MATLAB/R DictionaryR meetup NYC

January 7, 2010

Harlan Harrisharlan@harris.name

@HarlanH

Marck Vaismanmarck@vaisman.us

@wahalulu

MATLAB and the MATLAB logo are registered trademarks of The Mathworks.

About MATLAB

What is MATLAB• 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

MATLAB History• 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-Evaluate-Print 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*BSquare the matrix: A^2Raise to power k: A^k

A %*% BA %*% AA %*% A %*% A …

Element-by-element Operations:

A.*BA./BA.^k

A*BA/BA^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-by-element on vectors/matrices)

a < b, a > b, a <= b, a >= ba == ba ~= bAND: a && b

OR: a || b

XOR: xor(a,b)NOT: ~a

a < b, a > b, a <= b, a >= ba == ba != bAND: a && b (short-circuit) a & b (element-wise)OR: a || b a | bXOR: 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 arrayR: list

v=cell(1,n) In general, cell(m,n) makes an m × n cellarray. Then you can do e.g.:v{1}=12v{2}=’hi there’v{3}=rand(3)

v<-vector(’list’,n) Then you can do e.g.:v[[1]]<-12v[[2]]<-’hi there’v[[3]]<-matrix(runif(9),3)

Create a matrix-like object with different named columns.MATLAB: struct arrayR: 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=vcommand1command2

end

If only one command:for (i in v)

command

If multiple commands:for (i in v) {

command1command2

}

If/else statement if condcommand1command2

elsecommand3command4

end

MATLAB also has the elseif statement.

if (cond) {command1command2

} else {command3command4

}

R uses chained “else if” statements.

ifelse() function > 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 Datasetsepal_length,sepal_width,petal_length,petal_width,species5.1,3.5,1.4,0.2,setosa4.9,3.0,1.4,0.2,setosa4.7,3.2,1.3,0.2,setosa4.6,3.1,1.5,0.2,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 functionsVarying 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

% if minmax.m in path[smallest, largest] = …

minmax([1 30 3])

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 was created in current

# environmentx <- 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-of-data-analysis-packages-r-matlab-scipy-excel-sas-spss-stata/)

• R.matlab package• stackoverflow

References used for this talk

• David Hiebeler MATLAB/R Reference document: http://www.math.umaine.edu/~hiebeler/comp/matlabR.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!