Add final revisions for the qualification exam

Author: danielvartan

.Rbuildignore

@@ -1,11 +1,11 @@
 # See <https://git-scm.com/docs/gitignore>.
 
+_freeze/
+_targets/
 .auth/
 .quarto/
 .temp/
 .ssh/
-_targets/
-# docs/
 .Rapp.history
 .RData
 .Renviron

.gitignore

@@ -34,9 +34,21 @@
               },
               "pinned": true
             }
+          },
+          {
+            "id": "0f3fffc213ca6f8b",
+            "type": "leaf",
+            "state": {
+              "type": "markdown",
+              "state": {
+                "file": "qmd/list-of-abbreviations.qmd",
+                "mode": "source",
+                "source": false
+              }
+            }
           }
         ],
-        "currentTab": 1
+        "currentTab": 2
       }
     ],
     "direction": "vertical"
@@ -113,7 +125,7 @@
             "state": {
               "type": "backlink",
               "state": {
-                "file": "qmd/chapter-1.qmd",
+                "file": "qmd/list-of-abbreviations.qmd",
                 "collapseAll": false,
                 "extraContext": false,
                 "sortOrder": "alphabetical",
@@ -130,7 +142,7 @@
             "state": {
               "type": "outgoing-link",
               "state": {
-                "file": "qmd/chapter-1.qmd",
+                "file": "qmd/list-of-abbreviations.qmd",
                 "linksCollapsed": false,
                 "unlinkedCollapsed": true
               }
@@ -149,7 +161,7 @@
             "state": {
               "type": "outline",
               "state": {
-                "file": "qmd/chapter-1.qmd"
+                "file": "qmd/list-of-abbreviations.qmd"
               }
             }
           }
@@ -169,9 +181,12 @@
       "obsidian-grammarly-plugin:Enable Grammarly": false
     }
   },
-  "active": "8356ee2ff131600b",
+  "active": "0f3fffc213ca6f8b",
   "lastOpenFiles": [
+    "qmd/chapter-1.qmd",
     "qmd/chapter-6.qmd",
+    "README.html",
+    "README.knit.md",
     "Ecology-of-sleep-and-circadian-phenotypes-of-the-Brazilian-population.tex",
     "Ecology-of-sleep-and-circadian-phenotypes-of-the-Brazilian-population.pdf",
     "index.pdf",
@@ -180,8 +195,6 @@
     "index.lot",
     "index.lof",
     "index.aux",
-    "tesesusp.cls",
-    "index.tex",
     "qmd/appendice-ch-6.knit.md",
     "qmd/appendice-ch-6_files/figure-pdf/unnamed-chunk-36-1.png",
     "qmd/appendice-ch-6_files/figure-pdf/unnamed-chunk-31-1.png",
@@ -215,7 +228,6 @@
     "qmd/acknowledgments.knit.md",
     "qmd/inscription.knit.md",
     "qmd/errata.knit.md",
-    "renv/library/R-4.3/x86_64-w64-mingw32/targets/tar_watch/about.md",
-    "renv/library/R-4.3/x86_64-w64-mingw32/targets/paper/paper.md"
+    "renv/library/R-4.3/x86_64-w64-mingw32/targets/tar_watch/about.md"
   ]
 }

.obsidian/workspace.json

@@ -29,33 +29,32 @@
 # rutils:::bbt_scan_citation_keys()
 # rutils:::bbt_write_quarto_bib()
 # rutils:::set_quarto_speel_check()
-# rutils:::gather_words_from_spell_check()
-# rutils:::spell_check_quarto()
-# rutils:::update_quarto_wordlist()
+# rutils:::gather_words_from_spell_check(pattern = "\\.qmd$|\\.Rmd$")
+# rutils:::spell_check_quarto(pattern = "\\.qmd$|\\.Rmd$")
+# rutils:::update_quarto_wordlist(pattern = "\\.qmd$|\\.Rmd$")
 # rutils:::clean_quarto_mess()
 # rutils:::quarto_status("drafting")
 # spelling::spell_check_files("index.qmd")
 # urlchecker::url_check()
 # urlchecker::url_update()
 
-# # Pandoc
-#
-# rmarkdown::pandoc_convert(
-#   input = "qmd/acknowledgments.qmd",
-#   from = "markdown",
-#   to = "latex",
-#   wd = here::here()
-# )
-
 # # Quarto (see <https://quarto.org/docs/projects/quarto-projects.html>)
 #
+# source(here::here("R", "quarto-pre-render-pdf.R"))
+# source(here::here("R", "quarto-pre-render-html.R"))
+#
 # quarto render
 # quarto render --profile pdf
-# quarto render --profile pdf --cache-refresh
 # quarto render --profile html
-# quarto render --profile html --cache-refresh
 # quarto publish gh-pages
 
+# # LaTeX
+#
+# \BeforeBeginEnvironment{}{} # {etoolbox}
+# \AtBeginEnvironment{}{}
+# \AtEndEnvironment{}{}
+# \AfterEndEnvironment{}{}
+
 # # Google Cloud Storage
 #
 # library(googleCloudStorageR)
@@ -83,6 +82,5 @@
 # # TODO
 #
 # * Document functions.
-# * Finish version of 'tesesusp' Quarto format.
-# * Document and promote quarto util functions on {rutils}
-# * Create check_quarto_urls()
+# * Finish version of 'abnt' Quarto format.
+# * Create a new R package named {quartoutils}.

R/_dev.R

@@ -0,0 +1,25 @@
+# library(checkmate, quietly = TRUE)
+# library(here, quietly = TRUE)
+# library(yaml, quietly = TRUE)
+
+# Set variables -----
+
+quarto_yml_path <- here::here("_quarto.yml")
+quarto_yml_html_path <- here::here("_quarto-html.yml")
+quarto_yml_pdf_path <- here::here("_quarto-pdf.yml")
+
+quarto_yml_vars <- yaml::read_yaml(quarto_yml_path)
+quarto_yml_html_vars <- yaml::read_yaml(quarto_yml_html_path)
+quarto_yml_pdf_vars <- yaml::read_yaml(quarto_yml_pdf_path)
+
+github_user <- "danielvartan"
+project_name <- here::here() |> basename() # rstudioapi::getActiveProject()
+
+# Create output folders if they don't exist -----
+
+output_dir_pdf <- here::here(quarto_yml_pdf_vars$project$`output-dir`)
+output_dir_html <- here::here(quarto_yml_html_vars$project$`output-dir`)
+
+for (i in c(output_dir_html, output_dir_pdf)) {
+  if (!checkmate::test_directory_exists(i)) dir.create(i)
+}

R/quarto-post-render-common.R

@@ -3,32 +3,11 @@
 # library(rutils, quietly = TRUE)
 # library(yaml, quietly = TRUE)
 
-# Set variables ----------
+source(here::here("R", "quarto-post-render-common.R"))
 
-quarto_yml_path <- here::here("_quarto.yml")
-quarto_yml_html_path <- here::here("_quarto-html.yml")
-quarto_yml_pdf_path <- here::here("_quarto-pdf.yml")
+# Copy PDF (if exists) to `output_dir_html` folder ----------
 
-quarto_yml_vars <- yaml::read_yaml(quarto_yml_path)
-quarto_yml_html_vars <- yaml::read_yaml(quarto_yml_html_path)
-quarto_yml_pdf_vars <- yaml::read_yaml(quarto_yml_pdf_path)
-
-github_user <- "danielvartan"
-project_name <- here::here() |> basename() # rstudioapi::getActiveProject()
-
-# Set output variables and create output folders if they don't exist ----------
-
-output_dir_html <- here::here(quarto_yml_html_vars$project$`output-dir`)
-output_dir_pdf <- here::here(quarto_yml_pdf_vars$project$`output-dir`)
-pdf_dir <- here::here("pdf")
-
-for (i in c(output_dir_html, output_dir_pdf, pdf_dir)) {
-  if (!checkmate::test_directory_exists(i)) dir.create(i) |> invisible()
-}
-
-# Copy PDF (if exists) to `docs` folder ----------
-
-pdf_file <- list.files(pdf_dir, full.names = TRUE, pattern = ".pdf$")
+pdf_file <- list.files(output_dir_pdf, full.names = TRUE, pattern = ".pdf$")
 
 if (length(pdf_file) == 1) {
   rutils:::copy_file(pdf_file, file.path(output_dir_html, "index.pdf"))
@@ -56,13 +35,13 @@ writeLines(
   con = robots_file
 )
 
-# Delete unnecessary files and folders ----------
+# Delete unnecessary files and folders -----
 
 rutils:::clean_quarto_mess(
-  wd = here::here(),
   file = NULL,
   dir = c(".temp", "index_cache", "index_files", "qmd/images"),
-  ext = NULL,
-  keep = NULL,
-  quarto_yaml = NULL
+  ext = c("aux", "bbx", "cbx", "dbx", "fdb_latexmk", "lbx", "loa", "log",
+          "pdf", "scss", "tex", "xdv"),
+  ignore = NULL,
+  wd = here::here()
 )

R/quarto-post-render-html.R

@@ -1,52 +1,33 @@
-# library(checkmate, quietly = TRUE)
 # library(here, quietly = TRUE)
 # library(rutils, quietly = TRUE)
-# library(yaml, quietly = TRUE)
 
-# Set variables ----------
+source(here::here("R", "quarto-post-render-common.R"))
 
-quarto_yml_path <- here::here("_quarto.yml")
-quarto_yml_html_path <- here::here("_quarto-html.yml")
-quarto_yml_pdf_path <- here::here("_quarto-pdf.yml")
+# Copy and rename the PDF file (if exists) to `output_dir_pdf` folder -----
 
-quarto_yml_vars <- yaml::read_yaml(quarto_yml_path)
-quarto_yml_html_vars <- yaml::read_yaml(quarto_yml_html_path)
-quarto_yml_pdf_vars <- yaml::read_yaml(quarto_yml_pdf_path)
+pdf_file <- list.files(output_dir_pdf, full.names = TRUE, pattern = "\\.pdf$")
 
-github_user <- "danielvartan"
-project_name <- here::here() |> basename() # rstudioapi::getActiveProject()
-
-# Set output variables and create output folders if they don't exist ----------
-
-output_dir_html <- here::here(quarto_yml_html_vars$project$`output-dir`)
-output_dir_pdf <- here::here(quarto_yml_pdf_vars$project$`output-dir`)
-pdf_dir <- here::here("pdf")
-
-for (i in c(output_dir_html, output_dir_pdf, pdf_dir)) {
-  if (!checkmate::test_directory_exists(i)) dir.create(i) |> invisible()
+if (length(pdf_file) == 1) {
+  rutils:::copy_file(pdf_file, file.path(output_dir_pdf, "index.pdf"))
+  rutils:::copy_file(pdf_file, file.path(output_dir_html, "index.pdf"))
+  rutils:::delete_file(pdf_file)
 }
 
-# Copy PDF file (if exists) to `docs` folder ----------
+# Copy and rename the TeX file (if exists) to `output_dir_pdf` folder -----
 
-pdf_file <- list.files(output_dir_pdf, full.names = TRUE, pattern = ".pdf$")
-
-if (length(pdf_file) == 1) {
-  rutils:::remove_pdf_cover(pdf_file)
-
-  rutils:::copy_file(pdf_file, file.path(pdf_dir, "index.pdf"))
-  rutils:::copy_file(pdf_file, file.path(output_dir_html, "index.pdf"))
+tex_file <- list.files(here::here(), full.names = TRUE, pattern = ".tex$")
 
-  list.files(here::here(), full.names = TRUE, pattern = ".tex$") |>
-    rutils:::copy_file(file.path("pdf", "index.tex"))
+if (length(tex_file) == 1) {
+  rutils:::copy_file(tex_file, file.path(output_dir_pdf, "index.tex"))
 }
 
-# Delete unnecessary files and folders ----------
+# Delete unnecessary files and folders -----
 
 rutils:::clean_quarto_mess(
-  wd = here::here(),
   file = NULL,
   dir = c(".temp", "index_cache", "index_files"),
-  ext = c("aux", "cls", "loa", "log", "pdf", "tex"),
-  keep = NULL,
-  quarto_yaml = NULL
+  ext = c("aux", "bbx", "cbx", "dbx", "fdb_latexmk", "lbx", "loa", "log",
+          "otf", "pdf", "tex", "xdv"),
+  ignore = NULL,
+  wd = here::here()
 )