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Why R Markdown?
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Reproducible research is key for scientific advancement.
R Markdown can help you to organize, have better control over and produce reproducible research.
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Getting Started with R Markdown
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Starting a new Rmd File
Anatomy of an Rmd File (YAML header, Text, Code chunks)
How to knit an Rmd File to html
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R Markdown Syntax: Headings & Lists
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Heading syntax (#,
Bulleted lists (*, - , or +)
Numbered lists (1., 2., etc.)
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R Markdown Syntax: Hyperlinks, Images & Tables
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R Markdown syntax for hyperlinks
R Markdown syntax for images
You can resize images with R Markdown
You can easily create basic tables with R Markdown
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R Markdown Syntax: Emphasis, Formulas & Footnotes
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You can add *italicized* and *bolded* texts in R Markdown
There is an extensive LaTeX guideline for mathematics formatting
You can add create superscript text & linked footnotes
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R Markdown Syntax: Citations & Bibliography
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Finding & Applying Existing Journal Templates
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The rticles pachage provides some journal templates
Whenever available, if you already know which journal you are submitting to, start your paper using the template
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Knitr Syntax: Inline Code & Code Chunks
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Knitr Syntax: Styling Code Outputs
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Use kable() to create tables from dataframes
add captions to figures and images generated by code chunks
Set global chunk settings to automatically size & align outputs
Use bookdown to enable cross referencing
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Publishing a Report
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Define a new function for knit in the yaml to change your outputs
R-Studio lets you Knit and Publish to R-pubs
Github has Github Pages to publish work as a free webpage
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