DEB_euler: Dynamic Energy Budget model
In mrke/NicheMapR: R implementation of Niche Mapper software for biophysical modelling
DEB_euler R Documentation
Dynamic Energy Budget model
Description
Implementation of the Standarad Dynamic Energy Budget model of Kooijman
Note does not do a proper integration, i.e. rate of change is the difference between two fixed time periods
which is ok as long as the timestep is very small relative to the dynamics - hourly time steps or shorter
are ok for long-lived (months to years) animals
Michael Kearney Dec 2015
Usage
DEB_euler(
step = 1/24,
z = 7.997,
del_M = 0.242,
p_Xm = 13290 * step,
kap_X = 0.85,
v = 0.065 * step,
kap = 0.886,
p_M = 32 * step,
p_T = 0,
E_G = 7767,
kap_R = 0.95,
k_J = 0.002 * step,
E_Hb = 73590,
E_Hj = E_Hb,
E_Hp = 186500,
h_a = 2.16e-11/(step^2),
s_G = 0.01,
T_REF = 20 + 273.15,
T_A = 8085,
T_AL = 18721,
T_AH = 90000,
T_L = 288,
T_H = 315,
T_A2 = T_A,
T_AL2 = T_AL,
T_AH2 = T_AH,
T_L2 = T_L,
T_H2 = T_H,
E_0 = 1040000,
f = 1,
E_sm = 1116,
K = 1,
andens_deb = 1,
d_V = 0.3,
d_E = 0.3,
d_Egg = 0.3,
stoich_mode = 0,
mu_X = 525000,
mu_E = 585000,
mu_V = 5e+05,
mu_P = 480000,
mu_N = 244000/5,
kap_X_P = 0.1,
n_X = c(1, 1.8, 0.5, 0.15),
n_E = c(1, 1.8, 0.5, 0.15),
n_V = c(1, 1.8, 0.5, 0.15),
n_P = c(1, 1.8, 0.5, 0.15),
n_M_nitro = c(1, 4/5, 3/5, 4/5),
h_N = 384238,
clutchsize = 2,
clutch_ab = c(0.085, 0.7),
minclutch = 0,
batch = 1,
lambda = 1/2,
VTMIN = 26,
VTMAX = 39,
ma = 1e-04,
mi = 0,
mh = 0.5,
arrhenius = matrix(data = matrix(data = c(rep(T_A, 8), rep(T_AL, 8), rep(T_AH, 8),
rep(T_L, 8), rep(T_H, 8)), nrow = 8, ncol = 5), nrow = 8, ncol = 5),
arrhenius2 = matrix(data = matrix(data = c(rep(T_A2, 8), rep(T_AL2, 8), rep(T_AH2, 8),
rep(T_L2, 8), rep(T_H2, 8)), nrow = 8, ncol = 5), nrow = 8, ncol = 5),
acthr = 1,
X = 10,
E_pres = E_0/3e-09,
V_pres = 3e-09,
E_H_pres = 0,
q_pres = 0,
hs_pres = 0,
p_surv = 1,
E_s_pres = 0,
p_B_pres = 0,
E_R = 0,
E_B = 0,
stages = 7,
stage = 0,
breeding = 0,
Tb = 33,
starve_mode = 1,
fdry = 0.3,
L_b = 0.42,
L_j = 1.376,
S_instar = rep(1.618, stages),
spawnday = 1,
day = 1,
metab_mode = 0,
age = 0
)
Arguments
step
= 1/24, step size (days)
z
= 7.997, Zoom factor (cm)
del_M
= 0.242, Shape coefficient (-)
p_Xm
= 13290*step, Surface area-specific maximum feeding rate J/cm2/h
kap_X
= 0.85, Digestive efficiency (decimal %)
v
= 0.065*step, Energy conductance (cm/h)
kap
= 0.886, fraction of mobilised reserve allocated to soma
p_M
= 32*step, Volume-specific somatic maintenance (J/cm3/h)
p_T
= 0, (Structural-)Surface-area-specific heating cost (J/cm2/h)
E_G
= 7767, Cost of structure (J/cm3)
kap_R
= 0.95, Fraction of reproduction energy fixed in eggs
k_J
= 0.002*step, Maturity maintenance rate coefficient (1/h)
E_Hb
= 7.359e+04, Maturity at birth (J)
E_Hj
= E_Hb, Maturity at metamorphosis (J)
E_Hp
= 1.865e+05, Maturity at puberty
h_a
= 2.16e-11*(step^2), Weibull ageing acceleration (1/h2)
s_G
= 0.01, Gompertz stress coefficient (-)
T_REF
= 20+273.15, Reference temperature for rate correction (deg C)
T_A
= 8085 Arrhenius temperature
T_AL
= 18721, Arrhenius temperature for decrease below lower boundary of tolerance range T_L
T_AH
= 90000, Arrhenius temperature for decrease above upper boundary of tolerance range T_H
T_L
= 288, Lower boundary (K) of temperature tolerance range for Arrhenius thermal response
T_H
= 315, Upper boundary (K) of temperature tolerance range for Arrhenius thermal response
T_A2
= 8085 Arrhenius temperature for maturity maintenance (causes 'Temperature Size Rule' effect)
T_AL2
= 18721, Arrhenius temperature for decrease below lower boundary of tolerance range T_L for maturity maintenance (causes 'Temperature Size Rule' effect)
T_AH2
= 90000, Arrhenius temperature for decrease above upper boundary of tolerance range T_H for maturity maintenance (causes 'Temperature Size Rule' effect)
T_L2
= 288, Lower boundary (K) of temperature tolerance range for Arrhenius thermal response for maturity maintenance (causes 'Temperature Size Rule' effect)
T_H2
= 315, Upper boundary (K) of temperature tolerance range for Arrhenius thermal response for maturity maintenance (causes 'Temperature Size Rule' effect)
E_0
= 1.04e+06, Energy content of the egg (derived from core parameters) (J)
f
= 1, functional response (-), usually kept at 1 because gut model controls food availability such that f=0 when gut empty
E_sm
= 1116, Maximum volume-specific energy density of stomach (J/cm3)
K
= 500, Half saturation constant (#/cm2)
andens_deb
= 1, Animal density (g/cm3)
d_V
= 0.3, Dry mass fraction of structure
d_E
= 0.3, Dry mass fraction of reserve
d_Egg
= 0.3, Dry mass fraction of egg
stoich_mode
= 0, adjust chemical indices to chemical potentials (0) or vice versa (1), or leave as is (2)
mu_X
= 525000, Molar Gibbs energy (chemical potential) of food (J/mol)
mu_E
= 585000, Molar Gibbs energy (chemical potential) of reserve (J/mol)
mu_V
= 500000, Molar Gibbs energy (chemical potential) of structure (J/mol)
mu_P
= 480000, Molar Gibbs energy (chemical potential) of faeces (J/mol)
mu_N
= 244e3/5, Molar Gibbs energy (chemical potential) of nitrogenous waste (J/mol), synthesis from NH3, Withers page 119
kap_X_P
= 0.1, Faecation efficiency of food to faeces (-)
n_X
= c(1,1.8,0.5,.15), Chem. indices of C, O, H and N in food
n_E
= c(1,1.8,0.5,.15), Chem. indices of C, O, H and N in reserve
n_V
= c(1,1.8,0.5,.15), Chem. indices of C, O, H and N in structure
n_P
= c(1,1.8,0.5,.15), Chem. indices of C, O, H and N in faeces
n_M_nitro
= c(1,4/5,3/5,4/5), Chem. indices of C, O, H and N in nitrogenous waste
h_N
= 384238, molar enthalpy of nitrogenous waste (combustion frame of reference) (J/mol), overridden if n_M_nitro specified as urea, uric acid or ammonia
clutchsize
= 2, Clutch size (#), overridden by clutch_ab
clutch_ab
= c(0,0), paramters for relationship between length (cm) and clutch size: clutch size = a*L_w-b, make a and b zero if fixed clutch size
minclutch
= 0, Minimum clutch size if not enough in reproduction buffer for clutch size predicted by clutch_ab - if zero, will not operate
batch
= 1, Invoke Pequerie et al.'s batch laying model?
lambda
= 1/2
VTMIN
= 26, Voluntary thermal maximum, degrees C, controls whether repro event can occur at a given time
VTMAX
= 39, Voluntary thermal maximum, degrees C, controls whether repro event can occur at a given time
arrhenius
= matrix(data = matrix(data = c(rep(T_A,8),rep(T_AL,8),rep(T_AH,8),rep(T_L,8),rep(T_H,8)), nrow = 8, ncol = 5), nrow = 8, ncol = 5), Stage-specific 5-parameter Arrhenius thermal response for DEB model (T_A,T_AL,T_AH,T_L,T_H)
arrhenius2
= matrix(data = matrix(data = c(rep(T_A2,8),rep(T_AL2,8),rep(T_AH2,8),rep(T_L2,8),rep(T_H2,8)), nrow = 8, ncol = 5), nrow = 8, ncol = 5), Stage-specific 5-parameter Arrhenius thermal response for maturity maintenance (causes 'Temperature Size Rule' effect) DEB model (T_A2,T_AL2,T_AH2,T_L2,T_H2)
acthr
= 1
X
= 11
E_pres
= E_0/3e-9
V_pres
= 3e-9
E_H_pres
= 0
q_pres
= 0
hs_pres
= 0
p_surv
= 1
E_s_pres
= 0
E_R
= 0
E_B
= 0
stages
= 7, how many life stages?
stage
= 0
breeding
= 0
Tb
= 33
starve_mode
= 1, Determines how reproduction buffer is used during starvation, where 0 means it is not used, 1 means it is used before structure is mobilised and 2 means it is used to maximise reserve density
fdry
= 0.3, Dry mass fraction of food
S_instar
= rep(1.6, stages), stress at instar n: L_n^2/ L_n-1^2 (-)
p_B_past
= 0
Value
stage Life cycle stage, -
V Structure, cm^3
E Reserve density, J/cm^3
E_H Maturity, J
E_s Stomach energy content, J
E_R Reproduction buffer energy, J
E_B Reproduction batch energy, J
q Ageing acceleration, 1/time^2
hs Hazard rate
length Physical length, cm
wetmass Total wet mass, g
wetgonad Wet mass of gonad, g
wetgut Wet mass of food in gut, g
wetstorage Wet mass of reserve, g
p_surv Survival probability, -
fecundity Eggs produced at a given time point, #
clutches Clutches produced at a given time point
JMO2 Oxygen flux, mol/time
JMCO2 Carbon dioxide flux, mol/time
JMH2O metabolic water flux, mol/time
JMNWASTE nitrogenous waste flux, mol/time
O2ML Oxgen consumption rate, ml/hour
CO2ML Carbon dioxide production rate, ml/time
GH2OML Metabolic water production rate, ml/time
DEBQMET Metabolic heat generation, J/time
GDRYFOOD Dry food intake, g/time
GFAECES Faeces production, g/time
GNWASTE Nitrogenous waste production, g/time
p_A Assimilation power, J/time
p_C Catabolic power, J/time
p_M Somatic maintenance power, J/time
p_G Growth power, J/time
p_D Dissipation power, J/time
p_J Maturity power, J/time
p_R Reproduction power, J/time
p_B Reproduction batch power, J/time
L_b Structural length at birth, cm
L_j Structural length at end of metabolic acceleration (if occurring), cm
Examples
# simulate growth and reproduction at different constant body temperatures at
# constant food for a lizard (Tiliqua rugosa - default parameter values, starting
# as an egg)
n <- 3000 # time steps
step <- 1 # step size (days)
Tbs=seq(25, 35, 5) # sequence of body temperatures to use
for(j in 1:length(Tbs)){
debout<-matrix(data = 0, nrow = n, ncol = 38)
deb.names <- c("stage", "V", "E", "E_H", "E_s", "E_R", "E_B", "q", "hs", "length", "wetmass", "wetgonad", "wetgut", "wetstorage", "p_surv", "fecundity", "clutches", "JMO2", "JMCO2", "JMH2O", "JMNWASTE", "O2ML", "CO2ML", "GH2OMET", "DEBQMETW", "GDRYFOOD", "GFAECES", "GNWASTE", "p_A", "p_C", "p_M", "p_G", "p_D", "p_J", "p_R", "p_B", "L_b", "L_j")
colnames(debout)<-deb.names
# initialise
debout[1,]<-DEB_euler(Tb = Tbs[j], step = step)
for(i in 2:n){
debout[i,] <- DEB_euler(Tb = Tbs[j], breeding = 1, step = step, E_pres = debout[(i - 1), 3], V_pres = debout[(i - 1), 2], E_H_pres = debout[(i - 1), 4], q = debout[(i - 1), 8], hs = debout[(i - 1), 9], p_surv = debout[(i - 1), 15], E_s_pres = debout[(i - 1), 5], E_R = debout[(i - 1), 6], E_B = debout[(i - 1), 7])
}
if(j == 1){
plot((seq(1, n) / 365), debout[, 11], ylim = c(100, 1500), type = 'l', xlab = 'years', ylab = 'wet mass, g', col = j)
}else{
points((seq(1,n) / 365), debout[, 11], ylim = c(100, 1500), type = 'l', xlab = 'years', ylab = 'wet mass, g',col = j)
}
} #end loop through body temperatures
mrke/NicheMapR documentation built on Jan. 13, 2025, 9:11 p.m.
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| DEB_euler | R Documentation |
Dynamic Energy Budget model
Description
Implementation of the Standarad Dynamic Energy Budget model of Kooijman Note does not do a proper integration, i.e. rate of change is the difference between two fixed time periods which is ok as long as the timestep is very small relative to the dynamics - hourly time steps or shorter are ok for long-lived (months to years) animals Michael Kearney Dec 2015
Usage
DEB_euler(
step = 1/24,
z = 7.997,
del_M = 0.242,
p_Xm = 13290 * step,
kap_X = 0.85,
v = 0.065 * step,
kap = 0.886,
p_M = 32 * step,
p_T = 0,
E_G = 7767,
kap_R = 0.95,
k_J = 0.002 * step,
E_Hb = 73590,
E_Hj = E_Hb,
E_Hp = 186500,
h_a = 2.16e-11/(step^2),
s_G = 0.01,
T_REF = 20 + 273.15,
T_A = 8085,
T_AL = 18721,
T_AH = 90000,
T_L = 288,
T_H = 315,
T_A2 = T_A,
T_AL2 = T_AL,
T_AH2 = T_AH,
T_L2 = T_L,
T_H2 = T_H,
E_0 = 1040000,
f = 1,
E_sm = 1116,
K = 1,
andens_deb = 1,
d_V = 0.3,
d_E = 0.3,
d_Egg = 0.3,
stoich_mode = 0,
mu_X = 525000,
mu_E = 585000,
mu_V = 5e+05,
mu_P = 480000,
mu_N = 244000/5,
kap_X_P = 0.1,
n_X = c(1, 1.8, 0.5, 0.15),
n_E = c(1, 1.8, 0.5, 0.15),
n_V = c(1, 1.8, 0.5, 0.15),
n_P = c(1, 1.8, 0.5, 0.15),
n_M_nitro = c(1, 4/5, 3/5, 4/5),
h_N = 384238,
clutchsize = 2,
clutch_ab = c(0.085, 0.7),
minclutch = 0,
batch = 1,
lambda = 1/2,
VTMIN = 26,
VTMAX = 39,
ma = 1e-04,
mi = 0,
mh = 0.5,
arrhenius = matrix(data = matrix(data = c(rep(T_A, 8), rep(T_AL, 8), rep(T_AH, 8),
rep(T_L, 8), rep(T_H, 8)), nrow = 8, ncol = 5), nrow = 8, ncol = 5),
arrhenius2 = matrix(data = matrix(data = c(rep(T_A2, 8), rep(T_AL2, 8), rep(T_AH2, 8),
rep(T_L2, 8), rep(T_H2, 8)), nrow = 8, ncol = 5), nrow = 8, ncol = 5),
acthr = 1,
X = 10,
E_pres = E_0/3e-09,
V_pres = 3e-09,
E_H_pres = 0,
q_pres = 0,
hs_pres = 0,
p_surv = 1,
E_s_pres = 0,
p_B_pres = 0,
E_R = 0,
E_B = 0,
stages = 7,
stage = 0,
breeding = 0,
Tb = 33,
starve_mode = 1,
fdry = 0.3,
L_b = 0.42,
L_j = 1.376,
S_instar = rep(1.618, stages),
spawnday = 1,
day = 1,
metab_mode = 0,
age = 0
)
Arguments
step |
= 1/24, step size (days) |
z |
= 7.997, Zoom factor (cm) |
del_M |
= 0.242, Shape coefficient (-) |
p_Xm |
= 13290*step, Surface area-specific maximum feeding rate J/cm2/h |
kap_X |
= 0.85, Digestive efficiency (decimal %) |
v |
= 0.065*step, Energy conductance (cm/h) |
kap |
= 0.886, fraction of mobilised reserve allocated to soma |
p_M |
= 32*step, Volume-specific somatic maintenance (J/cm3/h) |
p_T |
= 0, (Structural-)Surface-area-specific heating cost (J/cm2/h) |
E_G |
= 7767, Cost of structure (J/cm3) |
kap_R |
= 0.95, Fraction of reproduction energy fixed in eggs |
k_J |
= 0.002*step, Maturity maintenance rate coefficient (1/h) |
E_Hb |
= 7.359e+04, Maturity at birth (J) |
E_Hj |
= E_Hb, Maturity at metamorphosis (J) |
E_Hp |
= 1.865e+05, Maturity at puberty |
h_a |
= 2.16e-11*(step^2), Weibull ageing acceleration (1/h2) |
s_G |
= 0.01, Gompertz stress coefficient (-) |
T_REF |
= 20+273.15, Reference temperature for rate correction (deg C) |
T_A |
= 8085 Arrhenius temperature |
T_AL |
= 18721, Arrhenius temperature for decrease below lower boundary of tolerance range |
T_AH |
= 90000, Arrhenius temperature for decrease above upper boundary of tolerance range |
T_L |
= 288, Lower boundary (K) of temperature tolerance range for Arrhenius thermal response |
T_H |
= 315, Upper boundary (K) of temperature tolerance range for Arrhenius thermal response |
T_A2 |
= 8085 Arrhenius temperature for maturity maintenance (causes 'Temperature Size Rule' effect) |
T_AL2 |
= 18721, Arrhenius temperature for decrease below lower boundary of tolerance range |
T_AH2 |
= 90000, Arrhenius temperature for decrease above upper boundary of tolerance range |
T_L2 |
= 288, Lower boundary (K) of temperature tolerance range for Arrhenius thermal response for maturity maintenance (causes 'Temperature Size Rule' effect) |
T_H2 |
= 315, Upper boundary (K) of temperature tolerance range for Arrhenius thermal response for maturity maintenance (causes 'Temperature Size Rule' effect) |
E_0 |
= 1.04e+06, Energy content of the egg (derived from core parameters) (J) |
f |
= 1, functional response (-), usually kept at 1 because gut model controls food availability such that f=0 when gut empty |
E_sm |
= 1116, Maximum volume-specific energy density of stomach (J/cm3) |
K |
= 500, Half saturation constant (#/cm2) |
andens_deb |
= 1, Animal density (g/cm3) |
d_V |
= 0.3, Dry mass fraction of structure |
d_E |
= 0.3, Dry mass fraction of reserve |
d_Egg |
= 0.3, Dry mass fraction of egg |
stoich_mode |
= 0, adjust chemical indices to chemical potentials (0) or vice versa (1), or leave as is (2) |
mu_X |
= 525000, Molar Gibbs energy (chemical potential) of food (J/mol) |
mu_E |
= 585000, Molar Gibbs energy (chemical potential) of reserve (J/mol) |
mu_V |
= 500000, Molar Gibbs energy (chemical potential) of structure (J/mol) |
mu_P |
= 480000, Molar Gibbs energy (chemical potential) of faeces (J/mol) |
mu_N |
= 244e3/5, Molar Gibbs energy (chemical potential) of nitrogenous waste (J/mol), synthesis from NH3, Withers page 119 |
kap_X_P |
= 0.1, Faecation efficiency of food to faeces (-) |
n_X |
= c(1,1.8,0.5,.15), Chem. indices of C, O, H and N in food |
n_E |
= c(1,1.8,0.5,.15), Chem. indices of C, O, H and N in reserve |
n_V |
= c(1,1.8,0.5,.15), Chem. indices of C, O, H and N in structure |
n_P |
= c(1,1.8,0.5,.15), Chem. indices of C, O, H and N in faeces |
n_M_nitro |
= c(1,4/5,3/5,4/5), Chem. indices of C, O, H and N in nitrogenous waste |
h_N |
= 384238, molar enthalpy of nitrogenous waste (combustion frame of reference) (J/mol), overridden if n_M_nitro specified as urea, uric acid or ammonia |
clutchsize |
= 2, Clutch size (#), overridden by |
clutch_ab |
= c(0,0), paramters for relationship between length (cm) and clutch size: clutch size = a*L_w-b, make a and b zero if fixed clutch size |
minclutch |
= 0, Minimum clutch size if not enough in reproduction buffer for clutch size predicted by |
batch |
= 1, Invoke Pequerie et al.'s batch laying model? |
lambda |
= 1/2 |
VTMIN |
= 26, Voluntary thermal maximum, degrees C, controls whether repro event can occur at a given time |
VTMAX |
= 39, Voluntary thermal maximum, degrees C, controls whether repro event can occur at a given time |
arrhenius |
= matrix(data = matrix(data = c(rep(T_A,8),rep(T_AL,8),rep(T_AH,8),rep(T_L,8),rep(T_H,8)), nrow = 8, ncol = 5), nrow = 8, ncol = 5), Stage-specific 5-parameter Arrhenius thermal response for DEB model (T_A,T_AL,T_AH,T_L,T_H) |
arrhenius2 |
= matrix(data = matrix(data = c(rep(T_A2,8),rep(T_AL2,8),rep(T_AH2,8),rep(T_L2,8),rep(T_H2,8)), nrow = 8, ncol = 5), nrow = 8, ncol = 5), Stage-specific 5-parameter Arrhenius thermal response for maturity maintenance (causes 'Temperature Size Rule' effect) DEB model (T_A2,T_AL2,T_AH2,T_L2,T_H2) |
acthr |
= 1 |
X |
= 11 |
E_pres |
= E_0/3e-9 |
V_pres |
= 3e-9 |
E_H_pres |
= 0 |
q_pres |
= 0 |
hs_pres |
= 0 |
p_surv |
= 1 |
E_s_pres |
= 0 |
E_R |
= 0 |
E_B |
= 0 |
stages |
= 7, how many life stages? |
stage |
= 0 |
breeding |
= 0 |
Tb |
= 33 |
starve_mode |
= 1, Determines how reproduction buffer is used during starvation, where 0 means it is not used, 1 means it is used before structure is mobilised and 2 means it is used to maximise reserve density |
fdry |
= 0.3, Dry mass fraction of food |
S_instar |
= rep(1.6, stages), stress at instar n: L_n^2/ L_n-1^2 (-) |
p_B_past |
= 0 |
Value
stage Life cycle stage, -
V Structure, cm^3
E Reserve density, J/cm^3
E_H Maturity, J
E_s Stomach energy content, J
E_R Reproduction buffer energy, J
E_B Reproduction batch energy, J
q Ageing acceleration, 1/time^2
hs Hazard rate
length Physical length, cm
wetmass Total wet mass, g
wetgonad Wet mass of gonad, g
wetgut Wet mass of food in gut, g
wetstorage Wet mass of reserve, g
p_surv Survival probability, -
fecundity Eggs produced at a given time point, #
clutches Clutches produced at a given time point
JMO2 Oxygen flux, mol/time
JMCO2 Carbon dioxide flux, mol/time
JMH2O metabolic water flux, mol/time
JMNWASTE nitrogenous waste flux, mol/time
O2ML Oxgen consumption rate, ml/hour
CO2ML Carbon dioxide production rate, ml/time
GH2OML Metabolic water production rate, ml/time
DEBQMET Metabolic heat generation, J/time
GDRYFOOD Dry food intake, g/time
GFAECES Faeces production, g/time
GNWASTE Nitrogenous waste production, g/time
p_A Assimilation power, J/time
p_C Catabolic power, J/time
p_M Somatic maintenance power, J/time
p_G Growth power, J/time
p_D Dissipation power, J/time
p_J Maturity power, J/time
p_R Reproduction power, J/time
p_B Reproduction batch power, J/time
L_b Structural length at birth, cm
L_j Structural length at end of metabolic acceleration (if occurring), cm
Examples
# simulate growth and reproduction at different constant body temperatures at
# constant food for a lizard (Tiliqua rugosa - default parameter values, starting
# as an egg)
n <- 3000 # time steps
step <- 1 # step size (days)
Tbs=seq(25, 35, 5) # sequence of body temperatures to use
for(j in 1:length(Tbs)){
debout<-matrix(data = 0, nrow = n, ncol = 38)
deb.names <- c("stage", "V", "E", "E_H", "E_s", "E_R", "E_B", "q", "hs", "length", "wetmass", "wetgonad", "wetgut", "wetstorage", "p_surv", "fecundity", "clutches", "JMO2", "JMCO2", "JMH2O", "JMNWASTE", "O2ML", "CO2ML", "GH2OMET", "DEBQMETW", "GDRYFOOD", "GFAECES", "GNWASTE", "p_A", "p_C", "p_M", "p_G", "p_D", "p_J", "p_R", "p_B", "L_b", "L_j")
colnames(debout)<-deb.names
# initialise
debout[1,]<-DEB_euler(Tb = Tbs[j], step = step)
for(i in 2:n){
debout[i,] <- DEB_euler(Tb = Tbs[j], breeding = 1, step = step, E_pres = debout[(i - 1), 3], V_pres = debout[(i - 1), 2], E_H_pres = debout[(i - 1), 4], q = debout[(i - 1), 8], hs = debout[(i - 1), 9], p_surv = debout[(i - 1), 15], E_s_pres = debout[(i - 1), 5], E_R = debout[(i - 1), 6], E_B = debout[(i - 1), 7])
}
if(j == 1){
plot((seq(1, n) / 365), debout[, 11], ylim = c(100, 1500), type = 'l', xlab = 'years', ylab = 'wet mass, g', col = j)
}else{
points((seq(1,n) / 365), debout[, 11], ylim = c(100, 1500), type = 'l', xlab = 'years', ylab = 'wet mass, g',col = j)
}
} #end loop through body temperatures
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