Zotero

Zotero is an open-source online reference manager, where references can be readily saved from Google scholar using a browser plugin.

Getting started

  1. Load Zotero and create a login

  2. Download Zotero to your computer

  3. Install Zotero Connector to create a browser plugin so that you can directly save google scholar citations to your online reference list

  4. Link Rstudio to your Zotero library

Adding Citations to Zotero

Add via Google Scholar

  1. Find article on Google Scholar, click on double quotes at bottom of citation

  2. Select ‘RefMan’ and OK to save to Zotero

  3. Add citation to the NMFS-PAM group

Add via Browser Plug-In

  1. Open Zotero on your coputer
  2. Go to publication website
  3. Click on the Zotero browser icon (top right of browser) and save to selected Zotero folder

Zotero Group Libraries

Group libraries are a means of crowd-sourcing literature on specific topics. Here we suggest how to create a new group library, and how to join/participate in an existing group library.

How to Join Existing Group Libraray

To find an existing group library, you can search on Zotero.

If you are interested in Acoustics specific libraries, you can use the ‘reference’ tag within Bioacoustics Stack Exchange.

Click the red ‘Join’ button to add the library to your account

Create a New Zotero Group Library

  1. Once Zotero is installed on your computer and you have a Zotero account, navigate to the Zotero Groups and select “Create New Group”

  2. If you intend to make this a publicly accessible Zotero Group, select and save the following settings

    • Group Type = “Public Open”

    • Library Reading = “Anyone on the internet”

    • Library Editing = “Any group members”

    • File Editing = “No group file storage”

Share Your Group Library

Post in Bioacoustics Stack Exchange as a Question/Answer and tag as ‘reference’ (in addition to other relevant tags) so that this information is searchable on the web and accessible to the public.

  1. Log into Bioacoustics Stack Exchange or follow these instructions to create an account: join bioacoustics stack exchange
  2. Post a question (or have a colleague post a question), similar to the examples below, and be sure to select the tag ‘references’ and any additional tag references. You can either answer your own question, or work with a colleague such that one of you asks the question, and then the other answers the question. Be sure to accept the answer once posted.
  3. Here are two examples to follow: Soundscape Zotero Group Library and PAM-Glider Group Library

Zotero and RStudio

You can integrate Zotero directly to your Quarto/RMarkdown document in RStudio, or to your Microsoft Word document. Here are some basics for using in Quarto/RMarkdown

Choose CSL: Citation Style Language

Use Zotero to download the csl file for the journal you want to use.

  1. Go to the Zotero Preferences menu (Zotero > Preferences on Mac, Edit > Preferences on PC)

  2. Click on the ‘Cite’ menu

  3. Below the list of pre-installed styles, click the link for ‘Get additional styles’

  4. Search for your desired style in the provided search field

  5. Select the style you want to install

Add CSL to Your yaml

title: "My Document" 
bibliography: references.bib 
csl: nature.csl

Export Zotero Library to Your R Project

  1. Open Zotero and select a folder/library
  2. Click File > Export Library…
  3. Select Format > BibText and save the *.bib file in your R project folder

Add Your References Into the Document

Inline Citation:

Citations are inserted into your document using square brackets and are separated by semicolons. Each citation must have a key, composed of an ‘@’ symbol plus the citation identifier from the database. For example;

[@wickham2015]

Bibliography:

A list of works cited will be automatically generated and placed in the document if the style calls for it. You may insert divs such as this;

### References
For more information, see Quarto Citations Guide and Zotero Citations