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MATLAB 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];

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outline
Outline
  • Examples
  • What is Matlab?
  • History
  • Characteristics
  • Organization of Matlab – Toolboxes
  • Basic Applications
  • Programming
example i
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

c code
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
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
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 cond7
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
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

what is matlab
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
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
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
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
MATLAB SYSTEM

MATLAB

Simulink

Applications

Develop Tools

Stateflow

Toolboxes

Module Libraries

Data-Accessing Tools

DATA

Generating-Codes Tools

C

Third parties modules

buildup of 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
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
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
elementary matrices
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
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 =1.8X10308

programming
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
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
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

slide23
Loop Cond.

>>%Obtain the result is a root of the polynomial x3 - 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
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
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
  • 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
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

function head comments
Function Head (Comments)

%AICad Function

%Date:Dec.29th, 2008

%Purpose: Calculate the adjusted

% Akaike’s 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
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
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
Function Example II
  • Background of PCA

Comparing more than two communities or samples

background of pca cond
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 responsevariables (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
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 window34
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 file35
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
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 cond37
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 in MCSR
  • Matlab is available on willow and sweetgum
  • www.mcsr.olemiss.edu
  • assist@mcsr.olemiss.edu
slide41
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

take home message
Take Home Message

More Practise,

More Confidence!