R Observatory: Metrics for crosshap version 1.4.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

crosshap

1.4.0Package record

Local Haplotype Clustering and Visualization

0packages depend

3.5Kdownloads / year

89.3%test coverage

13/13flavors OK

Overview

About

Maintained by Jacob MarshCRAN page ↗GitHub ↗Website ↗Issues ↗

A local haplotyping visualization toolbox to capture major patterns of co-inheritance between clusters of linked variants, whilst connecting findings to phenotypic and demographic traits across individuals. 'crosshap' enables users to explore and understand genomic variation across a trait-associated region. For an example of successful local haplotype analysis, see Marsh et al. (2022) doi:10.1007/s00122-022-04045-8.

Install

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

install.packages("crosshap", 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("jacobimarsh/crosshap")

Development version from jacobimarsh/crosshap. 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-crosshap

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-crosshap

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-crosshap

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

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 1.4.0

READMEYes · 331 wordsVignettesNoNEWSNoCitation fileNoWebsiteYes · pkgdown

The repository also keeps web-only articles.

Help pages: 28 (2 internal)includes a package overview page
Examples that run: 100%7 run in a plain check
Exported functions with examples: 32%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

How these are measured

Downloads

3.5K

CRAN downloads in the past year

Rank #12,178 · ~10/day · ~295/mo

Releases R versions

Daily download trend is not available in this view yet.

31930 days

89890 days

3.5K1 year

Compare downloads with other packages →

Also on80 r2u8 autocran

How downloads are counted

Repository

jacobimarsh/crosshap ↗Account: jacobimarsh

13Stars

2Forks

0Open issues

0Open PRs

0Releases

224Commits

5Commit identities

224 commits · Last activity 2024-11-04 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 50%
Median days to close, 50 most recently updated closed issues: 14
Median days to close, 50 most recently updated closed PRs: 3

Stars over time

2025-04-14 · 122026-08-29 · 13

How these are measured

PracticesBeta

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

Checks run against github.com/jacobimarsh/crosshap on 2026-10-18.

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 (4)

README.Rmdpkgdown

GitHub Pages site last deployed 2024-11-04 · The repository has a site deploy workflow

pkgdown site last built 2024-11-04

Coverage (1)

Coverage reporting (Codecov)

Reproducibility and dev environment (1)

renv

Show all practicesHide 2 practices

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

22 external dependencies (excludes base and recommended)

Installing crosshap adds 63 packages (40 with compiled code, 69 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, data.table 5.7 MB.

Depends (1)

R >= 4.00

Imports (16)

cli clustree data.table dbscan dplyr ggdist ggplot2 ggpp gridExtra gtable magrittr patchwork rlang scales tibble tidyr

LinkingTo (0)

none

Suggests (6)

covr knitr rmarkdown testthat umap vdiffr

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)

Jacob Marsh

Author, Maintainer since 1.1.0 (2023)

Brady Johnston

Author

Jakob Petereit

Author

Releases (3)

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
R
R 4.4.0 released · 2024-04-24
1.4.0Latest
record
2024-03-31 · current release · diff ↗
1.2.2
record
2023-05-02 · diff ↗
R
R 4.3.0 released · 2023-04-21
1.1.0
record
2023-04-12
R
R 4.2.0 released · 2022-04-22

Package metadata

First published: 2023-04-12
Total releases: 3 / 3 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.00
Bundled data: 1.5 MB / 5 files
Download size: 1.5 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("crosshap")

Format

Marsh, J., Johnston, B., & Petereit, J. (2024). crosshap: Local Haplotype Clustering and Visualization (Version 1.4.0) [Computer software]. https://doi.org/10.32614/CRAN.package.crosshap

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 crosshap version 1.4.0 [Data set]. HJJB, LLC. Data release v2026-10-20. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-20, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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