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

PeerJ

article

M. Umut Caglar¹  Ashley I. Teufel¹  Claus O. Wilke¹ 

[1] Department of Integrative Biology, University of Texas at Austin

关键词: R package;    Curve fitting;    Sigmoidal growth;    Double-sigmoidal growth;   

DOI  :  10.7717/peerj.4251

学科分类：社会科学、人文和艺术（综合）

来源: Inra

【 摘 要 】

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.

【 授权许可】

CC BY