The IQUIT R video series

A series of introductory R videos.

I’ve uploaded 20+ R tutorials to YouTube for a new undergraduate course in Ecology and Evolutionary Biology at CU developed by Andrew Martin and Brett Melbourne, which in jocular anticipation was named IQUIT: an introduction to quantitative inference and thinking.

We made the videos to address the most common R programming problems that arose for students in the first iteration of the course. These short tutorials may be of use elsewhere:

Introduction to R

• everything is an object
• addition, subtraction, multiplication
• assignment

Numeric vectors: 1

• vectors vs. scalars
• create vectors with c()

Numeric vectors: 2

• how to explore the structure of a vector
• class, length, str

Functions in R

• input and output
• single argument functions: sqrt, log, exp
• multi-argument functions: round

Creating special vectors: sequences and repetition

• generate integer sequence: :
• create sequence seq (hit args)
• repeat something rep (also note argument structure)

Relational operators and logical data types

• logical types (intro to relational operators)
• ==, !=, >, <, >=, <=
• TRUE and FALSE

Character data

• character objects
• character vectors
• relational operators on character vectors

2-d data structures: matrices and data frames

• data frames can hold lots of different data types
• matrix elements must be of the same type

Intro to indexing: matrices and vectors

• indexing and subsetting with [
• review str
• a bit with relational operators

Data frame subsetting and indexing

• indexing with relational operators
• 3 ways to subset data frame: df[c("column names")], df$column, df[, 1]

R style & other secrets to happiness

• basics of R style: spacing, alignment,
• breaking up run-on lines
• workspace management
• ls, rm
• choosing good names for files and objects
• commenting

Working with data in R: 1

• reading in data with read.csv
• automatic conversion of missing values to NA

Working with data in R: 2

• mixed type errors (numbers read in as characters because one cell has a letter)
• search path errors
• is.na

Visualization part 1: intro to plot()

• plot
• arguments: xlab, ylab, col

Visualization part 2: other types of plots

• histograms, jitter plots, line graphs

Visualization part 3: adding data to plots

• adding points
• adding lines, and segments (also abline)

Visualization part 4: annotation and legends

• annotation via text
• adding legends

Visualization part 5: graphical parameters

• commonly used parameters
• for points: col, cex, pch (see ?points for pch options)
• for lines: col, lwd, lty

Looping repetitive tasks

• the power of the for loop
• creating objects to hold results ahead of time, rather than growing objects

Summarizing data

• mean, sd, var, median

Randomization & sampling distributions

• sample and rep

Debugging R code 1: letting R find your data

• working directory errors when reading in data
• problems with typos, using objects that don’t exist

Debugging R code 2: unreported errors

• errors do not always bring error messages
• steps to finding & fixing errors

Replication and sample size

• explore the effect of n on the uncertainty in a sample mean

Conveying uncertainty with confidence intervals while not obscuring the data

• constructing confidence intervals
• plot CIs using the segments function

Differences in means

• given two populations, simulate the null sampling distribution of the difference in means
• randomly assign individuals to a group using sample or some other scheme, then iteratively simulate differences in means with CIs

Figure 1: Toby Hudson [CC BY-SA 2.5 au (https://creativecommons.org/licenses/by-sa/2.5/au/deed.en)], from Wikimedia Commons