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Programming I

Joy

Outline

Examples

What is Matlab?

History

Characteristics

Organization of Matlab Toolboxes

Basic Applications

Programming

Example I

Obtain the result of matrix multiply

Matlab Code

>>A=[4,6; 9,15; 8,7];

>>B=[3,24,5; 7,19,2];

>>C=A*B

C =

54 210 32

132 501 75

73 325 54

4 6

3 24 5

9 15

7 19 2

8 7

(

(

(

(

(

(

C Code

#include <cstdlib>

#include <iostream>

#include <fstream>

#include <sstream>

#include <iomanip>

#include <vector>

using namespace std;

typedef vector<vector<int> > Mat;

void input(istream& in, Mat& a);

Mat matrix_product(const Mat& a, const Mat& b);

void print(const Mat& a);

C Codes

int main(int argc, char *argv[])

{

ifstream in1 ( "Matrix A.txt" );

ifstream in2 ( "Matrix B.txt" );

int row, row1, col, col1;

in1>>row>>col;

in2>>row1>>col1;

Mat a(row, vector<int>(col));

input(in1, a);

Mat b(row1, vector<int>(col1));

input(in2, b);

print(matrix_product(a,b));

system("PAUSE");

return EXIT_SUCCESS;

}

C Code Cond.

void input(istream& in, Mat& a)

{

for(int i = 0; i < a.size(); ++i)

for(int j = 0; j < a[0].size(); ++j)

in>>a[i][j];

}

void print(const Mat& a)

{

for(int i = 0; i < a.size(); ++i)

{ cout<<endl;

for(int j = 0; j < a[0].size(); ++j)

cout<<setw(5)<<a[i][j];

}

cout<<endl;

}

C Code Cond.

Mat matrix_product(const Mat& a, const Mat& b)

{

Mat c(a.size(), vector<int>(b[0].size()));

for(int i = 0; i < c.size(); ++i)

for(int j = 0; j < c[0].size(); ++j)

{

c[i][j] = 0;

for(int k = 0; k < b.size() ; ++k)

c[i][j] = c[i][j] + a[i][k] * b[k][j];

}

return c;

}

Example II

Calculate the transpose of the matrix:

Matlab Code

>>A=[3,17,2;5,19,7;6,4,54]

>>A^(-1)

ans =

-0.9327 0.8505 -0.0757

0.2131 -0.1402 0.0103

0.0879 -0.0841 0.0262

3 17 2

5 19 7

6 4 54

(

(

(

(

What is MATLAB?

Abbreviation of MATrix LABoratory

Is a high-performance language for

technical computing

It integrates computation, visualization,

and programming in an easy-to-use

environment where problems and

solutions are expressed in familiar

mathematical notation.

Usage of MATLAB

Math and computation

Algorithm development

Data acquisition

Modeling, simulation, and prototyping

Data analysis, exploration, and visualization

Scientific and engineering graphics

Application development

including graphical user interface building

History

In 1970s Dr.Cleve Moler

Based on Fortran on EISPACK and LINPACK

Only solve basic matrix calculation and graphic

1984 MathWorks Company by Cleve Moler and

Jack Little

Matlab 1.0 based on C

Included image manipulations, multimedia etc.

toolboxes

In 1990 run on Windows

Simulink, Notebook, Symbol Operation, etc.

21 Century

Main Features

Powerful tool for matrix calculations

Basic data type is double complex matrix with subscript is 1

High efficient/reliable algorithms

Multi-paradigm

- interactive environment (no compiler)

- programming

Most input/output parameters in Matlab

functions are variable

User friendly with extensively help system

MATLAB SYSTEM

Develop Tools

Toolboxes

Data-Accessing Tools

Stateflow

Generating-Codes Tools

Module Libraries

Third parties modules

Applications

DATA

C

Simulink

MATLAB

Buildup of MATLAB

Development Environment

MATLAB desktop and Command Window, a command history, an editor

and debugger, and browsers for viewing help, the workspace, files, and the

search path.

The MATLAB Mathematical Function Library

A vast collection of computational algorithms ranging from elementary

functions to more sophisticated functions

The MATLAB Language

A high-level matrix/array language with control flow statements,

functions, data structures, input/output, and object-oriented

programming features

Graphics

Display vectors and matrices as graphs

two-dimensional and three-dimensional data visualization

image processing

animation and presentation graphics

The MATLAB Application Program Interface (API)

Interchange the C/Fortran codes with Matlab codes

Basic Applications I

Matrices and Arrays

Generating Arrays/Matrices

Elementary Matrices:

sum, transpose, diagonal, subscripts

Variables: does not require any type

declarations or dimension statements

Operators: +,-,*,/, ^, etc.

Examples of Expressions

Generating Matrices

Directly enter

A = [16 3 2 13; 5 10 11 8; 9 6 7 12; 4 15 14 1]

Use Functions

Example: B = zeros(1,5) row vector/array

C = ones(7,1) column vector/array

D = rand(5,8,3) multiple dimension matrix

Load/Import from files

zeros All 0s

ones All 1s

rand Uniformly distributed random elements

randn Normally distributed random elements

Elementary Matrices

>>D=rand(3,2,3)

D(:,:,1) = D(:,:,2) = D(:,:,3) =

0.9501 0.4860 0.4565 0.4447 0.9218 0.4057

0.2311 0.8913 0.0185 0.6154 0.7382 0.9355

0.6068 0.7621 0.8214 0.7919 0.1763 0.9169

>> sum(D(:,1,1))

ans =

1.7881

>> E=D(:,:,2)'

E =

0.4565 0.0185 0.8214

0.4447 0.6154 0.7919

>> a=diag(D(:,:,3))

a =

0.9218

0.9355

>> F=[D(1,:,1),D(2,:,3); D(1,:,1)+1, D(2,:,3)-1]

F =

0.9501 0.4860 0.7382 0.9355

1.9501 1.4860 -0.2618 -0.0645

>>F(:,2)=[]

F =

0.9501 0.7382 0.9355

1.9501 -0.2618 -0.0645

>> F(2:1:4)=[]

F =

0.9501 0.9355 -0.0645

Examples of Expression

>>rho = (1+sqrt(5))/2

rho =

1.6180

>>a = abs(3+4i)

a =

5

>>huge = exp(log(realmax))

huge =

1.7977e+308 =1.8X10

308

Basic Application II

Graphic

Programming

Flow Control

Selector: if, switch & case

Loop: for, while, continue, break, try & catch

Other: return

Other Data Structures

Multidimensional arrays, Cell arrays, Structures,

etc.

Scripts and Functions

Flow Control Examples I

Selector:

2-way:

if rand < 0.3 %Condition

flag = 0; %then_expression_1

else

flag = 1; %then_expression_2

end %endif

Multiple-ways:

if A > B | switch (grade)

'greater | case 0

elseif A < B | Excellent

'less | case 1

elseif A == B | Good

'equal | case 2

else | Average

error('Unexpected situation') | otherwise

end | Failed

| end

Flow Control Examples II

Loop

>>Generate a matrix

for i = 1:2

for j = 1:6

H(i,j) = 1/(i+j);

end

end

>>H

H =

0.5000 0.3333 0.2500 0.2000 0.1667 0.1429

0.3333 0.2500 0.2000 0.1667 0.1429 0.1250

Loop Cond.

>>%Obtain the result is a root of the polynomial x

3

- 2x 5

a = 0; fa = -Inf;

b = 3; fb = Inf;

while b-a > eps*b

x = (a+b)/2;

fx = x^3-2*x-5;

if sign(fx) == sign(fa)

a = x; fa = fx;

else

b = x; fb = fx;

end

end

>>x

x =

2.09455148154233

Scripts

MATLAB simply executes the commands found

in the file

Example

% Investigate the rank of magic squares

r = zeros(1,32); %generation a row array 1X 32

% ; tell the system does not display

% the result on the screen

for n = 3:32

r(n) = rank(magic(n));

end

r

bar(r) %display r in bar figure

Scripts Cond.

Note:

No input/output parameters

(Different from functions! )

Write the script in editor, which can be

activated by command edit in command

window, save it with its specific name

Next time you want to execute the script just

call the name in the command window

Functions

Functions are M-files that can accept input

arguments and return output arguments.

The names of the M-file and of the

function should be the same.

Function Example I

Background of AIC

AIC is used to compare the quality of nested

models

AIC requires a bias-adjustment in small sample

sizes

1

2 ln( ) 2

2 ( 1)

2 ln( ) 2

1

min( )

exp( 0.5 )

exp( 0.5 )

i i

i

i R

r

r

AIC likelihood K

K K

AICad likelihood K

n K

delta AIC AIC

delta

w

delta

=

= +

+

= + +

=

=

%AICad Function

%Date:Dec.29th, 2008

%Purpose: Calculate the adjusted

% Akaikes Information Criteria (AIC)

%InPut: AIC

% n (the sample size)

% K (the number of parameters in the model)

%OutPut: AICad

% delta

% weight

%Functions Called: None

%Called by: None

IN Command Window

>>AIC=[-123; -241.7; -92.4; -256.9];

>>n=12;

>>K=[4;8;2;6];

>>[AICad, delta, w] = CalAIC(AIC, n, K)

AICad = delta = w =

-83.0000 89.9000 0.0000

-97.7000 75.2000 0.0000

-80.4000 92.5000 0.0000

-172.9000 0 1.0000

M file

function[AICad,delta,w]=CalAIC(AIC,n,K)

AICad = AIC+2.*K.*(K+1);

a = min(AICad);

delta = AICad - a;

b = exp(-0.5.*delta);

c = sum(b);

w = b./c;

Function Example II

Background of PCA

Comparing more than two communities or samples

Sample Post Oak Red Oak Water Oak

1 66 25 24

2 48 30 31

3 26 55 42

4 15 20 49

5 11 50 58

combine post post red red water water

Y w x w x w x = + +

Background of PCA

Cond.

Principal Components Analysis (PCA)

It finds weighted sums of samples or

observations (linear combinations) that are

highly correlated with the values of the response

variables (e.g., species abundances)

PCA objectively chooses these weights in such a way

as to maximize the variance in the weighted sums

Based on correlations between response variables

.

Function Head

%Principle Component Analysis Function

%Date:Dec.29th, 2008

%Purpose: Obtain the axis scores of PCA

%InPut: the abundance of 3 species

% in 5 different samples

%OutPut: sample scores of PCA axis

%Functions Called: None

%Called by: None

IN Command Window

>>a=[66;48;26;15;11];

>>b=[25;30;55;20;50];

>>c=[24;31;42;49;58];

>>[score1, score2]=PCA(a,b,c)

score1 = score2 =

-2.2233 -0.1963

-1.1519 -0.0743

0.8734 -1.0888

0.4871 1.5120

2.0147 -0.1526

M file

function[x11,x12,x13,x21,x22,x23]=PCA(a,b,c)

%Calculate the mean and population standard deviation of 3 species

for i=1:5

d(i)=(a(i)-mean(a))^2;

stda=sqrt(sum(d)/5);

e(i)=(b(i)-mean(b))^2;

stdb=sqrt(sum(e)/5);

f(i)=(c(i)-mean(c))^2;

stdc=sqrt(sum(f)/5);

end

%Obtain the z-scores of 3 species

for i=1:5

za(i)=(a(i)-mean(a))/stda;

zb(i)=(b(i)-mean(b))/stdb;

zc(i)=(c(i)-mean(c))/stdc;

end

N=[za',zb',zc'];

M file Cond.

%Obtain the original correlation matrix

M=[1,corr(a,b),corr(a,c);corr(a,b),1,corr(b,c);corr(a,c),corr(b,c),1];

[V1,D1]= eig(M); %Calculate the eigenvector and eigenvalues

weight1=V1(:,3); %Get the maximum eigenvector

score1=N*weight1;

%We use the exact same procedure that we used for axis 1,

%except that we use a partial correlation matrix

%The partial correlation matrix is made up of all pairwise correlations

%among the 3 species, independent of their correlation with the axis 1

%sample scores. Hence, axis 2 sample scores will be uncorrelated

%with (or orthogonal to) axis 1 scores.

M file Cond.

new=[a,b,c,score1];

M2=[1,corr(a,b),corr(a,c),corr(a,score1);

corr(a,b),1,corr(b,c),corr(b,score1);

corr(a,c), corr(b, c), 1, corr(c,score1);

corr(a,score1),corr(b,score1),corr(c,score1),1];

for i=1:3

for j=1:3

corrnew(i,j)=M2(i,j);

end

end

g=[M2(4,1)*M2(4,1),M2(4,1)*M2(4,2),M2(4,1)*M2(4,3);

M2(4,2)*M2(4,1),M2(4,2)*M2(4,2),M2(4,2)*M2(4,3);

M2(4,3)*M2(4,1),M2(4,3)*M2(4,2),M2(4,3)*M2(4,3)];

corrmatrix=corrnew-g;

[V2,D2]=eig(corrmatrix);

weight2=V2(:,3); %signs needs to be checked with JMP

score2=N*weight2;

MATLAB in MCSR

Matlab is available on willow and sweetgum

www.mcsr.olemiss.edu

assist@mcsr.olemiss.edu

Enter matlab can activate Matlab in willow

or sweetgum

Use ver to obtain the version of Matlab,

which can tell you which toolboxes of

Matlab in that machine

Price of personal purchase is 500$ include update

releases (only include MATLAB & Simulink)

You need pay separate fee for each toolbox such as

statistical, bioinformatics, etc

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