R Observatory: Metrics for mvMAPIT version 2.0.4

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

mvMAPIT

2.0.4Package record

Multivariate Genome Wide Marginal Epistasis Test

1packages depend

4.4Kdownloads / year

97.2%test coverage

13/13flavors OK

Overview

About

Maintained by Julian StampCRAN page ↗GitHub ↗Website ↗

Epistasis, commonly defined as the interaction between genetic loci, is known to play an important role in the phenotypic variation of complex traits. As a result, many statistical methods have been developed to identify genetic variants that are involved in epistasis, and nearly all of these approaches carry out this task by focusing on analyzing one trait at a time. Previous studies have shown that jointly modeling multiple phenotypes can often dramatically increase statistical power for association mapping. In this package, we present the 'multivariate MArginal ePIstasis Test' ('mvMAPIT') – a multi-outcome generalization of a recently proposed epistatic detection method which seeks to detect marginal epistasis or the combined pairwise interaction effects between a given variant and all other variants. By searching for marginal epistatic effects, one can identify genetic variants that are involved in epistasis without the need to identify the exact partners with which the variants interact – thus, potentially alleviating much of the statistical and computational burden associated with conventional explicit search based methods. Our proposed 'mvMAPIT' builds upon this strategy by taking advantage of correlation structure between traits to improve the identification of variants involved in epistasis. We formulate 'mvMAPIT' as a multivariate linear mixed model and develop a multi-trait variance component estimation algorithm for efficient parameter inference and P-value computation. Together with reasonable model approximations, our proposed approach is scalable to moderately sized genome-wide association studies. Crawford et al. (2017) doi:10.1371/journal.pgen.1006869. Stamp et al. (2023) doi:10.1093/g3journal/jkad118. Stamp et al. (2025) doi:10.1016/j.ajhg.2025.07.004.

Changes in 2.0.4

Fix Bonferroni correction in the mvMAPIT.Rmd vignette.
New function binary_to_liability for LT-MAPIT support and corresponding vignette
Fix CRAN Notes - dependency compatibility.
Performance improvements in C++ implementation:
Eliminated redundant matrix inverse computation in projection operations
Optimized triple matrix products in Q matrix computation
Added benchmark suite for tracking performance improvements
Typical speedup: 3-8% depending on problem size and test method

From NEWS.md in the release

Install

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

install.packages("mvMAPIT", 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("lcrawlab/mvMAPIT")

Development version from lcrawlab/mvMAPIT. 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-mvmapit

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-mvMAPIT

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-mvMAPIT

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: 7.7 min · r-devel-windows-x86_64

Status changes

OK13 OK2026-09-09
ERROR12 OK, 1 ERROR2026-09-04
OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09

Show 7 earlier changesHide 7 earlier changes

ERROR12 OK, 1 ERROR2026-06-08
OK12 OK2026-04-25
NOTE12 OK, 2 NOTE2026-04-22
ERROR11 OK, 2 NOTE, 1 ERROR2026-04-18
NOTE12 OK, 2 NOTE2026-04-10
ERROR11 OK, 2 NOTE, 1 ERROR2026-04-09
NOTE12 OK, 2 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.0.4

READMEYes · 1,183 wordsVignettesYes · 7 · dynamicNEWSYes · 100% structured · mentions 2.0.4Citation fileNoWebsiteYes · pkgdown

Help pages: 9
Examples that run: 100%5 run in a plain check
Exported functions with examples: 83%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (7)

How these are measured

Downloads

4.4K

CRAN downloads in the past year

Rank #13,072 · ~12/day · ~366/mo

Releases R versions

Daily download trend is not available in this view yet.

36530 days

87390 days

4.4K1 year

Compare downloads with other packages →

Also on380 r2u4 autocran

How downloads are counted

Repository

lcrawlab/mvmapit ↗Organization: lcrawlab

14Stars

2Forks

3Open issues

0Open PRs

13Releases

125Commits

3Commit identities

epistasismapitmvmapitrvariance-componentscppcranepistasis-analysis

License file reads as GPL-3.0 · 125 commits · Last activity 2026-02-20 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 92%
Median days to close, 50 most recently updated closed issues: 154
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-06-26 · 122026-07-07 · 14

How these are measured

PracticesBeta

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

Checks run against github.com/lcrawlab/mvmapit on 2026-10-18.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows

Governance and community (1)

CODEOWNERS

Docs source (3)

pkgdown

GitHub Pages site last deployed 2026-02-20 · The repository has a site deploy workflow

pkgdown site last built 2026-02-20, before release 2.0.4 (2026-02-22)

Reproducibility and dev environment (2)

data-raw/Dockerfile

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

Dependencies

Declared dependencies

25 external dependencies (excludes base and recommended)

Installing mvMAPIT adds 52 packages (29 with compiled code, 29 MB of source tarballs). Heaviest: stringi 11 MB, Rcpp 1.8 MB, fs 1.4 MB.

Depends (1)

R >= 3.5

Imports (12)

checkmate CompQuadForm dplyr foreach harmonicmeanp logging mvtnorm Rcppstatstidyr truncnormutils

LinkingTo (6)

Rcpp RcppArmadillo RcppParallel RcppProgress RcppSpdlog testthat

Suggests (9)

GGally ggplot2 ggrepel kableExtra knitr markdown RcppAlgos rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

Imports 1

Depends, Imports or LinkingTo, most downloaded first

smer

How these are counted

Code & Tests

Datasets

People & History

People (2)

Julian Stamp

Maintainer since 2.0.0 (2022), Author

Lorin Crawford

Author

Releases (5)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
2.0.4Latest
record
2026-02-22 · current release · diff ↗ ·
added 1 export
binary_to_liability
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
2.0.3
record
2023-09-26 · diff ↗
2.0.2
record
2023-09-22 · diff ↗ ·
added 1 export
cauchy_combined
R
R 4.3.0 released · 2023-04-21
unarchivedReturned to CRAN
2023-02-09
2.0.1
record
2023-02-09 · diff ↗
archivedRemoved from CRAN
2023-01-10
issues were not corrected in time
2.0.0
record
2022-12-05
R
R 4.2.0 released · 2022-04-22

Package metadata

First published: 2022-12-05
Total releases: 5 / 4 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 3.5
Bundled data: 205 KB / 3 files
Download size: 903 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("mvMAPIT")

Format

Stamp, J., & Crawford, L. (2026). mvMAPIT: Multivariate Genome Wide Marginal Epistasis Test (Version 2.0.4) [Computer software]. https://doi.org/10.32614/CRAN.package.mvMAPIT

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 mvMAPIT version 2.0.4 [Data set]. HJJB, LLC. Data release v2026-10-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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