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Intro to R Markdown (CVC 2015)

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Nicholas Horton

on 13 July 2015

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Transcript of Intro to R Markdown (CVC 2015)

Intro to
R Markdown

Traditional Lab Report
Data Analysis
descriptive statistics
plots and tables
statistical model output
Write-Up
research question and context
interpretation of plots
drawing conclusions
Lab Report
copy + paste
copy + paste
the good
the bad
familiar format (Word)
impossible to reproduce
very difficult to update
very easy for mistakes to creep in
difficult for team work
messy
Markdown Lab Report (Reproducible analysis)
Text Block
Text Block
Text Block
Data Analysis
Data Analysis
the good
the bad
easy to reproduce
easy to update
easy to collaborate
standardized format
faster
must learn syntax
must be immaculate to compile
Text Block
Text Options
Data Analysis
aka: the R Chunk
Data Analysis
aka: the R Chunk
Text Block
R Chunk
Text Block
Things to remember
Don't forget to load the data. Markdown has a separate workspace from your console
The file must include the
minimal reproducible
code necessary
Comments encouraged (and should be in context)
All R chunks must be opened and closed with three ticks, ```
The PDF, Word, or HTML file will be generated in the same folder as the .Rmd file.

Andrew Bray and Nicholas Horton
based on Baumer et al (2014)
R Markdown: Integrating A Reproducible Analysis Tool into Introductory Statistics, Technology Innovations in Statistics Education, http://escholarship.org/uc/item/90b2f5xh
A quick intro to reproducibility and reproducible analysis
Reproducible analysis is a necessary (but not sufficient) precursor to reproducible research)
Of increasing importance to the research community
How do I replicate the analyses for the revisions of my paper (if myself from six months ago doesn't respond to emails...)
When do we teach these key skills to students?
A snapshot of recent papers and articles in
Science
A snapshot of recent papers and articles in
Science
A snapshot of recent papers and articles in
Science
YAML and the R Markdown header
YAML: YAML Ain’t Markup Language
There's some special markup in the header (to allow access to more advanced options and set metadata)
R Markdown templates in the mosaic package
We've added some templates to get you started quickly
fancy: to demo some neat features
plain: as a starting point for a new project
select "File > New File > New Markdown"
Full transcript