Thesis written using thesisdown. This was altered to comply with the University of Bristol's regulations by Matt Lee: bristolthesis.
Current version of the thesis can be found here
Plan for September/October:
| Task | Comments needed | Comments needed from | Complete |
|---|---|---|---|
| Discussion V1 | N | Y | |
| EWAS-GWAS comparisons V2 | N | N | |
| Chapters integrated into thesis | N | N | |
| Properties of EWAS V2 | N | N | |
| Discussion V2 | Y | TG + NT | N |
| Intro V3 | Y | TG | N |
| DNAm-lung cancer MR V2 | N | TG + GH | N |
Meeting notes and items can be found in meetings
Add \usepackage[hidelinks]{hyperref} to template.tex -- this can replace \usepackage{hyperref}
Within chunk header, use fig.scap='small caption'. In this example small caption will appear in the list of figures and the figure caption will remain as what was stated for the option fig.cap
To manually change the toc depth, in index.Rmd, swap thesisdown::thesis_pdf: default for
thesisdown::thesis_pdf: toc: true toc-depth: TOC-DEPTH-CHOICE -- remember indents (not sure how to show on readme)
To make sure the depth of heading numbers matches the toc depth, add \setcounter{secnumdepth}{$toc-depth$} to template.tex below \setcounter{tocdepth}{$toc-depth$} -- around line 155.
Extra details: This occured when copying text over from a paper into a chapter. Unicode character (U+2003) is just whitespace.
Solution: Just re-entered the text part by part and re-built the thesis each time to check it worked.
Solution: Only knit to word + remove abstract, abbreviations, acknowledgements etc. from yaml header. NOTE: to knit to pdf, it requires these in the yaml header to be present!