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growthODEs.m
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growthODEs.m
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% [[file:mutual_ide.org::*Function definition][Function definition:1]]
function dydt = growthODEs(t, y, varargin)
% Function definition:1 ends here
% [[file:mutual_ide.org::*Default parameter values][Default parameter values:1]]
%% Default ODE parameter values
default_nodes = (2^16) + 1;
% intrinsic growth
default_rP = 0.3;
default_rF1 = 0.3;
default_rF2 = 0.3;
% mutualism benefits
default_alphaPF1 = 0.01;
default_alphaPF2 = 0.01;
default_alphaF1P = 0.5;
default_alphaF2P = 0.5;
default_qP = 1.0;
default_qF1 = 1.0;
default_qF2 = 1.0;
% mutualism costs
default_betaP = 0.0;
default_betaF1 = 0.0;
default_betaF2 = 0.0;
default_cP = 1.0;
default_cF1 = 1.0;
default_cF2 = 1.0;
% death rate
default_dP = 0.1;
default_dF1 = 0.1;
default_dF2 = 0.1;
% saturation
default_hPF1 = 0.3;
default_hPF2 = 0.3;
default_hF1P = 0.3;
default_hF2P = 0.3;
default_eP = 0.3;
default_eF1 = 0.3;
default_eF2 = 0.3;
% = 0.0;
default_deltaP = 1.0;
default_deltaF1 = 0.9;
default_deltaF2 = 0.1;
% competition: tau12 is the effect F2 has on F1; tau21 is effect of F1 on F2
default_tau12 = 0.0;
default_tau21 = 0.0;
% Default parameter values:1 ends here
% [[file:mutual_ide.org::*Adding parameters with =inputParser=][Adding parameters with =inputParser=:1]]
p = inputParser;
p.KeepUnmatched = true;
addRequired(p, 't');
addRequired(p, 'y');
%% Optional ODE parameters
addParameter(p, 'nodes', default_nodes);
% intrinsic growth rates
addParameter(p, 'rP', default_rP);
addParameter(p, 'rF1', default_rF1);
addParameter(p, 'rF2', default_rF2);
% mutualism benefits
addParameter(p, 'alphaPF1', default_alphaPF1);
addParameter(p, 'alphaPF2', default_alphaPF2);
addParameter(p, 'alphaF1P', default_alphaF1P);
addParameter(p, 'alphaF2P', default_alphaF2P);
addParameter(p, 'qP', default_qP );
addParameter(p, 'qF1', default_qF1);
addParameter(p, 'qF2', default_qF2);
% mutualism costs
addParameter(p, 'betaP', default_betaP);
addParameter(p, 'betaF1', default_betaF1);
addParameter(p, 'betaF2', default_betaF2);
addParameter(p, 'cP', default_cP);
addParameter(p, 'cF1', default_cF1);
addParameter(p, 'cF2', default_cF2);
% death rate
addParameter(p, 'dP', default_dP);
addParameter(p, 'dF1', default_dF1);
addParameter(p, 'dF2', default_dF2);
% saturation
addParameter(p, 'hPF1', default_hPF1);
addParameter(p, 'hPF2', default_hPF2);
addParameter(p, 'hF1P', default_hF1P);
addParameter(p, 'hF2P', default_hF2P);
addParameter(p, 'eP', default_eP);
addParameter(p, 'eF1', default_eF1);
addParameter(p, 'eF2', default_eF2);
% mutualism dependence
addParameter(p, 'deltaP', default_deltaP);
addParameter(p, 'deltaF1', default_deltaF1);
addParameter(p, 'deltaF2', default_deltaF2);
% competition
addParameter(p, 'tau12', default_tau12);
addParameter(p, 'tau21', default_tau21);
parse(p, t, y, varargin{:});
% relabel variables so they're easier to read in the equation
t = p.Results.t;
y = p.Results.y;
nodes = p.Results.nodes;
% intrinsic growth
rP = p.Results.rP;
rF1 = p.Results.rF1;
rF2 = p.Results.rF2;
% mutualism benefits
alphaPF1 = p.Results.alphaPF1;
alphaPF2 = p.Results.alphaPF2;
alphaF1P = p.Results.alphaF1P;
alphaF2P = p.Results.alphaF2P;
cP = p.Results.cP;
cF1 = p.Results.cF1;
cF2 = p.Results.cF2;
% death rate
dP = p.Results.dP;
dF1 = p.Results.dF1;
dF2 = p.Results.dF2;
% saturation
hPF1 = p.Results.hPF1;
hPF2 = p.Results.hPF2;
hF1P = p.Results.hF1P;
hF2P = p.Results.hF2P;
% mutualism dependence
deltaF1 = p.Results.deltaF1;
deltaF2 = p.Results.deltaF2;
% competition: tau12 is the effect F2 has on F1; tau21 is effect of F1 on F2
tau12 = p.Results.tau12;
tau21 = p.Results.tau21;
y = reshape(y,3,nodes);
dydt = zeros(size(y));
% Adding parameters with =inputParser=:1 ends here
% [[file:mutual_ide.org::*Species /P/][Species /P/:2]]
% rename variables so equations are easier to read
P = y(1,:);
F1 = y(2,:);
F2 = y(3,:);
dydt(1,:) = P .* (rP + (cP * (alphaPF1 .* F1 ./ (hPF1 + F1) + alphaPF2 .* F2 ./ (hPF2 + F2))) - dP .* P);
% Species /P/:2 ends here
% [[file:mutual_ide.org::*Species /F/, Phenotype 1][Species /F/, Phenotype 1:2]]
dydt(2,:) = F1 .* ((1 - deltaF1) * rF1 + deltaF1 * (cF1 * (alphaF1P .* P) ./ (hF1P + P)) - (tau12 .* F2) - dF1 .* F1);
% Species /F/, Phenotype 1:2 ends here
% [[file:mutual_ide.org::*Species /F/, Phenotype 2][Species /F/, Phenotype 2:2]]
dydt(3,:) = F2 .* ((1 - deltaF2) * rF2 + deltaF2 * (cF2 * (alphaF2P .* P) ./ (hF2P + P)) - (tau21 .* F1) - dF2 .* F2);
% Species /F/, Phenotype 2:2 ends here
% [[file:mutual_ide.org::*Reshape][Reshape:1]]
dydt = reshape(dydt,3*nodes,1);
end
% Reshape:1 ends here