R Observatory: Metrics for HTRX version 1.2.4

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

HTRX

1.2.4Package record

Haplotype Trend Regression with eXtra Flexibility (HTRX)

0packages depend

2.4Kdownloads / year

–test coverage

11/13flavors OK

Overview

About

Maintained by Yaoling YangCRAN page ↗

Detection of haplotype patterns that include single nucleotide polymorphisms (SNPs) and non-contiguous haplotypes that are associated with a phenotype. Methods for implementing HTRX are described in Yang Y, Lawson DJ (2023) doi:10.1093/bioadv/vbad038 and Barrie W, Yang Y, Irving-Pease E.K, et al (2024) doi:10.1038/s41586-023-06618-z.

Install

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

install.packages("HTRX", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

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-htrx

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-HTRX

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-HTRX

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

2NOTE11OK

Check messages

NOTEdependencies in R coder-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Namespaces in Imports field not imported from:
  ‘recipes’ ‘tune’
All declared Imports should be used.

CRAN check page ↗

Slowest check: 3.1 min · r-oldrel-windows-x86_64

Status changes

NOTE11 OK, 2 NOTE2026-06-09
ERROR10 OK, 2 NOTE, 1 ERROR2026-06-08
NOTE11 OK, 2 NOTE2026-05-02
ERROR9 OK, 2 NOTE, 1 ERROR2026-04-25
NOTE12 OK, 2 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.2.4

READMEYes · 297 wordsVignettesYes · 1 · dynamicNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 13includes a package overview page
Examples that run: 100%12 run in a plain check
Exported functions with examples: 100%
Documented parameters: not tracked
Return-value docs: not tracked
Help pages citing references: 38%

Vignettes (1)

HTRX_vignette HTML

How these are measured

Downloads

2.4K

CRAN downloads in the past year

Rank #18,834 · ~7/day · ~201/mo

Releases R versions

Daily download trend is not available in this view yet.

29330 days

68290 days

2.4K1 year

Compare downloads with other packages →

Also on64 r2u5 autocran

How downloads are counted

Dependencies

Declared dependencies

7 external dependencies (excludes base and recommended)

Installing HTRX adds 110 packages (57 with compiled code, 96 MB of source tarballs). Heaviest: BH 14 MB, stringi 11 MB, ggplot2 6.0 MB.

Depends (1)

R >= 4.0.0

Imports (8)

fastglm caretparallelmethodsstatsglmnet tune recipes

LinkingTo (0)

none

Suggests (2)

knitr rmarkdown

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 (2)

Yaoling Yang

Author, Maintainer since 1.0.7 (2022)

Daniel Lawson

Author

Releases (5)

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
1.2.4Latest
record
2024-02-09 · current release · diff ↗
R
R 4.3.0 released · 2023-04-21
1.2.2
record
2023-03-27 · diff ↗
1.2.1
record
2023-02-14 · diff ↗
1.1.0
record
2022-11-24 · diff ↗
1.0.7
record
2022-10-11
R
R 4.2.0 released · 2022-04-22

Package metadata

First published: 2022-10-11
Total releases: 5 / 4 yrs
License: GPL-3 OSI
Minimum R: ≥ 4.0.0
Bundled data: 404 KB / 3 files
Download size: 658 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("HTRX")

Format

Yang, Y., & Lawson, D. (2024). HTRX: Haplotype Trend Regression with eXtra Flexibility (HTRX) (Version 1.2.4) [Computer software]. https://doi.org/10.32614/CRAN.package.HTRX

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 HTRX version 1.2.4 [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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