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 =16;
end
% There are a total of 3 entries in each of the rate and state variable arrays.
% There are a total of 37 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 (hour)');
LEGEND_CONSTANTS(:,1) = strpad('T_a in component model_parameters (celsius)');
LEGEND_CONSTANTS(:,2) = strpad('T_b in component model_parameters (celsius)');
LEGEND_CONSTANTS(:,3) = strpad('delta_T in component model_parameters (celsius)');
LEGEND_CONSTANTS(:,4) = strpad('kinc in component model_parameters (W_per_kg_C2)');
LEGEND_CONSTANTS(:,5) = strpad('tdose1 in component model_parameters (hour)');
LEGEND_CONSTANTS(:,6) = strpad('tdose2 in component model_parameters (hour)');
LEGEND_CONSTANTS(:,7) = strpad('tdose3 in component model_parameters (hour)');
LEGEND_ALGEBRAIC(:,6) = strpad('M_c in component M_c (W_per_kg)');
LEGEND_CONSTANTS(:,8) = strpad('t_day in component M_c (hour)');
LEGEND_CONSTANTS(:,9) = strpad('t_night in component M_c (hour)');
LEGEND_ALGEBRAIC(:,2) = strpad('tprime in component M_c (second)');
LEGEND_CONSTANTS(:,10) = strpad('day_length in component M_c (second)');
LEGEND_CONSTANTS(:,36) = strpad('M_day in component M_day (W_per_kg)');
LEGEND_ALGEBRAIC(:,4) = strpad('M_night in component M_night (W_per_kg)');
LEGEND_STATES(:,1) = strpad('M in component M (W_per_kg)');
LEGEND_CONSTANTS(:,11) = strpad('km in component M (per_hour)');
LEGEND_STATES(:,2) = strpad('T in component T (celsius)');
LEGEND_CONSTANTS(:,12) = strpad('c in component T (kJ_per_kg_C)');
LEGEND_ALGEBRAIC(:,1) = strpad('k in component k (W_per_kg_C)');
LEGEND_STATES(:,3) = strpad('BR in component k (dimensionless)');
LEGEND_CONSTANTS(:,13) = strpad('pEtot in component k (dimensionless)');
LEGEND_CONSTANTS(:,14) = strpad('kR in component k (per_day)');
LEGEND_CONSTANTS(:,15) = strpad('AMT_dose in component k (mg_per_kg)');
LEGEND_CONSTANTS(:,16) = strpad('pEf1 in component k (per_day)');
LEGEND_CONSTANTS(:,17) = strpad('pEs1 in component k (kg_per_day_mg)');
LEGEND_CONSTANTS(:,18) = strpad('pEf2 in component k (per_day)');
LEGEND_CONSTANTS(:,19) = strpad('pEs2 in component k (kg_per_day_mg)');
LEGEND_CONSTANTS(:,20) = strpad('pEf3 in component k (per_day)');
LEGEND_CONSTANTS(:,21) = strpad('pEs3 in component k (kg_per_day_mg)');
LEGEND_ALGEBRAIC(:,14) = strpad('E_slow in component k (per_day)');
LEGEND_ALGEBRAIC(:,16) = strpad('E_fast in component k (per_day)');
LEGEND_CONSTANTS(:,31) = strpad('f2_drug in component k (W_per_kg_C)');
LEGEND_CONSTANTS(:,35) = strpad('kb in component kb (W_per_kg_C)');
LEGEND_ALGEBRAIC(:,3) = strpad('f_prime in component M_night (dimensionless)');
LEGEND_ALGEBRAIC(:,7) = strpad('gNsTs1 in component gNT (dimensionless)');
LEGEND_ALGEBRAIC(:,10) = strpad('gNsTs2 in component gNT (dimensionless)');
LEGEND_ALGEBRAIC(:,13) = strpad('gNsTs3 in component gNT (dimensionless)');
LEGEND_ALGEBRAIC(:,8) = strpad('gNfTf1 in component gNT (dimensionless)');
LEGEND_ALGEBRAIC(:,11) = strpad('gNfTf2 in component gNT (dimensionless)');
LEGEND_ALGEBRAIC(:,15) = strpad('gNfTf3 in component gNT (dimensionless)');
LEGEND_CONSTANTS(:,30) = strpad('T_day in component T_day (celsius)');
LEGEND_CONSTANTS(:,33) = strpad('T_night in component T_night (celsius)');
LEGEND_CONSTANTS(:,22) = strpad('M_b in component kb (W_per_kg)');
LEGEND_CONSTANTS(:,23) = strpad('t_prime in component M_night (hour)');
LEGEND_CONSTANTS(:,24) = strpad('alpha in component M_night (per_hour)');
LEGEND_CONSTANTS(:,25) = strpad('delta_high_dose in component M_night (dimensionless)');
LEGEND_CONSTANTS(:,37) = strpad('M_night_baseline in component M_night (W_per_kg)');
LEGEND_CONSTANTS(:,26) = strpad('Ns in component gNT (dimensionless)');
LEGEND_CONSTANTS(:,27) = strpad('Nf in component gNT (dimensionless)');
LEGEND_CONSTANTS(:,28) = strpad('Ts in component gNT (day)');
LEGEND_CONSTANTS(:,29) = strpad('Tf in component gNT (day)');
LEGEND_ALGEBRAIC(:,5) = strpad('X1 in component gNT (day)');
LEGEND_ALGEBRAIC(:,9) = strpad('X2 in component gNT (day)');
LEGEND_ALGEBRAIC(:,12) = strpad('X3 in component gNT (day)');
LEGEND_CONSTANTS(:,32) = strpad('Kf in component gNT (per_day)');
LEGEND_CONSTANTS(:,34) = strpad('Ks in component gNT (per_day)');
LEGEND_RATES(:,1) = strpad('d/dt M in component M (W_per_kg)');
LEGEND_RATES(:,2) = strpad('d/dt T in component T (celsius)');
LEGEND_RATES(:,3) = strpad('d/dt BR in component k (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 = [];
CONSTANTS(:,1) = 21.0;
CONSTANTS(:,2) = 38.0;
CONSTANTS(:,3) = 1.57;
CONSTANTS(:,4) = 0.0258;
CONSTANTS(:,5) = 24.0;
CONSTANTS(:,6) = 72.0;
CONSTANTS(:,7) = 120.0;
CONSTANTS(:,8) = 17.5;
CONSTANTS(:,9) = 6.73;
CONSTANTS(:,10) = 86400;
STATES(:,1) = 3.5;
CONSTANTS(:,11) = 1.1375;
STATES(:,2) = 38.785;
CONSTANTS(:,12) = 3.47;
STATES(:,3) = 0.0;
CONSTANTS(:,13) = 0.144;
CONSTANTS(:,14) = 5.35;
CONSTANTS(:,15) = 3.0;
CONSTANTS(:,16) = 1.0;
CONSTANTS(:,17) = 0.2;
CONSTANTS(:,18) = 3.57;
CONSTANTS(:,19) = 2.43;
CONSTANTS(:,20) = 8.0;
CONSTANTS(:,21) = 50.0;
CONSTANTS(:,22) = 3.0;
CONSTANTS(:,23) = 45.12;
CONSTANTS(:,24) = 0.2229166;
CONSTANTS(:,25) = 1.0;
CONSTANTS(:,26) = 4.0;
CONSTANTS(:,27) = 4.0;
CONSTANTS(:,28) = 2.45;
CONSTANTS(:,29) = 0.368;
CONSTANTS(:,30) = CONSTANTS(:,2)+CONSTANTS(:,3)./2.00000;
CONSTANTS(:,31) = 0.00000;
CONSTANTS(:,32) = CONSTANTS(:,27)./CONSTANTS(:,29);
CONSTANTS(:,33) = CONSTANTS(:,2) - CONSTANTS(:,3)./2.00000;
CONSTANTS(:,34) = CONSTANTS(:,26)./CONSTANTS(:,28);
CONSTANTS(:,35) = CONSTANTS(:,22)./(CONSTANTS(:,2) - CONSTANTS(:,1));
CONSTANTS(:,36) = (CONSTANTS(:,35)+ CONSTANTS(:,4).*(CONSTANTS(:,30) - CONSTANTS(:,2))).*(CONSTANTS(:,30) - CONSTANTS(:,1));
CONSTANTS(:,37) = (CONSTANTS(:,35)+ CONSTANTS(:,4).*(CONSTANTS(:,33) - CONSTANTS(:,2))).*(CONSTANTS(:,33) - CONSTANTS(:,1));
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
ALGEBRAIC(:,1) = CONSTANTS(:,35)+ CONSTANTS(:,4).*(STATES(:,2) - CONSTANTS(:,2).*(1.00000+ CONSTANTS(:,13).*STATES(:,3)))+CONSTANTS(:,31);
RATES(:,2) = power(CONSTANTS(:,12), -1.00000).*(STATES(:,1) - ALGEBRAIC(:,1).*(STATES(:,2) - CONSTANTS(:,1)));
ALGEBRAIC(:,2) = rem( VOI.*3600.00.*1.00000, CONSTANTS(:,10));
ALGEBRAIC(:,3) = CONSTANTS(:,25).*power(1.00000+exp( - CONSTANTS(:,24).*(VOI - (CONSTANTS(:,5)+CONSTANTS(:,23)))), -1.00000);
ALGEBRAIC(:,4) = (1.00000 - ALGEBRAIC(:,3)).*CONSTANTS(:,37)+ ALGEBRAIC(:,3).*CONSTANTS(:,36);
ALGEBRAIC(:,6) = piecewise({ALGEBRAIC(:,2)./3600.00>=CONSTANTS(:,9)&ALGEBRAIC(:,2)./3600.00<CONSTANTS(:,8), ALGEBRAIC(:,4) }, CONSTANTS(:,36));
RATES(:,1) = - CONSTANTS(:,11).*(STATES(:,1) - ALGEBRAIC(:,6));
ALGEBRAIC(:,5) = (VOI - CONSTANTS(:,5))./24.0000;
ALGEBRAIC(:,7) = piecewise({ALGEBRAIC(:,5)>0.00000, (power(CONSTANTS(:,34), CONSTANTS(:,26))./6.00000).*exp( - CONSTANTS(:,34).*ALGEBRAIC(:,5)).*power(ALGEBRAIC(:,5), CONSTANTS(:,26) - 1.00000) }, 0.00000);
ALGEBRAIC(:,9) = (VOI - CONSTANTS(:,6))./24.0000;
ALGEBRAIC(:,10) = piecewise({ALGEBRAIC(:,9)>0.00000, (power(CONSTANTS(:,34), CONSTANTS(:,26))./6.00000).*exp( - CONSTANTS(:,34).*ALGEBRAIC(:,9)).*power(ALGEBRAIC(:,9), CONSTANTS(:,26) - 1.00000) }, 0.00000);
ALGEBRAIC(:,12) = (VOI - CONSTANTS(:,7))./24.0000;
ALGEBRAIC(:,13) = piecewise({ALGEBRAIC(:,12)>0.00000, (power(CONSTANTS(:,34), CONSTANTS(:,26))./6.00000).*exp( - CONSTANTS(:,34).*ALGEBRAIC(:,12)).*power(ALGEBRAIC(:,12), CONSTANTS(:,26) - 1.00000) }, 0.00000);
ALGEBRAIC(:,14) = CONSTANTS(:,15).*CONSTANTS(:,19).*(ALGEBRAIC(:,7)+ALGEBRAIC(:,10)+ALGEBRAIC(:,13));
ALGEBRAIC(:,8) = piecewise({ALGEBRAIC(:,5)>0.00000, (power(CONSTANTS(:,32), CONSTANTS(:,27))./6.00000).*exp( - CONSTANTS(:,32).*ALGEBRAIC(:,5)).*power(ALGEBRAIC(:,5), CONSTANTS(:,27) - 1.00000) }, 0.00000);
ALGEBRAIC(:,11) = piecewise({ALGEBRAIC(:,9)>0.00000, (power(CONSTANTS(:,32), CONSTANTS(:,27))./6.00000).*exp( - CONSTANTS(:,32).*ALGEBRAIC(:,9)).*power(ALGEBRAIC(:,9), CONSTANTS(:,27) - 1.00000) }, 0.00000);
ALGEBRAIC(:,15) = piecewise({ALGEBRAIC(:,12)>0.00000, (power(CONSTANTS(:,32), CONSTANTS(:,27))./6.00000).*exp( - CONSTANTS(:,32).*ALGEBRAIC(:,12)).*power(ALGEBRAIC(:,12), CONSTANTS(:,27) - 1.00000) }, 0.00000);
ALGEBRAIC(:,16) = CONSTANTS(:,18).*(ALGEBRAIC(:,8)+ALGEBRAIC(:,11)+ALGEBRAIC(:,15));
RATES(:,3) = ( ALGEBRAIC(:,3).*(ALGEBRAIC(:,14)+ALGEBRAIC(:,16))).*(1.00000 - STATES(:,3)) - CONSTANTS(:,14).*STATES(:,3);
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) = CONSTANTS(:,35)+ CONSTANTS(:,4).*(STATES(:,2) - CONSTANTS(:,2).*(1.00000+ CONSTANTS(:,13).*STATES(:,3)))+CONSTANTS(:,31);
ALGEBRAIC(:,2) = rem( VOI.*3600.00.*1.00000, CONSTANTS(:,10));
ALGEBRAIC(:,3) = CONSTANTS(:,25).*power(1.00000+exp( - CONSTANTS(:,24).*(VOI - (CONSTANTS(:,5)+CONSTANTS(:,23)))), -1.00000);
ALGEBRAIC(:,4) = (1.00000 - ALGEBRAIC(:,3)).*CONSTANTS(:,37)+ ALGEBRAIC(:,3).*CONSTANTS(:,36);
ALGEBRAIC(:,6) = piecewise({ALGEBRAIC(:,2)./3600.00>=CONSTANTS(:,9)&ALGEBRAIC(:,2)./3600.00<CONSTANTS(:,8), ALGEBRAIC(:,4) }, CONSTANTS(:,36));
ALGEBRAIC(:,5) = (VOI - CONSTANTS(:,5))./24.0000;
ALGEBRAIC(:,7) = piecewise({ALGEBRAIC(:,5)>0.00000, (power(CONSTANTS(:,34), CONSTANTS(:,26))./6.00000).*exp( - CONSTANTS(:,34).*ALGEBRAIC(:,5)).*power(ALGEBRAIC(:,5), CONSTANTS(:,26) - 1.00000) }, 0.00000);
ALGEBRAIC(:,9) = (VOI - CONSTANTS(:,6))./24.0000;
ALGEBRAIC(:,10) = piecewise({ALGEBRAIC(:,9)>0.00000, (power(CONSTANTS(:,34), CONSTANTS(:,26))./6.00000).*exp( - CONSTANTS(:,34).*ALGEBRAIC(:,9)).*power(ALGEBRAIC(:,9), CONSTANTS(:,26) - 1.00000) }, 0.00000);
ALGEBRAIC(:,12) = (VOI - CONSTANTS(:,7))./24.0000;
ALGEBRAIC(:,13) = piecewise({ALGEBRAIC(:,12)>0.00000, (power(CONSTANTS(:,34), CONSTANTS(:,26))./6.00000).*exp( - CONSTANTS(:,34).*ALGEBRAIC(:,12)).*power(ALGEBRAIC(:,12), CONSTANTS(:,26) - 1.00000) }, 0.00000);
ALGEBRAIC(:,14) = CONSTANTS(:,15).*CONSTANTS(:,19).*(ALGEBRAIC(:,7)+ALGEBRAIC(:,10)+ALGEBRAIC(:,13));
ALGEBRAIC(:,8) = piecewise({ALGEBRAIC(:,5)>0.00000, (power(CONSTANTS(:,32), CONSTANTS(:,27))./6.00000).*exp( - CONSTANTS(:,32).*ALGEBRAIC(:,5)).*power(ALGEBRAIC(:,5), CONSTANTS(:,27) - 1.00000) }, 0.00000);
ALGEBRAIC(:,11) = piecewise({ALGEBRAIC(:,9)>0.00000, (power(CONSTANTS(:,32), CONSTANTS(:,27))./6.00000).*exp( - CONSTANTS(:,32).*ALGEBRAIC(:,9)).*power(ALGEBRAIC(:,9), CONSTANTS(:,27) - 1.00000) }, 0.00000);
ALGEBRAIC(:,15) = piecewise({ALGEBRAIC(:,12)>0.00000, (power(CONSTANTS(:,32), CONSTANTS(:,27))./6.00000).*exp( - CONSTANTS(:,32).*ALGEBRAIC(:,12)).*power(ALGEBRAIC(:,12), CONSTANTS(:,27) - 1.00000) }, 0.00000);
ALGEBRAIC(:,16) = CONSTANTS(:,18).*(ALGEBRAIC(:,8)+ALGEBRAIC(:,11)+ALGEBRAIC(:,15));
end
% Compute result of a piecewise function
function x = piecewise(cases, default)
set = [0];
for i = 1:2:length(cases)
if (length(cases{i+1}) == 1)
x(cases{i} & ~set,:) = cases{i+1};
else
x(cases{i} & ~set,:) = cases{i+1}(cases{i} & ~set);
end
set = set | cases{i};
if(set), break, end
end
if (length(default) == 1)
x(~set,:) = default;
else
x(~set,:) = default(~set);
end
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