animalruns a demo for the standard model, after editing parameter values in
shmics: temp correction, embryo weights, reproduction, reserve residence times
shtime_animal: length, reprod, weight, survival
shphase: phase diagram
shflux: fluxes of compounds
shflux_struc: structure-specific fluxes
shflux_weight: weight-specific fluxes
shratio: Repiration, Watering, Urination Quotients
shpower: powers and specific powers
shscale: variables versus species' max body weight
shssd_iso: population characteristics versus functional response
The animal (or other organism) is decomposed in:
structure (V) and reserve (E)
X = food, V = structure, E = reserve, P = faeces
C = carbon dioxide, H = water, O = dioxygen, N = nitrogen waste
The animal develops through an embryonic, juvenile and adult phase.
Assimilation is switched on at birth
Allocation to maturation is redirected to reproduction at puberty
Uptake is proportional to surface area, which is taken to be proportional to the structural volume^(2/3): isomorph
The heating length (this is the volumetric length reduction due to the energy drain that goes into heating or osmotic work) is set to a fixed length in this implementation. The DEB theory has a module on the water balance, with implications for the costs of heating. These implications make the heating length a function of other variables.
All lengths refer to volumetric lengths. Lengths should be divided by a shape coefficients to arrive at shape-specific lengths.
Script shtraject runs a simulation of the stochastic variant, where food searching is a time-inhomogeneous Poisson process.
DEB theory quantifies aging directly in terms of the hazard rate, so for the aging process no deterministic equivalent is available.
The scripts plot variables as function of scaled time since birth.
shphase presents phase diagrams, which indicate how reserve and structure chnage relative to each other.
statistics computes quantities that depend on food density,
parscomp computes quantities that are independent of food density,
so functions of parameters, called compound parameters.
plots the various powers as function of scaled length.
It is based on
It is similar to
for mass fluxes and
for structure-specific mass fluxes and
for body weight-specific mass fluxes.
plots ratio's of mineral fluxes.
Maturity is, at constant food density, found from length by functions
The functions relate to non-acceleration, tyupe M acceleration and delayed type M acceleration.
They can be applied for the full life cycle (although maturity remains constant for adults).
Since food denisity trajectories uniquely determine state trajectories, the inverse mapping also exists:
from states trajectories to trajectories of scaled functional response.
The pair of functions
o2f is and example for (fish) otoliths, where otoliths are considered to be products,
with contributions from assimilations, dissipation and growth.
See section 4.11.4 of the DEB book.
Isotops, their dynamics is discussed in Section 4.7, add to the reconstruction to include temperature trajectories as well.
get_ue0for eggs and
get_ue0_foetusfor foetusses. The latter amounts to the cumulative energy investment till birth. The functions
initial_scaled reserve_foetusare shells around these function for vector-arguments and they are not scaled down to dimensionless quantities.
Scaled maturity at birth should not exceed a threshold that is computed in
The scaled length at birth is computed by
The functions differ in numerical method, from fast and dirty to slow and robust.
get_lb_foetus for foetal development.
The scaled time at birth is computed by
These functions also compute scaled length at birth.
Age, reserve, length (and maturity) at birth is produced by
get_tul_i for egg development and
get_aulh_f for foetal development.
The results are obtained by integration and can to used to check the results of other embryo-functions.
The numerical methods differ between these functions.
The scaled reserve density at which growth and/or maturition ceases at birth is computed by
The levels can be seen as minimum levels to reach birth.
The cumulative energy investment to the various endpoints at birth can be obtained numerically with functions
and graphically with functions
get_txand start acceleration
get_tp_foetusare computed in combination with other scaled times and scaled lengths at life history events. If you only need scaled lengths, it is more economic to use the corresponding
get_lp_foetus. If you only need states at birth, see under embryo
The scaled reserve density at which growth and maturition ceases at puberty is computed by
get_ep_min without acceleration,
get_ep_min_metam with acceleration.
Scaled functional response is reconstructed from scaled length by functions
They apply to the juvenile and adult stages.
The reserve residence time as function of length is computed by
and fluxes of masses for parameters and states by
It applies to the juvenile and adult stages.
reprod_rate_foetus. In case of type M acceleration, use functions
Likewise, the cumulative reproduction as function of time can be obtained with function
In case of type M acceleration, use functions
The cumulative energy investment in milk production (most by mammals) from birth to weaning is computed by
The median age at death due to ageing is computed by
for short growth periods.
The scaled mean age at death due to aging is computed by
get_tm_s for short growth periods and for arbitrary growth periods by
get_leh get state variables as functions of time over the whole life cycle.
get_pars_*obtain compound DEB parameters from easy-to-observe quantities and the functions
iget_pars_*do the reverse, which can be used for checking. The theory is discussed in KooySous2008. The heating length LT is assumed to be zero in all
get_pars_*functions. An example of use is given in
mydata_get_pars. The routines are organized as follows:
|constraint||kJ = kM||kJ != kM||kJ = kM||kJ = kM||kJ != kM||kJ = kM|
|growth & reprod||
elas_pars_rgive elasticity coefficients. Function
get_pars_uconverts compound parameters into unscaled primary parameters at abundant food.
Another group of
get_pars functions obtain primary (rather than compound) parameters from data at abundant food.
This strategy comes with assumptions about particular (chemical) parameter values (chemical potentials and the like).
Again, all functions assume absence of surface-area linked maintenance.
They don't make use of the assumption k_J = k_M, but assume that k_J is known.
By increasing the number of known parameters, we can decrease the amount of data that is needed to get the remaining parameters, as reflected in the different
iget_pars_8 are inverse functions, from parameters to data.
iget_pars_9_foetus are for foetal development.
One strategy to set values of "known" parameters is to use the generalized animal settings of Table 8.1 in the DEB-book.
The maximum number of parameters than can be obtained at abundant food only is 9.
filter_data_9 filter allowable parameter and data combinations in the case of 9 parameters (including type M acceleration).
filter_data_8 filter allowable parameter and data combinations in the case of 8 parameters (no acceleration).
sgr_iso_metam. The latter accounts for type M accleration. Likewise, the mean age, length, squared and cubed length in the population at constant food density is computed by
The scaled functional response at which the specific population growth rate is zero is found by
Population characteristics are plotted against scaled functional response by
scaleobtains eco-physiological qantities as function of the zoom-factor and function
shscaleplots these quanties against maximum body weight, which itself is just one such quantity.