nspyrison / thesis_ns

Nick's PhD research at Monash University, Australia

PhD Thesis, Monash University {-}

html version
pdf version

Directory {-}

• docs/: Output folder, compiled content ends up here as .pdf and .html (open with index.html)
• Rmd/: R Markdown source documents for thesis document
• figures/: Images made with other tools to illustrate ideas.
• data/: Cleaned data from other repositories
• template/: Monash thesis template from robjhydman/MonashThesis.
• renv/: Automated information of packages versions and such for reproducing this work

Reproducibility {-}

The environment and R packages used to construct this thesis can be recovered using the renv package. Run the following code to install the packages used in this thesis:

# install.packages("renv")
renv::restore()

The thesis can be compiled into both html and pdf format. This can be done in RStudio > Build pane > Build Book or run the following codes in the terminal:

Rscript --quiet _render.R "bookdown::pdf_book"
Rscript --quiet _render.R "bookdown::gitbook"

---

Dev notes {-}

• ! LaTeX Error: Missing \begin{document} is caused by a rouge .aux file; delete root level .aux file & rebuild. Thanks to Dan Simpson via NUMBAT slack.
• ! Package biblatex Error: Nested citation command. is caused by reference citations. [@ref1, @ref2] needs to change to [@ref1; @ref2] to work; find and replace, rebuild.
• _bookdown.yml: Higher level bookdown YAML settings (& specifies where/which rmd files)
• _render.R: Code ran at build; spell check, convert .pdf to .png, bookdown::render_book
  • nb: .png only created if it doesn't exist in docs/figures; delete/clean when updating figures.
• ./index.Rmd: Knitr setup and local functions. MUST print a splash page content for HTML version to work
• template/monashthesis.cls: Styling template and title page
• template/monashthesis.tex: LaTeX packages and preamble

Session info {-}

R> sessionInfo()
R version 4.1.2 (2021-11-01)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19044)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252