Reproducible research with Reinarhj/education/tcrenv2016/pre/r-markdown.pdflibrary(knitr)...

Reproducible research with R

Bjarki Þór Elvarsson and Einar Hjörleifsson

Marine Research Institute

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Reproducible research

Overview

1 Reproducible research

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Reproducible research

How did you do that?

What data did you use?

What scripts were used to do what?

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Typical workflow

Prepare data

Perform analysis

Generate report

Realise that something waswrong in the data or analysis

Do it all over again

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What is reproducible research?

"The final product of research is not only the paper itself, but also the fullcomputation environment used to produce the results in the paper such asthe code and data necessary for reproduction of the results and buildingupon the research." (Xie, 2014).

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Reproducible research

Rmarkdown

A convenient tool to generate reproducible document.

MarkdownRemove HTML tag for higher readibility.Inline HTML is avaliable.

R markdownMarkdown + embedded R code chunksRmd -> md -> docx, pdf,html

Why R MarkdownConsolidate your code and document into single file.Easy for version control.

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Reproducible research

Markdown

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Markdown quick refefence

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Markdown commands

Text formatting

# 1st level header *a* italics

## 2nd level header **b** bold

### 3rd level header

List: Hyperlinks

* item 1 [Hafro](www.hafro.is)

* item 2

+ subitem

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Markdown equations

Markdown also supports LaTeX equation so

$x^2 + \sum_i a_i y_i^n$

becomesx2 +

∑i

aiyni

Further reading: https://en.wikibooks.org/wiki/LaTeX/Mathematics

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Embedding R

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Chunks

Input from R in Markdown is evaluated in chunks:```{r}

<insert R code for Markdown>

```

Chunks have a plethora of options available by default:Allows you to display or hide codeSimilarly display or hide its outputFigure dimensions can be set (if created by in the chunk)

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R code chunks

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Helpful chunk output options

eval = TRUE : Evaluate all or part of the current chunkecho = TRUE : Show all or part of the source coderesults = ’asis’ : Writes raw output from R to the output documentwithout markup. Helpful for creating tables with xtable. markup is thedefault.include = TRUE : Code chunk will be included in output. If you don’twant a chunk in the output but still evaluated set this to FALSE

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Figure settings

fig.width controls the figure width (in inches)fig.height controls the figure height (in inches)fig.cap is the figure captionfig.align sets the alignmentdev allows the user to specify the file type of the plot (png, pdf, bmp,etc..)

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Reproducible research

Creating tables in RMarkdown

Tables in Markdown are fairly easy:

First Header | Second Header

------------- | -------------

Content Cell | Content Cell

Content Cell | Content Ce

But one can also use R command to create tables. Note: Set results=’asis’to write raw results from R into the output document

library(knitr)

kable(tab,caption = 'This is a table')

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Output options

Html, both slides and normal webpages

Word, requires either Word or Libreoffice to display

Pdf, requires LaTeX:Linux do ’yum install texlive’Windows: install miktex from miktex.orgMacOsX: install MacTeX from tug.org/mactex

Custom output

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Other notable features

Bibtex style citations

Theming available based on reference word documents, css files andlatex templates

Allows the creation of interactive webpages using shiny

Support for presentations (beamer, ioslides, slidy)

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Reproducible research

Class exercise

Play around with Einar’s ggplot2 document

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