Introduction to R for Geospatial Data: Reference

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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 Frames
• ?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.