Chapter 14, 15, and appendix

ch14.Rmd

@@ -415,11 +415,11 @@ As of this writing, the patchwork package is not available on CRAN, so you need
 ```
 
 Once you have installed patchwork, you can start stiching plots together (Figure \@ref(fig:FIG-OUTPUT-PATCHWORK)).
-```{r FIG-OUTPUT-PATCHWORK, fig.show="hold", fig.cap="Combining two plots together using `patchwork()`", fig.height=4, fig.width=7}
+```{r FIG-OUTPUT-PATCHWORK, fig.show="hold", fig.cap="Combining two plots together using `patchwork()`", fig.height=3.5, fig.width=7}
 library(patchwork)
 
 plot1 <- ggplot(PlantGrowth, aes(x = weight)) +
-  geom_histogram(bins = 20)
+  geom_histogram(bins = 12)
 
 plot2 <- ggplot(PlantGrowth, aes(x = group, y = weight, group = group)) +
   geom_boxplot()
@@ -431,9 +431,9 @@ plot1 + plot2
 
 Patchwork also allows you to determine how you want to lay out the ggplots in relation to each other, by adding a `plot_layout()` call. You can use this call to determine the number of columns you want the pplots to be arranged in (Figure \@ref(fig:FIG-OUTPUT-PATCHWORK-COLS)), and the size of the plots (Figure \@ref(fig:FIG-OUTPUT-PATCHWORK-HEIGHT)):
 
-```{r FIG-OUTPUT-PATCHWORK-COLS, fig.show="hold", fig.cap="Using `plot_layout()` to specify that the plots should be arranged in 2 columns", fig.height=7, fig.width=7}
+```{r FIG-OUTPUT-PATCHWORK-COLS, fig.show="hold", fig.cap="Using `plot_layout()` to specify that the plots should be arranged in 2 columns", fig.height=7, fig.width=8}
 plot3 <- ggplot(PlantGrowth, aes(x = weight, fill = group)) +
-  geom_histogram(bins = 20, position = "dodge")
+  geom_density(alpha = 0.25)
 
 plot1 + plot2 + plot3 +
   plot_layout(ncol = 2)

ch15.Rmd

@@ -11,17 +11,12 @@ editor_options:
 # persist across cached builds.
 
 source("utils.R", local = TRUE)
-knitr::opts_chunk$set(fig.width=3.5, fig.height=3.5)
-
-
-# Need to load MASS before dplyr because of conflict with select()
-suppressPackageStartupMessages({
-    library(MASS)
-    library(dplyr)
-})
-
-# Print less for the examples in this chapter
-options(knit_print_df_rows = 4)
+knitr::opts_chunk$set(
+  fig.width = 3.5,
+  fig.height = 3.5,
+  # Print less for the examples in this chapter
+  print_df_rows = c(2, 2)
+)
 ```
 
 Getting Your Data into Shape {#CHAPTER-DATAPREP}
@@ -293,6 +288,7 @@ Renaming a column using base R is a bit more verbose. It uses the `names()` func
 ToothGrowth2 <- ToothGrowth
 
 names(ToothGrowth2)  # Print the names of the columns
+
 # Rename "len" to "length"
 names(ToothGrowth2)[names(ToothGrowth2) == "len"] <- "length"
 
@@ -453,7 +449,7 @@ factor(sizes, levels = c("small", "medium", "large"))
 
 The order can also be specified with `levels` when the factor is first created:
 
-```{r echo=FALSE}
+```{r eval=FALSE}
 factor(c("small", "large", "large", "small", "medium"),
        levels = c("small", "medium", "large"))
 ```
@@ -571,8 +567,10 @@ mappings
 
 # Create a list of the arguments to pass to fct_recode
 args <- c(list(sizes), mappings)
+
 # Look at the structure of the list
 str(args)
+
 # Use do.call to call fct_recode with the arguments
 do.call(fct_recode, args)
 ```
@@ -1198,7 +1196,7 @@ ggplot(c2b, aes(x = Date, fill = Cult, y = Weight)) +
   geom_col(position = "dodge")
 ```
 
-```{r, FIG-DATAPREP-SUMMARIZE-MISSING-COMBO, ref.label=c("FIG-DATAPREP-SUMMARIZE-MISSING-COMBO-1", "FIG-DATAPREP-SUMMARIZE-MISSING-COMBO-2"), fig.show="hold", fig.cap="Bar graph with a missing combination (left); With missing combination filled (right)", fig.width=4, fig.height=3}
+```{r, FIG-DATAPREP-SUMMARIZE-MISSING-COMBO, ref.label=c("FIG-DATAPREP-SUMMARIZE-MISSING-COMBO-1", "FIG-DATAPREP-SUMMARIZE-MISSING-COMBO-2"), fig.show="hold", fig.cap="Bar graph with a missing combination (left); With missing combination filled (right)", fig.width=4, fig.height=3, warning=FALSE}
 ```
 
 When we used `complete()`, it filled in the missing combinations with `NA`. It's possible to fill with a different value, with the `fill` parameter. See `?complete` for more information.

ggplot-appendix.Rmd

@@ -11,7 +11,6 @@ editor_options:
 # persist across cached builds.
 
 source("utils.R", local = TRUE)
-knitr::opts_chunk$set(fig.width=4, fig.height=3.5)
 ```
 
 (APPENDIX) Appendix {-}

utils.R

@@ -1,21 +1,27 @@
 # options(warn = -1)
 
-library(ggplot2)
-library(dplyr)
+suppressPackageStartupMessages({
+  # Need to load MASS before dplyr because of conflict with select()
+  library(MASS)
+  library(ggplot2)
+  library(dplyr)
+})
+
 
 options(width = 95)
 
 knitr::opts_chunk$set(
-    collapse = TRUE,
-    comment = "#>",
-    cache = TRUE,
-    fig.show = "hold",
-    # out.width = NULL,
-    fig.align = "center",
-    fig.width = 5,
-    fig.height = 4,
-    out.width = NULL,
-    print_df_rows = c(3, 3)
+  collapse = TRUE,
+  comment = "#>",
+  cache = TRUE,
+  fig.show = "hold",
+  # out.width = NULL,
+  fig.align = "center",
+  fig.width = 5,
+  fig.height = 4,
+  out.width = NULL,
+  print_df_rows = c(3, 3),
+  print_tbl_rows = 6
 )
 
 # Seems to be necessary for captions for multiple images in a single Figure.
@@ -72,7 +78,7 @@ knit_print_data.frame <- function(x, ..., rows = knitr::opts_current$get("print_
   # Need to print the head and tail of data frame in one go, so that
   # alignment is correct.
   output <- capture.output(
-    print(x[rownums, ], ...)
+    print(x[rownums, , drop = FALSE], ...)
   )
 
   if (nrow(x) > sum(rows)) {
@@ -131,6 +137,10 @@ knit_print_table <- function(x, ...) {
   invisible()
 }
 
+knit_print_tbl <-   function(x, ..., maxrows = knitr::opts_current$get("print_tbl_rows")) {
+  print(x, ..., n = maxrows)
+}
+
 # Need this explicit registration step because of some change in R 3.5
 register_s3_method("knitr", "knit_print", "data.frame", knit_print_data.frame)
 register_s3_method("knitr", "knit_print", "matrix",     knit_print_data.frame)
@@ -141,6 +151,9 @@ register_s3_method("knitr", "knit_print", "ts",         knit_print_ts)
 
 register_s3_method("knitr", "knit_print", "table",      knit_print_table)
 
+register_s3_method("knitr", "knit_print", "grouped_df", knit_print_tbl)
+register_s3_method("knitr", "knit_print", "tbl_df", knit_print_tbl)
+register_s3_method("knitr", "knit_print", "tbl", knit_print_tbl)
 
 
 register_s3_method("knitr", "knit_print", "sf",
@@ -149,14 +162,3 @@ register_s3_method("knitr", "knit_print", "sf",
   }
 )
 
-register_s3_method("knitr", "knit_print", "tbl_df",
-  function(x, ..., maxrows = 8) {
-    tibble:::print.tbl_df(x, ..., n = maxrows)
-  }
-)
-
-register_s3_method("knitr", "knit_print", "tbl",
-  function(x, ..., maxrows = 8) {
-    tibble:::print.tbl(x, ..., n = maxrows)
-  }
-)