Package: iimi
Title: Identifying Infection with Machine Intelligence
Version: 1.2.2
Authors@R: c(
    person("Haochen", "Ning", , "hning@uvic.ca", role = c("aut")),
    person("Ian", "Boyes", , "ian.boyes@inspection.gc.ca", role = c("aut")),
    person("Ibrahim", "Numanagić", , "inumanag@uvic.ca", role = c("aut"),
    comment = c(ORCID = "0000-0002-2970-7937")),
    person("Michael", "Rott", , "mike.rott@inspection.gc.ca", role = c("aut")),
    person("Li", "Xing", , "lix491@math.usask.ca", role = c("aut"),
    comment = c(ORCID = "0000-0002-4186-7909")),
    person("Xuekui", "Zhang", , "xuekui@uvic.ca", role = c("aut", "cre"), 
    comment = c(ORCID = "0000-0003-4728-2343")))
Description: 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.
Encoding: UTF-8
RoxygenNote: 7.3.2
LazyData: true
VignetteBuilder: knitr
Imports: Biostrings, caret, data.table, dplyr, GenomicAlignments,
        IRanges, mltools, randomForest, Rsamtools, stats, xgboost,
        MTPS, stringr, R.utils, Rdpack
Depends: R (>= 3.5.0)
Suggests: rmarkdown, testthat (>= 3.0.0), knitr, httr
RdMacros: Rdpack
License: MIT + file LICENSE
LazyDataCompression: xz
NeedsCompilation: no
Packaged: 2026-06-15 08:45:16 UTC; root
Author: Haochen Ning [aut], Ian Boyes [aut], Ibrahim Numanagić [aut]
        (ORCID: <https://orcid.org/0000-0002-2970-7937>), Michael Rott
        [aut], Li Xing [aut] (ORCID:
        <https://orcid.org/0000-0002-4186-7909>), Xuekui Zhang [aut,
        cre] (ORCID: <https://orcid.org/0000-0003-4728-2343>)
Maintainer: Xuekui Zhang <xuekui@uvic.ca>
Config/pak/sysreqs: make libbz2-dev libicu-dev liblzma-dev xz-utils
        zlib1g-dev
Repository: https://ubcxzhang.r-universe.dev
Date/Publication: 2025-12-04 06:50:17 UTC
RemoteUrl: https://github.com/cran/iimi
RemoteRef: HEAD
RemoteSha: 833fa4762f4b4f959e108613a145c51ef6fccbda