R Observatory: Metrics for HaploCatcher version 2.0.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

HaploCatcher

2.0.1Package record

A Predictive Haplotyping Package

0packages depend

6.5Kdownloads / year

0.0%test coverage

13/13flavors OK

Overview

About

Maintained by Zachary WinnCRAN page ↗GitHub ↗Issues ↗

Used for predicting a genotype's allelic state at a specific locus/QTL/gene. This is accomplished by using both a genotype matrix and a separate file which has categorizations about loci/QTL/genes of interest for the individuals in the genotypic matrix. A training population can be created from a panel of individuals who have been previously screened for specific loci/QTL/genes, and this previous screening could be summarized into a category. Using the categorization of individuals which have been genotyped using a genome wide marker platform, a model can be trained to predict what category (haplotype) an individual belongs in based on their genetic sequence in the region associated with the locus/QTL/gene. These trained models can then be used to predict the haplotype of a locus/QTL/gene for individuals which have been genotyped with a genome wide platform yet not genotyped for the specific locus/QTL/gene. This package is based off work done by Winn et al 2021. For more specific information on this method, refer to doi:10.1007/s00122-022-04178-w.

Install

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

install.packages("HaploCatcher", 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("zjwinn/HaploCatcher")

Development version from zjwinn/HaploCatcher. 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-haplocatcher

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-HaploCatcher

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-HaploCatcher

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: 5.8 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK13 OK2026-05-02

Show 2 earlier changesHide 2 earlier changes

ERROR11 OK, 1 ERROR2026-04-25
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.0.1

READMEYes · 214 wordsVignettesYes · 1 · dynamicNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 10 (1 internal)includes a package overview page
Examples that run: 100%9 run in a plain check
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (1)

An Introduction to HaploCatcher HTML

How these are measured

Downloads

6.5K

CRAN downloads in the past year

Rank #18,001 · ~18/day · ~544/mo

Releases R versions

Daily download trend is not available in this view yet.

27230 days

71790 days

6.5K1 year

Compare downloads with other packages →

Also on75 r2u5 autocran

How downloads are counted

Repository

zjwinn/haplocatcher ↗Account: zjwinn

1Stars

0Forks

0Open issues

0Open PRs

1Releases

87Commits

2Commit identities

geneticsmachine-learningplantbreedinggeneslocusmolecular-geneticspipeliner-package

87 commits · Last activity 2026-06-08

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: 81

How these are measured

PracticesBeta

4 development-tooling and community-health practices detected across 2 families in the upstream repository

Checks run against github.com/zjwinn/haplocatcher on 2026-10-21.

CRAN release process (3)

cran-comments.mdrevdep/CRAN-SUBMISSION

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

9 external dependencies (excludes base and recommended)

Installing HaploCatcher adds 71 packages (37 with compiled code, 53 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, data.table 5.7 MB.

Depends (1)

R >= 2.10

Imports (10)

paralleldoParallel foreach caret ggplot2graphicsknitr patchwork randomForeststats

LinkingTo (0)

none

Suggests (2)

rmarkdown testthat

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 (1)

Zachary Winn

Author, Maintainer since 1.0.3 (2023)

Releases (3)

Pick two releases to compare their code metrics.

2.0.1Latest
record
2026-06-09 · current release · diff ↗
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
1.0.4
record
2023-04-22 · diff ↗
R
R 4.3.0 released · 2023-04-21
1.0.3
record
2023-04-04
R
R 4.2.0 released · 2022-04-22

Package metadata

First published: 2023-04-04
Total releases: 3 / 3 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 2.10
Bundled data: 283 KB / 3 files
Download size: 741 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("HaploCatcher")

Format

Winn, Z. (2026). HaploCatcher: A Predictive Haplotyping Package (Version 2.0.1) [Computer software]. https://doi.org/10.32614/CRAN.package.HaploCatcher

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 HaploCatcher version 2.0.1 [Data set]. HJJB, LLC. Data release v2026-10-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

Report a problem with this page →