System Identification for epidemic modeling
显示 更早的评论
I am trying to estimate parameters using the system identification toolbox. I used the example of three ecological systems provided in the documentation, and worked on it o build my own model.
Here is my model:
function [dx, y] = shigella(t, u, x,a,b,q,m,r,varargin)
y = [x(1); x(2); x(3)];
dx = [q - m*x(1) - b*x(1)*x(2) + a*x(3); (b*x(1)) - (m+r)*x(2); (r*x(2)) - (m+a)*x(3)];
-----------------------------------------------------------------------------------------------
And the system Id code:
FileName = 'shigella'; % File describing the model structure.
Order = [3 0 3]; % Model orders [ny nu nx].
Parameters = struct('Name', {'Loss of immunity', 'infectivity rate', 'population renewal', 'death rate', 'recovery rate'}, ...
'Unit', {'1/week' '1/week' '1/week' '1/week', '1/week'}, ...
'Value', {0.25 0.002 10 0.012 0.14}, ...
'Minimum', {-Inf -Inf -Inf -Inf -Inf}, ...
'Maximum', {Inf Inf Inf Inf Inf}, ...
'Fixed', {false false false false false}); % Estimate all 4 parameters.
InitialStates = struct('Name', {'Susceptible', 'Infected', 'Recovered'}, ...
'Unit', {'Size (in thousands)' 'Size (in thousands)', 'Size(inthousands)'}, ...
'Value', {20 5 10}, ...
'Minimum', {0 0 0}, ...
'Maximum', {Inf Inf Inf}, ...
'Fixed', {false false false}); % Estimate both initial states.
Ts = 0; % Time-continuous system.
nlgr = idnlgrey(FileName,Order, Parameters, InitialStates, Ts, ...
'Name', 'Population Variation', ...
'OutputName', {'Susceptible', 'Infected', 'Recovered'}, ...
'OutputUnit', {'Size (in thousands)' 'Size (in thousands)', 'Size (in thousands)'}, ...
'TimeUnit', 'week');
present(nlgr)
w = [1000 5 0];
u = [80 15 3];
v = [65 24 10];
f = [90 27 8];
z = [87 20 10];
g = [w; u; v; f; z];
z = iddata(g,[], 1, 'Name', 'Population Variation');
set(z, 'OutputName', {'Susceptible', 'Infected', 'Recovered'}, ...
'Tstart', 0, 'TimeUnit', 'Week');
compare(z, nlgr, 1)
opt = nlgreyestOptions;
opt.Display = 'on';
opt.SearchOption.MaxIter = 50;
nlgr = nlgreyest(nlgr, opt);
disp(' True Estimated parameter vector');
ptrue = [0.25 0.002 10 0.012 0.14];
fprintf(' %6.3f %6.3f\n', [ptrue'; getpvec(nlgr)']);
disp(' ');
disp(' True Estimated initial states');
x0true = [20 5 10];
fprintf(' %6.3f %6.3f\n', [x0true'; cell2mat(getinit(nlgr, 'Value'))']);
--------------------------------------------------------------------------------------------
When I run the code part by part, i get the following errors:
??? Error using ==> idnlgrey.isvalid at 165 Error or mismatch in the specified ODE file 'shigella'. The error message is: 'Attempted to access x(1); index out of bounds because numel(x)=0.'
I tried to get rid of the compare part and move on, but i got this error
??? Undefined function or variable 'nlgreyestOptions'.
---------------------------------------------------------------------------
I would really appreciate any help I can get on this.
4 个评论
Ojaswita
2015-4-13
Star Strider
2015-4-13
Just looking at your code, I find it difficult to understand your ‘shigella’ ODE. Before you use it with the System Identification Toolbox, be certain your ODE works with ode45 (or whatever solver is appropriate for it). See the documentation for ode45 to use the correct syntax for your ‘shigella’ function.
Ojaswita
2015-4-15
Ojaswita
2015-5-13
回答（0 个）
类别
在 帮助中心 和 File Exchange 中查找有关 Nonlinear Grey-Box Models 的更多信息
Community Treasure Hunt
Find the treasures in MATLAB Central and discover how the community can help you!
Start Hunting!
Translated by 
