Programming with R

Reference

Basic Operation

  • # this is a comment in R
  • Use x <- 3 to assign a value, 3, to a variable, x
  • R counts from 1, unlike many other programming languages (e.g., Python)
  • length(thing) returns the number of elements contained in the variable collection
  • c(value1, value2, value3) creates a vector
  • container[i] selects the i’th element from the variable container

List objects in current environment ls()

Remove objects in current environment rm(x)

Remove all objects from current environment rm(list = ls())

Control Flow

  • Create a contitional using if, else if, and else

    if(x > 0){
        print("value is positive")
    } else if (x < 0){
        print("value is negative")
    } else{
        print("value is neither positive nor negative")
    }
  • create a for loop to process elements in a collection one at a time

    for (i in 1:5) {
        print(i)
    }

This will print:

    1
    2
    3
    4
    5
  • Use == to test for equality
  • 3 == 3, will return TRUE,
  • 'apple' == 'orange' will return FALSE
  • X & Y is TRUE is both X and Y are true
  • X | Y is TRUE if either X or Y, or both are true

Functions

  • Defining a function:

    is_positive <- function(integer_value){
        if(integer_value > 0){
           TRUE
        } 
        else{
           FALSE
        {
    }

In R, the last executed line of a function is automatically returned

  • Specifying a default value for a function argument

    increment_me <- function(value_to_increment, value_to_increment_by = 1){
        value_to_increment + value_to_increment_by
    }

increment_me(4), will return 5

intrement_me(4, 6), will return 10

  • Call a function by using function_name(function_arguments)

    • apply family of functions:

      apply()
      sapply()
      lapply()
      mapply()

apply(dat, MARGIN = 2, mean) will return the average (mean) of each column in dat

Packages

  • Install package by using install.packages("package-name")
  • Update packages by using update.packages("package-name")
  • Load packages by using library("package-name")

Glossary

argument

A value given to a function or program when it runs. The term is often used interchangeably (and inconsistently) with parameter.

call stack

A data structure inside a running program that keeps track of active function calls. Each call’s variables are stored in a stack frame; a new stack frame is put on top of the stack for each call, and discarded when the call is finished.

comma-separated values (CSV)

A common textual representation for tables in which the values in each row are separated by commas.

comment

A remark in a program that is intended to help human readers understand what is going on, but is ignored by the computer. Comments in Python, R, and the Unix shell start with a # character and run to the end of the line; comments in SQL start with --, and other languages have other conventions.

conditional statement

A statement in a program that might or might not be executed depending on whether a test is true or false.

documentation

Human-language text written to explain what software does, how it works, or how to use it.

encapsulation

The practice of hiding something’s implementation details so that the rest of a program can worry about what it does rather than how it does it.

for loop

A loop that is executed once for each value in some kind of set, list, or range. See also: while loop.

function body

The statements that are executed inside a function.

function call

A use of a function in another piece of software.

function composition

The immediate application of one function to the result of another, such as f(g(x)).

index

A subscript that specifies the location of a single value in a collection, such as a single pixel in an image.

loop variable

The variable that keeps track of the progress of the loop.

notional machine

An abstraction of a computer used to think about what it can and will do.

parameter

A variable named in the function’s declaration that is used to hold a value passed into the call. The term is often used interchangeably (and inconsistently) with argument.

pipe

A connection from the output of one program to the input of another. When two or more programs are connected in this way, they are called a “pipeline”.

return statement

A statement that causes a function to stop executing and return a value to its caller immediately.

shape (of an array)

An array’s dimensions, represented as a vector. For example, a 5×3 array’s shape is (5,3).

silent failure

Failing without producing any warning messages. Silent failures are hard to detect and debug.

slice

A regular subsequence of a larger sequence, such as the first five elements or every second element.

stack frame

A data structure that provides storage for a function’s local variables. Each time a function is called, a new stack frame is created and put on the top of the call stack. When the function returns, the stack frame is discarded.

standard input (stdin)

A process’s default input stream. In interactive command-line applications, it is typically connected to the keyboard; in a pipe, it receives data from the standard output of the preceding process.

standard output (stdout)

A process’s default output stream. In interactive command-line applications, data sent to standard output is displayed on the screen; in a pipe, it is passed to the standard input of the next process.

string

Short for “character string”, a sequence of zero or more characters.

while loop

A loop that keeps executing as long as some condition is true. See also: for loop.