ans =
Contenuto principale
Risultati per
This project discusses predator-prey system, particularly the Lotka-Volterra equations,which model the interaction between two sprecies: prey and predators. Let's solve the Lotka-Volterra equations numerically and visualize the results.% Define parameters
% Define parameters
alpha = 1.0; % Prey birth rate
beta = 0.1; % Predator success rate
gamma = 1.5; % Predator death rate
delta = 0.075; % Predator reproduction rate
% Define the symbolic variables
syms R W
% Define the equations
eq1 = alpha * R - beta * R * W == 0;
eq2 = delta * R * W - gamma * W == 0;
% Solve the equations
equilibriumPoints = solve([eq1, eq2], [R, W]);
% Extract the equilibrium point values
Req = double(equilibriumPoints.R);
Weq = double(equilibriumPoints.W);
% Display the equilibrium points
equilibriumPointsValues = [Req, Weq]
% Solve the differential equations using ode45
lotkaVolterra = @(t,Y)[alpha*Y(1)-beta*Y(1)*Y(2);
delta*Y(1)*Y(2)-gamma*Y(2)];
% Initial conditions
R0 = 40;
W0 = 9;
Y0 = [R0, W0];
tspan = [0, 100];
% Solve the differential equations
[t, Y] = ode45(lotkaVolterra, tspan, Y0);
% Extract the populations
R = Y(:, 1);
W = Y(:, 2);
% Plot the results
figure;
subplot(2,1,1);
plot(t, R, 'r', 'LineWidth', 1.5);
hold on;
plot(t, W, 'b', 'LineWidth', 1.5);
xlabel('Time (months)');
ylabel('Population');
legend('R', 'W');
grid on;
subplot(2,1,2);
plot(R, W, 'k', 'LineWidth', 1.5);
xlabel('R');
ylabel('W');
grid on;
hold on;
plot(Req, Weq, 'ro', 'MarkerSize', 8, 'MarkerFaceColor', 'r');
legend('Phase Trajectory', 'Equilibrium Point');
Now, we need to handle a modified version of the Lotka-Volterra equations. These modified equations incorporate logistic growth fot the prey population.
These equations are:
% Define parameters
alpha = 1.0;
K = 100; % Carrying Capacity of the prey population
beta = 0.1;
gamma = 1.5;
delta = 0.075;
% Define the symbolic variables
syms R W
% Define the equations
eq1 = alpha*R*(1 - R/K) - beta*R*W == 0;
eq2 = delta*R*W - gamma*W == 0;
% Solve the equations
equilibriumPoints = solve([eq1, eq2], [R, W]);
% Extract the equilibrium point values
Req = double(equilibriumPoints.R);
Weq = double(equilibriumPoints.W);
% Display the equilibrium points
equilibriumPointsValues = [Req, Weq]
% Solve the differential equations using ode45
modified_lv = @(t,Y)[alpha*Y(1)*(1-Y(1)/K)-beta*Y(1)*Y(2);
delta*Y(1)*Y(2)-gamma*Y(2)];
% Initial conditions
R0 = 40;
W0 = 9;
Y0 = [R0, W0];
tspan = [0, 100];
% Solve the differential equations
[t, Y] = ode45(modified_lv, tspan, Y0);
% Extract the populations
R = Y(:, 1);
W = Y(:, 2);
% Plot the results
figure;
subplot(2,1,1);
plot(t, R, 'r', 'LineWidth', 1.5);
hold on;
plot(t, W, 'b', 'LineWidth', 1.5);
xlabel('Time (months)');
ylabel('Population');
legend('R', 'W');
grid on;
subplot(2,1,2);
plot(R, W, 'k', 'LineWidth', 1.5);
xlabel('R');
ylabel('W');
grid on;
hold on;
plot(Req, Weq, 'ro', 'MarkerSize', 8, 'MarkerFaceColor', 'r');
legend('Phase Trajectory', 'Equilibrium Point');
Swimming, diving
16%
Other water-based sport
4%
Gymnastics
20%
Other indoor arena sport
15%
track, field
24%
Other outdoor sport
21%
346 voti
Does your company or organization require that all your Word Documents and Excel workbooks be labeled with a Microsoft Azure Information Protection label or else they can't be saved? These are the labels that are right below the tool ribbon that apply a category label such as "Public", "Business Use", or "Highly Restricted". If so, you can either
- Create and save a "template file" with the desired label and then call copyfile to make a copy of that file and then write your results to the new copy, or
- If using Windows you can create and/or open the file using ActiveX and then apply the desired label from your MATLAB program's code.
For #1 you can do
copyfile(templateFileName, newDataFileName);
writematrix(myData, newDataFileName);
If the template has the AIP label applied to it, then the copy will also inherit the same label.
For #2, here is a demo for how to apply the code using ActiveX.
% Test to set the Microsoft Azure Information Protection label on an Excel workbook.
% Reference support article:
% https://www.mathworks.com/matlabcentral/answers/1901140-why-does-azure-information-protection-popup-pause-the-matlab-script-when-i-use-actxserver?s_tid=ta_ans_results
clc; % Clear the command window.
close all; % Close all figures (except those of imtool.)
clear; % Erase all existing variables. Or clearvars if you want.
workspace; % Make sure the workspace panel is showing.
format compact;
% Define your workbook file name.
excelFullFileName = fullfile(pwd, '\testAIP.xlsx');
% Make sure it exists. Open Excel as an ActiveX server if it does.
if isfile(excelFullFileName)
% If the workbook exists, launch Excel as an ActiveX server.
Excel = actxserver('Excel.Application');
Excel.visible = true; % Make the server visible.
fprintf('Excel opened successfully.\n');
fprintf('Your workbook file exists:\n"%s".\nAbout to try to open it.\n', excelFullFileName);
% Open up the existing workbook named in the variable fullFileName.
Excel.Workbooks.Open(excelFullFileName);
fprintf('Excel opened file successfully.\n');
else
% File does not exist. Alert the user.
warningMessage = sprintf('File does not exist:\n\n"%s"\n', excelFullFileName);
fprintf('%s\n', warningMessage);
errordlg(warningMessage);
return;
end
% If we get here, the workbook file exists and has been opened by Excel.
% Ask Excel for the Microsoft Azure Information Protection (AIP) label of the workbook we just opened.
label = Excel.ActiveWorkbook.SensitivityLabel.GetLabel
% See if there is a label already. If not, these will be null:
existingLabelID = label.LabelId
existingLabelName = label.LabelName
% Create a label.
label = Excel.ActiveWorkbook.SensitivityLabel.CreateLabelInfo
label.LabelId = "a518e53f-798e-43aa-978d-c3fda1f3a682";
label.LabelName = "Business Use";
% Assign the label to the workbook.
fprintf('Setting Microsoft Azure Information Protection to "Business Use", GUID of a518e53f-798e-43aa-978d-c3fda1f3a682\n');
Excel.ActiveWorkbook.SensitivityLabel.SetLabel(label, label);
% Save this workbook with the new AIP setting we just created.
Excel.ActiveWorkbook.Save;
% Shut down Excel.
Excel.ActiveWorkbook.Close;
Excel.Quit;
% Excel is now closed down. Delete the variable from the MATLAB workspace.
clear Excel;
% Now check to see if the AIP label has been set
% by opening up the file in Excel and looking at the AIP banner.
winopen(excelFullFileName)
Note that there is a line in there that gets an AIP label from the existing workbook, if there is one at all. If there is not one, you can set one. But to determine what the proper LabelId (that crazy long hexadecimal number) should be, you will probably need to open an existing document that already has the label that you want set (applied to it) and then read that label with this line:
label = Excel.ActiveWorkbook.SensitivityLabel.GetLabel
This stems purely from some play on my part. Suppose I asked you to work with the sequence formed as 2*n*F_n + 1, where F_n is the n'th Fibonacci number? Part of me would not be surprised to find there is nothing simple we could do. But, then it costs nothing to try, to see where MATLAB can take me in an explorative sense.
n = sym(0:100).';
Fn = fibonacci(n);
Sn = 2*n.*Fn + 1;
Sn(1:10) % A few elements
For kicks, I tried asking ChatGPT. Giving it nothing more than the first 20 members of thse sequence as integers, it decided this is a Perrin sequence, and gave me a recurrence relation, but one that is in fact incorrect. Good effort from the Ai, but a fail in the end.
Is there anything I can do? Try null! (Look carefully at the array generated by Toeplitz. It is at least a pretty way to generate the matrix I needed.)
X = toeplitz(Sn,[1,zeros(1,4)]);
rank(X(5:end,:))
Hmm. So there is no linear combination of those columns that yields all zeros, since the resulting matrix was full rank.
X = toeplitz(Sn,[1,zeros(1,5)]);
rank(X(6:end,:))
But if I take it one step further, we see the above matrix is now rank deficient. What does that tell me? It says there is some simple linear combination of the columns of X(6:end,:) that always yields zero. The previous test tells me there is no shorter constant coefficient recurrence releation, using fewer terms.
null(X(6:end,:))
Let me explain what those coefficients tell me. In fact, they yield a very nice recurrence relation for the sequence S_n, not unlike the original Fibonacci sequence it was based upon.
S(n+1) = 3*S(n) - S_(n-1) - 3*S(n-2) + S(n-3) + S(n-4)
where the first 5 members of that sequence are given as [1 3 5 13 25]. So a 6 term linear constant coefficient recurrence relation. If it reminds you of the generating relation for the Fibonacci sequence, that is good, because it should. (Remember I started the sequence at n==0, IF you decide to test it out.) We can test it out, like this:
SfunM = memoize(@(N) Sfun(N));
SfunM(25)
2*25*fibonacci(sym(25)) + 1
And indeed, it works as expected.
function Sn = Sfun(n)
switch n
case 0
Sn = 1;
case 1
Sn = 3;
case 2
Sn = 5;
case 3
Sn = 13;
case 4
Sn = 25;
otherwise
Sn = Sfun(n-5) + Sfun(n-4) - 3*Sfun(n-3) - Sfun(n-2) +3*Sfun(n-1);
end
end
A beauty of this, is I started from nothing but a sequence of integers, derived from an expression where I had no rational expectation of finding a formula, and out drops something pretty. I might call this explorational mathematics.
The next step of course is to go in the other direction. That is, given the derived recurrence relation, if I substitute the formula for S_n in terms of the Fibonacci numbers, can I prove it is valid in general? (Yes.) After all, without some proof, it may fail for n larger than 100. (I'm not sure how much I can cram into a single discussion, so I'll stop at this point for now. If I see interest in the ideas here, I can proceed further. For example, what was I doing with that sequence in the first place? And of course, can I prove the relation is valid? Can I do so using MATLAB?)
(I'll be honest, starting from scratch, I'm not sure it would have been obvious to find that relation, so null was hugely useful here.)
Hello, MATLAB enthusiasts! 🌟
Over the past few weeks, our community has been buzzing with insightful questions, vibrant discussions, and innovative ideas. Whether you're a seasoned expert or a curious beginner, there's something here for everyone to learn and enjoy. Let's take a moment to highlight some of the standout contributions that have sparked interest and inspired many. Dive in and see how you can join the conversation or find solutions to your own challenges!
Interesting Questions
How can i edit my code which works on r2014b version at work but not on my personal r2024a version? by Oluwadamilola Oke
Oluwadamilola Oke is seeking assistance with a MATLAB code that works on version r2014b but encounters errors on version r2024a. The issue seems to be related to file location or the use of specific commands like movefile. If you have experience with these versions of MATLAB, your expertise could be invaluable.
Yohay has been working on a simulation to measure particle speed and fit it to the Maxwell-Boltzmann distribution. However, the fit isn't aligning perfectly with the data. Yohay has shared the code and histogram data for community members to review and provide suggestions.
Alessandro Livi is toggling between C++ for Arduino Pico and MATLAB App Designer. They suggest an enhancement where typing // for comments in MATLAB automatically converts to %. This small feature could improve the workflow for many users who switch between programming languages.
Popular Discussions
Athanasios Paraskevopoulos has started an engaging discussion on Gabriel's Horn, a shape with infinite surface area but finite volume. The conversation delves into the mathematical intricacies and integral calculations required to understand this paradoxical shape.
Honzik has brought up an interesting topic about custom fonts for MATLAB. While popular coding fonts handle characters like 0 and O well, they often fail to distinguish between different types of brackets. Honzik suggests that MathWorks could develop a custom font optimized for MATLAB syntax to reduce coding errors.
From the Blogs
Guy Rouleau addresses a common error in Simulink models: "Derivative of state '1' in block 'X/Y/Integrator' at time 0.55 is not finite." The blog post explores various tools and methods to diagnose and resolve this issue, making it a valuable read for anyone facing similar challenges.
Guest writer Gianluca Carnielli, featured by Adam Danz, shares insights on creating time-sensitive animations using MATLAB. The article covers controlling the motion of multiple animated objects, organizing data with timetables, and simplifying animations with the retime function. This is a must-read for anyone interested in scientific animations.
Feel free to check out these fascinating contributions and join the discussions! Your input and expertise can make a significant difference in our community.
hello i found the following tools helpful to write matlab programs. copilot.microsoft.com chatgpt.com/gpts gemini.google.com and ai.meta.com. thanks a lot and best wishes.
I have picked the title but don't know which direction to take it. Looking for any and all inspiration. I took the project as it sounded interesting when reading into it, but I'm a satellite novice, and my degree is in electronics.
Check out the LLMs with MATLAB project on File Exchange to access Large Language Models from MATLAB.
Along with the latest support for GPT-4o mini, you can use LLMs with MATLAB to generate images, categorize data, and provide semantic analyis.
function ans = your_fcn_name(n)
n;
j=sum(1:n);
a=zeros(1,j);
for i=1:n
a(1,((sum(1:(i-1))+1)):(sum(1:(i-1))+i))=i.*ones(1,i);
end
disp
Gabriel's horn is a shape with the paradoxical property that it has infinite surface area, but a finite volume.
Gabriel’s horn is formed by taking the graph of with the domain and rotating it in three dimensions about the axis.
There is a standard formula for calculating the volume of this shape, for a general function .Wwe will just state that the volume of the solid between a and b is:
The surface area of the solid is given by:
One other thing we need to consider is that we are trying to find the value of these integrals between 1 and ∞. An integral with a limit of infinity is called an improper integral and we can't evaluate it simply by plugging the value infinity into the normal equation for a definite integral. Instead, we must first calculate the definite integral up to some finite limit b and then calculate the limit of the result as b tends to ∞:
Volume
We can calculate the horn's volume using the volume integral above, so
The total volume of this infinitely long trumpet isπ.
Surface Area
To determine the surface area, we first need the function’s derivative:
Now plug it into the surface area formula and we have:
This is an improper integral and it's hard to evaluate, but since in our interval
So, we have :
Now,we evaluate this last integral
So the surface are is infinite.
% Define the function for Gabriel's Horn
gabriels_horn = @(x) 1 ./ x;
% Create a range of x values
x = linspace(1, 40, 4000); % Increase the number of points for better accuracy
y = gabriels_horn(x);
% Create the meshgrid
theta = linspace(0, 2 * pi, 6000); % Increase theta points for a smoother surface
[X, T] = meshgrid(x, theta);
Y = gabriels_horn(X) .* cos(T);
Z = gabriels_horn(X) .* sin(T);
% Plot the surface of Gabriel's Horn
figure('Position', [200, 100, 1200, 900]);
surf(X, Y, Z, 'EdgeColor', 'none', 'FaceAlpha', 0.9);
hold on;
% Plot the central axis
plot3(x, zeros(size(x)), zeros(size(x)), 'r', 'LineWidth', 2);
% Set labels
xlabel('x');
ylabel('y');
zlabel('z');
% Adjust colormap and axis properties
colormap('gray');
shading interp; % Smooth shading
% Adjust the view
view(3);
axis tight;
grid on;
% Add formulas as text annotations
dim1 = [0.4 0.7 0.3 0.2];
annotation('textbox',dim1,'String',{'$$V = \pi \int_{1}^{a} \left( \frac{1}{x} \right)^2 dx = \pi \left( 1 - \frac{1}{a} \right)$$', ...
'', ... % Add an empty line for larger gap
'$$\lim_{a \to \infty} V = \lim_{a \to \infty} \pi \left( 1 - \frac{1}{a} \right) = \pi$$'}, ...
'Interpreter','latex','FontSize',12, 'EdgeColor','none', 'FitBoxToText', 'on');
dim2 = [0.4 0.5 0.3 0.2];
annotation('textbox',dim2,'String',{'$$A = 2\pi \int_{1}^{a} \frac{1}{x} \sqrt{1 + \left( -\frac{1}{x^2} \right)^2} dx > 2\pi \int_{1}^{a} \frac{dx}{x} = 2\pi \ln(a)$$', ...
'', ... % Add an empty line for larger gap
'$$\lim_{a \to \infty} A \geq \lim_{a \to \infty} 2\pi \ln(a) = \infty$$'}, ...
'Interpreter','latex','FontSize',12, 'EdgeColor','none', 'FitBoxToText', 'on');
% Add Gabriel's Horn label
dim3 = [0.3 0.9 0.3 0.1];
annotation('textbox',dim3,'String','Gabriel''s Horn', ...
'Interpreter','latex','FontSize',14, 'EdgeColor','none', 'HorizontalAlignment', 'center');
hold off
daspect([3.5 1 1]) % daspect([x y z])
view(-27, 15)
lightangle(-50,0)
lighting('gouraud')
The properties of this figure were first studied by Italian physicist and mathematician Evangelista Torricelli in the 17th century.
Acknowledgment
I would like to express my sincere gratitude to all those who have supported and inspired me throughout this project.
First and foremost, I would like to thank the mathematician and my esteemed colleague, Stavros Tsalapatis, for inspiring me with the fascinating subject of Gabriel's Horn.
I am also deeply thankful to Mr. @Star Strider for his invaluable assistance in completing the final code.
References:
When it comes to MOS tube burnout, it is usually because it is not working in the SOA workspace, and there is also a case where the MOS tube is overcurrent.
For example, the maximum allowable current of the PMOS transistor in this circuit is 50A, and the maximum current reaches 80+ at the moment when the MOS transistor is turned on, then the current is very large.
At this time, the PMOS is over-specified, and we can see on the SOA curve that it is not working in the SOA range, which will cause the PMOS to be damaged.
So what if you choose a higher current PMOS? Of course you can, but the cost will be higher.
We can choose to adjust the peripheral resistance or capacitor to make the PMOS turn on more slowly, so that the current can be lowered.
For example, when adjusting R1, R2, and the jumper capacitance between gs, when Cgs is adjusted to 1uF, The Ids are only 40A max, which is fine in terms of current, and meets the 80% derating.
(50 amps * 0.8 = 40 amps).
Next, let’s look at the power, from the SOA curve, the opening time of the MOS tube is about 1ms, and the maximum power at this time is 280W.
The normal thermal resistance of the chip is 50°C/W, and the maximum junction temperature can be 302°F.
Assuming the ambient temperature is 77°F, then the instantaneous power that 1ms can withstand is about 357W.
The actual power of PMOS here is 280W, which does not exceed the limit, which means that it works normally in the SOA area.
Therefore, when the current impact of the MOS transistor is large at the moment of turning, the Cgs capacitance can be adjusted appropriately to make the PMOS Working in the SOA area, you can avoid the problem of MOS corruption.
I am trying to earn my Intro to MATLAB badge in Cody, but I cannot click the Roll the Dice! problem. It simply is not letting me click it, therefore I cannot earn my badge. Does anyone know who I should contact or what to do?
Hello everyone, i hope you all are in good health. i need to ask you about the help about where i should start to get indulge in matlab. I am an electrical engineer but having experience of construction field. I am new here. Please do help me. I shall be waiting forward to hear from you. I shall be grateful to you. Need recommendations and suggestions from experienced members. Thank you.
I recently wrote up a document which addresses the solution of ordinary and partial differential equations in Matlab (with some Python examples thrown in for those who are interested). For ODEs, both initial and boundary value problems are addressed. For PDEs, it addresses parabolic and elliptic equations. The emphasis is on finite difference approaches and built-in functions are discussed when available. Theory is kept to a minimum. I also provide a discussion of strategies for checking the results, because I think many students are too quick to trust their solutions. For anyone interested, the document can be found at https://blanchard.neep.wisc.edu/SolvingDifferentialEquationsWithMatlab.pdf
Kindly link me to the Channel Modeling Group.
I read and compreheneded a paper on channel modeling "An Adaptive Geometry-Based Stochastic Model for Non-Isotropic MIMO Mobile-to-Mobile Channels" except the graphical results obtained from the MATLAB codes. I have tried to replicate the same graphs but to no avail from my codes. And I am really interested in the topic, i have even written to the authors of the paper but as usual, there is no reply from them. Kindly assist if possible.
Hi, I'm looking for sites where I can find coding & algorithms problems and their solutions. I'm doing this workshop in college and I'll need some problems to go over with the students and explain how Matlab works by solving the problems with them and then reviewing and going over different solution options. Does anyone know a website like that? I've tried looking in the Matlab Cody By Mathworks, but didn't exactly find what I'm looking for. Thanks in advance.
Hello, everyone! I’m Mark Hayworth, but you might know me better in the community as Image Analyst. I've been using MATLAB since 2006 (18 years). My background spans a rich career as a former senior scientist and inventor at The Procter & Gamble Company (HQ in Cincinnati). I hold both master’s & Ph.D. degrees in optical sciences from the College of Optical Sciences at the University of Arizona, specializing in imaging, image processing, and image analysis. I have 40+ years of military, academic, and industrial experience with image analysis programming and algorithm development. I have experience designing custom light booths and other imaging systems. I also work with color and monochrome imaging, video analysis, thermal, ultraviolet, hyperspectral, CT, MRI, radiography, profilometry, microscopy, NIR, and Raman spectroscopy, etc. on a huge variety of subjects.
I'm thrilled to participate in MATLAB Central's Ask Me Anything (AMA) session, a fantastic platform for knowledge sharing and community engagement. Following Adam Danz’s insightful AMA on staff contributors in the Answers forum, I’d like to discuss topics in the area of image analysis and processing. I invite you to ask me anything related to this field, whether you're seeking recommendations on tools, looking for tips and tricks, my background, or career development advice. Additionally, I'm more than willing to share insights from my experiences in the MATLAB Answers community, File Exchange, and my role as a member of the Community Advisory Board. If you have questions related to your specific images or your custom MATLAB code though, I'll invite you to ask those in the Answers forum. It's a more appropriate forum for those kinds of questions, plus you can get the benefit of other experts offering their solutions in addition to me.
For the coming weeks, I'll be here to engage with your questions and help shed light on any topics you're curious about.
Hello, everyone!
Over the past few weeks, our community has been buzzing with activity, showcasing the incredible depth of knowledge, creativity, and innovation that makes this forum such a vibrant place. Today, we're excited to highlight some of the noteworthy contributions that have sparked discussions, offered insights, and shared knowledge across various topics. Let's dive in!
Interesting Questions
Fatima Majeed brings us a thought-provoking mathematical challenge, delving into inequalities and the realms beyond (e^e). If you're up for a mathematical journey, this question is a must-see!
lil brain tackles a practical problem many of us have faced: efficiently segmenting a CSV file based on specific criteria. This post is not only a query but a learning opportunity for anyone dealing with similar data manipulation challenges.
Popular Discussions
Discover a simple yet effective trick for digit manipulation from goc3. This tip is especially handy for those frequenting Cody challenges or anyone interested in enhancing their number handling skills in MATLAB.
Chen Lin shares an exciting update about the 'Run Code' feature in the Discussions area, highlighting how our community can now directly execute and share code snippets within discussions. This feature marks a significant enhancement in how we interact and solve problems together.
From the Blogs
A Deep Dive into EEG Analysis for Predicting Neurological Outcomes By Tanya Kuruvilla
Connell D`Souza, alongside Team Swarthbeat, explores the cutting-edge application of EEG analysis in predicting neurological outcomes post-cardiac arrest. This blog post offers an in-depth look into the challenges and methodologies of modern medical data analysis.
Mihir Acharya discusses the pivotal role of MATLAB and Simulink in the future of robotics simulation. Through an engaging conversation with industry analyst George Chowdhury, this post sheds light on overcoming simulation challenges and the exciting possibilities that lie ahead.
We encourage everyone to explore these contributions further and engage with the authors and the community. Your participation is what fuels this community's continual growth and innovation.
Here's to many more discussions, discoveries, and breakthroughs together!
We are modeling the introduction of a novel pathogen into a completely susceptible population. In the cells below, I have provided you with the Matlab code for a simple stochastic SIR model, implemented using the "GillespieSSA" function
Simulating the stochastic model 100 times for
Since γ is 0.4 per day, per day
% Define the parameters
beta = 0.36;
gamma = 0.4;
n_sims = 100;
tf = 100; % Time frame changed to 100
% Calculate R0
R0 = beta / gamma
% Initial state values
initial_state_values = [1000000; 1; 0; 0]; % S, I, R, cum_inc
% Define the propensities and state change matrix
a = @(state) [beta * state(1) * state(2) / 1000000, gamma * state(2)];
nu = [-1, 0; 1, -1; 0, 1; 0, 0];
% Define the Gillespie algorithm function
function [t_values, state_values] = gillespie_ssa(initial_state, a, nu, tf)
t = 0;
state = initial_state(:); % Ensure state is a column vector
t_values = t;
state_values = state';
while t < tf
rates = a(state);
rate_sum = sum(rates);
if rate_sum == 0
break;
end
tau = -log(rand) / rate_sum;
t = t + tau;
r = rand * rate_sum;
cum_sum_rates = cumsum(rates);
reaction_index = find(cum_sum_rates >= r, 1);
state = state + nu(:, reaction_index);
% Update cumulative incidence if infection occurred
if reaction_index == 1
state(4) = state(4) + 1; % Increment cumulative incidence
end
t_values = [t_values; t];
state_values = [state_values; state'];
end
end
% Function to simulate the stochastic model multiple times and plot results
function simulate_stoch_model(beta, gamma, n_sims, tf, initial_state_values, R0, plot_type)
% Define the propensities and state change matrix
a = @(state) [beta * state(1) * state(2) / 1000000, gamma * state(2)];
nu = [-1, 0; 1, -1; 0, 1; 0, 0];
% Set random seed for reproducibility
rng(11);
% Initialize plot
figure;
hold on;
for i = 1:n_sims
[t, output] = gillespie_ssa(initial_state_values, a, nu, tf);
% Check if the simulation had only one step and re-run if necessary
while length(t) == 1
[t, output] = gillespie_ssa(initial_state_values, a, nu, tf);
end
if strcmp(plot_type, 'cumulative_incidence')
plot(t, output(:, 4), 'LineWidth', 2, 'Color', rand(1, 3));
elseif strcmp(plot_type, 'prevalence')
plot(t, output(:, 2), 'LineWidth', 2, 'Color', rand(1, 3));
end
end
xlabel('Time (days)');
if strcmp(plot_type, 'cumulative_incidence')
ylabel('Cumulative Incidence');
ylim([0 inf]);
elseif strcmp(plot_type, 'prevalence')
ylabel('Prevalence of Infection');
ylim([0 50]);
end
title(['Stochastic model output for R0 = ', num2str(R0)]);
subtitle([num2str(n_sims), ' simulations']);
xlim([0 tf]);
grid on;
hold off;
end
% Simulate the model 100 times and plot cumulative incidence
simulate_stoch_model(beta, gamma, n_sims, tf, initial_state_values, R0, 'cumulative_incidence');
% Simulate the model 100 times and plot prevalence
simulate_stoch_model(beta, gamma, n_sims, tf, initial_state_values, R0, 'prevalence');