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lemna

Overview

lemna is a software package for the language R. It implements model equations and default parameters to simulate the toxicokinetic-toxicodynamic (TKTD) model of the Lemna aquatic plant. Lemna is a standard test macrophyte used in ecotox effect studies. The model was described and published by the SETAC Europe Interest Group Effect Modeling (Klein et al. 2022). It is a refined description of the Lemna TKTD model published by Schmitt et al. (2013). This package contains the model’s reference implementation which is provided by the SETAC interest group.

Installation

## install directly from CRAN
install.packages("lemna")

## install latest development version from GitHub
#install.packages("remotes")
remotes::install_github("nkehrein/lemna", dependencies=TRUE)

Usage

The lemna package provides model equations and some useful helpers to simulate the growth of Lemna (duckweed) aquatic plant populations. A simulation is run by using the lemna() function. The required scenario data are either supplied individually on function call or are passed as a pre-defined scenario object, such as the focusd1 sample scenario:

library(lemna)

# simulate sample scenario
result <- lemna(focusd1)
head(result)
#>   time       BM     M_int        C_int  FrondNo
#> 1    0 80.00000 0.0000000 0.0000000000 200000.0
#> 2    1 79.48177 0.6614503 0.0004983256 198704.4
#> 3    2 79.00414 2.2061048 0.0016720907 197510.3
#> 4    3 78.57538 4.1750616 0.0031817050 196438.5
#> 5    4 78.23362 6.2899397 0.0048143381 195584.0
#> 6    5 78.01035 8.3810150 0.0064332127 195025.9

plot(result)

Learning lemna

The package contains two vignettes that may help you getting started:

License

The package and its source code is free and open-source software available under the MIT license.

Issues

If you find any issues or bugs within the package, please create a new issue on GitHub.

References

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.