R Observatory: Metrics for MiRKAT version 1.2.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

MiRKAT

1.2.3

Microbiome Regression-Based Kernel Association Tests

1packages depend

5.4Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Anna PlantingaFirst published 2017-07-2511 releasesCRAN page ↗

Test for overall association between microbiome composition data and phenotypes via phylogenetic kernels. The phenotype can be univariate continuous or binary (Zhao et al. (2015) doi:10.1016/j.ajhg.2015.04.003), survival outcomes (Plantinga et al. (2017) doi:10.1186/s40168-017-0239-9), multivariate (Zhan et al. (2017) doi:10.1002/gepi.22030) and structured phenotypes (Zhan et al. (2017) doi:10.1111/biom.12684). The package can also use robust regression (unpublished work) and integrated quantile regression (Wang et al. (2021) doi:10.1093/bioinformatics/btab668). In each case, the microbiome community effect is modeled nonparametrically through a kernel function, which can incorporate phylogenetic tree information.

Install

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

install.packages("MiRKAT", 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-mirkat

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-MiRKAT

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-MiRKAT

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

Health

CRAN checks

13OK

Slowest check: 5.9 min · r-oldrel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

11

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 60%

Downloads

5.4K

CRAN downloads in the past year

Rank #10,627 · ~15/day · ~447/mo

Releases R versions

Daily download trend is not available in this view yet.

22630 days

91790 days

5.4K1 year

Compare downloads with other packages →

Also on98 r2u6 autocran

Dependencies

Declared dependencies

12 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.1.0

Imports (11)

MASSCompQuadForm quantreg GUniFrac PearsonDS lme4Matrixpermute mixtoolssurvivalstats

LinkingTo (0)

none

Suggests (5)

knitr vegan rmarkdown magrittr kableExtra

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

ROKET

Code & Tests

Datasets

People & History

People (8)

Maintainer (1)

Anna Plantinga

Author, Maintainer

Authors (8)

Anna Plantinga

Author, Maintainer

Jun Chen

Author · added in 1.0.1

Tianying Wang

Author, Contributor · added in 1.2.1

Nehemiah Wilson

Author, Contributor · added in 1.1.0

Author

Author, Contributor

Author, Contributor

Author, Contributor

Contributors (5)

Tianying Wang

Author, Contributor · added in 1.2.1

Nehemiah Wilson

Author, Contributor · added in 1.1.0

Xiang Zhan

Author, Contributor

Ni Zhao

Author, Contributor

Haotian Zheng

Author, Contributor

Listed in earlier versions (1)

Hongjiao Liu

no longer listed · 1.1.3 to 1.1.5

Package Timeline

11 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
R
R 4.3.0 released · 2023-04-21
1.2.3Latest
2023-02-17 · current release · diff ↗
1.2.2
2022-11-15 · diff ↗
R
R 4.2.0 released · 2022-04-22
1.2.1
2021-09-24 · diff ↗
1.1.5
2021-08-23 · diff ↗
1.1.4
2021-06-08 · diff ↗
1.1.3
2021-05-26 · diff ↗
R
R 4.1.0 released · 2021-05-18
1.1.2
2021-01-22 · diff ↗
1.1.1
2020-08-27 · diff ↗
R
R 4.0.0 released · 2020-04-24
1.1.0
2020-04-14 · diff ↗

Show 7 earlier events

unarchivedReturned to CRAN
2020-04-14
archivedRemoved from CRAN
2020-02-19
check problems were not corrected despite reminders
R
R 3.6.0 released · 2019-04-26
1.0.1
2018-04-25 · diff ↗
R
R 3.5.0 released · 2018-04-23
1.0
2017-07-25
R
R 3.4.0 released · 2017-04-21

Package metadata

First published: 2017-07-25
Total releases: 11 / 9 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 3.1.0
Bundled data: 164 KB / 6 files
Download size: 234 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("MiRKAT")

Format

Plantinga, A., Chen, J., Wang, T., Wilson, N., Wu, M., Zhan, X., Zhao, N., & Zheng, H. (2023). MiRKAT: Microbiome Regression-Based Kernel Association Tests (Version 1.2.3) [Computer software]. https://doi.org/10.32614/CRAN.package.MiRKAT

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 MiRKAT version 1.2.3 [Data set]. HJJB, LLC. Data release v2026-08-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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