DEBtox {cvasi} | R Documentation |
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 to1
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 is1
. -
Tbp
, optional brood-pouch delay (d). Set toNA
or zero to disable. Default value is0
. -
MoA
, mode of action switches (-). Default value is0
. -
FB
, feedback on damage dynamics switches (-). Default value is0
.
-
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()
.
Simulation output
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
Solver settings
The arguments to ODE solver deSolve::ode()
control how model equations
are numerically integrated. The settings influence stability of the numerical
integration scheme as well as numerical precision of model outputs. Generally, the
default settings as defined by deSolve are used, but all deSolve settings
can be modified in cvasi workflows by the user, if needed. Please refer
to e.g. simulate()
on how to pass arguments to deSolve in cvasi
workflows.
Some default settings of deSolve were adapted for this model by expert judgement to enable precise, but also computationally efficient, simulations for most model parameters. These settings can be modified by the user, if needed:
-
method = 'ode45'
Selects the Dormand-Prince 4(5) method of the Runge-Kutta family, seedeSolve::rkMethod()
for details.
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 ofDEBtox()
References
Jager T, 2020: Revisiting simplified DEBtox models for analysing ecotoxicity data. Ecol Model 416. 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. doi:10.1002/etc.5795
See Also
Other DEB models:
DEB-models
,
DEB_abj()