KEY HELP TOPICS IN BASE R
Brett Melbourne University of Colorado Updated 22 Aug 2022
It is often frustrating to find what you need in the labyrinthine R help system. This list is a quick reference to the key, basic functionality of base R. It is based on a list originally compiled by Richard O'Keefe http://www.cs.otago.ac.nz/staffpriv/ok/R-help.txt
A more exhaustive search for help topics is from the html help under keywords by topic. Start html help: help.start().
THE R LANGUAGE AND PROGRAMMING
?Syntax Operators and their precedence
?Control if, while, for etc
?"function"
?switch
?Extract or ?"[" [] Read carefully and often
?Paren () {}
ARITHMETIC, LOGICAL, AND MATH FUNCTIONS
?Arithmetic + - * %% etc
?Comparison > < == != etc
?Logic & && | ! etc
?abs Absolute value
?sqrt Square root
?exp Exponents
?log Logarithms
?pi and other constants
?round and ceiling, floor, signif etc
?Trig cos, sin etc
?Special beta, gamma, binomial coef. (choose), factorial
BASIC DATA TYPES AND STRUCTURES
?numeric Continuous values
?integer Discrete values
?character Text values
?logical TRUE FALSE values
?matrix Row by column of numbers
?array Like a matrix but more than 2 dimensions
?list To store mixed data types
?data.frame Data in columns
?NA Missing values
?class Find out what type of object
?factor Categorical variables (typically for regression models)
CREATING VECTORS
?c Combine/concatonate
?":" Integer sequences
?gl Create factors
?interaction Interaction factor
?rep Repeat
?seq Sequence
BASIC OPERATIONS ON VECTORS
?length Number of elements
?"[" Indexing to extract or insert
?sum Add the elements
?max and min
?order What order are the elements in?
?sort Sort the elements
?cumsum
?lapply
?names
?rank
LOGICAL VECTORS
?"&" Logical operators, AND NOT OR
?all Is every element TRUE
?any Is any element TRUE
?identical
?ifelse If TRUE A, else B. A function, not a control structure.
?which Which indices are TRUE?
?"%in%" Same as ?match. Indices of matches
STRING (CHARACTER) OPERATORS
?paste Probably the most useful
?grep Character matching, see also help topics within
?nchar Number of characters
?sprintf
?strsplit
?strwidth
?strwrap
?substr
MATRICES
?colMeans and rowMeans
?colSums and rowSums
?ncol and nrow
?t Transpose
?"[" Indexing to extract or insert, with special attention to 'drop'
?"%*%" Matrix multiplication
?"%o%" Outer product
?"%x%" Kronecker product
?col
?colnames
?det
?diag
?dim
?dimnames
?drop
?eigen
?lower.tri
?qr
?rowsum
?solve
?svd
ELEMENTARY STATISTICS
?mean
?median
?var Variance
?sd Standard deviation
?range
?quantile
?IQR
?fivenum
?summary
LINEAR MODEL FITTING
?lm Fit a linear model to data
?summary.lm Output of the model fit
?formula Essential reading for linear model fitting
?coef Parameter estimates
?residuals
?fitted.values
?plot.lm Diagnostic plots
?predict
?AIC
?anova
?aov
?glm Fits generalized linear models
?glmer Generalized linear mixed models: library(lme4)
?lmer Linear mixed models: library(lme4)
?vcov
ECOLOGICAL AND EVOLUTIONARY MODELS (INCLUDING FITTING)
?mle Maximum likelihood: library(stats4)
?optim Workhorse for optimization
?optimize For one dimensional optimization
?logLik
?AIC
?coef
?confint
?ode Differential equations: library(deSolve)
INPUT/OUTPUT
?read.csv Read a csv data file
?write.csv Write a csv data file
?head Show the first few rows of data
?tail Show the last few rows of data
?library Load an R package
?source Read in code
?data Built in data sets in R
?save Save a dataset to an R file
?load Load a saved R data file
?scan
?read.table
?write.table
DATA/OBJECT HANDLING AND MANIPULATION
?subset Subset a data frame
?cbind and rbind. Join vectors, matrices, data frames.
?names Names of an object.
?ncol and nrow. Number of columns.
?length
?table
?aggregate
?apply
?reshape
?stack
PLOTTING
help.search("hplot") Lots of plot types and related functions
?plot Scatterplot (or default plot for object class)
?dotplot Dotplots (often a better choice than barcharts)
?barplot Barcharts
?boxplot Boxplot
?hist Histogram
?matplot Plot columns of a matrix
?pairs Scatterplot matrices
?points Add points
?lines Add lines
?curve Add a curve
?axis Add an axis
?abline Add a line (y=a+b*x)
?box Add a box outline/frame
?grid Add a grid
?segments Add line segments and arrows
?arrows Add arrows
?text Add text within a plot
?mtext Add text to plot margins
?legend Add a legend
?plotmath Add mathematical equations
?par Set line types, fonts, colors, margins, plot layouts etc
?colors See also help topics within
?jitter To jitter data points in a plot
?quartz Open a graphics window in Mac OS X
?windows Open a graphics window in Microsoft Windows
?Devices
?dev.off
DISTRIBUTIONS, RANDOM NUMBERS, AND RANDOM SAMPLES Distributions have d density, p pdf, q inverse pdf, and r random generator functions.
?dbeta
?dbinom
?dchisq
?dexp
?df
?dgamma
?dlnorm
?dmultinom
?dnbinom
?dnorm
?dpois
?dt
?dunif
?dweibull
?sample Random samples