Package: phase 1.2.9

Lakshman Abhilash

phase: Analyse Biological Time-Series Data

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>.

Authors:Lakshman Abhilash [aut, cre]

phase_1.2.9.tar.gz
phase_1.2.9.tar.gz(r-4.5-noble)phase_1.2.9.tar.gz(r-4.4-noble)
phase_1.2.9.tgz(r-4.4-emscripten)phase_1.2.9.tgz(r-4.3-emscripten)
phase.pdf |phase.html
phase/json (API)

# Install 'phase' in R:
install.packages('phase', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:
  • df - Example DAM data

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

1.78 score 227 downloads 6 mentions 22 exports 94 dependencies

Last updated 2 years agofrom:d8bba13e36. Checks:OK: 1 NOTE: 1. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 01 2024
R-4.5-linuxNOTEDec 01 2024

Exports:allActogramsallPeriodogramsActallPeriodogramsSleepallSomnogramsanticipationActbinDataCoMindActogramindPeriodogramActindPeriodogramSleepindSomnogrampeakIdentifierprofilesActprofilesSleeprosePlotsActrosePlotsSleepsleepDatasleepOnsetBoutLengthsleepStagessleepStattransitionProbstrimData

Dependencies:askpassbase64encbehavrbootbslibcachemcircularclicolorspacecommonmarkcpp11crayoncrosstalkcurldata.tabledigestdplyrevaluatefansifarverfastmapfontawesomefsgenericsggplot2gluegridExtragtablehighrhtmltoolshtmlwidgetshttpuvhttrisobandjquerylibjsonliteknitrlabelinglaterlatticelazyevallifecyclelomblubridatemagrittrMASSMatrixmemoisemgcvmimemunsellmvtnormnlmeopensslpillarpkgconfigplotlypracmapromisespurrrR6rappdirsRColorBrewerRcpprlangrmarkdownsassscalesshinyshinycssloadersshinydashboardshinyFilesshinythemessignalsourcetoolsstringistringrsystibbletidyrtidyselecttimechangetinytexutf8vctrsviridisLiteWaveletCompwesandersonwithrxfunxtableyamlzeitgebrzoo