funkycells

1.1.1

Functional Data Analysis for Multiplexed Cell Images

0packages depend

2.7Kdownloads / year

56.2%test coverage

13/13checks pass

Overview

About

Maintained by Jeremy VanderDoesFirst published 2023-08-091 releasesCRAN page ↗GitHub ↗

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.

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.

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).

Health

CRAN checks

13OK

Slowest check: 5.2 min · r-devel-linux-x86_64-fedora-clang

Code health

Yes

Tests · ratio 0.09

56.2%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 206 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 77%
Return-value docs: 100%
References docs: 0%

Downloads

2.7K

CRAN downloads in the past year

Rank #13,504 · ~7/day · ~224/mo

Releases R versions

Daily download trend is not available in this view yet.

28830 days

80390 days

2.7K1 year

Compare downloads with other packages →

Also on129 r2u29 autocran

Repository

GitHub ↗ jrvanderdoes/funkycells

1Stars

0Forks

1Open issues

0Open PRs

1Releases

176Commits

1Contributors

License GPL-3.0 · 176 commits · Last activity 2025-03-25

Stars over time

2022-11-03 · 12026-07-07 · 1

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/jrvanderdoes/funkycells on 2026-07-19.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (1)

data-raw/

CRAN release process (1)

cran-comments.md

Docs source (1)

README.Rmd

Show all practices

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

11 external dependencies (excludes base and recommended)

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.

Code & Tests

Datasets

People & History

People (3)

Maintainer (1)

Jeremy VanderDoes

Author, Maintainer, Copyright holder

Authors (3)

Jeremy VanderDoes

Author, Maintainer, Copyright holder

Jack Hywood

Author

Gregory Rice

Author

Jeremy VanderDoes

Author, Maintainer, Copyright holder

Package Timeline

1 release. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
1.1.1Latest
2026-03-10 · current release
R
R 4.5.0 released · 2025-04-11

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

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