R Observatory: Metrics for phase version 1.2.9

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

phase

1.2.9Package record

Analyse Biological Time-Series Data

0packages depend

2.9Kdownloads / year

–test coverage

0/13flavors OK

Overview

About

Maintained by Lakshman AbhilashCRAN page ↗

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>.

Install

R (CRAN)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("phase", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-phase

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-phase

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-phase

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

13NOTE

Check messages

NOTERd filesr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64, r-patched-linux-x86_64, r-release-linux-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64

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.
       |                            ^

CRAN check page ↗

Slowest check: 3.1 min · r-oldrel-windows-x86_64

Status changes

NOTE13 NOTE2026-06-09
ERROR12 NOTE, 1 ERROR2026-06-08
NOTE14 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.2.9

READMENoVignettesNoNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 23
Examples that run: 82%18 run in a plain check · 4 never run
Exported functions with examples: 100%
Documented parameters: 99%
Return-value docs: 100%
Help pages citing references: 0%

How these are measured

Downloads

2.9K

CRAN downloads in the past year

Rank #15,078 · ~8/day · ~243/mo

Releases R versions

Daily download trend is not available in this view yet.

33130 days

80990 days

2.9K1 year

Compare downloads with other packages →

Also on64 r2u6 autocran

How downloads are counted

Dependencies

Declared dependencies

14 external dependencies (excludes base and recommended)

Installing phase adds 86 packages (44 with compiled code, 77 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, data.table 5.7 MB.

Depends (1)

R >= 2.10

Imports (14)

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

LinkingTo (0)

none

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (1)

Lakshman Abhilash

Author, Maintainer since 1.1.1 (2021)

Releases (11)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
1.2.9Latest
record
2023-03-09 · current release · diff ↗
1.2.8
record
2023-03-08 · diff ↗ ·
added 2 exports
sleepStages, transitionProbs
1.2.7
record
2022-11-15 · diff ↗
1.2.6
record
2022-11-05 · diff ↗
1.2.5
record
2022-10-26 · diff ↗
1.2.3
record
2022-10-13 · diff ↗ ·
removed 7 exports
allActogramsWake, allPeriodogramsWake, indActogramWake, indPeriodogramWake, profilesWake, rosePlotsWake, wakeData
1.2.2
record
2022-09-25 · diff ↗
R
R 4.2.0 released · 2022-04-22
1.2.1
record
2021-08-16 · diff ↗ ·
added 1 export
sleepOnsetBoutLength
1.1.3
record
2021-08-06 · diff ↗
1.1.2
record
2021-07-17 · diff ↗
1.1.1
record
2021-07-02

Show 1 earlier eventHide 1 earlier event

R
R 4.1.0 released · 2021-05-18

Package metadata

First published: 2021-07-02
Total releases: 11 / 5 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 2.10
Bundled data: 138 KB / 1 file
Download size: 180 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("phase")

Format

Abhilash, L. (2023). phase: Analyse Biological Time-Series Data (Version 1.2.9) [Computer software]. https://doi.org/10.32614/CRAN.package.phase

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for phase version 1.2.9 [Data set]. HJJB, LLC. Data release v2026-10-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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