Hi i've been asked to solve SIR model using fsolve command in MATLAB, and Euler 3 point backward. I'm really confused on how to proceed, please help. This is what i have so far. I created a function for 3BDF scheme but i'm not sure how to proceed with fsolve and solve the system of nonlinear ODEs. The SIR model is shown as and 3BDF scheme is formulated as
clc
clear all
gamma=1/7;
beta=1/3;
ode1= #(R,S,I) -(beta*I*S)/(S+I+R);
ode2= #(R,S,I) (beta*I*S)/(S+I+R)-I*gamma;
ode3= #(I) gamma*I;
f(t,[S,I,R]) = [-(beta*I*S)/(S+I+R); (beta*I*S)/(S+I+R)-I*gamma; gamma*I];
R0=0;
I0=10;
S0=8e6;
odes={ode1;ode2;ode3}
fun = #root2d;
x0 = [0,0];
x = fsolve(fun,x0)
function [xs,yb] = ThreePointBDF(f,x0, xmax, h, y0)
% This function should return the numerical solution of y at x = xmax.
% (It should not return the entire time history of y.)
% TO BE COMPLETED
xs=x0:h:xmax;
y=zeros(1,length(xs));
y(1)=y0;
yb(1)=y0+f(x0,y0)*h;
for i=1:length(xs)-1
R =R0;
y1(i+1,:) = fsolve(#(u) u-2*h/3*f(t(i+1),u) - R, y1(i-1,:)+2*h*F(i,:))
S = S0;
y2(i+1,:) = fsolve(#(u) u-2*h/3*f(t(i+1),u) - S, y2(i-1,:)+2*h*F(i,:))
I= I0;
y3(i+1,:) = fsolve(#(u) u-2*h/3*f(t(i+1),u) - I, y3(i-1,:)+2*h*F(i,:))
end
end
You have an implicit equation
y(i+1) - 2*h/3*f(t(i+1),y(i+1)) = G = (4*y(i) - y(i-1))/3
where the right-side term G is constant in the call to fsolve, that is, during the solution of the implicit step equation.
Note that this is for the vector valued system y'(t)=f(t,y(t)) where
f(t,[S,I,R]) = [-(beta*I*S)/(S+I+R); (beta*I*S)/(S+I+R)-I*gamma; gamma*I];
To solve this write
G = (4*y(i,:) - y(i-1,:))/3
y(i+1,:) = fsolve(#(u) u-2*h/3*f(t(i+1),u) - G, y(i-1,:)+2*h*F(i,:))
where a midpoint step is used to get an order 2 approximation as initial guess, F(i,:)=f(t(i),y(i,:)). Add solver options for error tolerances as necessary, you want the error in the implicit equation smaller than the truncation error O(h^3) of the step. One can also keep only a short array of function values, then one has to be careful for the correspondence of the position in the short array to the time index.
Using all that and a reference solution by a higher order standard solver produces the following error graphs for the components
where one can see that the first order error of the constant first step results in a first order global error, while with a second order error in the first step using the Euler method results in a clear second order global error.
Implement the method in general terms
from scipy.optimize import fsolve
def BDF2(f,t,y0,y1):
N, h = len(t)-1, t[1]-t[0];
y = (N+1)*[np.asarray(y0)];
y[1] = y1;
for i in range(1,N):
t1, G = t[i+1], (4*y[i]-y[i-1])/3
y[i+1] = fsolve(lambda u: u-2*h/3*f(t1,u)-G, y[i-1]+2*h*f(t[i],y[i]), xtol=1e-3*h**3)
return np.vstack(y)
Set up the model to be solved
gamma=1/7;
beta=1/3;
print beta, gamma
y0 = np.array([8e6, 10, 0])
P = sum(y0); y0 = y0/P
def f(t,y): S,I,R = y; trns = beta*S*I/(S+I+R); recv=gamma*I; return np.array([-trns, trns-recv, recv])
Compute a reference solution and method solutions for the two initialization variants
from scipy.integrate import odeint
tg = np.linspace(0,120,25*128)
yg = odeint(f,y0,tg,atol=1e-12, rtol=1e-14, tfirst=True)
M = 16; # 8,4
t = tg[::M];
h = t[1]-t[0];
y1 = BDF2(f,t,y0,y0)
e1 = y1-yg[::M]
y2 = BDF2(f,t,y0,y0+h*f(0,y0))
e2 = y2-yg[::M]
Plot the errors, computation as above, but embedded in the plot commands, could be separated in principle by first computing a list of solutions
fig,ax = plt.subplots(3,2,figsize=(12,6))
for M in [16, 8, 4]:
t = tg[::M];
h = t[1]-t[0];
y = BDF2(f,t,y0,y0)
e = (y-yg[::M])
for k in range(3): ax[k,0].plot(t,e[:,k],'-o', ms=1, lw=0.5, label = "h=%.3f"%h)
y = BDF2(f,t,y0,y0+h*f(0,y0))
e = (y-yg[::M])
for k in range(3): ax[k,1].plot(t,e[:,k],'-o', ms=1, lw=0.5, label = "h=%.3f"%h)
for k in range(3):
for j in range(2): ax[k,j].set_ylabel(["$e_S$","$e_I$","$e_R$"][k]); ax[k,j].legend(); ax[k,j].grid()
ax[0,0].set_title("Errors: first step constant");
ax[0,1].set_title("Errors: first step Euler")
I'm having some issues getting my RK2 algorithm to work for a certain second-order linear differential equation. I have posted my current code (with the provided parameters) below. For some reason, the value of y1 deviates from the true value by a wider margin each iteration. Any input would be greatly appreciated. Thanks!
Code:
f = #(x,y1,y2) [y2; (1+y2)/x];
a = 1;
b = 2;
alpha = 0;
beta = 1;
n = 21;
h = (b-a)/(n-1);
yexact = #(x) 2*log(x)/log(2) - x +1;
ye = yexact((a:h:b)');
s = (beta - alpha)/(b - a);
y0 = [alpha;s];
[y1, y2] = RungeKuttaTwo2D(f, a, b, h, y0);
error = abs(ye - y1);
function [y1, y2] = RungeKuttaTwo2D(f, a, b, h, y0)
n = floor((b-a)/h);
y1 = zeros(n+1,1); y2 = y1;
y1(1) = y0(1); y2(1) = y0(2);
for i=1:n-1
ti = a+(i-1)*h;
fvalue1 = f(ti,y1(i),y2(i));
k1 = h*fvalue1;
fvalue2 = f(ti+h/2,y1(i)+k1(1)/2,y2(i)+k1(2)/2);
k2 = h*fvalue2;
y1(i+1) = y1(i) + k2(1);
y2(i+1) = y2(i) + k2(2);
end
end
Your exact solution is wrong. It is possible that your differential equation is missing a minus sign.
y2'=(1+y2)/x has as its solution y2(x)=C*x-1 and as y1'=y2 then y1(x)=0.5*C*x^2-x+D.
If the sign in the y2 equation were flipped, y2'=-(1+y2)/x, one would get y2(x)=C/x-1 with integral y1(x)=C*log(x)-x+D, which contains the given exact solution.
0=y1(1) = -1+D ==> D=1
1=y1(2) = C*log(2)-1 == C=1/log(2)
Additionally, the arrays in the integration loop have length n+1, so that the loop has to be from i=1 to n. Else the last element remains zero, which gives wrong residuals for the second boundary condition.
Correcting that and enlarging the computation to one secant step finds the correct solution for the discretization, as the ODE is linear. The error to the exact solution is bounded by 0.000285, which is reasonable for a second order method with step size 0.05.
I've noticed some weird facts about integral2. These are probably due to my limitations in understanding how it works. I have some difficulties in integrating out variables when I have particular functions. For instance, look at the following Code:
function Output = prova(p,Y)
x = p(1);
y = p(2);
w = p(3);
z = p(4);
F1 = #(Data,eta_1,eta_2,x,y,w,z) F2(eta_1,eta_2,Data) .* normpdf(eta_1,x,y) .* normpdf(eta_2,w,z);
Output = integral2(#(eta_1,eta_2)F1(Y,eta_1,eta_2,0,1,10,2),-5,5,-5,5);
end
function O = F2(pp1,pp2,D)
O = pp1 + pp2 + sum(D);
end
In this case the are no problems in evaluating the integral. But if I change the code in this way I obtain some errors, although the output of F2 is exactly the same:
function Output = prova(p,Y)
x = p(1);
y = p(2);
w = p(3);
z = p(4);
F1 = #(Data,eta_1,eta_2,x,y,w,z) F2(eta_1,eta_2,Data) .* normpdf(eta_1,x,y) .* normpdf(eta_2,w,z);
Output = integral2(#(eta_1,eta_2)F1(Y,eta_1,eta_2,0,1,10,2),-5,5,-5,5);
end
function O = F2(pp1,pp2,D)
o = sum([pp1 pp2]);
O = o + sum(D);
end
The problems increase if F2 for example have some matrix multiplication in which "eta_1" and "eta_2", which I want to integrate out, are involved. This problems makes practically impossible to solve computations in which, for instance, we have to integrate out a variable X which is inside a Likelihood Function (whose calculation could require some internal Loop, or Sum, or Prod involving our variable X). What is the solution?
I wrote a simple MatLab script to evaluate forward, backward and central difference approximations of first and second derivatives for a spesific function
(y = x^3-5x)
at two different x values
(x=0.5 and x = 1.5)
and for 7 different step sizes h and compare the relative errors of the approximations to the analytical derivatives.
However, i need to enter x and h values manually every time. Question is, how do I create a loop for 7 different h values and 2 different x values and get all the results as a matrix?
clc
clear all
close all
h = 0.00001;
x1 = 0.5;
y = #(x) x.^3 - 5*x;
dy = #(x) 3*x.^2 - 5;
ddy = #(x) 6*x;
d1 = dy(x1);
d2 = ddy(x1);
%Forward Differencing
f1 = (y(x1+h) - y(x1))/h;
f2 = (y(x1+2*h) - 2*y(x1+h) + y(x1))/(h.^2);
%Central Differencing
c1 = (y(x1+h)-y(x1-h))/(2*h);
c2 = (y(x1+h)-2*y(x1)+y(x1-h))/(h.^2);
% Backward Differencing
b1 = (y(x1) - y(x1-h))/h;
b2 = (y(x1)-2*y(x1-h)+y(x1-2*h))/(h.^2);
% Relative Errors
ForwardError1 = (f1 - dy(x1))/dy(x1);
ForwardError2 = (f2 - ddy(x1))/ddy(x1);
CentralError1 = (c1 - dy(x1))/dy(x1);
CentralError2 = (c2 - ddy(x1))/ddy(x1);
BackwardError1 = (b1 - dy(x1))/dy(x1);
BackwardError2 = (b2 - ddy(x1))/ddy(x1);
You don't need a loop. You can use meshgrid to create all combinations of your arguments (x and h in your case) and use these as inputs to your functions.
To get combinations of x = [0.5, 1.5] and h=0.00001:0.00001:0.00007 (I assume since you did not specify h values in the question), you would do:
[x, h] = meshgrid([0.5, 1.5], 0.00001:0.00001:0.00007);
y = #(x) x.^3 - 5*x;
f1 = (y(x1+h) - y(x1))./h;
Here x,h are matrices of size 7x2, and so is the result f1. Note that / was changed to ./ as h is a matrix and we want per-element operations.
Following code throws out an error.
syms z positive;
syms n;
syms m;
N = 10;
Ms = 10;
Es = 1;
pd = 0.9;
pd_dash = 1-pd;
pf = 0.1;
pf_dash = 1-pf;
pr = 0.1;
qr = 1-pr;
p = 0.005
pi = pf_dash*p;
pb = pd_dash*p;
qi = 1-pi;
qb = 1-pb;
sm = symsum( z^((n+1)*Es), n, 0, N-1 );
temp_sum = symsum(z^((n+m+1)*Es)*qr^(n+m)*pr, m, 0, N-1);
z=1; %assume a value of z
x = eval(sm); %works fine
y = eval(temp_sum);
% Error:The expression to the left of the equals sign is not a valid target for an assignment.
Please suggest a way to resolve this.
The problem that I suspect is: the temp_sum comes out to be in piecewise(...) which eval is not capable of evaluating.
What you actually did:
Create a symbolic expression
Create a variable z which is unused
Call a undocumented function sym/eval
I assume you wanted to:
Create a symbolic expression
Substitute z with 1: temp_sum=subs(temp_sum,z,1)
get the result. Here I don't know what you really have because I don't know which variables are symbolic unknowns and which constants. Try simplify(temp_sum). If you substituted all unknowns it should return a number.