R Observatory: Metrics for gateR version 0.1.16

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

gateR

0.1.16Package record

Flow/Mass Cytometry Gating via Spatial Kernel Density Estimation

0packages depend

3.3Kdownloads / year

74.4%test coverage

13/13flavors OK

Overview

About

Maintained by Ian D. BullerCRAN page ↗GitHub ↗Issues ↗

Estimates statistically significant marker combination values within which one immunologically distinctive group (i.e., disease case) is more associated than another group (i.e., healthy control), successively, using various combinations (i.e., "gates") of markers to examine features of cells that may be different between groups. For a two-group comparison, the 'gateR' package uses the spatial relative risk function estimated using the 'sparr' package. Details about the 'sparr' package methods can be found in the tutorial: Davies et al. (2018) doi:10.1002/sim.7577. Details about kernel density estimation can be found in J. F. Bithell (1990) doi:10.1002/sim.4780090616. More information about relative risk functions using kernel density estimation can be found in J. F. Bithell (1991) doi:10.1002/sim.4780101112.

Changes in 0.1.16

Renamed 'package.R' to 'gateR-package.R' after Roxygen (>=7.3.0) update
Fixed Rd \link{} targets missing package within 'gateR-package.Rd'
Updated vignette with updated package version and dependencies

From NEWS.md in the release

Install

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

install.packages("gateR", 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("lance-waller-lab/gateR")

Development version from lance-waller-lab/gateR. 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-gater

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-gateR

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-gateR

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: 7.0 min · r-release-linux-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 0.1.16

READMEYes · 644 wordsVignettesYes · 2 · dynamicNEWSYes · 100% structured · mentions 0.1.16Citation fileYes · software entry onlyWebsitenot declared in DESCRIPTION

Help pages: 8 (3 internal)includes a package overview page
Examples that run: 100%4 run in a plain check (1 of them under a condition)
Exported functions with examples: 50%
Documented parameters: 96%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (2)

How these are measured

Downloads

3.3K

CRAN downloads in the past year

Rank #10,851 · ~9/day · ~273/mo

Releases R versions

Daily download trend is not available in this view yet.

35930 days

97290 days

3.3K1 year

Compare downloads with other packages →

Also on64 r2u4 autocran

How downloads are counted

Repository

lance-waller-lab/gater ↗Organization: lance-waller-lab

2Stars

3Forks

0Open issues

0Open PRs

13Releases

72Commits

5Commit identities

rrstatscrancran-rcytometryflow-cytometrygatingkernel-density-estimation

License file reads as Apache-2.0 · 72 commits · Last activity 2025-08-29 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 1
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2023-02-01 · 22026-07-07 · 2

How these are measured

PracticesBeta

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

Checks run against github.com/lance-waller-lab/gater on 2026-10-22.

Continuous integration (2)

GitHub ActionsR CMD check workflow

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

Reproducibility and dev environment (1)

data-raw/

CRAN release process (1)

cran-comments.md

Lint, format, editor (1)

RStudio project

Show all practicesHide 1 practice

Git structural (1)

.gitattributes

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

Dependencies

Declared dependencies

13 external dependencies (excludes base and recommended)

Installing gateR adds 40 packages (26 with compiled code, 30 MB of source tarballs). Heaviest: spatstat 4.3 MB, fields 3.9 MB, spam 3.1 MB.

Depends (1)

R >= 3.5.0

Imports (11)

fieldsgraphicsgrDeviceslifecycle rlang sparr SpatialPack spatstat.geomstatsterra tibble

LinkingTo (0)

none

Suggests (6)

dplyr R.rsp spelling testthat usethisutils

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 (5)

Contributor

Contributor

Contributor

Copyright holder

Releases (13)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
0.1.16Latest
record
2025-08-29 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
0.1.15
record
2024-01-23 · diff ↗
R
R 4.3.0 released · 2023-04-21
0.1.13
record
2023-02-02 · diff ↗
0.1.12
record
2022-12-01 · diff ↗
unarchivedReturned to CRAN
2022-08-27
0.1.11
record
2022-08-27 · diff ↗
archivedRemoved from CRAN
2022-08-08
requires archived package 'SpatialPack'
R
R 4.2.0 released · 2022-04-22
0.1.10
record
2022-02-05 · diff ↗
0.1.9
record
2021-06-26 · diff ↗
R
R 4.1.0 released · 2021-05-18
0.1.8
record
2021-03-15 · diff ↗

Show 6 earlier eventsHide 6 earlier events

0.1.7
record
2021-02-04 · diff ↗
0.1.6
record
2021-01-07 · diff ↗
0.1.4
record
2020-11-30 · diff ↗
0.1.3
record
2020-11-17 · diff ↗
0.1.2
record
2020-11-10
R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2020-11-10
Total releases: 13 / 6 yrs
License: Apache License (>= 2.0)
Minimum R: ≥ 3.5.0
Bundled data: 553 KB / 1 file
Download size: 860 KB

Cite

Cite this package

Run in R for the authors' entry:

citation("gateR")

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

It points to 10.32614/cran.package.gater.

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 gateR version 0.1.16 [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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