Creating a number of matrices/vectors based on a number - matlab

I have a simple for loop that is used to simulated data,
for t=2:T;
Y_star(t,1,b)=[Y_star(t-1,1,b) X_1_star(t-1,1,b) X_2_star(t-1,1,b) 1]*beta(:,i)+w(t-1)*e(t-1,i);
X_1_star(t,1,b)=Theta(1,1)+Phi(1,:,1)*[X_1_star(t-1,1,b) ; X_2_star(t-1,1,b)]+w(t-1)*v(t-1,1,i);
X_2_star(t,1,b)=Theta(2,1)+Phi(2,:,1)*[X_1_star(t-1,1,b) ; X_2_star(t-1,1,b)]+w(t-1)*v(t-1,2,i);
end;
The issue I am having is this is fine when I have two X variables, however, I would like to write the code so that I can increase the number of variables to change each time, 4 say.
In this case, I would need X_1_star, X_2_star, X_3_star and X_4_star.
I can handle the Phi and Theta coefficients, as well as the w and v and e however I am struggling with creating the matrices for X's.
Any ideas would be greatly, I have tried storing the matrices within cells but I struggled to get this working.
Following the commnets, here is a simple example
%% Simple example
%-------------------------------------------------------------------------%
Phi = [0.9954 0.0195;
0.0012 0.9567];
Theta= [0.007;0.051];
beta = [0.06;-0.10;1.66;-0.88];
N = 1;
e = rand(370,1);
v = randn(370,2);
t = 371;
T = 371;
yy = rand(370,1);
X_1 = rand(370,1);
X_2 = rand(370,1);
B=50;
Y_star=zeros(T,N,B);
X_1_star=zeros(T,N,B);
X_2_star=zeros(T,N,B);
for b=1:B;
Y_star(1,:,b)=yy(1,:);
X_1_star(1,:,b)=X_1(1,:);
X_2_star(1,:,b)=X_2(1,:);
w=randn(T-1,1);
for t=2:T;
for i=1:N;
Y_star(t,i,b)=[Y_star(t-1,i,b) X_1_star(t-1,i,b) ...
X_2_star(t-1,i,b) 1]*beta(:,i)+w(t-1)*e(t-1,i);
X_1_star(t,i,b)=Theta(1,i)+Phi(1,:,i)*[X_1_star(t-1,i,b) ; ...
X_2_star(t-1,i,b)]+w(t-1)*v(t-1,1,i);
X_2_star(t,i,b)=Theta(2,i)+Phi(2,:,i)*[X_1_star(t-1,i,b) ; ...
X_2_star(t-1,i,b)]+w(t-1)*v(t-1,2,i);
end;
end;
disp(b);
end;
I ideally this to do the same thing but not be dependent upon writing X_1 and X_2, as I would like to increase this sometimes to a larger number.
I have tried reshaping as the commnets suggested but not sure how this would or could work in this example.

I think this problem is simply one of matrix algebra.
With the X variables it appears like you are simulating a small VAR model.
Instead of dynamic matrices as the answer above, I think it would make more sense to simulating the x data as a larger matrix instead of vectors.
Here is a simple example,
First, I show you a two variable case, both in the method you use, and by jointly simulating the data...
Then I show with a 3 variable case how to extend this...
All you have to do is take the size of the beta matrix (or alpha) as I guessing these are determined before the matrix...
%Simulating a small VAR model
%% 2 - variable case
rng('default')
b = [0.4 0.5;0.6 0.07];
a = [0.1 0.2];
v=randn(100,2);
x1 = zeros(100,1);
x2 = zeros(100,1);
xm=zeros(100,2);
T=100;
for t=2:T;
x1(t)=a(1)+b(1,:)*[x1(t-1) ; x2(t-1)]+v(t-1,1);
x2(t)=a(2)+b(2,:)*[x1(t-1) ; x2(t-1)]+v(t-1,2);
end;
for t=2:T;
xm(t,:)=a+xm(t-1,:)*b'+v(t-1,:)
end;
[xm x1 x2]
%% 3 - variable case
rng('default')
b = [0.4 0.5 0.1;0.6 0.07 0.1; 0.3 0.4 0.7];
a = [0.1 0.2 0.3];
v=randn(100,size(b,2));
xm=zeros(100,size(b,2));
for t=2:T;
xm(t,:)=a+xm(t-1,:)*b'+v(t-1,:)
end;

I generally find structure arrays more useful for this kind of dynamic indexing (where you don't know how many you'll have of X_1_star, X_2_star...)
I didn't try to reproduce the whole example, but it might go something like this if you're trying to get up to X_4_star:
...
nX=4;
for i=1:N
Y_star(t,i,b)=[Y_star(t-1,i,b) X_1_star(t-1,i,b) ...
X_2_star(t-1,i,b) 1]*beta(:,i)+w(t-1)*e(t-1,i);
for n=1:nX
X(n).star(t,i,b)=...
end
end

Related

Strange wrong result for (un)coupled PDEs using MATLAB's pdepe, time is doubled

I am trying to solve two coupled reaction diffusion equations in 1d, using pdpe, namely
$\partial_t u_1 = \nabla^2 u_1 + 2k(-u_1^2+u_2)$
$\partial_t u_2 = \nabla^2 u_1 + k(u_1^2-u_2)$
The solution is in the domain $x\in[0,1]$, with initial conditions being two identical Gaussian profiles centered at $x=1/2$. The boundary conditions are absorbing for both components, i.e. $u_1(0)=u_2(0)=u_1(1)=u_2(1)=0$.
Pdepe gives me a solution without prompting any errors. However, I think the solutions must be wrong, because when I set the coupling to zero, i.e. $k=0$ (and also if I set it to be very small, say $k=0.001$), the solutions do not coincide with the solution of the simple diffusion equation
$\partial_t u = \nabla^2 u$
as obtained from pdepe itself.
Strangely enough, the solutions $u_1(t)=u_2(t)$ from the "coupled" case with coupling set to zero, and the solution for the case uncoupled by construction $u(t')$ coincide if we set $t'=2t$, that is, the solution of the "coupled" case evolves twice as fast as the solution of the uncoupled case.
Here's a minimal working example:
Coupled case
function [xmesh,tspan,sol] = coupled(k) %argument is the coupling k
std=0.001; %width of initial gaussian
center=1/2; %center of gaussian
xmesh=linspace(0,1,10000);
tspan=linspace(0,1,1000);
sol = pdepe(0,#pdefun,#icfun,#bcfun,xmesh,tspan);
function [c,f,s] = pdefun(x,t,u,dudx)
c=ones(2,1);
f=zeros(2,1);
f(1) = dudx(1);
f(2) = dudx(2);
s=zeros(2,1);
s(1) = 2*k*(u(2)-u(1)^2);
s(2) = k*(u(1)^2-u(2));
end
function u0 = icfun(x)
u0=ones(2,1);
u0(1) = exp(-(x-center)^2/(2*std^2))/(sqrt(2*pi)*std);
u0(2) = exp(-(x-center)^2/(2*std^2))/(sqrt(2*pi)*std);
end
function [pL,qL,pR,qR] = bcfun(xL,uL,xR,uR,t)
pL=zeros(2,1);
pL(1) = uL(1);
pL(2) = uL(2);
pR=zeros(2,1);
pR(1) = uR(1);
pR(2) = uR(2);
qL = [0 0;0 0];
qR = [0 0;0 0];
end
end
Uncoupled case
function [xmesh,tspan,sol] = uncoupled()
std=0.001; %width of initial gaussian
center=1/2; %center of gaussian
xmesh=linspace(0,1,10000);
tspan=linspace(0,1,1000);
sol = pdepe(0,#pdefun,#icfun,#bcfun,xmesh,tspan);
function [c,f,s] = pdefun(x,t,u,dudx)
c=1;
f = dudx;
s=0;
end
function u0 = icfun(x)
u0=exp(-(x-center)^2/(2*std^2))/(sqrt(2*pi)*std);
end
function [pL,qL,pR,qR] = bcfun(xL,uL,xR,uR,t)
pL=uL;
pR=uR;
qL = 0;
qR = 0;
end
end
Now, suppose we run
[xmesh,tspan,soluncoupled] = uncoupled();
[xmesh,tspan,solcoupled] = coupled(0); %coupling k=0, i.e. uncoupled solutions
One can directly check by plotting the solutions for any time index $it$ that, even if they should be identical, the solutions given by each function are not identical, e.g.
hold all
plot(xmesh,soluncoupled(it+1,:),'b')
plot(xmesh,solcoupled(it+1,:,1),'r')
plot(xmesh,solcoupled(it+1,:,2),'g')
On the other hand, if we double the time of the uncoupled solution, the solutions are identical
hold all
plot(xmesh,soluncoupled(2*it+1,:),'b')
plot(xmesh,solcoupled(it+1,:,1),'r')
plot(xmesh,solcoupled(it+1,:,2),'g')
The case $k=0$ is not singular, one can set $k$ to be small but finite, and the deviations from the case $k=0$ are minimal, i.e. the solution still goes twice as fast as the uncoupled solution.
I really don't understand what is going on. I need to work on the coupled case, but obviously I don't trust the results if it does not give the right limit when $k\to 0$. I don't see where I could be making a mistake. Could it be a bug?
I found the source of the error. The problem lies in the qL and qR variables of bcfun for the coupled() function. The MATLAB documentation, see here and here, is slightly ambiguous on whether the q's should be matrices or column vectors. I had used matrices
qL = [0 0;0 0];
qR = [0 0;0 0];
but in reality I should have used column vectors
qL = [0;0];
qR = [0;0];
Amazingly, pdpe didn't throw an error, and simply gave wrong results. This should perhaps be fixed by the developers.

How to setup equation that involves a sum from x=1 to infinity and loops?

I am getting confused on how to properly set up this equation. To find a value of V(i,j). The end result would be plotting V over time. I understand that there needs to be loops to allow this equation to work, however I am lost when it comes to setting it up. Basically I am trying to take the sum from n=1 to infinity of (1-(-1)^n)/(n^4 *pi^4)*sin((n*pi*c*j)/L)*sin((n*pi*i)/L)
I originally thought that I should make it a while loop to increment n by 1 until I reach say 10 or so just to get an idea of what the output would look like. All of the variables were unknown and values were added again to see what the plot would look like.
I have down another code where the equation is just dependent on i and j. However with this n term, I am thrown off. Any advice would be great as to setting up the equation. Thank you.
L=10;
x=linspace(0,L,30);
t1= 50;
X=30;
p=1
c=t1/1000;
V=zeros(X,t1);
V(1,:)=0;
V(30,:)=0;
R=((4*p*L^3)/c);
n=1;
t=1:50;
while n < 10
for i=1:31
for j=1:50
V(i,j)=R*sum((1-(-1)^n)/(n^4 *pi^4)*sin((n*pi*c*j)/L)*sin((n*pi*i)/L));
end
end
n=n+1;
end
figure(1)
plot(V(i,j),t)
Various ways of doing so:
1) Computing the sum up to one Nmax in one shot:
Nmax = 30;
Vijn = #(i,j,n) R*((1-(-1)^n)/(n^4 *pi^4)*sin((n*pi*c*j)/L)*sin((n*pi*i)/L));
i = 1:31;
j = 1:50;
n = 1:Nmax;
[I,J,N] = ndgrid(i,j,n);
V = arrayfun(Vijn,I,J,N);
Vc = cumsum(V,3);
% now Vc(:,:,k) is sum_n=1^{k+1} V(i,j,n)
figure(1);clf;imagesc(Vc(:,:,end));
2) Looping indefinitely
n = 1;
V = 0;
i = 1:31;
j = 1:50;
[I,J] = meshgrid(i,j);
while true
V = V + R*((1-(-1)^n)/(n^4 *pi^4)*sin((n*pi*c*J)/L).*sin((n*pi*I)/L));
n = n + 1;
figure(1);clf;
imagesc(V);
title(sprintf('N = %d',n))
drawnow;
pause(0.25);
end
Note that in your example you won't need many terms, since:
Every second term is zero (for even n, the term 1-(-1)^n is zero).
The terms decay with 1/n^4. In norms: n=1 contributes ~2e4, n=3 contributes ~4e2, n=5 contributes 5e1, n=7 contributes ~14, etc. Visually, there is a small difference between n=1 and n=1+n=3 but barely a noticeable one for n=1+n=3+n=5.
Given that so few terms are needed, the first approach is probably the better one. Also, skip the even indices, as you don't need them.

separate 'entangled' vectors in Matlab

I have a set of three vectors (stored into a 3xN matrix) which are 'entangled' (e.g. some value in the second row should be in the third row and vice versa). This 'entanglement' is based on looking at the figure in which alpha2 is plotted. To separate the vector I use a difference based approach where I calculate the difference of one value with respect the three next values (e.g. comparing (1,i) with (:,i+1)). Then I take the minimum and store that. The method works to separate two of the three vectors, but not for the last.
I was wondering if you guys can share your ideas with me how to solve this problem (if possible). I have added my coded below.
Thanks in advance!
Problem in figures:
clear all; close all; clc;
%%
alpha2 = [-23.32 -23.05 -22.24 -20.91 -19.06 -16.70 -13.83 -10.49 -6.70;
-0.46 -0.33 0.19 2.38 5.44 9.36 14.15 19.80 26.32;
-1.58 -1.13 0.06 0.70 1.61 2.78 4.23 5.99 8.09];
%%% Original
figure()
hold on
plot(alpha2(1,:))
plot(alpha2(2,:))
plot(alpha2(3,:))
%%% Store start values
store1(1,1) = alpha2(1,1);
store2(1,1) = alpha2(2,1);
store3(1,1) = alpha2(3,1);
for i=1:size(alpha2,2)-1
for j=1:size(alpha2,1)
Alpha1(j,i) = abs(store1(1,i)-alpha2(j,i+1));
Alpha2(j,i) = abs(store2(1,i)-alpha2(j,i+1));
Alpha3(j,i) = abs(store3(1,i)-alpha2(j,i+1));
[~, I] = min(Alpha1(:,i));
store1(1,i+1) = alpha2(I,i+1);
[~, I] = min(Alpha2(:,i));
store2(1,i+1) = alpha2(I,i+1);
[~, I] = min(Alpha3(:,i));
store3(1,i+1) = alpha2(I,i+1);
end
end
%%% Plot to see if separation worked
figure()
hold on
plot(store1)
plot(store2)
plot(store3)
Solution using extrapolation via polyfit:
The idea is pretty simple: Iterate over all positions i and use polyfit to fit polynomials of degree d to the d+1 values from F(:,i-(d+1)) up to F(:,i). Use those polynomials to extrapolate the function values F(:,i+1). Then compute the permutation of the real values F(:,i+1) that fits those extrapolations best. This should work quite well, if there are only a few functions involved. There is certainly some room for improvement, but for your simple setting it should suffice.
function F = untangle(F, maxExtrapolationDegree)
%// UNTANGLE(F) untangles the functions F(i,:) via extrapolation.
if nargin<2
maxExtrapolationDegree = 4;
end
extrapolate = #(f) polyval(polyfit(1:length(f),f,length(f)-1),length(f)+1);
extrapolateAll = #(F) cellfun(extrapolate, num2cell(F,2));
fitCriterion = #(X,Y) norm(X(:)-Y(:),1);
nFuncs = size(F,1);
nPoints = size(F,2);
swaps = perms(1:nFuncs);
errorOfFit = zeros(1,size(swaps,1));
for i = 1:nPoints-1
nextValues = extrapolateAll(F(:,max(1,i-(maxExtrapolationDegree+1)):i));
for j = 1:size(swaps,1)
errorOfFit(j) = fitCriterion(nextValues, F(swaps(j,:),i+1));
end
[~,j_bestSwap] = min(errorOfFit);
F(:,i+1) = F(swaps(j_bestSwap,:),i+1);
end
Initial solution: (not that pretty - Skip this part)
This is a similar solution that tries to minimize the sum of the derivatives up to some degree of the vector valued function F = #(j) alpha2(:,j). It does so by stepping through the positions i and checks all possible permutations of the coordinates of i to get a minimal seminorm of the function F(1:i).
(I'm actually wondering right now if there is any canonical mathematical way to define the seminorm so we get our expected results... I initially was going for the H^1 and H^2 seminorms, but they didn't quite work...)
function F = untangle(F)
nFuncs = size(F,1);
nPoints = size(F,2);
seminorm = #(x,i) sum(sum(abs(diff(x(:,1:i),1,2)))) + ...
sum(sum(abs(diff(x(:,1:i),2,2)))) + ...
sum(sum(abs(diff(x(:,1:i),3,2)))) + ...
sum(sum(abs(diff(x(:,1:i),4,2))));
doSwap = #(x,swap,i) [x(:,1:i-1), x(swap,i:end)];
swaps = perms(1:nFuncs);
normOfSwap = zeros(1,size(swaps,1));
for i = 2:nPoints
for j = 1:size(swaps,1)
normOfSwap(j) = seminorm(doSwap(F,swaps(j,:),i),i);
end
[~,j_bestSwap] = min(normOfSwap);
F = doSwap(F,swaps(j_bestSwap,:),i);
end
Usage:
The command alpha2 = untangle(alpha2); will untangle your functions:
It should even work for more complicated data, like these shuffled sine-waves:
nPoints = 100;
nFuncs = 5;
t = linspace(0, 2*pi, nPoints);
F = bsxfun(#(a,b) sin(a*b), (1:nFuncs).', t);
for i = 1:nPoints
F(:,i) = F(randperm(nFuncs),i);
end
Remark: I guess if you already know that your functions will be quadratic or some other special form, RANSAC would be a better idea for larger number of functions. This could also be useful if the functions are not given with the same x-value spacing.

Plotting time graph in MATLAB

I have a function of this form in MATLAB,
C=S*e^(L*t)*inv(S)*C_0
where my
S=[-2 -3;3 -2]
L=[0.5 0; 0 1.5]
C_0=[1; 1]
I need to plot this function with respect to time. My output C is a 2-by-1 matrix.
What I have done is computed e^L separately using b=expm(L) and then I inserted mpower(b,t) into the function. So my resulting function in the script looks like
b=expm(L);
C=S*mpower(b,t)*inv(S)*C_0;
Now, how should I go about plotting this w.r.t time. I tried defining the time vector and then using it, but quite obviously I get the error message which says matrix dimensions do not agree. Can someone give me a suggestion?
You can probably do this in a vectorised manner but if you're not worried about speed or succinct code, why not just write a for loop?
ts = 1 : 100;
Cs = zeros(2, length(ts) );
S = [-2 -3;3 -2];
L = [0.5 0; 0 1.5];
C_0 = [1; 1];
for ii = 1 : length(ts)
b = expm(L);
Cs(:,ii) = S*mpower(b,ts(ii))*inv(S)*C_0;
end
ts contains the time values, Cs contains the values of C at each time.

tensile tests in matlab

The problem says:
Three tensile tests were carried out on an aluminum bar. In each test the strain was measured at the same values of stress. The results were
where the units of strain are mm/m.Use linear regression to estimate the modulus of elasticity of the bar (modulus of elasticity = stress/strain).
I used this program for this problem:
function coeff = polynFit(xData,yData,m)
% Returns the coefficients of the polynomial
% a(1)*x^(m-1) + a(2)*x^(m-2) + ... + a(m)
% that fits the data points in the least squares sense.
% USAGE: coeff = polynFit(xData,yData,m)
% xData = x-coordinates of data points.
% yData = y-coordinates of data points.
A = zeros(m); b = zeros(m,1); s = zeros(2*m-1,1);
for i = 1:length(xData)
temp = yData(i);
for j = 1:m
b(j) = b(j) + temp;
temp = temp*xData(i);
end
temp = 1;
for j = 1:2*m-1
s(j) = s(j) + temp;
temp = temp*xData(i);
end
end
for i = 1:m
for j = 1:m
A(i,j) = s(i+j-1);
end
end
% Rearrange coefficients so that coefficient
% of x^(m-1) is first
coeff = flipdim(gaussPiv(A,b),1);
The problem is solved without a program as follows
MY ATTEMPT
T=[34.5,69,103.5,138];
D1=[.46,.95,1.48,1.93];
D2=[.34,1.02,1.51,2.09];
D3=[.73,1.1,1.62,2.12];
Mod1=T./D1;
Mod2=T./D2;
Mod3=T./D3;
xData=T;
yData1=Mod1;
yData2=Mod2;
yData3=Mod3;
coeff1 = polynFit(xData,yData1,2);
coeff2 = polynFit(xData,yData2,2);
coeff3 = polynFit(xData,yData3,2);
x1=(0:.5:190);
y1=coeff1(2)+coeff1(1)*x1;
subplot(1,3,1);
plot(x1,y1,xData,yData1,'o');
y2=coeff2(2)+coeff2(1)*x1;
subplot(1,3,2);
plot(x1,y2,xData,yData2,'o');
y3=coeff3(2)+coeff3(1)*x1;
subplot(1,3,3);
plot(x1,y3,xData,yData3,'o');
What do I have to do to get this result?
As a general advice:
avoid for loops wherever possible.
avoid using i and j as variable names, as they are Matlab built-in names for the imaginary unit (I really hope that disappears in a future release...)
Due to m being an interpreted language, for-loops can be very slow compared to their compiled alternatives. Matlab is named MATtrix LABoratory, meaning it is highly optimized for matrix/array operations. Usually, when there is an operation that cannot be done without a loop, Matlab has a built-in function for it that runs way way faster than a for-loop in Matlab ever will. For example: computing the mean of elements in an array: mean(x). The sum of all elements in an array: sum(x). The standard deviation of elements in an array: std(x). etc. Matlab's power comes from these built-in functions.
So, your problem. You have a linear regression problem. The easiest way in Matlab to solve this problem is this:
%# your data
stress = [ %# in Pa
34.5 69 103.5 138] * 1e6;
strain = [ %# in m/m
0.46 0.95 1.48 1.93
0.34 1.02 1.51 2.09
0.73 1.10 1.62 2.12]' * 1e-3;
%# make linear array for the data
yy = strain(:);
xx = repmat(stress(:), size(strain,2),1);
%# re-formulate the problem into linear system Ax = b
A = [xx ones(size(xx))];
b = yy;
%# solve the linear system
x = A\b;
%# modulus of elasticity is coefficient
%# NOTE: y-offset is relatively small and can be ignored)
E = 1/x(1)
What you did in the function polynFit is done by A\b, but the \-operator is capable of doing it way faster, way more robust and way more flexible than what you tried to do yourself. I'm not saying you shouldn't try to make these thing yourself (please keep on doing that, you learn a lot from it!), I'm saying that for the "real" results, always use the \-operator (and check your own results against it as well).
The backslash operator (type help \ on the command prompt) is extremely useful in many situations, and I advise you learn it and learn it well.
I leave you with this: here's how I would write your polynFit function:
function coeff = polynFit(X,Y,m)
if numel(X) ~= numel(X)
error('polynFit:size_mismathc',...
'number of elements in matrices X and Y must be equal.');
end
%# bad condition number, rank errors, etc. taken care of by \
coeff = bsxfun(#power, X(:), m:-1:0) \ Y(:);
end
I leave it up to you to figure out how this works.