{"id":32206330,"url":"https://github.com/cvasi-tktd/cvasi","last_synced_at":"2026-02-18T22:36:42.413Z","repository":{"id":237686231,"uuid":"791783745","full_name":"cvasi-tktd/cvasi","owner":"cvasi-tktd","description":"An R package to simulate ecotox TK/TD models, calculate effects, derive effect profiles, and to fit model parameters to observed data.","archived":false,"fork":false,"pushed_at":"2025-11-24T09:46:30.000Z","size":14188,"stargazers_count":5,"open_issues_count":2,"forks_count":2,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-12-08T22:00:56.361Z","etag":null,"topics":["ecotoxicology","modeling","simulation"],"latest_commit_sha":null,"homepage":"","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/cvasi-tktd.png","metadata":{"files":{"readme":"README.Rmd","changelog":"NEWS.md","contributing":"CONTRIBUTING.md","funding":null,"license":"LICENSE.md","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":".github/CODEOWNERS","security":null,"support":null,"governance":null,"roadmap":"ROADMAP.md","authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2024-04-25T11:12:17.000Z","updated_at":"2025-09-30T08:40:31.000Z","dependencies_parsed_at":null,"dependency_job_id":"8f407647-f9d4-4f6c-812e-23ddbc0babd5","html_url":"https://github.com/cvasi-tktd/cvasi","commit_stats":null,"previous_names":["cvasi-tktd/cvasi"],"tags_count":10,"template":false,"template_full_name":null,"purl":"pkg:github/cvasi-tktd/cvasi","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cvasi-tktd%2Fcvasi","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cvasi-tktd%2Fcvasi/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cvasi-tktd%2Fcvasi/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cvasi-tktd%2Fcvasi/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/cvasi-tktd","download_url":"https://codeload.github.com/cvasi-tktd/cvasi/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/cvasi-tktd%2Fcvasi/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":29597266,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-02-18T22:25:43.180Z","status":"ssl_error","status_checked_at":"2026-02-18T22:25:42.766Z","response_time":162,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.5:443 state=error: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"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":["ecotoxicology","modeling","simulation"],"created_at":"2025-10-22T05:21:19.627Z","updated_at":"2026-02-18T22:36:42.389Z","avatar_url":"https://github.com/cvasi-tktd.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 = \"doc/figures/readme-\",\n  fig.height=4,\n  fig.align='center',\n  out.width = \"100%\"\n)\n\nlibrary(cvasi)\nlibrary(purrr)\n```\n\n# cvasi: Calibration, Validation, and Simulation of TKTD models in R\n\n\u003c!-- badges: start --\u003e\n[![CRAN status](https://www.r-pkg.org/badges/version/cvasi)](https://cran.r-project.org/package=cvasi)\n[![R-CMD-check](https://github.com/cvasi-tktd/cvasi/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/cvasi-tktd/cvasi/actions/workflows/R-CMD-check.yaml)\n\u003c!--[![Codecov test coverage](https://codecov.io/gh/xy/cvasi/branch/main/graph/badge.svg)](https://app.codecov.io/gh/xy/cvasi?branch=main)--\u003e\n\u003c!-- badges: end --\u003e\n\nThe `cvasi` package aims to ease the use of ecotox effect models by providing an\nintuitive workflow. Model inputs and parameters are encapsulated in scenario\nobjects which can be piped to other functions. Operations can be chained using\nthe `tidyr` syntax. The most time-consuming processes can be run in parallel if\nrequested.\n\nThe package provides facilities to\n\n* Simulate effect models such as *GUTS*, *GUTS-RED*, *DEB*, *Lemna* based on\n  Schmitt et al. (2013), and algae models based on Weber et al. (2012),\n* Calculate effect endpoints,\n* Derive effect profiles (*EPx* values),\n* Import exposure time-series from *FOCUS TOXSWA*,\n* Import fitted parameters from *morse*,\n* And much more.\n\nA graphical user interface implemented in [Shiny](https://posit.co/products/open-source/rstudio/)\nis also available, see the *[cvasi.ui](https://github.com/cvasi-tktd/cvasi.ui/)*\npackage. Please have a look at the [Changelog](NEWS.md)\nfor an overview of user-facing updates and changes.\n\n\n## Installation\n\nInstall the package from CRAN:\n\n```{r eval=FALSE}\ninstall.packages(\"cvasi\", dependencies=TRUE)\n```\n\nOr install the newest development version from *GitHub*:\n\n```{r eval=FALSE}\ninstall.packages(\"remotes\", dependencies=TRUE)\nremotes::install_github(\"cvasi-tktd/cvasi\", dependencies=TRUE)\n```\n\nFor installing `cvasi` from *GitHub* on Windows computers, please make sure that\nyou also have [*Rtools*](https://cran.r-project.org/bin/windows/Rtools/) installed\non your machine. *Rtools* are required to compile the package's C code.\n\n\n## Documentation\n\nThe package contains the following vignettes\n\n* [User Manual](https://github.com/cvasi-tktd/cvasi/blob/main/doc/cvasi-1-manual.md)\n* [Modeling Howto](https://github.com/cvasi-tktd/cvasi/blob/main/doc/cvasi-2-howto.md)\n\nThey can also be accessed locally by executing an *R* statement such as:\n```{r, eval=FALSE}\nvignette(\"cvasi-1-manual\", package=\"cvasi\")\n```\n\n\n## Usage\n\nBasic usage:\n```{r,message=FALSE,out.width=\"70%\"}\nlibrary(cvasi)\n\n# create and parameterize a GUTS-RED-IT scenario\nscenario \u003c- GUTS_RED_IT() %\u003e%\n  set_param(c(kd=0.0005, hb=0, alpha=0.4, beta=1.5)) %\u003e%\n  set_exposure(data.frame(time=c(0, 100, 101, 200, 201, 400),\n                          conc=c(0, 0, 0.1, 0.1, 0, 0))) %\u003e%\n  set_times(1:400)\n\n# simulate scenario\nresults \u003c- scenario %\u003e% simulate()\ntail(results)\n\n# ... and plot simulation results\nplot(results)\n```\n\nCalculation of effects:\n```{r out.width=\"60%\",warning=FALSE}\n# calculate effect level\nscenario %\u003e% effect()\n\n# create a dose-response curve\ndrc \u003c- scenario %\u003e% dose_response()\nhead(drc)\n\n# plot the dose-response curve\nplot(drc)\n\n# derive EPx values\nscenario %\u003e% epx()\n```\n\nMultiple scenarios can be processed in parallel without modifications to the workflow:\n```{r eval=FALSE}\n# enable parallel processing\nfuture::plan(future::multisession)\n\n# derive EPx for a list of 100 scenarios in parallel\nrep(c(scenario), 100) %\u003e% epx()\n\n# disable parallel processing\nfuture::plan(future::sequential)\n```\n\n## License\n\nThe package and its source code is free and open-source software available under\nthe [GPL-3.0 license](https://github.com/cvasi-tktd/cvasi/blob/main/LICENSE.md).\n\n## Issues\n\nIf you find any issues or bugs within the package, please create a\n[new issue](https://github.com/cvasi-tktd/cvasi/issues) on GitHub.\n\n## Contributing\n\nContributions to the project are welcome! Please have a look at the\n[Contribution Guidelines](https://github.com/cvasi-tktd/cvasi/blob/main/CONTRIBUTING.md) before submitting a Pull Request.\n\n\n## Acknowledgements\n\nFinancial support for creation and release of this software project was provided\nby Bayer Crop Science. This R package started as an internal project at Bayer\nCrop Science and the project owners would like to thank the people who have\ncontributed (in no particular order):\n\nNils Kehrein, Johannes Witt, André Gergs, Thomas Preuss, Julian Heinrich,\nZhenglei Gao, Tjalling Jager, Dirk Nickisch, Torben Wittwer, and Peter Vermeiren.\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcvasi-tktd%2Fcvasi","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fcvasi-tktd%2Fcvasi","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcvasi-tktd%2Fcvasi/lists"}