DEB_abj: DEB_abj

In cvasi: Calibration, Validation, and Simulation of TKTD Models

DEB_abj

Description

Creates a DEB abj scenario. The abj model with type M acceleration is like model std, but acceleration occurs between birth and metamorphosis (V1-morph). Isomorphy is assumed before and after acceleration. Metamorphosis is before puberty and occurs at maturity E_Hj, which might or might not correspond with changes in morphology. The abj model is a one-parameter extension of model std (DEB Wiki).

Usage

DEB_abj()

Details

State variables

The following list describes the default names and standard units of the model's state variables:

• L, structural length (cm)

• E, energy reserve (J)

• H, energy invested in maturity (J)

• R, reproduction buffer (J)

• cV, internal concentration (C)

• Lmax, maximum structural length (cm)

All state variables are initialized with zero. See set_init() on how to set the initial state.

Parameters

The following model parameters are required:

• p_M, vol-spec somatic maintenance (J/d.cm^3)

• v, energy conductance (cm/d)

• k_J, maturity maint rate coefficient (1/d)

• p_Am, surface-area specific maximum assimilation rate (J/d.cm^2)

• kap, allocation fraction to soma (-)

• E_G, spec cost for structure (J/cm^3)

• f, scaled functional response (-)

• E_Hj, maturity at metamorphosis (J)

• E_Hp, maturity at puberty (J)

• kap_R, reproduction efficiency (-)

• L_b, structural length at birth (cm)

• L_j, structural length at metamorphosis (cm)

• ke, elimination rate constant (d-1)

• c0, no-effect concentration sub-lethal (C)

• cT, tolerance concentration (C)

• MoA, mode of action switch (-)

Mode of Actions

Any combination of the following mode of actions (MoA) can be considered by the model:

• MoA = 1: effect on feeding

• MoA = 2: effect on maintenance costs

• MoA = 4: effect on overhead costs for making an egg

• MoA = 8: hazard during oogenesis

• MoA = 16: energy conductance

To activate more than one MoA, simply add up the corresponding codes. To disable all MoAs, set the parameter to zero. See also set_mode_of_action().

Effects

The state variables L (structural length) and R (reproduction buffer) are set as effect endpoints by default. All state variables are available as potential endpoints. The list of considered endpoints can be modified by using set_endpoints().

To calculate effects, each DEB scenario is simulated twice: One simulation which considers exposure to a toxicant and one simulation without exposure, i.e. a control. See also effect().

Value

an S4 object of type DebAbj

See Also

Other DEB models: DEB-models, DEBtox()

Examples

# Create an abj scenario from scratch and simulate it
DEB_abj() %>%
  set_init(c(L=0.02,E=0.1,H=0.01)) %>%
  set_param(c(p_M=3000,v=0.02,k_J=0.6,p_Am=300,kap=0.9,E_G=4000,f=1,
              E_Hj=0.05,E_Hp=0.3,kap_R=0.9,ke=1,c0=0,cT=1,L_b=0.02,
              L_j=0.04,MoA=0)) %>%
  set_exposure(no_exposure()) %>%
  set_times(0:10) %>%
  simulate()

# Print information about sample scenario 'americamysis'
americamysis

# Simulate 'americamysis' scenario
americamysis %>% simulate()

cvasi documentation built on Sept. 23, 2024, 9:08 a.m.