Appendix B

R commands

(Very rough summary of the most useful command)

B.1 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 (comma separated)

x=c(1,2,4,8,16 ) #create a data vector with specified elements

y=c(1:8,1:4) #creat a data vector with 12 entries
matr=rbind(1:8,1:4) #create two rows in a 2 * 8 matrix
matc=cbind(1:8,1:4) #create two columns in a 8 * 2 matrix
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 bino-
mialitem
sample(x, size, replace = FALSE, prob = NULL) #take a sample (with or without replace-
ment) of size from x

vect=c(x,y) #combine them into one vector of length 2n

mat=cbind(x,y) #combine them into a n x 2 matrix (column wise)
mat[4,2] #display the 4th row and the 2nd column
mat[3,] #display the 3rd row
mat[,2] #display the 2nd column
mat=cbind(rep(1:4,2),rep(4:1,2)) #create a 8 * 2 matrix with repeating elements
subset(data,logical) #those objects meeting a logical criterion
subset(data.df,select=variables,logical) #get those objects from a data frame that meet a
criterion

363
364 B R commands

B.2 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 available
detach(mat) #releases the names
new=old[,-n] #drop the nth column
new=old[n,] #drop the nth row
new=subset(old,logical) #select those cases that meet the logical condition
complete = subset(data,complete.cases(data)) #find those cases with no missing values
new=old[n1:n2,n3:n4] #select the n1 through n2 rows of variables n3 through n4)

B.3 data manipulation

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
factor() #converts a numeric variable into a factor (essential for ANOVA)
gl(n,k,length) #makes an n-level,k replicates, length long vectof factors
y <- edit(x) #opens a screen editor and saves changes made to x intoy
fix(x) #opens a screen editor window and makes and saves changes to x

B.4 Statistics and transformations

max()
min()
mean()
median()
interp.median() #for interpolated values sum()
var() #produces the variance covariance matrix
sd() #standard deviation
mad() #(median absolute deviation)
fivenum() #Tukey fivenumbers min, lowerhinge, median, upper hinge, max
scale(data,scale=T) #centers around the mean and scales by the sd)
colSums(), rowSums(), colMeans(), rowMeans() #see also apply(x,1,sum)
rowsum(x,group) #sum by group
cor(x,y,use=”pair”) #correlation matrix for pairwise complete data, use=”complete” for com-
plete cases
B.6 Graphics 365

t.test(x,y) #x is a data vector, y is a grouping vector independent groups

t.test(x,y,pair=TRUE) #x is a data vector, y is a grouping vector – paired groups
pairwise.t.test(x,g) does multiple comparisons of all groups defined by g
aov(x y,data=datafile) #where x and y can be matrices
aov.ex1 = aov(Alertness Dosage,data=data.ex1) #do the analysis of variance or
aov.ex2 = aov(Alertness Gender*Dosage,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 sub-
jects/cell
boxplot(Alertness Dosage,data=data.ex1) #graphical summary appears in graphics window

lm(x y,data=dataset) #basic linear model where x and y can be matrices

lm(Y X) #Y and X can be matrices
lm(Y X1+X2)
lm(Y X|W) #separate analyses for each level of W
solve(A,B) #inverse of A * B - used for linear regression
solve(A) #inverse of A

B.5 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

B.6 Graphics

stem() #stem and leaf diagram

par(mfrow=c(2,1)) #number of rows and columns to graph

boxplot(x,notch=T,names= grouping, main=”title”) #boxplot (box and whiskers)

366 B R commands

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(x,y,pch=symb[group],col=colors[group],bg=colors[condit],cex=1.5,main=”main title”)
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()
pairs() #SPLOM (scatter plot Matrix)

matplot () #ordinate is row of the matrix

biplot () #factor loadings and factor scores on same graph
coplot(x y|z) #x by y conditioned on z
symb=c(19,25,3,23) #choose some nice plotting symbols
colors=c(”black”,”red”,”green”,”blue”) #choose some nice colors

barplot() #simple bar plot

interaction.plot () #shows means for an ANOVA design

plot(degreedays,therms) #show the data points

by(heating,Location,function(x) abline(lm(therms degreedays,data=x))) #show the best fit-
ting regression for each group

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
B.6 Graphics 367

Table B.1 Functions used in this chapter. *are part of the psych package.

Function Use Example

? Help about a function. Same as help. ?round or help(round)
%*% Binary operator to do vector or matrix multiplication A %*% B
%+% *Binary operator to do vector or matrix like sums A %+% B
== Test of equality A == B
<- Assignment A is replaced by B. This notation is preferred to = A <- B
= Assignment A is replaced by B. (see <- ) A=B
[,] Evaluate an element of a matrix , array or data.frame. A[i,j] is xi j = X[i, j]
the ith row, jth column.
$ Evaluate an element of a list or data.frame. A$B is the element a.b = A$B
with name B in A.
as.vector() Make a set of numbers into a vector A <- as.vector(A)
c() Combine two or more items. A <- c(B,C)
colnames() Find or make the column names (also see rownames) A <- colnames(B) finds col-
rownames() names(A) <- B makes
colMeans() Find column or row means of each column or row in a data.frame Ac <- colMeans(A) Ar <-
rowMeans() or matrix rowMeans(A)
curve() Plot the curve for a specified function. curve(1/(1+exp(-x)),-3,3)
data.frame() Create a data.frame. (Similar to a matrix, but can have different A <- data.frame(x,y,z)
types of elements)
describe() *Report basic descriptive statistics for a vector, matrix, or describe(X)
dataframe
diag() Create or find the diagonal of a square matrix A <- diag(B) finds
diag(B) <- A creates
dim Report the dimensions (rows,cols) of a data.frame or matrix. n.rows <- dim(x.df)[1]
exp() Raise e to the A power exp(A)
for() Execute a loop from start to finish for (i in start:finish) {some
operation using i}
function() Create a new function to do something. new.f <- function(x,y) {
new <- x + y}
if() ... else Do something if a logical condition holds. Do something else if it if(A < B) {print(“B”) } else
does not hold. {print(“A”) }
length() Report the number of elements in a vector n <- length(v)
list() A general way of storing results. A <- list(a=1,b=2,c=3.4)
log() Find the natural logarithm of X A <- log(X)
lower.tri() Logical function, true if an element is in lower triangular subma- A <- lower.tri(B)
trix of a matrix (see upper.tri)
matrix() Create a matrix of m*n elements with m rows and n columns A <- matrix(B,ncol=n)
mean() median() Find the mean, or median of a data.frame, vector, or matrix A.m <- mean(A)
model.fit() *Calculate 3 alternative goodness of fit indices (see text)
paste() Combine several numeric or text variable into a string A <- paste(‘B’,‘is’,‘4’)
pairs.panels() *Plot the scatter plot matrices (SPLOM) and report the corre- pairs.panels(x.df)
lations for a data.frame or matrix
pnorm() What is the probability of an observation, z, given the normal p <- pnorm(z)
distribution −∞ < z < ∞
qnorm() What is the z score associated with a particular quantile (prob- z <- qnorm(x)
ability) in a normal distribution 0 < x < 1
read.clipboard() *Read a data matrix or data table from the clipboard A <- read.clipboard()
rep() Repeat A N times rep(A,N)
round() Round off numbers to n digits round(x,n)
runif() Create n random numbers, uniformly distributed between a and runif(n,a,b)
b. (Defaults to a=0, b=1)
sample() Draw n samples (with or without replacement) from x sample(2,100))
set.seed() Supply a particular start value to the random number generator set.seed(42)
seq() Form the sequence from lower to upper by step size x <- seq(lower,upper,step)
t() Transpose a vector or matrix ta <- t(A)
upper.tri() Logical function, true if an element is in upper triangular sub- A <- lower.tri(B)
matrix of a matrix (see lower.tri)