updated to latest version of bookdown and pandoc.

Author: clauswilke

_bookdown.yml

@@ -1,8 +1,7 @@
 new_session: yes
 output_dir: "_book"
-delete_merged_file: false
+delete_merged_file: true
 
-#rmd_files_draft: [
 rmd_files: [
   "index.Rmd",
 
@@ -20,40 +19,6 @@ rmd_files: [
   "overlapping_points.Rmd", # completed
   "avoid_line_drawings.Rmd", # completed
 
-  # Part II
-  "directory_of_visualizations.Rmd",
-  ##"visualizing_amounts.Rmd",
-  "visualizing_proportions.Rmd", # completed
-  "visualizing_distributions_I.Rmd", # completed
-  "visualizing_distributions_II.Rmd", # completed
-  "boxplots_violins.Rmd",
-
-  # Part III
-  "image_file_formats.Rmd", # completed
-
-  "notes.Rmd",
-
-  "references.Rmd"
-]
-
-rmd_files_final: [
-#rmd_files: [
-  "index.Rmd",
-
-  "introduction.Rmd",
-
-  # Part I
-  #"aesthetic_mapping.Rmd",
-  #"color_basics.Rmd",
-  "pitfalls_of_color_use.Rmd", # completed
-  #"redundant_coding.Rmd",
-  "small_axis_labels.Rmd", # completed
-  ##"aspect_ratio.Rmd",
-  "background_grids.Rmd", # completed
-  ##"proportional_ink.Rmd",
-  "overlapping_points.Rmd", # completed
-  "avoid_line_drawings.Rmd", # completed
-
   # Part II
   "directory_of_visualizations.Rmd",
   ##"visualizing_amounts.Rmd",
@@ -65,7 +30,7 @@ rmd_files_final: [
   # Part III
   "image_file_formats.Rmd", # completed
 
-  #"notes.Rmd",
+  "notes.Rmd",
 
   "references.Rmd"
 ]

_bookdown_final.yml

@@ -0,0 +1,36 @@
+new_session: no
+output_dir: "_book_final"
+delete_merged_file: true
+
+rmd_files: [
+  "index.Rmd",
+
+  "introduction.Rmd",
+
+  # Part I
+  #"aesthetic_mapping.Rmd",
+  "color_basics.Rmd",
+  "pitfalls_of_color_use.Rmd", # completed
+  #"redundant_coding.Rmd",
+  "small_axis_labels.Rmd", # completed
+  ##"aspect_ratio.Rmd",
+  "background_grids.Rmd", # completed
+  ##"proportional_ink.Rmd",
+  "overlapping_points.Rmd", # completed
+  "avoid_line_drawings.Rmd", # completed
+
+  # Part II
+  "directory_of_visualizations.Rmd",
+  ##"visualizing_amounts.Rmd",
+  "visualizing_proportions.Rmd", # completed
+  "visualizing_distributions_I.Rmd", # completed
+  "visualizing_distributions_II.Rmd", # completed
+  "boxplots_violins.Rmd", # completed
+
+  # Part III
+  "image_file_formats.Rmd", # completed
+
+  #"notes.Rmd",
+
+  "references.Rmd"
+]

_build_final.sh

@@ -0,0 +1,4 @@
+#!/bin/sh
+
+rm -rf ./book_final/
+Rscript -e "bookdown::render_book(input = 'index.Rmd', output_format = 'bookdown::gitbook', config_file = '_bookdown_final.yml')"

_deploy.sh

@@ -2,5 +2,5 @@
 
 rm -rf ./docs/
 mkdir ./docs
-cp -r ./_book/* ./docs/
+cp -r ./_book_final/* ./docs/
 git add ./docs/

aesthetic_mapping.Rmd

@@ -3,6 +3,4 @@
 source("_common.R")
 ```
 
-# (PART\*) Part I: General principles of figure design {-}
-
 # Visualizing data: mapping data onto aesthetics

background_grids.Rmd

@@ -103,7 +103,7 @@ Grid lines that run perpendicular to the key variable of interest tend to be the
 ```
 
 
-Background grids along both axis directions can make sense, however, for scatter plots where there is no primary axis of interest. This presentation frequently looks best without axis lines. Figure \@ref(fig:iris-scatter) provides an example.
+Background grids along both axis directions can make sense, however, for scatter plots where there is no primary axis of interest. This presentation frequently looks best without axis lines. Figure \@ref(fig:Aus-athletes-grid) provides an example.
 
 (ref:Aus-athletes-grid) Percent bodyfat versus height in professional male Australian athletes. (Each point represents one athlete.)