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Compiles functions to trim, bin, visualise, and analyse activity/sleep time-series data collected from the Drosophila Activity Monitor (DAM) system (Trikinetics, USA). The following methods were used to compute periodograms - Chi-square periodogram: Sokolove and Bushell (1978) <doi:10.1016/0022-5193(78)90022-X>, Lomb-Scargle periodogram: Lomb (1976) <doi:10.1007/BF00648343>, Scargle (1982) <doi:10.1086/160554> and Ruf (1999) <doi:10.1076/brhm.30.2.178.1422>, and Autocorrelation: Eijzenbach et al. (1986) <doi:10.1111/j.1440-1681.1986.tb00943.x>. Identification of activity peaks is done after using a Savitzky-Golay filter (Savitzky and Golay (1964) <doi:10.1021/ac60214a047>) to smooth raw activity data. Three methods to estimate anticipation of activity are used based on the following papers - Slope method: Fernandez et al. (2020) <doi:10.1016/j.cub.2020.04.025>, Harrisingh method: Harrisingh et al. (2007) <doi:10.1523/JNEUROSCI.3680-07.2007>, and Stoleru method: Stoleru et al. (2004) <doi:10.1038/nature02926>. Rose plots and circular analysis are based on methods from - Batschelet (1981) <ISBN:0120810506> and Zar (2010) <ISBN:0321656865>.
Version: | 1.2.9 |
Depends: | R (≥ 2.10) |
Imports: | circular, lubridate, plotly, pracma, signal, zeitgebr, zoo, behavr, wesanderson, shiny, shinythemes, shinydashboard, shinycssloaders, shinyFiles |
Published: | 2023-03-09 |
DOI: | 10.32614/CRAN.package.phase |
Author: | Lakshman Abhilash |
Maintainer: | Lakshman Abhilash <labhilash at gc.cuny.edu> |
License: | MIT + file LICENSE |
NeedsCompilation: | no |
CRAN checks: | phase results |
Reference manual: | phase.pdf |
Package source: | phase_1.2.9.tar.gz |
Windows binaries: | r-devel: phase_1.2.9.zip, r-release: phase_1.2.9.zip, r-oldrel: phase_1.2.9.zip |
macOS binaries: | r-release (arm64): phase_1.2.9.tgz, r-oldrel (arm64): phase_1.2.9.tgz, r-release (x86_64): phase_1.2.9.tgz, r-oldrel (x86_64): phase_1.2.9.tgz |
Old sources: | phase archive |
Please use the canonical form https://CRAN.R-project.org/package=phase to link to this page.
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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