R Observatory: Metrics for scSpatialSIM version 0.1.4

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

scSpatialSIM

0.1.4Package record

A Point Pattern Simulator for Spatial Cellular Data

0packages dependsuggested by 1

3Kdownloads / year

2.3%test coverage

13/13flavors OK

Overview

About

Maintained by Fridley LabCRAN page ↗GitHub ↗

Single cell resolution data has been valuable in learning about tissue microenvironments and interactions between cells or spots. This package allows for the simulation of this level of data, be it single cell or ‘spots’, in both a univariate (single metric or cell type) and bivariate (2 or more metrics or cell types) ways. As more technologies come to marker, more methods will be developed to derive spatial metrics from the data which will require a way to benchmark methods against each other. Additionally, as the field currently stands, there is not a gold standard method to be compared against. We set out to develop an R package that will allow users to simulate point patterns that can be biologically informed from different tissue domains, holes, and varying degrees of clustering/colocalization. The data can be exported as spatial files and a summary file (like 'HALO'). https://github.com/FridleyLab/scSpatialSIM/.

Install

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

install.packages("scSpatialSIM", 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("FridleyLab/scSpatialSIM")

Development version from FridleyLab/scSpatialSIM. 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-scspatialsim

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-scSpatialSIM

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-scSpatialSIM

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: 12.6 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-04
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 0.1.4

READMEYes · 79 wordsVignettesYes · 3 · dynamicNEWSNoCitation fileNo

Help pages: 16 (1 internal)
Examples that run: 100%8 run in a plain check
Exported functions with examples: 62%
Documented parameters: 93%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (3)

How these are measured

Downloads

3K

CRAN downloads in the past year

Rank #15,160 · ~8/day · ~248/mo

Releases R versions

Daily download trend is not available in this view yet.

33630 days

78890 days

3K1 year

Compare downloads with other packages →

Also on86 r2u10 autocran

How downloads are counted

Repository

fridleylab/scspatialsim ↗Organization: FridleyLab

4Stars

2Forks

2Open issues

0Open PRs

6Releases

91Commits

1Commit identities

91 commits · Last activity 2026-02-16 · 0% stars, 30d

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

2024-05-24 · 42026-07-07 · 4

How these are measured

PracticesBeta

6 development-tooling and community-health practices detected across 4 families in the upstream repository

Checks run against github.com/fridleylab/scspatialsim on 2026-10-11.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel

Docs source (2)

pkgdown

GitHub Pages site last deployed 2026-02-16

Reproducibility and dev environment (1)

data-raw/

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

15 external dependencies (excludes base and recommended)

Installing scSpatialSIM adds 80 packages (42 with compiled code, 69 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, doBy 4.3 MB.

Depends (1)

R >= 4.00

Imports (12)

dplyr ggplot2 magrittr spatstat.geom crayon ggpubr pbmcapply spatstat.random tidyrutilsmethodsproxy

LinkingTo (0)

none

Suggests (5)

knitr rmarkdown testthat spatialTIME spdep

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Suggested by 1

Suggests, most downloaded first

spatialGE

How these are counted

Code & Tests

Datasets

People & History

People (7)

Fridley Lab

Maintainer since 0.1.3.2 (2023)

Jordan Creed

Author

Brooke Fridley

Author, Copyright holder

Author

Author

Author

Author

Releases (4)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
0.1.4Latest
record
2026-02-16 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
0.1.3.4
record
2024-10-01 · diff ↗
R
R 4.4.0 released · 2024-04-24
0.1.3.3
record
2023-12-19 · diff ↗
0.1.3.2
record
2023-10-12
R
R 4.3.0 released · 2023-04-21

Package metadata

First published: 2023-10-12
Total releases: 4 / 3 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.00
Bundled data: 1.1 KB / 1 file
Download size: 1.3 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("scSpatialSIM")

Format

Lab, F., Creed, J., Fridley, B., Ospina, O., Soupir, A., Wilson, C., & Wrobel, J. (2026). scSpatialSIM: A Point Pattern Simulator for Spatial Cellular Data (Version 0.1.4) [Computer software]. https://doi.org/10.32614/CRAN.package.scSpatialSIM

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 scSpatialSIM version 0.1.4 [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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