DEBtox: DEBtox model

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

DEBtox model

Description

Creates a DEBtox scenario as described by Jager (2020). It represents a simplified DEBtox model based on DEBkiss. In the BYOM application [link], this model is referred to as DEBtox 2019, version 4.7. It supports an optional feature of the ERA special model variant, which can consider a reference Lm parameter to compare results of multiple datasets.

Usage

DEBtox()

DEB_Daphnia()

Details

State variables

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

• D, scaled damage ([C])

• L, body length (mm)

• R, cumulative reproduction (-)

• S, survival probability (-)

State variables D, L, and R are initialized with zero. Variable S is initialized with one (1.0). See set_init() on how to set the initial state manually.

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)

  • a, Weibull background hazard coefficient (-). Set to 1 to disable.

• 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)

• TK/TD 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))

• Other parameters (formerly globals in BYOM)

  • 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, optional reference max length for scaling rate constants (mm). Set to zero to disable the reference length. Disabled by default.

  • len, a switch to control body length dynamics: 1 organism can shrink, 2 organism cannot shrink. Default value is 1.

  • Tbp, optional brood-pouch delay (d). Set to NA or zero to disable. Default value is 0.

  • MoA, mode of action switches (-). Default value is 0.

  • FB, feedback on damage dynamics switches (-). Default value is 0.

A reference Lm_ref is needed to properly compare different data sets, or when calibrating on more than one data set. If Lm differs, one would not want to have different rate constants at the same length.

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 mode of action, simply add up the corresponding codes and set parameter MoA to the desired value. To disable all mode of actions, set parameter MoA to zero. See also set_moa().

As an example, to consider effects on feeding and maintenance, set the mode of action to three (3):

DEBtox() %>% set_param(c(MoA=3))

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 DEBtox 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. Simply set the optional parameter nout to the required output level and pass it to simulate().

• nout >= 1: f, actual scaled response

• nout >= 2: fR, actual f considering starvation

• nout >= 3: kd, actual kd

• nout >= 4: s, stress level

• nout >= 5: h, hazard rate

• nout >= 6: sA, stress factor on assimilation/feeding

• nout >= 7: sM, stress factor on maintenance

• nout >= 8: sG, stress factor on growth costs

• nout >= 9: sR, stress factor on reproduction costs

• nout >= 10: sH, stress factor on hazard to reproduction

• nout >= 11: xu, damage feedback factor for surf:vol scaling uptake rate

• nout >= 12: xe, damage feedback factor for surf:vol scaling elimination rate

• nout >= 13: xG, damage feedback factor for growth dilution

• nout >= 14: xR, damage feedback factor for losses with repro

Model history and changes

• cvasi v1.0.0

  • The DEB_Daphnia() model implemented BYOM's DEBtox 2019 model version 4.5

• cvasi v1.2.0

  • The model equations were updated to conform with BYOM's DEBtox 2019 version 4.7. This introduced a new model parameter a, the Weibull background hazard coefficient, and limited the maximum hazard rate to 99% per hour.

  • The scenario constructor was renamed to DEBtox().

  • Additional intermediary model variables available as optional simulation output

Value

an S4 object of type DebTox

Functions

• DEB_Daphnia(): Deprecated model variant of DEBtox()

References

Jager T, 2020: Revisiting simplified DEBtox models for analysing ecotoxicity data. Ecol Model 416. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1016/j.ecolmodel.2019.108904")}

Romoli et al., 2024: Environmental risk assessment with energy budget models: a comparison between two models of different complexity. Environ Toxicol Chem 43(2):440-449. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1002/etc.5795")}

See Also

Other DEB models: DEB-models, DEB_abj()

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