{"id":32209382,"url":"https://github.com/nkehrein/lemna","last_synced_at":"2025-10-22T06:05:40.320Z","repository":{"id":56922511,"uuid":"440140490","full_name":"nkehrein/lemna","owner":"nkehrein","description":"An implementation of the toxicokinetic-toxicodynamic model of the Lemna aquatic plant","archived":false,"fork":false,"pushed_at":"2025-03-31T13:13:55.000Z","size":1981,"stargazers_count":1,"open_issues_count":0,"forks_count":1,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-09-07T12:02:35.900Z","etag":null,"topics":["r","r-package","simulation"],"latest_commit_sha":null,"homepage":"","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/nkehrein.png","metadata":{"files":{"readme":"README.Rmd","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null}},"created_at":"2021-12-20T11:09:00.000Z","updated_at":"2025-03-31T13:13:48.000Z","dependencies_parsed_at":"2022-08-21T04:50:24.784Z","dependency_job_id":"943d9a2b-921e-44a2-bdac-45914bd11606","html_url":"https://github.com/nkehrein/lemna","commit_stats":{"total_commits":9,"total_committers":1,"mean_commits":9.0,"dds":0.0,"last_synced_commit":"32bfde5a3d21b46c50920f10a573b4c4dca32a92"},"previous_names":[],"tags_count":5,"template":false,"template_full_name":null,"purl":"pkg:github/nkehrein/lemna","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nkehrein%2Flemna","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nkehrein%2Flemna/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nkehrein%2Flemna/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nkehrein%2Flemna/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/nkehrein","download_url":"https://codeload.github.com/nkehrein/lemna/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nkehrein%2Flemna/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":280389354,"owners_count":26322513,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","status":"online","status_checked_at":"2025-10-22T02:00:06.515Z","response_time":63,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["r","r-package","simulation"],"created_at":"2025-10-22T06:03:38.395Z","updated_at":"2025-10-22T06:05:40.312Z","avatar_url":"https://github.com/nkehrein.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"---\noutput: github_document\n---\n\n\u003c!-- README.md is generated from README.Rmd. Please edit that file --\u003e\n\n```{r, include = FALSE}\nknitr::opts_chunk$set(\n  collapse = TRUE,\n  comment = \"#\u003e\",\n  fig.path = \"man/figures/README-\",\n  out.width = \"100%\"\n)\n```\n\n# lemna\n\n\u003c!-- badges: start --\u003e\n[![CRAN status](https://www.r-pkg.org/badges/version/lemna)](https://cran.r-project.org/package=lemna)\n[![R-CMD-check](https://github.com/nkehrein/lemna/workflows/R-CMD-check/badge.svg)](https://github.com/nkehrein/lemna/actions)\n\u003c!-- badges: end --\u003e\n\n## Overview\n\n\n*lemna* is a software package for the language [*R*](https://www.r-project.org/).\nIt implements model equations and default parameters to simulate the\ntoxicokinetic-toxicodynamic (TKTD) model of the *Lemna* aquatic plant.\n*Lemna* is a standard test macrophyte used in ecotox effect studies. The model\nwas described and published by the *SETAC Europe Interest Group Effect Modeling*\n(Klein *et al.* 2021). It is a refined description of the *Lemna* TKTD model\npublished by Schmitt *et al.* (2013). This package contains the model's reference\nimplementation which is provided by the *SETAC* interest group.\n\n\n## Installation\n\n```{r, eval=FALSE}\n## install directly from CRAN\ninstall.packages(\"lemna\")\n\n## install latest development version from GitHub\n#install.packages(\"remotes\")\nremotes::install_github(\"nkehrein/lemna\", dependencies=TRUE)\n```\n\n## Usage\n\nThe lemna package provides model equations and some useful helpers to simulate\nthe growth of *Lemna* (duckweed) aquatic plant populations. A simulation is run\nby using the `lemna()` function. The required scenario data are either supplied\nindividually on function call or are passed as a pre-defined scenario object,\nsuch as the `focusd1` sample scenario:\n\n```{r example}\nlibrary(lemna)\n\n# simulate sample scenario\nresult \u003c- lemna(focusd1)\nhead(result)\n\nplot(result)\n```\n\n## Learning lemna\n\nThe package contains two vignettes that may help you getting started:\n\n - [Introduction to the Lemna package](https://nkehrein.github.io/lemna/lemna-introduction.html)\u003cbr /\u003e\n   A general *Tutorial* and guide to the package functions\n - [Lemna model verification](https://nkehrein.github.io/lemna/lemna-verification.html)\u003cbr /\u003e\n   A verification of the model implementation against results of the Schmitt\n   *et al.* implementation. Contains advanced workflows of package features.\n\n## License\n\nThe package and its source code is free and open-source software available under\nthe MIT license.\n\n## Issues\n\nIf you find any issues or bugs within the package, please create a\n[new issue](https://github.com/nkehrein/lemna/issues) on GitHub.\n\n## References\n\n- Klein J., Cedergreen N., Heine S., Kehrein N., Reichenberger S., Rendal C.,\n  Schmitt W., Hommen U., 2021: Refined description of the *Lemna* TKTD growth model\n  based on *Schmitt et al.* (2013) – equation system and default parameters,\n  implementation in R.\n  Report of the working group *Lemna* of the SETAC Europe Interest Group Effect\n  Modeling. Version 1.3, September 2025.\n  https://www.setac.org/group/effect-modeling.html\n- Schmitt W., Bruns E., Dollinger M., Sowig P., 2013: Mechanistic TK/TD-model\n  simulating the effect of growth inhibitors on *Lemna* populations. Ecol Model\n  255, pp. 1-10. DOI: [10.1016/j.ecolmodel.2013.01.017](https://doi.org/10.1016/j.ecolmodel.2013.01.017)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnkehrein%2Flemna","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fnkehrein%2Flemna","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnkehrein%2Flemna/lists"}