Add patch changes

danielvartan · Oct 12, 2024 · 1be76d1 · 1be76d1
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diff --git a/LICENSE.md b/LICENSE.md
@@ -1,6 +1,6 @@
 # MIT License
 
-Copyright (c) Daniel Vartanian
+Copyright (c) 2024 Daniel Vartanian
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

diff --git a/R/_dev.R b/R/_dev.R
@@ -49,10 +49,10 @@
 # source(here::here("R", "_pre-render-revealjs.R"))
 #
 # quarto render
+# quarto render --profile gfm
 # quarto render --profile pdf
 # quarto render --profile html
 # quarto render --profile revealjs
-# quarto publish gh-pages
 
 # # LaTeX
 #

diff --git a/R/_post-render-end.R b/R/_post-render-end.R
@@ -1,6 +1,8 @@
-# library(rutils, quietly = TRUE)
-# library(here, quietly = TRUE)
-# library(magrittr, quietly = TRUE)
+# library(rutils)
+# library(here)
+# library(magrittr)
+# library(readr)
+# library(stringr)
 
 # Copy output to `docs` folder -----
 
@@ -64,6 +66,20 @@ for (i in seq_along(output_docs_new_files)) {
   )
 }
 
+# Update `LICENSE.md` year -----
+
+file <- here::here("LICENSE.md")
+
+data <-
+  file |>
+  readr::read_lines() |>
+  stringr::str_replace_all(
+    pattern = "20\\d{2}",
+    replacement = as.character(Sys.Date() |> lubridate::year())
+  )
+
+data |> readr::write_lines(file)
+
 # Delete unnecessary files and folders -----
 
 dir_list <-

diff --git a/R/_post-render-gfm.R b/R/_post-render-gfm.R
@@ -0,0 +1,11 @@
+# library(beepr)
+# library(groomr) # github.com/danielvartan/groomr
+# library(here)
+
+# Remove empty lines from `README.md` -----
+
+groomr::remove_blank_line_dups(here::here("README.md"))
+
+# Check if the script ran successfully -----
+
+# beepr::beep(1)
diff --git a/R/_pre-render-begin.R b/R/_pre-render-begin.R
@@ -89,9 +89,11 @@ env_vars |> yaml::write_yaml(env_vars_file_path)
 quarto_yml_pdf_path <- here::here("_quarto-pdf.yml")
 quarto_yml_pdf_vars <- yaml::read_yaml(quarto_yml_pdf_path)
 
-# (2024-06-05)
-# This function only works with BetterBibTeX (BBT) for Zotero version v6.7.140
-# or lower.
+# (2024-08-25)
+# This function should work with any version of BetterBibTeX (BBT) for Zotero.
+# Verify if @wmoldham PR was merged in the `rbbt` package (see issue #47
+# <https://github.com/paleolimbot/rbbt/issues/47>). If not, install `rbbt`
+# from @wmoldham fork `remotes::install_github("wmoldham/rbbt")`.
 
 if (isTRUE(quarto_yml_pdf_vars$format$`abnt-pdf`$zotero)) {
   rutils:::bbt_write_quarto_bib(

diff --git a/R/test_normality.R b/R/test_normality.R
@@ -219,7 +219,7 @@ plot_hist <- function(x,
   checkmate::assert_flag(print)
 
   if (isTRUE(na_rm)) x <- x |> rutils:::drop_na()
-  y_lab <- ifelse("count", "Frequency", "Density")
+  y_lab <- ifelse(stat == "count", "Frequency", "Density")
 
   plot <-
     dplyr::tibble(y = x) |>

diff --git a/R/utils-stats.R b/R/utils-stats.R
@@ -41,7 +41,12 @@ std_error <- function(x){
 # library(stats, quietly = TRUE)
 
 # TODO: Move to `rutils`.
-is_outlier <- function(x, method = "iqr", iqr_mult = 1.5, sd_mult = 3) {
+is_outlier <- function( # Change name to `test_outlier`
+    x,
+    method = "iqr",
+    iqr_mult = 1.5,
+    sd_mult = 3
+) {
   checkmate::assert_numeric(x)
   checkmate::assert_choice(method, c("iqr", "sd"))
   checkmate::assert_number(iqr_mult)
@@ -62,11 +67,23 @@ is_outlier <- function(x, method = "iqr", iqr_mult = 1.5, sd_mult = 3) {
 # library(checkmate, quietly = TRUE)
 
 # TODO: Move to `rutils`.
-remove_outliers <- function(x, method = "iqr", iqr_mult = 1.5, sd_mult = 3) {
+remove_outliers <- function(
+    x,
+    method = "iqr",
+    iqr_mult = 1.5,
+    sd_mult = 3
+) {
   checkmate::assert_numeric(x)
   checkmate::assert_choice(method, c("iqr", "sd"))
-  checkmate::assert_number(iqr_mult)
-  checkmate::assert_number(sd_mult)
-
-  x[!is_outlier(x, method = method, iqr_mult = iqr_mult, sd_mult = sd_mult)]
+  checkmate::assert_number(iqr_mult, lower = 1)
+  checkmate::assert_number(sd_mult, lower = 0)
+
+  x |>
+    test_outlier(
+      method = method,
+      iqr_mult = iqr_mult,
+      sd_mult = sd_mult
+    ) %>%
+    `!`() %>%
+    magrittr::extract(x, .)
 }
diff --git a/README.md b/README.md
@@ -1,17 +1,13 @@
-
-<!-- README.md is generated from README.Rmd. Please edit that file -->
-
 # mastersthesis
 
 <!-- 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)
 [![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/)
+MIT](https://img.shields.io/badge/license-MIT-green.png)](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/)
 <!-- badges: end -->
@@ -40,17 +36,14 @@ 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`). The
+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 were used under the approval of a
-Research Ethics Committee (REC) linked to the [Brazilian National
-Research Ethics Committee
-(CONEP)](https://conselho.saude.gov.br/Web_comissoes/conep/index.html).
-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.
+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.
 
 To reproduce the analyses do the following steps:
 
@@ -65,13 +58,12 @@ 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.had.co.nz/) and the Coursera course from John
 Hopkins University [Data Science: Foundations using
-R](https://www.coursera.org/specializations/data-science-foundations-r)
-(free for audit students).
+R](https://www.coursera.org/specializations/data-science-foundations-r).
 
 ## License
 
 [![License:
-MIT](https://img.shields.io/badge/license-MIT-green)](https://opensource.org/license/mit/)
+MIT](https://img.shields.io/badge/license-MIT-green.png)](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/)
 
@@ -80,24 +72,21 @@ 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 main research data were used under the approval of a Research Ethics
-Committee (REC) linked to the [Brazilian National Research Ethics
-Committee
-(CONEP)](https://conselho.saude.gov.br/Web_comissoes/conep/index.html);
-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.
+The main research data contain personal and sensitive data, hence it
+cannot be publicly shared. However, the data can be provided by the
+author upon reasonable request.
 
 ## Citation
 
 You can find the thesis citation below.
 
-    Vartanian, D. (2024). Is latitude associated with the regulation of circadian rhythms in humans? [Master's thesis, University of São Paulo]. https://github.com/danielvartan/mastersthesis
+Vartanian, D. (2024). Is latitude associated with the regulation of
+circadian rhythms in humans? \[Master’s thesis, University of São
+Paulo\]. https://github.com/danielvartan/mastersthesis
 
 A BibTeX entry for LaTeX users is
 
-    @mastersthesis{vartanian_2023,
+    @mastersthesis{vartanian2024,
       title = {Is latitude associated with the regulation of circadian rhythms in humans?},
       author = {Daniel Vartanian},
       year = {2024},

diff --git a/README.Rmd → README.qmd b/README.Rmd → README.qmd
@@ -1,18 +1,3 @@
----
-output: github_document
----
-
-<!-- README.md is generated from README.Rmd. Please edit that file -->
-
-```{r, include = FALSE}
-knitr::opts_chunk$set(
-  collapse = TRUE,
-  comment = "#>",
-  fig.path = "man/figures/README-",
-  out.width = "100%"
-)
-```
-
 # mastersthesis
 
 <!-- badges: start -->
@@ -34,9 +19,9 @@ The assemble of this repository was inspired by Ben Marwick, Carl Boettiger & Li
 
 ## 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`). The computational notebooks can be found in the `qmd` directory.
+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.
 
-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)](https://conselho.saude.gov.br/Web_comissoes/conep/index.html). 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.
+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.
 
 To reproduce the analyses do the following steps:
 
@@ -45,7 +30,7 @@ To reproduce the analyses do the following steps:
 3. Run [`renv::restore()`](https://rstudio.github.io/renv//reference/restore.html) to install all software dependencies.
 4. 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](https://r4ds.had.co.nz/) and the Coursera course from John Hopkins University [Data Science: Foundations using R](https://www.coursera.org/specializations/data-science-foundations-r) (free for audit students).
+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.had.co.nz/) and the Coursera course from John Hopkins University [Data Science: Foundations using R](https://www.coursera.org/specializations/data-science-foundations-r).
 
 ## License
 
@@ -55,20 +40,18 @@ MIT](https://img.shields.io/badge/license-MIT-green)](https://opensource.org/lic
 
 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 main research data were used under the approval of a Research Ethics Committee (REC) linked to the [Brazilian National Research Ethics Committee (CONEP)](https://conselho.saude.gov.br/Web_comissoes/conep/index.html); 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.
+The main research data contain personal and sensitive data, hence it cannot be publicly shared. However, the data can be provided by the author upon reasonable request.
 
 ## Citation
 
 You can find the thesis citation below.
 
-```         
 Vartanian, D. (2024). Is latitude associated with the regulation of circadian rhythms in humans? [Master's thesis, University of São Paulo]. https://github.com/danielvartan/mastersthesis
-```
 
 A BibTeX entry for LaTeX users is
 
 ```         
-@mastersthesis{vartanian_2023,
+@mastersthesis{vartanian2024,
   title = {Is latitude associated with the regulation of circadian rhythms in humans?},
   author = {Daniel Vartanian},
   year = {2024},

diff --git a/_quarto-gfm.yml b/_quarto-gfm.yml
@@ -0,0 +1,6 @@
+project:
+  output-dir: "."
+  render: [README.qmd]
+  post-render: "R/_post-render-gfm.R"
+
+format: gfm
diff --git a/_quarto.yml b/_quarto.yml
@@ -6,20 +6,20 @@ execute:
 
 profile:
   group:
-    - [html, pdf, revealjs]
+    - [gfm, html, pdf, revealjs]
   default: pdf
 
 book:
   title: "Is latitude associated with human circadian rhythms?"
   author: "Daniel Vartanian"
   keyword: >
-    Chronobiology. Biological rhythms. Chronotype. Circadian phenotype. Sleep.
-    Complex systems. Entrainment. Latitude. MCTQ.
+    chronobiology. biological rhythms. chronotype. circadian phenotype. sleep.
+    complex systems. entrainment. latitude. mctq.
   language: en-us
   license: "Creative Commons Attribution 4.0 International (CC BY 4.0)"
   publisher: "University of São Paulo"
   publisher-place: "São Paulo, SP, Brazil"
-  submitted: 2023
+  submitted: 2024
   url: https://danielvartan.github.io/mastersthesis/
   site-url: https://danielvartan.github.io/mastersthesis/
   repo-url: https://github.com/danielvartan/mastersthesis/

diff --git a/qmd/appendice-chapter-4.qmd b/qmd/appendice-chapter-4.qmd
@@ -20,7 +20,7 @@ rutils:::quarto_status(
   )
 ```
 
-## Data wrangling
+## Data munging
 
 The data wrangling processes were performed using the  [`targets`](https://github.com/ropensci/targets) R package. The full pipeline can be seen in the `_targets.R` file at the root of the [research compendium](https://github.com/danielvartan/mastersthesis).
 

diff --git a/qmd/appendice-chapter-6.qmd b/qmd/appendice-chapter-6.qmd
@@ -295,7 +295,7 @@ lubritime:::link_to_timeline(data) |>
 
 See [`targets` R package manual](https://books.ropensci.org/targets/walkthrough.html).
 
-### Data wrangling
+### Data munging
 
 ```{r}
 #| label: data-preparation
@@ -390,6 +390,8 @@ $$
 ```{r}
 #| code-fold: false
 
+# recipes::step_BoxCox()
+
 lambda <- box_cox$x[which.max(box_cox$y)]
 
 sprintf("%.50f", lambda) # Only ~16 digit precision
@@ -542,15 +544,9 @@ source(here::here("R/test_normality.R"))
 
 # res_model |> olsrr::ols_plot_resid_qq()
 
-qq_plot <- res_model |> 
-  stats::residuals() |>
-  plot_qq(print = FALSE)
-
-hist_plot <- res_model |>
+res_model |> 
   stats::residuals() |>
-  plot_hist(print = FALSE)
-
-cowplot::plot_grid(hist_plot, qq_plot, ncol = 2, nrow = 1)
+  test_normality()
 ```
 
 [Source: Created by the author.]{.legend}
-Original file line number
+Diff line change
@@ Expand Up / @@ -20,7 +20,7 @@ rutils:::quarto_status( @@
       )
     ```
-    ## Data wrangling
+    ## Data munging
     The data wrangling processes were performed using the  [`targets`](https://github.com/ropensci/targets) R package. The full pipeline can be seen in the `_targets.R` file at the root of the [research compendium](https://github.com/danielvartan/mastersthesis).
@@ Expand Down @@