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README.qmd
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---
html-table-processing: none
---
# mastersthesis
<!-- quarto render --profile gfm -->
```{r}
#| label: setup
#| include: false
source(here::here("R", "_setup.R"))
```
<!-- badges: start -->
[](https://www.repostatus.org/#active)
[](https://doi.org/10.17605/OSF.IO/YGKTS)
[](https://choosealicense.com/licenses/mit/)
[](https://creativecommons.org/licenses/by/4.0/)
<!-- badges: end -->
## Overview
☀️🌙⏰🛌💤🌍🗺️🧭📅🧬🧠🕰️📊📓
This repository contains the [Quarto book](https://quarto.org/docs/books/) of my Master's Thesis: *Is Latitude Associated with Chronotype?* The research compendium is accessible via [The Open Science Framework](https://osf.io/) by clicking [here](https://doi.org/10.17605/OSF.IO/YGKTS).
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)](https://doi.org/10.1080/00031305.2017.1375986).
## How to use
All analyses in this thesis are fully reproducible and were conducted using the [R programming language](https://www.r-project.org/) alongside the [Quarto](https://quarto.org/) publishing system. The [`renv`](https://rstudio.github.io/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](https://r4ds.hadley.nz/) and the Coursera course from John Hopkins University [Data Science: Foundations using R](https://www.coursera.org/specializations/data-science-foundations-r).
To reproduce the analyses do the following steps:
(@) Make sure that you have the latest R version and the following R packages installed in your machine:
```{r}
#| eval: false
install.packages(
c("cli", "here" ,"magrittr", "ragg", "renv", "stats", "stringr")
)
```
(@) Clone this repository.
(@) Open the R project (`mastersthesis.Rproj`).
(@) Run [`renv::restore()`](https://rstudio.github.io/renv//reference/restore.html) to install all software dependencies.
(@) Set all the keys provided by the author in the `.Renviron` file and the `_ssh` folder.
(@) Run `targets::tar_make()` to create every point of the data wrangling process (from the raw data to the cleaned and weighted data).
(@) 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`](https://bookdown.org/csgillespie/efficientR/set-up.html#:~:text=2.4.6%20The%20.Renviron%20file) file:
- `OSF_PAT`: Your [OSF](https://osf.io/) 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
[](https://opensource.org/license/mit/)
[](https://creativecommons.org/licenses/by/4.0/)
The code accompanying this thesis is distributed under the [MIT License](https://opensource.org/license/mit/). All documents are released under the [Creative Commons Attribution 4.0 International Public License](https://creativecommons.org/licenses/by/4.0/).
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. (`r env_vars[["year"]]`). *`r env_vars[["title"]] |> stringr::str_to_sentence()`* [`r env_vars[["academic-title"]]`'s `r env_vars[["type-of-work"]]`, `r env_vars[["university"]]`]. [https://doi.org/10.17605/OSF.IO/YGKTS](https://doi.org/10.17605/OSF.IO/YGKTS)
A BibTeX entry for LaTeX users is:
```
@mastersthesis{vartanian`r env_vars[["year"]]`,
title = {`r env_vars[["title"]] |> stringr::str_to_sentence()`},
author = {Daniel Vartanian},
year = {`r env_vars[["year"]]`},
address = {`r env_vars[["location"]]`},
school = {`r env_vars[["university"]]`},
langid = {`r env_vars[["language"]]`},
url = {https://doi.org/10.17605/OSF.IO/YGKTS},
note = {`r env_vars[["version-note"]]`}
}
```
## Acknowledgments
```{r}
#| echo: false
#| output: asis
htmltools::tags$table(
htmltools::tags$tr(
htmltools::tags$td(
htmltools::tags$br(),
htmltools::tags$br(),
htmltools::tags$p(
htmltools::tags$a(
htmltools::tags$img(
src = "images/usp-logo.svg",
width = 150
),
href = paste0(
"https://www.prpg.usp.br/pt-br/faca-pos-na-usp/",
"programas-de-pos-graduacao/621-modelagem-de-sistemas-complexos"
)
),
align = "center"
),
htmltools::tags$br(),
width = "30%"
),
htmltools::tags$td(
htmltools::tags$p(
"This thesis was developed in the Graduate Program in Modeling ",
"Complex Systems (",
htmltools::tags$a(
"PPGSCX",
href = paste0(
"https://www.prpg.usp.br/pt-br/faca-pos-na-usp/",
"programas-de-pos-graduacao/621-modelagem-de-sistemas-complexos"
),
.noWS = "outside"
),
") at the University of São Paulo (",
htmltools::tags$a(
"USP",
href = "https://www5.usp.br/",
.noWS = "outside"
),
") under the supervision of",
htmltools::tags$a(
"Prof. Dr. Camilo Rodrigues Neto",
href = "https://orcid.org/0000-0001-6783-6695",
.noWS = "after"
),
"."
),
width = "70%"
)
)
) |>
knitr::raw_html()
htmltools::tags$table(
htmltools::tags$tr(
htmltools::tags$td(
htmltools::tags$br(),
htmltools::tags$p(
htmltools::tags$a(
htmltools::tags$img(
src = "images/capes-logo-original.svg",
width = 120
),
href = "https://www.gov.br/capes/"
),
align = "center"
),
htmltools::tags$br(),
width = "30%"
),
htmltools::tags$td(
htmltools::tags$p(
"This study was financed by the Coordenação de Aperfeiçoamento de ",
"Pessoal de Nível Superior - Brazil (",
htmltools::tags$a(
"CAPES",
href = "https://orcid.org/0000-0001-6783-6695",
.noWS = "outside"
),
") - Finance Code 001, Grant Number 88887.703720/2022-00."
),
width = "70%"
)
)
) |>
knitr::raw_html()
```