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 =2;
end
% There are a total of 9 entries in each of the rate and state variable arrays.
% There are a total of 38 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_CONSTANTS(:,1) = strpad('BW in component main (kilogram)');
LEGEND_CONSTANTS(:,2) = strpad('Qcc in component main (litre_per_hr_kg)');
LEGEND_CONSTANTS(:,3) = strpad('Qliv in component main (dimensionless)');
LEGEND_CONSTANTS(:,4) = strpad('Qfat in component main (dimensionless)');
LEGEND_CONSTANTS(:,5) = strpad('Qbrain in component main (dimensionless)');
LEGEND_CONSTANTS(:,6) = strpad('Qslow in component main (dimensionless)');
LEGEND_CONSTANTS(:,21) = strpad('Qc in component main (litre_per_hr)');
LEGEND_CONSTANTS(:,29) = strpad('Ql in component main (litre_per_hr)');
LEGEND_CONSTANTS(:,34) = strpad('Qf in component main (litre_per_hr)');
LEGEND_CONSTANTS(:,36) = strpad('Qbr in component main (litre_per_hr)');
LEGEND_CONSTANTS(:,37) = strpad('Qs in component main (litre_per_hr)');
LEGEND_CONSTANTS(:,38) = strpad('Qr in component main (litre_per_hr)');
LEGEND_CONSTANTS(:,7) = strpad('Vblood in component main (dimensionless)');
LEGEND_CONSTANTS(:,8) = strpad('Vbrain in component main (dimensionless)');
LEGEND_CONSTANTS(:,9) = strpad('Vliver in component main (dimensionless)');
LEGEND_CONSTANTS(:,22) = strpad('Vfat in component main (dimensionless)');
LEGEND_CONSTANTS(:,10) = strpad('Vslow in component main (dimensionless)');
LEGEND_CONSTANTS(:,30) = strpad('Vrap in component main (dimensionless)');
LEGEND_CONSTANTS(:,31) = strpad('Vf in component main (litre)');
LEGEND_CONSTANTS(:,23) = strpad('Vs in component main (litre)');
LEGEND_CONSTANTS(:,24) = strpad('Vl in component main (litre)');
LEGEND_CONSTANTS(:,35) = strpad('Vr in component main (litre)');
LEGEND_CONSTANTS(:,25) = strpad('Vbr in component main (litre)');
LEGEND_CONSTANTS(:,26) = strpad('Vb in component main (litre)');
LEGEND_CONSTANTS(:,32) = strpad('Vven in component main (litre)');
LEGEND_CONSTANTS(:,33) = strpad('Vart in component main (litre)');
LEGEND_CONSTANTS(:,11) = strpad('Pfat_bl in component main (dimensionless)');
LEGEND_CONSTANTS(:,12) = strpad('Pslow_bl in component main (dimensionless)');
LEGEND_CONSTANTS(:,13) = strpad('Pliv_bl in component main (dimensionless)');
LEGEND_CONSTANTS(:,14) = strpad('Prapid_bl in component main (dimensionless)');
LEGEND_CONSTANTS(:,15) = strpad('Pbrain_bl in component main (dimensionless)');
LEGEND_CONSTANTS(:,16) = strpad('dose in component main (mg_per_kg)');
LEGEND_CONSTANTS(:,17) = strpad('F in component main (dimensionless)');
LEGEND_CONSTANTS(:,27) = strpad('D0 in component main (mg)');
LEGEND_CONSTANTS(:,18) = strpad('Ka in component main (per_hr)');
LEGEND_CONSTANTS(:,19) = strpad('Kfc in component main (per_hr)');
LEGEND_CONSTANTS(:,28) = strpad('KF in component main (per_hr_kg)');
LEGEND_VOI = strpad('t in component main (hr)');
LEGEND_STATES(:,1) = strpad('A_fat in component main (mg)');
LEGEND_STATES(:,2) = strpad('A_slow in component main (mg)');
LEGEND_STATES(:,3) = strpad('A_liv in component main (mg)');
LEGEND_STATES(:,4) = strpad('A_rapid in component main (mg)');
LEGEND_STATES(:,5) = strpad('A_brain in component main (mg)');
LEGEND_CONSTANTS(:,20) = strpad('A_blood in component main (mg)');
LEGEND_STATES(:,6) = strpad('A_stomach in component main (mg)');
LEGEND_STATES(:,7) = strpad('A_ven in component main (mg)');
LEGEND_STATES(:,8) = strpad('A_art in component main (mg)');
LEGEND_STATES(:,9) = strpad('A_liv_CL in component main (mg)');
LEGEND_ALGEBRAIC(:,1) = strpad('C_art in component main (mg_per_litre)');
LEGEND_ALGEBRAIC(:,2) = strpad('C_brain in component main (mg_per_litre)');
LEGEND_RATES(:,7) = strpad('d/dt A_ven in component main (mg)');
LEGEND_RATES(:,8) = strpad('d/dt A_art in component main (mg)');
LEGEND_RATES(:,1) = strpad('d/dt A_fat in component main (mg)');
LEGEND_RATES(:,2) = strpad('d/dt A_slow in component main (mg)');
LEGEND_RATES(:,5) = strpad('d/dt A_brain in component main (mg)');
LEGEND_RATES(:,4) = strpad('d/dt A_rapid in component main (mg)');
LEGEND_RATES(:,6) = strpad('d/dt A_stomach in component main (mg)');
LEGEND_RATES(:,3) = strpad('d/dt A_liv in component main (mg)');
LEGEND_RATES(:,9) = strpad('d/dt A_liv_CL in component main (mg)');
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 = [];
CONSTANTS(:,1) = 0.1615;
CONSTANTS(:,2) = 14;
CONSTANTS(:,3) = 0.25;
CONSTANTS(:,4) = 0.09;
CONSTANTS(:,5) = 0.03;
CONSTANTS(:,6) = 0.278;
CONSTANTS(:,7) = 0.05;
CONSTANTS(:,8) = 0.0116;
CONSTANTS(:,9) = 0.04;
CONSTANTS(:,10) = 0.63;
CONSTANTS(:,11) = 186;
CONSTANTS(:,12) = 3.4;
CONSTANTS(:,13) = 6.1;
CONSTANTS(:,14) = 6.1;
CONSTANTS(:,15) = 3;
CONSTANTS(:,16) = 60;
CONSTANTS(:,17) = 0.8;
CONSTANTS(:,18) = 0.1;
CONSTANTS(:,19) = 6;
STATES(:,1) = 0;
STATES(:,2) = 0;
STATES(:,3) = 0;
STATES(:,4) = 0;
STATES(:,5) = 0;
CONSTANTS(:,20) = 0;
STATES(:,7) = 0;
STATES(:,8) = 0;
STATES(:,9) = 0;
CONSTANTS(:,21) = CONSTANTS(:,2).*power(CONSTANTS(:,1), 0.740000);
CONSTANTS(:,22) = 0.0100000.*( 20.0000.*CONSTANTS(:,1)+1.66400);
CONSTANTS(:,23) = CONSTANTS(:,10).*CONSTANTS(:,1);
CONSTANTS(:,24) = CONSTANTS(:,9).*CONSTANTS(:,1);
CONSTANTS(:,25) = CONSTANTS(:,8).*CONSTANTS(:,1);
CONSTANTS(:,26) = CONSTANTS(:,7).*CONSTANTS(:,1);
CONSTANTS(:,27) = CONSTANTS(:,17).*CONSTANTS(:,16).*CONSTANTS(:,1);
CONSTANTS(:,28) = CONSTANTS(:,19)./power(CONSTANTS(:,1), 0.300000);
CONSTANTS(:,29) = CONSTANTS(:,3).*CONSTANTS(:,21);
CONSTANTS(:,30) = (((1.00000 - CONSTANTS(:,7)) - CONSTANTS(:,9)) - CONSTANTS(:,22)) - CONSTANTS(:,10);
CONSTANTS(:,31) = CONSTANTS(:,22).*CONSTANTS(:,1);
CONSTANTS(:,32) = 0.750000.*CONSTANTS(:,26);
CONSTANTS(:,33) = 0.250000.*CONSTANTS(:,26);
CONSTANTS(:,34) = CONSTANTS(:,4).*CONSTANTS(:,21);
CONSTANTS(:,35) = CONSTANTS(:,30).*CONSTANTS(:,1);
CONSTANTS(:,36) = CONSTANTS(:,5).*CONSTANTS(:,21);
CONSTANTS(:,37) = CONSTANTS(:,6).*CONSTANTS(:,21);
CONSTANTS(:,38) = (((CONSTANTS(:,21) - CONSTANTS(:,29)) - CONSTANTS(:,34)) - CONSTANTS(:,36)) - CONSTANTS(:,37);
STATES(:,6) = CONSTANTS(:,27);
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(:,34).*STATES(:,1))./CONSTANTS(:,31))./CONSTANTS(:,11)+(( CONSTANTS(:,36).*STATES(:,5))./CONSTANTS(:,25))./CONSTANTS(:,15)+(( CONSTANTS(:,37).*STATES(:,2))./CONSTANTS(:,23))./CONSTANTS(:,12)+(( CONSTANTS(:,29).*STATES(:,3))./CONSTANTS(:,24))./CONSTANTS(:,13)+(( CONSTANTS(:,38).*STATES(:,4))./CONSTANTS(:,35))./CONSTANTS(:,14);
RATES(:,1) = CONSTANTS(:,34).*(STATES(:,8)./CONSTANTS(:,26) - (STATES(:,1)./CONSTANTS(:,31))./CONSTANTS(:,11));
RATES(:,2) = CONSTANTS(:,37).*(STATES(:,8)./CONSTANTS(:,26) - (STATES(:,2)./CONSTANTS(:,23))./CONSTANTS(:,12));
RATES(:,5) = CONSTANTS(:,36).*(STATES(:,8)./CONSTANTS(:,26) - (STATES(:,5)./CONSTANTS(:,25))./CONSTANTS(:,15));
RATES(:,4) = CONSTANTS(:,38).*(STATES(:,8)./CONSTANTS(:,26) - (STATES(:,4)./CONSTANTS(:,35))./CONSTANTS(:,14));
RATES(:,6) = - CONSTANTS(:,18).*STATES(:,6);
RATES(:,3) = ( CONSTANTS(:,29).*(STATES(:,8)./CONSTANTS(:,26) - (STATES(:,3)./CONSTANTS(:,24))./CONSTANTS(:,13)) - (( CONSTANTS(:,28).*CONSTANTS(:,24).*STATES(:,3))./CONSTANTS(:,24))./CONSTANTS(:,13))+ CONSTANTS(:,18).*STATES(:,6);
RATES(:,9) = (( CONSTANTS(:,28).*CONSTANTS(:,24).*STATES(:,3))./CONSTANTS(:,24))./CONSTANTS(:,13);
RATES(:,8) = RATES(:,7) - ( CONSTANTS(:,21).*STATES(:,8))./CONSTANTS(:,26);
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(:,8)./CONSTANTS(:,26);
ALGEBRAIC(:,2) = STATES(:,5)./CONSTANTS(:,25);
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