R Observatory: Metrics for spatialTIME version 1.3.4-5

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

spatialTIME

1.3.4-5Package record

Spatial Analysis of Vectra Immunoflourescent Data

0packages dependsuggested by 2

8.2Kdownloads / year

1.1%test coverage

13/13flavors OK

Overview

About

Maintained by Fridley LabCRAN page ↗GitHub ↗Issues ↗

Visualization and analysis of Vectra Immunoflourescent data. Options for calculating both the univariate and bivariate Ripley's K are included. Calculations are performed using a permutation-based approach presented by Wilson et al. doi:10.1101/2021.04.27.21256104.

Install

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

install.packages("spatialTIME", 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/spatialTIME")

Development version from FridleyLab/spatialTIME. 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-spatialtime

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-spatialTIME

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-spatialTIME

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: 9.7 min · r-devel-linux-x86_64-debian-clang

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 1.3.4-5

READMEYes · 114 wordsVignettesYes · 1 · dynamicNEWSNoCitation fileYes · cites a publication

Help pages: 18 (1 internal)
Examples that run: 100%11 run in a plain check
Exported functions with examples: 71%
Documented parameters: 94%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (1)

Introduction to spatialTIME HTML

How these are measured

Downloads

8.2K

CRAN downloads in the past year

Rank #6,775 · ~22/day · ~680/mo

Releases R versions

Daily download trend is not available in this view yet.

44830 days

1.3K90 days

8.2K1 year

Compare downloads with other packages →

Also on116 r2u7 autocran

How downloads are counted

Repository

fridleylab/spatialtime ↗Organization: FridleyLab

6Stars

5Forks

3Open issues

2Open PRs

0Releases

313Commits

10Commit identities

313 commits · Last activity 2024-08-08 · 0% stars, 30d · Discussions: 1 post

Responsiveness

How these are sampled

PRs merged (all time): 67%
Median days to close, 50 most recently updated closed issues: 3
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-06-17 · 52026-07-07 · 6

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/fridleylab/spatialtime on 2026-10-25.

Continuous integration (3)

GitHub ActionsR CMD check workflowtic

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

Docs source (3)

README.Rmdpkgdown

GitHub Pages site last deployed 2026-10-06

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

24 external dependencies (excludes base and recommended)

Installing spatialTIME adds 55 packages (32 with compiled code, 45 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, sp 4.3 MB.

Depends (1)

R >= 2.10

Imports (19)

magrittr dplyr tidyr ggplot2 scalesgrDevicespurrr spatstat.univar spatstat.geom spatstat.explore RColorBrewer furrr future tidyselect crayon pbmcapply dixon tibble stringr

LinkingTo (0)

none

Suggests (6)

knitr devtools rmarkdown testthat gridExtra pheatmap

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Suggested by 2

Suggests, most downloaded first

mxfda scSpatialSIM

How these are counted

Code & Tests

Datasets

People & History

People (8)

Fridley Lab

Maintainer since 1.0.0 (2021)

Jordan Creed

Author

Oscar Ospina

Author · added in 1.2.1

Alex Soupir

Author · added in 1.1.0

Ram Thapa

Author

Christopher Wilson

Author

Julia Wrobel

Author · added in 1.3.3-3

Brooke Fridley

Copyright holder

Releases (10)

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
1.3.4-5Latest
record
2024-06-04 · current release · diff ↗
1.3.4-4
record
2024-05-30 · diff ↗
R
R 4.4.0 released · 2024-04-24
1.3.4-3
record
2024-03-11 · diff ↗
1.3.4-2
record
2023-12-19 · diff ↗ ·
added 5 exports
bi_pair_correlation, bi_ripleys_k_WSI, dixons_s, interaction_variable, pair_correlation
R
R 4.3.0 released · 2023-04-21
1.3.3-3
record
2023-03-22 · diff ↗ ·
added 1 export
merge_mifs
1.2.2
record
2022-11-22 · diff ↗
1.2.1
record
2022-06-23 · diff ↗
R
R 4.2.0 released · 2022-04-22
1.2.0
record
2021-09-11 · diff ↗
1.1.0
record
2021-08-21 · diff ↗ ·
added 3 exports
NN_G, bi_NN_G, subset_mif
R
R 4.1.0 released · 2021-05-18
1.0.0
record
2021-05-14

Show 1 earlier eventHide 1 earlier event

R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2021-05-14
Total releases: 10 / 5 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 2.10
Bundled data: 1.0 MB / 3 files
Download size: 2.9 MB

Cite

Cite this package

Run in R for the authors' entry:

citation("spatialTIME")

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

It points to 10.1093/bioinformatics/btab757.

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 spatialTIME version 1.3.4-5 [Data set]. HJJB, LLC. Data release v2026-10-26. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-26, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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