diff --git a/src/nature/energy.jl b/src/nature/energy.jl
index 74937b9bf8ab6dd1f56576e236205743be3b6066..e6e9c844b1463cf87861988b081f15c627773d64 100644
--- a/src/nature/energy.jl
+++ b/src/nature/energy.jl
@@ -3,6 +3,9 @@
### This file contains structs and functions for implementing Dynamic Energy Budgets.
###
+
+## STRUCTS
+
"""
DEBparameters
@@ -10,13 +13,18 @@ An immutable struct to save the parameter list for a species' Dynamic Energy Bud
model. (See Sousa et al., 2010.)
"""
struct DEBparameters
+ maxsearchrate::Float64 # maximum amount of food handled per day (F_m)
assimilation::Float64 # percentage of food biomass assimilated (y_EX)
+ growthefficiency::Float64 # yield of structure on reserve (y_VE)
+ v::Float64 # energy conductance
+ surfacesomaticmaintenance::Float64 # surface-specific somatic maintenance (J_ET)
+ volumesomaticmaintenance::Float64 # volume-specific somatic maintenance (J_EM)
+ #maturitymaintenance::Float64 # specific maturity maintenance (k_J)
kappa::Float64 # percentage allocated to somatic maintenance and growth (k)
- juvenilesize::Float64 # structure size at which an embryo becomes a juvenile (MHb)
- adultsize::Float64 # structure size at which a juvenile becomes an adult (MHp)
- maintenance::Float64 # daily percentage of body size needed per update for somatic and maturity maintenance
- reproduction::Float64 # energy needed to produce an egg (= initial amount of reserve)
- v::Float64 # energy conductance (XXX ???)
+ reproductionefficiency::Float64 # overhead cost of reproduction (k_R)
+ eggsize::Float64 # weight of an egg/embryo, = initial amount of reserve (M_E0)
+ juvenilesize::Float64 # structure size at which an embryo becomes a juvenile (M_Hb)
+ adultsize::Float64 # structure size at which a juvenile becomes an adult (M_Hp)
end
"""
@@ -50,32 +58,111 @@ Ecology, 85(7), 1771–1789. https://doi.org/10.1890/03-9000
"""
mutable struct EnergyBudget
params::DEBparameters
- reserve::Float64
- structure::Float64
- offspring::Float64
+ reserve::Float64 # M_E
+ structure::Float64 # M_V
+ #maturity::Float64 # M_H
+ offspring::Float64 # M_ER
end
+
+## INTERNAL CALCULATIONS
+
"""
- biomass(energybudget)
+ volumetriclength(energybudget)
-Calculate the total biomass of an individual based on its energy budget.
-(Sum of the reserve, structure, and offspring buffers; Sibly et al. 2013.)
+Calculate the structural length in cm based on an individual's weight
+(assuming a density of 1 g/cm³ to calculate volume, see Kooijman 2009).
"""
-function biomass(deb::EnergyBudget)
- deb.reserve + deb.structure + deb.offspring
+function volumetriclength(deb::EnergyBudget)
+ #TODO is cm the right unit?
+ weight = deb.reserve + deb.structure + deb.offspring
+ vlength = weight ^ (1/3)
+ vlength
end
"""
- feed!(biomass, energybudget)
+ maturitymaintenance(energybudget)
-Consume a given quantity of food. Expands the energy reserve by an
-amount determined by the assimilation rate.
+Calculate the specific maturity maintenance k_J.
+(Internal function.)
+"""
+function maturitymaintenance(deb::EnergyBudget)
+ y_VE = deb.params.growthefficiency
+ J_EM = deb.params.volumesomaticmaintenance
+ M_V = deb.structure
+ k_J = (y_VE * J_EM) / M_V
+ k_J
+end
+
+"""
+ scaledreservedensity(energybudget)
+
+Calculate the scaled reserve density e.
+(Internal function.)
"""
-function feed!(biomass::Float64, deb::EnergyBudget)
- deb.reserve += biomass * deb.params.assimilation
- #TODO reserve doesn't grow infinitely
+function scaledreservedensity(deb::EnergyBudget)
+ J_EAm = deb.params.assimilation * deb.params.maxsearchrate
+ m_E = deb.reserve / deb.structure
+ m_Em = J_EAm / (deb.params.v * deb.structure)
+ e = m_E / m_Em
+ e
end
+"""
+ investmentratio(energybudget)
+
+Calculate the investment ratio g.
+(Internal function.)
+"""
+function investmentratio(deb::EnergyBudget)
+ J_EAm = deb.params.assimilation * deb.params.maxsearchrate
+ y_VE = deb.params.growthefficiency
+ k = deb.params.kappa
+ v = deb.params.v
+ M_V = deb.structure
+ g = (v * M_V) / (k * J_EAm * y_VE)
+ g
+end
+
+"""
+ growthrate(energybudget)
+
+Calculate the specific growth rate r.
+(Internal function.)
+"""
+function growthrate(deb::EnergyBudget)
+ J_EAm = deb.params.assimilation * deb.params.maxsearchrate
+ J_ET = deb.params.surfacesomaticmaintenance
+ J_EM = deb.params.volumesomaticmaintenance
+ k = deb.params.kappa
+ v = deb.params.v
+ e = scaledreservedensity(deb)
+ g = investmentratio(deb)
+ L = volumetriclength(deb)
+ L_m = k * (J_EAm / J_EM) # max length
+ L_T = J_ET / J_EM # heating length
+ r = v * (e/L - (1+L_T/L)/L_m) / (e+g)
+ r
+end
+
+"""
+ mobilisation(energybudget)
+
+Calculate the mobilisation rate J_EC.
+(Internal function.)
+"""
+function mobilisation(deb::EnergyBudget)
+ M_E = deb.reserve
+ r = growthrate(deb)
+ v = deb.params.v
+ L = volumetriclength(deb)
+ J_EC = M_E * (v/L - r)
+ J_EC
+end
+
+
+## PUBLIC INTERFACE
+
"""
update!(energybudget)
@@ -86,25 +173,76 @@ Return `true` if the individual has enough energy to survive, or `false` if the
reserve is empty and it starves.
"""
function update!(deb::EnergyBudget)
- #TODO
- mobilisation = 0
- somaticmaintenance = deb.params.maintenance # J_ES
- maturitymaintenance = deb.params.maintenance # J_EJ
+ J_ET = deb.params.surfacesomaticmaintenance
+ J_EM = deb.params.volumesomaticmaintenance
+ k_R = deb.params.reproductionefficiency
+ y_VE = deb.params.growthefficiency
+ #k_J = deb.params.maturitymaintenance
+ k_J = maturitymaintenance(deb)
+ L = volumetriclength(deb)
+ k = deb.params.kappa
+ M_V = deb.structure
+ #M_H = deb.maturity
+ M_E = deb.reserve
+
+ J_EC = mobilisation(deb)
+
+ ## Somatic maintenance and growth
+ J_ES = J_EM * (L^3) + J_ET * (L^2) # somatic maintenance
+ J_EG = J_EC * k - J_ES # energy devoted to growth
+ J_VG = J_EG * y_VE # actual growth
+ #J_VG = growthrate(deb) * deb.structure # r*M_V
+ #XXX check if J_VG == J_EG * y_VE == r * M_V
+ deb.structure += J_VG
+
# juveniles grow until they reach adult size
+ #XXX growth should stop automatically at M_V == M_Hp
if deb.structure < adultsize
growth = (mobilisation*deb.params.kappa) - somaticmaintenance
deb.structure += growth
end
+
# juveniles increase in maturity, adults invest into reproduction
- maturityreproduction = (mobilisation*(1-deb.params.kappa)) - maturitymaintenance
- if deb.structure >= adultsize
- deb.offspring += maturityreproduction
+ J_EJ = k_J * M_H # maturity maintenance
+ J_ER = J_EC*(1-k) - J_EJ # resources for reproduction
+ if M_V >= deb.params.adultsize
+ deb.offspring += J_ER * k_R
+ else
+ #deb.maturity += J_ER #XXX I'm ignoring the maturity buffer for now
end
-
- deb.reserve -= mobilisation
+
+ #XXX Check that J_EC == J_ES + J_EG + J_EJ + J_ER
+ deb.reserve -= J_EC
return deb.reserve > 0
end
+"""
+ feed!(quantity, energybudget)
+
+Consume a given quantity of food. Expands the energy reserve by an
+amount determined by the assimilation rate. Returns `true` if successful,
+`false` if the reserve is already full.
+"""
+function feed!(quantity::Float64, deb::EnergyBudget)
+ F_m = deb.params.maxsearchrate
+ y_EX = deb.params.assimilation
+ M_V = deb.structure
+ M_E = deb.reserve
+ v = deb.params.v
+
+ J_EAm = y_EX * F_m # max assimilation rate
+ m_E = M_E / M_V # reserve density
+ m_Em = J_EAm / (v * M_V) # max reserve density
+
+ # only feed if the reserve is not yet at maximum capacity
+ if m_E < m_Em
+ deb.reserve += quantity * y_EX
+ return true
+ else
+ return false
+ end
+end
+
"""
reproduce!(energybudget)
@@ -113,9 +251,14 @@ embryo/egg, reducing the parent energy in the process. Returns the embryo's ener
budget, or `nothing` if the conditions are not met.
"""
function reproduce!(deb::EnergyBudget)
- if deb.structure >= deb.params.adultsize && deb.offspring >= deb.params.reproduction
- deb.offspring -= deb.params.reproduction
- return EnergyBudget(deb.params, deb.params.reproduction, 0.0, 0.0)
+ M_V = deb.structure
+ M_ER = deb.offspring
+ M_Hp = deb.params.adultsize
+ M_E0 = deb.params.eggsize
+
+ if M_V >= M_Hp && M_ER >= M_E0
+ deb.offspring -= M_E0
+ return EnergyBudget(deb.params, M_E0, 0.0, 0.0)
else
return nothing
end