R Observatory: Metrics for simphony version 1.0.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

simphony

1.0.3Package record

Simulating Large-Scale, Rhythmic Data

0packages depend

2.8Kdownloads / year

62.6%test coverage

13/13flavors OK

Overview

About

Maintained by Jake HugheyCRAN page ↗GitHub ↗Website ↗

A tool for simulating rhythmic data: transcriptome data using Gaussian or negative binomial distributions, and behavioral activity data using Bernoulli or Poisson distributions. See Singer et al. (2019) doi:10.7717/peerj.6985.

Changes in 1.0.3

Tweaked syntax for linter.

From NEWS.md in the release

Install

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

install.packages("simphony", 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("hugheylab/simphony")

Development version from hugheylab/simphony. 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-simphony

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-simphony

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-simphony

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: 1.6 min · r-release-macos-x86_64

Status changes

OK13 OK2026-08-04
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.0.3

README· In the repository, left out of the releaseVignettesYes · 2 · dynamicNEWSYes · 100% structured · mentions 1.0.3Citation fileNoWebsiteYes · pkgdown

Help pages: 6
Examples that run: 100%6 run in a plain check
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (2)

How these are measured

Downloads

2.8K

CRAN downloads in the past year

Rank #19,504 · ~8/day · ~236/mo

Releases R versions

Daily download trend is not available in this view yet.

23530 days

68090 days

2.8K1 year

Compare downloads with other packages →

Also on68 r2u6 autocran

How downloads are counted

Repository

hugheylab/simphony ↗Organization: hugheylab

3Stars

1Forks

0Open issues

0Open PRs

1Releases

290Commits

6Commit identities

simphonyrhythmic-datar

290 commits · Last activity 2022-12-01

Responsiveness

How these are sampled

PRs merged (all time): 92%
Median days to close, 50 most recently updated closed issues: 10
Median days to close, 50 most recently updated closed PRs: 1

Stars over time

2023-09-29 · 32026-07-07 · 3

How these are measured

PracticesBeta

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

Checks run against github.com/hugheylab/simphony on 2026-10-21.

Continuous integration (1)

GitHub Actions

Docs source (2)

pkgdown

GitHub Pages site last deployed 2020-08-04

pkgdown site last built 2022-12-01

Coverage (1)

Coverage reporting

Reproducibility and dev environment (1)

data-raw/

Show all practicesHide 3 practices

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Lint, format, editor (1)

RStudio project

Git structural (1)

.gitattributes

How this is detected·Detection ruleset v4 (2026-10-20)

Dependencies

Declared dependencies

9 external dependencies (excludes base and recommended)

Installing simphony adds 3 packages (1 with compiled code, 6.1 MB of source tarballs). Heaviest: data.table 5.7 MB, iterators 293 KB, foreach 88 KB.

Depends (1)

R >= 3.4

Imports (2)

data.table foreach

LinkingTo (0)

none

Suggests (7)

ggplot2 kableExtra knitr limma precrec 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 (3)

Jake Hughey

Author, Maintainer since 1.0.0 (2022)

Jordan Singer

Author

Darwin Fu

Contributor

Releases (2)

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
unarchivedReturned to CRAN
2022-08-09
1.0.3Latest
record
2022-08-09 · current release · diff ↗
archivedRemoved from CRAN
2022-08-08
issues were not corrected in time
R
R 4.2.0 released · 2022-04-22
1.0.0
record
2022-02-09
R
R 4.1.0 released · 2021-05-18

Package metadata

First published: 2022-02-09
Total releases: 2 / 4 yrs
License: GPL-2 OSI
Minimum R: ≥ 3.4
Bundled data: 23 KB / 1 file
Download size: 853 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("simphony")

Format

Hughey, J., Fu, D., & Singer, J. (2022). simphony: Simulating Large-Scale, Rhythmic Data (Version 1.0.3) [Computer software]. https://doi.org/10.32614/CRAN.package.simphony

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 simphony version 1.0.3 [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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