# 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 7 entries in each of the rate and state variable arrays.
% There are a total of 13 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(:,10) = strpad('T in component T (per_ml)');
LEGEND_CONSTANTS(:,1) = strpad('k in component kinetic_parameters (ml_per_day)');
LEGEND_CONSTANTS(:,2) = strpad('p in component kinetic_parameters (first_order_rate_constant)');
LEGEND_CONSTANTS(:,3) = strpad('c in component kinetic_parameters (first_order_rate_constant)');
LEGEND_CONSTANTS(:,4) = strpad('delta in component kinetic_parameters (first_order_rate_constant)');
LEGEND_STATES(:,1) = strpad('I in component I (per_ml)');
LEGEND_CONSTANTS(:,11) = strpad('I_0 in component I (per_ml)');
LEGEND_CONSTANTS(:,12) = strpad('k_ in component kinetic_parameters (ml_per_day)');
LEGEND_STATES(:,2) = strpad('E4 in component E4 (per_ml)');
LEGEND_CONSTANTS(:,5) = strpad('VI_0 in component VI (per_ml)');
LEGEND_STATES(:,3) = strpad('VI in component VI (per_ml)');
LEGEND_ALGEBRAIC(:,1) = strpad('h in component Heavyside_function (dimensionless)');
LEGEND_STATES(:,4) = strpad('VNI in component VNI (per_ml)');
LEGEND_ALGEBRAIC(:,2) = strpad('V in component virus_total (per_ml)');
LEGEND_STATES(:,5) = strpad('E1 in component E1 (per_ml)');
LEGEND_CONSTANTS(:,13) = strpad('b_ in component kinetic_parameters (day)');
LEGEND_STATES(:,6) = strpad('E2 in component E2 (per_ml)');
LEGEND_STATES(:,7) = strpad('E3 in component E3 (per_ml)');
LEGEND_CONSTANTS(:,6) = strpad('tau_p in component Heavyside_function (day)');
LEGEND_CONSTANTS(:,7) = strpad('b in component kinetic_parameters (day)');
LEGEND_CONSTANTS(:,8) = strpad('m in component kinetic_parameters (first_order_rate_constant)');
LEGEND_CONSTANTS(:,9) = strpad('n in component kinetic_parameters (dimensionless)');
LEGEND_RATES(:,1) = strpad('d/dt I in component I (per_ml)');
LEGEND_RATES(:,3) = strpad('d/dt VI in component VI (per_ml)');
LEGEND_RATES(:,4) = strpad('d/dt VNI in component VNI (per_ml)');
LEGEND_RATES(:,5) = strpad('d/dt E1 in component E1 (per_ml)');
LEGEND_RATES(:,6) = strpad('d/dt E2 in component E2 (per_ml)');
LEGEND_RATES(:,7) = strpad('d/dt E3 in component E3 (per_ml)');
LEGEND_RATES(:,2) = strpad('d/dt E4 in component E4 (per_ml)');
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) = 2.4e-5;
CONSTANTS(:,2) = 774;
CONSTANTS(:,3) = 3;
CONSTANTS(:,4) = 0.5;
STATES(:,1) = 0.1;
STATES(:,2) = 0;
CONSTANTS(:,5) = 200000;
STATES(:,3) = 200000;
STATES(:,4) = 0;
STATES(:,5) = 0;
STATES(:,6) = 0;
STATES(:,7) = 0;
CONSTANTS(:,6) = 0;
CONSTANTS(:,7) = 0.25;
CONSTANTS(:,8) = 0.01;
CONSTANTS(:,9) = 4;
CONSTANTS(:,10) = ( CONSTANTS(:,3).*CONSTANTS(:,4))./( CONSTANTS(:,1).*CONSTANTS(:,2));
CONSTANTS(:,11) =  (CONSTANTS(:,3)./CONSTANTS(:,2)).*CONSTANTS(:,5);
CONSTANTS(:,12) = CONSTANTS(:,1)./power(1.00000+ CONSTANTS(:,8).*CONSTANTS(:,7), CONSTANTS(:,9));
CONSTANTS(:,13) = CONSTANTS(:,7)./(1.00000+ CONSTANTS(:,8).*CONSTANTS(:,7));
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(:,12).*CONSTANTS(:,10).*STATES(:,2) -  CONSTANTS(:,4).*STATES(:,1);
RATES(:,5) = (STATES(:,3) - STATES(:,5))./CONSTANTS(:,13);
RATES(:,6) = (STATES(:,5) - STATES(:,6))./CONSTANTS(:,13);
RATES(:,7) = (STATES(:,6) - STATES(:,7))./CONSTANTS(:,13);
RATES(:,2) = (STATES(:,7) - STATES(:,2))./CONSTANTS(:,13);
ALGEBRAIC(:,1) = piecewise({VOI<CONSTANTS(:,6), 0.00000 }, 1.00000);
RATES(:,3) =  (1.00000 - ALGEBRAIC(:,1)).*CONSTANTS(:,2).*STATES(:,1) -  CONSTANTS(:,3).*STATES(:,3);
RATES(:,4) =  ALGEBRAIC(:,1).*CONSTANTS(:,2).*STATES(:,1) -  CONSTANTS(:,3).*STATES(:,4);
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) = piecewise({VOI<CONSTANTS(:,6), 0.00000 }, 1.00000);
ALGEBRAIC(:,2) = STATES(:,3)+STATES(:,4);
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

```
Source
Derived from workspace Mittler, Sulzer, Neumann, Perelson, 1998 at changeset 41a3b72cac7f.
Collaboration
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