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<!DOCTYPE html>
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<title>PhD Thesis, Monash University | README</title>
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<li class="chapter" data-level="" data-path=""><a href="#phd-thesis-monash-university"><i class="fa fa-check"></i>PhD Thesis, Monash University</a>
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<li class="chapter" data-level="" data-path=""><a href="#directory"><i class="fa fa-check"></i>Directory</a></li>
<li class="chapter" data-level="" data-path=""><a href="#reproducibility"><i class="fa fa-check"></i>Reproducibility</a></li>
<li class="chapter" data-level="" data-path=""><a href="#dev-notes"><i class="fa fa-check"></i>Dev notes</a></li>
<li class="chapter" data-level="" data-path=""><a href="#session-info"><i class="fa fa-check"></i>Session info</a></li>
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<!--bookdown:title:end-->
<!--bookdown:title:start-->
<div id="phd-thesis-monash-university" class="section level1 unnumbered">
<h1>PhD Thesis, Monash University</h1>
<p><a href="https://nspyrison.github.io/thesis_ns/">html version</a><br />
<a href="https://github.com/nspyrison/thesis_ns/blob/master/docs/thesis_ns.pdf">pdf version</a></p>
<!--
## Milestone deliverable:
Confirmation report: https://github.com/nspyrison/thesis_monash_phd/blob/master/_book/_confirmation_report_ns.pdf \
Confirmation presentation: https://github.com/nspyrison/confirmation_talk \
Mid candidature report: https://github.com/nspyrison/mid_candidature/blob/master/_mid_candidature_document.pdf \
Mid candidature presentation: https://github.com/nspyrison/mid_candidature/tree/master/_slides
-->
<div id="directory" class="section level2 unnumbered">
<h2>Directory</h2>
<ul>
<li><code>docs/</code>: Output folder, compiled content ends up here as .pdf and .html (open with index.html)</li>
<li><code>Rmd/</code>: R Markdown source documents for thesis document</li>
<li><code>figures/</code>: Images made with other tools to illustrate ideas.</li>
<li><code>data/</code>: Cleaned data from other repositories</li>
<li><code>template/</code>: Monash thesis template from <a href="https://github.com/robjhyndman/MonashThesis">robjhydman/MonashThesis</a>.</li>
<li><code>renv/</code>: Automated information of packages versions and such for reproducing this work</li>
</ul>
</div>
<div id="reproducibility" class="section level2 unnumbered">
<h2>Reproducibility</h2>
<p>The environment and R packages used to construct this thesis
can be recovered using the <strong>renv</strong> package. Run the following
code to install the packages used in this thesis:</p>
<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="co"># install.packages("renv")</span></span>
<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a>renv<span class="sc">::</span><span class="fu">restore</span>()</span></code></pre></div>
<p>The thesis can be compiled into both html and pdf format. This can be done in RStudio > Build pane > <code>Build Book</code> or run the following codes in the terminal:</p>
<div class="sourceCode" id="cb2"><pre class="sourceCode zsh"><code class="sourceCode zsh"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a>Rscript --quiet _render.R <span class="st">"bookdown::pdf_book"</span></span>
<span id="cb2-2"><a href="#cb2-2" aria-hidden="true" tabindex="-1"></a>Rscript --quiet _render.R <span class="st">"bookdown::gitbook"</span></span></code></pre></div>
<hr />
</div>
<div id="dev-notes" class="section level2 unnumbered">
<h2>Dev notes</h2>
<ul>
<li><code>! LaTeX Error: Missing \begin{document}</code> is caused by a rouge .aux file; delete root level .aux file & rebuild. Thanks to Dan Simpson via NUMBAT slack.</li>
<li><code>! Package biblatex Error: Nested citation command.</code> is caused by reference citations.
<span class="citation">[@ref1, @ref2]</span> needs to change to <span class="citation">[@ref1; @ref2]</span> to work; find and replace, rebuild.</li>
<li><code>_bookdown.yml</code>: Higher level bookdown YAML settings (& specifies where/which rmd files)</li>
<li><code>_render.R</code>: Code ran at build; spell check, convert .pdf to .png, <code>bookdown::render_book</code>
<ul>
<li><em>nb</em>: .png only created if it doesn’t exist in <code>docs/figures</code>; delete/clean when updating figures.</li>
</ul></li>
<li><code>./index.Rmd</code>: Knitr setup and local functions. MUST print a splash page content for HTML version to work</li>
<li><code>template/monashthesis.cls</code>: Styling template and title page</li>
<li><code>template/monashthesis.tex</code>: LaTeX packages and preamble</li>
</ul>
</div>
<div id="session-info" class="section level2 unnumbered">
<h2>Session info</h2>
<pre><code>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 </code></pre>
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