NumPy for R (and S-Plus) users

Help
R/S-Plus Python Description
help.start() help() Browse help interactively
help() help Help on using help
help(plot) or ?plot help(plot) or ?plot Help for a function
help(package='splines') help(pylab) Help for a toolbox/library
package
demo() Demonstration examples
example(plot) Example using a function

Searching available documentation

R/S-Plus Python Description
help.search('plot') Search help files
apropos('plot') Find objects by partial name
library() help(); modules [Numeric] List available packages
find(plot) help(plot) Locate functions
methods(plot) List available methods for a
function

Using interactively
R/S-Plus Python Description
Rgui ipython -pylab Start session
TAB Auto completion
source('foo.R') execfile('foo.py') or run Run code from file
foo.py
history() hist -n Command history
savehistory(file=".Rhistory") Save command history
q(save='no') CTRL-D End session
CTRL-Z # windows
sys.exit()

Operators
R/S-Plus Python Description
help(Syntax) Help on operator syntax

Arithmetic operators
R/S-Plus Python Description
a<-1; b<-2 a=1; b=1 Assignment; defining a
number
a + b a + b or add(a,b) Addition
a - b a - b or subtract(a,b) Subtraction
a * b a * b or multiply(a,b) Multiplication
a / b a / b or divide(a,b) Division
a ^ b a ** b Power, $a^b$
power(a,b)
pow(a,b)
a %% b a % b Remainder
remainder(a,b)
fmod(a,b)
a %/% b Integer division
a+=b or add(a,b,a) In place operation to save
array creation overhead
factorial(a) Factorial, $n!$

Relational operators
R/S-Plus Python Description
a == b a == b or equal(a,b) Equal
a < b a < b or less(a,b) Less than
a > b a > b or greater(a,b) Greater than
a <= b a <= b or less_equal(a,b) Less than or equal
a >= b a >= b or greater_equal(a,b) Greater than or equal
a != b a != b or not_equal(a,b) Not Equal

Logical operators
R/S-Plus Python Description
a && b a and b Short-circuit logical AND
a || b a or b Short-circuit logical OR
a & b logical_and(a,b) or a and b Element-wise logical AND
a | b logical_or(a,b) or a or b Element-wise logical OR
xor(a, b) logical_xor(a,b) Logical EXCLUSIVE OR
!a logical_not(a) or not a Logical NOT

root and logarithm

R/S-Plus Python Description
sqrt(a) math.sqrt(a) Square root
log(a) math.log(a) Logarithm, base $e$ (natural)
log10(a) math.log10(a) Logarithm, base 10
log2(a) math.log(a, 2) Logarithm, base 2 (binary)
exp(a) math.exp(a) Exponential function

Round off
R/S-Plus Python Description
round(a) around(a) or math.round(a) Round
ceil(a) ceil(a) Round up
floor(a) floor(a) Round down
 fix(a) Round towards zero

Mathematical constants
R/S-Plus Python Description
pi math.pi $\pi=3.141592$
exp(1) math.e or math.exp(1) $e=2.718281$

Missing values; IEEE-754 floating point status flags

R/S-Plus Python Description
nan Not a Number
inf Infinity, $\infty$
plus_inf Infinity, $+\infty$
minus_inf Infinity, $-\infty$
plus_zero Plus zero, $+0$
minus_zero Minus zero, $-0$

Complex numbers
R/S-Plus Python Description
1i z = 1j Imaginary unit
z <- 3+4i z = 3+4j or z = A complex number, $3+4i$
complex(3,4)
abs(3+4i) or Mod(3+4i) abs(3+4j) Absolute value (modulus)
Re(3+4i) z.real Real part
Im(3+4i) z.imag Imaginary part
Arg(3+4i) Argument
Conj(3+4i) z.conj(); z.conjugate() Complex conjugate

Trigonometry
R/S-Plus Python Description
atan2(b,a) atan2(b,a) Arctangent, $\arctan(b/a)$
hypot(x,y) Hypotenus; Euclidean distance

Generate random numbers

R/S-Plus Python Description
runif(10) random.random((10,)) Uniform distribution
random.uniform((10,))
runif(10, min=2, max=7) random.uniform(2,7,(10,)) Uniform: Numbers
between 2 and 7
matrix(runif(36),6) random.uniform(0,1,(6,6)) Uniform: 6,6 array
rnorm(10) random.standard_normal((10,)) Normal distribution

Vectors
R/S-Plus Python Description
a <- c(2,3,4,5) a=array([2,3,4,5]) Row vector, $1 \times n$-
matrix
adash <- t(c(2,3,4,5)) array([2,3,4,5])[:,NewAxis] Column vector, $m \times
array([2,3,4,5]).reshape(-1,1)
r_[1:10,'c'] 1$-matrix

Sequences
R/S-Plus Python Description
seq(10) or 1:10 arange(1,11, dtype=Float) 1,2,3, ... ,10
range(1,11)
seq(0,length=10) arange(10.) 0.0,1.0,2.0, ... ,9.0
seq(1,10,by=3) arange(1,11,3) 1,4,7,10
seq(10,1) or 10:1 arange(10,0,-1) 10,9,8, ... ,1
seq(from=10,to=1,by=-3) arange(10,0,-3) 10,7,4,1
seq(1,10,length=7) linspace(1,10,7) Linearly spaced vector of
n=7 points
rev(a) a[::-1] or Reverse
a.fill(3), a[:] = 3 Set all values to same scalar
value

Concatenation (vectors)
R/S-Plus Python Description
c(a,a) concatenate((a,a)) Concatenate two vectors
c(1:4,a) concatenate((range(1,5),a),
axis=1)

Repeating
R/S-Plus Python Description
rep(a,times=2) concatenate((a,a)) 1 2 3, 1 2 3
rep(a,each=3) a.repeat(3) or 1 1 1, 2 2 2, 3 3 3
rep(a,a) a.repeat(a) or 1, 2 2, 3 3 3

Miss those elements out

R/S-Plus Python Description
a[-1] a[1:] miss the first element
a[-10] miss the tenth element
a[-seq(1,50,3)] miss 1,4,7, ...
a[-1] last element
a[-2:] last two elements

Maximum and minimum

R/S-Plus Python Description
pmax(a,b) maximum(a,b) pairwise max
max(a,b) concatenate((a,b)).max() max of all values in two
 vectors
v <- max(a) ; i <- v,i = a.max(0),a.argmax(0)
which.max(a)

Vector multiplication
R/S-Plus Python Description
a*a a*a Multiply two vectors
dot(u,v) Vector dot product, $u \cdot v$

Matrices
R/S-Plus Python Description
rbind(c(2,3),c(4,5)) a = array([[2,3],[4,5]]) Define a matrix
array(c(2,3,4,5), dim=c(2,2))

Concatenation (matrices); rbind and cbind

R/S-Plus Python Description
rbind(a,b) concatenate((a,b), axis=0) Bind rows
vstack((a,b))
cbind(a,b) concatenate((a,b), axis=1) Bind columns
hstack((a,b))
concatenate((a,b), axis=2) Bind slices (three-
dstack((a,b))
way arrays)
concatenate((a,b), axis=None) Concatenate matrices
into one vector
rbind(1:4,1:4) concatenate((r_[1:5],r_[1:5])).reshape(2,- Bind rows (from
1)
vstack((r_[1:5],r_[1:5])) vectors)
cbind(1:4,1:4) Bind columns (from
vectors)

Array creation
R/S-Plus Python Description
matrix(0,3,5) or array(0,c(3,5)) zeros((3,5),Float) 0 filled array
zeros((3,5)) 0 filled array of integers
matrix(1,3,5) or array(1,c(3,5)) ones((3,5),Float) 1 filled array
matrix(9,3,5) or array(9,c(3,5)) Any number filled array
diag(1,3) identity(3) Identity matrix
diag(c(4,5,6)) diag((4,5,6)) Diagonal
a = empty((3,3)) Empty array

Reshape and flatten matrices

R/S-Plus Python Description
matrix(1:6,nrow=3,byrow=T) arange(1,7).reshape(2,-1) Reshaping (rows first)
a.setshape(2,3)
matrix(1:6,nrow=2) arange(1,7).reshape(- Reshaping (columns
array(1:6,c(2,3)) 1,2).transpose()
first)
as.vector(t(a)) a.flatten() or Flatten to vector (by
rows, like comics)
as.vector(a) a.flatten(1) Flatten to vector (by
columns)
a[row(a) <= col(a)] Flatten upper triangle
(by columns)

Shared data (slicing)

R/S-Plus Python Description
b = a b = a.copy() Copy of a

Indexing and accessing elements (Python: slicing)

R/S-Plus Python Description
a <- rbind(c(11, 12, 13, a = array([[ 11, 12, 13, 14 ], Input is a 3,4 array
14), [ 21, 22, 23, 24 ],
c(21, 22, 23, 24), [ 31, 32, 33, 34 ]])
c(31, 32, 33, 34))
a[2,3] a[1,2] Element 2,3 (row,col)
a[1,] a[0,] First row
a[,1] a[:,0] First column
a.take([0,2]).take([0,3], Array as indices
axis=1)
a[-1,] a[1:,] All, except first row
a[-2:,] Last two rows
a[::2,:] Strides: Every other row
a[...,2] Third in last dimension
(axis)
a[-2,-3] All, except row,column
(2,3)
a[,-2] a.take([0,2,3],axis=1) Remove one column
a.diagonal(offset=0) Diagonal

Assignment
R/S-Plus Python Description
a[,1] <- 99 a[:,0] = 99
a[,1] <- c(99,98,97) a[:,0] = array([99,98,97])
a[a>90] <- 90 (a>90).choose(a,90) Clipping: Replace all
a.clip(min=None, max=90)
elements over 90
a.clip(min=2, max=5) Clip upper and lower values

Transpose and inverse

R/S-Plus Python Description
t(a) a.conj().transpose() Transpose
a.transpose() Non-conjugate transpose
det(a) linalg.det(a) or Determinant
solve(a) linalg.inv(a) or Inverse
ginv(a) linalg.pinv(a) Pseudo-inverse
norm(a) Norms
eigen(a)$values linalg.eig(a)[0] Eigenvalues
svd(a)$d linalg.svd(a) Singular values
linalg.cholesky(a) Cholesky factorization
eigen(a)$vectors linalg.eig(a)[1] Eigenvectors
rank(a) rank(a) Rank

Sum
R/S-Plus Python Description
apply(a,2,sum) a.sum(axis=0) Sum of each column
apply(a,1,sum) a.sum(axis=1) Sum of each row
sum(a) a.sum() Sum of all elements
a.trace(offset=0) Sum along diagonal
apply(a,2,cumsum) a.cumsum(axis=0) Cumulative sum (columns)

Sorting
R/S-Plus Python Description
a = array([[4,3,2],[2,8,6], Example data
[1,4,7]])
t(sort(a)) a.ravel().sort() or Flat and sorted
apply(a,2,sort) a.sort(axis=0) or msort(a) Sort each column
t(apply(a,1,sort)) a.sort(axis=1) Sort each row
a[a[:,0].argsort(),] Sort rows (by first row)
order(a) a.ravel().argsort() Sort, return indices
a.argsort(axis=0) Sort each column,
return indices
a.argsort(axis=1) Sort each row, return
indices

Maximum and minimum

R/S-Plus Python Description
apply(a,2,max) a.max(0) or amax(a [,axis=0]) max in each column
apply(a,1,max) a.max(1) or amax(a, axis=1) max in each row
max(a) a.max() or max in array
i <- apply(a,1,which.max) return indices, i
pmax(b,c) maximum(b,c) pairwise max
apply(a,2,cummax)
a.ptp(); a.ptp(0) max-to-min range

Matrix manipulation
R/S-Plus Python Description
a[,4:1] fliplr(a) or a[:,::-1] Flip left-right
a[3:1,] flipud(a) or a[::-1,] Flip up-down
rot90(a) Rotate 90 degrees
kronecker(matrix(1,2,3),a) kron(ones((2,3)),a) Repeat matrix: [ a a a ; a a
a]
a[lower.tri(a)] <- 0 triu(a) Triangular, upper
a[upper.tri(a)] <- 0 tril(a) Triangular, lower

Equivalents to "size"
R/S-Plus Python Description
dim(a) a.shape or a.getshape() Matrix dimensions
ncol(a) a.shape[1] or size(a, axis=1) Number of columns
prod(dim(a)) a.size or size(a[, axis=None]) Number of elements
a.ndim Number of dimensions
object.size(a) a.nbytes Number of bytes used in
memory

Matrix- and elementwise- multiplication

R/S-Plus Python Description
a * b a * b or multiply(a,b) Elementwise operations
a %*% b matrixmultiply(a,b) Matrix product (dot
product)
inner(a,b) or Inner matrix vector
multiplication $a\cdot b'$
outer(a,b) or a %o% b outer(a,b) or Outer product
crossprod(a,b) or t(a) %*% b Cross product
kronecker(a,b) kron(a,b) Kronecker product
solve(a,b) linalg.solve(a,b) Left matrix division, $b^{-
1}{\cdot}a$ \newline (solve
linear equations)
vdot(a,b) Vector dot product
cross(a,b) Cross product

Find; conditional indexing

R/S-Plus Python Description
which(a != 0) a.ravel().nonzero() Non-zero elements, indices
which(a != 0, arr.ind=T) (i,j) = a.nonzero() Non-zero elements, array
(i,j) = where(a!=0)
indices
ij <- which(a != 0, v = a.compress((a!=0).flat) Vector of non-zero values
arr.ind=T); v <- a[ij] v = extract(a!=0,a)
which(a>5.5) (a>5.5).nonzero() Condition, indices
ij <- which(a>5.5, a.compress((a>5.5).flat) Return values
arr.ind=T); v <- a[ij]
where(a>5.5,0,a) or a * (a>5.5) Zero out elements above 5.5
a.put(2,indices) Replace values
Multi-way arrays
R/S-Plus Python Description
a = array([[[1,2],[1,2]], Define a 3-way array
[[3,4],[3,4]]])
a[0,...]

File input and output

R/S-Plus Python Description
f <- read.table("data.txt") f = fromfile("data.txt") Reading from a file
f = load("data.txt")
(2d)
f <- read.table("data.txt") f = load("data.txt") Reading from a file
(2d)
f <- f = load('data.csv', Reading fram a CSV
read.table(file="data.csv", delimiter=';')
sep=";") file (2d)
write(f,file="data.txt") save('data.csv', f, Writing to a file (2d)
fmt='%.6f', delimiter=';')
f.tofile(file='data.csv', Writing to a file (1d)
format='%.6f', sep=';')
f = fromfile(file='data.csv', Reading from a file
sep=';')
(1d)

Plotting

Basic x-y plots

R/S-Plus Python Description
plot(a, type="l") plot(a) 1d line plot
plot(x[,1],x[,2]) plot(x[:,0],x[:,1],'o') 2d scatter plot
plot(x1,y1,'bo', x2,y2,'go') Two graphs in one plot
plot(x1,y1) plot(x1,y1,'o') Overplotting: Add new
matplot(x2,y2,add=T) plot(x2,y2,'o')
show() # as normal plots to current
subplot(211) subplots
plot(x,y,type="b",col="red") plot(x,y,'ro-') Plotting symbols and
color

Axes and titles

R/S-Plus Python Description
grid() grid() Turn on grid lines
plot(c(1:10,10:1), asp=1) figure(figsize=(6,6)) 1:1 aspect ratio
plot(x,y, xlim=c(0,10), axis([ 0, 10, 0, 5 ]) Set axes manually
ylim=c(0,5))
plot(1:10, main="title", Axis labels and titles
xlab="x-axis", ylab="y-
axis")
text(2,25,'hello') Insert text

Log plots
R/S-Plus Python Description
plot(x,y, log="y") semilogy(a) logarithmic y-axis
plot(x,y, log="x") semilogx(a) logarithmic x-axis
plot(x,y, log="xy") loglog(a) logarithmic x and y axes

Filled plots and bar plots

R/S-Plus Python Description
plot(t,s, type="n", xlab="", fill(t,s,'b', t,c,'g', Filled plot
ylab="") alpha=0.2)
polygon(t,s, col="lightblue")
polygon(t,c,
col="lightgreen")
stem(x[,3]) Stem-and-Leaf plot

Functions
R/S-Plus Python Description
f <- function(x) sin(x/3) - Defining functions
cos(x/5)
plot(f, xlim=c(0,40), x = arrayrange(0,40,.5) Plot a function for given
type='p') y = sin(x/3) - cos(x/5)
plot(x,y, 'o') range

Polar plots
R/S-Plus Python Description
theta = arange(0,2*pi,0.001)
r = sin(2*theta)
polar(theta, rho)

Histogram plots
R/S-Plus Python Description
hist(rnorm(1000))
hist(rnorm(1000), breaks= -4:4)
hist(rnorm(1000), breaks=c(seq(-
5,0,0.25), seq(0.5,5,0.5)),
freq=F)
plot(apply(a,1,sort),type="l")

3d data

Contour and image plots

R/S-Plus Python Description
contour(z) levels, colls = contour(Z, V, Contour plot
origin='lower', extent=(-3,3,-
3,3))
clabel(colls, levels,
inline=1,
fmt='%1.1f', fontsize=10)
filled.contour(x,y,z, contourf(Z, V, Filled contour plot
nlevels=7, color=gray.colors) cmap=cm.gray,
origin='lower',
 extent=(-3,3,-3,3))
image(z, im = imshow(Z, Plot image data
col=gray.colors(256)) interpolation='bilinear',
origin='lower',
extent=(-3,3,-3,3))
# imshow() and contour() as Image with contours
above
quiver() Direction field vectors

Perspective plots of surfaces over the x-y plane

R/S-Plus Python Description
f <- function(x,y) x*exp(- n=arrayrange(-2,2,.1)
x^2-y^2) [x,y] = meshgrid(n,n)
n <- seq(-2,2, length=40) z = x*power(math.e,-x**2-
z <- outer(n,n,f) y**2)
persp(x,y,z, Mesh plot
theta=30, phi=30, expand=0.6,
ticktype='detailed')
persp(x,y,z, Surface plot
theta=30, phi=30, expand=0.6,
col='lightblue', shade=0.75,
ltheta=120,
ticktype='detailed')

Scatter (cloud) plots

R/S-Plus Python Description
cloud(z~x*y) 3d scatter plot

Save plot to a graphics file

R/S-Plus Python Description
postscript(file="foo.eps") savefig('foo.eps') PostScript
plot(1:10)
dev.off()
pdf(file='foo.pdf') savefig('foo.pdf') PDF
devSVG(file='foo.svg') savefig('foo.svg') SVG (vector graphics for
www)
png(filename = "Rplot%03d.png" savefig('foo.png') PNG (raster graphics)

Data analysis

Set membership operators

R/S-Plus Python Description
a <- c(1,2,2,5,2) a = array([1,2,2,5,2]) Create sets
b <- c(2,3,4) b = array([2,3,4])
a = set([1,2,2,5,2])
b = set([2,3,4])
unique(a) unique1d(a) Set unique
unique(a)
set(a)
union(a,b) union1d(a,b) Set union
a.union(b)
intersect(a,b) intersect1d(a) Set intersection
a.intersection(b)
setdiff(a,b) setdiff1d(a,b) Set difference
a.difference(b)
setdiff(union(a,b),intersect(a,b)) setxor1d(a,b) Set exclusion
a.symmetric_difference(b)
is.element(2,a) or 2 %in% a 2 in a True for set member
setmember1d(2,a)
contains(a,2)

Statistics
R/S-Plus Python Description
apply(a,2,mean) a.mean(axis=0) Average
mean(a [,axis=0])
apply(a,2,median) median(a) or median(a [,axis=0]) Median
apply(a,2,sd) a.std(axis=0) or std(a [,axis=0]) Standard deviation
apply(a,2,var) a.var(axis=0) or var(a) Variance
cor(x,y) correlate(x,y) or corrcoef(x,y) Correlation coefficient
cov(x,y) cov(x,y) Covariance

Interpolation and regression

R/S-Plus Python Description
z <- lm(y~x) (a,b) = polyfit(x,y,1) Straight line fit
plot(x,y) plot(x,y,'o', x,a*x+b,'-')
abline(z)
solve(a,b) linalg.lstsq(x,y) Linear least squares $y = ax +
b$
polyfit(x,y,3) Polynomial fit

Non-linear methods

Polynomials, root finding

R/S-Plus Python Description
poly() Polynomial
polyroot(c(1,-1,-1)) roots() Find zeros of
polynomial
polyval(array([1,2,1,2]),arange(1,11)) Evaluate polynomial

Differential equations
R/S-Plus Python Description
diff(x, n=1, axis=0) Discrete difference function and
approximate derivative

Fourier analysis
R/S-Plus Python Description
fft(a) fft(a) or Fast fourier transform
fft(a, inverse=TRUE) ifft(a) or Inverse fourier transform
convolve(x,y) Linear convolution
Symbolic algebra; calculus
R/S-Plus Python Description

Programming
R/S-Plus Python Description
.R .py Script file extension
# # Comment symbol (rest of
line)
library(RSvgDevice) from pylab import * Import library functions
string <- "a <- 234" string="a=234" Eval
eval(parse(text=string)) eval(string)

Loops
R/S-Plus Python Description
for(i in 1:5) print(i) for i in range(1,6): for-statement
print(i)
for(i in 1:5) { for i in range(1,6): Multiline for statements
print(i) print(i)
print(i*2) print(i*2)
}

Conditionals
R/S-Plus Python Description
if (1>0) a <- 100 if 1>0: a=100 if-statement
ifelse(a>0,a,0) Ternary operator (if?true:false)

Debugging
R/S-Plus Python Description
.Last.value Most recent evaluated
expression
objects() List variables loaded into
memory
rm(x) Clear variable $x$ from
memory
print(a) print a Print

Working directory and OS

R/S-Plus Python Description
list.files() or dir() os.listdir(".") List files in directory
list.files(pattern="\.r$") grep.grep("*.py") List script files in
directory
getwd() os.getcwd() Displays the current
working directory
setwd('foo') os.chdir('foo') Change working
 directory
system("notepad") os.system('notepad') Invoke a System
os.popen('notepad')
Command