The different elements of a {iheiddown} thesis
After this initial preview, let’s look at how the thesis project is
structured to better understand how to edit it.
The index file
The index file contains two things: the YAML header and the preface
of your thesis. It is also the backbone of your thesis in the sense that
this is where you will want to knit your whole thesis from.
The YAML header is the place where the main options, metadata and
formatting parameters are set. You can set the title of your
presentation here, add your name, change the front matter of your thesis
(abstract, acknowledgments, table of content, etc.).
The second element in this file is the preface. The only crucial
thing to know here is that in order to create your package bibliography
(the software you use to render your thesis) you need to leave the first
code chunk there.
The chapters
The chapters contain the meat of your thesis, this is where you will
outline your idea, run your analyses and draw your conclusions.
Chapters are structured in a similar way, so let us open the
01-introduction.Rmd chapter. In it, you will first find a
YAML header that where you can set various chapter level metadata and
options.
Note that if for some reason you rename the chapter, you will need to
specify the new name in the YAML header too under the input
option. Once you have done this you can write away!
The last thing to know about individual chapters is that you can knit
them individually. This comes in handy when you want to generate only
one part of your thesis for preview purposes.
The appendix and the references files
These files are a bit special as you might notice when you open
them.
The 99-references.Rmd file generates the bibliography.
This happens automatically, so you will most likely not need to alter
this file. Just know that you can set the title of the reference section
in the first line.
The 98-appendix.Rmd file allows you to showcase code,
additional outputs and more in a separate section to avoid unnecessarily
cluttering the main body of your thesis. This can be done by referencing
code chunks from your main body and printing the computations you
did in your R chunks or by adding new ones.
The _bookdown.yml file
The _bookdown.yml file contains additional information
for the YAML header of the main .Rmd file. A standard user
should not have to edit it. If for some reason or another you still feel
like it, you need to know that you can set additional .Rmd
subdirectories, set another output file than the standard
\versions file, and toggle the deletion of merged files
after the knitting process ended here.
The \bib folder
The bibliography folder contains two files; packages.bib
and references.bib. The former is automatically generated
by the first code chunk in the index.Rmd file and cites the
packages you have loaded when running your code chunks. You will not
need to alter this.
On the other hand, the references.bib file is the place
to dump the bibtex citations that you will cite in your thesis.
The \data folder
The data folder is the place to put all the data that you use in the
code chunk of your analysis. Remember to keep it tidy so you can easily
link data to outputs down the line such as graphs and tables.
The \front-matter folder
The front matter folder contains the front matter of your thesis.
This is where you will be able to edit the abbreviations part in the
corresponding Latex file, the acknowledgments section or the abstract of
your thesis in their respective .Rmd files.
The \versions folder
This is where you will find the pdf file after your thesis has been
knitted by {iheiddown}.
