MIC

2.0.1

Analysis of Antimicrobial Minimum Inhibitory Concentration Data

0packages depend

2.8Kdownloads / year

77.5%test coverage

13/13checks pass

Overview

About

Maintained by Alessandro GeradaFirst published 2025-02-075 releasesCRAN page ↗GitHub ↗

Analyse, plot, and tabulate antimicrobial minimum inhibitory concentration (MIC) data. Validate the results of an MIC experiment by comparing observed MIC values to a gold standard assay, in line with standards from the International Organization for Standardization (2021) https://www.iso.org/standard/79377.html.

Install

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

install.packages("MIC", 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("agerada/MIC")

Development version from agerada/MIC. 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-mic

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-MIC

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-MIC

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

Health

CRAN checks

13OK

Slowest check: 6.7 min · r-oldrel-macos-x86_64

Code health

Yes

Tests · ratio 0.27

77.5%

Coverage · measured lines

100%

Documentation · exports

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

Documentation

READMEYes · 479 wordsVignettesNopkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 19%

Downloads

2.8K

CRAN downloads in the past year

Rank #19,846 · ~8/day · ~232/mo

Releases R versions

Daily download trend is not available in this view yet.

18930 days

60790 days

2.8K1 year

Compare downloads with other packages →

Also on445 r2u34 autocran

Repository

GitHub ↗ agerada/mic

0Stars

0Forks

4Open issues

1Open PRs

4Releases

310Commits

4Contributors

License GPL-3.0 · 310 commits · Last activity 2026-07-21

Releases over time

2025-06-04 · 22026-07-07 · 4

Repository practices

Upstream repositoryBeta

7 development-tooling and community-health practices detected across 5 families in the upstream repository

Checks run against github.com/agerada/mic on 2026-07-19.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (2)

renvdata-raw/

CRAN release process (2)

cran-comments.mdrevdep/

Docs source (1)

README.Rmd

Show all practices

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

13 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.1.0

Imports (10)

AMR glue dplyr stringr rlang ggh4x ggplot2 forcats purrr tibble

LinkingTo (0)

none

Suggests (3)

testthat flextable lifecycle

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Code Composition

R 2,848 (70%)Rd 1,218 (30%)

Code characteristics

Object systems

S310

Cyclomatic complexity: 4.0 median / 36 max
Test cases: 21 / 0.27 per code line

Test coverage

Line coverage

77%

Expression

78.1%

Tests / Examples

77.5% / – ex

Functions

32 16 exported

Complexity

5.9 avg / 36 max

Call network

32 nodes / 31 edges

Call graph

Open call graph →

Loading call graph…

Lowest coverage

32 functions

Function	Cyclo	Coverage
clean_raw_mic exp	1	0%
table exp	1	0%
plot.mic_validation	3	0%
print.mic_validation	2	0%
print.mic_validation_summary	4	0%
table.default	1	0%

Datasets

Bundled datasets · 2

Name	Class	Rows × Cols	Also ships in
ecoffs	tbl_df/tbl/data.frame	85 × 25	–
example_mics	data.frame	300 × 4	–

1 internal object is bundled for the package's own use and not listed here.

People & History

People (1)

Maintainer (1)

Alessandro Gerada

Author, Maintainer, Copyright holder

Authors (1)

Alessandro Gerada

Author, Maintainer, Copyright holder

Alessandro Gerada

Author, Maintainer, Copyright holder

Package Timeline

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

2.0.1Latest
2026-07-21 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
2.0.0
2025-12-04 · diff ↗
1.2.0
2025-10-12 · diff ↗
1.1.0
2025-06-05 · diff ↗
R
R 4.5.0 released · 2025-04-11
1.0.2
2025-02-07
R
R 4.4.0 released · 2024-04-24

Package metadata

First published: 2025-02-07
Total releases: 5 / 1 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 4.1.0
Bundled data: 8.5 KB / 2 files
Download size: 740 KB
Installed size: not tracked yet
With dependencies: not tracked yet

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