Sicegar: R package for sigmoidal and double-sigmoidal curve fitting
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Abstract
Sigmoidal and double-sigmoidal dynamics are commonly observed in many areas of biology. Here we present sicegar, an R package for the automated fitting and classification of sigmoidal and double-sigmodial data. The package categorizes data into one of three categories, "no signal", "sigmodial", or "double sigmoidal", by rigorously fitting a series of mathematical models to the data. The data is labeled as "ambiguous" if neither the sigmoidal nor double-sigmoidal model fit the data well. In addition to performing the classification, the package also reports a wealth of metrics as well as biologically meaningful parameters describing the sigmoidal or double-sigmoidal curves. In extensive simulations, we find that the package performs well, can recover the original dynamics even under fairly high noise levels, and will typically classify curves as "ambiguous" rather than misclassifying them. The package is available on CRAN and comes with extensive documentation and usage examples.
Cite this as
2017. Sicegar: R package for sigmoidal and double-sigmoidal curve fitting. PeerJ Preprints 5:e3116v1 https://doi.org/10.7287/peerj.preprints.3116v1note This preprint is not peer-reviewed. You may wish to reference the subsequent peer-reviewed version of this article.
Author comment
This preprint describes the sicegar R package available on CRAN at: https://cran.r-project.org/package=sicegar
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Competing Interests
Claus O. Wilke is an Academic Editor for PeerJ.
Author Contributions
M. Umut Caglar conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.
Ashley I. Teufel contributed reagents/materials/analysis tools, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.
Claus O Wilke conceived and designed the experiments, contributed reagents/materials/analysis tools, wrote the paper, reviewed drafts of the paper.
Data Deposition
The following information was supplied regarding data availability:
Funding
This work was supported by National Institutes of Health grant R01 AI120560. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
