Original version submitted on 11/27/2024

R/utils.R

@@ -100,18 +100,30 @@ list_as_tibble <- function(list) {
 library(magrittr)
 # library(prettycheck) # github.com/danielvartan/prettycheck
 
-format_to_md_latex <- function(x, after = NULL, round = 3, key = "$") {
+format_to_md_latex <- function(
+    x,
+    after = NULL,
+    round = 3,
+    decimal_mark = ".",
+    big_mark = ",",
+    key = "$"
+  ) {
   prettycheck:::assert_numeric(x)
   prettycheck:::assert_string(after, null.ok = TRUE)
+  prettycheck:::assert_string(decimal_mark)
+  prettycheck:::assert_string(big_mark)
   prettycheck:::assert_number(round, lower = 0)
   prettycheck:::assert_string(key)
 
   if (is.null(after)) after <- ""
 
-  x <-
-    x |>
+  x |>
     round(round) |>
-    format(big.mark = ",", scientific = FALSE) %>% # Don't change the pipe!
+    format(
+      decimal.mark = decimal_mark,
+      big.mark = big_mark,
+      scientific = FALSE
+    ) %>% # Don't change the pipe!
     paste0(key, ., after, key)
 }
 

README.md

@@ -2,9 +2,9 @@
 
 <!-- quarto render --profile gfm -->
 <!-- badges: start -->
-[![Project Status: WIP – Initial development is in progress, but there
-has not yet been a stable, usable release suitable for the
-public.](https://www.repostatus.org/badges/latest/wip.svg)](https://www.repostatus.org/#wip)
+[![Project Status: Active – The project has reached a stable, usable
+state and is being actively
+developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
 [![OSF
 DOI](https://img.shields.io/badge/DOI-10.17605/OSF.IO/YGKTS-1284C5.svg)](https://doi.org/10.17605/OSF.IO/YGKTS)
 [![License:
@@ -19,7 +19,7 @@ MIT](https://img.shields.io/badge/license-MIT-green.png)](https://choosealicense
 
 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
+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).
 
@@ -30,8 +30,8 @@ Friends)](https://doi.org/10.1080/00031305.2017.1375986).
 
 ## How to use
 
-The analyses contained in this thesis are 100% reproducible. They were
-made using the [R programming language](https://www.r-project.org/) and
+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
@@ -92,12 +92,12 @@ MIT](https://img.shields.io/badge/license-MIT-green.png)](https://opensource.org
 [![License: CC BY
 4.0](https://img.shields.io/badge/License-CC_BY_4.0-lightgrey.svg)](https://creativecommons.org/licenses/by/4.0/)
 
-Code related to this repository is released under the [MIT
-license](https://opensource.org/license/mit/). Documents are released
-under the [Creative Commons Attribution 4.0 International
-license](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 under a private license and is not publicly
+The research data is subject to a private license and is not publicly
 available due to privacy and ethical considerations.
 
 ## Citation
@@ -108,7 +108,7 @@ Vartanian, D. (2024). *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
+A BibTeX entry for LaTeX users is:
 
     @mastersthesis{vartanian2024,
       title = {Is latitude associated with chronotype?},
@@ -123,14 +123,14 @@ A BibTeX entry for LaTeX users is
 
 ## Acknowledgments
 
-This Master’s thesis was developed in the Graduate Program in Modeling
-Complex Systems ([PPG-SCX](https://sites.usp.br/scx/en/apresentacao/))
-at the University of São Paulo ([USP](https://www5.usp.br/)), under the
+This thesis was developed in the Graduate Program in Modeling Complex
+Systems ([PPG-SCX](https://sites.usp.br/scx/en/apresentacao/)) at the
+University of São Paulo ([USP](https://www5.usp.br/)), under the
 supervision of [Prof. Dr. Camilo Rodrigues
 Neto](https://orcid.org/0000-0001-6783-6695).
 
 <a href="https://www.gov.br/capes/"><img src= "images/capes_logo_horizontal_rgb.png" height="35"/></a>
 
 This study was financed by the Coordenação de Aperfeiçoamento de Pessoal
 de Nível Superior - Brazil ([CAPES](https://www.gov.br/capes/)) -
-Finance Code 001, Grant Number: 88887.703720/2022-00.
+Finance Code 001, Grant Number 88887.703720/2022-00.

README.qmd

@@ -3,7 +3,7 @@
 <!-- quarto render --profile gfm -->
 
 <!-- badges: start -->
-[![Project Status: WIP – Initial development is in progress, but there has not yet been a stable, usable release suitable for the public.](https://www.repostatus.org/badges/latest/wip.svg)](https://www.repostatus.org/#wip)
+[![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
 [![OSF DOI](https://img.shields.io/badge/DOI-10.17605/OSF.IO/YGKTS-1284C5.svg)](https://doi.org/10.17605/OSF.IO/YGKTS)
 [![License: MIT](https://img.shields.io/badge/license-MIT-green)](https://choosealicense.com/licenses/mit/)
 [![License: CC BY 4.0](https://img.shields.io/badge/License-CC_BY_4.0-lightgrey.svg)](https://creativecommons.org/licenses/by/4.0/)
@@ -13,13 +13,13 @@
 
 ☀🌙⏰🛌💤🌍🗺️🧭📅🧬🧠🕰️📊📉📈📝
 
-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).
+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
 
-The analyses contained in this thesis are 100% reproducible. They were made using the [R programming language](https://www.r-project.org/) and 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.
+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 the keys section below).
 
@@ -53,17 +53,17 @@ These project's keys will be provided by the author of the thesis upon reasonabl
 MIT](https://img.shields.io/badge/license-MIT-green)](https://opensource.org/license/mit/)
 [![License: CC BY 4.0](https://img.shields.io/badge/License-CC_BY_4.0-lightgrey.svg)](https://creativecommons.org/licenses/by/4.0/)
 
-Code related to this repository is released under the [MIT license](https://opensource.org/license/mit/). Documents are released under the [Creative Commons Attribution 4.0 International license](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 under a private license and is not publicly available due to privacy and ethical considerations.
+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. (2024). *Is latitude associated with chronotype?* [Master's thesis, University of São Paulo]. [https://doi.org/10.17605/OSF.IO/YGKTS](https://doi.org/10.17605/OSF.IO/YGKTS)
 
-A BibTeX entry for LaTeX users is
+A BibTeX entry for LaTeX users is:
 
 ```         
 @mastersthesis{vartanian2024,
@@ -80,8 +80,8 @@ A BibTeX entry for LaTeX users is
 
 ## Acknowledgments
 
-This Master's thesis was developed in the Graduate Program in Modeling Complex Systems ([PPG-SCX](https://sites.usp.br/scx/en/apresentacao/)) at the University of São Paulo ([USP](https://www5.usp.br/)), under the supervision of [Prof. Dr. Camilo Rodrigues Neto](https://orcid.org/0000-0001-6783-6695).
+This thesis was developed in the Graduate Program in Modeling Complex Systems ([PPG-SCX](https://sites.usp.br/scx/en/apresentacao/)) at the University of São Paulo ([USP](https://www5.usp.br/)), under the supervision of [Prof. Dr. Camilo Rodrigues Neto](https://orcid.org/0000-0001-6783-6695).
 
 <a href="https://www.gov.br/capes/"><img src= "images/capes_logo_horizontal_rgb.png" height="35"/></a>
 
-This study was financed by the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - Brazil ([CAPES](https://www.gov.br/capes/)) - Finance Code 001, Grant Number: 88887.703720/2022-00.
+This study was financed by the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - Brazil ([CAPES](https://www.gov.br/capes/)) - Finance Code 001, Grant Number 88887.703720/2022-00.

_quarto-html.yml

@@ -39,7 +39,6 @@ book:
     - qmd/supplementary-material-6.qmd
     - qmd/supplementary-material-7.qmd
     - qmd/supplementary-material-8.qmd
-    - qmd/supplementary-material-9.qmd
     - qmd/supplementary-material-10.qmd
   comments:
     hypothesis:
@@ -62,7 +61,3 @@ format:
     callout-appearance: simple
     csl: csl/english-apa-author-date.csl
     theme: [cosmo, scss/web.scss]
-    link-external-newwindow: true
-    other-links:
-      - text: "Research compendium"
-        href: "https://doi.org/10.17605/OSF.IO/YGKTS"

_quarto-pdf.yml

@@ -18,6 +18,7 @@ book:
   chapters:
     - index.qmd
     - qmd/chapter-2.qmd
+    - qmd/chapter-4.qmd
     - qmd/chapter-5.qmd
     - qmd/chapter-6.qmd
 

_variables.yml

@@ -21,7 +21,7 @@ university: University of São Paulo
 version-note: Original version
 url: https://danielvartan.github.io/mastersthesis/
 language: en
-title: Is latitude associated with chronotype?
-date: '2024-11-26'
+title: Is Latitude Associated with Chronotype?
+date: '2024-11-27'
 year: '2024'
-format: html
+format: pdf

docs/index.html

@@ -4,24 +4,24 @@
 	<meta charset="utf-8">
 	<meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-	<title>Is latitude associated with chronotype?</title>
+	<title>Is Latitude Associated with Chronotype?</title>
 
-	<link href="https://cdn.jsdelivr.net/npm/bootstrap@5.3.3/dist/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-QWTKZyjpPEjISv5WaRU9OFeRpok6YctnYmDr5pNlyT2bRjXh0JMhjY6hW+ALEwIH" crossorigin="anonymous">
-	<link rel="stylesheet" href="style.css">
+	<link rel="stylesheet" href="css/bootstrap.min.css">
+	<link rel="stylesheet" href="css/style.css">
 	<link rel="icon" type="image/x-icon" href="favicon.png">
 </head>
 <body style="background-color:#FFFFFF;">
 
 <div class="container-sm mt-5 px-5">
 <div class="d-grid gap-3">
-	<h2>Is latitude associated with chronotype?</h2>
+	<h2>Is Latitude Associated with Chronotype? [Master's Thesis]</h2>
 
-	<p>Choose your destination.</p>
+	<p>Select your preferred destination.</p>
 
-	<a href="web/index.html" class="btn btn-outline-primary btn-block" role="button">Web version</a>
-	<a href="print/index.pdf" class="btn btn-outline-primary btn-block" role="button">Print version</a>
+	<a href="web/index.html" class="btn btn-outline-primary btn-block" role="button">Web Version</a>
+	<a href="print/index.pdf" class="btn btn-outline-primary btn-block" role="button">Print Version</a>
 	<a href="slides/index.html" class="btn btn-outline-primary btn-block" role="button">Presentation</a>
 </div>
-<script src="https://cdn.jsdelivr.net/npm/bootstrap@5.3.3/dist/js/bootstrap.bundle.min.js" integrity="sha384-YvpcrYf0tY3lHB60NNkmXc5s9fDVZLESaAA55NDzOxhy9GkcIdslK1eN7N6jIeHz" crossorigin="anonymous"></script>
+<script src="js/bootstrap.bundle.min.js"></script>
 </body>
 </html>