grofit: Fitting Biological Growth Curves with R
By Matthias Kahm, G. Hasenbrink, Hella Lichtenberg-Fraté, J. Ludwig, Maik Kschischo. 2010
508 citations recorded by the source corpus.
The grofit package was developed to fit many growth curves obtained under different conditions in order to derive a conclusive dose-response curve, for instance for a compound that potentially affects growth. grofit fits data to different parametric models and in addition provides a model free spline method to circumvent systematic errors that might occur within application of parametric methods. This amendment increases the reliability of the characteristic parameters (e.g.,lag phase, maximal growth rate, stationary phase) derived from a single growth curve. By relating obtained parameters to the respective condition (e.g.,concentration of a compound) a dose response curve can be derived that enables the calculation of descriptive pharma-/toxicological values like half maximum effective concentration (EC50). Bootstrap and cross-validation techniques are used for estimating confidence intervals of all derived parameters.
Subfields: Management Science and Operations Research, Plant Science
View Paper: https://www.semanticscholar.org/paper/82f157ab3579400717d01903f26dbce6993825a0
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In Management Science and Operations Research
- M. Delignette-Muller
- Sandrine Charles
- Christian Ritz
- Florent Baty
- Martin H. Brutsche
- Jens Carl Streibig
- Jean-Pierre Flandrois
- M. Rees
In Plant Science
Citations in the corpus
- A Toolbox for Nonlinear Regression in R: The Package nlstools (2015, methodology): “Specifically for dose-response and growth curve modeling, the packages drc [Ritz and Streibig, 2005], drfit [Ranke, 2006], and grofit [Kahm et al., 2010] among others offer infrastructure for automatically providing data-driven, informed starting values so that the user need not think about providing…”
- Growthcurver: an R package for obtaining interpretable metrics from microbial growth curves (2016, methodology): “Other recent methods fit the growth data to a variety of parametric growth models [11], but have a strong focus on generating dose response curves.”
- Dose-Response Analysis Using R (2015, background): “There also exist a number of other R packages related to dose-response analysis: DoseFinding [3], drfit [4], grofit [5],MCPMod [6], and nlstools [7].”
- How to fit nonlinear plant growth models and calculate growth rates: an update for ecologists (2012, methodology): “R’s grofit package may facilitate model fitting in certain cases, and for some mixed-effects models, the functions in the lme4 package converge more readily than do those of nlme (Kahm et al. 2010; Bates,Maechler &Bolker 2011).”