PRCC sensitive analysis graphs

I have tried to get prcc sensitve analysis graph, but unfortunately i got an error.I request you please help to overcome the error.

CODE:

% Define parameter ranges

paramRanges = struct('beta', [0.1, 0.5], 'sigma', [0.1, 0.3], 'gamma', [0.1, 0.4]);

% Number of samples

nSamples = 100;

% Number of parameters

paramNames = fieldnames(paramRanges);

nParams = numel(paramNames);

% Generate LHS samples

lhsSamples = lhsdesign(nSamples, nParams);

% Scale samples to parameter ranges

scaledSamples = zeros(nSamples, nParams);

for i = 1:nParams

low = paramRanges.(paramNames{i})(1);

high = paramRanges.(paramNames{i})(2);

scaledSamples(:, i) = low + lhsSamples(:, i) * (high - low);

end

% Define SEIR model parameters and calculate R0

% Run simulations to compute R0 for each parameter set

R0Values = zeros(nSamples, 1);

for i = 1:nSamples

R0Values(i) = calculateR0(scaledSamples(i, :));

end

% Calculate PRCC

function prcc = calculatePRCC(outputs, samples)

nParams = size(samples, 2);

prcc = zeros(nParams, 1);

for i = 1:nParams

% Rank data

ranksSamples = tiedrank(samples(:, i));

ranksOutputs = tiedrank(outputs);

% Compute correlation

prcc(i) = corr(ranksSamples, ranksOutputs);

end

end

% Perform PRCC analysis for R0 values

prccValues = calculatePRCC(R0Values, scaledSamples);

function R0 = calculateR0(params)

beta = params(1);

sigma = params(2);

gamma = params(3);

% Basic reproduction number for SEIR model

R0 = beta / gamma;

end

% Display results

for i = 1:nParams

fprintf('PRCC for %s: %.4f\n', paramNames{i}, prccValues(i));

end

ERROR:

Function definitions in a script must appear at the end of the file.

Move all statements after the "calculateR0" function definition to before the first local function definition.

Answer 1

[Shivam Gothi]

Hello @mallela ankamma rao,

I executed the code shared by you in MATLAB R2021a. I was able to reproduce the error as highlighted by you.

But, when I run the same code in MATLAB R2024a, it was executed without throwing error.

In older versions, all the function definations should go at the end of the file. This is not the case with R2024a version.

Therefore, there are two possible work arounds for this problem:

1) modify your code.

Upon inspecting the code provided by you in the comment section, I found that you have writen MATLAB commands after/in-between function definations, which is violating the defination:

"all the function definations should go at the end of the file"

I have re-organised your code and attached the corresponding (.m) file with this answer. I have compiled it in R2021a version and it is found to be executed without any error.

2) Update your MATLAB version

You can install the updated MATLAB version (R2024b) by refering the link:

https://in.mathworks.com/help/install/ug/install-products-with-internet-connection.html

R2024b allows to compile your code (shared in the question) without any error.

I hope this helps !

[mallela ankamma rao]

Thank you very much Shivam gothi sir

I request you please guide me to write prcc graph like below image by taking three parameters values

beta: 0.7196

sigma: 0.0342

gamma: -0.6795

[Shivam Gothi]

Hello @mallela ankamma rao

I appreciate your efforts in seeking solutions. It might be beneficial to ask this as a new question in the MATLAB Answers community. There are many experts who might be able to assist you more effectively.

Additionally, if you find any of the responses you've received helpful, it would be great to provide the feedback or marking an answer as accepted.

Answer 2

[Shivam Gothi]

Hello @mallela ankamma rao,

I copied the same code provided by you in a new (.m) file and saved it with some name. Then I executed the file and it did not throw any error. Also, running the above code in the below given "code section" does not produce any error. But, I can suggest the possible cause behind it.

% Define parameter ranges
paramRanges = struct('beta', [0.1, 0.5], 'sigma', [0.1, 0.3], 'gamma', [0.1, 0.4]);
% Number of samples
nSamples = 100;
% Number of parameters
paramNames = fieldnames(paramRanges);
nParams = numel(paramNames);
% Generate LHS samples
lhsSamples = lhsdesign(nSamples, nParams);
% Scale samples to parameter ranges
scaledSamples = zeros(nSamples, nParams);
for i = 1:nParams
    low = paramRanges.(paramNames{i})(1);
    high = paramRanges.(paramNames{i})(2);
    scaledSamples(:, i) = low + lhsSamples(:, i) * (high - low);
end
% Define SEIR model parameters and calculate R0
% Run simulations to compute R0 for each parameter set
R0Values = zeros(nSamples, 1);
for i = 1:nSamples
    R0Values(i) = calculateR0(scaledSamples(i, :));
end
% Calculate PRCC
function prcc = calculatePRCC(outputs, samples)
    nParams = size(samples, 2);
    prcc = zeros(nParams, 1);
    for i = 1:nParams
        % Rank data
        ranksSamples = tiedrank(samples(:, i));
        ranksOutputs = tiedrank(outputs);
        % Compute correlation
        prcc(i) = corr(ranksSamples, ranksOutputs);
    end
end
% Perform PRCC analysis for R0 values
prccValues = calculatePRCC(R0Values, scaledSamples);
function R0 = calculateR0(params)
    beta = params(1);
    sigma = params(2);
    gamma = params(3);
    
    % Basic reproduction number for SEIR model
    R0 = beta / gamma;
end
% Display results
for i = 1:nParams
    fprintf('PRCC for %s: %.4f\n', paramNames{i}, prccValues(i));
end

PRCC for beta: 0.7334
PRCC for sigma: -0.1026
PRCC for gamma: -0.6995

In MATLAB, all the function definations should go at the end of the file. Refer to the below MATLAB answer:

https://in.mathworks.com/matlabcentral/answers/1734390-i-don-t-understand-this-error-function-definitions-in-a-script-must-appear-at-the-end-of-the-file

Therefore, I think that the compilation error in your case can be resolved by putting the "for loop" before the function definations as shown in below code:

I hope this helps !

[mallela ankamma rao]

Thank you for your reply sir

But i face the same problem sir

I request you if possible please modify the code sir

[mallela ankamma rao]

I did according to your suggestion sir but still i faced same problem sir.

CODE:

% Define parameter ranges

paramRanges = struct('beta', [0.1, 0.5], 'sigma', [0.1, 0.3], 'gamma', [0.1, 0.4]);

% Number of samples

nSamples = 100;

% Number of parameters

paramNames = fieldnames(paramRanges);

nParams = numel(paramNames);

% Generate LHS samples

lhsSamples = lhsdesign(nSamples, nParams);

% Scale samples to parameter ranges

scaledSamples = zeros(nSamples, nParams);

for i = 1:nParams

low = paramRanges.(paramNames{i})(1);

high = paramRanges.(paramNames{i})(2);

scaledSamples(:, i) = low + lhsSamples(:, i) * (high - low);

end

% Define SEIR model parameters and calculate R0

% Run simulations to compute R0 for each parameter set

R0Values = zeros(nSamples, 1);

for i = 1:nSamples

R0Values(i) = calculateR0(scaledSamples(i, :));

end

% Calculate PRCC

% Perform PRCC analysis for R0 values

prccValues = calculatePRCC(R0Values, scaledSamples);

function R0 = calculateR0(params)

beta = params(1);

sigma = params(2);

gamma = params(3);

% Basic reproduction number for SEIR model

R0 = beta / gamma;

end

% Display results

for i = 1:n Params

fprintf('PRCC for %s: %.4f\n', paramNames{i}, prccValues(i));

end

function prcc = calculatePRCC(outputs, samples)

nParams = size(samples, 2);

prcc = zeros(nParams, 1);

for i = 1:nParams

% Rank data

ranksSamples = tiedrank(samples(:, i));

ranksOutputs = tiedrank(outputs);

% Compute correlation

prcc(i) = corr(ranksSamples, ranksOutputs);

end

end

ERROR:

Function definitions in a script must appear at the end of the file.

Move all statements after the "calculateR0" function definition to before the first local function definition.

[mallela ankamma rao]

Whenever I removed the following code and the run the program, there is no error arised but it did not show the prcc values of parameters.

for i = 1:n Params

fprintf('PRCC for %s: %.4f\n', paramNames{i}, prccValues(i));

end

[Shivam Gothi]

Hello @mallela ankamma rao

Which version of MATLAB are you using?

[mallela ankamma rao]

MATLAB R2021a version sir

Answer 3

[Pavl M.]

%just made it working on both TCE NCE MPPL Matlab versions:
clc
clear all
close all

% Define parameter ranges
paramRanges = struct('beta', [0.1, 0.5], 'sigma', [0.1, 0.3], 'gamma', [0.1, 0.4]);
% Number of samples
nSamples = 100;
% Number of parameters
paramNames = fieldnames(paramRanges);
nParams = numel(paramNames);
% Generate LHS samples
lhsSamples = lhsdesign(nSamples, nParams);
% Scale samples to parameter ranges
scaledSamples = zeros(nSamples, nParams);
for i = 1:nParams
    low = paramRanges.(paramNames{i})(1);
    high = paramRanges.(paramNames{i})(2);
    scaledSamples(:, i) = low + lhsSamples(:, i) * (high - low);
end
% Define SEIR model parameters and calculate R0
% Run simulations to compute R0 for each parameter set
R0Values = zeros(nSamples, 1);
for i = 1:nSamples
    R0Values(i) = calculateR0(scaledSamples(i, :));
end
% Calculate PRCC
% Perform PRCC analysis for R0 values
prccValues = calculatePRCC(R0Values, scaledSamples);



% Display results
for i = 1:nParams
    fprintf('PRCC for %s: %.4f\n', paramNames{i}, prccValues(i));
end

PRCC for beta: 0.7228
PRCC for sigma: -0.1311
PRCC for gamma: -0.6203

function R0 = calculateR0(params)
    beta = params(1);
    sigma = params(2);
    gamma = params(3);

    % Basic reproduction number for SEIR model
    R0 = beta / gamma;
end

function prcc = calculatePRCC(outputs, samples)
    nParams = size(samples, 2);
    prcc = zeros(nParams, 1);
    for i = 1:nParams
        % Rank data
        ranksSamples = tiedrank(samples(:, i));
        ranksOutputs = tiedrank(outputs);
        % Compute correlation
        prcc(i) = corr(ranksSamples, ranksOutputs);
    end
end