DEBtox | R Documentation |
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.
DEBtox()
DEB_Daphnia()
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.
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.
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))
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.
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()
.
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
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
an S4 object of type DebTox
DEB_Daphnia()
: Deprecated model variant of DEBtox()
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")}
Other DEB models:
DEB-models
,
DEB_abj()
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.