R Markdown Workshop

Challenge: YAML

Change the YAML of this document to achieve the following (hint check ?rmarkdown::html_document):

1. Made change
2. Add numbers to the sections.
3. A button to download the code.
4. Enable code_folding = "hide".
5. Change the printing of the data frame to “kable”.
6. Change the output to a pdf (you will need to comment out YAML keys that does not work with pdf).
7. Get the tex file for previous pdf (hint ?rmarkdown::pdf_document).
8. Change it so that the figures are pdf instead of png.

library(tidyverse)
library(knitr)
opts_chunk$set(fig.path = "figure/c07-")

1 Header 1

Let’s have a look at the iris data set. The dataset contains 150 observations.

1.1 Sub1-header 1

iris %>% 
  group_by(Species) %>% 
  count(name = "Count") 

1.2 Sub1-header 2

iris %>% 
  ggplot(aes(Sepal.Length, Sepal.Width, color = Species)) + 
  geom_point() + 
  labs(title = "The iris data-set") +
  theme_bw(base_size = 18) + 
  theme(legend.position = "bottom")

1.3 Sub1-header 3

iris %>% 
  ggplot(aes(Species, Sepal.Length)) + 
  geom_violin(aes(fill = Species)) +
  geom_boxplot(width = 0.1) + 
  theme_bw(base_size = 18) +
  guides(fill = FALSE)

2 Header 2

Let’s now have a look at ChickWeight data. The dataset contains 578 observations and 50 chicks.

2.1 Sub2-Header 1

ChickWeight %>% 
  ggplot(aes(Time, weight, color = Diet)) + 
  geom_point() +
  facet_wrap(~Chick) + 
  theme_minimal(base_size = 18)

2.2 Sub2-Header 2

sumdat <- ChickWeight %>% 
  filter(Time == max(Time)) %>% 
  group_by(Diet) %>% 
  summarise(Median = median(weight))

ChickWeight %>% 
  filter(Time == max(Time)) %>% 
  ggplot(aes(Diet, weight)) + 
  geom_point(size = 3, alpha = 1/3) +
  theme_minimal(base_size = 18) +
  geom_point(data = sumdat, aes(Diet, Median), color = "red", size = 5)