abx-inoculum-effects/SingleSp_PtoODEfcn2.m at main · GaTechBrownLab/abx-inoculum-effects · GitHub

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function xsol = SingleSp_PtoODEfcn2(p,time,dt,abx,x0,fcnname)
% p = set of parameters (open)
% time = time points
% x0 = initial value
% abx = abx values
% fcnname = functional form to use (string = 'logistic', 'logpoly','poly2', 'poly3')

% Cooperation
if strcmp(fcnname,'logextralosscoopabx')
    % p = [r,k,l,A,h,A50,b]
    dx = @(x) p(1).*x.*(1 - x./p(2)) + p(7).*x.^2 - (p(3).*(p(4).^p(5))./(p(6).^p(5) + p(4).^p(5))).*x;

% Cooperation, A = indep var
elseif strcmp(fcnname,'logextralosscoopabxindep')
    % p = [r,k,l,h,A50,b]
    dx = @(x,a) p(1).*x.*(1 - x./p(2)) + p(6).*x.^2 - (p(3).*(a.^p(4))./(p(5).^p(4) + a.^p(4))).*x;
    %dx = @(x,a) p(1).*x.*(1 + p(6).*x - x./p(2)) - (p(3).*(a.^p(4))./(p(5).^p(4) + a.^p(4))).*x;

% Logistic saturating loss
elseif strcmp(fcnname,'logextralossabx')
    % p = [r,k,l,A,h,A50]
    dx = @(x) p(1).*x.*(1 - x./p(2)) - (p(3).*(p(4).^p(5))./(p(6).^p(5) + p(4).^p(5))).*x;

% Logistic saturating loss, A = indep var
elseif strcmp(fcnname,'logextralossabxindep')
    % p = [r,k,l,h,A50]
    dx = @(x,a) p(1).*x.*(1 - x./p(2)) - (p(3).*(a.^p(4))./(p(5).^p(4) + a.^p(4))).*x;

% Logistic linear loss, A = indep var
elseif strcmp(fcnname,'logextralosslinabxindep')
    % p = [r,k,l,MIC]
    dx = @(x,a) p(1).*x.*(1 - x./p(2)) - (p(3).*(a./p(4))).*x;

% Effective antibiotic
elseif strcmp(fcnname,'logextralossAeff')
    % p = [r,k,l,A,h,A50]
    dx = @(x) p(1).*x.*(1 - x./p(2)) - (p(3).*((p(4)./x).^p(5))./(p(6).^p(5) + (p(4)./x).^p(5))).*x;

% Effective antibiotic, A = indep var
elseif strcmp(fcnname,'logextralossAeffindep')
    % p = [r,k,l,h,A50]
    dx = @(x,a) p(1).*x.*(1 - x./p(2)) - (p(3).*((a./x).^p(4))./(p(5).^p(4) + (a./x).^p(4))).*x;

% Strong Allee (original, in thesis)
elseif strcmp(fcnname,'logextralossalleeabx')
    % p = [r,k,l,A,h,A50,a]
    dx = @(x) (p(1).*x.*(1 - x./p(2)) - (p(3).*((p(4)./x).^p(5))./(p(6).^p(5) + (p(4)./x).^p(5))).*x).*(x - p(7))./p(2);    %applied to abx term (outside)
    %dx = @(x) (p(1).*x.*(1 - x./p(2)).*(x - p(7))./p(2) - (p(3).*((p(4)./x).^p(5))./(p(6).^p(5) + (p(4)./x).^p(5))).*x);    %just applied to growth (inside)

% Strong Allee (original, in thesis), A = indep var
elseif strcmp(fcnname,'logextralossalleeabxindep')
    % p = [r,k,l,h,A50,a]
    dx = @(x,a) (p(1).*x.*(1 - x./p(2)) - (p(3).*(a.^p(4))./(p(5).^p(4) + a.^p(4))).*x).*(x - p(6))./p(2);   %f(N) modifies abx loss term
    %dx = @(x,a) (p(1).*x.*(1 - x./p(2))).*(x - p(6))./p(2) - (p(3).*(a.^p(4))./(p(5).^p(4) + a.^p(4))).*x;  %f(N) doesn't modify abx loss term

% Weak Allee with abx or density threshold, A = indep var
elseif strcmp(fcnname,'logextralossWalleeabxindep')
    % p = [r,k,l,h,A50,a,Athresh or Nthresh]

    % This works but below is better
    %dx = @(x,a) (p(1).*x.*(1 - x./p(2))).*((x>p(7)).*(((x-p(7))./p(6))+1) + (x<=p(7))) - (p(3).*(a.^p(4))./(p(5).^p(4) + a.^p(4))).*x;

    % THE MODEL
    dx = @(x,a) (p(1).*x.*(1 - x./p(2))).*((a>p(7)).*((x./p(6))+1) + (a<=p(7))) - (p(3).*(a.^p(4))./(p(5).^p(4) + a.^p(4))).*x;

% Expanded logistic, A = indep var
elseif strcmp(fcnname,'logextralossdelayabxindep')
    % p = [r,k,l,h,A50,a,b]
    %dx = @(x,a) (p(1).*x.^p(6)).*(1-x./p(2)).^p(7) - (p(3).*(a.^p(4))./(p(5).^p(4) + a.^p(4))).*x;
    dx = @(x,a) (p(1).*x.^p(6)).*(1-x./p(2)) - (p(3).*(a.^p(4))./(p(5).^p(4) + a.^p(4))).*x;

% Expanded logistic with density threshold, A = indep var
elseif strcmp(fcnname,'logextralossdelayabxindep2')
    % p = [r,k,l,h,A50,a,b]
    dx = @(x,a) (p(1).*x.^((x>p(7))*p(6) + (x<=p(7)))).*(1-x./p(2)) - (p(3).*(a.^p(4))./(p(5).^p(4) + a.^p(4))).*x;

end

[t,a,x] = odesolver2(dt,time,abx,x0,dx);
xsol = x';

end