Exposure 672 - ExposureFile guyton_antidiuretic_hormone_2008.cellml
This is cellml_codegen, at path matlab
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 =4;
end
% There are a total of 1 entries in each of the rate and state variable arrays.
% There are a total of 17 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('CNA in component antidiuretic_hormone (monovalent_mEq_per_litre)');
LEGEND_CONSTANTS(:,2) = strpad('PA1 in component antidiuretic_hormone (mmHg)');
LEGEND_CONSTANTS(:,13) = strpad('ADHNA in component osmotic_control_of_ADH_secretion (dimensionless)');
LEGEND_CONSTANTS(:,3) = strpad('CNR in component parameter_values (monovalent_mEq_per_litre)');
LEGEND_CONSTANTS(:,12) = strpad('ADHNA1 in component osmotic_control_of_ADH_secretion (dimensionless)');
LEGEND_CONSTANTS(:,15) = strpad('ADHPR in component pressure_control_of_ADH_secretion (dimensionless)');
LEGEND_CONSTANTS(:,4) = strpad('ADHPUL in component parameter_values (mmHg)');
LEGEND_CONSTANTS(:,5) = strpad('ADHPAM in component parameter_values (per_mmHg2)');
LEGEND_CONSTANTS(:,14) = strpad('ADHPA in component pressure_control_of_ADH_secretion (mmHg)');
LEGEND_CONSTANTS(:,17) = strpad('ADH in component total_ADH_secretion (dimensionless)');
LEGEND_CONSTANTS(:,6) = strpad('ADHINF in component parameter_values (dimensionless)');
LEGEND_CONSTANTS(:,16) = strpad('ADH1 in component total_ADH_secretion (dimensionless)');
LEGEND_STATES(:,1) = strpad('ADHC in component ADH_in_blood (dimensionless)');
LEGEND_CONSTANTS(:,7) = strpad('ADHTC in component parameter_values (minute)');
LEGEND_ALGEBRAIC(:,3) = strpad('ADHMV in component ADH_effect_on_nonrenal_vascular_resistance (dimensionless)');
LEGEND_CONSTANTS(:,8) = strpad('ADHVUL in component parameter_values (dimensionless)');
LEGEND_CONSTANTS(:,9) = strpad('ADHVLL in component parameter_values (dimensionless)');
LEGEND_ALGEBRAIC(:,1) = strpad('ADHMV1 in component ADH_effect_on_nonrenal_vascular_resistance (dimensionless)');
LEGEND_ALGEBRAIC(:,4) = strpad('ADHMK in component ADH_effect_on_kidney (dimensionless)');
LEGEND_CONSTANTS(:,10) = strpad('ADHKLL in component parameter_values (dimensionless)');
LEGEND_CONSTANTS(:,11) = strpad('ADHKUL in component parameter_values (dimensionless)');
LEGEND_ALGEBRAIC(:,2) = strpad('ADHMK1 in component ADH_effect_on_kidney (dimensionless)');
LEGEND_RATES(:,1) = strpad('d/dt ADHC in component ADH_in_blood (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) = 142.035;
CONSTANTS(:,2) = 103.525;
CONSTANTS(:,3) = 139;
CONSTANTS(:,4) = 85;
CONSTANTS(:,5) = 0.3;
CONSTANTS(:,6) = 0;
STATES(:,1) = 1.0;
CONSTANTS(:,7) = 15;
CONSTANTS(:,8) = 2.5;
CONSTANTS(:,9) = 0.93617;
CONSTANTS(:,10) = 0.2;
CONSTANTS(:,11) = 5;
CONSTANTS(:,12) = (CONSTANTS(:,1) - CONSTANTS(:,3))./(142.000 - CONSTANTS(:,3));
CONSTANTS(:,13) = piecewise({CONSTANTS(:,12)<0.00000, 0.00000 }, CONSTANTS(:,12));
CONSTANTS(:,14) = piecewise({CONSTANTS(:,2)>CONSTANTS(:,4), CONSTANTS(:,4) }, CONSTANTS(:,2));
CONSTANTS(:,15) = power(CONSTANTS(:,4) - CONSTANTS(:,14), 2.00000).*CONSTANTS(:,5);
CONSTANTS(:,16) = CONSTANTS(:,13)+CONSTANTS(:,15)+CONSTANTS(:,6);
CONSTANTS(:,17) = piecewise({CONSTANTS(:,16)<0.00000, 0.00000 }, CONSTANTS(:,16));
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(:,17) - STATES(:,1))./CONSTANTS(:,7);
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(:,8) - (CONSTANTS(:,8) - 1.00000)./( ((CONSTANTS(:,9) - 1.00000)./(CONSTANTS(:,9) - CONSTANTS(:,8))).*(STATES(:,1) - 1.00000)+1.00000);
ALGEBRAIC(:,2) = CONSTANTS(:,11) - (CONSTANTS(:,11) - 1.00000)./( ((CONSTANTS(:,10) - 1.00000)./(CONSTANTS(:,10) - CONSTANTS(:,11))).*(STATES(:,1) - 1.00000)+1.00000);
ALGEBRAIC(:,3) = piecewise({ALGEBRAIC(:,1)<CONSTANTS(:,9), CONSTANTS(:,9) }, ALGEBRAIC(:,1));
ALGEBRAIC(:,4) = piecewise({ALGEBRAIC(:,2)<CONSTANTS(:,10), CONSTANTS(:,10) }, ALGEBRAIC(:,2));
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