Chapman and Hall style applied

.gitignore

@@ -8,3 +8,5 @@ docs/*
 !docs/healthyr-book.pdf
 rsconnect
 healthyr-book.rds
+my_saved_plot.png
+render*.rds

01_first_interaction.Rmd

@@ -1,3 +1,4 @@
+\mainmatter
 # (PART) Always plot your data first {-}
 # Your first R plots
 

03_summarising.Rmd

@@ -31,7 +31,7 @@ mydata %>%
 Most of the functions introduced in this session come from the tidyverse family (http://tidyverse.org/), rather than Base R. Including `library(tidyverse)` in your script loads a list of packages: ggplot2, dplyr, tidry, forcats, etc.
 
 
-```{r, out.width = "400px", echo = FALSE}
+```{r, echo = FALSE}
 knitr::include_graphics("images/library_vs_package.png")
 ```
 
@@ -197,7 +197,7 @@ mydata %>%
 ## Wide vs long: `spread()` and `gather()`
 
 
-```{r, out.width = "700px", echo = FALSE}
+```{r, echo = FALSE}
 knitr::include_graphics("images/wide_long.png")
 ```
 

_bookdown.yml

@@ -1,7 +1,12 @@
 book_filename: "healthyr-book"
+clean: [packages.bib, bookdown.bbl]
+delete_merged_file: true
 language:
+  label:
+    fig: "FIGURE "
+    tab: "TABLE "
   ui:
+    edit: "Edit"
     chapter_name: "Chapter "
-delete_merged_file: true
 new_session: yes
 output_dir: "docs"

_output.yml

@@ -1,9 +1,9 @@
 bookdown::gitbook:
-  css: style.css
+  css: css/style.css
   split_by: section
   config:
     toc:
-      collapse: section
+      collapse: none
       before: |
         <li><a href="./">R for healthcare data analysis</a></li>
       after: |
@@ -12,8 +12,19 @@ bookdown::gitbook:
     download: ["pdf", "epub"]
 bookdown::pdf_book:
   includes:
-    in_header: preamble.tex
-  latex_engine: pdflatex
+    in_header: latex/preamble.tex
+    before_body: latex/before_body.tex
+    after_body: latex/after_body.tex
+  keep_tex: true
+  dev: "cairo_pdf"
+  latex_engine: xelatex
   citation_package: natbib
-  keep_tex: yes
-bookdown::epub_book: default
+  template: null
+  pandoc_args: --top-level-division=chapter
+  toc_depth: 3
+  toc_unnumbered: false
+  toc_appendix: true
+  quote_footer: ["\\VA{", "}{}"]
+  highlight_bw: false
+bookdown::epub_book:
+  stylesheet: css/style.css

style.css → css/style.css

@@ -12,7 +12,15 @@ pre {
 pre code {
   white-space: inherit;
 }
-
+p.flushright {
+  text-align: right;
+}
+blockquote > p:last-child {
+  text-align: right;
+}
+blockquote > p:first-child {
+  text-align: inherit;
+}
 .healthyr, .warning, .error {
   padding: 1em 1em 1em 8em;
   margin-bottom: 10px;