bayesnec: An R Package for Concentration-Response Modeling and Estimation of Toxicity Metrics
The bayesnec package has been developed for R to fit concentration (dose)-response curves (CR) to toxicity data for the purpose of deriving no-effect-concentration (NEC), no-significant-effect-concentration (NSEC), and effect-concentration (of specified percentage "x", ECx) thresholds fro...
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| Format: | Article |
| Language: | English |
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Foundation for Open Access Statistics
2024-08-01
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| Series: | Journal of Statistical Software |
| Online Access: | https://www.jstatsoft.org/index.php/jss/article/view/4916 |
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| author | Rebecca Fisher Diego R. Barneche Gerard F. Ricardo David R. Fox |
| author_facet | Rebecca Fisher Diego R. Barneche Gerard F. Ricardo David R. Fox |
| author_sort | Rebecca Fisher |
| collection | DOAJ |
| description |
The bayesnec package has been developed for R to fit concentration (dose)-response curves (CR) to toxicity data for the purpose of deriving no-effect-concentration (NEC), no-significant-effect-concentration (NSEC), and effect-concentration (of specified percentage "x", ECx) thresholds from non-linear models fitted using Bayesian Hamiltonian Monte Carlo (HMC) via R packages brms and rstan or cmdstanr. In bayesnec it is possible to fit a single model, custom model-set, specific model-set or all of the available models. When multiple models are specified, the bnec() function returns a model weighted average estimate of predicted posterior values. A range of support functions and methods is also included to work with the returned single, or multi-model objects that allow extraction of raw, or model averaged predicted, NEC, NSEC and ECx values and to interrogate the fitted model or model-set. By combining Bayesian methods with model averaging, bayesnec provides a single estimate of toxicity and associated uncertainty that can be directly integrated into risk assessment frameworks.
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| format | Article |
| id | doaj-art-4dc76477c2c74f72a634dc39e0f6d0e6 |
| institution | Kabale University |
| issn | 1548-7660 |
| language | English |
| publishDate | 2024-08-01 |
| publisher | Foundation for Open Access Statistics |
| record_format | Article |
| series | Journal of Statistical Software |
| spelling | doaj-art-4dc76477c2c74f72a634dc39e0f6d0e62024-12-29T00:12:42ZengFoundation for Open Access StatisticsJournal of Statistical Software1548-76602024-08-01110110.18637/jss.v110.i05bayesnec: An R Package for Concentration-Response Modeling and Estimation of Toxicity MetricsRebecca Fisher0Diego R. Barneche1Gerard F. Ricardo2David R. Fox3Australian Institute of Marine ScienceAustralian Institute of Marine ScienceThe University of QueenslandThe University of Melbourne The bayesnec package has been developed for R to fit concentration (dose)-response curves (CR) to toxicity data for the purpose of deriving no-effect-concentration (NEC), no-significant-effect-concentration (NSEC), and effect-concentration (of specified percentage "x", ECx) thresholds from non-linear models fitted using Bayesian Hamiltonian Monte Carlo (HMC) via R packages brms and rstan or cmdstanr. In bayesnec it is possible to fit a single model, custom model-set, specific model-set or all of the available models. When multiple models are specified, the bnec() function returns a model weighted average estimate of predicted posterior values. A range of support functions and methods is also included to work with the returned single, or multi-model objects that allow extraction of raw, or model averaged predicted, NEC, NSEC and ECx values and to interrogate the fitted model or model-set. By combining Bayesian methods with model averaging, bayesnec provides a single estimate of toxicity and associated uncertainty that can be directly integrated into risk assessment frameworks. https://www.jstatsoft.org/index.php/jss/article/view/4916 |
| spellingShingle | Rebecca Fisher Diego R. Barneche Gerard F. Ricardo David R. Fox bayesnec: An R Package for Concentration-Response Modeling and Estimation of Toxicity Metrics Journal of Statistical Software |
| title | bayesnec: An R Package for Concentration-Response Modeling and Estimation of Toxicity Metrics |
| title_full | bayesnec: An R Package for Concentration-Response Modeling and Estimation of Toxicity Metrics |
| title_fullStr | bayesnec: An R Package for Concentration-Response Modeling and Estimation of Toxicity Metrics |
| title_full_unstemmed | bayesnec: An R Package for Concentration-Response Modeling and Estimation of Toxicity Metrics |
| title_short | bayesnec: An R Package for Concentration-Response Modeling and Estimation of Toxicity Metrics |
| title_sort | bayesnec an r package for concentration response modeling and estimation of toxicity metrics |
| url | https://www.jstatsoft.org/index.php/jss/article/view/4916 |
| work_keys_str_mv | AT rebeccafisher bayesnecanrpackageforconcentrationresponsemodelingandestimationoftoxicitymetrics AT diegorbarneche bayesnecanrpackageforconcentrationresponsemodelingandestimationoftoxicitymetrics AT gerardfricardo bayesnecanrpackageforconcentrationresponsemodelingandestimationoftoxicitymetrics AT davidrfox bayesnecanrpackageforconcentrationresponsemodelingandestimationoftoxicitymetrics |