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 =5;
end
% There are a total of 7 entries in each of the rate and state variable arrays.
% There are a total of 34 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('phi_I in component phi_I (cells_per_mm3)');
LEGEND_ALGEBRAIC(:,4) = strpad('alpha in component model_parameters (dimensionless)');
LEGEND_CONSTANTS(:,1) = strpad('k1 in component model_parameters (dimensionless)');
LEGEND_CONSTANTS(:,2) = strpad('k2 in component model_parameters (per_day)');
LEGEND_CONSTANTS(:,3) = strpad('k3 in component model_parameters (mm3_per_cells)');
LEGEND_CONSTANTS(:,4) = strpad('k5 in component model_parameters (mm3_per_cells)');
LEGEND_CONSTANTS(:,5) = strpad('k6 in component model_parameters (mm3_per_microg)');
LEGEND_CONSTANTS(:,6) = strpad('d1 in component model_parameters (per_day)');
LEGEND_STATES(:,2) = strpad('phi_R in component phi_R (cells_per_mm3)');
LEGEND_ALGEBRAIC(:,1) = strpad('K_T in component K_T (cells_per_mm3_per_day)');
LEGEND_STATES(:,3) = strpad('F in component F (cells_per_mm3)');
LEGEND_STATES(:,4) = strpad('C in component C (microg_per_mm3)');
LEGEND_STATES(:,5) = strpad('T in component T (pg_per_mm3)');
LEGEND_CONSTANTS(:,7) = strpad('k4 in component model_parameters (pg_per_cells_per_day)');
LEGEND_CONSTANTS(:,8) = strpad('k7 in component model_parameters (pg_per_cells_per_day)');
LEGEND_CONSTANTS(:,9) = strpad('d2 in component model_parameters (per_day)');
LEGEND_STATES(:,6) = strpad('P in component P (pg_per_mm3)');
LEGEND_CONSTANTS(:,10) = strpad('k8 in component model_parameters (pg_per_cells_per_day)');
LEGEND_CONSTANTS(:,11) = strpad('k9 in component model_parameters (pg_per_cells_per_day)');
LEGEND_CONSTANTS(:,12) = strpad('d3 in component model_parameters (per_day)');
LEGEND_CONSTANTS(:,13) = strpad('k10 in component model_parameters (per_day)');
LEGEND_CONSTANTS(:,14) = strpad('d4 in component model_parameters (per_day)');
LEGEND_ALGEBRAIC(:,2) = strpad('M_P in component M_P (cells_per_mm3_per_day)');
LEGEND_CONSTANTS(:,15) = strpad('k11 in component model_parameters (microg_per_cells_per_day)');
LEGEND_ALGEBRAIC(:,3) = strpad('f_T in component f_T (dimensionless)');
LEGEND_ALGEBRAIC(:,5) = strpad('g_C in component g_C (dimensionless)');
LEGEND_CONSTANTS(:,16) = strpad('d5 in component model_parameters (mm3_per_cells_per_day)');
LEGEND_STATES(:,7) = strpad('H in component H (microg_per_mm3)');
LEGEND_CONSTANTS(:,17) = strpad('k12 in component model_parameters (microg_per_cells_per_day)');
LEGEND_CONSTANTS(:,18) = strpad('d6 in component model_parameters (per_day)');
LEGEND_CONSTANTS(:,19) = strpad('tau1 in component K_T (mm6_cells_per_pg3_day)');
LEGEND_CONSTANTS(:,20) = strpad('tau2 in component K_T (mm3_cells_per_pg2_day)');
LEGEND_CONSTANTS(:,21) = strpad('tau3 in component K_T (cells_per_pg_per_day)');
LEGEND_CONSTANTS(:,22) = strpad('tau4 in component K_T (cells_per_mm3_per_day)');
LEGEND_CONSTANTS(:,23) = strpad('tau1 in component M_P (mm6_cells_per_pg3_day)');
LEGEND_CONSTANTS(:,24) = strpad('tau2 in component M_P (mm3_cells_per_pg2_day)');
LEGEND_CONSTANTS(:,25) = strpad('tau3 in component M_P (cells_per_pg_per_day)');
LEGEND_CONSTANTS(:,26) = strpad('tau4 in component M_P (cells_per_mm3_per_day)');
LEGEND_CONSTANTS(:,27) = strpad('tau1 in component f_T (mm9_per_pg3)');
LEGEND_CONSTANTS(:,28) = strpad('tau2 in component f_T (mm6_per_pg2)');
LEGEND_CONSTANTS(:,29) = strpad('tau3 in component f_T (mm3_per_pg)');
LEGEND_CONSTANTS(:,30) = strpad('tau4 in component f_T (dimensionless)');
LEGEND_CONSTANTS(:,31) = strpad('tau1 in component g_C (mm9_per_microg3)');
LEGEND_CONSTANTS(:,32) = strpad('tau2 in component g_C (mm6_per_microg2)');
LEGEND_CONSTANTS(:,33) = strpad('tau3 in component g_C (mm3_per_microg)');
LEGEND_CONSTANTS(:,34) = strpad('tau4 in component g_C (dimensionless)');
LEGEND_RATES(:,1) = strpad('d/dt phi_I in component phi_I (cells_per_mm3)');
LEGEND_RATES(:,2) = strpad('d/dt phi_R in component phi_R (cells_per_mm3)');
LEGEND_RATES(:,5) = strpad('d/dt T in component T (pg_per_mm3)');
LEGEND_RATES(:,6) = strpad('d/dt P in component P (pg_per_mm3)');
LEGEND_RATES(:,3) = strpad('d/dt F in component F (cells_per_mm3)');
LEGEND_RATES(:,4) = strpad('d/dt C in component C (microg_per_mm3)');
LEGEND_RATES(:,7) = strpad('d/dt H in component H (microg_per_mm3)');
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) = 200.0;
CONSTANTS(:,1) = 0.05;
CONSTANTS(:,2) = 0.693;
CONSTANTS(:,3) = 0.002;
CONSTANTS(:,4) = 0.0025;
CONSTANTS(:,5) = 0.0004;
CONSTANTS(:,6) = 0.2;
STATES(:,2) = 200.0;
STATES(:,3) = 50.0;
STATES(:,4) = 10.0;
STATES(:,5) = 6.0;
CONSTANTS(:,7) = 0.07;
CONSTANTS(:,8) = 0.004;
CONSTANTS(:,9) = 9.1;
STATES(:,6) = 2.0;
CONSTANTS(:,10) = 0.015;
CONSTANTS(:,11) = 0.0015;
CONSTANTS(:,12) = 4.0;
CONSTANTS(:,13) = 0.924;
CONSTANTS(:,14) = 1.0;
CONSTANTS(:,15) = 20.0;
CONSTANTS(:,16) = 1.5E-5;
STATES(:,7) = 0.01;
CONSTANTS(:,17) = 0.01;
CONSTANTS(:,18) = 0.7;
CONSTANTS(:,19) = -2.47;
CONSTANTS(:,20) = 21.94;
CONSTANTS(:,21) = 6.41;
CONSTANTS(:,22) = 1.75;
CONSTANTS(:,23) = 15.333;
CONSTANTS(:,24) = -167.21;
CONSTANTS(:,25) = 452.38;
CONSTANTS(:,26) = 2.6593;
CONSTANTS(:,27) = 0.0092;
CONSTANTS(:,28) = -0.1552;
CONSTANTS(:,29) = 0.6279;
CONSTANTS(:,30) = 0.2527;
CONSTANTS(:,31) = -4.33E-10;
CONSTANTS(:,32) = 0.0000009;
CONSTANTS(:,33) = -0.00055;
CONSTANTS(:,34) = 0.13;
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(:,5) = ( CONSTANTS(:,7).*STATES(:,1)+ CONSTANTS(:,8).*STATES(:,3)) - CONSTANTS(:,9).*STATES(:,5);
RATES(:,6) = ( CONSTANTS(:,10).*(STATES(:,1)+STATES(:,2))+ CONSTANTS(:,11).*STATES(:,3)) - CONSTANTS(:,12).*STATES(:,6);
RATES(:,7) = CONSTANTS(:,17).*STATES(:,3) - CONSTANTS(:,18).*STATES(:,7);
ALGEBRAIC(:,2) = CONSTANTS(:,23).*power(STATES(:,6), 3.00000)+ CONSTANTS(:,24).*power(STATES(:,6), 2.00000)+ CONSTANTS(:,25).*STATES(:,6)+CONSTANTS(:,26);
RATES(:,3) = (ALGEBRAIC(:,2)+ CONSTANTS(:,13).*STATES(:,3).*(1.00000 - ( CONSTANTS(:,3).*(STATES(:,1)+STATES(:,2))+ CONSTANTS(:,4).*STATES(:,3)+ CONSTANTS(:,5).*STATES(:,4)))) - CONSTANTS(:,14).*STATES(:,3);
ALGEBRAIC(:,4) = - ( 0.197000.*arbitrary_log(STATES(:,7), 10))+0.440700;
ALGEBRAIC(:,1) = CONSTANTS(:,19).*power(STATES(:,5), 3.00000)+ CONSTANTS(:,20).*power(STATES(:,5), 2.00000)+ CONSTANTS(:,21).*STATES(:,5)+CONSTANTS(:,22);
RATES(:,1) = ( ALGEBRAIC(:,4).*ALGEBRAIC(:,1)+ CONSTANTS(:,1).*CONSTANTS(:,2).*STATES(:,1).*(1.00000 - ( CONSTANTS(:,3).*(STATES(:,1)+STATES(:,2))+ CONSTANTS(:,4).*STATES(:,3)+ CONSTANTS(:,5).*STATES(:,4)))) - CONSTANTS(:,6).*STATES(:,1);
RATES(:,2) = ( (1.00000 - ALGEBRAIC(:,4)).*ALGEBRAIC(:,1)+ CONSTANTS(:,1).*CONSTANTS(:,2).*STATES(:,2).*(1.00000 - ( CONSTANTS(:,3).*(STATES(:,1)+STATES(:,2))+ CONSTANTS(:,4).*STATES(:,3)+ CONSTANTS(:,5).*STATES(:,4)))) - CONSTANTS(:,6).*STATES(:,2);
ALGEBRAIC(:,3) = CONSTANTS(:,27).*power(STATES(:,5), 3.00000)+ CONSTANTS(:,28).*power(STATES(:,5), 2.00000)+ CONSTANTS(:,29).*STATES(:,5)+CONSTANTS(:,30);
ALGEBRAIC(:,5) = CONSTANTS(:,31).*power(STATES(:,4), 3.00000)+ CONSTANTS(:,32).*power(STATES(:,4), 2.00000)+ CONSTANTS(:,33).*STATES(:,4)+CONSTANTS(:,34);
RATES(:,4) = CONSTANTS(:,15).*STATES(:,3).*ALGEBRAIC(:,3).*ALGEBRAIC(:,5) - CONSTANTS(:,16).*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(:,2) = CONSTANTS(:,23).*power(STATES(:,6), 3.00000)+ CONSTANTS(:,24).*power(STATES(:,6), 2.00000)+ CONSTANTS(:,25).*STATES(:,6)+CONSTANTS(:,26);
ALGEBRAIC(:,4) = - ( 0.197000.*arbitrary_log(STATES(:,7), 10))+0.440700;
ALGEBRAIC(:,1) = CONSTANTS(:,19).*power(STATES(:,5), 3.00000)+ CONSTANTS(:,20).*power(STATES(:,5), 2.00000)+ CONSTANTS(:,21).*STATES(:,5)+CONSTANTS(:,22);
ALGEBRAIC(:,3) = CONSTANTS(:,27).*power(STATES(:,5), 3.00000)+ CONSTANTS(:,28).*power(STATES(:,5), 2.00000)+ CONSTANTS(:,29).*STATES(:,5)+CONSTANTS(:,30);
ALGEBRAIC(:,5) = CONSTANTS(:,31).*power(STATES(:,4), 3.00000)+ CONSTANTS(:,32).*power(STATES(:,4), 2.00000)+ CONSTANTS(:,33).*STATES(:,4)+CONSTANTS(:,34);
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