3rd Year Report

Preface

This year has been mostly focused on building up knowledge on how to put into action the idea of making a more ethical and reproducible PhD. In order to understand the progress I have made this year, I describe in the following capters the importance of thinking about ethics and reproducibility, what are and how to use Data Hazards, as well as a breakdown of creating reproducible computer models.

At this point in time I am in a place where I have started writing my thesis in ways which allow me to keep good version control, which helps manage the source code and documents by keeping track of all the version modifications. In fact, I am using this year’s annual report as an exercise to write an example book using Quarto, which allows for a dynamic implementation of markdown files and python code all in one project, which can be version controlled via Git.

This is a Quarto Book:

This document is written using a Quarto book. Quarto allows for a dynamic implementation of different types of files that can be version controlled, which is extremely helpful to create a pipeline of work all in one place and that is traceable too.

Quarto is an open-source scientific and technical publishing system built on Pandoc.Pandoc acts kind of like a swiss-army knife (a tool that can be used for multiple tasks), it converts files from one markup format to another, which makes working with Quarto a smooth experience. You can create your outputs in multiple formats such as documents, web pages, books and more. This is showcased in how this report can be viewed on dfferent modes (pdf, web, and source code in GitHub).

Quarto allows you to have your code and narrative text all in one place. Likewise, thanks to Quarto I can write my thesis chapters using markdown, which is a lot more intuitive than LaTeX, in my opinion. Moreover, it allows for much better version control compared to Microsoft Word, and allows for helpful traceability of materials included in the document I am writing; which in itself has many benefits as it immensely helps to be able to go back to a previous version where everything was working before I broke the code (yet again).

Part of my work includes work which runs with different python scripts, and using Quarto means that I can embed python code if needed to explain how certain functionalities of the models work. It also allows for code using R to run within a Quarto document, as well as Jupyter Notebooks, and includes HTML implementations, which can all help with functionalities such as creating tables, adding images, and rendering the document in different formats (website html, or pdf, for example).

Different modes to view this report

• In an internet browser: through this url.

• In .pdf format: If you are viewing this document in your browser through a url, you can click on the top left icons of the document to download it.

• Source code in GitHub: You can also click on the top left icons of the document to access the source code.