Transcript MATLAB/R Dictionary R meetup NYC January 7, 2010 Harlan Harris [email protected] @HarlanH Marck Vaisman [email protected] @wahalulu MATLAB and the MATLAB logo are registered trademarks of The Mathworks.

MATLAB/R Dictionary
R meetup NYC
January 7, 2010
Harlan Harris
[email protected]
@HarlanH
Marck Vaisman
[email protected]
@wahalulu
MATLAB and the MATLAB logo are registered trademarks of The Mathworks.
About MATLAB
What is MATLAB
MATLAB History
• Commercial numerical
programming language,
simulation and visualization
• One million users (engineers,
scientists, academics)
• MATrix LABoratory –
specializes in matrix
operations
• Mathworks - base & add-ons
• Open-source Octave project
• Developed by Cleve Moler
(Math/CS Prof at UNM) in the
1970’s as a higher-level
numerical programming
language (vs. Fortran LINPACK)
• Adopted by engineers for
signal processing, control
modeling
• Multipurpose programming
language
Notes
• Today’s focus: Compare MATLAB & R for data
analysis, contrast as programming languages
• MATLAB is Base plus many toolboxes
– Base includes: descriptive stats, covariance and
correlation, linear and nonlinear regression
– Statistics toolbox adds: dataset and category (like
data.frames and factors) arrays, more visualizations,
distributions, ANOVA, multivariate regression, hypothesis
tests
->
• Interactive programming: Scripts and Read-EvaluatePrint Loop
• Similar representations of data
– Both use vectors/arrays as the primary data structures
• Matlab is based on 2-D matricies; R is based on 1-D vectors
– Both prefer vectorized functions to for loops
– Variables are declared dynamically
• Can do most MATLAB functionality in R; can do most
R functionality in MATLAB.
The basics: vectors, matrices and indexing
Task
Create a row vector
v = [1 2 3 4]
v<-c(1,2,3,4)
Create a column vector
v=[1;2;3;4] or v=[1 2 3 4]’
v<-c(1,2,3,4)
Note: R does not distinguish
between row and column vectors
Enter a matrix A
A=[1 2 3; 4 5 6]
Enter values by row:
A<-matrix(c(1,2,3,4,5,6),
nrow=2, byrow=TRUE)
Enter values by column:
A<-matrix(c(1,4,2,5,3,6),
nrow=2)
Access third element of vector v
v(3)
v[3] or v[[3]]
Access element of matrix A
A(2,3)
A[2,3]
“Glue” two matrices a1 and a2,
same number of rows, side by side
A=[a1 a2]
A<-cbind(a1,a2)
“Stack” two matrices a1 and a2,
same number of columns
A=[a1;a2]
A<-rbind(a1,a2)
Reshape* matrix A, making it an m
x n matrix with elements taken
columnwise from A
A=reshape(A,m,n)
dim(A)<-c(m,n)
Operators
Task
Assignment
=
<- or =
Whole Matrix Operations:
Multiplication: A*B
Square the matrix: A^2
Raise to power k: A^k
A %*% B
A %*% A
A %*% A %*% A …
Element-by-element
Operations:
A.*B
A./B
A.^k
A*B
A/B
A^k
Compute A-1B
A\B
A%*% solve(B)
Sums
Columns of matrix: sum(A)
Rows of matrix: sum(A,2)
colSums(A)
rowSums(A)
Logical operators (element-byelement on vectors/matrices)
a < b, a > b, a <= b, a >= b
a == b
a ~= b
AND: a && b
a < b, a > b, a <= b, a >= b
a == b
a != b
AND: a && b (short-circuit)
a & b (element-wise)
OR: a || b
a | b
XOR: xor(a,b)
NOT: !a
OR: a || b
XOR: xor(a,b)
NOT: ~a
Working with data structures
Task
Build a structure v of length n,
capable of containing different
data types in different elements.
MATLAB: cell array
R: list
v=cell(1,n) In general,
cell(m,n) makes an m × n cell
array. Then you can do e.g.:
v{1}=12
v{2}=’hi there’
v{3}=rand(3)
v<-vector(’list’,n)
Then you can do e.g.:
v[[1]]<-12
v[[2]]<-’hi there’
v[[3]]<-matrix(runif(9),3)
Create a matrix-like object with
different named columns.
MATLAB: struct array
R: data.frame
avals=2*ones(1,6);
yvals=6:-1:1; v=[1 5 3 2 3 7];
d=struct(’a’, avals,
’yy’, yyvals, ’fac’, v);
v<-c(1,5,3,2,3,7)
d<-data.frame(cbind(a=2,
yy=6:1), v)
Conditionals, control structures, loops
Task
for loops over values in vector
v
for i=v
command1
command2
end
If only one command:
for (i in v)
command
If multiple commands:
for (i in v) {
command1
command2
}
If/else statement
ifelse() function
if cond
command1
command2
else
command3
command4
end
if (cond) {
command1
command2
} else {
command3
command4
}
MATLAB also has the elseif
statement.
R uses chained “else if”
statements.
> print(ifelse(c(T,F), 2, 3))
[1] 2 3
Help!
Task
Get help on a function
help fminsearch
help(pmin)
or
?pmin
Search the help for a word
lookfor inverse
??inverse
Describe a variable
class(a)
class(a)
str(a)
Show variables in environment
who
ls()
Underlying type of variable
whos(‘a’)
typeof(a)
Example: k-means clustering of Fisher Iris data
Fisher Iris Dataset
sepal_length,sepal_width,petal_length,petal_width,species
5.1,3.5,1.4,0.2,setosa
4.9,3.0,1.4,0.2,setosa
4.7,3.2,1.3,0.2,setosa
4.6,3.1,1.5,0.2,setosa
…
Matlab and R as programming languages
Scripting, real-time analysis
Scripting, real-time analysis
File-based environments
Files unimportant
Imperative programming style
Functional programming style (impure)
Statically scoped
Dynamically scoped
Functions with multiple return values
Functions with named arguments, lazy
evaluation
Evolving OOP system
Multiple competing OOP systems
Can be compiled
Cannot be compiled
Large library of functions
Professional developed, cost money
Large library of functions
Varying quality and support
Can embed (in) many other languages
Can embed (in) many other languages
Functions
function [a, b] = minmax(z)
% one function per .m file!
% assign to formal return names
a = min(z)
b = max(z)
end
minmax <- function(c, opt=12) {
# functions are assigned to
# variables
ret <- list(min = min(z),
max = max(z))
ret
# last statement is
# return value
}
% if minmax.m in path
[smallest, largest] = …
minmax([1 30 3])
# if minmax was created in current
# environment
x <- minmax(c(1, 30, 3))
smallest <- x$min
Object-Oriented Programming
• Formerly: objects were
defined by a directory
tree, with one method
per file
• As of 2008: new
classdef syntax
resembles other
languages
• S3 classes: attributes +
syntax
– class(object)
– plot.lm()
• S4 classes: definitions +
methods
• R.oo, proto, etc…
Other notes
• r.matlab package
• Graphics
– Matlab has much better 3-d/interactive graphics support
– R has ggplot2 and much better statistical graphics
Additional Resources
•
•
•
•
•
Will Dwinell, Data Mining in MATLAB
Computerworld article on Cleve Moler
Mathworks
Matlabcentral
Comparison of Data Analysis packages
(http://anyall.org/blog/2009/02/comparison-ofdata-analysis-packages-r-matlab-scipy-excel-sas-spssstata/)
• R.matlab package
• stackoverflow
References used for this talk
• David Hiebeler MATLAB/R Reference document:
http://www.math.umaine.edu/~hiebeler/comp/matl
abR.html
• http://www.cyclismo.org/tutorial/R/index.html
• http://www.stat.berkeley.edu/~spector/R.pdf
• MATLAB documentation
• http://www.r-cookbook.com/node/23
Thank You!