R: Myriophyllum model with logistic growth

Myrio_log {cvasi}

R Documentation

Myriophyllum model with logistic growth

Description

The Myriophyllum model is derived from the Lemna TKTD model by Klein et al. (2021). Myrio_log() modifies the Myrio() model to feature logistic growth, i.e. control growth is described by the differential equation ⁠d BM/dt = k_photo_max*BM*(1 - BM/BM_L)⁠ where BM_L is the carrying capacity.

Usage

Myrio_log()

Value

an S4 object of type MyrioLogScenario

Model parameters

Growth model
- k_photo_max, Maximum photosynthesis rate (d-1), default: 0.47
- BM_L, Carrying capacity (g dw m-2)
Concentration response (Toxicodynamics)
- EC50_int, Internal concentration resulting in 50% effect (ug L-1)
- E_max, Maximum inhibition (-), default: 1
- b, Slope parameter (-)
Internal concentration (Toxicokinetics)
- P, Permeability (cm d-1)
- r_A_DW, Area per dry-weight ratio (cm2 g-1), default: 1000
- r_FW_DW, Fresh weight per dry weight ratio (-), default: 16.7
- r_FW_V, Fresh weight density (g cm-3), default: 1
- r_DW_TSL, Dry weight per total shoot length ratio (?)
- K_pw, Partitioning coefficient plant:water (-), default: 1
- k_met, Metabolisation rate (d-1), default: 0

State variables

The model has two state variables:

BM, Biomass (g dw m-2)
M_int, Mass of toxicant in plant population (mass per m2, e.g. ug m-2)

Environmental factors

None.

Simulation output

Simulation results will contain two additional columns besides state variables:

C_int, internal concentration of toxicant (mass per volume)
TSL, total shoot length (?)

The available output levels are as follows:

nout >= 1
- C_int, internal concentration (mass per volume)
nout >= 2
- TSL, total shoot length (?)
nout >= 3
- f_photo, photosynthesis dependency function (-)
nout >= 5, growth and TK/TD
- C_int_unb, unbound internal concentration (mass per volume)
- C_ext, external concentration (mass per volume)
nout >= 7, environmental factors
- dBM, biomass derivative (g dw m-2 d-1)
- dM_int, mass of toxicant in plants derivative (mass per m2 d-1)

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.

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().

Any transfer time point must also be an output time point. If a transfer occurs, simulation results of that time point will report the model state before the transfer. Be aware that in order to use transfers at regular intervals, the simulation must start at time point zero.

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