Sicegar: R package for sigmoidal and double-sigmoidal curve fitting
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 “...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
| Published: |
PeerJ Inc.
2018-01-01
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| Series: | PeerJ |
| Subjects: | |
| Online Access: | https://peerj.com/articles/4251.pdf |
| _version_ | 1797425719603625984 |
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| author | M. Umut Caglar Ashley I. Teufel Claus O. Wilke |
| author_facet | M. Umut Caglar Ashley I. Teufel Claus O. Wilke |
| author_sort | M. Umut Caglar |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-09T08:20:18Z |
| format | Article |
| id | doaj.art-fadbd81c86ab46d291084639138fea33 |
| institution | Directory Open Access Journal |
| issn | 2167-8359 |
| language | English |
| last_indexed | 2024-03-09T08:20:18Z |
| publishDate | 2018-01-01 |
| publisher | PeerJ Inc. |
| record_format | Article |
| series | PeerJ |
| spelling | doaj.art-fadbd81c86ab46d291084639138fea332023-12-02T21:53:50ZengPeerJ Inc.PeerJ2167-83592018-01-016e425110.7717/peerj.4251Sicegar: R package for sigmoidal and double-sigmoidal curve fittingM. Umut CaglarAshley I. TeufelClaus O. WilkeSigmoidal 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.https://peerj.com/articles/4251.pdfR packageCurve fittingSigmoidal growthDouble-sigmoidal growth |
| spellingShingle | M. Umut Caglar Ashley I. Teufel Claus O. Wilke Sicegar: R package for sigmoidal and double-sigmoidal curve fitting PeerJ R package Curve fitting Sigmoidal growth Double-sigmoidal growth |
| title | Sicegar: R package for sigmoidal and double-sigmoidal curve fitting |
| title_full | Sicegar: R package for sigmoidal and double-sigmoidal curve fitting |
| title_fullStr | Sicegar: R package for sigmoidal and double-sigmoidal curve fitting |
| title_full_unstemmed | Sicegar: R package for sigmoidal and double-sigmoidal curve fitting |
| title_short | Sicegar: R package for sigmoidal and double-sigmoidal curve fitting |
| title_sort | sicegar r package for sigmoidal and double sigmoidal curve fitting |
| topic | R package Curve fitting Sigmoidal growth Double-sigmoidal growth |
| url | https://peerj.com/articles/4251.pdf |
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