From beb48005b34eb45f8bb7f5032ea85c0d8d38f732 Mon Sep 17 00:00:00 2001
From: GitHub Actions <actions@github.com>
Date: Tue, 7 May 2024 00:22:04 +0000
Subject: [PATCH] differences for PR #889

---
 01-rstudio-intro.md             |   52 +-
 02-project-intro.md             |    8 +-
 03-seeking-help.md              |   14 +-
 04-data-structures-part1.md     |  156 ++---
 05-data-structures-part2.md     |   48 +-
 06-data-subsetting.md           |  130 ++--
 07-control-flow.md              |   22 +-
 08-plot-ggplot2.md              |   10 +-
 09-vectorization.md             |   48 +-
 10-functions.md                 |   20 +-
 11-writing-data.md              |    4 +-
 12-dplyr.md                     |   36 +-
 13-tidyr.md                     |   38 +-
 config.yaml                     |   95 ---
 fig/06-rmd-generate-figures.sh  |    0
 fig/12-plyr-generate-figures.sh |    0
 md5sum.txt                      |   50 +-
 renv.lock                       | 1021 -------------------------------
 18 files changed, 318 insertions(+), 1434 deletions(-)
 delete mode 100644 config.yaml
 mode change 100755 => 100644 fig/06-rmd-generate-figures.sh
 mode change 100755 => 100644 fig/12-plyr-generate-figures.sh
 delete mode 100644 renv.lock

diff --git a/01-rstudio-intro.md b/01-rstudio-intro.md
index 0124a77d6..b6ca3b0a9 100644
--- a/01-rstudio-intro.md
+++ b/01-rstudio-intro.md
@@ -150,7 +150,7 @@ The simplest thing you could do with R is to do arithmetic:
 1 + 100
 ```
 
-```{.output}
+```output
 [1] 101
 ```
 
@@ -205,7 +205,7 @@ From highest to lowest precedence:
 3 + 5 * 2
 ```
 
-```{.output}
+```output
 [1] 13
 ```
 
@@ -218,7 +218,7 @@ intend.
 (3 + 5) * 2
 ```
 
-```{.output}
+```output
 [1] 16
 ```
 
@@ -243,7 +243,7 @@ Really small or large numbers get a scientific notation:
 2/10000
 ```
 
-```{.output}
+```output
 [1] 2e-04
 ```
 
@@ -257,7 +257,7 @@ You can write numbers in scientific notation too:
 5e3  # Note the lack of minus here
 ```
 
-```{.output}
+```output
 [1] 5000
 ```
 
@@ -279,7 +279,7 @@ doesn't require an argument, whereas for the next set of mathematical functions
 sin(1)  # trigonometry functions
 ```
 
-```{.output}
+```output
 [1] 0.841471
 ```
 
@@ -288,7 +288,7 @@ sin(1)  # trigonometry functions
 log(1)  # natural logarithm
 ```
 
-```{.output}
+```output
 [1] 0
 ```
 
@@ -297,7 +297,7 @@ log(1)  # natural logarithm
 log10(10) # base-10 logarithm
 ```
 
-```{.output}
+```output
 [1] 1
 ```
 
@@ -306,7 +306,7 @@ log10(10) # base-10 logarithm
 exp(0.5) # e^(1/2)
 ```
 
-```{.output}
+```output
 [1] 1.648721
 ```
 
@@ -336,7 +336,7 @@ We can also do comparisons in R:
 1 == 1  # equality (note two equals signs, read as "is equal to")
 ```
 
-```{.output}
+```output
 [1] TRUE
 ```
 
@@ -345,7 +345,7 @@ We can also do comparisons in R:
 1 != 2  # inequality (read as "is not equal to")
 ```
 
-```{.output}
+```output
 [1] TRUE
 ```
 
@@ -354,7 +354,7 @@ We can also do comparisons in R:
 1 < 2  # less than
 ```
 
-```{.output}
+```output
 [1] TRUE
 ```
 
@@ -363,7 +363,7 @@ We can also do comparisons in R:
 1 <= 1  # less than or equal to
 ```
 
-```{.output}
+```output
 [1] TRUE
 ```
 
@@ -372,7 +372,7 @@ We can also do comparisons in R:
 1 > 0  # greater than
 ```
 
-```{.output}
+```output
 [1] TRUE
 ```
 
@@ -381,7 +381,7 @@ We can also do comparisons in R:
 1 >= -9 # greater than or equal to
 ```
 
-```{.output}
+```output
 [1] TRUE
 ```
 
@@ -424,7 +424,7 @@ in something called a **variable**. `x` now contains the **value** `0.025`:
 x
 ```
 
-```{.output}
+```output
 [1] 0.025
 ```
 
@@ -439,7 +439,7 @@ have appeared. Our variable `x` can be used in place of a number in any calculat
 log(x)
 ```
 
-```{.output}
+```output
 [1] -3.688879
 ```
 
@@ -550,7 +550,7 @@ same data type. For example:
 1:5
 ```
 
-```{.output}
+```output
 [1] 1 2 3 4 5
 ```
 
@@ -558,7 +558,7 @@ same data type. For example:
 2^(1:5)
 ```
 
-```{.output}
+```output
 [1]  2  4  8 16 32
 ```
 
@@ -567,7 +567,7 @@ x <- 1:5
 2^x
 ```
 
-```{.output}
+```output
 [1]  2  4  8 16 32
 ```
 
@@ -587,7 +587,7 @@ ls()
 ```
 
 
-```{.output}
+```output
 [1] "x" "y"
 ```
 
@@ -611,7 +611,7 @@ If we type `ls` by itself, R prints a bunch of code instead of a listing of obje
 ls
 ```
 
-```{.output}
+```output
 function (name, pos = -1L, envir = as.environment(pos), all.names = FALSE, 
     pattern, sorted = TRUE) 
 {
@@ -643,7 +643,7 @@ function (name, pos = -1L, envir = as.environment(pos), all.names = FALSE,
     }
     else all.names
 }
-<bytecode: 0x55beb9d90918>
+<bytecode: 0x55651f0c89e8>
 <environment: namespace:base>
 ```
 
@@ -658,7 +658,7 @@ created earlier contains 1, 2, 3, 4, 5:
 x
 ```
 
-```{.output}
+```output
 [1] 1 2 3 4 5
 ```
 
@@ -694,7 +694,7 @@ If instead we use `<-`, there will be unintended side effects, or you may get an
 rm(list <- ls())
 ```
 
-```{.error}
+```error
 Error in rm(list <- ls()): ... must contain names or character strings
 ```
 
@@ -804,7 +804,7 @@ One way of answering this question in R is to use the `>` to set up the followin
 mass > age
 ```
 
-```{.output}
+```output
 [1] TRUE
 ```
 
diff --git a/02-project-intro.md b/02-project-intro.md
index 56fed2799..5a8c5d428 100644
--- a/02-project-intro.md
+++ b/02-project-intro.md
@@ -189,8 +189,8 @@ By running these commands in the shell:
 ls -lh data/gapminder_data.csv
 ```
 
-```{.output}
--rw-r--r-- 1 runner docker 80K Apr 12 01:44 data/gapminder_data.csv
+```output
+-rw-r--r-- 1 runner docker 80K May  7 00:20 data/gapminder_data.csv
 ```
 
 The file size is 80K.
@@ -200,7 +200,7 @@ The file size is 80K.
 wc -l data/gapminder_data.csv
 ```
 
-```{.output}
+```output
 1705 data/gapminder_data.csv
 ```
 
@@ -211,7 +211,7 @@ There are 1705 lines. The data looks like:
 head data/gapminder_data.csv
 ```
 
-```{.output}
+```output
 country,year,pop,continent,lifeExp,gdpPercap
 Afghanistan,1952,8425333,Asia,28.801,779.4453145
 Afghanistan,1957,9240934,Asia,30.332,820.8530296
diff --git a/03-seeking-help.md b/03-seeking-help.md
index 438790423..828a4c6f5 100644
--- a/03-seeking-help.md
+++ b/03-seeking-help.md
@@ -159,7 +159,7 @@ be copied and pasted by others into their own R session.
 sessionInfo()
 ```
 
-```{.output}
+```output
 R version 4.3.3 (2024-02-29)
 Platform: x86_64-pc-linux-gnu (64-bit)
 Running under: Ubuntu 22.04.4 LTS
@@ -181,7 +181,7 @@ attached base packages:
 [1] stats     graphics  grDevices utils     datasets  methods   base     
 
 loaded via a namespace (and not attached):
-[1] compiler_4.3.3 tools_4.3.3    yaml_2.3.8     knitr_1.45     xfun_0.43     
+[1] compiler_4.3.3 tools_4.3.3    yaml_2.3.8     knitr_1.46     xfun_0.43     
 [6] renv_1.0.7     evaluate_0.23 
 ```
 
@@ -255,7 +255,7 @@ e.g.
 paste(c("a","b"), "c")
 ```
 
-```{.output}
+```output
 [1] "a c" "b c"
 ```
 
@@ -263,7 +263,7 @@ paste(c("a","b"), "c")
 paste(c("a","b"), "c", ",")
 ```
 
-```{.output}
+```output
 [1] "a c ," "b c ,"
 ```
 
@@ -271,7 +271,7 @@ paste(c("a","b"), "c", ",")
 paste(c("a","b"), "c", sep = ",")
 ```
 
-```{.output}
+```output
 [1] "a,c" "b,c"
 ```
 
@@ -279,7 +279,7 @@ paste(c("a","b"), "c", sep = ",")
 paste(c("a","b"), "c", collapse = "|")
 ```
 
-```{.output}
+```output
 [1] "a c|b c"
 ```
 
@@ -287,7 +287,7 @@ paste(c("a","b"), "c", collapse = "|")
 paste(c("a","b"), "c", sep = ",", collapse = "|")
 ```
 
-```{.output}
+```output
 [1] "a,c|b,c"
 ```
 
diff --git a/04-data-structures-part1.md b/04-data-structures-part1.md
index 2dbd076d2..66a838662 100644
--- a/04-data-structures-part1.md
+++ b/04-data-structures-part1.md
@@ -73,7 +73,7 @@ cats <- read.csv(file = "data/feline-data.csv")
 cats
 ```
 
-```{.output}
+```output
     coat weight likes_string
 1 calico    2.1            1
 2  black    5.0            0
@@ -128,7 +128,7 @@ them using the `$` operator:
 cats$weight
 ```
 
-```{.output}
+```output
 [1] 2.1 5.0 3.2
 ```
 
@@ -136,7 +136,7 @@ cats$weight
 cats$coat
 ```
 
-```{.output}
+```output
 [1] "calico" "black"  "tabby" 
 ```
 
@@ -148,7 +148,7 @@ We can do other operations on the columns:
 cats$weight + 2
 ```
 
-```{.output}
+```output
 [1] 4.1 7.0 5.2
 ```
 
@@ -156,7 +156,7 @@ cats$weight + 2
 paste("My cat is", cats$coat)
 ```
 
-```{.output}
+```output
 [1] "My cat is calico" "My cat is black"  "My cat is tabby" 
 ```
 
@@ -167,7 +167,7 @@ But what about
 cats$weight + cats$coat
 ```
 
-```{.error}
+```error
 Error in cats$weight + cats$coat: non-numeric argument to binary operator
 ```
 
@@ -185,7 +185,7 @@ data something is:
 typeof(cats$weight)
 ```
 
-```{.output}
+```output
 [1] "double"
 ```
 
@@ -197,7 +197,7 @@ For historic reasons, `double` is also called `numeric`.
 typeof(3.14)
 ```
 
-```{.output}
+```output
 [1] "double"
 ```
 
@@ -205,7 +205,7 @@ typeof(3.14)
 typeof(1L) # The L suffix forces the number to be an integer, since by default R uses float numbers
 ```
 
-```{.output}
+```output
 [1] "integer"
 ```
 
@@ -213,7 +213,7 @@ typeof(1L) # The L suffix forces the number to be an integer, since by default R
 typeof(1+1i)
 ```
 
-```{.output}
+```output
 [1] "complex"
 ```
 
@@ -221,7 +221,7 @@ typeof(1+1i)
 typeof(TRUE)
 ```
 
-```{.output}
+```output
 [1] "logical"
 ```
 
@@ -229,7 +229,7 @@ typeof(TRUE)
 typeof('banana')
 ```
 
-```{.output}
+```output
 [1] "character"
 ```
 
@@ -263,7 +263,7 @@ cats <- read.csv(file="data/feline-data_v2.csv")
 typeof(cats$weight)
 ```
 
-```{.output}
+```output
 [1] "character"
 ```
 
@@ -275,7 +275,7 @@ we did on them before, we run into trouble:
 cats$weight + 2
 ```
 
-```{.error}
+```error
 Error in cats$weight + 2: non-numeric argument to binary operator
 ```
 
@@ -295,7 +295,7 @@ is written by the `str()` function:
 str(cats)
 ```
 
-```{.output}
+```output
 'data.frame':	4 obs. of  3 variables:
  $ coat        : chr  "calico" "black" "tabby" "tabby"
  $ weight      : chr  "2.1" "5" "3.2" "2.3 or 2.4"
@@ -340,7 +340,7 @@ my_vector <- vector(length = 3)
 my_vector
 ```
 
-```{.output}
+```output
 [1] FALSE FALSE FALSE
 ```
 
@@ -355,7 +355,7 @@ another_vector <- vector(mode='character', length=3)
 another_vector
 ```
 
-```{.output}
+```output
 [1] "" "" ""
 ```
 
@@ -366,7 +366,7 @@ You can check if something is a vector:
 str(another_vector)
 ```
 
-```{.output}
+```output
  chr [1:3] "" "" ""
 ```
 
@@ -381,7 +381,7 @@ empty character strings. If we similarly do
 str(cats$weight)
 ```
 
-```{.output}
+```output
  num [1:3] 2.1 5 3.2
 ```
 
@@ -423,7 +423,7 @@ combine_vector <- c(2,6,3)
 combine_vector
 ```
 
-```{.output}
+```output
 [1] 2 6 3
 ```
 
@@ -446,7 +446,7 @@ coercion_vector <- c('a', TRUE)
 coercion_vector
 ```
 
-```{.output}
+```output
 [1] "a"    "TRUE"
 ```
 
@@ -455,7 +455,7 @@ another_coercion_vector <- c(0, TRUE)
 another_coercion_vector
 ```
 
-```{.output}
+```output
 [1] 0 1
 ```
 
@@ -471,7 +471,7 @@ example, combining `logical` and `character` transforms the result to
 c('a', TRUE)
 ```
 
-```{.output}
+```output
 [1] "a"    "TRUE"
 ```
 
@@ -487,7 +487,7 @@ character_vector_example <- c('0','2','4')
 character_vector_example
 ```
 
-```{.output}
+```output
 [1] "0" "2" "4"
 ```
 
@@ -496,7 +496,7 @@ character_coerced_to_double <- as.double(character_vector_example)
 character_coerced_to_double
 ```
 
-```{.output}
+```output
 [1] 0 2 4
 ```
 
@@ -505,7 +505,7 @@ double_coerced_to_logical <- as.logical(character_coerced_to_double)
 double_coerced_to_logical
 ```
 
-```{.output}
+```output
 [1] FALSE  TRUE  TRUE
 ```
 
@@ -527,7 +527,7 @@ using the `as.logical` function:
 cats$likes_string
 ```
 
-```{.output}
+```output
 [1] 1 0 1
 ```
 
@@ -536,7 +536,7 @@ cats$likes_string <- as.logical(cats$likes_string)
 cats$likes_string
 ```
 
-```{.output}
+```output
 [1]  TRUE FALSE  TRUE
 ```
 
@@ -731,7 +731,7 @@ ab_vector <- c('a', 'b')
 ab_vector
 ```
 
-```{.output}
+```output
 [1] "a" "b"
 ```
 
@@ -740,7 +740,7 @@ combine_example <- c(ab_vector, 'SWC')
 combine_example
 ```
 
-```{.output}
+```output
 [1] "a"   "b"   "SWC"
 ```
 
@@ -752,7 +752,7 @@ mySeries <- 1:10
 mySeries
 ```
 
-```{.output}
+```output
  [1]  1  2  3  4  5  6  7  8  9 10
 ```
 
@@ -760,7 +760,7 @@ mySeries
 seq(10)
 ```
 
-```{.output}
+```output
  [1]  1  2  3  4  5  6  7  8  9 10
 ```
 
@@ -768,7 +768,7 @@ seq(10)
 seq(1,10, by=0.1)
 ```
 
-```{.output}
+```output
  [1]  1.0  1.1  1.2  1.3  1.4  1.5  1.6  1.7  1.8  1.9  2.0  2.1  2.2  2.3  2.4
 [16]  2.5  2.6  2.7  2.8  2.9  3.0  3.1  3.2  3.3  3.4  3.5  3.6  3.7  3.8  3.9
 [31]  4.0  4.1  4.2  4.3  4.4  4.5  4.6  4.7  4.8  4.9  5.0  5.1  5.2  5.3  5.4
@@ -786,7 +786,7 @@ sequence_example <- 20:25
 head(sequence_example, n=2)
 ```
 
-```{.output}
+```output
 [1] 20 21
 ```
 
@@ -794,7 +794,7 @@ head(sequence_example, n=2)
 tail(sequence_example, n=4)
 ```
 
-```{.output}
+```output
 [1] 22 23 24 25
 ```
 
@@ -802,7 +802,7 @@ tail(sequence_example, n=4)
 length(sequence_example)
 ```
 
-```{.output}
+```output
 [1] 6
 ```
 
@@ -810,7 +810,7 @@ length(sequence_example)
 typeof(sequence_example)
 ```
 
-```{.output}
+```output
 [1] "integer"
 ```
 
@@ -822,7 +822,7 @@ first_element <- sequence_example[1]
 first_element
 ```
 
-```{.output}
+```output
 [1] 20
 ```
 
@@ -834,7 +834,7 @@ sequence_example[1] <- 30
 sequence_example
 ```
 
-```{.output}
+```output
 [1] 30 21 22 23 24 25
 ```
 
@@ -872,7 +872,7 @@ list_example <- list(1, "a", TRUE, 1+4i)
 list_example
 ```
 
-```{.output}
+```output
 [[1]]
 [1] 1
 
@@ -894,7 +894,7 @@ elements:
 str(list_example)
 ```
 
-```{.output}
+```output
 List of 4
  $ : num 1
  $ : chr "a"
@@ -915,7 +915,7 @@ To retrieve one of the elements of a list, use the **double bracket**:
 list_example[[2]]
 ```
 
-```{.output}
+```output
 [1] "a"
 ```
 
@@ -928,7 +928,7 @@ another_list <- list(title = "Numbers", numbers = 1:10, data = TRUE )
 another_list
 ```
 
-```{.output}
+```output
 $title
 [1] "Numbers"
 
@@ -947,7 +947,7 @@ We can access single elements by an additional way!
 another_list$title
 ```
 
-```{.output}
+```output
 [1] "Numbers"
 ```
 
@@ -976,7 +976,7 @@ The way to retrieve elements is different, though:
 pizza_price["pizzasubito"]
 ```
 
-```{.output}
+```output
 pizzasubito 
        5.64 
 ```
@@ -988,7 +988,7 @@ The approach used for the list does not work:
 pizza_price$pizzafresh
 ```
 
-```{.error}
+```error
 Error in pizza_price$pizzafresh: $ operator is invalid for atomic vectors
 ```
 
@@ -1005,7 +1005,7 @@ If you are only interested in the names, use the `names()` function:
 names(pizza_price)
 ```
 
-```{.output}
+```output
 [1] "pizzasubito" "pizzafresh"  "callapizza" 
 ```
 
@@ -1017,7 +1017,7 @@ possible for names:
 names(pizza_price)[3]
 ```
 
-```{.output}
+```output
 [1] "callapizza"
 ```
 
@@ -1026,7 +1026,7 @@ names(pizza_price)[3] <- "call-a-pizza"
 pizza_price
 ```
 
-```{.output}
+```output
  pizzasubito   pizzafresh call-a-pizza 
         5.64         6.60         4.50 
 ```
@@ -1106,7 +1106,7 @@ data frame:
 cats
 ```
 
-```{.output}
+```output
     coat weight likes_string
 1 calico    2.1         TRUE
 2  black    5.0        FALSE
@@ -1121,7 +1121,7 @@ if we run:
 typeof(cats)
 ```
 
-```{.output}
+```output
 [1] "list"
 ```
 
@@ -1144,7 +1144,7 @@ like any other list, but as a table?
 class(cats)
 ```
 
-```{.output}
+```output
 [1] "data.frame"
 ```
 
@@ -1166,7 +1166,7 @@ we have seen already, each column of data.frame is a vector.
 cats$coat
 ```
 
-```{.output}
+```output
 [1] "calico" "black"  "tabby" 
 ```
 
@@ -1174,7 +1174,7 @@ cats$coat
 cats[,1]
 ```
 
-```{.output}
+```output
 [1] "calico" "black"  "tabby" 
 ```
 
@@ -1182,7 +1182,7 @@ cats[,1]
 typeof(cats[,1])
 ```
 
-```{.output}
+```output
 [1] "character"
 ```
 
@@ -1190,7 +1190,7 @@ typeof(cats[,1])
 str(cats[,1])
 ```
 
-```{.output}
+```output
  chr [1:3] "calico" "black" "tabby"
 ```
 
@@ -1202,7 +1202,7 @@ thus can be composed of elements of different types.
 cats[1,]
 ```
 
-```{.output}
+```output
     coat weight likes_string
 1 calico    2.1         TRUE
 ```
@@ -1211,7 +1211,7 @@ cats[1,]
 typeof(cats[1,])
 ```
 
-```{.output}
+```output
 [1] "list"
 ```
 
@@ -1219,7 +1219,7 @@ typeof(cats[1,])
 str(cats[1,])
 ```
 
-```{.output}
+```output
 'data.frame':	1 obs. of  3 variables:
  $ coat        : chr "calico"
  $ weight      : num 2.1
@@ -1254,7 +1254,7 @@ Try out these examples and explain what is returned by each one.
 cats[1]
 ```
 
-```{.output}
+```output
     coat
 1 calico
 2  black
@@ -1270,7 +1270,7 @@ first column of the data frame.
 cats[[1]]
 ```
 
-```{.output}
+```output
 [1] "calico" "black"  "tabby" 
 ```
 
@@ -1282,7 +1282,7 @@ it is the contents of the first column, a *vector* of type *character*.
 cats$coat
 ```
 
-```{.output}
+```output
 [1] "calico" "black"  "tabby" 
 ```
 
@@ -1294,7 +1294,7 @@ first column of the data frame, again a *vector* of type *character*.
 cats["coat"]
 ```
 
-```{.output}
+```output
     coat
 1 calico
 2  black
@@ -1309,7 +1309,7 @@ the column name. Like example 1, the returned object is a *list*.
 cats[1, 1]
 ```
 
-```{.output}
+```output
 [1] "calico"
 ```
 
@@ -1322,7 +1322,7 @@ is a *vector* of type *character*.
 cats[, 1]
 ```
 
-```{.output}
+```output
 [1] "calico" "black"  "tabby" 
 ```
 
@@ -1335,7 +1335,7 @@ value as all the elements in this *column* and returns them as a *vector*.
 cats[1, ]
 ```
 
-```{.output}
+```output
     coat weight likes_string
 1 calico    2.1         TRUE
 ```
@@ -1361,7 +1361,7 @@ Data frames have column names, which can be accessed with the `names()` function
 names(cats)
 ```
 
-```{.output}
+```output
 [1] "coat"         "weight"       "likes_string"
 ```
 
@@ -1373,7 +1373,7 @@ names(cats)[2] <- "weight_kg"
 cats
 ```
 
-```{.output}
+```output
     coat weight_kg likes_string
 1 calico       2.1         TRUE
 2  black       5.0        FALSE
@@ -1394,7 +1394,7 @@ matrix_example <- matrix(0, ncol=6, nrow=3)
 matrix_example
 ```
 
-```{.output}
+```output
      [,1] [,2] [,3] [,4] [,5] [,6]
 [1,]    0    0    0    0    0    0
 [2,]    0    0    0    0    0    0
@@ -1408,7 +1408,7 @@ What makes it special is the `dim()` attribute:
 dim(matrix_example)
 ```
 
-```{.output}
+```output
 [1] 3 6
 ```
 
@@ -1419,7 +1419,7 @@ And similar to other data structures, we can ask things about our matrix:
 typeof(matrix_example)
 ```
 
-```{.output}
+```output
 [1] "double"
 ```
 
@@ -1427,7 +1427,7 @@ typeof(matrix_example)
 class(matrix_example)
 ```
 
-```{.output}
+```output
 [1] "matrix" "array" 
 ```
 
@@ -1435,7 +1435,7 @@ class(matrix_example)
 str(matrix_example)
 ```
 
-```{.output}
+```output
  num [1:3, 1:6] 0 0 0 0 0 0 0 0 0 0 ...
 ```
 
@@ -1443,7 +1443,7 @@ str(matrix_example)
 nrow(matrix_example)
 ```
 
-```{.output}
+```output
 [1] 3
 ```
 
@@ -1451,7 +1451,7 @@ nrow(matrix_example)
 ncol(matrix_example)
 ```
 
-```{.output}
+```output
 [1] 6
 ```
 
@@ -1477,7 +1477,7 @@ matrix_example <- matrix(0, ncol=6, nrow=3)
 length(matrix_example)
 ```
 
-```{.output}
+```output
 [1] 18
 ```
 
@@ -1560,7 +1560,7 @@ to remind people of the importance of these basics.
 Consider the R output of the matrix below:
 
 
-```{.output}
+```output
      [,1] [,2]
 [1,]    4    1
 [2,]    9    5
@@ -1583,7 +1583,7 @@ Think about what matrices the other commands will produce.
 Consider the R output of the matrix below:
 
 
-```{.output}
+```output
      [,1] [,2]
 [1,]    4    1
 [2,]    9    5
diff --git a/05-data-structures-part2.md b/05-data-structures-part2.md
index 04d1fc1b9..e56b7392f 100644
--- a/05-data-structures-part2.md
+++ b/05-data-structures-part2.md
@@ -40,7 +40,7 @@ age <- c(2, 3, 5)
 cats
 ```
 
-```{.output}
+```output
     coat weight likes_string
 1 calico    2.1            1
 2  black    5.0            0
@@ -54,7 +54,7 @@ We can then add this as a column via:
 cbind(cats, age)
 ```
 
-```{.output}
+```output
     coat weight likes_string age
 1 calico    2.1            1   2
 2  black    5.0            0   3
@@ -69,7 +69,7 @@ age <- c(2, 3, 5, 12)
 cbind(cats, age)
 ```
 
-```{.error}
+```error
 Error in data.frame(..., check.names = FALSE): arguments imply differing number of rows: 3, 4
 ```
 
@@ -78,7 +78,7 @@ age <- c(2, 3)
 cbind(cats, age)
 ```
 
-```{.error}
+```error
 Error in data.frame(..., check.names = FALSE): arguments imply differing number of rows: 3, 2
 ```
 
@@ -90,7 +90,7 @@ for every row in the table:
 nrow(cats)
 ```
 
-```{.output}
+```output
 [1] 3
 ```
 
@@ -98,7 +98,7 @@ nrow(cats)
 length(age)
 ```
 
-```{.output}
+```output
 [1] 2
 ```
 
@@ -126,7 +126,7 @@ Let's confirm that our new row was added correctly.
 cats
 ```
 
-```{.output}
+```output
            coat weight likes_string age
 1        calico    2.1            1   2
 2         black    5.0            0   3
@@ -144,7 +144,7 @@ We now know how to add rows and columns to our data frame in R. Now let's learn
 cats
 ```
 
-```{.output}
+```output
            coat weight likes_string age
 1        calico    2.1            1   2
 2         black    5.0            0   3
@@ -159,7 +159,7 @@ We can ask for a data frame minus the last row:
 cats[-4, ]
 ```
 
-```{.output}
+```output
     coat weight likes_string age
 1 calico    2.1            1   2
 2  black    5.0            0   3
@@ -181,7 +181,7 @@ We can also remove columns in our data frame. What if we want to remove the colu
 cats[,-4]
 ```
 
-```{.output}
+```output
            coat weight likes_string
 1        calico    2.1            1
 2         black    5.0            0
@@ -199,7 +199,7 @@ drop <- names(cats) %in% c("age")
 cats[,!drop]
 ```
 
-```{.output}
+```output
            coat weight likes_string
 1        calico    2.1            1
 2         black    5.0            0
@@ -221,7 +221,7 @@ cats <- rbind(cats, cats)
 cats
 ```
 
-```{.output}
+```output
            coat weight likes_string age
 1        calico    2.1            1   2
 2         black    5.0            0   3
@@ -321,7 +321,7 @@ out what the data looks like with `str`:
 str(gapminder)
 ```
 
-```{.output}
+```output
 'data.frame':	1704 obs. of  6 variables:
  $ country  : chr  "Afghanistan" "Afghanistan" "Afghanistan" "Afghanistan" ...
  $ year     : int  1952 1957 1962 1967 1972 1977 1982 1987 1992 1997 ...
@@ -338,7 +338,7 @@ An additional method for examining the structure of gapminder is to use the `sum
 summary(gapminder)
 ```
 
-```{.output}
+```output
    country               year           pop             continent        
  Length:1704        Min.   :1952   Min.   :6.001e+04   Length:1704       
  Class :character   1st Qu.:1966   1st Qu.:2.794e+06   Class :character  
@@ -362,7 +362,7 @@ Along with the `str` and `summary` functions, we can examine individual columns
 typeof(gapminder$year)
 ```
 
-```{.output}
+```output
 [1] "integer"
 ```
 
@@ -370,7 +370,7 @@ typeof(gapminder$year)
 typeof(gapminder$country)
 ```
 
-```{.output}
+```output
 [1] "character"
 ```
 
@@ -378,7 +378,7 @@ typeof(gapminder$country)
 str(gapminder$country)
 ```
 
-```{.output}
+```output
  chr [1:1704] "Afghanistan" "Afghanistan" "Afghanistan" "Afghanistan" ...
 ```
 
@@ -391,7 +391,7 @@ variables in gapminder, what do you think the following will produce, and why?
 length(gapminder)
 ```
 
-```{.output}
+```output
 [1] 6
 ```
 
@@ -404,7 +404,7 @@ is a *list of vectors and factors*:
 typeof(gapminder)
 ```
 
-```{.output}
+```output
 [1] "list"
 ```
 
@@ -416,7 +416,7 @@ columns. To get the number of rows and columns in our dataset, try:
 nrow(gapminder)
 ```
 
-```{.output}
+```output
 [1] 1704
 ```
 
@@ -424,7 +424,7 @@ nrow(gapminder)
 ncol(gapminder)
 ```
 
-```{.output}
+```output
 [1] 6
 ```
 
@@ -435,7 +435,7 @@ Or, both at once:
 dim(gapminder)
 ```
 
-```{.output}
+```output
 [1] 1704    6
 ```
 
@@ -447,7 +447,7 @@ ask for them later:
 colnames(gapminder)
 ```
 
-```{.output}
+```output
 [1] "country"   "year"      "pop"       "continent" "lifeExp"   "gdpPercap"
 ```
 
@@ -466,7 +466,7 @@ to start digging into our data proper. Check out the first few lines:
 head(gapminder)
 ```
 
-```{.output}
+```output
       country year      pop continent lifeExp gdpPercap
 1 Afghanistan 1952  8425333      Asia  28.801  779.4453
 2 Afghanistan 1957  9240934      Asia  30.332  820.8530
diff --git a/06-data-subsetting.md b/06-data-subsetting.md
index f52de0833..a940a9bc1 100644
--- a/06-data-subsetting.md
+++ b/06-data-subsetting.md
@@ -36,7 +36,7 @@ names(x) <- c('a', 'b', 'c', 'd', 'e')
 x
 ```
 
-```{.output}
+```output
   a   b   c   d   e 
 5.4 6.2 7.1 4.8 7.5 
 ```
@@ -63,7 +63,7 @@ from one:
 x[1]
 ```
 
-```{.output}
+```output
   a 
 5.4 
 ```
@@ -73,7 +73,7 @@ x[1]
 x[4]
 ```
 
-```{.output}
+```output
   d 
 4.8 
 ```
@@ -88,7 +88,7 @@ We can ask for multiple elements at once:
 x[c(1, 3)]
 ```
 
-```{.output}
+```output
   a   c 
 5.4 7.1 
 ```
@@ -100,7 +100,7 @@ Or slices of the vector:
 x[1:4]
 ```
 
-```{.output}
+```output
   a   b   c   d 
 5.4 6.2 7.1 4.8 
 ```
@@ -112,7 +112,7 @@ the `:` operator creates a sequence of numbers from the left element to the righ
 1:4
 ```
 
-```{.output}
+```output
 [1] 1 2 3 4
 ```
 
@@ -120,7 +120,7 @@ the `:` operator creates a sequence of numbers from the left element to the righ
 c(1, 2, 3, 4)
 ```
 
-```{.output}
+```output
 [1] 1 2 3 4
 ```
 
@@ -131,7 +131,7 @@ We can ask for the same element multiple times:
 x[c(1,1,3)]
 ```
 
-```{.output}
+```output
   a   a   c 
 5.4 5.4 7.1 
 ```
@@ -143,7 +143,7 @@ If we ask for an index beyond the length of the vector, R will return a missing
 x[6]
 ```
 
-```{.output}
+```output
 <NA> 
   NA 
 ```
@@ -157,7 +157,7 @@ If we ask for the 0th element, we get an empty vector:
 x[0]
 ```
 
-```{.output}
+```output
 named numeric(0)
 ```
 
@@ -181,7 +181,7 @@ every element *except* for the one specified:
 x[-2]
 ```
 
-```{.output}
+```output
   a   c   d   e 
 5.4 7.1 4.8 7.5 
 ```
@@ -193,7 +193,7 @@ We can skip multiple elements:
 x[c(-1, -5)]  # or x[-c(1,5)]
 ```
 
-```{.output}
+```output
   b   c   d 
 6.2 7.1 4.8 
 ```
@@ -214,7 +214,7 @@ x[-1:3]
 This gives a somewhat cryptic error:
 
 
-```{.error}
+```error
 Error in x[-1:3]: only 0's may be mixed with negative subscripts
 ```
 
@@ -230,7 +230,7 @@ that the `-` operator applies to the result:
 x[-(1:3)]
 ```
 
-```{.output}
+```output
   d   e 
 4.8 7.5 
 ```
@@ -246,7 +246,7 @@ x <- x[-4]
 x
 ```
 
-```{.output}
+```output
   a   b   c   e 
 5.4 6.2 7.1 7.5 
 ```
@@ -264,7 +264,7 @@ names(x) <- c('a', 'b', 'c', 'd', 'e')
 print(x)
 ```
 
-```{.output}
+```output
   a   b   c   d   e 
 5.4 6.2 7.1 4.8 7.5 
 ```
@@ -272,7 +272,7 @@ print(x)
 Come up with at least 2 different commands that will produce the following output:
 
 
-```{.output}
+```output
   b   c   d 
 6.2 7.1 4.8 
 ```
@@ -288,7 +288,7 @@ After you find 2 different commands, compare notes with your neighbour. Did you
 x[2:4]
 ```
 
-```{.output}
+```output
   b   c   d 
 6.2 7.1 4.8 
 ```
@@ -298,7 +298,7 @@ x[2:4]
 x[-c(1,5)]
 ```
 
-```{.output}
+```output
   b   c   d 
 6.2 7.1 4.8 
 ```
@@ -308,7 +308,7 @@ x[-c(1,5)]
 x[c(2,3,4)]
 ```
 
-```{.output}
+```output
   b   c   d 
 6.2 7.1 4.8 
 ```
@@ -327,7 +327,7 @@ x <- c(a=5.4, b=6.2, c=7.1, d=4.8, e=7.5) # we can name a vector 'on the fly'
 x[c("a", "c")]
 ```
 
-```{.output}
+```output
   a   c 
 5.4 7.1 
 ```
@@ -345,7 +345,7 @@ We can also use any logical vector to subset:
 x[c(FALSE, FALSE, TRUE, FALSE, TRUE)]
 ```
 
-```{.output}
+```output
   c   e 
 7.1 7.5 
 ```
@@ -359,7 +359,7 @@ the same result as the previous one.
 x[x > 7]
 ```
 
-```{.output}
+```output
   c   e 
 7.1 7.5 
 ```
@@ -376,7 +376,7 @@ We can use `==` to mimic the previous method of indexing by name
 x[names(x) == "a"]
 ```
 
-```{.output}
+```output
   a 
 5.4 
 ```
@@ -427,7 +427,7 @@ names(x) <- c('a', 'b', 'c', 'd', 'e')
 print(x)
 ```
 
-```{.output}
+```output
   a   b   c   d   e 
 5.4 6.2 7.1 4.8 7.5 
 ```
@@ -444,7 +444,7 @@ x_subset <- x[x<7 & x>4]
 print(x_subset)
 ```
 
-```{.output}
+```output
   a   b   d 
 5.4 6.2 4.8 
 ```
@@ -468,7 +468,7 @@ x <- 1:3
 x
 ```
 
-```{.output}
+```output
 [1] 1 2 3
 ```
 
@@ -477,7 +477,7 @@ names(x) <- c('a', 'a', 'a')
 x
 ```
 
-```{.output}
+```output
 a a a 
 1 2 3 
 ```
@@ -486,7 +486,7 @@ a a a
 x['a']  # only returns first value
 ```
 
-```{.output}
+```output
 a 
 1 
 ```
@@ -495,7 +495,7 @@ a
 x[names(x) == 'a']  # returns all three values
 ```
 
-```{.output}
+```output
 a a a 
 1 2 3 
 ```
@@ -521,7 +521,7 @@ x <- c(a=5.4, b=6.2, c=7.1, d=4.8, e=7.5) # we start again by naming a vector 'o
 x[-"a"]
 ```
 
-```{.error}
+```error
 Error in -"a": invalid argument to unary operator
 ```
 
@@ -532,7 +532,7 @@ However, we can use the `!=` (not-equals) operator to construct a logical vector
 x[names(x) != "a"]
 ```
 
-```{.output}
+```output
   b   c   d   e 
 6.2 7.1 4.8 7.5 
 ```
@@ -544,12 +544,12 @@ Skipping multiple named indices is a little bit harder still. Suppose we want to
 x[names(x)!=c("a","c")]
 ```
 
-```{.warning}
+```warning
 Warning in names(x) != c("a", "c"): longer object length is not a multiple of
 shorter object length
 ```
 
-```{.output}
+```output
   b   c   d   e 
 6.2 7.1 4.8 7.5 
 ```
@@ -567,12 +567,12 @@ Let's take a look at the comparison component of this code:
 names(x) != c("a", "c")
 ```
 
-```{.warning}
+```warning
 Warning in names(x) != c("a", "c"): longer object length is not a multiple of
 shorter object length
 ```
 
-```{.output}
+```output
 [1] FALSE  TRUE  TRUE  TRUE  TRUE
 ```
 
@@ -598,7 +598,7 @@ The way to get R to do what we really want (match *each* element of the left arg
 x[! names(x) %in% c("a","c") ]
 ```
 
-```{.output}
+```output
   b   d   e 
 6.2 4.8 7.5 
 ```
@@ -688,7 +688,7 @@ f <- factor(c("a", "a", "b", "c", "c", "d"))
 f[f == "a"]
 ```
 
-```{.output}
+```output
 [1] a a
 Levels: a b c d
 ```
@@ -697,7 +697,7 @@ Levels: a b c d
 f[f %in% c("b", "c")]
 ```
 
-```{.output}
+```output
 [1] b c c
 Levels: a b c d
 ```
@@ -706,7 +706,7 @@ Levels: a b c d
 f[1:3]
 ```
 
-```{.output}
+```output
 [1] a a b
 Levels: a b c d
 ```
@@ -719,7 +719,7 @@ even if no more of that category exists in the factor:
 f[-3]
 ```
 
-```{.output}
+```output
 [1] a a c c d
 Levels: a b c d
 ```
@@ -737,7 +737,7 @@ m <- matrix(rnorm(6*4), ncol=4, nrow=6)
 m[3:4, c(3,1)]
 ```
 
-```{.output}
+```output
             [,1]       [,2]
 [1,]  1.12493092 -0.8356286
 [2,] -0.04493361  1.5952808
@@ -751,7 +751,7 @@ rows or columns respectively:
 m[, c(3,4)]
 ```
 
-```{.output}
+```output
             [,1]        [,2]
 [1,] -0.62124058  0.82122120
 [2,] -2.21469989  0.59390132
@@ -769,7 +769,7 @@ to a vector:
 m[3,]
 ```
 
-```{.output}
+```output
 [1] -0.8356286  0.5757814  1.1249309  0.9189774
 ```
 
@@ -781,7 +781,7 @@ If you want to keep the output as a matrix, you need to specify a *third* argume
 m[3, , drop=FALSE]
 ```
 
-```{.output}
+```output
            [,1]      [,2]     [,3]      [,4]
 [1,] -0.8356286 0.5757814 1.124931 0.9189774
 ```
@@ -794,7 +794,7 @@ R will throw an error:
 m[, c(3,6)]
 ```
 
-```{.error}
+```error
 Error in m[, c(3, 6)]: subscript out of bounds
 ```
 
@@ -816,7 +816,7 @@ also subset using only one argument:
 m[5]
 ```
 
-```{.output}
+```output
 [1] 0.3295078
 ```
 
@@ -829,7 +829,7 @@ vector are arranged column-wise:
 matrix(1:6, nrow=2, ncol=3)
 ```
 
-```{.output}
+```output
      [,1] [,2] [,3]
 [1,]    1    3    5
 [2,]    2    4    6
@@ -842,7 +842,7 @@ If you wish to populate the matrix by row, use `byrow=TRUE`:
 matrix(1:6, nrow=2, ncol=3, byrow=TRUE)
 ```
 
-```{.output}
+```output
      [,1] [,2] [,3]
 [1,]    1    2    3
 [2,]    4    5    6
@@ -863,7 +863,7 @@ m <- matrix(1:18, nrow=3, ncol=6)
 print(m)
 ```
 
-```{.output}
+```output
      [,1] [,2] [,3] [,4] [,5] [,6]
 [1,]    1    4    7   10   13   16
 [2,]    2    5    8   11   14   17
@@ -906,7 +906,7 @@ xlist <- list(a = "Software Carpentry", b = 1:10, data = head(mtcars))
 xlist[1]
 ```
 
-```{.output}
+```output
 $a
 [1] "Software Carpentry"
 ```
@@ -924,7 +924,7 @@ data structures.
 xlist[1:2]
 ```
 
-```{.output}
+```output
 $a
 [1] "Software Carpentry"
 
@@ -940,7 +940,7 @@ bracket function: `[[`.
 xlist[[1]]
 ```
 
-```{.output}
+```output
 [1] "Software Carpentry"
 ```
 
@@ -953,7 +953,7 @@ You can't extract more than one element at once:
 xlist[[1:2]]
 ```
 
-```{.error}
+```error
 Error in xlist[[1:2]]: subscript out of bounds
 ```
 
@@ -964,7 +964,7 @@ Nor use it to skip elements:
 xlist[[-1]]
 ```
 
-```{.error}
+```error
 Error in xlist[[-1]]: invalid negative subscript in get1index <real>
 ```
 
@@ -975,7 +975,7 @@ But you can use names to both subset and extract elements:
 xlist[["a"]]
 ```
 
-```{.output}
+```output
 [1] "Software Carpentry"
 ```
 
@@ -986,7 +986,7 @@ The `$` function is a shorthand way for extracting elements by name:
 xlist$data
 ```
 
-```{.output}
+```output
                    mpg cyl disp  hp drat    wt  qsec vs am gear carb
 Mazda RX4         21.0   6  160 110 3.90 2.620 16.46  0  1    4    4
 Mazda RX4 Wag     21.0   6  160 110 3.90 2.875 17.02  0  1    4    4
@@ -1019,7 +1019,7 @@ Hint: the number 2 is contained within the "b" item in the list.
 xlist$b[2]
 ```
 
-```{.output}
+```output
 [1] 2
 ```
 
@@ -1028,7 +1028,7 @@ xlist$b[2]
 xlist[[2]][2]
 ```
 
-```{.output}
+```output
 [1] 2
 ```
 
@@ -1037,7 +1037,7 @@ xlist[[2]][2]
 xlist[["b"]][2]
 ```
 
-```{.output}
+```output
 [1] 2
 ```
 
@@ -1089,7 +1089,7 @@ element corresponds to a column. The resulting object will be a data frame:
 head(gapminder[3])
 ```
 
-```{.output}
+```output
        pop
 1  8425333
 2  9240934
@@ -1106,7 +1106,7 @@ Similarly, `[[` will act to extract *a single column*:
 head(gapminder[["lifeExp"]])
 ```
 
-```{.output}
+```output
 [1] 28.801 30.332 31.997 34.020 36.088 38.438
 ```
 
@@ -1117,7 +1117,7 @@ And `$` provides a convenient shorthand to extract columns by name:
 head(gapminder$year)
 ```
 
-```{.output}
+```output
 [1] 1952 1957 1962 1967 1972 1977
 ```
 
@@ -1128,7 +1128,7 @@ With two arguments, `[` behaves the same way as for matrices:
 gapminder[1:3,]
 ```
 
-```{.output}
+```output
       country year      pop continent lifeExp gdpPercap
 1 Afghanistan 1952  8425333      Asia  28.801  779.4453
 2 Afghanistan 1957  9240934      Asia  30.332  820.8530
@@ -1143,7 +1143,7 @@ the elements are mixed types):
 gapminder[3,]
 ```
 
-```{.output}
+```output
       country year      pop continent lifeExp gdpPercap
 3 Afghanistan 1962 10267083      Asia  31.997  853.1007
 ```
diff --git a/07-control-flow.md b/07-control-flow.md
index aac41dfa4..355b96172 100644
--- a/07-control-flow.md
+++ b/07-control-flow.md
@@ -56,7 +56,7 @@ if (x >= 10) {
 x
 ```
 
-```{.output}
+```output
 [1] 8
 ```
 
@@ -73,7 +73,7 @@ if (x >= 10) {
 }
 ```
 
-```{.output}
+```output
 [1] "x is less than 10"
 ```
 
@@ -92,7 +92,7 @@ if (x >= 10) {
 }
 ```
 
-```{.output}
+```output
 [1] "x is greater than 5, but less than 10"
 ```
 
@@ -110,7 +110,7 @@ if (x) {
 }
 ```
 
-```{.output}
+```output
 [1] "4 does not equal 3"
 ```
 
@@ -122,7 +122,7 @@ x <- 4 == 3
 x
 ```
 
-```{.output}
+```output
 [1] FALSE
 ```
 
@@ -186,7 +186,7 @@ if(any(gapminder$year == 2002)){
 Did anyone get a warning message like this?
 
 
-```{.error}
+```error
 Error in if (gapminder$year == 2012) {: the condition has length > 1
 ```
 
@@ -222,7 +222,7 @@ y <- -3
 ifelse(y < 0, "y is a negative number", "y is either positive or zero")
 ```
 
-```{.output}
+```output
 [1] "y is a negative number"
 ```
 
@@ -273,7 +273,7 @@ for (i in 1:10) {
 }
 ```
 
-```{.output}
+```output
 [1] 1
 [1] 2
 [1] 3
@@ -301,7 +301,7 @@ for (i in 1:5) {
 }
 ```
 
-```{.output}
+```output
 [1] "1 a"
 [1] "1 b"
 [1] "1 c"
@@ -348,7 +348,7 @@ for (i in 1:5) {
 output_vector
 ```
 
-```{.output}
+```output
  [1] "1 a" "1 b" "1 c" "1 d" "1 e" "2 a" "2 b" "2 c" "2 d" "2 e" "3 a" "3 b"
 [13] "3 c" "3 d" "3 e" "4 a" "4 b" "4 c" "4 d" "4 e" "5 a" "5 b" "5 c" "5 d"
 [25] "5 e"
@@ -394,7 +394,7 @@ output_vector2 <- as.vector(output_matrix)
 output_vector2
 ```
 
-```{.output}
+```output
  [1] "1 a" "2 a" "3 a" "4 a" "5 a" "1 b" "2 b" "3 b" "4 b" "5 b" "1 c" "2 c"
 [13] "3 c" "4 c" "5 c" "1 d" "2 d" "3 d" "4 d" "5 d" "1 e" "2 e" "3 e" "4 e"
 [25] "5 e"
diff --git a/08-plot-ggplot2.md b/08-plot-ggplot2.md
index f278811e8..de0df23a0 100644
--- a/08-plot-ggplot2.md
+++ b/08-plot-ggplot2.md
@@ -315,7 +315,7 @@ ggplot(data = gapminder, mapping = aes(x = gdpPercap, y = lifeExp)) +
   geom_point(alpha = 0.5) + scale_x_log10() + geom_smooth(method="lm")
 ```
 
-```{.output}
+```output
 `geom_smooth()` using formula = 'y ~ x'
 ```
 
@@ -330,7 +330,7 @@ ggplot(data = gapminder, mapping = aes(x = gdpPercap, y = lifeExp)) +
   geom_point(alpha = 0.5) + scale_x_log10() + geom_smooth(method="lm", size=1.5)
 ```
 
-```{.warning}
+```warning
 Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
 ℹ Please use `linewidth` instead.
 This warning is displayed once every 8 hours.
@@ -338,7 +338,7 @@ Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
 generated.
 ```
 
-```{.output}
+```output
 `geom_smooth()` using formula = 'y ~ x'
 ```
 
@@ -374,7 +374,7 @@ ggplot(data = gapminder, mapping = aes(x = gdpPercap, y = lifeExp)) +
  geom_smooth(method="lm", size=1.5)
 ```
 
-```{.output}
+```output
 `geom_smooth()` using formula = 'y ~ x'
 ```
 
@@ -409,7 +409,7 @@ ggplot(data = gapminder, mapping = aes(x = gdpPercap, y = lifeExp, color = conti
  geom_smooth(method="lm", size=1.5)
 ```
 
-```{.output}
+```output
 `geom_smooth()` using formula = 'y ~ x'
 ```
 
diff --git a/09-vectorization.md b/09-vectorization.md
index 9e751ed08..528e0d02c 100644
--- a/09-vectorization.md
+++ b/09-vectorization.md
@@ -30,7 +30,7 @@ x <- 1:4
 x * 2
 ```
 
-```{.output}
+```output
 [1] 2 4 6 8
 ```
 
@@ -44,7 +44,7 @@ y <- 6:9
 x + y
 ```
 
-```{.output}
+```output
 [1]  7  9 11 13
 ```
 
@@ -70,7 +70,7 @@ for (i in 1:4) {
 output_vector
 ```
 
-```{.output}
+```output
 [1]  7  9 11 13
 ```
 
@@ -82,7 +82,7 @@ sum_xy <- x + y
 sum_xy
 ```
 
-```{.output}
+```output
 [1]  7  9 11 13
 ```
 
@@ -114,7 +114,7 @@ gapminder$pop_millions <- gapminder$pop / 1e6
 head(gapminder)
 ```
 
-```{.output}
+```output
       country year      pop continent lifeExp gdpPercap pop_millions
 1 Afghanistan 1952  8425333      Asia  28.801  779.4453     8.425333
 2 Afghanistan 1957  9240934      Asia  30.332  820.8530     9.240934
@@ -176,7 +176,7 @@ vectorized:
 x > 2
 ```
 
-```{.output}
+```output
 [1] FALSE FALSE  TRUE  TRUE
 ```
 
@@ -188,7 +188,7 @@ a <- x > 3  # or, for clarity, a <- (x > 3)
 a
 ```
 
-```{.output}
+```output
 [1] FALSE FALSE FALSE  TRUE
 ```
 
@@ -212,7 +212,7 @@ x <- 1:4
 log(x)
 ```
 
-```{.output}
+```output
 [1] 0.0000000 0.6931472 1.0986123 1.3862944
 ```
 
@@ -224,7 +224,7 @@ m <- matrix(1:12, nrow=3, ncol=4)
 m * -1
 ```
 
-```{.output}
+```output
      [,1] [,2] [,3] [,4]
 [1,]   -1   -4   -7  -10
 [2,]   -2   -5   -8  -11
@@ -243,7 +243,7 @@ To do matrix multiplication, we need to use the `%*%` operator:
 m %*% matrix(1, nrow=4, ncol=1)
 ```
 
-```{.output}
+```output
      [,1]
 [1,]   22
 [2,]   26
@@ -254,7 +254,7 @@ m %*% matrix(1, nrow=4, ncol=1)
 matrix(1:4, nrow=1) %*% matrix(1:4, ncol=1)
 ```
 
-```{.output}
+```output
      [,1]
 [1,]   30
 ```
@@ -277,7 +277,7 @@ m <- matrix(1:12, nrow=3, ncol=4)
 m
 ```
 
-```{.output}
+```output
      [,1] [,2] [,3] [,4]
 [1,]    1    4    7   10
 [2,]    2    5    8   11
@@ -305,7 +305,7 @@ m <- matrix(1:12, nrow=3, ncol=4)
 m
 ```
 
-```{.output}
+```output
      [,1] [,2] [,3] [,4]
 [1,]    1    4    7   10
 [2,]    2    5    8   11
@@ -317,7 +317,7 @@ Write down what you think will happen when you run:
 1. `m ^ -1`
 
 
-```{.output}
+```output
           [,1]      [,2]      [,3]       [,4]
 [1,] 1.0000000 0.2500000 0.1428571 0.10000000
 [2,] 0.5000000 0.2000000 0.1250000 0.09090909
@@ -327,7 +327,7 @@ Write down what you think will happen when you run:
 2. `m * c(1, 0, -1)`
 
 
-```{.output}
+```output
      [,1] [,2] [,3] [,4]
 [1,]    1    4    7   10
 [2,]    0    0    0    0
@@ -337,7 +337,7 @@ Write down what you think will happen when you run:
 3. `m > c(0, 20)`
 
 
-```{.output}
+```output
       [,1]  [,2]  [,3]  [,4]
 [1,]  TRUE FALSE  TRUE FALSE
 [2,] FALSE  TRUE FALSE  TRUE
@@ -386,7 +386,7 @@ How about when n=10,000?
 sum(1/(1:100)^2)
 ```
 
-```{.output}
+```output
 [1] 1.634984
 ```
 
@@ -394,7 +394,7 @@ sum(1/(1:100)^2)
 sum(1/(1:1e04)^2)
 ```
 
-```{.output}
+```output
 [1] 1.644834
 ```
 
@@ -403,7 +403,7 @@ n <- 10000
 sum(1/(1:n)^2)
 ```
 
-```{.output}
+```output
 [1] 1.644834
 ```
 
@@ -417,7 +417,7 @@ inverse_sum_of_squares <- function(n) {
 inverse_sum_of_squares(100)
 ```
 
-```{.output}
+```output
 [1] 1.634984
 ```
 
@@ -425,7 +425,7 @@ inverse_sum_of_squares(100)
 inverse_sum_of_squares(10000)
 ```
 
-```{.output}
+```output
 [1] 1.644834
 ```
 
@@ -434,7 +434,7 @@ n <- 10000
 inverse_sum_of_squares(n)
 ```
 
-```{.output}
+```output
 [1] 1.644834
 ```
 
@@ -458,12 +458,12 @@ y <- c(1, 2, 3, 4, 5, 6, 7)
 x + y
 ```
 
-```{.warning}
+```warning
 Warning in x + y: longer object length is not a multiple of shorter object
 length
 ```
 
-```{.output}
+```output
 [1] 2 4 6 5 7 9 8
 ```
 
diff --git a/10-functions.md b/10-functions.md
index bf2bea211..d911ea3f3 100644
--- a/10-functions.md
+++ b/10-functions.md
@@ -114,7 +114,7 @@ Calling our own function is no different from calling any other function:
 fahr_to_kelvin(32)
 ```
 
-```{.output}
+```output
 [1] 273.15
 ```
 
@@ -124,7 +124,7 @@ fahr_to_kelvin(32)
 fahr_to_kelvin(212)
 ```
 
-```{.output}
+```output
 [1] 373.15
 ```
 
@@ -278,7 +278,7 @@ It still works when given proper input.
 fahr_to_kelvin(temp = 32)
 ```
 
-```{.output}
+```output
 [1] 273.15
 ```
 
@@ -290,7 +290,7 @@ But fails instantly if given improper input.
 fahr_to_kelvin(temp = as.factor(32))
 ```
 
-```{.error}
+```error
 Error in fahr_to_kelvin(temp = as.factor(32)): is.numeric(temp) is not TRUE
 ```
 
@@ -360,7 +360,7 @@ whatever command is executed on the last line of the function.
 calcGDP(head(gapminder))
 ```
 
-```{.output}
+```output
 [1]  6567086330  7585448670  8758855797  9648014150  9678553274 11697659231
 ```
 
@@ -409,7 +409,7 @@ Let's take a look at what happens when we specify the year:
 head(calcGDP(gapminder, year=2007))
 ```
 
-```{.output}
+```output
        country year      pop continent lifeExp  gdpPercap          gdp
 12 Afghanistan 2007 31889923      Asia  43.828   974.5803  31079291949
 24     Albania 2007  3600523    Europe  76.423  5937.0295  21376411360
@@ -426,7 +426,7 @@ Or for a specific country:
 calcGDP(gapminder, country="Australia")
 ```
 
-```{.output}
+```output
      country year      pop continent lifeExp gdpPercap          gdp
 61 Australia 1952  8691212   Oceania  69.120  10039.60  87256254102
 62 Australia 1957  9712569   Oceania  70.330  10949.65 106349227169
@@ -449,7 +449,7 @@ Or both:
 calcGDP(gapminder, year=2007, country="Australia")
 ```
 
-```{.output}
+```output
      country year      pop continent lifeExp gdpPercap          gdp
 72 Australia 2007 20434176   Oceania  81.235  34435.37 703658358894
 ```
@@ -572,7 +572,7 @@ best_practice <- c("Write", "programs", "for", "people", "not", "computers")
 paste(best_practice, collapse=" ")
 ```
 
-```{.output}
+```output
 [1] "Write programs for people not computers"
 ```
 
@@ -607,7 +607,7 @@ best_practice <- c("Write", "programs", "for", "people", "not", "computers")
 fence(text=best_practice, wrapper="***")
 ```
 
-```{.output}
+```output
 [1] "*** Write programs for people not computers ***"
 ```
 
diff --git a/11-writing-data.md b/11-writing-data.md
index ea076a0b8..8ff3ff209 100644
--- a/11-writing-data.md
+++ b/11-writing-data.md
@@ -116,7 +116,7 @@ OK:
 head cleaned-data/gapminder-aus.csv
 ```
 
-```{.output}
+```output
 "country","year","pop","continent","lifeExp","gdpPercap"
 "61","Australia",1952,8691212,"Oceania",69.12,10039.59564
 "62","Australia",1957,9712569,"Oceania",70.33,10949.64959
@@ -163,7 +163,7 @@ Now lets look at the data again using our shell skills:
 head cleaned-data/gapminder-aus.csv
 ```
 
-```{.output}
+```output
 country,year,pop,continent,lifeExp,gdpPercap
 Australia,1952,8691212,Oceania,69.12,10039.59564
 Australia,1957,9712569,Oceania,70.33,10949.64959
diff --git a/12-dplyr.md b/12-dplyr.md
index a332e936b..a6e39d500 100644
--- a/12-dplyr.md
+++ b/12-dplyr.md
@@ -31,7 +31,7 @@ do these operations using the normal base R operations:
 mean(gapminder$gdpPercap[gapminder$continent == "Africa"])
 ```
 
-```{.output}
+```output
 [1] 2193.755
 ```
 
@@ -39,7 +39,7 @@ mean(gapminder$gdpPercap[gapminder$continent == "Africa"])
 mean(gapminder$gdpPercap[gapminder$continent == "Americas"])
 ```
 
-```{.output}
+```output
 [1] 7136.11
 ```
 
@@ -47,7 +47,7 @@ mean(gapminder$gdpPercap[gapminder$continent == "Americas"])
 mean(gapminder$gdpPercap[gapminder$continent == "Asia"])
 ```
 
-```{.output}
+```output
 [1] 7902.15
 ```
 
@@ -154,7 +154,7 @@ tidy_gdp <- year_country_gdp %>% rename(gdp_per_capita = gdpPercap)
 head(tidy_gdp)
 ```
 
-```{.output}
+```output
   year     country gdp_per_capita
 1 1952 Afghanistan       779.4453
 2 1957 Afghanistan       820.8530
@@ -232,7 +232,7 @@ could have used in filter.
 str(gapminder)
 ```
 
-```{.output}
+```output
 'data.frame':	1704 obs. of  6 variables:
  $ country  : chr  "Afghanistan" "Afghanistan" "Afghanistan" "Afghanistan" ...
  $ year     : int  1952 1957 1962 1967 1972 1977 1982 1987 1992 1997 ...
@@ -246,7 +246,7 @@ str(gapminder)
 str(gapminder %>% group_by(continent))
 ```
 
-```{.output}
+```output
 gropd_df [1,704 × 6] (S3: grouped_df/tbl_df/tbl/data.frame)
  $ country  : chr [1:1704] "Afghanistan" "Afghanistan" "Afghanistan" "Afghanistan" ...
  $ year     : int [1:1704] 1952 1957 1962 1967 1972 1977 1982 1987 1992 1997 ...
@@ -326,7 +326,7 @@ lifeExp_bycountry %>%
    filter(mean_lifeExp == min(mean_lifeExp) | mean_lifeExp == max(mean_lifeExp))
 ```
 
-```{.output}
+```output
 # A tibble: 2 × 2
   country      mean_lifeExp
   <chr>               <dbl>
@@ -347,7 +347,7 @@ lifeExp_bycountry %>%
    head(1)
 ```
 
-```{.output}
+```output
 # A tibble: 1 × 2
   country      mean_lifeExp
   <chr>               <dbl>
@@ -360,7 +360,7 @@ lifeExp_bycountry %>%
    head(1)
 ```
 
-```{.output}
+```output
 # A tibble: 1 × 2
   country mean_lifeExp
   <chr>          <dbl>
@@ -376,7 +376,7 @@ lifeExp_bycountry %>%
    head(1)
 ```
 
-```{.output}
+```output
 # A tibble: 1 × 2
   country  mean_lifeExp
   <chr>           <dbl>
@@ -396,7 +396,7 @@ gdp_bycontinents_byyear <- gapminder %>%
     summarize(mean_gdpPercap = mean(gdpPercap))
 ```
 
-```{.output}
+```output
 `summarise()` has grouped output by 'continent'. You can override using the
 `.groups` argument.
 ```
@@ -413,7 +413,7 @@ gdp_pop_bycontinents_byyear <- gapminder %>%
               sd_pop = sd(pop))
 ```
 
-```{.output}
+```output
 `summarise()` has grouped output by 'continent'. You can override using the
 `.groups` argument.
 ```
@@ -435,7 +435,7 @@ gapminder %>%
     count(continent, sort = TRUE)
 ```
 
-```{.output}
+```output
   continent  n
 1    Africa 52
 2      Asia 33
@@ -454,7 +454,7 @@ gapminder %>%
     summarize(se_le = sd(lifeExp)/sqrt(n()))
 ```
 
-```{.output}
+```output
 # A tibble: 5 × 2
   continent se_le
   <chr>     <dbl>
@@ -478,7 +478,7 @@ gapminder %>%
       se_le = sd(lifeExp)/sqrt(n()))
 ```
 
-```{.output}
+```output
 # A tibble: 5 × 5
   continent mean_le min_le max_le se_le
   <chr>       <dbl>  <dbl>  <dbl> <dbl>
@@ -506,7 +506,7 @@ gdp_pop_bycontinents_byyear <- gapminder %>%
               sd_gdp_billion = sd(gdp_billion))
 ```
 
-```{.output}
+```output
 `summarise()` has grouped output by 'continent'. You can override using the
 `.groups` argument.
 ```
@@ -533,7 +533,7 @@ gdp_pop_bycontinents_byyear_above25 <- gapminder %>%
               sd_gdp_billion = sd(gdp_billion))
 ```
 
-```{.output}
+```output
 `summarise()` has grouped output by 'continent'. You can override using the
 `.groups` argument.
 ```
@@ -548,7 +548,7 @@ gdp_future_bycontinents_byyear_high_lifeExp <- gapminder %>%
               mean_gdpPercap_expected = mean(gdp_futureExpectation))
 ```
 
-```{.output}
+```output
 `summarise()` has grouped output by 'continent'. You can override using the
 `.groups` argument.
 ```
diff --git a/13-tidyr.md b/13-tidyr.md
index 840c1a31b..e8debdc6c 100644
--- a/13-tidyr.md
+++ b/13-tidyr.md
@@ -68,7 +68,7 @@ First, lets look at the structure of our original gapminder data frame:
 str(gapminder)
 ```
 
-```{.output}
+```output
 'data.frame':	1704 obs. of  6 variables:
  $ country  : chr  "Afghanistan" "Afghanistan" "Afghanistan" "Afghanistan" ...
  $ year     : int  1952 1957 1962 1967 1972 1977 1982 1987 1992 1997 ...
@@ -133,7 +133,7 @@ gap_wide <- read.csv("data/gapminder_wide.csv", stringsAsFactors = FALSE)
 str(gap_wide)
 ```
 
-```{.output}
+```output
 'data.frame':	142 obs. of  38 variables:
  $ continent     : chr  "Africa" "Africa" "Africa" "Africa" ...
  $ country       : chr  "Algeria" "Angola" "Benin" "Botswana" ...
@@ -191,7 +191,7 @@ gap_long <- gap_wide %>%
 str(gap_long)
 ```
 
-```{.output}
+```output
 tibble [5,112 × 4] (S3: tbl_df/tbl/data.frame)
  $ continent   : chr [1:5112] "Africa" "Africa" "Africa" "Africa" ...
  $ country     : chr [1:5112] "Algeria" "Algeria" "Algeria" "Algeria" ...
@@ -227,7 +227,7 @@ gap_long <- gap_wide %>%
 str(gap_long)
 ```
 
-```{.output}
+```output
 tibble [5,112 × 4] (S3: tbl_df/tbl/data.frame)
  $ continent   : chr [1:5112] "Africa" "Africa" "Africa" "Africa" ...
  $ country     : chr [1:5112] "Algeria" "Algeria" "Algeria" "Algeria" ...
@@ -266,12 +266,12 @@ gap_long %>% group_by(continent, obs_type) %>%
    summarize(means=mean(obs_values))
 ```
 
-```{.output}
+```output
 `summarise()` has grouped output by 'continent'. You can override using the
 `.groups` argument.
 ```
 
-```{.output}
+```output
 # A tibble: 15 × 3
 # Groups:   continent [5]
    continent obs_type       means
@@ -314,7 +314,7 @@ gap_normal <- gap_long %>%
 dim(gap_normal)
 ```
 
-```{.output}
+```output
 [1] 1704    6
 ```
 
@@ -322,7 +322,7 @@ dim(gap_normal)
 dim(gapminder)
 ```
 
-```{.output}
+```output
 [1] 1704    6
 ```
 
@@ -330,7 +330,7 @@ dim(gapminder)
 names(gap_normal)
 ```
 
-```{.output}
+```output
 [1] "continent" "country"   "year"      "gdpPercap" "lifeExp"   "pop"      
 ```
 
@@ -338,7 +338,7 @@ names(gap_normal)
 names(gapminder)
 ```
 
-```{.output}
+```output
 [1] "country"   "year"      "pop"       "continent" "lifeExp"   "gdpPercap"
 ```
 
@@ -352,7 +352,7 @@ gap_normal <- gap_normal[, names(gapminder)]
 all.equal(gap_normal, gapminder)
 ```
 
-```{.output}
+```output
 [1] "Attributes: < Component \"class\": Lengths (3, 1) differ (string compare on first 1) >"
 [2] "Attributes: < Component \"class\": 1 string mismatch >"                                
 [3] "Component \"country\": 1704 string mismatches"                                         
@@ -366,7 +366,7 @@ all.equal(gap_normal, gapminder)
 head(gap_normal)
 ```
 
-```{.output}
+```output
 # A tibble: 6 × 6
   country  year      pop continent lifeExp gdpPercap
   <chr>   <int>    <dbl> <chr>       <dbl>     <dbl>
@@ -382,7 +382,7 @@ head(gap_normal)
 head(gapminder)
 ```
 
-```{.output}
+```output
       country year      pop continent lifeExp gdpPercap
 1 Afghanistan 1952  8425333      Asia  28.801  779.4453
 2 Afghanistan 1957  9240934      Asia  30.332  820.8530
@@ -401,7 +401,7 @@ gap_normal <- gap_normal %>% arrange(country, year)
 all.equal(gap_normal, gapminder)
 ```
 
-```{.output}
+```output
 [1] "Attributes: < Component \"class\": Lengths (3, 1) differ (string compare on first 1) >"
 [2] "Attributes: < Component \"class\": 1 string mismatch >"                                
 ```
@@ -422,7 +422,7 @@ gap_temp <- gap_long %>% unite(var_ID, continent, country, sep = "_")
 str(gap_temp)
 ```
 
-```{.output}
+```output
 tibble [5,112 × 4] (S3: tbl_df/tbl/data.frame)
  $ var_ID    : chr [1:5112] "Africa_Algeria" "Africa_Algeria" "Africa_Algeria" "Africa_Algeria" ...
  $ obs_type  : chr [1:5112] "gdpPercap" "gdpPercap" "gdpPercap" "gdpPercap" ...
@@ -437,7 +437,7 @@ gap_temp <- gap_long %>%
 str(gap_temp)
 ```
 
-```{.output}
+```output
 tibble [5,112 × 3] (S3: tbl_df/tbl/data.frame)
  $ ID_var    : chr [1:5112] "Africa_Algeria" "Africa_Algeria" "Africa_Algeria" "Africa_Algeria" ...
  $ var_names : chr [1:5112] "gdpPercap_1952" "gdpPercap_1957" "gdpPercap_1962" "gdpPercap_1967" ...
@@ -457,7 +457,7 @@ gap_wide_new <- gap_long %>%
 str(gap_wide_new)
 ```
 
-```{.output}
+```output
 tibble [142 × 37] (S3: tbl_df/tbl/data.frame)
  $ ID_var        : chr [1:142] "Africa_Algeria" "Africa_Angola" "Africa_Benin" "Africa_Botswana" ...
  $ gdpPercap_1952: num [1:142] 2449 3521 1063 851 543 ...
@@ -534,7 +534,7 @@ gap_wide_betterID <- gap_long %>%
 str(gap_wide_betterID)
 ```
 
-```{.output}
+```output
 tibble [142 × 38] (S3: tbl_df/tbl/data.frame)
  $ continent     : chr [1:142] "Africa" "Africa" "Africa" "Africa" ...
  $ country       : chr [1:142] "Algeria" "Angola" "Benin" "Botswana" ...
@@ -580,7 +580,7 @@ tibble [142 × 38] (S3: tbl_df/tbl/data.frame)
 all.equal(gap_wide, gap_wide_betterID)
 ```
 
-```{.output}
+```output
 [1] "Attributes: < Component \"class\": Lengths (1, 3) differ (string compare on first 1) >"
 [2] "Attributes: < Component \"class\": 1 string mismatch >"                                
 ```
diff --git a/config.yaml b/config.yaml
deleted file mode 100644
index e94fdac68..000000000
--- a/config.yaml
+++ /dev/null
@@ -1,95 +0,0 @@
-#------------------------------------------------------------
-# Values for this lesson.
-#------------------------------------------------------------
-
-# Which carpentry is this (swc, dc, lc, or cp)?
-# swc: Software Carpentry
-# dc: Data Carpentry
-# lc: Library Carpentry
-# cp: Carpentries (to use for instructor training for instance)
-# incubator: The Carpentries Incubator
-carpentry: 'swc'
-
-# Overall title for pages.
-title: 'R for Reproducible Scientific Analysis'
-
-# Date the lesson was created (YYYY-MM-DD, this is empty by default)
-created: '2015-04-18'
-
-# Comma-separated list of keywords for the lesson
-keywords: 'software, data, lesson, The Carpentries'
-
-# Life cycle stage of the lesson
-# possible values: pre-alpha, alpha, beta, stable
-life_cycle: 'stable'
-
-# License of the lesson materials (recommended CC-BY 4.0)
-license: 'CC-BY 4.0'
-
-# Link to the source repository for this lesson
-source: 'https://github.com/swcarpentry/r-novice-gapminder'
-
-# Default branch of your lesson
-branch: 'main'
-
-# Who to contact if there are any issues
-contact: 'team@carpentries.org'
-
-# Navigation ------------------------------------------------
-#
-# Use the following menu items to specify the order of
-# individual pages in each dropdown section. Leave blank to
-# include all pages in the folder.
-#
-# Example -------------
-#
-# episodes:
-# - introduction.md
-# - first-steps.md
-#
-# learners:
-# - setup.md
-#
-# instructors:
-# - instructor-notes.md
-#
-# profiles:
-# - one-learner.md
-# - another-learner.md
-
-# Order of episodes in your lesson
-episodes: 
-- 01-rstudio-intro.Rmd
-- 02-project-intro.Rmd
-- 03-seeking-help.Rmd
-- 04-data-structures-part1.Rmd
-- 05-data-structures-part2.Rmd
-- 06-data-subsetting.Rmd
-- 07-control-flow.Rmd
-- 08-plot-ggplot2.Rmd
-- 09-vectorization.Rmd
-- 10-functions.Rmd
-- 11-writing-data.Rmd
-- 12-dplyr.Rmd
-- 13-tidyr.Rmd
-- 14-knitr-markdown.Rmd
-- 15-wrap-up.Rmd
-
-# Information for Learners
-learners: 
-
-# Information for Instructors
-instructors: 
-
-# Learner Profiles
-profiles: 
-
-# Customisation ---------------------------------------------
-#
-# This space below is where custom yaml items (e.g. pinning
-# sandpaper and varnish versions) should live
-
-
-url: 'https://swcarpentry.github.io/r-novice-gapminder'
-analytics: carpentries
-lang: en
diff --git a/fig/06-rmd-generate-figures.sh b/fig/06-rmd-generate-figures.sh
old mode 100755
new mode 100644
diff --git a/fig/12-plyr-generate-figures.sh b/fig/12-plyr-generate-figures.sh
old mode 100755
new mode 100644
diff --git a/md5sum.txt b/md5sum.txt
index 7729d2096..5d03a125a 100644
--- a/md5sum.txt
+++ b/md5sum.txt
@@ -1,26 +1,26 @@
 "file" "checksum" "built" "date"
-"CODE_OF_CONDUCT.md" "c93c83c630db2fe2462240bf72552548" "site/built/CODE_OF_CONDUCT.md" "2024-04-12"
-"LICENSE.md" "b24ebbb41b14ca25cf6b8216dda83e5f" "site/built/LICENSE.md" "2024-04-12"
-"config.yaml" "8b9d63dd3c46d5b4d5fa4219b51a0dfc" "site/built/config.yaml" "2024-04-12"
-"index.md" "86c8fb559b13d1695d55b52dd6cbf574" "site/built/index.md" "2024-04-12"
-"episodes/01-rstudio-intro.Rmd" "04f6b758558750cef962768d78dd63b0" "site/built/01-rstudio-intro.md" "2024-04-16"
-"episodes/02-project-intro.Rmd" "cd60cc3116d4f6be92f03f5cc51bcc3b" "site/built/02-project-intro.md" "2024-04-12"
-"episodes/03-seeking-help.Rmd" "d24c310b8f36930e70379458f3c93461" "site/built/03-seeking-help.md" "2024-04-12"
-"episodes/04-data-structures-part1.Rmd" "5ec938f71a9cec633cef9329d214c3a0" "site/built/04-data-structures-part1.md" "2024-04-12"
-"episodes/05-data-structures-part2.Rmd" "95c5dd30b8288090ce89ecbf2d3072bd" "site/built/05-data-structures-part2.md" "2024-04-12"
-"episodes/06-data-subsetting.Rmd" "5d4ce8731ab37ddea81874d63ae1ce86" "site/built/06-data-subsetting.md" "2024-04-12"
-"episodes/07-control-flow.Rmd" "6a8691c8668737e4202f49b52aeb8ac6" "site/built/07-control-flow.md" "2024-04-12"
-"episodes/08-plot-ggplot2.Rmd" "a9a97a1eee46dc82b83c6c740a4412cf" "site/built/08-plot-ggplot2.md" "2024-04-12"
-"episodes/09-vectorization.Rmd" "e229eb061b3f072a132c4b31bbc2fdb0" "site/built/09-vectorization.md" "2024-04-12"
-"episodes/10-functions.Rmd" "14edd4cf50edb8fefeb987a17d740e1a" "site/built/10-functions.md" "2024-04-12"
-"episodes/11-writing-data.Rmd" "8b26e062dddd2394d00c6847ff0b7505" "site/built/11-writing-data.md" "2024-04-12"
-"episodes/12-dplyr.Rmd" "fc20e35f891f0bb624647d69816c3220" "site/built/12-dplyr.md" "2024-04-12"
-"episodes/13-tidyr.Rmd" "1c59c3bea4cec5e0c47654a546294f07" "site/built/13-tidyr.md" "2024-04-12"
-"episodes/14-knitr-markdown.Rmd" "0c63ce92263a32f19fbec9f7b619b682" "site/built/14-knitr-markdown.md" "2024-04-12"
-"episodes/15-wrap-up.Rmd" "c5ce0d34a37b7a99624ad1d6ac482256" "site/built/15-wrap-up.md" "2024-04-12"
-"instructors/instructor-notes.md" "e61e7587564a6c4c11dbb6beea127764" "site/built/instructor-notes.md" "2024-04-12"
-"learners/discuss.md" "42ad66ab1907e030914dbb2a94376a47" "site/built/discuss.md" "2024-04-12"
-"learners/reference.md" "1cd851cc85adc26ea172da91e8c564f7" "site/built/reference.md" "2024-04-12"
-"learners/setup.md" "f888f8a54b071715c0cf56896e650c00" "site/built/setup.md" "2024-04-12"
-"profiles/learner-profiles.md" "60b93493cf1da06dfd63255d73854461" "site/built/learner-profiles.md" "2024-04-12"
-"renv/profiles/lesson-requirements/renv.lock" "c5c7ba2c4747ed796cf48687124c6f9e" "site/built/renv.lock" "2024-04-12"
+"CODE_OF_CONDUCT.md" "c93c83c630db2fe2462240bf72552548" "site/built/CODE_OF_CONDUCT.md" "2024-05-07"
+"LICENSE.md" "b24ebbb41b14ca25cf6b8216dda83e5f" "site/built/LICENSE.md" "2024-05-07"
+"config.yaml" "8b9d63dd3c46d5b4d5fa4219b51a0dfc" "site/built/config.yaml" "2024-05-07"
+"index.md" "86c8fb559b13d1695d55b52dd6cbf574" "site/built/index.md" "2024-05-07"
+"episodes/01-rstudio-intro.Rmd" "04f6b758558750cef962768d78dd63b0" "site/built/01-rstudio-intro.md" "2024-05-07"
+"episodes/02-project-intro.Rmd" "cd60cc3116d4f6be92f03f5cc51bcc3b" "site/built/02-project-intro.md" "2024-05-07"
+"episodes/03-seeking-help.Rmd" "d24c310b8f36930e70379458f3c93461" "site/built/03-seeking-help.md" "2024-05-07"
+"episodes/04-data-structures-part1.Rmd" "5ec938f71a9cec633cef9329d214c3a0" "site/built/04-data-structures-part1.md" "2024-05-07"
+"episodes/05-data-structures-part2.Rmd" "95c5dd30b8288090ce89ecbf2d3072bd" "site/built/05-data-structures-part2.md" "2024-05-07"
+"episodes/06-data-subsetting.Rmd" "5d4ce8731ab37ddea81874d63ae1ce86" "site/built/06-data-subsetting.md" "2024-05-07"
+"episodes/07-control-flow.Rmd" "6a8691c8668737e4202f49b52aeb8ac6" "site/built/07-control-flow.md" "2024-05-07"
+"episodes/08-plot-ggplot2.Rmd" "a9a97a1eee46dc82b83c6c740a4412cf" "site/built/08-plot-ggplot2.md" "2024-05-07"
+"episodes/09-vectorization.Rmd" "e229eb061b3f072a132c4b31bbc2fdb0" "site/built/09-vectorization.md" "2024-05-07"
+"episodes/10-functions.Rmd" "14edd4cf50edb8fefeb987a17d740e1a" "site/built/10-functions.md" "2024-05-07"
+"episodes/11-writing-data.Rmd" "8b26e062dddd2394d00c6847ff0b7505" "site/built/11-writing-data.md" "2024-05-07"
+"episodes/12-dplyr.Rmd" "fc20e35f891f0bb624647d69816c3220" "site/built/12-dplyr.md" "2024-05-07"
+"episodes/13-tidyr.Rmd" "1c59c3bea4cec5e0c47654a546294f07" "site/built/13-tidyr.md" "2024-05-07"
+"episodes/14-knitr-markdown.Rmd" "0c63ce92263a32f19fbec9f7b619b682" "site/built/14-knitr-markdown.md" "2024-05-07"
+"episodes/15-wrap-up.Rmd" "c5ce0d34a37b7a99624ad1d6ac482256" "site/built/15-wrap-up.md" "2024-05-07"
+"instructors/instructor-notes.md" "e61e7587564a6c4c11dbb6beea127764" "site/built/instructor-notes.md" "2024-05-07"
+"learners/discuss.md" "42ad66ab1907e030914dbb2a94376a47" "site/built/discuss.md" "2024-05-07"
+"learners/reference.md" "1cd851cc85adc26ea172da91e8c564f7" "site/built/reference.md" "2024-05-07"
+"learners/setup.md" "f888f8a54b071715c0cf56896e650c00" "site/built/setup.md" "2024-05-07"
+"profiles/learner-profiles.md" "60b93493cf1da06dfd63255d73854461" "site/built/learner-profiles.md" "2024-05-07"
+"renv/profiles/lesson-requirements/renv.lock" "a1ea73c0f46232383431e5531d0bb733" "site/built/renv.lock" "2024-05-07"
diff --git a/renv.lock b/renv.lock
deleted file mode 100644
index 53c910915..000000000
--- a/renv.lock
+++ /dev/null
@@ -1,1021 +0,0 @@
-{
-  "R": {
-    "Version": "4.3.3",
-    "Repositories": [
-      {
-        "Name": "carpentries",
-        "URL": "https://carpentries.r-universe.dev"
-      },
-      {
-        "Name": "carpentries_archive",
-        "URL": "https://carpentries.github.io/drat"
-      },
-      {
-        "Name": "CRAN",
-        "URL": "https://cran.rstudio.com"
-      }
-    ]
-  },
-  "Packages": {
-    "DiagrammeR": {
-      "Package": "DiagrammeR",
-      "Version": "1.0.11",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "RColorBrewer",
-        "cli",
-        "dplyr",
-        "glue",
-        "htmltools",
-        "htmlwidgets",
-        "igraph",
-        "magrittr",
-        "purrr",
-        "readr",
-        "rlang",
-        "rstudioapi",
-        "scales",
-        "stringr",
-        "tibble",
-        "tidyr",
-        "viridisLite",
-        "visNetwork"
-      ],
-      "Hash": "584c1e1cbb6f9b6c3b0f4ef0ad960966"
-    },
-    "MASS": {
-      "Package": "MASS",
-      "Version": "7.3-60.0.1",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "grDevices",
-        "graphics",
-        "methods",
-        "stats",
-        "utils"
-      ],
-      "Hash": "b765b28387acc8ec9e9c1530713cb19c"
-    },
-    "Matrix": {
-      "Package": "Matrix",
-      "Version": "1.6-5",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "grDevices",
-        "graphics",
-        "grid",
-        "lattice",
-        "methods",
-        "stats",
-        "utils"
-      ],
-      "Hash": "8c7115cd3a0e048bda2a7cd110549f7a"
-    },
-    "R6": {
-      "Package": "R6",
-      "Version": "2.5.1",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "R"
-      ],
-      "Hash": "470851b6d5d0ac559e9d01bb352b4021"
-    },
-    "RColorBrewer": {
-      "Package": "RColorBrewer",
-      "Version": "1.1-3",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R"
-      ],
-      "Hash": "45f0398006e83a5b10b72a90663d8d8c"
-    },
-    "base64enc": {
-      "Package": "base64enc",
-      "Version": "0.1-3",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "R"
-      ],
-      "Hash": "543776ae6848fde2f48ff3816d0628bc"
-    },
-    "bit": {
-      "Package": "bit",
-      "Version": "4.0.5",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R"
-      ],
-      "Hash": "d242abec29412ce988848d0294b208fd"
-    },
-    "bit64": {
-      "Package": "bit64",
-      "Version": "4.0.5",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "bit",
-        "methods",
-        "stats",
-        "utils"
-      ],
-      "Hash": "9fe98599ca456d6552421db0d6772d8f"
-    },
-    "bslib": {
-      "Package": "bslib",
-      "Version": "0.7.0",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "base64enc",
-        "cachem",
-        "fastmap",
-        "grDevices",
-        "htmltools",
-        "jquerylib",
-        "jsonlite",
-        "lifecycle",
-        "memoise",
-        "mime",
-        "rlang",
-        "sass"
-      ],
-      "Hash": "8644cc53f43828f19133548195d7e59e"
-    },
-    "cachem": {
-      "Package": "cachem",
-      "Version": "1.0.8",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "fastmap",
-        "rlang"
-      ],
-      "Hash": "c35768291560ce302c0a6589f92e837d"
-    },
-    "cli": {
-      "Package": "cli",
-      "Version": "3.6.2",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "utils"
-      ],
-      "Hash": "1216ac65ac55ec0058a6f75d7ca0fd52"
-    },
-    "clipr": {
-      "Package": "clipr",
-      "Version": "0.8.0",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "utils"
-      ],
-      "Hash": "3f038e5ac7f41d4ac41ce658c85e3042"
-    },
-    "colorspace": {
-      "Package": "colorspace",
-      "Version": "2.1-0",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "grDevices",
-        "graphics",
-        "methods",
-        "stats"
-      ],
-      "Hash": "f20c47fd52fae58b4e377c37bb8c335b"
-    },
-    "cpp11": {
-      "Package": "cpp11",
-      "Version": "0.4.7",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R"
-      ],
-      "Hash": "5a295d7d963cc5035284dcdbaf334f4e"
-    },
-    "crayon": {
-      "Package": "crayon",
-      "Version": "1.5.2",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "grDevices",
-        "methods",
-        "utils"
-      ],
-      "Hash": "e8a1e41acf02548751f45c718d55aa6a"
-    },
-    "digest": {
-      "Package": "digest",
-      "Version": "0.6.35",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "utils"
-      ],
-      "Hash": "698ece7ba5a4fa4559e3d537e7ec3d31"
-    },
-    "dplyr": {
-      "Package": "dplyr",
-      "Version": "1.1.4",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "R6",
-        "cli",
-        "generics",
-        "glue",
-        "lifecycle",
-        "magrittr",
-        "methods",
-        "pillar",
-        "rlang",
-        "tibble",
-        "tidyselect",
-        "utils",
-        "vctrs"
-      ],
-      "Hash": "fedd9d00c2944ff00a0e2696ccf048ec"
-    },
-    "evaluate": {
-      "Package": "evaluate",
-      "Version": "0.23",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "methods"
-      ],
-      "Hash": "daf4a1246be12c1fa8c7705a0935c1a0"
-    },
-    "fansi": {
-      "Package": "fansi",
-      "Version": "1.0.6",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "grDevices",
-        "utils"
-      ],
-      "Hash": "962174cf2aeb5b9eea581522286a911f"
-    },
-    "farver": {
-      "Package": "farver",
-      "Version": "2.1.1",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Hash": "8106d78941f34855c440ddb946b8f7a5"
-    },
-    "fastmap": {
-      "Package": "fastmap",
-      "Version": "1.1.1",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Hash": "f7736a18de97dea803bde0a2daaafb27"
-    },
-    "fontawesome": {
-      "Package": "fontawesome",
-      "Version": "0.5.2",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "htmltools",
-        "rlang"
-      ],
-      "Hash": "c2efdd5f0bcd1ea861c2d4e2a883a67d"
-    },
-    "fs": {
-      "Package": "fs",
-      "Version": "1.6.3",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "methods"
-      ],
-      "Hash": "47b5f30c720c23999b913a1a635cf0bb"
-    },
-    "generics": {
-      "Package": "generics",
-      "Version": "0.1.3",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "R",
-        "methods"
-      ],
-      "Hash": "15e9634c0fcd294799e9b2e929ed1b86"
-    },
-    "ggplot2": {
-      "Package": "ggplot2",
-      "Version": "3.5.0",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "MASS",
-        "R",
-        "cli",
-        "glue",
-        "grDevices",
-        "grid",
-        "gtable",
-        "isoband",
-        "lifecycle",
-        "mgcv",
-        "rlang",
-        "scales",
-        "stats",
-        "tibble",
-        "vctrs",
-        "withr"
-      ],
-      "Hash": "52ef83f93f74833007f193b2d4c159a2"
-    },
-    "glue": {
-      "Package": "glue",
-      "Version": "1.7.0",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "methods"
-      ],
-      "Hash": "e0b3a53876554bd45879e596cdb10a52"
-    },
-    "gtable": {
-      "Package": "gtable",
-      "Version": "0.3.4",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "cli",
-        "glue",
-        "grid",
-        "lifecycle",
-        "rlang"
-      ],
-      "Hash": "b29cf3031f49b04ab9c852c912547eef"
-    },
-    "highr": {
-      "Package": "highr",
-      "Version": "0.10",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "R",
-        "xfun"
-      ],
-      "Hash": "06230136b2d2b9ba5805e1963fa6e890"
-    },
-    "hms": {
-      "Package": "hms",
-      "Version": "1.1.3",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "lifecycle",
-        "methods",
-        "pkgconfig",
-        "rlang",
-        "vctrs"
-      ],
-      "Hash": "b59377caa7ed00fa41808342002138f9"
-    },
-    "htmltools": {
-      "Package": "htmltools",
-      "Version": "0.5.8",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "base64enc",
-        "digest",
-        "fastmap",
-        "grDevices",
-        "rlang",
-        "utils"
-      ],
-      "Hash": "149431ee39aba5bdc264112c8ff94444"
-    },
-    "htmlwidgets": {
-      "Package": "htmlwidgets",
-      "Version": "1.6.4",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "grDevices",
-        "htmltools",
-        "jsonlite",
-        "knitr",
-        "rmarkdown",
-        "yaml"
-      ],
-      "Hash": "04291cc45198225444a397606810ac37"
-    },
-    "igraph": {
-      "Package": "igraph",
-      "Version": "2.0.3",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "Matrix",
-        "R",
-        "cli",
-        "cpp11",
-        "grDevices",
-        "graphics",
-        "lifecycle",
-        "magrittr",
-        "methods",
-        "pkgconfig",
-        "rlang",
-        "stats",
-        "utils",
-        "vctrs"
-      ],
-      "Hash": "c3b7d801d722e26e4cd888e042bf9af5"
-    },
-    "isoband": {
-      "Package": "isoband",
-      "Version": "0.2.7",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "grid",
-        "utils"
-      ],
-      "Hash": "0080607b4a1a7b28979aecef976d8bc2"
-    },
-    "jquerylib": {
-      "Package": "jquerylib",
-      "Version": "0.1.4",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "htmltools"
-      ],
-      "Hash": "5aab57a3bd297eee1c1d862735972182"
-    },
-    "jsonlite": {
-      "Package": "jsonlite",
-      "Version": "1.8.8",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "methods"
-      ],
-      "Hash": "e1b9c55281c5adc4dd113652d9e26768"
-    },
-    "knitr": {
-      "Package": "knitr",
-      "Version": "1.45",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "evaluate",
-        "highr",
-        "methods",
-        "tools",
-        "xfun",
-        "yaml"
-      ],
-      "Hash": "1ec462871063897135c1bcbe0fc8f07d"
-    },
-    "labeling": {
-      "Package": "labeling",
-      "Version": "0.4.3",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "graphics",
-        "stats"
-      ],
-      "Hash": "b64ec208ac5bc1852b285f665d6368b3"
-    },
-    "lattice": {
-      "Package": "lattice",
-      "Version": "0.22-6",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "grDevices",
-        "graphics",
-        "grid",
-        "stats",
-        "utils"
-      ],
-      "Hash": "cc5ac1ba4c238c7ca9fa6a87ca11a7e2"
-    },
-    "lifecycle": {
-      "Package": "lifecycle",
-      "Version": "1.0.4",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "cli",
-        "glue",
-        "rlang"
-      ],
-      "Hash": "b8552d117e1b808b09a832f589b79035"
-    },
-    "magrittr": {
-      "Package": "magrittr",
-      "Version": "2.0.3",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "R"
-      ],
-      "Hash": "7ce2733a9826b3aeb1775d56fd305472"
-    },
-    "memoise": {
-      "Package": "memoise",
-      "Version": "2.0.1",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "cachem",
-        "rlang"
-      ],
-      "Hash": "e2817ccf4a065c5d9d7f2cfbe7c1d78c"
-    },
-    "mgcv": {
-      "Package": "mgcv",
-      "Version": "1.9-1",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "Matrix",
-        "R",
-        "graphics",
-        "methods",
-        "nlme",
-        "splines",
-        "stats",
-        "utils"
-      ],
-      "Hash": "110ee9d83b496279960e162ac97764ce"
-    },
-    "mime": {
-      "Package": "mime",
-      "Version": "0.12",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "tools"
-      ],
-      "Hash": "18e9c28c1d3ca1560ce30658b22ce104"
-    },
-    "munsell": {
-      "Package": "munsell",
-      "Version": "0.5.0",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "colorspace",
-        "methods"
-      ],
-      "Hash": "6dfe8bf774944bd5595785e3229d8771"
-    },
-    "nlme": {
-      "Package": "nlme",
-      "Version": "3.1-164",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "R",
-        "graphics",
-        "lattice",
-        "stats",
-        "utils"
-      ],
-      "Hash": "a623a2239e642806158bc4dc3f51565d"
-    },
-    "pillar": {
-      "Package": "pillar",
-      "Version": "1.9.0",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "cli",
-        "fansi",
-        "glue",
-        "lifecycle",
-        "rlang",
-        "utf8",
-        "utils",
-        "vctrs"
-      ],
-      "Hash": "15da5a8412f317beeee6175fbc76f4bb"
-    },
-    "pkgconfig": {
-      "Package": "pkgconfig",
-      "Version": "2.0.3",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "utils"
-      ],
-      "Hash": "01f28d4278f15c76cddbea05899c5d6f"
-    },
-    "prettyunits": {
-      "Package": "prettyunits",
-      "Version": "1.2.0",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R"
-      ],
-      "Hash": "6b01fc98b1e86c4f705ce9dcfd2f57c7"
-    },
-    "progress": {
-      "Package": "progress",
-      "Version": "1.2.3",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "R6",
-        "crayon",
-        "hms",
-        "prettyunits"
-      ],
-      "Hash": "f4625e061cb2865f111b47ff163a5ca6"
-    },
-    "purrr": {
-      "Package": "purrr",
-      "Version": "1.0.2",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "cli",
-        "lifecycle",
-        "magrittr",
-        "rlang",
-        "vctrs"
-      ],
-      "Hash": "1cba04a4e9414bdefc9dcaa99649a8dc"
-    },
-    "rappdirs": {
-      "Package": "rappdirs",
-      "Version": "0.3.3",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "R"
-      ],
-      "Hash": "5e3c5dc0b071b21fa128676560dbe94d"
-    },
-    "readr": {
-      "Package": "readr",
-      "Version": "2.1.5",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "R6",
-        "cli",
-        "clipr",
-        "cpp11",
-        "crayon",
-        "hms",
-        "lifecycle",
-        "methods",
-        "rlang",
-        "tibble",
-        "tzdb",
-        "utils",
-        "vroom"
-      ],
-      "Hash": "9de96463d2117f6ac49980577939dfb3"
-    },
-    "renv": {
-      "Package": "renv",
-      "Version": "1.0.5",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "utils"
-      ],
-      "Hash": "32c3f93e8360f667ca5863272ec8ba6a"
-    },
-    "rlang": {
-      "Package": "rlang",
-      "Version": "1.1.3",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "utils"
-      ],
-      "Hash": "42548638fae05fd9a9b5f3f437fbbbe2"
-    },
-    "rmarkdown": {
-      "Package": "rmarkdown",
-      "Version": "2.26",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "bslib",
-        "evaluate",
-        "fontawesome",
-        "htmltools",
-        "jquerylib",
-        "jsonlite",
-        "knitr",
-        "methods",
-        "tinytex",
-        "tools",
-        "utils",
-        "xfun",
-        "yaml"
-      ],
-      "Hash": "9b148e7f95d33aac01f31282d49e4f44"
-    },
-    "rstudioapi": {
-      "Package": "rstudioapi",
-      "Version": "0.16.0",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Hash": "96710351d642b70e8f02ddeb237c46a7"
-    },
-    "sass": {
-      "Package": "sass",
-      "Version": "0.4.9",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R6",
-        "fs",
-        "htmltools",
-        "rappdirs",
-        "rlang"
-      ],
-      "Hash": "d53dbfddf695303ea4ad66f86e99b95d"
-    },
-    "scales": {
-      "Package": "scales",
-      "Version": "1.3.0",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "R6",
-        "RColorBrewer",
-        "cli",
-        "farver",
-        "glue",
-        "labeling",
-        "lifecycle",
-        "munsell",
-        "rlang",
-        "viridisLite"
-      ],
-      "Hash": "c19df082ba346b0ffa6f833e92de34d1"
-    },
-    "stringi": {
-      "Package": "stringi",
-      "Version": "1.8.3",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "R",
-        "stats",
-        "tools",
-        "utils"
-      ],
-      "Hash": "058aebddea264f4c99401515182e656a"
-    },
-    "stringr": {
-      "Package": "stringr",
-      "Version": "1.5.1",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "cli",
-        "glue",
-        "lifecycle",
-        "magrittr",
-        "rlang",
-        "stringi",
-        "vctrs"
-      ],
-      "Hash": "960e2ae9e09656611e0b8214ad543207"
-    },
-    "tibble": {
-      "Package": "tibble",
-      "Version": "3.2.1",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "R",
-        "fansi",
-        "lifecycle",
-        "magrittr",
-        "methods",
-        "pillar",
-        "pkgconfig",
-        "rlang",
-        "utils",
-        "vctrs"
-      ],
-      "Hash": "a84e2cc86d07289b3b6f5069df7a004c"
-    },
-    "tidyr": {
-      "Package": "tidyr",
-      "Version": "1.3.1",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "cli",
-        "cpp11",
-        "dplyr",
-        "glue",
-        "lifecycle",
-        "magrittr",
-        "purrr",
-        "rlang",
-        "stringr",
-        "tibble",
-        "tidyselect",
-        "utils",
-        "vctrs"
-      ],
-      "Hash": "915fb7ce036c22a6a33b5a8adb712eb1"
-    },
-    "tidyselect": {
-      "Package": "tidyselect",
-      "Version": "1.2.1",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "cli",
-        "glue",
-        "lifecycle",
-        "rlang",
-        "vctrs",
-        "withr"
-      ],
-      "Hash": "829f27b9c4919c16b593794a6344d6c0"
-    },
-    "tinytex": {
-      "Package": "tinytex",
-      "Version": "0.50",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "xfun"
-      ],
-      "Hash": "be7a76845222ad20adb761f462eed3ea"
-    },
-    "tzdb": {
-      "Package": "tzdb",
-      "Version": "0.4.0",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "R",
-        "cpp11"
-      ],
-      "Hash": "f561504ec2897f4d46f0c7657e488ae1"
-    },
-    "utf8": {
-      "Package": "utf8",
-      "Version": "1.2.4",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R"
-      ],
-      "Hash": "62b65c52671e6665f803ff02954446e9"
-    },
-    "vctrs": {
-      "Package": "vctrs",
-      "Version": "0.6.5",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "cli",
-        "glue",
-        "lifecycle",
-        "rlang"
-      ],
-      "Hash": "c03fa420630029418f7e6da3667aac4a"
-    },
-    "viridisLite": {
-      "Package": "viridisLite",
-      "Version": "0.4.2",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R"
-      ],
-      "Hash": "c826c7c4241b6fc89ff55aaea3fa7491"
-    },
-    "visNetwork": {
-      "Package": "visNetwork",
-      "Version": "2.1.2",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "grDevices",
-        "htmltools",
-        "htmlwidgets",
-        "jsonlite",
-        "magrittr",
-        "methods",
-        "stats",
-        "utils"
-      ],
-      "Hash": "3e48b097e8d9a91ecced2ed4817a678d"
-    },
-    "vroom": {
-      "Package": "vroom",
-      "Version": "1.6.5",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "bit64",
-        "cli",
-        "cpp11",
-        "crayon",
-        "glue",
-        "hms",
-        "lifecycle",
-        "methods",
-        "progress",
-        "rlang",
-        "stats",
-        "tibble",
-        "tidyselect",
-        "tzdb",
-        "vctrs",
-        "withr"
-      ],
-      "Hash": "390f9315bc0025be03012054103d227c"
-    },
-    "withr": {
-      "Package": "withr",
-      "Version": "3.0.0",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "grDevices",
-        "graphics"
-      ],
-      "Hash": "d31b6c62c10dcf11ec530ca6b0dd5d35"
-    },
-    "xfun": {
-      "Package": "xfun",
-      "Version": "0.43",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "grDevices",
-        "stats",
-        "tools"
-      ],
-      "Hash": "ab6371d8653ce5f2f9290f4ec7b42a8e"
-    },
-    "yaml": {
-      "Package": "yaml",
-      "Version": "2.3.8",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Hash": "29240487a071f535f5e5d5a323b7afbd"
-    }
-  }
-}