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R Markdown Workshop



Reproducible Reports

Presented by Emi Tanaka

School of Mathematics and Statistics


dr.emi.tanaka@gmail.com @statsgen

19th Nov 2019 @ SSA Vic | Melbourne, Australia

These slides are viewed best by Chrome and occasionally need to be refreshed if elements did not load properly. See here for PDF .

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🔎 Open and inspect the file

demo-header.Rmd

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Cross Reference

  • When you make a header via Rmd
    # Some Header
    an id is created automatically.
  • The id is created by replacing space with - and making it all lower case.
  • Now you can link to this header by [some text](#some-header).
  • Cross references work for both pdf and html outputs.
3/27

Direct Reference for html


  • For html output, you can also give a link directly to the relevant section
  • E.g. open demo-header.html in a web browser
  • Append say #chicken-data to the url. It should look like

    demo-header.html#chicken-data

  • It should have taken you to straight to the corresponding header 🏃‍♀
4/27

User-defined id


  • You can define your own id by appending {#your-id}.
# Some header {#header1}
  • Now you can link to this header with the id header1.
  • Note there should be no space in the id name!
5/27

🔎 Open and inspect the file

demo.bib

6/27

Bibliography

  • BibTeX citation style format is used to store references in .bib files.
  • Remember that you can get most BibTeX citation for R packages citation function. (Scroll below to see the BibTeX citation).
citation("xaringan")
  To cite package 'xaringan' in publications use:
    Yihui Xie (2019). xaringan: Presentation Ninja. R package version 0.13. https://CRAN.R-project.org/package=xaringan
  A BibTeX entry for LaTeX users is
    @Manual{,
      title = {xaringan: Presentation Ninja},
      author = {Yihui Xie},
      year = {2019},
      note = {R package version 0.13},
      url = {https://CRAN.R-project.org/package=xaringan},
    }
7/27

🔍 Open, inspect and knit the file

demo-citation.Rmd

8/27

Citations


  • You can include BibTeX by specifying the bib file at YAML as:
bibliography: bibliography.bib

[@bibtex-key] (Author et al. 2019)

or

@bibtex-key Author et al. 2019

  • See demo-citation.Rmd
9/27

Figure References

  • Support for figure references are included for output format type bookdown::pdf_document2 for pdf or bookdown::html_document2 for html.
```{r plot1, fig.cap = "Caption"}
ggplot(cars, aes(dist, speed)) + geom_point()
```

  • Above figure number can be referenced as \@ref(fig:plot1)

  • The reference label has the prefix fig: before the chunk label.

10/27

Table References

  • Support for table references are also included for output format type bookdown::pdf_document2 for pdf or bookdown::html_document2 for html.
```{r table1}
knitr::kable(cars, booktabs = TRUE, caption = "Caption")
```

  • Above table number can be referenced as \@ref(tab:table1)

  • The reference label has the prefix tab: before the chunk label.

11/27

Markdown for Captions

```{r plot1, fig.cap = "(ref:label)"}
ggplot(cars, aes(dist, speed)) + geom_point()
```
  • Then the caption can be entered in a separate paragraph with empty lines above and below it
(ref:label) This is the *caption* with **markdown**.
  • You can substitute label with another unique label composed of alphanumeric characters, :, -, or /
  • This caption supports markdown syntax
  • This is great for long captions
  • It also works for tables!
12/27

🔧 Open and work through

challenge-08-references.Rmd

05:00
13/27

Parametrized Report

---
title: "Parameterized Report"
params:
   species: setosa 
output: html_document
---
```{r, message = FALSE, fig.dim = c(3,2)}
library(tidyverse)
iris %>% 
   filter(Species==params$species) %>% 
   ggplot(aes(Sepal.Length, Sepal.Width)) +
   geom_point(aes(color=Species))
```

14/27

Knit with Parameters

---
title: "Parameterized Report"
params:
  species: 
    label: "Species"
    value: setosa
    input: select
    choices: [setosa, versicolor, virginica]
  color: red
  max:
    label: "Maximum Sepal Width"
    value: 4
    input: slider
    min: 4
    max: 5
    step: 0.1
output: html_document
---

```{r, message = params$printmsg}
library(tidyverse)
iris %>% 
  filter(Species==params$species) %>% 
  filter(Sepal.Width < params$max) %>% 
  ggplot(aes(Sepal.Length, Sepal.Width)) +
  geom_point(color = params$color) + 
  labs(title = params$species)
```
15/27

Shiny Report Generator

---
title: "Parameterized Report"
params:
  species: 
    label: "Species"
    value: setosa
    input: select
    choices: [setosa, versicolor, virginica]
  color: red
  max:
    label: "Maximum Sepal Width"
    value: 5
    input: slider
    min: 4
    max: 5
    step: 0.05
output: html_document
---

16/27

🔧 Open and work through

challenge-09-params.Rmd

05:00
17/27

R Markdown via Command Line

demo-render.Rmd

---
title: "Parameterized Report"
params:
   species: setosa
output: html_document
---
```{r, message = FALSE, fig.dim = c(3,2)}
library(tidyverse)
iris %>% 
   filter(Species==params$species) %>% 
   ggplot(aes(Sepal.Length, Sepal.Width)) +
   geom_point(aes(color=Species))
```

You can knit this file via R command by
using the render function:

library(rmarkdown)
render("demo-render.Rmd")


You can overwrite the YAML values
by supplying arguments to render:

library(rmarkdown)
render("demo-render.Rmd", 
       output_format = "pdf_document",
       params = list(species = "virginica"))
18/27

🔧 Open and work through

challenge-10-letters.Rmd

10:00
19/27

Themes: html_document

You can change the look of the html document by specifying themes:

  • default default
  • cerulean cerulean
  • journal journal
  • flatly flatly
  • darkly darkly
  • readable readable
  • spacelab spacelab
  • united united
  • cosmo cosmo
  • lumen lumen
  • paper paper
  • sandstone sandstone
  • simplex simplex
  • yeti yeti
  • NULL null 
output: 
  html_document:
    theme: cerulean

These bootswatch themes attach the whole bootstrap library which makes your html file size larger.

20/27

prettydoc

prettydoc 📦 is a community contributed theme that is light-weight:

  • cayman cayman
  • tactile tactile
  • architect architect
  • leonids leonids
  • hpstr hpstr 
output: 
  prettydoc::html_pretty:
    theme: cayman

See more about it below:

https://prettydoc.statr.me/

21/27

rmdformats

rmdformats 📦 contains four built-in html formats:

  • readthedown readthedown
  • html_clean html_clean
  • html_docco html_docco
  • material material

You can use these formats by simply specifying the output in YAML as below:

output: rmdformats::readthedown

See more about it below:

https://github.com/juba/rmdformats

22/27

rticles - LaTeX Journal Article Templates

  • acm acm_article
  • acs acs_article
  • aea aea_article
  • agu agu_article
  • amq amq_article
  • ams ams_article
  • asa asa_article
  • biometrics biometrics_article
  • copernicus copernicus_article
  • elsevier elsevier_article
  • frontiers frontiers_article
  • ieee ieee_article
  • jss jss_article
  • mdpi mdpi_article
  • mnras mnras_article
  • peerj peerj_article
  • plos plos_article
  • pnas pnas_article
  • rjournal rjournal_article
  • rsos rsos_article
  • rss rss_article
  • sage sage_article
  • sim sim_article
  • springer springer_article
  • tf tf_article
Go to RStudio > File > New File > R Markdown ... > From Template
23/27

External Files in Templating

  • When using rticles, each journal usually require external files (e.g. cls or image files).
  • These external components are stored within the package.
  • So use draft instead of render!

GUI

  • RStudio > File > New File > R Markdown ... > From Template

Command line

rmarkdown::draft("file.Rmd", 
 template = "biometrics_article",
 package = "rticles")
24/27

Making your own R Markdown template

  • You need to make an R package first!
    Go to RStudio > New Project > New Directory > R Package or usethis::create_package()
  • When you are in your R package project,
usethis::use_rmarkdown_template("<Name>")
  • Modify the skeleton/skeleton.Rmd to how you want and add all external files to the skeleton folder.
  • Install your package.
  • 🎉 And now find it at RStudio > File > New File > R Markdown > From Template.
25/27

🔧 Create your own
R Markdown Template Package!

15:00
26/27

Session Information

devtools::session_info()
  ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
   setting  value                       
   version  R version 3.6.1 (2019-07-05)
   os       macOS Mojave 10.14.4        
   system   x86_64, darwin15.6.0        
   ui       X11                         
   language (EN)                        
   collate  en_AU.UTF-8                 
   ctype    en_AU.UTF-8                 
   tz       Australia/Sydney            
   date     2019-11-18                  
  ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
   package     * version    date       lib source                              
   anicon        0.1.0      2019-11-07 [1] Github (emitanaka/anicon@0b756df)   
   assertthat    0.2.1      2019-03-21 [1] CRAN (R 3.6.0)                      
   backports     1.1.5      2019-10-02 [1] CRAN (R 3.6.0)                      
   broom         0.5.2      2019-04-07 [1] CRAN (R 3.6.0)                      
   callr         3.3.2      2019-09-22 [1] CRAN (R 3.6.0)                      
   cellranger    1.1.0      2016-07-27 [1] CRAN (R 3.6.0)                      
   cli           1.1.0      2019-03-19 [1] CRAN (R 3.6.0)                      
   colorspace    1.4-1      2019-03-18 [1] CRAN (R 3.6.0)                      
   countdown     0.3.3      2019-11-18 [1] Github (gadenbuie/countdown@5c895d9)
   crayon        1.3.4      2017-09-16 [1] CRAN (R 3.6.0)                      
   desc          1.2.0      2018-05-01 [1] CRAN (R 3.6.0)                      
   devtools      2.2.1      2019-09-24 [1] CRAN (R 3.6.0)                      
   digest        0.6.22     2019-10-21 [1] CRAN (R 3.6.0)                      
   dplyr       * 0.8.3      2019-07-04 [1] CRAN (R 3.6.0)                      
   ellipsis      0.3.0      2019-09-20 [1] CRAN (R 3.6.0)                      
   emo           0.0.0.9000 2019-11-11 [1] Github (hadley/emo@02a5206)         
   evaluate      0.14       2019-05-28 [1] CRAN (R 3.6.0)                      
   forcats     * 0.4.0      2019-02-17 [1] CRAN (R 3.6.0)                      
   fs            1.3.1      2019-05-06 [1] CRAN (R 3.6.0)                      
   generics      0.0.2      2018-11-29 [1] CRAN (R 3.6.0)                      
   ggplot2     * 3.2.1      2019-08-10 [1] CRAN (R 3.6.0)                      
   glue          1.3.1      2019-03-12 [1] CRAN (R 3.6.0)                      
   gtable        0.3.0      2019-03-25 [1] CRAN (R 3.6.0)                      
   haven         2.1.1      2019-07-04 [1] CRAN (R 3.6.0)                      
   hms           0.5.2      2019-10-30 [1] CRAN (R 3.6.0)                      
   htmltools     0.4.0      2019-10-04 [1] CRAN (R 3.6.0)                      
   httr          1.4.1      2019-08-05 [1] CRAN (R 3.6.0)                      
   icon          0.1.0      2019-11-07 [1] Github (emitanaka/icon@8458546)     
   jsonlite      1.6        2018-12-07 [1] CRAN (R 3.6.0)                      
   knitr         1.25       2019-09-18 [1] CRAN (R 3.6.0)                      
   lattice       0.20-38    2018-11-04 [1] CRAN (R 3.6.1)                      
   lazyeval      0.2.2      2019-03-15 [1] CRAN (R 3.6.0)                      
   lifecycle     0.1.0      2019-08-01 [1] CRAN (R 3.6.0)                      
   lubridate     1.7.4      2018-04-11 [1] CRAN (R 3.6.0)                      
   magrittr      1.5        2014-11-22 [1] CRAN (R 3.6.0)                      
   memoise       1.1.0      2017-04-21 [1] CRAN (R 3.6.0)                      
   modelr        0.1.5      2019-08-08 [1] CRAN (R 3.6.0)                      
   munsell       0.5.0      2018-06-12 [1] CRAN (R 3.6.0)                      
   nlme          3.1-140    2019-05-12 [1] CRAN (R 3.6.1)                      
   pillar        1.4.2      2019-06-29 [1] CRAN (R 3.6.0)                      
   pkgbuild      1.0.6      2019-10-09 [1] CRAN (R 3.6.0)                      
   pkgconfig     2.0.3      2019-09-22 [1] CRAN (R 3.6.0)                      
   pkgload       1.0.2      2018-10-29 [1] CRAN (R 3.6.0)                      
   prettyunits   1.0.2      2015-07-13 [1] CRAN (R 3.6.0)                      
   processx      3.4.1      2019-07-18 [1] CRAN (R 3.6.0)                      
   ps            1.3.0      2018-12-21 [1] CRAN (R 3.6.0)                      
   purrr       * 0.3.3      2019-10-18 [1] CRAN (R 3.6.0)                      
   R6            2.4.0      2019-02-14 [1] CRAN (R 3.6.0)                      
   Rcpp          1.0.2      2019-07-25 [1] CRAN (R 3.6.0)                      
   readr       * 1.3.1      2018-12-21 [1] CRAN (R 3.6.0)                      
   readxl        1.3.1      2019-03-13 [1] CRAN (R 3.6.0)                      
   remotes       2.1.0      2019-06-24 [1] CRAN (R 3.6.0)                      
   rlang         0.4.1      2019-10-24 [1] CRAN (R 3.6.0)                      
   rmarkdown     1.16       2019-10-01 [1] CRAN (R 3.6.0)                      
   rprojroot     1.3-2      2018-01-03 [1] CRAN (R 3.6.0)                      
   rstudioapi    0.10       2019-03-19 [1] CRAN (R 3.6.0)                      
   rvest         0.3.4      2019-05-15 [1] CRAN (R 3.6.0)                      
   scales        1.0.0      2018-08-09 [1] CRAN (R 3.6.0)                      
   sessioninfo   1.1.1      2018-11-05 [1] CRAN (R 3.6.0)                      
   stringi       1.4.3      2019-03-12 [1] CRAN (R 3.6.0)                      
   stringr     * 1.4.0      2019-02-10 [1] CRAN (R 3.6.0)                      
   testthat      2.2.1      2019-07-25 [1] CRAN (R 3.6.0)                      
   tibble      * 2.1.3      2019-06-06 [1] CRAN (R 3.6.0)                      
   tidyr       * 1.0.0      2019-09-11 [1] CRAN (R 3.6.0)                      
   tidyselect    0.2.5      2018-10-11 [1] CRAN (R 3.6.0)                      
   tidyverse   * 1.2.1      2017-11-14 [1] CRAN (R 3.6.0)                      
   usethis       1.5.1      2019-07-04 [1] CRAN (R 3.6.0)                      
   vctrs         0.2.0      2019-07-05 [1] CRAN (R 3.6.0)                      
   whisker       0.4        2019-08-28 [1] CRAN (R 3.6.0)                      
   withr         2.1.2      2018-03-15 [1] CRAN (R 3.6.0)                      
   xaringan      0.13       2019-10-30 [1] CRAN (R 3.6.0)                      
   xfun          0.10       2019-10-01 [1] CRAN (R 3.6.0)                      
   xml2          1.2.2      2019-08-09 [1] CRAN (R 3.6.0)                      
   yaml          2.2.0      2018-07-25 [1] CRAN (R 3.6.0)                      
   zeallot       0.1.0      2018-01-28 [1] CRAN (R 3.6.0)                      
  [1] /Library/Frameworks/R.framework/Versions/3.6/Resources/library

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demo-header.Rmd

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