class: center, middle, inverse, title-slide

# Managing Citation In R Bookdown
## with Zotero
### Lin Yu
### University of Alberta
### 2021/07/31

---

class: inverse, center, middle

# Get Started

---

# Create R Bookdown Project

If you do not have a R bookdown project yet, you will need to build one first.

--

Create a new R bookdown<sup>1</sup> project from the menu `File - New 
Project -> New Directory -> Book Project using bookdown`

- The contents of the book are wrote with R markdown, by default, the name of each R markdown file has the following format: chapter number and chapter title. For example, _01_introduction_.

--

- The bibliographies are stored in the .bib file(s), in this case, book.bib and packages.bib.

--

.footnote[
[1] See the [official tutorial](https://bookdown.org/yihui/bookdown/get-started.html) for more details

]

---
class: inverse, center, middle

# Have Zotero ready

### Install Zotero is quite simple, so I decided to skip this part:)

---
class: inverse, middle, center

# Better-bibtex extension

---

# better-bibtex addin

After downloading Zotero, you need to install the 'better-bibtex' extension, which help create **citekeys** for your bibliographies. [Here](https://github.com/retorquere/zotero-better-bibtex/releases/tag/v5.4.28) is where you can get the better-bibtex addin. then

--

- Go to Tools on Zotero's main menu. Then click on Add-ons, select ‘Extensions’

--

- Click on the gear in the top-right corner and choose ‘Install Add-on From File…’

--

- Choose .xpi file that you have just downloaded, click ‘Install’

--

- Restart Zotero

--

You can [customize](https://retorque.re/zotero-better-bibtex/citing/) the format of citekey as you like:)

- You can think of the _citekey_ as the name or identifier of the bibliography

- The _citekey_ is used in R markdown files for citation
---

# How to Cite?

In R markdown, there are a few different ways to cite a bibliography.:

--

The simplest method is to use the visual mode's *insert citation* option.

- Swith to the [visual mode](https://rstudio.github.io/visual-markdown-editing/), then you can find the insert button, where you can click on **citation**

--

Alternatively, use *insert citation* addin in the **citr** R pacakge

- why?: You may prefer source mode; you do not have visual mode in your current R environment.
 
 - install [citr](https://github.com/crsh/citr) package (you may want to use `devtools::install_github("crsh/citr")`)
 
 - afte installation, you can find it in the *Addins*, and you can even define a [keyboard shortcut](http://rstudio.github.io/rstudioaddins/#keyboard-shorcuts) to call the addin.
 
--

---

# How to Cite? (Continued)

The third method for citation:

--

Manually export bibliographies into the R project.

- [Export the collection](https://www.zotero.org/support/kb/exporting) as Better BibTex format, put the .bib file under the root directory of the R bookdown project; 
 
 - in the R markdown file, use syntax `\cite{@citekey}` to cite 
 
 - Not recommended: (i) you need to **manually** update the .bib file (ii) using `\cite{@citekey}` is not efficient

---

class: inverse, center, middle

# Almost there:)

---

# One Last Step

--

Change the bibliography setting in the index.Rmd file: (see below codes)

```r
documentclass: book
bibliography: [YOUR_REFERENCE.bib]
```

If you use the *insert citation* option, then .bib file with a defualt name of "reference.bib" will be generated and updated every time you add new citations.

--

You are all set now! The default citation style is (author year)

However, you can change the citation style as you like!

---

# Change Citation Style

[Two easy steps](https://stackoverflow.com/questions/48965247/use-csl-file-for-pdf-output-in-bookdown) are required if you want to change the citation style:

--

Step 1: Download .csl file

- Download the desired .csl file (e.g., the-lancet.csl), .csl file can be downloaded from the [Zotero Style Repo](https://www.zotero.org/styles), then you need to store it under the root directory of the R bookdown project

- A trick here: by default, the .csl file will be downloaded to the Zotero folder.

--

Step 2: modify index.Rmd and _output.yml

- comment the biblio-style and specify the csl as follow:

```r
bibliography: [book.bib, packages.bib,testbib.bib, references.bib]
#biblio-style: apalike 
csl: the-lancet.csl
```

- add `pandoc_args: [ "--csl", "the-lancet.csl" ]` to the _output.yml (see next page)

---

# Change Citation Style (Cont'd)

- add `pandoc_args: [ "--csl", "the-lancet.csl" ]` to the _output.yml (see next page)

```r
bookdown::gitbook:
  css: style.css
  pandoc_args: [ "--csl", "the-lancet.csl" ]
  config:
    toc:
      before: |
        <li><a href="./">A Minimal Book Example</a></li>
      after: |
        <li><a href="https://github.com/rstudio/bookdown" target="blank">Published with bookdown</a></li>
    download: ["pdf", "epub"]
bookdown::pdf_book:
  includes:
    in_header: preamble.tex
  latex_engine: xelatex
  citation_package: default
  pandoc_args: [ "--csl", "the-lancet.csl" ]
  keep_tex: yes
bookdown::epub_book:
  pandoc_args: [ "--csl", "the-lancet.csl" ]
```

---

background-image: url(data:image/png;base64,#https://media4.giphy.com/media/fGU4lCGuH1sSffgNIE/200w.gif?cid=82a1493btnd325t1jxs7tfuglukb10rdhy9jzydo7b6h1b9n&rid=200w.gif&ct=g)
background-position: 50% 40%
class: center
# I am so happy

---
class: center, middle, inverse

# Thank you

Notes for current slide

Notes for next slide

Managing Citation In R Bookdownwith ZoteroLin YuUniversity of Alberta2021/07/311 / 14

Get Started2 / 14

Create R Bookdown Project

If you do not have a R bookdown project yet, you will need to build one first.

3 / 14

Create R Bookdown Project

If you do not have a R bookdown project yet, you will need to build one first.

Create a new R bookdown¹ project from the menu File - New Project -> New Directory -> Book Project using bookdown

The contents of the book are wrote with R markdown, by default, the name of each R markdown file has the following format: chapter number and chapter title. For example, 01_introduction.

3 / 14

Create R Bookdown Project

If you do not have a R bookdown project yet, you will need to build one first.

Create a new R bookdown¹ project from the menu File - New Project -> New Directory -> Book Project using bookdown

The contents of the book are wrote with R markdown, by default, the name of each R markdown file has the following format: chapter number and chapter title. For example, 01_introduction.
The bibliographies are stored in the .bib file(s), in this case, book.bib and packages.bib.

3 / 14

Create R Bookdown Project

If you do not have a R bookdown project yet, you will need to build one first.

Create a new R bookdown¹ project from the menu File - New Project -> New Directory -> Book Project using bookdown

The contents of the book are wrote with R markdown, by default, the name of each R markdown file has the following format: chapter number and chapter title. For example, 01_introduction.
The bibliographies are stored in the .bib file(s), in this case, book.bib and packages.bib.

[1] See the official tutorial for more details

3 / 14

Have Zotero readyInstall Zotero is quite simple, so I decided to skip this part:)4 / 14

Better-bibtex extension5 / 14

better-bibtex addin

After downloading Zotero, you need to install the 'better-bibtex' extension, which help create citekeys for your bibliographies. Here is where you can get the better-bibtex addin. then

6 / 14

better-bibtex addin

After downloading Zotero, you need to install the 'better-bibtex' extension, which help create citekeys for your bibliographies. Here is where you can get the better-bibtex addin. then

Go to Tools on Zotero's main menu. Then click on Add-ons, select ‘Extensions’

6 / 14

better-bibtex addin

After downloading Zotero, you need to install the 'better-bibtex' extension, which help create citekeys for your bibliographies. Here is where you can get the better-bibtex addin. then

Go to Tools on Zotero's main menu. Then click on Add-ons, select ‘Extensions’
Click on the gear in the top-right corner and choose ‘Install Add-on From File…’

6 / 14

better-bibtex addin

After downloading Zotero, you need to install the 'better-bibtex' extension, which help create citekeys for your bibliographies. Here is where you can get the better-bibtex addin. then

Go to Tools on Zotero's main menu. Then click on Add-ons, select ‘Extensions’
Click on the gear in the top-right corner and choose ‘Install Add-on From File…’
Choose .xpi file that you have just downloaded, click ‘Install’

6 / 14

better-bibtex addin

After downloading Zotero, you need to install the 'better-bibtex' extension, which help create citekeys for your bibliographies. Here is where you can get the better-bibtex addin. then

Go to Tools on Zotero's main menu. Then click on Add-ons, select ‘Extensions’
Click on the gear in the top-right corner and choose ‘Install Add-on From File…’
Choose .xpi file that you have just downloaded, click ‘Install’
Restart Zotero

6 / 14

better-bibtex addin

After downloading Zotero, you need to install the 'better-bibtex' extension, which help create citekeys for your bibliographies. Here is where you can get the better-bibtex addin. then

Go to Tools on Zotero's main menu. Then click on Add-ons, select ‘Extensions’
Click on the gear in the top-right corner and choose ‘Install Add-on From File…’
Choose .xpi file that you have just downloaded, click ‘Install’
Restart Zotero

You can customize the format of citekey as you like:)

You can think of the citekey as the name or identifier of the bibliography
The citekey is used in R markdown files for citation

6 / 14

How to Cite?

In R markdown, there are a few different ways to cite a bibliography.:

7 / 14

How to Cite?

In R markdown, there are a few different ways to cite a bibliography.:

The simplest method is to use the visual mode's insert citation option.

Swith to the visual mode, then you can find the insert button, where you can click on citation

7 / 14

How to Cite?

In R markdown, there are a few different ways to cite a bibliography.:

The simplest method is to use the visual mode's insert citation option.

Swith to the visual mode, then you can find the insert button, where you can click on citation

Alternatively, use insert citation addin in the citr R pacakge

why?: You may prefer source mode; you do not have visual mode in your current R environment.
install citr package (you may want to use devtools::install_github("crsh/citr"))
afte installation, you can find it in the Addins, and you can even define a keyboard shortcut to call the addin.

7 / 14

How to Cite?

In R markdown, there are a few different ways to cite a bibliography.:

The simplest method is to use the visual mode's insert citation option.

Swith to the visual mode, then you can find the insert button, where you can click on citation

Alternatively, use insert citation addin in the citr R pacakge

why?: You may prefer source mode; you do not have visual mode in your current R environment.
install citr package (you may want to use devtools::install_github("crsh/citr"))
afte installation, you can find it in the Addins, and you can even define a keyboard shortcut to call the addin.

7 / 14

How to Cite? (Continued)

The third method for citation:

8 / 14

How to Cite? (Continued)

The third method for citation:

Manually export bibliographies into the R project.

Export the collection as Better BibTex format, put the .bib file under the root directory of the R bookdown project;
in the R markdown file, use syntax \cite{@citekey} to cite
Not recommended: (i) you need to manually update the .bib file (ii) using \cite{@citekey} is not efficient

8 / 14

Almost there:)9 / 14

One Last Step10 / 14

One Last Step

Change the bibliography setting in the index.Rmd file: (see below codes)

documentclass: book
bibliography: [YOUR_REFERENCE.bib]

If you use the insert citation option, then .bib file with a defualt name of "reference.bib" will be generated and updated every time you add new citations.

10 / 14

One Last Step

Change the bibliography setting in the index.Rmd file: (see below codes)

documentclass: book
bibliography: [YOUR_REFERENCE.bib]

If you use the insert citation option, then .bib file with a defualt name of "reference.bib" will be generated and updated every time you add new citations.

You are all set now! The default citation style is (author year)

However, you can change the citation style as you like!

10 / 14

Change Citation Style

Two easy steps are required if you want to change the citation style:

11 / 14

Change Citation Style

Two easy steps are required if you want to change the citation style:

Step 1: Download .csl file

Download the desired .csl file (e.g., the-lancet.csl), .csl file can be downloaded from the Zotero Style Repo, then you need to store it under the root directory of the R bookdown project
A trick here: by default, the .csl file will be downloaded to the Zotero folder.

11 / 14

Change Citation Style

Two easy steps are required if you want to change the citation style:

Step 1: Download .csl file

Download the desired .csl file (e.g., the-lancet.csl), .csl file can be downloaded from the Zotero Style Repo, then you need to store it under the root directory of the R bookdown project
A trick here: by default, the .csl file will be downloaded to the Zotero folder.

Step 2: modify index.Rmd and _output.yml

comment the biblio-style and specify the csl as follow:

bibliography: [book.bib, packages.bib,testbib.bib, references.bib]
#biblio-style: apalike 
csl: the-lancet.csl

add pandoc_args: [ "--csl", "the-lancet.csl" ] to the _output.yml (see next page)

11 / 14

Change Citation Style (Cont'd)

add pandoc_args: [ "--csl", "the-lancet.csl" ] to the _output.yml (see next page)

bookdown::gitbook:
  css: style.css
  pandoc_args: [ "--csl", "the-lancet.csl" ]
  config:
    toc:
      before: |
        <li><a href="./">A Minimal Book Example</a></li>
      after: |
        <li><a href="https://github.com/rstudio/bookdown" target="blank">Published with bookdown</a></li>
    download: ["pdf", "epub"]
bookdown::pdf_book:
  includes:
    in_header: preamble.tex
  latex_engine: xelatex
  citation_package: default
  pandoc_args: [ "--csl", "the-lancet.csl" ]
  keep_tex: yes
bookdown::epub_book:
  pandoc_args: [ "--csl", "the-lancet.csl" ]

12 / 14

I am so happy13 / 14

Thank you14 / 14

Get Started2 / 14

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