ZIM4rv

0.1.1

Gene‐based Association Tests of Zero‐inflated Count Phenotype for Rare Variants

0packages depend

2.1Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Xiaomin LiuFirst published 2024-12-191 releasesCRAN page ↗GitHub ↗

Gene‐based association tests to model count data with excessive zeros and rare variants using zero-inflated Poisson/zero-inflated negative Binomial regression framework. This method was originally described by Fan, Sun, and Li in Genetic Epidemiology 46(1):73-86 doi:10.1002/gepi.22438.

Install

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

install.packages("ZIM4rv", 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("fanx0037/ZIM4rv")

Development version from fanx0037/ZIM4rv. 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-zim4rv

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-ZIM4rv

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-ZIM4rv

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13OK

Slowest check: 1.9 min · r-devel-linux-x86_64-fedora-clang

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

Dependencies · direct

Check history

OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 72 wordsVignettesNopkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 44%

Downloads

2.1K

CRAN downloads in the past year

Rank #22,741 · ~6/day · ~173/mo

Releases R versions

Daily download trend is not available in this view yet.

15830 days

51390 days

2.1K1 year

Compare downloads with other packages →

Also on84 r2u25 autocran

Repository

GitHub ↗ fanx0037/zim4rv

0Stars

0Forks

2Open issues

0Open PRs

0Releases

Last activity 2024-12-18

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/fanx0037/zim4rv on 2026-07-19.

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

7 external dependencies (excludes base and recommended)

Depends (7)

data.table pscl CompQuadFormstatsSKAT RNOmni R (>= 3.5.0)

Imports (0)

none

LinkingTo (0)

none

Suggests (1)

testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Code Composition

R 720 (57%)Rd 552 (43%)

Code characteristics

Cyclomatic complexity: 1.0 median / 9 max

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

11 11 exported

Complexity

3 avg / 9 max

Call network

11 nodes / 7 edges

Call graph

Open call graph →

Loading call graph…

Lowest coverage

Per-function coverage is not measured for this package yet.

Datasets

Bundled datasets · 7

Name	Class	Rows × Cols	Also ships in
Ex1_genedata	data.frame	200 × 5	–
Ex1_phenodata	data.frame	200 × 8	–
Ex2_covar	data.frame	15 × 4	–
Ex2_dosage	data.frame	7 × 21	–
Ex2_fam	data.frame	15 × 6	–
Ex2_pheno	data.frame	15 × 4	–
Ex2_region	data.frame	3 × 4	–

People & History

People (1)

Maintainer (1)

Xiaomin Liu

Author, Maintainer, Copyright holder

Authors (1)

Xiaomin Liu

Author, Maintainer, Copyright holder

Xiaomin Liu

Author, Maintainer, Copyright holder

Package Timeline

1 release. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
0.1.1Latest
2026-03-10 · current release
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2024-12-19
Total releases: 1 / 2 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.5.0
Bundled data: 5.7 KB / 7 files
Download size: 226 KB
Installed size: not tracked yet
With dependencies: not tracked yet

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