R Observatory: Metrics for funkycells version 1.1.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

funkycells

1.1.1Package record

Functional Data Analysis for Multiplexed Cell Images

0packages depend

2.9Kdownloads / year

56.2%test coverage

13/13flavors OK

Overview

About

Maintained by Jeremy VanderDoesCRAN page ↗GitHub ↗Website ↗Issues ↗

Compare variables of interest between (potentially large numbers of) spatial interactions and meta-variables. Spatial variables are summarized using K, or other, functions, and projected for use in a modified random forest model. The model allows comparison of functional and non-functional variables to each other and to noise, giving statistical significance to the results. Included are preparation, modeling, and interpreting tools along with example datasets, as described in VanderDoes et al., (2023) doi:10.1101/2023.07.18.549619.

Changes in 1.1.1

Update package title
Remove don't run examples
Update vignettes to not save to home directory (via temp directory and variable to not run those sections)

From NEWS.md in the release

Install

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

install.packages("funkycells", 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("jrvanderdoes/funkycells")

Development version from jrvanderdoes/funkycells. 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-funkycells

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-funkycells

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-funkycells

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: 4.4 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
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.1.1

READMEYes · 206 wordsVignettesYes · 5 · dynamicNEWSYes · 100% structured · mentions 1.1.1Citation fileYes · cites a publicationWebsiteYes · pkgdown

Help pages: 14
Examples that run: 100%11 run in a plain check
Exported functions with examples: 100%
Documented parameters: 77%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (5)

How these are measured

Downloads

2.9K

CRAN downloads in the past year

Rank #15,511 · ~8/day · ~241/mo

Releases R versions

Daily download trend is not available in this view yet.

28030 days

79690 days

2.9K1 year

Compare downloads with other packages →

Also on96 r2u4 autocran

How downloads are counted

Repository

jrvanderdoes/funkycells ↗Account: jrvanderdoes

1Stars

0Forks

1Open issues

0Open PRs

1Releases

176Commits

1Commit identities

License file reads as GPL-3.0 · 176 commits · Last activity 2023-08-11 · 0% stars, 30d · Default branch at 1.1.1.9000, ahead of CRAN 1.1.1 (checked 2026-10-21)

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: not measured
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2022-11-03 · 12026-07-07 · 1

How these are measured

PracticesBeta

9 development-tooling and community-health practices detected across 5 families in the upstream repository

Checks run against github.com/jrvanderdoes/funkycells on 2026-10-21.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux

Docs source (4)

README.Rmdpkgdown

GitHub Pages site last deployed 2023-08-11 · The repository has a site deploy workflow

pkgdown site last built 2023-08-11

Reproducibility and dev environment (1)

data-raw/

CRAN release process (1)

cran-comments.md

Show all practicesHide 1 practice

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

11 external dependencies (excludes base and recommended)

Installing funkycells adds 61 packages (40 with compiled code, 52 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, fds 3.7 MB.

Depends (1)

R >= 2.10

Imports (8)

fda ggplot2rpartspatstat.explore spatstat.geomstatsstringr tidyr

LinkingTo (0)

none

Suggests (5)

knitr pROC rmarkdown scales 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)

Jeremy VanderDoes

Jack Hywood

Author

Gregory Rice

Author

Releases (1)

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
1.1.1Latest
record
2023-08-09 · current release
R
R 4.3.0 released · 2023-04-21

Package metadata

First published: 2023-08-09
Total releases: 1 / 3 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 2.10
Bundled data: 1.9 MB / 3 files
Download size: 2.2 MB

Cite

Cite this package

Run in R for the authors' entry:

citation("funkycells")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.1101/2023.07.18.549619.

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 funkycells version 1.1.1 [Data set]. HJJB, LLC. Data release v2026-10-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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