MiRKAT

1.2.3

Microbiome Regression-Based Kernel Association Tests

1packages depend

5.6Kdownloads / 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 The package can also use robust regression (unpublished work) and integrated quantile regression (Wang et al.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: 8.0 min · r-devel-linux-x86_64-fedora-gcc

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

Yes

Vignettes

README

Dependencies · direct

Check history

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

Downloads

5.6K

CRAN downloads in the past year

Rank #10,521 · ~15/day · ~470/mo

Releases R versions

Daily download trend is not available in this view yet.

41630 days

1K90 days

5.6K1 year

Compare downloads with other packages →

Also on91 r2u14 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

Code Composition

R 2,865 (63%)Rd 1,266 (28%)Vignettes 390 (9%)

Code characteristics

Cyclomatic complexity: 3.0 median / 58 max
Documented parameters: 100%

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

40 9 exported

Complexity

8.2 avg / 58 max

Call network

40 nodes / 41 edges

Test coverage has not been measured for this package yet; nodes fall back to a neutral fill.

Call graph

Open call graph →

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Lowest coverage

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

People & History

People (8)

Maintainer (1)

Anna Plantinga

Author, Maintainer

Authors (8)

Author, Maintainer

Author

Author, Contributor

Author, Contributor

Author

Author, Contributor

Author, Contributor

Author, Contributor

Contributors (5)

Author, Contributor

Author, Contributor

Author, Contributor

Author, Contributor

Author, Contributor

Release 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 5 earlier events

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