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1
MATLAB °R / R Reference
May 25, 2010
David Hiebeler
Dept. of Mathematics and Statistics
University of Maine
Orono, ME 04469-5752
http://www.math.umaine.edu/~hiebeler
I wrote the first version of this reference during the Spring 2007 semester, as I learned R while
teaching my Modeling & Simulation course at the University of Maine. The course covers population
and epidemiological modeling, including deterministic and stochastic models in discrete and continuous
time, along with spatial models. Half of the class meetings are in a regular classroom, and half are in
a computer lab where students work through modeling & simulation exercises. When I taught earlier
versions of the course, it was based on Matlab only. In Spring 2007, some biology graduate students in
the class who had learned R in statistics courses asked if they could use R in my class as well, and I said
yes. My colleague Bill Halteman was a great help as I frantically learned R to stay ahead of the class.
As I went, every time I learned how to do something in R for the course, I added it to this reference, so
that I wouldn’t forget it later. Some items took a huge amount of time searching for a simple way to do
what I wanted, but at the end of the semester, I was pleasantly surprised that almost everything I do
in Matlab had an equivalent in R. I was also inspired to do this after seeing the “R for Octave Users”
reference written by Robin Hankin. I’ve continued to add to the document, with many additions based
on topics that came up while teaching courses on Advanced Linear Algebra and Numerical Analysis.
This reference is organized into general categories. There is also a Matlab index and an R index at
the end, which should make it easy to look up a command you know in one of the languages and learn
how to do it in the other (or if you’re trying to read code in whichever language is unfamiliar to you,
allow you to translate back to the one you are more familiar with). The index entries refer to the item
numbers in the first column of the reference document, rather than page numbers.
Any corrections, suggested improvements, or even just notification that the reference has been useful
are appreciated. I hope all the time I spent on this will prove useful for others in addition to myself and
my students. Note that sometimes I don’t necessarily do things in what you may consider the “best” way
in a particular language. I often tried to do things in a similar way in both languages, and where possible
I’ve avoided the use of Matlab toolboxes or R packages which are not part of the core distributions.
But if you believe you have a “better” way (either simpler, or more computationally efficient) to do
something, feel free to let me know.
Acknowledgements: Thanks to Alan Cobo-Lewis and Isaac Michaud for correcting some errors; and
Robert Bryce, Thomas Clerc, Richard Cotton, Stephen Eglen, Andreas Handel, Niels Richard Hansen,
David Khabie-Zeitoune, Michael Kiparsky, Andy Moody, Ben Morin, Lee Pang, Manas A. Pathak, Rachel
Rier, Rune Schjellerup Philosof, and Corey Yanofsky for contributions.
Permission is granted to make and distribute verbatim copies of this manual provided this permission
notice is preserved on all copies.
Permission is granted to copy and distribute modified versions of this manual under the conditions
for verbatim copying, provided that the entire resulting derived work is distributed under the terms of a
permission notice identical to this one.
Permission is granted to copy and distribute translations of this manual into another language, under the above conditions for modified versions, except that this permission notice may be stated in a
translation approved by the Free Software Foundation.
c
Copyright °2007–2010
David Hiebeler
D. Hiebeler, Matlab / R Reference
2
Contents
1 Help
3
2 Entering/building/indexing matrices
2.1 Cell arrays and lists . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
2.2 Structs and data frames . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
3
6
6
3 Computations
3.1 Basic computations . . . . . . . . . .
3.2 Complex numbers . . . . . . . . . .
3.3 Matrix/vector computations . . . . .
3.4 Root-finding . . . . . . . . . . . . . .
3.5 Function optimization/minimization
3.6 Numerical integration / quadrature .
3.7 Curve fitting . . . . . . . . . . . . .
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6
6
7
8
14
14
15
16
4 Conditionals, control structure, loops
17
5 Functions, ODEs
21
6 Probability and random values
23
7 Graphics
7.1 Various types of plotting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
7.2 Printing/saving graphics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
7.3 Animating cellular automata / lattice simulations . . . . . . . . . . . . . . . . . . . . . . .
27
27
35
36
8 Working with files
37
9 Miscellaneous
9.1 Variables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
9.2 Strings and Misc. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
38
38
39
10 Spatial Modeling
42
Index of MATLAB commands and concepts
43
Index of R commands and concepts
48
D. Hiebeler, Matlab / R Reference
1
No.
1
3
Help
Description
Show help for a function (e.g.
sqrt)
Show help for a built-in keyword (e.g. for)
General list of many help topics
Matlab
help sqrt, or helpwin sqrt to see
it in a separate window
help for
R
help(sqrt) or ?sqrt
help
4
Explore main documentation
in browser
5
Search documentation for
keyword or partial keyword
(e.g. functions which refer to
“binomial”)
doc or helpbrowser (previously it
was helpdesk, which is now being
phased out)
lookfor binomial
library() to see available libraries,
or library(help=’base’) for very
long list of stuff in base package which
you can see help for
help.start()
2
3
2
No.
6
7
Description
Enter
a row ¤ vector ~v
£
1 2 3 4
=
1
2
Enter a column vector
3
4
·
1 2
4 5
3
6
¸
Enter a matrix
9
10
Access an element of vector v
Access an element of matrix
A
Access an element of matrix
A using a single index: indices count down the first column, then down the second
column, etc.
Build the vector [2 3 4 5 6 7]
Build the vector [7 6 5 4 3 2]
Build the vector [2 5 8 11 14]
12
13
14
help.search(’binomial’)
Entering/building/indexing matrices
8
11
help(’for’) or ?’for’
Matlab
v=[1 2 3 4]
R
v=c(1,2,3,4)
or
alternatively
v=scan() then enter “1 2 3 4” and
press Enter twice (the blank line
terminates input)
[1; 2; 3; 4]
c(1,2,3,4)
(R does not distinguish between row
and column vectors.)
v(3)
A(2,3)
To
enter
values
by
row:
matrix(c(1,2,3,4,5,6), nrow=2,
byrow=TRUE) To enter values by
column: matrix(c(1,4,2,5,3,6),
nrow=2)
v[3]
A[2,3]
A(5)
A[5]
2:7
7:-1:2
2:3:14
2:7
7:2
seq(2,14,3)
[1 2 3 ; 4 5 6]
D. Hiebeler, Matlab / R Reference
No.
15
4
Description
Build a vector containing
n equally-spaced values between a and b inclusive
Build a vector containing
n logarithmically equallyspaced values between 10a
and 10b inclusive
Build a vector of length k
containing all zeros
Build a vector of length k
containing the value j in all
positions
Build an m×n matrix of zeros
Matlab
linspace(a,b,n)
R
seq(a,b,length.out=n)
seq(a,b,len=n)
logspace(a,b,n)
10^seq(a,b,len=n)
zeros(k,1) (for a column vector) or
zeros(1,k) (for a row vector)
j*ones(k,1) (for a column vector)
or j*ones(1,k) (for a row vector)
rep(0,k)
zeros(m,n)
j*ones(m,n)
v=diag(A)
[a1 a2]
cbind(a1,a2)
[a1; a2]
rbind(a1,a2)
28
Build an m × n matrix containing j in all positions
n × n identity matrix In
Build diagonal matrix A using elements of vector v as diagonal entries
Extract diagonal elements of
matrix A
“Glue” two matrices a1 and
a2 (with the same number of
rows) side-by-side
“Stack” two matrices a1 and
a2 (with the same number of
columns) on top of each other
Given vectors x and y of
lengths m and n respectively,
build n×m matrices X whose
rows are copies of x and Y
whose columns are copies of
y
Reverse the order of elements
in vector v
Column 2 of matrix A
matrix(0,nrow=m,ncol=n) or just
matrix(0,m,n)
matrix(j,nrow=m,ncol=n) or just
matrix(j,m,n)
diag(n)
diag(v,nrow=length(v)) (Note: if
you are sure the length of vector v is 2
or more, you can simply say diag(v).)
v=diag(A)
29
Row 7 of matrix A
A(7,:)
30
All elements of A as a vector,
column-by-column
Rows 2–4, columns 6–10 of A
(this is a 3 × 5 matrix)
A 3 × 2 matrix consisting of
rows 7, 7, and 6 and columns
2 and 1 of A (in that order)
Circularly shift the rows of
matrix A down by s1 elements, and right by s2 elements
16
17
18
19
20
21
22
23
24
25
26
27
31
32
33
eye(n)
diag(v)
or
just
rep(j,k)
[X,Y]=meshgrid(x,y)
m=length(x); n=length(y);
X=matrix(rep(x,each=n),nrow=n);
Y=matrix(rep(y,m),nrow=n)
v(end:-1:1)
rev(v)
A(:,2)
A(:) (gives a column vector)
A[,2] Note: that gives the result as a
vector. To make the result a m×1 matrix instead, do A[,2,drop=FALSE]
A[7,] Note: that gives the result as a
vector. To make the result a 1×n matrix instead, do A[7,,drop=FALSE]
c(A)
A(2:4,6:10)
A[2:4,6:10]
A([7 7 6], [2 1])
A[c(7,7,6),c(2,1)]
circshift(A, [s1 s2])
No simple way, but modulo arithmetic
on indices will work: m=dim(A)[1];
n=dim(A)[2]; A[(1:m-s1-1)%%m+1,
(1:n-s2-1)%%n+1]
D. Hiebeler, Matlab / R Reference
No.
34
35
36
37
38
39
40
41
42
43
44
45
46
47
5
Description
Flip the order of elements in
each row of matrix A
Flip the order of elements in
each column of matrix A
Given a single index ind into
an m × n matrix A, compute
the row r and column c of
that position (also works if
ind is a vector)
Given the row r and column
c of an element of an m × n
matrix A, compute the single
index ind which can be used
to access that element of A
(also works if r and c are vectors)
Given equal-sized vectors r
and c (each of length k), set
elements in rows (given by r)
and columns (given by c) of
matrix A equal to 12. That
is, k elements of A will be
modified.
Truncate vector v, keeping
only the first 10 elements
Extract elements of vector v
from position a to the end
All but the k th element of
vector v
All but the j th and k th elements of vector v
Reshape matrix A, making it
an m × n matrix with elements taken columnwise from
the original A (which must
have mn elements)
Extract the lower-triangular
portion of matrix A
Extract the upper-triangular
portion of matrix A
Enter n × n Hilbert matrix H
where Hij = 1/(i + j − 1)
Matlab
fliplr(A)
R
t(apply(A,1,rev))
flipud(A)
apply(A,2,rev)
[r,c] = ind2sub(size(A), ind)
r = ((ind-1) %% m) + 1
c = floor((ind-1) / m) + 1
ind = sub2ind(size(A), r, c)
ind = (c-1)*m + r
inds = sub2ind(size(A),r,c);
A(inds) = 12;
inds = cbind(r,c)
A[inds] = 12
v = v(1:10)
v(a:end)
v = v[1:10], or length(v) = 10
also works
v[a:length(v)]
v([1:(k-1) (k+1):end])
v[-k]
No simple way? Generalize the previous item
A = reshape(A,m,n)
v[c(-j,-k)]
L = tril(A)
L = A; L[upper.tri(L)]=0
U = triu(A)
U = A; U[lower.tri(U)]=0
hilb(n)
Enter an n-dimensional array,
e.g. a 3 × 4 × 2 array with the
values 1 through 24
reshape(1:24, 3, 4, 2)
reshape(1:24, [3 4 2])
Hilbert(n), but this is part of the
Matrix package which you’ll need to
install (see item 331 for how to install/load packages).
array(1:24, c(3,4,2)) (Note that
a matrix is 2-D, i.e.
rows and
columns, while an array is more generally N -D)
or
dim(A) = c(m,n)
D. Hiebeler, Matlab / R Reference
2.1
No.
48
50
Then
you
v[[1]] = 12
v[[2]] = ’hi there’
v[[3]] = matrix(runif(9),3)
w = v[[i]]
Set the name of the ith element in a list.
If you use regular indexing, i.e. w
= v(i), then w will be a 1 × 1 cell
matrix containing the contents of the
ith element of v.
(Matlab does not have names associated with elements of cell arrays.)
If you use regular indexing, i.e. w =
v[i], then w will be a list of length 1
containing the contents of the ith element of v.
names(v)[3] = ’myrandmatrix’
Use names(v) to see all names, and
names(v)=NULL to clear all names.
Structs and data frames
Description
Matlab
R
Create a matrix-like object avals=2*ones(1,6);
v=c(1,5,3,2,3,7); d=data.frame(
with different named columns yvals=6:-1:1; v=[1 5 3 2 3 7]; cbind(a=2, yy=6:1), v)
(a struct in Matlab, or a d=struct(’a’,avals,
data frame in R)
’yy’, yyvals, ’fac’, v);
Note that I (surprisingly) don’t use R for statistics, and therefore have very little experience with data
frames (and also very little with Matlab structs). I will try to add more to this section later on.
Computations
3.1
56
57
58
59
60
61
62
v{1} = 12
v{2} = ’hi there’
v{3} = rand(3)
R
v = vector(’list’,n)
can do e.g.:
w = v{i}
3
No.
52
53
54
55
Matlab
v = cell(1,n)
In general,
cell(m,n) makes an m × n cell
array. Then you can do e.g.:
Extract the ith element of a
cell/list vector v
2.2
No.
51
Cell arrays and lists
Description
Build a vector v of length n,
capable of containing different data types in different elements (called a cell array in
Matlab, and a list in R)
49
6
Basic computations
Description
a + b, a − b, ab, a/b
√
a
ab
|a| (note: for complex arguments, this computes the
modulus)
ea
ln(a)
log2 (a), log10 (a)
sin(a), cos(a), tan(a)
sin−1 (a), cos−1 (a), tan−1 (a)
sinh(a), cosh(a), tanh(a)
sinh−1 (a),
cosh−1 (a),
−1
tanh (a)
Matlab
a+b, a-b, a*b, a/b
sqrt(a)
a^b
abs(a)
R
a+b, a-b, a*b, a/b
sqrt(a)
a^b
abs(a)
exp(a)
log(a)
log2(a), log10(a)
sin(a), cos(a), tan(a)
asin(a), acos(a), atan(a)
sinh(a), cosh(a), tanh(a)
asinh(a), acosh(a), atanh(a)
exp(a)
log(a)
log2(a), log10(a)
sin(a), cos(a), tan(a)
asin(a), acos(a), atan(a)
sinh(a), cosh(a), tanh(a)
asinh(a), acosh(a), atanh(a)
D. Hiebeler, Matlab / R Reference
No.
63
64
65
66
67
68
69
70
71
7
Description
n MOD k (modulo arithmetic)
Round to nearest integer
Matlab
mod(n,k)
R
n %% k
round(x)
Round down to next lowest
integer
Round up to next largest integer
Sign of x (+1, 0, or -1)
floor(x)
round(x) (Note: R uses IEC 60559
standard, rounding 5 to the even digit
— so e.g. round(0.5) gives 0, not 1.)
floor(x)
ceil(x)
ceiling(x)
sign(x) (Note: for complex values,
this computes x/abs(x).)
erf(x)
sign(x) (Does not work with complex values)
2*pnorm(x*sqrt(2))-1
erfc(x)
2*pnorm(x*sqrt(2),lower=FALSE)
Error function erf(x)
√ Rx
2
(2/ π) 0 e−t dt
=
Complementary
error function cerf(x) =
√ R∞
2
(2/ π) x e−t dt = 1-erf(x)
Inverse error function
erfinv(x)
qnorm((1+x)/2)/sqrt(2)
Inverse complementary error erfcinv(x)
qnorm(x/2,lower=FALSE)/sqrt(2)
function
72
Binomial
coefficient nchoosek(n,k)
choose(n,k)
¶
µ
n
= n!/(n!(n − k)!)
k
Note: the various functions above (logarithm, exponential, trig, abs, and rounding functions) all work
with vectors and matrices, applying the function to each element, as well as with scalars.
3.2
No.
73
74
75
76
77
78
Complex numbers
Description
Enter a complex number
Modulus (magnitude)
Argument (angle)
Complex conjugate
Real part of z
Imaginary part of z
Matlab
1+2i
abs(z)
angle(z)
conj(z)
real(z)
imag(z)
R
1+2i
abs(z) or Mod(z)
Arg(z)
Conj(z)
Re(z)
Im(z)
D. Hiebeler, Matlab / R Reference
3.3
No.
79
8
Matrix/vector computations
Description
Vector dot product ~x · ~y =
~xT ~y
Vector cross product ~x × ~y
Matlab
dot(x,y)
R
sum(x*y)
cross(x,y)
A * B
A .* B
83
Matrix multiplication AB
Element-by-element multiplication of A and B
Transpose of a matrix, AT
Not in base R, but e.g. the xprod
function from the RSEIS package will
do it (see item 331 for how to install/load packages)
A %*% B
A * B
84
Solve A~x = ~b
85
86
87
88
89
90
Reduced echelon form of A
Determinant of A
Inverse of A
Trace of A
Compute AB −1
Element-by-element division
of A and B
Compute A−1 B
Square the matrix A
Raise matrix A to the k th
power
80
81
82
91
92
93
94
95
96
97
Raise each element of A to
the k th power
Rank of matrix A
Set w to be a vector of eigenvalues of A, and V a matrix
containing the corresponding
eigenvectors
Permuted LU factorization of
a matrix
A’ (This is actually the complex conjugate (i.e. Hermitian) transpose;
use A.’ for the non-conjugate transpose if you like; they are equivalent
for real matrices.)
A\b Warning: if there is no solution,
Matlab gives you a least-squares
“best fit.” If there are many solutions, Matlab just gives you one of
them.
rref(A)
det(A)
inv(A)
trace(A)
A/B
A ./ B
t(A) for transpose, or Conj(t(A)) for
conjugate (Hermitian) transpose
A\B
A^2
A^k
solve(A,B)
A %*% A
(No easy way to do this in R
other than repeated multiplication
A %*% A %*% A...)
A^k
A.^k
solve(A,b) Warning: this only works
with square invertible matrices.
R does not have a function to do this
det(A)
solve(A)
sum(diag(A))
A %*% solve(B)
A / B
rank(A)
[V,D]=eig(A) and then w=diag(D)
since Matlab returns the eigenvalues on the diagonal of D
qr(A)$rank
tmp=eigen(A); w=tmp$values;
V=tmp$vectors
[L,U,P]=lu(A) then the matrices
satisfy P A = LU . Note that this
works even with non-square matrices
tmp=expand(lu(Matrix(A)));
L=tmp$L; U=tmp$U; P=tmp$P then
the matrices satisfy A = P LU , i.e.
P −1 A = LU . Note that the lu and
expand functions are part of the Matrix package (see item 331 for how to
install/load packages). Also note that
this doesn’t seem to work correctly
with non-square matrices. L, U, and
P will be of class Matrix rather than
class matrix; to make them the latter,
instead do L=as.matrix(tmp$L),
U=as.matrix(tmp$U),
and
P=as.matrix(tmp$P) above.
D. Hiebeler, Matlab / R Reference
No.
98
9
Description
Singular-value
decomposition: given m × n matrix
A with rank r, find m × r
matrix P with orthonormal
columns, diagonal r × r
matrix S, and r × n matrix
QT with orthonormal rows
so that P SQT = A
Schur
decomposition of square matrix,
A = QT QH = QT Q−1 where
Q is unitary (i.e. QH Q = I)
and T is upper triangular;
QH = QT is the Hermitian
(conjugate) transpose
Matlab
[P,S,Q]=svd(A,’econ’)
R
tmp=svd(A); U=tmp$u; V=tmp$v;
S=diag(tmp$d)
[Q,T]=schur(A)
Cholesky factorization of a
square, symmetric, positive
definite matrix A = RT R,
where R is upper-triangular
QR factorization of matrix A,
where Q is orthogonal (satisfying QQT = I) and R is
upper-triangular
R = chol(A)
tmp=Schur(Matrix(A)); T=tmp@T;
Q=tmp@Q Note that Schur is part of
the Matrix package (see item 331 for
how to install/load packages). T and
Q will be of class Matrix rather than
class matrix; to make them the latter,
instead do T=as.matrix(tmp@T) and
Q=as.matrix(tmp@Q) above.
R = chol(A) Note that chol is part
of the Matrix package (see item 331
for how to install/load packages).
102
Vector norms
norm(v,1)
for
1-norm
k~v k1 ,
norm(v,2) for Euclidean norm
k~v k2 , norm(v,inf) for infinity-norm
k~v k∞ , and norm(v,p) for p-norm
P
1/p
k~v kp = ( |vi |p )
103
Matrix norms
104
Condition number cond(A) =
kAk1 kA−1 k1 of A, using 1norm
105
Condition number cond(A) =
kAk2 kA−1 k2 of A, using 2norm
Condition number cond(A) =
kAk∞ kA−1 k∞ of A, using
infinity-norm
norm(A,1) for 1-norm kAk1 ,
norm(A)
for
2-norm
kAk2 ,
norm(A,inf)
for
infinity-norm
kAk∞ , and norm(A,’fro’) for
¡P T
¢1/2
Frobenius norm
i (A A)ii
cond(A,1) (Note: Matlab also has
a function rcond(A) which computes
reciprocal condition estimator using
the 1-norm)
cond(A,2)
99
100
101
106
[Q,R]=qr(A) satisfying QR = A, or
[Q,R,E]=qr(A) to do permuted QR
factorization satisfying AE = QR
cond(A,inf)
z=qr(A); Q=qr.Q(z); R=qr.R(z);
E=diag(n)[,z$pivot] (where n is
the number of columns in A) gives
permuted QR factorization satisfying
AE = QR
R does not have a norm function for vectors; only one for
matrices.
But the following will
work:
norm(matrix(v),’1’) for
1-norm k~v k1 , norm(matrix(v),’i’)
for
infinity-norm
k~v k∞ ,
and
sum(abs(v)^p)^(1/p) for p-norm
P
1/p
k~v kp = ( |vi |p )
norm(A,’1’) for 1-norm kAk1 ,
max(svd(A)$d) for 2-norm kAk2 ,
norm(A,’i’) for infinity-norm kAk∞ ,
and norm(A,’f’) for Frobenius norm
¡P T
¢1/2
i (A A)ii
1/rcond(A,’1’)
kappa(A, exact=TRUE) (leave out
the “exact=TRUE” for an estimate)
1/rcond(A,’I’)
D. Hiebeler, Matlab / R Reference
No.
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
Description
Compute mean of all elements in vector or matrix
Compute means of columns
of a matrix
Compute means of rows of a
matrix
Compute standard deviation
of all elements in vector or
matrix
Compute standard deviations
of columns of a matrix
Compute standard deviations
of rows of a matrix
Compute variance of all elements in vector or matrix
Compute variance of columns
of a matrix
Compute variance of rows of
a matrix
Compute covariance for two
vectors of observations
Compute covariance matrix,
giving covariances between
columns of matrix A
Given matrices A and B,
build covariance matrix C
where cij is the covariance between column i of A and column j of B
Compute Pearson’s linear
correlation coefficient between elements of vectors v
and w
Compute Kendall’s tau correlation statistic for vectors v
and w
Compute Spearman’s rho
correlation
statistic
for
vectors v and w
Compute pairwise Pearson’s
correlation coefficient between columns of matrix
A
Compute matrix C of pairwise Pearson’s correlation coefficients between each pair of
columns of matrices A and B,
i.e. so cij is the correlation
between column i of A and
column j of B
10
Matlab
mean(v) for vectors, mean(A(:)) for
matrices
mean(A)
R
mean(v) or mean(A)
mean(A,2)
rowMeans(A)
std(v) for vectors, std(A(:)) for
matrices. This normalizes by n − 1.
Use std(v,1) to normalize by n.
std(A). This normalizes by n − 1.
Use std(A,1) to normalize by n
std(A,0,2) to normalize by n − 1,
std(A,1,2) to normalize by n
var(v) for vectors, var(A(:)) for
matrices. This normalizes by n − 1.
Use var(v,1) to normalize by n.
var(A). This normalizes by n − 1.
Use var(A,1) to normalize by n
var(A,0,2) to normalize by n − 1,
var(A,1,2) to normalize by n
cov(v,w) computes the 2 × 2 covariance matrix; the off-diagonal elements give the desired covariance
cov(A)
sd(v) for vectors, sd(c(A)) for matrices. This normalizes by n − 1.
colMeans(A)
sd(A). This normalizes by n − 1.
apply(A,1,sd). This normalizes by
n − 1.
var(v) for vectors, var(c(A)) for
matrices. This normalizes by n − 1.
apply(A,2,var). This normalizes by
n − 1.
apply(A,1,var). This normalizes by
n − 1.
cov(v,w)
var(A) or cov(A)
I don’t know of a direct way to
do this in Matlab. But one way is
[Y,X]=meshgrid(std(B),std(A));
X.*Y.*corr(A,B)
cov(A,B)
corr(v,w) Note: v and w must
be column vectors.
To make it
work regardless of whether they
are row or column vectors, do
corr(v(:),w(:))
corr(v,w,’type’,’kendall’)
cor(v,w)
corr(v,w,’type’,’spearman’)
cor(v,w,method=’spearman’)
corr(A) The ’type’ argument may
also be used as in the previous two
items
cor(A) The method argument may
also be used as in the previous two
items
corr(A,B) The ’type’ argument
may also be used as just above
cor(A,B) The method argument
may also be used as just above
cor(v,w,method=’kendall’)
D. Hiebeler, Matlab / R Reference
No.
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
Description
Compute sum of all elements
in vector or matrix
Compute sums of columns of
matrix
Compute sums of rows of matrix
Compute product of all elements in vector or matrix
Compute
products
of
columns of matrix
Compute products of rows of
matrix
Compute
P∞ matrix exponential
eA = k=0 Ak /k!
Compute cumulative sum of
values in vector
Compute cumulative sums of
columns of matrix
Compute cumulative sums of
rows of matrix
Compute cumulative sum
of all elements of matrix
(column-by-column)
Cumulative product of elements in vector v
Cumulative minimum or
maximum of elements in
vector v
Compute differences between
consecutive elements of vector v. Result is a vector
w 1 element shorter than v,
where element i of w is element i + 1 of v minus element
i of v
Make a vector y the same size
as vector x, which equals 4
everywhere that x is greater
than 5, and equals 3 everywhere else (done via a vectorized computation).
Compute minimum of values
in vector v
Compute minimum of all values in matrix A
Compute minimum value of
each column of matrix A
Compute minimum value of
each row of matrix A
11
Matlab
sum(v) for vectors, sum(A(:)) for
matrices
sum(A)
R
sum(v) or sum(A)
sum(A,2)
rowSums(A)
prod(v) for vectors, prod(A(:)) for
matrices
prod(A)
prod(v) or prod(A)
prod(A,2)
apply(A,1,prod)
expm(A)
cumsum(v)
expm(Matrix(A)), but this is part of
the Matrix package which you’ll need
to install (see item 331 for how to install/load packages).
cumsum(v)
cumsum(A)
apply(A,2,cumsum)
cumsum(A,2)
t(apply(A,1,cumsum))
cumsum(A(:))
cumsum(A)
cumprod(v) (Can also be used in the
various ways cumsum can)
I don’t know of an easy way to do
this in Matlab
cumprod(v) (Can also be used in the
various ways cumsum can)
cummin(v) or cummax(v)
diff(v)
diff(v)
z = [3 4]; y = z((x > 5)+1)
y = ifelse(x > 5, 4, 3)
min(v)
min(v)
min(A(:))
min(A)
min(A) (returns a row vector)
apply(A,2,min) (returns a vector)
min(A, [ ], 2) (returns a column
vector)
apply(A,1,min) (returns a vector)
colSums(A)
apply(A,2,prod)
D. Hiebeler, Matlab / R Reference
No.
143
144
145
146
Description
Given matrices A and B,
compute a matrix where each
element is the minimum of
the corresponding elements of
A and B
Given matrix A and scalar
c, compute a matrix where
each element is the minimum
of c and the corresponding element of A
Find minimum among all values in matrices A and B
Find index of the first time
min(v) appears in v, and
store that index in ind
Notes:
12
Matlab
min(A,B)
R
pmin(A,B)
min(A,c)
pmin(A,c)
min([A(:)
; B(:)])
[y,ind] = min(v)
min(A,B)
ind = which.min(v)
• Matlab and R both have a max function (and R has pmax and which.max as well) which behaves
in the same ways as min but to compute maxima rather than minima.
• Functions like exp, sin, sqrt etc. will operate on arrays in both Matlab and R, doing the
computations for each element of the matrix.
No.
147
148
149
150
151
152
153
154
155
156
Description
Number of rows in A
Number of columns in A
Dimensions of A, listed in a
vector
Number of elements in vector
v
Total number of elements in
matrix A
Max. dimension of A
Sort values in vector v
Sort values in v, putting
sorted values in s, and indices
in idx, in the sense that s[k]
= x[idx[k]]
Sort the order of the rows of
matrix m
Matlab
size(A,1)
size(A,2)
size(A)
R
nrow(A)
ncol(A)
dim(A)
length(v)
length(v)
numel(A)
length(A)
length(A)
sort(v)
[s,idx]=sort(v)
max(dim(A))
sort(v)
tmp=sort(v,index.return=TRUE);
s=tmp$x; idx=tmp$ix
sortrows(m)
This sorts according to the first column, then uses column 2 to break
ties, then column 3 for remaining
ties, etc.
Complex numbers are
sorted by abs(x), and ties are then
broken by angle(x).
Sort order of rows of matrix
m, specifying to use columns
c1, c2, c3 as the sorting
“keys”
sortrows(m, [c1 c2 c2])
m[order(m[,1]),]
This only sorts according to the first
column. To use column 2 to break
ties, and then column 3 to break further ties, do
m[order(m[,1], m[,2], m[,3]),]
Complex numbers are sorted first by
real part, then by imaginary part.
m[order(m[,c1], m[,c2],
m[,c3]),]
D. Hiebeler, Matlab / R Reference
No.
157
158
159
160
161
162
163
164
165
Description
Same as previous item, but
sort in decreasing order for
columns c1 and c2
Sort order of rows of matrix
m, and keep indices used for
sorting
To count how many values in
the vector v are between 4
and 7 (inclusive on the upper
end)
Given vector v, return list of
indices of elements of v which
are greater than 5
Given matrix A, return list
of indices of elements of A
which are greater than 5, using single-indexing
Given matrix A, generate
vectors r and c giving rows
and columns of elements of A
which are greater than 5
Given vector x (of presumably discrete values), build a
vector v listing unique values in x, and corresponding
vector c indicating how many
times those values appear in
x
Given vector x (of presumably continuous values), divide the range of values into k
equally-sized bins, and build
a vector m containing the
midpoints of the bins and a
corresponding vector c containing the counts of values in
the bins
Convolution / polynomial
multiplication (given vectors
x and y containing polynomial coefficients, their convolution is a vector containing
coefficients of the product of
the two polynomials)
13
Matlab
sortrows(m, [-c1 -c2 c2])
R
m[order(-m[,c1], -m[,c2],
m[,c3]),]
[y,i] = sortrows(m)
i=order(m[1,]); y=m[i,]
sum((v > 4) & (v <= 7))
sum((v > 4) & (v <= 7))
find(v > 5)
which(v > 5)
find(A > 5)
which(A > 5)
[r,c] = find(A > 5)
w = which(A > 5, arr.ind=TRUE);
r=w[,1]; c=w[,2]
v = unique(x); c = hist(x,v);
w=table(x); c=as.numeric(w);
v=as.numeric(names(w))
[c,m] = hist(x,k)
w=hist(x,seq(min(x),max(x),
length.out=k+1), plot=FALSE);
m=w$mids; c=w$counts
conv(x,y)
convolve(x,rev(y),type=’open’)
Note: the accuracy of this is not
as good as Matlab; e.g.
doing
v=c(1,-1); for (i in 2:20)
v=convolve(v,c(-i,1),
type=’open’) to generate the
20th -degree
Q20 Wilkinson polynomial
W (x) = i=1 (x−i) gives a coefficient
of ≈ −780.19 for x19 , rather than the
correct value -210.
D. Hiebeler, Matlab / R Reference
3.4
No.
166
167
No.
168
169
170
171
Root-finding
Description
Find roots of polynomial
whose coefficients are stored
in vector v (coefficients in v
are highest-order first)
Find zero (root) of a function
f (x) of one variable
3.5
14
Matlab
roots(v)
Define function f(x), then do
fzero(f,x0) to search for a root
near x0, or fzero(f,[a b]) to find
a root between a and b, assuming
the sign of f (x) differs at x = a
and x = b. Default forward error
tolerance (i.e. error in x) is machine
epsilon ǫmach .
R
polyroot(rev(v))
(This function
really wants the vector to have the
constant coefficient first in v; rev reverses their order to achieve this.)
Define function f(x), then do
uniroot(f, c(a,b)) to find a root
between a and b, assuming the sign
of f (x) differs at x = a and x = b.
Default forward error tolerance (i.e.
error in x) is fourth root of machine
epsilon, (ǫmach )0.25 . To specify e.g.
a tolerance of 2−52 , do uniroot(f,
c(a,b), tol=2^-52).
Function optimization/minimization
Description
Find value m which minimizes a function f (x) of one
variable within the interval
from a to b
Find value m which minimizes a function f (x, p1 , p2 )
with given extra parameters
(but minimization is only occuring over the first argument), in the interval from a
to b.
Find values of x, y, z which
minimize function f (x, y, z),
using a starting guess of x =
1, y = 2.2, and z = 3.4.
Find
values
of
x, y, z
which minimize function
f (x, y, z, p1 , p2 ),
using a
starting guess of x = 1,
y = 2.2, and z = 3.4, where
the function takes some extra
parameters (useful e.g. for
doing things like nonlinear
least-squares
optimization
where you pass in some data
vectors as extra parameters).
Matlab
Define function f(x), then do
R
Define function f(x), then do
m = fminbnd(f, a, b)
m = optimize(f,c(a,b))$minimum
Define function f(x,p1,p2), then use
an “anonymous function”:
Define function f(x,p1,p2), then:
% first define values for p1
% and p2, and then do:
m=fminbnd(@(x) f(x,p1,p2),a,b)
# first define values for p1
# and p2, and then do:
m = optimize(f, c(a,b), p1=p1,
p2=p2)$minimum
First write function f(v) which accepts a vector argument v containing
values of x, y, and z, and returns the
scalar value f (x, y, z), then do:
First write function f(v) which accepts a vector argument v containing
values of x, y, and z, and returns the
scalar value f (x, y, z), then do:
fminsearch(@f,[1 2.2 3.4])
optim(c(1,2.2,3.4),f)$par
First write function f(v,p1,p2)
which accepts a vector argument
v containing values of x, y, and
z, along with the extra parameters, and returns the scalar value
f (x, y, z, p1 , p2 ), then do:
First write function f(v,p1,p2) which
accepts a vector argument v containing values of x, y, and z, along with
the extra parameters, and returns the
scalar value f (x, y, z, p1 , p2 ), then do:
fminsearch(@f,[1 2.2 3.4], ...
[ ], p1, p2)
Or use an anonymous function:
fminsearch(@(x) f(x,p1,p2), ...
[1 2.2 3.4])
optim(c(1,2.2,3.4), f, p1=p1,
p2=p2)$par
D. Hiebeler, Matlab / R Reference
3.6
15
Numerical integration / quadrature
No.
172
Description
Numerically integrate function f (x) over interval from
a to b
Matlab
quad(f,a,b) uses
son’s quadrature,
absolute tolerance
specify absolute
quad(f,a,b,tol)
173
Simple trapezoidal numerical
integration using (x, y) values
in vectors x and y
trapz(x,y)
adaptive Simpwith a default
of 10−6 .
To
tolerance, use
R
integrate(f,a,b) uses adaptive
quadrature with default absolute
and relative error tolerances being
the fourth root of machine epsilon,
(ǫmach )0.25 ≈ 1.22 × 10−4 .
Tolerances can be specified by using
integrate(f,a,b, rel.tol=tol1,
abs.tol=tol2). Note that the function f must be written to work even
when given a vector of x values as its
argument.
sum(diff(x)*(y[-length(y)]+
y[-1])/2)
D. Hiebeler, Matlab / R Reference
3.7
No.
174
175
176
177
178
179
16
Curve fitting
Description
Fit the line y = c1 x + c0 to
data in vectors x and y.
Fit the quadratic polynomial
y = c2 x2 + c1 x + c0 to data in
vectors x and y.
Fit nth degree polynomial
y = cn xn + cn−1 xn−1 + . . . +
c1 x + c0 to data in vectors x
and y.
Fit the quadratic polynomial
with zero intercept, y =
c2 x2 + c1 x to data in vectors
x and y.
Fit natural cubic spline
(S ′′ (x) = 0 at both endpoints) to points (xi , yi )
whose coordinates are in
vectors x and y; evaluate at
points whose x coordinates
are in vector xx, storing
corresponding y’s in yy
Fit cubic spline using
Forsythe,
Malcolm
and
Moler method (third derivatives at endpoints match
third derivatives of exact cubics through the four points
at each end) to points (xi , yi )
whose coordinates are in
vectors x and y; evaluate at
points whose x coordinates
are in vector xx, storing
corresponding y’s in yy
Matlab
R
p = polyfit(x,y,1)
p = coef(lm(y ~ x))
The return vector p has the coefficients in descending order, i.e. p(1)
is c1 , and p(2) is c0 .
The return vector p has the coefficients in ascending order, i.e. p[1] is
c0 , and p[2] is c1 .
p = polyfit(x,y,2)
p = coef(lm(y ~ x + I(x^2)))
The return vector p has the coefficients in descending order, i.e. p(1)
is c2 , p(2) is c1 , and p(3) is c0 .
The return vector p has the coefficients in ascending order, i.e. p[1] is
c0 , p[2] is c1 , and p[3] is c2 .
No simple built-in way. But this will
work: coef(lm(as.formula(paste(
’y~’,paste(’I(x^’,1:n,’)’,
sep=’’,collapse=’+’)))))
This
more
concise
“lowerlevel” method will also work:
coef(lm.fit(outer(x,0:n,’^’),y))
Note that both of the above return
the coefficients in ascending order.
Also see the polyreg function in the
mda package (see item 331 for how
to install/load packages).
p = polyfit(x,y,n)
The return vector p has the coefficients in descending order, p(1) is
cn , p(2) is cn−1 , etc.
(I don’t know a simple way do this
in Matlab, other than to write a
function which computes the sum
of squared residuals and use fminsearch on that function. There is
likely an easy way to do it in the
Statistics Toolbox.)
pp=csape(x,y,’variational’);
yy=ppval(pp,xx) but note that
csape is in Matlab’s Spline
Toolbox
I’m not aware of a function to do this
in Matlab
p=coef(lm(y ~ -1 + x + I(x^2)))
The return vector p has the coefficients in ascending order, i.e. p[1] is
c1 , and p[2] is c2 .
tmp=spline(x,y,method=’natural’,
xout=xx); yy=tmp$y
tmp=spline(x,y,xout=xx);
yy=tmp$y
D. Hiebeler, Matlab / R Reference
No.
180
Description
Fit cubic spline such that
first derivatives at endpoints
match first derivatives of exact cubics through the four
points at each end) to points
(xi , yi ) whose coordinates are
in vectors x and y; evaluate
at points whose x coordinates
are in vector xx, storing corresponding y’s in yy
Fit cubic spline with periodic
boundaries, i.e. so that first
and second derivatives match
at the left and right ends
(the first and last y values
of the provided data should
also agree), to points (xi , yi )
whose coordinates are in vectors x and y; evaluate at
points whose x coordinates
are in vector xx, storing corresponding y’s in yy
Fit cubic spline with “nota-knot” conditions (the first
two piecewise cubics coincide,
as do the last two), to points
(xi , yi ) whose coordinates are
in vectors x and y; evaluate
at points whose x coordinates
are in vector xx, storing corresponding y’s in yy
181
182
4
No.
183
17
Matlab
pp=csape(x,y); yy=ppval(pp,xx)
but csape is in Matlab’s Spline
Toolbox
R
I’m not aware of a function to do this
in R
pp=csape(x,y,’periodic’);
yy=ppval(pp,xx) but csape is in
Matlab’s Spline Toolbox
tmp=spline(x,y,method=
’periodic’, xout=xx); yy=tmp$y
yy=spline(x,y,xx)
I’m not aware of a function to do this
in R
Conditionals, control structure, loops
Description
“for” loops over values in a
vector v (the vector v is often constructed via a:b)
Matlab
R
If only one command inside the loop:
for i=v
command1
command2
end
for (i in v)
command
or
for (i in v) command
If multiple commands inside the loop:
for (i in v) {
command1
command2
}
D. Hiebeler, Matlab / R Reference
No.
184
Description
“if” statements with no else
clause
18
Matlab
R
If only one command inside the clause:
if cond
command1
command2
end
if (cond)
command
or
if (cond) command
If multiple commands:
if (cond) {
command1
command2
}
185
“if/else” statement
If one command in clauses:
if cond
command1
command2
else
command3
command4
end
Note: Matlab also has an “elseif”
statement, e.g.:
if cond1
command1
elseif cond2
command2
elseif cond3
command3
else
command4
end
if (cond)
command1 else
command2
or
if (cond) cmd1 else cmd2
If multiple commands:
if (cond) {
command1
command2
} else {
command3
command4
}
Warning: the “else” must be on the
same line as command1 or the “}”
(when typed interactively at the command prompt), otherwise R thinks the
“if” statement was finished and gives
an error.
R does not have an “elseif” statement.
Logical comparisons which can be used on scalars in “if” statements, or which operate element-byelement on vectors/matrices:
Matlab
xa
x <= a
x >= a
x == a
x ~= a
R
x
x
x
x
x
x
a
<= a
>= a
== a
!= a
Description
True if x is less than a
True if x is greater than a
True if x is less than or equal to a
True if x is greater than or equal to a
True if x is equal to a
True if x is not equal to a
D. Hiebeler, Matlab / R Reference
19
Scalar logical operators:
Description
a AND b
a OR b
a XOR b
NOT a
Matlab
a && b
a || b
xor(a,b)
~a
R
a && b
a || b
xor(a,b)
!a
The && and || operators are short-circuiting, i.e. && stops as soon as any of its terms are FALSE, and
|| stops as soon as any of its terms are TRUE.
Matrix logical operators (they operate element-by-element):
Description
a AND b
a OR b
a XOR b
NOT a
No.
186
187
188
189
Description
To test whether a scalar value
x is between 4 and 7 (inclusive on the upper end)
To count how many values in
the vector x are between 4
and 7 (inclusive on the upper
end)
Test whether all values in
a logical/boolean vector are
TRUE
Test whether any values in
a logical/boolean vector are
TRUE
Matlab
a & b
a | b
xor(a,b)
~a
R
a & b
a | b
xor(a,b)
!a
Matlab
if ((x > 4) && (x <= 7))
R
if ((x > 4) && (x <= 7))
sum((x > 4) & (x <= 7))
sum((x > 4) & (x <= 7))
all(v)
all(v)
any(v)
any(v)
D. Hiebeler, Matlab / R Reference
No.
190
191
192
Description
“while” statements to do iteration (useful when you don’t
know ahead of time how
many iterations you’ll need).
E.g. to add uniform random numbers between 0 and
1 (and their squares) until
their sum is greater than 20:
More flow control: these commands exit or move on to the
next iteration of the innermost while or for loop, respectively.
“Switch” statements for integers
20
Matlab
R
mysum = 0;
mysumsqr = 0;
while (mysum < 20)
r = rand;
mysum = mysum + r;
mysumsqr = mysumsqr + r^2;
end
mysum = 0
mysumsqr = 0
while (mysum < 20) {
r = runif(1)
mysum = mysum + r
mysumsqr = mysumsqr + r^2
}
break and continue
(As with “if” statements and “for”
loops, the curly brackets are not necessary if there’s only one statement inside the “while” loop.)
break and next
switch (x)
case 10
disp(’ten’)
case {12,13}
disp(’dozen (bakers?)’)
otherwise
disp(’unrecognized’)
end
R doesn’t have a switch statement capable of doing this. It has a function
which is fairly limited for integers, but
can which do string matching. See
?switch for more. But a basic example of what it can do for integers is
below, showing that you can use it to
return different expressions based on
whether a value is 1, 2, . . ..
mystr = switch(x, ’one’, ’two’,
’three’); print(mystr)
Note that switch returns NULL if x is
larger than 3 in the above case. Also,
continuous values of x will be truncated to integers.
D. Hiebeler, Matlab / R Reference
5
No.
193
Functions, ODEs
Description
Implement
add(x,y)
a
function
Matlab
Put the following in add.m:
function retval=add(x,y)
retval = x+y;
Then you can do e.g. add(2,3)
194
21
Implement
a
function
f(x,y,z) which returns multiple values, and store those
return values in variables u
and v
Write function as follows:
function [a,b] = f(x,y,z)
a = x*y+z; b=2*sin(x-z);
Then call the function by doing:
[u,v] = f(2,8,12)
R
Enter the following, or put it in a file
and source that file:
add = function(x,y) {
return(x+y)
}
Then you can do e.g. add(2,3).
Note, the curly brackets aren’t needed
if your function only has one line.
Also, the return keyword is optional
in the above example, as the value of
the last expression in a function gets
returned, so just x+y would work
too.
Write function as follows:
f = function(x,y,z) {
a = x*y+z; b=2*sin(x-z)
return(list(a,b))
}
Then call the function by doing: tmp=f(2,8,12); u=tmp[[1]];
v=tmp[[2]]. The above is most general, and will work even when u and
v are different types of data. If they
are both scalars, the function could
simply return them packed in a vector, i.e. return(c(a,b)). If they
are vectors of the same size, the function could return them packed together into the columns of a matrix,
i.e. return(cbind(a,b)).
D. Hiebeler, Matlab / R Reference
No.
195
196
197
Description
Numerically
solve
ODE
dx/dt = 5x from t = 3 to
t = 12 with initial condition
x(3) = 7
Numerically solve system of
ODEs dw/dt = 5w, dz/dt =
3w + 7z from t = 3 to t = 12
with initial conditions w(3) =
7, z(3) = 8.2
Pass parameters such as r =
1.3 and K = 50 to an ODE
function from the command
line, solving dx/dt = rx(1 −
x/K) from t = 0 to t = 20
with initial condition x(0) =
2.5.
22
Matlab
First implement function
R
First implement function
function retval=f(t,x)
retval = 5*x;
f = function(t,x,parms) {
return(list(5*x))
}
Then
do
ode45(@f,[3,12],7)
to
plot
solution,
or
[t,x]=ode45(@f,[3,12],7) to get
back vector t containing time values
and vector x containing corresponding function values. If you want
function values at specific times,
e.g. 3, 3.1, 3.2, . . . , 11.9, 12, you can
do [t,x]=ode45(@f,3:0.1:12,7).
Note: in older versions of Matlab,
use ’f’ instead of @f.
First implement function
function retval=myfunc(t,x)
w = x(1); z = x(2);
retval = zeros(2,1);
retval(1) = 5*w;
retval(2) = 3*w + 7*z;
Then do
ode45(@myfunc,[3,12],[7;
8.2]) to plot solution,
or
[t,x]=ode45(@myfunc,[3,12],[7;
8.2]) to get back vector t containing time values and matrix x, whose
first column containing corresponding w(t) values and second column
contains z(t) values. If you want
function values at specific times, e.g.
3, 3.1, 3.2, . . . , 11.9, 12, you can do
[t,x]=ode45(@myfunc,3:0.1:12,[7;
8.2]). Note: in older versions of
Matlab, use ’f’ instead of @f.
First implement function
function retval=func2(t,x,r,K)
retval = r*x*(1-x/K)
Then do ode45(@func2,[0 20],
2.5, [ ], 1.3, 50). The empty
matrix is necessary between the initial condition and the beginning of
your extra parameters.
Then do y=lsoda(7, seq(3,12,
0.1), f,NA) to obtain solution
values at times 3, 3.1, 3.2, . . . , 11.9, 12.
The first column of y, namely y[,1]
contains the time values; the second
column y[,2] contains the corresponding function values.
Note:
lsoda is part of the deSolve package
(see item 331 for how to install/load
packages).
First implement function
myfunc = function(t,x,parms) {
w = x[1]; z = x[2];
return(list(c(5*w, 3*w+7*z)))
}
Then
do
y=lsoda(c(7,8.2),
seq(3,12, 0.1), myfunc,NA)
to obtain solution values at times
3, 3.1, 3.2, . . . , 11.9, 12.
The first
column of y, namely y[,1] contains
the time values; the second column
y[,2] contains the corresponding
values of w(t); and the third column
contains z(t). Note: lsoda is part of
the deSolve package (see item 331
for how to install/load packages).
First implement function
func2=function(t,x,parms) {
r=parms[1]; K=parms[2]
return(list(r*x*(1-x/K)))
}
Then do
y=lsoda(2.5,seq(0,20,0.1),
func2,c(1.3,50))
Note: lsoda is part of the deSolve
package (see item 331 for how to install/load packages).
D. Hiebeler, Matlab / R Reference
6
No.
198
199
200
201
202
203
204
205
206
207
208
209
210
23
Probability and random values
Description
Generate a continuous uniform random value between 0
and 1
Generate vector of n uniform
random vals between 0 and 1
Generate m×n matrix of uniform random values between
0 and 1
Generate m×n matrix of continuous uniform random values between a and b
Generate a random integer
between 1 and k
Matlab
rand
R
runif(1)
rand(n,1) or rand(1,n)
runif(n)
rand(m,n)
matrix(runif(m*n),m,n)
matrix(runif(m*n),m)
a+rand(m,n)*(b-a) or if you
have the Statistics toolbox then
unifrnd(a,b,m,n)
floor(k*rand) + 1
matrix(runif(m*n,a,b),m)
Generate m×n matrix of discrete uniform random integers between 1 and k
Generate m × n matrix where
each entry is 1 with probability p, otherwise is 0
floor(k*rand(m,n))+1 or if you
have the Statistics toolbox then
unidrnd(k,m,n)
(rand(m,n)=0)*exp(-x/mu)/mu will work
even without the Statistics Toolbox,
as long as mu is positive.
normpdf(x,mu,sigma)
or
exp(-(x-mu)^2/(2*sigma^2))/
(sqrt(2*pi)*sigma) will work even
without the Statistics Toolbox.
R
dbinom(x,n,p)
unifpdf(x,a,b)
or
((x>=a)&&(x<=b))/(b-a)
will
work even without the Statistics
Toolbox.
dunif(x,a,b)
dpois(x,lambda)
dexp(x,1/mu)
dnorm(x,mu,sigma)
unidpdf(x,n) or ((x==floor(x)) ((x==round(x)) && (x >= 1) &&
&& (x>=1)&&(x<=n))/n will work (x <= n))/n
even without the Statistics Toolbox,
as long as n is a positive integer.
228
mnpdf(x,p)
dmultinom(x,prob=p)
Note: vector p must sum to one.
Also, x and p can be vectors of
length k, or if one or both are m × k
matrices then the computations are
performed for each row.
Note: one or more of the parameters in the above “*pdf” (Matlab) or “d*” (R) functions can be
vectors, but they must be the same size. Scalars are promoted to arrays of the appropriate size.
D. Hiebeler, Matlab / R Reference
No.
229
230
231
232
233
234
The corresponding CDF functions are below:
Description
Matlab
Compute probability that a binocdf(x,n,p).
Without the
random variable from the Statistics
Toolbox,
as
long
Binomial(n, p) distribution is as n is a non-negative inless than or equal to x (i.e. teger,
this will work:
r =
the cumulative distribution 0:floor(x); sum(factorial(n)./
function, or cdf).
(factorial(r).*factorial(n-r))
.*p.^r.*(1-p).^(n-r)).
(Unfortunately, Matlab’s nchoosek
function won’t take a vector argument for k.)
Compute probability that a poisscdf(x,lambda).
Withrandom variable from the out the Statistics Toolbox, as
Poisson(λ) distribution is less long as lambda ≥
0, this
than or equal to x.
will work:
r = 0:floor(x);
sum(exp(-lambda)*lambda.^r
./factorial(r))
Compute cumulative distri- expcdf(x,mu)
or
bution function at x for a (x>=0)*(1-exp(-x/mu))
will
random variable from the ex- work even without the Statistics
ponential distribution with Toolbox, as long as mu is positive.
mean µ.
Compute cumulative distri- normcdf(x,mu,sigma) or 1/2 bution function at x for a ran- erf(-(x-mu)/(sigma*sqrt(2)))/2
dom variable from the Nor- will work even without the Statismal distribution with mean µ tics Toolbox, as long as sigma is
and standard deviation σ.
positive.
Compute cumulative distri- unifcdf(x,a,b)
or
bution function at x for a ran- (x>a)*(min(x,b)-a)/(b-a)
will
dom variable from the contin- work even without the Statistics
uous uniform distribution on Toolbox, as long as b > a.
interval (a, b).
Compute probability that a unidcdf(x,n)
or
random variable from the dis- (x>=1)*min(floor(x),n)/n
will
crete uniform distribution on work even without the Statistics
integers 1 . . . n is less than or Toolbox, as long as n is a positive
equal to x.
integer.
26
R
pbinom(x,n,p)
ppois(x,lambda)
pexp(x,1/mu)
pnorm(x,mu,sigma)
punif(x,a,b)
(x>=1)*min(floor(x),n)/n
D. Hiebeler, Matlab / R Reference
7
Graphics
7.1
Various types of plotting
No.
235
Description
Create a new figure window
Matlab
figure
236
Select figure number n
figure(n) (will create the figure if it
doesn’t exist)
237
gcf
238
Determine which figure window is currently active
List open figure windows
239
Close figure window(s)
240
241
Plot points using open circles
Plot points using solid lines
242
Plotting: color, point markers, linestyle
243
27
Plotting
axes
with
logarithmic
get(0,’children’) (The 0 handle
refers to the root graphics object.)
close to close the current figure window, close(n) to close a specified
figure, and close all to close all figures
plot(x,y,’o’)
plot(x,y)
plot(x,y,str) where str is a
string specifying color, point marker,
and/or linestyle (see table below)
(e.g. ’gs--’ for green squares with
dashed line)
semilogx, semilogy, and loglog
functions take arguments like plot,
and plot with logarithmic scales for
x, y, and both axes, respectively
R
dev.new() Notes:
internally, on
Windows this calls windows(), on
MacOS it calls quartz(), and on
Linux it calls X11(). X11() is also
available on MacOS; you can tell
R to use it by default by doing
options(device=’X11’).
In R
sometime after 2.7.0, X11 graphics
started doing antialising by default,
which makes plots look smoother
but takes longer to draw. If you are
using X11 graphics in R and notice
that figure plotting is extremely slow
(especially if making many plots),
do this before calling dev.new():
X11.options(type=’Xlib’)
or
X11.options(antialias=’none’).
Or just use e.g. X11(type=’Xlib’)
to make new figure windows. They
are uglier (lines are more jagged), but
render much more quickly.
dev.set(n) (returns the actual device selected; will be different from n
if there is no figure device with number n)
dev.cur()
dev.list()
dev.off() to close the currently active figure device, dev.off(n) to close
a specified one, and graphics.off()
to close all figure devices.
plot(x,y)
plot(x,y,type=’l’) (Note: that’s a
lower-case ’L’, not the number 1)
plot(x,y,type=str1,
pch=arg2,col=str3,
lty=arg4)
See tables below for possible values of
the 4 parameters
plot(..., log=’x’),
plot(...,
log=’y’),
and
plot(...,
log=’xy’) plot with logarithmic
scales for x, y, and both axes,
respectively
D. Hiebeler, Matlab / R Reference
No.
244
Description
Make bar graph where the x
coordinates of the bars are in
x, and their heights are in y
245
Make histogram of values in
x
Given vector x containing
discrete values, make a bar
graph where the x coordinates of bars are the values,
and heights are the counts of
how many times the values
appear in x
Given vector x containing
continuous values, lump the
data into k bins and make a
histogram / bar graph of the
binned data
Make a plot containing errorbars of height s above and below (x, y) points
246
247
248
28
Matlab
bar(x,y) Or just bar(y) if you only
want to specify heights. Note: if A
is a matrix, bar(A) interprets each
column as a separate set of observations, and each row as a different observation within a set. So a 20 × 2
matrix is plotted as 2 sets of 20 observations, while a 2 × 20 matrix is
plotted as 20 sets of 2 observations.
hist(x)
R
Can’t do this in R; but barplot(y)
makes a bar graph where you specify
the heights, barplot(y,w) also specifies the widths of the bars, and hist
can make plots like this too.
v=unique(x); c=hist(x,v);
bar(v,c)
barplot(table(x))
[c,m] = hist(x,k); bar(m,c) or
for slightly different plot style use
hist(x,k)
hist(x,seq(min(x), max(x),
length.out=k+1))
errorbar(x,y,s)
errbar(x,y,y+s,y-s) Note: errbar
is part of the Hmisc package (see
item 331 for how to install/load packages).
errbar(x,y,y+a,y-b) Note: errbar
is part of the Hmisc package (see
item 331 for how to install/load packages).
pie(v)
249
Make a plot containing errorbars of height a above and b
below (x, y) points
errorbar(x,y,b,a)
250
Other types of 2-D plots
stem(x,y)
and
stairs(x,y)
for other types of 2-D plots.
polar(theta,r) to use polar
coordinates for plotting.
hist(x)
D. Hiebeler, Matlab / R Reference
No.
251
Description
Make a 3-D plot of some data
points with given x, y, z coordinates in the vectors x, y,
and z.
252
Surface plot of data in matrix
A
253
Surface plot
√
sin(x + y) y
of x between
90 values of y
8
of f (x, y) =
for 100 values
0 and 10, and
between 2 and
29
Matlab
plot3(x,y,z) This works much like
plot, as far as plotting symbols, linetypes, and colors.
R
cloud(z~x*y) You can also use
arguments pch and col as with
plot. To make a 3-D plot with
lines, do cloud(z~x*y,type=’l’,
panel.cloud=panel.3dwire)
surf(A)
persp(A)
You can then click on the small
curved arrow in the figure window
(or choose “Rotate 3D” from the
“Tools” menu), and then click and
drag the mouse in the figure to rotate it in three dimensions.
You can include shading in the image via e.g. persp(A,shade=0.5).
There are two viewing angles you
can also specify, among other parameters, e.g. persp(A, shade=0.5,
theta=50, phi=35).
x = linspace(0,10,100);
y = linspace(2,8,90);
[X,Y] = meshgrid(x,y);
Z = sin(X+Y).*sqrt(Y);
surf(X,Y,Z)
shading flat
x = seq(0,10,len=100)
y = seq(2,8,len=90)
f = function(x,y)
return(sin(x+y)*sqrt(y))
z = outer(x,y,f)
persp(x,y,z)
contour(x,y,z)
Or
do
s=expand.grid(x=x,y=y),
and
then
wireframe(z~x*y,s)
or
wireframe(z~x*y,s,shade=TRUE)
(Note: wireframe is part of the
lattice package; see item 331 for how
to load packages). If you have vectors
x, y, and z all the same length, you
can also do symbols(x,y,z).
You have to do this when
you
make
the
plot,
e.g.
plot(x,y,xlim=c(x1,x2),
ylim=c(y1,y2))
title(main=’somestring’)
adds
a
main
title,
title(sub=’somestring’)
adds
a subtitle.
You can also include
main= and sub= arguments in a
plot command.
title(xlab=’somestring’,
ylab=’anotherstr’).
You can
also include xlab= and ylab=
arguments in a plot command.
254
Other ways of plotting the
data from the previous command
mesh(X,Y,Z),
surfc(X,Y,Z),
surfl(X,Y,Z),
contour(X,Y,Z),
pcolor(X,Y,Z),
waterfall(X,Y,Z). Also see the
slice command.
255
Set axis ranges in a figure
window
axis([x1 x2 y1 y2])
256
Add title to plot
title(’somestring’)
257
Add axis labels to plot
xlabel(’somestring’)
ylabel(’somestring’)
and
D. Hiebeler, Matlab / R Reference
No.
258
Description
Include Greek letters or symbols in plot axis labels
259
Change font size to 16 in plot
labels
260
Add grid lines to plot
grid on (and grid off to turn off)
261
262
Add a text label to a plot
Add set of text labels to a
plot. xv and yv are vectors.
Add an arrow to current plot,
with tail at (xt, yt) and head
at (xh, yh)
text(x,y,’hello’)
s={’hi’, ’there’};
text(xv,yv,s)
annotation(’arrow’, [xt xh],
[yt yh]) Note: coordinates should
be normalized figure coordinates, not
coordinates within your displayed
axes. Find and download from The
Mathworks the file dsxy2figxy.m
which converts for you, then do this:
[fx,fy]=dsxy2figxy([xt xh],
[yt yh]); annotation(’arrow’,
fx, fy)
annotation(’doublearrow’, [x0
x1], [y0 y1]) See note in previous item about normalized figure
coordinates.
legend(’first’, ’second’,
’Location’, ’NorthWest’)
263
264
Add a double-headed arrow
to current plot, with coordinates (x0, y0) and (x1, y1)
265
Add figure legend to top-left
corner of plot
Matlab
You can use basic TeX commands,
e.g.
plot(x,y);
xlabel(’\phi^2 + \mu_{i,j}’)
or
xlabel(’fecundity \phi’)
See also help tex and parts of
doc text props for more about
building labels using general LaTeX
commands
For the legends and numerical axis
labels, use set(gca, ’FontSize’,
16), and for text labels on axes
do e.g.
xlabel(’my x var’,
’FontSize’, 16)
30
R
plot(x,y,xlab=
expression(phi^2 + mu[’i,j’]))
or
plot(x,y,xlab=expression(
paste(’fecundity ’, phi)))
See also help(plotmath) and p.
98 of the R Graphics book by Paul
Murrell for more.
For
on-screen
graphics,
do
par(ps=16) followed by e.g. a plot
command. For PostScript or PDF
plots, add a pointsize=16 argument,
e.g. pdf(’myfile.pdf’, width=8,
height=8, pointsize=16)
(see
items 275 and 276)
grid()
Note that if you’ll be
printing the plot, the default style
for grid-lines is to use gray dotted lines, which are almost invisible on some printers.
You may
want to do e.g. grid(lty=’dashed’,
col=’black’) to use black dashed
lines which are easier to see.
text(x,y,’hello’)
s=c(’hi’, ’there’);
text(xv,yv,s)
arrows(xt, yt, xh, yh)
arrows(x0, y0, x1, y1, code=3)
legend(’topleft’,
legend=c(’first’, ’second’),
col=c(’red’, ’blue’),
pch=c(’*’,’o’))
Matlab note: sometimes you build a graph piece-by-piece, and then want to manually add a legend
which doesn’t correspond with the order you put things in the plot. You can manually construct a legend
by plotting “invisible” things, then building the legend using them. E.g. to make a legend with black stars
and solid lines, and red circles and dashed lines: h1=plot(0,0,’k*-’); set(h1,’Visible’, ’off’);
h2=plot(0,0,’k*-’); set(h2,’Visible’, ’off’); legend([h1 h2], ’blah, ’whoa’). Just be sure
to choose coordinates for your “invisible” points within the current figure’s axis ranges.
D. Hiebeler, Matlab / R Reference
31
No.
266
Description
Adding more things to a figure
Matlab
hold on means everything plotted
from now on in that figure window is
added to what’s already there. hold
off turns it off. clf clears the figure
and turns off hold.
267
Plot multiple data sets at
once
268
Plot sin(2x) for x between 7
and 18
plot(x,y) where x and y are 2-D
matrices. Each column of x is plotted against the corresponding column of y. If x has only one column,
it will be re-used.
fplot(’sin(2*x)’, [7 18])
269
Plot color image of integer
values in matrix A
image(A) to use array values as
raw indices into colormap, or
imagesc(A) to automatically scale
values first (these both draw row
1 of the matrix at the top of the
image); or pcolor(A) (draws row
1 of the matrix at the bottom of
the image). After using pcolor,
try the commands shading flat or
shading interp.
270
Add colorbar legend to image
plot
colorbar,
pcolor.
271
Set colormap in image
colormap(hot). Instead of hot, you
can also use gray, flag, jet (the
default), cool, bone, copper, pink,
hsv, prism. By default, the length
of the new colormap is the same as
the currently-installed one; use e.g.
colormap(hot(256)) to specify the
number of entries.
after using image or
R
points(...) and lines(...) work
like plot, but add to what’s already
in the figure rather than clearing the
figure first. points and lines are
basically identical, just with different
default plotting styles. Note: axes
are not recalculated/redrawn when
adding more things to a figure.
matplot(x,y) where x and y are 2-D
matrices. Each column of x is plotted
against the corresponding column of
y. If x has only one column, it will be
re-used.
curve(sin(2*x), 7, 18, 200)
makes the plot, by sampling the
value of the function at 200 values
between 7 and 18 (if you don’t
specify the number of points, 101
is the default). You could do this
manually yourself via commands
like
tmpx=seq(7,18,len=200);
plot(tmpx, sin(2*tmpx)).
image(A) (it rotates the matrix 90 degrees counterclockwise: it draws row
1 of A as the left column of the image, and column 1 of A as the bottom
row of the image, so the row number
is the x coord and column number is
the y coord). It also rescales colors. If
you are using a colormap with k entries, but the value k does not appear
in A, use image(A,zlim=c(1,k))
to avoid rescaling of colors.
Or
e.g. image(A,zlim=c(0,k-1)) if you
want values 0 through k−1 to be plotted using the k colors.
Use
filled.contour(A)
rather
than image(A), although it “blurs”
the data via interpolation, or
use levelplot(A) from the lattice package (see item 331 for
how to load packages).
To use
a colormap with the latter, do
e.g.
levelplot(A,col.regions=
terrain.colors(100)).
image(A,col=terrain.colors(100)).
The parameter 100 specifies the
length of the colormap.
Other
colormaps
are
heat.colors(),
topo.colors(), and cm.colors().
D. Hiebeler, Matlab / R Reference
No.
272
Description
Build your own colormap using Red/Green/Blue triplets
Matlab plotting specifications,
Symbol Color
Symbol
b
blue
.
g
green
o
r
red
x
c
cyan
+
m
magenta
*
y
yellow
s
k
black
d
w
white
v
^
<
>
p
h
Matlab
Use an n × 3 matrix; each row
gives R,G,B intensities between 0
and 1. Can use as argument with
colormap. E.g. for 2 colors: mycmap
= [0.5 0.8 0.2 ; 0.2 0.2 0.7]
32
R
Use a vector of hexadecimal strings,
each beginning with ’#’ and giving
R,G,B intensities between 00 and FF.
E.g. c(’#80CC33’,’#3333B3’); can
use as argument to col= parameter
to image. You can build such a
vector of strings from vectors of Red,
Green, and Blue intensities (each
between 0 and 1) as follows (for a
2-color example):
r=c(0.5,0.2);
g=c(0.8,0.2); b=c(0.2,0.7);
mycolors=rgb(r,g,b).
for use with plot, fplot, semilogx, semilogy, loglog, etc:
Marker
Symbol Linestyle
point (.)
solid line
circle (◦)
:
dotted line
cross (×)
-.
dash-dot line
plus sign (+)
-dashed line
asterisk (∗)
square (¤)
diamond (♦)
triangle (down) (▽)
triangle (up) (△)
triangle (left) (⊳)
triangle (right) (⊲)
pentragram star
hexagram star
R plotting specifications for col (color), pch (plotting character), and type arguments, for use with plot,
matplot, points, and lines:
col
Description
pch Description
type Description
’blue’
Blue
’a’ a (similarly for other
p
points
characters, but see ’.’
below for an exception
’green’
Green
0
open square
l
lines
’red’
Red
1
open circle
b
both
’cyan’
Cyan
2
triangle point-up
c
lines part only of “b”
’magenta’
Magenta
3
+ (plus)
o
lines, points overplotted
’yellow’
Yellow
4
× (cross)
h
histogram-like lines
’black’
Black
5
diamond
s
steps
’#RRGGBB’
hexadecimal specifica6
triangle point-down
S
another kind of steps
tion of Red, Green,
Blue
(Other names) See colors() for list of ’.’ rectangle of size 0.01
n
no plotting (can be useavailable color names.
inch, 1 pixel, or 1 point
ful for setting up axis
(1/72 inch) depending
ranges, etc.)
on device
(See table on next page
for more)
D. Hiebeler, Matlab / R Reference
33
R plotting specifications for lty (line-type) argument, for use with plot, matplot, points, and lines:
lty Description
0
blank
1
solid
2
dashed
3
dotted
4
dotdash
5
longdash
6
twodash
# #
24
25
A A
b b
18
19
20
21
22
23
12
13
14
15
16
17
6
7
8
9
10
11
0
1
2
3
4
5
.
R plotting characters, i.e. values for pch argument (from the book R Graphics, by Paul Murrell,
Chapman & Hall / CRC, 2006)
D. Hiebeler, Matlab / R Reference
No.
273
Description
Divide up a figure window
into smaller sub-figures
Matlab
subplot(m,n,k) divides the current
figure window into an m × n array of subplots, and draws in subplot number k as numbered in “reading order,” i.e. left-to-right, top-tobottom. E.g. subplot(2,3,4) selects the first sub-figure in the second
row of a 2 × 3 array of sub-figures.
You can do more complex things,
e.g. subplot(5,5,[1 2 6 7]) selects the first two subplots in the first
row, and first two subplots in the
second row, i.e. gives you a bigger
subplot within a 5 × 5 array of subplots. (If you that command followed
by e.g. subplot(5,5,3) you’ll see
what’s meant by that.)
274
Force graphics windows to
update
drawnow (Matlab normally only
updates figure windows when a
script/function finishes and returns
control to the Matlab prompt, or
under a couple of other circumstances. This forces it to update
figure windows to reflect any recent
plotting commands.)
34
R
There are several ways to do this, e.g.
using layout or split.screen, although they aren’t quite as friendly
as
Matlab’s. E.g. if you let A =
1 1 2
1 1 3 , then layout(A) will
4 5 6
divide the figure into 6 sub-figures:
you can imagine the figure divide into
a 3 × 3 matrix of smaller blocks; subfigure 1 will take up the upper-left
2 × 2 portion, and sub-figures 2–6 will
take up smaller portions, according to
the positions of those numbers in the
matrix A. Consecutive plotting commands will draw into successive subfigures; there doesn’t seem to be a way
to explicitly specify which sub-figure
to draw into next.
To use split.screen, you can
do e.g. split.screen(c(2,1)) to
split into a 2 × 1 matrix of subfigures (numbered 1 and 2). Then
split.screen(c(1,3),2) splits subfigure 2 into a 1 × 3 matrix of smaller
sub-figures (numbered 3, 4, and 5).
screen(4) will then select sub-figure
number 4, and subsequent plotting
commands will draw into it.
A third way to accomplish this is
via the commands par(mfrow=) or
par(mfcol=) to split the figure window, and par(mfg=) to select which
sub-figure to draw into.
Note that the above methods are all
incompatible with each other.
R automatically updates graphics
windows even before functions/scripts
finish executing, so it’s not necessary to explictly request it. But note
that some graphics functions (particularly those in the lattice package)
don’t display their results when called
from scripts or functions; e.g. rather
than levelplot(...) you need to do
print(levelplot(...)). Such functions will automatically display their
plots when called interactively from
the command prompt.
D. Hiebeler, Matlab / R Reference
7.2
35
Printing/saving graphics
No.
275
Description
To print/save to a PDF file
named fname.pdf
Matlab
print -dpdf fname saves the contents of currently active figure window
276
To print/save to a PostScript
file fname.ps or fname.eps
print -dps fname for black &
white PostScript;
print -dpsc
fname for color PostScript; print
-deps fname for black & white
Encapsulated PostScript;
print
-depsc fname for color Encapsulated PostScript. The first two save
to fname.ps, while the latter two
save to fname.eps.
277
To print/save to a JPEG file
fname.jpg with jpeg quality = 90 (higher quality looks
better but makes the file
larger)
print -djpeg90 fname
R
First do pdf(’fname.pdf’). Then,
do various plotting commands
to make your image, as if you
were plotting in a window.
Finally, do dev.off() to close/save
the PDF file. To print the contents of the active figure window,
do dev.copy(device=pdf,
file=’fname.pdf’); dev.off().
(But this will not work if you’ve
turned off the display list via
dev.control(displaylist=
’inhibit’).) You can also simply use
dev.copy2pdf(file=’fname.pdf’).
postscript(’fname.eps’), followed
by your plotting commands, followed by dev.off() to close/save
the file. Note: you may want to
use
postscript(’fname.eps’,
horizontal=FALSE) to save your figure in portrait mode rather than the
default landscape mode. To print the
contents of the active figure window,
do dev.copy(device=postscript,
file=’fname.eps’); dev.off().
(But this will not work if you’ve
turned off the display list via
dev.control(displaylist=
’inhibit’).) You can also include
the horizontal=FALSE argument
with dev.copy().
The command
dev.copy2eps(file=’fname.eps’)
also saves in portrait mode.
jpeg(’fname.jpg’,quality=90),
followed by your plotting commands,
followed by dev.off() to close/save
the file.
D. Hiebeler, Matlab / R Reference
7.3
No.
278
36
Animating cellular automata / lattice simulations
Description
To display images of cellular automata or other lattice
simulations while running in
real time
Matlab
Repeatedly use either pcolor or
image to display the data. Don’t
forget to call drawnow as well, otherwise the figure window will not be
updated with each image.
R
If you simply call image repeatedly,
there is a great deal of flickering/flashing. To avoid this, after
drawing the image for the first time
using e.g.
image(A), from then
on only use image(A,add=TRUE),
which avoids redrawing the entire
image (and the associated flicker).
However, this will soon consume a
great deal of memory, as all drawn
images are saved in the image buffer.
There are two solutions to that
problem: (1) every k time steps,
leave off the “add=TRUE” argument
to flush the image buffer (and get
occasional flickering), where you
choose k to balance the flickering
vs.
memory-usage tradeoff; or
(2) after drawing the first image,
do
dev.control(displaylist=
’inhibit’) to prohibit retaining the
data. However, the latter solution
means that after the simulation is
done, the figure window will not be
redrawn if it is resized, or temporarily
obscured by another window. (A
call to dev.control(displaylist=
’enable’) and then one final
image(A) at the end of the simulation will re-enable re-drawing
after resizing or obscuring, without
consuming extra memory.)
D. Hiebeler, Matlab / R Reference
8
No.
279
280
281
282
283
284
285
37
Working with files
Description
Create a folder (also known
as a “directory”)
Set/change working directory
See list of files in current
working directory
Run commands in file ‘foo.m’
or ‘foo.R’ respectively
Read data from text file
“data.txt” into matrix A
Read data from text file
“data.txt” into matrix A,
skipping the first s lines of the
file
Write data from matrix A
into text file “data.txt”
Matlab
mkdir dirname
R
dir.create(’dirname’)
cd dirname
dir
setwd(’dirname’)
dir()
foo
source(’foo.R’)
A=load(’data.txt’)
or
A=importdata(’data.txt’) Note
that both routines will ignore comments (anything on a line following
a “%” character)
A=as.matrix(read.table(
’data.txt’)) This will ignore
comments (anything on a line
following a “#” character). To ignore comments indicated by “%”,
do
A=as.matrix(read.table(
’data.txt’, comment.char=’%’))
A=as.matrix(read.table(
’data.txt’, skip=s))
tmp=importdata(’data.txt’,
’ ’,s);
a=tmp.data
save data.txt A -ascii
write(t(A), file=’data.txt’,
ncolumn=dim(A)[2])
D. Hiebeler, Matlab / R Reference
9
38
Miscellaneous
9.1
Variables
No.
286
Description
Assigning to variables
Matlab
x = 5
287
From within a function, assign a value to variable y
in the base environment (i.e.
the command prompt environment)
From within a function, access the value of variable y
in the base environment (i.e.
the command prompt environment)
assignin(’base’, ’y’, 7)
who
whos
whos ab
whos *ab*
ls.str(pattern=’ab’)
openvar(A), or double-click on the
variable in the Workspace pane (if
it’s being displayed) of your Matlabdesktop
fix(A)
294
295
296
297
Short list of defined variables
Long list of defined variables
See detailed info about the
variable ab
See detailed info about all
variables with “ab” in their
name
Open graphical data editor,
to edit the value of variable
A (useful for editing values in
a matrix, though it works for
non-matrix variables as well)
Clear one variable
Clear two variables
Clear all variables
See what type of object x is
get(’y’, envir=globalenv())
Though note that inside a function,
if there isn’t a local variable y, then
just the expression y will look for one
in the base environment, but if there
is a local y then that one will be used
instead.
ls()
ls.str()
str(ab)
clear x
clear x y
clear all
class(x)
298
(Variable names)
Variable names must begin with a
letter, but after that they may contain any combination of letters, digits, and the underscore character.
Names are case-sensitive.
299
Result of last command
ans contains the result of the last
command which did not assign its
value to a variable. E.g. after 2+5;
x=3, then ans will contain 7.
rm(x)
rm(x,y)
rm(list=ls())
class(x) and typeof(x) give different aspects of the “type” of x
Variable names may contain letters,
digits, the period, and the underscore
character. They cannot begin with a
digit or underscore, or with a period
followed by a digit. Names are casesensitive.
.Last.value contains the result of
the last command, whether or not its
value was assigned to a variable. E.g.
after 2+5; x=3, then .Last.value will
contain 3.
288
289
290
291
292
293
evalin(’base’, ’y’)
R
x <- 5 or x = 5 Note: for compatibility with S-plus, many people prefer
the first form.
y <<- 7
D. Hiebeler, Matlab / R Reference
9.2
39
Strings and Misc.
No.
300
Description
Line continuation
301
Controlling
output
formatting
Matlab
If you want to break up a Matlab
command over more than one line,
end all but the last line with three
periods: “...”. E.g.:
x = 3 + ...
4
or
x = 3 ...
+ 4
of
format short g
format long g are
help format
handy;
and
see
302
303
304
Exit the program
Comments
Display a string
quit or exit
% this is a comment
disp(’hi there’)
or
omit
trailing
newline
fprintf(’hi there’)
305
Display a string containing
single quotes
306
Give prompt and read numerical input from user
disp(’It’’s nice’)
or
to
omit
trailing
newline
fprintf(’It’’s nice’)
x = input(’Enter data:’)
307
Give prompt and read character (string) input from user
Concatenate strings
Concatenate strings stored in
a vector
308
309
310
Extract substring of a string
311
Determine whether elements
of a vector are in a set, and
give positions of corresponding elements in the set.
to
use
x = input(’Enter string:’,’s’)
[’two hal’ ’ves’]
v={’two ’, ’halves’};
strcat(v{:}) But note that
this drops trailing spaces on
strings. To avoid that, instead do
strcat([v{:}])
text1=’hi there’;
text2=text(2:6)
x = {’a’, ’aa’, ’bc’, ’c’}; y
= {’da’, ’a’, ’bc’, ’a’, ’bc’,
’aa’}; [tf, loc]=ismember(x,y)
Then loc contains the locations of
last occurrences of elements of x
in the set y, and 0 for unmatched
elements.
R
In R, you can spread commands out
over multiple lines, and nothing extra is necessary. R will continue reading input until the command is complete. However, this only works when
the syntax makes it clear that the first
line was not complete. E.g.:
x = 3 +
4
works, but
x = 3
+ 4
does not treat the second line as a continuation of the first.
options(digits=6) tells R you’d like
to use 6 digits of precision in values it
displays (it is only a suggestion, not
strictly followed)
q() or quit()
# this is a comment
print(’hi there’) Note:
to
avoid
having
double-quotes
around the displayed string, do
print(’hi there’, quote=FALSE)
or print(noquote(’hi there’)).
print(’It\’s nice’)
or
print("It’s nice")
print(’Enter data:’); x=scan()
But note: if in a script and you use
the Edit → Execute menu item to
run it, the selected text after the
scan statement will be used as source
for the input, rather than keyboard.
x = readline(’Enter string:’)
paste(’two hal’, ’ves’, sep=’’)
v=c(’two ’, ’halves’);
paste(v, collapse=’’)
text1=’hi there’;
text2=substr(text1,2,6)
x = c(’a’, ’aa’, ’bc’, ’c’); y
= c(’da’, ’a’, ’bc’, ’a’, ’bc’,
’aa’); loc=match(x,y) Then loc
contains the locations of first occurences of elements of x in the set
y, and NA for unmatched elements.
D. Hiebeler, Matlab / R Reference
No.
312
Description
Find indices of regular expression pattern p in string s
313
Perform some commands
only if the regular expression
p is contained in the string s
314
315
316
317
318
319
320
321
322
323
324
40
Matlab
v=regexp(s,p)
R
v=gregexpr(p,s)[[1]]
(The
returned
vector
also
has
a
“match.length”
attribute
giving lengths of the matches; this
attribute can be removed via
attributes(v)=NULL.)
if (regexp(s,p)
...commands...
end
if (grepl(p,s)) {
...commands...
}
Convert number to string
Use sprintf to create a
formatted string. Use %d for
integers (“d” stands for “decimal”, i.e. base 10), %f for
floating-point numbers, %e
for scientific-notation floating
point, %g to automatically
choose %e or %f based on
the value. You can specify
field-widths/precisions,
e.g. %5d for integers with
padding to 5 spaces, or %.7f
for floating-point with 7
digits of precision. There are
many other options too; see
the docs.
Machine epsilon ǫmach , i.e.
difference between 1 and the
next largest double-precision
floating-point number
Pause for x seconds
Wait for user to press any key
num2str(x)
as.character(x)
x=2; y=3.5;
s=sprintf(’x is %d, y=%g’, ...
x, y)
x=2; y=3.5
s=sprintf(’x is %d, y is %g’,
x, y)
eps (See help eps for various other
things eps can give.)
.Machine$double.eps
pause(x)
pause
Produce a beep (or possibly
a visual signal, depending on
preferences set)
Measure CPU time used to
do some commands
Measure elapsed (“wallclock”) time used to do some
commands
Print an error message an interrupt execution
Print a warning message
Putting multiple statements
on one line
beep
Sys.sleep(x)
Don’t know of a way to do this in R,
but scan(quiet=TRUE) will wait until
the user presses the Enter key
alarm()
t1=cputime; ...commands... ;
cputime-t1
tic; ...commands... ; toc or
t1=clock; ...commands... ;
etime(clock,t1)
error(’Problem!’)
t1=proc.time(); ...commands...
; (proc.time()-t1)[1]
t1=proc.time(); ...commands...
; (proc.time()-t1)[3]
warning(’Smaller problem!’)
Separate statements by commas or
semicolons. A semicolon at the end
of a statement suppresses display of
the results (also useful even with just
a single statement on a line), while a
comma does not.
warning(’Smaller problem!’)
Separate statements by semicolons.
stop(’Problem!’)
D. Hiebeler, Matlab / R Reference
No.
325
326
Description
Evaluate contents of a string
s as command(s).
Get a command prompt for
debugging, while executing a
script or function. While at
that prompt, you can type expressions to see the values of
variables, etc.
327
Show where a command is
328
Query/set the search path.
41
Matlab
eval(s)
R
eval(parse(text=s))
Insert the command keyboard in
your file. Note that your prompt will
change to K>>. When you are done
debugging and want to continue executing the file, type return.
Insert the command browser() in
your file. Note that your prompt will
change to Browse[1]>. When you are
done debugging and want to continue
executing the file, either type c or just
press return (i.e. enter a blank line).
Note, if you type n, you enter the step
debugger.
R does not execute commands directly
from files, so there is no equivalent
command.
which sqrt shows you where the file
defining the sqrt function is (but
note that many basic functions are
“built in,” so the Matlab function file is really just a stub containing documentation). This is useful if a command is doing something
strange, e.g. sqrt isn’t working. If
you’ve accidentally defined a variable
called sqrt, then which sqrt will
tell you, so you can clear sqrt to
erase it so that you can go back to
using the function sqrt.
path displays the current search path
(the list of places Matlab searches
for commands you enter). To add a
directory ~/foo to the beginning of
the search path, do
R does not use a search path to look
for files.
addpath ~/foo -begin
329
Startup sequence
330
Shutdown sequence
or to add it to the end of the path,
do addpath ~/foo -end (Note: you
should generally add the full path
of a directory, i.e. in Linux or Mac
OS-X something like ~/foo as above
or of the form /usr/local/lib/foo,
while under Windows it would be
something like C:/foo)
If a file startup.m exists in the
startup directory for Matlab, its
contents are executed.
(See the
Matlab docs for how to change the
startup directory.)
Upon typing quit or exit, Matlab
will run the script finish.m if present
somewhere in the search path.
If a file .Rprofile exists in the current directory or the user’s home directory (in that order), its contents
are sourced; saved data from the file
.RData (if it exists) are then loaded.
If a function .First() has been defined, it is then called (so the obvious
place to define this function is in your
.Rprofile file).
Upon typing q() or quit(), R will call
the function .Last() if it has been defined (one obvious place to define it
would be in the .Rprofile file)
D. Hiebeler, Matlab / R Reference
No.
331
Description
Install and load a package.
10
No.
332
333
334
335
Matlab
Matlab does not have packages. It
has toolboxes, which you can purchase and install. “Contributed”
code (written by end users) can simply be downloaded and put in a directory which you then add to Matlab’s path (see item 328 for how to
add things to Matlab’s path).
42
R
To install e.g. the deSolve package, you can use the command
install.packages(’deSolve’).
You then need to load the package
in order to use it, via the command
library(’deSolve’). When running
R again later you’ll need to load the
package again to use it, but you
should not need to re-install it. Note
that the lattice package is typically
included with binary distributions of
R, so it only needs to be loaded, not
installed.
Spatial Modeling
Description
Take an L×L matrix A of
0s and 1s, and “seed” fraction p of the 0s (turn them
into 1s), not changing entries
which are already 1.
Take an L × L matrix A of 0s
and 1s, and “kill” fraction p
of the 1s (turn them into 0s),
not changing the rest of the
entries
Do “wraparound” on a coordinate newx that you’ve already calculated. You can
replace newx with x+dx if
you want to do wraparound
on an offset x coordinate.
Randomly initialize a portion
of an array: set fraction p of
sites in rows iy1 through iy2
and columns ix1 through ix2
equal to 1 (and set the rest of
the sites in that block equal
to zero). Note: this assume
iy1 < iy2 and ix1 < ix2.
Matlab
A = (A | (rand(L) < p))*1;
R
A = (A | (matrix(runif(L^2),L)
< p))*1
A = (A & (rand(L) < 1-p))*1;
A = (A & (matrix(runif(L^2),L)
< 1-p))*1
mod(newx-1,L)+1 Note: for portability with other languages such as
C which handle MOD of negative
values differently, you may want to
get in the habit of instead doing
mod(newx-1+L,L)+1
dx=ix2-ix1+1; dy=iy2-iy1+1;
A(iy1:iy2,ix1:ix2) = ...
(rand(dy,dx) < p0)*1;
((newx-1) %% L) + 1 Note:
for
portability with other languages such
as C which handle MOD of negative values differently, you may want
to get in the habit of instead doing
((newx-1+L)%%L) + 1
dx=ix2-ix1+1; dy=iy2-iy1+1;
A[iy1:iy2,ix1:ix2] =
(matrix(runif(dy*dx),dy) <
p0)*1
INDEX OF MATLAB COMMANDS AND CONCEPTS
43
Index of MATLAB commands and concepts
’, 83
,, 324
.*, 82
..., 300
./, 90
.^, 94
/, 89
:, 12–14
;, 324
=, 286
[, 6–8
%, 303
&, 186, 187
^, 54, 92, 93
\, 84, 91
{ 49
abs, 55, 74
acos, 60
acosh, 62
addpath, 328
all, 188
angle, 75
annotation, 263, 264
ans, 299
any, 189
arrows in plots, 263, 264
asin, 60
asinh, 62
assignin, 287
atan, 60
atanh, 62
average, see mean
axis, 255
bar, 244, 246, 247
beep, 319
binocdf, 229
binopdf, 222
binornd, 213
boolean tests
scalar, 186
vector, 187–189
break, 191
cd, 280
ceil, 66
cell, 48
cell arrays, 48
extracting elements of, 49
cellular automata animation, 278
chol, 100
circshift, 33
class, 297
clear, 294–296
clf, 266
clock, 321
close, 239
colon, see :
colorbar, 270
colormap
building your own, 272
colormap, 271, 272
column vector, 7
comments, 303
complex numbers, 73–78
cond, 104–106
conj, 76
continue, 191
contour, 254
conv, 165
corr, 118–123
cos, 59
cosh, 61
cov, 116, 117
cputime, 320
cross, 80
csape, 178, 180, 181
cubic splines, 179, 180
natural, 178
not-a-knot, 182
periodic, 181
cumprod, 135
cumsum, 131–134
cumulative distribution functions
binomial, 229
continuous uniform on interval (a, b), 233
discrete uniform from 1..n, 234
exponential, 231
normal, 232
Poisson, 230
debugging, 326
det, 86
diag, 22, 23
diff, 137
differential equations, see ode45
dir, 281
disp, 304, 305
doc, 4
dot, 79
INDEX OF MATLAB COMMANDS AND CONCEPTS
drawnow, 274, 278
echelon form, see matrix
eig, 96
element-by-element matrix operations, see matrix
else, 185
elseif, 185
end, 40
eps, 316
erf, 68
erfc, 69
erfcinv, 71
erfinv, 70
error, 322
errorbar, 248, 249
etime, 321
eval, 325
evalin, 288
exit, 302, 330
exp, 56
expcdf, 231
expm, 130
exppdf, 224
exprnd, 215
eye, 21
figure, 235, 236
file
running commands in, 282
text
reading data from, 283, 284
saving data to, 285
find, 160–162
finish.m, 330
fliplr, 34
flipud, 35
floor, 65
fminbnd, 168, 169
fminsearch, 170, 171
font size in plots, 259
for, 183
format, 301
fplot, 268
fprintf, 304, 305
function
multi-variable
minimization, 170
minimization over first parameter only, 169
minimization over only some parameters,
171
single-variable
minimization, 168
user-written, 193
returning multiple values, 194
fzero, 167
gca, 259
gcf, 237
get, 238
Greek letters
in plot labels, 258
grid, 260
help, 1–3
helpbrowser, 4
helpdesk, 4
hilb, 46
hist, 163, 164, 245, 246
hold, 266
identity, see matrix
if, 184–186
imag, 78
image, 269, 278
imagesc, 269
importdata, 283, 284
ind2sub, 36
indexing
matrix, 10
with a single index, 11
vector, 9
input, 306, 307
inv, 87
inverse, see matrix
ismember, 311
keyboard, 326
legend, 265
length, 150, 152
linspace, 15
load, 283
log, 57
log10, 58
log2, 58
loglog, 243
logspace, 16
lookfor, 5
lu, 97
matrix, 8
boolean operations on, 161, 162
changing shape of, 43
Cholesky factorization, 100
circular shift, 33
condition number, 104–106
44
INDEX OF MATLAB COMMANDS AND CONCEPTS
containing all indentical entries, 20
containing all zeros, 19
converting row, column to single index, 37
converting single-index to row, column, 36
cumulative sums of all elements of, 134
cumulative sums of columns, 132
cumulative sums of rows, 133
determinant, 86
diagonal, 22
echelon form, 85
eigenvalues and eigenvectors of, 96
equation
solving, 84
exponential of, 130
extracting a column of, 28
extracting a rectangular piece of, 31
extracting a row of, 29
extracting specified rows and columns of, 32
“gluing” together, 24, 25
identity, 21
inverse, 87
lower-triangular portion of, 44
LU factorization, 97
minimum of values of, 140
minimum value of each column of, 141
minimum value of each row of, 142
modifying elements given lists of rows and
columns, 38
multiplication, 81
element-by-element, 82
N -dimensional, 47
norm, 103
powers of, 93
product
of all elements, 127
of columns of, 128
of rows of, 129
QR factorization, 101
rank, 95
re-shaping its elements into a vector, 30
reverse elements in columns, 35
reverse elements in rows, 34
Schur decomposition, 99
singular value decomposition, 98
size of, 147–149, 151, 152
sum
of all elements, 124
of columns of, 125
of rows of, 126
trace, 88
transpose, 83
upper-triangular portion of, 45
max, see min
45
mean, 107–109
mesh, 254
meshgrid, 26, 118, 253
min, 139–142, 144–146
mind, 143
mkdir, 279
mnpdf, 228
mnrnd, 220, 221
mod, 63, 334
modulo arithmetic, 63, 334
multiple statements on one line, 324
nchoosek, 72
norm, 102, 103
normcdf, 232
normpdf, 225
normrnd, 219
num2str, 314
numel, 151
ode45, 195–197
ones, 18, 20
openvar, 293
optimization, 168–171
path, 328
pause, 317, 318
pcolor, 254, 269, 278
perform some commands with probability p, 207
permutation of integers 1..n, 208
plot, 240–242, 267
Greek letters in axis labels, 258
plot3, 251
poisscdf, 230
poisspdf, 223
poissrnd, 214
polar, 250
polyfit, 174–176
polynomial
least-squares fitted, 175–177
multiplication, 165
roots of, 166
ppval, 178, 180, 181
print, 275–277
probability density functions
binomial, 222
continuous uniform on interval (a, b), 226
discrete uniform from 1..n, 227
exponential, 224
multinomial, 228
normal, 225
Poisson, 223
prod, 127–129
INDEX OF MATLAB COMMANDS AND CONCEPTS
qr, 101
quad, 172
quit, 302, 330
rand, 198–206, 212
random values
Bernoulli, 204
binomial, 213
continuous uniform distribution on interval
(a, b), 201, 218
continuous uniform distribution on interval
(0,1), 198–200
discrete uniform distribution from a..b, 206
discrete uniform distribution from 1..k, 203,
216, 217
discrete uniform distribution, 202
exponential, 215
k unique values sampled from integers 1..n,
209
multinomial, 220, 221
normal, 219
Poisson, 214
setting the seed, 212
randperm, 208, 209
randsample, 209–211
rank, 95
rcond, 104
real, 77
regexp, 312, 313
reshape, 43, 47
roots
of general single-variable function, 167
polynomial, 166
roots, 166
round, 64
row vector, 6
rref, 85
sampling values from a vector, 210, 211
save, 285
schur, 99
semilogx, 243
semilogy, 243
set, 259
shading, 269
sign, 67
sin, 59
sinh, 61
size, 147–149
slice, 254
sort, 153, 154, 209
sortrows, 155–158
spline, 182
46
splines, see cubic splines
sprintf, 315
sqrt, 53
stairs, 250
standard deviation, see std
startup.m, 329
std, 110–112
stem, 250
stop, 322
strcat, 309
string
concatenation, 308
converting number to, 314
pattern matching, 312, 313
substrings, 310
struct, 51
sub2ind, 37, 38
subplot, 273
sum, 124–126, 187
surf, 252, 253
surfc, 254
surfl, 254
svd, 98
switch, 192
tan, 59
tanh, 61
text, 261, 262
tic, 321
title, 256
toc, 321
trace, 88
transpose, see matrix
trapz, 173
tril, 44
triu, 45
unidcdf, 234
unidpdf, 227
unidrnd, 216, 217
unifcdf, 233
unifpdf, 226
unifrnd, 218
unique, 163, 246
var, 113–115
variables
assigning, 286
assigning in base environment from function, 287
evaluating from base environment within function, 288
names, 298
variance, see var
INDEX OF MATLAB COMMANDS AND CONCEPTS
vector
boolean operations on, 159, 160
containing all indentical entries, 18
containing all zeros, 17
counts of binned values in, 164
counts of discrete values in, 163
cross product, 80
cumulative sum of elements of, 131
differences between consecutive elements of,
137
dot product, 79
minimum of values of, 139
norm, 102
position of first occurance of minimum value
in, 146
product of all elements, 127
reversing order of elements in, 27
size of, 150
sum of all elements, 124
truncating, 39
warning, 323
waterfall, 254
which, 327
while, 190
who, 289
whos, 290–292
xlabel, 257–259
ylabel, 257, 258
zeros, 17, 19
47
INDEX OF R COMMANDS AND CONCEPTS
48
Index of R commands and concepts
*, 92
/, 90
:, 12, 13
;, 324
<-, 286
<<-, 287
=, 286
?, 1, 2
[[, 49
#, 303
%%, 63, 334
&, 186, 187
^, 54, 94
abs, 55, 74
acos, 60
acosh, 62
alarm, 319
all, 188
any, 189
apply, 34, 35, 112, 114, 115, 128, 141, 142
Arg, 75
array, 47
arrows, 263, 264
as.character, 314
as.formula, 176
as.numeric, 163
asin, 60
asinh, 62
atan, 60
atanh, 62
average, see mean
barplot, 244, 246
boolean tests
scalar, 186
vector, 187–189
break, 191
browser, 326
c, 6, 7
cbind, 24, 38
ceiling, 66
cellular automata animation, 278
chol, 100
choose, 72
class, 297
cloud, 251
coef, 174–177
colMeans, 108
colon, see :
colormap
building your own, 272
for image, 271
colSums, 125
column vector, 7
comments, 303
complex numbers, 73–78
Conj, 76
contour, 254
convolve, 165
cor, 119–123
cos, 59
cosh, 61
cov, 116–118
cubic splines, 179, 180, 182
natural, 178
periodic, 181
cummax, 136
cummin, 136
cumprod, 135
cumsum, 131–134
cumulative distribution functions
binomial, 229
continuous uniform on interval (a, b), 233
discrete uniform from 1..n, 234
exponential, 231
normal, 232
Poisson, 230
curve, 268
data.frame, 51
dbinom, 222
debugging, 326
det, 86
dev.control, 275, 276, 278
dev.copy, 275, 276
dev.copy2eps, 276
dev.copy2pdf, 275
dev.cur(), 237
dev.list, 238
dev.new, 235
dev.off, 239, 275–277
dev.set, 236
dexp, 224
diag, 21–23
diff, 137
differential equations, see lsoda
dim, 43, 149, 152
dir, 281
dir.create, 279
INDEX OF R COMMANDS AND CONCEPTS
dmultinom, 228
dnorm, 225
dpois, 223
dunif, 226
echelon form, see matrix
eig, 96
element-by-element matrix operations, see matrix
else, 185
errbar, 248, 249
eval, 325
exp, 56
expand, 97
expand.grid, 254
expm, 130
file
running commands in, 282
text
reading data from, 283, 284
saving data to, 285
filled.contour, 270
.First, 329
fix, 293
floor, 65
font size in plots, 259
for, 183
function
multi-variable
minimization, 170
minimization over first parameter only, 169
minimization over only some parameters,
171
single-variable
minimization, 168
user-written, 193
returning multiple values, 194
get, 288
globalenv, 288
graphics
not being displayed from scripts/functions,
274
Greek letters
in plot labels, 258
gregexpr, 312
grepl, 313
grid, 260
help, 1, 2
help.search, 5
help.start, 4
Hilbert, 46
49
hist, 164, 244, 245, 247
identity, see matrix
if, 184–186
ifelse, 138
Im, 78
image, 269, 278
indexing
matrix, 10
with a single index, 11
vector, 9
install.packages, 331
integrate, 172
inverse, see matrix
jpeg, 277
kappa, 105
.Last, 330
.Last.value, 299
lattice package, 254, 270, 274, 331
layout, 273
legend, 265
length, 39, 40, 150, 151
levelplot, 270, 274
library, 3, 331
lines, 266
lists, 48
extracting elements of, 49
lm, 174–177
lm.fit, 176
log, 57
log10, 58
log2, 58
lower.tri, 45
ls, 289
ls.str, 290, 292
lsoda, 195–197
.Machine$double.eps, 316
match, 311
matplot, 267
matrix, 8
boolean operations on, 161, 162
changing shape of, 43
Cholesky factorization, 100
circular shift, 33
condition number, 104–106
containing all indentical entries, 20
containing all zeros, 19
converting row, column to single index, 37
converting single-index to row, column, 36
cumulative sums of all elements of, 134
INDEX OF R COMMANDS AND CONCEPTS
cumulative sums of columns, 132
cumulative sums of rows, 133
determinant, 86
diagonal, 22
echelon form, 85
eigenvalues and eigenvectors of, 96
equation
solving, 84
exponential of, 130
extracting a column of, 28
extracting a rectangular piece of, 31
extracting a row of, 29
extracting specified rows and columns of, 32
“gluing” together, 24, 25
identity, 21
inverse, 87
lower-triangular portion of, 44
LU factorization, 97
minimum of values of, 140
minimum value of each column of, 141
minimum value of each row of, 142
modifying elements given lists of rows and
columns, 38
multiplication, 81
element-by-element, 82
N -dimensional, 47
norm, 103
powers of, 93
product
of all elements, 127
of columns of, 128
of rows of, 129
QR factorization, 101
rank, 95
re-shaping its elements into a vector, 30
reverse elements in columns, 35
reverse elements in rows, 34
Schur decomposition, 99
singular value decomposition, 98
size of, 147–149, 151, 152
sum
of all elements, 124
of columns of, 125
of rows of, 126
trace, 88
transpose, 83
upper-triangular portion of, 45
matrix, 8, 19, 20
max, see min
mean, 107
min, 139–142, 145
Mod, 74
modulo arithmetic, 63, 334
50
multiple statements on one line, 324
names, 50, 163
ncol, 148
next, 191
norm, 102, 103
nrow, 147
optim, 170, 171
optimization, 168–171
optimize, 168, 169
options
digits=, 301
order, 155–158
outer, 176, 253
packages
installing, 331
loading, 331
par, 259
par
mfcol=, 273
mfrow=, 273
parse, 325
paste, 176, 308, 309
pbinom, 229
pdf, 259, 275
perform some commands with probability p, 207
permutation of integers 1..n, 208
persp, 252, 253
pexp, 231
pie, 250
plot, 240–243
Greek letters in axis labels, 258
main=, 256
sub=, 256
xlab=, 257, 258
xlim=, 255
ylab=, 257, 258
ylim=, 255
pmin, 143, 144
pnorm, 68, 69, 232
points, 266
polynomial
least-squares fitted, 175–177
multiplication, 165
roots of, 166
polyreg, 176
polyroot, 166
postscript, 276
ppois, 230
print, 274, 304, 305
probability density functions
binomial, 222
INDEX OF R COMMANDS AND CONCEPTS
continuous uniform on interval (a, b), 226
discrete uniform from 1..n, 227
exponential, 224
multinomial, 228
normal, 225
Poisson, 223
proc.time, 320, 321
prod, 127–129
punif, 233
q, 302, 330
qnorm, 70, 71
qr, 95, 101
quartz, 235
quit, 302, 330
rand, 205
random values
Bernoulli, 204
binomial, 213
continuous uniform distribution on interval
(a, b), 201, 218
continuous uniform distribution on interval
(0,1), 198, 200
continuous uniform distribution on inteval
(0,1), 199
discrete uniform distribution from a..b, 206
discrete uniform distribution from 1..k, 203,
216, 217
discrete uniform distribution, 202
exponential, 215
k unique values sampled from integers 1..n,
209
multinomial, 220, 221
normal, 219
Poisson, 214
setting the seed, 212
rbind, 25
rbinom, 213
rcond, 104, 106
.RData, 329
Re, 77
read.table, 283, 284
readline, 307
rep, 17, 18
rev, 27
rexp, 215
rgb, 272
rm, 294–296
rmultinom, 220, 221
rnorm, 219
roots
of general single-variable function, 167
51
polynomial, 166
round, 64
row vector, 6
rowMeans, 109
rpois, 214
.Rprofile, 329
runif, 198–204, 206, 218
sample, 208–211, 216, 217
sampling values from a vector, 210, 211
scan, 306, 318
Schur, 99
sd, 110–112
seq, 14–16
set.seed, 212
setwd, 280
sign, 67
sin, 59
sinh, 61
solve, 84, 87, 89, 91
sort, 153, 154
source, 282
spline, 178, 179, 181
splines, see cubic splines
split.screen, 273
sprintf, 315
sqrt, 53
standard deviation, see sd
str, 291
string
concatenation, 308
converting number to, 314
pattern matching, 312, 313
substrings, 310
substr, 310
sum, 124, 126, 187
svd, 98
switch, 192
symbols, 254
Sys.sleep, 317
t, 83
table, 163, 246
tan, 59
tanh, 61
text, 261, 262
title, 256, 257
transpose, see matrix
typeof, 297
uniroot, 167
upper.tri, 44
var, 113–115, 117
INDEX OF R COMMANDS AND CONCEPTS
variables
assigning, 286
assigning in base environment from function, 287
evaluating from base environment within function, 288
names, 298
variance, see var
vector
boolean operations on, 159, 160
containing all indentical entries, 18
containing all zeros, 17
counts of binned values in, 164
counts of discrete values in, 163
cross product, 80
cumulative sum of elements of, 131
differences between consecutive elements of,
137
dot product, 79
minimum of values of, 139
norm, 102
position of first occurance of minimum value
in, 146
product of all elements, 127
reversing order of elements in, 27
size of, 150
sum of all elements, 124
truncating, 39
vector, 48
warning, 323
which, 160–162
which.max, see which.min
which.min, 146
while, 190
windows, 235
wireframe, 254
write, 285
x11, 235
52
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