index.Rmd

---
### Title page
title: "Towards prediction"
subtitle: Studying the mind and brain in the age of machine learning

author: "Lukas Snoek"
date: "woensdag 9 februari 2022"
aula: false 
time: "13.00"
birthplace: "Hoevelaken"

### Colophon 
# This paragraph begins with "This thesis was typeset using (R) Markdown, \LaTeX\ and the \verb+bookdown+ R-package"
# and is optionally followed by:
ISBN: "978-94-6458-013-6"
printing: "Ridderprint | www.ridderprint.nl"
cover: "Designed by author using a *neural style transfer* implementation by Reiichiro Nakano."
thesis_url: "https://lukas-snoek.com/thesis"
license: "CC BY" # optional, otherwise this bit is omitted

### Committee
promotores: 
- title: dr.
  initials: H.S.
  surname: Scholte
  affiliation: Universiteit van Amsterdam
one_promotor: true

copromotores:
- title: dr. 
  initials: S.
  surname: Oosterwijk
  affiliation: Universiteit van Amsterdam 
one_copromotor: true

members:
- title: prof. dr.
  initials: B.U.
  surname: Forstmann
  affiliation: Universiteit van Amsterdam
- title: prof. dr.
  initials: A.H.
  surname: Fischer
  affiliation: Universiteit van Amsterdam
- title: prof. dr.
  initials: C.
  surname: Keysers
  affiliation: Universiteit van Amsterdam
- title: prof. dr.
  initials: P.G.
  surname: Schyns
  affiliation: University of Glasgow
- title: prof. dr.
  initials: R.W.
  surname: Goebel
  affiliation: Maastricht University
- title: prof. dr.
  initials: D.
  surname: Borsboom
  affiliation: Universiteit van Amsterdam

faculty: Faculteit der Maatschappij- en Gedragswetenschappen

### Book settings
documentclass: memoir
book_size: false # "true" if you want to render a pdf for printing as a book; "false" if you want to print loose pages
           # if book_size is set to false, forces A4 paper size, and the "oneside" classoption
           # if book_size is set to true, forces standard "thesis B5 size" (170mm wide by 240mm high), and the "twoside" classoption
# geometry: "left=2.5cm, right=2.5cm, top=2.5cm, bottom=2.5cm" # use this if you want to change the margins
            # 2.5cm equal margins are often recommended by printers (so when book_size: true)
fontsize: 12pt # 12pt is recommened when book_size is false; 10 or 11pt is recommended when book_size is true
lang: en-US # default language for the thesis. Change to en-GB or en-US if you want a specific flavor of English (or to nl for Dutch)
site: bookdown::bookdown_site # to get a "Build" button in RStudio to render the book

output:
  # HTML
  bookdown::gitbook:
    css: css/style.css
    pandoc_args: [ "--csl", "bib/apa.csl" ]
    sharing:
      facebook: no
      github: yes
      twitter: yes
      all: ['facebook', 'twitter', 'linkedin']

    config:
      toolbar:
        download: 'thesis.pdf'
      toc: 
        #this text will print on top ("before") or at the bottom ("after") of the table of contents
        before: | 
          <li><a href="./">PhD thesis of Lukas Snoek</a></li>
        after: |
          <li><a href="https://github.com/rstudio/bookdown" target="blank">Published with bookdown</a></li>
          
  # PDF through Latex
  bookdown::pdf_book: 
    template: template.tex
    keep_tex: yes
    pandoc_args: [ "--csl", "bib/apa.csl" ]
    latex_engine: xelatex  # for the fontspec package
    #citation_package: biblatex
    includes:
      in_header: tex/preamble.tex

indent: true # indent new paragraphs, instead of leaving whitespace
links-as-notes: true # in the pdf, print hyperlink URLS as footnotes (as they can't be clicked on)
bibliography:
  - bib/introduction_discussion.bib
  - bib/misc.bib
  - bib/shared-states.bib
  - bib/confounds-decoding.bib
  - bib/aomic.bib
  - bib/morbid-curiosity.bib
  - bib/hypothesis-kernel-analysis.bib
  - bib/static-vs-dynamic.bib

citation_package: none
biblio-style: "apa"
colorlinks: true
#citecolor: gray
link-citations: true # make clickable hyperlinks from in-text citations to bibliography at the end
---

```{r, include = FALSE, child = if (knitr::is_html_output()) '_00-preface.Rmd'}
```