R Observatory: Metrics for squid version 0.2.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

squid

0.2.1Package record

Statistical Quantification of Individual Differences

0packages depend

3.2Kdownloads / year

37.1%test coverage

0/13flavors OK

Overview

About

Maintained by Hassen AllegueCRAN page ↗GitHub ↗Website ↗Issues ↗

A simulation-based tool made to help researchers to become familiar with multilevel variations, and to build up sampling designs for their study. This tool has two main objectives: First, it provides an educational tool useful for students, teachers and researchers who want to learn to use mixed-effects models. Users can experience how the mixed-effects model framework can be used to understand distinct biological phenomena by interactively exploring simulated multilevel data. Second, it offers research opportunities to those who are already familiar with mixed-effects models, as it enables the generation of data sets that users may download and use for a range of simulation-based statistical analyses such as power and sensitivity analysis of multilevel and multivariate data [Allegue, H., Araya-Ajoy, Y.G., Dingemanse, N.J., Dochtermann N.A., Garamszegi, L.Z., Nakagawa, S., Reale, D., Schielzeth, H. and Westneat, D.F. (2016) <doi: 10.1111/2041-210X.12659>].

Changes in 0.2.1

Fix directory error in squidApp() e740983

From NEWS.md in the release

Install

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

install.packages("squid", 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("squid-group/squid")

Development version from squid-group/squid. 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-squid

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-squid

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-squid

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) squidR.Rd:83: Lost braces; missing escapes or markup?
    83 |   \item \code{X1_sto_shared} (default \code{TRUE}): {logical}; if \code{TRUE}, the stochastic environmental effect included in the environmental effect x1 will be shared between individuals. If \code{FALSE}, each individual will experience a different stochastic environmental effect x1 (i.e. a new stochastic environmental effect is generated for each individual).
       |                                                     ^

NOTEdependencies in R coder-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Namespaces in Imports field not imported from:
  ‘arm’ ‘brms’ ‘lme4’ ‘plotly’ ‘shinyMatrix’
All declared Imports should be used.

CRAN check page ↗

Slowest check: 1.1 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 0.2.1

READMEYes · 1,469 wordsVignettesNoNEWSYes · 100% structured · mentions 0.2.1Citation fileNoWebsiteYes · pkgdown

Help pages: 3includes a package overview page
Examples that run: 50%1 run in a plain check · 1 never run
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 50%
Help pages citing references: 0%

How these are measured

Downloads

3.2K

CRAN downloads in the past year

Rank #13,511 · ~9/day · ~267/mo

Releases R versions

Daily download trend is not available in this view yet.

30930 days

84390 days

3.2K1 year

Compare downloads with other packages →

Also on109 r2u6 autocran

How downloads are counted

Repository

squidgroup/squid ↗Organization: squidgroup

Moved from squid-group/squid.

36Stars

7Forks

1Open issues

0Open PRs

5Releases

285Commits

6Commit identities

linear-mixed-effects-modellingmultilevel-dataphenotypic-equationvariance-componentsphenotypic-plasticityreaction-normrepeatabilitypersonality

285 commits · Last activity 2025-08-04 · 0% stars, 30d · Default branch at 0.2.1.9000, ahead of CRAN 0.2.1 (checked 2026-10-11) · Discussions: 1 post

Responsiveness

How these are sampled

PRs merged (all time): 92%
Median days to close, 50 most recently updated closed issues: 22
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-05-11 · 352026-08-20 · 36

How these are measured

PracticesBeta

7 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/squid-group/squid on 2026-10-11.

Continuous integration (2)

GitHub ActionsTravis CI (config file)

Docs source (4)

README.Rmdpkgdown

GitHub Pages site last deployed 2025-08-04 · The repository has a site deploy workflow

pkgdown site last built 2022-04-25

CRAN release process (1)

cran-comments.md

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

Dependencies

Declared dependencies

9 external dependencies (excludes base and recommended)

Installing squid adds 117 packages (60 with compiled code, 120 MB of source tarballs). Heaviest: BH 14 MB, stringi 11 MB, ggplot2 6.0 MB.

Depends (1)

R >= 4.1.0

Imports (11)

statsshiny shinyMatrix ggplot2 (>= 3.3.5)plotlygridMASSlme4 arm data.table brms

LinkingTo (0)

none

Suggests (1)

testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (9)

Hassen Allegue

Author, Maintainer since 0.1.0 (2016)

Ned A. Dochtermann

Author · added in 0.1.1

David F. Westneat

Author · added in 0.1.1

Yimen G. Araya-Ajoy

Author · added in 0.1.1

Niels J. Dingemanse

Author · added in 0.1.1

Shinichi Nakagawa

Author

Denis Reale

Author · added in 0.1.1

Holger Schielzeth

Author

Laszlo Z. Garamszegi

Author · added in 0.1.1

Listed in earlier versions (5)

Show 5 peopleHide 5 people

Yimen Araya

no longer listed · 0.1.0

Niels Dingemanse

no longer listed · 0.1.0

Ned Dochtermann

no longer listed · 0.1.0

Laszlo Garamszegi

no longer listed · 0.1.0

Dave Westneat

no longer listed · 0.1.0

Releases (5)

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
R
R 4.2.0 released · 2022-04-22
0.2.1Latest
record
2022-01-21 · current release · diff ↗
0.2.0
record
2022-01-11 · diff ↗
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
0.1.2
record
2019-08-06 · diff ↗
R
R 3.6.0 released · 2019-04-26
R
R 3.5.0 released · 2018-04-23
R
R 3.4.0 released · 2017-04-21
0.1.1
record
2016-06-20 · diff ↗
0.1.0
record
2016-06-01
R
R 3.3.0 released · 2016-05-03

Package metadata

First published: 2016-06-01
Total releases: 5 / 10 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.1.0
Download size: 3.8 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("squid")

Format

Allegue, H., A. Dochtermann, N., F. Westneat, D., G. Araya-Ajoy, Y., J. Dingemanse, N., Nakagawa, S., Reale, D., Schielzeth, H., & Z. Garamszegi, L. (2022). squid: Statistical Quantification of Individual Differences (Version 0.2.1) [Computer software]. https://doi.org/10.32614/CRAN.package.squid

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 squid version 0.2.1 [Data set]. HJJB, LLC. Data release v2026-10-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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