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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