function [prdData, info] = predict_Gallus_gallus_IR(par, data, auxData) % unpack par, data, auxData cPar = parscomp_st(par); vars_pull(par); vars_pull(cPar); vars_pull(data); vars_pull(auxData); if E_Hb >= E_Hx || E_Hx >= E_Hp prdData = []; info = 0; return end % compute temperature correction factors TC_ab = tempcorr(temp.ab, T_ref, T_A); TC = tempcorr(temp.am, T_ref, T_A); kT_M = TC * k_M; % zero-variate data % life cycle pars_tR = [g; k; l_T; v_Hb; v_Hx; v_Hp; t_N * kT_M]; % compose parameter vector [t_R, t_p, t_x, t_b, l_R, l_p, l_x, l_b, info] = get_tR(pars_tR, f); % -, scaled times & lengths at f % birth L_b = L_m * l_b; % cm, structural length at birth at f Ww_b = L_b^3 * (1 + f * w); % g, wet weight at birth at f aT_b = t_0 + t_b/ k_M/ TC_ab; % d, age at birth at f and T % fledging tT_x = (t_x - t_b)/ kT_M; % d, time since birth at fledching at f and T % puberty tT_p = (t_p - t_b)/ kT_M; % d, time since birth at fledching at f and T % ultimate l_i = f - l_T; % -, scaled ultimate length L_i = L_m * l_i; % cm, ultimate structural length at f Ww_i = L_i^3 * (1 + f * w); % g, ultimate wet weight % reproduction pars_R = [kap; kap_R; g; k_J; k_M; L_T; v; U_Hb; U_Hp]; % compose parameter vector at T RT_i = TC * reprod_rate(L_i, f, pars_R); % #/d, ultimate reproduction rate at T tT_R = (t_R - t_b)/ kT_M; % d, time since birth at 1st brood at f and T L_R = L_m * l_R; % cm, structural length at 1st brood at f Ww_R = L_R^3 * (1 + f * w); % g, wet weight 1st brood % life span pars_tm = [g; l_T; h_a/ k_M^2; s_G]; % compose parameter vector at T_ref t_m = get_tm_s(pars_tm, f, l_b); % -, scaled mean life span at T_ref aT_m = t_m/ kT_M; % d, mean life span at T % males p_Am_m = z_m * p_M/ kap; % J/d.cm^2, {p_Am} spec assimilation flux pT_Am_m = p_Am_m * TC; % J/d.cm^2, {p_Am} spec assimilation flux, temp corrected E_m_m = p_Am_m/ v; % J/cm^3, reserve capacity [E_m] g_m = E_G/ (kap* E_m_m); % -, energy investment ratio m_Em_m = y_E_V * E_m_m/ E_G; % mol/mol, reserve capacity w_m = m_Em_m * w_E/ w_V; % -, contribution of reserve to weight L_mm = v/ k_M/ g_m; % cm, max struct length L_im = (f - l_T) * L_mm; % cm, ultimate structural length Ww_im = L_im^3 * (1 + f * w_m); % g, ultimate wet weight pars_tRm = [g_m; k; l_T; v_Hb; v_Hx; v_Hpm; t_N * kT_M]; % compose parameter vector [t_Rm, t_pm, t_xm, t_bm, l_Rm, l_pm, l_xm, l_bm, info] = get_tR(pars_tRm, f); % -, scaled times & lengths at f Ww_Rm = (l_Rm * L_mm)^3 * (1 + f * w_m); % g, wet weight at 1st brood tT_Rm = (t_Rm - t_bm)/ kT_M; % d, time since birth at 1st brood % pack to output prdData.ab = aT_b; prdData.tx = tT_x; prdData.tp = tT_p; prdData.tR = tT_R; prdData.tRm = tT_Rm; prdData.am = aT_m; prdData.Wwb = Ww_b; prdData.WwR = Ww_R; prdData.WwRm = Ww_Rm; prdData.Wwi = Ww_i; prdData.Wwim = Ww_im; prdData.Ri = RT_i; % uni-variate data % time-weight at varying f vT = v * TC; pT_Am = p_Am * TC; pT_M = p_M * TC; kT_J = k_J * TC; %females tJ_X = feed.tW_f; tJ_X(:,2) = tJ_X(:,2)/ w_X; [a eL] = ode45(@dget_eL, tW_f(:,1), [1; L_b], [], vT, g, L_T, L_m, pT_Am, tJ_X, 0, kap_Xf, mu_Xf); pT_C = E_m * eL(:,1) .* eL(:,2).^3 .* (E_G * vT ./ eL(:,2) + pT_M) ./ (kap * eL(:,1) * E_m + E_G); % contribution of egg production to weight for eggs laid one at a time is half the investment per day EW_R = 0.5 * ((1 - kap) * pT_C - kT_J * E_Hp) * w_E/ mu_E; % 0.5 * weight of eggs per day EWw_f = EW_R + eL(:,2).^3 .* (1 + eL(:,1) * w); % g, wet weight % tR_f and tW0_f have the same time points n = size(tR,1); EW_R = zeros(n,1); EWw_0 = EW_R; pars_UE0 = [V_Hb; g; k_J; k_M; v]; t = [-1e-10; tR(:,1)]; [a eL] = ode45(@dget_eL, t, [1; L_b], [], vT, g, L_T, L_m, pT_Am, tJ_X, 0, kap_Xf, mu_Xf); eL(1,:) = []; for i = 1:n EWw_0(i) = w_E * J_E_Am * initial_scaled_reserve(eL(i,1), pars_UE0)/ d_E; % g, egg wet weight EW_R(i) = EWw_0(i) * TC * reprod_rate(eL(i,2), eL(i,1), pars_R); % #/d, ultimate reproduction rate at T end % tJ_X = feed.tW2_f; tJ_X(:,2) = tJ_X(:,2)/ w_X; % d,mol/d: time, food intake [a eL] = ode45(@dget_eL, tW2_f(:,1), [1; L_b], [], vT, g, L_T, L_m, pT_Am, tJ_X, 1, kap_X, mu_X); pT_C = E_m * eL(:,1) .* eL(:,2).^3 .* (E_G * vT ./ eL(:,2) + pT_M) ./ (kap * eL(:,1) * E_m + E_G); % contribution of egg production to weight for eggs laid one at a time is half the investment per day W_R = 0.5 * ((1 - kap) * pT_C - kT_J * E_Hp) * w_E/ mu_E; % 0.5 * weight of eggs per day EWw_f2 = W_R + eL(:,2).^3 .* (1 + eL(:,1) * w); % g, wet weight % males tJ_X = feed.tW_m; tJ_X(:,2) = tJ_X(:,2)/ w_X; [a eL] = ode45(@dget_eL, tW_m(:,1), [1; L_b], [], vT, g_m, L_T, L_mm, pT_Am_m, tJ_X, 0, kap_Xf, mu_Xf); EWw_m = eL(:,2).^3 .* (1 + eL(:,1) * w); % g, wet weight % tJ_X = feed.tW2_m; tJ_X(:,2) = tJ_X(:,2)/ w_X; % d,mol/d: time, food intake [a eL] = ode45(@dget_eL, tW2_m(:,1), [1; L_b], [], vT, g_m, L_T, L_mm, pT_Am_m, tJ_X, 1, kap_X, mu_X); EWw_m2 = eL(:,2).^3 .* (1 + eL(:,1) * w); % g, wet weight % pack to output prdData.tW_f = EWw_f; prdData.tW_m = EWw_m; prdData.tW2_f = EWw_f2; prdData.tW2_m = EWw_m2; prdData.tW0 = EWw_0; prdData.tR = EW_R; end %% subfunctions function deL = dget_eL(t, eL, v, g, L_T, L_m, p_Am, tJ_X, i, kap_X, mu_X) e = eL(1); % -, scaled reserve density L = eL(2); % structural length if i == 0 && t < 7 f = 1; else p_A = kap_X * mu_X * spline1(t, tJ_X); % J/d, intake rate f = p_A/ (p_Am * L^2); % -, scaled functional response end de = (f - e) * v/ L; r = v * (e/ L - (1 + L_T/ L)/ L_m)/ (e + g); dL = L * r/ 3; % de/dt and dL/dt deL = [de; dL]; end