This repository contains the research compendium and Quarto book of my master’s thesis: Ecology of sleep and circadian phenotypes of the Brazilian population. Its aim is to facilitate research work and to improve reproducibility.
Click here to access the thesis documents.
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).
The analyses contained in this thesis are 100% reproducible. They were
made using the R programming language and
the Quarto publishing system. The
renv package was used to ensure
that the R environment used can be restored (see renv.lock). 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 were used under the approval of a Research Ethics Committee (REC) linked to the Brazilian National Research Ethics Committee (CONEP). 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.
To reproduce the analyses do the following steps:
- Clone this repository.
- Open the R project (
mastersthesis.Rproj). - Run
renv::restore()to install all software dependencies. - Open and run the analysis in the computational notebook.
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 (free for audit students).
Code related to this repository is released under the MIT license. Documents are released under the Creative Commons Attribution 4.0 International license.
The main research data were used under the approval of a Research Ethics Committee (REC) linked to the Brazilian National Research Ethics Committee (CONEP); therefore, it cannot be publicly shared. However, it can be provided by the author upon reasonable request. If the intention is to use the data for new research, the request will need approval from CONEP, which must be made with the author’s approval and participation.
You can find the thesis citation below.
Vartanian, D. (2023). Ecology of sleep and circadian phenotypes of the Brazilian
population [Master's thesis, University of São Paulo].
A BibTeX entry for LaTeX users is
@mastersthesis{vartanian_2023,
title = {Ecology of sleep and circadian phenotypes of the Brazilian population},
author = {Daniel Vartanian},
year = {2023},
address = {São Paulo},
school = {University of São Paulo},
langid = {en-us},
url = {https://github.com/danielvartan/mastersthesis},
note = {Preliminary version}
}
This thesis was developed in the Graduate Program in Modeling Complex Systems (PPG-SCX) at the University of Sao Paulo (USP), under the supervision of Prof. Dr. Camilo Rodrigues Neto.
Financial support was provided by the Coordination for the Improvement of Higher Education Personnel (CAPES) (Grant number: 88887.703720/2022-00).