Lemna_SETAC {cvasi}R Documentation

Lemna model (Klein et al. 2021)

Description

The model was described and published by the SETAC Europe Interest Group Effect Modeling (Klein et al. 2022). It is based on the Lemna model by Schmitt (2013). The model is a mechanistic combined toxicokinetic-toxicodynamic (TK/TD) and growth model for the aquatic macrophytes Lemna spp.. The model simulates the development of Lemna biomass under laboratory and environmental conditions. Growth of the Lemna population is simulated on basis of photosynthesis and respiration rates which are functions of environmental conditions. The toxicodynamic sub-model describes the effects of growth-inhibiting substances by a respective reduction in the photosynthesis rate based on internal concentrations.

Usage

Lemna_SETAC()

Value

an S4 object of type LemnaSetac

State variables

The model has two state variables:

Model parameters

Forcings

Besides exposure, the model requires four environmental properties as time-series input:

Forcings time-series are represented by data.frame objects consisting of two columns. The first for time and the second for the environmental factor in question.

Entries of the data.frame need to be ordered chronologically. A time-series can consist of only a single row; in this case it will represent constant environmental conditions. See scenarios for more details.

Effects

Supported effect endpoints include BM (biomass) and r (average growth rate during simulation). The effect on biomass is calculated from the last state of a simulation. Be aware that endpoint r is incompatible with biomass transfers.

Simulation output

For reasons of convenience, the return value contains by default two additional variables derived from simulation results: the internal concentration C_int as well as the number of fronds FrondNo. These can be disabled by setting the argument nout = 0.

The available output levels are as follows:

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:

Biomass transfer

Models supporting biomass transfer can be instructed to move a fixed amount of biomass to a new medium after a period of time. This feature replicates a procedure occurring in e.g. Lemna effect studies and may be necessary to recreate study results.

The biomass transfer feature assumes that always a fixed amount of biomass is transferred. Transfers can occur at any fixed point in time or in regular intervals. During a transfer, the biomass is reset to the transferred amount and additional compartments can be scaled 1:1 accordingly, to e.g. reflect the change in internal toxicant mass when biomass is modified. Transfer settings can be modified using set_transfer().

If a transfer occurs, simulation results of that time point will report the model state before the transfer. Be aware that if transfers are defined using the interval argument, the transfers will always occur relative to time point zero (t = 0). As an example, setting a regular transfer of seven days, interval = 7, will result at transfers occurring at time points which are integer multiplicates of seven, such as t=0, t=7, t=14 and so forth. The starting and end times of a scenario do not influece when a regular transfer occurs, only if it occurs.

References

Klein J., Cedergreen N., Heine S., Reichenberger S., Rendal C., Schmitt W., Hommen U., 2021: Refined description of the Lemna TKTD growth model based on Schmitt et al. (2013) - equation system and default parameters. Report of the working group Lemna of the SETAC Europe Interest Group Effect Modeling. Version 1, uploaded on 22. Sept. 2021. https://www.setac.org/group/effect-modeling.html

Schmitt W., Bruns E., Dollinger M., and Sowig P., 2013: Mechanistic TK/TD-model simulating the effect of growth inhibitors on Lemna populations. Ecol Model 255, pp. 1-10. doi:10.1016/j.ecolmodel.2013.01.017

See Also

Lemna-models, Macrophyte-models, Transferable, Scenarios

Other Lemna models: Lemna-models, Lemna_Schmitt()

Other macrophyte models: Lemna_Schmitt(), Macrophyte-models, Myrio(), Myrio_log()


[Package cvasi version 1.4.0 Index]