In biostats-r/biostats.tutorials: Apps and tutorials for statistics and data handling in R

knitr::opts_chunk$set(echo = TRUE)
library("learnr")

Assigning an object to a name

If you run an R command, the resulting object will be printed to the screen.

mean(1:10) # mean of sequence of numbers from 1:10
# result printed to screen

If you want to use the object again, you need to assign it to a name so it can be stored.

The usual assign operator is <-. The name is put on the left of the arrow and the object on the right. The result can be accessed by typing the name of the object.

result <- mean(1:10) # mean of sequence of numbers from 1:10
result
# result printed to screen

The object can now be used in further calculations.

result * result

question_checkbox(
  "Select all statements that are true",
  answer("The arrow `<-` is the best way to assign an object to a name.", correct = TRUE),
  answer("If the result of a function is not assigned to an name, it is printed to the screen and lost.", correct = TRUE),
  answer("Forgetting to assign an object is a  common error.", correct = TRUE),
  random_answer_order = TRUE,
  allow_retry = TRUE
)

Legal names

Allowed characters

Object names can only include

lower case letters
UPPER case letters
numbers
dots . and underscores _

The first character must be a letter or a dot.

question_checkbox(
  "Select all the names that are legal",
  answer("tomato", correct = TRUE),
  answer("_apple", correct = FALSE, message = "Names cannot start with an underscore"),
  answer("BASil", correct = TRUE),
  answer("extra virgin olive oil", correct = FALSE, message = "Names cannot include spaces"),
  answer(".banana", message = "The object `.banana` will be invisible", correct = TRUE),
  answer("2onions", correct = FALSE, message = "Names cannot start with a number"),
  answer("mushroom2", correct = TRUE),
  answer("carrot/cabbage", correct = FALSE, message = "Names can only include letters, numbers, `.` and `_`"),
  answer(".", correct = TRUE, message = "The object `.` will be invisible"),
  answer("spinach_potato", correct = TRUE),
  answer("kål", correct = TRUE, message = "Names with `æ`, `ø`, or `å` are legal but can cause problems. Avoid."),
  random_answer_order = TRUE,
  allow_retry = TRUE,
  try_again = "Be sure to select all seven legal names!"
)

Invisible objects

If the first character in a name is a dot, the object is invisible (this is sometime useful). Use ls(all.names = TRUE) to find any invisible objects.

question_checkbox(
  "Select all statements that are true",
  answer("Object names that start with a `.` are invisible", correct = TRUE),
  answer("Object names cannot start with a `.`", correct = FALSE),
  answer("Invisible objects appear in the RStudio Environment tab", correct = FALSE),
  answer("The R command `ls(all.names = TRUE)` will show invisible objects", correct = TRUE),
  random_answer_order = TRUE,
  allow_retry = TRUE
)

Special characters

Object names can include characters with diacritics such as æ, ø, and å but these are best avoided.

You may collaborate with people who do not have these characters on their keyboard.
Worse, computers with different locales may fail to read code with these characters (see Sys.getlocale() to find your current locale)
There are several characters that look like å but are treated as different characters by R.
Representing these characters depends on the file encoding. File encoding and locale problems open up a whole world of pain you will want to avoid!

question_checkbox(
  "Select all statements that are true",
  answer("Object names can include characters with diacritics such as `ø` and `å`.", correct = TRUE),
  answer("Using characters with diacritics is a very bad idea.", correct = TRUE),
  random_answer_order = TRUE,
  allow_retry = TRUE
)

Reserved names

Some names are reserved for R. These include function, if, else, for, while, next and TRUE. You can see the full list with ?Reserved. If you try to use one of these names, you will get an error.

Here are examples of the errors you can get trying to use reserved words as names.

function <- 7 #error

next <- 1 #error

TRUE <- FALSE #error!

question_checkbox(
  "Select all the legal names",
  answer("TRUE", correct = FALSE),
  answer("false", correct = TRUE),
  answer("T", correct = TRUE, message = "Some people use `T` as a shortcut for TRUE. Using `T` as an object name will ruin their code."),
  answer("function", correct = FALSE),
  answer("NULL", correct = FALSE),
  answer("na", correct = TRUE),
  answer("mean", correct = TRUE, message = "It is legal but can be confusing to give objects the same name existing R functions such as `mean`"),
  answer("Bergen", correct = TRUE),
  answer("Function", correct = TRUE),
  random_answer_order = TRUE,
  allow_retry = TRUE,
  try_again = "Be sure to select all six legal names!"
)

Case Sensitivity

R is a case sensitive language. This means that fun, Fun and FUN are all different objects.

question_checkbox(
  "Select all statements that are true",
  answer("R is a case sensitive language", correct = TRUE),
  answer("The names `data`, `Data`, and `DATA` refer to the same object.", correct = FALSE),
  random_answer_order = TRUE,
  allow_retry = TRUE
)

Good names

“There are only two hard things in Computer Science: cache invalidation and naming things.”

— Phil Karlton

Naming things is surprisingly hard.

Names should be legal
Names should be concise
Names should be meaningful
Avoid using names of common functions

question_checkbox(
  "Select all the good names",
  answer("T", correct = FALSE, message = "Some people use `T` as a shortcut for TRUE. Using `T` as an object name will ruin their code."),
  answer("bird_raw", correct = TRUE),
  answer("weather", correct = TRUE),
  answer("fish_clean", correct = TRUE),
  answer("jja1b", correct = FALSE),
  answer("mean", correct = FALSE, message = "It is legal but can be confusing to give objects the same name existing R functions such as `mean`"),
  answer("data", correct = FALSE, message = "`data` is not very informative, especially if you have multiple datasets to analyse"),
  answer("ddd", correct = FALSE, message = "You will never remember what `ddd` represents."),
  random_answer_order = TRUE,
  allow_retry = TRUE,
  try_again = "Be sure to select all three good names!"
)