Setup & Q&A

• Open RStudio

• Open your fundRmentals R Project (click the blue cube in the top right corner of RStudio)

• Open a new Rmd file for today

• In a new code chunk, load tidyverse, palmerpenguins, knitr, & kableExtra, using the library() command (install them in the console if you need to)

• In another code chunk, create a peng_data_smry table by copying & running the below code:

peng_data_smry <- palmerpenguins::penguins %>% na.omit() %>% dplyr::group_by(., species) %>%
  dplyr::summarise(., avg_mass = mean(body_mass_g), sd_mass = sd(body_mass_g), 
                   avg_flipper_l = mean(flipper_length_mm), 
                   sd_flipper_l = sd(flipper_length_mm), n = n())Copy Code

Overview

• kable tables

• Code chunk options

• Next steps

knitr::kable() tables

• knitr::kable() is just one function we can use in R to create tables

  • papaja::apa_table() is also a great one to use (install info here..)

• For a very basic table we can use kable() like this:

knitr::kable(data)Copy Code

Task: try out knitr::kable() on our peng_data_smry, knit your doc to see it!

knitr::kable() tables

To make our table prettier, we can set some basic options within the kable() function, including col.names, caption & digits:

knitr::kable(data, 
             col.names = c("New Column Name 1", "New Column Name 2", "New Column Name 3"), 
             caption = "This is the caption for my pretty table made with knitr::kable().", 
             digits = 3)Copy Code

Task: modify our kable table so that the column names are more presentable (with capital letters & spaces) & to have 2 decimal places

Solution

knitr::kable(peng_data_smry, 
             col.names = c("Species", "Mean Body Mass", "SD Body Mass", "Mean Flipper Length", 
                           "SD Flipper Length", "Frequencies"),
             digits = 2)Copy Code

kableExtra::kable_styling()

• The kableExtra package extends the functionality of knitr::kable() to make our tables super pretty

• You can pipe %>% the output of knitr::kable() into the styling functions of kableExtra

• The most common function we're going to use is kableExtra::kable_styling()

• The most useful arguments of kableExtra::kable_styling() are font_size, full_width, position, & bootstrap_options with the following options:

font_size = 12 # any number for font size
full_width = TRUE or FALSE  
position = "left", "right" or "center"
bootstrap_options = "basic", "striped", "bordered", "hover", or "condensed"Copy Code

Piping it all together %>%

To put it all together, we could write something like this:

knitr::kable(data, 
             col.names = c("New Column Name 1", "New Column Name 2", "New Column Name 3"), 
             caption = "This is the caption for my pretty table made with knitr::kable().", 
             digits = 3) %>% 
  kableExtra::kable_styling(
    font_size = 10, 
    full_width = TRUE, 
    position = "right", 
    bootstrap_options = "striped")Copy Code

Task: add in some kableExtra::kable_styling() to our kable table, choose any font_size you like, set full_width to be FALSE, position it in the center, and set bootstrap_options to be bordered, then knit your doc!

Solution

knitr::kable(peng_data_smry, 
             col.names = c("Species", "Mean Body Mass", "SD Body Mass", "Mean Flipper Length", 
                           "SD Flipper Length", "Frequencies"), 
             digits = 2) %>% 
  kableExtra::kable_styling(
    font_size = 12, 
    full_width = FALSE, 
    position = "center", 
    bootstrap_options = "bordered")Copy Code

Code Chunk Options

• Our knitted file doesn't look so great with all our code included! 😢

• But not to fear! We can easily change this by setting different code chunk options such as:

  • eval = FALSE (code is not run)
  • echo = FALSE (code is not shown, but the output is)
  • message = FALSE (messages are not shown)
  • warning = FALSE (warnings are not shown)

• We can even use a mix of these in the same code chunk to get the desired output

An example code chunk with a name & eval = TRUE set

Task: set the code chunk options so that the code creating your tables is not shown in the knitted file & see how it looks!

You made it to the end!!

• Well done for getting through to the end of this whirlwind couRse!! 🥳
• You've all done amazingly and I'm very grateful for your patience and motivation (I know deep, deep down that maybe everyone doesn't absolutely love R... so huge well done for sticking with it!)

• As a reminder, you can access all materials on the website along with some additional resources:
  • R-DEX: find teaching materials from previous UG modules
  • Useful functions from the course
  • Submit your how do I questions

• For supervising projects, students will have access to an R help desk and analyses workshops with me and Jennifer Mankin, they also have access to the R-DEX which you can refer them to if you get any 'How do I?' questions

FundRmentals feedback form

• Please feel free to answer a few questions here about the course, and also comment any things you might want or find helpful in the future
• You can be brutally honest, I'll try not to take it to heaRt 😄