DEB_var: Dynamic Energy Budget model
In mrke/NicheMapR: R implementation of Niche Mapper software for biophysical modelling
DEB_var R Documentation
Dynamic Energy Budget model
Description
Implementation of the Standard Dynamic Energy Budget model of Kooijman
Note that this uses the deSolve package 'ode' function with events and
can handle variable food and variable temperature. It runs faster than the 'DEB'
function.
Michael Kearney May 2021
Usage
DEB_var(
ndays = 365,
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,
E_He = E_Hp,
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),
batch = 1,
lambda = 1/2,
E_init = E_0/3e-09,
V_init = 3e-09,
E_H_init = 0,
q_init = 0,
hs_init = 0,
p_surv_init = 1,
E_s_init = 0,
p_B_init = 0,
E_R_init = 0,
E_B_init = 0,
stages = 7,
starve_mode = 1,
fdry = 0.3,
L_b = 0.07101934,
L_j = 1.376,
s_j = 0.9977785,
k_EV = 0.002948759 * step,
kap_V = 0.8,
S_instar = rep(1.618, stages),
day = 1,
metab_mode = 0,
age = 0,
foetal = 0
)
Arguments
ndays
= 365, length of simulation (days)
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
batch
= 1, Invoke Pequerie et al.'s batch laying model?
lambda
= 1/2
E_init
= 6011.93
V_init
= 3.9752^3
E_H_init
= 73592
q_init
= 0
hs_init
= 0
p_surv_init
= 1
E_s_init
= 0
E_R_init
= 0
E_B_init
= 0
stages
= 3, how many life stages?
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 (-)
stage
= 0, Initial stage (0=embryo, for STD 1=juvenile, 2=mature but not yet reproducing, 3=beyond first reproduction, for ABP 1-(stages-1) = instars, stages = adult)
minclutch
= 0, Minimum clutch size if not enough in reproduction buffer for clutch size predicted by clutch_ab - if zero, will not operate
acthr
= 1
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 Aging 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 fluctuating body temperatures (Tb = 5 cm air temperature) 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(Tb = Tbs[j], step = step)
for(i in 2:n){
debout[i,] <- DEB(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 April 3, 2024, 10:05 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
| DEB_var | R Documentation |
Dynamic Energy Budget model
Description
Implementation of the Standard Dynamic Energy Budget model of Kooijman Note that this uses the deSolve package 'ode' function with events and can handle variable food and variable temperature. It runs faster than the 'DEB' function. Michael Kearney May 2021
Usage
DEB_var(
ndays = 365,
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,
E_He = E_Hp,
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),
batch = 1,
lambda = 1/2,
E_init = E_0/3e-09,
V_init = 3e-09,
E_H_init = 0,
q_init = 0,
hs_init = 0,
p_surv_init = 1,
E_s_init = 0,
p_B_init = 0,
E_R_init = 0,
E_B_init = 0,
stages = 7,
starve_mode = 1,
fdry = 0.3,
L_b = 0.07101934,
L_j = 1.376,
s_j = 0.9977785,
k_EV = 0.002948759 * step,
kap_V = 0.8,
S_instar = rep(1.618, stages),
day = 1,
metab_mode = 0,
age = 0,
foetal = 0
)
Arguments
ndays |
= 365, length of simulation (days) |
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 |
batch |
= 1, Invoke Pequerie et al.'s batch laying model? |
lambda |
= 1/2 |
E_init |
= 6011.93 |
V_init |
= 3.9752^3 |
E_H_init |
= 73592 |
q_init |
= 0 |
hs_init |
= 0 |
p_surv_init |
= 1 |
E_s_init |
= 0 |
E_R_init |
= 0 |
E_B_init |
= 0 |
stages |
= 3, how many life stages? |
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 (-) |
stage |
= 0, Initial stage (0=embryo, for STD 1=juvenile, 2=mature but not yet reproducing, 3=beyond first reproduction, for ABP 1-(stages-1) = instars, stages = adult) |
minclutch |
= 0, Minimum clutch size if not enough in reproduction buffer for clutch size predicted by |
acthr |
= 1 |
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 Aging 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 fluctuating body temperatures (Tb = 5 cm air temperature) 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(Tb = Tbs[j], step = step)
for(i in 2:n){
debout[i,] <- DEB(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
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.