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Bioassay Analysis Using R

Author

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  • Ritz, Christian
  • Streibig, Jens C.

Abstract

We describe an add-on package for the language and environment R which allows simultaneous fitting of several non-linear regression models. The focus is on analysis of dose response curves, but the functionality is applicable to arbitrary non-linear regression models. Features of the package is illustrated in examples.

Suggested Citation

  • Ritz, Christian & Streibig, Jens C., 2005. "Bioassay Analysis Using R," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 12(i05).
    • Handle: RePEc:jss:jstsof:v:012:i05
    DOI: http://hdl.handle.net/10.18637/jss.v012.i05
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    1. Lea A I Vaas & Johannes Sikorski & Victoria Michael & Markus Göker & Hans-Peter Klenk, 2012. "Visualization and Curve-Parameter Estimation Strategies for Efficient Exploration of Phenotype Microarray Kinetics," PLOS ONE, Public Library of Science, vol. 7(4), pages 1-18, April.
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    3. Hector Sanz & John J Aponte & Jaroslaw Harezlak & Yan Dong & Aintzane Ayestaran & Augusto Nhabomba & Maxmillian Mpina & Obiang Régis Maurin & Núria Díez-Padrisa & Ruth Aguilar & Gemma Moncunill & Agna, 2017. "drLumi: An open-source package to manage data, calibrate, and conduct quality control of multiplex bead-based immunoassays data analysis," PLOS ONE, Public Library of Science, vol. 12(11), pages 1-18, November.
    4. Euro Pannacci & Marco Masi & Michela Farneselli & Francesco Tei, 2020. "Evaluation of Mugwort ( Artemisia vulgaris L.) Aqueous Extract as a Potential Bioherbicide to Control Amaranthus retroflexus L. in Maize," Agriculture, MDPI, vol. 10(12), pages 1-13, December.
    5. Holst, Niels & Lang, Andreas & Lövei, Gabor & Otto, Mathias, 2013. "Increased mortality is predicted of Inachis io larvae caused by Bt-maize pollen in European farmland," Ecological Modelling, Elsevier, vol. 250(C), pages 126-133.
    6. Euro Pannacci & Selene Baratta & Beatrice Falcinelli & Michela Farneselli & Francesco Tei, 2022. "Mugwort ( Artemisia vulgaris L.) Aqueous Extract: Hormesis and Biostimulant Activity for Seed Germination and Seedling Growth in Vegetable Crops," Agriculture, MDPI, vol. 12(9), pages 1-10, August.
    7. Christian Andreasen & Zahra Bitarafan & Johanna Fenselau & Christoph Glasner, 2018. "Exploiting Waste Heat from Combine Harvesters to Damage Harvested Weed Seeds and Reduce Weed Infestation," Agriculture, MDPI, vol. 8(3), pages 1-12, March.
    8. Christoph Kunz & Dominic J. Sturm & Markus Sökefeld & Roland Gerhards, 2017. "Weed suppression and early sugar beet development under different cover crop mulches," Plant Protection Science, Czech Academy of Agricultural Sciences, vol. 53(3), pages 187-193.
    9. Muhammad Javaid Akhter & Solvejg Kopp Mathiassen & Zelalem Eshetu Bekalu & Henrik Brinch-Pedersen & Per Kudsk, 2021. "Increased Activity of 5-Enolpyruvylshikimate-3-phosphate Synthase (EPSPS) Enzyme Describe the Natural Tolerance of Vulpia myuros to Glyphosate in Comparison with Apera spica-venti," Agriculture, MDPI, vol. 11(8), pages 1-15, July.
    10. Floriane Larras & Agnès Bouchez & Frédéric Rimet & Bernard Montuelle, 2012. "Using Bioassays and Species Sensitivity Distributions to Assess Herbicide Toxicity towards Benthic Diatoms," PLOS ONE, Public Library of Science, vol. 7(8), pages 1-9, August.
    11. Christian Ritz & Florent Baty & Jens C Streibig & Daniel Gerhard, 2015. "Dose-Response Analysis Using R," PLOS ONE, Public Library of Science, vol. 10(12), pages 1-13, December.
    12. LonÄ arić, Željka & K. Hackenberger, Branimir, 2013. "Stage and age structured Aedes vexans and Culex pipiens (Diptera: Culicidae) climate-dependent matrix population model," Theoretical Population Biology, Elsevier, vol. 83(C), pages 82-94.
    13. Hyun Seung Won & Wong Weng Kee, 2015. "Multiple-Objective Optimal Designs for Studying the Dose Response Function and Interesting Dose Levels," The International Journal of Biostatistics, De Gruyter, vol. 11(2), pages 253-271, November.
    14. Marcos Krull, 2020. "Comparing statistical analyses to estimate thresholds in ecotoxicology," PLOS ONE, Public Library of Science, vol. 15(4), pages 1-16, April.
    15. Baty, Florent & Ritz, Christian & Charles, Sandrine & Brutsche, Martin & Flandrois, Jean-Pierre & Delignette-Muller, Marie-Laure, 2015. "A Toolbox for Nonlinear Regression in R: The Package nlstools," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 66(i05).
    16. Fox, John & Leanage, Allison, 2016. "R and the Journal of Statistical Software," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 73(i02).
    17. repec:jss:jstsof:33:i07 is not listed on IDEAS
    18. Camilo Guzmán & Manish Bagga & Amanpreet Kaur & Jukka Westermarck & Daniel Abankwa, 2014. "ColonyArea: An ImageJ Plugin to Automatically Quantify Colony Formation in Clonogenic Assays," PLOS ONE, Public Library of Science, vol. 9(3), pages 1-9, March.
    19. Y. Fong & J. Wakefield & S. De Rosa & N. Frahm, 2012. "A Robust Bayesian Random Effects Model for Nonlinear Calibration Problems," Biometrics, The International Biometric Society, vol. 68(4), pages 1103-1112, December.
    20. Euro Pannacci & Daniele Del Buono & Maria Luce Bartucca & Luigi Nasini & Primo Proietti & Francesco Tei, 2020. "Herbicide Uptake and Regrowth Ability of Tall Fescue and Orchardgrass in S-Metolachlor-Contaminated Leachates from Sand Pot Experiment," Agriculture, MDPI, vol. 10(10), pages 1-10, October.
    21. Gianna S. Monti & Peter Filzmoser & Roland C. Deutsch, 2018. "A Robust Approach to Risk Assessment Based on Species Sensitivity Distributions," Risk Analysis, John Wiley & Sons, vol. 38(10), pages 2073-2086, October.
    22. Signe M. Jensen & Christian Ritz, 2015. "Simultaneous Inference for Model Averaging of Derived Parameters," Risk Analysis, John Wiley & Sons, vol. 35(1), pages 68-76, January.
    23. Erickson, Richard A. & Cox, Stephen B. & Oates, Jessica L. & Anderson, Todd A. & Salice, Christopher J. & Long, Kevin R., 2014. "A Daphnia population model that considers pesticide exposure and demographic stochasticity," Ecological Modelling, Elsevier, vol. 275(C), pages 37-47.
    24. Kahm, Matthias & Hasenbrink, Guido & Lichtenberg-Fraté, Hella & Ludwig, Jost & Kschischo, Maik, 2010. "grofit: Fitting Biological Growth Curves with R," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 33(i07).
    25. Ádám Z Lendvai & Çağlar Akçay & Jenny Q Ouyang & Roslyn Dakin & Alice D Domalik & Prianka S St John & Mark Stanback & Ignacio T Moore & Frances Bonier, 2015. "Analysis of the Optimal Duration of Behavioral Observations Based on an Automated Continuous Monitoring System in Tree Swallows (Tachycineta bicolor): Is One Hour Good Enough?," PLOS ONE, Public Library of Science, vol. 10(11), pages 1-11, November.

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