Add a new print version

Author: danielvartan

.Rprofile

@@ -1,3 +1,7 @@
+# Set session ID -----
+
+session_id <- Sys.time() |> as.character()
+
 # Load functions -----
 
 single_quote <- function(x) paste0("'", x, "'")
@@ -64,13 +68,34 @@ require_pkg <- function(...) {
   invisible()
 }
 
-rprofile_message <- function(x, id) {
-  if (Sys.getenv(paste0("RPROFILE_MESSAGE_", id)) == "") {
+rprofile_cat_line <- function(session_id, env_var = "RPROFILE_MESSAGES") {
+  if (Sys.getenv(env_var) == session_id) cat("\n")
+
+  invisible()
+}
+
+rprofile_message <- function(
+    x,
+    session_id,
+    env_var = "RPROFILE_MESSAGES",
+    cat_line = TRUE,
+    info = FALSE
+  ) {
+  if (Sys.getenv(env_var) %in% c("", session_id)) {
     do.call(
       what = Sys.setenv,
-      args = list(TRUE) |> magrittr::set_names(paste0("RPROFILE_MESSAGE_", id))
+      args =
+        list(session_id) |>
+        magrittr::set_names(env_var)
     )
-    cli::cli_alert(x, wrap = TRUE)
+
+    if (isTRUE(info)) {
+      cli::cli_alert_info(x, wrap = TRUE)
+    } else {
+      cli::cli_alert(x, wrap = TRUE)
+    }
+
+    if (isTRUE(cat_line)) cat("\n")
   }
 
   invisible()
@@ -85,13 +110,21 @@ require_pkg(c("cli", "here" ,"magrittr", "ragg", "renv", "stats", "stringr"))
 library(magrittr)
 library(ragg)
 
+# Show session message -----
+
+rprofile_message(
+  x = "The messages below are shown only once per R session.",
+  session_id = session_id,
+  info = TRUE
+)
+
 # Activate `renv` -----
 
-rprofile_message("`renv` activation settings:", 1)
+rprofile_message("`renv` activation settings:", session_id)
 
 source(here::here("renv", "activate.R"))
 
-cat("\n")
+rprofile_cat_line(session_id)
 
 # Set options -----
 
@@ -102,24 +135,22 @@ options(scipen = 999)
 rprofile_message(
   paste0(
     "If you haven't already set it, configure {.strong AGG} ",
-    "as the RStudio graphic device backend. Learn more in ",
+    "as the RStudio graphic device backend. Learn more at ",
     "<https://ragg.r-lib.org/#use-ragg-in-rstudio>."
   ),
-  2
+  session_id
 )
 
-cat("\n")
-
 # Set system locale -----
 
 source(here::here("R", "set_locale.R"))
 
-set_locale()
+set_locale(session_id)
 
-# Clean the global environment -----
+# End line -----
 
-rm(list = ls())
+rprofile_cat_line(session_id = session_id, env_var = "SET_LOCALE_MESSAGES")
 
-# .Rprofile end -----
+# Clean the global environment -----
 
-cat("\n")
+rm(list = ls())

R/_post-render-gfm.R

@@ -10,7 +10,10 @@ groomr::remove_blank_line_dups(here::here("README.md"))
 
 # Update project year -----
 
-files <- here::here("LICENSE.md")
+files <- c(
+  here::here("CITATION.cff"),
+  here::here("LICENSE.md")
+)
 
 for (i in files) {
   data <-

R/_pre-render-pdf.R

@@ -105,6 +105,30 @@ swap_list <- list(
     end_tag = "%:::% foreign-abstract keywords end %:::%",
     value = NULL,
     quarto_render = FALSE
+  ),
+  other_in_header = list(
+    from = here::here("qmd", "_config.qmd"),
+    to = here::here("tex", "include-in-header.tex"),
+    begin_tag = "%:::% other-in-header begin %:::%",
+    end_tag = "%:::% other-in-header end %:::%",
+    value = NULL,
+    quarto_render = FALSE
+  ),
+  other_before_body = list(
+    from = here::here("qmd", "_config.qmd"),
+    to = here::here("tex", "include-before-body.tex"),
+    begin_tag = "%:::% other-before-body begin %:::%",
+    end_tag = "%:::% other-before-body end %:::%",
+    value = NULL,
+    quarto_render = FALSE
+  ),
+  other_after_body = list(
+    from = here::here("qmd", "_config.qmd"),
+    to = here::here("tex", "include-after-body.tex"),
+    begin_tag = "%:::% other-after-body begin %:::%",
+    end_tag = "%:::% other-after-body end %:::%",
+    value = NULL,
+    quarto_render = FALSE
   )
 )
 

R/_setup.R

@@ -30,7 +30,7 @@ options(
   pillar.max_footer_lines = 2,
   pillar.min_chars = 15,
   scipen = 10,
-  digits = 5,
+  digits = 10,
   stringr.view_n = 6,
   pillar.bold = TRUE,
   width = 77 # 80 - 3 for #> comment
@@ -83,29 +83,19 @@ sysfonts::font_paths(
   c(
     here::here("otf"),
     here::here("ttf"),
+    here::here("_extensions", "abnt", "otf"),
     here::here("_extensions", "abnt", "ttf")
   )
 )
 
-if (env_vars$format == "pdf") {
-  sysfonts::font_add(
-    family = "helvetica-neue",
-    regular = here::here("otf", "helveticaneueltstd-roman.otf"),
-    bold = here::here("otf", "helveticaneueltstd-bd.otf"),
-    italic = here::here("otf", "helveticaneueltstd-it.otf"),
-    bolditalic = here::here("otf", "helveticaneueltstd-bdit.otf"),
-    symbol = NULL
-  )
-} else {
-  sysfonts::font_add(
-    family = "dm-sans",
-    regular = here::here("ttf", "dmsans-regular.ttf"),
-    bold = here::here("ttf", "dmsans-bold.ttf"),
-    italic = here::here("ttf", "dmsans-italic.ttf"),
-    bolditalic = here::here("ttf", "dmsans-bolditalic.ttf"),
-    symbol = NULL
-  )
-}
+sysfonts::font_add(
+  family = "dm-sans",
+  regular = here::here("ttf", "dmsans-regular.ttf"),
+  bold = here::here("ttf", "dmsans-bold.ttf"),
+  italic = here::here("ttf", "dmsans-italic.ttf"),
+  bolditalic = here::here("ttf", "dmsans-bolditalic.ttf"),
+  symbol = NULL
+)
 
 showtext::showtext_auto()
 
@@ -120,11 +110,7 @@ ggplot2::theme_set(
   ggplot2::theme(
     text = ggplot2::element_text(
       color = get_brand_color("secondary"),
-      family = ifelse(
-        env_vars$format == "pdf",
-        "helvetica-neue",
-        "dm-sans"
-      ),
+      family = "dm-sans",
       face = "plain"
     ),
     panel.background = ggplot2::element_rect(fill = "transparent"),

R/set_locale.R

@@ -11,7 +11,7 @@
 # library(stats)
 # library(stringr)
 
-set_locale <- function() {
+set_locale <- function(session_id = Sys.time() |> as.character()) {
   locale_values <- c(
     "en_US.utf8", "en_US.UTF-8", "en_US", "en-US", "en", "English_United States"
   )
@@ -68,30 +68,17 @@ set_locale <- function() {
   }
 
   if (Sys.getenv("SET_LOCALE_MESSAGES") == "") {
-    Sys.setenv(SET_LOCALE_MESSAGES = TRUE)
+    Sys.setenv(SET_LOCALE_MESSAGES = session_id)
 
-    get_locale(periodic_message = TRUE)
+    get_locale()
   }
 
   invisible()
 }
 
 # library(cli)
 
-get_locale <- function(periodic_message = FALSE) {
-  prettycheck:::assert_flag(periodic_message)
-
-  if (isTRUE(periodic_message)) {
-    cli::cli_alert_info(
-      paste0(
-        "The messages below are shown only once per R session."
-      ),
-      wrap = TRUE
-    )
-  }
-
-  cat("\n")
-
+get_locale <- function() {
   cli::cli_alert(
     paste0(
       "The current system locale is:\n\n",

R/utils.R

@@ -104,7 +104,7 @@ write_in_results_yml <- function(
 
   for (i in seq_along(x)) {
     if (is.numeric(x[[i]])) {
-      x[[i]] <- x[[i]] |> signif(10)
+      x[[i]] <- x[[i]] |> signif(digits)
     }
 
     if (names(x)[i] %in% names(out)) {

README.md

@@ -1,11 +1,8 @@
-
-
 # mastersthesis
 
 <!-- quarto render --profile gfm -->
 
 <!-- badges: start -->
-
 [![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)
@@ -45,30 +42,31 @@ 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).
+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:
 
 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", "renv", "stats", "stringr"))`.
+    `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()`](https://rstudio.github.io/renv//reference/restore.html)
     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 and get every point of the data
-    wrangling process (from the raw_data to the cleaned and weighted
+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.  Open and run any analysis present in the computational notebooks.
-
-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).
+7.  Run any analysis present in the computational notebooks (`qmd`
+    directory).
 
 ## Keys
 
@@ -114,28 +112,29 @@ available due to privacy and ethical considerations.
 
 To cite this work, please use the following format:
 
-Vartanian, D. (2024). *Is latitude associated with chronotype?*
-\[Master’s thesis, University of São Paulo\].
+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{vartanian2024,
+    @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 = {Original version}
+      note = {Corrected version}
     }
 
 ## Acknowledgments
 
 The 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
+Systems
+([PPG-SCX](https://www.prpg.usp.br/pt-br/faca-pos-na-usp/programas-de-pos-graduacao/621-modelagem-de-sistemas-complexos))
+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).