Add final adjustments to revealjs presentation

Author: danielvartan

CITATION.cff

@@ -3,39 +3,17 @@
 cff-version: 1.2.0
 message: "To cite this master's thesis in publications use:"
 title: "Ecology of sleep and circadian phenotypes of the Brazilian population"
-abstract: "Chronotypes are temporal phenotypes. Observable traits, like weight
-  and eye color. Our current understanding of these traits is that they are
-  linked to our environment and are the result of evolution pressures for
-  creating an inner temporal organization. A way that organisms have found to
-  anticipate events. Having such an important function in nature, these internal
-  rhythms need to be closely aligned with environmental changes. The agents
-  that shift these oscillations towards the environment are called zeitgebers
-  and the shift phenomenon is called entrainment. The main zeitgeber for
-  humans is light exposure, particularly the light of the sun. Considering
-  the major role of light on entrainment, several studies hypothesized that
-  the latitude shift of the sun could influence or even define the chronotypes
-  of different populations. For example, populations that live close to the
-  equator would be, on average, more entrained to the light-dark cycle and
-  have morning-leaning characteristics. Here we test this hypothesis using
-  a biological measure, the chronotype state, provided by the Munich ChronoType
-  Questionnaire. We tested the latitude hypothesis on a sample with 73,825
-  subjects living in different latitudes in Brazil. Our results show that,
-  even with a wide, big, and aligned sample, the latitude is associated only
-  with negligible effect sizes. The entrainment phenomenon appears to be much
-  more complex than previously imagined, opening new questions and
-  contradictions that need to be further investigated."
 keywords:
-  - masters-thesis
-  - chronobiology
-  - chronotype
-  - circadian phenotypes
-  - sleep
-  - sleep-wake cycle
-  - complex-systems
-  - entrainment
-  - latitude
-  - ecology
-  - mctq
+  - Chronobiology
+  - Biological rhythms
+  - Chronotype
+  - Circadian phenotype
+  - Sleep
+  - Complex systems
+  - Entrainment
+  - Latitude
+  - Ecology
+  - MCTQ
 authors:
 - family-names: Vartanian
   given-names: Daniel
@@ -63,5 +41,8 @@ preferred-citation:
     email: danvartan@gmail.com
     orcid: https://orcid.org/0000-0001-7782-759X
   year: "2023"
+  address: São Paulo
+  school: University of São Paulo
+  langid: en-us
   url: https://danielvartan.github.io/mastersthesis/
-  notes: "Quarto Book"
+  note: Preliminary version

R/plot_ggally.R

@@ -6,6 +6,9 @@ library(ggplot2, quietly = TRUE)
 # library(tidyr, quietly = TRUE)
 # library(viridis, quietly = TRUE)
 
+source(here::here("R/utils.R"))
+
+# ggplot2::aes(colour = sex)
 plot_ggally <- function(data,
                         cols,
                         mapping = NULL,
@@ -55,9 +58,6 @@ plot_ggally <- function(data,
         mapping = mapping,
         axisLabels = axis_labels
       ) +
-      ggplot2::theme(
-        text = ggplot2::element_text(size = text_size)
-      ) +
       viridis::scale_color_viridis(
         begin = 0.25,
         end = 0.75,

R/quarto-pre-render-revealjs.R

@@ -9,6 +9,22 @@ source(here::here("R", "quarto-pre-render-begin.R"))
 # Update Quarto files -----
 
 swap_list <- list(
+  preface = list(
+    from = here::here("qmd", "slides-preface.qmd"),
+    to = here::here("qmd", "_index-revealjs.qmd"),
+    begin_tag = "%:::% slides-preface begin %:::%",
+    end_tag = "%:::% slides-preface end %:::%",
+    value = NULL,
+    quarto_render = FALSE
+  ),
+  objectives = list(
+    from = here::here("qmd", "slides-objectives.qmd"),
+    to = here::here("qmd", "_index-revealjs.qmd"),
+    begin_tag = "%:::% slides-objectives begin %:::%",
+    end_tag = "%:::% slides-objectives end %:::%",
+    value = NULL,
+    quarto_render = FALSE
+  ),
   introduction = list(
     from = here::here("qmd", "slides-introduction.qmd"),
     to = here::here("qmd", "_index-revealjs.qmd"),
@@ -17,6 +33,22 @@ swap_list <- list(
     value = NULL,
     quarto_render = FALSE
   ),
+  thesis_outline = list(
+    from = here::here("qmd", "slides-thesis-outline.qmd"),
+    to = here::here("qmd", "_index-revealjs.qmd"),
+    begin_tag = "%:::% slides-thesis-outline begin %:::%",
+    end_tag = "%:::% slides-thesis-outline end %:::%",
+    value = NULL,
+    quarto_render = FALSE
+  ),
+  methods = list(
+    from = here::here("qmd", "slides-methods.qmd"),
+    to = here::here("qmd", "_index-revealjs.qmd"),
+    begin_tag = "%:::% slides-methods begin %:::%",
+    end_tag = "%:::% slides-methods end %:::%",
+    value = NULL,
+    quarto_render = FALSE
+  ),
   results = list(
     from = here::here("qmd", "slides-results.qmd"),
     to = here::here("qmd", "_index-revealjs.qmd"),
@@ -25,6 +57,30 @@ swap_list <- list(
     value = NULL,
     quarto_render = FALSE
   ),
+  discussion = list(
+    from = here::here("qmd", "slides-discussion.qmd"),
+    to = here::here("qmd", "_index-revealjs.qmd"),
+    begin_tag = "%:::% slides-discussion begin %:::%",
+    end_tag = "%:::% slides-discussion end %:::%",
+    value = NULL,
+    quarto_render = FALSE
+  ),
+  final_remarks = list(
+    from = here::here("qmd", "slides-final-remarks.qmd"),
+    to = here::here("qmd", "_index-revealjs.qmd"),
+    begin_tag = "%:::% slides-final-remarks begin %:::%",
+    end_tag = "%:::% slides-final-remarks end %:::%",
+    value = NULL,
+    quarto_render = FALSE
+  ),
+  references = list(
+    from = here::here("qmd", "slides-references.qmd"),
+    to = here::here("qmd", "_index-revealjs.qmd"),
+    begin_tag = "%:::% slides-references begin %:::%",
+    end_tag = "%:::% slides-references end %:::%",
+    value = NULL,
+    quarto_render = FALSE
+  ),
   index = list(
     from = here::here("qmd", "_index-revealjs.qmd"),
     to = here::here("index.qmd"),

_quarto-revealjs.yml

@@ -7,15 +7,17 @@ project:
 
 title: "Ecology of sleep and circadian phenotypes of the Brazilian population"
 author: "Daniel Vartanian"
+institute: "University of São Paulo"
+date: today
 
 format:
   revealjs:
-    date: today
+
     lang: en
     csl: english-apa-author-date.csl
     keyboard: true
     controls: true
     controls-layout: bottom-right
     preview-links: auto
-    theme: default
+    theme: [default, scss/slides.scss]
     chalkboard: true

_variables.yml

@@ -22,6 +22,6 @@ version-note: Preliminary version
 url: https://danielvartan.github.io/mastersthesis/
 language: en-us
 title: Ecology of sleep and circadian phenotypes of the Brazilian population
-date: '2023-11-15'
+date: '2023-11-16'
 year: '2023'
 format: revealjs

docs/index.html

@@ -21,7 +21,7 @@
 </head>
 <body style="background-color:#FFFFFF;">
 
-<div class="container p-5" style="width: 500px;">
+<div class="container p-5" style="width: 50%;">
 <div class="d-grid gap-3">
 	<h2>Ecology of sleep and circadian phenotypes of the Brazilian population</h2>