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 =9;
end
% There are a total of 8 entries in each of the rate and state variable arrays.
% There are a total of 20 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_CONSTANTS(:,1) = strpad('mu_T in component uninfected_CD4 (per_day)');
LEGEND_CONSTANTS(:,2) = strpad('r in component uninfected_CD4 (per_day)');
LEGEND_STATES(:,1) = strpad('T_1 in component latently_infected_CD4 (per_micro_L)');
LEGEND_CONSTANTS(:,3) = strpad('T_max in component uninfected_CD4 (per_micro_L)');
LEGEND_CONSTANTS(:,4) = strpad('k_1 in component HIV1 (micro_L_per_day)');
LEGEND_STATES(:,2) = strpad('V in component HIV1 (per_micro_L)');
LEGEND_CONSTANTS(:,5) = strpad('k_1_ in component hybrid_HIV1 (micro_L_per_day)');
LEGEND_STATES(:,3) = strpad('V_ in component hybrid_HIV1 (per_micro_L)');
LEGEND_CONSTANTS(:,6) = strpad('s_0 in component uninfected_CD4 (per_micro_L_day)');
LEGEND_CONSTANTS(:,7) = strpad('theta in component uninfected_CD4 (per_micro_L)');
LEGEND_ALGEBRAIC(:,1) = strpad('s_V in component uninfected_CD4 (per_micro_L_day)');
LEGEND_STATES(:,4) = strpad('T in component uninfected_CD4 (per_micro_L)');
LEGEND_CONSTANTS(:,8) = strpad('k_2 in component latently_infected_CD4 (per_day)');
LEGEND_CONSTANTS(:,9) = strpad('k_1D in component actively_infected_CD4 (micro_L_per_day)');
LEGEND_ALGEBRAIC(:,2) = strpad('D in component DIV (per_micro_L)');
LEGEND_CONSTANTS(:,10) = strpad('mu_b in component actively_infected_CD4 (per_day)');
LEGEND_STATES(:,5) = strpad('T_2 in component actively_infected_CD4 (per_micro_L)');
LEGEND_CONSTANTS(:,11) = strpad('k_s in component actively_coinfected_CD4 (per_day)');
LEGEND_CONSTANTS(:,12) = strpad('mu_bD in component actively_coinfected_CD4 (per_day)');
LEGEND_STATES(:,6) = strpad('T_D2 in component actively_coinfected_CD4 (per_micro_L)');
LEGEND_CONSTANTS(:,13) = strpad('mu_TD in component stably_coinfected_CD4 (per_day)');
LEGEND_STATES(:,7) = strpad('T_D1 in component stably_coinfected_CD4 (per_micro_L)');
LEGEND_ALGEBRAIC(:,5) = strpad('N_D_t in component DIV (dimensionless)');
LEGEND_ALGEBRAIC(:,8) = strpad('pi_D_t in component DIV (per_day)');
LEGEND_CONSTANTS(:,14) = strpad('mu_D in component DIV (per_day)');
LEGEND_ALGEBRAIC(:,3) = strpad('N_t in component production_function (dimensionless)');
LEGEND_CONSTANTS(:,15) = strpad('t_DIV in component DIV (day)');
LEGEND_STATES(:,8) = strpad('D_ode in component DIV (per_micro_L)');
LEGEND_CONSTANTS(:,16) = strpad('D_0 in component DIV (per_micro_L)');
LEGEND_ALGEBRAIC(:,6) = strpad('N_2_t in component HIV1 (dimensionless)');
LEGEND_CONSTANTS(:,17) = strpad('mu_V in component HIV1 (per_day)');
LEGEND_ALGEBRAIC(:,7) = strpad('N_t_ in component hybrid_HIV1 (dimensionless)');
LEGEND_ALGEBRAIC(:,9) = strpad('pi_t_ in component hybrid_HIV1 (per_day)');
LEGEND_CONSTANTS(:,18) = strpad('N_0 in component production_function (dimensionless)');
LEGEND_CONSTANTS(:,19) = strpad('gamma in component production_function (dimensionless)');
LEGEND_CONSTANTS(:,20) = strpad('t_c in component production_function (day)');
LEGEND_ALGEBRAIC(:,4) = strpad('T_tot in component cell_population (per_micro_L)');
LEGEND_RATES(:,4) = strpad('d/dt T in component uninfected_CD4 (per_micro_L)');
LEGEND_RATES(:,1) = strpad('d/dt T_1 in component latently_infected_CD4 (per_micro_L)');
LEGEND_RATES(:,5) = strpad('d/dt T_2 in component actively_infected_CD4 (per_micro_L)');
LEGEND_RATES(:,6) = strpad('d/dt T_D2 in component actively_coinfected_CD4 (per_micro_L)');
LEGEND_RATES(:,7) = strpad('d/dt T_D1 in component stably_coinfected_CD4 (per_micro_L)');
LEGEND_RATES(:,8) = strpad('d/dt D_ode in component DIV (per_micro_L)');
LEGEND_RATES(:,2) = strpad('d/dt V in component HIV1 (per_micro_L)');
LEGEND_RATES(:,3) = strpad('d/dt V_ in component hybrid_HIV1 (per_micro_L)');
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) = 0.02;
CONSTANTS(:,2) = 0.03;
STATES(:,1) = 0;
CONSTANTS(:,3) = 1500;
CONSTANTS(:,4) = 2.4E-5;
STATES(:,2) = 1E-3;
CONSTANTS(:,5) = 2.4E-7;
STATES(:,3) = 0;
CONSTANTS(:,6) = 10;
CONSTANTS(:,7) = 1;
STATES(:,4) = 1000;
CONSTANTS(:,8) = 0.017;
CONSTANTS(:,9) = 2.4E-5;
CONSTANTS(:,10) = 0.24;
STATES(:,5) = 0;
CONSTANTS(:,11) = 0.48;
CONSTANTS(:,12) = 0.12;
STATES(:,6) = 0;
CONSTANTS(:,13) = 0.02;
STATES(:,7) = 0;
CONSTANTS(:,14) = 0.76;
CONSTANTS(:,15) = 2557;
STATES(:,8) = 0;
CONSTANTS(:,16) = 0.1;
CONSTANTS(:,17) = 2.4;
CONSTANTS(:,18) = 300;
CONSTANTS(:,19) = 25;
CONSTANTS(:,20) = 7305;
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(:,4).*STATES(:,2).*STATES(:,4)+ CONSTANTS(:,5).*STATES(:,3).*STATES(:,4)) - CONSTANTS(:,1).*STATES(:,1)) - CONSTANTS(:,8).*STATES(:,1);
RATES(:,7) = CONSTANTS(:,11).*STATES(:,6) - CONSTANTS(:,13).*STATES(:,7);
ALGEBRAIC(:,1) = ( CONSTANTS(:,6).*CONSTANTS(:,7))./(CONSTANTS(:,7)+STATES(:,2));
RATES(:,4) = (((ALGEBRAIC(:,1) - CONSTANTS(:,1).*STATES(:,4))+ CONSTANTS(:,2).*STATES(:,4).*(1.00000 - (STATES(:,4)+STATES(:,1))./CONSTANTS(:,3))) - CONSTANTS(:,4).*STATES(:,2).*STATES(:,4)) - CONSTANTS(:,5).*STATES(:,3).*STATES(:,4);
ALGEBRAIC(:,2) = piecewise({VOI<CONSTANTS(:,15), 0.00000 }, STATES(:,8));
RATES(:,5) = ( CONSTANTS(:,8).*STATES(:,1) - CONSTANTS(:,9).*ALGEBRAIC(:,2).*STATES(:,5)) - CONSTANTS(:,10).*STATES(:,5);
RATES(:,6) = ( CONSTANTS(:,9).*ALGEBRAIC(:,2).*STATES(:,5) - CONSTANTS(:,11).*STATES(:,6)) - CONSTANTS(:,12).*STATES(:,6);
ALGEBRAIC(:,3) = CONSTANTS(:,18).*(1.00000+ CONSTANTS(:,19).*(power(VOI, 2.00000)./(power(VOI, 2.00000)+power(CONSTANTS(:,20), 2.00000))));
ALGEBRAIC(:,6) = 0.100000.*ALGEBRAIC(:,3);
RATES(:,2) = (( ALGEBRAIC(:,3).*CONSTANTS(:,10).*STATES(:,5)+ ALGEBRAIC(:,6).*CONSTANTS(:,12).*STATES(:,6)) - CONSTANTS(:,4).*STATES(:,2).*STATES(:,4)) - CONSTANTS(:,17).*STATES(:,2);
ALGEBRAIC(:,5) = 0.200000.*ALGEBRAIC(:,3);
ALGEBRAIC(:,8) = 0.500000.*CONSTANTS(:,10).*ALGEBRAIC(:,3);
RATES(:,8) = piecewise({VOI<CONSTANTS(:,15), CONSTANTS(:,16)./CONSTANTS(:,15) }, ( ALGEBRAIC(:,5).*CONSTANTS(:,12).*STATES(:,6)+ ALGEBRAIC(:,8).*STATES(:,7)) - CONSTANTS(:,14).*STATES(:,8));
ALGEBRAIC(:,7) = 0.100000.*ALGEBRAIC(:,3);
ALGEBRAIC(:,9) = 0.0100000.*CONSTANTS(:,10).*ALGEBRAIC(:,3);
RATES(:,3) = (( ALGEBRAIC(:,7).*CONSTANTS(:,12).*STATES(:,6)+ ALGEBRAIC(:,9).*STATES(:,7)) - CONSTANTS(:,17).*STATES(:,3)) - CONSTANTS(:,5).*STATES(:,4).*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(:,6).*CONSTANTS(:,7))./(CONSTANTS(:,7)+STATES(:,2));
ALGEBRAIC(:,2) = piecewise({VOI<CONSTANTS(:,15), 0.00000 }, STATES(:,8));
ALGEBRAIC(:,3) = CONSTANTS(:,18).*(1.00000+ CONSTANTS(:,19).*(power(VOI, 2.00000)./(power(VOI, 2.00000)+power(CONSTANTS(:,20), 2.00000))));
ALGEBRAIC(:,6) = 0.100000.*ALGEBRAIC(:,3);
ALGEBRAIC(:,5) = 0.200000.*ALGEBRAIC(:,3);
ALGEBRAIC(:,8) = 0.500000.*CONSTANTS(:,10).*ALGEBRAIC(:,3);
ALGEBRAIC(:,7) = 0.100000.*ALGEBRAIC(:,3);
ALGEBRAIC(:,9) = 0.0100000.*CONSTANTS(:,10).*ALGEBRAIC(:,3);
ALGEBRAIC(:,4) = STATES(:,4)+STATES(:,1)+STATES(:,5)+STATES(:,6)+STATES(:,7);
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