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lshtm_msc_project_template

The goal of lshtm_msc_project_template is to provide a template Quarto book for a MSc project at LSHTM

It provides a title page, with all the required components configurable through _quarto.yml, and a framework for writing up various sections of a project.

Install

Either clone this git repository:

git clone https://github.com/bakenzua/lshtm_msc_project_template.git

or download the zip file and extract somewhere appropriate on your pc.

Configure

Configuration of the title page can be made by editing the metadata in _quarto.yml

Editable options are indicated via comments.

################################################
#   Title page metadata - edit accordingly     #
################################################
candidate-number: "007"
msc-course: "Medical Statistics"
academic-year: "2023-24"
page-count: "0"
project-length: "Standard" # Extended (MSc IID only)
################################################

Output file

Extra care should be taken with the output-file option as this does not compile from the other options:

# edit line below...
  output-file: "[Candidate Number]_[MSc]_[Year of Submission]_Project"

Replacing

  • [Candidate Number] with the candidate number, e.g. 1234

  • [MSc] with MSc title, e.g. MedSats

  • [Year of Submission] with year of submission, e.g. 2023

Will produce an output file: 1234_MedStats_2023_Project.pdf as required

Use

The project includes the following quarto files that are applicable for different sections of a project.

  • index.qmd

    • Title page

    • Table of contents

    • Abstract

    • Acknowledgements

  • intro.qmd

    • Introduction

    • Aims and Objectives

  • methods.qmd

  • results.qmd

  • discussion.qmd

  • references.qmd

  • appendices.qmd

Please refer to the Quarto documentation for guidance on incorporating workings and write up into these files.

Note that each of the files is rendered within it's own R environment, meaning data frames and functions are not passed from e.g. methods.qmd to results.qmd. If there is a need for common objects between files, some custom caching or common set-up code must be implemented. One method might be to implement a {targets} pipeline with this book as a quarto target, which loads parent objects as required. Alternatively concatenate different chapters into one file, i.e. write up methods and results section in the same qmd file

The easiest way to compile the template to a pdf, is via the render button in RStudio.

Citations and References

The references.bib file is a bibliography file as described in Quarto documentation. This can be exported from a reference manager, e.g. Zotero. To cite an article from the bibliography in the text, use @ followed by the citation identifier, as per the standard pandoc citation syntax. An example is given in intro.qmd. Cited articles will then automatically be compiled to the references page.

The vancouver.csl file is a citation style definition which uses the Vancouver referencing and citation system. Alternative citation and reference styles can be downloaded from https://github.com/citation-style-language/styles. The csl: vancouver.csl field of _quarto.yml should be amended accordingly.

Attribution

  • This template was inspired by the latex template for LSHTM MSc projects by Robert Greener.
  • It borrows heavily from this post by Patrick Cameron.
  • The LSHTM Logo (lshtm_logo.jpg and lshtm_logo_small.jpg) remains property of the London School of Hygiene and Tropical Medicine
    • Everything else is MIT licensed