Contents
parameters for 'animal'
created 2000/11/02 by Bas Kooijman, modified 2009/09/29 not all parameters are required for any particular application warning: length units refer to volumetric lengths multiply by the shape coefficient for physical length suggestion: copy pars_animal first to pars_mydata before changing values then run pars_mydata
mydata = 0; foetus = 0; % for compatibility with pars_my_pet in add_my_pet global T T_ref pars_T TC pT_Am pT_M k global n_O n_M w_O d_O mu_T mu_M mu_O mu_E eta_O M_Vb M_Vp M_Vm M_E0 M_Em m_Em p_ref M_V global f K eb_min ep_min y_E_X y_X_E y_V_E y_E_V y_P_X y_X_P kap kap_R global jT_X_Am jT_E_Am JT_X_Am JT_E_Am jT_E_M jT_E_J global vT g kT_M kT_J E_G R_m hT_a s_G a_m global L_d L_b L_p L_m L_T l_b l_p l_T V_Hb v_Hb v_Hp u_Hb u_Hp U_Hb U_Hp
temperature parameters (in Kelvin)
these pars are not relevant if T = T_1
T = 293; % K, actual body temperature T_ref = 293; % K, temp for which rate pars are given T_A = 8000; % K, Arrhenius temp T_L = 277; % K, lower boundary tolerance range T_H = 318; % K, upper boundary tolerance range T_AL = 20000; % K, Arrhenius temp for lower boundary T_AH =190000; % K, Arrhenius temp for upper boundary pars_T = [T_A T_L T_H T_AL T_AH];
food abundance
values computed in routine statistics depend on this
f = 1.0; % scaled functional response % this is the food intake relative to the max for individuals of that size
chemical indices (relative elemental frequencies)
notice that these values relate to dry mass wet mass has ten times more H and O, relative to C organic compounds columns: food, structure, reserve, faeces X V E P
n_O = [1.00, 1.00, 1.00, 1.00; % C/C, equals 1 by definition 1.80, 1.80, 2.00, 1.80; % H/C 0.50, 0.50, 0.75, 0.50; % O/C 0.20, 0.15, 0.20, 0.15]; % N/C % minerals % rows: elements carbon, hydrogen, oxygen, nitrogen % columns: carbon dioxide (C), water (H), dioxygen (O), ammonia (N) % CO2 H2O O2 NH3 n_M = [1, 0, 0, 0; % C 0, 2, 0, 3; % H 2, 1, 2, 0; % O 0, 0, 0, 1]; % N
parameters that link moles to grams (wet weight), volumes and energy
% given in vector form for food, structure, reserve, feaces % these parameters do not affect the dynamics; just output mapping d_O = [.1; .1; .1; .1]; % g/cm^3, specific densities for organics % dry mass per wet volume mu_X = 525000; % J/mol, chemical potential of food mu_V = 500000; % J/mol, chemical potential of structure mu_E = 550000; % J/mol, chemical potential of reserve mu_P = 480000; % J/mol, chemical potential of faeces mu_O = [mu_X; mu_V; mu_E; mu_P]; %J/mol, chemical potentials of organics mu_M = [0; 0; 0; 0]; % kJ/mol, chemical potentials of minerals % C: CO2, H: H2O, O: O2, N: NH3 % molar volume of gas at 1 bar and 20 C is 24.4 L/mol X_gas = T_ref/ T/ 24.4; % M, mol of gas per litre at 20 C and 1 bar
conversion parameters
z = 1; % zoom factor rel to reference L_m = 1 cm to compare species del_M = .16; % -, shape coefficient to convert vol-length to physical length
primary parameters of the standard DEB model in energy
only p_Am, E_Hb, E_Hp, h_a depend on zoom factor z (interspecifically)
F_m = 6.5; % l/d.cm^2, {F_m} max spec searching rate kap_X = 0.8; % -, digestion efficiency of food to reserve kap_X_P = 0.1; % -, faecation efficiency of food to faeces % kap_X_P does not affect state varables, only mineral and faeces fluxes v = 0.02; % cm/d, energy conductance kap = 0.8; % -, alloaction fraction to soma = growth + somatic maintenance kap_R = 0.95; % -, reproduction efficiency p_M = 18; % J/d.cm^3, [p_M] vol-specific somatic maintenance p_T = 0; % J/d.cm^2, {p_T} surface-specific som maintenance k_J = 0.002; % 1/d, < k_M = p_M/E_G, maturity maint rate coefficient E_G = 2800; % J/cm^3, [E_G], spec cost for structure % life stage parameters: b = birth; i = metamorphosis; p = puberty % E_H is the cumulated energy from reserve invested in maturation E_Hb = 1e-3 * 275 * z^3; % J, E_H^b E_Hj = E_Hb; % J, E_H^j, no metamorphosis E_Hp = 50 * z^3; % J, E_H^p % aging process h_a = z * 1e-6; % 1/d^2, Weibull aging acceleration s_G = 1e-4; % -, Gompertz stress coefficient parscomp % compound parameters statistics % food-dependend quantities report_animal % print result to screen
Parameter values
reference temp, T_ref, K 293
actual temp, T, K 293
temperature correction factor, c_T, - 1
initial reserve mass at growth ceasing at birth, M_E^0, mol 2.619e-06
initial reserve mass at maturation ceasing at birth, M_E^0, mol 2.605e-06
initial reserve mass at maturation ceasing at puberty, M_E^0, mol 2.76e-06
initial reserve mass at f, M_E^0, mol 3.312e-06
initial reserve energy at f, E_0, J 1.822
initial dry weight at f, W_d^0, g 9.539e-05
fraction of reserve left at birth, U_E^b/ U_E^0, - 0.2367
structural length at birth, L_b, cm 0.07264
structural mass at birth, M_V^b, mol 1.604e-06
physical length at birth, L_w^b, cm 0.454
dry weight at birth, W_d^b, g 6.092e-05
birth weight as fraction of max, W_b/ W_m, - 0.0003833
structural length at metamorphosis, L_j, cm 0.07264
structural mass at metamorphosis, M_V^j, mol 1.604e-06
physical length at metamorphosis, L_w^j, cm 0.454
dry weight at metamorphosis, W_d^j, g 6.092e-05
metamorphosis weight as fraction of max, W_j/ W_m, - 0.0003833
structural length at puberty, L_p, cm 0.3774
structural mass at puberty, M_V^p, mol 0.000225
physical length at puberty, L_w^p, cm 2.359
dry weight at puberty, W_d^p, g 0.008545
puberty weight as fraction of max, W_p/ W_m, - 0.05377
maximum structural length, L_m, cm 1
ultimate structural length, L_i, cm 1
ultimate structural mass, M_V^i, mol 0.004184
physical ultimate length, L_w^i, cm 6.25
maximum dry weight, W_d^m, g 0.1589
ultimate dry weight, W_d^i, g 0.1589
fraction of weight that is structure, del_V, - 0.6293
max spec searching rate at T, {F_m}, l/d.cm^2 6.5
clearance rate at birth, CR_b, l/d 0.0343
clearance rate at puberty, CR_p, l/d 0.926
ultimate clearance rate, CR_i, l/d 6.5
half saturation coefficient, K, M 8.242e-06
food dens for maturation ceasing at birth, X_J^b, M 6.384e-07
food dens for growth ceasing at birth, X_G^b, M 1.985e-07
food dens for maturation and growth ceasing at puberty, X_J^p, M 3.223e-06
scaled functional response, f, - 1
func resp for growth ceasing at birth, f_G^b, - 0.07189
func resp for maturation ceasing at birth, f_J^b, - 0.02352
func resp for maturation and growth ceasing at puberty, f_J^p, - 0.2811
max surface-spec feeding rate, {p_Xm}, J/d.cm^2 28.13
max surface-spec feeding rate, {J_XAm}, mol/d.cm^2 5.357e-05
food energy intake at birth, p_Xb, J/d 0.1484
food mass intake at birth, J_XAb, mol/d 2.827e-07
food energy intake at puberty, p_Xp, J/d 4.007
food mass intake at puberty, J_XAp, mol/d 7.632e-06
ultimate food energy intake, p_Xi, J/d 28.13
ultimate food mass intake, J_XAi, mol/d 5.357e-05
max survival time when starved, [E_m]/[p_M], d 62.5
max spec assimilation rate at T, {p_Am}, J/d.cm^2 22.5
max surface-spec assimilation rate, {J_EAm}, mol/d.cm^2 4.091e-05
yield of reserve on food, y_EX, mol/mol 0.7636
yield of faeces on food, y_PX, mol/mol 0.1094
energy conductance at T, v, cm/d 0.02
maximum reserve residence time, t_E, d 50
reserve capacity, [E_m], J/cm^3 1125
reserve capacity, m_Em, mol/mol 0.4889
vol-specific somatic maintenance at T, [p_M], J/d.cm^3 18
surface-specific som maintenance at T, {p_T}, J/d.cm^2 0
heating length, L_T, cm 0
somatic maintenance rate coeff, k_M, 1/d 0.006429
maturity maint rate coefficient at T, k_J, 1/d 0.002
maintenance ratio, k, - 0.3111
volume-spec som maint costs, [J_EM], mol/d.cm^3 3.273e-05
surface-spec som maint costs, {J_ET}, mol/d.cm^2 0
mass-spec somatic maint costs, j_EM, mol/mol.d 0.007822
mass-spec maturity maint costs, j_EJ, mol/mol.d 0.002433
specific dynamic action, SDA, mol O/ mol X 0.1865
respiration quotient for L = L_m, RQ, mol C/ mol O 1.026
urination quotient for L = L_m, UQ, mol N/ mol O 0.2051
watering quotient for L = L_m, WQ, mol H/ mol O 0.7179
heat dissipation for L = L_i, p_T^+, J/d 21.13
dioxygen use per gram max dry weight, L/g.h -0.0002078
yield of structure on reserve, y_VE, mol/mol 0.8219
growth efficiency, kappa_G, - 0.7472
energy investment ratio, g, - 3.111
von Bertalanffy growth rate, r_B, 1/d 0.001622
ultimate reproduction rate, R_i, 1/d 2.295
gonado-somatic index, GSI, mol/mol 0.4687
age at birth, a_b, d 15.2
age at metamorphosis, a_j, d 15.2
age at puberty, a_p, d 261
age at 99% of ultimate length, d 2809
mean life span, a_m, d 597.7
survival probability at birth, S_b, - 1
survival probability at puberty, S_p, - 0.9425
Weibull aging acceleration at T, h_a , 1/d^2 1e-06
Weibull aging rate at T, h_W, 1/d 0.001494
Gompertz aging rate at T, h_G, 1/d 2e-06
vol-spec structural mass, [M_V], mol/cm^3 0.004184
vol-spec structural energy, [E_V], J/cm^3 2092
energy density of whole dry body, <E + E_V>, J/g 2.024e+04
maximum specific population growth rate, r_m, 1/d 0.01225
mean age of juveniles + adults at f=1, Ea, d 94.3
mean structural length of juveniles + adults at f=1, EL, cm 0.1783
mean squared structural length of juv + adults at f=1, EL^2, cm^2 0.04038
mean structural cubed length of juv + adults at f=1, EL^3, cm^3 0.01131
scaled func response at no pop growth, f_0, - 0.2868
mean age of juveniles + adults at r=0, Ea, d 298.9
mean structural length of juveniles + adults at r=0, EL, cm 0.1551
mean squared structural length of juv + adults at r=0, EL^2, cm^2 0.02638
mean cubed structural length of juv + adults at r=0, EL^3, cm^3 0.00471