# 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 =0;
end
% There are a total of 5 entries in each of the rate and state variable arrays.
% There are a total of 10 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_STATES(:,1) = strpad('x in component x (cell)');
LEGEND_CONSTANTS(:,1) = strpad('lamda in component x (cell_per_mm3_day)');
LEGEND_CONSTANTS(:,2) = strpad('d in component x (first_order_rate_constant)');
LEGEND_CONSTANTS(:,3) = strpad('beta in component model_parameters (mm3_per_vir_day)');
LEGEND_STATES(:,2) = strpad('v in component v (vir)');
LEGEND_STATES(:,3) = strpad('y in component y (cell)');
LEGEND_CONSTANTS(:,4) = strpad('a in component y (first_order_rate_constant)');
LEGEND_CONSTANTS(:,5) = strpad('alpha in component model_parameters (mm3_per_vir_day)');
LEGEND_STATES(:,4) = strpad('w in component w (vir)');
LEGEND_STATES(:,5) = strpad('z in component z (cell)');
LEGEND_CONSTANTS(:,6) = strpad('b in component z (first_order_rate_constant)');
LEGEND_CONSTANTS(:,7) = strpad('k in component v (vir_per_cell_day)');
LEGEND_CONSTANTS(:,8) = strpad('u in component v (first_order_rate_constant)');
LEGEND_CONSTANTS(:,9) = strpad('c in component w (vir_per_cell_day)');
LEGEND_CONSTANTS(:,10) = strpad('q in component w (first_order_rate_constant)');
LEGEND_RATES(:,1) = strpad('d/dt x in component x (cell)');
LEGEND_RATES(:,3) = strpad('d/dt y in component y (cell)');
LEGEND_RATES(:,5) = strpad('d/dt z in component z (cell)');
LEGEND_RATES(:,2) = strpad('d/dt v in component v (vir)');
LEGEND_RATES(:,4) = strpad('d/dt w in component w (vir)');
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 = [];
STATES(:,1) = 3;
CONSTANTS(:,1) = 2.0;
CONSTANTS(:,2) = 0.01;
CONSTANTS(:,3) = 0.004;
STATES(:,2) = 149;
STATES(:,3) = 6;
CONSTANTS(:,4) = 0.33;
CONSTANTS(:,5) = 0.004;
STATES(:,4) = 1;
STATES(:,5) = 0;
CONSTANTS(:,6) = 2.0;
CONSTANTS(:,7) = 50.0;
CONSTANTS(:,8) = 2.0;
CONSTANTS(:,9) = 2000.0;
CONSTANTS(:,10) = 2.0;
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) =  1.00000.*CONSTANTS(:,1) - ( CONSTANTS(:,2).*STATES(:,1)+ 1.00000.*CONSTANTS(:,3).*STATES(:,1).*STATES(:,2));
RATES(:,3) =  1.00000.*CONSTANTS(:,3).*STATES(:,1).*STATES(:,2) - ( CONSTANTS(:,4).*STATES(:,3)+ 1.00000.*CONSTANTS(:,5).*STATES(:,4).*STATES(:,3));
RATES(:,5) =  1.00000.*CONSTANTS(:,5).*STATES(:,4).*STATES(:,3) -  CONSTANTS(:,6).*STATES(:,5);
RATES(:,2) =  CONSTANTS(:,7).*STATES(:,3) -  CONSTANTS(:,8).*STATES(:,2);
RATES(:,4) =  CONSTANTS(:,9).*STATES(:,5) -  CONSTANTS(:,10).*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
end

% Pad out or shorten strings to a set length
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 Revilla, Garcia-Ramos, 2003 at changeset fdf8ed9269a0.
Collaboration
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