https://github.com/nkehrein/lemna
An implementation of the toxicokinetic-toxicodynamic model of the Lemna aquatic plant
https://github.com/nkehrein/lemna
r r-package simulation
Last synced: 8 months ago
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An implementation of the toxicokinetic-toxicodynamic model of the Lemna aquatic plant
- Host: GitHub
- URL: https://github.com/nkehrein/lemna
- Owner: nkehrein
- License: other
- Created: 2021-12-20T11:09:00.000Z (over 4 years ago)
- Default Branch: master
- Last Pushed: 2025-03-31T13:13:55.000Z (about 1 year ago)
- Last Synced: 2025-09-07T12:02:35.900Z (10 months ago)
- Topics: r, r-package, simulation
- Language: R
- Homepage:
- Size: 1.89 MB
- Stars: 1
- Watchers: 1
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.Rmd
- License: LICENSE
Awesome Lists containing this project
README
---
output: github_document
---
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
# lemna
[](https://cran.r-project.org/package=lemna)
[](https://github.com/nkehrein/lemna/actions)
## Overview
*lemna* is a software package for the language [*R*](https://www.r-project.org/).
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.* 2021). 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
```{r, eval=FALSE}
## 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:
```{r example}
library(lemna)
# simulate sample scenario
result <- lemna(focusd1)
head(result)
plot(result)
```
## Learning lemna
The package contains two vignettes that may help you getting started:
- [Introduction to the Lemna package](https://nkehrein.github.io/lemna/lemna-introduction.html)
A general *Tutorial* and guide to the package functions
- [Lemna model verification](https://nkehrein.github.io/lemna/lemna-verification.html)
A verification of the model implementation against results of the Schmitt
*et al.* implementation. Contains advanced workflows of package features.
## 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](https://github.com/nkehrein/lemna/issues) on GitHub.
## References
- Klein J., Cedergreen N., Heine S., Kehrein N., 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,
implementation in R.
Report of the working group *Lemna* of the SETAC Europe Interest Group Effect
Modeling. Version 1.3, September 2025.
https://www.setac.org/group/effect-modeling.html
- Schmitt W., Bruns E., Dollinger M., 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](https://doi.org/10.1016/j.ecolmodel.2013.01.017)