• Abschlussarbeit mit bookdown
  • Vorbereitung und Vorwort
    • Contribute!
    • Get started
      • RStudio und Packrat
    • Links und Tipps
      • Auswertungsskript ausführen
  • 1 Buchbestandteile
    • 1.1 Überschriften, Labels und Absätze
    • 1.2 Abbildungen
    • 1.3 Tabellen
      • 1.3.1 knitr-Tabelle
      • 1.3.2 komplexere (LaTeX-)Tabellen
      • 1.3.3 xTable()
      • 1.3.4 interaktive Tabellen
    • 1.4 Inline R-Code
      • 1.4.1 Referenzieren mit Inline-Bedingung
      • 1.4.2 Inline R-Output und bedingte Textanzeige
  • 2 Verfassen
    • 2.1 Zitationen
    • 2.2 Text wiederholen und Blockquote
    • 2.3 Spracheinstellungen
    • 2.4 Spell Check
    • 2.5 Collaboration
  • 3 To Be Done
  • Literatur
  • Published with bookdown

Thesis Writing in RStudio Using Bookdown

Links und Tipps

  • Yihui Xie wrote a great book, explaining all you need to know about bookdown. (https://bookdown.org/yihui/bookdown/)
    • Actually I edited his Minimal Book Example to create this book. See his original book here: https://bookdown.org/yihui/bookdown-demo/ (or download it from GitHub).
    • See how the Bookdown-book works under the hood or to follow Yihui’s example: https://github.com/rstudio/bookdown/tree/master/inst/examples
  • I agree with Sean Kross who says “getting started with bookdown is not yet a totally straightforward process”. Read his How to Start a Bookdown Book here!
    • Actually he provides a minimal bookdown example as well, but for some reasons his didn’t work for me. You can download it from GitHub.

  • Rosanna van Hespen wrote a great and very straight forward blog on “Writing your thesis with R Markdown” (read at Rosanna’s Research) with a focus on solely creating a PDF file. Special thanks to her for eventually showing me how to use inline R code in a Markdown report. I was haunted by this idea for years and thank to her blog I came in contact with Pandoc and Co.

  • Into Microsoft Word? http://rmarkdown.rstudio.com/articles_docx.html

  • If you move or share your own project, it migth be a good idea to delete the folder /packrat/lib/ before starting the RProject on a new machine in order to have a clean installation of the packages.

  • There are some cool addins for RStudio, e. g.
    • citr Just install it like any other R-package and then you can easily insert citations browsing your bib-file within Rstudio.
    • ggThemeAssist or ggedit
    • Find more https://github.com/daattali/addinslist

  • To speed up knitting you should use cache. Via knitr::opts_chunk$set() you can set your preferred default chunk options. See mine in the source code of index.Rmd. For all options see https://yihui.name/knitr/options/ and for cool ideas regarding dependent caching see https://github.com/yihui/knitr/issues/238!

  • Annotations: hypothes.is lets you easily and in collaboration with others (or several supervisors) annotate text on any website. Of course PDF annotations, (Online-)Word’s markups, an HTML comment area (e.g. Disqus) or Git issues could fit your needs as well.

Auswertungsskript ausführen

Damit alle Ergebnisse, Grafiken und Variablen vorhanden sind, müssen erst die Berechnungen in R vorgenommen werden. Theoretisch könnten alle R-Berechnungn auch in einem R-Chunk im Buch ausgeführt werden. Da das aber bei langen Skripten sehr unübersichtlich werden kann, habe ich ein klassischen R-Skript zur Auswertung erstellt, dass vor dem Kompilieren des Buches (ggf. mit Dummy-Daten) ausgeführt werden muss. Entweder per Hand oder per Source-Befehl. Die Ergebnissen können/sollten für ein schnelles Kompilieren des Buches während der Bearbeitung gecached werden.

source('_Auswertungsskript.r')