DEB_Daphnia {cvasi}

DEBtox Daphnia

Description

Creates a DEBtox Daphnia scemarop.

Usage

DEB_Daphnia()

Details

State variables

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

• D, scaled damage (C)

• L, body length (mm)

• R, cumulative reproduction (-)

• S, survival probability (-)

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

Parameters

The following parameters are required:

• General

  • L0, body length at start (mm)

  • Lp, body length at puberty (mm)

  • Lm, maximum body length (mm)

  • rB, von Bertalanffy growth rate constant (1/d)

  • Rm, maximum reproduction rate (#/d)

  • f, scaled functional response (-)

  • hb, background hazard rate (d-1)

• Extra parameters

  • Lf, body length at half-saturation feeding (mm)

  • Lj, body length at which acceleration stops (mm)

  • Tlag, lag time for start development (d)

• TKTD parameters

  • kd, dominant rate constant (d-1)

  • zb, effect threshold energy budget (C)

  • bb, effect strength energy-budget effects (1/C)

  • zs, effect threshold survival (C)

  • bs, effect strength survival (1/(C d))

• Global parameters

  • FBV, dry weight egg as fraction of structural body weight (-)

  • KRV, part. coeff. repro buffer and structure (kg/kg) (for losses with reproduction)

  • kap, approximation for kappa (for starvation response)

  • yP, product of yVA and yAV (for starvation response)

  • Lm_ref, reference max length for scaling rate constants (mm)

  • len, switch to fit length 1) with shrinking, 2) without shrinking

  • Tbp, brood-pouch delay (d)

• MoA, mode of action switch (-)

• FB, feedback on damage dynamics switch (-)

Mode of Action

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

• MoA = 1: assimilation/feeding

• MoA = 2: costs for maintenance

• MoA = 4: costs for growth and reproduction

• MoA = 8: costs for reproduction

• MoA = 16: hazard for reproduction

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().

Feedbacks

Any combination of the following damage feedbacks can be considered by the model:

• 1: surf:vol scaling uptake rate

• 2: surf:vol scaling elimination rate

• 4: growth dilution

• 8: losses with reproduction

To activate more than one feedback, simply add up the corresponding codes. To disable all feedbacks, set the parameter to zero.

Effects

The state variables L (body length), R (cumulative reproduction), and S (survival probability) 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().

Output variables

The following intermediary model variables can be added to the model output on demand, see simulate() for details:

• nout >= 3

  • f, actual f

  • fR, actual f considering starvation

  • kd, actual kd

• nout >= 6

  • s, stress level for metabolic effects

  • sA, stress factor on assimilation/feeding

  • h, hazard rate for effects on survival

• nout >= 10, damage feedbacks

  • xu, factor for surf:vol scaling uptake rate

  • xe, factor for surf:vol scaling elimination rate

  • xG, factor for growth dilution

  • xR, factor for losses with repro

Value

an S4 object of type DebDaphnia

See Also

Other DEB models: DEB-models, DEB_abj()