R Observatory: Metrics for phase version 1.2.9

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

phase

1.2.9

Analyse Biological Time-Series Data

0packages depend

2.7Kdownloads / year

–test coverage

0/13checks pass

Overview

About

Maintained by Lakshman AbhilashFirst published 2021-07-0211 releasesCRAN 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.

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).

Health

CRAN checks

13NOTE

Failing flavors

NOTE r-devel-linux-x86_64-debian-clang
NOTE r-devel-linux-x86_64-debian-gcc
NOTE r-devel-linux-x86_64-fedora-clang
NOTE r-devel-linux-x86_64-fedora-gcc
NOTE r-devel-windows-x86_64
NOTE r-oldrel-macos-arm64
NOTE r-oldrel-macos-x86_64
NOTE r-oldrel-windows-x86_64
NOTE r-patched-linux-x86_64
NOTE r-release-linux-x86_64
NOTE r-release-macos-arm64
NOTE r-release-macos-x86_64
NOTE r-release-windows-x86_64

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

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

14

Dependencies · direct

Check history

NOTE2026-06-09
0 OK · 13 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
0 OK · 12 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
0 OK · 14 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 82%
Documented parameters: 99%
Return-value docs: 100%
References docs: 0%

Downloads

2.7K

CRAN downloads in the past year

Rank #15,429 · ~7/day · ~226/mo

Releases R versions

Daily download trend is not available in this view yet.

15530 days

67690 days

2.7K1 year

Compare downloads with other packages →

Also on91 r2u19 autocran

Dependencies

Declared dependencies

14 external dependencies (excludes base and recommended)

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.

Code & Tests

Datasets

People & History

People (1)

Maintainer (1)

Lakshman Abhilash

Author, Maintainer

Authors (1)

Lakshman Abhilash

Author, Maintainer

Package Timeline

11 releases. Pick two to compare their code metrics. R releases are shown for context.

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
2023-03-09 · current release · diff ↗
1.2.8
2023-03-08 · diff ↗
1.2.7
2022-11-15 · diff ↗
1.2.6
2022-11-05 · diff ↗
1.2.5
2022-10-26 · diff ↗
1.2.3
2022-10-13 · diff ↗
1.2.2
2022-09-25 · diff ↗
R
R 4.2.0 released · 2022-04-22
1.2.1
2021-08-16 · diff ↗
1.1.3
2021-08-06 · diff ↗
1.1.2
2021-07-17 · diff ↗
1.1.1
2021-07-02

Show 1 earlier events

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
Installed size: not tracked yet
With dependencies: not tracked yet

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 is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

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 v2026-08-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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