this course we have an academic problem that is used for learning the method: “Water scarcity or floods are increasingly a problem during the anthropocene. How is this problem solved in varouis regions, and what has the scientific community suggested in previous research?”

However, feel free to limit the scope of the problem, or use your own academic problem in episode 2. You must be able to easily find at least 500 references treating the chosen subject. We do this in order to simulate how to easily get an overview over a relatively good search on the literature on the chosen subject.

Check the functionality After the installation. Check your usual text editor. For Word users: Do you see the tab for Zotero functionality somewhere to the right? If not, you may use googles solution:

Zotero tab does not appear in the Word Ribbon Open the Templates and Add-ins window by going to File → Options → Add-ins, selecting “Word Add-ins” in the Manage drop-down at the bottom, and clicking “Go…”. Then, make sure Zotero.dotm is present and ticked.

Zotero supports the text editors Google Docs, Microsoft Word and Libre Office.

Installing the Zotero Word Processor Plugins Vitit this site: https://www.zotero.org/support/word_processor_plugin_installation

Overview

Questions

  • How do you write a lesson using Markdown and sandpaper?

Objectives

  • Have all the installations ready on your PC/ Mac
  • Be technically ready to start working with Zotero

Introduction

This is a lesson created via The Carpentries Workbench. It is written in Pandoc-flavored Markdown for static files and R Markdown for dynamic files that can render code into output. Please refer to the Introduction to The Carpentries Workbench for full documentation.

What you need to know is that there are three sections required for a valid Carpentries lesson:

  1. questions are displayed at the beginning of the episode to prime the learner for the content.
  2. objectives are the learning objectives for an episode displayed with the questions.
  3. keypoints are displayed at the end of the episode to reinforce the objectives.

Challenge 1: Can you do it?

How did you organize your references the last time you wrote an assignment?

  1. Endnote

  2. I did it manually

  3. Zotero

the right answer should be c) Zotero

Challenge 2: how do you nest solutions within challenge blocks?

You can add a line with at least three colons and a solution tag.

Figures

You can use standard markdown for static figures with the following syntax:

![optional caption that appears below the figure](figure url){alt='alt text for accessibility purposes'}

Blue Carpentries hex person logo with no text.
You belong in The Carpentries!

Math

One of our episodes contains \(\LaTeX\) equations when describing how to create dynamic reports with {knitr}, so we now use mathjax to describe this:

$\alpha = \dfrac{1}{(1 - \beta)^2}$ becomes: \(\alpha = \dfrac{1}{(1 - \beta)^2}\)

Cool, right?

Key Points

  • Use .md files for episodes when you want static content
  • Use .Rmd files for episodes when you need to generate output
  • Run sandpaper::check_lesson() to identify any issues with your lesson
  • Run sandpaper::build_lesson() to preview your lesson locally