mastersthesis

Overview

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This repository contains the Quarto book of my Master’s Thesis: Is Latitude Associated with Chronotype? The research compendium is accessible via The Open Science Framework by clicking here.

The assemble of this repository was inspired by Ben Marwick, Carl Boettiger & Lincoln Mullen’s article Packaging Data Analytical Work Reproducibly Using R (and Friends).

How to use

All analyses in this thesis are fully reproducible and were conducted using the R programming language alongside the Quarto publishing system. The renv package was used to ensure that the R environment used can be restored (see renv.lock). All the computational notebooks can be found in the qmd directory.

It’s important to note that some restrictions apply to the availability of the main research data, which contain personal and sensitive information. As a result, this data cannot be publicly shared. To run the analyses, users must have an internet connection and request a set of access keys from the author (see Keys section).

If you don’t feel comfortable with R, I strongly recommend checking Hadley Wickham and Garrett Grolemund’s free and online book R for Data Science and the Coursera course from John Hopkins University Data Science: Foundations using R.

To reproduce the analyses do the following steps:

1. Make sure that you have the latest R version and the following R packages installed in your machine: install.packages(c("cli", "here" ,"magrittr", "ragg", "renv", "stats", "stringr")).
2. Clone this repository.
3. Open the R project (mastersthesis.Rproj).
4. Run renv::restore() to install all software dependencies.
5. Set all the keys provided by the author in the .Renviron file and the _ssh folder.
6. Run targets::tar_make() to create every point of the data wrangling process (from the raw data to the cleaned and weighted data).
7. Run any analysis present in the computational notebooks (qmd directory).

Keys

To access the data and run the notebooks, you will need to set the following keys in the .Renviron file:

• OSF_PAT: Your OSF Personal Access Token (PAT). If you don’t have one, go to the settings section of your OSF account and create a new token.
• MASTERSTHESIS_PASSWORD: The password for the project’s RSA private key (32 bytes).

Additionally, you will need the following keys in the project’s _ssh folder:

• id_rsa: The project’s private RSA key (RSA 4096 bits (OpenSSL)).
• id_rsa.pub: The project’s public RSA key.

These project’s keys will be provided by the author of the thesis upon reasonable request. As reasonable requests, I consider those made by researchers with a legitimate interest in the thesis topic, whose projects are of high quality, ethically conducted, and who have obtained all necessary approvals for their research proposal.

License

The code accompanying this thesis is distributed under the MIT License. All documents are released under the Creative Commons Attribution 4.0 International Public License.

The research data is subject to a private license and is not publicly available due to privacy and ethical considerations.

Citation

To cite this work, please use the following format:

Vartanian, D. (2025). Is latitude associated with chronotype? [Master’s Thesis, University of São Paulo]. https://doi.org/10.17605/OSF.IO/YGKTS

A BibTeX entry for LaTeX users is:

@mastersthesis{vartanian2025,
  title = {Is latitude associated with chronotype?},
  author = {Daniel Vartanian},
  year = {2025},
  address = {São Paulo},
  school  = {University of São Paulo},
  langid = {en},
  url = {https://doi.org/10.17605/OSF.IO/YGKTS},
  note = {Corrected version}
}

Acknowledgments

The thesis was developed in the Graduate Program in Modeling Complex Systems (PPG-SCX) at the University of São Paulo (USP), under the supervision of Prof. Dr. Camilo Rodrigues Neto.

This study was financed by the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - Brazil (CAPES) - Finance Code 001, Grant Number 88887.703720/2022-00.