Generated Code
The following is matlab code generated by the CellML API from this CellML file. (Back to language selection)
The raw code is available.
function [VOI, STATES, ALGEBRAIC, CONSTANTS] = mainFunction()
% This is the "main function". In Matlab, things work best if you rename this function to match the filename.
[VOI, STATES, ALGEBRAIC, CONSTANTS] = solveModel();
end
function [algebraicVariableCount] = getAlgebraicVariableCount()
% Used later when setting a global variable with the number of algebraic variables.
% Note: This is not the "main method".
algebraicVariableCount =4;
end
% There are a total of 10 entries in each of the rate and state variable arrays.
% There are a total of 14 entries in the constant variable array.
%
function [VOI, STATES, ALGEBRAIC, CONSTANTS] = solveModel()
% Create ALGEBRAIC of correct size
global algebraicVariableCount; algebraicVariableCount = getAlgebraicVariableCount();
% Initialise constants and state variables
[INIT_STATES, CONSTANTS] = initConsts;
% Set timespan to solve over
tspan = [0, 10];
% Set numerical accuracy options for ODE solver
options = odeset('RelTol', 1e-06, 'AbsTol', 1e-06, 'MaxStep', 1);
% Solve model with ODE solver
[VOI, STATES] = ode15s(@(VOI, STATES)computeRates(VOI, STATES, CONSTANTS), tspan, INIT_STATES, options);
% Compute algebraic variables
[RATES, ALGEBRAIC] = computeRates(VOI, STATES, CONSTANTS);
ALGEBRAIC = computeAlgebraic(ALGEBRAIC, CONSTANTS, STATES, VOI);
% Plot state variables against variable of integration
[LEGEND_STATES, LEGEND_ALGEBRAIC, LEGEND_VOI, LEGEND_CONSTANTS] = createLegends();
figure();
plot(VOI, STATES);
xlabel(LEGEND_VOI);
l = legend(LEGEND_STATES);
set(l,'Interpreter','none');
end
function [LEGEND_STATES, LEGEND_ALGEBRAIC, LEGEND_VOI, LEGEND_CONSTANTS] = createLegends()
LEGEND_STATES = ''; LEGEND_ALGEBRAIC = ''; LEGEND_VOI = ''; LEGEND_CONSTANTS = '';
LEGEND_VOI = strpad('time in component environment (day)');
LEGEND_STATES(:,1) = strpad('S in component S (dimensionless)');
LEGEND_CONSTANTS(:,1) = strpad('r in component S (first_order_rate_constant)');
LEGEND_CONSTANTS(:,2) = strpad('epsilon in component S (dimensionless)');
LEGEND_ALGEBRAIC(:,1) = strpad('H in component S (dimensionless)');
LEGEND_CONSTANTS(:,3) = strpad('d in component kinetic_parameters (first_order_rate_constant)');
LEGEND_CONSTANTS(:,4) = strpad('g in component memory_duration (first_order_rate_constant)');
LEGEND_CONSTANTS(:,5) = strpad('beta_1 in component kinetic_parameters (first_order_rate_constant)');
LEGEND_CONSTANTS(:,6) = strpad('beta_2 in component kinetic_parameters (first_order_rate_constant)');
LEGEND_STATES(:,2) = strpad('R_1 in component R1 (dimensionless)');
LEGEND_STATES(:,3) = strpad('R_2 in component R2 (dimensionless)');
LEGEND_STATES(:,4) = strpad('R_12 in component R12 (dimensionless)');
LEGEND_STATES(:,5) = strpad('P_1 in component P1 (dimensionless)');
LEGEND_STATES(:,6) = strpad('P_2 in component P2 (dimensionless)');
LEGEND_STATES(:,7) = strpad('I_1 in component I1 (dimensionless)');
LEGEND_STATES(:,8) = strpad('I_2 in component I2 (dimensionless)');
LEGEND_STATES(:,9) = strpad('I_12 in component I12 (dimensionless)');
LEGEND_STATES(:,10) = strpad('I_21 in component I21 (dimensionless)');
LEGEND_ALGEBRAIC(:,2) = strpad('P in component S (dimensionless)');
LEGEND_CONSTANTS(:,7) = strpad('a_1 in component kinetic_parameters (first_order_rate_constant)');
LEGEND_CONSTANTS(:,8) = strpad('alpha_1 in component kinetic_parameters (first_order_rate_constant)');
LEGEND_CONSTANTS(:,9) = strpad('a_2 in component kinetic_parameters (first_order_rate_constant)');
LEGEND_CONSTANTS(:,10) = strpad('alpha_2 in component kinetic_parameters (first_order_rate_constant)');
LEGEND_CONSTANTS(:,11) = strpad('k_1 in component P1 (first_order_rate_constant)');
LEGEND_CONSTANTS(:,12) = strpad('u in component kinetic_parameters (first_order_rate_constant)');
LEGEND_ALGEBRAIC(:,3) = strpad('log_P1 in component P1 (dimensionless)');
LEGEND_CONSTANTS(:,13) = strpad('k_2 in component P2 (first_order_rate_constant)');
LEGEND_ALGEBRAIC(:,4) = strpad('log_P2 in component P2 (dimensionless)');
LEGEND_CONSTANTS(:,14) = strpad('G in component memory_duration (dimensionless)');
LEGEND_RATES(:,1) = strpad('d/dt S in component S (dimensionless)');
LEGEND_RATES(:,7) = strpad('d/dt I_1 in component I1 (dimensionless)');
LEGEND_RATES(:,8) = strpad('d/dt I_2 in component I2 (dimensionless)');
LEGEND_RATES(:,9) = strpad('d/dt I_12 in component I12 (dimensionless)');
LEGEND_RATES(:,10) = strpad('d/dt I_21 in component I21 (dimensionless)');
LEGEND_RATES(:,2) = strpad('d/dt R_1 in component R1 (dimensionless)');
LEGEND_RATES(:,3) = strpad('d/dt R_2 in component R2 (dimensionless)');
LEGEND_RATES(:,4) = strpad('d/dt R_12 in component R12 (dimensionless)');
LEGEND_RATES(:,5) = strpad('d/dt P_1 in component P1 (dimensionless)');
LEGEND_RATES(:,6) = strpad('d/dt P_2 in component P2 (dimensionless)');
LEGEND_STATES = LEGEND_STATES';
LEGEND_ALGEBRAIC = LEGEND_ALGEBRAIC';
LEGEND_RATES = LEGEND_RATES';
LEGEND_CONSTANTS = LEGEND_CONSTANTS';
end
function [STATES, CONSTANTS] = initConsts()
VOI = 0; CONSTANTS = []; STATES = []; ALGEBRAIC = [];
STATES(:,1) = 100;
CONSTANTS(:,1) = 0.5;
CONSTANTS(:,2) = 0.1;
CONSTANTS(:,3) = 0.01;
CONSTANTS(:,4) = 0.01;
CONSTANTS(:,5) = 1;
CONSTANTS(:,6) = 1;
STATES(:,2) = 0;
STATES(:,3) = 0;
STATES(:,4) = 0;
STATES(:,5) = 1;
STATES(:,6) = 1;
STATES(:,7) = 0;
STATES(:,8) = 0;
STATES(:,9) = 0;
STATES(:,10) = 0;
CONSTANTS(:,7) = 0.03;
CONSTANTS(:,8) = 0.1;
CONSTANTS(:,9) = 1;
CONSTANTS(:,10) = 0.1;
CONSTANTS(:,11) = 1;
CONSTANTS(:,12) = 0.5;
CONSTANTS(:,13) = 1;
CONSTANTS(:,14) = 1.00000./CONSTANTS(:,4);
if (isempty(STATES)), warning('Initial values for states not set');, end
end
function [RATES, ALGEBRAIC] = computeRates(VOI, STATES, CONSTANTS)
global algebraicVariableCount;
statesSize = size(STATES);
statesColumnCount = statesSize(2);
if ( statesColumnCount == 1)
STATES = STATES';
ALGEBRAIC = zeros(1, algebraicVariableCount);
utilOnes = 1;
else
statesRowCount = statesSize(1);
ALGEBRAIC = zeros(statesRowCount, algebraicVariableCount);
RATES = zeros(statesRowCount, statesColumnCount);
utilOnes = ones(statesRowCount, 1);
end
RATES(:,7) = ( CONSTANTS(:,5).*STATES(:,1).*STATES(:,5) - CONSTANTS(:,7).*STATES(:,7)) - CONSTANTS(:,8).*STATES(:,7);
RATES(:,8) = ( CONSTANTS(:,6).*STATES(:,1).*STATES(:,6) - CONSTANTS(:,9).*STATES(:,8)) - CONSTANTS(:,10).*STATES(:,8);
RATES(:,9) = ( CONSTANTS(:,6).*STATES(:,2).*STATES(:,6) - CONSTANTS(:,9).*STATES(:,9)) - CONSTANTS(:,10).*STATES(:,9);
RATES(:,10) = ( CONSTANTS(:,5).*STATES(:,3).*STATES(:,5) - CONSTANTS(:,7).*STATES(:,10)) - CONSTANTS(:,8).*STATES(:,10);
RATES(:,2) = (( CONSTANTS(:,8).*STATES(:,7) - CONSTANTS(:,3).*STATES(:,2)) - CONSTANTS(:,4).*STATES(:,2)) - CONSTANTS(:,6).*STATES(:,2).*STATES(:,6);
RATES(:,3) = (( CONSTANTS(:,10).*STATES(:,8) - CONSTANTS(:,3).*STATES(:,3)) - CONSTANTS(:,4).*STATES(:,3)) - CONSTANTS(:,5).*STATES(:,3).*STATES(:,5);
RATES(:,4) = (( CONSTANTS(:,10).*STATES(:,9)+ CONSTANTS(:,8).*STATES(:,10)) - CONSTANTS(:,3).*STATES(:,4)) - CONSTANTS(:,4).*STATES(:,4);
RATES(:,5) = CONSTANTS(:,11).*(STATES(:,7)+STATES(:,10)) - CONSTANTS(:,12).*STATES(:,5);
RATES(:,6) = CONSTANTS(:,13).*(STATES(:,8)+STATES(:,9)) - CONSTANTS(:,12).*STATES(:,6);
ALGEBRAIC(:,1) = STATES(:,1)+STATES(:,7)+STATES(:,2)+STATES(:,8)+STATES(:,3)+STATES(:,9)+STATES(:,10)+STATES(:,4);
RATES(:,1) = (((( CONSTANTS(:,1).*ALGEBRAIC(:,1))./( CONSTANTS(:,2).*ALGEBRAIC(:,1)+1.00000) - CONSTANTS(:,3).*STATES(:,1)) - CONSTANTS(:,5).*STATES(:,1).*STATES(:,5)) - CONSTANTS(:,6).*STATES(:,1).*STATES(:,6))+ CONSTANTS(:,4).*(STATES(:,2)+STATES(:,3)+STATES(:,4));
RATES = RATES';
end
% Calculate algebraic variables
function ALGEBRAIC = computeAlgebraic(ALGEBRAIC, CONSTANTS, STATES, VOI)
statesSize = size(STATES);
statesColumnCount = statesSize(2);
if ( statesColumnCount == 1)
STATES = STATES';
utilOnes = 1;
else
statesRowCount = statesSize(1);
utilOnes = ones(statesRowCount, 1);
end
ALGEBRAIC(:,1) = STATES(:,1)+STATES(:,7)+STATES(:,2)+STATES(:,8)+STATES(:,3)+STATES(:,9)+STATES(:,10)+STATES(:,4);
ALGEBRAIC(:,2) = STATES(:,5)+STATES(:,6);
ALGEBRAIC(:,3) = arbitrary_log(STATES(:,5), 10);
ALGEBRAIC(:,4) = arbitrary_log(STATES(:,6), 10);
end
% Compute a logarithm to any base" +
function x = arbitrary_log(a, base)
x = log(a) ./ log(base);
end
% Pad out or shorten strings to a set length
function strout = strpad(strin)
req_length = 160;
insize = size(strin,2);
if insize > req_length
strout = strin(1:req_length);
else
strout = [strin, blanks(req_length - insize)];
end
end