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 =11;
end
% There are a total of 2 entries in each of the rate and state variable arrays.
% There are a total of 11 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 (minute)');
LEGEND_CONSTANTS(:,1) = strpad('VPF in component pulmonary_O2_uptake (litre)');
LEGEND_CONSTANTS(:,2) = strpad('DOB in component pulmonary_O2_uptake (mL_per_minute)');
LEGEND_CONSTANTS(:,3) = strpad('QRO in component pulmonary_O2_uptake (L_per_minute)');
LEGEND_CONSTANTS(:,4) = strpad('RMO in component pulmonary_O2_uptake (mL_per_minute)');
LEGEND_CONSTANTS(:,5) = strpad('HM in component pulmonary_O2_uptake (dimensionless)');
LEGEND_CONSTANTS(:,10) = strpad('O2UTIL in component total_O2_utilization (mL_per_minute)');
LEGEND_ALGEBRAIC(:,6) = strpad('O2VAD2 in component progressive_chemoreceptor_adaptation_of_alveolar_ventilation (dimensionless)');
LEGEND_ALGEBRAIC(:,5) = strpad('O2VTS2 in component acute_chemoreceptor_adaptation_of_alveolar_ventilation (dimensionless)');
LEGEND_ALGEBRAIC(:,8) = strpad('ALVENT in component alveolar_ventilation (L_per_minute)');
LEGEND_CONSTANTS(:,6) = strpad('VNTSTM in component parameter_values (dimensionless)');
LEGEND_ALGEBRAIC(:,9) = strpad('PO2ALV in component alveolar_PO2 (mmHg)');
LEGEND_CONSTANTS(:,7) = strpad('PO2AMB in component parameter_values (mmHg)');
LEGEND_ALGEBRAIC(:,2) = strpad('PO2ART in component arterial_PO2 (mmHg)');
LEGEND_ALGEBRAIC(:,10) = strpad('O2DFS in component respiratory_O2_diffusion_into_capillaries (mL_per_minute)');
LEGEND_CONSTANTS(:,8) = strpad('PL2 in component parameter_values (L_mL_per_minute_per_mmHg)');
LEGEND_CONSTANTS(:,9) = strpad('VPTISS in component parameter_values (litre)');
LEGEND_CONSTANTS(:,11) = strpad('RSPDFC in component respiratory_O2_diffusion_into_capillaries (mL_per_minute_per_mmHg)');
LEGEND_STATES(:,1) = strpad('OVA in component O2_volume_of_arterial_blood (mL_per_L)');
LEGEND_ALGEBRAIC(:,11) = strpad('DOVA in component O2_volume_of_arterial_blood (mL_per_L_per_minute)');
LEGEND_ALGEBRAIC(:,1) = strpad('OSA in component arterial_PO2 (dimensionless)');
LEGEND_ALGEBRAIC(:,4) = strpad('O2VTST in component acute_chemoreceptor_adaptation_of_alveolar_ventilation (dimensionless)');
LEGEND_ALGEBRAIC(:,3) = strpad('O2VTST1 in component acute_chemoreceptor_adaptation_of_alveolar_ventilation (dimensionless)');
LEGEND_ALGEBRAIC(:,7) = strpad('DO2VAD in component progressive_chemoreceptor_adaptation_of_alveolar_ventilation (per_minute)');
LEGEND_STATES(:,2) = strpad('O2VAD1 in component progressive_chemoreceptor_adaptation_of_alveolar_ventilation (dimensionless)');
LEGEND_RATES(:,1) = strpad('d/dt OVA in component O2_volume_of_arterial_blood (mL_per_L)');
LEGEND_RATES(:,2) = strpad('d/dt O2VAD1 in component progressive_chemoreceptor_adaptation_of_alveolar_ventilation (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) = 0.0123238;
CONSTANTS(:,2) = 163.508;
CONSTANTS(:,3) = 4.97838;
CONSTANTS(:,4) = 56.8057;
CONSTANTS(:,5) = 40.0381;
CONSTANTS(:,6) = 1;
CONSTANTS(:,7) = 150;
CONSTANTS(:,8) = 1.8;
CONSTANTS(:,9) = 0.0175;
STATES(:,1) = 204.497;
STATES(:,2) = 2.368e-07;
CONSTANTS(:,10) = CONSTANTS(:,2)+CONSTANTS(:,4);
CONSTANTS(:,11) = CONSTANTS(:,8)./(CONSTANTS(:,9)+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) = (STATES(:,1)./CONSTANTS(:,5))./5.25000;
ALGEBRAIC(:,2) = piecewise({ALGEBRAIC(:,1)>1.00000, 114.000+ (ALGEBRAIC(:,1) - 1.00000).*6667.00 , ALGEBRAIC(:,1)>0.936000&ALGEBRAIC(:,1)<=1.00000, 74.0000+ (ALGEBRAIC(:,1) - 0.936000).*625.000 , ALGEBRAIC(:,1)>0.800000&ALGEBRAIC(:,1)<=0.936000, 46.0000+ (ALGEBRAIC(:,1) - 0.800000).*205.882 }, ALGEBRAIC(:,1).*57.5000);
ALGEBRAIC(:,3) = (ALGEBRAIC(:,2) - 67.0000)./30.0000;
ALGEBRAIC(:,4) = piecewise({ALGEBRAIC(:,3)>1.00000, 1.00000 , ALGEBRAIC(:,3)<0.600000, 0.600000 }, ALGEBRAIC(:,3));
ALGEBRAIC(:,5) = 1.00000./ALGEBRAIC(:,4);
ALGEBRAIC(:,7) = ( (ALGEBRAIC(:,5) - 1.00000).*3.00000 - STATES(:,2)).*0.000500000;
RATES(:,2) = ALGEBRAIC(:,7);
ALGEBRAIC(:,6) = STATES(:,2)+1.00000;
ALGEBRAIC(:,8) = CONSTANTS(:,10).*CONSTANTS(:,6).*0.0266670.*ALGEBRAIC(:,5).*ALGEBRAIC(:,6);
ALGEBRAIC(:,9) = CONSTANTS(:,7) - (CONSTANTS(:,10)./ALGEBRAIC(:,8))./0.761000;
ALGEBRAIC(:,10) = (ALGEBRAIC(:,9) - ALGEBRAIC(:,2)).*CONSTANTS(:,11);
ALGEBRAIC(:,11) = (ALGEBRAIC(:,10) - CONSTANTS(:,10))./( CONSTANTS(:,3).*1.00000);
RATES(:,1) = ALGEBRAIC(:,11);
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)./CONSTANTS(:,5))./5.25000;
ALGEBRAIC(:,2) = piecewise({ALGEBRAIC(:,1)>1.00000, 114.000+ (ALGEBRAIC(:,1) - 1.00000).*6667.00 , ALGEBRAIC(:,1)>0.936000&ALGEBRAIC(:,1)<=1.00000, 74.0000+ (ALGEBRAIC(:,1) - 0.936000).*625.000 , ALGEBRAIC(:,1)>0.800000&ALGEBRAIC(:,1)<=0.936000, 46.0000+ (ALGEBRAIC(:,1) - 0.800000).*205.882 }, ALGEBRAIC(:,1).*57.5000);
ALGEBRAIC(:,3) = (ALGEBRAIC(:,2) - 67.0000)./30.0000;
ALGEBRAIC(:,4) = piecewise({ALGEBRAIC(:,3)>1.00000, 1.00000 , ALGEBRAIC(:,3)<0.600000, 0.600000 }, ALGEBRAIC(:,3));
ALGEBRAIC(:,5) = 1.00000./ALGEBRAIC(:,4);
ALGEBRAIC(:,7) = ( (ALGEBRAIC(:,5) - 1.00000).*3.00000 - STATES(:,2)).*0.000500000;
ALGEBRAIC(:,6) = STATES(:,2)+1.00000;
ALGEBRAIC(:,8) = CONSTANTS(:,10).*CONSTANTS(:,6).*0.0266670.*ALGEBRAIC(:,5).*ALGEBRAIC(:,6);
ALGEBRAIC(:,9) = CONSTANTS(:,7) - (CONSTANTS(:,10)./ALGEBRAIC(:,8))./0.761000;
ALGEBRAIC(:,10) = (ALGEBRAIC(:,9) - ALGEBRAIC(:,2)).*CONSTANTS(:,11);
ALGEBRAIC(:,11) = (ALGEBRAIC(:,10) - CONSTANTS(:,10))./( CONSTANTS(:,3).*1.00000);
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