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 =13;
end
% There are a total of 2 entries in each of the rate and state variable arrays.
% There are a total of 41 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('PA in component autonomics (mmHg)');
LEGEND_CONSTANTS(:,2) = strpad('PO2ART in component autonomics (mmHg)');
LEGEND_CONSTANTS(:,3) = strpad('PLA in component autonomics (mmHg)');
LEGEND_CONSTANTS(:,4) = strpad('PRA in component autonomics (mmHg)');
LEGEND_CONSTANTS(:,5) = strpad('PPA in component autonomics (mmHg)');
LEGEND_CONSTANTS(:,32) = strpad('PA1 in component pressure_driving_autonomic_receptors (mmHg)');
LEGEND_CONSTANTS(:,6) = strpad('CRRFLX in component parameter_values (mmHg)');
LEGEND_CONSTANTS(:,7) = strpad('EXE in component parameter_values (mmHg)');
LEGEND_CONSTANTS(:,33) = strpad('AUC in component chemoreceptors_effect_of_PA (dimensionless)');
LEGEND_CONSTANTS(:,8) = strpad('AUC1 in component parameter_values (dimensionless)');
LEGEND_CONSTANTS(:,38) = strpad('AUC3 in component chemoreceptors_effect_of_art_PO2 (dimensionless)');
LEGEND_CONSTANTS(:,9) = strpad('O2CHMO in component parameter_values (per_mmHg)');
LEGEND_CONSTANTS(:,35) = strpad('AUC2 in component chemoreceptors_effect_of_art_PO2 (dimensionless)');
LEGEND_ALGEBRAIC(:,1) = strpad('AU6C in component arterial_baroreceptor_reflex (dimensionless)');
LEGEND_CONSTANTS(:,10) = strpad('AUX in component parameter_values (dimensionless)');
LEGEND_CONSTANTS(:,11) = strpad('AUK in component parameter_values (per_minute)');
LEGEND_CONSTANTS(:,12) = strpad('BAROTC in component parameter_values (minute)');
LEGEND_CONSTANTS(:,34) = strpad('AUB in component arterial_baroreceptor_reflex (dimensionless)');
LEGEND_CONSTANTS(:,36) = strpad('A1B in component arterial_baroreceptor_reflex (dimensionless)');
LEGEND_CONSTANTS(:,37) = strpad('AU6A in component arterial_baroreceptor_reflex (dimensionless)');
LEGEND_CONSTANTS(:,13) = strpad('AU4 in component arterial_baroreceptor_reflex (dimensionless)');
LEGEND_STATES(:,1) = strpad('AU6 in component arterial_baroreceptor_reflex (dimensionless)');
LEGEND_CONSTANTS(:,39) = strpad('AUN in component CNS_ischemic_reflex (dimensionless)');
LEGEND_CONSTANTS(:,14) = strpad('AUN1 in component parameter_values (dimensionless)');
LEGEND_CONSTANTS(:,40) = strpad('AULP in component autonomic_response_to_vasculature_pressure (dimensionless)');
LEGEND_CONSTANTS(:,15) = strpad('AULPM in component parameter_values (dimensionless)');
LEGEND_CONSTANTS(:,41) = strpad('AUEX in component autonomic_response_to_exercise (dimensionless)');
LEGEND_CONSTANTS(:,16) = strpad('EXC in component parameter_values (dimensionless)');
LEGEND_CONSTANTS(:,17) = strpad('EXCXP in component parameter_values (dimensionless)');
LEGEND_ALGEBRAIC(:,5) = strpad('AUTTL in component total_autonomic_stimulation (dimensionless)');
LEGEND_ALGEBRAIC(:,3) = strpad('AUTTL1 in component total_autonomic_stimulation (dimensionless)');
LEGEND_CONSTANTS(:,18) = strpad('EXCML in component parameter_values (dimensionless)');
LEGEND_ALGEBRAIC(:,4) = strpad('AU in component actual_autonomic_stimulation (dimensionless)');
LEGEND_CONSTANTS(:,19) = strpad('AUDMP in component parameter_values (minute)');
LEGEND_CONSTANTS(:,20) = strpad('AUMAX in component parameter_values (dimensionless)');
LEGEND_CONSTANTS(:,21) = strpad('AUMIN in component parameter_values (dimensionless)');
LEGEND_CONSTANTS(:,22) = strpad('AUSLP in component parameter_values (dimensionless)');
LEGEND_ALGEBRAIC(:,8) = strpad('DAU in component actual_autonomic_stimulation (per_minute)');
LEGEND_STATES(:,2) = strpad('AU1 in component actual_autonomic_stimulation (dimensionless)');
LEGEND_ALGEBRAIC(:,2) = strpad('AUT in component actual_autonomic_stimulation (dimensionless)');
LEGEND_ALGEBRAIC(:,6) = strpad('VVR in component autonomic_drive_on_target_organs_and_tissues (litre)');
LEGEND_ALGEBRAIC(:,9) = strpad('AUH in component autonomic_drive_on_target_organs_and_tissues (dimensionless)');
LEGEND_ALGEBRAIC(:,10) = strpad('AUR in component autonomic_drive_on_target_organs_and_tissues (dimensionless)');
LEGEND_ALGEBRAIC(:,11) = strpad('AOM in component autonomic_drive_on_target_organs_and_tissues (dimensionless)');
LEGEND_ALGEBRAIC(:,12) = strpad('AUM in component autonomic_drive_on_target_organs_and_tissues (dimensionless)');
LEGEND_ALGEBRAIC(:,13) = strpad('AVE in component autonomic_drive_on_target_organs_and_tissues (dimensionless)');
LEGEND_CONSTANTS(:,23) = strpad('VV9 in component parameter_values (litre)');
LEGEND_CONSTANTS(:,24) = strpad('AUL in component parameter_values (litre)');
LEGEND_CONSTANTS(:,25) = strpad('AUV in component parameter_values (dimensionless)');
LEGEND_CONSTANTS(:,26) = strpad('AUS in component parameter_values (dimensionless)');
LEGEND_CONSTANTS(:,27) = strpad('O2A in component parameter_values (dimensionless)');
LEGEND_CONSTANTS(:,28) = strpad('AUM1 in component parameter_values (dimensionless)');
LEGEND_CONSTANTS(:,29) = strpad('AUM2 in component parameter_values (dimensionless)');
LEGEND_CONSTANTS(:,30) = strpad('AUY in component parameter_values (dimensionless)');
LEGEND_ALGEBRAIC(:,7) = strpad('AUO in component autonomic_drive_on_target_organs_and_tissues (dimensionless)');
LEGEND_CONSTANTS(:,31) = strpad('MDMP in component parameter_values (dimensionless)');
LEGEND_RATES(:,1) = strpad('d/dt AU6 in component arterial_baroreceptor_reflex (dimensionless)');
LEGEND_RATES(:,2) = strpad('d/dt AU1 in component actual_autonomic_stimulation (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) = 103.525;
CONSTANTS(:,2) = 97.0439;
CONSTANTS(:,3) = 2;
CONSTANTS(:,4) = 0.00852183;
CONSTANTS(:,5) = 15.6376;
CONSTANTS(:,6) = 0;
CONSTANTS(:,7) = 0;
CONSTANTS(:,8) = 0.3;
CONSTANTS(:,9) = 0.01;
CONSTANTS(:,10) = 1;
CONSTANTS(:,11) = 0.004;
CONSTANTS(:,12) = 0.16;
CONSTANTS(:,13) = -0.060024;
STATES(:,1) = 1.00132;
CONSTANTS(:,14) = 0.5;
CONSTANTS(:,15) = 0;
CONSTANTS(:,16) = 1;
CONSTANTS(:,17) = 1.0;
CONSTANTS(:,18) = 0.01;
CONSTANTS(:,19) = 0.3;
CONSTANTS(:,20) = 5.0;
CONSTANTS(:,21) = 0.4;
CONSTANTS(:,22) = 1.5;
STATES(:,2) = 1.00007;
CONSTANTS(:,23) = 2.51;
CONSTANTS(:,24) = 1.5;
CONSTANTS(:,25) = 0.55;
CONSTANTS(:,26) = 1;
CONSTANTS(:,27) = 0.1;
CONSTANTS(:,28) = 3;
CONSTANTS(:,29) = 1;
CONSTANTS(:,30) = 0;
CONSTANTS(:,31) = 0;
CONSTANTS(:,32) = piecewise({CONSTANTS(:,6)>1.00000e-07, CONSTANTS(:,6) }, CONSTANTS(:,1) - CONSTANTS(:,7));
CONSTANTS(:,33) = piecewise({CONSTANTS(:,32)<80.0000&CONSTANTS(:,32)>=40.0000, 0.00500000.*(80.0000 - CONSTANTS(:,32)).*CONSTANTS(:,8) , CONSTANTS(:,32)<40.0000, 0.200000.*CONSTANTS(:,8) }, 0.00000);
CONSTANTS(:,34) = piecewise({CONSTANTS(:,32)<160.000&CONSTANTS(:,32)>=80.0000, 0.0166670.*(160.000 - CONSTANTS(:,32)) , CONSTANTS(:,32)<80.0000, 1.33360 }, 0.00000);
CONSTANTS(:,35) = piecewise({CONSTANTS(:,2)<80.0000&CONSTANTS(:,2)>=40.0000, CONSTANTS(:,9).*(80.0000 - CONSTANTS(:,2)) , CONSTANTS(:,2)<40.0000, CONSTANTS(:,9).*40.0000 }, 0.00000);
CONSTANTS(:,36) = (CONSTANTS(:,34) - 1.00000).*CONSTANTS(:,10)+1.00000;
CONSTANTS(:,37) = CONSTANTS(:,36) - CONSTANTS(:,13);
CONSTANTS(:,38) = CONSTANTS(:,33)+CONSTANTS(:,35);
CONSTANTS(:,39) = piecewise({CONSTANTS(:,32)<40.0000, 0.0400000.*(40.0000 - CONSTANTS(:,32)).*CONSTANTS(:,14) }, 0.00000);
CONSTANTS(:,40) = (15.0000./(CONSTANTS(:,3)+CONSTANTS(:,4)+CONSTANTS(:,5)) - 1.00000).*CONSTANTS(:,15)+1.00000;
CONSTANTS(:,41) = power(CONSTANTS(:,16), CONSTANTS(:,17));
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(:,1) = (CONSTANTS(:,37) - STATES(:,1))./CONSTANTS(:,12);
ALGEBRAIC(:,1) = STATES(:,1);
ALGEBRAIC(:,3) = ( CONSTANTS(:,41).*CONSTANTS(:,40).*(CONSTANTS(:,38)+ALGEBRAIC(:,1)+CONSTANTS(:,39)) - 1.00000).*CONSTANTS(:,18)+1.00000;
ALGEBRAIC(:,5) = piecewise({ALGEBRAIC(:,3)<0.00000, 0.00000 }, ALGEBRAIC(:,3));
ALGEBRAIC(:,8) = (ALGEBRAIC(:,5) - STATES(:,2))./CONSTANTS(:,19);
RATES(:,2) = ALGEBRAIC(:,8);
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);
ALGEBRAIC(:,3) = ( CONSTANTS(:,41).*CONSTANTS(:,40).*(CONSTANTS(:,38)+ALGEBRAIC(:,1)+CONSTANTS(:,39)) - 1.00000).*CONSTANTS(:,18)+1.00000;
ALGEBRAIC(:,5) = piecewise({ALGEBRAIC(:,3)<0.00000, 0.00000 }, ALGEBRAIC(:,3));
ALGEBRAIC(:,8) = (ALGEBRAIC(:,5) - STATES(:,2))./CONSTANTS(:,19);
ALGEBRAIC(:,2) = CONSTANTS(:,20) - (CONSTANTS(:,20) - 1.00000)./exp( CONSTANTS(:,22).*(STATES(:,2) - 1.00000));
ALGEBRAIC(:,4) = piecewise({ALGEBRAIC(:,2)<CONSTANTS(:,21), CONSTANTS(:,21) }, ALGEBRAIC(:,2));
ALGEBRAIC(:,6) = (CONSTANTS(:,23) - ALGEBRAIC(:,4).*CONSTANTS(:,24))+CONSTANTS(:,24);
ALGEBRAIC(:,7) = ALGEBRAIC(:,4) - 1.00000;
ALGEBRAIC(:,9) = ALGEBRAIC(:,7).*CONSTANTS(:,25)+1.00000;
ALGEBRAIC(:,10) = ALGEBRAIC(:,7).*CONSTANTS(:,26)+1.00000;
ALGEBRAIC(:,11) = ALGEBRAIC(:,7).*CONSTANTS(:,27)+1.00000;
ALGEBRAIC(:,12) = power( ALGEBRAIC(:,7).*CONSTANTS(:,28)+1.00000, CONSTANTS(:,29));
ALGEBRAIC(:,13) = ALGEBRAIC(:,7).*CONSTANTS(:,30)+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