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All in one – Reporting with RStudio (slides)
Presentation · December 2016
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SLIDE 2
All in one
Reporting with RStudio Satu Helske 8 December 2016
SLIDE 3 Learning R
◮ Online courses
◮ Lynda ◮ DataCamp ◮ Code School
◮ Books
◮ Getting used to R, RStudio, and R Markdown by Chester Ismay ◮ R for Data Science by Garrett Grolemund and Hadley Wickham ◮ R for Stata Users by Robert A. Muenchen and Joseph M. Hilbe
SLIDE 4
Rstudio
◮ Open source graphical interface for R and related tools ◮ Code completion, syntax highlighting, code diagnostics ◮ Autosave, command history, plotting history, environment
browser, integrated searchable help
◮ R projects for easy return to and switching between jobs ◮ https://www.rstudio.com/
SLIDE 5
Reporting with knitr
SLIDE 6
What?
◮ Mix text, R code, R output, R graphics, mathematics ◮ Notes, reports, exercises, slides, research papers ◮ PDF, Word, html etc.
SLIDE 7 Why?
◮ Reproducible research
◮ Change in data → Change in report ◮ Sharing work with others
◮ Easier to adjust font sizes in figures ◮ No copy-paste errors
SLIDE 8 How?
◮ knitr with R Markdown
◮ Simple, fast ◮ Limited functionalities ◮ Rmd file
◮ knitr with LaTeX
◮ Precice control ◮ Requires LaTeX skills ◮ Rnw file
SLIDE 9
R Markdown
SLIDE 10
R Markdown
◮ Simple formatting syntax ◮ Fully reproducible documents ◮ Closely integrated to Rstudio ◮ Based on Markdown language, knitr, and pandoc ◮ http://rmarkdown.rstudio.com/
SLIDE 11
Workflow
SLIDE 12
Open R Markdown file
SLIDE 13
Write
SLIDE 14
Add R code
SLIDE 15
Render
SLIDE 16
Markdown syntax
SLIDE 17 YAML header
subtitle: RStudio for reporting author: Satu Helske date: 8 December 2016
- utput: ioslides_presentation
SLIDE 18
Headers
# Header 1 ## Header 2 ### Header 3
SLIDE 19
Typesetting examples
◮ _italics_ or *italics* produces italics ◮ __bold__ or **bold** produces bold ◮ superscriptˆ2ˆ produces superscript2 ◮ subscripts~2~ produces subscripts2
SLIDE 20 Lists
+ Item A * Item B
produces
◮ Item 1
◮ Item A ◮ Item B
◮ Item 2
(-, +, and * are equivalents)
SLIDE 21 Tables
Type | Freq | %
Apples | 7 | 44 Oranges | 9 | 56 produces Type Freq % Apples 7 44 Oranges 9 56
SLIDE 22
Mathematics
Mathematics like in LaTex: y_i = \beta_0 + \beta_1 x_i + \epsilon_i produces yi = β0 + β1xi + ǫi
SLIDE 23
Embedding R code
SLIDE 24 Code chunks
◮ Start with three backticks followed by {r}
◮ Optional own chunk name (unique, no spaces or periods) ◮ Optional options (R expressions)
◮ R code in between ◮ End with three backticks
SLIDE 25 Some options for code chunks
◮ eval: run R code (TRUE/FALSE) ◮ echo: show R code in output ◮ warning, error, message: show warnings/errors/messages in
◮ cache: save objects
◮ chunk only evaluated 1st time, later objects are loaded
◮ fig.width, fig.height, fig.asp: settings for figure size ◮ fig.cap: caption for figure
SLIDE 26 Dynamic tables
library(knitr) regression_table <- lm(dist ~ speed, data = cars) kable(summary(regression_table)$coefficients, digits = c(2, 2, 2, 3)) Estimate
t value Pr(>|t|) (Intercept)
6.76
0.012 speed 3.93 0.42 9.46 0.000
SLIDE 27 Figures
plot(cars)
5 10 15 20 25 20 40 60 80 100 120 speed dist
SLIDE 28
Dynamic code within text
The sample size was `r nrow(cars)`. The average distance that was travelled was `r mean(cars$dist)`. produces The sample size was 50. The average distance that was travelled was 42.98.
SLIDE 29
Writing papers
SLIDE 30 Bookdown
◮ R package built on top of R Markdown ◮ Book or “book” from several R Markdown documents ◮ Numbering, cross-referencing, appendices ◮ Output options (YAML)
◮ bookdown::html_document2 ◮ bookdown::word_document2 ◮ bookdown::pdf_book
◮ https://bookdown.org/yihui/bookdown/
SLIDE 31 Abstract
Option abstract in YAML
- title: All in one - RStudio for reporting
author: Satu Helske
abstract: "This is my abstract."
SLIDE 32 Numbers and cross-references
◮ Use bookdown outputs (e.g., bookdown::pdf_document2) ◮ Figures
◮ Name chunk (e.g., my-plot), fig.cap in R chunk options ◮ Cross-reference in text: \@ref(fig:my-plot)
◮ Tables
◮ Name chunk (e.g., my-table) ◮ kable function in knitr; add caption argument ◮ Cross-reference: \@ref(tab:my-table)
◮ Sections
◮ Add {#my-section} after section header ◮ Cross-reference: \@ref(my-section)
SLIDE 33 Bibliographies
◮ BibTeX bibliographies (.bib) recommended
@Book{Author2015, author = {Author, Alice and Writer, William}, title = {Book of something}, publisher = {Publisher P}, year = {2015}, address = {City, Country} }
◮ Add bibliography + options in YAML, e.g.
- bibliography: my_bibliography.bib
biblio-style: apalike link-citations: true
SLIDE 34
Citing
◮ Citing in text: @Author2015 ◮ Citing in brackets: [@Author2015; @Writer2016] ◮ References printed at the end of the document →
Last line is section header, e.g. # References
SLIDE 35
LaTeX
SLIDE 36
knitr with LaTeX
◮ Normal LaTeX with embedded R code ◮ Inline code: \Sexpr{} ◮ Code chunks:
<<my_cars_plot, fig.height=6, fig.width=8>>= plot(cars) @
SLIDE 37
Open Rnw document
SLIDE 38
Before rendering with knitr
◮ Change RStudio default from Sweave to knitr
SLIDE 39
Rendering
SLIDE 40 Tips
◮ When writing, use html output
◮ Fast to render ◮ No need to worry about pages, margins etc.
◮ Cache time-consuming code chunks with the cache option
◮ Note: cached chunks only change if you change the contents →
Subsequent chunks do not automatically change (unless cache cleared)
◮ For data cleaning, manipulation, and visualization, see
tidyverse
◮ Finding help
◮ Stack overflow ◮ Github project pages
SLIDE 41 Tips for collaboration
◮ Share the Rmd (R Markdown) file
◮ Use commenting (Crtl + Shift + C) to suggest changes or to
show where you have modified the file
◮ Share the Word file
◮ Use the commenting options in Word ◮ Copy and paste changes into the Rmd file
◮ Use version control such as Git
◮ Integrated in RStudio ◮ Automatically keeps track of all changes in all previous versions ◮ Might be a steep learning curve, but for small projects learning
the very basics is usually enough
◮ Learn (enough) Git in 15 minutes: https://try.github.io
SLIDE 42 Useful links
◮ R Markdown cheat sheet by RStudio ◮ knitr in a knutshell by Karl Broman ◮ knitr by Yihui Xie ◮ LaTeX by the LaTeX Project ◮ Citing
◮ BibTex by Martin J. Osborne ◮ Bibliographies and citations by Rstudio ◮ Citing with Mendeley by Rosanna van Hespen
◮ Tables
◮ Precise control: xtables by David B. Dahl, David Scott,
Jonathan Swinton and others
◮ Good-looking tables with minimal effort, e.g., summarizing
multiple models: stargazer by Marek Hlavac
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