R Observatory: Metrics for iimi version 1.2.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

iimi needs mltools, which CRAN will archive unless its check problems are fixed by Nov 11.

iimi

1.2.2Package record

Identifying Infection with Machine Intelligence

0packages depend

3.6Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Xuekui ZhangCRAN page ↗

A novel machine learning method for plant viruses diagnostic using genome sequencing data. This package includes three different machine learning models, random forest, XGBoost, and elastic net, to train and predict mapped genome samples. Mappability profile and unreliable regions are introduced to the algorithm, and users can build a mappability profile from scratch with functions included in the package. Plotting mapped sample coverage information is provided.

Install

R (CRAN)Ubuntu (r2u)

install.packages("iimi", 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-iimi

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

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 8.4 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK13 OK2026-05-10

Show 4 earlier changesHide 4 earlier changes

ERROR12 OK, 1 ERROR2026-05-03
OK13 OK2026-05-02
ERROR11 OK, 1 ERROR2026-04-25
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.2.2

READMENoVignettesYes · 1 · dynamicNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 14
Examples that run: 14%1 run in a plain check · 6 never run
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0% with Rdpack citation macros

Vignettes (1)

Introduction to the iimi package

How these are measured

Downloads

3.6K

CRAN downloads in the past year

Rank #10,553 · ~10/day · ~301/mo

Releases R versions

Daily download trend is not available in this view yet.

35930 days

98190 days

3.6K1 year

Compare downloads with other packages →

Also on104 r2u

How downloads are counted

Dependencies

Declared dependencies

18 external dependencies (excludes base and recommended)

Installing iimi adds 75 packages (40 with compiled code, 58 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, data.table 5.7 MB. 4 more not on CRAN are not measured.

Depends (1)

R >= 3.5.0

Imports (15)

Biostrings caret data.table dplyr GenomicAlignments IRanges mltools randomForest Rsamtoolsstatsxgboost MTPS stringr R.utils Rdpack

LinkingTo (0)

none

Suggests (4)

rmarkdown testthat knitr httr

Enhances (0)

none

Dependencies facing archival

CRAN will archive these unless their check problems are fixed by the date shown. This package needs each one to install.

mltoolsfix by Nov 11

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (6)

Xuekui Zhang

Author, Maintainer since 1.0.2 (2024)

Author

Author

Author

Author

Author

Releases (5)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
1.2.2Latest
record
2025-12-04 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
1.2.1
record
2024-11-01 · diff ↗
1.1.1
record
2024-07-26 · diff ↗
1.1.0
record
2024-07-18 · diff ↗
R
R 4.4.0 released · 2024-04-24
1.0.2
record
2024-03-07
R
R 4.3.0 released · 2023-04-21

Package metadata

First published: 2024-03-07
Total releases: 5 / 2 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 3.5.0
Bundled data: 2.4 MB / 7 files
Download size: 2.5 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("iimi")

Format

Zhang, X., Boyes, I., Ning, H., Numanagić, I., Rott, M., & Xing, L. (2025). iimi: Identifying Infection with Machine Intelligence (Version 1.2.2) [Computer software]. https://doi.org/10.32614/CRAN.package.iimi

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 iimi version 1.2.2 [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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