phase

Analyse Biological Time-Series Data

v1.2.9 · Mar 8, 2023 · MIT + file LICENSE

Description

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>.

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14 NOTE

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Flavor	Status	Time
r-devel-linux-x86_64-debian-clang	NOTE	145.4s
r-devel-linux-x86_64-debian-gcc	NOTE	97.8s
r-devel-linux-x86_64-fedora-clang	NOTE	212.9s
r-devel-linux-x86_64-fedora-gcc	NOTE	211.3s
r-devel-macos-arm64	NOTE	32s
r-devel-windows-x86_64	NOTE	139s
r-oldrel-macos-arm64	NOTE
r-oldrel-macos-x86_64	NOTE	78s
r-oldrel-windows-x86_64	NOTE	184s
r-patched-linux-x86_64	NOTE	134.4s
r-release-linux-x86_64	NOTE	134.9s
r-release-macos-arm64	NOTE
r-release-macos-x86_64	NOTE	121s
r-release-windows-x86_64	NOTE	141s

Check details (14 non-OK)

NOTE r-devel-linux-x86_64-debian-clang

Rd files

checkRd: (-1) rosePlotsAct.Rd:19: Lost braces; missing escapes or markup?
    19 | A \code{plotly} {htmlwidget} with rose plots for locomotor activity.
       |                 ^
checkRd: (-1) rosePlotsSleep.Rd:19: Lost braces; missing escapes or markup?
    19 | #' @return A \code{plotly} {htmlwidget} with rose plots for sleep data.
       |                            ^

NOTE r-devel-linux-x86_64-debian-gcc

Rd files

checkRd: (-1) rosePlotsAct.Rd:19: Lost braces; missing escapes or markup?
    19 | A \code{plotly} {htmlwidget} with rose plots for locomotor activity.
       |                 ^
checkRd: (-1) rosePlotsSleep.Rd:19: Lost braces; missing escapes or markup?
    19 | #' @return A \code{plotly} {htmlwidget} with rose plots for sleep data.
       |                            ^

NOTE r-devel-linux-x86_64-fedora-clang

Rd files

checkRd: (-1) rosePlotsAct.Rd:19: Lost braces; missing escapes or markup?
    19 | A \code{plotly} {htmlwidget} with rose plots for locomotor activity.
       |                 ^
checkRd: (-1) rosePlotsSleep.Rd:19: Lost braces; missing escapes or markup?
    19 | #' @return A \code{plotly} {htmlwidget} with rose plots for sleep data.
       |                            ^

NOTE r-devel-linux-x86_64-fedora-gcc

Rd files

checkRd: (-1) rosePlotsAct.Rd:19: Lost braces; missing escapes or markup?
    19 | A \code{plotly} {htmlwidget} with rose plots for locomotor activity.
       |                 ^
checkRd: (-1) rosePlotsSleep.Rd:19: Lost braces; missing escapes or markup?
    19 | #' @return A \code{plotly} {htmlwidget} with rose plots for sleep data.
       |                            ^

NOTE r-devel-macos-arm64

Rd files

checkRd: (-1) rosePlotsAct.Rd:19: Lost braces; missing escapes or markup?
    19 | A \code{plotly} {htmlwidget} with rose plots for locomotor activity.
       |                 ^
checkRd: (-1) rosePlotsSleep.Rd:19: Lost braces; missing escapes or markup?
    19 | #' @return A \code{plotly} {htmlwidget} with rose plots for sleep data.
       |                            ^

NOTE r-devel-windows-x86_64

Rd files

checkRd: (-1) rosePlotsAct.Rd:19: Lost braces; missing escapes or markup?
    19 | A \code{plotly} {htmlwidget} with rose plots for locomotor activity.
       |                 ^
checkRd: (-1) rosePlotsSleep.Rd:19: Lost braces; missing escapes or markup?
    19 | #' @return A \code{plotly} {htmlwidget} with rose plots for sleep data.
       |                            ^

NOTE r-oldrel-macos-arm64

Rd files

checkRd: (-1) rosePlotsAct.Rd:19: Lost braces; missing escapes or markup?
    19 | A \code{plotly} {htmlwidget} with rose plots for locomotor activity.
       |                 ^
checkRd: (-1) rosePlotsSleep.Rd:19: Lost braces; missing escapes or markup?
    19 | #' @return A \code{plotly} {htmlwidget} with rose plots for sleep data.
       |                            ^

NOTE r-oldrel-macos-x86_64

Rd files

checkRd: (-1) rosePlotsAct.Rd:19: Lost braces; missing escapes or markup?
    19 | A \code{plotly} {htmlwidget} with rose plots for locomotor activity.
       |                 ^
checkRd: (-1) rosePlotsSleep.Rd:19: Lost braces; missing escapes or markup?
    19 | #' @return A \code{plotly} {htmlwidget} with rose plots for sleep data.
       |                            ^

NOTE r-oldrel-windows-x86_64

Rd files

checkRd: (-1) rosePlotsAct.Rd:19: Lost braces; missing escapes or markup?
    19 | A \code{plotly} {htmlwidget} with rose plots for locomotor activity.
       |                 ^
checkRd: (-1) rosePlotsSleep.Rd:19: Lost braces; missing escapes or markup?
    19 | #' @return A \code{plotly} {htmlwidget} with rose plots for sleep data.
       |                            ^

NOTE r-patched-linux-x86_64

Rd files

checkRd: (-1) rosePlotsAct.Rd:19: Lost braces; missing escapes or markup?
    19 | A \code{plotly} {htmlwidget} with rose plots for locomotor activity.
       |                 ^
checkRd: (-1) rosePlotsSleep.Rd:19: Lost braces; missing escapes or markup?
    19 | #' @return A \code{plotly} {htmlwidget} with rose plots for sleep data.
       |                            ^

NOTE r-release-linux-x86_64

Rd files

checkRd: (-1) rosePlotsAct.Rd:19: Lost braces; missing escapes or markup?
    19 | A \code{plotly} {htmlwidget} with rose plots for locomotor activity.
       |                 ^
checkRd: (-1) rosePlotsSleep.Rd:19: Lost braces; missing escapes or markup?
    19 | #' @return A \code{plotly} {htmlwidget} with rose plots for sleep data.
       |                            ^

NOTE r-release-macos-arm64

Rd files

checkRd: (-1) rosePlotsAct.Rd:19: Lost braces; missing escapes or markup?
    19 | A \code{plotly} {htmlwidget} with rose plots for locomotor activity.
       |                 ^
checkRd: (-1) rosePlotsSleep.Rd:19: Lost braces; missing escapes or markup?
    19 | #' @return A \code{plotly} {htmlwidget} with rose plots for sleep data.
       |                            ^

NOTE r-release-macos-x86_64

Rd files

checkRd: (-1) rosePlotsAct.Rd:19: Lost braces; missing escapes or markup?
    19 | A \code{plotly} {htmlwidget} with rose plots for locomotor activity.
       |                 ^
checkRd: (-1) rosePlotsSleep.Rd:19: Lost braces; missing escapes or markup?
    19 | #' @return A \code{plotly} {htmlwidget} with rose plots for sleep data.
       |                            ^

NOTE r-release-windows-x86_64

Rd files

checkRd: (-1) rosePlotsAct.Rd:19: Lost braces; missing escapes or markup?
    19 | A \code{plotly} {htmlwidget} with rose plots for locomotor activity.
       |                 ^
checkRd: (-1) rosePlotsSleep.Rd:19: Lost braces; missing escapes or markup?
    19 | #' @return A \code{plotly} {htmlwidget} with rose plots for sleep data.
       |                            ^

Check History

NOTE 0 OK · 14 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Mar 9, 2026

NOTE r-devel-linux-x86_64-debian-clang

Rd files

checkRd: (-1) rosePlotsAct.Rd:19: Lost braces; missing escapes or markup?
    19 | A \code{plotly} {htmlwidget} with rose plots for locomotor activity.
       |                 ^
checkRd: (-1) rosePlotsSleep.Rd:19: Lost braces; missing escapes or markup?
    19 | #' @return A \code{plotly} {htmlwidget} with rose plots for sleep data.
       |                            ^

NOTE r-devel-linux-x86_64-debian-gcc

Rd files

checkRd: (-1) rosePlotsAct.Rd:19: Lost braces; missing escapes or markup?
    19 | A \code{plotly} {htmlwidget} with rose plots for locomotor activity.
       |                 ^
checkRd: (-1) rosePlotsSleep.Rd:19: Lost braces; missing escapes or markup?
    19 | #' @return A \code{plotly} {htmlwidget} with rose plots for sleep data.
       |                            ^

NOTE r-devel-linux-x86_64-fedora-clang

Rd files

checkRd: (-1) rosePlotsAct.Rd:19: Lost braces; missing escapes or markup?
    19 | A \code{plotly} {htmlwidget} with rose plots for locomotor activity.
       |                 ^
checkRd: (-1) rosePlotsSleep.Rd:19: Lost braces; missing escapes or markup?
    19 | #' @return A \code{plotly} {htmlwidget} with rose plots for sleep data.
       |                            ^

NOTE r-devel-linux-x86_64-fedora-gcc

Rd files

checkRd: (-1) rosePlotsAct.Rd:19: Lost braces; missing escapes or markup?
    19 | A \code{plotly} {htmlwidget} with rose plots for locomotor activity.
       |                 ^
checkRd: (-1) rosePlotsSleep.Rd:19: Lost braces; missing escapes or markup?
    19 | #' @return A \code{plotly} {htmlwidget} with rose plots for sleep data.
       |                            ^

NOTE r-devel-macos-arm64

Rd files

checkRd: (-1) rosePlotsAct.Rd:19: Lost braces; missing escapes or markup?
    19 | A \code{plotly} {htmlwidget} with rose plots for locomotor activity.
       |                 ^
checkRd: (-1) rosePlotsSleep.Rd:19: Lost braces; missing escapes or markup?
    19 | #' @return A \code{plotly} {htmlwidget} with rose plots for sleep data.
       |                            ^

NOTE r-devel-windows-x86_64

Rd files

checkRd: (-1) rosePlotsAct.Rd:19: Lost braces; missing escapes or markup?
    19 | A \code{plotly} {htmlwidget} with rose plots for locomotor activity.
       |                 ^
checkRd: (-1) rosePlotsSleep.Rd:19: Lost braces; missing escapes or markup?
    19 | #' @return A \code{plotly} {htmlwidget} with rose plots for sleep data.
       |                            ^

NOTE r-patched-linux-x86_64

Rd files

checkRd: (-1) rosePlotsAct.Rd:19: Lost braces; missing escapes or markup?
    19 | A \code{plotly} {htmlwidget} with rose plots for locomotor activity.
       |                 ^
checkRd: (-1) rosePlotsSleep.Rd:19: Lost braces; missing escapes or markup?
    19 | #' @return A \code{plotly} {htmlwidget} with rose plots for sleep data.
       |                            ^

NOTE r-release-linux-x86_64

Rd files

checkRd: (-1) rosePlotsAct.Rd:19: Lost braces; missing escapes or markup?
    19 | A \code{plotly} {htmlwidget} with rose plots for locomotor activity.
       |                 ^
checkRd: (-1) rosePlotsSleep.Rd:19: Lost braces; missing escapes or markup?
    19 | #' @return A \code{plotly} {htmlwidget} with rose plots for sleep data.
       |                            ^

NOTE r-release-macos-arm64

Rd files

checkRd: (-1) rosePlotsAct.Rd:19: Lost braces; missing escapes or markup?
    19 | A \code{plotly} {htmlwidget} with rose plots for locomotor activity.
       |                 ^
checkRd: (-1) rosePlotsSleep.Rd:19: Lost braces; missing escapes or markup?
    19 | #' @return A \code{plotly} {htmlwidget} with rose plots for sleep data.
       |                            ^

NOTE r-release-macos-x86_64

Rd files

checkRd: (-1) rosePlotsAct.Rd:19: Lost braces; missing escapes or markup?
    19 | A \code{plotly} {htmlwidget} with rose plots for locomotor activity.
       |                 ^
checkRd: (-1) rosePlotsSleep.Rd:19: Lost braces; missing escapes or markup?
    19 | #' @return A \code{plotly} {htmlwidget} with rose plots for sleep data.
       |                            ^

NOTE r-release-windows-x86_64

Rd files

checkRd: (-1) rosePlotsAct.Rd:19: Lost braces; missing escapes or markup?
    19 | A \code{plotly} {htmlwidget} with rose plots for locomotor activity.
       |                 ^
checkRd: (-1) rosePlotsSleep.Rd:19: Lost braces; missing escapes or markup?
    19 | #' @return A \code{plotly} {htmlwidget} with rose plots for sleep data.
       |                            ^

NOTE r-oldrel-macos-arm64

Rd files

checkRd: (-1) rosePlotsAct.Rd:19: Lost braces; missing escapes or markup?
    19 | A \code{plotly} {htmlwidget} with rose plots for locomotor activity.
       |                 ^
checkRd: (-1) rosePlotsSleep.Rd:19: Lost braces; missing escapes or markup?
    19 | #' @return A \code{plotly} {htmlwidget} with rose plots for sleep data.
       |                            ^

NOTE r-oldrel-macos-x86_64

Rd files

checkRd: (-1) rosePlotsAct.Rd:19: Lost braces; missing escapes or markup?
    19 | A \code{plotly} {htmlwidget} with rose plots for locomotor activity.
       |                 ^
checkRd: (-1) rosePlotsSleep.Rd:19: Lost braces; missing escapes or markup?
    19 | #' @return A \code{plotly} {htmlwidget} with rose plots for sleep data.
       |                            ^

NOTE r-oldrel-windows-x86_64

Rd files

checkRd: (-1) rosePlotsAct.Rd:19: Lost braces; missing escapes or markup?
    19 | A \code{plotly} {htmlwidget} with rose plots for locomotor activity.
       |                 ^
checkRd: (-1) rosePlotsSleep.Rd:19: Lost braces; missing escapes or markup?
    19 | #' @return A \code{plotly} {htmlwidget} with rose plots for sleep data.
       |                            ^

Dependency Network

Version History

new 1.2.9 Mar 9, 2026

Maintainer

Lakshman Abhilash

Dependencies

Depends

R (>= 2.10)

Imports

circular lubridate plotly pracma signal zeitgebr zoo behavr wesanderson shiny shinythemes shinydashboard shinycssloaders shinyFiles

Compilation

No compilation needed

First Published

Mar 9, 2026

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