Reference

Last updated on 2024-10-16 | Edit this page

Reference

Introduction to R and RStudio

  • Use the escape key to cancel incomplete commands or running code (Ctrl+C) if you’re using R from the shell.
  • Basic arithmetic operations follow standard order of precedence:
    • Brackets: (, )
    • Exponents: ^ or **
    • Divide: /
    • Multiply: *
    • Add: +
    • Subtract: -
  • Scientific notation is available, e.g: 2e-3
  • Anything to the right of a # is a comment, R will ignore this!
  • Functions are denoted by function_name(). Expressions inside the brackets are evaluated before being passed to the function, and functions can be nested.
  • Comparison operators: <, <=, >, >=, ==, !=
  • Use all.equal to compare numbers!
  • <- is the assignment operator. Anything to the right is evaluate, then stored in a variable named to the left.
  • ls lists all variables and functions you’ve created
  • rm can be used to remove them
  • When assigning values to function arguments, you must use =.

Project management with RStudio

  • To create a new project, go to File -> New Project
  • Some best practices:
    • Treat data as read-only
    • Keep cleaned data separate from raw dirty data
    • Treat generated output as disposable
    • Keep related data together
    • Use a consistent naming scheme

Data Structures

  • Use read.csv() to import data in memory
  • class() gives you the data class of your object
  • R automatic converts data types
  • The functions: length(), nrow(), head(), tail(), and str() can be useful to explore data.
  • Factors are a special class to deal with categorical data.
  • Lists provide a flexible data type.
  • Data frames are a special case of lists.

Exploring Data Frames

  • R makes it easy to import datasets storred remotely
  • ?data.frame is a key data structure. It is a list of vectors.
  • cbind() will add a column (vector) to a data.frame.
  • rbind() will add a row (list) to a data.frame.

Useful functions for querying data structures:

  • ?str structure, prints out a summary of the whole data structure

  • ?class what is the data structure?

  • ?head print the first n elements (rows for two-dimensional objects)

  • ?tail print the last n elements (rows for two-dimensional objects)

  • ?rownames, ?colnames, ?dimnames retrieve or modify the row names and column names of an object.

  • ?length get the number of elements in an atomic vector

  • ?nrow, ?ncol, ?dim get the dimensions of a n-dimensional object (Won’t work on atomic vectors or lists).

  • If your data frame contains factors, you need to take extra steps to add rows that contain new level values.

  • read.csv to read in data in a regular structure

    • sep argument to specify the separator
      • “,” for comma separated
      • “\t” for tab separated
    • Other arguments:
      • header=TRUE if there is a header row

Subsetting data

  • Elements can be accessed by:

    • Index
    • Name
    • Logical vectors

  • [ single square brackets:

    • extract single elements or subset vectors
    • e.g.x[1] extracts the first item from vector x.
    • extract single elements of a list. The returned value will be another list().
    • extract columns from a data.frame

  • [ with two arguments to:

    • extract rows and/or columns of
      • matrices
      • data.frames
      • e.g. x[1,2] will extract the value in row 1, column 2.
      • e.g. x[2,:] will extract the entire second column of values.

  • [[ double square brackets to extract items from lists.

  • $ to access columns or list elements by name

  • negative indices skip elements

Data frame manipulation with dplyr

  • ?select to extract variables by name.
  • ?filter return rows with matching conditions.
  • ?group_by group data by one of more variables.
  • ?summarize summarize multiple values to a single value.
  • ?mutate add new variables to a data.frame.
  • ?count and ?n to tally values in the data frame.
  • Combine operations using the ?"%>%" pipe operator.

Control flow

  • figures can be created with the grammar of graphics:
    • library(ggplot2)
    • ggplot to create the base figure
    • aesthetics specify the data axes, shape, color, and data size
    • geometry functions specify the type of plot, e.g. point, line, density, box
    • geometry functions also add statistical transforms, e.g. geom_smooth
    • scale functions change the mapping from data to aesthetics
    • facet functions stratify the figure into panels
    • aesthetics apply to individual layers, or can be set for the whole plot inside ggplot.
    • theme functions change the overall look of the plot
    • order of layers matters!
    • ggsave to save a figure.

Writing data

  • write.table to write out objects in regular format

Glossary

argument
A value given to a function or program when it runs. The term is often used interchangeably (and inconsistently) with parameter.
assign
To give a value a name by associating a variable with it.
body
(of a function): the statements that are executed when a function runs.
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.
comma-separated values
(CSV) A common textual representation for tables in which the values in each row are separated by commas.
delimiter
A character or characters used to separate individual values, such as the commas between columns in a CSV file.
documentation
Human-language text written to explain what software does, how it works, or how to use it.
floating-point number
A number containing a fractional part and an exponent. See also: integer.
for loop
A loop that is executed once for each value in some kind of set, list, or range. See also: while loop.
index
A subscript that specifies the location of a single value in a collection, such as a single pixel in an image.
integer
A whole number, such as -12343. See also: floating-point number.
library
In R, the directory(ies) where packages are stored.
package
A collection of R functions, data and compiled code in a well-defined format. Packages are stored in a library and loaded using the library() function.
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.
return statement
A statement that causes a function to stop executing and return a value to its caller immediately.
sequence
A collection of information that is presented in a specific order.
shape
An array’s dimensions, represented as a vector. For example, a 5×3 array’s shape is (5,3).
string
Short for “character string”, a sequence of zero or more characters.
syntax error
A programming error that occurs when statements are in an order or contain characters not expected by the programming language.
type
The classification of something in a program (for example, the contents of a variable) as a kind of number (e.g. floating-point, integer), string, or something else. In R the command typeof() is used to query a variables type.
while loop
A loop that keeps executing as long as some condition is true. See also: for loop.