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Sicegar: R package for sigmoidal and double-sigmoidal curve fitting.

Authors
  • Caglar, M Umut1
  • Teufel, Ashley I1
  • Wilke, Claus O1
  • 1 Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA.
Type
Published Article
Journal
PeerJ
Publisher
PeerJ
Publication Date
Jan 01, 2018
Volume
6
Identifiers
DOI: 10.7717/peerj.4251
PMID: 29362694
Source
Medline
Keywords
License
Unknown

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-sigmoidal data. The package categorizes data into one of three categories, "no signal," "sigmoidal," 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.

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