R Observatory: Metrics for HTRX version 1.2.4

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

HTRX

1.2.4

Haplotype Trend Regression with eXtra Flexibility (HTRX)

0packages depend

2.2Kdownloads / year

–test coverage

11/13checks pass

Overview

About

Maintained by Yaoling YangFirst published 2022-10-115 releasesCRAN 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.

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).

Health

CRAN checks

2NOTE11OK

Failing flavors

NOTE r-devel-linux-x86_64-fedora-clang
NOTE r-devel-linux-x86_64-fedora-gcc

Slowest check: 3.3 min · r-oldrel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

8

Dependencies · direct

Check history

NOTE2026-06-09
11 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
10 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-05-02
11 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-25
9 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 297 wordsVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: not tracked
Return-value docs: not tracked
References docs: 38%

Downloads

2.2K

CRAN downloads in the past year

Rank #19,015 · ~6/day · ~186/mo

Releases R versions

Daily download trend is not available in this view yet.

12530 days

57890 days

2.2K1 year

Compare downloads with other packages →

Also on91 r2u17 autocran

Dependencies

Declared dependencies

7 external dependencies (excludes base and recommended)

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.

Code & Tests

Datasets

People & History

People (2)

Maintainer (1)

Yaoling Yang

Author, Maintainer

Authors (2)

Yaoling Yang

Author, Maintainer

Daniel Lawson

Author

Package Timeline

5 releases. Pick two to compare their code metrics. R releases are shown for context.

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
2024-02-09 · current release · diff ↗
R
R 4.3.0 released · 2023-04-21
1.2.2
2023-03-27 · diff ↗
1.2.1
2023-02-14 · diff ↗
1.1.0
2022-11-24 · diff ↗
1.0.7
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
Installed size: not tracked yet
With dependencies: not tracked yet

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 is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

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 v2026-08-15. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-15, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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