This repository contains the sources files for my PhD thesis at Leiden University (defended on July 2nd, 2025), which was made using Quarto and koma-script. The pdf of the thesis is freely available at Leiden University Scholarly Publications (online repository).
If you want to directly access the individual chapters (all were/are going to be published open access) + associated code, you can use the Table below:
| Chapter | Journal | DOI | Code repository |
|---|---|---|---|
| Handling missing covariate data in clinical studies in haematology (Chapter 2) | Best Practice & Research Clinical Haematology | 10.1016/j.beha.2023.101477 | https://github.com/survival-lumc/ReviewHaemaMissing |
| Multiple imputation for cause-specific Cox models: Assessing methods for estimation and prediction (Chapter 3) | Statistical Methods in Medical Research | 10.1177/09622802221102623 | https://github.com/survival-lumc/CauseSpecCovarMI |
| Impact of comorbidities and body mass index on the outcomes of allogeneic hematopoietic cell transplantation in myelofibrosis: A study on behalf of the Chronic Malignancies Working Party of EBMT (Chapter 4) | American Journal of Hematology | 10.1002/ajh.27262 | Not publicly available :( |
| Multiple imputation of missing covariates when using the Fine–Gray model (Chapter 5) | Statistics in Medicine | 10.1002/sim.70166 | https://github.com/survival-lumc/FineGrayCovarMI |
| Why you should avoid using multiple Fine–Gray models: insights from (attempts at) simulating proportional subdistribution hazards data (Chapter 6) | Journal of the Royal Statistical Society, Series A (Statistics in Society) | 10.1093/jrsssa/qnae056 | https://github.com/survival-lumc/FineGrayDGM |
| Joint models quantify associations between immune cell kinetics and allo-immunological events after allogeneic stem cell transplantation and subsequent donor lymphocyte infusion (Chapter 7) | Frontiers in Immunology | 10.3389/fimmu.2023.1208814 | https://github.com/survival-lumc/ImmuneReconstJM |
After cloning this repository using
git clone https://github.com/edbonneville/phd-thesis.git
..the thesis can be rendered with
quarto::quarto_render(output_format = "pdf")..but most likely that will not work for you from the off as I have unfortunately done a fairly lackluster job of documenting the various R/LaTex/system dependencies here (oopsies). In any case, you need all of R, Quarto, and Git installed. The suggested TinyTex workflow suggested by Quarto worked nicely for me, including auto-installing LaTex packages on the fly.
Most of the heavy lifting for the formatting is done in _quarto.yml, but the following non-standard stuff might be useful:
- chapterthumb.sty are the koma-script-based thumb indices for the chapters, with minor formatting edits also allowing for bleed correction when sending to the printers.
- tex/preamble-global.tex is the overall preamble, with some font settings + headings set-up.
- tex/koma-chapter-titles.tex is the koma-script-based emulation of the 'Lenny' chapter title style from fncychap, again with some minor edits.
- tex/before-body.tex is my set-up for the 'non-scientific' part of the thesis required by Leiden University, and uses some pandoc variables.
Credit to the following repositories and blog posts helping me put this thesis together: