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UHHthesis

The UHHthesis ecosystem provides ready-to-use thesis templates for Bachelor’s and Master’s theses at the University of Hamburg (UHH), designed for students in the MIN faculty (primarily Biology). Two tools are available: an R package built on bookdown and R Markdown, and a Quarto extension for the modern Quarto publishing framework. Both tools produce PDF and Word output that conforms to the official UHH/MIN submission standards, and aim to encourage reproducible research.

Thesis Guide: General guidance on planning, structuring, and writing your BSc or MSc thesis — from the initial research question to the final submission: English (PDF) | Deutsch (PDF)

R package – UHHthesis

The UHHthesis R package wraps bookdown and provides four R Markdown output format functions. It creates a multi-file project with pre-filled chapters, a front matter, and a bibliography folder. It is the right choice if your workflow is entirely in R and RStudio.

Template Language Output Function
PDF thesis German PDF (LaTeX) thesis_pdf_de()
PDF thesis English PDF (LaTeX) thesis_pdf_en()
Word thesis German DOCX thesis_word_de()
Word thesis English DOCX thesis_word_en()

Quarto Extension – quarto-UHHthesis

The quarto-UHHthesis extension delivers the same UHH thesis templates for the Quarto framework. It supports R, Python, and Julia in a single document, works in VS Code, Positron, RStudio, and any text editor, and is the recommended choice for new thesis projects.

Prerequisites

Tool Required for Min. version How to get
R R Markdown templates ≥ 4.2 cran.r-project.org
RStudio or Positron both current posit.co/downloads
bookdown R Markdown any install.packages(“bookdown”)
LaTeX / TinyTeX PDF output (both tools) any tinytex::install_tinytex()
Quarto Quarto extension ≥ 1.3 quarto.org

Quick installation guide

R package 

# Using the package 'pak' (recommended)
if (!require("pak")) install.packages("pak")
pak::pak("uham-bio/UHHthesis")

# Alternatively, using 'remotes'
if (!require("remotes")) install.packages("remotes")
remotes::install_github("uham-bio/UHHthesis")

For step-by-step instructions including prerequisites and project creation, see the Getting Started guides: Getting Started (EN) | Erste Schritte (DE)

Quarto extension

Open a terminal in the folder where you want to create your thesis project, then run one of the following:

# English template
quarto use template uham-bio/quarto-UHHthesis/en

# German template
quarto use template uham-bio/quarto-UHHthesis/de

For step-by-step instructions including prerequisites and metadata configuration, see the Getting Started guides: Getting Started (EN) | Erste Schritte (DE)

Project structure

R Markdown (UHHthesis) 

your-thesis/
├── index.Rmd              # Main file — the ONLY file to knit
├── _bookdown.yml          # Chapter order and output settings
├── template.tex           # LaTeX template (do not edit)
├── chapter/               # One .Rmd file per thesis chapter
├── prelim/                # Abstract, Zusammenfassung, Abbreviations
├── bib/                   # references.bib + citation style (.csl)
├── data/                  # Data files
├── images/                # Logos and external images
└── thesis-output/         # Generated PDF / DOCX (created on first knit)

Quarto (quarto-UHHthesis) 

your-thesis/
├── _quarto.yml            # Main configuration (title, author, formats, bibliography)
├── index.qmd              # Title page metadata and abstract includes
├── _extensions/UHHthesis/ # Format extension (do not edit)
├── chapter/               # One .qmd file per thesis chapter
├── prelim/                # Abstract, Zusammenfassung, Abbreviations
├── bib/                   # references.bib + citation style (.csl)
├── data/                  # Data files
├── images/                # Logos and external images
└── thesis-output/         # Generated PDF / DOCX (created on first render)

Documentation

Full documentation is available on the UHHthesis website:

R Markdown (UHHthesis)

Quarto Extension (quarto-UHHthesis)

Useful resources

Author

Saskia A. Otto University of Hamburg · Department of Biology · Institute of Marine Ecosystem and Fisheries Science · GitHub · Website