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add some tips about rstudio
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James Brusey committed Oct 7, 2022
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@@ -10,6 +10,7 @@ For this reason, the recommendations here may differ somewhat from recommendatio
** Also see
| [[file:meetings.org][Meetings]] |
| [[file:planning.org][Planning]] |
| [[file:rstudio-tips.org][RStudio tips]] |

* About novelty
Doing a master's project is similar to doing a PhD but whereas a PhD dissertation is required to be novel, a master's dissertation is definitely not required to involve a novel element.
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#+title: Tips for using RStudio to produce your dissertation

If you are using RStudio, here are some tips that might help make your report look great.

* Number sections
By default, RStudio / pandoc does not number section headings.
To fix this, in the YAML header, use something like:
#+BEGIN_SRC
---
...
output:
pdf_document:
number_sections: true
---
#+END_SRC
This should automatically number your sections.

* Selecting the LaTeX class
I personally prefer the KOMA report class over the LaTeX default.
#+BEGIN_SRC
---
...
documentclass: scrreprt
...
---
#+END_SRC

* Citations
The first thing to know is that to cite a paper with RMarkdown, you need to use the =@= [[https://pandoc.org/MANUAL.html#citation-syntax][citation syntax]].
The thing after =@= is the citation key.
Note that you either put the citation in square brackets (for parenthetical citations) or put it without brackets when you want to refer directly to something that the authors did.
For example, if we have a paper with key =Krizhevsky2012=, we might refer to it as, "The ImageNet classification problem has been examined using DCNNs =[@Krizhevsky2012]=".
In this case, we use square brackets so that the citation is formatted with parentheses.
Alternatively, we can put the authors as actors by saying, "=@Krizhevsky2012= applied DCNNs to ImageNet".

There's great information on using Zotero with RStudio [[https://christopherjunk.netlify.app/blog/2019/02/25/zotero-rmarkdown/][online]].
You will probably need to install the Better BibTex add-in for Zotero.
I also recommend the Chrome extension for capturing papers to your Zotero library.

Don't forget to use Better BibTex to export your bibliography to a =bib= file and refer to it in your document
#+BEGIN_SRC
---
...
bibliography: "zotero-export.bib"
...
---
#+END_SRC

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