A short list of the most useful R commands

A summary of the most important commands with minimal examples. See the relevant part of
the guide for better examples. For all of these commands, using the help(function) or ? function
is the most useful source of information. Unfortunately, knowing what to ask for help about is
the hardest problem.
See the R-reference card by Tom Short for a much more complete list.
Input and display
#read files with labels in first row
read.table(filename,header=TRUE)

#read a tab or space delimited file

read.table(filename,header=TRUE,sep=',')

#read csv files

x=c(1,2,4,8,16 )

#create a data vector with specified elements

y=c(1:10)

#creat a data vector with elements 1-10

n=10
x1=c(rnorm(n))

#create a n item vector of random normal

deviates

y1=c(runif(n))+n

#create another n item vector that has n added

to each random uniform distribution

z=rbinom(n,size,prob)

#create n samples of size "size" with

probability prob from the binomial

vect=c(x,y)

#combine them into one vector of length 2n

mat=cbind(x,y)

#combine them into a n x 2 matrix

mat[4,2]

#display the 4th row and the 2nd column

mat[3,]

#display the 3rd row

mat[,2]

#display the 2nd column

subset(dataset,logical)

#those objects meeting a logical criterion

subset(data.df,select=variables,logical)

#get those objects from a data frame that meet

a criterion

data.df[data.df=logical]

#yet another way to get a subset

x[order(x$B),]

#sort a dataframe by the order of the elements

in B

x[rev(order(x$B)),]

#sort the dataframe in reverse order

browse.workspace

#a menu command that creates a window with

information about all variables in the
workspace

moving around

ls()

#list the variables in the workspace

rm(x)

#remove x from the workspace

rm(list=ls())

#remove all the variables from the workspace

attach(mat)

#make the names of the variables in the matrix

or data frame available in the workspace

detach(mat)

#releases the names

new=old[,-n]

#drop the nth column

new=old[n,]
new=subset(old,logical)

#drop the nth row

#select those cases that meet the logical
condition

complete = subset(data.df,complete.cases(data.df)) #find those cases with no missing values

new=old[n1:n2,n3:n4]

#select the n1 through n2 rows of variables n3

through n4)

distributions
beta(a, b)
gamma(x)
choose(n, k)
factorial(x)
dnorm(x, mean=0, sd=1, log = FALSE) #normal distribution
pnorm(q, mean=0, sd=1, lower.tail = TRUE, log.p = FALSE)
qnorm(p, mean=0, sd=1, lower.tail = TRUE, log.p = FALSE)
rnorm(n, mean=0, sd=1)
dunif(x, min=0, max=1, log = FALSE) #uniform distribution
punif(q, min=0, max=1, lower.tail = TRUE, log.p = FALSE)
qunif(p, min=0, max=1, lower.tail = TRUE, log.p = FALSE)
runif(n, min=0, max=1)
data manipulation

replace(x, list, values)

#remember to assign this to some object i.e., x <replace(x,x==-9,NA)

#similar to the operation x[x==-9] <- NA

cut(x, breaks, labels = NULL,

include.lowest = FALSE, right = TRUE, dig.lab = 3, ...)
x.df=data.frame(x1,x2,x3 ...)

#combine different kinds of data into a data frame

as.data.frame()
is.data.frame()
x=as.matrix()
scale()

#converts a data frame to standardized scores

round(x,n)

#rounds the values of x to n decimal places

ceiling(x)

#vector x of smallest integers > x

floor(x)

#vector x of largest interger < x

as.integer(x)

#truncates real x to integers (compare to

round(x,0)

as.integer(x < cutpoint)

#vector x of 0 if less than cutpoint, 1 if greater

than cutpoint)

factor(ifelse(a < cutpoint, "Neg", "Pos"))

#is another way to dichotomize and to make a

factor for analysis

transform(data.df,variable names = some operation) #can be part of a set up for a data set
x%in%y

#tests each element of x for membership in y

y%in%x

#tests each element of y for membership in x

all(x%in%y)

#true if x is a proper subset of y

all(x)

# for a vector of logical values, are they all true?

any(x)

#for a vector of logical values, is at least one

true?

Statistics and transformations

max()
min()
mean()

median()
sum()
var()

#produces the variance covariance matrix

sd()

#standard deviation

mad()

#(median absolute deviation)

fivenum()

#Tukey fivenumbers min, lowerhinge, median, upper hinge, max

table()

#frequency counts of entries, ideally the entries are factors(although it

works with integers or even reals)

scale(data,scale=T)

#centers around the mean and scales by the sd)

cumsum(x)

#cumulative sum, etc.

cumprod(x)
cummax(x)
cummin(x)
rev(x)

#reverse the order of values in x

cor(x,y,use="pair")

#correlation matrix for pairwise complete data, use="complete" for

complete cases

aov(x~y,data=datafile) #where x and y can be matrices

aov.ex1 = aov(DV~IV,data=data.ex1)

#do the analysis of variance or

aov.ex2 = aov(DV~IV1*IV21,data=data.ex2)

#do a two way analysis of variance

summary(aov.ex1)

#show the summary table

print(model.tables(aov.ex1,"means"),digits=3)

#report the means and the number of

subjects/cell

boxplot(DV~IV,data=data.ex1)

#graphical summary appears in graphics

window

lm(x~y,data=dataset)

#basic linear model where x and y can be

matrices (see plot.lm for plotting options)

t.test(x,g)
pairwise.t.test(x,g)
power.anova.test(groups = NULL, n = NULL, between.var = NULL,
within.var = NULL, sig.level = 0.05, power = NULL)
power.t.test(n = NULL, delta = NULL, sd = 1, sig.level = 0.05,
power = NULL, type = c("two.sample", "one.sample", "paired"),
alternative = c("two.sided", "one.sided"),strict = FALSE)

More statistics: Regression and Linear model

lm(Y~X)

#Y and X can be matrices

lm(Y~X1+X2)
lm(Y~X|W)
solve(A,B)

#inverse of A * B - used for linear regression

solve(A)

#inverse of A

factanal()
princomp()

Useful additional commands

colSums (x, na.rm = FALSE, dims = 1)
rowSums (x, na.rm = FALSE, dims = 1)
colMeans(x, na.rm = FALSE, dims = 1)
rowMeans(x, na.rm = FALSE, dims = 1)
rowsum(x, group, reorder = TRUE, ...)

#finds row sums for each level of a grouping

variable

apply(X, MARGIN, FUN, ...)

#applies the function (FUN) to either rows (1) or

columns (2) on object X

apply(x,1,min)

#finds the minimum for each row

apply(x,2,max)

#finds the maximum for each column

col.max(x)

#another way to find which column has the

maximum value for each row

which.min(x)
which.max(x)
z=apply(big5r,1,which.min)

#tells the row with the minimum value for every

column

Graphics

par(mfrow=c(nrow,mcol))

#number of rows and columns to graph

par(ask=TRUE)

#ask for user input before drawing a new graph

par(omi=c(0,0,1,0) )

#set the size of the outer margins

mtext("some global title",3,outer=TRUE,line=1,cex=1.5)

#note that we seem to need to add

the global title last

#cex = character expansion factor
boxplot(x,main="title")

#boxplot (box and whiskers)

title( "some title")

#add a title to the first graph

hist()

#histogram

plot()
plot(x,y,xlim=range(-1,1),ylim=range(-1,1),main=title)
par(mfrow=c(1,1))

#change the graph window back to one figure

symb=c(19,25,3,23)
colors=c("black","red","green","blue")
charact=c("S","T","N","H")
plot(PA,NAF,pch=symb[group],col=colors[group],bg=colors[condit],cex=1.5,main="P
ostive vs. Negative Affect by Film condition")
points(mPA,mNA,pch=symb[condit],cex=4.5,col=colors[condit],bg=colors[condit])
curve()
abline(a,b)
abline(a, b, untf = FALSE, ...)
abline(h=, untf = FALSE, ...)
abline(v=, untf = FALSE, ...)
abline(coef=, untf = FALSE, ...)
abline(reg=, untf = FALSE, ...)
identify()
plot(eatar,eanta,xlim=range(-1,1),ylim=range(-1,1),main=title)
identify(eatar,eanta,labels=labels(energysR[,1]) )

#dynamically puts names

on the plots
locate()
legend()
pairs()

#SPLOM (scatter plot Matrix)

pairs.panels ()

#SPLOM on lower off diagonal, histograms on diagonal, correlations on

diagonal
#not standard R, but uses a function found in useful.r

matplot ()
biplot ())
plot(table(x))

#plot the frequencies of levels in x

x= recordPlot()

#save the current plot device output in the object x

replayPlot(x)

#replot object x

dev.control

#various control functions for printing/saving graphic files

pdf(height=6, width=6)

#create a pdf file for output

dev.of()

#close the pdf file created with pdf

layout(mat)

#specify where multiple graphs go on the page

#experiment with the magic code from Paul Murrell to do fancy

graphic location
layout(rbind(c(1, 1, 2, 2, 3, 3),c(0, 4, 4, 5, 5, 0)))
for (i in 1:5) {
plot(i, type="n")
text(1, i, paste("Plot", i), cex=4)
}

Distributions
To generate random samples from a variety of distributions
runif(n,lower,upper)
rnorm(n,mean,sd)
rbinom(n,size,p)
sample(x, size, replace = FALSE, prob = NULL)

#samples with or without replacement

Working with Dates

date <-strptime(as.character(date), "%m/%d/%y")

#change the date field to a internal form

for time
#see ?formats and ?POSIXlt
as.Date
month= months(date)

#see also weekdays, Julian

Additional functions that I have created because I needed some specific operation may be
included in the workspace by issuing the source command:

source(http://personality-project.org/r/useful.r)

These functions include:

#alpha.scale

#find coefficient alpha for a scale and a dataframe of items

#describe

give means, sd, skew, n, and se

#summ.stats

#basic summary statistics by a grouping variable

#error.crosses

(error bars in two space)

#skew

find skew

#panel.cor

taken from the examples for pairs

#pairs.panels

adapted from panel.cor --

gives a splom, histogram, and correlation

matrix
#multi.hist

#plot multiple histograms

#correct.cor

#given a correlation matrix and a vector of reliabilities, correct for reliability

#fisherz

#convert pearson r to fisher z

#paired.r

#test for difference of dependent correlations

#count.pairwise

#count the number of good cases when doing pairwise analysis

#eigen.loadings #convert eigen vector vectors to factor loadings by unnormalizing them

#principal

#yet another way to do a principal components analysis -- brute force

eignvalue decomp

#factor.congruence #find the factor congruence coeffiecints

#factor.model

#given a factor model, find the correlation matrix

#factor.residuals

#how well does it fit?

#factor.rotate

# rotate two columns of a factor matrix by theta (in degrees)

#phi2poly

#convert a matrix of phi coefficients to polychoric correlations

part of a short guide to R

Version of February 20, 2005
William Revelle
Department of Psychology
Northwestern University