From f997393f7b88960631f5166eb3d67f7a8d2e885f Mon Sep 17 00:00:00 2001
From: Jon Harmon <jonthegeek@gmail.com>
Date: Tue, 25 Jun 2024 08:07:01 -0500
Subject: [PATCH] Cohort3 (#49)

* Add new cohort to README.

* Update TOC to match current book.

* Disable broken blocks.

* Use latest R version.
---
 .github/workflows/deploy_bookdown.yml         |  2 --
 .github/workflows/pr_check.yml                |  2 --
 01-introduction.Rmd                           |  2 ++
 03-0.Rmd                                      | 21 -------------
 03-individual_geoms.Rmd                       |  2 ++
 10-Position_scales_and_axes.Rmd               |  2 ++
 11-Colour_scales_and_legends.Rmd              |  3 +-
 12-Other_aesthetics.Rmd                       | 30 ++++---------------
 14-build-plot.Rmd => 13-build-plot.Rmd        |  2 ++
 ...and-guides.Rmd => 14-Scales-and-guides.Rmd |  0
 ...e-systems.Rmd => 15-Coordinate-systems.Rmd |  0
 17-Faceting.Rmd => 16-Faceting.Rmd            |  0
 18-themes.Rmd => 17-themes.Rmd                |  0
 ...ot2.Rmd => 18-Programming-with-ggplot2.Rmd |  3 +-
 ...-internals.Rmd => 19-ggplot2-internals.Rmd |  6 ++--
 ...ng-ggplot2.Rmd => 20-Extending-ggplot2.Rmd |  0
 22-Case-Study.Rmd => 21-Case-Study.Rmd        |  0
 ...rammar.Rmd => 99-Mastering-the-Grammar.Rmd |  4 ++-
 README.md                                     |  1 +
 19 files changed, 24 insertions(+), 56 deletions(-)
 delete mode 100644 03-0.Rmd
 rename 14-build-plot.Rmd => 13-build-plot.Rmd (99%)
 rename 15-Scales-and-guides.Rmd => 14-Scales-and-guides.Rmd (100%)
 rename 16-Coordinate-systems.Rmd => 15-Coordinate-systems.Rmd (100%)
 rename 17-Faceting.Rmd => 16-Faceting.Rmd (100%)
 rename 18-themes.Rmd => 17-themes.Rmd (100%)
 rename 19-Programming-with-ggplot2.Rmd => 18-Programming-with-ggplot2.Rmd (99%)
 rename 20-ggplot2-internals.Rmd => 19-ggplot2-internals.Rmd (99%)
 rename 21-Extending-ggplot2.Rmd => 20-Extending-ggplot2.Rmd (100%)
 rename 22-Case-Study.Rmd => 21-Case-Study.Rmd (100%)
 rename 13-Mastering-the-Grammar.Rmd => 99-Mastering-the-Grammar.Rmd (98%)

diff --git a/.github/workflows/deploy_bookdown.yml b/.github/workflows/deploy_bookdown.yml
index 6e78e59..c38b129 100644
--- a/.github/workflows/deploy_bookdown.yml
+++ b/.github/workflows/deploy_bookdown.yml
@@ -14,8 +14,6 @@ jobs:
     steps:
       - uses: actions/checkout@v2
       - uses: r-lib/actions/setup-r@v2
-        with:
-          r-version: '4.2.0'
       - uses: r-lib/actions/setup-pandoc@v2
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
diff --git a/.github/workflows/pr_check.yml b/.github/workflows/pr_check.yml
index 1fdda39..4b57a53 100644
--- a/.github/workflows/pr_check.yml
+++ b/.github/workflows/pr_check.yml
@@ -13,8 +13,6 @@ jobs:
     steps:
       - uses: actions/checkout@v2
       - uses: r-lib/actions/setup-r@v2
-        with:
-          r-version: '4.2.1'
       - uses: r-lib/actions/setup-pandoc@v2
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
diff --git a/01-introduction.Rmd b/01-introduction.Rmd
index 61643ff..ab88db6 100644
--- a/01-introduction.Rmd
+++ b/01-introduction.Rmd
@@ -1,3 +1,5 @@
+# (PART\*) Getting Started {-}
+
 # Introduction
 
 **Learning objectives:**
diff --git a/03-0.Rmd b/03-0.Rmd
deleted file mode 100644
index 93a4538..0000000
--- a/03-0.Rmd
+++ /dev/null
@@ -1,21 +0,0 @@
-# Layers {-}
-
-*Introduction*
-
-- Based on the *Grammar of Graphics*, GGplot2 encourages you to build plots in a structured manner building upon on your plots with various layers. 
-- The purposes of the layers are: 
-- to display the **data**. 
-- to display a **statistical summary** of the data.
-- to add **metadata** such as context, annotations or references to your plot.
-
-## Layers: Chapters {-}
-
-**The section on layers is broken up into the following chapters:**
-
-- Chapter 3. Individual Geoms
-- Chapter 4. Collective Geoms
-- Chapter 5. Statistical Summaries
-- Chapter 6. Maps
-- Chapter 7. Networks
-- Chapter 8. Annotations
-- Chapter 9. Arranging Plots
diff --git a/03-individual_geoms.Rmd b/03-individual_geoms.Rmd
index b871b70..a6932a2 100644
--- a/03-individual_geoms.Rmd
+++ b/03-individual_geoms.Rmd
@@ -1,3 +1,5 @@
+# (PART\*) Layers {-}
+
 # Individual Geoms
 
 ```{r 03-individualgeoms, include=FALSE}
diff --git a/10-Position_scales_and_axes.Rmd b/10-Position_scales_and_axes.Rmd
index 9cc968d..97f0dab 100644
--- a/10-Position_scales_and_axes.Rmd
+++ b/10-Position_scales_and_axes.Rmd
@@ -1,3 +1,5 @@
+# (PART\*) Scales {-}
+
 # Position scales and axes
 
 **Learning Objectives**
diff --git a/11-Colour_scales_and_legends.Rmd b/11-Colour_scales_and_legends.Rmd
index 8c0d1f5..51e822f 100644
--- a/11-Colour_scales_and_legends.Rmd
+++ b/11-Colour_scales_and_legends.Rmd
@@ -1,10 +1,9 @@
 # Colour Scales and Legends
 
 ```{r 11-library, include=FALSE}
-
 library(ggplot2)
 library(dplyr)
-
+library(scico)
 ```
 
 
diff --git a/12-Other_aesthetics.Rmd b/12-Other_aesthetics.Rmd
index 3a48e60..cf4fcac 100644
--- a/12-Other_aesthetics.Rmd
+++ b/12-Other_aesthetics.Rmd
@@ -15,12 +15,8 @@ To learn about several other aesthetics that ggplot2 can use to represent data,
 - identity scales
 
 
-
-
 ```{r 12-library 01, include=FALSE}
-
 library(ggplot2)
-
 ```
 
 
@@ -35,7 +31,6 @@ base <- ggplot(mpg, aes(displ, hwy, size = cyl)) +
 
 base
 base + scale_size(range = c(1, 2))
-
 ```
 
 There are several size scales:
@@ -54,7 +49,7 @@ There are several size scales:
 There are situations where area scaling is undesirable, and for such situations *scale_radius()* may be more appropriate. For example,  consider a data set containing astronomical data that includes the radius of different planets:
 
 
-```{r radius size scales 01, echo=FALSE }
+```{r radius size scales 01, echo = FALSE}
 planets <- data.frame(
   name = c("Mercury", "Venus", "Earth", "Mars", "Jupiter", "Saturn", "Uranus", "Neptune"),
   type = c(rep("Inner", 4), rep("Outer", 4)),
@@ -87,25 +82,19 @@ Binned size scales work similarly to binned scales for colour and position aesth
 
 
 ```{r binned size scales 01}
-
 base <- ggplot(mpg, aes(displ, manufacturer, size = hwy)) +
   geom_point(alpha = .2) +
   scale_size_binned()
 
 base
-
 ```
 
 Unlike *guide_legend()*, the guide created for a binned scale by *guide_bins()* does not organize the individual keys into a table. Instead they are arranged in a column (or row) along a single vertical (or horizontal) axis, which by default is displayed with its own axis. The important arguments to guide_bins() are listed below:
 
 - **axis** indicates whether the axis should be drawn (default is TRUE)
 
-
-
 ```{r binned size scales 02}
-
 base + guides(size = guide_bins(axis = FALSE))
-
 ```
 
 - **direction** is a character string specifying the direction of the guide, either "vertical" (the default) or "horizontal"
@@ -149,13 +138,11 @@ The default *scale_shape()* function contains a single argument: **set solid = T
 
 
 ```{r shape 01}
-
 base <- ggplot(mpg, aes(displ, hwy, shape = factor(cyl))) + 
   geom_point()
 
 base
 base + scale_shape(solid = FALSE)
-
 ```
 
 
@@ -176,10 +163,8 @@ It is possible to map a variable onto the linetype aesthetic, which works best f
 
 
 ```{r line type 01}
-
 ggplot(economics_long, aes(date, value01, linetype = variable)) +
   geom_line()
-
 ```
 
 With five categories the above plot is quite difficult to read. 
@@ -187,7 +172,6 @@ With five categories the above plot is quite difficult to read.
 The default “palette” for linetype is supplied by the *scales::linetype_pal()* function, and includes the 13 linetypes shown below:
 
 
-
 ```{r line types 02}
 df <- data.frame(value = letters[1:13])
 base <- ggplot(df, aes(linetype = value)) +
@@ -211,7 +195,8 @@ This allows you to specify your own line types using *scale_linetype_manual()*,
 
 Note that the last four lines are blank, because the *linetypes()* function defined above returns NA when the number of categories exceeds 9. 
 
-```{r line types 03}
+```{r line types 03, eval = FALSE}
+# TODO: Eval turned off due to error, you should fix this!
 linetypes <- function(n) {
   types <- c("55",  "75", "95", "1115", "111115", "11111115",
              "5158", "9198", "c1c8")
@@ -227,7 +212,8 @@ The *scale_linetype()* function contains a na.value argument used to specify wha
 
 
 
-```{r line types 04}
+```{r line types 04, eval = FALSE}
+# TODO: Eval turned off due to error, you should fix this!
 base + scale_linetype(palette = linetypes, na.value = "dotted")
 ```
 
@@ -262,23 +248,17 @@ ggplot(huron, aes(year)) +
 ggplot(huron, aes(year)) +
   geom_line(aes(y = level + 5, colour = "above")) +
   geom_line(aes(y = level - 5, colour = "below"))
-
-
 ```
 
 - And then tell the scale how to map labels to colours:
 
-
-
 ```{r manual scales 03}
-
 ggplot(huron, aes(year)) +
   geom_line(aes(y = level + 5, colour = "above")) +
   geom_line(aes(y = level - 5, colour = "below")) +
   scale_colour_manual("Direction",
     values = c("above" = "red", "below" = "blue")
   )
-
 ```
 
 
diff --git a/14-build-plot.Rmd b/13-build-plot.Rmd
similarity index 99%
rename from 14-build-plot.Rmd
rename to 13-build-plot.Rmd
index 3d92a39..5b94764 100644
--- a/14-build-plot.Rmd
+++ b/13-build-plot.Rmd
@@ -1,3 +1,5 @@
+# (PART\*) The Grammar {-}
+
 # Build a plot layer by layer
 
 **Learning objectives:**
diff --git a/15-Scales-and-guides.Rmd b/14-Scales-and-guides.Rmd
similarity index 100%
rename from 15-Scales-and-guides.Rmd
rename to 14-Scales-and-guides.Rmd
diff --git a/16-Coordinate-systems.Rmd b/15-Coordinate-systems.Rmd
similarity index 100%
rename from 16-Coordinate-systems.Rmd
rename to 15-Coordinate-systems.Rmd
diff --git a/17-Faceting.Rmd b/16-Faceting.Rmd
similarity index 100%
rename from 17-Faceting.Rmd
rename to 16-Faceting.Rmd
diff --git a/18-themes.Rmd b/17-themes.Rmd
similarity index 100%
rename from 18-themes.Rmd
rename to 17-themes.Rmd
diff --git a/19-Programming-with-ggplot2.Rmd b/18-Programming-with-ggplot2.Rmd
similarity index 99%
rename from 19-Programming-with-ggplot2.Rmd
rename to 18-Programming-with-ggplot2.Rmd
index 547605a..d1c6559 100644
--- a/19-Programming-with-ggplot2.Rmd
+++ b/18-Programming-with-ggplot2.Rmd
@@ -1,5 +1,6 @@
-# Programming with ggplot2
+# (PART\*) Advanced Topics {-}
 
+# Programming with ggplot2
 
 **Learning objectives:**
 
diff --git a/20-ggplot2-internals.Rmd b/19-ggplot2-internals.Rmd
similarity index 99%
rename from 20-ggplot2-internals.Rmd
rename to 19-ggplot2-internals.Rmd
index 9baf796..0a1c8c3 100644
--- a/20-ggplot2-internals.Rmd
+++ b/19-ggplot2-internals.Rmd
@@ -662,14 +662,16 @@ p +
 
 This is the output of the `guide_train()` method defined for `guide_legend()`. The most important piece of it is `key`, which is the data associated with the legend.
 
-```{r 20-57}
+```{r 20-57, eval = FALSE}
+# TODO: The unexported function no longer exists, so we had to turn off eval.
 names( ggtrace_inspect_return(p, ggplot2:::guide_train.legend) )
 ggtrace_inspect_return(p, ggplot2:::guide_train.legend)$key
 ```
 
 The output of `guide_train()` is passed to `guide_gengrob()`. This is the output of the `guide_gebgrob()` method defined for `guide_legend()`:
 
-```{r 20-58}
+```{r 20-58, eval = FALSE}
+# TODO: The unexported function no longer exists, so we had to turn off eval.
 legend_gengrob <- ggtrace_inspect_return(p, ggplot2:::guide_gengrob.legend)
 grid.newpage()
 grid.draw(legend_gengrob)
diff --git a/21-Extending-ggplot2.Rmd b/20-Extending-ggplot2.Rmd
similarity index 100%
rename from 21-Extending-ggplot2.Rmd
rename to 20-Extending-ggplot2.Rmd
diff --git a/22-Case-Study.Rmd b/21-Case-Study.Rmd
similarity index 100%
rename from 22-Case-Study.Rmd
rename to 21-Case-Study.Rmd
diff --git a/13-Mastering-the-Grammar.Rmd b/99-Mastering-the-Grammar.Rmd
similarity index 98%
rename from 13-Mastering-the-Grammar.Rmd
rename to 99-Mastering-the-Grammar.Rmd
index 08046b1..b0f283c 100644
--- a/13-Mastering-the-Grammar.Rmd
+++ b/99-Mastering-the-Grammar.Rmd
@@ -1,6 +1,8 @@
 # Mastering the Grammar
 
-```{r setup, include=FALSE}
+***This was previously covered as chapter 13, but it does not exist as a separate chapter in the current version of the book.***
+
+```{r 99-setup, include=FALSE}
 #library(knitr)
 #knitr::opts_chunk$set(cache=TRUE, cache.lazy= FALSE, warning = FALSE, 
                       
diff --git a/README.md b/README.md
index a62e7a3..0125a83 100644
--- a/README.md
+++ b/README.md
@@ -12,6 +12,7 @@ If you would like to present, please see the sign-up sheet for your cohort (link
 
 - Cohort 1 (started 2021-08-30, ended 2022-07-18): [meeting videos](https://www.youtube.com/playlist?list=PL3x6DOfs2NGhUxGvu46tXQtBl0qyTcDet)
 - Cohort 2 (started 2023-04-06, ended 2024-01-19): [meeting videos](https://youtube.com/playlist?list=PL3x6DOfs2NGhw3rkmaGipc21j0a7sCPNy)
+- [Cohort 3](https://docs.google.com/spreadsheets/d/1vMD-FxWj9YakVAngHg67ctRVc0izzCu81L_UoaOSWqM/edit?usp=sharing) (starts 2024-07-10): [meeting videos](https://www.youtube.com/playlist?list=PL3x6DOfs2NGi0FPmGOBAeU1LRNp4lRC9-)
 
 ## How to Present