R Observatory: Metrics for SqueakR version 1.3.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

SqueakR

1.3.0Package record

An Experiment Interface for 'DeepSqueak' Bioacoustics Research

0packages depend

2.6Kdownloads / year

27.0%test coverage

13/13flavors OK

Overview

About

Maintained by Simon OgundareCRAN page ↗GitHub ↗Website ↗

Data processing and visualizations for rodent vocalizations exported from 'DeepSqueak'. These functions are compatible with the 'SqueakR' Shiny Dashboard, which can be used to visualize experimental results and analyses.

Changes in 1.3.0

version 1.3.0 [GitHub release] [CRAN release]

---

Added animal field for each added experiment data, which updates experiment metadata for animals field. Updated compatibility to match semi-automatic and automatic SqueakR pipelines, as well as describe_experiment() function. Updated documentation to reflect the change
Added Plotly sunburst plot (to functions list and dashboard) to graph proportions of collected data done per experimenter, as well as data collected per animal per group
Added Plotly 3D surface plot (plotSurface()) using 2D kernel density estimation to represent call density against principal frequency and call length
Added functions for unblinding experimenters to data

Show all changes in 1.3.0Hide the rest of the changes in 1.3.0

Added function — plotContours() — which renders plotSurface() as a 2D rendering, flanked by histograms displaying distributions of principal frequency and call length
Standardized some function naming (plotSurface instead of plotCallDataSurface, etc)

version 1.2.8

---

Used report package for analyses: added functions for reporting descriptive statistics for grouped data in SqueakR Dashboard tab
Deprecated SqueakR Dashboard repository on GitHub and merged functions into SqueakR
Added 3D cluster plot visualization function plotClusters() against call length (z), principal frequency (x) and mean power (y) using plotly, available in base SqueakR and on dashboard

version 1.2.5

---

Merged SqueakR dashboard into SqueakR package! Dashboard can now be run after loading the package by running squeakRDashboard()
Added function for calculating ANOVA between groups
Added ANOVA tab on SqueakR Dashboard for determining statistical significance between call features

version 1.2.0

---

Added fully-automatic pipeline function (autosqueakRpipeline()) which references Google Sheet to add data without experimenter input for every file
Renamed experiment_pipeline() to semisqueakRpipeline()
Added function (remove_experiment_data()) to remove data from experiment object
Updated vignette to reflect package changes

version 1.0.0

---

Recreated NEWS.md file to track changes to the package.
Added functions for generating experiment and analyzing data between experimental groups.
Added visualizations including ethnograms, histograms, box-plots, and correlation matrices.

version 0.5.1

---

Basic set of functions without all plotting functions
Bug fixes
Prepared development release for Mac
Prepared development release for Windows

version 0.0.0.9000

---

NEWS.md setup

added development NEWS.md file

From NEWS.md in the release

Install

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

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

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

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("osimon81/SqueakR")

Development version from osimon81/SqueakR. Installs pak first if it is not already available.

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-squeakr

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-SqueakR

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-SqueakR

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

13OK

CRAN check page ↗

Slowest check: 3.5 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK12 OK2026-04-25

Show 1 earlier changeHide 1 earlier change

NOTE11 OK, 3 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.3.0

READMEYes · 279 wordsVignettesYes · 1 · dynamicNEWSYes · 100% structured · mentions 1.3.0Citation fileNoWebsiteYes · pkgdown

Help pages: 36 (1 internal)includes a package overview page
Examples that run: 6%2 run in a plain check · 33 never run
Exported functions with examples: 100%
Documented parameters: 96%
Return-value docs: 100%
Help pages citing references: 3%

Vignettes (1)

SqueakR

How these are measured

Downloads

2.6K

CRAN downloads in the past year

Rank #17,535 · ~7/day · ~215/mo

Releases R versions

Daily download trend is not available in this view yet.

26530 days

72790 days

2.6K1 year

Compare downloads with other packages →

Also on97 r2u3 autocran

How downloads are counted

Repository

osimon81/squeakr ↗Account: osimon81

8Stars

0Forks

0Open issues

0Open PRs

2Releases

67Commits

1Commit identities

bioacousticsdeepsqueakrcran

67 commits · Last activity 2022-06-25 · Discussions: 1 post

Responsiveness

How these are sampled

PRs merged (all time): 0%
Median days to close, 50 most recently updated closed issues: 3
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-01-21 · 82026-07-07 · 8

How these are measured

PracticesBeta

9 development-tooling and community-health practices detected across 6 families in the upstream repository

Checks run against github.com/osimon81/squeakr on 2026-10-18.

Continuous integration (1)

GitHub Actions

Docs source (3)

pkgdown

GitHub Pages site last deployed 2022-06-25 · The repository has a site deploy workflow

Coverage (1)

Coverage reporting

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Show all practicesHide 2 practices

Research and citation (1)

codemeta.json

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

18 external dependencies (excludes base and recommended)

Installing SqueakR adds 135 packages (60 with compiled code, 124 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, data.table 5.7 MB.

Depends (1)

R >= 2.10

Imports (17)

dplyr ggcorrplot ggeasy gghighlight ggplot2 ggpubr googlesheets4MASSplotly RColorBrewer readxl report rlist rstatix shiny shinydashboardutils

LinkingTo (0)

none

Suggests (3)

knitr rmarkdown testthat

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)

Simon Ogundare

Author, Maintainer since 1.0.0 (2022)

Releases (3)

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
1.3.0Latest
record
2022-06-28 · current release · diff ↗ ·
added 9 exports
plotClusters, plotContours, plotSunburstAnimals, plotSunburstExperimenters, plotSurface, squeakrSummary, unblind_all_ids, unblind_data_id, unblind_data_name
1.2.5
record
2022-06-22 · diff ↗ ·
removed 1 export
experiment_pipeline

added 5 exports
autosqueakRpipeline, remove_experiment_data, semisqueakRpipeline, squeakRDashboard, squeakrANOVA
1.0.0
record
2022-06-17
R
R 4.2.0 released · 2022-04-22

Package metadata

First published: 2022-06-17
Total releases: 3 / 4 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 2.10
Bundled data: 73 KB / 1 file
Download size: 4.1 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("SqueakR")

Format

Ogundare, S. (2022). SqueakR: An Experiment Interface for 'DeepSqueak' Bioacoustics Research (Version 1.3.0) [Computer software]. https://doi.org/10.32614/CRAN.package.SqueakR

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 SqueakR version 1.3.0 [Data set]. HJJB, LLC. Data release v2026-10-21. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-21, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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