papaja: Reproducible APA
manuscripts with R Markdown
Preface
1
Introduction
1.1
Motivation
1.1.1
Reproducible scientific reports
1.2
Implementation
1.2.1
Guiding principles
1.2.2
Document compilation
1.3
Alternatives
1.4
Getting started
1.4.1
Software requirements
1.4.2
Installing papaja
1.4.3
Creating a document
2
R Markdown components
2.1
YAML front matter
2.1.1
Manuscript metadata
2.1.2
Rendering options
2.2
Body
2.2.1
Markdown
2.2.2
R code
3
Writing
3.1
Markdown text formatting
3.2
Citations
3.2.1
Citation styles
3.2.2
Works ‘in press’
3.2.3
Conveniently inserting citations with
citr
3.2.4
Meta-analysis references
3.2.5
Citing R and its packages
3.3
Equations
3.4
Cross-referencing
3.5
Appendices
3.6
Counting words
3.7
Comparing document versions
4
Reporting
4.1
Numerical values
4.2
Figures
4.2.1
R-generated figures
4.2.2
External images
4.2.3
Figure captions
4.3
Tables
4.3.1
Fixed-width columns
4.3.2
Table captions
4.3.3
Alternatives
4.4
Statistical Models and Tests
4.4.1
Reporting models and tests in a table
4.4.2
Supported analysis methods
4.5
Caching expensive computations
4.5.1
Inserting variables before they have been computed
5
Tips and Tricks
5.1
Global chunk options
5.2
Meaningful chunk names
5.3
Text references
5.4
Useful RStudio Addins
5.5
Reproducible software environments
5.5.1
Docker
5.5.2
CodeOcean
5.6
RStudio
5.7
Splitting an R Markdown document
5.8
Best practices
5.9
Troubleshooting
5.9.1
YAML
5.9.2
R
5.9.3
bookdown
5.9.4
pandoc
5.9.5
\(\LaTeX\)
6
Collaborative writing
7
Published manuscripts
8
Limitations
8.1
PDF documents
8.1.1
Customizing the document preamble
8.2
Microsoft Word documents
9
Customizations
9.1
Author name disambiguation
9.2
Adjusting line spacing
9.3
Writing dissertations
9.4
Customizing
apa_print()
10
Future directions
10.1
Contributions
10.1.1
Workflow
References
papaja on GitHub
Published with bookdown
papaja: Reproducible APA manuscripts with R Markdown
6
Collaborative writing
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